1	antibody	antibody	NN	_	_	_
2	:	:	:	_	_	_
3	Flag	flag	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	ChIP-Seq	chip-seq	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Cultures	culture	NNS	_	_	_
8	of	of	IN	_	_	_
9	Caulobacter	caulobacter	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	TLS1631-TLS1633	tls1631-tls1633	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	were	be	VBD	_	_	_
14	grown	grow	VBN	_	_	_
15	at	at	IN	_	_	_
16	30oC	30oC	NNP	_	_	_
17	in	in	IN	_	_	_
18	PYE	PYE	NNP	_	_	_
19	and	and	CC	_	_	_
20	supplemented	supplement	VBN	_	_	_
21	with	with	IN	_	_	_
22	antibiotics	antibiotic	NNS	_	_	_
23	,	,	,	_	_	_
24	as	as	RB	_	_	_
25	necessary	necessary	JJ	_	_	_
26	,	,	,	_	_	_
27	at	at	IN	_	_	_
28	appropriate	appropriate	JJ	_	_	_
29	concentrations	concentration	NNS	_	_	_
30	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	deplete	deplete	VB	_	_	_
3	wild-type	wild-type	JJ	_	_	_
4	non-tagged	non-tagged	JJ	_	_	_
5	ParB	parb	NN	_	_	_
6	,	,	,	_	_	_
7	exponential-phase	exponential-phase	NN	_	_	_
8	cells	cell	NNS	_	_	_
9	were	be	VBD	_	_	_
10	washed	wash	VBN	_	_	_
11	off	off	RP	_	_	_
12	xylose	xylose	NN	_	_	_
13	and	and	CC	_	_	_
14	re-introduced	re-introduced	JJ	_	_	_
15	to	to	TO	_	_	_
16	PYE	PYE	NNP	_	_	_
17	+0.2	+0.2	CD	_	_	_
18	%	%	NN	_	_	_
19	glucose	glucose	NN	SUPP	_	_
20	for	for	IN	_	_	_
21	an	a	DT	_	_	_
22	additional	additional	JJ	_	_	_
23	5	5	CD	_	_	_
24	hours	hour	NNS	_	_	_
25	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	4	4	CD	_	_	_
3	hours	hour	NNS	_	_	_
4	,	,	,	_	_	_
5	vanillate	vanillate	NN	_	_	_
6	was	be	VBD	_	_	_
7	added	add	VBN	_	_	_
8	to	to	TO	_	_	_
9	induce	induce	VB	_	_	_
10	the	the	DT	_	_	_
11	expression	expression	NN	_	_	_
12	of	of	IN	_	_	_
13	flag-parB	flag-parb	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	WT	wt	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	or	or	CC	_	_	_
18	flag-parB	flag-parb	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	G101S	g101s	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	developmental	developmental	JJ	_	_	_
23	stage	stage	NN	_	_	_
24	:	:	:	_	_	_
25	mixed	mixed	JJ	_	_	_
26	population	population	NN	_	_	_
27	,	,	,	_	_	_
28	exponential	exponential	JJ	GrowthPhase	_	_
29	phase	phase	NN	GrowthPhase	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	DNA	dna	NN	_	_	_
32	was	be	VBD	_	_	_
33	isolated	isolate	VBN	_	_	_
34	using	use	VBG	_	_	_
35	the	the	DT	_	_	_
36	Qiagen	Qiagen	NNP	_	_	_
37	Cell	cell	NN	_	_	_
38	Lysis	lysis	NN	_	_	_
39	and	and	CC	_	_	_
40	Protein	protein	NN	_	_	_
41	Precipitation	precipitation	NN	_	_	_
42	solutions	solution	NNS	_	_	_
43	.	.	.	_	_	_

1	Detailed	detailed	JJ	_	_	_
2	protocols	protocol	NNS	_	_	_
3	are	be	VBP	_	_	_
4	listed	list	VBN	_	_	_
5	in	in	IN	_	_	_
6	the	the	DT	_	_	_
7	Supplementary	Supplementary	NNP	_	_	_
8	Materials	Materials	NNPS	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	Escherichia	escherichia	FW	Organism	_	_
11	coli	coli	FW	Organism	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	Escherichia	escherichia	FW	Organism	_	_
14	coli	coli	FW	Organism	_	_
15	AB1157	ab1157	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	For	for	IN	_	_	_
18	analysis	analysis	NN	_	_	_
19	of	of	IN	_	_	_
20	ChIP-seq	ChIP-seq	NNP	_	_	_
21	data	datum	NNS	_	_	_
22	,	,	,	_	_	_
23	Hiseq	Hiseq	NNP	_	_	_
24	2500	2500	CD	_	_	_
25	Illumina	Illumina	NNP	_	_	_
26	short	short	JJ	_	_	_
27	reads	read	VBZ	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	50	50	CD	_	_	_
30	bp	bp	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	were	be	VBD	_	_	_
33	mapped	map	VBN	_	_	_
34	back	back	RB	_	_	_
35	to	to	TO	_	_	_
36	the	the	DT	_	_	_
37	Caulobacter	Caulobacter	NNP	_	_	_
38	NA1000	na1000	NN	_	_	_
39	reference	reference	NN	_	_	_
40	genome	genome	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	NCBI	ncbi	NN	_	_	_
43	Reference	Reference	NNP	_	_	_
44	Sequence	sequence	NN	_	_	_
45	:	:	:	_	_	_
46	NC-011916.1	nc-011916.1	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	using	use	VBG	_	_	_
49	Bowtie	Bowtie	NNP	_	_	_
50	1	1	CD	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	Langmead	Langmead	NNP	_	_	_
53	et	et	FW	_	_	_
54	al.	al.	FW	_	_	_
55	,	,	,	_	_	_
56	2009	2009	CD	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	and	and	CC	_	_	_
59	the	the	DT	_	_	_
60	following	follow	VBG	_	_	_
61	command	command	NN	_	_	_
62	:	:	:	_	_	_
63	bowtie	bowtie	NN	_	_	_
64	-	-	:	_	_	_
65	m	m	NN	_	_	_
66	1	1	CD	_	_	_
67	-	-	:	_	_	_
68	n	n	NN	_	_	_
69	1	1	CD	_	_	_
70	--	--	:	_	_	_
71	best	best	JJS	_	_	_
72	--	--	:	_	_	_
73	strata	strata	SYM	_	_	_
74	-	-	:	_	_	_
75	p	p	NN	_	_	_
76	4	4	CD	_	_	_
77	--	--	:	_	_	_
78	chunkmbs	chunkmb	NNS	_	_	_
79	512	512	CD	_	_	_
80	NA1000-bowtie	na1000-bowtie	NN	_	_	_
81	--	--	:	_	_	_
82	sam	sam	NN	_	_	_
83	*	*	NN	_	_	_
84	.	.	.	_	_	_

1	fastq	fastq	NN	_	_	_
2	>	>	JJR	_	_	_
3	output.sam	output.sam	NN	_	_	_
4	.	.	.	_	_	_

1	Subsequently	subsequently	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	sequencing	sequencing	NN	_	_	_
5	coverage	coverage	NN	_	_	_
6	at	at	IN	_	_	_
7	each	each	DT	_	_	_
8	nucleotide	nucleotide	NN	_	_	_
9	position	position	NN	_	_	_
10	was	be	VBD	_	_	_
11	computed	compute	VBN	_	_	_
12	using	use	VBG	_	_	_
13	BEDTools	bedtool	NNS	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Quinlan	Quinlan	NNP	_	_	_
16	and	and	CC	_	_	_
17	Hall	Hall	NNP	_	_	_
18	,	,	,	_	_	_
19	2010	2010	CD	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	using	use	VBG	_	_	_
22	the	the	DT	_	_	_
23	following	follow	VBG	_	_	_
24	command	command	NN	_	_	_
25	:	:	:	_	_	_
26	bedtools	bedtool	NNS	_	_	_
27	genomecov	genomecov	NN	_	_	_
28	-	-	:	_	_	_
29	d	d	SYM	_	_	_
30	-	-	:	_	_	_
31	ibam	ibam	NN	_	_	_
32	output.sorted.bam	output.sorted.bam	NN	_	_	_
33	-	-	:	_	_	_
34	g	g	NN	_	_	_
35	NA1000.fna	na1000.fna	NN	_	_	_
36	>	>	JJR	_	_	_
37	coverage_output.txt	coverage_output.txt	NN	_	_	_
38	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	analysis	analysis	NN	_	_	_
3	of	of	IN	_	_	_
4	E.	e.	FW	_	_	_
5	coli	coli	FW	_	_	_
6	ChIP-seq	ChIP-seq	NNP	_	_	_
7	data	datum	NNS	_	_	_
8	,	,	,	_	_	_
9	reference	reference	NN	_	_	_
10	genomes	genome	NNS	_	_	_
11	were	be	VBD	_	_	_
12	first	first	JJ	_	_	_
13	reconstructed	reconstruct	VBN	_	_	_
14	in	in	IN	_	_	_
15	silico	silico	NN	_	_	_
16	by	by	IN	_	_	_
17	inserting	insert	VBG	_	_	_
18	the	the	DT	_	_	_
19	nucleotide	nucleotide	NN	_	_	_
20	sequence	sequence	NN	_	_	_
21	of	of	IN	_	_	_
22	parS	pars	NN	_	_	_
23	and	and	CC	_	_	_
24	apramycin	apramycin	NN	_	_	_
25	antibiotic	antibiotic	JJ	_	_	_
26	resistance	resistance	NN	_	_	_
27	cassette	cassette	NN	_	_	_
28	to	to	TO	_	_	_
29	the	the	DT	_	_	_
30	ybbD	ybbd	NN	GEN	_	_
31	locus	locus	NN	_	_	_
32	of	of	IN	_	_	_
33	E.	e.	FW	_	_	_
34	coli	coli	FW	_	_	_
35	MG1655	mg1655	NN	_	_	_
36	genome	genome	NN	_	_	_
37	.	.	.	_	_	_

1	Afterwards	afterwards	RB	_	_	_
2	,	,	,	_	_	_
3	Hiseq	Hiseq	NNP	_	_	_
4	2500	2500	CD	_	_	_
5	Illumina	Illumina	NNP	_	_	_
6	short	short	JJ	_	_	_
7	reads	read	VBZ	_	_	_
8	were	be	VBD	_	_	_
9	mapped	map	VBN	_	_	_
10	back	back	RB	_	_	_
11	to	to	TO	_	_	_
12	these	these	DT	_	_	_
13	reconstructed	reconstruct	VBN	_	_	_
14	reference	reference	NN	_	_	_
15	genomes	genome	NNS	_	_	_
16	using	use	VBG	_	_	_
17	Bowtie	Bowtie	NNP	_	_	_
18	1	1	CD	_	_	_
19	.	.	.	_	_	_

1	Sequence	sequence	NN	_	_	_
2	coverage	coverage	NN	_	_	_
3	at	at	IN	_	_	_
4	each	each	DT	_	_	_
5	nucleotide	nucleotide	NN	_	_	_
6	position	position	NN	_	_	_
7	was	be	VBD	_	_	_
8	also	also	RB	_	_	_
9	computed	compute	VBN	_	_	_
10	using	use	VBG	_	_	_
11	BEDTools	bedtool	NNS	_	_	_
12	.	.	.	_	_	_

1	Finally	finally	RB	_	_	_
2	,	,	,	_	_	_
3	ChIP-seq	chip-seq	JJ	_	_	_
4	profiles	profile	NNS	_	_	_
5	were	be	VBD	_	_	_
6	plotted	plot	VBN	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	x-axis	x-axis	JJ	_	_	_
10	representing	represent	VBG	_	_	_
11	genomic	genomic	JJ	_	_	_
12	positions	position	NNS	_	_	_
13	and	and	CC	_	_	_
14	the	the	DT	_	_	_
15	y-axis	y-axis	NN	_	_	_
16	is	be	VBZ	_	_	_
17	the	the	DT	_	_	_
18	number	number	NN	_	_	_
19	of	of	IN	_	_	_
20	reads	read	VBZ	_	_	_
21	per	per	IN	_	_	_
22	base	base	NN	_	_	_
23	pair	pair	NN	_	_	_
24	per	per	IN	_	_	_
25	million	million	CD	_	_	_
26	mapped	map	VBD	_	_	_
27	reads	read	VBZ	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	RPBPM	rpbpm	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	using	use	VBG	_	_	_
32	custom	custom	NN	_	_	_
33	R	r	NN	_	_	_
34	scripts	script	NNS	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	For	for	IN	_	_	_
3	analysis	analysis	NN	_	_	_
4	of	of	IN	_	_	_
5	IDAP-seq	idap-seq	JJ	_	_	_
6	data	datum	NNS	_	_	_
7	,	,	,	_	_	_
8	Hiseq	Hiseq	NNP	_	_	_
9	2500	2500	CD	_	_	_
10	Illumina	Illumina	NNP	_	_	_
11	short	short	JJ	_	_	_
12	reads	read	VBZ	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	50	50	CD	_	_	_
15	bp	bp	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	were	be	VBD	_	_	_
18	mapped	map	VBN	_	_	_
19	back	back	RB	_	_	_
20	to	to	TO	_	_	_
21	the	the	DT	_	_	_
22	Caulobacter	Caulobacter	NNP	_	_	_
23	NA1000	na1000	NN	_	_	_
24	reference	reference	NN	_	_	_
25	genome	genome	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	NCBI	ncbi	NN	_	_	_
28	Reference	Reference	NNP	_	_	_
29	Sequence	sequence	NN	_	_	_
30	:	:	:	_	_	_
31	NC-011916.1	nc-011916.1	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	using	use	VBG	_	_	_
34	Bowtie	Bowtie	NNP	_	_	_
35	1	1	CD	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	Langmead	Langmead	NNP	_	_	_
38	et	et	FW	_	_	_
39	al.	al.	FW	_	_	_
40	,	,	,	_	_	_
41	2009	2009	CD	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	and	and	CC	_	_	_
44	the	the	DT	_	_	_
45	following	follow	VBG	_	_	_
46	command	command	NN	_	_	_
47	:	:	:	_	_	_
48	bowtie	bowtie	NN	_	_	_
49	-	-	:	_	_	_
50	m	m	NN	_	_	_
51	1	1	CD	_	_	_
52	-	-	:	_	_	_
53	n	n	NN	_	_	_
54	1	1	CD	_	_	_
55	--	--	:	_	_	_
56	best	best	JJS	_	_	_
57	--	--	:	_	_	_
58	strata	strata	SYM	_	_	_
59	-	-	:	_	_	_
60	p	p	NN	_	_	_
61	4	4	CD	_	_	_
62	--	--	:	_	_	_
63	chunkmbs	chunkmb	NNS	_	_	_
64	512	512	CD	_	_	_
65	NA1000-bowtie	na1000-bowtie	NN	_	_	_
66	--	--	:	_	_	_
67	sam	sam	NN	_	_	_
68	*	*	NN	_	_	_
69	.	.	.	_	_	_

1	fastq	fastq	NN	_	_	_
2	>	>	JJR	_	_	_
3	output.sam	output.sam	NN	_	_	_
4	.	.	.	_	_	_

1	Subsequently	subsequently	RB	_	_	_
2	,	,	,	_	_	_
3	sequencing	sequencing	NN	_	_	_
4	reads	read	VBZ	_	_	_
5	were	be	VBD	_	_	_
6	sorted	sort	VBN	_	_	_
7	to	to	TO	_	_	_
8	either	either	CC	_	_	_
9	being	be	VBG	_	_	_
10	mapped	map	VBN	_	_	_
11	to	to	TO	_	_	_
12	the	the	DT	_	_	_
13	upper	upper	JJ	_	_	_
14	DNA	dna	NN	_	_	_
15	strand	strand	NN	_	_	_
16	or	or	CC	_	_	_
17	to	to	TO	_	_	_
18	the	the	DT	_	_	_
19	lower	lower	JJR	_	_	_
20	strand	strand	NN	_	_	_
21	of	of	IN	_	_	_
22	the	the	DT	_	_	_
23	reference	reference	NN	_	_	_
24	genome	genome	NN	_	_	_
25	,	,	,	_	_	_
26	as	as	IN	_	_	_
27	suggested	suggest	VBN	_	_	_
28	in	in	IN	_	_	_
29	the	the	DT	_	_	_
30	original	original	JJ	_	_	_
31	IDAP-seq	idap-seq	JJ	_	_	_
32	publication	publication	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	Belitsky	Belitsky	NNP	_	_	_
35	and	and	CC	_	_	_
36	Sonenshein	Sonenshein	NNP	_	_	_
37	,	,	,	_	_	_
38	2013	2013	CD	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	number	number	NN	_	_	_
3	of	of	IN	_	_	_
4	5	5	CD	_	_	_
5	'	'	''	_	_	_
6	end	end	NN	_	_	_
7	of	of	IN	_	_	_
8	reads	read	VBZ	_	_	_
9	that	that	DT	_	_	_
10	were	be	VBD	_	_	_
11	mapped	map	VBN	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	upper	upper	JJ	_	_	_
15	strand	strand	NN	_	_	_
16	was	be	VBD	_	_	_
17	counted	count	VBN	_	_	_
18	for	for	IN	_	_	_
19	each	each	DT	_	_	_
20	nucleotide	nucleotide	NN	_	_	_
21	position	position	NN	_	_	_
22	along	along	IN	_	_	_
23	the	the	DT	_	_	_
24	Caulobacter	Caulobacter	NNP	_	_	_
25	genome	genome	NN	_	_	_
26	using	use	VBG	_	_	_
27	BEDTools	bedtool	NNS	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Quinlan	Quinlan	NNP	_	_	_
30	&	&	CC	_	_	_
31	Hall	Hall	NNP	_	_	_
32	,	,	,	_	_	_
33	2010	2010	CD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	and	and	CC	_	_	_
36	the	the	DT	_	_	_
37	following	follow	VBG	_	_	_
38	command	command	NN	_	_	_
39	:	:	:	_	_	_
40	bedtools	bedtool	NNS	_	_	_
41	genomecov	genomecov	NN	_	_	_
42	-	-	:	_	_	_
43	d	d	NN	_	_	_
44	-5	-5	CD	_	_	_
45	-	-	:	_	_	_
46	strand	strand	NN	_	_	_
47	+	+	CC	_	_	_
48	-	-	:	_	_	_
49	ibam	ibam	NN	_	_	_
50	output.sorted.bam	output.sorted.bam	NN	_	_	_
51	-	-	:	_	_	_
52	g	g	NN	_	_	_
53	NA1000.fna	na1000.fna	NN	_	_	_
54	>	>	JJR	_	_	_
55	upper_strand_output.txt	upper_strand_output.txt	NN	_	_	_
56	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	count	count	VB	_	_	_
3	the	the	DT	_	_	_
4	number	number	NN	_	_	_
5	of	of	IN	_	_	_
6	5	5	CD	_	_	_
7	'	'	''	_	_	_
8	end	end	NN	_	_	_
9	of	of	IN	_	_	_
10	reads	read	VBZ	_	_	_
11	that	that	DT	_	_	_
12	were	be	VBD	_	_	_
13	mapped	map	VBN	_	_	_
14	to	to	TO	_	_	_
15	the	the	DT	_	_	_
16	lower	lower	JJR	_	_	_
17	strand	strand	NN	_	_	_
18	,	,	,	_	_	_
19	the	the	DT	_	_	_
20	following	follow	VBG	_	_	_
21	command	command	NN	_	_	_
22	was	be	VBD	_	_	_
23	used	use	VBN	_	_	_
24	instead	instead	RB	_	_	_
25	:	:	:	_	_	_
26	bedtools	bedtool	NNS	_	_	_
27	genomecov	genomecov	NN	_	_	_
28	-	-	:	_	_	_
29	d	d	NN	_	_	_
30	-5	-5	CD	_	_	_
31	-	-	:	_	_	_
32	strand	strand	NN	_	_	_
33	-	-	:	_	_	_
34	-	-	:	_	_	_
35	ibam	ibam	NN	_	_	_
36	output.sorted.bam	output.sorted.bam	NN	_	_	_
37	-	-	:	_	_	_
38	g	g	NN	_	_	_
39	NA1000.fna	na1000.fna	NN	_	_	_
40	>	>	JJR	_	_	_
41	lower_strand_output.txt	lower_strand_output.txt	NN	_	_	_
42	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	IDAP-seq	idap-seq	JJ	_	_	_
3	profile	profile	NN	_	_	_
4	was	be	VBD	_	_	_
5	then	then	RB	_	_	_
6	plotted	plot	VBN	_	_	_
7	using	use	VBG	_	_	_
8	R	r	NN	_	_	_
9	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	sequence	sequence	NN	_	_	_
3	in	in	IN	_	_	_
4	between	between	IN	_	_	_
5	the	the	DT	_	_	_
6	summit	summit	NN	_	_	_
7	of	of	IN	_	_	_
8	upper	upper	JJ	_	_	_
9	strand	strand	NN	_	_	_
10	profile	profile	NN	_	_	_
11	and	and	CC	_	_	_
12	that	that	IN	_	_	_
13	of	of	IN	_	_	_
14	the	the	DT	_	_	_
15	lower	lower	JJR	_	_	_
16	strand	strand	NN	_	_	_
17	profile	profile	NN	_	_	_
18	defines	define	VBZ	_	_	_
19	the	the	DT	_	_	_
20	minimal	minimal	JJ	_	_	_
21	parS	pars	NN	_	_	_
22	sequence	sequence	NN	_	_	_
23	required	require	VBN	_	_	_
24	for	for	IN	_	_	_
25	binding	bind	VBG	_	_	_
26	to	to	TO	_	_	_
27	ParB	parb	NN	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	NC	NC	NNP	_	_	_
7	_	_	NNP	_	_	_
8	000913.3	000913.3	CD	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	Genome	Genome	NNP	_	_	_
11	_	_	NNP	_	_	_
12	build	build	VB	_	_	_
13	:	:	:	_	_	_
14	NC	NC	NNP	_	_	_
15	_	_	NNP	_	_	_
16	011916.1	011916.1	CD	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	genotype	genotype	NN	_	_	_
19	:	:	:	_	_	_
20	AB1157	ab1157	NN	_	_	_
21	ybbD	ybbd	NN	GEN	_	_
22	:	:	:	_	_	_
23	:	:	:	_	_	_
24	parS	pars	NN	_	_	_
25	scrambled	scramble	VBD	_	_	_
26	site	site	NN	_	_	_
27	3	3	CD	_	_	_
28	pUTC18	putc18	NN	_	_	_
29	:	:	:	_	_	_
30	:	:	:	_	_	_
31	parB	parb	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	G101S	g101s	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	genotype	genotype	NN	_	_	_
37	:	:	:	_	_	_
38	AB1157	ab1157	NN	_	_	_
39	ybbD	ybbd	NN	GEN	_	_
40	:	:	:	_	_	_
41	:	:	:	_	_	_
42	parS	pars	NN	_	_	_
43	scrambled	scramble	VBD	_	_	_
44	site	site	NN	_	_	_
45	3	3	CD	_	_	_
46	pUTC18	putc18	NN	_	_	_
47	:	:	:	_	_	_
48	:	:	:	_	_	_
49	parB	parb	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	WT	wt	NN	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	genotype	genotype	NN	_	_	_
55	:	:	:	_	_	_
56	AB1157	ab1157	NN	_	_	_
57	ybbD	ybbd	NN	GEN	_	_
58	:	:	:	_	_	_
59	:	:	:	_	_	_
60	parS	pars	NN	_	_	_
61	site	site	NN	_	_	_
62	1	1	CD	_	_	_
63	pUTC18	putc18	NN	_	_	_
64	:	:	:	_	_	_
65	:	:	:	_	_	_
66	parB	parb	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	WT	wt	NN	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	genotype	genotype	NN	_	_	_
72	:	:	:	_	_	_
73	AB1157	ab1157	NN	_	_	_
74	ybbD	ybbd	NN	GEN	_	_
75	:	:	:	_	_	_
76	:	:	:	_	_	_
77	parS	pars	NN	_	_	_
78	site	site	NN	_	_	_
79	2	2	CD	_	_	_
80	pUTC18	putc18	NN	_	_	_
81	:	:	:	_	_	_
82	:	:	:	_	_	_
83	parB	parb	NN	_	_	_
84	-LRB-	-lrb-	-LRB-	_	_	_
85	G101S	g101s	NN	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	genotype	genotype	NN	_	_	_
89	:	:	:	_	_	_
90	AB1157	ab1157	NN	_	_	_
91	ybbD	ybbd	NN	GEN	_	_
92	:	:	:	_	_	_
93	:	:	:	_	_	_
94	parS	pars	NN	_	_	_
95	site	site	NN	_	_	_
96	2	2	CD	_	_	_
97	pUTC18	putc18	NN	_	_	_
98	:	:	:	_	_	_
99	:	:	:	_	_	_
100	parB	parb	NN	_	_	_
101	-LRB-	-lrb-	-LRB-	_	_	_
102	WT	wt	NN	_	_	_
103	-RRB-	-rrb-	-RRB-	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	genotype	genotype	NN	_	_	_
106	:	:	:	_	_	_
107	AB1157	ab1157	NN	_	_	_
108	ybbD	ybbd	NN	GEN	_	_
109	:	:	:	_	_	_
110	:	:	:	_	_	_
111	parS	pars	NN	_	_	_
112	site	site	NN	_	_	_
113	3	3	CD	_	_	_
114	pUTC18	putc18	NN	_	_	_
115	:	:	:	_	_	_
116	:	:	:	_	_	_
117	parB	parb	NN	_	_	_
118	-LRB-	-lrb-	-LRB-	_	_	_
119	G101S	g101s	NN	_	_	_
120	-RRB-	-rrb-	-RRB-	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	genotype	genotype	NN	_	_	_
123	:	:	:	_	_	_
124	AB1157	ab1157	NN	_	_	_
125	ybbD	ybbd	NN	GEN	_	_
126	:	:	:	_	_	_
127	:	:	:	_	_	_
128	parS	pars	NN	_	_	_
129	site	site	NN	_	_	_
130	3	3	CD	_	_	_
131	pUTC18	putc18	NN	_	_	_
132	:	:	:	_	_	_
133	:	:	:	_	_	_
134	parB	parb	NN	_	_	_
135	-LRB-	-lrb-	-LRB-	_	_	_
136	WT	wt	NN	_	_	_
137	-RRB-	-rrb-	-RRB-	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	genotype	genotype	NN	_	_	_
140	:	:	:	_	_	_
141	AB1157	ab1157	NN	_	_	_
142	ybbD	ybbd	NN	GEN	_	_
143	:	:	:	_	_	_
144	:	:	:	_	_	_
145	parS	pars	NN	_	_	_
146	site	site	NN	_	_	_
147	4	4	CD	_	_	_
148	pUTC18	putc18	NN	_	_	_
149	:	:	:	_	_	_
150	:	:	:	_	_	_
151	parB	parb	NN	_	_	_
152	-LRB-	-lrb-	-LRB-	_	_	_
153	G101S	g101s	NN	_	_	_
154	-RRB-	-rrb-	-RRB-	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	genotype	genotype	NN	_	_	_
157	:	:	:	_	_	_
158	AB1157	ab1157	NN	_	_	_
159	ybbD	ybbd	NN	GEN	_	_
160	:	:	:	_	_	_
161	:	:	:	_	_	_
162	parS	pars	NN	_	_	_
163	site	site	NN	_	_	_
164	4	4	CD	_	_	_
165	pUTC18	putc18	NN	_	_	_
166	:	:	:	_	_	_
167	:	:	:	_	_	_
168	parB	parb	NN	_	_	_
169	-LRB-	-lrb-	-LRB-	_	_	_
170	WT	wt	NN	_	_	_
171	-RRB-	-rrb-	-RRB-	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	genotype	genotype	NN	_	_	_
174	:	:	:	_	_	_
175	AB1157	ab1157	NN	_	_	_
176	ybbD	ybbd	NN	GEN	_	_
177	:	:	:	_	_	_
178	:	:	:	_	_	_
179	parS	pars	NN	_	_	_
180	site	site	NN	_	_	_
181	5	5	CD	_	_	_
182	pUTC18	putc18	NN	_	_	_
183	:	:	:	_	_	_
184	:	:	:	_	_	_
185	parB	parb	NN	_	_	_
186	-LRB-	-lrb-	-LRB-	_	_	_
187	G101S	g101s	NN	_	_	_
188	-RRB-	-rrb-	-RRB-	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	genotype	genotype	NN	_	_	_
191	:	:	:	_	_	_
192	AB1157	ab1157	NN	_	_	_
193	ybbD	ybbd	NN	GEN	_	_
194	:	:	:	_	_	_
195	:	:	:	_	_	_
196	parS	pars	NN	_	_	_
197	site	site	NN	_	_	_
198	5	5	CD	_	_	_
199	pUTC18	putc18	NN	_	_	_
200	:	:	:	_	_	_
201	:	:	:	_	_	_
202	parB	parb	NN	_	_	_
203	-LRB-	-lrb-	-LRB-	_	_	_
204	WT	wt	NN	_	_	_
205	-RRB-	-rrb-	-RRB-	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	genotype	genotype	NN	_	_	_
208	:	:	:	_	_	_
209	AB1157	ab1157	NN	_	_	_
210	ybbD	ybbd	NN	GEN	_	_
211	:	:	:	_	_	_
212	:	:	:	_	_	_
213	parS	pars	NN	_	_	_
214	site	site	NN	_	_	_
215	6	6	CD	_	_	_
216	pUTC18	putc18	NN	_	_	_
217	:	:	:	_	_	_
218	:	:	:	_	_	_
219	parB	parb	NN	_	_	_
220	-LRB-	-lrb-	-LRB-	_	_	_
221	WT	wt	NN	_	_	_
222	-RRB-	-rrb-	-RRB-	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	genotype	genotype	NN	_	_	_
225	:	:	:	_	_	_
226	AB1157	ab1157	NN	_	_	_
227	ybbD	ybbd	NN	GEN	_	_
228	:	:	:	_	_	_
229	:	:	:	_	_	_
230	parS	pars	NN	_	_	_
231	site	site	NN	_	_	_
232	7	7	CD	_	_	_
233	pUTC18	putc18	NN	_	_	_
234	:	:	:	_	_	_
235	:	:	:	_	_	_
236	parB	parb	NN	_	_	_
237	-LRB-	-lrb-	-LRB-	_	_	_
238	G101S	g101s	NN	_	_	_
239	-RRB-	-rrb-	-RRB-	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
241	genotype	genotype	NN	_	_	_
242	:	:	:	_	_	_
243	AB1157	ab1157	NN	_	_	_
244	ybbD	ybbd	NN	GEN	_	_
245	:	:	:	_	_	_
246	:	:	:	_	_	_
247	parS	pars	NN	_	_	_
248	site	site	NN	_	_	_
249	7	7	CD	_	_	_
250	pUTC18	putc18	NN	_	_	_
251	:	:	:	_	_	_
252	:	:	:	_	_	_
253	parB	parb	NN	_	_	_
254	-LRB-	-lrb-	-LRB-	_	_	_
255	WT	wt	NN	_	_	_
256	-RRB-	-rrb-	-RRB-	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	Hiseq	hiseq	JJ	_	_	_
259	2500	2500	CD	_	_	_
260	Illumina	Illumina	NNP	_	_	_
261	short	short	JJ	_	_	_
262	reads	read	VBZ	_	_	_
263	-LRB-	-lrb-	-LRB-	_	_	_
264	50	50	CD	_	_	_
265	bp	bp	NN	_	_	_
266	-RRB-	-rrb-	-RRB-	_	_	_
267	were	be	VBD	_	_	_
268	mapped	map	VBN	_	_	_
269	back	back	RB	_	_	_
270	to	to	TO	_	_	_
271	the	the	DT	_	_	_
272	Caulobacter	Caulobacter	NNP	_	_	_
273	NA1000	na1000	NN	_	_	_
274	reference	reference	NN	_	_	_
275	genome	genome	NN	_	_	_
276	-LRB-	-lrb-	-LRB-	_	_	_
277	NCBI	ncbi	NN	_	_	_
278	Reference	Reference	NNP	_	_	_
279	Sequence	sequence	NN	_	_	_
280	:	:	:	_	_	_
281	NC-011916.1	nc-011916.1	NN	_	_	_
282	-RRB-	-rrb-	-RRB-	_	_	_
283	using	use	VBG	_	_	_
284	Bowtie	Bowtie	NNP	_	_	_
285	1	1	CD	_	_	_
286	-LRB-	-lrb-	-LRB-	_	_	_
287	Langmead	Langmead	NNP	_	_	_
288	et	et	FW	_	_	_
289	al.	al.	FW	_	_	_
290	,	,	,	_	_	_
291	2009	2009	CD	_	_	_
292	-RRB-	-rrb-	-RRB-	_	_	_
293	and	and	CC	_	_	_
294	the	the	DT	_	_	_
295	following	follow	VBG	_	_	_
296	command	command	NN	_	_	_
297	:	:	:	_	_	_
298	bowtie	bowtie	NN	_	_	_
299	-	-	:	_	_	_
300	m	m	NN	_	_	_
301	1	1	CD	_	_	_
302	-	-	:	_	_	_
303	n	n	NN	_	_	_
304	1	1	CD	_	_	_
305	--	--	:	_	_	_
306	best	best	JJS	_	_	_
307	--	--	:	_	_	_
308	strata	strata	SYM	_	_	_
309	-	-	:	_	_	_
310	p	p	NN	_	_	_
311	4	4	CD	_	_	_
312	--	--	:	_	_	_
313	chunkmbs	chunkmb	NNS	_	_	_
314	512	512	CD	_	_	_
315	NA1000-bowtie	na1000-bowtie	NN	_	_	_
316	--	--	:	_	_	_
317	sam	sam	NN	_	_	_
318	*	*	NN	_	_	_
319	.	.	.	_	_	_

1	fastq	fastq	NN	_	_	_
2	>	>	JJR	_	_	_
3	output.sam	output.sam	NN	_	_	_
4	.	.	.	_	_	_

1	Subsequently	subsequently	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	sequencing	sequencing	NN	_	_	_
5	coverage	coverage	NN	_	_	_
6	for	for	IN	_	_	_
7	each	each	DT	_	_	_
8	nucleotide	nucleotide	NN	_	_	_
9	position	position	NN	_	_	_
10	was	be	VBD	_	_	_
11	computed	compute	VBN	_	_	_
12	using	use	VBG	_	_	_
13	BEDTools	bedtool	NNS	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Quinlan	Quinlan	NNP	_	_	_
16	&	&	CC	_	_	_
17	Hall	Hall	NNP	_	_	_
18	,	,	,	_	_	_
19	2010	2010	CD	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	and	and	CC	_	_	_
22	the	the	DT	_	_	_
23	following	follow	VBG	_	_	_
24	command	command	NN	_	_	_
25	:	:	:	_	_	_
26	bedtools	bedtool	NNS	_	_	_
27	genomecov	genomecov	NN	_	_	_
28	-	-	:	_	_	_
29	d	d	SYM	_	_	_
30	-	-	:	_	_	_
31	ibam	ibam	NN	_	_	_
32	output.sorted.bam	output.sorted.bam	NN	_	_	_
33	-	-	:	_	_	_
34	g	g	NN	_	_	_
35	NA1000.fna	na1000.fna	NN	_	_	_
36	>	>	JJR	_	_	_
37	coverage_output.txt	coverage_output.txt	NN	_	_	_
38	.	.	.	_	_	_

1	Finally	finally	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	ratio	ratio	NN	_	_	_
5	between	between	IN	_	_	_
6	the	the	DT	_	_	_
7	number	number	NN	_	_	_
8	of	of	IN	_	_	_
9	reads	read	VBZ	_	_	_
10	of	of	IN	_	_	_
11	libraries	library	NNS	_	_	_
12	generated	generate	VBN	_	_	_
13	from	from	IN	_	_	_
14	pMCS1-Tn5-ME-R6Kγ-kanR-ME	pmcs1-tn5-me-r6kγ-kanr-me	NN	_	_	_
15	or	or	CC	_	_	_
16	pMCS1-Tn5-ME-R6Kγ-kanR-parS456-ME	pmcs1-tn5-me-r6kγ-kanr-pars456-me	NN	_	_	_
17	were	be	VBD	_	_	_
18	calculated	calculate	VBN	_	_	_
19	.	.	.	_	_	_

1	Results	result	NNS	_	_	_
2	were	be	VBD	_	_	_
3	binned	bin	VBN	_	_	_
4	over	over	IN	_	_	_
5	1	1	CD	_	_	_
6	kb	kb	NN	_	_	_
7	and	and	CC	_	_	_
8	represented	represent	VBN	_	_	_
9	as	as	IN	_	_	_
10	a	a	DT	_	_	_
11	log10	log10	NN	_	_	_
12	scale	scale	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	LELab	lelab	NN	_	_	_
3	_	_	CD	_	_	_
4	ChIP	chip	NN	_	_	_
5	_	_	SYM	_	_	_
6	seq	seq	FW	_	_	_
7	_	_	FW	_	_	_
8	TLS1637	tls1637	NN	_	_	_
9	_	_	NN	_	_	_
10	anti	anti	JJ	_	_	_
11	_	_	CD	_	_	_
12	FLAG	flag	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	LELab	lelab	NN	_	_	_
15	_	_	CD	_	_	_
16	ChIP	chip	NN	_	_	_
17	_	_	SYM	_	_	_
18	seq	seq	FW	_	_	_
19	_	_	FW	_	_	_
20	TLS1638	tls1638	NN	_	_	_
21	_	_	NN	_	_	_
22	anti	anti	JJ	_	_	_
23	_	_	CD	_	_	_
24	FLAG	flag	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	LELab	lelab	NN	_	_	_
27	_	_	CD	_	_	_
28	ChIP	chip	NN	_	_	_
29	_	_	SYM	_	_	_
30	seq	seq	FW	_	_	_
31	_	_	FW	_	_	_
32	TLS1639	tls1639	NN	_	_	_
33	_	_	NN	_	_	_
34	anti	anti	JJ	_	_	_
35	_	_	CD	_	_	_
36	FLAG	flag	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	LELab	lelab	NN	_	_	_
39	_	_	CD	_	_	_
40	ChIP	chip	NN	_	_	_
41	_	_	SYM	_	_	_
42	seq	seq	FW	_	_	_
43	_	_	FW	_	_	_
44	TLS1640	tls1640	NN	_	_	_
45	_	_	NN	_	_	_
46	anti	anti	JJ	_	_	_
47	_	_	CD	_	_	_
48	FLAG	flag	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	LELab	lelab	NN	_	_	_
51	_	_	CD	_	_	_
52	ChIP	chip	NN	_	_	_
53	_	_	SYM	_	_	_
54	seq	seq	FW	_	_	_
55	_	_	FW	_	_	_
56	TLS1641	tls1641	NN	_	_	_
57	_	_	NN	_	_	_
58	anti	anti	JJ	_	_	_
59	_	_	CD	_	_	_
60	FLAG	flag	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	LELab	lelab	NN	_	_	_
63	_	_	CD	_	_	_
64	ChIP	chip	NN	_	_	_
65	_	_	SYM	_	_	_
66	seq	seq	FW	_	_	_
67	_	_	FW	_	_	_
68	TLS1642	tls1642	NN	_	_	_
69	_	_	NN	_	_	_
70	anti	anti	JJ	_	_	_
71	_	_	CD	_	_	_
72	FLAG	flag	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	LELAb	lelab	NN	_	_	_
75	_	_	CD	_	_	_
76	ChIP	chip	NN	_	_	_
77	_	_	SYM	_	_	_
78	seq	seq	FW	_	_	_
79	_	_	FW	_	_	_
80	TLS1643	tls1643	NN	_	_	_
81	_	_	NN	_	_	_
82	anti	anti	JJ	_	_	_
83	_	_	CD	_	_	_
84	FLAG	flag	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	LELab	lelab	NN	_	_	_
87	_	_	CD	_	_	_
88	ChIP	chip	NN	_	_	_
89	_	_	SYM	_	_	_
90	seq	seq	FW	_	_	_
91	_	_	FW	_	_	_
92	TLS1644	tls1644	NN	_	_	_
93	_	_	NN	_	_	_
94	anti	anti	JJ	_	_	_
95	_	_	CD	_	_	_
96	FLAG	flag	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	LELab	lelab	NN	_	_	_
99	_	_	CD	_	_	_
100	ChIP	chip	NN	_	_	_
101	_	_	SYM	_	_	_
102	seq	seq	FW	_	_	_
103	_	_	FW	_	_	_
104	TLS1645	tls1645	NN	_	_	_
105	_	_	NN	_	_	_
106	anti	anti	JJ	_	_	_
107	_	_	CD	_	_	_
108	FLAG	flag	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	LELab	lelab	NN	_	_	_
111	_	_	CD	_	_	_
112	ChIP	chip	NN	_	_	_
113	_	_	SYM	_	_	_
114	seq	seq	FW	_	_	_
115	_	_	FW	_	_	_
116	TLS1646	tls1646	NN	_	_	_
117	_	_	NN	_	_	_
118	anti	anti	JJ	_	_	_
119	_	_	CD	_	_	_
120	FLAG	flag	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	LELab	lelab	NN	_	_	_
123	_	_	CD	_	_	_
124	ChIP	chip	NN	_	_	_
125	_	_	SYM	_	_	_
126	seq	seq	FW	_	_	_
127	_	_	FW	_	_	_
128	TLS1647	tls1647	NN	_	_	_
129	_	_	NN	_	_	_
130	anti	anti	JJ	_	_	_
131	_	_	CD	_	_	_
132	FLAG	flag	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	LELab	lelab	NN	_	_	_
135	_	_	CD	_	_	_
136	ChIP	chip	NN	_	_	_
137	_	_	SYM	_	_	_
138	seq	seq	FW	_	_	_
139	_	_	FW	_	_	_
140	TLS1648	tls1648	NN	_	_	_
141	_	_	NN	_	_	_
142	anti	anti	JJ	_	_	_
143	_	_	CD	_	_	_
144	FLAG	flag	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	LELab	lelab	NN	_	_	_
147	_	_	CD	_	_	_
148	ChIP	chip	NN	_	_	_
149	_	_	SYM	_	_	_
150	seq	seq	FW	_	_	_
151	_	_	FW	_	_	_
152	TLS1649	tls1649	NN	_	_	_
153	_	_	NN	_	_	_
154	anti	anti	JJ	_	_	_
155	_	_	CD	_	_	_
156	FLAG	flag	NN	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	LELab	lelab	NN	_	_	_
159	_	_	CD	_	_	_
160	ChIP	chip	NN	_	_	_
161	_	_	SYM	_	_	_
162	seq	seq	FW	_	_	_
163	_	_	FW	_	_	_
164	TLS1650	tls1650	NN	_	_	_
165	_	_	NN	_	_	_
166	anti	anti	JJ	_	_	_
167	_	_	CD	_	_	_
168	FLAG	flag	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	None	none	NN	_	_	_
171	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
172	Standard	Standard	NNP	_	_	_
173	library	library	NN	_	_	_
174	construction	construction	NN	_	_	_
175	for	for	IN	_	_	_
176	Illumina	Illumina	NNP	_	_	_
177	Hiseq2500	hiseq2500	NN	_	_	_
178	sequencing	sequencing	NN	_	_	_
179	platform	platform	NN	_	_	_
180	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
181	Supplementary	Supplementary	NNP	_	_	_
182	_	_	VBD	_	_	_
183	files	file	NNS	_	_	_
184	_	_	IN	_	_	_
185	format	format	NN	_	_	_
186	_	_	NN	_	_	_
187	and	and	CC	_	_	_
188	_	_	NN	_	_	_
189	content	content	NN	_	_	_
190	:	:	:	_	_	_
191	Files	file	NNS	_	_	_
192	ending	end	VBG	_	_	_
193	with	with	IN	_	_	_
194	_	_	CD	_	_	_
195	coverage.txt	coverage.txt	NN	_	_	_
196	:	:	:	_	_	_
197	tab-delimited	tab-delimited	JJ	_	_	_
198	text	text	NN	_	_	_
199	file	file	NN	_	_	_
200	of	of	IN	_	_	_
201	nucleotide-resolution	nucleotide-resolution	JJ	_	_	_
202	coverage	coverage	NN	_	_	_
203	from	from	IN	_	_	_
204	RNA-seq	rna-seq	JJ	_	_	_
205	data	datum	NNS	_	_	_
206	-LRB-	-lrb-	-LRB-	_	_	_
207	column	column	NN	_	_	_
208	1	1	CD	_	_	_
209	:	:	:	_	_	_
210	genome	genome	NN	_	_	_
211	ID	id	NN	_	_	_
212	,	,	,	_	_	_
213	column	column	NN	_	_	_
214	2	2	CD	_	_	_
215	:	:	:	_	_	_
216	nucleotide	nucleotide	NN	_	_	_
217	position	position	NN	_	_	_
218	,	,	,	_	_	_
219	column	column	NN	_	_	_
220	3	3	CD	_	_	_
221	:	:	:	_	_	_
222	coverage	coverage	NN	_	_	_
223	-RRB-	-rrb-	-RRB-	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
225	T18-ParB	t18-parb	NN	_	_	_
226	-LRB-	-lrb-	-LRB-	_	_	_
227	G101S	g101s	NN	_	_	_
228	-RRB-	-rrb-	-RRB-	_	_	_
229	were	be	VBD	_	_	_
230	produced	produce	VBN	_	_	_
231	by	by	IN	_	_	_
232	addition	addition	NN	_	_	_
233	of	of	IN	_	_	_
234	0.5	0.5	CD	_	_	_
235	mM	mm	NN	KWSUPP	_	_
236	IPTG	iptg	NN	_	_	_
237	for	for	IN	_	_	_
238	an	a	DT	_	_	_
239	hour	hour	NN	_	_	_
240	before	before	IN	_	_	_
241	formadehyde	formadehyde	NN	_	_	_
242	to	to	TO	_	_	_
243	1	1	CD	_	_	_
244	%	%	NN	_	_	_
245	-LRB-	-lrb-	-LRB-	_	_	_
246	final	final	JJ	_	_	_
247	concentration	concentration	NN	_	_	_
248	-RRB-	-rrb-	-RRB-	_	_	_
249	was	be	VBD	_	_	_
250	added	add	VBN	_	_	_
251	to	to	TO	_	_	_
252	fix	fix	VB	_	_	_
253	cells	cell	NNS	_	_	_
254	for	for	IN	_	_	_
255	ChIP-seq	ChIP-seq	NNP	_	_	_
256	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
257	T18-ParB	t18-parb	NN	_	_	_
258	-LRB-	-lrb-	-LRB-	_	_	_
259	WT	wt	NN	_	_	_
260	-RRB-	-rrb-	-RRB-	_	_	_
261	were	be	VBD	_	_	_
262	produced	produce	VBN	_	_	_
263	by	by	IN	_	_	_
264	addition	addition	NN	_	_	_
265	of	of	IN	_	_	_
266	0.5	0.5	CD	_	_	_
267	mM	mm	NN	KWSUPP	_	_
268	IPTG	iptg	NN	_	_	_
269	for	for	IN	_	_	_
270	an	a	DT	_	_	_
271	hour	hour	NN	_	_	_
272	before	before	IN	_	_	_
273	formadehyde	formadehyde	NN	_	_	_
274	to	to	TO	_	_	_
275	1	1	CD	_	_	_
276	%	%	NN	_	_	_
277	-LRB-	-lrb-	-LRB-	_	_	_
278	final	final	JJ	_	_	_
279	concentration	concentration	NN	_	_	_
280	-RRB-	-rrb-	-RRB-	_	_	_
281	was	be	VBD	_	_	_
282	added	add	VBN	_	_	_
283	to	to	TO	_	_	_
284	fix	fix	VB	_	_	_
285	cells	cell	NNS	_	_	_
286	for	for	IN	_	_	_
287	ChIP-seq	ChIP-seq	NNP	_	_	_
288	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
289	Adapter	Adapter	NNP	_	_	_
290	cutting	cut	VBG	_	_	_
291	using	use	VBG	_	_	_
292	cutadapt	cutadapt	NN	_	_	_
293	,	,	,	_	_	_
294	version	version	NN	_	_	_
295	1.8.3	1.8.3	CD	_	_	_
296	,	,	,	_	_	_
297	parameters	parameter	NNS	_	_	_
298	-	-	:	_	_	_
299	e	e	SYM	_	_	_
300	0.1	0.1	CD	_	_	_
301	-	-	:	_	_	_
302	O	o	NN	_	_	_
303	1	1	CD	_	_	_
304	-	-	:	_	_	_
305	m	m	NN	_	_	_
306	12	12	CD	_	_	_
307	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
308	E.	E.	NNP	_	_	_
309	coli	coli	NN	_	_	_
310	CMA540	cma540	NN	_	_	_
311	-LRB-	-lrb-	-LRB-	_	_	_
312	MG1693	mg1693	NN	_	_	_
313	∆	∆	CD	_	_	_
314	hfq	hfq	NN	GEN	_	_
315	:	:	:	_	_	_
316	:	:	:	_	_	_
317	cat	cat	NN	_	_	_
318	-RRB-	-rrb-	-RRB-	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
320	E.	e.	FW	_	_	_
321	coli	coli	FW	_	_	_
322	MG1693	mg1693	NN	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	Escherichia	escherichia	FW	Organism	_	_
325	coli	coli	FW	Organism	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	Genome	Genome	NNP	_	_	_
328	_	_	NNP	_	_	_
329	build	build	VB	_	_	_
330	:	:	:	_	_	_
331	U00096	u00096	NN	_	_	_
332	.3	.3	NN	_	_	_
333	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
334	Genome	Genome	NNP	_	_	_
335	mapping	mapping	NN	_	_	_
336	using	use	VBG	_	_	_
337	Bowtie	Bowtie	NNP	_	_	_
338	,	,	,	_	_	_
339	version	version	NN	_	_	_
340	1.1.2	1.1.2	CD	_	_	_
341	,	,	,	_	_	_
342	parameters	parameter	NNS	_	_	_
343	for	for	IN	_	_	_
344	samples	sample	NNS	_	_	_
345	1-2	1-2	CD	_	_	_
346	:	:	:	_	_	_
347	-	-	:	_	_	_
348	v	v	LS	_	_	_
349	2	2	CD	_	_	_
350	--	--	:	_	_	_
351	best	best	JJS	_	_	_
352	--	--	:	_	_	_
353	strata	strata	SYM	_	_	_
354	-	-	:	_	_	_
355	m	m	NN	_	_	_
356	1	1	CD	_	_	_
357	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
358	growth	growth	NN	_	_	_
359	phase	phase	NN	_	_	_
360	:	:	:	_	_	_
361	Exponential	exponential	JJ	_	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
363	Hfq	hfq	NN	_	_	_
364	mut	mut	NN	_	_	_
365	exp	exp	NN	_	_	_
366	mRNA	mrna	NN	_	_	_
367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
368	Hfq	hfq	NN	_	_	_
369	mut	mut	NN	_	_	_
370	exp	exp	NN	_	_	_
371	RPF	rpf	NN	_	_	_
372	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
373	Quality	quality	JJ	_	_	_
374	trimming	trim	VBG	_	_	_
375	using	use	VBG	_	_	_
376	FASTX-toolkit	fastx-toolkit	NN	_	_	_
377	,	,	,	_	_	_
378	version	version	NN	_	_	_
379	0.0.13.2	0.0.13.2	CD	_	_	_
380	,	,	,	_	_	_
381	parameters	parameter	NNS	_	_	_
382	-	-	:	_	_	_
383	v	v	LS	_	_	_
384	-	-	:	_	_	_
385	t	t	NN	_	_	_
386	20	20	CD	_	_	_
387	-	-	:	_	_	_
388	l	l	NN	_	_	_
389	10	10	CD	_	_	_
390	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
391	Read	read	VBP	_	_	_
392	counting	count	VBG	_	_	_
393	using	use	VBG	_	_	_
394	bedtools	bedtool	NNS	_	_	_
395	,	,	,	_	_	_
396	version	version	NN	_	_	_
397	2.17.0	2.17.0	CD	_	_	_
398	,	,	,	_	_	_
399	parameter	parameter	NN	_	_	_
400	:	:	:	_	_	_
401	-	-	:	_	_	_
402	s	s	NNS	_	_	_
403	,	,	,	_	_	_
404	the	the	DT	_	_	_
405	middle	middle	JJ	_	_	_
406	nucleotide	nucleotide	NN	_	_	_
407	of	of	IN	_	_	_
408	each	each	DT	_	_	_
409	read	read	NN	_	_	_
410	was	be	VBD	_	_	_
411	taken	take	VBN	_	_	_
412	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
413	RNA-Seq	rna-seq	NN	_	_	_
414	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
415	RNA-size	rna-size	NN	_	_	_
416	selection	selection	NN	_	_	_
417	and	and	CC	_	_	_
418	generation	generation	NN	_	_	_
419	of	of	IN	_	_	_
420	the	the	DT	_	_	_
421	cDNA	cdna	NN	_	_	_
422	libraries	library	NNS	_	_	_
423	was	be	VBD	_	_	_
424	performed	perform	VBN	_	_	_
425	as	as	IN	_	_	_
426	described	describe	VBN	_	_	_
427	-LCB-	-lcb-	-LRB-	_	_	_
428	Ingolia	Ingolia	NNP	_	_	_
429	,	,	,	_	_	_
430	2009	2009	CD	_	_	_
431	-RCB-	-rcb-	-RRB-	_	_	_
432	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
433	strain	strain	NN	_	_	_
434	:	:	:	_	_	_
435	CMA540	cma540	NN	_	_	_
436	-LRB-	-lrb-	-LRB-	_	_	_
437	MG1693	mg1693	NN	_	_	_
438	delta	delta	NN	_	_	_
439	_	_	NN	_	_	_
440	hfq	hfq	NN	GEN	_	_
441	:	:	:	_	_	_
442	:	:	:	_	_	_
443	cat	cat	NN	_	_	_
444	-RRB-	-rrb-	-RRB-	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	strain	strain	NN	_	_	_
447	:	:	:	_	_	_
448	MG1693	mg1693	NN	_	_	_
449	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
450	Strains	strain	NNS	_	_	_
451	were	be	VBD	_	_	_
452	grown	grow	VBN	_	_	_
453	in	in	IN	_	_	_
454	LB	lb	NN	MED	_	_
455	medium	medium	NN	MED	_	_
456	-LRB-	-lrb-	-LRB-	_	_	_
457	Difco	Difco	NNP	_	_	_
458	-RRB-	-rrb-	-RRB-	_	_	_
459	supplemented	supplement	VBN	_	_	_
460	with	with	IN	_	_	_
461	thymine	thymine	NN	_	_	_
462	-LRB-	-lrb-	-LRB-	_	_	_
463	50	50	CD	_	_	_
464	µg	µg	NN	_	_	_
465	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
466	Supplementary	supplementary	JJ	_	_	_
467	_	_	NN	_	_	_
468	files	file	NNS	_	_	_
469	_	_	IN	_	_	_
470	format	format	NN	_	_	_
471	_	_	NN	_	_	_
472	and	and	CC	_	_	_
473	_	_	NN	_	_	_
474	content	content	NN	_	_	_
475	:	:	:	_	_	_
476	Read	read	VB	_	_	_
477	counts	count	NNS	_	_	_
478	were	be	VBD	_	_	_
479	normalized	normalize	VBN	_	_	_
480	by	by	IN	_	_	_
481	the	the	DT	_	_	_
482	length	length	NN	_	_	_
483	of	of	IN	_	_	_
484	the	the	DT	_	_	_
485	unique	unique	JJ	_	_	_
486	CDS	cds	NN	_	_	_
487	per	per	IN	_	_	_
488	kilobase	kilobase	NN	_	_	_
489	-LRB-	-lrb-	-LRB-	_	_	_
490	RPKM	rpkm	NN	_	_	_
491	-RRB-	-rrb-	-RRB-	_	_	_
492	and	and	CC	_	_	_
493	the	the	DT	_	_	_
494	total	total	JJ	_	_	_
495	mapped	map	VBN	_	_	_
496	reads	read	VBZ	_	_	_
497	per	per	IN	_	_	_
498	million	million	CD	_	_	_
499	-LRB-	-lrb-	-LRB-	_	_	_
500	RPM	rpm	NN	_	_	_
501	-RRB-	-rrb-	-RRB-	_	_	_
502	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
503	Total	total	JJ	_	_	_
504	RNA	rna	NN	_	_	_
505	was	be	VBD	_	_	_
506	extracted	extract	VBN	_	_	_
507	using	use	VBG	_	_	_
508	TRI	TRI	NNP	_	_	_
509	Reagent	Reagent	NNP	_	_	_
510	-LRB-	-lrb-	-LRB-	_	_	_
511	Sigma	Sigma	NNP	_	_	_
512	Aldrich	Aldrich	NNP	_	_	_
513	-RRB-	-rrb-	-RRB-	_	_	_
514	,	,	,	_	_	_
515	enriched	enrich	VBN	_	_	_
516	by	by	IN	_	_	_
517	depleting	deplete	VBG	_	_	_
518	small	small	JJ	_	_	_
519	RNAs	rna	NNS	_	_	_
520	with	with	IN	_	_	_
521	GeneJET	GeneJET	NNP	_	_	_
522	Purification	purification	NN	_	_	_
523	Kit	kit	NN	_	_	_
524	-LRB-	-lrb-	-LRB-	_	_	_
525	Fermentas	fermentas	NN	_	_	_
526	-RRB-	-rrb-	-RRB-	_	_	_
527	and	and	CC	_	_	_
528	rRNA	rrna	NN	_	_	_
529	with	with	IN	_	_	_
530	MICROBExpres	microbexpre	NNS	_	_	_
531	Bacterial	bacterial	JJ	_	_	_
532	mRNA	mrna	NN	_	_	_
533	Enrichment	Enrichment	NNP	_	_	_
534	Kit	kit	NN	_	_	_
535	-LRB-	-lrb-	-LRB-	_	_	_
536	Ambion	ambion	NN	_	_	_
537	-RRB-	-rrb-	-RRB-	_	_	_
538	and	and	CC	_	_	_
539	fragmented	fragmented	JJ	_	_	_
540	in	in	IN	_	_	_
541	alkaline	alkaline	NN	_	_	_
542	solution	solution	NN	_	_	_
543	-LRB-	-lrb-	-LRB-	_	_	_
544	2	2	CD	_	_	_
545	mM	mm	NN	KWSUPP	_	_
546	EDTA	edta	NN	_	_	_
547	and	and	CC	_	_	_
548	100	100	CD	_	_	_
549	mM	mm	NN	KWSUPP	_	_
550	Na2CO3	na2co3	NN	_	_	_
551	pH	ph	NN	_	_	_
552	9.2	9.2	CD	_	_	_
553	for	for	IN	_	_	_
554	40	40	CD	_	_	_
555	min	min	NN	_	_	_
556	at	at	IN	_	_	_
557	95	95	CD	_	_	_
558	°C	°c	NN	_	_	_
559	-RRB-	-rrb-	-RRB-	_	_	_
560	to	to	TO	_	_	_
561	fragments	fragment	NNS	_	_	_
562	with	with	IN	_	_	_
563	size	size	NN	_	_	_
564	of	of	IN	_	_	_
565	24-35	24-35	CD	_	_	_
566	nts	nt	NNS	_	_	_
567	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	RPFS	rpf	NNS	_	_	_
3	,	,	,	_	_	_
4	cells	cell	NNS	_	_	_
5	were	be	VBD	_	_	_
6	lysed	lyse	VBN	_	_	_
7	by	by	IN	_	_	_
8	freeze-rupturing	freeze-rupturing	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Retch	Retch	NNP	_	_	_
11	Mill	Mill	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	100	100	CD	_	_	_
15	A260	a260	NN	_	_	_
16	units	unit	NNS	_	_	_
17	of	of	IN	_	_	_
18	ribosome-bound	ribosome-bound	JJ	_	_	_
19	mRNA	mrna	NN	_	_	_
20	fraction	fraction	NN	_	_	_
21	were	be	VBD	_	_	_
22	directly	directly	RB	_	_	_
23	used	use	VBN	_	_	_
24	for	for	IN	_	_	_
25	polysomal	polysomal	JJ	_	_	_
26	analysis	analysis	NN	_	_	_
27	or	or	CC	_	_	_
28	subjected	subject	VBN	_	_	_
29	to	to	TO	_	_	_
30	nucleolytic	nucleolytic	JJ	_	_	_
31	digestion	digestion	NN	_	_	_
32	with	with	IN	_	_	_
33	10	10	CD	_	_	_
34	units	unit	NNS	_	_	_
35	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
36	WT	WT	NNP	_	_	_
37	exp	exp	NN	_	_	_
38	mRNA	mrna	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	WT	wt	JJ	_	_	_
41	exp	exp	NN	_	_	_
42	RPF	rpf	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
44	All	all	DT	_	_	_
45	cultures	culture	NNS	_	_	_
46	were	be	VBD	_	_	_
47	grown	grow	VBN	_	_	_
48	at	at	IN	_	_	_
49	37C	37c	NN	_	_	_
50	in	in	IN	_	_	_
51	well-mixed	well-mixed	JJ	_	_	_
52	minimal	minimal	JJ	_	_	_
53	media	media	NNS	_	_	_
54	modified	modify	VBN	_	_	_
55	with	with	IN	_	_	_
56	M63	m63	NN	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	mM63	mm63	NN	_	_	_
59	:	:	:	_	_	_
60	pH	ph	NN	_	_	_
61	7.0	7.0	CD	_	_	_
62	,	,	,	_	_	_
63	62	62	CD	_	_	_
64	mM	mm	NN	KWSUPP	_	_
65	K2HPO4	k2hpo4	NN	_	_	_
66	,	,	,	_	_	_
67	39	39	CD	_	_	_
68	mM	mm	NN	KWSUPP	_	_
69	KH2PO4	kh2po4	NN	_	_	_
70	,	,	,	_	_	_
71	15	15	CD	_	_	_
72	mM	mm	NN	KWSUPP	_	_
73	ammonium	ammonium	NN	SUPP	_	_
74	sulfate	sulfate	NN	SUPP	_	_
75	,	,	,	_	_	_
76	1.8	1.8	CD	_	_	_
77	µM	µm	NN	_	_	_
78	FeSO4-7H2O	feso4-7h2o	NN	_	_	_
79	,	,	,	_	_	_
80	15	15	CD	_	_	_
81	µM	µm	NN	_	_	_
82	thiamine	thiamine	NN	SUPP	_	_
83	hydrochloride	hydrochloride	NN	SUPP	_	_
84	,	,	,	_	_	_
85	0.2	0.2	CD	_	_	_
86	mM	mm	NN	KWSUPP	_	_
87	MgSO4-7H2O	mgso4-7h2o	NN	_	_	_
88	and	and	CC	_	_	_
89	22	22	CD	_	_	_
90	mM	mm	NN	KWSUPP	_	_
91	glucose	glucose	NN	SUPP	_	_
92	-RRB-	-rrb-	-RRB-	_	_	_
93	.	.	.	_	_	_

1	One	one	CD	_	_	_
2	amino	amino	NN	_	_	_
3	acid	acid	NN	_	_	_
4	,	,	,	_	_	_
5	Ile	ile	NN	_	_	_
6	or	or	CC	_	_	_
7	Leu	leu	NN	_	_	_
8	,	,	,	_	_	_
9	was	be	VBD	_	_	_
10	added	add	VBN	_	_	_
11	to	to	TO	_	_	_
12	the	the	DT	_	_	_
13	monoculture	monoculture	NN	_	_	_
14	medium	medium	NN	_	_	_
15	when	when	WRB	_	_	_
16	appropriate	appropriate	JJ	_	_	_
17	.	.	.	_	_	_

1	Prior	prior	RB	_	_	_
2	to	to	TO	_	_	_
3	coculturing	coculturing	NN	_	_	_
4	,	,	,	_	_	_
5	at	at	IN	_	_	_
6	both	both	CC	_	_	_
7	the	the	DT	_	_	_
8	initial	initial	JJ	_	_	_
9	inoculation	inoculation	NN	_	_	_
10	and	and	CC	_	_	_
11	transfer	transfer	NN	_	_	_
12	,	,	,	_	_	_
13	we	we	PRP	_	_	_
14	washed	wash	VBD	_	_	_
15	the	the	DT	_	_	_
16	E.	e.	FW	_	_	_
17	coli	coli	FW	_	_	_
18	cells	cell	NNS	_	_	_
19	with	with	IN	_	_	_
20	fresh	fresh	JJ	_	_	_
21	mM63	mm63	NN	_	_	_
22	without	without	IN	_	_	_
23	amino	amino	NN	SUPP	_	_
24	acids	acid	NNS	SUPP	_	_
25	to	to	TO	_	_	_
26	exclude	exclude	VB	_	_	_
27	the	the	DT	_	_	_
28	carry-over	carry-over	NN	_	_	_
29	of	of	IN	_	_	_
30	supplements	supplement	NNS	_	_	_
31	from	from	IN	_	_	_
32	the	the	DT	_	_	_
33	pre-culture	pre-culture	JJ	_	_	_
34	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	coculture	coculture	NN	_	_	_
3	samples	sample	NNS	_	_	_
4	,	,	,	_	_	_
5	we	we	PRP	_	_	_
6	used	use	VBD	_	_	_
7	cell	cell	NN	_	_	_
8	culture	culture	NN	_	_	_
9	inserts	insert	NNS	_	_	_
10	with	with	IN	_	_	_
11	a	a	DT	_	_	_
12	pore	pore	NN	_	_	_
13	size	size	NN	_	_	_
14	of	of	IN	_	_	_
15	0.45	0.45	CD	_	_	_
16	µm	µm	NN	_	_	_
17	at	at	IN	_	_	_
18	a	a	DT	_	_	_
19	density	density	NN	_	_	_
20	of	of	IN	_	_	_
21	10	10	CD	_	_	_
22	^	^	CD	_	_	_
23	8	8	CD	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
25	Ancestral	ancestral	JJ	_	_	_
26	I	I	PRP	_	_	_
27	-	-	:	_	_	_
28	cells	cell	NNS	_	_	_
29	at	at	IN	_	_	_
30	amino	amino	NN	_	_	_
31	acid	acid	NN	_	_	_
32	starvation	starvation	NN	_	_	_
33	in	in	IN	_	_	_
34	monoculture	monoculture	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
36	Ancestral	ancestral	JJ	_	_	_
37	I	I	PRP	_	_	_
38	-	-	:	_	_	_
39	cells	cell	NNS	_	_	_
40	at	at	IN	_	_	_
41	log	log	NN	_	_	_
42	phase	phase	NN	_	_	_
43	in	in	IN	_	_	_
44	monoculture	monoculture	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
46	Ancestral	ancestral	JJ	_	_	_
47	I	I	PRP	_	_	_
48	-	-	:	_	_	_
49	cells	cell	NNS	_	_	_
50	in	in	IN	_	_	_
51	coculture	coculture	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	Ancestral	ancestral	JJ	_	_	_
54	I	I	PRP	_	_	_
55	-	-	:	_	_	_
56	cells	cell	NNS	_	_	_
57	in	in	IN	_	_	_
58	coculture	coculture	NN	_	_	_
59	,	,	,	_	_	_
60	a	a	DT	_	_	_
61	biological	biological	JJ	_	_	_
62	replicate	replicate	VB	_	_	_
63	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
64	Ancestral	ancestral	JJ	_	_	_
65	L	l	NN	_	_	_
66	-	-	:	_	_	_
67	cells	cell	NNS	_	_	_
68	at	at	IN	_	_	_
69	amino	amino	NN	_	_	_
70	acid	acid	NN	_	_	_
71	starvation	starvation	NN	_	_	_
72	in	in	IN	_	_	_
73	monoculture	monoculture	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	Ancestral	ancestral	JJ	_	_	_
76	L	l	NN	_	_	_
77	-	-	:	_	_	_
78	cells	cell	NNS	_	_	_
79	at	at	IN	_	_	_
80	log	log	NN	_	_	_
81	phase	phase	NN	_	_	_
82	in	in	IN	_	_	_
83	monoculture	monoculture	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	Ancestral	ancestral	JJ	_	_	_
86	L	l	NN	_	_	_
87	-	-	:	_	_	_
88	cells	cell	NNS	_	_	_
89	at	at	IN	_	_	_
90	log	log	NN	_	_	_
91	phase	phase	NN	_	_	_
92	in	in	IN	_	_	_
93	monoculture	monoculture	NN	_	_	_
94	,	,	,	_	_	_
95	a	a	DT	_	_	_
96	technical	technical	JJ	_	_	_
97	replicate	replicate	VB	_	_	_
98	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
99	Ancestral	ancestral	JJ	_	_	_
100	L	l	NN	_	_	_
101	-	-	:	_	_	_
102	cells	cell	NNS	_	_	_
103	in	in	IN	_	_	_
104	coculture	coculture	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	Ancestral	ancestral	JJ	_	_	_
107	L	l	NN	_	_	_
108	-	-	:	_	_	_
109	cells	cell	NNS	_	_	_
110	in	in	IN	_	_	_
111	coculture	coculture	NN	_	_	_
112	,	,	,	_	_	_
113	a	a	DT	_	_	_
114	biological	biological	JJ	_	_	_
115	replicate	replicate	VBP	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	cell	cell	NN	_	_	_
118	type	type	NN	_	_	_
119	:	:	:	_	_	_
120	Ancestral	ancestral	JJ	_	_	_
121	I	I	PRP	_	_	_
122	-	-	:	_	_	_
123	cells	cell	NNS	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	cell	cell	NN	_	_	_
126	type	type	NN	_	_	_
127	:	:	:	_	_	_
128	Ancestral	ancestral	JJ	_	_	_
129	L	l	NN	_	_	_
130	-	-	:	_	_	_
131	cells	cell	NNS	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	cell	cell	NN	_	_	_
134	type	type	NN	_	_	_
135	:	:	:	_	_	_
136	Evolved	evolve	VBN	_	_	_
137	I	I	PRP	_	_	_
138	-	-	:	_	_	_
139	cells	cell	NNS	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	cell	cell	NN	_	_	_
142	type	type	NN	_	_	_
143	:	:	:	_	_	_
144	Evolved	evolve	VBN	_	_	_
145	L	l	NN	_	_	_
146	-	-	:	_	_	_
147	cells	cell	NNS	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	cell	cell	NN	_	_	_
150	type	type	NN	_	_	_
151	:	:	:	_	_	_
152	Original	original	JJ	_	_	_
153	prototroph	prototroph	NN	_	_	_
154	DH1	dh1	NN	_	_	_
155	cells	cell	NNS	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
157	culture	culture	NN	_	_	_
158	type	type	NN	_	_	_
159	:	:	:	_	_	_
160	coculture	coculture	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	culture	culture	NN	_	_	_
163	type	type	NN	_	_	_
164	:	:	:	_	_	_
165	monoculture	monoculture	NN	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	DH1-log	dh1-log	JJ	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	DH1-log-tr	dh1-log-tr	JJ	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	Escherichia	escherichia	FW	Organism	_	_
172	coli	coli	FW	Organism	_	_
173	K-12	k-12	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	Evolved	evolve	VBD	_	_	_
176	I	I	PRP	_	_	_
177	-	-	:	_	_	_
178	cells	cell	NNS	_	_	_
179	at	at	IN	_	_	_
180	amino	amino	NN	_	_	_
181	acid	acid	NN	_	_	_
182	starvation	starvation	NN	_	_	_
183	in	in	IN	_	_	_
184	monoculture	monoculture	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	Evolved	evolve	VBD	_	_	_
187	I	I	PRP	_	_	_
188	-	-	:	_	_	_
189	cells	cell	NNS	_	_	_
190	at	at	IN	_	_	_
191	log	log	NN	_	_	_
192	phase	phase	NN	_	_	_
193	in	in	IN	_	_	_
194	monoculture	monoculture	NN	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	Evolved	evolve	VBD	_	_	_
197	I	I	PRP	_	_	_
198	-	-	:	_	_	_
199	cells	cell	NNS	_	_	_
200	in	in	IN	_	_	_
201	coculture	coculture	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	Evolved	evolve	VBD	_	_	_
204	I	I	PRP	_	_	_
205	-	-	:	_	_	_
206	cells	cell	NNS	_	_	_
207	in	in	IN	_	_	_
208	coculture	coculture	NN	_	_	_
209	,	,	,	_	_	_
210	a	a	DT	_	_	_
211	biological	biological	JJ	_	_	_
212	replicate	replicate	VBP	_	_	_
213	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
214	Evolved	evolve	VBD	_	_	_
215	L	l	NN	_	_	_
216	-	-	:	_	_	_
217	cells	cell	NNS	_	_	_
218	at	at	IN	_	_	_
219	amino	amino	NN	_	_	_
220	acid	acid	NN	_	_	_
221	starvation	starvation	NN	_	_	_
222	in	in	IN	_	_	_
223	monoculture	monoculture	NN	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
225	Evolved	evolve	VBD	_	_	_
226	L	l	NN	_	_	_
227	-	-	:	_	_	_
228	cells	cell	NNS	_	_	_
229	at	at	IN	_	_	_
230	log	log	NN	_	_	_
231	phase	phase	NN	_	_	_
232	in	in	IN	_	_	_
233	monoculture	monoculture	NN	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	Evolved	evolve	VBD	_	_	_
236	L	l	NN	_	_	_
237	-	-	:	_	_	_
238	cells	cell	NNS	_	_	_
239	at	at	IN	_	_	_
240	log	log	NN	_	_	_
241	phase	phase	NN	_	_	_
242	in	in	IN	_	_	_
243	monoculture	monoculture	NN	_	_	_
244	,	,	,	_	_	_
245	a	a	DT	_	_	_
246	technical	technical	JJ	_	_	_
247	replicate	replicate	VBP	_	_	_
248	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
249	Evolved	evolve	VBD	_	_	_
250	L	l	NN	_	_	_
251	-	-	:	_	_	_
252	cells	cell	NNS	_	_	_
253	in	in	IN	_	_	_
254	coculture	coculture	NN	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	Evolved	evolve	VBD	_	_	_
257	L	l	NN	_	_	_
258	-	-	:	_	_	_
259	cells	cell	NNS	_	_	_
260	in	in	IN	_	_	_
261	coculture	coculture	NN	_	_	_
262	,	,	,	_	_	_
263	a	a	DT	_	_	_
264	biological	biological	JJ	_	_	_
265	replicate	replicate	VBP	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
267	genotype	genotype	NN	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	growth	growth	NN	_	_	_
270	type	type	NN	_	_	_
271	:	:	:	_	_	_
272	amino	amino	NN	_	_	_
273	acid	acid	NN	_	_	_
274	starvation	starvation	NN	_	_	_
275	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
276	growth	growth	NN	_	_	_
277	type	type	NN	_	_	_
278	:	:	:	_	_	_
279	log	log	NN	_	_	_
280	phase	phase	NN	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	IA-co1	ia-co1	NN	_	_	_
283	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
284	IA-co2	ia-co2	NN	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
286	IA-log	ia-log	JJ	_	_	_
287	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
288	IA-starve	ia-starve	JJ	_	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
290	IE-co1	ie-co1	NN	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	IE-co2	ie-co2	NN	_	_	_
293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
294	IE-log	ie-log	JJ	_	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	IE-starve	ie-starve	JJ	_	_	_
297	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
298	LA-co1	la-co1	NN	_	_	_
299	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
300	LA-co2	la-co2	NN	_	_	_
301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
302	LA-log	la-log	NN	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
304	LA-log-tr	la-log-tr	NN	_	_	_
305	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
306	LA-starve	la-starve	JJ	_	_	_
307	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
308	LE-co1	le-co1	NN	_	_	_
309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
310	LE-co2	le-co2	NN	_	_	_
311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
312	LE-log	le-log	JJ	_	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
314	LE-log-tr	le-log-tr	NN	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
316	LE-starve	le-starve	JJ	_	_	_
317	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
318	Metabolome	metabolome	NN	_	_	_
319	data	datum	NNS	_	_	_
320	for	for	IN	_	_	_
321	these	these	DT	_	_	_
322	cultures	culture	NNS	_	_	_
323	are	be	VBP	_	_	_
324	also	also	RB	_	_	_
325	provided	provide	VBN	_	_	_
326	in	in	IN	_	_	_
327	the	the	DT	_	_	_
328	supplementary	supplementary	JJ	_	_	_
329	file	file	NN	_	_	_
330	\	\	SYM	_	_	_
331	Ecoli	Ecoli	NNP	_	_	_
332	_	_	SYM	_	_	_
333	co	co	FW	_	_	_
334	_	_	FW	_	_	_
335	results.xlsx	results.xlsx	FW	_	_	_
336	\	\	FW	_	_	_
337	,	,	,	_	_	_
338	just	just	RB	_	_	_
339	for	for	IN	_	_	_
340	information	information	NN	_	_	_
341	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Microarray	Microarray	NNP	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	processed	process	VBN	_	_	_
6	using	use	VBG	_	_	_
7	a	a	DT	_	_	_
8	custom	custom	NN	_	_	_
9	R	r	NN	_	_	_
10	software	software	NN	_	_	_
11	for	for	IN	_	_	_
12	the	the	DT	_	_	_
13	finite	finite	JJ	_	_	_
14	hybridisation	hybridisation	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	FH	fh	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	model	model	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Ono	Ono	NNP	_	_	_
21	et	et	FW	_	_	_
22	al.	al.	FW	_	_	_
23	,	,	,	_	_	_
24	2008	2008	CD	_	_	_
25	,	,	,	_	_	_
26	Bioinformatics	Bioinformatics	NNP	_	_	_
27	24	24	CD	_	_	_
28	,	,	,	_	_	_
29	p1278	p1278	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Original	original	JJ	_	_	_
3	prototroph	prototroph	NN	_	_	_
4	DH1	dh1	NN	_	_	_
5	cells	cell	NNS	_	_	_
6	at	at	IN	_	_	_
7	log	log	NN	_	_	_
8	phase	phase	NN	_	_	_
9	in	in	IN	_	_	_
10	monoculture	monoculture	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Original	original	JJ	_	_	_
13	prototroph	prototroph	NN	_	_	_
14	DH1	dh1	NN	_	_	_
15	cells	cell	NNS	_	_	_
16	at	at	IN	_	_	_
17	log	log	NN	_	_	_
18	phase	phase	NN	_	_	_
19	in	in	IN	_	_	_
20	monoculture	monoculture	NN	_	_	_
21	,	,	,	_	_	_
22	a	a	DT	_	_	_
23	technical	technical	JJ	_	_	_
24	replicate	replicate	VBP	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	strain	strain	NN	_	_	_
27	:	:	:	_	_	_
28	K-12	k-12	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	substrain	substrain	NN	_	_	_
31	:	:	:	_	_	_
32	DH1	dh1	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
34	The	the	DT	_	_	_
35	cell	cell	NN	_	_	_
36	cultures	culture	NNS	_	_	_
37	were	be	VBD	_	_	_
38	interrupted	interrupt	VBN	_	_	_
39	by	by	IN	_	_	_
40	placing	place	VBG	_	_	_
41	them	they	PRP	_	_	_
42	directly	directly	RB	_	_	_
43	into	into	IN	_	_	_
44	a	a	DT	_	_	_
45	cold	cold	JJ	_	_	_
46	phenol-ethanol	phenol-ethanol	NN	_	_	_
47	solution	solution	NN	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	0.1g-phenol	0.1g-phenol	JJ	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
51	The	the	DT	_	_	_
52	processed	process	VBN	_	_	_
53	gene	gene	NN	_	_	_
54	expression	expression	NN	_	_	_
55	data	datum	NNS	_	_	_
56	in	in	IN	_	_	_
57	log10	log10	NN	_	_	_
58	scale	scale	NN	_	_	_
59	are	be	VBP	_	_	_
60	provided	provide	VBN	_	_	_
61	in	in	IN	_	_	_
62	the	the	DT	_	_	_
63	supplementary	supplementary	JJ	_	_	_
64	file	file	NN	_	_	_
65	\	\	SYM	_	_	_
66	Ecoli	Ecoli	NNP	_	_	_
67	_	_	SYM	_	_	_
68	co	co	FW	_	_	_
69	_	_	FW	_	_	_
70	results.xlsx	results.xlsx	FW	_	_	_
71	\	\	FW	_	_	_
72	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	total	total	JJ	_	_	_
4	RNA	rna	NN	_	_	_
5	was	be	VBD	_	_	_
6	extracted	extract	VBN	_	_	_
7	using	use	VBG	_	_	_
8	an	a	DT	_	_	_
9	RNeasy	rneasy	JJ	_	_	_
10	kit	kit	NN	_	_	_
11	,	,	,	_	_	_
12	Qiagen	Qiagen	NNP	_	_	_
13	,	,	,	_	_	_
14	in	in	IN	_	_	_
15	accordance	accordance	NN	_	_	_
16	with	with	IN	_	_	_
17	the	the	DT	_	_	_
18	manufacturer	manufacturer	NN	_	_	_
19	's	's	POS	_	_	_
20	instructions	instruction	NNS	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	After	after	IN	_	_	_
3	normalization	normalization	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	read	read	NN	_	_	_
7	counts	count	NNS	_	_	_
8	were	be	VBD	_	_	_
9	estimated	estimate	VBN	_	_	_
10	in	in	IN	_	_	_
11	the	the	DT	_	_	_
12	running	run	VBG	_	_	_
13	windows	window	NNS	_	_	_
14	of	of	IN	_	_	_
15	35	35	CD	_	_	_
16	bp	bp	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	the	the	DT	_	_	_
20	ratios	ratio	NNS	_	_	_
21	R	r	NN	_	_	_
22	between	between	IN	_	_	_
23	values	value	NNS	_	_	_
24	obtained	obtain	VBN	_	_	_
25	for	for	IN	_	_	_
26	experimental	experimental	JJ	_	_	_
27	and	and	CC	_	_	_
28	control	control	JJ	_	_	_
29	libraries	library	NNS	_	_	_
30	were	be	VBD	_	_	_
31	calculated	calculate	VBN	_	_	_
32	.	.	.	_	_	_

1	Peaks	peak	NNS	_	_	_
2	were	be	VBD	_	_	_
3	localized	localized	JJ	_	_	_
4	requiring	require	VBG	_	_	_
5	R	r	NN	_	_	_
6	≥	≥	CD	_	_	_
7	1.5	1.5	CD	_	_	_
8	for	for	IN	_	_	_
9	at	at	IN	_	_	_
10	least	least	JJS	_	_	_
11	50	50	CD	_	_	_
12	%	%	NN	_	_	_
13	positions	position	NNS	_	_	_
14	of	of	IN	_	_	_
15	at	at	IN	_	_	_
16	least	least	JJS	_	_	_
17	60	60	CD	_	_	_
18	bp	bp	NN	_	_	_
19	genomic	genomic	JJ	_	_	_
20	region	region	NN	_	_	_
21	in	in	IN	_	_	_
22	length	length	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2	antibody	antibody	NN	_	_	_
3	:	:	:	_	_	_
4	Anti-Dps	anti-dps	JJ	_	_	_
5	antibodies	antibody	NNS	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
7	antibody	antibody	NN	_	_	_
8	:	:	:	_	_	_
9	rabbit	rabbit	NN	_	_	_
10	pre-immune	pre-immune	JJ	_	_	_
11	IgG	igg	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	Bacterial	bacterial	JJ	_	_	_
14	cells	cell	NNS	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
16	Bacterial	bacterial	JJ	_	_	_
17	cells	cell	NNS	_	_	_
18	were	be	VBD	_	_	_
19	grown	grow	VBN	_	_	_
20	aerobically	aerobically	RB	_	_	_
21	in	in	IN	_	_	_
22	M9	m9	NN	_	_	_
23	medium	medium	NN	_	_	_
24	supplemented	supplement	VBN	_	_	_
25	with	with	IN	_	_	_
26	0.2	0.2	CD	_	_	_
27	%	%	NN	_	_	_
28	glucose	glucose	NN	SUPP	_	_
29	and	and	CC	_	_	_
30	5	5	CD	_	_	_
31	%	%	NN	_	_	_
32	LB	lb	NN	_	_	_
33	at	at	IN	_	_	_
34	37	37	CD	_	_	_
35	°C	°c	NN	_	_	_
36	under	under	IN	_	_	_
37	constant	constant	JJ	_	_	_
38	shaking	shake	VBG	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	~	~	NN	_	_	_
41	120	120	CD	_	_	_
42	rpm	rpm	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	in	in	IN	_	_	_
45	a	a	DT	_	_	_
46	water	water	NN	_	_	_
47	bath	bath	NN	_	_	_
48	and	and	CC	_	_	_
49	harvested	harvest	VBN	_	_	_
50	at	at	IN	_	_	_
51	OD	od	NN	_	_	_
52	~	~	NN	_	_	_
53	0.6	0.6	CD	_	_	_
54	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	ChIP-Seq	chip-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	ChIP-seq	chip-seq	NN	_	_	_
5	experiments	experiment	NNS	_	_	_
6	were	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	in	in	IN	_	_	_
9	duplicate	duplicate	VB	_	_	_
10	using	use	VBG	_	_	_
11	similar	similar	JJ	_	_	_
12	growth	growth	NN	_	_	_
13	condition	condition	NN	_	_	_
14	and	and	CC	_	_	_
15	protocols	protocol	NNS	_	_	_
16	for	for	IN	_	_	_
17	chromatin	chromatin	NN	_	_	_
18	immunoprecipitation	immunoprecipitation	NN	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	first	first	JJ	_	_	_
3	experiment	experiment	NN	_	_	_
4	was	be	VBD	_	_	_
5	done	do	VBN	_	_	_
6	in	in	IN	_	_	_
7	the	the	DT	_	_	_
8	Centre	Centre	NNP	_	_	_
9	for	for	IN	_	_	_
10	Genomic	genomic	JJ	_	_	_
11	Regulation	regulation	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	CRG	crg	NN	_	_	_
14	,	,	,	_	_	_
15	Barcelona	Barcelona	NNP	_	_	_
16	,	,	,	_	_	_
17	Spain	Spain	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	while	while	IN	_	_	_
21	the	the	DT	_	_	_
22	second	second	JJ	_	_	_
23	one	one	CD	_	_	_
24	in	in	IN	_	_	_
25	the	the	DT	_	_	_
26	Immanuel	Immanuel	NNP	_	_	_
27	Kant	Kant	NNP	_	_	_
28	Baltic	Baltic	NNP	_	_	_
29	Federal	Federal	NNP	_	_	_
30	University	University	NNP	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Kaliningrad	Kaliningrad	NNP	_	_	_
33	,	,	,	_	_	_
34	Russia	Russia	NNP	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	both	both	DT	_	_	_
3	cases	case	NNS	_	_	_
4	,	,	,	_	_	_
5	bacterial	bacterial	JJ	_	_	_
6	cells	cell	NNS	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	aerobically	aerobically	RB	_	_	_
10	at	at	IN	_	_	_
11	37	37	CD	_	_	_
12	°C	°c	NN	_	_	_
13	until	until	IN	_	_	_
14	OD600	od600	NN	_	_	_
15	~	~	NN	_	_	_
16	0.6	0.6	CD	_	_	_
17	were	be	VBD	_	_	_
18	treated	treat	VBN	_	_	_
19	with	with	IN	_	_	_
20	formaldehyde	formaldehyde	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	final	final	JJ	_	_	_
23	concentration	concentration	NN	_	_	_
24	of	of	IN	_	_	_
25	1	1	CD	_	_	_
26	%	%	NN	_	_	_
27	,	,	,	_	_	_
28	20	20	CD	_	_	_
29	min	min	NN	_	_	_
30	incubation	incubation	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	.	.	.	_	_	_

1	Cross-linking	cross-linking	NN	_	_	_
2	was	be	VBD	_	_	_
3	stopped	stop	VBN	_	_	_
4	with	with	IN	_	_	_
5	glycine	glycine	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	final	final	JJ	_	_	_
8	concentration	concentration	NN	_	_	_
9	of	of	IN	_	_	_
10	450	450	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	5	5	CD	_	_	_
3	minutes	minute	NNS	_	_	_
4	of	of	IN	_	_	_
5	incubation	incubation	NN	_	_	_
6	the	the	DT	_	_	_
7	cells	cell	NNS	_	_	_
8	were	be	VBD	_	_	_
9	pelleted	pellete	VBN	_	_	_
10	by	by	IN	_	_	_
11	centrifugation	centrifugation	NN	_	_	_
12	at	at	IN	_	_	_
13	14,000	14,000	CD	_	_	_
14	rpm	rpm	NN	_	_	_
15	for	for	IN	_	_	_
16	15	15	CD	_	_	_
17	minutes	minute	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	+4	+4	CD	_	_	_
20	°C	°c	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	,	,	,	_	_	_
23	washed	wash	VBN	_	_	_
24	twice	twice	RB	_	_	_
25	with	with	IN	_	_	_
26	5	5	CD	_	_	_
27	ml	ml	NN	_	_	_
28	of	of	IN	_	_	_
29	PBS	PBS	NNP	_	_	_
30	and	and	CC	_	_	_
31	resuspended	resuspend	VBN	_	_	_
32	in	in	IN	_	_	_
33	1.3	1.3	CD	_	_	_
34	ml	ml	NN	_	_	_
35	of	of	IN	_	_	_
36	ice-cold	ice-cold	JJ	_	_	_
37	immunoprecipitation	immunoprecipitation	NN	_	_	_
38	buffer	buffer	NN	_	_	_
39	prepared	prepare	VBN	_	_	_
40	from	from	IN	_	_	_
41	50	50	CD	_	_	_
42	ml	ml	NN	_	_	_
43	of	of	IN	_	_	_
44	buffer	buffer	NN	_	_	_
45	containing	contain	VBG	_	_	_
46	100	100	CD	_	_	_
47	mM	mm	NN	KWSUPP	_	_
48	NaCl	nacl	NN	_	_	_
49	,	,	,	_	_	_
50	50	50	CD	_	_	_
51	mM	mm	NN	KWSUPP	_	_
52	Tris-HCl	tris-hcl	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	pH	ph	NN	_	_	_
55	8.1	8.1	CD	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	,	,	,	_	_	_
58	5	5	CD	_	_	_
59	mM	mm	NN	KWSUPP	_	_
60	EDTA	edta	NN	_	_	_
61	,	,	,	_	_	_
62	0.2	0.2	CD	_	_	_
63	%	%	NN	_	_	_
64	NaN3	nan3	NN	_	_	_
65	,	,	,	_	_	_
66	0.5	0.5	CD	_	_	_
67	%	%	NN	_	_	_
68	SDS	sds	NN	_	_	_
69	,	,	,	_	_	_
70	and	and	CC	_	_	_
71	25	25	CD	_	_	_
72	ml	ml	NN	_	_	_
73	of	of	IN	_	_	_
74	buffer	buffer	NN	_	_	_
75	containing	contain	VBG	_	_	_
76	100	100	CD	_	_	_
77	mM	mm	NN	KWSUPP	_	_
78	Tris-HCl	tris-hcl	NN	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	pH	ph	NN	_	_	_
81	8.6	8.6	CD	_	_	_
82	-RRB-	-rrb-	-RRB-	_	_	_
83	;	;	:	_	_	_
84	100	100	CD	_	_	_
85	mM	mm	NN	KWSUPP	_	_
86	NaCl	nacl	NN	_	_	_
87	;	;	:	_	_	_
88	5	5	CD	_	_	_
89	mM	mm	NN	KWSUPP	_	_
90	EDTA	edta	NN	_	_	_
91	;	;	:	_	_	_
92	0,2	0,2	CD	_	_	_
93	%	%	NN	_	_	_
94	NaN3	nan3	NN	_	_	_
95	,	,	,	_	_	_
96	5	5	CD	_	_	_
97	%	%	NN	_	_	_
98	Triton-X-100	triton-x-100	NN	_	_	_
99	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	phenylmethylsulfonyl	phenylmethylsulfonyl	NN	_	_	_
3	fluoride	fluoride	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	final	final	JJ	_	_	_
6	concentration	concentration	NN	_	_	_
7	of	of	IN	_	_	_
8	1	1	CD	_	_	_
9	mM	mm	NN	KWSUPP	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	or	or	CC	_	_	_
12	20	20	CD	_	_	_
13	μl	μl	NN	_	_	_
14	of	of	IN	_	_	_
15	Protease	protease	NN	_	_	_
16	Inhibitor	inhibitor	NN	_	_	_
17	Cocktail	cocktail	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	PIC	pic	NN	_	_	_
20	,	,	,	_	_	_
21	Sigma	Sigma	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	for	for	IN	_	_	_
24	the	the	DT	_	_	_
25	first	first	JJ	_	_	_
26	and	and	CC	_	_	_
27	the	the	DT	_	_	_
28	second	second	JJ	_	_	_
29	experiment	experiment	NN	_	_	_
30	,	,	,	_	_	_
31	respectively	respectively	RB	_	_	_
32	,	,	,	_	_	_
33	were	be	VBD	_	_	_
34	added	add	VBN	_	_	_
35	followed	follow	VBN	_	_	_
36	by	by	IN	_	_	_
37	incubation	incubation	NN	_	_	_
38	for	for	IN	_	_	_
39	30	30	CD	_	_	_
40	min	min	NN	_	_	_
41	at	at	IN	_	_	_
42	+4	+4	CD	_	_	_
43	°C	°c	NN	_	_	_
44	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	ChIP-seq	chip-seq	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	prepared	prepare	VBN	_	_	_
6	from	from	IN	_	_	_
7	5-10	5-10	CD	_	_	_
8	ng	ng	NN	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	DNA	dna	NN	_	_	_
12	samples	sample	NNS	_	_	_
13	with	with	IN	_	_	_
14	the	the	DT	_	_	_
15	NebNext	NebNext	NNP	_	_	_
16	®	®	SYM	_	_	_
17	Ultra	ultra	FW	_	_	_
18	™	™	FW	_	_	_
19	DNA	dna	NN	_	_	_
20	Library	Library	NNP	_	_	_
21	Prep	Prep	NNP	_	_	_
22	Kit	kit	NN	_	_	_
23	for	for	IN	_	_	_
24	Illumina	Illumina	NNP	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	New	New	NNP	_	_	_
27	England	England	NNP	_	_	_
28	Biolabs	Biolabs	NNP	_	_	_
29	,	,	,	_	_	_
30	MA	MA	NNP	_	_	_
31	,	,	,	_	_	_
32	USA	USA	NNP	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	following	follow	VBG	_	_	_
35	the	the	DT	_	_	_
36	manufacturer	manufacturer	NN	_	_	_
37	's	's	POS	_	_	_
38	instructions	instruction	NNS	_	_	_
39	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	the	the	DT	_	_	_
3	final	final	JJ	_	_	_
4	amplification	amplification	NN	_	_	_
5	of	of	IN	_	_	_
6	the	the	DT	_	_	_
7	library	library	NN	_	_	_
8	15	15	CD	_	_	_
9	PCR	pcr	NN	_	_	_
10	cycles	cycle	NNS	_	_	_
11	were	be	VBD	_	_	_
12	used	use	VBN	_	_	_
13	.	.	.	_	_	_

1	Size	size	NN	_	_	_
2	distribution	distribution	NN	_	_	_
3	and	and	CC	_	_	_
4	concentration	concentration	NN	_	_	_
5	of	of	IN	_	_	_
6	the	the	DT	_	_	_
7	amplicons	amplicon	NNS	_	_	_
8	was	be	VBD	_	_	_
9	checked	check	VBN	_	_	_
10	on	on	IN	_	_	_
11	the	the	DT	_	_	_
12	Bioanalyzer	Bioanalyzer	NNP	_	_	_
13	2100	2100	CD	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Agilent	Agilent	NNP	_	_	_
16	,	,	,	_	_	_
17	USA	USA	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	the	the	DT	_	_	_
3	first	first	JJ	_	_	_
4	experiment	experiment	NN	_	_	_
5	,	,	,	_	_	_
6	the	the	DT	_	_	_
7	maximum	maximum	NN	_	_	_
8	was	be	VBD	_	_	_
9	at	at	IN	_	_	_
10	about	about	IN	_	_	_
11	300	300	CD	_	_	_
12	bp	bp	NN	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	ChIP	chip	NN	_	_	_
16	libraries	library	NNS	_	_	_
17	were	be	VBD	_	_	_
18	sequenced	sequence	VBN	_	_	_
19	using	use	VBG	_	_	_
20	50	50	CD	_	_	_
21	nt	nt	NNS	_	_	_
22	single-end	single-end	JJ	_	_	_
23	read	read	NN	_	_	_
24	protocol	protocol	NN	_	_	_
25	on	on	IN	_	_	_
26	the	the	DT	_	_	_
27	Illumina	Illumina	NNP	_	_	_
28	HiSeq	hiseq	NN	_	_	_
29	system	system	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Illumina	Illumina	NNP	_	_	_
32	,	,	,	_	_	_
33	USA	USA	NNP	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	of	of	IN	_	_	_
36	the	the	DT	_	_	_
37	Genomics	Genomics	NNP	_	_	_
38	Facility	Facility	NNP	_	_	_
39	in	in	IN	_	_	_
40	the	the	DT	_	_	_
41	Centre	Centre	NNP	_	_	_
42	for	for	IN	_	_	_
43	Genomic	genomic	JJ	_	_	_
44	Regulation	regulation	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	Barcelona	Barcelona	NNP	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	the	the	DT	_	_	_
3	second	second	JJ	_	_	_
4	experiment	experiment	NN	_	_	_
5	,	,	,	_	_	_
6	the	the	DT	_	_	_
7	maximum	maximum	NN	_	_	_
8	was	be	VBD	_	_	_
9	at	at	IN	_	_	_
10	about	about	IN	_	_	_
11	450	450	CD	_	_	_
12	bp	bp	NN	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	samples	sample	NNS	_	_	_
16	were	be	VBD	_	_	_
17	sequenced	sequence	VBN	_	_	_
18	using	use	VBG	_	_	_
19	standard	standard	JJ	_	_	_
20	paired-end	paired-end	NN	_	_	_
21	2	2	CD	_	_	_
22	*	*	SYM	_	_	_
23	150	150	CD	_	_	_
24	nt	nt	NNS	_	_	_
25	protocol	protocol	NN	_	_	_
26	on	on	IN	_	_	_
27	the	the	DT	_	_	_
28	MiSeq	miseq	NN	_	_	_
29	system	system	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Illumina	Illumina	NNP	_	_	_
32	,	,	,	_	_	_
33	USA	USA	NNP	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	in	in	IN	_	_	_
36	the	the	DT	_	_	_
37	Immanuel	Immanuel	NNP	_	_	_
38	Kant	Kant	NNP	_	_	_
39	Baltic	Baltic	NNP	_	_	_
40	Federal	Federal	NNP	_	_	_
41	University	University	NNP	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	Kaliningrad	Kaliningrad	NNP	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Exp	exp	NN	_	_	_
4	1	1	CD	_	_	_
5	_	_	NN	_	_	_
6	control	control	NN	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	Exp	Exp	NNP	_	_	_
9	1	1	CD	_	_	_
10	_	_	CD	_	_	_
11	IP	IP	NNP	_	_	_
12	sample	sample	NN	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Exp	exp	NN	_	_	_
15	2	2	CD	_	_	_
16	_	_	NN	_	_	_
17	control	control	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
19	Exp	exp	NN	_	_	_
20	2	2	CD	_	_	_
21	_	_	CD	_	_	_
22	IP	IP	NNP	_	_	_
23	sample	sample	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	For	for	IN	_	_	_
26	immunoprecipitation	immunoprecipitation	NN	_	_	_
27	,	,	,	_	_	_
28	800	800	CD	_	_	_
29	μl	μl	NN	_	_	_
30	of	of	IN	_	_	_
31	collected	collect	VBN	_	_	_
32	chromatin	chromatin	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	~	~	CD	_	_	_
35	1000	1000	CD	_	_	_
36	μg	μg	NN	_	_	_
37	of	of	IN	_	_	_
38	protein	protein	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	were	be	VBD	_	_	_
41	incubated	incubate	VBN	_	_	_
42	on	on	IN	_	_	_
43	a	a	DT	_	_	_
44	rotating	rotate	VBG	_	_	_
45	wheel	wheel	NN	_	_	_
46	over	over	IN	_	_	_
47	night	night	NN	_	_	_
48	at	at	IN	_	_	_
49	4	4	CD	_	_	_
50	°C	°c	NN	_	_	_
51	with	with	IN	_	_	_
52	10	10	CD	_	_	_
53	μg	μg	NN	_	_	_
54	of	of	IN	_	_	_
55	either	either	CC	_	_	_
56	rabbit	rabbit	NN	_	_	_
57	anti-Dps	anti-dps	JJ	_	_	_
58	antibodies	antibody	NNS	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	experimental	experimental	JJ	_	_	_
61	sample	sample	NN	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	or	or	CC	_	_	_
64	rabbit	rabbit	NN	_	_	_
65	pre-immune	pre-immune	JJ	_	_	_
66	IgG	igg	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	negative	negative	JJ	_	_	_
69	control	control	NN	_	_	_
70	-RRB-	-rrb-	-RRB-	_	_	_
71	.	.	.	_	_	_

1	Next	next	JJ	_	_	_
2	day	day	NN	_	_	_
3	30	30	CD	_	_	_
4	μl	μl	NN	_	_	_
5	of	of	IN	_	_	_
6	Ultra	Ultra	NNP	_	_	_
7	Link	Link	NNP	_	_	_
8	Protein	protein	NN	_	_	_
9	A	a	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Genome	Genome	NNP	_	_	_
12	_	_	NNP	_	_	_
13	build	build	VB	_	_	_
14	:	:	:	_	_	_
15	E.	e.	FW	_	_	_
16	coli	coli	FW	_	_	_
17	K-12	k-12	NN	_	_	_
18	MG1655	mg1655	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	U00096	u00096	NN	_	_	_
21	.3	.3	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	growth	growth	NN	_	_	_
25	stage	stage	NN	_	_	_
26	:	:	:	_	_	_
27	log-phase	log-phase	JJ	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	medium	medium	NN	_	_	_
30	:	:	:	_	_	_
31	M9	m9	NN	_	_	_
32	medium	medium	NN	_	_	_
33	supplemented	supplement	VBN	_	_	_
34	with	with	IN	_	_	_
35	0.2	0.2	CD	_	_	_
36	%	%	NN	_	_	_
37	glucose	glucose	NN	SUPP	_	_
38	and	and	CC	_	_	_
39	5	5	CD	_	_	_
40	%	%	NN	_	_	_
41	LB	lb	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	ngs	ng	NNS	_	_	_
44	platform	platform	NN	_	_	_
45	:	:	:	_	_	_
46	Illumina	Illumina	NNP	_	_	_
47	HiSeq	HiSeq	NNP	_	_	_
48	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
49	ngs	ng	NNS	_	_	_
50	platform	platform	NN	_	_	_
51	:	:	:	_	_	_
52	Illumina	Illumina	NNP	_	_	_
53	MiSeq	MiSeq	NNP	_	_	_
54	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
55	Only	only	RB	_	_	_
56	ideal	ideal	JJ	_	_	_
57	correspondence	correspondence	NN	_	_	_
58	of	of	IN	_	_	_
59	sequence	sequence	NN	_	_	_
60	reads	read	VBZ	_	_	_
61	to	to	TO	_	_	_
62	the	the	DT	_	_	_
63	genome	genome	NN	_	_	_
64	in	in	IN	_	_	_
65	both	both	DT	_	_	_
66	cases	case	NNS	_	_	_
67	was	be	VBD	_	_	_
68	permitted	permit	VBN	_	_	_
69	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	profiles	profile	NNS	_	_	_
3	obtained	obtain	VBN	_	_	_
4	for	for	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	and	and	CC	_	_	_
7	control	control	JJ	_	_	_
8	samples	sample	NNS	_	_	_
9	were	be	VBD	_	_	_
10	normalized	normalize	VBN	_	_	_
11	by	by	IN	_	_	_
12	the	the	DT	_	_	_
13	scaling	scaling	NN	_	_	_
14	method	method	NN	_	_	_
15	initially	initially	RB	_	_	_
16	offered	offer	VBN	_	_	_
17	by	by	IN	_	_	_
18	Affymetrix	Affymetrix	NNP	_	_	_
19	for	for	IN	_	_	_
20	microarray	microarray	NN	_	_	_
21	data	data	NN	_	_	_
22	analysis	analysis	NN	_	_	_
23	and	and	CC	_	_	_
24	later	later	RB	_	_	_
25	implemented	implement	VBD	_	_	_
26	in	in	IN	_	_	_
27	several	several	JJ	_	_	_
28	other	other	JJ	_	_	_
29	approaches	approach	NNS	_	_	_
30	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	method	method	NN	_	_	_
3	assumes	assume	VBZ	_	_	_
4	unaffected	unaffected	JJ	_	_	_
5	protein	protein	NN	_	_	_
6	occupancy	occupancy	NN	_	_	_
7	at	at	IN	_	_	_
8	most	most	JJS	_	_	_
9	genomic	genomic	JJ	_	_	_
10	positions	position	NNS	_	_	_
11	and	and	CC	_	_	_
12	quantifies	quantify	VBZ	_	_	_
13	the	the	DT	_	_	_
14	scaling	scaling	NN	_	_	_
15	factor	factor	NN	_	_	_
16	on	on	IN	_	_	_
17	the	the	DT	_	_	_
18	basis	basis	NN	_	_	_
19	of	of	IN	_	_	_
20	corrected	correct	VBN	_	_	_
21	mean	mean	NN	_	_	_
22	values	value	NNS	_	_	_
23	obtained	obtain	VBN	_	_	_
24	after	after	IN	_	_	_
25	removal	removal	NN	_	_	_
26	of	of	IN	_	_	_
27	2	2	CD	_	_	_
28	%	%	NN	_	_	_
29	signals	signal	NNS	_	_	_
30	with	with	IN	_	_	_
31	highest	highest	JJS	_	_	_
32	and	and	CC	_	_	_
33	lowest	lowest	JJS	_	_	_
34	intensities	intensity	NNS	_	_	_
35	from	from	IN	_	_	_
36	both	both	DT	_	_	_
37	control	control	NN	_	_	_
38	and	and	CC	_	_	_
39	experimental	experimental	JJ	_	_	_
40	sets	set	NNS	_	_	_
41	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	quality	quality	JJ	_	_	_
6	filtered	filter	VBN	_	_	_
7	on	on	IN	_	_	_
8	the	the	DT	_	_	_
9	Galaxy	Galaxy	NNP	_	_	_
10	server	server	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Filter	Filter	NNP	_	_	_
13	by	by	IN	_	_	_
14	Quality	Quality	NNP	_	_	_
15	tool	tool	NN	_	_	_
16	,	,	,	_	_	_
17	Q	Q	NNP	_	_	_
18	≥	≥	SYM	_	_	_
19	20	20	CD	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	providing	provide	VBG	_	_	_
22	99	99	CD	_	_	_
23	%	%	NN	_	_	_
24	probability	probability	NN	_	_	_
25	of	of	IN	_	_	_
26	correct	correct	JJ	_	_	_
27	sequencing	sequencing	NN	_	_	_
28	for	for	IN	_	_	_
29	all	all	DT	_	_	_
30	nucleotides	nucleotide	NNS	_	_	_
31	in	in	IN	_	_	_
32	each	each	DT	_	_	_
33	read	read	NN	_	_	_
34	.	.	.	_	_	_

1	As	as	IN	_	_	_
2	a	a	DT	_	_	_
3	result	result	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	sets	set	NNS	_	_	_
7	contain	contain	VBP	_	_	_
8	31,656,551	31,656,551	CD	_	_	_
9	and	and	CC	_	_	_
10	45,396,252	45,396,252	CD	_	_	_
11	sequences	sequence	NNS	_	_	_
12	in	in	IN	_	_	_
13	the	the	DT	_	_	_
14	control	control	NN	_	_	_
15	and	and	CC	_	_	_
16	immunoprecipitated	immunoprecipitate	VBN	_	_	_
17	samples	sample	NNS	_	_	_
18	of	of	IN	_	_	_
19	the	the	DT	_	_	_
20	first	first	JJ	_	_	_
21	experiment	experiment	NN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	,	,	,	_	_	_
25	respectively	respectively	RB	_	_	_
26	,	,	,	_	_	_
27	7,493,528	7,493,528	CD	_	_	_
28	and	and	CC	_	_	_
29	8,214,737	8,214,737	CD	_	_	_
30	reads	read	VBZ	_	_	_
31	for	for	IN	_	_	_
32	the	the	DT	_	_	_
33	second	second	JJ	_	_	_
34	experiment	experiment	NN	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	sequencing	sequencing	NN	_	_	_
3	mode	mode	NN	_	_	_
4	:	:	:	_	_	_
5	50	50	CD	_	_	_
6	nt	nt	NNS	_	_	_
7	single-end	single-end	JJ	_	_	_
8	read	read	NN	_	_	_
9	protocol	protocol	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	sequencing	sequencing	NN	_	_	_
12	mode	mode	NN	_	_	_
13	:	:	:	_	_	_
14	paired-end	paired-end	NN	_	_	_
15	2	2	CD	_	_	_
16	*	*	SYM	_	_	_
17	150	150	CD	_	_	_
18	nt	nt	NNS	_	_	_
19	protocol	protocol	NN	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	Supplementary	Supplementary	NNP	_	_	_
22	_	_	VBD	_	_	_
23	files	file	NNS	_	_	_
24	_	_	IN	_	_	_
25	format	format	NN	_	_	_
26	_	_	NN	_	_	_
27	and	and	CC	_	_	_
28	_	_	NN	_	_	_
29	content	content	NN	_	_	_
30	:	:	:	_	_	_
31	Processed	process	VBN	_	_	_
32	data	datum	NNS	_	_	_
33	include	include	VBP	_	_	_
34	read	read	VBN	_	_	_
35	pileups	pileup	NNS	_	_	_
36	obtained	obtain	VBN	_	_	_
37	in	in	IN	_	_	_
38	two	two	CD	_	_	_
39	ChIP-seq	chip-seq	JJ	_	_	_
40	experiments	experiment	NNS	_	_	_
41	by	by	IN	_	_	_
42	two	two	CD	_	_	_
43	different	different	JJ	_	_	_
44	approaches	approach	NNS	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	files	file	NNS	_	_	_
47	1-4	1-4	CD	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	,	,	,	_	_	_
50	the	the	DT	_	_	_
51	set	set	NN	_	_	_
52	of	of	IN	_	_	_
53	regions	region	NNS	_	_	_
54	bound	bind	VBN	_	_	_
55	by	by	IN	_	_	_
56	Dps	dp	NNS	_	_	_
57	in	in	IN	_	_	_
58	both	both	DT	_	_	_
59	experiments	experiment	NNS	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	file	file	NN	_	_	_
62	5	5	CD	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	and	and	CC	_	_	_
65	the	the	DT	_	_	_
66	set	set	NN	_	_	_
67	of	of	IN	_	_	_
68	regions	region	NNS	_	_	_
69	unbound	unbound	JJ	_	_	_
70	by	by	IN	_	_	_
71	Dps	dp	NNS	_	_	_
72	in	in	IN	_	_	_
73	both	both	DT	_	_	_
74	experiments	experiment	NNS	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	file	file	NN	_	_	_
77	6	6	CD	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	processed	process	VBN	_	_	_
3	data	datum	NNS	_	_	_
4	are	be	VBP	_	_	_
5	provided	provide	VBN	_	_	_
6	as	as	IN	_	_	_
7	tab-delimited	tab-delimited	JJ	_	_	_
8	.	.	.	_	_	_

1	txt	txt	NN	_	_	_
2	files	file	NNS	_	_	_
3	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	To	to	TO	_	_	_
3	apply	apply	VB	_	_	_
4	the	the	DT	_	_	_
5	second	second	JJ	_	_	_
6	approach	approach	NN	_	_	_
7	variable	variable	NN	_	_	_
8	in	in	IN	_	_	_
9	length	length	NN	_	_	_
10	reads	read	VBZ	_	_	_
11	from	from	IN	_	_	_
12	Illumina	Illumina	NNP	_	_	_
13	MiSeq	MiSeq	NNP	_	_	_
14	were	be	VBD	_	_	_
15	first	first	JJ	_	_	_
16	trimmed	trim	VBN	_	_	_
17	from	from	IN	_	_	_
18	both	both	DT	_	_	_
19	sides	side	NNS	_	_	_
20	to	to	TO	_	_	_
21	obtain	obtain	VB	_	_	_
22	a	a	DT	_	_	_
23	set	set	NN	_	_	_
24	of	of	IN	_	_	_
25	standard	standard	JJ	_	_	_
26	50	50	CD	_	_	_
27	nt	nt	NNS	_	_	_
28	sequences	sequence	NNS	_	_	_
29	taken	take	VBN	_	_	_
30	from	from	IN	_	_	_
31	the	the	DT	_	_	_
32	middle	middle	NN	_	_	_
33	of	of	IN	_	_	_
34	longer	longer	JJR	_	_	_
35	reads	read	VBZ	_	_	_
36	.	.	.	_	_	_

1	Reads	read	NNS	_	_	_
2	shorter	shorter	JJR	_	_	_
3	than	than	IN	_	_	_
4	50	50	CD	_	_	_
5	nt	nt	NNS	_	_	_
6	were	be	VBD	_	_	_
7	discarded	discard	VBN	_	_	_
8	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	,	,	,	_	_	_
3	all	all	DT	_	_	_
4	four	four	CD	_	_	_
5	sets	set	NNS	_	_	_
6	from	from	IN	_	_	_
7	both	both	DT	_	_	_
8	experiments	experiment	NNS	_	_	_
9	were	be	VBD	_	_	_
10	aligned	align	VBN	_	_	_
11	to	to	TO	_	_	_
12	the	the	DT	_	_	_
13	genome	genome	NN	_	_	_
14	using	use	VBG	_	_	_
15	the	the	DT	_	_	_
16	Matcher	Matcher	NNP	_	_	_
17	program	program	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	available	available	JJ	_	_	_
20	at	at	IN	_	_	_
21	:	:	:	_	_	_
22	http	http	NN	_	_	_
23	:	:	:	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
25	Two	two	CD	_	_	_
26	different	different	JJ	_	_	_
27	approaches	approach	NNS	_	_	_
28	were	be	VBD	_	_	_
29	used	use	VBN	_	_	_
30	to	to	TO	_	_	_
31	align	align	VB	_	_	_
32	sequence	sequence	NN	_	_	_
33	reads	read	VBZ	_	_	_
34	to	to	TO	_	_	_
35	the	the	DT	_	_	_
36	genome	genome	NN	_	_	_
37	of	of	IN	_	_	_
38	E.	e.	FW	_	_	_
39	coli	coli	FW	_	_	_
40	K-12	k-12	NN	_	_	_
41	MG1655	mg1655	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	U00096	u00096	NN	_	_	_
44	.3	.3	NN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	.	.	.	_	_	_

1	First	first	RB	_	_	_
2	,	,	,	_	_	_
3	quality	quality	NN	_	_	_
4	controlled	controlled	JJ	_	_	_
5	reads	read	VBZ	_	_	_
6	were	be	VBD	_	_	_
7	mapped	map	VBN	_	_	_
8	using	use	VBG	_	_	_
9	the	the	DT	_	_	_
10	CLC	clc	NN	_	_	_
11	Genomics	genomic	NNS	_	_	_
12	Workbench	workbench	JJ	_	_	_
13	version	version	NN	_	_	_
14	7.5.1	7.5.1	CD	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	CLC	clc	NN	_	_	_
17	GW	gw	NN	_	_	_
18	,	,	,	_	_	_
19	Bio-Qiagen	bio-qiagen	NN	_	_	_
20	,	,	,	_	_	_
21	Aarhus	Aarhus	NNP	_	_	_
22	,	,	,	_	_	_
23	Denmark	Denmark	NNP	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	with	with	IN	_	_	_
26	either	either	CC	_	_	_
27	default	default	NN	_	_	_
28	settings	setting	NNS	_	_	_
29	for	for	IN	_	_	_
30	the	the	DT	_	_	_
31	length	length	NN	_	_	_
32	and	and	CC	_	_	_
33	similarity	similarity	NN	_	_	_
34	fractions	fraction	NNS	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	0.5	0.5	CD	_	_	_
37	and	and	CC	_	_	_
38	0.8	0.8	CD	_	_	_
39	,	,	,	_	_	_
40	respectively	respectively	RB	_	_	_
41	,	,	,	_	_	_
42	see	see	VB	_	_	_
43	supplemental	supplemental	JJ	_	_	_
44	Table	Table	NNP	_	_	_
45	2	2	CD	_	_	_
46	of	of	IN	_	_	_
47	the	the	DT	_	_	_
48	paper	paper	NN	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	or	or	CC	_	_	_
51	with	with	IN	_	_	_
52	the	the	DT	_	_	_
53	most	most	RBS	_	_	_
54	stringent	stringent	JJ	_	_	_
55	criteria	criterion	NNS	_	_	_
56	-LRB-	-lrb-	-LRB-	_	_	_
57	1.0	1.0	CD	_	_	_
58	and	and	CC	_	_	_
59	1.0	1.0	CD	_	_	_
60	,	,	,	_	_	_
61	respectively	respectively	RB	_	_	_
62	,	,	,	_	_	_
63	deposited	deposit	VBN	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	.	.	.	_	_	_

1	Reads	read	VBZ	_	_	_
2	with	with	IN	_	_	_
3	sequences	sequence	NNS	_	_	_
4	aligned	align	VBN	_	_	_
5	to	to	TO	_	_	_
6	multiple	multiple	JJ	_	_	_
7	genomic	genomic	JJ	_	_	_
8	regions	region	NNS	_	_	_
9	were	be	VBD	_	_	_
10	ignored	ignore	VBN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Agilent	Agilent	NNP	_	_	_
3	Scan	scan	VB	_	_	_
4	Control	Control	NNP	_	_	_
5	Software	Software	NNP	_	_	_
6	V.	V.	NNP	_	_	_
7	8.5	8.5	CD	_	_	_
8	at	at	IN	_	_	_
9	a	a	DT	_	_	_
10	resolution	resolution	NN	_	_	_
11	of	of	IN	_	_	_
12	3μm	3μm	NN	_	_	_
13	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	data	datum	NNS	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Agilent	Agilent	NNP	_	_	_
7	Feature	Feature	NNP	_	_	_
8	extraction	extraction	NN	_	_	_
9	software	software	NN	_	_	_
10	V	v	NN	_	_	_
11	10.10	10.10	CD	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	azide	azide	NN	_	_	_
14	treated	treat	VBN	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	Cells	cell	NNS	_	_	_
17	were	be	VBD	_	_	_
18	subcultured	subculture	VBN	_	_	_
19	from	from	IN	_	_	_
20	overnight	overnight	JJ	_	_	_
21	cultures	culture	NNS	_	_	_
22	into	into	IN	_	_	_
23	20	20	CD	_	_	_
24	ml	ml	NN	_	_	_
25	of	of	IN	_	_	_
26	LB	lb	NN	MED	_	_
27	media	media	NNS	MED	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	cultures	culture	NNS	_	_	_
30	were	be	VBD	_	_	_
31	split	split	VBN	_	_	_
32	into	into	IN	_	_	_
33	two	two	CD	_	_	_
34	10	10	CD	_	_	_
35	ml	ml	NN	_	_	_
36	cultures	culture	NNS	_	_	_
37	.	.	.	_	_	_

1	One	one	CD	_	_	_
2	half	half	NN	_	_	_
3	was	be	VBD	_	_	_
4	treated	treat	VBN	_	_	_
5	with	with	IN	_	_	_
6	2	2	CD	_	_	_
7	mM	mm	NN	KWSUPP	_	_
8	NaN3	nan3	NN	_	_	_
9	for	for	IN	_	_	_
10	10	10	CD	_	_	_
11	minutes	minute	NNS	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	other	other	JJ	_	_	_
15	half	half	NN	_	_	_
16	was	be	VBD	_	_	_
17	left	leave	VBN	_	_	_
18	untreated	untreated	JJ	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	Escherichia	escherichia	FW	Organism	_	_
21	coli	coli	FW	Organism	_	_
22	K-12	k-12	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	growth	growth	NN	_	_	_
25	media	media	NNS	_	_	_
26	:	:	:	_	_	_
27	LB	lb	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	od	od	NN	_	_	_
30	:	:	:	_	_	_
31	0.8	0.8	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	Sample	sample	NN	_	_	_
34	1	1	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	Sample	sample	NN	_	_	_
37	2	2	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	strain	strain	NN	_	_	_
40	:	:	:	_	_	_
41	BW25113	bw25113	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	Total	total	JJ	_	_	_
44	RNA	rna	NN	_	_	_
45	using	use	VBG	_	_	_
46	Qiagen	Qiagen	NNP	_	_	_
47	RNeasy	RNeasy	NNP	_	_	_
48	kit	kit	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	treatment	treatment	NN	_	_	_
51	:	:	:	_	_	_
52	2	2	CD	_	_	_
53	mM	mm	NN	KWSUPP	_	_
54	NaN3	nan3	NN	_	_	_
55	for	for	IN	_	_	_
56	10	10	CD	_	_	_
57	minutes	minute	NNS	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	treatment	treatment	NN	_	_	_
60	:	:	:	_	_	_
61	none	none	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	untreated	untreated	JJ	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	Adaptive	adaptive	JJ	_	_	_
66	threshold	threshold	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	quantitation	quantitation	NN	_	_	_
69	method	method	NN	_	_	_
70	-RRB-	-rrb-	-RRB-	_	_	_
71	uses	use	VBZ	_	_	_
72	the	the	DT	_	_	_
73	parameters	parameter	NNS	_	_	_
74	of	of	IN	_	_	_
75	the	the	DT	_	_	_
76	spot	spot	NN	_	_	_
77	diameter	diameter	NN	_	_	_
78	and	and	CC	_	_	_
79	background	background	NN	_	_	_
80	inner	inner	JJ	_	_	_
81	and	and	CC	_	_	_
82	outer	outer	JJ	_	_	_
83	dimensions	dimension	NNS	_	_	_
84	to	to	TO	_	_	_
85	create	create	VB	_	_	_
86	a	a	DT	_	_	_
87	spot	spot	NN	_	_	_
88	mask	mask	NN	_	_	_
89	and	and	CC	_	_	_
90	background	background	NN	_	_	_
91	mask	mask	NN	_	_	_
92	,	,	,	_	_	_
93	then	then	RB	_	_	_
94	refines	refine	VBZ	_	_	_
95	the	the	DT	_	_	_
96	mask	mask	NN	_	_	_
97	on	on	IN	_	_	_
98	a	a	DT	_	_	_
99	pixel-by-pixel	pixel-by-pixel	JJ	_	_	_
100	basis	basis	NN	_	_	_
101	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	normalization	normalization	NN	_	_	_
4	method	method	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	,	,	,	_	_	_
7	uses	use	VBZ	_	_	_
8	the	the	DT	_	_	_
9	intensity	intensity	NN	_	_	_
10	of	of	IN	_	_	_
11	each	each	DT	_	_	_
12	spot	spot	NN	_	_	_
13	in	in	IN	_	_	_
14	relation	relation	NN	_	_	_
15	to	to	TO	_	_	_
16	all	all	DT	_	_	_
17	spots	spot	NNS	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	,	,	,	_	_	_
5	glucose	glucose	NN	SUPP	_	_
6	limitation	limitation	NN	_	_	_
7	,	,	,	_	_	_
8	110	110	CD	_	_	_
9	min	min	NN	_	_	_
10	after	after	IN	_	_	_
11	depletion	depletion	NN	_	_	_
12	of	of	IN	_	_	_
13	extracellular	extracellular	JJ	_	_	_
14	acetate	acetate	NN	SUPP	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	E.	E.	NNP	_	_	_
17	coli	coli	NN	_	_	_
18	,	,	,	_	_	_
19	glucose	glucose	NN	SUPP	_	_
20	limitation	limitation	NN	_	_	_
21	,	,	,	_	_	_
22	170	170	CD	_	_	_
23	min	min	NN	_	_	_
24	after	after	IN	_	_	_
25	depletion	depletion	NN	_	_	_
26	of	of	IN	_	_	_
27	extracellular	extracellular	JJ	_	_	_
28	acetate	acetate	NN	SUPP	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	E.	E.	NNP	_	_	_
31	coli	coli	NN	_	_	_
32	,	,	,	_	_	_
33	glucose	glucose	NN	SUPP	_	_
34	limitation	limitation	NN	_	_	_
35	,	,	,	_	_	_
36	230	230	CD	_	_	_
37	min	min	NN	_	_	_
38	after	after	IN	_	_	_
39	depletion	depletion	NN	_	_	_
40	of	of	IN	_	_	_
41	extracellular	extracellular	JJ	_	_	_
42	acetate	acetate	NN	SUPP	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	E.	E.	NNP	_	_	_
45	coli	coli	NN	_	_	_
46	,	,	,	_	_	_
47	glucose	glucose	NN	SUPP	_	_
48	limitation	limitation	NN	_	_	_
49	,	,	,	_	_	_
50	30	30	CD	_	_	_
51	min	min	NN	_	_	_
52	after	after	IN	_	_	_
53	depletion	depletion	NN	_	_	_
54	of	of	IN	_	_	_
55	extracellular	extracellular	JJ	_	_	_
56	acetate	acetate	NN	SUPP	_	_
57	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
58	E.	E.	NNP	_	_	_
59	coli	coli	NN	_	_	_
60	,	,	,	_	_	_
61	glucose	glucose	NN	SUPP	_	_
62	limitation	limitation	NN	_	_	_
63	,	,	,	_	_	_
64	350	350	CD	_	_	_
65	min	min	NN	_	_	_
66	after	after	IN	_	_	_
67	depletion	depletion	NN	_	_	_
68	of	of	IN	_	_	_
69	extracellular	extracellular	JJ	_	_	_
70	acetate	acetate	NN	SUPP	_	_
71	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
72	E.	E.	NNP	_	_	_
73	coli	coli	NN	_	_	_
74	,	,	,	_	_	_
75	glucose	glucose	NN	SUPP	_	_
76	limitation	limitation	NN	_	_	_
77	,	,	,	_	_	_
78	50	50	CD	_	_	_
79	min	min	NN	_	_	_
80	after	after	IN	_	_	_
81	depletion	depletion	NN	_	_	_
82	of	of	IN	_	_	_
83	extracellular	extracellular	JJ	_	_	_
84	acetate	acetate	NN	SUPP	_	_
85	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
86	E.	E.	NNP	_	_	_
87	coli	coli	NN	_	_	_
88	,	,	,	_	_	_
89	glucose	glucose	NN	SUPP	_	_
90	limitation	limitation	NN	_	_	_
91	,	,	,	_	_	_
92	acetate	acetate	NN	SUPP	_	_
93	concentration	concentration	NN	_	_	_
94	≤	≤	CD	_	_	_
95	0.35	0.35	CD	_	_	_
96	gL-1	gl-1	NN	_	_	_
97	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
98	E.	E.	NNP	_	_	_
99	coli	coli	NN	_	_	_
100	,	,	,	_	_	_
101	glucose	glucose	NN	SUPP	_	_
102	limitation	limitation	NN	_	_	_
103	-LRB-	-lrb-	-LRB-	_	_	_
104	glucose	glucose	NN	SUPP	_	_
105	concentration	concentration	NN	_	_	_
106	<	<	JJR	_	_	_
107	0.05	0.05	CD	_	_	_
108	gL-1	gl-1	NN	_	_	_
109	-RRB-	-rrb-	-RRB-	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	E.	e.	FW	_	_	_
112	coli	coli	FW	_	_	_
113	,	,	,	_	_	_
114	glucose	glucose	NN	SUPP	_	_
115	limitation	limitation	NN	_	_	_
116	-LRB-	-lrb-	-LRB-	_	_	_
117	glucose	glucose	NN	SUPP	_	_
118	concentration	concentration	NN	_	_	_
119	<	<	JJR	_	_	_
120	0.05	0.05	CD	_	_	_
121	gL-1	gl-1	NN	_	_	_
122	-RRB-	-rrb-	-RRB-	_	_	_
123	,	,	,	_	_	_
124	fed-batch	fed-batch	JJ	_	_	_
125	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
126	E.	e.	FW	_	_	_
127	coli	coli	FW	_	_	_
128	K12	k12	NN	_	_	_
129	-LRB-	-lrb-	-LRB-	_	_	_
130	W3110	w3110	NN	_	_	_
131	-RRB-	-rrb-	-RRB-	_	_	_
132	,	,	,	_	_	_
133	fed-batch	fed-batch	JJ	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	E.coli	e.coli	NNS	_	_	_
136	_	_	VBP	_	_	_
137	RviaT1	rviat1	NN	_	_	_
138	_	_	CD	_	_	_
139	SR1	sr1	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	E.coli	e.coli	NNS	_	_	_
142	_	_	VBP	_	_	_
143	RviaT1	rviat1	NN	_	_	_
144	_	_	CD	_	_	_
145	SR2	sr2	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	E.coli	e.coli	NNS	_	_	_
148	_	_	VBP	_	_	_
149	RviaT1	rviat1	NN	_	_	_
150	_	_	CD	_	_	_
151	SR3	sr3	NN	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	E.coli	e.coli	NNS	_	_	_
154	_	_	VBP	_	_	_
155	RviaT2	rviat2	NN	_	_	_
156	_	_	CD	_	_	_
157	SR1	sr1	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	E.coli	e.coli	NNS	_	_	_
160	_	_	VBP	_	_	_
161	RviaT2	rviat2	NN	_	_	_
162	_	_	CD	_	_	_
163	SR2	sr2	NN	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	E.coli	e.coli	NNS	_	_	_
166	_	_	VBP	_	_	_
167	RviaT2	rviat2	NN	_	_	_
168	_	_	CD	_	_	_
169	SR3	sr3	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	E.coli	e.coli	NNS	_	_	_
172	_	_	VBP	_	_	_
173	RviaT3	rviat3	NN	_	_	_
174	_	_	CD	_	_	_
175	SR1	sr1	NN	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	E.coli	e.coli	NNS	_	_	_
178	_	_	VBP	_	_	_
179	RviaT3	rviat3	NN	_	_	_
180	_	_	CD	_	_	_
181	SR2	sr2	NN	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	E.coli	e.coli	NNS	_	_	_
184	_	_	VBP	_	_	_
185	RviaT3	rviat3	NN	_	_	_
186	_	_	CD	_	_	_
187	SR3	sr3	NN	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	E.coli	e.coli	NNS	_	_	_
190	_	_	VBP	_	_	_
191	RviaT4	rviat4	NN	_	_	_
192	_	_	CD	_	_	_
193	SR1	sr1	NN	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	E.coli	e.coli	NNS	_	_	_
196	_	_	VBP	_	_	_
197	RviaT4	rviat4	NN	_	_	_
198	_	_	CD	_	_	_
199	SR2	sr2	NN	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	E.coli	e.coli	NNS	_	_	_
202	_	_	VBP	_	_	_
203	RviaT4	rviat4	NN	_	_	_
204	_	_	CD	_	_	_
205	SR3	sr3	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	E.coli	e.coli	NNS	_	_	_
208	_	_	VBP	_	_	_
209	RviaT5	rviat5	NN	_	_	_
210	_	_	CD	_	_	_
211	SR2	sr2	NN	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	E.coli	e.coli	NNS	_	_	_
214	_	_	VBP	_	_	_
215	RviaT5	rviat5	NN	_	_	_
216	_	_	CD	_	_	_
217	SR3	sr3	NN	_	_	_
218	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
219	E.coli	e.coli	NNS	_	_	_
220	_	_	VBP	_	_	_
221	RviaT6	rviat6	NN	_	_	_
222	_	_	CD	_	_	_
223	SR2	sr2	NN	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
225	E.coli	e.coli	NNS	_	_	_
226	_	_	VBP	_	_	_
227	RviaT6	rviat6	NN	_	_	_
228	_	_	CD	_	_	_
229	SR3	sr3	NN	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
231	E.coli	e.coli	NNS	_	_	_
232	_	_	VBP	_	_	_
233	RviaT7	rviat7	NN	_	_	_
234	_	_	CD	_	_	_
235	SR2	sr2	NN	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	E.coli	e.coli	NNS	_	_	_
238	_	_	VBP	_	_	_
239	RviaT7	rviat7	NN	_	_	_
240	_	_	CD	_	_	_
241	SR3	sr3	NN	_	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
243	E.coli	e.coli	NNS	_	_	_
244	_	_	VBP	_	_	_
245	RviaT8	rviat8	NN	_	_	_
246	_	_	CD	_	_	_
247	SR2	sr2	NN	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
249	E.coli	e.coli	NNS	_	_	_
250	_	_	VBP	_	_	_
251	RviaT8	rviat8	NN	_	_	_
252	_	_	CD	_	_	_
253	SR3	sr3	NN	_	_	_
254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
255	E.coli	e.coli	NNS	_	_	_
256	_	_	VBP	_	_	_
257	T1viaR	t1viar	NN	_	_	_
258	_	_	CD	_	_	_
259	SR1	sr1	NN	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	E.coli	e.coli	NNS	_	_	_
262	_	_	VBP	_	_	_
263	T1viaR	t1viar	NN	_	_	_
264	_	_	CD	_	_	_
265	SR2	sr2	NN	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
267	E.coli	e.coli	NNS	_	_	_
268	_	_	VBP	_	_	_
269	T1viaR	t1viar	NN	_	_	_
270	_	_	CD	_	_	_
271	SR3	sr3	NN	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	E.coli	e.coli	NNS	_	_	_
274	_	_	VBP	_	_	_
275	T2viaR	t2viar	NN	_	_	_
276	_	_	CD	_	_	_
277	SR1	sr1	NN	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
279	E.coli	e.coli	NNS	_	_	_
280	_	_	VBP	_	_	_
281	T2viaR	t2viar	NN	_	_	_
282	_	_	CD	_	_	_
283	SR2	sr2	NN	_	_	_
284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
285	E.coli	e.coli	NNS	_	_	_
286	_	_	VBP	_	_	_
287	T2viaR	t2viar	NN	_	_	_
288	_	_	CD	_	_	_
289	SR3	sr3	NN	_	_	_
290	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
291	E.coli	e.coli	NNS	_	_	_
292	_	_	VBP	_	_	_
293	T3viaR	t3viar	NN	_	_	_
294	_	_	CD	_	_	_
295	SR1	sr1	NN	_	_	_
296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
297	E.coli	e.coli	NNS	_	_	_
298	_	_	VBP	_	_	_
299	T3viaR	t3viar	NN	_	_	_
300	_	_	CD	_	_	_
301	SR2	sr2	NN	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
303	E.coli	e.coli	NNS	_	_	_
304	_	_	VBP	_	_	_
305	T3viaR	t3viar	NN	_	_	_
306	_	_	CD	_	_	_
307	SR3	sr3	NN	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	E.coli	e.coli	NNS	_	_	_
310	_	_	VBP	_	_	_
311	T4viaR	t4viar	NN	_	_	_
312	_	_	CD	_	_	_
313	SR1	sr1	NN	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	E.coli	e.coli	NNS	_	_	_
316	_	_	VBP	_	_	_
317	T4viaR	t4viar	NN	_	_	_
318	_	_	CD	_	_	_
319	SR2	sr2	NN	_	_	_
320	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
321	E.coli	e.coli	NNS	_	_	_
322	_	_	VBP	_	_	_
323	T4viaR	t4viar	NN	_	_	_
324	_	_	CD	_	_	_
325	SR3	sr3	NN	_	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	E.coli	e.coli	NNS	_	_	_
328	_	_	VBP	_	_	_
329	T5viaR	t5viar	NN	_	_	_
330	_	_	CD	_	_	_
331	SR2	sr2	NN	_	_	_
332	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
333	E.coli	e.coli	NNS	_	_	_
334	_	_	VBP	_	_	_
335	T5viaR	t5viar	NN	_	_	_
336	_	_	CD	_	_	_
337	SR3	sr3	NN	_	_	_
338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
339	E.coli	e.coli	NNS	_	_	_
340	_	_	VBP	_	_	_
341	T6viaR	t6viar	NN	_	_	_
342	_	_	CD	_	_	_
343	SR2	sr2	NN	_	_	_
344	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
345	E.coli	e.coli	NNS	_	_	_
346	_	_	VBP	_	_	_
347	T6viaR	t6viar	NN	_	_	_
348	_	_	CD	_	_	_
349	SR3	sr3	NN	_	_	_
350	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
351	E.coli	e.coli	NNS	_	_	_
352	_	_	VBP	_	_	_
353	T7viaR	t7viar	NN	_	_	_
354	_	_	CD	_	_	_
355	SR2	sr2	NN	_	_	_
356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
357	E.coli	e.coli	NNS	_	_	_
358	_	_	VBP	_	_	_
359	T7viaR	t7viar	NN	_	_	_
360	_	_	CD	_	_	_
361	SR3	sr3	NN	_	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
363	E.coli	e.coli	NNS	_	_	_
364	_	_	VBP	_	_	_
365	T8viaR	t8viar	NN	_	_	_
366	_	_	CD	_	_	_
367	SR2	sr2	NN	_	_	_
368	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
369	E.coli	e.coli	NNS	_	_	_
370	_	_	VBP	_	_	_
371	T8viaR	t8viar	NN	_	_	_
372	_	_	CD	_	_	_
373	SR3	sr3	NN	_	_	_
374	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
375	E.	E.	NNP	_	_	_
376	coli	coli	NN	_	_	_
377	,	,	,	_	_	_
378	unlimited	unlimited	JJ	_	_	_
379	growth	growth	NN	_	_	_
380	-LRB-	-lrb-	-LRB-	_	_	_
381	batch	batch	NN	_	_	_
382	-RRB-	-rrb-	-RRB-	_	_	_
383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
384	E.	e.	FW	_	_	_
385	coli	coli	FW	_	_	_
386	,	,	,	_	_	_
387	unlimited	unlimited	JJ	_	_	_
388	growth	growth	NN	_	_	_
389	-LRB-	-lrb-	-LRB-	_	_	_
390	batch	batch	NN	_	_	_
391	-RRB-	-rrb-	-RRB-	_	_	_
392	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
393	Escherichia	escherichia	FW	Organism	_	_
394	coli	coli	FW	Organism	_	_
395	str	str	FW	_	_	_
396	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	W3110	w3110	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Raw	raw	NN	_	_	_
4	data	datum	NNS	_	_	_
5	were	be	VBD	_	_	_
6	created	create	VBN	_	_	_
7	by	by	IN	_	_	_
8	analyzing	analyze	VBG	_	_	_
9	16-bit	16-bit	JJ	_	_	_
10	tiff	tiff	NN	_	_	_
11	files	file	NNS	_	_	_
12	with	with	IN	_	_	_
13	the	the	DT	_	_	_
14	Scan	scan	VB	_	_	_
15	Array	Array	NNP	_	_	_
16	Express	Express	NNP	_	_	_
17	imaging	imaging	NN	_	_	_
18	software	software	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	microarray	microarray	NN	_	_	_
21	analysis	analysis	NN	_	_	_
22	system	system	NN	_	_	_
23	,	,	,	_	_	_
24	version	version	NN	_	_	_
25	3.0.0.0016	3.0.0.0016	CD	_	_	_
26	,	,	,	_	_	_
27	PerkinElmer	PerkinElmer	NNP	_	_	_
28	,	,	,	_	_	_
29	Massachusetts	Massachusetts	NNP	_	_	_
30	,	,	,	_	_	_
31	USA	USA	NNP	_	_	_
32	;	;	:	_	_	_
33	adaptive	adaptive	JJ	_	_	_
34	treshold	treshold	NN	_	_	_
35	method	method	NN	_	_	_
36	,	,	,	_	_	_
37	total	total	JJ	_	_	_
38	normalization	normalization	NN	_	_	_
39	method	method	NN	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cell	cell	NN	_	_	_
4	samples	sample	NNS	_	_	_
5	were	be	VBD	_	_	_
6	collected	collect	VBN	_	_	_
7	directly	directly	RB	_	_	_
8	into	into	IN	_	_	_
9	RNAprotect	rnaprotect	NN	_	_	_
10	Bacteria	bacterium	NNS	_	_	_
11	Reagent	reagent	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Qiagen	Qiagen	NNP	_	_	_
14	,	,	,	_	_	_
15	Hilden	Hilden	NNP	_	_	_
16	,	,	,	_	_	_
17	Germany	Germany	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	to	to	TO	_	_	_
20	avoid	avoid	VB	_	_	_
21	RNA	rna	NN	_	_	_
22	degradation	degradation	NN	_	_	_
23	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	centrifuged	centrifuge	VBN	_	_	_
5	according	accord	VBG	_	_	_
6	to	to	TO	_	_	_
7	the	the	DT	_	_	_
8	manufacturer	manufacturer	NN	_	_	_
9	's	's	POS	_	_	_
10	protocol	protocol	NN	_	_	_
11	and	and	CC	_	_	_
12	frozen	freeze	VBN	_	_	_
13	at	at	IN	_	_	_
14	-	-	:	_	_	_
15	80	80	CD	_	_	_
16	°C	°c	NN	_	_	_
17	until	until	IN	_	_	_
18	RNA	rna	NN	_	_	_
19	isolation	isolation	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	culture	culture	NN	_	_	_
4	medium	medium	NN	_	_	_
5	samples	sample	NNS	_	_	_
6	were	be	VBD	_	_	_
7	withdrawn	withdraw	VBN	_	_	_
8	with	with	IN	_	_	_
9	a	a	DT	_	_	_
10	capillary	capillary	JJ	_	_	_
11	sampling	sampling	NN	_	_	_
12	probe	probe	NN	_	_	_
13	as	as	IN	_	_	_
14	developed	develop	VBN	_	_	_
15	by	by	IN	_	_	_
16	Theobald	Theobald	NNP	_	_	_
17	et	et	FW	_	_	_
18	al.	al.	FW	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	1997	1997	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	,	,	,	_	_	_
23	however	however	RB	_	_	_
24	,	,	,	_	_	_
25	without	without	IN	_	_	_
26	using	use	VBG	_	_	_
27	membrane-covered	membrane-covered	JJ	_	_	_
28	glass	glass	NN	_	_	_
29	tubes	tube	NNS	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	fed-batch	fed-batch	JJ	_	_	_
4	cultivations	cultivation	NNS	_	_	_
5	were	be	VBD	_	_	_
6	carried	carry	VBN	_	_	_
7	out	out	RP	_	_	_
8	with	with	IN	_	_	_
9	the	the	DT	_	_	_
10	bacterial	bacterial	JJ	_	_	_
11	strain	strain	NN	_	_	_
12	E.	e.	FW	_	_	_
13	coli	coli	FW	_	_	_
14	K-12	k-12	NN	_	_	_
15	W3110	w3110	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	DSM	DSM	NNP	_	_	_
18	5911	5911	CD	_	_	_
19	,	,	,	_	_	_
20	German	german	JJ	_	_	_
21	Collection	collection	NN	_	_	_
22	of	of	IN	_	_	_
23	Microorganisms	microorganism	NNS	_	_	_
24	and	and	CC	_	_	_
25	Cell	cell	NN	_	_	_
26	Cultures	culture	NNS	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	in	in	IN	_	_	_
29	a	a	DT	_	_	_
30	30-l	30-l	JJ	_	_	_
31	bioreactor	bioreactor	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	Bioengineering	bioengineer	VBG	_	_	_
34	AG	AG	NNP	_	_	_
35	,	,	,	_	_	_
36	Wald	Wald	NNP	_	_	_
37	,	,	,	_	_	_
38	Switzerland	Switzerland	NNP	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	.	.	.	_	_	_

1	Minimal	minimal	JJ	_	_	_
2	medium	medium	NN	_	_	_
3	supplemented	supplement	VBN	_	_	_
4	with	with	IN	_	_	_
5	glucose	glucose	NN	SUPP	_	_
6	as	as	IN	_	_	_
7	the	the	DT	_	_	_
8	carbon	carbon	NN	_	_	_
9	source	source	NN	_	_	_
10	was	be	VBD	_	_	_
11	used	use	VBN	_	_	_
12	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	batch	batch	NN	_	_	_
3	medium	medium	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	batch	batch	NN	_	_	_
6	volume	volume	NN	_	_	_
7	VR	vr	NN	_	_	_
8	,0	,0	NN	_	_	_
9	=	=	JJ	_	_	_
10	17	17	CD	_	_	_
11	l	l	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	consisted	consist	VBD	_	_	_
14	of	of	IN	_	_	_
15	8.8	8.8	CD	_	_	_
16	g	g	NN	_	_	_
17	l	l	NN	_	_	_
18	−	−	CD	_	_	_
19	1	1	CD	_	_	_
20	glucose	glucose	NN	SUPP	_	_
21	•	•	SYM	_	_	_
22	H2O	h2o	NN	_	_	_
23	,	,	,	_	_	_
24	2.0	2.0	CD	_	_	_
25	g	g	NN	_	_	_
26	l	l	NN	_	_	_
27	−	−	CD	_	_	_
28	1	1	CD	_	_	_
29	Na2SO4	na2so4	NN	_	_	_
30	•	•	SYM	_	_	_
31	10H2O	10h2o	CD	_	_	_
32	,	,	,	_	_	_
33	2.68	2.68	CD	_	_	_
34	g	g	NN	_	_	_
35	l	l	NN	_	_	_
36	−	−	CD	_	_	_
37	1	1	CD	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	NH4	nh4	NN	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	2SO4	2so4	NN	_	_	_
42	,	,	,	_	_	_
43	1.0	1.0	CD	_	_	_
44	g	g	NN	_	_	_
45	l	l	NN	_	_	_
46	−	−	CD	_	_	_
47	1	1	CD	_	_	_
48	NH4Cl	nh4cl	NN	_	_	_
49	,	,	,	_	_	_
50	14.6	14.6	CD	_	_	_
51	g	g	NN	_	_	_
52	l	l	NN	_	_	_
53	−	−	CD	_	_	_
54	1	1	CD	_	_	_
55	K2HPO4	k2hpo4	NN	_	_	_
56	,	,	,	_	_	_
57	4.02	4.02	CD	_	_	_
58	g	g	NN	_	_	_
59	l	l	NN	_	_	_
60	−	−	CD	_	_	_
61	1	1	CD	_	_	_
62	NaH2PO4	nah2po4	NN	_	_	_
63	•	•	SYM	_	_	_
64	2H2O	2h2o	NN	_	_	_
65	,	,	,	_	_	_
66	0.01	0.01	CD	_	_	_
67	g	g	NN	_	_	_
68	l	l	NN	_	_	_
69	−	−	CD	_	_	_
70	1	1	CD	_	_	_
71	thiamine	thiamine	NN	SUPP	_	_
72	HCl	hcl	NN	_	_	_
73	;	;	:	_	_	_
74	0.3	0.3	CD	_	_	_
75	mM	mm	NN	KWSUPP	_	_
76	CaCl2	cacl2	NN	_	_	_
77	•	•	SYM	_	_	_
78	2H2O	2h2o	NN	_	_	_
79	,	,	,	_	_	_
80	2mM	2mm	NN	_	_	_
81	MgSO4	mgso4	NN	_	_	_
82	•	•	SYM	_	_	_
83	7H2O	7h2o	CD	_	_	_
84	;	;	:	_	_	_
85	3	3	CD	_	_	_
86	ml	ml	NN	_	_	_
87	l	l	NN	_	_	_
88	−	−	CD	_	_	_
89	1	1	CD	_	_	_
90	of	of	IN	_	_	_
91	trace	trace	NN	_	_	_
92	element	element	NN	_	_	_
93	solution	solution	NN	_	_	_
94	-LRB-	-lrb-	-LRB-	_	_	_
95	TES	tes	NN	_	_	_
96	:	:	:	_	_	_
97	16.7	16.7	CD	_	_	_
98	g	g	NN	_	_	_
99	l	l	NN	_	_	_
100	−	−	CD	_	_	_
101	1	1	CD	_	_	_
102	FeCl3	fecl3	NN	_	_	_
103	•	•	SYM	_	_	_
104	6H2O	6h2o	CD	_	_	_
105	,	,	,	_	_	_
106	20.1	20.1	CD	_	_	_
107	g	g	NN	_	_	_
108	l	l	NN	_	_	_
109	−	−	CD	_	_	_
110	1	1	CD	_	_	_
111	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
112	Theobald	Theobald	NNP	_	_	_
113	,	,	,	_	_	_
114	U.	U.	NNP	_	_	_
115	,	,	,	_	_	_
116	Mailinger	Mailinger	NNP	_	_	_
117	,	,	,	_	_	_
118	W.	W.	NNP	_	_	_
119	,	,	,	_	_	_
120	Baltes	Baltes	NNP	_	_	_
121	,	,	,	_	_	_
122	M.	M.	NNP	_	_	_
123	,	,	,	_	_	_
124	Rizzi	Rizzi	NNP	_	_	_
125	,	,	,	_	_	_
126	M.	M.	NNP	_	_	_
127	,	,	,	_	_	_
128	Reuss	Reuss	NNP	_	_	_
129	,	,	,	_	_	_
130	M.	M.	NNP	_	_	_
131	,	,	,	_	_	_
132	1997	1997	CD	_	_	_
133	.	.	.	_	_	_

1	In	in	FW	_	_	_
2	vivo	vivo	FW	_	_	_
3	analysis	analysis	NN	_	_	_
4	of	of	IN	_	_	_
5	metabolic	metabolic	JJ	_	_	_
6	dynamics	dynamics	NNS	_	_	_
7	in	in	IN	_	_	_
8	Saccharomyces	saccharomyces	FW	_	_	_
9	cerevisiae	cerevisiae	FW	_	_	_
10	.	.	.	_	_	_

1	1	1	LS	_	_	_
2	.	.	.	_	_	_

1	Experimental	experimental	JJ	_	_	_
2	observations	observation	NNS	_	_	_
3	.	.	.	_	_	_

1	Biotechnol	Biotechnol	NNP	_	_	_
2	.	.	.	_	_	_

1	Bioeng	Bioeng	NNP	_	_	_
2	.	.	.	_	_	_

1	55	55	CD	_	_	_
2	,	,	,	_	_	_
3	305	305	CD	_	_	_
4	--	--	:	_	_	_
5	316	316	CD	_	_	_
6	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	VALUE	VALUE	NNP	_	_	_
4	data	datum	NNS	_	_	_
5	are	be	VBP	_	_	_
6	normalized	normalize	VBN	_	_	_
7	log2	log2	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	test	test	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Total	total	JJ	_	_	_
12	RNA	rna	NN	_	_	_
13	from	from	IN	_	_	_
14	8.1	8.1	CD	_	_	_
15	*	*	SYM	_	_	_
16	10exp9	10exp9	CD	_	_	_
17	cells	cell	NNS	_	_	_
18	was	be	VBD	_	_	_
19	isolated	isolate	VBN	_	_	_
20	using	use	VBG	_	_	_
21	the	the	DT	_	_	_
22	RNeasy	RNeasy	NNP	_	_	_
23	Kit	kit	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Qiagen	qiagen	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	according	accord	VBG	_	_	_
28	to	to	TO	_	_	_
29	the	the	DT	_	_	_
30	manufacturer	manufacturer	NN	_	_	_
31	's	's	POS	_	_	_
32	protocol	protocol	NN	_	_	_
33	.	.	.	_	_	_

1	On-column	on-column	JJ	_	_	_
2	DNase	dnase	NN	_	_	_
3	digestion	digestion	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	RNase	rnase	NN	_	_	_
8	free	free	JJ	_	_	_
9	DNase	dnase	NN	_	_	_
10	set	set	NN	_	_	_
11	,	,	,	_	_	_
12	Qiagen	Qiagen	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	concentration	concentration	NN	_	_	_
3	and	and	CC	_	_	_
4	quality	quality	NN	_	_	_
5	were	be	VBD	_	_	_
6	assessed	assess	VBN	_	_	_
7	photometrically	photometrically	RB	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Nanodrop	nanodrop	JJ	_	_	_
10	ND	nd	NN	_	_	_
11	1000	1000	CD	_	_	_
12	,	,	,	_	_	_
13	NanoDrop	NanoDrop	NNP	_	_	_
14	Technologies	Technologies	NNPS	_	_	_
15	,	,	,	_	_	_
16	Inc.	Inc.	NNP	_	_	_
17	,	,	,	_	_	_
18	Delaware	Delaware	NNP	_	_	_
19	,	,	,	_	_	_
20	USA	USA	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	,	,	,	_	_	_
23	by	by	IN	_	_	_
24	formaldehyde	formaldehyde	NN	_	_	_
25	gel	gel	NN	_	_	_
26	electrophoresis	electrophoresis	NN	_	_	_
27	and	and	CC	_	_	_
28	bioanalyzer	bioanalyzer	NN	_	_	_
29	analysis	analysis	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	RNA	rna	NN	_	_	_
32	6000	6000	CD	_	_	_
33	Nano	Nano	NNP	_	_	_
34	LabChip	LabChip	NNP	_	_	_
35	Kit	kit	NN	_	_	_
36	,	,	,	_	_	_
37	Agilent	Agilent	NNP	_	_	_
38	Bioanalyzer	Bioanalyzer	NNP	_	_	_
39	2100	2100	CD	_	_	_
40	,	,	,	_	_	_
41	Agilent	Agilent	NNP	_	_	_
42	Technologies	Technologies	NNPS	_	_	_
43	,	,	,	_	_	_
44	California	California	NNP	_	_	_
45	,	,	,	_	_	_
46	USA	USA	NNP	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	.	.	.	_	_	_

1	Only	only	RB	_	_	_
2	RNA	rna	NN	_	_	_
3	with	with	IN	_	_	_
4	260	260	CD	_	_	_
5	nm	nm	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	An	a	DT	_	_	_
8	RNeasy	rneasy	NN	_	_	_
9	minikit	minikit	NN	_	_	_
10	was	be	VBD	_	_	_
11	used	use	VBN	_	_	_
12	to	to	TO	_	_	_
13	prepare	prepare	VB	_	_	_
14	total	total	JJ	_	_	_
15	RNA	rna	NN	_	_	_
16	according	accord	VBG	_	_	_
17	to	to	TO	_	_	_
18	the	the	DT	_	_	_
19	manufacturer	manufacturer	NN	_	_	_
20	's	's	POS	_	_	_
21	instructions	instruction	NNS	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	QIAGEN	QIAGEN	NNP	_	_	_
24	Ltd.	Ltd.	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	Any	any	DT	_	_	_
2	contaminating	contaminate	VBG	_	_	_
3	DNA	dna	NN	_	_	_
4	was	be	VBD	_	_	_
5	removed	remove	VBN	_	_	_
6	using	use	VBG	_	_	_
7	a	a	DT	_	_	_
8	DNAase	dnaase	NN	_	_	_
9	column	column	NN	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	QIAGEN	QIAGEN	NNP	_	_	_
13	Ltd	Ltd	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Escherichia	escherichia	FW	Organism	_	_
6	coli	coli	FW	Organism	_	_
7	O157	o157	NN	_	_	_
8	TUV93-0	tuv93-0	NN	_	_	_
9	MEM-HEPES	mem-hepes	NN	_	_	_
10	+	+	CC	_	_	_
11	20uM	20um	NN	_	_	_
12	ME0052	me0052	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	in	in	IN	_	_	_
15	DMSO	dmso	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Escherichia	escherichia	FW	Organism	_	_
19	coli	coli	FW	Organism	_	_
20	O157	o157	NN	_	_	_
21	TUV93-0	tuv93-0	NN	_	_	_
22	MEM-HEPES	mem-hepes	NN	_	_	_
23	+	+	CC	_	_	_
24	20uM	20um	NN	_	_	_
25	ME0053	me0053	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	in	in	IN	_	_	_
28	DMSO	dmso	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Escherichia	escherichia	FW	Organism	_	_
32	coli	coli	FW	Organism	_	_
33	O157	o157	NN	_	_	_
34	TUV93-0	tuv93-0	NN	_	_	_
35	MEM-HEPES	mem-hepes	NN	_	_	_
36	+	+	CC	_	_	_
37	20uM	20um	NN	_	_	_
38	ME0054	me0054	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	in	in	IN	_	_	_
41	DMSO	dmso	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Escherichia	escherichia	FW	Organism	_	_
45	coli	coli	FW	Organism	_	_
46	O157	o157	NN	_	_	_
47	TUV93-0	tuv93-0	NN	_	_	_
48	MEM-HEPES	mem-hepes	NN	_	_	_
49	+	+	CC	_	_	_
50	20uM	20um	NN	_	_	_
51	ME0055	me0055	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	in	in	IN	_	_	_
54	DMSO	dmso	NN	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	Escherichia	escherichia	FW	Organism	_	_
58	coli	coli	FW	Organism	_	_
59	O157	o157	NN	_	_	_
60	TUV93-0	tuv93-0	NN	_	_	_
61	MEM-HEPES	mem-hepes	NN	_	_	_
62	+	+	CC	_	_	_
63	DMSO	dmso	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
65	Escherichia	escherichia	FW	Organism	_	_
66	coli	coli	FW	Organism	_	_
67	O157	o157	NN	_	_	_
68	TUV93-0	tuv93-0	NN	_	_	_
69	was	be	VBD	_	_	_
70	grown	grow	VBN	_	_	_
71	at	at	IN	_	_	_
72	37	37	CD	_	_	_
73	degrees	degree	NNS	_	_	_
74	C	c	NN	_	_	_
75	to	to	TO	_	_	_
76	OD	od	NN	_	_	_
77	0.7	0.7	CD	_	_	_
78	in	in	IN	_	_	_
79	MEM-HEPES	mem-hepes	NN	_	_	_
80	supplemented	supplement	VBN	_	_	_
81	with	with	IN	_	_	_
82	0.1	0.1	CD	_	_	_
83	%	%	NN	_	_	_
84	Glucose	glucose	NN	_	_	_
85	and	and	CC	_	_	_
86	250nM	250nm	NN	_	_	_
87	Fe	Fe	NNP	_	_	_
88	-LRB-	-lrb-	-LRB-	_	_	_
89	NO3	no3	NN	_	_	_
90	-RRB-	-rrb-	-RRB-	_	_	_
91	2	2	CD	_	_	_
92	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	O157	o157	NN	_	_	_
5	TUV93-0	tuv93-0	NN	_	_	_
6	was	be	VBD	_	_	_
7	grown	grow	VBN	_	_	_
8	at	at	IN	_	_	_
9	37	37	CD	_	_	_
10	degrees	degree	NNS	_	_	_
11	C	c	NN	_	_	_
12	to	to	TO	_	_	_
13	OD	od	NN	_	_	_
14	0.7	0.7	CD	_	_	_
15	in	in	IN	_	_	_
16	MEM-HEPES	mem-hepes	NN	_	_	_
17	supplemented	supplement	VBN	_	_	_
18	with	with	IN	_	_	_
19	0.1	0.1	CD	_	_	_
20	%	%	NN	_	_	_
21	Glucose	glucose	NN	_	_	_
22	and	and	CC	_	_	_
23	250nM	250nm	NN	_	_	_
24	Fe	Fe	NNP	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	NO3	no3	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	2	2	CD	_	_	_
29	and	and	CC	_	_	_
30	and	and	CC	_	_	_
31	equivalent	equivalent	JJ	_	_	_
32	volume	volume	NN	_	_	_
33	of	of	IN	_	_	_
34	DMSO	dmso	NN	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	O157	o157	NN	_	_	_
5	TUV93-0	tuv93-0	NN	_	_	_
6	was	be	VBD	_	_	_
7	grown	grow	VBN	_	_	_
8	in	in	IN	_	_	_
9	the	the	DT	_	_	_
10	presence	presence	NN	_	_	_
11	of	of	IN	_	_	_
12	20uM	20um	NN	_	_	_
13	ME0052	me0052	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Escherichia	escherichia	FW	Organism	_	_
16	coli	coli	FW	Organism	_	_
17	O157	o157	NN	_	_	_
18	TUV93-0	tuv93-0	NN	_	_	_
19	was	be	VBD	_	_	_
20	grown	grow	VBN	_	_	_
21	in	in	IN	_	_	_
22	the	the	DT	_	_	_
23	presence	presence	NN	_	_	_
24	of	of	IN	_	_	_
25	20uM	20um	NN	_	_	_
26	ME0053	me0053	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Escherichia	escherichia	FW	Organism	_	_
29	coli	coli	FW	Organism	_	_
30	O157	o157	NN	_	_	_
31	TUV93-0	tuv93-0	NN	_	_	_
32	was	be	VBD	_	_	_
33	grown	grow	VBN	_	_	_
34	in	in	IN	_	_	_
35	the	the	DT	_	_	_
36	presence	presence	NN	_	_	_
37	of	of	IN	_	_	_
38	20uM	20um	NN	_	_	_
39	ME0054	me0054	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	Escherichia	escherichia	FW	Organism	_	_
42	coli	coli	FW	Organism	_	_
43	O157	o157	NN	_	_	_
44	TUV93-0	tuv93-0	NN	_	_	_
45	was	be	VBD	_	_	_
46	grown	grow	VBN	_	_	_
47	in	in	IN	_	_	_
48	the	the	DT	_	_	_
49	presence	presence	NN	_	_	_
50	of	of	IN	_	_	_
51	20uM	20um	NN	_	_	_
52	ME0055	me0055	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Escherichia	escherichia	FW	Organism	_	_
55	coli	coli	FW	Organism	_	_
56	O157	o157	NN	_	_	_
57	TUV93-0	tuv93-0	NN	_	_	_
58	was	be	VBD	_	_	_
59	grown	grow	VBN	_	_	_
60	in	in	IN	_	_	_
61	the	the	DT	_	_	_
62	presence	presence	NN	_	_	_
63	of	of	IN	_	_	_
64	DMSO	dmso	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	inhibitor	inhibitor	NN	_	_	_
67	:	:	:	_	_	_
68	20uM	20um	NN	_	_	_
69	ME0052	me0052	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	inhibitor	inhibitor	NN	_	_	_
72	:	:	:	_	_	_
73	20uM	20um	NN	_	_	_
74	ME0053	me0053	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	inhibitor	inhibitor	NN	_	_	_
77	:	:	:	_	_	_
78	20uM	20um	NN	_	_	_
79	ME0054	me0054	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	inhibitor	inhibitor	NN	_	_	_
82	:	:	:	_	_	_
83	20uM	20um	NN	_	_	_
84	ME0055	me0055	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	LOWESS	lowess	NN	_	_	_
87	normalised	normalised	JJ	_	_	_
88	data	datum	NNS	_	_	_
89	that	that	WDT	_	_	_
90	represents	represent	VBZ	_	_	_
91	the	the	DT	_	_	_
92	average	average	NN	_	_	_
93	of	of	IN	_	_	_
94	the	the	DT	_	_	_
95	three	three	CD	_	_	_
96	replicate	replicate	VBP	_	_	_
97	experiments	experiment	NNS	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
99	ME0052	me0052	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	ME0053	me0053	NN	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	ME0054	me0054	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	ME0055	me0055	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	media	media	NNS	_	_	_
108	:	:	:	_	_	_
109	MEM-HEPES	mem-hepes	NN	_	_	_
110	supplemented	supplement	VBN	_	_	_
111	with	with	IN	_	_	_
112	0.1	0.1	CD	_	_	_
113	%	%	NN	_	_	_
114	Glucose	glucose	NN	_	_	_
115	and	and	CC	_	_	_
116	250nM	250nm	NN	_	_	_
117	Fe	Fe	NNP	_	_	_
118	-LRB-	-lrb-	-LRB-	_	_	_
119	NO3	no3	NN	_	_	_
120	-RRB-	-rrb-	-RRB-	_	_	_
121	2	2	CD	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
123	no	no	DT	_	_	_
124	inhibitor	inhibitor	NN	_	_	_
125	:	:	:	_	_	_
126	equivalent	equivalent	JJ	_	_	_
127	volume	volume	NN	_	_	_
128	of	of	IN	_	_	_
129	DMSO	dmso	NN	_	_	_
130	added	add	VBD	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	od	od	NN	_	_	_
133	:	:	:	_	_	_
134	0.7	0.7	CD	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	strain	strain	NN	_	_	_
137	:	:	:	_	_	_
138	O157	o157	NN	_	_	_
139	:	:	:	_	_	_
140	H7	h7	NN	_	_	_
141	EHEC	ehec	NN	_	_	_
142	TUV93-0	tuv93-0	NN	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
144	All	all	DT	_	_	_
145	culture	culture	NN	_	_	_
146	experiments	experiment	NNS	_	_	_
147	were	be	VBD	_	_	_
148	performed	perform	VBN	_	_	_
149	in	in	IN	_	_	_
150	MOPS	MOPS	NNP	MED	_	_
151	medium	medium	NN	_	_	_
152	supplemented	supplement	VBN	_	_	_
153	with	with	IN	_	_	_
154	0.2	0.2	CD	_	_	_
155	%	%	NN	_	_	_
156	glucose	glucose	NN	SUPP	_	_
157	,	,	,	_	_	_
158	19	19	CD	_	_	_
159	amino	amino	NN	SUPP	_	_
160	acids	acid	NNS	SUPP	_	_
161	-LRB-	-lrb-	-LRB-	_	_	_
162	without	without	IN	_	_	_
163	methionine	methionine	NN	SUPP	_	_
164	-RRB-	-rrb-	-RRB-	_	_	_
165	,	,	,	_	_	_
166	vitamins	vitamin	NNS	_	_	_
167	,	,	,	_	_	_
168	bases	basis	NNS	_	_	_
169	and	and	CC	_	_	_
170	micronutrients	micronutrient	NNS	_	_	_
171	-LRB-	-lrb-	-LRB-	_	_	_
172	MOPS	mop	NNS	MED	_	_
173	rich	rich	JJ	_	_	_
174	defined	define	VBN	_	_	_
175	medium	medium	NN	_	_	_
176	minus	minus	CC	_	_	_
177	methionine	methionine	NN	SUPP	_	_
178	,	,	,	_	_	_
179	Teknova	teknova	NN	_	_	_
180	-RRB-	-rrb-	-RRB-	_	_	_
181	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	grown	grow	VBN	_	_	_
4	in	in	IN	_	_	_
5	an	a	DT	_	_	_
6	overnight	overnight	JJ	_	_	_
7	liquid	liquid	JJ	_	_	_
8	culture	culture	NN	_	_	_
9	at	at	IN	_	_	_
10	37	37	CD	_	_	_
11	°C	°c	NN	_	_	_
12	,	,	,	_	_	_
13	diluted	dilute	VBN	_	_	_
14	to	to	TO	_	_	_
15	an	a	DT	_	_	_
16	OD420	od420	NN	_	_	_
17	=	=	JJ	_	_	_
18	.001	.001	CD	_	_	_
19	in	in	IN	_	_	_
20	fresh	fresh	JJ	_	_	_
21	medium	medium	NN	_	_	_
22	and	and	CC	_	_	_
23	grown	grow	VBN	_	_	_
24	until	until	IN	_	_	_
25	OD420	od420	NN	_	_	_
26	reached	reach	VBD	_	_	_
27	0.4	0.4	CD	_	_	_
28	where	where	WRB	_	_	_
29	samples	sample	NNS	_	_	_
30	were	be	VBD	_	_	_
31	collected	collect	VBN	_	_	_
32	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	10	10	CD	_	_	_
3	°C	°c	NN	_	_	_
4	samples	sample	NNS	_	_	_
5	,	,	,	_	_	_
6	cultures	culture	NNS	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	to	to	TO	_	_	_
10	OD420	od420	NN	_	_	_
11	=	=	JJ	_	_	_
12	1.1	1.1	CD	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	and	and	CC	_	_	_
17	cold	cold	JJ	_	_	_
18	shock	shock	NN	_	_	_
19	was	be	VBD	_	_	_
20	performed	perform	VBN	_	_	_
21	by	by	IN	_	_	_
22	mixing	mix	VBG	_	_	_
23	70mL	70ml	NN	_	_	_
24	of	of	IN	_	_	_
25	37	37	CD	_	_	_
26	°C	°c	NN	_	_	_
27	culture	culture	NN	_	_	_
28	with	with	IN	_	_	_
29	130mL	130ml	NN	_	_	_
30	of	of	IN	_	_	_
31	0	0	CD	_	_	_
32	°C	°c	NN	_	_	_
33	media	media	NNS	_	_	_
34	pre-chilled	pre-chill	VBN	_	_	_
35	in	in	IN	_	_	_
36	ice-water	ice-water	JJ	_	_	_
37	slurry	slurry	NN	_	_	_
38	,	,	,	_	_	_
39	with	with	IN	_	_	_
40	continued	continued	JJ	_	_	_
41	growth	growth	NN	_	_	_
42	of	of	IN	_	_	_
43	the	the	DT	_	_	_
44	culture	culture	NN	_	_	_
45	in	in	IN	_	_	_
46	a	a	DT	_	_	_
47	10	10	CD	_	_	_
48	°C	°c	NN	_	_	_
49	shaker	shaker	NN	_	_	_
50	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Basecalls	basecall	NNS	_	_	_
3	performed	perform	VBN	_	_	_
4	using	use	VBG	_	_	_
5	Casava	Casava	NNP	_	_	_
6	versions	version	NNS	_	_	_
7	1.6	1.6	CD	_	_	_
8	or	or	CC	_	_	_
9	1.7	1.7	CD	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Bowtie	Bowtie	NNP	_	_	_
3	alignments	alignment	NNS	_	_	_
4	against	against	IN	_	_	_
5	the	the	DT	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	genome	genome	NN	_	_	_
9	were	be	VBD	_	_	_
10	converted	convert	VBN	_	_	_
11	to	to	TO	_	_	_
12	wiggle	wiggle	VB	_	_	_
13	files	file	NNS	_	_	_
14	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	ribosome	ribosome	NN	_	_	_
3	footprints	footprint	NNS	_	_	_
4	and	and	CC	_	_	_
5	mRNA-seq	mrna-seq	NN	_	_	_
6	,	,	,	_	_	_
7	the	the	DT	_	_	_
8	position	position	NN	_	_	_
9	of	of	IN	_	_	_
10	each	each	DT	_	_	_
11	alignment	alignment	NN	_	_	_
12	is	be	VBZ	_	_	_
13	distributed	distribute	VBN	_	_	_
14	into	into	IN	_	_	_
15	several	several	JJ	_	_	_
16	nucleotides	nucleotide	NNS	_	_	_
17	in	in	IN	_	_	_
18	the	the	DT	_	_	_
19	center	center	NN	_	_	_
20	of	of	IN	_	_	_
21	each	each	DT	_	_	_
22	read	read	NN	_	_	_
23	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	read	read	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	center	center	NN	_	_	_
7	residues	residue	NNS	_	_	_
8	that	that	WDT	_	_	_
9	are	be	VBP	_	_	_
10	at	at	IN	_	_	_
11	least	least	JJS	_	_	_
12	10	10	CD	_	_	_
13	nucleotides	nucleotide	NNS	_	_	_
14	away	away	RB	_	_	_
15	from	from	IN	_	_	_
16	either	either	CC	_	_	_
17	ends	end	NNS	_	_	_
18	were	be	VBD	_	_	_
19	given	give	VBN	_	_	_
20	the	the	DT	_	_	_
21	same	same	JJ	_	_	_
22	score	score	NN	_	_	_
23	,	,	,	_	_	_
24	which	which	WDT	_	_	_
25	is	be	VBZ	_	_	_
26	weighted	weight	VBN	_	_	_
27	by	by	IN	_	_	_
28	the	the	DT	_	_	_
29	length	length	NN	_	_	_
30	of	of	IN	_	_	_
31	the	the	DT	_	_	_
32	fragment	fragment	NN	_	_	_
33	-LSB-	-lsb-	-LRB-	_	_	_
34	Oh	oh	UH	_	_	_
35	et	et	FW	_	_	_
36	al	al	FW	_	_	_
37	,	,	,	_	_	_
38	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	147	147	CD	_	_	_
3	,	,	,	_	_	_
4	1295	1295	CD	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	2011	2011	CD	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	-RSB-	-rsb-	-RRB-	_	_	_
9	.	.	.	_	_	_

1	Scores	score	NNS	_	_	_
2	therefore	therefore	RB	_	_	_
3	represent	represent	VBP	_	_	_
4	the	the	DT	_	_	_
5	number	number	NN	_	_	_
6	of	of	IN	_	_	_
7	read	read	VBN	_	_	_
8	alignments	alignment	NNS	_	_	_
9	attributed	attribute	VBD	_	_	_
10	to	to	TO	_	_	_
11	each	each	DT	_	_	_
12	genomic	genomic	JJ	_	_	_
13	position	position	NN	_	_	_
14	under	under	IN	_	_	_
15	each	each	DT	_	_	_
16	scoring	score	VBG	_	_	_
17	scheme	scheme	NN	_	_	_
18	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	DMS-seq	dms-seq	NN	_	_	_
3	,	,	,	_	_	_
4	the	the	DT	_	_	_
5	position	position	NN	_	_	_
6	of	of	IN	_	_	_
7	each	each	DT	_	_	_
8	alignment	alignment	NN	_	_	_
9	was	be	VBD	_	_	_
10	the	the	DT	_	_	_
11	position	position	NN	_	_	_
12	immediately	immediately	RB	_	_	_
13	5	5	CD	_	_	_
14	'	'	''	_	_	_
15	of	of	IN	_	_	_
16	the	the	DT	_	_	_
17	5	5	CD	_	_	_
18	'	'	''	_	_	_
19	end	end	NN	_	_	_
20	of	of	IN	_	_	_
21	the	the	DT	_	_	_
22	read	read	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	DMS-MaPSeq	dms-mapseq	NN	_	_	_
3	of	of	IN	_	_	_
4	purified	purify	VBN	_	_	_
5	cspA	cspa	NN	GEN	_	_
6	mRNA	mrna	NN	_	_	_
7	at	at	IN	_	_	_
8	10	10	CD	_	_	_
9	°C	°c	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	DMS-MaPSeq	dms-mapseq	NN	_	_	_
12	of	of	IN	_	_	_
13	purified	purify	VBN	_	_	_
14	cspA	cspa	NN	GEN	_	_
15	mRNA	mrna	NN	_	_	_
16	at	at	IN	_	_	_
17	10	10	CD	_	_	_
18	°C	°c	NN	_	_	_
19	,	,	,	_	_	_
20	rep1	rep1	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	DMS-MaPSeq	dms-mapseq	NN	_	_	_
23	of	of	IN	_	_	_
24	purified	purify	VBN	_	_	_
25	cspA	cspa	NN	GEN	_	_
26	mRNA	mrna	NN	_	_	_
27	at	at	IN	_	_	_
28	10	10	CD	_	_	_
29	°C	°c	NN	_	_	_
30	,	,	,	_	_	_
31	rep2	rep2	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	DMS-MaPSeq	dms-mapseq	NN	_	_	_
34	of	of	IN	_	_	_
35	purified	purify	VBN	_	_	_
36	cspA	cspa	NN	GEN	_	_
37	mRNA	mrna	NN	_	_	_
38	at	at	IN	_	_	_
39	10	10	CD	_	_	_
40	°C	°c	NN	_	_	_
41	,	,	,	_	_	_
42	rep	rep	NN	GEN	_	_
43	3	3	CD	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	DMS-MaPSeq	dms-mapseq	NN	_	_	_
46	of	of	IN	_	_	_
47	purified	purify	VBN	_	_	_
48	cspA	cspa	NN	GEN	_	_
49	mRNA	mrna	NN	_	_	_
50	at	at	IN	_	_	_
51	10	10	CD	_	_	_
52	°C	°c	NN	_	_	_
53	,	,	,	_	_	_
54	rep	rep	NN	GEN	_	_
55	4	4	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	DMS-MaPSeq	dms-mapseq	NN	_	_	_
58	of	of	IN	_	_	_
59	purified	purify	VBN	_	_	_
60	cspA	cspa	NN	GEN	_	_
61	mRNA	mrna	NN	_	_	_
62	at	at	IN	_	_	_
63	10	10	CD	_	_	_
64	°C	°c	NN	_	_	_
65	with	with	IN	_	_	_
66	0.025	0.025	CD	_	_	_
67	mM	mm	NN	KWSUPP	_	_
68	CspA	cspa	NN	TF	_	_
69	protein	protein	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	DMS-MaPSeq	dms-mapseq	NN	_	_	_
72	of	of	IN	_	_	_
73	purified	purify	VBN	_	_	_
74	cspA	cspa	NN	GEN	_	_
75	mRNA	mrna	NN	_	_	_
76	at	at	IN	_	_	_
77	10	10	CD	_	_	_
78	°C	°c	NN	_	_	_
79	with	with	IN	_	_	_
80	0.05	0.05	CD	_	_	_
81	mM	mm	NN	KWSUPP	_	_
82	CspA	cspa	NN	TF	_	_
83	protein	protein	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	DMS-MaPSeq	dms-mapseq	NN	_	_	_
86	of	of	IN	_	_	_
87	purified	purify	VBN	_	_	_
88	cspA	cspa	NN	GEN	_	_
89	mRNA	mrna	NN	_	_	_
90	at	at	IN	_	_	_
91	10	10	CD	_	_	_
92	°C	°c	NN	_	_	_
93	with	with	IN	_	_	_
94	0.1	0.1	CD	_	_	_
95	mM	mm	NN	KWSUPP	_	_
96	CspA	cspa	NN	TF	_	_
97	protein	protein	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	DMS-MaPSeq	dms-mapseq	NN	_	_	_
100	of	of	IN	_	_	_
101	purified	purify	VBN	_	_	_
102	cspA	cspa	NN	GEN	_	_
103	mRNA	mrna	NN	_	_	_
104	at	at	IN	_	_	_
105	10	10	CD	_	_	_
106	°C	°c	NN	_	_	_
107	with	with	IN	_	_	_
108	0.1	0.1	CD	_	_	_
109	mM	mm	NN	KWSUPP	_	_
110	CspA	cspa	NN	TF	_	_
111	protein	protein	NN	_	_	_
112	,	,	,	_	_	_
113	rep1	rep1	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	DMS-MaPSeq	dms-mapseq	NN	_	_	_
116	of	of	IN	_	_	_
117	purified	purify	VBN	_	_	_
118	cspA	cspa	NN	GEN	_	_
119	mRNA	mrna	NN	_	_	_
120	at	at	IN	_	_	_
121	10	10	CD	_	_	_
122	°C	°c	NN	_	_	_
123	with	with	IN	_	_	_
124	0.1	0.1	CD	_	_	_
125	mM	mm	NN	KWSUPP	_	_
126	CspA	cspa	NN	TF	_	_
127	protein	protein	NN	_	_	_
128	,	,	,	_	_	_
129	rep	rep	NN	GEN	_	_
130	2	2	CD	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	DMS-MaPSeq	dms-mapseq	NN	_	_	_
133	of	of	IN	_	_	_
134	purified	purify	VBN	_	_	_
135	cspA	cspa	NN	GEN	_	_
136	mRNA	mrna	NN	_	_	_
137	at	at	IN	_	_	_
138	10	10	CD	_	_	_
139	°C	°c	NN	_	_	_
140	with	with	IN	_	_	_
141	0.1	0.1	CD	_	_	_
142	mM	mm	NN	KWSUPP	_	_
143	CspA	cspa	NN	TF	_	_
144	protein	protein	NN	_	_	_
145	,	,	,	_	_	_
146	rep	rep	NN	GEN	_	_
147	3	3	CD	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	DMS-MaPSeq	dms-mapseq	NN	_	_	_
150	of	of	IN	_	_	_
151	purified	purify	VBN	_	_	_
152	cspA	cspa	NN	GEN	_	_
153	mRNA	mrna	NN	_	_	_
154	at	at	IN	_	_	_
155	10	10	CD	_	_	_
156	°C	°c	NN	_	_	_
157	with	with	IN	_	_	_
158	0.1	0.1	CD	_	_	_
159	mM	mm	NN	KWSUPP	_	_
160	CspA	cspa	NN	TF	_	_
161	protein	protein	NN	_	_	_
162	,	,	,	_	_	_
163	rep	rep	NN	GEN	_	_
164	4	4	CD	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	DMS-MaPSeq	dms-mapseq	NN	_	_	_
167	of	of	IN	_	_	_
168	purified	purify	VBN	_	_	_
169	cspA	cspa	NN	GEN	_	_
170	mRNA	mrna	NN	_	_	_
171	at	at	IN	_	_	_
172	37	37	CD	_	_	_
173	°C	°c	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	DMS-MaPSeq	dms-mapseq	NN	_	_	_
176	of	of	IN	_	_	_
177	purified	purify	VBN	_	_	_
178	cspA	cspa	NN	GEN	_	_
179	mRNA	mrna	NN	_	_	_
180	at	at	IN	_	_	_
181	37	37	CD	_	_	_
182	°C	°c	NN	_	_	_
183	,	,	,	_	_	_
184	rep1	rep1	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	DMS-MaPSeq	dms-mapseq	NN	_	_	_
187	of	of	IN	_	_	_
188	purified	purify	VBN	_	_	_
189	cspA	cspa	NN	GEN	_	_
190	mRNA	mrna	NN	_	_	_
191	at	at	IN	_	_	_
192	37	37	CD	_	_	_
193	°C	°c	NN	_	_	_
194	,	,	,	_	_	_
195	rep	rep	NN	GEN	_	_
196	2	2	CD	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	DMS-seq	dms-seq	NN	_	_	_
199	30	30	CD	_	_	_
200	min	min	NN	_	_	_
201	after	after	IN	_	_	_
202	shift	shift	NN	_	_	_
203	to	to	TO	_	_	_
204	10	10	CD	_	_	_
205	°C	°c	NN	_	_	_
206	in	in	IN	_	_	_
207	WT	wt	JJ	_	_	_
208	cells	cell	NNS	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	DMS-seq	dms-seq	NN	_	_	_
211	6	6	CD	_	_	_
212	hr	hr	NN	_	_	_
213	after	after	IN	_	_	_
214	shift	shift	NN	_	_	_
215	to	to	TO	_	_	_
216	10	10	CD	_	_	_
217	°C	°c	NN	_	_	_
218	in	in	IN	_	_	_
219	WT	wt	JJ	_	_	_
220	cells	cell	NNS	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	DMS-seq	dms-seq	NN	_	_	_
223	8	8	CD	_	_	_
224	hr	hr	NN	_	_	_
225	after	after	IN	_	_	_
226	shift	shift	NN	_	_	_
227	to	to	TO	_	_	_
228	10	10	CD	_	_	_
229	°C	°c	NN	_	_	_
230	in	in	IN	_	_	_
231	∆	∆	CD	_	_	_
232	cspABEG	cspabeg	NN	_	_	_
233	cells	cell	NNS	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	DMS-seq	dms-seq	NN	_	_	_
236	8	8	CD	_	_	_
237	hr	hr	NN	_	_	_
238	after	after	IN	_	_	_
239	shift	shift	NN	_	_	_
240	to	to	TO	_	_	_
241	10	10	CD	_	_	_
242	°C	°c	NN	_	_	_
243	in	in	IN	_	_	_
244	∆	∆	CD	_	_	_
245	cspBG	cspbg	NN	_	_	_
246	cells	cell	NNS	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	DMS-seq	dms-seq	NN	_	_	_
249	8	8	CD	_	_	_
250	hr	hr	NN	_	_	_
251	after	after	IN	_	_	_
252	shift	shift	NN	_	_	_
253	to	to	TO	_	_	_
254	10	10	CD	_	_	_
255	°C	°c	NN	_	_	_
256	in	in	IN	_	_	_
257	WT	wt	JJ	_	_	_
258	cells	cell	NNS	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	DMS-seq	dms-seq	NN	_	_	_
261	of	of	IN	_	_	_
262	purified	purify	VBN	_	_	_
263	mRNA	mrna	NN	_	_	_
264	in	in	FW	_	_	_
265	vitro	vitro	FW	_	_	_
266	at	at	IN	_	_	_
267	10	10	CD	_	_	_
268	°C	°c	NN	_	_	_
269	,	,	,	_	_	_
270	rep1	rep1	NN	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	DMS-seq	dms-seq	NN	_	_	_
273	of	of	IN	_	_	_
274	purified	purify	VBN	_	_	_
275	mRNA	mrna	NN	_	_	_
276	in	in	FW	_	_	_
277	vitro	vitro	FW	_	_	_
278	at	at	IN	_	_	_
279	10	10	CD	_	_	_
280	°C	°c	NN	_	_	_
281	,	,	,	_	_	_
282	rep2	rep2	NN	_	_	_
283	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
284	DMS-seq	dms-seq	NN	_	_	_
285	of	of	IN	_	_	_
286	WT	wt	JJ	_	_	_
287	cells	cell	NNS	_	_	_
288	after	after	IN	_	_	_
289	kasugamycin	kasugamycin	NN	_	_	_
290	treatment	treatment	NN	_	_	_
291	at	at	IN	_	_	_
292	10	10	CD	_	_	_
293	°C	°c	NN	_	_	_
294	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
295	Escherichia	escherichia	FW	Organism	_	_
296	coli	coli	FW	Organism	_	_
297	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
298	Escherichia	escherichia	FW	Organism	_	_
299	coli	coli	FW	Organism	_	_
300	str	str	FW	_	_	_
301	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Extraction	extraction	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	as	as	IN	_	_	_
7	described	describe	VBN	_	_	_
8	in	in	IN	_	_	_
9	detail	detail	NN	_	_	_
10	previously	previously	RB	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Li	Li	NNP	_	_	_
13	et	et	FW	_	_	_
14	al.	al.	FW	_	_	_
15	,	,	,	_	_	_
16	2012	2012	CD	_	_	_
17	;	;	:	_	_	_
18	Oh	oh	UH	_	_	_
19	et	et	FW	_	_	_
20	al.	al.	FW	_	_	_
21	,	,	,	_	_	_
22	2011	2011	CD	_	_	_
23	;	;	:	_	_	_
24	Rouskin	Rouskin	NNP	_	_	_
25	et	et	FW	_	_	_
26	al.	al.	FW	_	_	_
27	,	,	,	_	_	_
28	2014	2014	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	ribosome	ribosome	NN	_	_	_
3	profiling	profiling	NN	_	_	_
4	,	,	,	_	_	_
5	200	200	CD	_	_	_
6	ml	ml	NN	_	_	_
7	of	of	IN	_	_	_
8	cell	cell	NN	_	_	_
9	culture	culture	NN	_	_	_
10	was	be	VBD	_	_	_
11	rapidly	rapidly	RB	_	_	_
12	filtered	filter	VBN	_	_	_
13	by	by	IN	_	_	_
14	passing	pass	VBG	_	_	_
15	through	through	IN	_	_	_
16	a	a	DT	_	_	_
17	nitrocellulose	nitrocellulose	NN	_	_	_
18	filter	filter	NN	_	_	_
19	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	pellets	pellet	NNS	_	_	_
3	was	be	VBD	_	_	_
4	were	be	VBD	_	_	_
5	rapidly	rapidly	RB	_	_	_
6	collected	collect	VBN	_	_	_
7	using	use	VBG	_	_	_
8	a	a	DT	_	_	_
9	pre-warmed	pre-warmed	JJ	_	_	_
10	metal	metal	NN	_	_	_
11	table	table	NN	_	_	_
12	crumber	crumber	NN	_	_	_
13	,	,	,	_	_	_
14	flash	flash	NN	_	_	_
15	frozen	freeze	VBN	_	_	_
16	in	in	IN	_	_	_
17	liquid	liquid	JJ	_	_	_
18	nitrogen	nitrogen	NN	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	combined	combine	VBN	_	_	_
22	with	with	IN	_	_	_
23	frozen	frozen	JJ	_	_	_
24	droplets	droplet	NNS	_	_	_
25	of	of	IN	_	_	_
26	lysis	lysis	NN	_	_	_
27	buffer	buffer	NN	_	_	_
28	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	and	and	CC	_	_	_
3	lysis	lysis	NN	_	_	_
4	buffer	buffer	NN	_	_	_
5	were	be	VBD	_	_	_
6	pulverized	pulverize	VBN	_	_	_
7	in	in	IN	_	_	_
8	10	10	CD	_	_	_
9	ml	ml	NN	_	_	_
10	canisters	canister	NNS	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Retsch	retsch	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	pre-chilled	pre-chilled	JJ	_	_	_
15	in	in	IN	_	_	_
16	liquid	liquid	JJ	_	_	_
17	nitrogen	nitrogen	NN	_	_	_
18	using	use	VBG	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	TissueLyser	TissueLyser	NNP	_	_	_
21	II	II	NNP	_	_	_
22	.	.	.	_	_	_

1	Pulverized	pulverize	VBN	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	thawed	thaw	VBN	_	_	_
5	on	on	IN	_	_	_
6	ice	ice	NN	_	_	_
7	and	and	CC	_	_	_
8	clarified	clarify	VBN	_	_	_
9	by	by	IN	_	_	_
10	centrifugation	centrifugation	NN	_	_	_
11	at	at	IN	_	_	_
12	4	4	CD	_	_	_
13	°C	°c	NN	_	_	_
14	.	.	.	_	_	_

1	Lysate	lysate	NN	_	_	_
2	containing	contain	VBG	_	_	_
3	0.5	0.5	CD	_	_	_
4	mg	mg	NN	_	_	_
5	of	of	IN	_	_	_
6	RNA	rna	NN	_	_	_
7	was	be	VBD	_	_	_
8	digested	digest	VBN	_	_	_
9	for	for	IN	_	_	_
10	1	1	CD	_	_	_
11	h	h	NN	_	_	_
12	with	with	IN	_	_	_
13	750	750	CD	_	_	_
14	U	u	NN	_	_	_
15	of	of	IN	_	_	_
16	micrococcal	micrococcal	JJ	_	_	_
17	nuclease	nuclease	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Roche	Roche	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	at	at	IN	_	_	_
22	25	25	CD	_	_	_
23	°C	°c	NN	_	_	_
24	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	ribosome-protected	ribosome-protected	JJ	_	_	_
3	RNA	rna	NN	_	_	_
4	fragments	fragment	NNS	_	_	_
5	were	be	VBD	_	_	_
6	isolated	isolate	VBN	_	_	_
7	using	use	VBG	_	_	_
8	a	a	DT	_	_	_
9	sucrose	sucrose	NN	_	_	_
10	gradient	gradient	NN	_	_	_
11	followed	follow	VBN	_	_	_
12	by	by	IN	_	_	_
13	hot	hot	JJ	_	_	_
14	acid	acid	NN	_	_	_
15	phenol	phenol	NN	_	_	_
16	extraction	extraction	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	For	for	IN	_	_	_
3	DMS-MaPSeq	dms-mapseq	NN	_	_	_
4	,	,	,	_	_	_
5	reads	read	VBZ	_	_	_
6	were	be	VBD	_	_	_
7	aligned	align	VBN	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	5	5	CD	_	_	_
11	'	'	''	_	_	_
12	UTR	utr	NN	_	_	_
13	of	of	IN	_	_	_
14	cspA	cspa	NN	GEN	_	_
15	using	use	VBG	_	_	_
16	bowtie2	bowtie2	NN	_	_	_
17	and	and	CC	_	_	_
18	an	a	DT	_	_	_
19	alignment	alignment	NN	_	_	_
20	seed	seed	NN	_	_	_
21	of	of	IN	_	_	_
22	12nt	12nt	JJ	_	_	_
23	.	.	.	_	_	_

1	Low	low	JJ	_	_	_
2	sequence	sequence	NN	_	_	_
3	quality	quality	NN	_	_	_
4	bases	basis	NNS	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	Q	Q	NNP	_	_	_
7	score	score	NN	_	_	_
8	<	<	JJR	_	_	_
9	20	20	CD	_	_	_
10	%	%	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	and	and	CC	_	_	_
13	missing	miss	VBG	_	_	_
14	bases	basis	NNS	_	_	_
15	due	due	JJ	_	_	_
16	to	to	TO	_	_	_
17	truncated	truncate	VBN	_	_	_
18	reads	read	VBZ	_	_	_
19	were	be	VBD	_	_	_
20	set	set	VBN	_	_	_
21	to	to	TO	_	_	_
22	question	question	VB	_	_	_
23	marks	mark	NNS	_	_	_
24	.	.	.	_	_	_

1	Reads	read	NNS	_	_	_
2	that	that	WDT	_	_	_
3	consisted	consist	VBD	_	_	_
4	of	of	IN	_	_	_
5	more	more	JJR	_	_	_
6	than	than	IN	_	_	_
7	20	20	CD	_	_	_
8	%	%	NN	_	_	_
9	question	question	NN	_	_	_
10	marks	mark	NNS	_	_	_
11	were	be	VBD	_	_	_
12	filtered	filter	VBN	_	_	_
13	out	out	RP	_	_	_
14	.	.	.	_	_	_

1	Only	only	RB	_	_	_
2	mutations	mutation	NNS	_	_	_
3	that	that	WDT	_	_	_
4	agreed	agree	VBD	_	_	_
5	between	between	IN	_	_	_
6	the	the	DT	_	_	_
7	forward	forward	JJ	_	_	_
8	and	and	CC	_	_	_
9	the	the	DT	_	_	_
10	reverse	reverse	JJ	_	_	_
11	read	read	NN	_	_	_
12	were	be	VBD	_	_	_
13	considered	consider	VBN	_	_	_
14	true	true	JJ	_	_	_
15	mutations	mutation	NNS	_	_	_
16	.	.	.	_	_	_

1	Mutation	mutation	NN	_	_	_
2	rate	rate	NN	_	_	_
3	per	per	IN	_	_	_
4	base	base	NN	_	_	_
5	was	be	VBD	_	_	_
6	calculated	calculate	VBN	_	_	_
7	as	as	IN	_	_	_
8	number	number	NN	_	_	_
9	of	of	IN	_	_	_
10	reads	read	VBZ	_	_	_
11	with	with	IN	_	_	_
12	a	a	DT	_	_	_
13	mutation	mutation	NN	_	_	_
14	at	at	IN	_	_	_
15	the	the	DT	_	_	_
16	base	base	NN	_	_	_
17	divided	divide	VBN	_	_	_
18	by	by	IN	_	_	_
19	total	total	JJ	_	_	_
20	number	number	NN	_	_	_
21	of	of	IN	_	_	_
22	reads	read	VBZ	_	_	_
23	covering	cover	VBG	_	_	_
24	the	the	DT	_	_	_
25	base	base	NN	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	For	for	IN	_	_	_
3	in	in	FW	_	_	_
4	vivo	vivo	FW	_	_	_
5	DMS	dms	FW	_	_	_
6	modification	modification	NN	_	_	_
7	,	,	,	_	_	_
8	15	15	CD	_	_	_
9	mL	ml	NN	_	_	_
10	of	of	IN	_	_	_
11	E.	e.	FW	_	_	_
12	coli	coli	FW	_	_	_
13	culture	culture	NN	_	_	_
14	was	be	VBD	_	_	_
15	incubated	incubate	VBN	_	_	_
16	with	with	IN	_	_	_
17	750	750	CD	_	_	_
18	µL	µl	NN	_	_	_
19	DMS	dms	NN	_	_	_
20	.	.	.	_	_	_

1	Incubation	incubation	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	for	for	IN	_	_	_
5	2	2	CD	_	_	_
6	min	min	NN	_	_	_
7	at	at	IN	_	_	_
8	37	37	CD	_	_	_
9	°C	°c	NN	_	_	_
10	or	or	CC	_	_	_
11	for	for	IN	_	_	_
12	45	45	CD	_	_	_
13	min	min	NN	_	_	_
14	at	at	IN	_	_	_
15	10	10	CD	_	_	_
16	°C	°c	NN	_	_	_
17	.	.	.	_	_	_

1	DMS	dms	NN	_	_	_
2	was	be	VBD	_	_	_
3	quenched	quench	VBN	_	_	_
4	by	by	IN	_	_	_
5	adding	add	VBG	_	_	_
6	30	30	CD	_	_	_
7	mL	ml	NN	_	_	_
8	0	0	CD	_	_	_
9	°C	°c	NN	_	_	_
10	stop	stop	NN	_	_	_
11	solution	solution	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	30	30	CD	_	_	_
14	%	%	NN	_	_	_
15	β-mercaptoethanol	β-mercaptoethanol	NN	_	_	_
16	,	,	,	_	_	_
17	25	25	CD	_	_	_
18	%	%	NN	_	_	_
19	isoamyl	isoamyl	NN	_	_	_
20	alcohol	alcohol	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	,	,	,	_	_	_
23	after	after	IN	_	_	_
24	which	which	WDT	_	_	_
25	cells	cell	NNS	_	_	_
26	were	be	VBD	_	_	_
27	quickly	quickly	RB	_	_	_
28	put	put	VBN	_	_	_
29	on	on	IN	_	_	_
30	ice	ice	NN	_	_	_
31	,	,	,	_	_	_
32	collected	collect	VBN	_	_	_
33	by	by	IN	_	_	_
34	centrifugation	centrifugation	NN	_	_	_
35	at	at	IN	_	_	_
36	8000	8000	CD	_	_	_
37	x	x	CC	_	_	_
38	g	g	NN	_	_	_
39	,	,	,	_	_	_
40	4	4	CD	_	_	_
41	°C	°c	NN	_	_	_
42	for	for	IN	_	_	_
43	2	2	CD	_	_	_
44	min	min	NN	_	_	_
45	,	,	,	_	_	_
46	and	and	CC	_	_	_
47	washed	wash	VBN	_	_	_
48	with	with	IN	_	_	_
49	8	8	CD	_	_	_
50	mL	ml	NN	_	_	_
51	30	30	CD	_	_	_
52	%	%	NN	_	_	_
53	BME	bme	NN	_	_	_
54	solution	solution	NN	_	_	_
55	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	resuspended	resuspend	VBN	_	_	_
5	in	in	IN	_	_	_
6	450	450	CD	_	_	_
7	µL	µl	NN	_	_	_
8	total	total	JJ	_	_	_
9	RNA	rna	NN	_	_	_
10	lysis	lysis	NN	_	_	_
11	buffer	buffer	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	10	10	CD	_	_	_
14	mM	mm	NN	KWSUPP	_	_
15	EDTA	edta	NN	_	_	_
16	,	,	,	_	_	_
17	50	50	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	sodium	sodium	NN	SUPP	_	_
20	acetate	acetate	NN	SUPP	_	_
21	pH	ph	NN	_	_	_
22	5.5	5.5	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	total	total	JJ	_	_	_
27	RNA	rna	NN	_	_	_
28	was	be	VBD	_	_	_
29	purified	purify	VBN	_	_	_
30	with	with	IN	_	_	_
31	hot	hot	JJ	_	_	_
32	acid	acid	NN	_	_	_
33	phenol	phenol	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Ambion	ambion	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	NC000913	nc000913	NN	_	_	_
7	.2	.2	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	genotype	genotype	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	MG1655	mg1655	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	MG1655	mg1655	NN	_	_	_
14	∆	∆	CD	_	_	_
15	cspABCEG	cspabceg	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	MG1655	mg1655	NN	_	_	_
18	∆	∆	CD	_	_	_
19	cspABEG	cspabeg	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	MG1655	mg1655	NN	_	_	_
22	∆	∆	CD	_	_	_
23	cspBG	cspbg	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	MG1655	mg1655	NN	_	_	_
26	∆	∆	CD	_	_	_
27	rnr	rnr	NN	GEN	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	molecule	molecule	NN	_	_	_
30	subtype	subtype	NN	_	_	_
31	:	:	:	_	_	_
32	DMS-modified	dms-modified	JJ	_	_	_
33	mRNA	mrna	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	molecule	molecule	NN	_	_	_
36	subtype	subtype	NN	_	_	_
37	:	:	:	_	_	_
38	mRNA	mrna	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	molecule	molecule	NN	_	_	_
41	subtype	subtype	NN	_	_	_
42	:	:	:	_	_	_
43	Ribosome	ribosome	NN	_	_	_
44	protected	protect	VBD	_	_	_
45	mRNA	mrna	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	molecule	molecule	NN	_	_	_
48	subtype	subtype	NN	_	_	_
49	:	:	:	_	_	_
50	Total	total	JJ	_	_	_
51	RNA	rna	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	mRNA	mrna	NN	_	_	_
54	fragments	fragment	NNS	_	_	_
55	were	be	VBD	_	_	_
56	size	size	NN	_	_	_
57	selected	select	VBN	_	_	_
58	via	via	IN	_	_	_
59	gel	gel	NN	_	_	_
60	purification	purification	NN	_	_	_
61	,	,	,	_	_	_
62	and	and	CC	_	_	_
63	ligated	ligate	VBN	_	_	_
64	to	to	TO	_	_	_
65	5	5	CD	_	_	_
66	'	'	''	_	_	_
67	adenylated	adenylate	VBN	_	_	_
68	DNA	dna	NN	_	_	_
69	oligo	oligo	JJ	_	_	_
70	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	reverse	reverse	JJ	_	_	_
3	transcription	transcription	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	single	single	JJ	_	_	_
7	stranded	stranded	JJ	_	_	_
8	DNA	dna	NN	_	_	_
9	was	be	VBD	_	_	_
10	circularized	circularize	VBN	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	PCR	pcr	NN	_	_	_
14	amplified	amplify	VBD	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Oh	oh	UH	_	_	_
17	et	et	FW	_	_	_
18	al.	al.	FW	_	_	_
19	,	,	,	_	_	_
20	2011	2011	CD	_	_	_
21	;	;	:	_	_	_
22	Li	Li	NNP	_	_	_
23	et	et	FW	_	_	_
24	al.	al.	FW	_	_	_
25	,	,	,	_	_	_
26	2014	2014	CD	_	_	_
27	;	;	:	_	_	_
28	Rouskin	Rouskin	NNP	_	_	_
29	et	et	FW	_	_	_
30	al.	al.	FW	_	_	_
31	,	,	,	_	_	_
32	2014	2014	CD	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	mRNA-seq	mrna-seq	NN	_	_	_
3	10	10	CD	_	_	_
4	min	min	NN	_	_	_
5	after	after	IN	_	_	_
6	shift	shift	NN	_	_	_
7	to	to	TO	_	_	_
8	10	10	CD	_	_	_
9	°C	°c	NN	_	_	_
10	in	in	IN	_	_	_
11	WT	wt	JJ	_	_	_
12	cells	cell	NNS	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	mRNA-seq	mrna-seq	NN	_	_	_
15	2	2	CD	_	_	_
16	hr	hr	NN	_	_	_
17	after	after	IN	_	_	_
18	shift	shift	NN	_	_	_
19	to	to	TO	_	_	_
20	10	10	CD	_	_	_
21	°C	°c	NN	_	_	_
22	in	in	IN	_	_	_
23	WT	wt	JJ	_	_	_
24	cells	cell	NNS	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	mRNA-seq	mrna-seq	NN	_	_	_
27	30	30	CD	_	_	_
28	min	min	NN	_	_	_
29	after	after	IN	_	_	_
30	shift	shift	NN	_	_	_
31	to	to	TO	_	_	_
32	10	10	CD	_	_	_
33	°C	°c	NN	_	_	_
34	in	in	IN	_	_	_
35	WT	wt	JJ	_	_	_
36	cells	cell	NNS	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	mRNA-seq	mrna-seq	NN	_	_	_
39	3	3	CD	_	_	_
40	hr	hr	NN	_	_	_
41	after	after	IN	_	_	_
42	shift	shift	NN	_	_	_
43	to	to	TO	_	_	_
44	10	10	CD	_	_	_
45	°C	°c	NN	_	_	_
46	in	in	IN	_	_	_
47	WT	wt	JJ	_	_	_
48	cells	cell	NNS	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	mRNA-seq	mrna-seq	NN	_	_	_
51	4	4	CD	_	_	_
52	hr	hr	NN	_	_	_
53	after	after	IN	_	_	_
54	shift	shift	NN	_	_	_
55	to	to	TO	_	_	_
56	10	10	CD	_	_	_
57	°C	°c	NN	_	_	_
58	in	in	IN	_	_	_
59	WT	wt	JJ	_	_	_
60	cells	cell	NNS	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	mRNA-seq	mrna-seq	NN	_	_	_
63	6	6	CD	_	_	_
64	hr	hr	NN	_	_	_
65	after	after	IN	_	_	_
66	shift	shift	NN	_	_	_
67	to	to	TO	_	_	_
68	10	10	CD	_	_	_
69	°C	°c	NN	_	_	_
70	in	in	IN	_	_	_
71	WT	wt	JJ	_	_	_
72	cells	cell	NNS	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	mRNA-seq	mrna-seq	NN	_	_	_
75	8	8	CD	_	_	_
76	hr	hr	NN	_	_	_
77	after	after	IN	_	_	_
78	shift	shift	NN	_	_	_
79	to	to	TO	_	_	_
80	10	10	CD	_	_	_
81	°C	°c	NN	_	_	_
82	in	in	IN	_	_	_
83	∆	∆	CD	_	_	_
84	cspABEG	cspabeg	NN	_	_	_
85	cells	cell	NNS	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
87	mRNA-seq	mrna-seq	NN	_	_	_
88	8	8	CD	_	_	_
89	hr	hr	NN	_	_	_
90	after	after	IN	_	_	_
91	shift	shift	NN	_	_	_
92	to	to	TO	_	_	_
93	10	10	CD	_	_	_
94	°C	°c	NN	_	_	_
95	in	in	IN	_	_	_
96	WT	wt	JJ	_	_	_
97	cells	cell	NNS	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	mRNA-seq	mrna-seq	NN	_	_	_
100	at	at	IN	_	_	_
101	37	37	CD	_	_	_
102	°C	°c	NN	_	_	_
103	in	in	IN	_	_	_
104	∆	∆	CD	_	_	_
105	cspABCEG	cspabceg	NN	_	_	_
106	cells	cell	NNS	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
108	mRNA-seq	mrna-seq	NN	_	_	_
109	at	at	IN	_	_	_
110	37	37	CD	_	_	_
111	°C	°c	NN	_	_	_
112	in	in	IN	_	_	_
113	WT	wt	JJ	_	_	_
114	cells	cell	NNS	_	_	_
115	_	_	VBP	_	_	_
116	1	1	CD	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	mRNA-seq	mrna-seq	NN	_	_	_
119	at	at	IN	_	_	_
120	37	37	CD	_	_	_
121	°C	°c	NN	_	_	_
122	in	in	IN	_	_	_
123	WT	wt	JJ	_	_	_
124	cells	cell	NNS	_	_	_
125	_	_	VBP	_	_	_
126	2	2	CD	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
128	OTHER	other	JJ	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	Ribosome	ribosome	NN	_	_	_
131	profiling	profile	VBG	_	_	_
132	10	10	CD	_	_	_
133	min	min	NN	_	_	_
134	after	after	IN	_	_	_
135	shift	shift	NN	_	_	_
136	to	to	TO	_	_	_
137	10	10	CD	_	_	_
138	°C	°c	NN	_	_	_
139	in	in	IN	_	_	_
140	WT	wt	JJ	_	_	_
141	cells	cell	NNS	_	_	_
142	_	_	VBP	_	_	_
143	1	1	CD	_	_	_
144	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
145	Ribosome	Ribosome	NNP	_	_	_
146	profiling	profile	VBG	_	_	_
147	10	10	CD	_	_	_
148	min	min	NN	_	_	_
149	after	after	IN	_	_	_
150	shift	shift	NN	_	_	_
151	to	to	TO	_	_	_
152	10	10	CD	_	_	_
153	°C	°c	NN	_	_	_
154	in	in	IN	_	_	_
155	WT	wt	JJ	_	_	_
156	cells	cell	NNS	_	_	_
157	_	_	VBP	_	_	_
158	2	2	CD	_	_	_
159	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
160	Ribosome	Ribosome	NNP	_	_	_
161	profiling	profile	VBG	_	_	_
162	15	15	CD	_	_	_
163	min	min	NN	_	_	_
164	after	after	IN	_	_	_
165	shift	shift	NN	_	_	_
166	to	to	TO	_	_	_
167	10	10	CD	_	_	_
168	°C	°c	NN	_	_	_
169	in	in	IN	_	_	_
170	WT	wt	JJ	_	_	_
171	cells	cell	NNS	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
173	Ribosome	ribosome	NN	_	_	_
174	profiling	profiling	NN	_	_	_
175	2	2	CD	_	_	_
176	hr	hr	NN	_	_	_
177	after	after	IN	_	_	_
178	shift	shift	NN	_	_	_
179	to	to	TO	_	_	_
180	10	10	CD	_	_	_
181	°C	°c	NN	_	_	_
182	in	in	IN	_	_	_
183	WT	wt	JJ	_	_	_
184	cells	cell	NNS	_	_	_
185	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
186	Ribosome	Ribosome	NNP	_	_	_
187	profiling	profile	VBG	_	_	_
188	30	30	CD	_	_	_
189	min	min	NN	_	_	_
190	after	after	IN	_	_	_
191	shift	shift	NN	_	_	_
192	to	to	TO	_	_	_
193	10	10	CD	_	_	_
194	°C	°c	NN	_	_	_
195	in	in	IN	_	_	_
196	WT	wt	JJ	_	_	_
197	cells	cell	NNS	_	_	_
198	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
199	Ribosome	Ribosome	NNP	_	_	_
200	profiling	profile	VBG	_	_	_
201	3	3	CD	_	_	_
202	hr	hr	NN	_	_	_
203	after	after	IN	_	_	_
204	shift	shift	NN	_	_	_
205	to	to	TO	_	_	_
206	10	10	CD	_	_	_
207	°C	°c	NN	_	_	_
208	in	in	IN	_	_	_
209	WT	wt	JJ	_	_	_
210	cells	cell	NNS	_	_	_
211	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
212	Ribosome	Ribosome	NNP	_	_	_
213	profiling	profile	VBG	_	_	_
214	4	4	CD	_	_	_
215	hr	hr	NN	_	_	_
216	after	after	IN	_	_	_
217	shift	shift	NN	_	_	_
218	to	to	TO	_	_	_
219	10	10	CD	_	_	_
220	°C	°c	NN	_	_	_
221	in	in	IN	_	_	_
222	WT	wt	JJ	_	_	_
223	cells	cell	NNS	_	_	_
224	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
225	Ribosome	Ribosome	NNP	_	_	_
226	profiling	profile	VBG	_	_	_
227	5	5	CD	_	_	_
228	min	min	NN	_	_	_
229	after	after	IN	_	_	_
230	shift	shift	NN	_	_	_
231	to	to	TO	_	_	_
232	10	10	CD	_	_	_
233	°C	°c	NN	_	_	_
234	in	in	IN	_	_	_
235	WT	wt	JJ	_	_	_
236	cells	cell	NNS	_	_	_
237	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
238	Ribosome	Ribosome	NNP	_	_	_
239	profiling	profile	VBG	_	_	_
240	6	6	CD	_	_	_
241	hr	hr	NN	_	_	_
242	after	after	IN	_	_	_
243	shift	shift	NN	_	_	_
244	to	to	TO	_	_	_
245	10	10	CD	_	_	_
246	°C	°c	NN	_	_	_
247	in	in	IN	_	_	_
248	WT	wt	JJ	_	_	_
249	cells	cell	NNS	_	_	_
250	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
251	Ribosome	Ribosome	NNP	_	_	_
252	profiling	profile	VBG	_	_	_
253	8	8	CD	_	_	_
254	hr	hr	NN	_	_	_
255	after	after	IN	_	_	_
256	shift	shift	NN	_	_	_
257	to	to	TO	_	_	_
258	10	10	CD	_	_	_
259	°C	°c	NN	_	_	_
260	in	in	IN	_	_	_
261	∆	∆	CD	_	_	_
262	cspABEG	cspabeg	NN	_	_	_
263	cells	cell	NNS	_	_	_
264	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
265	Ribosome	Ribosome	NNP	_	_	_
266	profiling	profile	VBG	_	_	_
267	8	8	CD	_	_	_
268	hr	hr	NN	_	_	_
269	after	after	IN	_	_	_
270	shift	shift	NN	_	_	_
271	to	to	TO	_	_	_
272	10	10	CD	_	_	_
273	°C	°c	NN	_	_	_
274	in	in	IN	_	_	_
275	WT	wt	JJ	_	_	_
276	cells	cell	NNS	_	_	_
277	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
278	Ribosome	Ribosome	NNP	_	_	_
279	profiling	profile	VBG	_	_	_
280	at	at	IN	_	_	_
281	37	37	CD	_	_	_
282	°C	°c	NN	_	_	_
283	in	in	IN	_	_	_
284	∆	∆	CD	_	_	_
285	cspABCEG	cspabceg	NN	_	_	_
286	cells	cell	NNS	_	_	_
287	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
288	Ribosome	Ribosome	NNP	_	_	_
289	profiling	profile	VBG	_	_	_
290	at	at	IN	_	_	_
291	37	37	CD	_	_	_
292	°C	°c	NN	_	_	_
293	in	in	IN	_	_	_
294	WT	wt	JJ	_	_	_
295	cells	cell	NNS	_	_	_
296	_	_	VBP	_	_	_
297	1	1	CD	_	_	_
298	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
299	Ribosome	Ribosome	NNP	_	_	_
300	profiling	profile	VBG	_	_	_
301	at	at	IN	_	_	_
302	37	37	CD	_	_	_
303	°C	°c	NN	_	_	_
304	in	in	IN	_	_	_
305	WT	wt	JJ	_	_	_
306	cells	cell	NNS	_	_	_
307	_	_	VBP	_	_	_
308	2	2	CD	_	_	_
309	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
310	RNA-Seq	rna-seq	JJ	_	_	_
311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
312	Sequenced	sequence	VBN	_	_	_
313	reads	read	VBZ	_	_	_
314	were	be	VBD	_	_	_
315	trimmed	trim	VBN	_	_	_
316	for	for	IN	_	_	_
317	adaptor	adaptor	NN	_	_	_
318	sequence	sequence	NN	_	_	_
319	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	background	background	NN	_	_	_
4	:	:	:	_	_	_
5	MG1655	mg1655	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	strain	strain	NN	_	_	_
8	:	:	:	_	_	_
9	MG1655	mg1655	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Supplementary	supplementary	JJ	_	_	_
12	_	_	NN	_	_	_
13	files	file	NNS	_	_	_
14	_	_	IN	_	_	_
15	format	format	NN	_	_	_
16	_	_	NN	_	_	_
17	and	and	CC	_	_	_
18	_	_	NN	_	_	_
19	content	content	NN	_	_	_
20	:	:	:	_	_	_
21	Txt	txt	NN	_	_	_
22	files	file	NNS	_	_	_
23	are	be	VBP	_	_	_
24	processed	process	VBN	_	_	_
25	data	datum	NNS	_	_	_
26	for	for	IN	_	_	_
27	DMS-MaPseq	dms-mapseq	NN	_	_	_
28	with	with	IN	_	_	_
29	two	two	CD	_	_	_
30	columns	column	NNS	_	_	_
31	:	:	:	_	_	_
32	first	first	JJ	_	_	_
33	column	column	NN	_	_	_
34	containing	contain	VBG	_	_	_
35	chromosome	chromosome	NN	_	_	_
36	positions	position	NNS	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	relative	relative	JJ	_	_	_
39	to	to	TO	_	_	_
40	transcription	transcription	NN	_	_	_
41	start	start	NN	_	_	_
42	site	site	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	1	1	CD	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	of	of	IN	_	_	_
47	cspA	cspa	NN	GEN	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	and	and	CC	_	_	_
50	second	second	JJ	_	_	_
51	column	column	NN	_	_	_
52	containing	contain	VBG	_	_	_
53	the	the	DT	_	_	_
54	mutation	mutation	NN	_	_	_
55	rate	rate	NN	_	_	_
56	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Supplementary	Supplementary	NNP	_	_	_
3	_	_	VBD	_	_	_
4	files	file	NNS	_	_	_
5	_	_	IN	_	_	_
6	format	format	NN	_	_	_
7	_	_	NN	_	_	_
8	and	and	CC	_	_	_
9	_	_	NN	_	_	_
10	content	content	NN	_	_	_
11	:	:	:	_	_	_
12	Wiggle	Wiggle	NNP	_	_	_
13	files	file	VBZ	_	_	_
14	with	with	IN	_	_	_
15	two	two	CD	_	_	_
16	columns	column	NNS	_	_	_
17	:	:	:	_	_	_
18	first	first	JJ	_	_	_
19	column	column	NN	_	_	_
20	containing	contain	VBG	_	_	_
21	chromosome	chromosome	NN	_	_	_
22	positions	position	NNS	_	_	_
23	and	and	CC	_	_	_
24	second	second	JJ	_	_	_
25	column	column	NN	_	_	_
26	containing	contain	VBG	_	_	_
27	the	the	DT	_	_	_
28	number	number	NN	_	_	_
29	of	of	IN	_	_	_
30	reads	read	VBZ	_	_	_
31	mapped	map	VBN	_	_	_
32	to	to	TO	_	_	_
33	the	the	DT	_	_	_
34	position	position	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	see	see	VB	_	_	_
37	publication	publication	NN	_	_	_
38	for	for	IN	_	_	_
39	details	detail	NNS	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	temperature	temperature	NN	_	_	_
3	:	:	:	_	_	_
4	10	10	CD	_	_	_
5	°C	°c	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	temperature	temperature	NN	_	_	_
8	:	:	:	_	_	_
9	37	37	CD	_	_	_
10	°C	°c	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	The	the	DT	_	_	_
13	remaining	remain	VBG	_	_	_
14	reads	read	VBZ	_	_	_
15	were	be	VBD	_	_	_
16	aligned	align	VBN	_	_	_
17	using	use	VBG	_	_	_
18	Bowtie	Bowtie	NNP	_	_	_
19	v0	v0	NN	_	_	_
20	.12.7	.12.7	CD	_	_	_
21	against	against	IN	_	_	_
22	E.	e.	FW	_	_	_
23	coli	coli	FW	_	_	_
24	MG1655	mg1655	NN	_	_	_
25	genome	genome	NN	_	_	_
26	using	use	VBG	_	_	_
27	parameters	parameter	NNS	_	_	_
28	-	-	:	_	_	_
29	v1	v1	SYM	_	_	_
30	-	-	:	_	_	_
31	m2	m2	SYM	_	_	_
32	-	-	:	_	_	_
33	k1	k1	NN	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA-seq	RNA-seq	NNP	_	_	_
4	20	20	CD	_	_	_
5	min	min	NN	_	_	_
6	after	after	IN	_	_	_
7	shift	shift	NN	_	_	_
8	to	to	TO	_	_	_
9	10	10	CD	_	_	_
10	°C	°c	NN	_	_	_
11	in	in	IN	_	_	_
12	∆	∆	CD	_	_	_
13	rnr	rnr	NN	GEN	_	_
14	cells	cell	NNS	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
16	Total	total	JJ	_	_	_
17	RNA-seq	rna-seq	NN	_	_	_
18	20	20	CD	_	_	_
19	min	min	NN	_	_	_
20	after	after	IN	_	_	_
21	shift	shift	NN	_	_	_
22	to	to	TO	_	_	_
23	10	10	CD	_	_	_
24	°C	°c	NN	_	_	_
25	in	in	IN	_	_	_
26	WT	wt	JJ	_	_	_
27	cells	cell	NNS	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
29	Total	total	JJ	_	_	_
30	RNA-seq	rna-seq	NN	_	_	_
31	4	4	CD	_	_	_
32	hr	hr	NN	_	_	_
33	after	after	IN	_	_	_
34	shift	shift	NN	_	_	_
35	to	to	TO	_	_	_
36	10	10	CD	_	_	_
37	°C	°c	NN	_	_	_
38	in	in	IN	_	_	_
39	∆	∆	CD	_	_	_
40	rnr	rnr	NN	GEN	_	_
41	cells	cell	NNS	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
43	Total	total	JJ	_	_	_
44	RNA-seq	rna-seq	NN	_	_	_
45	4	4	CD	_	_	_
46	hr	hr	NN	_	_	_
47	after	after	IN	_	_	_
48	shift	shift	NN	_	_	_
49	to	to	TO	_	_	_
50	10	10	CD	_	_	_
51	°C	°c	NN	_	_	_
52	in	in	IN	_	_	_
53	WT	wt	JJ	_	_	_
54	cells	cell	NNS	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
56	Total	total	JJ	_	_	_
57	RNA-seq	rna-seq	NN	_	_	_
58	8	8	CD	_	_	_
59	hr	hr	NN	_	_	_
60	after	after	IN	_	_	_
61	shift	shift	NN	_	_	_
62	to	to	TO	_	_	_
63	10	10	CD	_	_	_
64	°C	°c	NN	_	_	_
65	in	in	IN	_	_	_
66	∆	∆	CD	_	_	_
67	rnr	rnr	NN	GEN	_	_
68	cells	cell	NNS	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
70	Total	total	JJ	_	_	_
71	RNA-seq	rna-seq	NN	_	_	_
72	8	8	CD	_	_	_
73	hr	hr	NN	_	_	_
74	after	after	IN	_	_	_
75	shift	shift	NN	_	_	_
76	to	to	TO	_	_	_
77	10	10	CD	_	_	_
78	°C	°c	NN	_	_	_
79	in	in	IN	_	_	_
80	WT	wt	JJ	_	_	_
81	cells	cell	NNS	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
83	Total	total	JJ	_	_	_
84	RNA-seq	rna-seq	NN	_	_	_
85	after	after	IN	_	_	_
86	rifampicin	rifampicin	NN	SUPP	_	_
87	treatment	treatment	NN	_	_	_
88	--	--	:	_	_	_
89	4	4	CD	_	_	_
90	hr	hr	NN	_	_	_
91	after	after	IN	_	_	_
92	shift	shift	NN	_	_	_
93	to	to	TO	_	_	_
94	10	10	CD	_	_	_
95	°C	°c	NN	_	_	_
96	in	in	IN	_	_	_
97	∆	∆	CD	_	_	_
98	rnr	rnr	NN	GEN	_	_
99	cells	cell	NNS	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
101	Total	total	JJ	_	_	_
102	RNA-seq	rna-seq	NN	_	_	_
103	after	after	IN	_	_	_
104	rifampicin	rifampicin	NN	SUPP	_	_
105	treatment	treatment	NN	_	_	_
106	--	--	:	_	_	_
107	4	4	CD	_	_	_
108	hr	hr	NN	_	_	_
109	after	after	IN	_	_	_
110	shift	shift	NN	_	_	_
111	to	to	TO	_	_	_
112	10	10	CD	_	_	_
113	°C	°c	NN	_	_	_
114	in	in	IN	_	_	_
115	WT	wt	JJ	_	_	_
116	cells	cell	NNS	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
118	Total	total	JJ	_	_	_
119	RNA-seq	rna-seq	NN	_	_	_
120	before	before	IN	_	_	_
121	rifampicin	rifampicin	NN	SUPP	_	_
122	treatment	treatment	NN	_	_	_
123	--	--	:	_	_	_
124	2	2	CD	_	_	_
125	hr	hr	NN	_	_	_
126	after	after	IN	_	_	_
127	shift	shift	NN	_	_	_
128	to	to	TO	_	_	_
129	10	10	CD	_	_	_
130	°C	°c	NN	_	_	_
131	in	in	IN	_	_	_
132	∆	∆	CD	_	_	_
133	rnr	rnr	NN	GEN	_	_
134	cells	cell	NNS	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
136	Total	total	JJ	_	_	_
137	RNA-seq	rna-seq	NN	_	_	_
138	before	before	IN	_	_	_
139	rifampicin	rifampicin	NN	SUPP	_	_
140	treatment	treatment	NN	_	_	_
141	--	--	:	_	_	_
142	2	2	CD	_	_	_
143	hr	hr	NN	_	_	_
144	after	after	IN	_	_	_
145	shift	shift	NN	_	_	_
146	to	to	TO	_	_	_
147	10	10	CD	_	_	_
148	°C	°c	NN	_	_	_
149	in	in	IN	_	_	_
150	WT	wt	JJ	_	_	_
151	cells	cell	NNS	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	treatment	treatment	NN	_	_	_
154	:	:	:	_	_	_
155	0.025	0.025	CD	_	_	_
156	mM	mm	NN	KWSUPP	_	_
157	CspA	cspa	NN	TF	_	_
158	protein	protein	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	treatment	treatment	NN	_	_	_
161	:	:	:	_	_	_
162	0.05	0.05	CD	_	_	_
163	mM	mm	NN	KWSUPP	_	_
164	CspA	cspa	NN	TF	_	_
165	protein	protein	NN	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	treatment	treatment	NN	_	_	_
168	:	:	:	_	_	_
169	0.1	0.1	CD	_	_	_
170	mM	mm	NN	KWSUPP	_	_
171	CspA	cspa	NN	TF	_	_
172	protein	protein	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	treatment	treatment	NN	_	_	_
175	:	:	:	_	_	_
176	After	after	IN	_	_	_
177	10	10	CD	_	_	_
178	mg	mg	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	treatment	treatment	NN	_	_	_
181	:	:	:	_	_	_
182	After	after	IN	_	_	_
183	250	250	CD	_	_	_
184	µg	µg	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	treatment	treatment	NN	_	_	_
187	:	:	:	_	_	_
188	Before	before	IN	_	_	_
189	rifampicin	rifampicin	NN	SUPP	_	_
190	treatment	treatment	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	treatment	treatment	NN	_	_	_
193	:	:	:	_	_	_
194	NA	NA	NNP	_	_	_
195	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
196	Trimmed	trim	VBD	_	_	_
197	reads	read	VBZ	_	_	_
198	were	be	VBD	_	_	_
199	sequentially	sequentially	RB	_	_	_
200	aligned	align	VBN	_	_	_
201	using	use	VBG	_	_	_
202	Bowtie	Bowtie	NNP	_	_	_
203	v0	v0	NN	_	_	_
204	.12.7	.12.7	CD	_	_	_
205	to	to	TO	_	_	_
206	E.	e.	FW	_	_	_
207	coli	coli	FW	_	_	_
208	rRNA	rrna	NN	_	_	_
209	and	and	CC	_	_	_
210	noncoding	noncoding	JJ	_	_	_
211	RNA	rna	NN	_	_	_
212	allowing	allow	VBG	_	_	_
213	one	one	CD	_	_	_
214	mismatch	mismatch	NN	_	_	_
215	.	.	.	_	_	_

1	Reads	read	VBZ	_	_	_
2	aligning	align	VBG	_	_	_
3	to	to	TO	_	_	_
4	any	any	DT	_	_	_
5	of	of	IN	_	_	_
6	these	these	DT	_	_	_
7	indices	index	NNS	_	_	_
8	were	be	VBD	_	_	_
9	discarded	discard	VBN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Bicyclomycin	bicyclomycin	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	BCM	bcm	NN	_	_	_
5	,	,	,	_	_	_
6	gift	gift	NN	_	_	_
7	of	of	IN	_	_	_
8	Schering-Plough	Schering-Plough	NNP	_	_	_
9	Animal	Animal	NNP	_	_	_
10	Health	Health	NNP	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	was	be	VBD	_	_	_
13	added	add	VBN	_	_	_
14	to	to	TO	_	_	_
15	the	the	DT	_	_	_
16	culture	culture	NN	_	_	_
17	at	at	IN	_	_	_
18	the	the	DT	_	_	_
19	indicated	indicate	VBN	_	_	_
20	dose	dose	NN	_	_	_
21	for	for	IN	_	_	_
22	20	20	CD	_	_	_
23	minutes	minute	NNS	_	_	_
24	.	.	.	_	_	_

1	Culture	culture	NN	_	_	_
2	was	be	VBD	_	_	_
3	added	add	VBN	_	_	_
4	to	to	TO	_	_	_
5	2	2	CD	_	_	_
6	volumes	volume	NNS	_	_	_
7	of	of	IN	_	_	_
8	RNAprotect	rnaprotect	NN	_	_	_
9	Bacterial	bacterial	JJ	_	_	_
10	Reagent	reagent	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	QIAGEN	qiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Coli-MDS42	coli-mds42	NN	_	_	_
3	_	_	CD	_	_	_
4	bcm-100mcg	bcm-100mcg	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Coli-MDS42	coli-mds42	NN	_	_	_
7	_	_	CD	_	_	_
8	del-nusA	del-nusa	NN	_	_	_
9	_	_	CD	_	_	_
10	rep1	rep1	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Coli-MDS42	coli-mds42	NN	_	_	_
13	_	_	CD	_	_	_
14	del-nusA	del-nusa	NN	_	_	_
15	_	_	CD	_	_	_
16	rep2	rep2	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Coli-MDS42	coli-mds42	NN	_	_	_
19	_	_	CD	_	_	_
20	del-nusG	del-nusg	NN	_	_	_
21	_	_	CD	_	_	_
22	rep1	rep1	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	Coli-MDS42	coli-mds42	NN	_	_	_
25	_	_	CD	_	_	_
26	del-nusG	del-nusg	NN	_	_	_
27	_	_	CD	_	_	_
28	rep2	rep2	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Coli-MDS42	coli-mds42	NN	_	_	_
31	_	_	CD	_	_	_
32	no-drug	no-drug	JJ	_	_	_
33	_	_	NN	_	_	_
34	rep1	rep1	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	Coli-MDS42	coli-mds42	NN	_	_	_
37	_	_	CD	_	_	_
38	no-drug	no-drug	JJ	_	_	_
39	_	_	NN	_	_	_
40	rep2	rep2	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	Coli-MG1655	coli-mg1655	NN	_	_	_
43	_	_	CD	_	_	_
44	bcm-100mcg	bcm-100mcg	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	Coli-MG1655	coli-mg1655	NN	_	_	_
47	_	_	CD	_	_	_
48	bcm-10mcg	bcm-10mcg	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	Coli-MG1655	coli-mg1655	NN	_	_	_
51	_	_	CD	_	_	_
52	bcm-25mcg	bcm-25mcg	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Coli-MG1655	coli-mg1655	NN	_	_	_
55	_	_	CD	_	_	_
56	no-drug	no-drug	JJ	_	_	_
57	_	_	NN	_	_	_
58	rep1	rep1	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	Coli-MG1655	coli-mg1655	NN	_	_	_
61	_	_	CD	_	_	_
62	no-drug	no-drug	JJ	_	_	_
63	_	_	NN	_	_	_
64	rep2	rep2	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	Coli-O157H7	coli-o157h7	NN	_	_	_
67	_	_	CD	_	_	_
68	bcm-100mcg	bcm-100mcg	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	Coli-O157H7	coli-o157h7	NN	_	_	_
71	_	_	CD	_	_	_
72	no-drug	no-drug	JJ	_	_	_
73	_	_	NN	_	_	_
74	rep1	rep1	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	Coli-O157H7	coli-o157h7	NN	_	_	_
77	_	_	CD	_	_	_
78	no-drug	no-drug	JJ	_	_	_
79	_	_	NN	_	_	_
80	rep2	rep2	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	Culture	culture	NN	_	_	_
83	conditions	condition	NNS	_	_	_
84	:	:	:	_	_	_
85	37	37	CD	_	_	_
86	C	c	NN	_	_	_
87	with	with	IN	_	_	_
88	shaking	shake	VBG	_	_	_
89	at	at	IN	_	_	_
90	220	220	CD	_	_	_
91	RPM	rpm	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	Drug	drug	NN	_	_	_
94	:	:	:	_	_	_
95	bicyclomycin	bicyclomycin	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	Drug	drug	NN	_	_	_
98	:	:	:	_	_	_
99	none	none	NN	_	_	_
100	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
101	Escherichia	escherichia	FW	Organism	_	_
102	coli	coli	FW	Organism	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	Extraction	extraction	NN	_	_	_
105	:	:	:	_	_	_
106	Rneasy	Rneasy	NNP	_	_	_
107	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
108	Extraction	Extraction	NNP	_	_	_
109	:	:	:	_	_	_
110	TRI	TRI	NNP	_	_	_
111	Reagent	Reagent	NNP	_	_	_
112	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
113	Feature	Feature	NNP	_	_	_
114	intensity	intensity	NN	_	_	_
115	was	be	VBD	_	_	_
116	extracted	extract	VBN	_	_	_
117	by	by	IN	_	_	_
118	GeneChip	GeneChip	NNP	_	_	_
119	Operating	Operating	NNP	_	_	_
120	System	System	NNP	_	_	_
121	as	as	IN	_	_	_
122	CEL	CEL	NNP	_	_	_
123	files	file	NNS	_	_	_
124	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	probe-level	probe-level	JJ	_	_	_
3	analysis	analysis	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	CEL	CEL	NNP	_	_	_
7	files	file	NNS	_	_	_
8	was	be	VBD	_	_	_
9	done	do	VBN	_	_	_
10	by	by	IN	_	_	_
11	the	the	DT	_	_	_
12	PLIER	plier	NN	_	_	_
13	algorithm	algorithm	NN	_	_	_
14	in	in	IN	_	_	_
15	the	the	DT	_	_	_
16	Affymetrix	Affymetrix	NNP	_	_	_
17	Expression	expression	NN	_	_	_
18	Console	console	NN	_	_	_
19	.	.	.	_	_	_

1	No	no	DT	_	_	_
2	further	further	JJ	_	_	_
3	adjustments	adjustment	NNS	_	_	_
4	were	be	VBD	_	_	_
5	made	make	VBN	_	_	_
6	to	to	TO	_	_	_
7	the	the	DT	_	_	_
8	data	datum	NNS	_	_	_
9	in	in	IN	_	_	_
10	the	the	DT	_	_	_
11	table	table	NN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Growth	Growth	NNP	_	_	_
3	medium	medium	NN	_	_	_
4	:	:	:	_	_	_
5	MOPS	mop	NNS	MED	_	_
6	minimal	minimal	JJ	_	_	_
7	,	,	,	_	_	_
8	0.4	0.4	CD	_	_	_
9	%	%	NN	_	_	_
10	glucose	glucose	NN	SUPP	_	_
11	,	,	,	_	_	_
12	0.5	0.5	CD	_	_	_
13	%	%	NN	_	_	_
14	casamino	casamino	NN	SUPP	_	_
15	acids	acid	NNS	SUPP	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Growth	Growth	NNP	_	_	_
18	phase	phase	NN	_	_	_
19	:	:	:	_	_	_
20	exponential	exponential	JJ	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	Growth	Growth	NNP	_	_	_
23	phase	phase	NN	_	_	_
24	:	:	:	_	_	_
25	OD600	od600	NN	_	_	_
26	=	=	JJ	_	_	_
27	0.3	0.3	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Isolate	isolate	VB	_	_	_
30	:	:	:	_	_	_
31	EDL933	edl933	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	Isolate	isolate	VB	_	_	_
34	:	:	:	_	_	_
35	MDS42	mds42	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Isolate	isolate	VB	_	_	_
38	:	:	:	_	_	_
39	MG1655	mg1655	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	K12	k12	NN	_	_	_
42	strain	strain	NN	_	_	_
43	MG1655	mg1655	NN	_	_	_
44	,	,	,	_	_	_
45	100	100	CD	_	_	_
46	mcg	mcg	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	K12	k12	NN	_	_	_
49	strain	strain	NN	_	_	_
50	MG1655	mg1655	NN	_	_	_
51	,	,	,	_	_	_
52	10	10	CD	_	_	_
53	mcg	mcg	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	K12	k12	NN	_	_	_
56	strain	strain	NN	_	_	_
57	MG1655	mg1655	NN	_	_	_
58	,	,	,	_	_	_
59	25	25	CD	_	_	_
60	mcg	mcg	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	K12	k12	NN	_	_	_
63	strain	strain	NN	_	_	_
64	MG1655	mg1655	NN	_	_	_
65	,	,	,	_	_	_
66	control	control	NN	_	_	_
67	sample	sample	NN	_	_	_
68	,	,	,	_	_	_
69	exponential	exponential	JJ	GrowthPhase	_	_
70	phase	phase	NN	GrowthPhase	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	O157	o157	NN	_	_	_
73	:	:	:	_	_	_
74	H7	h7	NN	_	_	_
75	strain	strain	NN	_	_	_
76	EDL933	edl933	NN	_	_	_
77	,	,	,	_	_	_
78	100	100	CD	_	_	_
79	mcg	mcg	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	O157	o157	NN	_	_	_
82	:	:	:	_	_	_
83	H7	h7	NN	_	_	_
84	strain	strain	NN	_	_	_
85	EDL933	edl933	NN	_	_	_
86	,	,	,	_	_	_
87	control	control	NN	_	_	_
88	sample	sample	NN	_	_	_
89	,	,	,	_	_	_
90	exponential	exponential	JJ	GrowthPhase	_	_
91	phase	phase	NN	GrowthPhase	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	Overnight	overnight	JJ	_	_	_
94	culture	culture	NN	_	_	_
95	in	in	IN	_	_	_
96	LB	lb	NN	MED	_	_
97	medium	medium	NN	MED	_	_
98	was	be	VBD	_	_	_
99	innoculated	innoculate	VBN	_	_	_
100	from	from	IN	_	_	_
101	a	a	DT	_	_	_
102	single	single	JJ	_	_	_
103	colony	colony	NN	_	_	_
104	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	overnight	overnight	JJ	_	_	_
3	culture	culture	NN	_	_	_
4	was	be	VBD	_	_	_
5	diluted	dilute	VBN	_	_	_
6	1	1	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Reduced	reduce	VBN	_	_	_
9	genome	genome	NN	_	_	_
10	strain	strain	NN	_	_	_
11	MDS42	mds42	NN	_	_	_
12	,	,	,	_	_	_
13	100	100	CD	_	_	_
14	mcg	mcg	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
16	Reduced	reduce	VBN	_	_	_
17	genome	genome	NN	_	_	_
18	strain	strain	NN	_	_	_
19	MDS42	mds42	NN	_	_	_
20	,	,	,	_	_	_
21	control	control	NN	_	_	_
22	sample	sample	NN	_	_	_
23	,	,	,	_	_	_
24	exponential	exponential	JJ	GrowthPhase	_	_
25	phase	phase	NN	GrowthPhase	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	Reduced	reduce	VBN	_	_	_
28	genome	genome	NN	_	_	_
29	strain	strain	NN	_	_	_
30	MDS42	mds42	NN	_	_	_
31	,	,	,	_	_	_
32	deletion	deletion	NN	_	_	_
33	of	of	IN	_	_	_
34	nusA	nusa	NN	GEN	_	_
35	gene	gene	NN	_	_	_
36	,	,	,	_	_	_
37	OD600	od600	NN	_	_	_
38	=	=	JJ	_	_	_
39	0.3	0.3	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	Reduced	reduce	VBN	_	_	_
42	genome	genome	NN	_	_	_
43	strain	strain	NN	_	_	_
44	MDS42	mds42	NN	_	_	_
45	,	,	,	_	_	_
46	deletion	deletion	NN	_	_	_
47	of	of	IN	_	_	_
48	nusG	nusg	NN	GEN	_	_
49	gene	gene	NN	_	_	_
50	,	,	,	_	_	_
51	OD600	od600	NN	_	_	_
52	=	=	JJ	_	_	_
53	0.3	0.3	CD	_	_	_
54	,	,	,	_	_	_
55	overnight	overnight	JJ	_	_	_
56	culture	culture	NN	_	_	_
57	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
58	Strain	Strain	NNP	_	_	_
59	:	:	:	_	_	_
60	K-12	k-12	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Strain	strain	NN	_	_	_
63	:	:	:	_	_	_
64	K-12	k-12	NN	_	_	_
65	reduced	reduce	VBD	_	_	_
66	genome	genome	NN	_	_	_
67	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
68	Strain	Strain	NNP	_	_	_
69	:	:	:	_	_	_
70	O157	o157	NN	_	_	_
71	:	:	:	_	_	_
72	H7	h7	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	TRI	TRI	NNP	_	_	_
75	Reagent	Reagent	NNP	_	_	_
76	-LRB-	-lrb-	-LRB-	_	_	_
77	Sigma	Sigma	NNP	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	or	or	CC	_	_	_
80	Rneasy	rneasy	NN	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	QIAGEN	qiagen	NN	_	_	_
83	-RRB-	-rrb-	-RRB-	_	_	_
84	according	accord	VBG	_	_	_
85	to	to	TO	_	_	_
86	manufacturer	manufacturer	NN	_	_	_
87	's	's	POS	_	_	_
88	protocol	protocol	NN	_	_	_
89	.	.	.	_	_	_

1	No	no	DT	_	_	_
2	Rnase	rnase	NN	_	_	_
3	treatment	treatment	NN	_	_	_
4	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Aligned	Aligned	NNP	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	designated	designate	VBN	_	_	_
6	to	to	TO	_	_	_
7	top	top	JJ	_	_	_
8	and	and	CC	_	_	_
9	bottom	bottom	JJ	_	_	_
10	strands	strand	NNS	_	_	_
11	using	use	VBG	_	_	_
12	Samtools	Samtools	NNP	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	At	at	IN	_	_	_
15	the	the	DT	_	_	_
16	appropriate	appropriate	JJ	_	_	_
17	optical	optical	JJ	_	_	_
18	density	density	NN	_	_	_
19	,	,	,	_	_	_
20	culture	culture	NN	_	_	_
21	growth	growth	NN	_	_	_
22	was	be	VBD	_	_	_
23	instantaneously	instantaneously	RB	_	_	_
24	arrested	arrest	VBN	_	_	_
25	by	by	IN	_	_	_
26	addition	addition	NN	_	_	_
27	of	of	IN	_	_	_
28	an	a	DT	_	_	_
29	equal	equal	JJ	_	_	_
30	volume	volume	NN	_	_	_
31	of	of	IN	_	_	_
32	chilled	chill	VBN	_	_	_
33	100	100	CD	_	_	_
34	%	%	NN	_	_	_
35	ethanol	ethanol	NN	_	_	_
36	,	,	,	_	_	_
37	and	and	CC	_	_	_
38	the	the	DT	_	_	_
39	cells	cell	NNS	_	_	_
40	were	be	VBD	_	_	_
41	stored	store	VBN	_	_	_
42	at	at	IN	_	_	_
43	--	--	:	_	_	_
44	80	80	CD	_	_	_
45	°C	°c	NN	_	_	_
46	until	until	IN	_	_	_
47	they	they	PRP	_	_	_
48	were	be	VBD	_	_	_
49	processed	process	VBN	_	_	_
50	for	for	IN	_	_	_
51	RNA	rna	NN	_	_	_
52	extraction	extraction	NN	_	_	_
53	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	lysed	lyse	VBN	_	_	_
5	and	and	CC	_	_	_
6	total	total	JJ	_	_	_
7	RNA	rna	NN	_	_	_
8	was	be	VBD	_	_	_
9	prepared	prepare	VBN	_	_	_
10	by	by	IN	_	_	_
11	the	the	DT	_	_	_
12	hot	hot	JJ	_	_	_
13	phenol	phenol	NN	_	_	_
14	method	method	NN	_	_	_
15	essentially	essentially	RB	_	_	_
16	as	as	IN	_	_	_
17	described	describe	VBN	_	_	_
18	,	,	,	_	_	_
19	after	after	IN	_	_	_
20	chromosomal	chromosomal	JJ	_	_	_
21	DNA	dna	NN	_	_	_
22	has	have	VBZ	_	_	_
23	been	be	VBN	_	_	_
24	digested	digest	VBN	_	_	_
25	with	with	IN	_	_	_
26	RNase-free	rnase-free	JJ	_	_	_
27	DNase	dnase	NN	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Bacterial	bacterial	JJ	_	_	_
3	cells	cell	NNS	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	bcl2fastq2	bcl2fastq2	NN	_	_	_
6	v2	v2	NN	_	_	_
7	.15.0	.15.0	CD	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Demultiplexing	demultiplexing	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	,	,	,	_	_	_
12	Fastqc	fastqc	NN	_	_	_
13	0.11.5	0.11.5	CD	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	read	read	VB	_	_	_
16	quality	quality	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	,	,	,	_	_	_
19	Cutadapt-1.9.1	cutadapt-1.9.1	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	adaptor	adaptor	NN	_	_	_
22	trimming	trim	VBG	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	Escherichia	escherichia	FW	Organism	_	_
26	coli	coli	FW	Organism	_	_
27	K-12	k-12	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Genome	Genome	NNP	_	_	_
30	_	_	NNP	_	_	_
31	build	build	VB	_	_	_
32	:	:	:	_	_	_
33	NC000913	nc000913	NN	_	_	_
34	.2	.2	NN	_	_	_
35	MG1655	mg1655	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	genotype	genotype	NN	_	_	_
38	:	:	:	_	_	_
39	-LCB-	-lcb-	-LRB-	_	_	_
40	delta	delta	NN	_	_	_
41	-RCB-	-rcb-	-RRB-	_	_	_
42	nusG	nusg	NN	GEN	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	genotype	genotype	NN	_	_	_
45	:	:	:	_	_	_
46	-LCB-	-lcb-	-LRB-	_	_	_
47	delta	delta	NN	_	_	_
48	-RCB-	-rcb-	-RRB-	_	_	_
49	rho	rho	NN	GEN	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	genotype	genotype	NN	_	_	_
52	:	:	:	_	_	_
53	wild	wild	JJ	_	_	_
54	type	type	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	∆	∆	CD	_	_	_
57	nusG	nusg	NN	GEN	_	_
58	UvsW	uvsw	NN	_	_	_
59	_	_	CD	_	_	_
60	replicate1	replicate1	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	∆	∆	CD	_	_	_
63	nusG	nusg	NN	GEN	_	_
64	UvsW	uvsw	NN	_	_	_
65	_	_	CD	_	_	_
66	replicate2	replicate2	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	∆	∆	CD	_	_	_
69	nusG	nusg	NN	GEN	_	_
70	UvsW	uvsw	NN	_	_	_
71	_	_	CD	_	_	_
72	replicate3	replicate3	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	Reads	read	NNS	_	_	_
75	were	be	VBD	_	_	_
76	aligned	align	VBN	_	_	_
77	using	use	VBG	_	_	_
78	MG15655	mg15655	NN	_	_	_
79	as	as	IN	_	_	_
80	reference	reference	NN	_	_	_
81	genome	genome	NN	_	_	_
82	-LRB-	-lrb-	-LRB-	_	_	_
83	NC000913	nc000913	NN	_	_	_
84	.2	.2	NN	_	_	_
85	-RRB-	-rrb-	-RRB-	_	_	_
86	using	use	VBG	_	_	_
87	Bowtie2	bowtie2	NN	_	_	_
88	tool	tool	NN	_	_	_
89	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	∆	∆	SYM	_	_	_
3	rho	rho	FW	GEN	_	_
4	UvsW	uvsw	NN	_	_	_
5	_	_	CD	_	_	_
6	replicate1	replicate1	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	∆	∆	CD	_	_	_
9	rho	rho	NN	GEN	_	_
10	UvsW	uvsw	NN	_	_	_
11	_	_	CD	_	_	_
12	replicate2	replicate2	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	∆	∆	CD	_	_	_
15	rho	rho	NN	GEN	_	_
16	UvsW	uvsw	NN	_	_	_
17	_	_	CD	_	_	_
18	replicate3	replicate3	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	ssRNA-seq	ssrna-seq	JJ	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Starting	start	VBG	_	_	_
23	from	from	IN	_	_	_
24	single	single	JJ	_	_	_
25	colonies	colony	NNS	_	_	_
26	,	,	,	_	_	_
27	the	the	DT	_	_	_
28	following	follow	VBG	_	_	_
29	cultures	culture	NNS	_	_	_
30	were	be	VBD	_	_	_
31	set	set	VBN	_	_	_
32	up	up	RP	_	_	_
33	in	in	IN	_	_	_
34	triplicate	triplicate	NN	_	_	_
35	for	for	IN	_	_	_
36	overnight	overnight	JJ	_	_	_
37	incubation	incubation	NN	_	_	_
38	:	:	:	_	_	_
39	GJ13507	gj13507	NN	_	_	_
40	,	,	,	_	_	_
41	GJ13531	gj13531	NN	_	_	_
42	,	,	,	_	_	_
43	and	and	CC	_	_	_
44	GJ13533	gj13533	NN	_	_	_
45	in	in	IN	_	_	_
46	glucose-minimal	glucose-minimal	JJ	_	_	_
47	A	a	NN	_	_	_
48	;	;	:	_	_	_
49	and	and	CC	_	_	_
50	GJ13519	gj13519	NN	_	_	_
51	also	also	RB	_	_	_
52	in	in	IN	_	_	_
53	0.2	0.2	CD	_	_	_
54	%	%	NN	_	_	_
55	glycerol-minimal	glycerol-minimal	JJ	_	_	_
56	A.	a.	NN	_	_	_
57	All	all	PDT	_	_	_
58	the	the	DT	_	_	_
59	cultures	culture	NNS	_	_	_
60	were	be	VBD	_	_	_
61	supplemented	supplement	VBN	_	_	_
62	with	with	IN	_	_	_
63	200	200	CD	_	_	_
64	μM	μm	NN	_	_	_
65	IPTG	iptg	NN	_	_	_
66	,	,	,	_	_	_
67	with	with	IN	_	_	_
68	the	the	DT	_	_	_
69	exception	exception	NN	_	_	_
70	of	of	IN	_	_	_
71	the	the	DT	_	_	_
72	cultures	culture	NNS	_	_	_
73	of	of	IN	_	_	_
74	GJ13507	gj13507	NN	_	_	_
75	whose	whose	WP$	_	_	_
76	supplementation	supplementation	NN	_	_	_
77	with	with	IN	_	_	_
78	IPTG	iptg	NN	_	_	_
79	was	be	VBD	_	_	_
80	at	at	IN	_	_	_
81	3	3	CD	_	_	_
82	μM	μm	NN	_	_	_
83	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	overnight-grown	overnight-grown	JJ	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	each	each	DT	_	_	_
6	subcultured	subculture	VBN	_	_	_
7	into	into	IN	_	_	_
8	20	20	CD	_	_	_
9	ml	ml	NN	_	_	_
10	of	of	IN	_	_	_
11	fresh	fresh	JJ	_	_	_
12	medium	medium	NN	_	_	_
13	of	of	IN	_	_	_
14	the	the	DT	_	_	_
15	same	same	JJ	_	_	_
16	composition	composition	NN	_	_	_
17	,	,	,	_	_	_
18	with	with	IN	_	_	_
19	an	a	DT	_	_	_
20	inoculum	inoculum	NN	_	_	_
21	of	of	IN	_	_	_
22	1:50	1:50	CD	_	_	_
23	for	for	IN	_	_	_
24	GJ13507	gj13507	NN	_	_	_
25	and	and	CC	_	_	_
26	GJ13531	gj13531	NN	_	_	_
27	and	and	CC	_	_	_
28	of	of	IN	_	_	_
29	1:100	1:100	CD	_	_	_
30	for	for	IN	_	_	_
31	the	the	DT	_	_	_
32	remainder	remainder	NN	_	_	_
33	,	,	,	_	_	_
34	and	and	CC	_	_	_
35	grown	grow	VBN	_	_	_
36	to	to	TO	_	_	_
37	an	a	DT	_	_	_
38	A600	a600	NN	_	_	_
39	of	of	IN	_	_	_
40	0.4	0.4	CD	_	_	_
41	to	to	TO	_	_	_
42	0.45	0.45	CD	_	_	_
43	,	,	,	_	_	_
44	before	before	IN	_	_	_
45	the	the	DT	_	_	_
46	cells	cell	NNS	_	_	_
47	were	be	VBD	_	_	_
48	harvested	harvest	VBN	_	_	_
49	for	for	IN	_	_	_
50	making	make	VBG	_	_	_
51	the	the	DT	_	_	_
52	RNA	rna	NN	_	_	_
53	preparations	preparation	NNS	_	_	_
54	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
55	Strand	Strand	NNP	_	_	_
56	specific	specific	JJ	_	_	_
57	base	base	NN	_	_	_
58	read	read	VBD	_	_	_
59	counts	count	NNS	_	_	_
60	were	be	VBD	_	_	_
61	determined	determine	VBN	_	_	_
62	for	for	IN	_	_	_
63	each	each	DT	_	_	_
64	of	of	IN	_	_	_
65	4091	4091	CD	_	_	_
66	ORFs	orf	NNS	_	_	_
67	for	for	IN	_	_	_
68	the	the	DT	_	_	_
69	15	15	CD	_	_	_
70	samples	sample	NNS	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	Strand-specific	strand-specific	JJ	_	_	_
73	RNA-Seq	rna-seq	NN	_	_	_
74	data	datum	NNS	_	_	_
75	were	be	VBD	_	_	_
76	generated	generate	VBN	_	_	_
77	,	,	,	_	_	_
78	following	follow	VBG	_	_	_
79	rRNA	rrna	NN	_	_	_
80	depletion	depletion	NN	_	_	_
81	with	with	IN	_	_	_
82	a	a	DT	_	_	_
83	Ribo-Zero	Ribo-Zero	NNP	_	_	_
84	kit	kit	NN	_	_	_
85	,	,	,	_	_	_
86	with	with	IN	_	_	_
87	the	the	DT	_	_	_
88	aid	aid	NN	_	_	_
89	of	of	IN	_	_	_
90	the	the	DT	_	_	_
91	di-tagged	di-tagged	JJ	_	_	_
92	cDNA	cdna	NN	_	_	_
93	strategy	strategy	NN	_	_	_
94	-LRB-	-lrb-	-LRB-	_	_	_
95	ScriptSeq	scriptseq	NN	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	on	on	IN	_	_	_
98	an	a	DT	_	_	_
99	Illumina	Illumina	NNP	_	_	_
100	NextSeq	NextSeq	NNP	_	_	_
101	platform	platform	NN	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	substrain	substrain	NN	_	_	_
104	:	:	:	_	_	_
105	GJ13507	gj13507	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	substrain	substrain	NN	_	_	_
108	:	:	:	_	_	_
109	GJ13519	gj13519	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	substrain	substrain	NN	_	_	_
112	:	:	:	_	_	_
113	GJ13531	gj13531	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	substrain	substrain	NN	_	_	_
116	:	:	:	_	_	_
117	GJ13533	gj13533	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	Supplementary	supplementary	JJ	_	_	_
120	_	_	NN	_	_	_
121	files	file	NNS	_	_	_
122	_	_	IN	_	_	_
123	format	format	NN	_	_	_
124	_	_	NN	_	_	_
125	and	and	CC	_	_	_
126	_	_	NN	_	_	_
127	content	content	NN	_	_	_
128	:	:	:	_	_	_
129	The	the	DT	_	_	_
130	text	text	NN	_	_	_
131	file	file	NN	_	_	_
132	contains	contain	VBZ	_	_	_
133	sense	sense	NN	_	_	_
134	and	and	CC	_	_	_
135	antisense	antisense	JJ	_	_	_
136	raw	raw	JJ	_	_	_
137	base	base	NN	_	_	_
138	read	read	VBD	_	_	_
139	counts	count	NNS	_	_	_
140	for	for	IN	_	_	_
141	each	each	DT	_	_	_
142	of	of	IN	_	_	_
143	the	the	DT	_	_	_
144	4091	4091	CD	_	_	_
145	ORFs	orf	NNS	_	_	_
146	for	for	IN	_	_	_
147	all	all	PDT	_	_	_
148	the	the	DT	_	_	_
149	15	15	CD	_	_	_
150	samples	sample	NNS	_	_	_
151	,	,	,	_	_	_
152	and	and	CC	_	_	_
153	the	the	DT	_	_	_
154	explanation	explanation	NN	_	_	_
155	key	key	NN	_	_	_
156	is	be	VBZ	_	_	_
157	included	include	VBN	_	_	_
158	in	in	IN	_	_	_
159	the	the	DT	_	_	_
160	file	file	NN	_	_	_
161	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Viable	viable	JJ	_	_	_
3	clones	clone	NNS	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	UvsW-expressing	uvsw-expressing	JJ	_	_	_
7	strains	strain	NNS	_	_	_
8	GJ13531	gj13531	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Δrho	δrho	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	and	and	CC	_	_	_
13	GJ13507	gj13507	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	ΔnusG	δnusg	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	were	be	VBD	_	_	_
18	obtained	obtain	VBN	_	_	_
19	as	as	IN	_	_	_
20	white	white	JJ	_	_	_
21	colonies	colony	NNS	_	_	_
22	from	from	IN	_	_	_
23	their	they	PRP$	_	_	_
24	respective	respective	JJ	_	_	_
25	shelter	shelter	NN	_	_	_
26	plasmid-carrying	plasmid-carrying	JJ	_	_	_
27	derivatives	derivative	NNS	_	_	_
28	GJ13531	gj13531	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	WT	wt	JJ	_	_	_
31	glucose	glucose	NN	SUPP	_	_
32	_	_	NN	_	_	_
33	replicate1	replicate1	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	WT	wt	JJ	_	_	_
36	glucose	glucose	NN	SUPP	_	_
37	_	_	NN	_	_	_
38	replicate2	replicate2	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	WT	wt	JJ	_	_	_
41	glucose	glucose	NN	SUPP	_	_
42	_	_	NN	_	_	_
43	replicate3	replicate3	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	WT	wt	JJ	_	_	_
46	_	_	NN	_	_	_
47	glycerol	glycerol	NN	SUPP	_	_
48	_	_	CD	_	_	_
49	replicate1	replicate1	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	WT	wt	JJ	_	_	_
52	_	_	NN	_	_	_
53	glycerol	glycerol	NN	SUPP	_	_
54	_	_	CD	_	_	_
55	replicate2	replicate2	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	WT	wt	JJ	_	_	_
58	_	_	NN	_	_	_
59	glycerol	glycerol	NN	SUPP	_	_
60	_	_	CD	_	_	_
61	replicate3	replicate3	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	WT	wt	JJ	_	_	_
64	UvsW	uvsw	NN	_	_	_
65	_	_	NN	_	_	_
66	replicate1	replicate1	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	WT	wt	JJ	_	_	_
69	UvsW	uvsw	NN	_	_	_
70	_	_	NN	_	_	_
71	replicate2	replicate2	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	WT	wt	JJ	_	_	_
74	UvsW	uvsw	NN	_	_	_
75	_	_	NN	_	_	_
76	replicate3	replicate3	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	cells	cell	NNS	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
80	Cells	cell	NNS	_	_	_
81	were	be	VBD	_	_	_
82	inoculated	inoculate	VBN	_	_	_
83	from	from	IN	_	_	_
84	overnight	overnight	JJ	_	_	_
85	grown	grown	JJ	_	_	_
86	culture	culture	NN	_	_	_
87	in	in	IN	_	_	_
88	Lysogeny	Lysogeny	NNP	_	_	_
89	Broth	Broth	NNP	_	_	_
90	-LRB-	-lrb-	-LRB-	_	_	_
91	LB	LB	NNP	_	_	_
92	-RRB-	-rrb-	-RRB-	_	_	_
93	and	and	CC	_	_	_
94	then	then	RB	_	_	_
95	harvested	harvest	VBN	_	_	_
96	in	in	IN	_	_	_
97	the	the	DT	_	_	_
98	early	early	JJ	_	_	_
99	exponential	exponential	JJ	_	_	_
100	growth	growth	NN	_	_	_
101	phase	phase	NN	_	_	_
102	and	and	CC	_	_	_
103	mid	mid	JJ	_	_	_
104	exponential	exponential	JJ	_	_	_
105	growth	growth	NN	_	_	_
106	phase	phase	NN	_	_	_
107	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	crpfis.rep1.ee	crpfis.rep1.ee	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	crpfis.rep1.me	crpfis.rep1.me	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	crpfis.rep2.ee	crpfis.rep2.ee	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	crpfis.rep2.me	crpfis.rep2.me	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	crp.rep1.ee	crp.rep1.ee	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	crp.rep1.me	crp.rep1.me	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	crp.rep2.ee	crp.rep2.ee	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	crp.rep2.me	crp.rep2.me	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	cya.rep1.ee	cya.rep1.ee	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	cya.rep1.me	cya.rep1.me	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	cya.rep2.ee	cya.rep2.ee	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	cya.rep2.me	cya.rep2.me	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Escherichia	escherichia	FW	Organism	_	_
27	coli	coli	FW	Organism	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	fis.rep1.ee	fis.rep1.ee	JJ	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	fis.rep1.me	fis.rep1.me	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	fis.rep2.ee	fis.rep2.ee	JJ	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	fis.rep2.me	fis.rep2.me	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Genome	Genome	NNP	_	_	_
38	_	_	NNP	_	_	_
39	build	build	VB	_	_	_
40	:	:	:	_	_	_
41	Escherichia	escherichia	FW	Organism	_	_
42	coli	coli	FW	Organism	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	NC000913	nc000913	NN	_	_	_
45	.2	.2	NN	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	genotype	genotype	NN	_	_	_
49	:	:	:	_	_	_
50	crpfis	crpfis	NN	_	_	_
51	mutant	mutant	JJ	_	_	_
52	background	background	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	genotype	genotype	NN	_	_	_
55	:	:	:	_	_	_
56	crp	crp	NN	GEN	_	_
57	mutant	mutant	JJ	_	_	_
58	background	background	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	genotype	genotype	NN	_	_	_
61	:	:	:	_	_	_
62	cya	cya	NN	_	_	_
63	mutant	mutant	JJ	_	_	_
64	background	background	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	genotype	genotype	NN	_	_	_
67	:	:	:	_	_	_
68	fis	fis	NN	GEN	_	_
69	mutant	mutant	JJ	_	_	_
70	background	background	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	genotype	genotype	NN	_	_	_
73	:	:	:	_	_	_
74	wildtype	wildtype	JJ	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	growth	growth	NN	_	_	_
77	phase	phase	NN	_	_	_
78	:	:	:	_	_	_
79	Early	early	JJ	_	_	_
80	exponential	exponential	JJ	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	growth	growth	NN	_	_	_
83	phase	phase	NN	_	_	_
84	:	:	:	_	_	_
85	Mid	Mid	NNP	_	_	_
86	exponential	exponential	JJ	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	NEXTflexRapid	nextflexrapid	NN	_	_	_
89	Directional	directional	JJ	_	_	_
90	RNA-Seq	rna-seq	NN	_	_	_
91	library	library	NN	_	_	_
92	kit	kit	NN	_	_	_
93	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
94	Raw	raw	NN	_	_	_
95	.	.	.	_	_	_

1	fastq	fastq	NN	_	_	_
2	files	file	NNS	_	_	_
3	were	be	VBD	_	_	_
4	mapped	map	VBN	_	_	_
5	to	to	TO	_	_	_
6	the	the	DT	_	_	_
7	reference	reference	NN	_	_	_
8	genome	genome	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	NC000913	nc000913	NN	_	_	_
11	.2	.2	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	using	use	VBG	_	_	_
14	BWA	bwa	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	version	version	NN	_	_	_
17	0.7	0.7	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	Mapped	map	VBN	_	_	_
2	reads	read	VBZ	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	converted	convert	VBN	_	_	_
6	to	to	TO	_	_	_
7	read	read	VB	_	_	_
8	count	count	NN	_	_	_
9	per	per	IN	_	_	_
10	gene	gene	NN	_	_	_
11	using	use	VBG	_	_	_
12	bedtools	bedtool	NNS	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	version	version	NN	_	_	_
15	2	2	CD	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	the	the	DT	_	_	_
3	case	case	NN	_	_	_
4	of	of	IN	_	_	_
5	Ion	ion	NN	_	_	_
6	torrent	torrent	NN	_	_	_
7	data	datum	NNS	_	_	_
8	.	.	.	_	_	_

1	bam	bam	NN	_	_	_
2	files	file	NNS	_	_	_
3	were	be	VBD	_	_	_
4	converted	convert	VBN	_	_	_
5	using	use	VBG	_	_	_
6	BWA	BWA	NNP	_	_	_
7	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Resulting	Resulting	NNP	_	_	_
3	read	read	VBD	_	_	_
4	count	count	NN	_	_	_
5	matrix	matrix	NN	_	_	_
6	was	be	VBD	_	_	_
7	used	use	VBN	_	_	_
8	as	as	IN	_	_	_
9	input	input	NN	_	_	_
10	for	for	IN	_	_	_
11	the	the	DT	_	_	_
12	differntial	differntial	JJ	_	_	_
13	expression	expression	NN	_	_	_
14	analysis	analysis	NN	_	_	_
15	in	in	IN	_	_	_
16	edgeR	edger	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	version	version	NN	_	_	_
19	3.12.1	3.12.1	CD	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	RNA	rna	NN	_	_	_
5	was	be	VBD	_	_	_
6	extracted	extract	VBN	_	_	_
7	from	from	IN	_	_	_
8	the	the	DT	_	_	_
9	harvested	harvest	VBN	_	_	_
10	cells	cell	NNS	_	_	_
11	using	use	VBG	_	_	_
12	Trizol	Trizol	NNP	_	_	_
13	reagent	reagent	NN	_	_	_
14	.	.	.	_	_	_

1	Depending	depend	VBG	_	_	_
2	upon	upon	IN	_	_	_
3	the	the	DT	_	_	_
4	concentration	concentration	NN	_	_	_
5	of	of	IN	_	_	_
6	total	total	JJ	_	_	_
7	RNA	rna	NN	_	_	_
8	,	,	,	_	_	_
9	sample	sample	NN	_	_	_
10	were	be	VBD	_	_	_
11	treated	treat	VBN	_	_	_
12	with	with	IN	_	_	_
13	Dnase	dnase	NN	_	_	_
14	and	and	CC	_	_	_
15	ribocleanup	ribocleanup	NN	_	_	_
16	was	be	VBD	_	_	_
17	given	give	VBN	_	_	_
18	according	accord	VBG	_	_	_
19	to	to	TO	_	_	_
20	the	the	DT	_	_	_
21	instruction	instruction	NN	_	_	_
22	manual	manual	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	srain	srain	NN	_	_	_
3	:	:	:	_	_	_
4	K12	k12	NN	_	_	_
5	MG1655	mg1655	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	srain	srain	NN	_	_	_
8	:	:	:	_	_	_
9	K12	k12	NN	_	_	_
10	MG1656	mg1656	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	srain	srain	NN	_	_	_
13	:	:	:	_	_	_
14	K12	k12	NN	_	_	_
15	MG1657	mg1657	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	srain	srain	NN	_	_	_
18	:	:	:	_	_	_
19	K12	k12	NN	_	_	_
20	MG1658	mg1658	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	srain	srain	NN	_	_	_
23	:	:	:	_	_	_
24	K12	k12	NN	_	_	_
25	MG1659	mg1659	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	srain	srain	NN	_	_	_
28	:	:	:	_	_	_
29	K12	k12	NN	_	_	_
30	MG1660	mg1660	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	srain	srain	NN	_	_	_
33	:	:	:	_	_	_
34	K12	k12	NN	_	_	_
35	MG1661	mg1661	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	srain	srain	NN	_	_	_
38	:	:	:	_	_	_
39	K12	k12	NN	_	_	_
40	MG1662	mg1662	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	srain	srain	NN	_	_	_
43	:	:	:	_	_	_
44	K12	k12	NN	_	_	_
45	MG1663	mg1663	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	srain	srain	NN	_	_	_
48	:	:	:	_	_	_
49	K12	k12	NN	_	_	_
50	MG1664	mg1664	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	srain	srain	NN	_	_	_
53	:	:	:	_	_	_
54	K12	k12	NN	_	_	_
55	MG1665	mg1665	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	srain	srain	NN	_	_	_
58	:	:	:	_	_	_
59	K12	k12	NN	_	_	_
60	MG1666	mg1666	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	srain	srain	NN	_	_	_
63	:	:	:	_	_	_
64	K12	k12	NN	_	_	_
65	MG1667	mg1667	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	srain	srain	NN	_	_	_
68	:	:	:	_	_	_
69	K12	k12	NN	_	_	_
70	MG1668	mg1668	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	srain	srain	NN	_	_	_
73	:	:	:	_	_	_
74	K12	k12	NN	_	_	_
75	MG1669	mg1669	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	srain	srain	NN	_	_	_
78	:	:	:	_	_	_
79	K12	k12	NN	_	_	_
80	MG1670	mg1670	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	srain	srain	NN	_	_	_
83	:	:	:	_	_	_
84	K12	k12	NN	_	_	_
85	MG1671	mg1671	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	srain	srain	NN	_	_	_
88	:	:	:	_	_	_
89	K12	k12	NN	_	_	_
90	MG1672	mg1672	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	srain	srain	NN	_	_	_
93	:	:	:	_	_	_
94	K12	k12	NN	_	_	_
95	MG1673	mg1673	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	srain	srain	NN	_	_	_
98	:	:	:	_	_	_
99	K12	k12	NN	_	_	_
100	MG1674	mg1674	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	Supplementary	supplementary	JJ	_	_	_
103	_	_	NN	_	_	_
104	files	file	NNS	_	_	_
105	_	_	IN	_	_	_
106	format	format	NN	_	_	_
107	_	_	NN	_	_	_
108	and	and	CC	_	_	_
109	_	_	NN	_	_	_
110	content	content	NN	_	_	_
111	:	:	:	_	_	_
112	.	.	.	_	_	_

1	txt	txt	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	log2	log2	NN	_	_	_
4	fold	fold	JJ	_	_	_
5	change	change	NN	_	_	_
6	values	value	NNS	_	_	_
7	,	,	,	_	_	_
8	p-values	p-value	NNS	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	wt.rep1.ee	wt.rep1.ee	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	wt.rep1.me	wt.rep1.me	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	wt.rep2.ee	wt.rep2.ee	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	wt.rep2.me	wt.rep2.me	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	cell	cell	NN	_	_	_
20	pellets	pellet	NNS	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	E.	e.	FW	_	_	_
23	coli	coli	FW	_	_	_
24	042	042	CD	_	_	_
25	WT	wt	JJ	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	E.	e.	FW	_	_	_
28	coli	coli	FW	_	_	_
29	hhahha2	hhahha2	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	E.	e.	FW	_	_	_
32	coli	coli	FW	_	_	_
33	hns	hns	FW	GEN	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	E.	e.	FW	_	_	_
36	coli	coli	FW	_	_	_
37	hns2	hns2	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	E.	e.	FW	_	_	_
40	coli	coli	FW	_	_	_
41	hnshns2	hnshns2	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	Escherichia	escherichia	FW	Organism	_	_
44	coli	coli	FW	Organism	_	_
45	042	042	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	For	for	IN	_	_	_
48	quantification	quantification	NN	_	_	_
49	of	of	IN	_	_	_
50	gene	gene	NN	_	_	_
51	expression	expression	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	read	read	NN	_	_	_
54	counting	counting	NN	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	,	,	,	_	_	_
57	the	the	DT	_	_	_
58	alignments	alignment	NNS	_	_	_
59	generated	generate	VBN	_	_	_
60	with	with	IN	_	_	_
61	the	the	DT	_	_	_
62	Genomics	Genomics	NNP	_	_	_
63	Workbench	Workbench	NNP	_	_	_
64	were	be	VBD	_	_	_
65	exported	export	VBN	_	_	_
66	in	in	IN	_	_	_
67	BAM	BAM	NNP	_	_	_
68	format	format	NN	_	_	_
69	.	.	.	_	_	_

1	Read	Read	NNP	_	_	_
2	counting	counting	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	performed	perform	VBN	_	_	_
6	with	with	IN	_	_	_
7	the	the	DT	_	_	_
8	FeatureCounts	FeatureCounts	NNP	_	_	_
9	v.	v.	CC	_	_	_
10	1.5.0-p1	1.5.0-p1	CD	_	_	_
11	program	program	NN	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	following	follow	VBG	_	_	_
15	parameters	parameter	NNS	_	_	_
16	;	;	:	_	_	_
17	Level	Level	NNP	_	_	_
18	:	:	:	_	_	_
19	meta-feature	meta-feature	JJ	_	_	_
20	leve	leve	NN	_	_	_
21	.	.	.	_	_	_

1	Paired-end	paired-end	NN	_	_	_
2	:	:	:	_	_	_
3	no	no	DT	_	_	_
4	.	.	.	_	_	_

1	Strand	strand	VB	_	_	_
2	specific	specific	JJ	_	_	_
3	:	:	:	_	_	_
4	yes	yes	UH	_	_	_
5	.	.	.	_	_	_

1	Multimapping	multimapp	VBG	_	_	_
2	reads	read	VBZ	_	_	_
3	:	:	:	_	_	_
4	counted	count	VBN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	as	as	IN	_	_	_
7	fractions	fraction	NNS	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	.	.	.	_	_	_

1	Multi-overlapping	multi-overlapping	JJ	_	_	_
2	reads	read	VBZ	_	_	_
3	:	:	:	_	_	_
4	not	not	RB	_	_	_
5	counted	count	VBN	_	_	_
6	.	.	.	_	_	_

1	Overlapping	overlapping	JJ	_	_	_
2	bases	basis	NNS	_	_	_
3	:	:	:	_	_	_
4	30	30	CD	_	_	_
5	.	.	.	_	_	_

1	Read	Read	NNP	_	_	_
2	orientations	orientation	NNS	_	_	_
3	:	:	:	_	_	_
4	fr	fr	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	From	from	IN	_	_	_
7	the	the	DT	_	_	_
8	rRNA	rrna	NN	_	_	_
9	depleted	deplete	VBN	_	_	_
10	RNA	rna	NN	_	_	_
11	samples	sample	NNS	_	_	_
12	,	,	,	_	_	_
13	first-strand	first-strand	JJ	_	_	_
14	cDNA	cdna	NN	_	_	_
15	was	be	VBD	_	_	_
16	synthesized	synthesize	VBN	_	_	_
17	using	use	VBG	_	_	_
18	a	a	DT	_	_	_
19	N6	n6	NN	_	_	_
20	randomized	randomize	VBD	_	_	_
21	primer	primer	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	fragmentation	fragmentation	NN	_	_	_
3	,	,	,	_	_	_
4	the	the	DT	_	_	_
5	Illumina	Illumina	NNP	_	_	_
6	TruSeq	TruSeq	NNP	_	_	_
7	sequencing	sequencing	NN	_	_	_
8	adapters	adapter	NNS	_	_	_
9	were	be	VBD	_	_	_
10	ligated	ligate	VBN	_	_	_
11	in	in	IN	_	_	_
12	a	a	DT	_	_	_
13	strand	strand	NN	_	_	_
14	specific	specific	JJ	_	_	_
15	manner	manner	NN	_	_	_
16	to	to	TO	_	_	_
17	the	the	DT	_	_	_
18	5	5	CD	_	_	_
19	'	'	''	_	_	_
20	and	and	CC	_	_	_
21	3	3	CD	_	_	_
22	'	'	''	_	_	_
23	ends	end	NNS	_	_	_
24	of	of	IN	_	_	_
25	the	the	DT	_	_	_
26	cDNA	cdna	NN	_	_	_
27	fragments	fragment	NNS	_	_	_
28	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cDNA	cdna	NN	_	_	_
3	was	be	VBD	_	_	_
4	finally	finally	RB	_	_	_
5	amplified	amplify	VBN	_	_	_
6	with	with	IN	_	_	_
7	PCR	pcr	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	15	15	CD	_	_	_
10	PCR	pcr	NN	_	_	_
11	cycles	cycle	NNS	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	using	use	VBG	_	_	_
14	a	a	DT	_	_	_
15	proof	proof	NN	_	_	_
16	reading	reading	NN	_	_	_
17	enzyme	enzyme	NN	_	_	_
18	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	Illumina	Illumina	NNP	_	_	_
3	sequencing	sequencing	NN	_	_	_
4	,	,	,	_	_	_
5	cDNA	cdna	NN	_	_	_
6	libraries	library	NNS	_	_	_
7	were	be	VBD	_	_	_
8	pooled	pool	VBN	_	_	_
9	in	in	IN	_	_	_
10	a	a	DT	_	_	_
11	25:1	25:1	CD	_	_	_
12	ratio	ratio	NN	_	_	_
13	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	library	library	NN	_	_	_
3	pool	pool	NN	_	_	_
4	was	be	VBD	_	_	_
5	fractionated	fractionate	VBN	_	_	_
6	in	in	IN	_	_	_
7	the	the	DT	_	_	_
8	size	size	NN	_	_	_
9	range	range	NN	_	_	_
10	of	of	IN	_	_	_
11	250-500	250-500	CD	_	_	_
12	bp	bp	NN	_	_	_
13	using	use	VBG	_	_	_
14	a	a	DT	_	_	_
15	differential	differential	JJ	_	_	_
16	clean	clean	JJ	_	_	_
17	-	-	:	_	_	_
18	up	up	RP	_	_	_
19	with	with	IN	_	_	_
20	the	the	DT	_	_	_
21	Agencourt	Agencourt	NNP	_	_	_
22	AMPure	AMPure	NNP	_	_	_
23	kit	kit	NN	_	_	_
24	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cDNA	cdna	NN	_	_	_
3	pool	pool	NN	_	_	_
4	was	be	VBD	_	_	_
5	sequenced	sequence	VBN	_	_	_
6	on	on	IN	_	_	_
7	an	a	DT	_	_	_
8	Illumina	Illumina	NNP	_	_	_
9	NextSeq	NextSeq	NNP	_	_	_
10	500	500	CD	_	_	_
11	system	system	NN	_	_	_
12	using	use	VBG	_	_	_
13	75	75	CD	_	_	_
14	bp	bp	NN	_	_	_
15	read	read	VBD	_	_	_
16	length	length	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	NCBI	ncbi	NN	_	_	_
7	reference	reference	NN	_	_	_
8	sequence	sequence	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	NC	nc	NN	_	_	_
11	_	_	CD	_	_	_
12	017626.1	017626.1	CD	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	genotype	genotype	NN	_	_	_
16	:	:	:	_	_	_
17	mutant	mutant	JJ	_	_	_
18	hhahha2	hhahha2	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	genotype	genotype	NN	_	_	_
21	:	:	:	_	_	_
22	mutant	mutant	JJ	_	_	_
23	hhs	hh	NNS	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
25	genotype	genotype	NN	_	_	_
26	:	:	:	_	_	_
27	mutant	mutant	JJ	_	_	_
28	hns2	hns2	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	genotype	genotype	NN	_	_	_
31	:	:	:	_	_	_
32	mutant	mutant	JJ	_	_	_
33	hnshns2	hnshns2	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	genotype	genotype	NN	_	_	_
36	:	:	:	_	_	_
37	wild	wild	JJ	_	_	_
38	type	type	NN	_	_	_
39	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
40	Illumina	Illumina	NNP	_	_	_
41	sequencing	sequencing	NN	_	_	_
42	instruments	instrument	NNS	_	_	_
43	generate	generate	VBP	_	_	_
44	per-cycle	per-cycle	JJ	_	_	_
45	BCL	BCL	NNP	_	_	_
46	base	base	NN	_	_	_
47	call	call	NN	_	_	_
48	files	file	NNS	_	_	_
49	as	as	IN	_	_	_
50	primary	primary	JJ	_	_	_
51	sequencing	sequencing	NN	_	_	_
52	output	output	NN	_	_	_
53	in	in	IN	_	_	_
54	bcl2	bcl2	NN	_	_	_
55	format	format	NN	_	_	_
56	.	.	.	_	_	_

1	Conversion	conversion	NN	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	bcl2	bcl2	NN	_	_	_
5	file	file	NN	_	_	_
6	to	to	TO	_	_	_
7	gzipped	gzipped	JJ	_	_	_
8	fastq	fastq	NN	_	_	_
9	files	file	NNS	_	_	_
10	was	be	VBD	_	_	_
11	performed	perform	VBN	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	bcl2fastq	bcl2fastq	NN	_	_	_
15	script	script	NN	_	_	_
16	v.	v.	CC	_	_	_
17	2.18.0.12	2.18.0.12	CD	_	_	_
18	provided	provide	VBN	_	_	_
19	by	by	IN	_	_	_
20	Illumina	Illumina	NNP	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	LB	LB	NNP	MED	_	_
3	medium	medium	NN	MED	_	_
4	at	at	IN	_	_	_
5	37ºC	37ºc	NN	_	_	_
6	with	with	IN	_	_	_
7	200rpm	200rpm	JJ	_	_	_
8	agitation	agitation	NN	_	_	_
9	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Mapping	mapping	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	trimmed	trimmed	RBR	_	_	_
6	reads	read	VBZ	_	_	_
7	to	to	TO	_	_	_
8	the	the	DT	_	_	_
9	reference	reference	NN	_	_	_
10	sequences	sequence	NNS	_	_	_
11	was	be	VBD	_	_	_
12	also	also	RB	_	_	_
13	performed	perform	VBN	_	_	_
14	with	with	IN	_	_	_
15	the	the	DT	_	_	_
16	CLC	clc	NN	_	_	_
17	Genomics	genomic	NNS	_	_	_
18	Workbench	workbench	JJ	_	_	_
19	9.0	9.0	CD	_	_	_
20	using	use	VBG	_	_	_
21	the	the	DT	_	_	_
22	`	`	``	_	_	_
23	Map	map	NN	_	_	_
24	Reads	read	VBZ	_	_	_
25	to	to	TO	_	_	_
26	Reference	Reference	NNP	_	_	_
27	'	'	POS	_	_	_
28	tool	tool	NN	_	_	_
29	with	with	IN	_	_	_
30	standard	standard	JJ	_	_	_
31	parameters	parameter	NNS	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Quality	Quality	NNP	_	_	_
3	and	and	CC	_	_	_
4	adapter	adapter	NN	_	_	_
5	trimming	trim	VBG	_	_	_
6	was	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	with	with	IN	_	_	_
9	the	the	DT	_	_	_
10	CLC	clc	NN	_	_	_
11	Genomics	genomic	NNS	_	_	_
12	Workbench	workbench	JJ	_	_	_
13	9.0	9.0	CD	_	_	_
14	software	software	NN	_	_	_
15	package	package	NN	_	_	_
16	using	use	VBG	_	_	_
17	the	the	DT	_	_	_
18	`	`	``	_	_	_
19	Trim	Trim	NNP	_	_	_
20	Sequences	sequence	NNS	_	_	_
21	'	'	POS	_	_	_
22	tool	tool	NN	_	_	_
23	with	with	IN	_	_	_
24	standard	standard	JJ	_	_	_
25	parameters	parameter	NNS	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Supplementary	supplementary	JJ	_	_	_
5	_	_	NN	_	_	_
6	files	file	NNS	_	_	_
7	_	_	IN	_	_	_
8	format	format	NN	_	_	_
9	_	_	NN	_	_	_
10	and	and	CC	_	_	_
11	_	_	NN	_	_	_
12	content	content	NN	_	_	_
13	:	:	:	_	_	_
14	Strain-expression	strain-expression	NN	_	_	_
15	.	.	.	_	_	_

1	xlsx	xlsx	NN	_	_	_
2	archive	archive	NN	_	_	_
3	contains	contain	VBZ	_	_	_
4	expression	expression	NN	_	_	_
5	values	value	NNS	_	_	_
6	in	in	IN	_	_	_
7	RPKM	rpkm	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Reads	read	NNS	_	_	_
10	Per	per	IN	_	_	_
11	Kb	kb	NN	_	_	_
12	exon	exon	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	contig	contig	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	per	per	IN	_	_	_
17	Million	Million	NNP	_	_	_
18	mapped	map	VBD	_	_	_
19	reads	read	VBZ	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	see	see	VB	_	_	_
22	Mortazavi	Mortazavi	NNP	_	_	_
23	et	et	FW	_	_	_
24	al.	al.	FW	_	_	_
25	2008	2008	CD	_	_	_
26	,	,	,	_	_	_
27	Nat	Nat	NNP	_	_	_
28	Methods	method	NNS	_	_	_
29	.	.	.	_	_	_

1	5	5	CD	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	7	7	CD	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	:	:	:	_	_	_
6	621-8	621-8	CD	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	and	and	CC	_	_	_
9	can	can	MD	GEN	_	_
10	be	be	VB	_	_	_
11	directly	directly	RB	_	_	_
12	compared	compare	VBN	_	_	_
13	to	to	TO	_	_	_
14	each	each	DT	_	_	_
15	other	other	JJ	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	tab-delimited	tab-delimited	JJ	_	_	_
18	text	text	NN	_	_	_
19	files	file	NNS	_	_	_
20	include	include	VBP	_	_	_
21	RPKM	rpkm	NN	_	_	_
22	values	value	NNS	_	_	_
23	for	for	IN	_	_	_
24	each	each	DT	_	_	_
25	Sample	Sample	NNP	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	from	from	IN	_	_	_
7	the	the	DT	_	_	_
8	cell	cell	NN	_	_	_
9	pellets	pellet	NNS	_	_	_
10	using	use	VBG	_	_	_
11	a	a	DT	_	_	_
12	bead	bead	NN	_	_	_
13	mill	mill	NN	_	_	_
14	and	and	CC	_	_	_
15	the	the	DT	_	_	_
16	mirVana	mirvana	NN	_	_	_
17	RNA	rna	NN	_	_	_
18	isolation	isolation	NN	_	_	_
19	kit	kit	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Ambion	ambion	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	including	include	VBG	_	_	_
24	DNase	dnase	NN	_	_	_
25	treatment	treatment	NN	_	_	_
26	.	.	.	_	_	_

1	From	from	IN	_	_	_
2	the	the	DT	_	_	_
3	total	total	JJ	_	_	_
4	RNA	rna	NN	_	_	_
5	samples	sample	NNS	_	_	_
6	,	,	,	_	_	_
7	ribosomal	ribosomal	JJ	_	_	_
8	RNA	rna	NN	_	_	_
9	molecules	molecule	NNS	_	_	_
10	were	be	VBD	_	_	_
11	depleted	deplete	VBN	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	Ribo-Zero	Ribo-Zero	NNP	_	_	_
15	rRNA	rrna	NN	_	_	_
16	Removal	removal	NN	_	_	_
17	Kit	kit	NN	_	_	_
18	for	for	IN	_	_	_
19	bacteria	bacterium	NNS	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Illumina	Illumina	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	We	we	PRP	_	_	_
3	used	use	VBD	_	_	_
4	an	a	DT	_	_	_
5	Illumina	Illumina	NNP	_	_	_
6	NextSeq	NextSeq	NNP	_	_	_
7	500	500	CD	_	_	_
8	system	system	NN	_	_	_
9	and	and	CC	_	_	_
10	a	a	DT	_	_	_
11	MID	mid	NN	_	_	_
12	150	150	CD	_	_	_
13	Kit	kit	NN	_	_	_
14	with	with	IN	_	_	_
15	1x75	1x75	CD	_	_	_
16	bp	bp	NN	_	_	_
17	read	read	VBD	_	_	_
18	length	length	NN	_	_	_
19	.	.	.	_	_	_

1	Base-calling	base-calling	NN	_	_	_
2	was	be	VBD	_	_	_
3	perform	perform	VB	_	_	_
4	online	online	NN	_	_	_
5	during	during	IN	_	_	_
6	the	the	DT	_	_	_
7	sequencing	sequencing	NN	_	_	_
8	procedure	procedure	NN	_	_	_
9	with	with	IN	_	_	_
10	the	the	DT	_	_	_
11	Real-Time	Real-Time	NNP	_	_	_
12	Analysis	analysis	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	RTA	rta	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	software	software	NN	_	_	_
17	version	version	NN	_	_	_
18	2.4.11	2.4.11	CD	_	_	_
19	and	and	CC	_	_	_
20	System	System	NNP	_	_	_
21	Suite	Suite	NNP	_	_	_
22	Version	Version	NNP	_	_	_
23	2.1.2.1	2.1.2.1	CD	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	E.coli	e.coli	NNS	_	_	_
3	_	_	VBP	_	_	_
4	∆	∆	SYM	_	_	_
5	ompR	ompr	NN	GEN	_	_
6	pH	ph	NN	_	_	_
7	5.6	5.6	CD	_	_	_
8	A	a	DT	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	E.coli	e.coli	NNS	_	_	_
11	_	_	VBP	_	_	_
12	∆	∆	SYM	_	_	_
13	ompR	ompr	NN	GEN	_	_
14	pH	ph	NN	_	_	_
15	5.6	5.6	CD	_	_	_
16	B	b	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	E.coli	e.coli	NNS	_	_	_
19	_	_	VBP	_	_	_
20	∆	∆	SYM	_	_	_
21	ompR	ompr	NN	GEN	_	_
22	pH	ph	NN	_	_	_
23	5.6	5.6	CD	_	_	_
24	C	c	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	E.coli	e.coli	NNS	_	_	_
27	_	_	VBP	_	_	_
28	∆	∆	SYM	_	_	_
29	ompR	ompr	NN	GEN	_	_
30	pH	ph	NN	_	_	_
31	7.2	7.2	CD	_	_	_
32	+15	+15	CD	_	_	_
33	%	%	NN	_	_	_
34	sucrose	sucrose	NN	_	_	_
35	A	a	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	E.coli	e.coli	NNS	_	_	_
38	_	_	VBP	_	_	_
39	∆	∆	SYM	_	_	_
40	ompR	ompr	NN	GEN	_	_
41	pH	ph	NN	_	_	_
42	7.2	7.2	CD	_	_	_
43	+15	+15	CD	_	_	_
44	%	%	NN	_	_	_
45	sucrose	sucrose	NN	_	_	_
46	B	b	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	E.	e.	FW	_	_	_
49	coli	coli	FW	_	_	_
50	strains	strain	NNS	_	_	_
51	was	be	VBD	_	_	_
52	grown	grow	VBN	_	_	_
53	in	in	IN	_	_	_
54	MgM	MgM	NNP	_	_	_
55	media	media	NNS	_	_	_
56	at	at	IN	_	_	_
57	pH	ph	NN	_	_	_
58	5.6	5.6	CD	_	_	_
59	,	,	,	_	_	_
60	7.2	7.2	CD	_	_	_
61	and	and	CC	_	_	_
62	7.2	7.2	CD	_	_	_
63	with	with	IN	_	_	_
64	15	15	CD	_	_	_
65	%	%	NN	_	_	_
66	-LRB-	-lrb-	-LRB-	_	_	_
67	w	w	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	E.coli	e.coli	NNS	_	_	_
70	_	_	VBP	_	_	_
71	WT	wt	JJ	_	_	_
72	pH	ph	NN	_	_	_
73	5.6	5.6	CD	_	_	_
74	A	a	DT	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	E.coli	e.coli	NN	_	_	_
77	_	_	CD	_	_	_
78	WT	WT	NNP	_	_	_
79	pH	ph	NN	_	_	_
80	5.6	5.6	CD	_	_	_
81	B	b	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	E.coli	e.coli	NNS	_	_	_
84	_	_	VBP	_	_	_
85	WT	wt	JJ	_	_	_
86	pH	ph	NN	_	_	_
87	5.6	5.6	CD	_	_	_
88	C	c	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	E.coli	e.coli	NNS	_	_	_
91	_	_	VBP	_	_	_
92	WT	wt	JJ	_	_	_
93	pH	ph	NN	_	_	_
94	7.2	7.2	CD	_	_	_
95	+15	+15	CD	_	_	_
96	%	%	NN	_	_	_
97	sucrose	sucrose	NN	_	_	_
98	A	a	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	E.coli	e.coli	NNS	_	_	_
101	_	_	VBP	_	_	_
102	WT	wt	JJ	_	_	_
103	pH	ph	NN	_	_	_
104	7.2	7.2	CD	_	_	_
105	+15	+15	CD	_	_	_
106	%	%	NN	_	_	_
107	sucrose	sucrose	NN	_	_	_
108	B	b	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	E.coli	e.coli	NNS	_	_	_
111	_	_	VBP	_	_	_
112	WT	wt	JJ	_	_	_
113	pH	ph	NN	_	_	_
114	7.2	7.2	CD	_	_	_
115	+15	+15	CD	_	_	_
116	%	%	NN	_	_	_
117	sucrose	sucrose	NN	_	_	_
118	C	c	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	Escherichia	escherichia	FW	Organism	_	_
121	coli	coli	FW	Organism	_	_
122	str	str	FW	_	_	_
123	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	genotype	genotype	NN	_	_	_
4	:	:	:	_	_	_
5	delta	delta	NN	_	_	_
6	_	_	CD	_	_	_
7	ompR	ompr	NN	GEN	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	genotype	genotype	NN	_	_	_
10	:	:	:	_	_	_
11	Wildtype	wildtype	JJ	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	∆	∆	CD	_	_	_
14	ompR	ompr	NN	GEN	_	_
15	pH	ph	NN	_	_	_
16	5.6	5.6	CD	_	_	_
17	A	a	DT	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	∆	∆	CD	_	_	_
20	ompR	ompr	NN	GEN	_	_
21	pH	ph	NN	_	_	_
22	5.6	5.6	CD	_	_	_
23	B	b	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	∆	∆	CD	_	_	_
26	ompR	ompr	NN	GEN	_	_
27	pH	ph	NN	_	_	_
28	5.6	5.6	CD	_	_	_
29	C	c	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	∆	∆	CD	_	_	_
32	ompR	ompr	NN	GEN	_	_
33	pH	ph	NN	_	_	_
34	7.2	7.2	CD	_	_	_
35	+15	+15	CD	_	_	_
36	%	%	NN	_	_	_
37	sucrose	sucrose	NN	_	_	_
38	A	a	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	∆	∆	CD	_	_	_
41	ompR	ompr	NN	GEN	_	_
42	pH	ph	NN	_	_	_
43	7.2	7.2	CD	_	_	_
44	+15	+15	CD	_	_	_
45	%	%	NN	_	_	_
46	sucrose	sucrose	NN	_	_	_
47	B	b	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	ph	ph	NN	_	_	_
50	:	:	:	_	_	_
51	5.6	5.6	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	ph	ph	NN	_	_	_
54	:	:	:	_	_	_
55	7.2	7.2	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
57	Raw	raw	NN	_	_	_
58	signal	signal	NN	_	_	_
59	data	datum	NNS	_	_	_
60	were	be	VBD	_	_	_
61	extracted	extract	VBN	_	_	_
62	from	from	IN	_	_	_
63	the	the	DT	_	_	_
64	TIFF	tiff	NN	_	_	_
65	image	image	NN	_	_	_
66	with	with	IN	_	_	_
67	Agilent	Agilent	NNP	_	_	_
68	Feature	Feature	NNP	_	_	_
69	Extraction	Extraction	NNP	_	_	_
70	Software	Software	NNP	_	_	_
71	-LRB-	-lrb-	-LRB-	_	_	_
72	V10	V10	NNP	_	_	_
73	.7.1.1	.7.1.1	CD	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	data	data	NN	_	_	_
3	analysis	analysis	NN	_	_	_
4	is	be	VBZ	_	_	_
5	done	do	VBN	_	_	_
6	using	use	VBG	_	_	_
7	a	a	DT	_	_	_
8	microarray	microarray	NN	_	_	_
9	specialized	specialized	JJ	_	_	_
10	analysis	analysis	NN	_	_	_
11	software	software	NN	_	_	_
12	,	,	,	_	_	_
13	Genespring	Genespring	NNP	_	_	_
14	GX	GX	NNP	_	_	_
15	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	this	this	DT	_	_	_
3	experiment	experiment	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	microarray	microarray	NN	_	_	_
7	type	type	NN	_	_	_
8	used	use	VBN	_	_	_
9	is	be	VBZ	_	_	_
10	a	a	DT	_	_	_
11	slide	slide	NN	_	_	_
12	having	have	VBG	_	_	_
13	8	8	CD	_	_	_
14	arrays	array	NNS	_	_	_
15	with	with	IN	_	_	_
16	60	60	CD	_	_	_
17	thousand	thousand	CD	_	_	_
18	features	feature	NNS	_	_	_
19	per	per	IN	_	_	_
20	array	array	NN	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	exact	exact	JJ	_	_	_
3	number	number	NN	_	_	_
4	of	of	IN	_	_	_
5	features	feature	NNS	_	_	_
6	in	in	IN	_	_	_
7	the	the	DT	_	_	_
8	each	each	DT	_	_	_
9	array	array	NN	_	_	_
10	,	,	,	_	_	_
11	inclusive	inclusive	NN	_	_	_
12	of	of	IN	_	_	_
13	control	control	NN	_	_	_
14	probes	probe	NNS	_	_	_
15	,	,	,	_	_	_
16	is	be	VBZ	_	_	_
17	10,751	10,751	CD	_	_	_
18	features	feature	NNS	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	microarray	microarray	NN	_	_	_
3	has	have	VBZ	_	_	_
4	a	a	DT	_	_	_
5	specific	specific	JJ	_	_	_
6	Agilent	Agilent	NNP	_	_	_
7	identifier	identifier	NN	_	_	_
8	called	call	VBD	_	_	_
9	an	a	DT	_	_	_
10	AMADID	amadid	NN	_	_	_
11	which	which	WDT	_	_	_
12	is	be	VBZ	_	_	_
13	used	use	VBN	_	_	_
14	to	to	TO	_	_	_
15	identify	identify	VB	_	_	_
16	what	what	WP	_	_	_
17	kind	kind	NN	_	_	_
18	of	of	IN	_	_	_
19	array	array	NN	_	_	_
20	is	be	VBZ	_	_	_
21	being	be	VBG	_	_	_
22	used	use	VBN	_	_	_
23	;	;	:	_	_	_
24	in	in	IN	_	_	_
25	this	this	DT	_	_	_
26	experiment	experiment	NN	_	_	_
27	the	the	DT	_	_	_
28	AMADID	AMADID	NNP	_	_	_
29	used	use	VBN	_	_	_
30	is	be	VBZ	_	_	_
31	the	the	DT	_	_	_
32	design	design	NN	_	_	_
33	ID	id	NN	_	_	_
34	020097	020097	CD	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	sucrose	sucrose	NN	_	_	_
7	status	status	NN	_	_	_
8	:	:	:	_	_	_
9	no	no	DT	_	_	_
10	sucrose	sucrose	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	sucrose	sucrose	NN	_	_	_
13	status	status	NN	_	_	_
14	:	:	:	_	_	_
15	with	with	IN	_	_	_
16	15	15	CD	_	_	_
17	%	%	NN	_	_	_
18	sucrose	sucrose	NN	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	Supplementary	Supplementary	NNP	_	_	_
21	files	file	VBZ	_	_	_
22	contain	contain	VBP	_	_	_
23	the	the	DT	_	_	_
24	following	following	NN	_	_	_
25	:	:	:	_	_	_
26	Raw	raw	NN	_	_	_
27	Signal	signal	NN	_	_	_
28	Values	value	NNS	_	_	_
29	:	:	:	_	_	_
30	The	the	DT	_	_	_
31	term	term	NN	_	_	_
32	``	``	``	_	_	_
33	raw	raw	JJ	_	_	_
34	''	''	''	_	_	_
35	signal	signal	NN	_	_	_
36	values	value	NNS	_	_	_
37	refer	refer	VBP	_	_	_
38	to	to	TO	_	_	_
39	the	the	DT	_	_	_
40	linear	linear	JJ	_	_	_
41	data	datum	NNS	_	_	_
42	after	after	IN	_	_	_
43	thresholding	threshold	VBG	_	_	_
44	and	and	CC	_	_	_
45	summarization	summarization	NN	_	_	_
46	Summarization	summarization	NN	_	_	_
47	is	be	VBZ	_	_	_
48	performed	perform	VBN	_	_	_
49	by	by	IN	_	_	_
50	computing	compute	VBG	_	_	_
51	the	the	DT	_	_	_
52	geometric	geometric	JJ	_	_	_
53	mean	mean	NN	_	_	_
54	.	.	.	_	_	_

1	Raw	raw	NN	_	_	_
2	data	datum	NNS	_	_	_
3	filtered	filter	VBN	_	_	_
4	on	on	IN	_	_	_
5	Expression	expression	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	20.0	20.0	CD	_	_	_
8	-	-	:	_	_	_
9	343943.344	343943.344	CD	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	•	•	SYM	_	_	_
12	Normalized	normalize	VBN	_	_	_
13	Signal	signal	NN	_	_	_
14	Values	value	NNS	_	_	_
15	:	:	:	_	_	_
16	``	``	``	_	_	_
17	Normalized	normalize	VBN	_	_	_
18	''	''	''	_	_	_
19	value	value	NN	_	_	_
20	is	be	VBZ	_	_	_
21	the	the	DT	_	_	_
22	value	value	NN	_	_	_
23	generated	generate	VBN	_	_	_
24	after	after	IN	_	_	_
25	log	log	NN	_	_	_
26	transformation	transformation	NN	_	_	_
27	and	and	CC	_	_	_
28	normalization	normalization	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Shift	shift	NN	_	_	_
31	to	to	TO	_	_	_
32	75	75	CD	_	_	_
33	percentile	percentile	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	and	and	CC	_	_	_
36	baseline	baseline	NN	_	_	_
37	transformation	transformation	NN	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	total	total	JJ	_	_	_
4	RNA	rna	NN	_	_	_
5	was	be	VBD	_	_	_
6	isolated	isolate	VBN	_	_	_
7	using	use	VBG	_	_	_
8	an	a	DT	_	_	_
9	RNeasy	rneasy	NN	_	_	_
10	mini	minus	NNS	_	_	_
11	kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Qiagen	qiagen	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	WT	WT	NNP	_	_	_
3	pH	ph	NN	_	_	_
4	5.6	5.6	CD	_	_	_
5	A	a	DT	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	WT	wt	NN	_	_	_
8	pH	ph	NN	_	_	_
9	5.6	5.6	CD	_	_	_
10	B	b	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	WT	wt	NN	_	_	_
13	pH	ph	NN	_	_	_
14	5.6	5.6	CD	_	_	_
15	C	c	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	WT	wt	JJ	_	_	_
18	pH	ph	NN	_	_	_
19	7.2	7.2	CD	_	_	_
20	+15	+15	CD	_	_	_
21	%	%	NN	_	_	_
22	sucrose	sucrose	NN	_	_	_
23	A	a	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	WT	wt	JJ	_	_	_
26	pH	ph	NN	_	_	_
27	7.2	7.2	CD	_	_	_
28	+15	+15	CD	_	_	_
29	%	%	NN	_	_	_
30	sucrose	sucrose	NN	_	_	_
31	B	b	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	WT	wt	JJ	_	_	_
34	pH	ph	NN	_	_	_
35	7.2	7.2	CD	_	_	_
36	+15	+15	CD	_	_	_
37	%	%	NN	_	_	_
38	sucrose	sucrose	NN	_	_	_
39	C	c	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	170	170	CD	_	_	_
42	μl	μl	NN	_	_	_
43	were	be	VBD	_	_	_
44	taken	take	VBN	_	_	_
45	from	from	IN	_	_	_
46	each	each	DT	_	_	_
47	of	of	IN	_	_	_
48	four	four	CD	_	_	_
49	wells	well	NNS	_	_	_
50	per	per	IN	_	_	_
51	time	time	NN	_	_	_
52	point	point	NN	_	_	_
53	and	and	CC	_	_	_
54	collected	collect	VBN	_	_	_
55	into	into	IN	_	_	_
56	a	a	DT	_	_	_
57	fresh	fresh	JJ	_	_	_
58	tube	tube	NN	_	_	_
59	were	be	VBD	_	_	_
60	1.360	1.360	CD	_	_	_
61	ml	ml	NN	_	_	_
62	of	of	IN	_	_	_
63	RNA	rna	NN	_	_	_
64	protection	protection	NN	_	_	_
65	buffer	buffer	NN	_	_	_
66	had	have	VBD	_	_	_
67	previously	previously	RB	_	_	_
68	been	be	VBN	_	_	_
69	added	add	VBN	_	_	_
70	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	left	leave	VBN	_	_	_
4	for	for	IN	_	_	_
5	5	5	CD	_	_	_
6	minutes	minute	NNS	_	_	_
7	at	at	IN	_	_	_
8	RT	rt	NN	_	_	_
9	and	and	CC	_	_	_
10	then	then	RB	_	_	_
11	centrifuged	centrifuge	VBD	_	_	_
12	at	at	IN	_	_	_
13	4	4	CD	_	_	_
14	°C	°c	NN	_	_	_
15	at	at	IN	_	_	_
16	maximum	maximum	JJ	_	_	_
17	speed	speed	NN	_	_	_
18	.	.	.	_	_	_

1	Supernatant	supernatant	NN	_	_	_
2	was	be	VBD	_	_	_
3	discarded	discard	VBN	_	_	_
4	and	and	CC	_	_	_
5	pellets	pellet	NNS	_	_	_
6	frozen	freeze	VBN	_	_	_
7	at	at	IN	_	_	_
8	-20	-20	CD	_	_	_
9	°C	°c	NN	_	_	_
10	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	extraction	extraction	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	using	use	VBG	_	_	_
6	RNeasy	RNeasy	NNP	_	_	_
7	Mini	Mini	NNP	_	_	_
8	Kit	kit	NN	_	_	_
9	from	from	IN	_	_	_
10	Qiagen	Qiagen	NNP	_	_	_
11	-LSB-	-lsb-	-LRB-	_	_	_
12	Cat	Cat	NNP	_	_	_
13	No	No	NNP	_	_	_
14	74104	74104	NN	_	_	_
15	-RSB-	-rsb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	remove	remove	VB	_	_	_
3	possible	possible	JJ	_	_	_
4	traces	trace	NNS	_	_	_
5	of	of	IN	_	_	_
6	genomic	genomic	JJ	_	_	_
7	DNA	dna	NN	_	_	_
8	contamination	contamination	NN	_	_	_
9	,	,	,	_	_	_
10	2	2	CD	_	_	_
11	μg	μg	NN	_	_	_
12	of	of	IN	_	_	_
13	each	each	DT	_	_	_
14	sample	sample	NN	_	_	_
15	were	be	VBD	_	_	_
16	treated	treat	VBN	_	_	_
17	for	for	IN	_	_	_
18	a	a	DT	_	_	_
19	second	second	JJ	_	_	_
20	time	time	NN	_	_	_
21	with	with	IN	_	_	_
22	DNAseI	dnasei	NN	_	_	_
23	from	from	IN	_	_	_
24	Qiagen	Qiagen	NNP	_	_	_
25	-LSB-	-lsb-	-LRB-	_	_	_
26	Cat	Cat	NNP	_	_	_
27	No	No	NNP	_	_	_
28	79254	79254	NN	_	_	_
29	-RSB-	-rsb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	quality	quality	NN	_	_	_
4	and	and	CC	_	_	_
5	integrity	integrity	NN	_	_	_
6	was	be	VBD	_	_	_
7	assessed	assess	VBN	_	_	_
8	using	use	VBG	_	_	_
9	Agilent	Agilent	NNP	_	_	_
10	2100	2100	CD	_	_	_
11	Bioanalyzer	Bioanalyzer	NNP	_	_	_
12	and	and	CC	_	_	_
13	Agilent	Agilent	NNP	_	_	_
14	RNA	rna	NN	_	_	_
15	6000	6000	CD	_	_	_
16	Nano	Nano	NNP	_	_	_
17	kit	kit	NN	_	_	_
18	-LSB-	-lsb-	-LRB-	_	_	_
19	Cat	cat	NN	_	_	_
20	No	no	DT	_	_	_
21	5067-1511	5067-1511	NN	_	_	_
22	-RSB-	-rsb-	-RRB-	_	_	_
23	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	had	have	VBD	_	_	_
3	an	a	DT	_	_	_
4	average	average	JJ	_	_	_
5	RIN	rin	NN	_	_	_
6	of	of	IN	_	_	_
7	9.5	9.5	CD	_	_	_
8	.	.	.	_	_	_

1	Enrichment	enrichment	NN	_	_	_
2	of	of	IN	_	_	_
3	mRNA	mrna	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	using	use	VBG	_	_	_
7	MicrobExpress	MicrobExpress	NNP	_	_	_
8	rRNA	rrna	NN	_	_	_
9	removal	removal	NN	_	_	_
10	kit	kit	NN	_	_	_
11	from	from	IN	_	_	_
12	Thermo	Thermo	NNP	_	_	_
13	Scientific	Scientific	NNP	_	_	_
14	-LSB-	-lsb-	-LRB-	_	_	_
15	Cat	Cat	NNP	_	_	_
16	No	No	NNP	_	_	_
17	AM1905	am1905	NN	_	_	_
18	-RSB-	-rsb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	Successful	successful	JJ	_	_	_
2	rRNA	rrna	NN	_	_	_
3	depletion	depletion	NN	_	_	_
4	was	be	VBD	_	_	_
5	assessed	assess	VBN	_	_	_
6	with	with	IN	_	_	_
7	analysis	analysis	NN	_	_	_
8	on	on	IN	_	_	_
9	Bioanalyzer	Bioanalyzer	NNP	_	_	_
10	.	.	.	_	_	_

1	Retrotranscription	retrotranscription	NN	_	_	_
2	was	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	performed	perform	VBN	_	_	_
5	starting	start	VBG	_	_	_
6	from	from	IN	_	_	_
7	50	50	CD	_	_	_
8	ng	ng	NN	_	_	_
9	total	total	JJ	_	_	_
10	enriched	enriched	JJ	_	_	_
11	mRNA	mrna	NN	_	_	_
12	using	use	VBG	_	_	_
13	Tetro	Tetro	NNP	_	_	_
14	cDNA	cdna	NN	_	_	_
15	synthesis	synthesis	NN	_	_	_
16	kit	kit	NN	_	_	_
17	from	from	IN	_	_	_
18	Bioline	Bioline	NNP	_	_	_
19	-LSB-	-lsb-	-LRB-	_	_	_
20	Cat	Cat	NNP	_	_	_
21	No	No	NNP	_	_	_
22	BIO-65043	bio-65043	NN	_	_	_
23	-RSB-	-rsb-	-RRB-	_	_	_
24	and	and	CC	_	_	_
25	6	6	CD	_	_	_
26	μl	μl	NN	_	_	_
27	of	of	IN	_	_	_
28	Random	Random	NNP	_	_	_
29	Hexamers	Hexamers	NNPS	_	_	_
30	-LSB-	-lsb-	-LRB-	_	_	_
31	Cat	Cat	NNP	_	_	_
32	No	No	NNP	_	_	_
33	BIO-38028	bio-38028	NN	_	_	_
34	-RSB-	-rsb-	-RRB-	_	_	_
35	per	per	IN	_	_	_
36	reaction	reaction	NN	_	_	_
37	.	.	.	_	_	_

1	Second	second	JJ	_	_	_
2	cDNA	cdna	NN	_	_	_
3	synthesis	synthesis	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	adding	add	VBG	_	_	_
7	to	to	TO	_	_	_
8	the	the	DT	_	_	_
9	first	first	JJ	_	_	_
10	strand	strand	NN	_	_	_
11	synthesis	synthesis	NN	_	_	_
12	mix	mix	NN	_	_	_
13	5	5	CD	_	_	_
14	μl	μl	NN	_	_	_
15	of	of	IN	_	_	_
16	Second	second	JJ	_	_	_
17	strand	strand	NN	_	_	_
18	synthesis	synthesis	NN	_	_	_
19	buffer	buffer	NN	_	_	_
20	-LSB-	-lsb-	-LRB-	_	_	_
21	Cat	cat	NN	_	_	_
22	No	no	DT	_	_	_
23	B6117S	b6117s	NN	_	_	_
24	-RSB-	-rsb-	-RRB-	_	_	_
25	,	,	,	_	_	_
26	3	3	CD	_	_	_
27	μl	μl	NN	_	_	_
28	of	of	IN	_	_	_
29	dNTPs	dntps	NN	_	_	_
30	-LSB-	-lsb-	-LRB-	_	_	_
31	Cat	cat	NN	_	_	_
32	No	no	DT	_	_	_
33	N0446S	n0446s	NN	_	_	_
34	-RSB-	-rsb-	-RRB-	_	_	_
35	,	,	,	_	_	_
36	2μl	2μl	NN	_	_	_
37	of	of	IN	_	_	_
38	RNAseH	rnaseh	NN	_	_	_
39	-LSB-	-lsb-	-LRB-	_	_	_
40	Cat	cat	NN	_	_	_
41	No	no	DT	_	_	_
42	M0297L	m0297l	NN	_	_	_
43	-RSB-	-rsb-	-RRB-	_	_	_
44	all	all	DT	_	_	_
45	from	from	IN	_	_	_
46	NEB	NEB	NNP	_	_	_
47	,	,	,	_	_	_
48	2	2	CD	_	_	_
49	μl	μl	NN	_	_	_
50	of	of	IN	_	_	_
51	Polymerase	polymerase	NN	_	_	_
52	I	I	PRP	_	_	_
53	from	from	IN	_	_	_
54	Thermo	Thermo	NNP	_	_	_
55	Scientific	Scientific	NNP	_	_	_
56	-LSB-	-lsb-	-LRB-	_	_	_
57	Cat	Cat	NNP	_	_	_
58	No	No	NNP	_	_	_
59	18010025	18010025	CD	_	_	_
60	-RSB-	-rsb-	-RRB-	_	_	_
61	and	and	CC	_	_	_
62	18	18	CD	_	_	_
63	μl	μl	NN	_	_	_
64	of	of	IN	_	_	_
65	water	water	NN	_	_	_
66	,	,	,	_	_	_
67	per	per	IN	_	_	_
68	reaction	reaction	NN	_	_	_
69	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	incubated	incubate	VBN	_	_	_
4	at	at	IN	_	_	_
5	16	16	CD	_	_	_
6	°C	°c	NN	_	_	_
7	for	for	IN	_	_	_
8	2.5	2.5	CD	_	_	_
9	h.	h.	NN	_	_	_
10	Purification	purification	NN	_	_	_
11	of	of	IN	_	_	_
12	cDNA	cdna	NN	_	_	_
13	was	be	VBD	_	_	_
14	performed	perform	VBN	_	_	_
15	using	use	VBG	_	_	_
16	MiniElute	MiniElute	NNP	_	_	_
17	PCR	pcr	NN	_	_	_
18	purification	purification	NN	_	_	_
19	kit	kit	NN	_	_	_
20	-LSB-	-lsb-	-LRB-	_	_	_
21	Cat	cat	NN	_	_	_
22	No	no	DT	_	_	_
23	28004	28004	NN	_	_	_
24	-RSB-	-rsb-	-RRB-	_	_	_
25	with	with	IN	_	_	_
26	final	final	JJ	_	_	_
27	elution	elution	NN	_	_	_
28	in	in	IN	_	_	_
29	10	10	CD	_	_	_
30	μl	μl	NN	_	_	_
31	of	of	IN	_	_	_
32	DEPC-treated	depc-treated	JJ	_	_	_
33	free	free	JJ	_	_	_
34	water	water	NN	_	_	_
35	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	was	be	VBD	_	_	_
3	quantified	quantify	VBN	_	_	_
4	using	use	VBG	_	_	_
5	a	a	DT	_	_	_
6	Qubit	qubit	NN	_	_	_
7	fluorometer	fluorometer	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Invitrogen	invitrogen	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	After	after	IN	_	_	_
3	60	60	CD	_	_	_
4	minutes	minute	NNS	_	_	_
5	into	into	IN	_	_	_
6	the	the	DT	_	_	_
7	incubation	incubation	NN	_	_	_
8	,	,	,	_	_	_
9	the	the	DT	_	_	_
10	plate	plate	NN	_	_	_
11	was	be	VBD	_	_	_
12	briefly	briefly	RB	_	_	_
13	removed	remove	VBN	_	_	_
14	so	so	RB	_	_	_
15	inducer	inducer	NN	_	_	_
16	could	could	MD	_	_	_
17	be	be	VB	_	_	_
18	added	add	VBN	_	_	_
19	to	to	TO	_	_	_
20	wells	well	NNS	_	_	_
21	,	,	,	_	_	_
22	and	and	CC	_	_	_
23	this	this	DT	_	_	_
24	time	time	NN	_	_	_
25	point	point	NN	_	_	_
26	was	be	VBD	_	_	_
27	set	set	VBN	_	_	_
28	as	as	IN	_	_	_
29	time	time	NN	_	_	_
30	0	0	CD	_	_	_
31	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	instead	instead	RB	_	_	_
4	removed	remove	VBN	_	_	_
5	from	from	IN	_	_	_
6	wells	well	NNS	_	_	_
7	at	at	IN	_	_	_
8	15	15	CD	_	_	_
9	and	and	CC	_	_	_
10	60	60	CD	_	_	_
11	minutes	minute	NNS	_	_	_
12	after	after	IN	_	_	_
13	induction	induction	NN	_	_	_
14	for	for	IN	_	_	_
15	processing	processing	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	B10	b10	NN	_	_	_
3	DH10BGFP	dh10bgfp	NN	_	_	_
4	_	_	CD	_	_	_
5	pSB1C3	psb1c3	NN	_	_	_
6	_	_	NN	_	_	_
7	2	2	CD	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	B17	b17	NN	_	_	_
10	MG1655GFP	mg1655gfp	NN	_	_	_
11	_	_	CD	_	_	_
12	pSB1C3	psb1c3	NN	_	_	_
13	_	_	NN	_	_	_
14	2	2	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	B22	b22	NN	_	_	_
17	MG1655GFP	mg1655gfp	NN	_	_	_
18	_	_	CD	_	_	_
19	pSB1C3	psb1c3	NN	_	_	_
20	_	_	CD	_	_	_
21	H3	h3	NN	_	_	_
22	_	_	NN	_	_	_
23	2	2	CD	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	B26	b26	NN	_	_	_
26	MG1655GFP	mg1655gfp	NN	_	_	_
27	_	_	CD	_	_	_
28	Lux	lux	FW	_	_	_
29	_	_	FW	_	_	_
30	2	2	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	B3	b3	NN	_	_	_
33	DH10BGFP	dh10bgfp	NN	_	_	_
34	_	_	CD	_	_	_
35	pSB1C3	psb1c3	NN	_	_	_
36	_	_	NN	_	_	_
37	2	2	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	B4	b4	NN	_	_	_
40	DH10BGFP	dh10bgfp	NN	_	_	_
41	_	_	CD	_	_	_
42	pLys	ply	VBZ	_	_	_
43	_	_	SYM	_	_	_
44	2	2	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	B7	b7	NN	_	_	_
47	DH10BGFP	dh10bgfp	NN	_	_	_
48	_	_	CD	_	_	_
49	pD864	pd864	NN	_	_	_
50	_	_	NN	_	_	_
51	2	2	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	B9	b9	NN	_	_	_
54	DH10BGFP	dh10bgfp	NN	_	_	_
55	_	_	CD	_	_	_
56	pLys	ply	VBZ	_	_	_
57	_	_	SYM	_	_	_
58	M1	m1	NN	_	_	_
59	_	_	NN	_	_	_
60	2	2	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
62	Bacterial	bacterial	JJ	_	_	_
63	cells	cell	NNS	_	_	_
64	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
65	E.	E.	NNP	_	_	_
66	coli	coli	NN	_	_	_
67	cells	cell	NNS	_	_	_
68	with	with	IN	_	_	_
69	construct	construct	NN	_	_	_
70	and	and	CC	_	_	_
71	control	control	NN	_	_	_
72	plasmids	plasmid	NNS	_	_	_
73	were	be	VBD	_	_	_
74	grown	grow	VBN	_	_	_
75	at	at	IN	_	_	_
76	37	37	CD	_	_	_
77	°C	°c	NN	_	_	_
78	overnight	overnight	JJ	_	_	_
79	with	with	IN	_	_	_
80	aeration	aeration	NN	_	_	_
81	in	in	IN	_	_	_
82	a	a	DT	_	_	_
83	shaking	shake	VBG	_	_	_
84	incubator	incubator	NN	_	_	_
85	in	in	IN	_	_	_
86	5	5	CD	_	_	_
87	ml	ml	NN	_	_	_
88	of	of	IN	_	_	_
89	defined	define	VBN	_	_	_
90	supplemented	supplement	VBN	_	_	_
91	M9	m9	NN	_	_	_
92	medium	medium	NN	_	_	_
93	with	with	IN	_	_	_
94	the	the	DT	_	_	_
95	appropriate	appropriate	JJ	_	_	_
96	antibiotic	antibiotic	JJ	_	_	_
97	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	the	the	DT	_	_	_
3	morning	morning	NN	_	_	_
4	,	,	,	_	_	_
5	60	60	CD	_	_	_
6	μl	μl	NN	_	_	_
7	of	of	IN	_	_	_
8	each	each	DT	_	_	_
9	sample	sample	NN	_	_	_
10	were	be	VBD	_	_	_
11	diluted	dilute	VBN	_	_	_
12	into	into	IN	_	_	_
13	3	3	CD	_	_	_
14	ml	ml	NN	_	_	_
15	of	of	IN	_	_	_
16	fresh	fresh	JJ	_	_	_
17	medium	medium	NN	_	_	_
18	and	and	CC	_	_	_
19	grown	grow	VBN	_	_	_
20	at	at	IN	_	_	_
21	37	37	CD	_	_	_
22	°C	°c	NN	_	_	_
23	with	with	IN	_	_	_
24	shaking	shake	VBG	_	_	_
25	for	for	IN	_	_	_
26	another	another	DT	_	_	_
27	hour	hour	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	outgrowth	outgrowth	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	200	200	CD	_	_	_
2	μl	μl	NN	_	_	_
3	of	of	IN	_	_	_
4	each	each	DT	_	_	_
5	sample	sample	NN	_	_	_
6	were	be	VBD	_	_	_
7	then	then	RB	_	_	_
8	transferred	transfer	VBN	_	_	_
9	in	in	IN	_	_	_
10	8	8	CD	_	_	_
11	wells	well	NNS	_	_	_
12	of	of	IN	_	_	_
13	a	a	DT	_	_	_
14	96-well	96-well	JJ	_	_	_
15	plate	plate	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Costar	costar	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	at	at	IN	_	_	_
20	approximately	approximately	RB	_	_	_
21	0.1	0.1	CD	_	_	_
22	OD	od	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	600	600	CD	_	_	_
25	nm	nm	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	placed	place	VBN	_	_	_
5	in	in	IN	_	_	_
6	a	a	DT	_	_	_
7	Synergy	synergy	NN	_	_	_
8	HT	ht	NN	_	_	_
9	Microplate	Microplate	NNP	_	_	_
10	Reader	Reader	NNP	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	BioTek	BioTek	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	and	and	CC	_	_	_
15	incubated	incubate	VBN	_	_	_
16	at	at	IN	_	_	_
17	37	37	CD	_	_	_
18	°C	°c	NN	_	_	_
19	with	with	IN	_	_	_
20	orbital	orbital	JJ	_	_	_
21	shaking	shake	VBG	_	_	_
22	at	at	IN	_	_	_
23	1,000	1,000	CD	_	_	_
24	rpm	rpm	NN	_	_	_
25	for	for	IN	_	_	_
26	1	1	CD	_	_	_
27	h	h	NN	_	_	_
28	,	,	,	_	_	_
29	performing	perform	VBG	_	_	_
30	measurements	measurement	NNS	_	_	_
31	of	of	IN	_	_	_
32	GFP	gfp	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	excitation	excitation	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	ex	ex	FW	_	_	_
37	.	.	.	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_

1	,	,	,	_	_	_
2	485	485	CD	_	_	_
3	nm	nm	NN	_	_	_
4	;	;	:	_	_	_
5	emission	emission	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	em	em	NN	_	_	_
8	.	.	.	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_

1	,	,	,	_	_	_
2	528	528	CD	_	_	_
3	nm	nm	NN	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	and	and	CC	_	_	_
6	OD	od	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	600	600	CD	_	_	_
9	nm	nm	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	every	every	DT	_	_	_
12	15	15	CD	_	_	_
13	minutes	minute	NNS	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	G21	g21	NN	_	_	_
6	MG1655GFP	mg1655gfp	NN	_	_	_
7	_	_	CD	_	_	_
8	pD864	pd864	NN	_	_	_
9	_	_	NN	_	_	_
10	3	3	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	G23	g23	NN	_	_	_
13	MG1655GFP	mg1655gfp	NN	_	_	_
14	_	_	CD	_	_	_
15	pLys	ply	VBZ	_	_	_
16	_	_	SYM	_	_	_
17	M1	m1	NN	_	_	_
18	_	_	NN	_	_	_
19	3	3	CD	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	G28	g28	NN	_	_	_
22	MG1655GFP	mg1655gfp	NN	_	_	_
23	_	_	CD	_	_	_
24	pD864	pd864	NN	_	_	_
25	_	_	NN	_	_	_
26	3	3	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	G29	g29	NN	_	_	_
29	DH10BGFP	dh10bgfp	NN	_	_	_
30	_	_	CD	_	_	_
31	None	none	NN	_	_	_
32	_	_	NN	_	_	_
33	3	3	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	G5	g5	NN	_	_	_
36	DH10BGFP	dh10bgfp	NN	_	_	_
37	_	_	CD	_	_	_
38	Lux	lux	FW	_	_	_
39	_	_	FW	_	_	_
40	3	3	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	G6	g6	NN	_	_	_
43	DH10BGFP	dh10bgfp	NN	_	_	_
44	_	_	CD	_	_	_
45	pD864	pd864	NN	_	_	_
46	_	_	CD	_	_	_
47	LacZ	lacz	NN	_	_	_
48	_	_	SYM	_	_	_
49	3	3	CD	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	Genome	Genome	NNP	_	_	_
52	_	_	NNP	_	_	_
53	build	build	VB	_	_	_
54	:	:	:	_	_	_
55	Samples	sample	NNS	_	_	_
56	from	from	IN	_	_	_
57	strain	strain	NN	_	_	_
58	DH10BGFP	dh10bgfp	NN	_	_	_
59	were	be	VBD	_	_	_
60	mapped	map	VBN	_	_	_
61	to	to	TO	_	_	_
62	the	the	DT	_	_	_
63	reference	reference	NN	_	_	_
64	geneome	geneome	NN	_	_	_
65	Escherichia	escherichia	FW	Organism	_	_
66	coli	coli	FW	Organism	_	_
67	str	str	FW	_	_	_
68	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	DH10B	dh10b	NN	_	_	_
2	,	,	,	_	_	_
3	assembly	assembly	NN	_	_	_
4	ASM1942v1	asm1942v1	NN	_	_	_
5	.31	.31	CD	_	_	_
6	complemented	complement	VBN	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	GFP	gfp	NN	_	_	_
10	sequence	sequence	NN	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	sequence	sequence	NN	_	_	_
15	of	of	IN	_	_	_
16	corresponding	corresponding	JJ	_	_	_
17	synthetic	synthetic	JJ	_	_	_
18	circuit	circuit	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	Samples	sample	NNS	_	_	_
7	from	from	IN	_	_	_
8	strain	strain	NN	_	_	_
9	MG1655GFP	mg1655gfp	NN	_	_	_
10	were	be	VBD	_	_	_
11	mapped	map	VBN	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	reference	reference	NN	_	_	_
15	geneome	geneome	NN	_	_	_
16	Escherichia	escherichia	FW	Organism	_	_
17	coli	coli	FW	Organism	_	_
18	str	str	FW	_	_	_
19	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	,	,	,	_	_	_
3	assembly	assembly	NN	_	_	_
4	ASM584v2	asm584v2	NN	_	_	_
5	.31	.31	CD	_	_	_
6	complemented	complement	VBN	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	GFP	gfp	NN	_	_	_
10	sequence	sequence	NN	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	sequence	sequence	NN	_	_	_
15	of	of	IN	_	_	_
16	corresponding	corresponding	JJ	_	_	_
17	synthetic	synthetic	JJ	_	_	_
18	circuit	circuit	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Library	Library	NNP	_	_	_
3	preparation	preparation	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	Nextera	Nextera	NNP	_	_	_
9	XT	XT	NNP	_	_	_
10	kit	kit	NN	_	_	_
11	from	from	IN	_	_	_
12	Illumina	Illumina	NNP	_	_	_
13	-LSB-	-lsb-	-LRB-	_	_	_
14	Cat	Cat	NNP	_	_	_
15	No	No	NNP	_	_	_
16	FC-131-1096	fc-131-1096	NN	_	_	_
17	-RSB-	-rsb-	-RRB-	_	_	_
18	starting	start	VBG	_	_	_
19	from	from	IN	_	_	_
20	1	1	CD	_	_	_
21	ng	ng	NN	_	_	_
22	of	of	IN	_	_	_
23	total	total	JJ	_	_	_
24	cDNA	cdna	NN	_	_	_
25	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	original	original	JJ	_	_	_
3	protocol	protocol	NN	_	_	_
4	was	be	VBD	_	_	_
5	modified	modify	VBN	_	_	_
6	where	where	WRB	_	_	_
7	3	3	CD	_	_	_
8	min	min	NN	_	_	_
9	tagmentation	tagmentation	NN	_	_	_
10	and	and	CC	_	_	_
11	13	13	CD	_	_	_
12	cycles	cycle	NNS	_	_	_
13	of	of	IN	_	_	_
14	step-limited	step-limited	JJ	_	_	_
15	PCR	pcr	NN	_	_	_
16	were	be	VBD	_	_	_
17	used	use	VBN	_	_	_
18	.	.	.	_	_	_

1	Ampure	ampure	JJ	_	_	_
2	beads	bead	NNS	_	_	_
3	from	from	IN	_	_	_
4	Beckman	Beckman	NNP	_	_	_
5	Coulter	Coulter	NNP	_	_	_
6	-LSB-	-lsb-	-LRB-	_	_	_
7	Cat	Cat	NNP	_	_	_
8	No	No	NNP	_	_	_
9	A63880	a63880	NN	_	_	_
10	-RSB-	-rsb-	-RRB-	_	_	_
11	were	be	VBD	_	_	_
12	used	use	VBN	_	_	_
13	for	for	IN	_	_	_
14	library	library	NN	_	_	_
15	purification	purification	NN	_	_	_
16	.	.	.	_	_	_

1	Library	Library	NNP	_	_	_
2	quality	quality	NN	_	_	_
3	assessment	assessment	NN	_	_	_
4	and	and	CC	_	_	_
5	quantification	quantification	NN	_	_	_
6	was	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	with	with	IN	_	_	_
9	Agilent	Agilent	NNP	_	_	_
10	2100	2100	CD	_	_	_
11	Bioanalyzer	Bioanalyzer	NNP	_	_	_
12	and	and	CC	_	_	_
13	Agilent	Agilent	NNP	_	_	_
14	high	high	JJ	_	_	_
15	sensitivity	sensitivity	NN	_	_	_
16	DNA	dna	NN	_	_	_
17	analysis	analysis	NN	_	_	_
18	kit	kit	NN	_	_	_
19	-LSB-	-lsb-	-LRB-	_	_	_
20	Cat	cat	NN	_	_	_
21	No	no	DT	_	_	_
22	5067-4626	5067-4626	CD	_	_	_
23	-RSB-	-rsb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	Finally	finally	RB	_	_	_
2	all	all	DT	_	_	_
3	90	90	CD	_	_	_
4	samples	sample	NNS	_	_	_
5	were	be	VBD	_	_	_
6	pooled	pool	VBN	_	_	_
7	together	together	RB	_	_	_
8	in	in	IN	_	_	_
9	the	the	DT	_	_	_
10	same	same	JJ	_	_	_
11	reaction	reaction	NN	_	_	_
12	tube	tube	NN	_	_	_
13	at	at	IN	_	_	_
14	a	a	DT	_	_	_
15	final	final	JJ	_	_	_
16	concentration	concentration	NN	_	_	_
17	of	of	IN	_	_	_
18	1	1	CD	_	_	_
19	nM	nm	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Numer	Numer	NNP	_	_	_
3	of	of	IN	_	_	_
4	reads	read	VBZ	_	_	_
5	per	per	IN	_	_	_
6	gene	gene	NN	_	_	_
7	were	be	VBD	_	_	_
8	counted	count	VBN	_	_	_
9	using	use	VBG	_	_	_
10	Bioconductor	Bioconductor	NNP	_	_	_
11	Rsubread	Rsubread	NNP	_	_	_
12	package	package	NN	_	_	_
13	v1	v1	NN	_	_	_
14	.12.6	.12.6	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
16	paired	paired	JJ	_	_	_
17	end	end	NN	_	_	_
18	sequencing	sequencing	NN	_	_	_
19	with	with	IN	_	_	_
20	Illumina	Illumina	NNP	_	_	_
21	HiSeq	HiSeq	NNP	_	_	_
22	2500	2500	CD	_	_	_
23	Sequencer	Sequencer	NNP	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	plasmid	plasmid	NN	_	_	_
26	:	:	:	_	_	_
27	None	none	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	plasmid	plasmid	NN	_	_	_
30	:	:	:	_	_	_
31	PD864	pd864	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	plasmid	plasmid	NN	_	_	_
34	:	:	:	_	_	_
35	PLYS	plys	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	plasmid	plasmid	NN	_	_	_
38	:	:	:	_	_	_
39	PSB1C3	psb1c3	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	R11	r11	NN	_	_	_
42	DH10BGFP	dh10bgfp	NN	_	_	_
43	_	_	CD	_	_	_
44	pLys	ply	VBZ	_	_	_
45	_	_	SYM	_	_	_
46	1	1	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	R16	r16	NN	_	_	_
49	MG1655GFP	mg1655gfp	NN	_	_	_
50	_	_	CD	_	_	_
51	pLys	ply	VBZ	_	_	_
52	_	_	SYM	_	_	_
53	M1	m1	NN	_	_	_
54	_	_	NN	_	_	_
55	1	1	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	R19	r19	NN	_	_	_
58	MG1655GFP	mg1655gfp	NN	_	_	_
59	_	_	CD	_	_	_
60	Lux	lux	FW	_	_	_
61	_	_	FW	_	_	_
62	1	1	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	R26	r26	NN	_	_	_
65	MG1655GFP	mg1655gfp	NN	_	_	_
66	_	_	CD	_	_	_
67	Lux	lux	FW	_	_	_
68	_	_	FW	_	_	_
69	1	1	CD	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	R27	r27	NN	_	_	_
72	MG1655GFP	mg1655gfp	NN	_	_	_
73	_	_	CD	_	_	_
74	pD864	pd864	NN	_	_	_
75	_	_	CD	_	_	_
76	LacZ	lacz	NN	_	_	_
77	_	_	NN	_	_	_
78	1	1	CD	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	R29	r29	NN	_	_	_
81	DH10BGFP	dh10bgfp	NN	_	_	_
82	_	_	CD	_	_	_
83	None	none	NN	_	_	_
84	_	_	NN	_	_	_
85	1	1	CD	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	R2	r2	NN	_	_	_
88	DH10BGFP	dh10bgfp	NN	_	_	_
89	_	_	CD	_	_	_
90	pLys	ply	VBZ	_	_	_
91	_	_	SYM	_	_	_
92	M1	m1	NN	_	_	_
93	_	_	NN	_	_	_
94	1	1	CD	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	R3	r3	NN	_	_	_
97	DH10BGFP	dh10bgfp	NN	_	_	_
98	_	_	CD	_	_	_
99	pSB1C3	psb1c3	NN	_	_	_
100	_	_	NN	_	_	_
101	1	1	CD	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	R6	r6	NN	_	_	_
104	DH10BGFP	dh10bgfp	NN	_	_	_
105	_	_	CD	_	_	_
106	pD864	pd864	NN	_	_	_
107	_	_	CD	_	_	_
108	LacZ	lacz	NN	_	_	_
109	_	_	NN	_	_	_
110	1	1	CD	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	RNA-Seq	rna-seq	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	Sequenced	sequence	VBN	_	_	_
115	reads	read	VBZ	_	_	_
116	were	be	VBD	_	_	_
117	trimmed	trim	VBN	_	_	_
118	for	for	IN	_	_	_
119	adaptor	adaptor	NN	_	_	_
120	sequence	sequence	NN	_	_	_
121	and	and	CC	_	_	_
122	low-quality	low-quality	JJ	_	_	_
123	sequence	sequence	NN	_	_	_
124	using	use	VBG	_	_	_
125	TrimGalore	trimgalore	NN	_	_	_
126	version	version	NN	_	_	_
127	0.4.1	0.4.1	CD	_	_	_
128	,	,	,	_	_	_
129	then	then	RB	_	_	_
130	mapped	map	VBD	_	_	_
131	to	to	TO	_	_	_
132	mm8	mm8	VB	_	_	_
133	whole	whole	JJ	_	_	_
134	genome	genome	NN	_	_	_
135	using	use	VBG	_	_	_
136	bwa	bwa	NN	_	_	_
137	mem	mem	NN	_	_	_
138	version	version	NN	_	_	_
139	0.7.12	0.7.12	CD	_	_	_
140	with	with	IN	_	_	_
141	default	default	NN	_	_	_
142	parameters	parameter	NNS	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	strain	strain	NN	_	_	_
145	:	:	:	_	_	_
146	DH10BGFP	dh10bgfp	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	strain	strain	NN	_	_	_
149	:	:	:	_	_	_
150	MG1655GFP	mg1655gfp	NN	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	Supplementary	supplementary	JJ	_	_	_
153	_	_	NN	_	_	_
154	files	file	NNS	_	_	_
155	_	_	IN	_	_	_
156	format	format	NN	_	_	_
157	_	_	NN	_	_	_
158	and	and	CC	_	_	_
159	_	_	NN	_	_	_
160	content	content	NN	_	_	_
161	:	:	:	_	_	_
162	CSV	CSV	NNP	_	_	_
163	files	file	VBZ	_	_	_
164	providing	provide	VBG	_	_	_
165	the	the	DT	_	_	_
166	number	number	NN	_	_	_
167	of	of	IN	_	_	_
168	reads	read	VBZ	_	_	_
169	mapping	map	VBG	_	_	_
170	to	to	TO	_	_	_
171	each	each	DT	_	_	_
172	genomic	genomic	JJ	_	_	_
173	gene	gene	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	synthetic	synthetic	JJ	_	_	_
176	circuit	circuit	NN	_	_	_
177	:	:	:	_	_	_
178	H3	h3	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	synthetic	synthetic	JJ	_	_	_
181	circuit	circuit	NN	_	_	_
182	:	:	:	_	_	_
183	LACZ	lacz	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	synthetic	synthetic	JJ	_	_	_
186	circuit	circuit	NN	_	_	_
187	:	:	:	_	_	_
188	Lux	lux	FW	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
190	synthetic	synthetic	JJ	_	_	_
191	circuit	circuit	NN	_	_	_
192	:	:	:	_	_	_
193	M1	m1	NN	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	synthetic	synthetic	JJ	_	_	_
196	circuit	circuit	NN	_	_	_
197	:	:	:	_	_	_
198	None	none	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	treatment	treatment	NN	_	_	_
201	:	:	:	_	_	_
202	15	15	CD	_	_	_
203	min	min	NN	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	treatment	treatment	NN	_	_	_
206	:	:	:	_	_	_
207	15	15	CD	_	_	_
208	min	min	NN	_	_	_
209	after	after	IN	_	_	_
210	induction	induction	NN	_	_	_
211	with	with	IN	_	_	_
212	arabinose	arabinose	NN	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	treatment	treatment	NN	_	_	_
215	:	:	:	_	_	_
216	15	15	CD	_	_	_
217	min	min	NN	_	_	_
218	after	after	IN	_	_	_
219	induction	induction	NN	_	_	_
220	with	with	IN	_	_	_
221	rhamnose	rhamnose	NN	_	_	_
222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
223	treatment	treatment	NN	_	_	_
224	:	:	:	_	_	_
225	60	60	CD	_	_	_
226	min	min	NN	_	_	_
227	after	after	IN	_	_	_
228	induction	induction	NN	_	_	_
229	with	with	IN	_	_	_
230	arabinose	arabinose	NN	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	treatment	treatment	NN	_	_	_
233	:	:	:	_	_	_
234	60	60	CD	_	_	_
235	min	min	NN	_	_	_
236	after	after	IN	_	_	_
237	induction	induction	NN	_	_	_
238	with	with	IN	_	_	_
239	rhamnose	rhamnose	NN	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
241	3C-seq	3c-seq	NN	_	_	_
242	:	:	:	_	_	_
243	5	5	CD	_	_	_
244	µg	µg	NN	_	_	_
245	of	of	IN	_	_	_
246	a	a	DT	_	_	_
247	3C	3c	NN	_	_	_
248	library	library	NN	_	_	_
249	was	be	VBD	_	_	_
250	suspended	suspend	VBN	_	_	_
251	in	in	IN	_	_	_
252	water	water	NN	_	_	_
253	-LRB-	-lrb-	-LRB-	_	_	_
254	final	final	JJ	_	_	_
255	volume	volume	NN	_	_	_
256	130	130	CD	_	_	_
257	µL	µl	NN	_	_	_
258	-RRB-	-rrb-	-RRB-	_	_	_
259	and	and	CC	_	_	_
260	sheared	shear	VBD	_	_	_
261	using	use	VBG	_	_	_
262	a	a	DT	_	_	_
263	Covaris	Covaris	NNP	_	_	_
264	S220	s220	NN	_	_	_
265	instrument	instrument	NN	_	_	_
266	-LRB-	-lrb-	-LRB-	_	_	_
267	Duty	duty	NN	_	_	_
268	cycle	cycle	NN	_	_	_
269	5	5	CD	_	_	_
270	,	,	,	_	_	_
271	Intensity	intensity	NN	_	_	_
272	5	5	CD	_	_	_
273	,	,	,	_	_	_
274	cycles	cycle	NNS	_	_	_
275	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBP	_	_	_
276	3C-seq	3c-seq	JJ	_	_	_
277	libraries	library	NNS	_	_	_
278	were	be	VBD	_	_	_
279	proccessed	proccess	VBN	_	_	_
280	using	use	VBG	_	_	_
281	the	the	DT	_	_	_
282	3C-seq	3c-seq	JJ	_	_	_
283	pipeline	pipeline	NN	_	_	_
284	available	available	JJ	_	_	_
285	at	at	IN	_	_	_
286	-LRB-	-lrb-	-LRB-	_	_	_
287	https	http	NNS	_	_	_
288	:	:	:	_	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
290	3C-seq	3c-seq	NN	_	_	_
291	of	of	IN	_	_	_
292	E.	e.	FW	_	_	_
293	coli	coli	FW	_	_	_
294	fis	fis	NN	GEN	_	_
295	cells	cell	NNS	_	_	_
296	in	in	IN	_	_	_
297	exponential	exponential	JJ	GrowthPhase	_	_
298	phase	phase	NN	GrowthPhase	_	_
299	30	30	CD	_	_	_
300	°C	°c	NN	_	_	_
301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
302	3C-seq	3c-seq	NN	_	_	_
303	of	of	IN	_	_	_
304	E.	e.	FW	_	_	_
305	coli	coli	FW	_	_	_
306	fis	fis	NN	GEN	_	_
307	cells	cell	NNS	_	_	_
308	in	in	IN	_	_	_
309	exponential	exponential	JJ	GrowthPhase	_	_
310	phase	phase	NN	GrowthPhase	_	_
311	30	30	CD	_	_	_
312	°C	°c	NN	_	_	_
313	-	-	:	_	_	_
314	Replicate	replicate	VB	_	_	_
315	1	1	CD	_	_	_
316	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
317	3C-seq	3c-seq	NN	_	_	_
318	of	of	IN	_	_	_
319	E.	e.	FW	_	_	_
320	coli	coli	FW	_	_	_
321	hns	hns	NN	GEN	_	_
322	cells	cell	NNS	_	_	_
323	in	in	IN	_	_	_
324	exponential	exponential	JJ	GrowthPhase	_	_
325	phase	phase	NN	GrowthPhase	_	_
326	30	30	CD	_	_	_
327	°C	°c	NN	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	3C-seq	3c-seq	NN	_	_	_
330	of	of	IN	_	_	_
331	E.	e.	FW	_	_	_
332	coli	coli	FW	_	_	_
333	hns	hns	NN	GEN	_	_
334	cells	cell	NNS	_	_	_
335	in	in	IN	_	_	_
336	exponential	exponential	JJ	GrowthPhase	_	_
337	phase	phase	NN	GrowthPhase	_	_
338	30	30	CD	_	_	_
339	°C	°c	NN	_	_	_
340	-	-	:	_	_	_
341	Replicate	replicate	VB	_	_	_
342	1	1	CD	_	_	_
343	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
344	3C-seq	3c-seq	NN	_	_	_
345	of	of	IN	_	_	_
346	E.	e.	FW	_	_	_
347	coli	coli	FW	_	_	_
348	hupAB	hupab	NN	_	_	_
349	cells	cell	NNS	_	_	_
350	in	in	IN	_	_	_
351	exponential	exponential	JJ	GrowthPhase	_	_
352	phase	phase	NN	GrowthPhase	_	_
353	37	37	CD	_	_	_
354	°C	°c	NN	_	_	_
355	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
356	3C-seq	3c-seq	NN	_	_	_
357	of	of	IN	_	_	_
358	E.	e.	FW	_	_	_
359	coli	coli	FW	_	_	_
360	hupAB	hupab	NN	_	_	_
361	cells	cell	NNS	_	_	_
362	in	in	IN	_	_	_
363	exponential	exponential	JJ	GrowthPhase	_	_
364	phase	phase	NN	GrowthPhase	_	_
365	37	37	CD	_	_	_
366	°C	°c	SYM	_	_	_
367	-	-	:	_	_	_
368	Replicate	replicate	VB	_	_	_
369	1	1	CD	_	_	_
370	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
371	3C-seq	3c-seq	NN	_	_	_
372	of	of	IN	_	_	_
373	E.	e.	FW	_	_	_
374	coli	coli	FW	_	_	_
375	matP	matp	NN	GEN	_	_
376	cells	cell	NNS	_	_	_
377	in	in	IN	_	_	_
378	exponential	exponential	JJ	GrowthPhase	_	_
379	phase	phase	NN	GrowthPhase	_	_
380	22	22	CD	_	_	_
381	°C	°c	NN	_	_	_
382	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
383	3C-seq	3c-seq	NN	_	_	_
384	of	of	IN	_	_	_
385	E.	e.	FW	_	_	_
386	coli	coli	FW	_	_	_
387	matP	matp	NN	GEN	_	_
388	cells	cell	NNS	_	_	_
389	in	in	IN	_	_	_
390	exponential	exponential	JJ	GrowthPhase	_	_
391	phase	phase	NN	GrowthPhase	_	_
392	30	30	CD	_	_	_
393	°C	°c	NN	_	_	_
394	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
395	3C-seq	3c-seq	NN	_	_	_
396	of	of	IN	_	_	_
397	E.	e.	FW	_	_	_
398	coli	coli	FW	_	_	_
399	matP	matp	NN	GEN	_	_
400	cells	cell	NNS	_	_	_
401	in	in	IN	_	_	_
402	exponential	exponential	JJ	GrowthPhase	_	_
403	phase	phase	NN	GrowthPhase	_	_
404	30	30	CD	_	_	_
405	°C	°c	NN	_	_	_
406	-	-	:	_	_	_
407	Replicate	replicate	VB	_	_	_
408	1	1	CD	_	_	_
409	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
410	3C-seq	3c-seq	NN	_	_	_
411	of	of	IN	_	_	_
412	E.	e.	FW	_	_	_
413	coli	coli	FW	_	_	_
414	matPDC20	matpdc20	NN	_	_	_
415	cells	cell	NNS	_	_	_
416	harbouring	harbour	VBG	_	_	_
417	plasmid	plasmid	NN	_	_	_
418	pGBM2-5xmatS	pgbm2-5xmats	NN	_	_	_
419	in	in	IN	_	_	_
420	exponential	exponential	JJ	GrowthPhase	_	_
421	phase	phase	NN	GrowthPhase	_	_
422	30	30	CD	_	_	_
423	°C	°c	NN	_	_	_
424	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
425	3C-seq	3c-seq	NN	_	_	_
426	of	of	IN	_	_	_
427	E.	e.	FW	_	_	_
428	coli	coli	FW	_	_	_
429	matPDC20	matpdc20	NN	_	_	_
430	cells	cell	NNS	_	_	_
431	harbouring	harbour	VBG	_	_	_
432	plasmid	plasmid	NN	_	_	_
433	pGBM2	pgbm2	NN	_	_	_
434	in	in	IN	_	_	_
435	exponential	exponential	JJ	GrowthPhase	_	_
436	phase	phase	NN	GrowthPhase	_	_
437	30	30	CD	_	_	_
438	°C	°c	NN	_	_	_
439	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
440	3C-seq	3c-seq	NN	_	_	_
441	of	of	IN	_	_	_
442	E.	e.	FW	_	_	_
443	coli	coli	FW	_	_	_
444	matPDC20	matpdc20	NN	_	_	_
445	cells	cell	NNS	_	_	_
446	in	in	IN	_	_	_
447	exponential	exponential	JJ	GrowthPhase	_	_
448	phase	phase	NN	GrowthPhase	_	_
449	30	30	CD	_	_	_
450	°C	°c	NN	_	_	_
451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
452	3C-seq	3c-seq	NN	_	_	_
453	of	of	IN	_	_	_
454	E.	e.	FW	_	_	_
455	coli	coli	FW	_	_	_
456	mukB	mukb	NN	GEN	_	_
457	cells	cell	NNS	_	_	_
458	in	in	IN	_	_	_
459	exponential	exponential	JJ	GrowthPhase	_	_
460	phase	phase	NN	GrowthPhase	_	_
461	22	22	CD	_	_	_
462	°C	°c	NN	_	_	_
463	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
464	3C-seq	3c-seq	NN	_	_	_
465	of	of	IN	_	_	_
466	E.	e.	FW	_	_	_
467	coli	coli	FW	_	_	_
468	mukB	mukb	NN	GEN	_	_
469	cells	cell	NNS	_	_	_
470	in	in	IN	_	_	_
471	exponential	exponential	JJ	GrowthPhase	_	_
472	phase	phase	NN	GrowthPhase	_	_
473	22	22	CD	_	_	_
474	°C	°c	NN	_	_	_
475	-	-	:	_	_	_
476	Replicate	replicate	VB	_	_	_
477	1	1	CD	_	_	_
478	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
479	3C-seq	3c-seq	NN	_	_	_
480	of	of	IN	_	_	_
481	E.	e.	FW	_	_	_
482	coli	coli	FW	_	_	_
483	mukBmatP	mukbmatp	NN	_	_	_
484	cells	cell	NNS	_	_	_
485	in	in	IN	_	_	_
486	exponential	exponential	JJ	GrowthPhase	_	_
487	phase	phase	NN	GrowthPhase	_	_
488	22	22	CD	_	_	_
489	°C	°c	NN	_	_	_
490	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
491	3C-seq	3c-seq	NN	_	_	_
492	of	of	IN	_	_	_
493	E.	e.	FW	_	_	_
494	coli	coli	FW	_	_	_
495	wt	wt	JJ	_	_	_
496	cells	cell	NNS	_	_	_
497	harbouring	harbour	VBG	_	_	_
498	plasmid	plasmid	NN	_	_	_
499	pGBM2-5xmatS	pgbm2-5xmats	NN	_	_	_
500	in	in	IN	_	_	_
501	exponential	exponential	JJ	GrowthPhase	_	_
502	phase	phase	NN	GrowthPhase	_	_
503	30	30	CD	_	_	_
504	°C	°c	NN	_	_	_
505	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
506	3C-seq	3c-seq	NN	_	_	_
507	of	of	IN	_	_	_
508	E.	e.	FW	_	_	_
509	coli	coli	FW	_	_	_
510	wt	wt	JJ	_	_	_
511	cells	cell	NNS	_	_	_
512	harbouring	harbour	VBG	_	_	_
513	plasmid	plasmid	NN	_	_	_
514	pGBM2-5xmatS	pgbm2-5xmats	NN	_	_	_
515	in	in	IN	_	_	_
516	exponential	exponential	JJ	GrowthPhase	_	_
517	phase	phase	NN	GrowthPhase	_	_
518	30	30	CD	_	_	_
519	°C	°c	NN	_	_	_
520	-	-	:	_	_	_
521	Replicate	replicate	VB	_	_	_
522	1	1	CD	_	_	_
523	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
524	3C-seq	3c-seq	NN	_	_	_
525	of	of	IN	_	_	_
526	E.	e.	FW	_	_	_
527	coli	coli	FW	_	_	_
528	wt	wt	JJ	_	_	_
529	cells	cell	NNS	_	_	_
530	harbouring	harbour	VBG	_	_	_
531	plasmid	plasmid	NN	_	_	_
532	pGBM2	pgbm2	NN	_	_	_
533	in	in	IN	_	_	_
534	exponential	exponential	JJ	GrowthPhase	_	_
535	phase	phase	NN	GrowthPhase	_	_
536	30	30	CD	_	_	_
537	°C	°c	NN	_	_	_
538	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
539	3C-seq	3c-seq	NN	_	_	_
540	of	of	IN	_	_	_
541	E.	e.	FW	_	_	_
542	coli	coli	FW	_	_	_
543	wt	wt	JJ	_	_	_
544	cells	cell	NNS	_	_	_
545	harbouring	harbour	VBG	_	_	_
546	plasmid	plasmid	NN	_	_	_
547	pGBM2	pgbm2	NN	_	_	_
548	in	in	IN	_	_	_
549	exponential	exponential	JJ	GrowthPhase	_	_
550	phase	phase	NN	GrowthPhase	_	_
551	30	30	CD	_	_	_
552	°C	°c	NN	_	_	_
553	-	-	:	_	_	_
554	Replicate	replicate	VB	_	_	_
555	1	1	CD	_	_	_
556	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
557	3C-seq	3c-seq	NN	_	_	_
558	of	of	IN	_	_	_
559	E.	e.	FW	_	_	_
560	coli	coli	FW	_	_	_
561	wt	wt	JJ	_	_	_
562	cells	cell	NNS	_	_	_
563	in	in	IN	_	_	_
564	exponential	exponential	JJ	GrowthPhase	_	_
565	phase	phase	NN	GrowthPhase	_	_
566	22	22	CD	_	_	_
567	°C	°c	NN	_	_	_
568	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
569	3C-seq	3c-seq	NN	_	_	_
570	of	of	IN	_	_	_
571	E.	e.	FW	_	_	_
572	coli	coli	FW	_	_	_
573	wt	wt	JJ	_	_	_
574	cells	cell	NNS	_	_	_
575	in	in	IN	_	_	_
576	exponential	exponential	JJ	GrowthPhase	_	_
577	phase	phase	NN	GrowthPhase	_	_
578	22	22	CD	_	_	_
579	°C	°c	NN	_	_	_
580	-	-	:	_	_	_
581	Replicate	replicate	VB	_	_	_
582	1	1	CD	_	_	_
583	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
584	3C-seq	3c-seq	NN	_	_	_
585	of	of	IN	_	_	_
586	E.	e.	FW	_	_	_
587	coli	coli	FW	_	_	_
588	wt	wt	JJ	_	_	_
589	cells	cell	NNS	_	_	_
590	in	in	IN	_	_	_
591	exponential	exponential	JJ	GrowthPhase	_	_
592	phase	phase	NN	GrowthPhase	_	_
593	30	30	CD	_	_	_
594	°C	°c	NN	_	_	_
595	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
596	3C-seq	3c-seq	NN	_	_	_
597	of	of	IN	_	_	_
598	E.	e.	FW	_	_	_
599	coli	coli	FW	_	_	_
600	wt	wt	JJ	_	_	_
601	cells	cell	NNS	_	_	_
602	in	in	IN	_	_	_
603	exponential	exponential	JJ	GrowthPhase	_	_
604	phase	phase	NN	GrowthPhase	_	_
605	30	30	CD	_	_	_
606	°C	°c	NN	_	_	_
607	-	-	:	_	_	_
608	Replicate	replicate	VB	_	_	_
609	1	1	CD	_	_	_
610	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
611	3C-seq	3c-seq	NN	_	_	_
612	of	of	IN	_	_	_
613	E.	e.	FW	_	_	_
614	coli	coli	FW	_	_	_
615	wt	wt	JJ	_	_	_
616	cells	cell	NNS	_	_	_
617	in	in	IN	_	_	_
618	exponential	exponential	JJ	GrowthPhase	_	_
619	phase	phase	NN	GrowthPhase	_	_
620	30	30	CD	_	_	_
621	°C	°c	NN	_	_	_
622	-	-	:	_	_	_
623	Replicate	replicate	VB	_	_	_
624	2	2	CD	_	_	_
625	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
626	3C-seq	3c-seq	NN	_	_	_
627	of	of	IN	_	_	_
628	E.	e.	FW	_	_	_
629	coli	coli	FW	_	_	_
630	wt	wt	JJ	_	_	_
631	cells	cell	NNS	_	_	_
632	in	in	IN	_	_	_
633	exponential	exponential	JJ	GrowthPhase	_	_
634	phase	phase	NN	GrowthPhase	_	_
635	37	37	CD	_	_	_
636	°C	°c	NN	_	_	_
637	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
638	3C-seq	3c-seq	NN	_	_	_
639	of	of	IN	_	_	_
640	E.	e.	FW	_	_	_
641	coli	coli	FW	_	_	_
642	wt	wt	JJ	_	_	_
643	cells	cell	NNS	_	_	_
644	in	in	IN	_	_	_
645	exponential	exponential	JJ	GrowthPhase	_	_
646	phase	phase	NN	GrowthPhase	_	_
647	37	37	CD	_	_	_
648	°C	°c	SYM	_	_	_
649	-	-	:	_	_	_
650	Replicate	replicate	VB	_	_	_
651	1	1	CD	_	_	_
652	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
653	3C-seq	3c-seq	NN	_	_	_
654	of	of	IN	_	_	_
655	E.	e.	FW	_	_	_
656	coli	coli	FW	_	_	_
657	wt	wt	JJ	_	_	_
658	cells	cell	NNS	_	_	_
659	in	in	IN	_	_	_
660	exponential	exponential	JJ	GrowthPhase	_	_
661	phase	phase	NN	GrowthPhase	_	_
662	LB	lb	NN	_	_	_
663	30	30	CD	_	_	_
664	°C	°c	NN	_	_	_
665	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
666	3C-seq	3c-seq	NN	_	_	_
667	of	of	IN	_	_	_
668	E.	e.	FW	_	_	_
669	coli	coli	FW	_	_	_
670	wt	wt	JJ	_	_	_
671	cells	cell	NNS	_	_	_
672	in	in	IN	_	_	_
673	exponential	exponential	JJ	GrowthPhase	_	_
674	phase	phase	NN	GrowthPhase	_	_
675	LB	lb	NN	_	_	_
676	30	30	CD	_	_	_
677	°C	°c	NN	_	_	_
678	-	-	:	_	_	_
679	Replicate	replicate	VB	_	_	_
680	1	1	CD	_	_	_
681	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
682	3C-seq	3c-seq	NN	_	_	_
683	of	of	IN	_	_	_
684	E.	e.	FW	_	_	_
685	coli	coli	FW	_	_	_
686	wt	wt	JJ	_	_	_
687	cells	cell	NNS	_	_	_
688	in	in	IN	_	_	_
689	stationary	stationary	JJ	GrowthPhase	_	_
690	phase	phase	NN	GrowthPhase	_	_
691	30	30	CD	_	_	_
692	°C	°c	NN	_	_	_
693	-LRB-	-lrb-	-LRB-	_	_	_
694	30h	30h	NN	_	_	_
695	-RRB-	-rrb-	-RRB-	_	_	_
696	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
697	3C-seq	3c-seq	NN	_	_	_
698	of	of	IN	_	_	_
699	E.	e.	FW	_	_	_
700	coli	coli	FW	_	_	_
701	wt	wt	JJ	_	_	_
702	cells	cell	NNS	_	_	_
703	in	in	IN	_	_	_
704	stationary	stationary	JJ	GrowthPhase	_	_
705	phase	phase	NN	GrowthPhase	_	_
706	30	30	CD	_	_	_
707	°C	°c	NN	_	_	_
708	-LRB-	-lrb-	-LRB-	_	_	_
709	30h	30h	NN	_	_	_
710	-RRB-	-rrb-	-RRB-	_	_	_
711	-	-	:	_	_	_
712	Replicate	replicate	VB	_	_	_
713	1	1	CD	_	_	_
714	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
715	3C-seq	3c-seq	NN	_	_	_
716	of	of	IN	_	_	_
717	E.	e.	FW	_	_	_
718	coli	coli	FW	_	_	_
719	zapB	zapb	NN	GEN	_	_
720	cells	cell	NNS	_	_	_
721	harbouring	harbour	VBG	_	_	_
722	plasmid	plasmid	NN	_	_	_
723	pGBM2-5xmatS	pgbm2-5xmats	NN	_	_	_
724	in	in	IN	_	_	_
725	exponential	exponential	JJ	GrowthPhase	_	_
726	phase	phase	NN	GrowthPhase	_	_
727	30	30	CD	_	_	_
728	°C	°c	NN	_	_	_
729	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
730	3C-seq	3c-seq	NN	_	_	_
731	of	of	IN	_	_	_
732	E.	e.	FW	_	_	_
733	coli	coli	FW	_	_	_
734	zapB	zapb	NN	GEN	_	_
735	cells	cell	NNS	_	_	_
736	harbouring	harbour	VBG	_	_	_
737	plasmid	plasmid	NN	_	_	_
738	pGBM2	pgbm2	NN	_	_	_
739	in	in	IN	_	_	_
740	exponential	exponential	JJ	GrowthPhase	_	_
741	phase	phase	NN	GrowthPhase	_	_
742	30	30	CD	_	_	_
743	°C	°c	NN	_	_	_
744	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
745	3C-seq	3c-seq	NN	_	_	_
746	of	of	IN	_	_	_
747	E.	e.	FW	_	_	_
748	coli	coli	FW	_	_	_
749	zapB	zapb	NN	GEN	_	_
750	cells	cell	NNS	_	_	_
751	in	in	IN	_	_	_
752	exponential	exponential	JJ	GrowthPhase	_	_
753	phase	phase	NN	GrowthPhase	_	_
754	30	30	CD	_	_	_
755	°C	°c	NN	_	_	_
756	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
757	Assignment	assignment	NN	_	_	_
758	to	to	TO	_	_	_
759	restriction	restriction	NN	_	_	_
760	fragment	fragment	NN	_	_	_
761	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
762	Binning	binning	NN	_	_	_
763	at	at	IN	_	_	_
764	5kb	5kb	JJ	_	_	_
765	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	E	e	NN	_	_	_
3	coli	coli	NN	_	_	_
4	cells	cell	NNS	_	_	_
5	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
6	E.	E.	NNP	_	_	_
7	coli	coli	NN	_	_	_
8	cells	cell	NNS	_	_	_
9	were	be	VBD	_	_	_
10	grown	grow	VBN	_	_	_
11	at	at	IN	_	_	_
12	22	22	CD	_	_	_
13	°C	°c	NN	_	_	_
14	,	,	,	_	_	_
15	30	30	CD	_	_	_
16	°C	°c	NN	_	_	_
17	and	and	CC	_	_	_
18	37	37	CD	_	_	_
19	°C	°c	NN	_	_	_
20	in	in	IN	_	_	_
21	either	either	CC	_	_	_
22	Lennox	Lennox	NNP	_	_	_
23	Broth	Broth	NNP	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	LB	LB	NNP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	or	or	CC	_	_	_
28	liquid	liquid	JJ	_	_	_
29	minimal	minimal	JJ	_	_	_
30	medium	medium	NN	_	_	_
31	A	a	DT	_	_	_
32	supplemented	supplement	VBN	_	_	_
33	with	with	IN	_	_	_
34	0.12	0.12	CD	_	_	_
35	%	%	NN	_	_	_
36	casamino	casamino	NN	SUPP	_	_
37	acids	acid	NNS	SUPP	_	_
38	and	and	CC	_	_	_
39	0.4	0.4	CD	_	_	_
40	%	%	NN	_	_	_
41	glucose	glucose	NN	SUPP	_	_
42	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	to	to	TO	_	_	_
6	OD600	od600	NN	_	_	_
7	=	=	JJ	_	_	_
8	0.2	0.2	CD	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	early	early	JJ	_	_	_
11	exponential	exponential	JJ	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	or	or	CC	_	_	_
14	2	2	CD	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	stationary	stationary	JJ	GrowthPhase	_	_
17	phase	phase	NN	GrowthPhase	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Filtering	filter	VBG	_	_	_
4	,	,	,	_	_	_
5	Mapping	mapping	NN	_	_	_
6	quality	quality	NN	_	_	_
7	=	=	JJ	_	_	_
8	30	30	CD	_	_	_
9	,	,	,	_	_	_
10	no	no	DT	_	_	_
11	ambiguous	ambiguous	JJ	_	_	_
12	reads	read	VBZ	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	For	for	IN	_	_	_
15	3C-seq	3c-seq	NN	_	_	_
16	:	:	:	_	_	_
17	≈	≈	SYM	_	_	_
18	1-2	1-2	CD	_	_	_
19	x	x	CC	_	_	_
20	109	109	CD	_	_	_
21	crosslinked	crosslink	VBN	_	_	_
22	cells	cell	NNS	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	7	7	CD	_	_	_
25	%	%	NN	_	_	_
26	formaldehyde	formaldehyde	NN	_	_	_
27	,	,	,	_	_	_
28	unless	unless	IN	_	_	_
29	otherwise	otherwise	RB	_	_	_
30	stated	state	VBN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	are	be	VBP	_	_	_
33	suspended	suspend	VBN	_	_	_
34	in	in	IN	_	_	_
35	600	600	CD	_	_	_
36	μl	μl	NN	_	_	_
37	Tris	Tris	NNP	_	_	_
38	10	10	CD	_	_	_
39	mM	mm	NN	KWSUPP	_	_
40	EDTA	edta	NN	_	_	_
41	0.5	0.5	CD	_	_	_
42	mM	mm	NN	KWSUPP	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	TE	te	NN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	pH	ph	NN	_	_	_
48	8	8	CD	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	with	with	IN	_	_	_
51	4	4	CD	_	_	_
52	μl	μl	NN	_	_	_
53	of	of	IN	_	_	_
54	lysozyme	lysozyme	NN	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	35	35	CD	_	_	_
57	U	U	NNP	_	_	_
58	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
59	For	for	IN	_	_	_
60	RNA-seq	RNA-seq	NNP	_	_	_
61	:	:	:	_	_	_
62	total	total	JJ	_	_	_
63	RNA	rna	NN	_	_	_
64	was	be	VBD	_	_	_
65	extracted	extract	VBN	_	_	_
66	using	use	VBG	_	_	_
67	RNeasy	RNeasy	NNP	_	_	_
68	Protect	protect	VB	_	_	_
69	Bacteria	bacterium	NNS	_	_	_
70	according	accord	VBG	_	_	_
71	to	to	TO	_	_	_
72	manufacturer	manufacturer	NN	_	_	_
73	instructions	instruction	NNS	_	_	_
74	-LRB-	-lrb-	-LRB-	_	_	_
75	QIAGEN	QIAGEN	NNP	_	_	_
76	-	-	:	_	_	_
77	#	#	#	_	_	_
78	74524	74524	CD	_	_	_
79	-RRB-	-rrb-	-RRB-	_	_	_
80	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
81	Genome	Genome	NNP	_	_	_
82	_	_	NNP	_	_	_
83	build	build	VB	_	_	_
84	:	:	:	_	_	_
85	E.	e.	FW	_	_	_
86	coli	coli	FW	_	_	_
87	MG1655	mg1655	NN	_	_	_
88	GenBank	genbank	NN	_	_	_
89	:	:	:	_	_	_
90	U00096	u00096	NN	_	_	_
91	.2	.2	NN	_	_	_
92	,	,	,	_	_	_
93	total	total	JJ	_	_	_
94	length	length	NN	_	_	_
95	:	:	:	_	_	_
96	4639675	4639675	CD	_	_	_
97	bp	bp	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	genotype	genotype	NN	_	_	_
100	:	:	:	_	_	_
101	F	f	NN	_	_	_
102	-	-	:	_	_	_
103	lambda	lambda	NN	_	_	_
104	-	-	:	_	_	_
105	ilvG	ilvg	NN	_	_	_
106	-	-	:	_	_	_
107	rfb-50	rfb-50	NN	_	_	_
108	rph-1	rph-1	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	genotype	genotype	NN	_	_	_
111	:	:	:	_	_	_
112	F	f	NN	_	_	_
113	-	-	:	_	_	_
114	lambda	lambda	NN	_	_	_
115	-	-	:	_	_	_
116	ilvG	ilvg	NN	_	_	_
117	-	-	:	_	_	_
118	rfb-50	rfb-50	NN	_	_	_
119	rph-1	rph-1	NN	_	_	_
120	-LSB-	-lsb-	-LRB-	_	_	_
121	delta	delta	NN	_	_	_
122	-RSB-	-rsb-	-RRB-	_	_	_
123	fis	fi	VBZ	GEN	_	_
124	:	:	:	_	_	_
125	:	:	:	_	_	_
126	frt-kan-frt	frt-kan-frt	JJ	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	genotype	genotype	NN	_	_	_
129	:	:	:	_	_	_
130	F	f	NN	_	_	_
131	-	-	:	_	_	_
132	lambda	lambda	NN	_	_	_
133	-	-	:	_	_	_
134	ilvG	ilvg	NN	_	_	_
135	-	-	:	_	_	_
136	rfb-50	rfb-50	NN	_	_	_
137	rph-1	rph-1	NN	_	_	_
138	-LSB-	-lsb-	-LRB-	_	_	_
139	delta	delta	NN	_	_	_
140	-RSB-	-rsb-	-RRB-	_	_	_
141	hns	hn	NNS	GEN	_	_
142	:	:	:	_	_	_
143	:	:	:	_	_	_
144	frt	frt	SYM	_	_	_
145	-	-	:	_	_	_
146	kan	kan	SYM	_	_	_
147	-	-	:	_	_	_
148	frt	frt	NN	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	genotype	genotype	NN	_	_	_
151	:	:	:	_	_	_
152	F	f	NN	_	_	_
153	-	-	:	_	_	_
154	lambda	lambda	NN	_	_	_
155	-	-	:	_	_	_
156	ilvG	ilvg	NN	_	_	_
157	-	-	:	_	_	_
158	rfb-50	rfb-50	NN	_	_	_
159	rph-1	rph-1	NN	_	_	_
160	-LSB-	-lsb-	-LRB-	_	_	_
161	delta	delta	NN	_	_	_
162	-RSB-	-rsb-	-RRB-	_	_	_
163	matP	matp	NN	GEN	_	_
164	:	:	:	_	_	_
165	:	:	:	_	_	_
166	frt-cam-frt	frt-cam-frt	JJ	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	genotype	genotype	NN	_	_	_
169	:	:	:	_	_	_
170	F	f	NN	_	_	_
171	-	-	:	_	_	_
172	lambda	lambda	NN	_	_	_
173	-	-	:	_	_	_
174	ilvG	ilvg	NN	_	_	_
175	-	-	:	_	_	_
176	rfb-50	rfb-50	NN	_	_	_
177	rph-1	rph-1	NN	_	_	_
178	-LSB-	-lsb-	-LRB-	_	_	_
179	delta	delta	NN	_	_	_
180	-RSB-	-rsb-	-RRB-	_	_	_
181	mukB	mukb	NN	GEN	_	_
182	:	:	:	_	_	_
183	:	:	:	_	_	_
184	frt	frt	SYM	_	_	_
185	-	-	:	_	_	_
186	kan	kan	NN	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	genotype	genotype	NN	_	_	_
189	:	:	:	_	_	_
190	F	f	NN	_	_	_
191	-	-	:	_	_	_
192	lambda	lambda	NN	_	_	_
193	-	-	:	_	_	_
194	ilvG	ilvg	NN	_	_	_
195	-	-	:	_	_	_
196	rfb-50	rfb-50	NN	_	_	_
197	rph-1	rph-1	NN	_	_	_
198	-LSB-	-lsb-	-LRB-	_	_	_
199	delta	delta	NN	_	_	_
200	-RSB-	-rsb-	-RRB-	_	_	_
201	zapB	zapb	NN	GEN	_	_
202	:	:	:	_	_	_
203	:	:	:	_	_	_
204	frt-kan-frt	frt-kan-frt	JJ	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	genotype	genotype	NN	_	_	_
207	:	:	:	_	_	_
208	F	f	NN	_	_	_
209	-	-	:	_	_	_
210	lambda	lambda	NN	_	_	_
211	-	-	:	_	_	_
212	ilvG	ilvg	NN	_	_	_
213	-	-	:	_	_	_
214	rfb-50	rfb-50	NN	_	_	_
215	rph-1	rph-1	NN	_	_	_
216	matP	matp	NN	GEN	_	_
217	-LSB-	-lsb-	-LRB-	_	_	_
218	delta	delta	NN	_	_	_
219	-RSB-	-rsb-	-RRB-	_	_	_
220	C20	c20	NN	_	_	_
221	:	:	:	_	_	_
222	:	:	:	_	_	_
223	frt-cam-frt	frt-cam-frt	JJ	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
225	genotype	genotype	NN	_	_	_
226	:	:	:	_	_	_
227	F	f	NN	_	_	_
228	-	-	:	_	_	_
229	lambda	lambda	NN	_	_	_
230	-	-	:	_	_	_
231	ilvG	ilvg	NN	_	_	_
232	-	-	:	_	_	_
233	rfb-50	rfb-50	NN	_	_	_
234	rph-1	rph-1	NN	_	_	_
235	phi80	phi80	NN	_	_	_
236	+	+	CC	_	_	_
237	-LSB-	-lsb-	-LRB-	_	_	_
238	delta	delta	NN	_	_	_
239	-RSB-	-rsb-	-RRB-	_	_	_
240	hupA	hupa	NN	GEN	_	_
241	:	:	:	_	_	_
242	:	:	:	_	_	_
243	frt	frt	SYM	_	_	_
244	-	-	:	_	_	_
245	kan	kan	SYM	_	_	_
246	-	-	:	_	_	_
247	frt	frt	NN	_	_	_
248	-LSB-	-lsb-	-LRB-	_	_	_
249	delta	delta	NN	_	_	_
250	-RSB-	-rsb-	-RRB-	_	_	_
251	hupB	hupb	NN	GEN	_	_
252	:	:	:	_	_	_
253	:	:	:	_	_	_
254	frt-cam-frt	frt-cam-frt	JJ	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	genotype	genotype	NN	_	_	_
257	:	:	:	_	_	_
258	F	f	NN	_	_	_
259	-	-	:	_	_	_
260	lambda	lambda	NN	_	_	_
261	-	-	:	_	_	_
262	ilvG	ilvg	NN	_	_	_
263	-	-	:	_	_	_
264	rfb-50	rfb-50	NN	_	_	_
265	rph-1phi80	rph-1phi80	NN	_	_	_
266	+	+	CC	_	_	_
267	-LSB-	-lsb-	-LRB-	_	_	_
268	delta	delta	NN	_	_	_
269	-RSB-	-rsb-	-RRB-	_	_	_
270	mukB	mukb	NN	GEN	_	_
271	:	:	:	_	_	_
272	:	:	:	_	_	_
273	frt	frt	SYM	_	_	_
274	-	-	:	_	_	_
275	apra	apra	NN	_	_	_
276	-LSB-	-lsb-	-LRB-	_	_	_
277	delta	delta	NN	_	_	_
278	-RSB-	-rsb-	-RRB-	_	_	_
279	matP	matp	NN	GEN	_	_
280	:	:	:	_	_	_
281	:	:	:	_	_	_
282	frt-cam-frt	frt-cam-frt	JJ	_	_	_
283	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
284	growth	growth	NN	_	_	_
285	condition	condition	NN	_	_	_
286	:	:	:	_	_	_
287	LB	lb	NN	_	_	_
288	at	at	IN	_	_	_
289	30	30	CD	_	_	_
290	°C	°c	NN	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	growth	growth	NN	_	_	_
293	condition	condition	NN	_	_	_
294	:	:	:	_	_	_
295	LB	lb	NN	_	_	_
296	at	at	IN	_	_	_
297	37	37	CD	_	_	_
298	°C	°c	NN	_	_	_
299	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
300	growth	growth	NN	_	_	_
301	condition	condition	NN	_	_	_
302	:	:	:	_	_	_
303	MM	mm	NN	_	_	_
304	+	+	CC	_	_	_
305	0.12	0.12	CD	_	_	_
306	%	%	NN	_	_	_
307	casaminoacids	casaminoacid	NNS	_	_	_
308	+0.4	+0.4	CD	_	_	_
309	%	%	NN	_	_	_
310	glucose	glucose	NN	SUPP	_	_
311	at	at	IN	_	_	_
312	22	22	CD	_	_	_
313	°C	°c	NN	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	growth	growth	NN	_	_	_
316	condition	condition	NN	_	_	_
317	:	:	:	_	_	_
318	MM	mm	NN	_	_	_
319	+	+	CC	_	_	_
320	0.12	0.12	CD	_	_	_
321	%	%	NN	_	_	_
322	casaminoacids	casaminoacid	NNS	_	_	_
323	+0.4	+0.4	CD	_	_	_
324	%	%	NN	_	_	_
325	glucose	glucose	NN	SUPP	_	_
326	at	at	IN	_	_	_
327	30	30	CD	_	_	_
328	°C	°c	NN	_	_	_
329	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
330	Iterative	iterative	JJ	_	_	_
331	alignment	alignment	NN	_	_	_
332	,	,	,	_	_	_
333	Min-leght	min-leght	NN	_	_	_
334	=	=	JJ	_	_	_
335	20	20	CD	_	_	_
336	,	,	,	_	_	_
337	step	step	NN	_	_	_
338	=	=	JJ	_	_	_
339	5	5	CD	_	_	_
340	,	,	,	_	_	_
341	bowtie2	bowtie2	NN	_	_	_
342	--	--	:	_	_	_
343	very-sensitive	very-sensitive	JJ	_	_	_
344	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
345	Library	Library	NNP	_	_	_
346	strategy	strategy	NN	_	_	_
347	:	:	:	_	_	_
348	3C-seq	3c-seq	JJ	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
350	OTHER	other	JJ	_	_	_
351	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
352	Removal	removal	NN	_	_	_
353	of	of	IN	_	_	_
354	PCR	pcr	NN	_	_	_
355	duplicates	duplicate	VBZ	_	_	_
356	based	base	VBN	_	_	_
357	on	on	IN	_	_	_
358	the	the	DT	_	_	_
359	20	20	CD	_	_	_
360	first	first	JJ	_	_	_
361	bp	bp	NN	_	_	_
362	of	of	IN	_	_	_
363	the	the	DT	_	_	_
364	read	read	NN	_	_	_
365	containing	contain	VBG	_	_	_
366	a	a	DT	_	_	_
367	6	6	CD	_	_	_
368	nt	nt	NN	_	_	_
369	random	random	JJ	_	_	_
370	tag	tag	NN	GEN	_	_
371	-LRB-	-lrb-	-LRB-	_	_	_
372	home	home	NN	_	_	_
373	made	make	VBN	_	_	_
374	script	script	NN	_	_	_
375	-RRB-	-rrb-	-RRB-	_	_	_
376	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Removal	removal	NN	_	_	_
3	of	of	IN	_	_	_
4	un-informative	un-informative	JJ	_	_	_
5	events	event	NNS	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	uncuts	uncut	NNS	_	_	_
8	,	,	,	_	_	_
9	loops	loop	NNS	_	_	_
10	etc	etc	FW	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	as	as	IN	_	_	_
13	described	describe	VBN	_	_	_
14	in	in	IN	_	_	_
15	Cournac	Cournac	NNP	_	_	_
16	et	et	FW	_	_	_
17	al.	al.	FW	_	_	_
18	.	.	.	_	_	_

1	BMC	BMC	NNP	_	_	_
2	2012	2012	CD	_	_	_
3	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	RNA-seq	rna-seq	NN	_	_	_
5	of	of	IN	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	wt	wt	JJ	_	_	_
9	cells	cell	NNS	_	_	_
10	in	in	IN	_	_	_
11	stationary	stationary	JJ	GrowthPhase	_	_
12	phase	phase	NN	GrowthPhase	_	_
13	30	30	CD	_	_	_
14	°C	°c	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	30h	30h	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	RNA-seq	rna-seq	NN	_	_	_
20	of	of	IN	_	_	_
21	E.	e.	FW	_	_	_
22	coli	coli	FW	_	_	_
23	wt	wt	JJ	_	_	_
24	cells	cell	NNS	_	_	_
25	in	in	IN	_	_	_
26	stationary	stationary	JJ	GrowthPhase	_	_
27	phase	phase	NN	GrowthPhase	_	_
28	30	30	CD	_	_	_
29	°C	°c	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	30h	30h	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	-	-	:	_	_	_
34	Replicate	replicate	VB	_	_	_
35	1	1	CD	_	_	_
36	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
37	Supplementary	Supplementary	NNP	_	_	_
38	_	_	VBD	_	_	_
39	files	file	NNS	_	_	_
40	_	_	IN	_	_	_
41	format	format	NN	_	_	_
42	_	_	NN	_	_	_
43	and	and	CC	_	_	_
44	_	_	NN	_	_	_
45	content	content	NN	_	_	_
46	:	:	:	_	_	_
47	rna-seq	rna-seq	NN	_	_	_
48	:	:	:	_	_	_
49	genomic	genomic	JJ	_	_	_
50	position	position	NN	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	middle	middle	NN	_	_	_
53	of	of	IN	_	_	_
54	the	the	DT	_	_	_
55	5kb-bin	5kb-bin	NN	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	to	to	TO	_	_	_
58	each	each	DT	_	_	_
59	count	count	NN	_	_	_
60	.	.	.	_	_	_

1	3C	3c	NN	_	_	_
2	seq	seq	NN	_	_	_
3	:	:	:	_	_	_
4	contact	contact	NN	_	_	_
5	maps	map	NNS	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	2D	2d	NN	_	_	_
8	array	array	NN	_	_	_
9	of	of	IN	_	_	_
10	928	928	CD	_	_	_
11	5kb-bins	5kb-bin	NNS	_	_	_
12	x	x	CC	_	_	_
13	928	928	CD	_	_	_
14	5kb-bins	5kb-bin	NNS	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Bacterial	bacterial	JJ	_	_	_
3	liquid	liquid	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
6	Counts	Counts	NNPS	_	_	_
7	were	be	VBD	_	_	_
8	depth	depth	NN	_	_	_
9	normalized	normalize	VBD	_	_	_
10	to	to	TO	_	_	_
11	a	a	DT	_	_	_
12	pseudo-reference	pseudo-reference	NN	_	_	_
13	sample	sample	NN	_	_	_
14	calculated	calculate	VBN	_	_	_
15	from	from	IN	_	_	_
16	all	all	DT	_	_	_
17	samples	sample	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	ribozero	ribozero	NN	_	_	_
20	treated	treat	VBN	_	_	_
21	samples	sample	NNS	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	or	or	CC	_	_	_
24	using	use	VBG	_	_	_
25	counts	count	NNS	_	_	_
26	per	per	IN	_	_	_
27	million	million	CD	_	_	_
28	counts	count	NNS	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	total	total	JJ	_	_	_
31	RNA	rna	NN	_	_	_
32	samples	sample	NNS	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	emptyvec	emptyvec	NN	_	_	_
3	_	_	NN	_	_	_
4	mRNA	mrna	NN	_	_	_
5	_	_	SYM	_	_	_
6	5m	5m	FW	_	_	_
7	_	_	FW	_	_	_
8	rep1	rep1	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	emptyvec	emptyvec	NN	_	_	_
11	_	_	NN	_	_	_
12	mRNA	mrna	NN	_	_	_
13	_	_	SYM	_	_	_
14	5m	5m	FW	_	_	_
15	_	_	FW	_	_	_
16	rep2	rep2	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	emptyvec	emptyvec	NN	_	_	_
19	_	_	CD	_	_	_
20	totalRNA	totalrna	NN	_	_	_
21	_	_	SYM	_	_	_
22	30m	30m	FW	_	_	_
23	_	_	FW	_	_	_
24	rep1	rep1	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	emptyvec	emptyvec	NN	_	_	_
27	_	_	CD	_	_	_
28	totalRNA	totalrna	NN	_	_	_
29	_	_	SYM	_	_	_
30	30m	30m	FW	_	_	_
31	_	_	FW	_	_	_
32	rep2	rep2	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	emptyvec	emptyvec	NN	_	_	_
35	_	_	CD	_	_	_
36	totalRNA	totalrna	NN	_	_	_
37	_	_	SYM	_	_	_
38	5m	5m	FW	_	_	_
39	_	_	FW	_	_	_
40	rep1	rep1	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	emptyvec	emptyvec	NN	_	_	_
43	_	_	CD	_	_	_
44	totalRNA	totalrna	NN	_	_	_
45	_	_	SYM	_	_	_
46	5m	5m	FW	_	_	_
47	_	_	FW	_	_	_
48	rep2	rep2	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	ercc	ercc	NN	_	_	_
51	spike-in	spike-in	NN	_	_	_
52	:	:	:	_	_	_
53	No	no	DT	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	ercc	ercc	NN	_	_	_
56	spike-in	spike-in	NN	_	_	_
57	:	:	:	_	_	_
58	Prior	prior	RB	_	_	_
59	to	to	TO	_	_	_
60	extraction	extraction	NN	_	_	_
61	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
62	Escherichia	escherichia	FW	Organism	_	_
63	coli	coli	FW	Organism	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	For	for	IN	_	_	_
66	each	each	DT	_	_	_
67	uniquely	uniquely	RB	_	_	_
68	mapped	map	VBN	_	_	_
69	fragment	fragment	NN	_	_	_
70	-LRB-	-lrb-	-LRB-	_	_	_
71	ribozero	ribozero	NN	_	_	_
72	treated	treat	VBN	_	_	_
73	samples	sample	NNS	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	or	or	CC	_	_	_
76	all	all	DT	_	_	_
77	mapped	map	VBN	_	_	_
78	fragments	fragment	NNS	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	total	total	JJ	_	_	_
81	RNA	rna	NN	_	_	_
82	samples	sample	NNS	_	_	_
83	-RRB-	-rrb-	-RRB-	_	_	_
84	,	,	,	_	_	_
85	at	at	IN	_	_	_
86	all	all	DT	_	_	_
87	aligned	align	VBN	_	_	_
88	positions	position	NNS	_	_	_
89	a	a	DT	_	_	_
90	count	count	NN	_	_	_
91	was	be	VBD	_	_	_
92	added	add	VBN	_	_	_
93	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	For	for	IN	_	_	_
3	ribozero	ribozero	NN	_	_	_
4	treated	treat	VBN	_	_	_
5	samples	sample	NNS	_	_	_
6	,	,	,	_	_	_
7	counts	count	VBZ	_	_	_
8	at	at	IN	_	_	_
9	all	all	DT	_	_	_
10	positions	position	NNS	_	_	_
11	were	be	VBD	_	_	_
12	log2	log2	NN	_	_	_
13	transformed	transform	VBN	_	_	_
14	and	and	CC	_	_	_
15	a	a	DT	_	_	_
16	cleavage	cleavage	NN	_	_	_
17	ratio	ratio	NN	_	_	_
18	was	be	VBD	_	_	_
19	calculated	calculate	VBN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	+	+	CC	_	_	_
22	MazF	mazf	NN	_	_	_
23	-	-	:	_	_	_
24	empty	empty	JJ	_	_	_
25	vector	vector	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	for	for	IN	_	_	_
28	assessing	assess	VBG	_	_	_
29	MazF	mazf	NN	_	_	_
30	cleavage	cleavage	NN	_	_	_
31	in	in	IN	_	_	_
32	transcripts	transcript	NNS	_	_	_
33	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	NCBI	ncbi	NN	_	_	_
7	reference	reference	NN	_	_	_
8	sequence	sequence	NN	_	_	_
9	:	:	:	_	_	_
10	NC	nc	NN	_	_	_
11	_	_	SYM	_	_	_
12	000913.2	000913.2	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	MazF	mazf	NN	_	_	_
15	_	_	NN	_	_	_
16	mRNA	mrna	NN	_	_	_
17	_	_	SYM	_	_	_
18	5m	5m	FW	_	_	_
19	_	_	FW	_	_	_
20	rep1	rep1	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	MazF	mazf	NN	_	_	_
23	_	_	NN	_	_	_
24	mRNA	mrna	NN	_	_	_
25	_	_	SYM	_	_	_
26	5m	5m	FW	_	_	_
27	_	_	FW	_	_	_
28	rep2	rep2	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	MazF	mazf	NN	_	_	_
31	_	_	CD	_	_	_
32	totalRNA	totalrna	NN	_	_	_
33	_	_	SYM	_	_	_
34	30m	30m	FW	_	_	_
35	_	_	FW	_	_	_
36	rep1	rep1	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	MazF	mazf	NN	_	_	_
39	_	_	CD	_	_	_
40	totalRNA	totalrna	NN	_	_	_
41	_	_	SYM	_	_	_
42	30m	30m	FW	_	_	_
43	_	_	FW	_	_	_
44	rep2	rep2	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	MazF	mazf	NN	_	_	_
47	_	_	CD	_	_	_
48	totalRNA	totalrna	NN	_	_	_
49	_	_	SYM	_	_	_
50	5m	5m	FW	_	_	_
51	_	_	FW	_	_	_
52	rep1	rep1	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	MazF	mazf	NN	_	_	_
55	_	_	CD	_	_	_
56	totalRNA	totalrna	NN	_	_	_
57	_	_	SYM	_	_	_
58	5m	5m	FW	_	_	_
59	_	_	FW	_	_	_
60	rep2	rep2	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	MazF	mazf	NN	_	_	_
63	_	_	CD	_	_	_
64	totalRNA	totalrna	NN	_	_	_
65	_	_	SYM	_	_	_
66	60m	60m	FW	_	_	_
67	_	_	FW	_	_	_
68	rep1	rep1	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	MazF	mazf	NN	_	_	_
71	_	_	CD	_	_	_
72	totalRNA	totalrna	NN	_	_	_
73	_	_	SYM	_	_	_
74	60m	60m	FW	_	_	_
75	_	_	FW	_	_	_
76	rep2	rep2	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	Paired-end	paired-end	NN	_	_	_
79	reads	read	VBZ	_	_	_
80	mapped	map	VBN	_	_	_
81	to	to	TO	_	_	_
82	MG1655	mg1655	NN	_	_	_
83	genome	genome	NN	_	_	_
84	using	use	VBG	_	_	_
85	bowtie2	bowtie2	NN	_	_	_
86	with	with	IN	_	_	_
87	default	default	NN	_	_	_
88	settings	setting	NNS	_	_	_
89	.	.	.	_	_	_

1	Any	any	DT	_	_	_
2	adapter	adapter	NN	_	_	_
3	sequences	sequence	NNS	_	_	_
4	were	be	VBD	_	_	_
5	removed	remove	VBN	_	_	_
6	prior	prior	RB	_	_	_
7	to	to	TO	_	_	_
8	mapping	mapping	NN	_	_	_
9	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	plasmid	plasmid	NN	_	_	_
3	:	:	:	_	_	_
4	pBAD30-empty	pbad30-empty	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	plasmid	plasmid	NN	_	_	_
7	:	:	:	_	_	_
8	pBAD30-MazF	pbad30-mazf	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	ribozero	ribozero	NN	_	_	_
11	:	:	:	_	_	_
12	No	no	DT	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	ribozero	ribozero	NN	_	_	_
15	:	:	:	_	_	_
16	Yes	yes	UH	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
18	RNA-Seq	rna-seq	JJ	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	RNA	rna	NN	_	_	_
21	was	be	VBD	_	_	_
22	extracted	extract	VBN	_	_	_
23	using	use	VBG	_	_	_
24	Trizol	Trizol	NNP	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	Invitrogen	Invitrogen	NNP	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	and	and	CC	_	_	_
29	Direct-zol	direct-zol	NN	_	_	_
30	RNA	rna	NN	_	_	_
31	MiniPrep	MiniPrep	NNP	_	_	_
32	kit	kit	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	Zymo	zymo	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	See	see	VB	_	_	_
3	publication	publication	NN	_	_	_
4	for	for	IN	_	_	_
5	complete	complete	JJ	_	_	_
6	protocol	protocol	NN	_	_	_
7	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	samples	sample	NNS	_	_	_
4	with	with	IN	_	_	_
5	rRNA	rrna	NN	_	_	_
6	subtraction	subtraction	NN	_	_	_
7	with	with	IN	_	_	_
8	treated	treat	VBN	_	_	_
9	with	with	IN	_	_	_
10	bacterial	bacterial	JJ	_	_	_
11	Ribo-Zero	Ribo-Zero	NNP	_	_	_
12	kit	kit	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Illumina	Illumina	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	Next	next	RB	_	_	_
2	,	,	,	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	fragmented	fragmented	JJ	_	_	_
6	with	with	IN	_	_	_
7	RNA	rna	NN	_	_	_
8	fragmentation	fragmentation	NN	_	_	_
9	reagents	reagent	NNS	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Ambion	Ambion	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	.	.	.	_	_	_

1	First	first	JJ	_	_	_
2	strand	strand	NN	_	_	_
3	cDNA	cdna	NN	_	_	_
4	synthesis	synthesis	NN	_	_	_
5	was	be	VBD	_	_	_
6	conducted	conduct	VBN	_	_	_
7	using	use	VBG	_	_	_
8	random	random	JJ	_	_	_
9	primers	primer	NNS	_	_	_
10	and	and	CC	_	_	_
11	Superscript	Superscript	NNP	_	_	_
12	III	III	NNP	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Invitrogen	Invitrogen	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	enable	enable	VB	_	_	_
3	strand	strand	NN	_	_	_
4	specificity	specificity	NN	_	_	_
5	,	,	,	_	_	_
6	second	second	JJ	_	_	_
7	strand	strand	NN	_	_	_
8	synthesis	synthesis	NN	_	_	_
9	was	be	VBD	_	_	_
10	conducted	conduct	VBN	_	_	_
11	using	use	VBG	_	_	_
12	dUTP	dutp	NN	_	_	_
13	instead	instead	RB	_	_	_
14	of	of	IN	_	_	_
15	dTTP	dttp	NN	_	_	_
16	with	with	IN	_	_	_
17	RNase	rnase	NN	_	_	_
18	H	h	NN	_	_	_
19	,	,	,	_	_	_
20	E.	e.	FW	_	_	_
21	coli	coli	FW	_	_	_
22	DNA	dna	NN	_	_	_
23	ligase	ligase	NN	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	E.	e.	FW	_	_	_
27	coli	coli	FW	_	_	_
28	DNA	dna	NN	_	_	_
29	polymerase	polymerase	NN	_	_	_
30	.	.	.	_	_	_

1	Ends	end	NNS	_	_	_
2	were	be	VBD	_	_	_
3	repaired	repair	VBN	_	_	_
4	with	with	IN	_	_	_
5	T4	t4	NN	_	_	_
6	DNA	dna	NN	_	_	_
7	polymerase	polymerase	NN	_	_	_
8	,	,	,	_	_	_
9	Klenow	Klenow	NNP	_	_	_
10	DNA	DNA	NNP	_	_	_
11	polymerase	polymerase	NN	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	T4	t4	NN	_	_	_
15	PNK	pnk	NN	_	_	_
16	.	.	.	_	_	_

1	3	3	CD	_	_	_
2	'	'	''	_	_	_
3	ends	end	NNS	_	_	_
4	were	be	VBD	_	_	_
5	adenylated	adenylate	VBN	_	_	_
6	with	with	IN	_	_	_
7	the	the	DT	_	_	_
8	Klenow	Klenow	NNP	_	_	_
9	fragment	fragment	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	3	3	CD	_	_	_
12	'	'	''	_	_	_
13	>	>	JJR	_	_	_
14	5	5	CD	_	_	_
15	'	'	''	_	_	_
16	exo	exo	SYM	_	_	_
17	-	-	:	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	Y-shaped	y-shaped	JJ	_	_	_
2	adapters	adapter	NNS	_	_	_
3	were	be	VBD	_	_	_
4	ligated	ligate	VBN	_	_	_
5	and	and	CC	_	_	_
6	9-12	9-12	CD	_	_	_
7	cycles	cycle	NNS	_	_	_
8	of	of	IN	_	_	_
9	PCR	pcr	NN	_	_	_
10	were	be	VBD	_	_	_
11	conducted	conduct	VBN	_	_	_
12	with	with	IN	_	_	_
13	standard	standard	JJ	_	_	_
14	Illumina	Illumina	NNP	_	_	_
15	primers	primer	NNS	_	_	_
16	with	with	IN	_	_	_
17	multiplexing	multiplex	VBG	_	_	_
18	indexes	index	NNS	_	_	_
19	.	.	.	_	_	_

1	Libraries	library	NNS	_	_	_
2	were	be	VBD	_	_	_
3	extracted	extract	VBN	_	_	_
4	from	from	IN	_	_	_
5	an	a	DT	_	_	_
6	acrylamide	acrylamide	NN	_	_	_
7	gel	gel	NN	_	_	_
8	and	and	CC	_	_	_
9	submitted	submit	VBN	_	_	_
10	for	for	IN	_	_	_
11	sequencing	sequencing	NN	_	_	_
12	at	at	IN	_	_	_
13	the	the	DT	_	_	_
14	MIT	MIT	NNP	_	_	_
15	BioMicro	BioMicro	NNP	_	_	_
16	Center	Center	NNP	_	_	_
17	using	use	VBG	_	_	_
18	standard	standard	JJ	_	_	_
19	Illumina	Illumina	NNP	_	_	_
20	protocols	protocol	NNS	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Separate	separate	JJ	_	_	_
3	E.	e.	FW	_	_	_
4	coli	coli	FW	_	_	_
5	colonies	colony	NNS	_	_	_
6	were	be	VBD	_	_	_
7	picked	pick	VBN	_	_	_
8	from	from	IN	_	_	_
9	LB	LB	NNP	_	_	_
10	agar	agar	NN	_	_	_
11	plates	plate	NNS	_	_	_
12	for	for	IN	_	_	_
13	each	each	DT	_	_	_
14	replicate	replicate	VBP	_	_	_
15	.	.	.	_	_	_

1	Overnight	overnight	JJ	_	_	_
2	cultures	culture	NNS	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	12-16	12-16	CD	_	_	_
5	hrs	hr	NNS	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	at	at	IN	_	_	_
10	37	37	CD	_	_	_
11	°C	°c	NN	_	_	_
12	in	in	IN	_	_	_
13	M9	m9	NN	_	_	_
14	media	media	NNS	_	_	_
15	supplemented	supplement	VBN	_	_	_
16	with	with	IN	_	_	_
17	0.1	0.1	CD	_	_	_
18	%	%	NN	_	_	_
19	casamino	casamino	NN	SUPP	_	_
20	acids	acid	NNS	SUPP	_	_
21	,	,	,	_	_	_
22	0.4	0.4	CD	_	_	_
23	%	%	NN	_	_	_
24	glycerol	glycerol	NN	SUPP	_	_
25	,	,	,	_	_	_
26	0.4	0.4	CD	_	_	_
27	%	%	NN	_	_	_
28	glucose	glucose	NN	SUPP	_	_
29	,	,	,	_	_	_
30	2	2	CD	_	_	_
31	mM	mm	NN	KWSUPP	_	_
32	MgSO4	mgso4	NN	_	_	_
33	,	,	,	_	_	_
34	and	and	CC	_	_	_
35	0.1	0.1	CD	_	_	_
36	mM	mm	NN	KWSUPP	_	_
37	CaCl2	cacl2	NN	_	_	_
38	.	.	.	_	_	_

1	Overnight	overnight	JJ	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	back	back	RB	_	_	_
5	diluted	dilute	VBN	_	_	_
6	into	into	IN	_	_	_
7	fresh	fresh	JJ	_	_	_
8	media	media	NNS	_	_	_
9	and	and	CC	_	_	_
10	grown	grow	VBN	_	_	_
11	3-4	3-4	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	to	to	TO	_	_	_
14	an	a	DT	_	_	_
15	OD600	od600	NN	_	_	_
16	of	of	IN	_	_	_
17	~	~	NN	_	_	_
18	0.35	0.35	CD	_	_	_
19	at	at	IN	_	_	_
20	37	37	CD	_	_	_
21	°C	°c	NN	_	_	_
22	in	in	IN	_	_	_
23	an	a	DT	_	_	_
24	orbital	orbital	JJ	_	_	_
25	shaker	shaker	NN	_	_	_
26	at	at	IN	_	_	_
27	200	200	CD	_	_	_
28	RPM	rpm	NN	_	_	_
29	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	centrifuged	centrifuge	VBN	_	_	_
4	,	,	,	_	_	_
5	washed	wash	VBN	_	_	_
6	,	,	,	_	_	_
7	and	and	CC	_	_	_
8	back	back	RB	_	_	_
9	diluted	dilute	VBN	_	_	_
10	into	into	IN	_	_	_
11	media	media	NNS	_	_	_
12	lacking	lack	VBG	_	_	_
13	glucose	glucose	NN	SUPP	_	_
14	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	at	at	IN	_	_	_
3	least	least	JJS	_	_	_
4	30	30	CD	_	_	_
5	minutes	minute	NNS	_	_	_
6	of	of	IN	_	_	_
7	recovery	recovery	NN	_	_	_
8	Para	para	NN	_	_	_
9	was	be	VBD	_	_	_
10	induced	induce	VBN	_	_	_
11	by	by	IN	_	_	_
12	adding	add	VBG	_	_	_
13	arabinose	arabinose	NN	_	_	_
14	to	to	TO	_	_	_
15	0.2	0.2	CD	_	_	_
16	%	%	NN	_	_	_
17	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	harvested	harvest	VBN	_	_	_
4	by	by	IN	_	_	_
5	centrifuging	centrifuge	VBG	_	_	_
6	1	1	CD	_	_	_
7	mL	ml	NN	_	_	_
8	of	of	IN	_	_	_
9	culture	culture	NN	_	_	_
10	for	for	IN	_	_	_
11	1	1	CD	_	_	_
12	minute	minute	NN	_	_	_
13	at	at	IN	_	_	_
14	maximum	maximum	JJ	_	_	_
15	speed	speed	NN	_	_	_
16	on	on	IN	_	_	_
17	a	a	DT	_	_	_
18	benchtop	benchtop	JJ	_	_	_
19	centrifuge	centrifuge	NN	_	_	_
20	.	.	.	_	_	_

1	Pellets	pellet	NNS	_	_	_
2	were	be	VBD	_	_	_
3	immediately	immediately	RB	_	_	_
4	flash	flash	VB	_	_	_
5	frozen	freeze	VBN	_	_	_
6	in	in	IN	_	_	_
7	lN2	ln2	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	delta	delta	NN	_	_	_
6	_	_	CD	_	_	_
7	mazF	mazf	NN	GEN	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Supplementary	supplementary	JJ	_	_	_
10	_	_	NN	_	_	_
11	files	file	NNS	_	_	_
12	_	_	IN	_	_	_
13	format	format	NN	_	_	_
14	_	_	NN	_	_	_
15	and	and	CC	_	_	_
16	_	_	NN	_	_	_
17	content	content	NN	_	_	_
18	:	:	:	_	_	_
19	5m_ribozero_counts_cleavage_ratio.csv.gz	5m_ribozero_counts_cleavage_ratio.csv.gz	NN	_	_	_
20	is	be	VBZ	_	_	_
21	a	a	DT	_	_	_
22	log-transformed	log-transformed	JJ	_	_	_
23	list	list	NN	_	_	_
24	of	of	IN	_	_	_
25	sequencing	sequencing	NN	_	_	_
26	depth-normalized	depth-normalized	JJ	_	_	_
27	counts	count	NNS	_	_	_
28	for	for	IN	_	_	_
29	every	every	DT	_	_	_
30	genomic	genomic	JJ	_	_	_
31	position	position	NN	_	_	_
32	at	at	IN	_	_	_
33	both	both	DT	_	_	_
34	strands	strand	NNS	_	_	_
35	for	for	IN	_	_	_
36	each	each	DT	_	_	_
37	ribozero	ribozero	NN	_	_	_
38	treated	treat	VBN	_	_	_
39	sample	sample	NN	_	_	_
40	as	as	RB	_	_	_
41	well	well	RB	_	_	_
42	as	as	IN	_	_	_
43	the	the	DT	_	_	_
44	average	average	JJ	_	_	_
45	cleavage	cleavage	NN	_	_	_
46	ratio	ratio	NN	_	_	_
47	calculated	calculate	VBN	_	_	_
48	from	from	IN	_	_	_
49	all	all	DT	_	_	_
50	samples	sample	NNS	_	_	_
51	.	.	.	_	_	_

1	total_RNA_rpm.csv.gz	total_rna_rpm.csv.gz	NN	_	_	_
2	is	be	VBZ	_	_	_
3	a	a	DT	_	_	_
4	list	list	NN	_	_	_
5	of	of	IN	_	_	_
6	sequencing	sequencing	NN	_	_	_
7	depth-normalized	depth-normalized	JJ	_	_	_
8	counts	count	NNS	_	_	_
9	for	for	IN	_	_	_
10	every	every	DT	_	_	_
11	genomic	genomic	JJ	_	_	_
12	position	position	NN	_	_	_
13	at	at	IN	_	_	_
14	both	both	DT	_	_	_
15	strans	stran	NNS	_	_	_
16	for	for	IN	_	_	_
17	all	all	DT	_	_	_
18	total	total	JJ	_	_	_
19	RNA	rna	NN	_	_	_
20	samples	sample	NNS	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	time	time	NN	_	_	_
3	induction	induction	NN	_	_	_
4	:	:	:	_	_	_
5	30	30	CD	_	_	_
6	minutes	minute	NNS	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
8	time	time	NN	_	_	_
9	induction	induction	NN	_	_	_
10	:	:	:	_	_	_
11	5	5	CD	_	_	_
12	minutes	minute	NNS	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
14	time	time	NN	_	_	_
15	induction	induction	NN	_	_	_
16	:	:	:	_	_	_
17	60	60	CD	_	_	_
18	minutes	minute	NNS	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Bacteria	bacterium	NNS	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Culture	culture	NN	_	_	_
23	of	of	IN	_	_	_
24	bacterial	bacterial	JJ	_	_	_
25	strains	strain	NNS	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	10	10	CD	_	_	_
28	mL	ml	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	were	be	VBD	_	_	_
31	centrifuged	centrifuge	VBN	_	_	_
32	20	20	CD	_	_	_
33	min	min	NN	_	_	_
34	at	at	IN	_	_	_
35	10,000	10,000	CD	_	_	_
36	g	g	NN	_	_	_
37	and	and	CC	_	_	_
38	bacterial	bacterial	JJ	_	_	_
39	pellets	pellet	NNS	_	_	_
40	were	be	VBD	_	_	_
41	washed	wash	VBN	_	_	_
42	3	3	CD	_	_	_
43	times	time	NNS	_	_	_
44	with	with	IN	_	_	_
45	2	2	CD	_	_	_
46	mL	ml	NN	_	_	_
47	of	of	IN	_	_	_
48	phosphate	phosphate	NN	_	_	_
49	buffered	buffer	VBN	_	_	_
50	saline	saline	NN	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	PBS	PBS	NNP	_	_	_
53	-RRB-	-rrb-	-RRB-	_	_	_
54	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	extraction	extraction	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	EasyDNA	easydna	NN	_	_	_
8	kit	kit	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Invitrogen	invitrogen	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	following	follow	VBG	_	_	_
13	the	the	DT	_	_	_
14	manufacturer	manufacturer	NN	_	_	_
15	instructions	instruction	NNS	_	_	_
16	slightly	slightly	RB	_	_	_
17	modified	modify	VBN	_	_	_
18	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	bacterial	bacterial	JJ	_	_	_
5	pellet	pellet	NN	_	_	_
6	was	be	VBD	_	_	_
7	incubated	incubate	VBN	_	_	_
8	5	5	CD	_	_	_
9	min	min	NN	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	μL	μl	NN	_	_	_
13	of	of	IN	_	_	_
14	PBS	PBS	NNP	_	_	_
15	and	and	CC	_	_	_
16	1	1	CD	_	_	_
17	μL	μl	NN	_	_	_
18	of	of	IN	_	_	_
19	protéinase	protéinase	NN	_	_	_
20	K	k	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	20	20	CD	_	_	_
23	mg	mg	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Escherichia	escherichia	FW	Organism	_	_
26	coli	coli	FW	Organism	_	_
27	K-12	k-12	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Fluorescence	fluorescence	NN	_	_	_
30	intensities	intensity	NNS	_	_	_
31	of	of	IN	_	_	_
32	oligonucleotide	oligonucleotide	NN	_	_	_
33	spots	spot	NNS	_	_	_
34	were	be	VBD	_	_	_
35	extracted	extract	VBN	_	_	_
36	from	from	IN	_	_	_
37	the	the	DT	_	_	_
38	scanned	scan	VBN	_	_	_
39	images	image	NNS	_	_	_
40	using	use	VBG	_	_	_
41	the	the	DT	_	_	_
42	Feature	Feature	NNP	_	_	_
43	Extraction	extraction	NN	_	_	_
44	software	software	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	V11	v11	NN	_	_	_
47	.0	.0	CD	_	_	_
48	,	,	,	_	_	_
49	Agilent	Agilent	NNP	_	_	_
50	Technologies	Technologies	NNPS	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	data	datum	NNS	_	_	_
3	were	be	VBD	_	_	_
4	processed	process	VBN	_	_	_
5	with	with	IN	_	_	_
6	dedicated	dedicated	JJ	_	_	_
7	scripts	script	NNS	_	_	_
8	based	base	VBN	_	_	_
9	on	on	IN	_	_	_
10	C++	C++	NNP	_	_	_
11	and	and	CC	_	_	_
12	Delphi	Delphi	NNP	_	_	_
13	languages	language	NNS	_	_	_
14	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	probe	probe	NN	_	_	_
4	,	,	,	_	_	_
5	median	median	JJ	_	_	_
6	intensity	intensity	NN	_	_	_
7	value	value	NN	_	_	_
8	of	of	IN	_	_	_
9	the	the	DT	_	_	_
10	3	3	CD	_	_	_
11	replicates	replicate	VBZ	_	_	_
12	was	be	VBD	_	_	_
13	conserved	conserve	VBN	_	_	_
14	and	and	CC	_	_	_
15	used	use	VBN	_	_	_
16	as	as	IN	_	_	_
17	the	the	DT	_	_	_
18	probe	probe	NN	_	_	_
19	signal	signal	NN	_	_	_
20	value	value	NN	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	SNR	snr	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	Signal-to-Noise	Signal-to-Noise	NNP	_	_	_
5	Ratio	Ratio	NNP	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	,	,	,	_	_	_
8	similar	similar	JJ	_	_	_
9	to	to	TO	_	_	_
10	the	the	DT	_	_	_
11	detection	detection	NN	_	_	_
12	threshold	threshold	NN	_	_	_
13	response	response	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	positive	positive	JJ	_	_	_
16	hybridization	hybridization	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	corresponding	correspond	VBG	_	_	_
20	to	to	TO	_	_	_
21	the	the	DT	_	_	_
22	probe	probe	NN	_	_	_
23	signal	signal	NN	_	_	_
24	value	value	NN	_	_	_
25	divided	divide	VBN	_	_	_
26	by	by	IN	_	_	_
27	the	the	DT	_	_	_
28	local	local	JJ	_	_	_
29	background	background	NN	_	_	_
30	intensity	intensity	NN	_	_	_
31	value	value	NN	_	_	_
32	,	,	,	_	_	_
33	was	be	VBD	_	_	_
34	calculated	calculate	VBN	_	_	_
35	for	for	IN	_	_	_
36	each	each	DT	_	_	_
37	probe	probe	NN	_	_	_
38	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	SNR	SNR	NNP	_	_	_
3	thresholds	threshold	NNS	_	_	_
4	were	be	VBD	_	_	_
5	set	set	VBN	_	_	_
6	to	to	TO	_	_	_
7	3	3	CD	_	_	_
8	for	for	IN	_	_	_
9	25-mer	25-mer	JJ	_	_	_
10	probes	probe	NNS	_	_	_
11	and	and	CC	_	_	_
12	6	6	CD	_	_	_
13	for	for	IN	_	_	_
14	54-mer	54-mer	JJ	_	_	_
15	probes	probe	NNS	_	_	_
16	.	.	.	_	_	_

1	Such	such	JJ	_	_	_
2	SNR	snr	NN	_	_	_
3	threshold	threshold	NN	_	_	_
4	values	value	NNS	_	_	_
5	ensured	ensure	VBD	_	_	_
6	a	a	DT	_	_	_
7	very	very	RB	_	_	_
8	specific	specific	JJ	_	_	_
9	response	response	NN	_	_	_
10	of	of	IN	_	_	_
11	the	the	DT	_	_	_
12	FibroChip	FibroChip	NNP	_	_	_
13	,	,	,	_	_	_
14	except	except	IN	_	_	_
15	for	for	IN	_	_	_
16	genes	gene	NNS	_	_	_
17	belonging	belong	VBG	_	_	_
18	to	to	TO	_	_	_
19	very	very	RB	_	_	_
20	close	close	JJ	_	_	_
21	strains	strain	NNS	_	_	_
22	from	from	IN	_	_	_
23	the	the	DT	_	_	_
24	same	same	JJ	_	_	_
25	species	species	NNS	_	_	_
26	.	.	.	_	_	_

1	Results	result	NNS	_	_	_
2	for	for	IN	_	_	_
3	25	25	CD	_	_	_
4	-	-	:	_	_	_
5	and	and	CC	_	_	_
6	54-mer	54-mer	JJ	_	_	_
7	probes	probe	NNS	_	_	_
8	were	be	VBD	_	_	_
9	treated	treat	VBN	_	_	_
10	independently	independently	RB	_	_	_
11	and	and	CC	_	_	_
12	for	for	IN	_	_	_
13	each	each	DT	_	_	_
14	probe	probe	NN	_	_	_
15	type	type	NN	_	_	_
16	,	,	,	_	_	_
17	a	a	DT	_	_	_
18	gene	gene	NN	_	_	_
19	was	be	VBD	_	_	_
20	considered	consider	VBN	_	_	_
21	as	as	IN	_	_	_
22	detected	detect	VBN	_	_	_
23	when	when	WRB	_	_	_
24	65	65	CD	_	_	_
25	%	%	NN	_	_	_
26	of	of	IN	_	_	_
27	probes	probe	NNS	_	_	_
28	were	be	VBD	_	_	_
29	positive	positive	JJ	_	_	_
30	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	SNR	snr	NN	_	_	_
3	value	value	NN	_	_	_
4	of	of	IN	_	_	_
5	a	a	DT	_	_	_
6	detected	detect	VBN	_	_	_
7	gene	gene	NN	_	_	_
8	was	be	VBD	_	_	_
9	then	then	RB	_	_	_
10	calculated	calculate	VBN	_	_	_
11	by	by	IN	_	_	_
12	the	the	DT	_	_	_
13	mean	mean	NN	_	_	_
14	of	of	IN	_	_	_
15	the	the	DT	_	_	_
16	SNR	snr	NN	_	_	_
17	of	of	IN	_	_	_
18	all	all	DT	_	_	_
19	25	25	CD	_	_	_
20	-	-	:	_	_	_
21	or	or	CC	_	_	_
22	54-mer	54-mer	JJ	_	_	_
23	probes	probe	NNS	_	_	_
24	targeting	target	VBG	_	_	_
25	this	this	DT	_	_	_
26	gene	gene	NN	_	_	_
27	,	,	,	_	_	_
28	meeting	meeting	NN	_	_	_
29	or	or	CC	_	_	_
30	not	not	RB	_	_	_
31	the	the	DT	_	_	_
32	defined	define	VBN	_	_	_
33	SNR	snr	NN	_	_	_
34	threshold	threshold	NN	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	gDNA	gdna	NN	_	_	_
3	_	_	CD	_	_	_
4	Ecoli	Ecoli	NNP	_	_	_
5	_	_	SYM	_	_	_
6	K12	k12	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
8	Genomic	genomic	JJ	_	_	_
9	DNA	dna	NN	_	_	_
10	was	be	VBD	_	_	_
11	extracted	extract	VBN	_	_	_
12	from	from	IN	_	_	_
13	4	4	CD	_	_	_
14	bacteria	bacterium	NNS	_	_	_
15	strains	strain	NNS	_	_	_
16	.	.	.	_	_	_

1	Strains	strain	NNS	_	_	_
2	Fibrobacter	fibrobacter	JJ	_	_	_
3	succinogenes	succinogene	NNS	_	_	_
4	S85	s85	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	ATCC	atcc	NN	_	_	_
7	19169	19169	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	,	,	,	_	_	_
10	Ruminococcus	ruminococcus	NN	_	_	_
11	albus	albus	NN	_	_	_
12	20	20	CD	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	ATCC	atcc	NN	_	_	_
15	27211	27211	CD	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	and	and	CC	_	_	_
18	Bacteroides	bacteroide	NNS	_	_	_
19	xylanisolvens	xylanisolven	NNS	_	_	_
20	XB1A	xb1a	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	DSM	DSM	NNP	_	_	_
23	18836T	18836T	NNP	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	were	be	VBD	_	_	_
26	grown	grow	VBN	_	_	_
27	15	15	CD	_	_	_
28	h	h	NN	_	_	_
29	under	under	IN	_	_	_
30	strictly	strictly	RB	_	_	_
31	anaerobic	anaerobic	JJ	_	_	_
32	conditions	condition	NNS	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	Hungate	Hungate	NNP	_	_	_
35	,	,	,	_	_	_
36	1950	1950	CD	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	in	in	IN	_	_	_
39	a	a	DT	_	_	_
40	complex	complex	JJ	_	_	_
41	medium	medium	NN	_	_	_
42	containing	contain	VBG	_	_	_
43	20	20	CD	_	_	_
44	%	%	NN	_	_	_
45	of	of	IN	_	_	_
46	clarified	clarify	VBN	_	_	_
47	rumen	ruman	NNS	_	_	_
48	fluid	fluid	NN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	Béra-Maillet	béra-maillet	JJ	_	_	_
51	et	et	FW	_	_	_
52	al.	al.	FW	_	_	_
53	,	,	,	_	_	_
54	2000	2000	CD	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	and	and	CC	_	_	_
57	0.2	0.2	CD	_	_	_
58	g	g	NN	_	_	_
59	of	of	IN	_	_	_
60	cellobiose	cellobiose	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	Sigma-Aldrich	sigma-aldrich	NN	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	as	as	IN	_	_	_
65	carbon	carbon	NN	_	_	_
66	source	source	NN	_	_	_
67	,	,	,	_	_	_
68	at	at	IN	_	_	_
69	39	39	CD	_	_	_
70	°C	°c	NN	_	_	_
71	for	for	IN	_	_	_
72	the	the	DT	_	_	_
73	two	two	CD	_	_	_
74	first	first	JJ	_	_	_
75	ones	one	NNS	_	_	_
76	and	and	CC	_	_	_
77	37	37	CD	_	_	_
78	°C	°c	NN	_	_	_
79	for	for	IN	_	_	_
80	the	the	DT	_	_	_
81	third	third	JJ	_	_	_
82	one	one	CD	_	_	_
83	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	strain	strain	NN	_	_	_
3	Escherichia	escherichia	FW	Organism	_	_
4	coli	coli	FW	Organism	_	_
5	K12	k12	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	ATCC	atcc	NN	_	_	_
8	10798	10798	CD	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	was	be	VBD	_	_	_
11	cultivated	cultivate	VBN	_	_	_
12	15	15	CD	_	_	_
13	h	h	NN	_	_	_
14	at	at	IN	_	_	_
15	37	37	CD	_	_	_
16	°C	°c	NN	_	_	_
17	in	in	IN	_	_	_
18	Luria-Bertani	luria-bertani	JJ	_	_	_
19	medium	medium	NN	_	_	_
20	under	under	IN	_	_	_
21	shaking	shake	VBG	_	_	_
22	and	and	CC	_	_	_
23	aerobic	aerobic	JJ	_	_	_
24	conditions	condition	NNS	_	_	_
25	.	.	.	_	_	_

1	-LRB-	-lrb-	-LRB-	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	gut	gut	NN	_	_	_
4	origin	origin	NN	_	_	_
5	:	:	:	_	_	_
6	Human	human	JJ	_	_	_
7	colon	colon	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
9	No	no	DT	_	_	_
10	treatment	treatment	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	AcrA-Negative	acra-negative	JJ	_	_	_
13	,	,	,	_	_	_
14	Multidrug	multidrug	JJ	_	_	_
15	Efflux	Efflux	NNP	_	_	_
16	Mutant	Mutant	NNP	_	_	_
17	Strain	Strain	NNP	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	AcrB	acrb	NN	_	_	_
20	-	-	:	_	_	_
21	and	and	CC	_	_	_
22	EmrAB-Negative	emrab-negative	JJ	_	_	_
23	,	,	,	_	_	_
24	Multidrug	multidrug	JJ	_	_	_
25	Efflux	Efflux	NNP	_	_	_
26	Mutant	Mutant	NNP	_	_	_
27	Strain	Strain	NNP	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	AcrB-Negative	AcrB-Negative	NNP	_	_	_
30	,	,	,	_	_	_
31	Multidrug	Multidrug	NNP	_	_	_
32	Efflux	Efflux	NNP	_	_	_
33	Mutant	Mutant	NNP	_	_	_
34	Strain	Strain	NNP	_	_	_
35	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
36	AG102MB	ag102mb	NN	_	_	_
37	is	be	VBZ	_	_	_
38	an	a	DT	_	_	_
39	isogenic	isogenic	JJ	_	_	_
40	mutant	mutant	JJ	_	_	_
41	derived	derive	VBN	_	_	_
42	from	from	IN	_	_	_
43	hyper-resistant	hyper-resistant	JJ	_	_	_
44	AG102	ag102	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	marR1	marr1	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	.	.	.	_	_	_

1	It	it	PRP	_	_	_
2	contains	contain	VBZ	_	_	_
3	a	a	DT	_	_	_
4	mutation	mutation	NN	_	_	_
5	at	at	IN	_	_	_
6	the	the	DT	_	_	_
7	acrB	acrb	NN	GEN	_	_
8	locus	locus	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	marR1	marr1	NN	_	_	_
11	,	,	,	_	_	_
12	acrB	acrb	NN	GEN	_	_
13	:	:	:	_	_	_
14	:	:	:	_	_	_
15	kan	kan	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	resulting	result	VBG	_	_	_
18	in	in	IN	_	_	_
19	a	a	DT	_	_	_
20	multidrug	multidrug	JJ	_	_	_
21	efflux	efflux	NN	_	_	_
22	negative	negative	JJ	_	_	_
23	phenotype	phenotype	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	to	to	TO	_	_	_
6	mid-log	mid-log	JJ	_	_	_
7	phase	phase	NN	_	_	_
8	in	in	IN	_	_	_
9	Luria-Bertani	Luria-Bertani	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Miller	Miller	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	broth	broth	JJ	_	_	_
14	medium	medium	NN	_	_	_
15	at	at	IN	_	_	_
16	37C	37c	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	to	to	TO	_	_	_
6	mid-log	mid-log	JJ	_	_	_
7	phase	phase	NN	_	_	_
8	in	in	IN	_	_	_
9	Luria-Bertani	Luria-Bertani	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Miller	Miller	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	broth	broth	JJ	_	_	_
14	medium	medium	NN	_	_	_
15	at	at	IN	_	_	_
16	37C	37c	NN	_	_	_
17	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	cultured	culture	VBN	_	_	_
4	with	with	IN	_	_	_
5	25	25	CD	_	_	_
6	ug	ug	NN	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	E.	E.	NNP	_	_	_
9	coli	coli	NN	_	_	_
10	AcrA	AcrA	NNP	_	_	_
11	Multidrug	Multidrug	NNP	_	_	_
12	Efflux	Efflux	NNP	_	_	_
13	Mutant	mutant	JJ	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	E.	e.	FW	_	_	_
16	coli	coli	FW	_	_	_
17	AcrB	acrb	NN	_	_	_
18	and	and	CC	_	_	_
19	EmrAB	EmrAB	NNP	_	_	_
20	Multidrug	Multidrug	NNP	_	_	_
21	Efflux	Efflux	NNP	_	_	_
22	Double	double	JJ	_	_	_
23	Mutant	mutant	JJ	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	E.	e.	FW	_	_	_
26	coli	coli	FW	_	_	_
27	AcrB	acrb	NN	_	_	_
28	Multidrug	multidrug	JJ	_	_	_
29	Efflux	efflux	NN	_	_	_
30	Mutant	mutant	JJ	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Efflux	efflux	NN	_	_	_
33	Mutant	mutant	JJ	_	_	_
34	Parent	Parent	NNP	_	_	_
35	Strain	Strain	NNP	_	_	_
36	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
37	Escherichia	escherichia	FW	Organism	_	_
38	coli	coli	FW	Organism	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	HNCE3	hnce3	NN	_	_	_
41	is	be	VBZ	_	_	_
42	an	a	DT	_	_	_
43	isogenic	isogenic	JJ	_	_	_
44	mutant	mutant	JJ	_	_	_
45	derived	derive	VBN	_	_	_
46	from	from	IN	_	_	_
47	hyper-resistant	hyper-resistant	JJ	_	_	_
48	AG102	ag102	NN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	marR1	marr1	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	.	.	.	_	_	_

1	It	it	PRP	_	_	_
2	contains	contain	VBZ	_	_	_
3	a	a	DT	_	_	_
4	nonpolar	nonpolar	JJ	_	_	_
5	mutation	mutation	NN	_	_	_
6	at	at	IN	_	_	_
7	the	the	DT	_	_	_
8	acrA	acra	NN	GEN	_	_
9	locus	locus	NN	_	_	_
10	which	which	WDT	_	_	_
11	allows	allow	VBZ	_	_	_
12	read-through	read-through	NN	_	_	_
13	for	for	IN	_	_	_
14	acrB	acrb	NN	GEN	_	_
15	expression	expression	NN	_	_	_
16	and	and	CC	_	_	_
17	results	result	VBZ	_	_	_
18	in	in	IN	_	_	_
19	a	a	DT	_	_	_
20	multidrug	multidrug	JJ	_	_	_
21	efflux	efflux	NN	_	_	_
22	negative	negative	JJ	_	_	_
23	phenotype	phenotype	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	HNCE4	hnce4	NN	_	_	_
3	is	be	VBZ	_	_	_
4	an	a	DT	_	_	_
5	isogenic	isogenic	JJ	_	_	_
6	mutant	mutant	JJ	_	_	_
7	derived	derive	VBN	_	_	_
8	from	from	IN	_	_	_
9	drug	drug	NN	_	_	_
10	sensitive	sensitive	JJ	_	_	_
11	AG102MB	ag102mb	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	marR1	marr1	NN	_	_	_
14	,	,	,	_	_	_
15	AcrB	acrb	NN	_	_	_
16	:	:	:	_	_	_
17	:	:	:	_	_	_
18	kan	kan	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	It	it	PRP	_	_	_
2	contains	contain	VBZ	_	_	_
3	an	a	DT	_	_	_
4	additional	additional	JJ	_	_	_
5	mutation	mutation	NN	_	_	_
6	at	at	IN	_	_	_
7	the	the	DT	_	_	_
8	emrAB	emrab	NN	_	_	_
9	locus	locus	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	marR1	marr1	NN	_	_	_
12	,	,	,	_	_	_
13	acrB	acrb	NN	GEN	_	_
14	:	:	:	_	_	_
15	:	:	:	_	_	_
16	kan	kan	NN	_	_	_
17	,	,	,	_	_	_
18	emrAB	emrab	NN	_	_	_
19	:	:	:	_	_	_
20	:	:	:	_	_	_
21	cat	cat	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	resulting	result	VBG	_	_	_
24	in	in	IN	_	_	_
25	a	a	DT	_	_	_
26	multidrug	multidrug	JJ	_	_	_
27	efflux	efflux	NN	_	_	_
28	negative	negative	JJ	_	_	_
29	phenotype	phenotype	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	analyzed	analyze	VBN	_	_	_
4	data	datum	NNS	_	_	_
5	were	be	VBD	_	_	_
6	imported	import	VBN	_	_	_
7	to	to	TO	_	_	_
8	ArrayTrack	ArrayTrack	NNP	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	NCTR	NCTR	NNP	_	_	_
11	Center	Center	NNP	_	_	_
12	for	for	IN	_	_	_
13	Toxicoinformatics	Toxicoinformatics	NNPS	_	_	_
14	;	;	:	_	_	_
15	http	http	NN	_	_	_
16	:	:	:	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
18	The	the	DT	_	_	_
19	parent	parent	NN	_	_	_
20	strain	strain	NN	_	_	_
21	,	,	,	_	_	_
22	AG102	ag102	NN	_	_	_
23	,	,	,	_	_	_
24	was	be	VBD	_	_	_
25	previously	previously	RB	_	_	_
26	derived	derive	VBN	_	_	_
27	from	from	IN	_	_	_
28	AG100	ag100	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	K-12	k-12	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	.	.	.	_	_	_

1	AG102	ag102	NN	_	_	_
2	is	be	VBZ	_	_	_
3	drug	drug	NN	_	_	_
4	hyper-resistant	hyper-resistant	JJ	_	_	_
5	due	due	JJ	_	_	_
6	to	to	TO	_	_	_
7	a	a	DT	_	_	_
8	mutation	mutation	NN	_	_	_
9	in	in	IN	_	_	_
10	marR	marr	NN	GEN	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	marR1	marr1	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	which	which	WDT	_	_	_
15	increases	increase	VBZ	_	_	_
16	expression	expression	NN	_	_	_
17	of	of	IN	_	_	_
18	MarA	mara	NN	TF	_	_
19	,	,	,	_	_	_
20	a	a	DT	_	_	_
21	global	global	JJ	_	_	_
22	regulator	regulator	NN	_	_	_
23	,	,	,	_	_	_
24	which	which	WDT	_	_	_
25	in	in	IN	_	_	_
26	turn	turn	NN	_	_	_
27	results	result	VBZ	_	_	_
28	in	in	IN	_	_	_
29	overexpression	overexpression	NN	_	_	_
30	of	of	IN	_	_	_
31	the	the	DT	_	_	_
32	AcrAB-TolC	acrab-tolc	NN	_	_	_
33	multidrug	multidrug	JJ	_	_	_
34	efflux	efflux	NN	_	_	_
35	system	system	NN	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	Qiagen	Qiagen	NNP	_	_	_
8	RNeasy	RNeasy	NNP	_	_	_
9	kit	kit	NN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Alignment	alignment	NN	_	_	_
3	:	:	:	_	_	_
4	reads	read	VBZ	_	_	_
5	were	be	VBD	_	_	_
6	mapped	map	VBN	_	_	_
7	to	to	TO	_	_	_
8	bespoke	bespeak	VB	_	_	_
9	reference	reference	NN	_	_	_
10	sequence	sequence	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	DL4201	dl4201	NN	_	_	_
13	_	_	NN	_	_	_
14	in	in	IN	_	_	_
15	_	_	NN	_	_	_
16	lab	lab	NN	_	_	_
17	_	_	CD	_	_	_
18	reference	reference	NN	_	_	_
19	_	_	NN	_	_	_
20	genome	genome	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	available	available	JJ	_	_	_
23	on	on	IN	_	_	_
24	series	series	NN	_	_	_
25	record	record	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	using	use	VBG	_	_	_
29	the	the	DT	_	_	_
30	default	default	NN	_	_	_
31	parameters	parameter	NNS	_	_	_
32	of	of	IN	_	_	_
33	software	software	NN	_	_	_
34	Bowtie	bowtie	NN	_	_	_
35	2	2	CD	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	Langmead	Langmead	NNP	_	_	_
38	,	,	,	_	_	_
39	B.	B.	NNP	_	_	_
40	and	and	CC	_	_	_
41	Salzberg	Salzberg	NNP	_	_	_
42	,	,	,	_	_	_
43	S.L.	S.L.	NNP	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	2012	2012	CD	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	Fast	fast	JJ	_	_	_
48	gapped-read	gapped-read	JJ	_	_	_
49	alignment	alignment	NN	_	_	_
50	with	with	IN	_	_	_
51	Bowtie	bowtie	NN	_	_	_
52	2	2	CD	_	_	_
53	.	.	.	_	_	_

1	Nat	Nat	NNP	_	_	_
2	Methods	method	NNS	_	_	_
3	,	,	,	_	_	_
4	9	9	CD	_	_	_
5	,	,	,	_	_	_
6	357-359	357-359	CD	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	All	All	NNP	_	_	_
3	samples	sample	NNS	_	_	_
4	were	be	VBD	_	_	_
5	processed	process	VBN	_	_	_
6	following	follow	VBG	_	_	_
7	NEB	NEB	NNP	_	_	_
8	's	's	POS	_	_	_
9	protocol	protocol	NN	_	_	_
10	from	from	IN	_	_	_
11	the	the	DT	_	_	_
12	NEBNext	nebnext	NN	_	_	_
13	®	®	NN	_	_	_
14	ChIP-Seq	chip-seq	JJ	_	_	_
15	library	library	NN	_	_	_
16	preparation	preparation	NN	_	_	_
17	kit	kit	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	background	background	NN	_	_	_
3	strain	strain	NN	_	_	_
4	:	:	:	_	_	_
5	BW27784	bw27784	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Bacterial	bacterial	JJ	_	_	_
8	Cell	cell	NN	_	_	_
9	Lysates	lysate	NNS	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Cells	cell	NNS	_	_	_
12	were	be	VBD	_	_	_
13	collected	collect	VBN	_	_	_
14	by	by	IN	_	_	_
15	centrifugation	centrifugation	NN	_	_	_
16	and	and	CC	_	_	_
17	washed	wash	VBN	_	_	_
18	three	three	CD	_	_	_
19	times	time	NNS	_	_	_
20	in	in	IN	_	_	_
21	ice-cold	ice-cold	JJ	_	_	_
22	1X	1x	NN	_	_	_
23	PBS	PBS	NNP	_	_	_
24	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	re-suspended	re-suspended	JJ	_	_	_
6	in	in	IN	_	_	_
7	250	250	CD	_	_	_
8	μl	μl	NN	_	_	_
9	ChIP	chip	NN	_	_	_
10	buffer	buffer	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	200	200	CD	_	_	_
13	mM	mm	NN	KWSUPP	_	_
14	Tris-HCl	tris-hcl	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	pH	ph	NN	_	_	_
17	8.0	8.0	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	600	600	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	NaCl	nacl	NN	_	_	_
23	4	4	CD	_	_	_
24	%	%	NN	_	_	_
25	Triton	Triton	NNP	_	_	_
26	X	X	NNP	_	_	_
27	,	,	,	_	_	_
28	Complete	complete	JJ	_	_	_
29	protease	protease	NN	_	_	_
30	inhibitor	inhibitor	NN	_	_	_
31	cocktail	cocktail	NN	_	_	_
32	EDTA-free	edta-free	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	Roche	Roche	NNP	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	.	.	.	_	_	_

1	Sonication	sonication	NN	_	_	_
2	of	of	IN	_	_	_
3	crosslinked	crosslink	VBN	_	_	_
4	samples	sample	NNS	_	_	_
5	was	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	using	use	VBG	_	_	_
8	the	the	DT	_	_	_
9	Diagenode	Diagenode	NNP	_	_	_
10	Bioruptor	Bioruptor	NNP	_	_	_
11	®	®	NN	_	_	_
12	at	at	IN	_	_	_
13	30s	30s	CD	_	_	_
14	intervals	interval	NNS	_	_	_
15	for	for	IN	_	_	_
16	10	10	CD	_	_	_
17	min	min	NN	_	_	_
18	at	at	IN	_	_	_
19	high	high	JJ	_	_	_
20	amplitude	amplitude	NN	_	_	_
21	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	sonication	sonication	NN	_	_	_
3	,	,	,	_	_	_
4	350	350	CD	_	_	_
5	μl	μl	NN	_	_	_
6	of	of	IN	_	_	_
7	ChIP	chip	NN	_	_	_
8	buffer	buffer	NN	_	_	_
9	was	be	VBD	_	_	_
10	added	add	VBN	_	_	_
11	to	to	TO	_	_	_
12	each	each	DT	_	_	_
13	sample	sample	NN	_	_	_
14	,	,	,	_	_	_
15	the	the	DT	_	_	_
16	samples	sample	NNS	_	_	_
17	were	be	VBD	_	_	_
18	mixed	mix	VBN	_	_	_
19	by	by	IN	_	_	_
20	gentle	gentle	JJ	_	_	_
21	pipetting	pipetting	NN	_	_	_
22	and	and	CC	_	_	_
23	100	100	CD	_	_	_
24	μl	μl	NN	_	_	_
25	of	of	IN	_	_	_
26	each	each	DT	_	_	_
27	lysate	lysate	NN	_	_	_
28	was	be	VBD	_	_	_
29	removed	remove	VBN	_	_	_
30	and	and	CC	_	_	_
31	stored	store	VBN	_	_	_
32	as	as	IN	_	_	_
33	`	`	``	_	_	_
34	input	input	NN	_	_	_
35	'	'	''	_	_	_
36	.	.	.	_	_	_

1	Immunoprecipitation	immunoprecipitation	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	overnight	overnight	RB	_	_	_
5	at	at	IN	_	_	_
6	4	4	CD	_	_	_
7	°C	°c	NN	_	_	_
8	using	use	VBG	_	_	_
9	1	1	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Cells	cell	NNS	_	_	_
12	were	be	VBD	_	_	_
13	grown	grow	VBN	_	_	_
14	in	in	IN	_	_	_
15	LB	LB	NNP	MED	_	_
16	media	media	NNS	MED	_	_
17	supplemented	supplement	VBN	_	_	_
18	with	with	IN	_	_	_
19	0.2	0.2	CD	_	_	_
20	%	%	NN	_	_	_
21	arabinose	arabinose	NN	_	_	_
22	at	at	IN	_	_	_
23	37	37	CD	_	_	_
24	°C	°c	NN	_	_	_
25	to	to	TO	_	_	_
26	and	and	CC	_	_	_
27	OD600nm	od600nm	NN	_	_	_
28	of	of	IN	_	_	_
29	0.2-0.25	0.2-0.25	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
31	ChIP-Seq	chip-seq	JJ	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	DL4184	dl4184	NN	_	_	_
34	biological	biological	JJ	_	_	_
35	repeat	repeat	NN	_	_	_
36	1	1	CD	_	_	_
37	RecA	reca	NN	_	_	_
38	ChIP	chip	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	DL4184	dl4184	NN	_	_	_
41	biological	biological	JJ	_	_	_
42	repeat	repeat	NN	_	_	_
43	2	2	CD	_	_	_
44	RecA	reca	NN	_	_	_
45	ChIP	chip	NN	_	_	_
46	_	_	NN	_	_	_
47	reanalyzed	reanalyze	VBN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	DL4201	dl4201	NN	_	_	_
50	biological	biological	JJ	_	_	_
51	repeat	repeat	NN	_	_	_
52	1	1	CD	_	_	_
53	RecA	reca	NN	_	_	_
54	ChIP	chip	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	DL4201	dl4201	NN	_	_	_
57	biological	biological	JJ	_	_	_
58	repeat	repeat	NN	_	_	_
59	2	2	CD	_	_	_
60	RecA	reca	NN	_	_	_
61	ChIP	chip	NN	_	_	_
62	_	_	NN	_	_	_
63	reanalyzed	reanalyze	VBN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	DL5699	dl5699	NN	_	_	_
66	biological	biological	JJ	_	_	_
67	repeat	repeat	NN	_	_	_
68	1	1	CD	_	_	_
69	RecA	reca	NN	_	_	_
70	ChIP	chip	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	DL5699	dl5699	NN	_	_	_
73	biological	biological	JJ	_	_	_
74	repeat	repeat	NN	_	_	_
75	2	2	CD	_	_	_
76	RecA	reca	NN	_	_	_
77	ChIP	chip	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	DL6204	dl6204	NN	_	_	_
80	biological	biological	JJ	_	_	_
81	repeat	repeat	NN	_	_	_
82	1	1	CD	_	_	_
83	RecA	reca	NN	_	_	_
84	ChIP	chip	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	DL6204	dl6204	NN	_	_	_
87	biological	biological	JJ	_	_	_
88	repeat	repeat	NN	_	_	_
89	2	2	CD	_	_	_
90	RecA	reca	NN	_	_	_
91	ChIP	chip	NN	_	_	_
92	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
93	Escherichia	escherichia	FW	Organism	_	_
94	coli	coli	FW	Organism	_	_
95	K-12	k-12	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	Genome	Genome	NNP	_	_	_
98	_	_	NNP	_	_	_
99	build	build	VB	_	_	_
100	:	:	:	_	_	_
101	DL4201	dl4201	NN	_	_	_
102	_	_	NN	_	_	_
103	in	in	IN	_	_	_
104	_	_	NN	_	_	_
105	lab	lab	NN	_	_	_
106	_	_	CD	_	_	_
107	reference	reference	NN	_	_	_
108	_	_	NN	_	_	_
109	genome	genome	NN	_	_	_
110	-LRB-	-lrb-	-LRB-	_	_	_
111	available	available	JJ	_	_	_
112	on	on	IN	_	_	_
113	series	series	NN	_	_	_
114	record	record	NN	_	_	_
115	-RRB-	-rrb-	-RRB-	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	genotype	genotype	NN	_	_	_
118	:	:	:	_	_	_
119	BW27784	bw27784	NN	_	_	_
120	delta	delta	NN	_	_	_
121	_	_	CD	_	_	_
122	recD	recd	NN	GEN	_	_
123	lacZ	lacz	NN	GEN	_	_
124	:	:	:	_	_	_
125	:	:	:	_	_	_
126	XXX	xxx	NN	_	_	_
127	mhpR	mhpr	NN	GEN	_	_
128	:	:	:	_	_	_
129	:	:	:	_	_	_
130	XXX	XXX	NNP	_	_	_
131	proA	proA	NNP	GEN	_	_
132	:	:	:	_	_	_
133	:	:	:	_	_	_
134	ISceIcs	isceic	NNS	_	_	_
135	tsx	tsx	NN	GEN	_	_
136	:	:	:	_	_	_
137	:	:	:	_	_	_
138	ISceIcs	isceic	NNS	_	_	_
139	PBAD-sbcDC	pbad-sbcdc	NN	_	_	_
140	lacZ	lacz	NN	GEN	_	_
141	+	+	CC	_	_	_
142	cynX	cynx	NN	GEN	_	_
143	:	:	:	_	_	_
144	:	:	:	_	_	_
145	GmR	gmr	NN	_	_	_
146	lacIq	laciq	NN	_	_	_
147	lacZX	laczx	NN	_	_	_
148	-	-	:	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	genotype	genotype	NN	_	_	_
151	:	:	:	_	_	_
152	BW27784	bw27784	NN	_	_	_
153	delta	delta	NN	_	_	_
154	_	_	CD	_	_	_
155	recD	recd	NN	GEN	_	_
156	lacZ	lacz	NN	GEN	_	_
157	:	:	:	_	_	_
158	:	:	:	_	_	_
159	XXX	xxx	NN	_	_	_
160	mhpR	mhpr	NN	GEN	_	_
161	:	:	:	_	_	_
162	:	:	:	_	_	_
163	XXX	XXX	NNP	_	_	_
164	proA	proA	NNP	GEN	_	_
165	:	:	:	_	_	_
166	:	:	:	_	_	_
167	ISceIcs	isceic	NNS	_	_	_
168	tsx	tsx	NN	GEN	_	_
169	:	:	:	_	_	_
170	:	:	:	_	_	_
171	ISceIcs	isceic	NNS	_	_	_
172	PBAD-sbcDC	pbad-sbcdc	NN	_	_	_
173	lacZ	lacz	NN	GEN	_	_
174	:	:	:	_	_	_
175	:	:	:	_	_	_
176	pal246	pal246	NN	_	_	_
177	cynX	cynx	NN	GEN	_	_
178	:	:	:	_	_	_
179	:	:	:	_	_	_
180	GmR	gmr	NN	_	_	_
181	lacIq	laciq	NN	_	_	_
182	lacZX	laczx	NN	_	_	_
183	-	-	:	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	genotype	genotype	NN	_	_	_
186	:	:	:	_	_	_
187	BW27784	bw27784	NN	_	_	_
188	lacZ	lacz	NN	GEN	_	_
189	:	:	:	_	_	_
190	:	:	:	_	_	_
191	XXX	xxx	NN	_	_	_
192	mhpR	mhpr	NN	GEN	_	_
193	:	:	:	_	_	_
194	:	:	:	_	_	_
195	XXX	XXX	NNP	_	_	_
196	proA	proA	NNP	GEN	_	_
197	:	:	:	_	_	_
198	:	:	:	_	_	_
199	ISceIcs	isceic	NNS	_	_	_
200	tsx	tsx	NN	GEN	_	_
201	:	:	:	_	_	_
202	:	:	:	_	_	_
203	ISceIcs	isceic	NNS	_	_	_
204	PBAD-sbcDC	pbad-sbcdc	NN	_	_	_
205	lacZ	lacz	NN	GEN	_	_
206	+	+	CC	_	_	_
207	cynX	cynx	NN	GEN	_	_
208	:	:	:	_	_	_
209	:	:	:	_	_	_
210	GmR	gmr	NN	_	_	_
211	lacIq	laciq	NN	_	_	_
212	lacZX	laczx	NN	_	_	_
213	-	-	:	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	genotype	genotype	NN	_	_	_
216	:	:	:	_	_	_
217	BW27784	bw27784	NN	_	_	_
218	lacZ	lacz	NN	GEN	_	_
219	:	:	:	_	_	_
220	:	:	:	_	_	_
221	XXX	xxx	NN	_	_	_
222	mhpR	mhpr	NN	GEN	_	_
223	:	:	:	_	_	_
224	:	:	:	_	_	_
225	XXX	XXX	NNP	_	_	_
226	proA	proA	NNP	GEN	_	_
227	:	:	:	_	_	_
228	:	:	:	_	_	_
229	ISceIcs	isceic	NNS	_	_	_
230	tsx	tsx	NN	GEN	_	_
231	:	:	:	_	_	_
232	:	:	:	_	_	_
233	ISceIcs	isceic	NNS	_	_	_
234	PBAD-sbcDC	pbad-sbcdc	NN	_	_	_
235	lacZ	lacz	NN	GEN	_	_
236	:	:	:	_	_	_
237	:	:	:	_	_	_
238	pal246	pal246	NN	_	_	_
239	cynX	cynx	NN	GEN	_	_
240	:	:	:	_	_	_
241	:	:	:	_	_	_
242	GmR	gmr	NN	_	_	_
243	lacIq	laciq	NN	_	_	_
244	lacZX	laczx	NN	_	_	_
245	-	-	:	_	_	_
246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
247	Normalisation	normalisation	NN	_	_	_
248	:	:	:	_	_	_
249	Counts	count	NNS	_	_	_
250	were	be	VBD	_	_	_
251	normalised	normalise	VBN	_	_	_
252	by	by	IN	_	_	_
253	applying	apply	VBG	_	_	_
254	a	a	DT	_	_	_
255	single	single	JJ	_	_	_
256	,	,	,	_	_	_
257	sample-specific	sample-specific	JJ	_	_	_
258	scaling	scaling	NN	_	_	_
259	factor	factor	NN	_	_	_
260	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	calculate	calculate	VB	_	_	_
3	this	this	DT	_	_	_
4	scaling	scaling	NN	_	_	_
5	factor	factor	NN	_	_	_
6	,	,	,	_	_	_
7	we	we	PRP	_	_	_
8	implemented	implement	VBD	_	_	_
9	the	the	DT	_	_	_
10	median	median	NN	_	_	_
11	of	of	IN	_	_	_
12	ratios	ratio	NNS	_	_	_
13	normalisation	normalisation	NN	_	_	_
14	of	of	IN	_	_	_
15	DESeq	deseq	NN	_	_	_
16	software	software	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Anders	Anders	NNP	_	_	_
19	,	,	,	_	_	_
20	S.	S.	NNP	_	_	_
21	and	and	CC	_	_	_
22	Huber	Huber	NNP	_	_	_
23	,	,	,	_	_	_
24	W.	W.	NNP	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	2010	2010	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	Differential	differential	JJ	_	_	_
29	expression	expression	NN	_	_	_
30	analysis	analysis	NN	_	_	_
31	for	for	IN	_	_	_
32	sequence	sequence	NN	_	_	_
33	count	count	NN	_	_	_
34	data	datum	NNS	_	_	_
35	.	.	.	_	_	_

1	Genome	Genome	NNP	_	_	_
2	Biol	Biol	NNP	_	_	_
3	,	,	,	_	_	_
4	11	11	CD	_	_	_
5	,	,	,	_	_	_
6	R106	r106	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	using	use	VBG	_	_	_
9	R.	R.	NNP	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Protein	protein	NN	_	_	_
12	DNA	dna	NN	_	_	_
13	interactions	interaction	NNS	_	_	_
14	were	be	VBD	_	_	_
15	crosslinked	crosslink	VBN	_	_	_
16	for	for	IN	_	_	_
17	10	10	CD	_	_	_
18	min	min	NN	_	_	_
19	at	at	IN	_	_	_
20	22.5	22.5	CD	_	_	_
21	C	c	NN	_	_	_
22	with	with	IN	_	_	_
23	1	1	CD	_	_	_
24	%	%	NN	_	_	_
25	formaldehyde	formaldehyde	NN	_	_	_
26	and	and	CC	_	_	_
27	quenched	quench	VBN	_	_	_
28	using	use	VBG	_	_	_
29	glycine	glycine	NN	_	_	_
30	to	to	TO	_	_	_
31	a	a	DT	_	_	_
32	final	final	JJ	_	_	_
33	concentration	concentration	NN	_	_	_
34	of	of	IN	_	_	_
35	0.5	0.5	CD	_	_	_
36	M	m	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
38	Raw	raw	NN	_	_	_
39	counts	count	NNS	_	_	_
40	of	of	IN	_	_	_
41	mapped	map	VBN	_	_	_
42	reads	read	VBZ	_	_	_
43	per	per	IN	_	_	_
44	reference	reference	NN	_	_	_
45	base	base	NN	_	_	_
46	pair	pair	NN	_	_	_
47	were	be	VBD	_	_	_
48	then	then	RB	_	_	_
49	calculated	calculate	VBN	_	_	_
50	using	use	VBG	_	_	_
51	SAMtools	samtool	NNS	_	_	_
52	software	software	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	with	with	IN	_	_	_
55	parameter	parameter	NN	_	_	_
56	--	--	:	_	_	_
57	d	d	NN	_	_	_
58	set	set	VBN	_	_	_
59	to	to	TO	_	_	_
60	10	10	CD	_	_	_
61	^	^	CD	_	_	_
62	6	6	CD	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	DL4184	dl4184	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	strain	strain	NN	_	_	_
7	:	:	:	_	_	_
8	DL4201	dl4201	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	strain	strain	NN	_	_	_
11	:	:	:	_	_	_
12	DL5966	dl5966	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	strain	strain	NN	_	_	_
15	:	:	:	_	_	_
16	DL6204	dl6204	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Supplementary	supplementary	JJ	_	_	_
19	_	_	NN	_	_	_
20	files	file	NNS	_	_	_
21	_	_	IN	_	_	_
22	format	format	NN	_	_	_
23	_	_	NN	_	_	_
24	and	and	CC	_	_	_
25	_	_	NN	_	_	_
26	content	content	NN	_	_	_
27	:	:	:	_	_	_
28	txt	txt	NN	_	_	_
29	files	file	NNS	_	_	_
30	of	of	IN	_	_	_
31	a	a	DT	_	_	_
32	matrix	matrix	NN	_	_	_
33	containing	contain	VBG	_	_	_
34	genome	genome	NN	_	_	_
35	position	position	NN	_	_	_
36	in	in	IN	_	_	_
37	column	column	NN	_	_	_
38	1	1	CD	_	_	_
39	and	and	CC	_	_	_
40	number	number	NN	_	_	_
41	of	of	IN	_	_	_
42	depth	depth	NN	_	_	_
43	of	of	IN	_	_	_
44	mapped	map	VBN	_	_	_
45	reads	read	VBZ	_	_	_
46	in	in	IN	_	_	_
47	column	column	NN	_	_	_
48	2	2	CD	_	_	_
49	.	.	.	_	_	_

1	Also	also	RB	_	_	_
2	,	,	,	_	_	_
3	in	in	IN	_	_	_
4	a	a	DT	_	_	_
5	CSV	CSV	NNP	_	_	_
6	file	file	NN	_	_	_
7	of	of	IN	_	_	_
8	a	a	DT	_	_	_
9	matrix	matrix	NN	_	_	_
10	containing	contain	VBG	_	_	_
11	genome	genome	NN	_	_	_
12	position	position	NN	_	_	_
13	in	in	IN	_	_	_
14	column	column	NN	_	_	_
15	1	1	CD	_	_	_
16	and	and	CC	_	_	_
17	subsequent	subsequent	JJ	_	_	_
18	coloumns	coloumn	NNS	_	_	_
19	with	with	IN	_	_	_
20	normalised	normalised	JJ	_	_	_
21	number	number	NN	_	_	_
22	of	of	IN	_	_	_
23	depth	depth	NN	_	_	_
24	of	of	IN	_	_	_
25	mapped	map	VBN	_	_	_
26	reads	read	VBZ	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	column	column	NN	_	_	_
29	names	name	NNS	_	_	_
30	have	have	VBP	_	_	_
31	the	the	DT	_	_	_
32	strain	strain	NN	_	_	_
33	number	number	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	.	.	.	_	_	_

1	CSV	CSV	NNP	_	_	_
2	file	file	NN	_	_	_
3	is	be	VBZ	_	_	_
4	on	on	IN	_	_	_
5	the	the	DT	_	_	_
6	series	series	NN	_	_	_
7	record	record	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	induced	induce	VBN	_	_	_
5	DNA	dna	NN	_	_	_
6	double	double	JJ	_	_	_
7	strand	strand	NN	_	_	_
8	break	break	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	treatment	treatment	NN	_	_	_
11	:	:	:	_	_	_
12	none	none	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	AG102	ag102	NN	_	_	_
15	was	be	VBD	_	_	_
16	previously	previously	RB	_	_	_
17	derived	derive	VBN	_	_	_
18	from	from	IN	_	_	_
19	AG100	ag100	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	K-12	k-12	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

1	AG102	ag102	NN	_	_	_
2	is	be	VBZ	_	_	_
3	drug	drug	NN	_	_	_
4	hyper-resistant	hyper-resistant	JJ	_	_	_
5	due	due	JJ	_	_	_
6	to	to	TO	_	_	_
7	a	a	DT	_	_	_
8	mutation	mutation	NN	_	_	_
9	in	in	IN	_	_	_
10	marR	marr	NN	GEN	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	marR1	marr1	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	which	which	WDT	_	_	_
15	increases	increase	VBZ	_	_	_
16	expression	expression	NN	_	_	_
17	of	of	IN	_	_	_
18	MarA	mara	NN	TF	_	_
19	,	,	,	_	_	_
20	a	a	DT	_	_	_
21	global	global	JJ	_	_	_
22	regulator	regulator	NN	_	_	_
23	,	,	,	_	_	_
24	which	which	WDT	_	_	_
25	in	in	IN	_	_	_
26	turn	turn	NN	_	_	_
27	results	result	VBZ	_	_	_
28	in	in	IN	_	_	_
29	overexpression	overexpression	NN	_	_	_
30	of	of	IN	_	_	_
31	the	the	DT	_	_	_
32	AcrAB-TolC	acrab-tolc	NN	_	_	_
33	multidrug	multidrug	JJ	_	_	_
34	efflux	efflux	NN	_	_	_
35	system	system	NN	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cholic	cholic	JJ	_	_	_
3	Acid	acid	NN	_	_	_
4	Treatment	treatment	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	DMSO-Only	dmso-only	JJ	_	_	_
7	Treatment	treatment	NN	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	E.	E.	NNP	_	_	_
10	coli	coli	NN	_	_	_
11	Cholic	Cholic	NNP	_	_	_
12	Acid	Acid	NNP	_	_	_
13	Treatment	treatment	NN	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	E.	E.	NNP	_	_	_
16	coli	coli	NN	_	_	_
17	Estradiol	Estradiol	NNP	_	_	_
18	Treatment	Treatment	NNP	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	E.	E.	NNP	_	_	_
21	coli	coli	NN	_	_	_
22	Hydrocortisone	Hydrocortisone	NNP	_	_	_
23	Treatment	Treatment	NNP	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	E.	E.	NNP	_	_	_
26	coli	coli	NN	_	_	_
27	Progesterone	progesterone	NN	_	_	_
28	Treatment	treatment	NN	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	E.	E.	NNP	_	_	_
31	coli	coli	NN	_	_	_
32	was	be	VBD	_	_	_
33	grown	grow	VBN	_	_	_
34	to	to	TO	_	_	_
35	mid-log	mid-log	JJ	_	_	_
36	phase	phase	NN	_	_	_
37	in	in	IN	_	_	_
38	Luria-Bertani	Luria-Bertani	NNP	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	Miller	Miller	NNP	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	broth	broth	JJ	_	_	_
43	medium	medium	NN	_	_	_
44	at	at	IN	_	_	_
45	37C	37c	NN	_	_	_
46	in	in	IN	_	_	_
47	the	the	DT	_	_	_
48	presence	presence	NN	_	_	_
49	of	of	IN	_	_	_
50	dimethyl	dimethyl	JJ	_	_	_
51	sulfoxide	sulfoxide	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	DMSO	dmso	NN	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	-	-	:	_	_	_
56	dissolved	dissolve	VBN	_	_	_
57	cholic	cholic	JJ	_	_	_
58	acid	acid	NN	_	_	_
59	at	at	IN	_	_	_
60	1	1	CD	_	_	_
61	mM	mm	NN	KWSUPP	_	_
62	final	final	JJ	_	_	_
63	culture	culture	NN	_	_	_
64	concentration	concentration	NN	_	_	_
65	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	was	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	to	to	TO	_	_	_
7	mid-log	mid-log	JJ	_	_	_
8	phase	phase	NN	_	_	_
9	in	in	IN	_	_	_
10	Luria-Bertani	Luria-Bertani	NNP	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Miller	Miller	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	broth	broth	JJ	_	_	_
15	medium	medium	NN	_	_	_
16	at	at	IN	_	_	_
17	37C	37c	NN	_	_	_
18	in	in	IN	_	_	_
19	the	the	DT	_	_	_
20	presence	presence	NN	_	_	_
21	of	of	IN	_	_	_
22	dimethyl	dimethyl	JJ	_	_	_
23	sulfoxide	sulfoxide	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	DMSO	dmso	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	-	-	:	_	_	_
28	dissolved	dissolve	VBN	_	_	_
29	estradiol	estradiol	NN	_	_	_
30	at	at	IN	_	_	_
31	1	1	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	final	final	JJ	_	_	_
34	culture	culture	NN	_	_	_
35	concentration	concentration	NN	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	was	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	to	to	TO	_	_	_
7	mid-log	mid-log	JJ	_	_	_
8	phase	phase	NN	_	_	_
9	in	in	IN	_	_	_
10	Luria-Bertani	Luria-Bertani	NNP	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Miller	Miller	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	broth	broth	JJ	_	_	_
15	medium	medium	NN	_	_	_
16	at	at	IN	_	_	_
17	37C	37c	NN	_	_	_
18	in	in	IN	_	_	_
19	the	the	DT	_	_	_
20	presence	presence	NN	_	_	_
21	of	of	IN	_	_	_
22	dimethyl	dimethyl	JJ	_	_	_
23	sulfoxide	sulfoxide	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	DMSO	dmso	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	-	-	:	_	_	_
28	dissolved	dissolve	VBN	_	_	_
29	hydrocortisone	hydrocortisone	NN	_	_	_
30	at	at	IN	_	_	_
31	1	1	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	final	final	JJ	_	_	_
34	culture	culture	NN	_	_	_
35	concentration	concentration	NN	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	was	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	to	to	TO	_	_	_
7	mid-log	mid-log	JJ	_	_	_
8	phase	phase	NN	_	_	_
9	in	in	IN	_	_	_
10	Luria-Bertani	Luria-Bertani	NNP	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Miller	Miller	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	broth	broth	JJ	_	_	_
15	medium	medium	NN	_	_	_
16	at	at	IN	_	_	_
17	37C	37c	NN	_	_	_
18	in	in	IN	_	_	_
19	the	the	DT	_	_	_
20	presence	presence	NN	_	_	_
21	of	of	IN	_	_	_
22	dimethyl	dimethyl	JJ	_	_	_
23	sulfoxide	sulfoxide	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	DMSO	dmso	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	-	-	:	_	_	_
28	dissolved	dissolve	VBN	_	_	_
29	progesterone	progesterone	NN	_	_	_
30	at	at	IN	_	_	_
31	1	1	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	final	final	JJ	_	_	_
34	culture	culture	NN	_	_	_
35	concentration	concentration	NN	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	was	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	to	to	TO	_	_	_
7	mid-log	mid-log	JJ	_	_	_
8	phase	phase	NN	_	_	_
9	in	in	IN	_	_	_
10	Luria-Bertani	Luria-Bertani	NNP	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Miller	Miller	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	broth	broth	JJ	_	_	_
15	medium	medium	NN	_	_	_
16	at	at	IN	_	_	_
17	37C	37c	NN	_	_	_
18	in	in	IN	_	_	_
19	the	the	DT	_	_	_
20	presence	presence	NN	_	_	_
21	of	of	IN	_	_	_
22	dimethyl	dimethyl	JJ	_	_	_
23	sulfoxide	sulfoxide	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	DMSO	dmso	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	-	-	:	_	_	_
28	only	only	RB	_	_	_
29	steroid	steroid	NN	_	_	_
30	carrier	carrier	NN	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Estradiol	estradiol	NN	_	_	_
6	Treatment	treatment	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Hydrocortisone	hydrocortisone	NN	_	_	_
9	Treatment	treatment	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Progesterone	progesterone	NN	_	_	_
12	Treatment	treatment	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
14	The	the	DT	_	_	_
15	analyzed	analyze	VBN	_	_	_
16	data	datum	NNS	_	_	_
17	were	be	VBD	_	_	_
18	imported	import	VBN	_	_	_
19	to	to	TO	_	_	_
20	ArrayTrack	ArrayTrack	NNP	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	NCTR	NCTR	NNP	_	_	_
23	Center	Center	NNP	_	_	_
24	for	for	IN	_	_	_
25	Toxicoinformatics	Toxicoinformatics	NNPS	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	raw	raw	JJ	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	normalized	normalize	VBN	_	_	_
6	by	by	IN	_	_	_
7	using	use	VBG	_	_	_
8	median	median	NN	_	_	_
9	channel	channel	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	intensity	intensity	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	scaling	scale	VBG	_	_	_
14	with	with	IN	_	_	_
15	no	no	DT	_	_	_
16	background	background	NN	_	_	_
17	subtraction	subtraction	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	Qiagen	Qiagen	NNP	_	_	_
8	RNeasy	RNeasy	NNP	_	_	_
9	kit	kit	NN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Bacteria	bacterium	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	batch	batch	NN	_	_	_
7	or	or	CC	_	_	_
8	bioreactor	bioreactor	NN	_	_	_
9	vessels	vessel	NNS	_	_	_
10	in	in	IN	_	_	_
11	M9	m9	NN	MED	_	_
12	minimal	minimal	JJ	MED	_	_
13	media	media	NNS	MED	_	_
14	supplemented	supplement	VBN	_	_	_
15	with	with	IN	_	_	_
16	0.4	0.4	CD	_	_	_
17	%	%	NN	_	_	_
18	glucose	glucose	NN	SUPP	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	DNA	dna	NN	_	_	_
3	extraction	extraction	NN	_	_	_
4	:	:	:	_	_	_
5	Genomic	genomic	JJ	_	_	_
6	DNA	dna	NN	_	_	_
7	was	be	VBD	_	_	_
8	isolated	isolate	VBN	_	_	_
9	and	and	CC	_	_	_
10	purified	purify	VBN	_	_	_
11	according	accord	VBG	_	_	_
12	to	to	TO	_	_	_
13	standard	standard	JJ	_	_	_
14	procedures	procedure	NNS	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Ausubel	Ausubel	NNP	_	_	_
17	et	et	FW	_	_	_
18	al.	al.	FW	_	_	_
19	1994	1994	CD	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	Genomic	genomic	JJ	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	fragmented	fragment	VBN	_	_	_
5	by	by	IN	_	_	_
6	nebulization	nebulization	NN	_	_	_
7	as	as	IN	_	_	_
8	described	describe	VBN	_	_	_
9	by	by	IN	_	_	_
10	Girgis	Girgis	NNP	_	_	_
11	et	et	FW	_	_	_
12	al.	al.	FW	_	_	_
13	.	.	.	_	_	_

1	PLoS	PLoS	NNP	_	_	_
2	Genetics	Genetics	NNP	_	_	_
3	3	3	CD	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	9	9	CD	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	:	:	:	_	_	_
8	e154	e154	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	2007	2007	CD	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	and	and	CC	_	_	_
13	purified	purify	VBN	_	_	_
14	by	by	IN	_	_	_
15	phenol	phenol	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Elements	element	NNS	_	_	_
18	with	with	IN	_	_	_
19	poor	poor	JJ	_	_	_
20	spot	spot	NN	_	_	_
21	morphology	morphology	NN	_	_	_
22	or	or	CC	_	_	_
23	exhibiting	exhibit	VBG	_	_	_
24	uneven	uneven	JJ	_	_	_
25	hybridization	hybridization	NN	_	_	_
26	caused	cause	VBN	_	_	_
27	by	by	IN	_	_	_
28	dust	dust	NN	_	_	_
29	particles	particle	NNS	_	_	_
30	or	or	CC	_	_	_
31	scratches	scratch	NNS	_	_	_
32	,	,	,	_	_	_
33	were	be	VBD	_	_	_
34	flagged	flag	VBN	_	_	_
35	manually	manually	RB	_	_	_
36	and	and	CC	_	_	_
37	excluded	exclude	VBN	_	_	_
38	from	from	IN	_	_	_
39	further	further	JJ	_	_	_
40	analyses	analysis	NNS	_	_	_
41	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	local	local	JJ	_	_	_
3	background	background	NN	_	_	_
4	subtraction	subtraction	NN	_	_	_
5	and	and	CC	_	_	_
6	global	global	JJ	_	_	_
7	normalization	normalization	NN	_	_	_
8	relative	relative	JJ	_	_	_
9	to	to	TO	_	_	_
10	the	the	DT	_	_	_
11	genomic	genomic	JJ	_	_	_
12	DNA	dna	NN	_	_	_
13	reference	reference	NN	_	_	_
14	,	,	,	_	_	_
15	duplicate	duplicate	VB	_	_	_
16	measurements	measurement	NNS	_	_	_
17	on	on	IN	_	_	_
18	the	the	DT	_	_	_
19	same	same	JJ	_	_	_
20	array	array	NN	_	_	_
21	were	be	VBD	_	_	_
22	averaged	average	VBN	_	_	_
23	,	,	,	_	_	_
24	yielding	yield	VBG	_	_	_
25	a	a	DT	_	_	_
26	single	single	JJ	_	_	_
27	vector	vector	NN	_	_	_
28	for	for	IN	_	_	_
29	each	each	DT	_	_	_
30	time-point	time-point	NN	_	_	_
31	across	across	IN	_	_	_
32	a	a	DT	_	_	_
33	perturbation	perturbation	NN	_	_	_
34	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	data	datum	NNS	_	_	_
3	from	from	IN	_	_	_
4	all	all	DT	_	_	_
5	hybridizations	hybridization	NNS	_	_	_
6	were	be	VBD	_	_	_
7	combined	combine	VBN	_	_	_
8	into	into	IN	_	_	_
9	a	a	DT	_	_	_
10	matrix	matrix	NN	_	_	_
11	and	and	CC	_	_	_
12	scaled	scale	VBD	_	_	_
13	relative	relative	JJ	_	_	_
14	to	to	TO	_	_	_
15	each	each	DT	_	_	_
16	other	other	JJ	_	_	_
17	using	use	VBG	_	_	_
18	quantile-normalization	quantile-normalization	NN	_	_	_
19	as	as	IN	_	_	_
20	implemented	implement	VBN	_	_	_
21	in	in	IN	_	_	_
22	the	the	DT	_	_	_
23	Matlab	Matlab	NNP	_	_	_
24	Bioinformatics	Bioinformatics	NNPS	_	_	_
25	toolbox	toolbox	NN	_	_	_
26	.	.	.	_	_	_

1	Biological	biological	JJ	_	_	_
2	duplicates	duplicate	NNS	_	_	_
3	from	from	IN	_	_	_
4	all	all	DT	_	_	_
5	experiments	experiment	NNS	_	_	_
6	were	be	VBD	_	_	_
7	averaged	average	VBN	_	_	_
8	,	,	,	_	_	_
9	leading	lead	VBG	_	_	_
10	to	to	TO	_	_	_
11	a	a	DT	_	_	_
12	single	single	JJ	_	_	_
13	set	set	NN	_	_	_
14	of	of	IN	_	_	_
15	time-series	time-series	NNS	_	_	_
16	data	datum	NNS	_	_	_
17	for	for	IN	_	_	_
18	each	each	DT	_	_	_
19	perturbation	perturbation	NN	_	_	_
20	.	.	.	_	_	_

1	Seven	seven	CD	_	_	_
2	time-points	time-point	NNS	_	_	_
3	were	be	VBD	_	_	_
4	assayed	assay	VBN	_	_	_
5	for	for	IN	_	_	_
6	each	each	DT	_	_	_
7	perturbation	perturbation	NN	_	_	_
8	,	,	,	_	_	_
9	corresponding	correspond	VBG	_	_	_
10	to	to	TO	_	_	_
11	0	0	CD	_	_	_
12	,	,	,	_	_	_
13	4	4	CD	_	_	_
14	,	,	,	_	_	_
15	8	8	CD	_	_	_
16	,	,	,	_	_	_
17	12	12	CD	_	_	_
18	,	,	,	_	_	_
19	20	20	CD	_	_	_
20	,	,	,	_	_	_
21	28	28	CD	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	44	44	CD	_	_	_
25	minutes	minute	NNS	_	_	_
26	post	post	JJ	_	_	_
27	transition	transition	NN	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	K-12	k-12	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	evolved	evolve	VBD	_	_	_
7	_	_	CD	_	_	_
8	temperature	temperature	NN	_	_	_
9	_	_	CD	_	_	_
10	Up	up	IN	_	_	_
11	_	_	CD	_	_	_
12	0	0	CD	_	_	_
13	min	min	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	evolved	evolve	VBD	_	_	_
16	_	_	CD	_	_	_
17	temperature	temperature	NN	_	_	_
18	_	_	VBD	_	_	_
19	Up	up	RP	_	_	_
20	_	_	SYM	_	_	_
21	16	16	CD	_	_	_
22	min	min	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	evolved	evolve	VBD	_	_	_
25	_	_	CD	_	_	_
26	temperature	temperature	NN	_	_	_
27	_	_	VBD	_	_	_
28	Up	up	RP	_	_	_
29	_	_	SYM	_	_	_
30	44	44	CD	_	_	_
31	min	min	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	evolved	evolve	VBD	_	_	_
34	temperature	temperature	NN	_	_	_
35	up	up	IN	_	_	_
36	shift	shift	NN	_	_	_
37	0	0	CD	_	_	_
38	min	min	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	evolved	evolve	VBD	_	_	_
41	temperature	temperature	NN	_	_	_
42	up	up	IN	_	_	_
43	shift	shift	NN	_	_	_
44	16	16	CD	_	_	_
45	min	min	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	evolved	evolve	VBD	_	_	_
48	temperature	temperature	NN	_	_	_
49	up	up	IN	_	_	_
50	shift	shift	NN	_	_	_
51	44	44	CD	_	_	_
52	min	min	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
54	genomic	genomic	JJ	_	_	_
55	DNA	dna	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
57	Genomic	genomic	JJ	_	_	_
58	DNA	dna	NN	_	_	_
59	served	serve	VBD	_	_	_
60	as	as	IN	_	_	_
61	a	a	DT	_	_	_
62	universal	universal	JJ	_	_	_
63	reference	reference	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	MG1655	mg1655	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	oxygen	oxygen	NN	_	_	_
68	_	_	CD	_	_	_
69	down	down	IN	_	_	_
70	_	_	CD	_	_	_
71	0	0	CD	_	_	_
72	min	min	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	oxygen	oxygen	NN	_	_	_
75	_	_	CD	_	_	_
76	down	down	IN	_	_	_
77	_	_	CD	_	_	_
78	12	12	CD	_	_	_
79	min	min	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	oxygen	oxygen	NN	_	_	_
82	_	_	CD	_	_	_
83	down	down	IN	_	_	_
84	_	_	CD	_	_	_
85	20	20	CD	_	_	_
86	min	min	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	oxygen	oxygen	NN	_	_	_
89	_	_	CD	_	_	_
90	down	down	IN	_	_	_
91	_	_	CD	_	_	_
92	28	28	CD	_	_	_
93	min	min	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	oxygen	oxygen	NN	_	_	_
96	_	_	CD	_	_	_
97	down	down	IN	_	_	_
98	_	_	CD	_	_	_
99	44	44	CD	_	_	_
100	min	min	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	oxygen	oxygen	NN	_	_	_
103	_	_	CD	_	_	_
104	down	down	IN	_	_	_
105	_	_	CD	_	_	_
106	4	4	CD	_	_	_
107	min	min	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	oxygen	oxygen	NN	_	_	_
110	_	_	CD	_	_	_
111	down	down	IN	_	_	_
112	_	_	CD	_	_	_
113	8	8	CD	_	_	_
114	min	min	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	oxygen	oxygen	NN	_	_	_
117	down	down	IN	_	_	_
118	shift	shift	NN	_	_	_
119	,	,	,	_	_	_
120	0	0	CD	_	_	_
121	min	min	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	oxygen	oxygen	NN	_	_	_
124	down	down	IN	_	_	_
125	shift	shift	NN	_	_	_
126	,	,	,	_	_	_
127	12	12	CD	_	_	_
128	min	min	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	oxygen	oxygen	NN	_	_	_
131	down	down	IN	_	_	_
132	shift	shift	NN	_	_	_
133	,	,	,	_	_	_
134	20	20	CD	_	_	_
135	min	min	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	oxygen	oxygen	NN	_	_	_
138	down	down	IN	_	_	_
139	shift	shift	NN	_	_	_
140	,	,	,	_	_	_
141	28	28	CD	_	_	_
142	min	min	NN	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	oxygen	oxygen	NN	_	_	_
145	down	down	IN	_	_	_
146	shift	shift	NN	_	_	_
147	,	,	,	_	_	_
148	44	44	CD	_	_	_
149	min	min	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	oxygen	oxygen	NN	_	_	_
152	down	down	IN	_	_	_
153	shift	shift	NN	_	_	_
154	,	,	,	_	_	_
155	4	4	CD	_	_	_
156	min	min	NN	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	oxygen	oxygen	NN	_	_	_
159	down	down	IN	_	_	_
160	shift	shift	NN	_	_	_
161	,	,	,	_	_	_
162	8	8	CD	_	_	_
163	min	min	NN	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	oxygen	oxygen	NN	_	_	_
166	_	_	CD	_	_	_
167	Up	up	IN	_	_	_
168	_	_	CD	_	_	_
169	0	0	CD	_	_	_
170	min	min	NN	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	oxygen	oxygen	NN	_	_	_
173	_	_	CD	_	_	_
174	Up	up	IN	_	_	_
175	_	_	CD	_	_	_
176	12	12	CD	_	_	_
177	min	min	NN	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	oxygen	oxygen	NN	_	_	_
180	_	_	CD	_	_	_
181	Up	up	IN	_	_	_
182	_	_	CD	_	_	_
183	20	20	CD	_	_	_
184	min	min	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	oxygen	oxygen	NN	_	_	_
187	_	_	CD	_	_	_
188	Up	up	IN	_	_	_
189	_	_	CD	_	_	_
190	28	28	CD	_	_	_
191	min	min	NN	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	oxygen	oxygen	NN	_	_	_
194	_	_	CD	_	_	_
195	Up	up	IN	_	_	_
196	_	_	CD	_	_	_
197	44	44	CD	_	_	_
198	min	min	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	oxygen	oxygen	NN	_	_	_
201	_	_	CD	_	_	_
202	Up	up	IN	_	_	_
203	_	_	CD	_	_	_
204	4	4	CD	_	_	_
205	min	min	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	oxygen	oxygen	NN	_	_	_
208	_	_	CD	_	_	_
209	Up	up	IN	_	_	_
210	_	_	CD	_	_	_
211	8	8	CD	_	_	_
212	min	min	NN	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	oxygen	oxygen	NN	_	_	_
215	up	up	IN	_	_	_
216	shift	shift	NN	_	_	_
217	,	,	,	_	_	_
218	0	0	CD	_	_	_
219	min	min	NN	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	oxygen	oxygen	NN	_	_	_
222	up	up	IN	_	_	_
223	shift	shift	NN	_	_	_
224	,	,	,	_	_	_
225	12	12	CD	_	_	_
226	min	min	NN	_	_	_
227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
228	oxygen	oxygen	NN	_	_	_
229	up	up	IN	_	_	_
230	shift	shift	NN	_	_	_
231	,	,	,	_	_	_
232	20	20	CD	_	_	_
233	min	min	NN	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	oxygen	oxygen	NN	_	_	_
236	up	up	IN	_	_	_
237	shift	shift	NN	_	_	_
238	,	,	,	_	_	_
239	28	28	CD	_	_	_
240	min	min	NN	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	oxygen	oxygen	NN	_	_	_
243	up	up	IN	_	_	_
244	shift	shift	NN	_	_	_
245	,	,	,	_	_	_
246	44	44	CD	_	_	_
247	min	min	NN	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
249	oxygen	oxygen	NN	_	_	_
250	up	up	IN	_	_	_
251	shift	shift	NN	_	_	_
252	,	,	,	_	_	_
253	4	4	CD	_	_	_
254	min	min	NN	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	oxygen	oxygen	NN	_	_	_
257	up	up	IN	_	_	_
258	shift	shift	NN	_	_	_
259	,	,	,	_	_	_
260	8	8	CD	_	_	_
261	min	min	NN	_	_	_
262	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
263	parental	parental	JJ	_	_	_
264	_	_	NN	_	_	_
265	temperature	temperature	NN	_	_	_
266	_	_	CD	_	_	_
267	Up	up	IN	_	_	_
268	_	_	CD	_	_	_
269	0	0	CD	_	_	_
270	min	min	NN	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	parental	parental	JJ	_	_	_
273	_	_	NN	_	_	_
274	temperature	temperature	NN	_	_	_
275	_	_	VBD	_	_	_
276	Up	up	RP	_	_	_
277	_	_	SYM	_	_	_
278	16	16	CD	_	_	_
279	min	min	NN	_	_	_
280	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
281	parental	parental	JJ	_	_	_
282	_	_	NN	_	_	_
283	temperature	temperature	NN	_	_	_
284	_	_	VBD	_	_	_
285	Up	up	RP	_	_	_
286	_	_	SYM	_	_	_
287	44	44	CD	_	_	_
288	min	min	NN	_	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
290	parental	parental	JJ	_	_	_
291	temperature	temperature	NN	_	_	_
292	up	up	IN	_	_	_
293	shift	shift	NN	_	_	_
294	0	0	CD	_	_	_
295	min	min	NN	_	_	_
296	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
297	parental	parental	JJ	_	_	_
298	temperature	temperature	NN	_	_	_
299	up	up	IN	_	_	_
300	shift	shift	NN	_	_	_
301	16	16	CD	_	_	_
302	min	min	NN	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
304	parental	parental	JJ	_	_	_
305	temperature	temperature	NN	_	_	_
306	up	up	IN	_	_	_
307	shift	shift	NN	_	_	_
308	44	44	CD	_	_	_
309	min	min	NN	_	_	_
310	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
311	Physiological	physiological	JJ	_	_	_
312	perturbations	perturbation	NNS	_	_	_
313	were	be	VBD	_	_	_
314	carried	carry	VBN	_	_	_
315	out	out	RP	_	_	_
316	under	under	IN	_	_	_
317	a	a	DT	_	_	_
318	controlled	controlled	JJ	_	_	_
319	environment	environment	NN	_	_	_
320	in	in	IN	_	_	_
321	the	the	DT	_	_	_
322	context	context	NN	_	_	_
323	of	of	IN	_	_	_
324	bioreactor	bioreactor	NN	_	_	_
325	-LRB-	-lrb-	-LRB-	_	_	_
326	Bioflo	bioflo	NN	_	_	_
327	110	110	CD	_	_	_
328	,	,	,	_	_	_
329	New	New	NNP	_	_	_
330	Brunswick	Brunswick	NNP	_	_	_
331	Scientific	Scientific	NNP	_	_	_
332	-RRB-	-rrb-	-RRB-	_	_	_
333	growth	growth	NN	_	_	_
334	.	.	.	_	_	_

1	Thermoelectric	Thermoelectric	NNP	_	_	_
2	sensors	sensor	NNS	_	_	_
3	and	and	CC	_	_	_
4	heaters	heater	NNS	_	_	_
5	were	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	to	to	TO	_	_	_
8	shift	shift	VB	_	_	_
9	temperature	temperature	NN	_	_	_
10	profiles	profile	NNS	_	_	_
11	between	between	IN	_	_	_
12	250	250	CD	_	_	_
13	C	c	NN	_	_	_
14	and	and	CC	_	_	_
15	370	370	CD	_	_	_
16	C	c	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	polarographic	polarographic	JJ	_	_	_
20	dissolved	dissolve	VBN	_	_	_
21	oxygen	oxygen	NN	_	_	_
22	sensors	sensor	NNS	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Mettler	Mettler	NNP	_	_	_
25	Toledo	Toledo	NNP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	and	and	CC	_	_	_
28	nitrogen	nitrogen	NN	_	_	_
29	gas	gas	NN	_	_	_
30	was	be	VBD	_	_	_
31	used	use	VBN	_	_	_
32	to	to	TO	_	_	_
33	rapidly	rapidly	RB	_	_	_
34	change	change	VB	_	_	_
35	oxygen	oxygen	NN	_	_	_
36	saturation	saturation	NN	_	_	_
37	between	between	IN	_	_	_
38	anaerobic	anaerobic	JJ	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	0	0	CD	_	_	_
41	%	%	NN	_	_	_
42	dissolved	dissolve	VBN	_	_	_
43	oxygen	oxygen	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	and	and	CC	_	_	_
46	aerobic	aerobic	JJ	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	16-21	16-21	CD	_	_	_
49	%	%	NN	_	_	_
50	dissolved	dissolve	VBN	_	_	_
51	oxygen	oxygen	NN	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	condition	condition	NN	_	_	_
54	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	extraction	extraction	NN	_	_	_
4	:	:	:	_	_	_
5	A	a	DT	_	_	_
6	hot-phenol	hot-phenol	NN	_	_	_
7	procedure	procedure	NN	_	_	_
8	was	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	to	to	TO	_	_	_
11	extract	extract	VB	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	pellets	pellet	NNS	_	_	_
3	were	be	VBD	_	_	_
4	lysed	lyse	VBN	_	_	_
5	with	with	IN	_	_	_
6	500	500	CD	_	_	_
7	μl	μl	NN	_	_	_
8	TE	te	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	pH8	ph8	NN	_	_	_
11	.0	.0	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	,	,	,	_	_	_
14	50	50	CD	_	_	_
15	μl	μl	NN	_	_	_
16	10	10	CD	_	_	_
17	%	%	NN	_	_	_
18	SDS	sds	NN	_	_	_
19	and	and	CC	_	_	_
20	lysozyme	lysozyme	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	0.5	0.5	CD	_	_	_
23	mg	mg	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	temperature	temperature	NN	_	_	_
26	_	_	CD	_	_	_
27	down	down	IN	_	_	_
28	_	_	CD	_	_	_
29	0	0	CD	_	_	_
30	min	min	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	temperature	temperature	NN	_	_	_
33	_	_	CD	_	_	_
34	down	down	IN	_	_	_
35	_	_	CD	_	_	_
36	12	12	CD	_	_	_
37	min	min	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	temperature	temperature	NN	_	_	_
40	_	_	CD	_	_	_
41	down	down	IN	_	_	_
42	_	_	CD	_	_	_
43	20	20	CD	_	_	_
44	min	min	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	temperature	temperature	NN	_	_	_
47	_	_	CD	_	_	_
48	down	down	IN	_	_	_
49	_	_	CD	_	_	_
50	28	28	CD	_	_	_
51	min	min	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	temperature	temperature	NN	_	_	_
54	_	_	CD	_	_	_
55	down	down	IN	_	_	_
56	_	_	CD	_	_	_
57	44	44	CD	_	_	_
58	min	min	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	temperature	temperature	NN	_	_	_
61	_	_	CD	_	_	_
62	down	down	IN	_	_	_
63	_	_	CD	_	_	_
64	4	4	CD	_	_	_
65	min	min	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	temperature	temperature	NN	_	_	_
68	_	_	CD	_	_	_
69	down	down	IN	_	_	_
70	_	_	CD	_	_	_
71	8	8	CD	_	_	_
72	min	min	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	temperature	temperature	NN	_	_	_
75	down	down	IN	_	_	_
76	shift	shift	NN	_	_	_
77	,	,	,	_	_	_
78	0	0	CD	_	_	_
79	min	min	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	temperature	temperature	NN	_	_	_
82	down	down	IN	_	_	_
83	shift	shift	NN	_	_	_
84	,	,	,	_	_	_
85	12	12	CD	_	_	_
86	min	min	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	temperature	temperature	NN	_	_	_
89	down	down	IN	_	_	_
90	shift	shift	NN	_	_	_
91	,	,	,	_	_	_
92	20	20	CD	_	_	_
93	min	min	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	temperature	temperature	NN	_	_	_
96	down	down	IN	_	_	_
97	shift	shift	NN	_	_	_
98	,	,	,	_	_	_
99	28	28	CD	_	_	_
100	min	min	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	temperature	temperature	NN	_	_	_
103	down	down	IN	_	_	_
104	shift	shift	NN	_	_	_
105	,	,	,	_	_	_
106	44	44	CD	_	_	_
107	min	min	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	temperature	temperature	NN	_	_	_
110	down	down	IN	_	_	_
111	shift	shift	NN	_	_	_
112	,	,	,	_	_	_
113	4	4	CD	_	_	_
114	min	min	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	temperature	temperature	NN	_	_	_
117	down	down	IN	_	_	_
118	shift	shift	NN	_	_	_
119	,	,	,	_	_	_
120	8	8	CD	_	_	_
121	min	min	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	temperature	temperature	NN	_	_	_
124	_	_	CD	_	_	_
125	Up	up	IN	_	_	_
126	_	_	CD	_	_	_
127	0	0	CD	_	_	_
128	min	min	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	temperature	temperature	NN	_	_	_
131	_	_	VBD	_	_	_
132	Up	up	RP	_	_	_
133	_	_	SYM	_	_	_
134	12	12	CD	_	_	_
135	min	min	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	temperature	temperature	NN	_	_	_
138	_	_	VBD	_	_	_
139	Up	up	RP	_	_	_
140	_	_	SYM	_	_	_
141	20	20	CD	_	_	_
142	min	min	NN	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	temperature	temperature	NN	_	_	_
145	_	_	VBD	_	_	_
146	Up	up	RP	_	_	_
147	_	_	SYM	_	_	_
148	28	28	CD	_	_	_
149	min	min	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	temperature	temperature	NN	_	_	_
152	_	_	VBD	_	_	_
153	Up	up	RP	_	_	_
154	_	_	SYM	_	_	_
155	44	44	CD	_	_	_
156	min	min	NN	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	temperature	temperature	NN	_	_	_
159	_	_	VBD	_	_	_
160	Up	up	RP	_	_	_
161	_	_	SYM	_	_	_
162	4	4	CD	_	_	_
163	min	min	NN	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	temperature	temperature	NN	_	_	_
166	_	_	VBD	_	_	_
167	Up	up	RP	_	_	_
168	_	_	SYM	_	_	_
169	8	8	CD	_	_	_
170	min	min	NN	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	temperature	temperature	NN	_	_	_
173	up	up	IN	_	_	_
174	shift	shift	NN	_	_	_
175	,	,	,	_	_	_
176	0	0	CD	_	_	_
177	min	min	NN	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	temperature	temperature	NN	_	_	_
180	up	up	IN	_	_	_
181	shift	shift	NN	_	_	_
182	,	,	,	_	_	_
183	12	12	CD	_	_	_
184	min	min	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	temperature	temperature	NN	_	_	_
187	up	up	IN	_	_	_
188	shift	shift	NN	_	_	_
189	,	,	,	_	_	_
190	20	20	CD	_	_	_
191	min	min	NN	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	temperature	temperature	NN	_	_	_
194	up	up	IN	_	_	_
195	shift	shift	NN	_	_	_
196	,	,	,	_	_	_
197	28	28	CD	_	_	_
198	min	min	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	temperature	temperature	NN	_	_	_
201	up	up	IN	_	_	_
202	shift	shift	NN	_	_	_
203	,	,	,	_	_	_
204	44	44	CD	_	_	_
205	min	min	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	temperature	temperature	NN	_	_	_
208	up	up	IN	_	_	_
209	shift	shift	NN	_	_	_
210	,	,	,	_	_	_
211	4	4	CD	_	_	_
212	min	min	NN	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	temperature	temperature	NN	_	_	_
215	up	up	IN	_	_	_
216	shift	shift	NN	_	_	_
217	,	,	,	_	_	_
218	8	8	CD	_	_	_
219	min	min	NN	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	Basecalling	basecalling	NN	_	_	_
222	performed	perform	VBN	_	_	_
223	by	by	IN	_	_	_
224	MiSeq	miseq	NN	_	_	_
225	-LRB-	-lrb-	-LRB-	_	_	_
226	RTA	rta	NN	_	_	_
227	-RRB-	-rrb-	-RRB-	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
229	carbon	carbon	NN	_	_	_
230	source	source	NN	_	_	_
231	:	:	:	_	_	_
232	Glucose	glucose	NN	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	carbon	carbon	NN	_	_	_
235	source	source	NN	_	_	_
236	:	:	:	_	_	_
237	Glycerol	glycerol	NN	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	cDNA	cdna	NN	_	_	_
240	libraries	library	NNS	_	_	_
241	were	be	VBD	_	_	_
242	barcoded	barcode	VBN	_	_	_
243	with	with	IN	_	_	_
244	the	the	DT	_	_	_
245	TruSeq	TruSeq	NNP	_	_	_
246	RNA	rna	NN	_	_	_
247	Sample	sample	NN	_	_	_
248	Prep	Prep	NNP	_	_	_
249	Kit	kit	NN	_	_	_
250	v2	v2	NN	_	_	_
251	-LRB-	-lrb-	-LRB-	_	_	_
252	Illumina	Illumina	NNP	_	_	_
253	Inc.	Inc.	NNP	_	_	_
254	,	,	,	_	_	_
255	San	San	NNP	_	_	_
256	Diego	Diego	NNP	_	_	_
257	,	,	,	_	_	_
258	CA	CA	NNP	_	_	_
259	-RRB-	-rrb-	-RRB-	_	_	_
260	.	.	.	_	_	_

1	Libraries	library	NNS	_	_	_
2	were	be	VBD	_	_	_
3	sequenced	sequence	VBN	_	_	_
4	on	on	IN	_	_	_
5	the	the	DT	_	_	_
6	Illumina	Illumina	NNP	_	_	_
7	MiSeq	MiSeq	NNP	_	_	_
8	to	to	TO	_	_	_
9	produce	produce	VB	_	_	_
10	50	50	CD	_	_	_
11	bp	bp	NN	_	_	_
12	single	single	JJ	_	_	_
13	reads	read	VBZ	_	_	_
14	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	steps	step	NNS	_	_	_
3	in	in	IN	_	_	_
4	library	library	NN	_	_	_
5	construction	construction	NN	_	_	_
6	and	and	CC	_	_	_
7	sequencing	sequencing	NN	_	_	_
8	were	be	VBD	_	_	_
9	performed	perform	VBN	_	_	_
10	according	accord	VBG	_	_	_
11	to	to	TO	_	_	_
12	manufacturer	manufacturer	NN	_	_	_
13	's	's	POS	_	_	_
14	standards	standard	NNS	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	CF104	cf104	NN	_	_	_
3	.3.3	.3.3	CD	_	_	_
4	_	_	NN	_	_	_
5	u1	u1	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	CF104	cf104	NN	_	_	_
8	.3.3	.3.3	CD	_	_	_
9	_	_	NN	_	_	_
10	u7	u7	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	CF104	cf104	NN	_	_	_
13	.3.3	.3.3	CD	_	_	_
14	_	_	NN	_	_	_
15	y2	y2	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	CF104	cf104	NN	_	_	_
18	.3.3	.3.3	CD	_	_	_
19	_	_	NN	_	_	_
20	y9	y9	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	CF108	cf108	NN	_	_	_
23	.4	.4	NN	_	_	_
24	B	b	NN	_	_	_
25	_	_	CD	_	_	_
26	u1	u1	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	CF108	cf108	NN	_	_	_
29	.4	.4	NN	_	_	_
30	B	b	NN	_	_	_
31	_	_	CD	_	_	_
32	u2	u2	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	CF108	cf108	NN	_	_	_
35	.4	.4	NN	_	_	_
36	B	b	NN	_	_	_
37	_	_	CD	_	_	_
38	y3	y3	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	CF108	cf108	NN	_	_	_
41	.4	.4	NN	_	_	_
42	B	b	NN	_	_	_
43	_	_	CD	_	_	_
44	y8	y8	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	Compile	compile	VB	_	_	_
47	annotated	annotated	JJ	_	_	_
48	counts	count	NNS	_	_	_
49	using	use	VBG	_	_	_
50	custom	custom	NN	_	_	_
51	Python	Python	NNP	_	_	_
52	script	script	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	ExtractMapCounts	extractmapcount	NNS	_	_	_
55	from	from	IN	_	_	_
56	http	http	NN	_	_	_
57	:	:	:	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	CON206	con206	NN	_	_	_
60	.3	.3	NN	_	_	_
61	A	a	NN	_	_	_
62	_	_	NN	_	_	_
63	u1	u1	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	CON206	con206	NN	_	_	_
66	.3	.3	NN	_	_	_
67	A	a	NN	_	_	_
68	_	_	NN	_	_	_
69	u2	u2	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	CON206	con206	NN	_	_	_
72	.3	.3	NN	_	_	_
73	A	a	NN	_	_	_
74	_	_	NN	_	_	_
75	y1	y1	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	CON206	con206	NN	_	_	_
78	.3	.3	NN	_	_	_
79	A	a	NN	_	_	_
80	_	_	NN	_	_	_
81	y2	y2	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	CON208	con208	NN	_	_	_
84	.3	.3	NN	_	_	_
85	A	a	NN	_	_	_
86	_	_	NN	_	_	_
87	u1	u1	NN	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	CON208	con208	NN	_	_	_
90	.3	.3	NN	_	_	_
91	A	a	NN	_	_	_
92	_	_	NN	_	_	_
93	u8	u8	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	CON208	con208	NN	_	_	_
96	.3	.3	NN	_	_	_
97	A	a	NN	_	_	_
98	_	_	NN	_	_	_
99	y2	y2	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	CON208	con208	NN	_	_	_
102	.3	.3	NN	_	_	_
103	A	a	NN	_	_	_
104	_	_	NN	_	_	_
105	y6	y6	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	disease	disease	NN	_	_	_
108	state	state	NN	_	_	_
109	:	:	:	_	_	_
110	control	control	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	disease	disease	NN	_	_	_
113	state	state	NN	_	_	_
114	:	:	:	_	_	_
115	cystic	cystic	JJ	_	_	_
116	fibrosis	fibrosis	NN	_	_	_
117	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
118	E.	E.	NNP	_	_	_
119	coli	coli	NN	_	_	_
120	strain	strain	NN	_	_	_
121	isolated	isolate	VBN	_	_	_
122	from	from	IN	_	_	_
123	CF	cf	NN	_	_	_
124	patient	patient	NN	_	_	_
125	stool	stool	VBP	_	_	_
126	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
127	E.	e.	FW	_	_	_
128	coli	coli	FW	_	_	_
129	strain	strain	NN	_	_	_
130	isolated	isolate	VBN	_	_	_
131	from	from	IN	_	_	_
132	healthy	healthy	JJ	_	_	_
133	child	child	NN	_	_	_
134	stool	stool	NN	_	_	_
135	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
136	Escherichia	escherichia	FW	Organism	_	_
137	coli	coli	FW	Organism	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	Experiments	experiment	NNS	_	_	_
140	were	be	VBD	_	_	_
141	performed	perform	VBN	_	_	_
142	at	at	IN	_	_	_
143	37	37	CD	_	_	_
144	°C	°c	NN	_	_	_
145	and	and	CC	_	_	_
146	followed	follow	VBD	_	_	_
147	three	three	CD	_	_	_
148	steps	step	NNS	_	_	_
149	:	:	:	_	_	_
150	seed	seed	NN	_	_	_
151	culture	culture	NN	_	_	_
152	,	,	,	_	_	_
153	pre-culture	pre-culture	JJ	_	_	_
154	and	and	CC	_	_	_
155	experimental	experimental	JJ	_	_	_
156	culture	culture	NN	_	_	_
157	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	the	the	DT	_	_	_
3	seed	seed	NN	_	_	_
4	culture	culture	NN	_	_	_
5	the	the	DT	_	_	_
6	cells	cell	NNS	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	overnight	overnight	RB	_	_	_
10	in	in	IN	_	_	_
11	Luria	Luria	NNP	_	_	_
12	Broth	Broth	NNP	_	_	_
13	,	,	,	_	_	_
14	then	then	RB	_	_	_
15	diluted	dilute	VBN	_	_	_
16	1:100	1:100	CD	_	_	_
17	in	in	IN	_	_	_
18	either	either	CC	_	_	_
19	M9	m9	NN	MED	_	_
20	minimal	minimal	JJ	MED	_	_
21	media	media	NNS	MED	_	_
22	with	with	IN	_	_	_
23	glycerol	glycerol	NN	SUPP	_	_
24	or	or	CC	_	_	_
25	glucose	glucose	NN	SUPP	_	_
26	for	for	IN	_	_	_
27	the	the	DT	_	_	_
28	pre-cultures	pre-culture	NNS	_	_	_
29	.	.	.	_	_	_

1	Finally	finally	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	experimental	experimental	JJ	_	_	_
5	cultures	culture	NNS	_	_	_
6	were	be	VBD	_	_	_
7	started	start	VBN	_	_	_
8	from	from	IN	_	_	_
9	the	the	DT	_	_	_
10	overnight	overnight	JJ	_	_	_
11	grown	grown	JJ	_	_	_
12	pre-cultures	pre-culture	NNS	_	_	_
13	containing	contain	VBG	_	_	_
14	the	the	DT	_	_	_
15	same	same	JJ	_	_	_
16	carbon	carbon	NN	_	_	_
17	source	source	NN	_	_	_
18	at	at	IN	_	_	_
19	a	a	DT	_	_	_
20	normalized	normalize	VBN	_	_	_
21	optical	optical	JJ	_	_	_
22	density	density	NN	_	_	_
23	at	at	IN	_	_	_
24	600	600	CD	_	_	_
25	nm	nm	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	OD600	od600	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	of	of	IN	_	_	_
30	0.05	0.05	CD	_	_	_
31	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	harvested	harvest	VBN	_	_	_
4	at	at	IN	_	_	_
5	mid-exponential	mid-exponential	JJ	_	_	_
6	phase	phase	NN	_	_	_
7	,	,	,	_	_	_
8	cells	cell	NNS	_	_	_
9	were	be	VBD	_	_	_
10	immediately	immediately	RB	_	_	_
11	spun	spin	VBN	_	_	_
12	down	down	RP	_	_	_
13	and	and	CC	_	_	_
14	cell	cell	NN	_	_	_
15	pellets	pellet	NNS	_	_	_
16	stored	store	VBD	_	_	_
17	at	at	IN	_	_	_
18	-80	-80	CD	_	_	_
19	°C	°c	NN	_	_	_
20	until	until	IN	_	_	_
21	processed	process	VBN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Filter	Filter	NNP	_	_	_
3	for	for	IN	_	_	_
4	map	map	NN	GEN	_	_
5	quality	quality	NN	_	_	_
6	>	>	JJR	_	_	_
7	=	=	JJ	_	_	_
8	20	20	CD	_	_	_
9	using	use	VBG	_	_	_
10	Samtools	samtool	NNS	_	_	_
11	0.1.18	0.1.18	CD	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
13	Filter	Filter	NNP	_	_	_
14	out	out	IN	_	_	_
15	rRNA	rrna	NN	_	_	_
16	reads	read	VBZ	_	_	_
17	,	,	,	_	_	_
18	multi-mapped	multi-mapped	JJ	_	_	_
19	reads	read	VBZ	_	_	_
20	,	,	,	_	_	_
21	>	>	JJR	_	_	_
22	3	3	CD	_	_	_
23	mismatches	mismatch	NNS	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	gapped	gap	VBD	_	_	_
27	mappings	mapping	NNS	_	_	_
28	using	use	VBG	_	_	_
29	custom	custom	NN	_	_	_
30	Python	Python	NNP	_	_	_
31	script	script	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	FilterBAM2BAM	filterbam2bam	NN	_	_	_
34	from	from	IN	_	_	_
35	http	http	NN	_	_	_
36	:	:	:	_	_	_
37	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
38	Genome	Genome	NNP	_	_	_
39	_	_	NNP	_	_	_
40	build	build	VB	_	_	_
41	:	:	:	_	_	_
42	Escherichia	escherichia	FW	Organism	_	_
43	coli	coli	FW	Organism	_	_
44	str	str	FW	_	_	_
45	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	U00096	u00096	NN	_	_	_
4	.3	.3	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	individual	individual	NN	_	_	_
8	:	:	:	_	_	_
9	CF	cf	NN	_	_	_
10	patient	patient	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	individual	individual	JJ	_	_	_
13	:	:	:	_	_	_
14	healthy	healthy	JJ	_	_	_
15	child	child	NN	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Map	map	NN	_	_	_
18	to	to	TO	_	_	_
19	MG1655	mg1655	NN	_	_	_
20	reference	reference	NN	_	_	_
21	using	use	VBG	_	_	_
22	BWA	BWA	NNP	_	_	_
23	0.7.4	0.7.4	CD	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	bwa	bwa	NN	_	_	_
26	mem	mem	NN	_	_	_
27	,	,	,	_	_	_
28	default	default	NN	_	_	_
29	parameters	parameter	NNS	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
32	replicate	replicate	VBP	_	_	_
33	:	:	:	_	_	_
34	1	1	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	replicate	replicate	VB	_	_	_
37	:	:	:	_	_	_
38	2	2	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	RNA-Seq	rna-seq	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	RNA	rna	NN	_	_	_
43	was	be	VBD	_	_	_
44	extracted	extract	VBN	_	_	_
45	using	use	VBG	_	_	_
46	Trizol	Trizol	NNP	_	_	_
47	and	and	CC	_	_	_
48	chloroform	chloroform	NN	_	_	_
49	in	in	IN	_	_	_
50	conjunction	conjunction	NN	_	_	_
51	with	with	IN	_	_	_
52	Qiagen	Qiagen	NNP	_	_	_
53	's	's	POS	_	_	_
54	RNeasy	RNeasy	NNP	_	_	_
55	Mini	Mini	NNP	_	_	_
56	kit	kit	NN	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	Qiagen	Qiagen	NNP	_	_	_
59	,	,	,	_	_	_
60	Valencia	Valencia	NNP	_	_	_
61	,	,	,	_	_	_
62	CA	CA	NNP	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	following	follow	VBG	_	_	_
65	the	the	DT	_	_	_
66	A.	a.	NN	_	_	_
67	Untergasser	Untergasser	NNP	_	_	_
68	protocol	protocol	NN	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	http	http	NN	_	_	_
71	:	:	:	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
73	Supplementary	supplementary	JJ	_	_	_
74	_	_	NN	_	_	_
75	files	file	NNS	_	_	_
76	_	_	IN	_	_	_
77	format	format	NN	_	_	_
78	_	_	NN	_	_	_
79	and	and	CC	_	_	_
80	_	_	NN	_	_	_
81	content	content	NN	_	_	_
82	:	:	:	_	_	_
83	expression	expression	NN	_	_	_
84	level	level	NN	_	_	_
85	files	file	NNS	_	_	_
86	are	be	VBP	_	_	_
87	tab-delimited	tab-delimited	JJ	_	_	_
88	text	text	NN	_	_	_
89	with	with	IN	_	_	_
90	columns	column	NNS	_	_	_
91	as	as	IN	_	_	_
92	follows	follow	VBZ	_	_	_
93	:	:	:	_	_	_
94	index	index	NN	_	_	_
95	,	,	,	_	_	_
96	hits	hit	VBZ	_	_	_
97	,	,	,	_	_	_
98	RPKM	rpkm	NN	_	_	_
99	,	,	,	_	_	_
100	RPM	RPM	NNP	_	_	_
101	,	,	,	_	_	_
102	start	start	VB	_	_	_
103	_	_	SYM	_	_	_
104	position	position	NN	_	_	_
105	,	,	,	_	_	_
106	end	end	NN	_	_	_
107	_	_	NN	_	_	_
108	position	position	NN	_	_	_
109	,	,	,	_	_	_
110	strand	strand	NN	_	_	_
111	,	,	,	_	_	_
112	feature	feature	NN	_	_	_
113	_	_	CD	_	_	_
114	type	type	NN	_	_	_
115	,	,	,	_	_	_
116	reference	reference	NN	_	_	_
117	_	_	NN	_	_	_
118	replicon	replicon	NN	_	_	_
119	-LRB-	-lrb-	-LRB-	_	_	_
120	type	type	NN	_	_	_
121	-RRB-	-rrb-	-RRB-	_	_	_
122	,	,	,	_	_	_
123	locus	locus	NN	_	_	_
124	_	_	NN	_	_	_
125	tag	tag	NN	GEN	_	_
126	,	,	,	_	_	_
127	gene	gene	NN	_	_	_
128	_	_	NN	_	_	_
129	name	name	NN	_	_	_
130	,	,	,	_	_	_
131	product	product	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
133	Bacterial	bacterial	JJ	_	_	_
134	cells	cell	NNS	_	_	_
135	were	be	VBD	_	_	_
136	grown	grow	VBN	_	_	_
137	in	in	IN	_	_	_
138	dYT	dyt	JJ	_	_	_
139	medium	medium	NN	_	_	_
140	-LRB-	-lrb-	-LRB-	_	_	_
141	Miller	Miller	NNP	_	_	_
142	,	,	,	_	_	_
143	JH	JH	NNP	_	_	_
144	-LRB-	-lrb-	-LRB-	_	_	_
145	1972	1972	CD	_	_	_
146	-RRB-	-rrb-	-RRB-	_	_	_
147	Experiments	experiment	NNS	_	_	_
148	in	in	IN	_	_	_
149	Molecular	molecular	JJ	_	_	_
150	Genetics	Genetics	NNP	_	_	_
151	-LRB-	-lrb-	-LRB-	_	_	_
152	Cold	Cold	NNP	_	_	_
153	Spring	Spring	NNP	_	_	_
154	Harbor	Harbor	NNP	_	_	_
155	Laboratory	Laboratory	NNP	_	_	_
156	,	,	,	_	_	_
157	Cold	Cold	NNP	_	_	_
158	Spring	Spring	NNP	_	_	_
159	Harbor	Harbor	NNP	_	_	_
160	,	,	,	_	_	_
161	NY	NY	NNP	_	_	_
162	-RRB-	-rrb-	-RRB-	_	_	_
163	supplemented	supplement	VBN	_	_	_
164	with	with	IN	_	_	_
165	kanamycin	kanamycin	NN	_	_	_
166	-LRB-	-lrb-	-LRB-	_	_	_
167	10	10	CD	_	_	_
168	mg	mg	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	E.coli	e.coli	JJ	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
172	E.	e.	FW	_	_	_
173	coli	coli	FW	_	_	_
174	B178	b178	NN	_	_	_
175	groESL	groesl	NN	_	_	_
176	-LRB-	-lrb-	-LRB-	_	_	_
177	-	-	:	_	_	_
178	-RRB-	-rrb-	-RRB-	_	_	_
179	expressing	express	VBG	_	_	_
180	human	human	JJ	_	_	_
181	Hsp60	hsp60	NN	_	_	_
182	and	and	CC	_	_	_
183	Hsp10	hsp10	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
185	E.	e.	FW	_	_	_
186	coli	coli	FW	_	_	_
187	B178	b178	NN	_	_	_
188	groESL	groesl	NN	_	_	_
189	-LRB-	-lrb-	-LRB-	_	_	_
190	-	-	:	_	_	_
191	-RRB-	-rrb-	-RRB-	_	_	_
192	expressing	express	VBG	_	_	_
193	human	human	JJ	_	_	_
194	wt	wt	JJ	_	_	_
195	and	and	CC	_	_	_
196	Val98Ile	val98ile	NN	_	_	_
197	Hsp60	hsp60	NN	_	_	_
198	and	and	CC	_	_	_
199	Hsp10	hsp10	NN	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
201	E.	e.	FW	_	_	_
202	coli	coli	FW	_	_	_
203	strain	strain	NN	_	_	_
204	B178	b178	NN	_	_	_
205	-LRB-	-lrb-	-LRB-	_	_	_
206	Georgopoulos	Georgopoulos	NNP	_	_	_
207	et	et	FW	_	_	_
208	al.	al.	FW	_	_	_
209	-LRB-	-lrb-	-LRB-	_	_	_
210	1973	1973	CD	_	_	_
211	-RRB-	-rrb-	-RRB-	_	_	_
212	J	J	NNP	_	_	_
213	Mol	Mol	NNP	_	_	_
214	Biol	Biol	NNP	_	_	_
215	76	76	CD	_	_	_
216	:	:	:	_	_	_
217	45-60	45-60	CD	_	_	_
218	-RRB-	-rrb-	-RRB-	_	_	_
219	in	in	IN	_	_	_
220	which	which	WDT	_	_	_
221	the	the	DT	_	_	_
222	endogenous	endogenous	JJ	_	_	_
223	groES	groes	NN	_	_	_
224	and	and	CC	_	_	_
225	groEL	groel	NN	_	_	_
226	genes	gene	NNS	_	_	_
227	have	have	VBP	_	_	_
228	been	be	VBN	_	_	_
229	deleted	delete	VBN	_	_	_
230	and	and	CC	_	_	_
231	that	that	DT	_	_	_
232	is	be	VBZ	_	_	_
233	maintained	maintain	VBN	_	_	_
234	alive	alive	JJ	_	_	_
235	by	by	IN	_	_	_
236	the	the	DT	_	_	_
237	pOFX-tac1-derived	pofx-tac1-derived	JJ	_	_	_
238	plasmid	plasmid	NN	_	_	_
239	carrying	carry	VBG	_	_	_
240	an	a	DT	_	_	_
241	IPTG-inducible	iptg-inducible	JJ	_	_	_
242	operon	operon	NN	_	_	_
243	with	with	IN	_	_	_
244	cDNA	cdna	NN	_	_	_
245	encoding	encode	VBG	_	_	_
246	human	human	JJ	_	_	_
247	Hsp10	hsp10	NN	_	_	_
248	and	and	CC	_	_	_
249	the	the	DT	_	_	_
250	mature	mature	JJ	_	_	_
251	part	part	NN	_	_	_
252	of	of	IN	_	_	_
253	human	human	JJ	_	_	_
254	wild	wild	JJ	_	_	_
255	type	type	NN	_	_	_
256	Hsp60	hsp60	NN	_	_	_
257	-LRB-	-lrb-	-LRB-	_	_	_
258	Hansen	Hansen	NNP	_	_	_
259	et	et	FW	_	_	_
260	al.	al.	FW	_	_	_
261	,	,	,	_	_	_
262	2002	2002	CD	_	_	_
263	-RRB-	-rrb-	-RRB-	_	_	_
264	.	.	.	_	_	_

1	These	these	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	subsequently	subsequently	RB	_	_	_
5	transformed	transform	VBN	_	_	_
6	by	by	IN	_	_	_
7	electroporation	electroporation	NN	_	_	_
8	with	with	IN	_	_	_
9	a	a	DT	_	_	_
10	second	second	JJ	_	_	_
11	plasmid	plasmid	NN	_	_	_
12	,	,	,	_	_	_
13	derivative	derivative	NN	_	_	_
14	of	of	IN	_	_	_
15	pBAD	pbad	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Escherichia	escherichia	FW	Organism	_	_
18	coli	coli	FW	Organism	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	MAS5	mas5	NN	_	_	_
21	.0	.0	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	Total	total	JJ	_	_	_
24	RNA	rna	NN	_	_	_
25	was	be	VBD	_	_	_
26	purified	purify	VBN	_	_	_
27	using	use	VBG	_	_	_
28	the	the	DT	_	_	_
29	RNAeasy	rnaeasy	NN	_	_	_
30	kit	kit	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Qiagen	qiagen	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	were	be	VBD	_	_	_
4	analyzed	analyze	VBN	_	_	_
5	using	use	VBG	_	_	_
6	custom	custom	NN	_	_	_
7	software	software	NN	_	_	_
8	based	base	VBN	_	_	_
9	on	on	IN	_	_	_
10	the	the	DT	_	_	_
11	R	r	NN	_	_	_
12	programming	programming	NN	_	_	_
13	environment	environment	NN	_	_	_
14	and	and	CC	_	_	_
15	BioConductor	BioConductor	NNP	_	_	_
16	packages	package	NNS	_	_	_
17	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	probe	probe	NN	_	_	_
3	was	be	VBD	_	_	_
4	randomly	randomly	RB	_	_	_
5	spotted	spot	VBN	_	_	_
6	in	in	IN	_	_	_
7	three	three	CD	_	_	_
8	to	to	TO	_	_	_
9	five	five	CD	_	_	_
10	replicates	replicate	VBZ	_	_	_
11	to	to	TO	_	_	_
12	control	control	VB	_	_	_
13	for	for	IN	_	_	_
14	positional	positional	JJ	_	_	_
15	effects	effect	NNS	_	_	_
16	on	on	IN	_	_	_
17	the	the	DT	_	_	_
18	array	array	NN	_	_	_
19	.	.	.	_	_	_

1	Data	datum	NNS	_	_	_
2	from	from	IN	_	_	_
3	replicate	replicate	VBP	_	_	_
4	probes	probe	NNS	_	_	_
5	were	be	VBD	_	_	_
6	summarized	summarize	VBN	_	_	_
7	by	by	IN	_	_	_
8	the	the	DT	_	_	_
9	median	median	NN	_	_	_
10	of	of	IN	_	_	_
11	the	the	DT	_	_	_
12	log2-transformed	log2-transformed	JJ	_	_	_
13	intensities	intensity	NNS	_	_	_
14	.	.	.	_	_	_

1	No	no	DT	_	_	_
2	normalization	normalization	NN	_	_	_
3	or	or	CC	_	_	_
4	background	background	NN	_	_	_
5	correction	correction	NN	_	_	_
6	was	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	E.coli	e.coli	NN	_	_	_
3	CFT073	cft073	NN	_	_	_
4	genomic	genomic	JJ	_	_	_
5	DNA	dna	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	E.coli	e.coli	NN	_	_	_
8	CFT073	cft073	NN	_	_	_
9	genomic	genomic	JJ	_	_	_
10	DNA	dna	NN	_	_	_
11	hybridization	hybridization	NN	_	_	_
12	to	to	TO	_	_	_
13	LLNL	llnl	NN	_	_	_
14	virulence	virulence	NN	_	_	_
15	mechanism	mechanism	NN	_	_	_
16	array	array	NN	_	_	_
17	v2A	v2a	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	E.coli	e.coli	NN	_	_	_
20	O157	o157	NN	_	_	_
21	:	:	:	_	_	_
22	H7	h7	NN	_	_	_
23	EDL	edl	NN	_	_	_
24	933	933	CD	_	_	_
25	genomic	genomic	JJ	_	_	_
26	DNA	dna	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	E.coli	e.coli	NN	_	_	_
29	O157	o157	NN	_	_	_
30	:	:	:	_	_	_
31	H7	h7	NN	_	_	_
32	EDL	edl	NN	_	_	_
33	933	933	CD	_	_	_
34	genomic	genomic	JJ	_	_	_
35	DNA	dna	NN	_	_	_
36	hybridization	hybridization	NN	_	_	_
37	to	to	TO	_	_	_
38	LLNL	llnl	NN	_	_	_
39	virulence	virulence	NN	_	_	_
40	mechanism	mechanism	NN	_	_	_
41	array	array	NN	_	_	_
42	v2A	v2a	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Escherichia	escherichia	FW	Organism	_	_
45	coli	coli	FW	Organism	_	_
46	CFT073	cft073	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	Escherichia	escherichia	FW	Organism	_	_
49	coli	coli	FW	Organism	_	_
50	O157	o157	NN	_	_	_
51	:	:	:	_	_	_
52	H7	h7	NN	_	_	_
53	str	str	NN	_	_	_
54	.	.	.	_	_	_

1	EDL933	edl933	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
3	Genomic	genomic	JJ	_	_	_
4	DNA	dna	NN	_	_	_
5	was	be	VBD	_	_	_
6	extracted	extract	VBN	_	_	_
7	using	use	VBG	_	_	_
8	the	the	DT	_	_	_
9	Epicentre	Epicentre	NNP	_	_	_
10	DNA	dna	NN	_	_	_
11	extraction	extraction	NN	_	_	_
12	kit	kit	NN	_	_	_
13	according	accord	VBG	_	_	_
14	to	to	TO	_	_	_
15	the	the	DT	_	_	_
16	manufacturer	manufacturer	NN	_	_	_
17	's	's	POS	_	_	_
18	protocols	protocol	NNS	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	serovar	serovar	NN	_	_	_
3	O157	o157	NN	_	_	_
4	:	:	:	_	_	_
5	H7	h7	NN	_	_	_
6	strain	strain	NN	_	_	_
7	EDL933	edl933	NN	_	_	_
8	;	;	:	_	_	_
9	GenBank	genbank	NN	_	_	_
10	accession	accession	NN	_	_	_
11	NC	nc	NN	_	_	_
12	_	_	CD	_	_	_
13	002655.2	002655.2	CD	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	strain	strain	NN	_	_	_
16	CFT073	cft073	NN	_	_	_
17	;	;	:	_	_	_
18	GenBank	genbank	NN	_	_	_
19	accession	accession	NN	_	_	_
20	AE014075	ae014075	NN	_	_	_
21	.1	.1	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	The	the	DT	_	_	_
24	bacterial	bacterial	JJ	_	_	_
25	culture	culture	NN	_	_	_
26	pellets	pellet	NNS	_	_	_
27	were	be	VBD	_	_	_
28	grown	grow	VBN	_	_	_
29	according	accord	VBG	_	_	_
30	to	to	TO	_	_	_
31	the	the	DT	_	_	_
32	instructions	instruction	NNS	_	_	_
33	from	from	IN	_	_	_
34	ATCC	atcc	NN	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Functional	functional	JJ	_	_	_
6	annotation	annotation	NN	_	_	_
7	was	be	VBD	_	_	_
8	done	do	VBN	_	_	_
9	using	use	VBG	_	_	_
10	the	the	DT	_	_	_
11	Database	database	NN	_	_	_
12	for	for	IN	_	_	_
13	Annotation	Annotation	NNP	_	_	_
14	,	,	,	_	_	_
15	Visualization	visualization	NN	_	_	_
16	and	and	CC	_	_	_
17	Integrated	Integrated	NNP	_	_	_
18	Discovery	Discovery	NNP	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	DAVID	DAVID	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	Bioinformatics	Bioinformatics	NNP	_	_	_
23	Resources	Resources	NNP	_	_	_
24	6.7	6.7	CD	_	_	_
25	,	,	,	_	_	_
26	NIAID	NIAID	NNP	_	_	_
27	,	,	,	_	_	_
28	NIH	NIH	NNP	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	http	http	JJ	_	_	_
31	:	:	:	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	incubation	incubation	NN	_	_	_
34	time	time	NN	_	_	_
35	:	:	:	_	_	_
36	5	5	CD	_	_	_
37	hr	hr	NN	_	_	_
38	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
39	Next	Next	NNP	_	_	_
40	,	,	,	_	_	_
41	a	a	DT	_	_	_
42	linear	linear	JJ	_	_	_
43	model	model	NN	_	_	_
44	was	be	VBD	_	_	_
45	built	build	VBN	_	_	_
46	for	for	IN	_	_	_
47	each	each	DT	_	_	_
48	comparison	comparison	NN	_	_	_
49	using	use	VBG	_	_	_
50	the	the	DT	_	_	_
51	R	r	NN	_	_	_
52	LIMMA	limma	NN	_	_	_
53	package	package	NN	_	_	_
54	and	and	CC	_	_	_
55	statistics	statistics	NNS	_	_	_
56	for	for	IN	_	_	_
57	differential	differential	JJ	_	_	_
58	expression	expression	NN	_	_	_
59	analysis	analysis	NN	_	_	_
60	were	be	VBD	_	_	_
61	computed	compute	VBN	_	_	_
62	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	filter	filter	NN	_	_	_
3	for	for	IN	_	_	_
4	differential	differential	JJ	_	_	_
5	expression	expression	NN	_	_	_
6	,	,	,	_	_	_
7	two	two	CD	_	_	_
8	fold	fold	JJ	_	_	_
9	or	or	CC	_	_	_
10	three-fold	three-fold	JJ	_	_	_
11	change	change	NN	_	_	_
12	with	with	IN	_	_	_
13	a	a	DT	_	_	_
14	FDR	FDR	NNP	_	_	_
15	≤	≤	SYM	_	_	_
16	0.05	0.05	CD	_	_	_
17	were	be	VBD	_	_	_
18	used	use	VBN	_	_	_
19	as	as	IN	_	_	_
20	the	the	DT	_	_	_
21	threshold	threshold	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	PA20	pa20	NN	_	_	_
3	cultures	culture	NNS	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	PA20	pa20	NN	_	_	_
6	cultures	culture	NNS	_	_	_
7	for	for	IN	_	_	_
8	RNA-seq	rna-seq	NN	_	_	_
9	were	be	VBD	_	_	_
10	grown	grow	VBN	_	_	_
11	on	on	IN	_	_	_
12	T-agar	t-agar	JJ	_	_	_
13	with	with	IN	_	_	_
14	and	and	CC	_	_	_
15	without	without	IN	_	_	_
16	added	add	VBN	_	_	_
17	Sulfamethoxazole	Sulfamethoxazole	NNP	_	_	_
18	-	-	:	_	_	_
19	Trimethoprim	Trimethoprim	NNP	_	_	_
20	at	at	IN	_	_	_
21	designated	designate	VBN	_	_	_
22	levels	level	NNS	_	_	_
23	for	for	IN	_	_	_
24	the	the	DT	_	_	_
25	indicated	indicated	JJ	_	_	_
26	times	time	NNS	_	_	_
27	and	and	CC	_	_	_
28	temperatures	temperature	NNS	_	_	_
29	.	.	.	_	_	_

1	Working	work	VBG	_	_	_
2	stocks	stock	NNS	_	_	_
3	were	be	VBD	_	_	_
4	tested	test	VBN	_	_	_
5	and	and	CC	_	_	_
6	maintained	maintain	VBN	_	_	_
7	using	use	VBG	_	_	_
8	LB	lb	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Miller	Miller	NNP	_	_	_
11	formulation	formulation	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	or	or	CC	_	_	_
14	LB	lb	NN	_	_	_
15	agar	agar	NN	_	_	_
16	.	.	.	_	_	_

1	Plasmid	plasmid	NN	_	_	_
2	pSE380	pse380	NN	_	_	_
3	derivatives	derivative	NNS	_	_	_
4	were	be	VBD	_	_	_
5	induced	induce	VBN	_	_	_
6	by	by	IN	_	_	_
7	IPTG	iptg	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	prepared	prepare	VBN	_	_	_
6	for	for	IN	_	_	_
7	sequencing	sequencing	NN	_	_	_
8	using	use	VBG	_	_	_
9	standard	standard	JJ	_	_	_
10	Illumina	Illumina	NNP	_	_	_
11	protocols	protocol	NNS	_	_	_
12	;	;	:	_	_	_
13	rRNAs	rrna	NNS	_	_	_
14	were	be	VBD	_	_	_
15	removed	remove	VBN	_	_	_
16	by	by	IN	_	_	_
17	Ribozero	ribozero	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	gram	gram	NN	_	_	_
20	negative	negative	JJ	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	,	,	,	_	_	_
23	libraries	library	NNS	_	_	_
24	were	be	VBD	_	_	_
25	prepared	prepare	VBN	_	_	_
26	using	use	VBG	_	_	_
27	TruSeq	TruSeq	NNP	_	_	_
28	protocol	protocol	NN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	RNA-seq	rna-seq	NN	_	_	_
5	data	datum	NNS	_	_	_
6	were	be	VBD	_	_	_
7	mapped	map	VBN	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	E.	e.	FW	_	_	_
11	coli	coli	FW	_	_	_
12	O157	o157	NN	_	_	_
13	:	:	:	_	_	_
14	H7	h7	NN	_	_	_
15	Sakai	Sakai	NNP	_	_	_
16	genome	genome	NN	_	_	_
17	using	use	VBG	_	_	_
18	the	the	DT	_	_	_
19	Subjunc	subjunc	NN	_	_	_
20	aligner	aligner	NN	_	_	_
21	program	program	NN	_	_	_
22	from	from	IN	_	_	_
23	the	the	DT	_	_	_
24	Subread	Subread	NNP	_	_	_
25	package	package	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	v1	v1	NN	_	_	_
28	.4.6	.4.6	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	http	http	NN	_	_	_
32	:	:	:	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
34	Supplementary	supplementary	JJ	_	_	_
35	_	_	NN	_	_	_
36	files	file	NNS	_	_	_
37	_	_	IN	_	_	_
38	format	format	NN	_	_	_
39	_	_	NN	_	_	_
40	and	and	CC	_	_	_
41	_	_	NN	_	_	_
42	content	content	NN	_	_	_
43	:	:	:	_	_	_
44	comma-delimited	comma-delimited	JJ	_	_	_
45	text	text	NN	_	_	_
46	files	file	NNS	_	_	_
47	include	include	VBP	_	_	_
48	RPKM	rpkm	NN	_	_	_
49	values	value	NNS	_	_	_
50	for	for	IN	_	_	_
51	each	each	DT	_	_	_
52	Sample	Sample	NNP	_	_	_
53	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
54	T5	t5	NN	_	_	_
55	_	_	SYM	_	_	_
56	1x	1x	FW	_	_	_
57	_	_	FW	_	_	_
58	4	4	CD	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	T5	t5	NN	_	_	_
61	_	_	CD	_	_	_
62	27x	27x	CD	_	_	_
63	_	_	NN	_	_	_
64	1	1	CD	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	The	the	DT	_	_	_
67	alignment	alignment	NN	_	_	_
68	Bam	bam	UH	_	_	_
69	files	file	NNS	_	_	_
70	were	be	VBD	_	_	_
71	compared	compare	VBN	_	_	_
72	against	against	IN	_	_	_
73	the	the	DT	_	_	_
74	gene	gene	NN	_	_	_
75	annotation	annotation	NN	_	_	_
76	general	general	JJ	_	_	_
77	feature	feature	NN	_	_	_
78	format	format	NN	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	GFF	gff	NN	_	_	_
81	-RRB-	-rrb-	-RRB-	_	_	_
82	file	file	NN	_	_	_
83	,	,	,	_	_	_
84	and	and	CC	_	_	_
85	raw	raw	JJ	_	_	_
86	counts	count	NNS	_	_	_
87	for	for	IN	_	_	_
88	each	each	DT	_	_	_
89	gene	gene	NN	_	_	_
90	were	be	VBD	_	_	_
91	generated	generate	VBN	_	_	_
92	using	use	VBG	_	_	_
93	the	the	DT	_	_	_
94	featureCounts	featureCounts	NNPS	_	_	_
95	tool	tool	NN	_	_	_
96	from	from	IN	_	_	_
97	Subread	Subread	NNP	_	_	_
98	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	raw	raw	JJ	_	_	_
3	counts	count	NNS	_	_	_
4	data	datum	NNS	_	_	_
5	of	of	IN	_	_	_
6	the	the	DT	_	_	_
7	expressed	express	VBN	_	_	_
8	genes	gene	NNS	_	_	_
9	was	be	VBD	_	_	_
10	normalized	normalize	VBN	_	_	_
11	for	for	IN	_	_	_
12	RNA	rna	NN	_	_	_
13	composition	composition	NN	_	_	_
14	using	use	VBG	_	_	_
15	the	the	DT	_	_	_
16	trimmed	trimmed	RBR	_	_	_
17	mean	mean	VB	_	_	_
18	of	of	IN	_	_	_
19	M	m	NN	_	_	_
20	values	value	NNS	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	TMM	tmm	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	method	method	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	http	http	NN	_	_	_
27	:	:	:	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
29	Total	total	JJ	_	_	_
30	RNA	rna	NN	_	_	_
31	samples	sample	NNS	_	_	_
32	were	be	VBD	_	_	_
33	isolated	isolate	VBN	_	_	_
34	using	use	VBG	_	_	_
35	RNAzol	rnazol	NN	_	_	_
36	RT	rt	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Molecular	molecular	JJ	_	_	_
39	Research	Research	NNP	_	_	_
40	Center	Center	NNP	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	by	by	IN	_	_	_
43	following	follow	VBG	_	_	_
44	manufature	manufature	NN	_	_	_
45	's	's	POS	_	_	_
46	instructions	instruction	NNS	_	_	_
47	.	.	.	_	_	_

1	Contaminating	contaminate	VBG	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	from	from	IN	_	_	_
6	RNA	rna	NN	_	_	_
7	samples	sample	NNS	_	_	_
8	by	by	IN	_	_	_
9	DNase	dnase	NN	_	_	_
10	I	i	CD	_	_	_
11	digestion	digestion	NN	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	TURBO	TURBO	NNP	_	_	_
15	DNA-free	dna-free	JJ	_	_	_
16	kit	kit	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Ambion	ambion	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	15degrees	15degree	NNS	_	_	_
3	replicate	replicate	VBP	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	15degrees	15degree	NNS	_	_	_
7	replicate	replicate	VBP	_	_	_
8	2	2	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
10	15degrees	15degree	NNS	_	_	_
11	replicate	replicate	VBP	_	_	_
12	3	3	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	46degrees	46degree	NNS	_	_	_
15	replicate	replicate	VBP	_	_	_
16	1	1	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	46degrees	46degree	NNS	_	_	_
19	replicate	replicate	VBP	_	_	_
20	2	2	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
22	46degrees	46degree	NNS	_	_	_
23	replicate	replicate	VBP	_	_	_
24	3	3	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	BC-7ppm	bc-7ppm	JJ	_	_	_
27	replicate	replicate	VB	_	_	_
28	1	1	CD	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	BC-7ppm	bc-7ppm	JJ	_	_	_
31	replicate	replicate	VB	_	_	_
32	2	2	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
34	BC-7ppm	bc-7ppm	JJ	_	_	_
35	replicate	replicate	VB	_	_	_
36	3	3	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	BC-9ppm	bc-9ppm	JJ	_	_	_
39	replicate	replicate	VB	_	_	_
40	1	1	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	BC-9ppm	bc-9ppm	JJ	_	_	_
43	replicate	replicate	VB	_	_	_
44	2	2	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
46	BC-9ppm	bc-9ppm	JJ	_	_	_
47	replicate	replicate	VB	_	_	_
48	3	3	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	CH3COOH	ch3cooh	NN	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	pH	ph	NN	_	_	_
53	5.9	5.9	CD	_	_	_
54	±	±	SYM	_	_	_
55	0.05	0.05	CD	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	;	;	:	_	_	_
58	HCl	hcl	NN	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	pH	ph	NN	_	_	_
61	4.75	4.75	CD	_	_	_
62	±	±	SYM	_	_	_
63	0.05	0.05	CD	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	;	;	:	_	_	_
66	NaOH	naoh	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	pH	ph	NN	_	_	_
69	9.6	9.6	CD	_	_	_
70	±	±	SYM	_	_	_
71	0.05	0.05	CD	_	_	_
72	-RRB-	-rrb-	-RRB-	_	_	_
73	;	;	:	_	_	_
74	EtOH	etoh	NN	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	5	5	CD	_	_	_
77	%	%	NN	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	;	;	:	_	_	_
80	NaCl	nacl	NN	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	4.5	4.5	CD	_	_	_
83	%	%	NN	_	_	_
84	-RRB-	-rrb-	-RRB-	_	_	_
85	;	;	:	_	_	_
86	Glycerol	glycerol	NN	_	_	_
87	-LRB-	-lrb-	-LRB-	_	_	_
88	15	15	CD	_	_	_
89	%	%	NN	_	_	_
90	-RRB-	-rrb-	-RRB-	_	_	_
91	;	;	:	_	_	_
92	BC	bc	NN	_	_	_
93	-LRB-	-lrb-	-LRB-	_	_	_
94	7	7	CD	_	_	_
95	and	and	CC	_	_	_
96	9	9	CD	_	_	_
97	mg	mg	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	CH3COOH	ch3cooh	NN	_	_	_
100	replicate	replicate	VBP	_	_	_
101	1	1	CD	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	CH3COOH	ch3cooh	NN	_	_	_
104	replicate	replicate	VBP	_	_	_
105	2	2	CD	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	CH3COOH	ch3cooh	NN	_	_	_
108	replicate	replicate	VBP	_	_	_
109	3	3	CD	_	_	_
110	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
111	Control	Control	NNP	_	_	_
112	replicate	replicate	VB	_	_	_
113	1	1	CD	_	_	_
114	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
115	Control	Control	NNP	_	_	_
116	replicate	replicate	VB	_	_	_
117	2	2	CD	_	_	_
118	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
119	Control	Control	NNP	_	_	_
120	replicate	replicate	VB	_	_	_
121	3	3	CD	_	_	_
122	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
123	Escherichia	escherichia	FW	Organism	_	_
124	coli	coli	FW	Organism	_	_
125	str	str	FW	_	_	_
126	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	EtBr	etbr	NN	_	_	_
4	replicate	replicate	VBP	_	_	_
5	1	1	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	EtBr	etbr	NN	_	_	_
8	replicate	replicate	VBP	_	_	_
9	2	2	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	EtBr	etbr	NN	_	_	_
12	replicate	replicate	VBP	_	_	_
13	3	3	CD	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	EtOH	etoh	NN	_	_	_
16	replicate	replicate	VBP	_	_	_
17	1	1	CD	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	EtOH	etoh	NN	_	_	_
20	replicate	replicate	VBP	_	_	_
21	2	2	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	EtOH	etoh	NN	_	_	_
24	replicate	replicate	VB	_	_	_
25	3	3	CD	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	Glycerol	Glycerol	NNP	_	_	_
28	replicate	replicate	VB	_	_	_
29	1	1	CD	_	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
31	Glycerol	Glycerol	NNP	_	_	_
32	replicate	replicate	VB	_	_	_
33	2	2	CD	_	_	_
34	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
35	Glycerol	Glycerol	NNP	_	_	_
36	replicate	replicate	VB	_	_	_
37	3	3	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	HCl	hcl	NN	_	_	_
40	replicate	replicate	VBP	_	_	_
41	1	1	CD	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	HCl	hcl	NN	_	_	_
44	replicate	replicate	VBP	_	_	_
45	3	3	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	NaCl	nacl	NN	_	_	_
48	replicate	replicate	VBP	_	_	_
49	1	1	CD	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	NaCl	nacl	NN	_	_	_
52	replicate	replicate	VBP	_	_	_
53	2	2	CD	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
55	NaCl	nacl	NN	_	_	_
56	replicate	replicate	VBP	_	_	_
57	3	3	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	NaOH	naoh	NN	_	_	_
60	replicate	replicate	VBP	_	_	_
61	1	1	CD	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	NaOH	naoh	NN	_	_	_
64	replicate	replicate	VBP	_	_	_
65	3	3	CD	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	pooled	pool	VBD	_	_	_
68	RNA	rna	NN	_	_	_
69	from	from	IN	_	_	_
70	all	all	DT	_	_	_
71	conditions	condition	NNS	_	_	_
72	including	include	VBG	_	_	_
73	the	the	DT	_	_	_
74	control	control	NN	_	_	_
75	,	,	,	_	_	_
76	reference	reference	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
78	The	the	DT	_	_	_
79	cultures	culture	NNS	_	_	_
80	were	be	VBD	_	_	_
81	prepared	prepare	VBN	_	_	_
82	by	by	IN	_	_	_
83	inoculating	inoculate	VBG	_	_	_
84	one	one	CD	_	_	_
85	colony	colony	NN	_	_	_
86	from	from	IN	_	_	_
87	tryptone	tryptone	NN	SUPP	_	_
88	soya	soya	NN	_	_	_
89	agar	agar	NN	_	_	_
90	-LRB-	-lrb-	-LRB-	_	_	_
91	TSA	tsa	NN	_	_	_
92	-RRB-	-rrb-	-RRB-	_	_	_
93	-LRB-	-lrb-	-LRB-	_	_	_
94	Oxoid	Oxoid	NNP	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	-LRB-	-lrb-	-LRB-	_	_	_
97	overnight	overnight	JJ	_	_	_
98	growth	growth	NN	_	_	_
99	at	at	IN	_	_	_
100	37	37	CD	_	_	_
101	°C	°c	NN	_	_	_
102	-RRB-	-rrb-	-RRB-	_	_	_
103	to	to	TO	_	_	_
104	5	5	CD	_	_	_
105	ml	ml	NN	_	_	_
106	TSB	tsb	NN	_	_	_
107	and	and	CC	_	_	_
108	incubating	incubate	VBG	_	_	_
109	overnight	overnight	JJ	_	_	_
110	at	at	IN	_	_	_
111	37	37	CD	_	_	_
112	°C	°c	NN	_	_	_
113	,	,	,	_	_	_
114	with	with	IN	_	_	_
115	shaking	shake	VBG	_	_	_
116	-LRB-	-lrb-	-LRB-	_	_	_
117	200	200	CD	_	_	_
118	rpm	rpm	NN	_	_	_
119	-RRB-	-rrb-	-RRB-	_	_	_
120	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	initially	initially	RB	_	_	_
5	diluted	dilute	VBN	_	_	_
6	1:10	1:10	CD	_	_	_
7	in	in	IN	_	_	_
8	medium	medium	NN	_	_	_
9	and	and	CC	_	_	_
10	used	use	VBN	_	_	_
11	to	to	TO	_	_	_
12	inoculate	inoculate	VB	_	_	_
13	room-temperature	room-temperature	JJ	_	_	_
14	TSB	tsb	NN	_	_	_
15	for	for	IN	_	_	_
16	each	each	DT	_	_	_
17	of	of	IN	_	_	_
18	the	the	DT	_	_	_
19	different	different	JJ	_	_	_
20	stress	stress	NN	_	_	_
21	factors	factor	NNS	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	40	40	CD	_	_	_
24	ml	ml	NN	_	_	_
25	total	total	JJ	_	_	_
26	volume	volume	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	to	to	TO	_	_	_
29	a	a	DT	_	_	_
30	final	final	JJ	_	_	_
31	concentration	concentration	NN	_	_	_
32	of	of	IN	_	_	_
33	approx.	approx.	RB	_	_	_
34	1	1	CD	_	_	_
35	'	'	''	_	_	_
36	107	107	CD	_	_	_
37	CFU	CFU	NNP	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
39	The	the	DT	_	_	_
40	fluorescent	fluorescent	JJ	_	_	_
41	spot	spot	NN	_	_	_
42	intensities	intensity	NNS	_	_	_
43	were	be	VBD	_	_	_
44	quantified	quantify	VBN	_	_	_
45	using	use	VBG	_	_	_
46	ImaGeneÔ	imageneô	NN	_	_	_
47	5.6.1	5.6.1	CD	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	BioDiscovery	BioDiscovery	NNP	_	_	_
50	Inc.	Inc.	NNP	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	software	software	NN	_	_	_
53	.	.	.	_	_	_

1	Background	background	NN	_	_	_
2	subtraction	subtraction	NN	_	_	_
3	and	and	CC	_	_	_
4	normalization	normalization	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	LOWESS	lowess	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	was	be	VBD	_	_	_
9	performed	perform	VBN	_	_	_
10	in	in	IN	_	_	_
11	GeneSpringä	GeneSpringä	NNP	_	_	_
12	7	7	CD	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Silicon	Silicon	NNP	_	_	_
15	Genetics	Genetics	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	-LRB-	-lrb-	-LRB-	_	_	_
2	A	a	DT	_	_	_
3	lowess	lowess	NN	_	_	_
4	curve	curve	NN	_	_	_
5	was	be	VBD	_	_	_
6	fit	fit	VBN	_	_	_
7	to	to	TO	_	_	_
8	the	the	DT	_	_	_
9	log-intensity	log-intensity	JJ	_	_	_
10	versus	versus	CC	_	_	_
11	log-ratio	log-ratio	JJ	_	_	_
12	plot	plot	NN	_	_	_
13	.	.	.	_	_	_

1	20	20	CD	_	_	_
2	%	%	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	data	datum	NNS	_	_	_
6	was	be	VBD	_	_	_
7	used	use	VBN	_	_	_
8	to	to	TO	_	_	_
9	calculate	calculate	VB	_	_	_
10	the	the	DT	_	_	_
11	lowess	lowess	NN	_	_	_
12	fit	fit	NN	_	_	_
13	at	at	IN	_	_	_
14	each	each	DT	_	_	_
15	point	point	NN	_	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	curve	curve	NN	_	_	_
3	was	be	VBD	_	_	_
4	used	use	VBN	_	_	_
5	to	to	TO	_	_	_
6	adjust	adjust	VB	_	_	_
7	the	the	DT	_	_	_
8	control	control	NN	_	_	_
9	value	value	NN	_	_	_
10	for	for	IN	_	_	_
11	each	each	DT	_	_	_
12	measurement	measurement	NN	_	_	_
13	.	.	.	_	_	_

1	If	if	IN	_	_	_
2	the	the	DT	_	_	_
3	control	control	NN	_	_	_
4	channel	channel	NN	_	_	_
5	was	be	VBD	_	_	_
6	lower	lower	JJR	_	_	_
7	than	than	IN	_	_	_
8	10	10	CD	_	_	_
9	then	then	RB	_	_	_
10	the	the	DT	_	_	_
11	value	value	NN	_	_	_
12	was	be	VBD	_	_	_
13	set	set	VBN	_	_	_
14	to	to	TO	_	_	_
15	10	10	CD	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	Only	only	RB	_	_	_
2	data	datum	NNS	_	_	_
3	from	from	IN	_	_	_
4	spots	spot	NNS	_	_	_
5	representing	represent	VBG	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	K-12	k-12	NN	_	_	_
9	MG1655	mg1655	NN	_	_	_
10	genes	gene	NNS	_	_	_
11	were	be	VBD	_	_	_
12	analyzed	analyze	VBN	_	_	_
13	in	in	IN	_	_	_
14	our	we	PRP$	_	_	_
15	studies	study	NNS	_	_	_
16	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	analyses	analysis	NNS	_	_	_
3	were	be	VBD	_	_	_
4	based	base	VBN	_	_	_
5	on	on	IN	_	_	_
6	3	3	CD	_	_	_
7	biological	biological	JJ	_	_	_
8	replicates	replicate	VBZ	_	_	_
9	with	with	IN	_	_	_
10	the	the	DT	_	_	_
11	exception	exception	NN	_	_	_
12	of	of	IN	_	_	_
13	the	the	DT	_	_	_
14	second	second	JJ	_	_	_
15	biological	biological	JJ	_	_	_
16	replicate	replicate	VB	_	_	_
17	from	from	IN	_	_	_
18	conditions	condition	NNS	_	_	_
19	HCl	hcl	NN	_	_	_
20	and	and	CC	_	_	_
21	NaOH	naoh	NN	_	_	_
22	.	.	.	_	_	_

1	These	these	DT	_	_	_
2	two	two	CD	_	_	_
3	observations	observation	NNS	_	_	_
4	were	be	VBD	_	_	_
5	removed	remove	VBN	_	_	_
6	due	due	JJ	_	_	_
7	to	to	TO	_	_	_
8	bad	bad	JJ	_	_	_
9	hybridization	hybridization	NN	_	_	_
10	giving	give	VBG	_	_	_
11	a	a	DT	_	_	_
12	total	total	NN	_	_	_
13	of	of	IN	_	_	_
14	34	34	CD	_	_	_
15	array	array	NN	_	_	_
16	hybridizations	hybridization	NNS	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	observations	observation	NNS	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	Genes	gene	NNS	_	_	_
2	not	not	RB	_	_	_
3	present	present	VB	_	_	_
4	in	in	IN	_	_	_
5	any	any	DT	_	_	_
6	of	of	IN	_	_	_
7	the	the	DT	_	_	_
8	34	34	CD	_	_	_
9	observations	observation	NNS	_	_	_
10	were	be	VBD	_	_	_
11	filtered	filter	VBN	_	_	_
12	out	out	RP	_	_	_
13	,	,	,	_	_	_
14	resulting	result	VBG	_	_	_
15	in	in	IN	_	_	_
16	the	the	DT	_	_	_
17	analysis	analysis	NN	_	_	_
18	of	of	IN	_	_	_
19	4279	4279	CD	_	_	_
20	out	out	IN	_	_	_
21	of	of	IN	_	_	_
22	4289	4289	CD	_	_	_
23	MG1655	mg1655	NN	_	_	_
24	genes	gene	NNS	_	_	_
25	on	on	IN	_	_	_
26	the	the	DT	_	_	_
27	array	array	NN	_	_	_
28	.	.	.	_	_	_

1	Missing	miss	VBG	_	_	_
2	values	value	NNS	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	data	datum	NNS	_	_	_
5	points	point	NNS	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	were	be	VBD	_	_	_
8	replaced	replace	VBN	_	_	_
9	by	by	IN	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	KNNimpute	knnimpute	NN	_	_	_
13	procedure	procedure	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	k	k	NN	_	_	_
16	=	=	JJ	_	_	_
17	10	10	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	on	on	IN	_	_	_
20	log2	log2	NN	_	_	_
21	transformed	transform	VBN	_	_	_
22	data	datum	NNS	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	from	from	IN	_	_	_
7	1	1	CD	_	_	_
8	ml	ml	NN	_	_	_
9	cells	cell	NNS	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	RNeasy	RNeasy	NNP	_	_	_
13	Protect	Protect	NNP	_	_	_
14	Bacteria	bacterium	NNS	_	_	_
15	Mini	Mini	NNP	_	_	_
16	Prep	Prep	NNP	_	_	_
17	kit	kit	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Qiagen	qiagen	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	as	as	IN	_	_	_
22	recommended	recommend	VBN	_	_	_
23	by	by	IN	_	_	_
24	the	the	DT	_	_	_
25	manufacturer	manufacturer	NN	_	_	_
26	including	include	VBG	_	_	_
27	the	the	DT	_	_	_
28	``	``	``	_	_	_
29	on-column	on-column	JJ	_	_	_
30	''	''	''	_	_	_
31	DNase	dnase	NN	_	_	_
32	treatment	treatment	NN	_	_	_
33	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	accession	accession	NN	_	_	_
3	:	:	:	_	_	_
4	NC	nc	NN	_	_	_
5	_	_	SYM	_	_	_
6	000913.2	000913.2	CD	_	_	_
7	+	+	CC	_	_	_
8	NC	NC	NNP	_	_	_
9	_	_	NNP	_	_	_
10	000913.3	000913.3	CD	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	After	after	IN	_	_	_
13	0.5	0.5	CD	_	_	_
14	M	m	NN	_	_	_
15	NaCl	nacl	NN	_	_	_
16	treatment	treatment	NN	_	_	_
17	for	for	IN	_	_	_
18	10	10	CD	_	_	_
19	min	min	NN	_	_	_
20	of	of	IN	_	_	_
21	the	the	DT	_	_	_
22	early-exponential	early-exponential	JJ	_	_	_
23	phase	phase	NN	_	_	_
24	cells	cell	NNS	_	_	_
25	,	,	,	_	_	_
26	samples	sample	NNS	_	_	_
27	were	be	VBD	_	_	_
28	collected	collect	VBN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	After	after	IN	_	_	_
3	0.5	0.5	CD	_	_	_
4	M	m	NN	_	_	_
5	NaCl	nacl	NN	_	_	_
6	treatment	treatment	NN	_	_	_
7	for	for	IN	_	_	_
8	20	20	CD	_	_	_
9	min	min	NN	_	_	_
10	of	of	IN	_	_	_
11	the	the	DT	_	_	_
12	early-exponential	early-exponential	JJ	_	_	_
13	phase	phase	NN	_	_	_
14	cells	cell	NNS	_	_	_
15	,	,	,	_	_	_
16	samples	sample	NNS	_	_	_
17	were	be	VBD	_	_	_
18	collected	collect	VBN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	After	after	IN	_	_	_
3	0.5	0.5	CD	_	_	_
4	M	m	NN	_	_	_
5	NaCl	nacl	NN	_	_	_
6	treatment	treatment	NN	_	_	_
7	for	for	IN	_	_	_
8	45	45	CD	_	_	_
9	min	min	NN	_	_	_
10	of	of	IN	_	_	_
11	the	the	DT	_	_	_
12	early-exponential	early-exponential	JJ	_	_	_
13	phase	phase	NN	_	_	_
14	cells	cell	NNS	_	_	_
15	,	,	,	_	_	_
16	samples	sample	NNS	_	_	_
17	were	be	VBD	_	_	_
18	collected	collect	VBN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Arrays	array	NNS	_	_	_
3	were	be	VBD	_	_	_
4	processed	process	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Nimblegen	Nimblegen	NNP	_	_	_
7	's	's	POS	_	_	_
8	standard	standard	JJ	_	_	_
9	protocol	protocol	NN	_	_	_
10	for	for	IN	_	_	_
11	Nimblescan	Nimblescan	NNP	_	_	_
12	ChIP	ChIP	NNP	_	_	_
13	data	datum	NNS	_	_	_
14	extraction	extraction	NN	_	_	_
15	.	.	.	_	_	_

1	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	chip	chip	NN	_	_	_
3	antibody	antibody	NN	_	_	_
4	:	:	:	_	_	_
5	none	none	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	chip	chip	NN	_	_	_
8	antibody	antibody	NN	_	_	_
9	:	:	:	_	_	_
10	RNAP	rnap	NN	_	_	_
11	beta	beta	NN	_	_	_
12	subunit	subunit	NN	_	_	_
13	antibody	antibody	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	E.	e.	FW	_	_	_
16	coli	coli	FW	_	_	_
17	CC72	cc72	NN	_	_	_
18	was	be	VBD	_	_	_
19	grown	grow	VBN	_	_	_
20	in	in	IN	_	_	_
21	water	water	NN	_	_	_
22	bath	bath	NN	_	_	_
23	to	to	TO	_	_	_
24	early-exponential	early-exponential	JJ	_	_	_
25	phase	phase	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	OD600	od600	NN	_	_	_
28	0.2	0.2	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	at	at	IN	_	_	_
31	37	37	CD	_	_	_
32	°C	°c	NN	_	_	_
33	in	in	IN	_	_	_
34	LB	lb	NN	MED	_	_
35	medium	medium	NN	MED	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	E.coli	e.coli	NNS	_	_	_
3	_	_	VBP	_	_	_
4	LB	lb	NN	_	_	_
5	_	_	CD	_	_	_
6	rep2	rep2	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	E.coli	e.coli	NNS	_	_	_
9	_	_	VBP	_	_	_
10	LB	lb	NN	_	_	_
11	_	_	CD	_	_	_
12	rep3	rep3	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	E.coli	e.coli	NNS	_	_	_
15	_	_	VBP	_	_	_
16	Na10	na10	NN	_	_	_
17	_	_	CD	_	_	_
18	rep1	rep1	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	E.coli	e.coli	NNS	_	_	_
21	_	_	VBP	_	_	_
22	Na10	na10	NN	_	_	_
23	_	_	CD	_	_	_
24	rep2	rep2	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	E.coli	e.coli	NNS	_	_	_
27	_	_	VBP	_	_	_
28	Na10	na10	NN	_	_	_
29	_	_	CD	_	_	_
30	rep3	rep3	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	E.coli	e.coli	NNS	_	_	_
33	_	_	VBP	_	_	_
34	Na20	na20	NN	_	_	_
35	_	_	CD	_	_	_
36	rep1	rep1	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	E.coli	e.coli	NNS	_	_	_
39	_	_	VBP	_	_	_
40	Na20	na20	NN	_	_	_
41	_	_	CD	_	_	_
42	rep2	rep2	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	E.coli	e.coli	NNS	_	_	_
45	_	_	VBP	_	_	_
46	Na20	na20	NN	_	_	_
47	_	_	CD	_	_	_
48	rep3	rep3	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	E.coli	e.coli	NNS	_	_	_
51	_	_	VBP	_	_	_
52	Na45	na45	NN	_	_	_
53	_	_	CD	_	_	_
54	rep1	rep1	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	E.coli	e.coli	NNS	_	_	_
57	_	_	VBP	_	_	_
58	Na45	na45	NN	_	_	_
59	_	_	CD	_	_	_
60	rep2	rep2	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	E.coli	e.coli	NNS	_	_	_
63	_	_	VBP	_	_	_
64	Na45	na45	NN	_	_	_
65	_	_	CD	_	_	_
66	rep3	rep3	NN	_	_	_
67	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
68	Escherichia	escherichia	FW	Organism	_	_
69	coli	coli	FW	Organism	_	_
70	str	str	FW	_	_	_
71	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	genotype	genotype	NN	_	_	_
4	:	:	:	_	_	_
5	Fusion	fusion	NN	_	_	_
6	of	of	IN	_	_	_
7	venus	venus	NN	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	3	3	CD	_	_	_
11	'	'	''	_	_	_
12	end	end	NN	_	_	_
13	of	of	IN	_	_	_
14	rpoC	rpoc	NN	GEN	_	_
15	in	in	IN	_	_	_
16	E.	e.	FW	_	_	_
17	coli	coli	FW	_	_	_
18	wild-type	wild-type	JJ	_	_	_
19	MG1655	mg1655	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	RNAP	rnap	NN	_	_	_
22	beta	beta	NN	_	_	_
23	subunit	subunit	NN	_	_	_
24	ChIP	chip	NN	_	_	_
25	DNA	dna	NN	_	_	_
26	from	from	IN	_	_	_
27	E.	e.	FW	_	_	_
28	coli	coli	FW	_	_	_
29	CC72	cc72	NN	_	_	_
30	10	10	CD	_	_	_
31	min	min	NN	_	_	_
32	after	after	IN	_	_	_
33	osmotic	osmotic	JJ	_	_	_
34	stress	stress	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	RNAP	rnap	NN	_	_	_
37	beta	beta	NN	_	_	_
38	subunit	subunit	NN	_	_	_
39	ChIP	chip	NN	_	_	_
40	DNA	dna	NN	_	_	_
41	from	from	IN	_	_	_
42	E.	e.	FW	_	_	_
43	coli	coli	FW	_	_	_
44	CC72	cc72	NN	_	_	_
45	20	20	CD	_	_	_
46	min	min	NN	_	_	_
47	after	after	IN	_	_	_
48	osmotic	osmotic	JJ	_	_	_
49	stress	stress	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	RNAP	rnap	NN	_	_	_
52	beta	beta	NN	_	_	_
53	subunit	subunit	NN	_	_	_
54	ChIP	chip	NN	_	_	_
55	DNA	dna	NN	_	_	_
56	from	from	IN	_	_	_
57	E.	e.	FW	_	_	_
58	coli	coli	FW	_	_	_
59	CC72	cc72	NN	_	_	_
60	45	45	CD	_	_	_
61	min	min	NN	_	_	_
62	after	after	IN	_	_	_
63	osmotic	osmotic	JJ	_	_	_
64	stress	stress	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	RNAP	rnap	NN	_	_	_
67	beta	beta	NN	_	_	_
68	subunit	subunit	NN	_	_	_
69	ChIP	chip	NN	_	_	_
70	DNA	dna	NN	_	_	_
71	from	from	IN	_	_	_
72	E.	e.	FW	_	_	_
73	coli	coli	FW	_	_	_
74	CC72	cc72	NN	_	_	_
75	at	at	IN	_	_	_
76	early-exponential	early-exponential	JJ	_	_	_
77	phase	phase	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
79	The	the	DT	_	_	_
80	ChIP	chip	NN	_	_	_
81	experiment	experiment	NN	_	_	_
82	was	be	VBD	_	_	_
83	performed	perform	VBN	_	_	_
84	essentially	essentially	RB	_	_	_
85	as	as	IN	_	_	_
86	described	describe	VBN	_	_	_
87	previously	previously	RB	_	_	_
88	-LRB-	-lrb-	-LRB-	_	_	_
89	Herring	Herring	NNP	_	_	_
90	,	,	,	_	_	_
91	Raffaelle	Raffaelle	NNP	_	_	_
92	et	et	FW	_	_	_
93	al.	al.	FW	_	_	_
94	2005	2005	CD	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	cell	cell	NN	_	_	_
5	cultures	culture	NNS	_	_	_
6	were	be	VBD	_	_	_
7	fixed	fix	VBN	_	_	_
8	by	by	IN	_	_	_
9	a	a	DT	_	_	_
10	1	1	CD	_	_	_
11	%	%	NN	_	_	_
12	formaldehyde	formaldehyde	NN	_	_	_
13	and	and	CC	_	_	_
14	10	10	CD	_	_	_
15	mM	mm	NN	KWSUPP	_	_
16	sodium	sodium	NN	_	_	_
17	phosphate	phosphate	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	pH	ph	NN	_	_	_
20	7.6	7.6	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	solution	solution	NN	_	_	_
23	for	for	IN	_	_	_
24	20	20	CD	_	_	_
25	min	min	NN	_	_	_
26	at	at	IN	_	_	_
27	room	room	NN	_	_	_
28	temperature	temperature	NN	_	_	_
29	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	cell	cell	NN	_	_	_
3	lysis	lysis	NN	_	_	_
4	,	,	,	_	_	_
5	RNase	rnase	NN	_	_	_
6	A	a	NN	_	_	_
7	treatment	treatment	NN	_	_	_
8	and	and	CC	_	_	_
9	sonication	sonication	NN	_	_	_
10	,	,	,	_	_	_
11	the	the	DT	_	_	_
12	chromosome	chromosome	NN	_	_	_
13	was	be	VBD	_	_	_
14	fragmented	fragmented	JJ	_	_	_
15	to	to	TO	_	_	_
16	100-1200	100-1200	CD	_	_	_
17	bp	bp	NN	_	_	_
18	.	.	.	_	_	_

1	RNAP	rnap	NN	_	_	_
2	binding	binding	NN	_	_	_
3	DNA	dna	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	IP	IP	NNP	_	_	_
6	DNA	dna	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	was	be	VBD	_	_	_
9	immunoprecipitated	immunoprecipitate	VBN	_	_	_
10	with	with	IN	_	_	_
11	RNAP	rnap	NN	_	_	_
12	using	use	VBG	_	_	_
13	an	a	DT	_	_	_
14	antibody	antibody	NN	_	_	_
15	against	against	IN	_	_	_
16	the	the	DT	_	_	_
17	RNAP	rnap	NN	_	_	_
18	β	β	NN	_	_	_
19	'	'	''	_	_	_
20	subunit	subunit	NN	_	_	_
21	and	and	CC	_	_	_
22	pan	pan	NN	_	_	_
23	mouse	mouse	NN	_	_	_
24	magnetic	magnetic	JJ	_	_	_
25	beads	bead	NNS	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	same	same	JJ	_	_	_
3	sample	sample	NN	_	_	_
4	without	without	IN	_	_	_
5	the	the	DT	_	_	_
6	β	β	NN	_	_	_
7	'	'	''	_	_	_
8	antibody	antibody	NN	_	_	_
9	was	be	VBD	_	_	_
10	used	use	VBN	_	_	_
11	as	as	IN	_	_	_
12	mock	mock	JJ	_	_	_
13	immunoprecipitation	immunoprecipitation	NN	_	_	_
14	DNA	dna	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	mock	mock	JJ	_	_	_
17	IP	IP	NNP	_	_	_
18	DNA	dna	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	washing	wash	VBG	_	_	_
3	and	and	CC	_	_	_
4	de-crosslinking	de-crosslinking	NN	_	_	_
5	,	,	,	_	_	_
6	DNA	dna	NN	_	_	_
7	was	be	VBD	_	_	_
8	purified	purify	VBN	_	_	_
9	using	use	VBG	_	_	_
10	the	the	DT	_	_	_
11	PCR	pcr	NN	_	_	_
12	purification	purification	NN	_	_	_
13	kit	kit	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Qiagen	qiagen	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	early-exponential	early-exponential	JJ	_	_	_
4	phase	phase	NN	_	_	_
5	cells	cell	NNS	_	_	_
6	were	be	VBD	_	_	_
7	collected	collect	VBN	_	_	_
8	without	without	IN	_	_	_
9	NaCl	nacl	NN	_	_	_
10	treatment	treatment	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	A	a	NN	_	_	_
3	culture	culture	NN	_	_	_
4	volume	volume	NN	_	_	_
5	of	of	IN	_	_	_
6	7	7	CD	_	_	_
7	ml	ml	NN	_	_	_
8	was	be	VBD	_	_	_
9	mixed	mix	VBN	_	_	_
10	with	with	IN	_	_	_
11	the	the	DT	_	_	_
12	same	same	JJ	_	_	_
13	volume	volume	NN	_	_	_
14	of	of	IN	_	_	_
15	boiling	boil	VBG	_	_	_
16	2	2	CD	_	_	_
17	%	%	NN	_	_	_
18	SDS	sds	NN	_	_	_
19	,	,	,	_	_	_
20	4mM	4mm	NN	_	_	_
21	EDTA	edta	NN	_	_	_
22	and	and	CC	_	_	_
23	heated	heat	VBN	_	_	_
24	at	at	IN	_	_	_
25	100	100	CD	_	_	_
26	°C	°c	NN	_	_	_
27	for	for	IN	_	_	_
28	3	3	CD	_	_	_
29	to	to	TO	_	_	_
30	5	5	CD	_	_	_
31	minutes	minute	NNS	_	_	_
32	then	then	RB	_	_	_
33	vortexed	vortex	VBD	_	_	_
34	.	.	.	_	_	_

1	At	at	IN	_	_	_
2	this	this	DT	_	_	_
3	stage	stage	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	extract	extract	NN	_	_	_
7	was	be	VBD	_	_	_
8	either	either	CC	_	_	_
9	processed	process	VBN	_	_	_
10	further	further	JJ	_	_	_
11	or	or	CC	_	_	_
12	stored	store	VBN	_	_	_
13	at	at	IN	_	_	_
14	-20	-20	CD	_	_	_
15	°C	°c	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Affymetrix	Affymetrix	NNP	_	_	_
3	.	.	.	_	_	_

1	CEL	CEL	NNP	_	_	_
2	files	file	VBZ	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	normalized	normalize	VBN	_	_	_
6	with	with	IN	_	_	_
7	dChip	dchip	NN	_	_	_
8	using	use	VBG	_	_	_
9	the	the	DT	_	_	_
10	array	array	NN	_	_	_
11	of	of	IN	_	_	_
12	median	median	JJ	_	_	_
13	brightness	brightness	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	BS	bs	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	Model	Model	NNP	_	_	_
2	method	method	NN	_	_	_
3	:	:	:	_	_	_
4	model-base	model-base	NN	_	_	_
5	expression	expression	NN	_	_	_
6	;	;	:	_	_	_
7	background	background	NN	_	_	_
8	substraction	substraction	NN	_	_	_
9	:	:	:	_	_	_
10	Mismatch	Mismatch	NNP	_	_	_
11	Probe	Probe	NNP	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	PM	PM	NNP	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	Escherichia	escherichia	FW	Organism	_	_
16	coli	coli	FW	Organism	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	exponential	exponential	JJ	GrowthPhase	_	_
19	phase	phase	NN	GrowthPhase	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	JO2057	jo2057	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	WT	wt	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	JO2057	jo2057	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	WT	wt	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	,	,	,	_	_	_
31	exponential	exponential	JJ	GrowthPhase	_	_
32	phase	phase	NN	GrowthPhase	_	_
33	,	,	,	_	_	_
34	repetition1	repetition1	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	JO2057	jo2057	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	WT	wt	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	,	,	,	_	_	_
41	exponential	exponential	JJ	GrowthPhase	_	_
42	phase	phase	NN	GrowthPhase	_	_
43	,	,	,	_	_	_
44	repetition2	repetition2	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	JO2057	jo2057	NN	_	_	_
47	WT	WT	NNP	_	_	_
48	,	,	,	_	_	_
49	LB	LB	NNP	_	_	_
50	,	,	,	_	_	_
51	exponential	exponential	JJ	GrowthPhase	_	_
52	phase	phase	NN	GrowthPhase	_	_
53	,	,	,	_	_	_
54	repetition1	repetition1	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	JO2057	jo2057	NN	_	_	_
57	WT	WT	NNP	_	_	_
58	,	,	,	_	_	_
59	LB	LB	NNP	_	_	_
60	,	,	,	_	_	_
61	exponential	exponential	JJ	GrowthPhase	_	_
62	phase	phase	NN	GrowthPhase	_	_
63	,	,	,	_	_	_
64	repetition2	repetition2	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	JO2057	jo2057	NN	_	_	_
67	WT	WT	NNP	_	_	_
68	,	,	,	_	_	_
69	LB	LB	NNP	_	_	_
70	,	,	,	_	_	_
71	stationary	stationary	JJ	GrowthPhase	_	_
72	phase	phase	NN	GrowthPhase	_	_
73	,	,	,	_	_	_
74	repetition1	repetition1	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	JO2057	jo2057	NN	_	_	_
77	WT	WT	NNP	_	_	_
78	,	,	,	_	_	_
79	LB	LB	NNP	_	_	_
80	,	,	,	_	_	_
81	stationary	stationary	JJ	GrowthPhase	_	_
82	phase	phase	NN	GrowthPhase	_	_
83	,	,	,	_	_	_
84	repetition2	repetition2	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	JO2057	jo2057	NN	_	_	_
87	WT	WT	NNP	_	_	_
88	,	,	,	_	_	_
89	LB	LB	NNP	_	_	_
90	,	,	,	_	_	_
91	transition	transition	NN	_	_	_
92	phase	phase	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	JO2057	jo2057	NN	_	_	_
95	-LRB-	-lrb-	-LRB-	_	_	_
96	WT	wt	NN	_	_	_
97	-RRB-	-rrb-	-RRB-	_	_	_
98	,	,	,	_	_	_
99	Min	min	NN	_	_	_
100	Glucose	glucose	NN	_	_	_
101	,	,	,	_	_	_
102	exponential	exponential	JJ	GrowthPhase	_	_
103	phase	phase	NN	GrowthPhase	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	JO2057	jo2057	NN	_	_	_
106	WT	WT	NNP	_	_	_
107	,	,	,	_	_	_
108	Min	Min	NNP	_	_	_
109	Glucose	Glucose	NNP	_	_	_
110	,	,	,	_	_	_
111	exponential	exponential	JJ	GrowthPhase	_	_
112	phase	phase	NN	GrowthPhase	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	JO2057	jo2057	NN	_	_	_
115	-LRB-	-lrb-	-LRB-	_	_	_
116	WT	wt	NN	_	_	_
117	-RRB-	-rrb-	-RRB-	_	_	_
118	,	,	,	_	_	_
119	Min	min	NN	_	_	_
120	Glucose	glucose	NN	_	_	_
121	,	,	,	_	_	_
122	stationary	stationary	JJ	GrowthPhase	_	_
123	phase	phase	NN	GrowthPhase	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	JO2057	jo2057	NN	_	_	_
126	WT	WT	NNP	_	_	_
127	,	,	,	_	_	_
128	Min	Min	NNP	_	_	_
129	Glucose	Glucose	NNP	_	_	_
130	,	,	,	_	_	_
131	stationary	stationary	JJ	GrowthPhase	_	_
132	phase	phase	NN	GrowthPhase	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	JO2057	jo2057	NN	_	_	_
135	-LRB-	-lrb-	-LRB-	_	_	_
136	WT	wt	NN	_	_	_
137	-RRB-	-rrb-	-RRB-	_	_	_
138	,	,	,	_	_	_
139	Min	Min	NNP	_	_	_
140	Glycerol	Glycerol	NNP	_	_	_
141	,	,	,	_	_	_
142	exponential	exponential	JJ	GrowthPhase	_	_
143	phase	phase	NN	GrowthPhase	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	JO2057	jo2057	NN	_	_	_
146	WT	WT	NNP	_	_	_
147	,	,	,	_	_	_
148	Min	Min	NNP	_	_	_
149	Glycerol	Glycerol	NNP	_	_	_
150	,	,	,	_	_	_
151	exponential	exponential	JJ	GrowthPhase	_	_
152	phase	phase	NN	GrowthPhase	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	JO2057	jo2057	NN	_	_	_
155	-LRB-	-lrb-	-LRB-	_	_	_
156	WT	wt	NN	_	_	_
157	-RRB-	-rrb-	-RRB-	_	_	_
158	,	,	,	_	_	_
159	Min	Min	NNP	_	_	_
160	Glycerol	Glycerol	NNP	_	_	_
161	,	,	,	_	_	_
162	stationary	stationary	JJ	GrowthPhase	_	_
163	phase	phase	NN	GrowthPhase	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	JO2057	jo2057	NN	_	_	_
166	WT	WT	NNP	_	_	_
167	,	,	,	_	_	_
168	Min	Min	NNP	_	_	_
169	Glycerol	Glycerol	NNP	_	_	_
170	,	,	,	_	_	_
171	stationary	stationary	JJ	GrowthPhase	_	_
172	phase	phase	NN	GrowthPhase	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	JO2057	jo2057	NN	_	_	_
175	-LRB-	-lrb-	-LRB-	_	_	_
176	WT	wt	NN	_	_	_
177	-RRB-	-rrb-	-RRB-	_	_	_
178	,	,	,	_	_	_
179	stationary	stationary	JJ	GrowthPhase	_	_
180	phase	phase	NN	GrowthPhase	_	_
181	,	,	,	_	_	_
182	repetition1	repetition1	NN	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	JO2057	jo2057	NN	_	_	_
185	-LRB-	-lrb-	-LRB-	_	_	_
186	WT	wt	NN	_	_	_
187	-RRB-	-rrb-	-RRB-	_	_	_
188	,	,	,	_	_	_
189	stationary	stationary	JJ	GrowthPhase	_	_
190	phase	phase	NN	GrowthPhase	_	_
191	,	,	,	_	_	_
192	repetition2	repetition2	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	JO2057	jo2057	NN	_	_	_
195	-LRB-	-lrb-	-LRB-	_	_	_
196	WT	wt	NN	_	_	_
197	-RRB-	-rrb-	-RRB-	_	_	_
198	,	,	,	_	_	_
199	transition	transition	NN	_	_	_
200	phase	phase	NN	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	JO2081	jo2081	NN	_	_	_
203	-LRB-	-lrb-	-LRB-	_	_	_
204	hupA	hupa	NN	GEN	_	_
205	-RRB-	-rrb-	-RRB-	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	JO2081	jo2081	NN	_	_	_
208	-LRB-	-lrb-	-LRB-	_	_	_
209	hupA	hupa	NN	GEN	_	_
210	-RRB-	-rrb-	-RRB-	_	_	_
211	,	,	,	_	_	_
212	exponential	exponential	JJ	GrowthPhase	_	_
213	phase	phase	NN	GrowthPhase	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	JO2081	jo2081	NN	_	_	_
216	hupA	hupa	NN	GEN	_	_
217	,	,	,	_	_	_
218	LB	lb	NN	_	_	_
219	,	,	,	_	_	_
220	exponential	exponential	JJ	GrowthPhase	_	_
221	phase	phase	NN	GrowthPhase	_	_
222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
223	JO2081	jo2081	NN	_	_	_
224	hupA	hupa	NN	GEN	_	_
225	,	,	,	_	_	_
226	LB	lb	NN	_	_	_
227	,	,	,	_	_	_
228	stationary	stationary	JJ	GrowthPhase	_	_
229	phase	phase	NN	GrowthPhase	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
231	JO2081	jo2081	NN	_	_	_
232	hupA	hupa	NN	GEN	_	_
233	,	,	,	_	_	_
234	LB	lb	NN	_	_	_
235	,	,	,	_	_	_
236	transition	transition	NN	_	_	_
237	phase	phase	NN	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	JO2081	jo2081	NN	_	_	_
240	-LRB-	-lrb-	-LRB-	_	_	_
241	hupA	hupa	NN	GEN	_	_
242	-RRB-	-rrb-	-RRB-	_	_	_
243	,	,	,	_	_	_
244	stationary	stationary	JJ	GrowthPhase	_	_
245	phase	phase	NN	GrowthPhase	_	_
246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
247	JO2081	jo2081	NN	_	_	_
248	-LRB-	-lrb-	-LRB-	_	_	_
249	hupA	hupa	NN	GEN	_	_
250	-RRB-	-rrb-	-RRB-	_	_	_
251	,	,	,	_	_	_
252	transition	transition	NN	_	_	_
253	phase	phase	NN	_	_	_
254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
255	JO2083	jo2083	NN	_	_	_
256	-LRB-	-lrb-	-LRB-	_	_	_
257	hupB	hupb	NN	GEN	_	_
258	-RRB-	-rrb-	-RRB-	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	JO2083	jo2083	NN	_	_	_
261	-LRB-	-lrb-	-LRB-	_	_	_
262	hupB	hupb	NN	GEN	_	_
263	-RRB-	-rrb-	-RRB-	_	_	_
264	,	,	,	_	_	_
265	exponential	exponential	JJ	GrowthPhase	_	_
266	phase	phase	NN	GrowthPhase	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	JO2083	jo2083	NN	_	_	_
269	hupB	hupb	NN	GEN	_	_
270	,	,	,	_	_	_
271	LB	lb	NN	_	_	_
272	,	,	,	_	_	_
273	exponential	exponential	JJ	GrowthPhase	_	_
274	phase	phase	NN	GrowthPhase	_	_
275	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
276	JO2083	jo2083	NN	_	_	_
277	hupB	hupb	NN	GEN	_	_
278	,	,	,	_	_	_
279	LB	lb	NN	_	_	_
280	,	,	,	_	_	_
281	stationary	stationary	JJ	GrowthPhase	_	_
282	phase	phase	NN	GrowthPhase	_	_
283	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
284	JO2083	jo2083	NN	_	_	_
285	hupB	hupb	NN	GEN	_	_
286	,	,	,	_	_	_
287	LB	lb	NN	_	_	_
288	,	,	,	_	_	_
289	transition	transition	NN	_	_	_
290	phase	phase	NN	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	JO2083	jo2083	NN	_	_	_
293	-LRB-	-lrb-	-LRB-	_	_	_
294	hupB	hupb	NN	GEN	_	_
295	-RRB-	-rrb-	-RRB-	_	_	_
296	,	,	,	_	_	_
297	stationary	stationary	JJ	GrowthPhase	_	_
298	phase	phase	NN	GrowthPhase	_	_
299	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
300	JO2083	jo2083	NN	_	_	_
301	-LRB-	-lrb-	-LRB-	_	_	_
302	hupB	hupb	NN	GEN	_	_
303	-RRB-	-rrb-	-RRB-	_	_	_
304	,	,	,	_	_	_
305	transition	transition	NN	_	_	_
306	phase	phase	NN	_	_	_
307	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
308	JO3020	jo3020	NN	_	_	_
309	-LRB-	-lrb-	-LRB-	_	_	_
310	hupAB	hupab	NN	_	_	_
311	-RRB-	-rrb-	-RRB-	_	_	_
312	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
313	JO3020	jo3020	NN	_	_	_
314	-LRB-	-lrb-	-LRB-	_	_	_
315	hupAB	hupab	NN	_	_	_
316	-RRB-	-rrb-	-RRB-	_	_	_
317	,	,	,	_	_	_
318	exponential	exponential	JJ	GrowthPhase	_	_
319	phase	phase	NN	GrowthPhase	_	_
320	,	,	,	_	_	_
321	repetition1	repetition1	NN	_	_	_
322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
323	JO3020	jo3020	NN	_	_	_
324	-LRB-	-lrb-	-LRB-	_	_	_
325	hupAB	hupab	NN	_	_	_
326	-RRB-	-rrb-	-RRB-	_	_	_
327	,	,	,	_	_	_
328	exponential	exponential	JJ	GrowthPhase	_	_
329	phase	phase	NN	GrowthPhase	_	_
330	,	,	,	_	_	_
331	repetition2	repetition2	NN	_	_	_
332	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
333	JO3020	jo3020	NN	_	_	_
334	hupAB	hupab	NN	_	_	_
335	,	,	,	_	_	_
336	LB	lb	NN	_	_	_
337	,	,	,	_	_	_
338	exponential	exponential	JJ	GrowthPhase	_	_
339	phase	phase	NN	GrowthPhase	_	_
340	,	,	,	_	_	_
341	repetition1	repetition1	NN	_	_	_
342	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
343	JO3020	jo3020	NN	_	_	_
344	hupAB	hupab	NN	_	_	_
345	,	,	,	_	_	_
346	LB	lb	NN	_	_	_
347	,	,	,	_	_	_
348	exponential	exponential	JJ	GrowthPhase	_	_
349	phase	phase	NN	GrowthPhase	_	_
350	,	,	,	_	_	_
351	repetition2	repetition2	NN	_	_	_
352	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
353	JO3020	jo3020	NN	_	_	_
354	hupAB	hupab	NN	_	_	_
355	,	,	,	_	_	_
356	LB	lb	NN	_	_	_
357	,	,	,	_	_	_
358	stationary	stationary	JJ	GrowthPhase	_	_
359	phase	phase	NN	GrowthPhase	_	_
360	,	,	,	_	_	_
361	repetition1	repetition1	NN	_	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
363	JO3020	jo3020	NN	_	_	_
364	hupAB	hupab	NN	_	_	_
365	,	,	,	_	_	_
366	LB	lb	NN	_	_	_
367	,	,	,	_	_	_
368	stationary	stationary	JJ	GrowthPhase	_	_
369	phase	phase	NN	GrowthPhase	_	_
370	,	,	,	_	_	_
371	repetition2	repetition2	NN	_	_	_
372	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
373	JO3020	jo3020	NN	_	_	_
374	hupAB	hupab	NN	_	_	_
375	,	,	,	_	_	_
376	LB	lb	NN	_	_	_
377	,	,	,	_	_	_
378	transition	transition	NN	_	_	_
379	phase	phase	NN	_	_	_
380	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
381	JO3020	jo3020	NN	_	_	_
382	-LRB-	-lrb-	-LRB-	_	_	_
383	hupAB	hupab	NN	_	_	_
384	-RRB-	-rrb-	-RRB-	_	_	_
385	,	,	,	_	_	_
386	Min	min	NN	_	_	_
387	Glucose	glucose	NN	_	_	_
388	,	,	,	_	_	_
389	exponential	exponential	JJ	GrowthPhase	_	_
390	phase	phase	NN	GrowthPhase	_	_
391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
392	JO3020	jo3020	NN	_	_	_
393	hupAB	hupab	NN	_	_	_
394	,	,	,	_	_	_
395	Min	min	NN	_	_	_
396	Glucose	glucose	NN	_	_	_
397	,	,	,	_	_	_
398	exponential	exponential	JJ	GrowthPhase	_	_
399	phase	phase	NN	GrowthPhase	_	_
400	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
401	JO3020	jo3020	NN	_	_	_
402	-LRB-	-lrb-	-LRB-	_	_	_
403	hupAB	hupab	NN	_	_	_
404	-RRB-	-rrb-	-RRB-	_	_	_
405	,	,	,	_	_	_
406	Min	min	NN	_	_	_
407	Glucose	glucose	NN	_	_	_
408	,	,	,	_	_	_
409	stationary	stationary	JJ	GrowthPhase	_	_
410	phase	phase	NN	GrowthPhase	_	_
411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
412	JO3020	jo3020	NN	_	_	_
413	hupAB	hupab	NN	_	_	_
414	,	,	,	_	_	_
415	Min	min	NN	_	_	_
416	Glucose	glucose	NN	_	_	_
417	,	,	,	_	_	_
418	stationary	stationary	JJ	GrowthPhase	_	_
419	phase	phase	NN	GrowthPhase	_	_
420	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
421	JO3020	jo3020	NN	_	_	_
422	-LRB-	-lrb-	-LRB-	_	_	_
423	hupAB	hupab	NN	_	_	_
424	-RRB-	-rrb-	-RRB-	_	_	_
425	,	,	,	_	_	_
426	Min	Min	NNP	_	_	_
427	Glycerol	Glycerol	NNP	_	_	_
428	exponential	exponential	JJ	GrowthPhase	_	_
429	phase	phase	NN	GrowthPhase	_	_
430	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
431	JO3020	jo3020	NN	_	_	_
432	hupAB	hupab	NN	_	_	_
433	,	,	,	_	_	_
434	Min	Min	NNP	_	_	_
435	Glycerol	Glycerol	NNP	_	_	_
436	exponential	exponential	JJ	GrowthPhase	_	_
437	phase	phase	NN	GrowthPhase	_	_
438	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
439	JO3020	jo3020	NN	_	_	_
440	-LRB-	-lrb-	-LRB-	_	_	_
441	hupAB	hupab	NN	_	_	_
442	-RRB-	-rrb-	-RRB-	_	_	_
443	,	,	,	_	_	_
444	Min	Min	NNP	_	_	_
445	Glycerol	Glycerol	NNP	_	_	_
446	stationary	stationary	JJ	GrowthPhase	_	_
447	phase	phase	NN	GrowthPhase	_	_
448	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
449	JO3020	jo3020	NN	_	_	_
450	hupAB	hupab	NN	_	_	_
451	,	,	,	_	_	_
452	Min	Min	NNP	_	_	_
453	Glycerol	Glycerol	NNP	_	_	_
454	stationary	stationary	JJ	GrowthPhase	_	_
455	phase	phase	NN	GrowthPhase	_	_
456	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
457	JO3020	jo3020	NN	_	_	_
458	-LRB-	-lrb-	-LRB-	_	_	_
459	hupAB	hupab	NN	_	_	_
460	-RRB-	-rrb-	-RRB-	_	_	_
461	,	,	,	_	_	_
462	stationary	stationary	JJ	GrowthPhase	_	_
463	phase	phase	NN	GrowthPhase	_	_
464	,	,	,	_	_	_
465	repetition1	repetition1	NN	_	_	_
466	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
467	JO3020	jo3020	NN	_	_	_
468	-LRB-	-lrb-	-LRB-	_	_	_
469	hupAB	hupab	NN	_	_	_
470	-RRB-	-rrb-	-RRB-	_	_	_
471	,	,	,	_	_	_
472	stationary	stationary	JJ	GrowthPhase	_	_
473	phase	phase	NN	GrowthPhase	_	_
474	,	,	,	_	_	_
475	repetition2	repetition2	NN	_	_	_
476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
477	JO3020	jo3020	NN	_	_	_
478	-LRB-	-lrb-	-LRB-	_	_	_
479	hupAB	hupab	NN	_	_	_
480	-RRB-	-rrb-	-RRB-	_	_	_
481	,	,	,	_	_	_
482	transition	transition	NN	_	_	_
483	phase	phase	NN	_	_	_
484	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
485	MW30	mw30	NN	_	_	_
486	-LRB-	-lrb-	-LRB-	_	_	_
487	rpoS	rpos	NN	GEN	_	_
488	-RRB-	-rrb-	-RRB-	_	_	_
489	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
490	MW30	mw30	NN	_	_	_
491	-LRB-	-lrb-	-LRB-	_	_	_
492	rpoS	rpos	NN	GEN	_	_
493	-RRB-	-rrb-	-RRB-	_	_	_
494	,	,	,	_	_	_
495	LB	lb	NN	_	_	_
496	,	,	,	_	_	_
497	exponential	exponential	JJ	GrowthPhase	_	_
498	phase	phase	NN	GrowthPhase	_	_
499	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
500	MW30	mw30	NN	_	_	_
501	rpoS	rpos	NN	GEN	_	_
502	,	,	,	_	_	_
503	LB	lb	NN	_	_	_
504	,	,	,	_	_	_
505	exponential	exponential	JJ	GrowthPhase	_	_
506	phase	phase	NN	GrowthPhase	_	_
507	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
508	MW30	mw30	NN	_	_	_
509	-LRB-	-lrb-	-LRB-	_	_	_
510	rpoS	rpos	NN	GEN	_	_
511	-RRB-	-rrb-	-RRB-	_	_	_
512	,	,	,	_	_	_
513	LB	lb	NN	_	_	_
514	,	,	,	_	_	_
515	stationary	stationary	JJ	GrowthPhase	_	_
516	phase	phase	NN	GrowthPhase	_	_
517	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
518	MW30	mw30	NN	_	_	_
519	rpoS	rpos	NN	GEN	_	_
520	,	,	,	_	_	_
521	LB	lb	NN	_	_	_
522	,	,	,	_	_	_
523	stationary	stationary	JJ	GrowthPhase	_	_
524	phase	phase	NN	GrowthPhase	_	_
525	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
526	Seven	seven	CD	_	_	_
527	mililiter	mililiter	NN	_	_	_
528	of	of	IN	_	_	_
529	phenol	phenol	NN	_	_	_
530	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
531	stationary	stationary	JJ	GrowthPhase	_	_
532	phase	phase	NN	GrowthPhase	_	_
533	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
534	The	the	DT	_	_	_
535	five	five	CD	_	_	_
536	bacterial	bacterial	JJ	_	_	_
537	strains	strain	NNS	_	_	_
538	-LRB-	-lrb-	-LRB-	_	_	_
539	JO2057	jo2057	NN	_	_	_
540	,	,	,	_	_	_
541	JO2081	jo2081	NN	_	_	_
542	,	,	,	_	_	_
543	JO2083	jo2083	NN	_	_	_
544	,	,	,	_	_	_
545	JO3020	jo3020	NN	_	_	_
546	and	and	CC	_	_	_
547	MW30	mw30	NN	_	_	_
548	-RRB-	-rrb-	-RRB-	_	_	_
549	were	be	VBD	_	_	_
550	grown	grow	VBN	_	_	_
551	in	in	IN	_	_	_
552	100	100	CD	_	_	_
553	ml	ml	NN	_	_	_
554	LB	lb	NN	_	_	_
555	0.5	0.5	CD	_	_	_
556	%	%	NN	_	_	_
557	NaCl	nacl	NN	_	_	_
558	,	,	,	_	_	_
559	M9	m9	NN	_	_	_
560	minimal	minimal	JJ	_	_	_
561	glucose	glucose	NN	SUPP	_	_
562	or	or	CC	_	_	_
563	M9	m9	NN	_	_	_
564	minimal	minimal	JJ	_	_	_
565	glycerol	glycerol	NN	SUPP	_	_
566	at	at	IN	_	_	_
567	200	200	CD	_	_	_
568	rpm	rpm	NN	_	_	_
569	in	in	IN	_	_	_
570	New	New	NNP	_	_	_
571	Brunswick	Brunswick	NNP	_	_	_
572	laboratory	laboratory	NN	_	_	_
573	shaker	shaker	NN	_	_	_
574	in	in	IN	_	_	_
575	2liter	2liter	JJ	_	_	_
576	flasks	flask	NNS	_	_	_
577	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	typical	typical	JJ	_	_	_
3	doubling	doubling	NN	_	_	_
4	time	time	NN	_	_	_
5	,	,	,	_	_	_
6	observed	observe	VBN	_	_	_
7	in	in	IN	_	_	_
8	exponential	exponential	JJ	GrowthPhase	_	_
9	phase	phase	NN	GrowthPhase	_	_
10	in	in	IN	_	_	_
11	LB	LB	NNP	_	_	_
12	,	,	,	_	_	_
13	was	be	VBD	_	_	_
14	40	40	CD	_	_	_
15	min	min	NN	_	_	_
16	for	for	IN	_	_	_
17	JO2057	jo2057	NN	_	_	_
18	,	,	,	_	_	_
19	JO2081	jo2081	NN	_	_	_
20	,	,	,	_	_	_
21	JO2083	jo2083	NN	_	_	_
22	,	,	,	_	_	_
23	MW30	mw30	NN	_	_	_
24	and	and	CC	_	_	_
25	75	75	CD	_	_	_
26	min	min	NN	_	_	_
27	for	for	IN	_	_	_
28	JO3020	jo3020	NN	_	_	_
29	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	growth	growth	NN	_	_	_
3	curve	curve	NN	_	_	_
4	calibration	calibration	NN	_	_	_
5	,	,	,	_	_	_
6	the	the	DT	_	_	_
7	various	various	JJ	_	_	_
8	growth	growth	NN	_	_	_
9	phase	phase	NN	_	_	_
10	sample	sample	NN	_	_	_
11	were	be	VBD	_	_	_
12	collected	collect	VBN	_	_	_
13	at	at	IN	_	_	_
14	the	the	DT	_	_	_
15	following	following	JJ	_	_	_
16	cell	cell	NN	_	_	_
17	densities	density	NNS	_	_	_
18	:	:	:	_	_	_
19	exponential	exponential	JJ	GrowthPhase	_	_
20	phase	phase	NN	GrowthPhase	_	_
21	:	:	:	_	_	_
22	OD600	od600	NN	_	_	_
23	0.6-0.7	0.6-0.7	CD	_	_	_
24	;	;	:	_	_	_
25	transition	transition	NN	_	_	_
26	:	:	:	_	_	_
27	2.2-2.5	2.2-2.5	CD	_	_	_
28	and	and	CC	_	_	_
29	stationary	stationary	JJ	_	_	_
30	:	:	:	_	_	_
31	4.6-4.8	4.6-4.8	CD	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	3.0	3.0	CD	_	_	_
34	for	for	IN	_	_	_
35	hupAB	hupab	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	transition	transition	NN	_	_	_
3	phase	phase	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Anaerobic	anaerobic	JJ	_	_	_
6	,	,	,	_	_	_
7	minus	minus	CC	_	_	_
8	nitrate	nitrate	NN	SUPP	_	_
9	,	,	,	_	_	_
10	IP	IP	NNP	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	Anaerobic	Anaerobic	NNP	_	_	_
13	,	,	,	_	_	_
14	plus	plus	CC	_	_	_
15	nitrate	nitrate	NN	SUPP	_	_
16	,	,	,	_	_	_
17	IP	IP	NNP	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Chromatin	Chromatin	NNP	_	_	_
20	was	be	VBD	_	_	_
21	extracted	extract	VBN	_	_	_
22	and	and	CC	_	_	_
23	processed	process	VBN	_	_	_
24	according	accord	VBG	_	_	_
25	to	to	TO	_	_	_
26	Oxford	Oxford	NNP	_	_	_
27	Gene	Gene	NNP	_	_	_
28	Technology	Technology	NNP	_	_	_
29	protocols	protocol	NNS	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	www.ogt.co.uk	www.ogt.co.uk	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Escherichia	escherichia	FW	Organism	_	_
6	coli	coli	FW	Organism	_	_
7	,	,	,	_	_	_
8	expressing	express	VBG	_	_	_
9	NsrR	nsrr	NN	TF	_	_
10	with	with	IN	_	_	_
11	a	a	DT	_	_	_
12	C-terminal	c-terminal	JJ	_	_	_
13	Flag-tag	flag-tag	NN	_	_	_
14	,	,	,	_	_	_
15	was	be	VBD	_	_	_
16	grown	grow	VBN	_	_	_
17	anaerobically	anaerobically	RB	_	_	_
18	in	in	IN	_	_	_
19	L	l	NN	_	_	_
20	broth	broth	NN	_	_	_
21	supplemented	supplement	VBN	_	_	_
22	with	with	IN	_	_	_
23	glucose	glucose	NN	SUPP	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	,	,	,	_	_	_
5	expressing	express	VBG	_	_	_
6	NsrR	nsrr	NN	TF	_	_
7	with	with	IN	_	_	_
8	a	a	DT	_	_	_
9	C-terminal	c-terminal	JJ	_	_	_
10	Flag-tag	flag-tag	NN	_	_	_
11	,	,	,	_	_	_
12	was	be	VBD	_	_	_
13	grown	grow	VBN	_	_	_
14	anaerobically	anaerobically	RB	_	_	_
15	in	in	IN	_	_	_
16	L	l	NN	_	_	_
17	broth	broth	NN	_	_	_
18	supplemented	supplement	VBN	_	_	_
19	with	with	IN	_	_	_
20	glucose	glucose	NN	SUPP	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	,	,	,	_	_	_
5	expressing	express	VBG	_	_	_
6	NsrR	nsrr	NN	TF	_	_
7	with	with	IN	_	_	_
8	a	a	DT	_	_	_
9	C-terminal	c-terminal	JJ	_	_	_
10	Flag-tag	flag-tag	NN	_	_	_
11	,	,	,	_	_	_
12	was	be	VBD	_	_	_
13	grown	grow	VBN	_	_	_
14	anaerobically	anaerobically	RB	_	_	_
15	in	in	IN	_	_	_
16	L	l	NN	_	_	_
17	broth	broth	NN	_	_	_
18	supplemented	supplement	VBN	_	_	_
19	with	with	IN	_	_	_
20	glucose	glucose	NN	SUPP	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	,	,	,	_	_	_
5	expressing	express	VBG	_	_	_
6	NsrR	nsrr	NN	TF	_	_
7	with	with	IN	_	_	_
8	a	a	DT	_	_	_
9	C-terminal	c-terminal	JJ	_	_	_
10	Flag-tag	flag-tag	NN	_	_	_
11	,	,	,	_	_	_
12	was	be	VBD	_	_	_
13	grown	grow	VBN	_	_	_
14	anaerobically	anaerobically	RB	_	_	_
15	in	in	IN	_	_	_
16	L	l	NN	_	_	_
17	broth	broth	NN	_	_	_
18	supplemented	supplement	VBN	_	_	_
19	with	with	IN	_	_	_
20	glucose	glucose	NN	SUPP	_	_
21	and	and	CC	_	_	_
22	nitrate	nitrate	NN	SUPP	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	,	,	,	_	_	_
5	expressing	express	VBG	_	_	_
6	NsrR	nsrr	NN	TF	_	_
7	with	with	IN	_	_	_
8	a	a	DT	_	_	_
9	C-terminal	c-terminal	JJ	_	_	_
10	Flag-tag	flag-tag	NN	_	_	_
11	,	,	,	_	_	_
12	was	be	VBD	_	_	_
13	grown	grow	VBN	_	_	_
14	anaerobically	anaerobically	RB	_	_	_
15	in	in	IN	_	_	_
16	L	l	NN	_	_	_
17	broth	broth	NN	_	_	_
18	supplemented	supplement	VBN	_	_	_
19	with	with	IN	_	_	_
20	glucose	glucose	NN	SUPP	_	_
21	and	and	CC	_	_	_
22	nitrate	nitrate	NN	SUPP	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	NsrR	nsrr	NN	TF	_	_
3	_	_	CD	_	_	_
4	Flagtag	Flagtag	NNP	_	_	_
5	_	_	CD	_	_	_
6	rep1	rep1	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	NsrR	nsrr	NN	TF	_	_
9	_	_	CD	_	_	_
10	Flagtag	Flagtag	NNP	_	_	_
11	_	_	CD	_	_	_
12	rep2	rep2	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	NsrR	nsrr	NN	TF	_	_
15	_	_	CD	_	_	_
16	Flagtag	Flagtag	NNP	_	_	_
17	_	_	CD	_	_	_
18	rep3	rep3	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	The	the	DT	_	_	_
21	value	value	NN	_	_	_
22	is	be	VBZ	_	_	_
23	the	the	DT	_	_	_
24	simple	simple	JJ	_	_	_
25	linear	linear	JJ	_	_	_
26	ratio	ratio	NN	_	_	_
27	of	of	IN	_	_	_
28	the	the	DT	_	_	_
29	processed	process	VBN	_	_	_
30	Cy3	cy3	NN	_	_	_
31	and	and	CC	_	_	_
32	Cy5	cy5	NN	_	_	_
33	signals	signal	NNS	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	value	value	NN	_	_	_
4	is	be	VBZ	_	_	_
5	the	the	DT	_	_	_
6	simple	simple	JJ	_	_	_
7	linear	linear	JJ	_	_	_
8	ratio	ratio	NN	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	processed	process	VBN	_	_	_
12	Cy5	cy5	NN	_	_	_
13	and	and	CC	_	_	_
14	Cy3	cy3	NN	_	_	_
15	signals	signal	NNS	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	bacteria	bacterium	NNS	_	_	_
3	harvested	harvest	VBN	_	_	_
4	from	from	IN	_	_	_
5	blood	blood	NN	_	_	_
6	of	of	IN	_	_	_
7	chickens	chicken	NNS	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	condition	condition	NN	_	_	_
10	:	:	:	_	_	_
11	in	in	FW	_	_	_
12	vivo	vivo	FW	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Data	Data	NNP	_	_	_
15	were	be	VBD	_	_	_
16	extracted	extract	VBN	_	_	_
17	with	with	IN	_	_	_
18	Feature	feature	NN	_	_	_
19	Extraction	extraction	NN	_	_	_
20	software	software	NN	_	_	_
21	10.7	10.7	CD	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Agilent	agilent	JJ	_	_	_
24	technologies	technology	NNS	_	_	_
25	,	,	,	_	_	_
26	Santa	Santa	NNP	_	_	_
27	Clara	Clara	NNP	_	_	_
28	,	,	,	_	_	_
29	CA	CA	NNP	_	_	_
30	,	,	,	_	_	_
31	US	US	NNP	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Raw	raw	NN	_	_	_
2	data	datum	NNS	_	_	_
3	were	be	VBD	_	_	_
4	normalized	normalize	VBN	_	_	_
5	by	by	IN	_	_	_
6	Quantile	quantile	JJ	_	_	_
7	algorithm	algorithm	NN	_	_	_
8	,	,	,	_	_	_
9	GeneSpring	GeneSpring	NNP	_	_	_
10	Software	Software	NNP	_	_	_
11	11.0	11.0	CD	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Agilent	agilent	JJ	_	_	_
14	technologies	technology	NNS	_	_	_
15	,	,	,	_	_	_
16	Santa	Santa	NNP	_	_	_
17	Clara	Clara	NNP	_	_	_
18	,	,	,	_	_	_
19	CA	CA	NNP	_	_	_
20	,	,	,	_	_	_
21	US	US	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	E058	e058	NN	_	_	_
3	in	in	FW	_	_	_
4	vivo	vivo	FW	_	_	_
5	,	,	,	_	_	_
6	biological	biological	JJ	_	_	_
7	rep1	rep1	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	E058	e058	NN	_	_	_
10	in	in	FW	_	_	_
11	vivo	vivo	FW	_	_	_
12	,	,	,	_	_	_
13	biological	biological	JJ	_	_	_
14	rep2	rep2	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	E058	e058	NN	_	_	_
17	in	in	FW	_	_	_
18	vivo	vivo	FW	_	_	_
19	,	,	,	_	_	_
20	biological	biological	JJ	_	_	_
21	rep3	rep3	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	E058ΔrstAB	e058δrstab	NN	_	_	_
24	in	in	FW	_	_	_
25	vivo	vivo	FW	_	_	_
26	,	,	,	_	_	_
27	biological	biological	JJ	_	_	_
28	rep1	rep1	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	E058ΔrstAB	e058δrstab	NN	_	_	_
31	in	in	FW	_	_	_
32	vivo	vivo	FW	_	_	_
33	,	,	,	_	_	_
34	biological	biological	JJ	_	_	_
35	rep2	rep2	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	E058ΔrstAB	e058δrstab	NN	_	_	_
38	in	in	FW	_	_	_
39	vivo	vivo	FW	_	_	_
40	,	,	,	_	_	_
41	biological	biological	JJ	_	_	_
42	rep3	rep3	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Escherichia	escherichia	FW	Organism	_	_
45	coli	coli	FW	Organism	_	_
46	APEC	apec	NN	_	_	_
47	O2	o2	CD	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	genotype	genotype	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	strain	strain	NN	_	_	_
52	:	:	:	_	_	_
53	E058	e058	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
55	The	the	DT	_	_	_
56	in	in	FW	_	_	_
57	vivo	vivo	FW	_	_	_
58	bacterial	bacterial	JJ	_	_	_
59	samples	sample	NNS	_	_	_
60	were	be	VBD	_	_	_
61	harvested	harvest	VBN	_	_	_
62	with	with	IN	_	_	_
63	two-step	two-step	JJ	_	_	_
64	centrifugation	centrifugation	NN	_	_	_
65	.	.	.	_	_	_

1	We	we	PRP	_	_	_
2	first	first	RB	_	_	_
3	centrifuged	centrifuge	VBD	_	_	_
4	the	the	DT	_	_	_
5	collected	collect	VBN	_	_	_
6	anticoagulated	anticoagulated	JJ	_	_	_
7	blood	blood	NN	_	_	_
8	samples	sample	NNS	_	_	_
9	at	at	IN	_	_	_
10	low	low	JJ	_	_	_
11	speed	speed	NN	_	_	_
12	to	to	TO	_	_	_
13	remove	remove	VB	_	_	_
14	the	the	DT	_	_	_
15	abundant	abundant	JJ	_	_	_
16	red	red	JJ	_	_	_
17	and	and	CC	_	_	_
18	white	white	JJ	_	_	_
19	blood	blood	NN	_	_	_
20	cells	cell	NNS	_	_	_
21	and	and	CC	_	_	_
22	collected	collect	VBN	_	_	_
23	the	the	DT	_	_	_
24	upper	upper	JJ	_	_	_
25	serum	serum	NN	_	_	_
26	layer	layer	NN	_	_	_
27	.	.	.	_	_	_

1	We	we	PRP	_	_	_
2	then	then	RB	_	_	_
3	used	use	VBD	_	_	_
4	high-speed	high-speed	JJ	_	_	_
5	centrifugation	centrifugation	NN	_	_	_
6	to	to	TO	_	_	_
7	precipitate	precipitate	VB	_	_	_
8	the	the	DT	_	_	_
9	bacteria	bacterium	NNS	_	_	_
10	from	from	IN	_	_	_
11	the	the	DT	_	_	_
12	serum	serum	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	To	to	TO	_	_	_
3	prepare	prepare	VB	_	_	_
4	the	the	DT	_	_	_
5	in	in	FW	_	_	_
6	vivo	vivo	FW	_	_	_
7	samples	sample	NNS	_	_	_
8	,	,	,	_	_	_
9	the	the	DT	_	_	_
10	bacteria	bacterium	NNS	_	_	_
11	was	be	VBD	_	_	_
12	harvested	harvest	VBN	_	_	_
13	from	from	IN	_	_	_
14	cardiac	cardiac	JJ	_	_	_
15	blood	blood	NN	_	_	_
16	in	in	IN	_	_	_
17	1-day-old	1-day-old	JJ	_	_	_
18	chickens	chicken	NNS	_	_	_
19	at	at	IN	_	_	_
20	5	5	CD	_	_	_
21	hours	hour	NNS	_	_	_
22	post	post	NN	_	_	_
23	infection	infection	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	from	from	IN	_	_	_
5	in	in	FW	_	_	_
6	vivo	vivo	FW	_	_	_
7	samples	sample	NNS	_	_	_
8	of	of	IN	_	_	_
9	APEC	APEC	NNP	_	_	_
10	E058	e058	NN	_	_	_
11	and	and	CC	_	_	_
12	E058ΔrstAB	e058δrstab	NN	_	_	_
13	was	be	VBD	_	_	_
14	extracted	extract	VBN	_	_	_
15	and	and	CC	_	_	_
16	purified	purify	VBN	_	_	_
17	using	use	VBG	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74106	74106	CD	_	_	_
25	,	,	,	_	_	_
26	QIAGEN	QIAGEN	NNP	_	_	_
27	,	,	,	_	_	_
28	GmBH	GmBH	NNP	_	_	_
29	,	,	,	_	_	_
30	Germany	Germany	NNP	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	following	follow	VBG	_	_	_
33	the	the	DT	_	_	_
34	manufacturer	manufacturer	NN	_	_	_
35	's	's	POS	_	_	_
36	instructions	instruction	NNS	_	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	10	10	CD	_	_	_
3	.	.	.	_	_	_

1	FHI9.IND.HUS	fhi9.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	11	11	CD	_	_	_
4	.	.	.	_	_	_

1	FHI12.nIND.HUS	fhi12.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	12	12	CD	_	_	_
4	.	.	.	_	_	_

1	FHI12.IND.HUS	fhi12.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	13	13	CD	_	_	_
4	.	.	.	_	_	_

1	FHI24.nIND.HUS	fhi24.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	15	15	CD	_	_	_
4	.	.	.	_	_	_

1	FHI25.nIND.HUS	fhi25.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	16	16	CD	_	_	_
4	.	.	.	_	_	_

1	FHI25.IND.HUS	fhi25.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	17	17	CD	_	_	_
4	.	.	.	_	_	_

1	FHI27.nIND.HUS	fhi27.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	18	18	CD	_	_	_
4	.	.	.	_	_	_

1	FHI27.IND.HUS	fhi27.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	19	19	CD	_	_	_
4	.	.	.	_	_	_

1	FHI36.nIND.nHUS	fhi36.nind.nhus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	1	1	CD	_	_	_
4	.	.	.	_	_	_

1	FHI4.nIND.HUS	fhi4.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	20	20	CD	_	_	_
4	.	.	.	_	_	_

1	FHI36.IND.nHUS	fhi36.ind.nhus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	21	21	CD	_	_	_
4	.	.	.	_	_	_

1	FHI43.nIND.nHUS	fhi43.nind.nhus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	22	22	CD	_	_	_
4	.	.	.	_	_	_

1	FHI43.IND.nHUS	fhi43.ind.nhus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	23	23	CD	_	_	_
4	.	.	.	_	_	_

1	FHI48.nIND.HUS	fhi48.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	25	25	CD	_	_	_
4	.	.	.	_	_	_

1	FHI79.nIND.HUS	fhi79.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	26	26	CD	_	_	_
4	.	.	.	_	_	_

1	FHI79.IND.HUS	fhi79.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	27	27	CD	_	_	_
4	.	.	.	_	_	_

1	FHI95.nIND.nHUS	fhi95.nind.nhus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	28	28	CD	_	_	_
4	.	.	.	_	_	_

1	FHI95.IND.nHUS	fhi95.ind.nhus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	29	29	CD	_	_	_
4	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav40.nIND.nHUS	olav40.nind.nhus	JJ	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	2	2	CD	_	_	_
5	.	.	.	_	_	_

1	FHI4.IND.HUS	fhi4.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	31	31	CD	_	_	_
4	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav104.nIND.nHUS	Olav104.nIND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	32	32	CD	_	_	_
5	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav104.IND.nHUS	Olav104.IND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	33	33	CD	_	_	_
5	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav157.nIND.nHUS	Olav157.nIND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	34	34	CD	_	_	_
5	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav157.IND.nHUS	Olav157.IND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	35	35	CD	_	_	_
5	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav172.nIND.nHUS	Olav172.nIND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	37	37	CD	_	_	_
5	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav174.nIND.nHUS	Olav174.nIND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	38	38	CD	_	_	_
5	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav174.IND.nHUS	Olav174.IND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	39	39	CD	_	_	_
5	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav178.nIND.nHUS	Olav178.nIND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	3	3	CD	_	_	_
5	.	.	.	_	_	_

1	FHI6.nIND.HUS	fhi6.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	40	40	CD	_	_	_
4	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav178.IND.nHUS	Olav178.IND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	41	41	CD	_	_	_
5	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav179.nIND.nHUS	Olav179.nIND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	42	42	CD	_	_	_
5	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav179.IND.nHUS	Olav179.IND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	43	43	CD	_	_	_
5	.	.	.	_	_	_

1	FHI63.nIND.HUS	fhi63.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	44	44	CD	_	_	_
4	.	.	.	_	_	_

1	FHI63.IND.HUS	fhi63.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	45	45	CD	_	_	_
4	.	.	.	_	_	_

1	FHI66.nIND.nHUS	fhi66.nind.nhus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	46	46	CD	_	_	_
4	.	.	.	_	_	_

1	FHI66.IND.nHUS	fhi66.ind.nhus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	47	47	CD	_	_	_
4	.	.	.	_	_	_

1	FHI83.nIND.HUS	fhi83.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	48	48	CD	_	_	_
4	.	.	.	_	_	_

1	FHI83.IND.HUS	fhi83.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	49	49	CD	_	_	_
4	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav17.nIND.nHUS	Olav17.nIND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	4	4	CD	_	_	_
5	.	.	.	_	_	_

1	FHI6.IND.HUS	fhi6.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	50	50	CD	_	_	_
4	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav17.IND.nHUS	Olav17.IND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	51	51	CD	_	_	_
5	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav39.IND.nHUS	Olav39.IND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	52	52	CD	_	_	_
5	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav63.nIND.nHUS	Olav63.nIND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	53	53	CD	_	_	_
5	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav63.IND.nHUS	Olav63.IND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	54	54	CD	_	_	_
5	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav164	Olav164	NNP	_	_	_
3	.	.	.	_	_	_

1	nIND.HUS	nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	55	55	CD	_	_	_
4	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav164	Olav164	NNP	_	_	_
3	.	.	.	_	_	_

1	IND.HUS	ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	56	56	CD	_	_	_
4	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav176.IND.HUS	Olav176.IND.HUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	57	57	CD	_	_	_
5	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav39.nIND.nHUS	Olav39.nIND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	59	59	CD	_	_	_
5	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav173.IND.nHUS	Olav173.IND.nHUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	5	5	CD	_	_	_
5	.	.	.	_	_	_

1	FHI7.nIND.HUS	fhi7.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	60	60	CD	_	_	_
4	.	.	.	_	_	_

1	St.	St.	NNP	_	_	_
2	Olav176.nIND.HUS	Olav176.nIND.HUS	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	6	6	CD	_	_	_
5	.	.	.	_	_	_

1	FHI7.IND.HUS	fhi7.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	7	7	CD	_	_	_
4	.	.	.	_	_	_

1	FHI8.nIND.HUS	fhi8.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	8	8	CD	_	_	_
4	.	.	.	_	_	_

1	FHI8.IND.HUS	fhi8.ind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	9	9	CD	_	_	_
4	.	.	.	_	_	_

1	FHI9.nIND.HUS	fhi9.nind.hus	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	A	a	NN	_	_	_
4	generalized	generalize	VBN	_	_	_
5	linear	linear	JJ	_	_	_
6	model	model	NN	_	_	_
7	likelihood	likelihood	NN	_	_	_
8	ratio	ratio	NN	_	_	_
9	test	test	NN	_	_	_
10	was	be	VBD	_	_	_
11	performed	perform	VBN	_	_	_
12	to	to	TO	_	_	_
13	test	test	VB	_	_	_
14	for	for	IN	_	_	_
15	differential	differential	JJ	_	_	_
16	expression	expression	NN	_	_	_
17	between	between	IN	_	_	_
18	groups	group	NNS	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	HUS	hus	NNS	_	_	_
21	vs.	vs.	CC	_	_	_
22	non-HUS	non-hus	JJ	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	and	and	CC	_	_	_
25	condition	condition	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	induced	induce	VBN	_	_	_
28	vs.	vs.	CC	_	_	_
29	non-induced	non-induced	JJ	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	,	,	,	_	_	_
32	with	with	IN	_	_	_
33	FDR-adjusted	fdr-adjusted	JJ	_	_	_
34	p-values	p-values	NN	_	_	_
35	<	<	JJR	_	_	_
36	0.05	0.05	CD	_	_	_
37	regarded	regard	VBN	_	_	_
38	as	as	IN	_	_	_
39	statistically	statistically	RB	_	_	_
40	significant	significant	JJ	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	Bacterial	bacterial	JJ	_	_	_
43	cells	cell	NNS	_	_	_
44	from	from	IN	_	_	_
45	an	a	DT	_	_	_
46	overnight	overnight	JJ	_	_	_
47	culture	culture	NN	_	_	_
48	were	be	VBD	_	_	_
49	washed	wash	VBN	_	_	_
50	and	and	CC	_	_	_
51	diluted	dilute	VBN	_	_	_
52	in	in	IN	_	_	_
53	fresh	fresh	JJ	_	_	_
54	SILAC	silac	NN	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	stable	stable	JJ	_	_	_
57	isotope	isotope	NN	_	_	_
58	labeling	labeling	NN	_	_	_
59	with	with	IN	_	_	_
60	amino	amino	NN	SUPP	_	_
61	acids	acid	NNS	SUPP	_	_
62	in	in	IN	_	_	_
63	cell	cell	NN	_	_	_
64	culture	culture	NN	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	medium	medium	NN	_	_	_
67	optimized	optimize	VBN	_	_	_
68	for	for	IN	_	_	_
69	non-auxotrophic	non-auxotrophic	JJ	_	_	_
70	E.	e.	FW	_	_	_
71	coli	coli	FW	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	Ping	ping	VB	_	_	_
74	LY	LY	NNP	_	_	_
75	et	et	FW	_	_	_
76	al.	al.	FW	_	_	_
77	.	.	.	_	_	_

1	J	J	NNP	_	_	_
2	Proteome	Proteome	NNP	_	_	_
3	Res.	Res.	NNP	_	_	_
4	,	,	,	_	_	_
5	2013	2013	CD	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	,	,	,	_	_	_
8	before	before	IN	_	_	_
9	incubation	incubation	NN	_	_	_
10	at	at	IN	_	_	_
11	37	37	CD	_	_	_
12	°C	°c	NN	_	_	_
13	with	with	IN	_	_	_
14	agitation	agitation	NN	_	_	_
15	until	until	IN	_	_	_
16	reaching	reach	VBG	_	_	_
17	an	a	DT	_	_	_
18	OD600	od600	NN	_	_	_
19	of	of	IN	_	_	_
20	approximately	approximately	RB	_	_	_
21	0.3	0.3	CD	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Differential	differential	JJ	_	_	_
3	expression	expression	NN	_	_	_
4	analysis	analysis	NN	_	_	_
5	was	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	with	with	IN	_	_	_
8	R	r	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	version	version	NN	_	_	_
11	3.1.1	3.1.1	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	edgeR	edger	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	version	version	NN	_	_	_
17	3.8.5	3.8.5	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Bioconductor	bioconductor	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	strain	strain	NN	_	_	_
5	FHI12	fhi12	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	E.	e.	FW	_	_	_
8	coli	coli	FW	_	_	_
9	strain	strain	NN	_	_	_
10	FHI24	fhi24	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	E.	e.	FW	_	_	_
13	coli	coli	FW	_	_	_
14	strain	strain	NN	_	_	_
15	FHI25	fhi25	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	E.	e.	FW	_	_	_
18	coli	coli	FW	_	_	_
19	strain	strain	NN	_	_	_
20	FHI27	fhi27	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	E.	e.	FW	_	_	_
23	coli	coli	FW	_	_	_
24	strain	strain	NN	_	_	_
25	FHI36	fhi36	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	E.	e.	FW	_	_	_
28	coli	coli	FW	_	_	_
29	strain	strain	NN	_	_	_
30	FHI4	fhi4	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	E.	e.	FW	_	_	_
33	coli	coli	FW	_	_	_
34	strain	strain	NN	_	_	_
35	FHI43	fhi43	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	E.	e.	FW	_	_	_
38	coli	coli	FW	_	_	_
39	strain	strain	NN	_	_	_
40	FHI48	fhi48	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	E.	e.	FW	_	_	_
43	coli	coli	FW	_	_	_
44	strain	strain	NN	_	_	_
45	FHI6	fhi6	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	E.	e.	FW	_	_	_
48	coli	coli	FW	_	_	_
49	strain	strain	NN	_	_	_
50	FHI63	fhi63	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	E.	e.	FW	_	_	_
53	coli	coli	FW	_	_	_
54	strain	strain	NN	_	_	_
55	FHI66	fhi66	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	E.	e.	FW	_	_	_
58	coli	coli	FW	_	_	_
59	strain	strain	NN	_	_	_
60	FHI7	fhi7	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	E.	e.	FW	_	_	_
63	coli	coli	FW	_	_	_
64	strain	strain	NN	_	_	_
65	FHI79	fhi79	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	E.	e.	FW	_	_	_
68	coli	coli	FW	_	_	_
69	strain	strain	NN	_	_	_
70	FHI8	fhi8	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	E.	e.	FW	_	_	_
73	coli	coli	FW	_	_	_
74	strain	strain	NN	_	_	_
75	FHI83	fhi83	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	E.	e.	FW	_	_	_
78	coli	coli	FW	_	_	_
79	strain	strain	NN	_	_	_
80	FHI9	fhi9	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	E.	e.	FW	_	_	_
83	coli	coli	FW	_	_	_
84	strain	strain	NN	_	_	_
85	FHI95	fhi95	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	E.	e.	FW	_	_	_
88	coli	coli	FW	_	_	_
89	strain	strain	NN	_	_	_
90	St.	St.	NNP	_	_	_
91	Olav104	Olav104	NNP	_	_	_
92	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
93	E.	E.	NNP	_	_	_
94	coli	coli	NN	_	_	_
95	strain	strain	NN	_	_	_
96	St.	St.	NNP	_	_	_
97	Olav157	Olav157	NNP	_	_	_
98	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
99	E.	E.	NNP	_	_	_
100	coli	coli	NN	_	_	_
101	strain	strain	NN	_	_	_
102	St.	St.	NNP	_	_	_
103	Olav164	Olav164	NNP	_	_	_
104	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
105	E.	E.	NNP	_	_	_
106	coli	coli	NN	_	_	_
107	strain	strain	NN	_	_	_
108	St.	St.	NNP	_	_	_
109	Olav17	Olav17	NNP	_	_	_
110	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
111	E.	E.	NNP	_	_	_
112	coli	coli	NN	_	_	_
113	strain	strain	NN	_	_	_
114	St.	St.	NNP	_	_	_
115	Olav172	Olav172	NNP	_	_	_
116	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
117	E.	E.	NNP	_	_	_
118	coli	coli	NN	_	_	_
119	strain	strain	NN	_	_	_
120	St.	St.	NNP	_	_	_
121	Olav173	Olav173	NNP	_	_	_
122	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
123	E.	E.	NNP	_	_	_
124	coli	coli	NN	_	_	_
125	strain	strain	NN	_	_	_
126	St.	St.	NNP	_	_	_
127	Olav174	Olav174	NNP	_	_	_
128	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
129	E.	E.	NNP	_	_	_
130	coli	coli	NN	_	_	_
131	strain	strain	NN	_	_	_
132	St.	St.	NNP	_	_	_
133	Olav176	Olav176	NNP	_	_	_
134	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
135	E.	E.	NNP	_	_	_
136	coli	coli	NN	_	_	_
137	strain	strain	NN	_	_	_
138	St.	St.	NNP	_	_	_
139	Olav178	Olav178	NNP	_	_	_
140	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
141	E.	E.	NNP	_	_	_
142	coli	coli	NN	_	_	_
143	strain	strain	NN	_	_	_
144	St.	St.	NNP	_	_	_
145	Olav179	Olav179	NNP	_	_	_
146	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
147	E.	E.	NNP	_	_	_
148	coli	coli	NN	_	_	_
149	strain	strain	NN	_	_	_
150	St.	St.	NNP	_	_	_
151	Olav39	Olav39	NNP	_	_	_
152	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
153	E.	E.	NNP	_	_	_
154	coli	coli	NN	_	_	_
155	strain	strain	NN	_	_	_
156	St.	St.	NNP	_	_	_
157	Olav40	Olav40	NNP	_	_	_
158	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
159	E.	E.	NNP	_	_	_
160	coli	coli	NN	_	_	_
161	strain	strain	NN	_	_	_
162	St.	St.	NNP	_	_	_
163	Olav63	Olav63	NNP	_	_	_
164	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
165	Escherichia	escherichia	FW	Organism	_	_
166	coli	coli	FW	Organism	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	genome	genome	NN	_	_	_
169	accession	accession	NN	_	_	_
170	:	:	:	_	_	_
171	GCA	gca	NN	_	_	_
172	_	_	SYM	_	_	_
173	000752975	000752975	CD	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	genome	genome	NN	_	_	_
176	accession	accession	NN	_	_	_
177	:	:	:	_	_	_
178	GCA	gca	NN	_	_	_
179	_	_	SYM	_	_	_
180	000753215	000753215	CD	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	genome	genome	NN	_	_	_
183	accession	accession	NN	_	_	_
184	:	:	:	_	_	_
185	GCA	gca	NN	_	_	_
186	_	_	SYM	_	_	_
187	000753275	000753275	CD	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	genome	genome	NN	_	_	_
190	accession	accession	NN	_	_	_
191	:	:	:	_	_	_
192	GCA	gca	NN	_	_	_
193	_	_	SYM	_	_	_
194	000936225	000936225	CD	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	genome	genome	NN	_	_	_
197	accession	accession	NN	_	_	_
198	:	:	:	_	_	_
199	GCA	gca	NN	_	_	_
200	_	_	SYM	_	_	_
201	000936245	000936245	CD	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	genome	genome	NN	_	_	_
204	accession	accession	NN	_	_	_
205	:	:	:	_	_	_
206	GCA	gca	NN	_	_	_
207	_	_	SYM	_	_	_
208	000936475	000936475	CD	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	genome	genome	NN	_	_	_
211	accession	accession	NN	_	_	_
212	:	:	:	_	_	_
213	GCA	gca	NN	_	_	_
214	_	_	SYM	_	_	_
215	000937275	000937275	CD	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	genome	genome	NN	_	_	_
218	accession	accession	NN	_	_	_
219	:	:	:	_	_	_
220	GCA	gca	NN	_	_	_
221	_	_	SYM	_	_	_
222	000938695	000938695	CD	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	genome	genome	NN	_	_	_
225	accession	accession	NN	_	_	_
226	:	:	:	_	_	_
227	GCA	gca	NN	_	_	_
228	_	_	SYM	_	_	_
229	000938995	000938995	CD	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
231	genome	genome	NN	_	_	_
232	accession	accession	NN	_	_	_
233	:	:	:	_	_	_
234	GCA	gca	NN	_	_	_
235	_	_	SYM	_	_	_
236	000939195	000939195	CD	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	genome	genome	NN	_	_	_
239	accession	accession	NN	_	_	_
240	:	:	:	_	_	_
241	GCA	gca	NN	_	_	_
242	_	_	SYM	_	_	_
243	000939755	000939755	CD	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	genome	genome	NN	_	_	_
246	accession	accession	NN	_	_	_
247	:	:	:	_	_	_
248	GCA	gca	NN	_	_	_
249	_	_	SYM	_	_	_
250	000939955	000939955	CD	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	genome	genome	NN	_	_	_
253	accession	accession	NN	_	_	_
254	:	:	:	_	_	_
255	GCA	gca	NN	_	_	_
256	_	_	SYM	_	_	_
257	000941395	000941395	CD	_	_	_
258	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
259	genome	genome	NN	_	_	_
260	accession	accession	NN	_	_	_
261	:	:	:	_	_	_
262	GCA	gca	NN	_	_	_
263	_	_	SYM	_	_	_
264	000941895	000941895	CD	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	genome	genome	NN	_	_	_
267	accession	accession	NN	_	_	_
268	:	:	:	_	_	_
269	GCA	gca	NN	_	_	_
270	_	_	SYM	_	_	_
271	000946755	000946755	CD	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	genome	genome	NN	_	_	_
274	accession	accession	NN	_	_	_
275	:	:	:	_	_	_
276	GCA	gca	NN	_	_	_
277	_	_	SYM	_	_	_
278	000947315	000947315	CD	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	genome	genome	NN	_	_	_
281	accession	accession	NN	_	_	_
282	:	:	:	_	_	_
283	GCA	gca	NN	_	_	_
284	_	_	SYM	_	_	_
285	000951835	000951835	CD	_	_	_
286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
287	genome	genome	NN	_	_	_
288	accession	accession	NN	_	_	_
289	:	:	:	_	_	_
290	GCA	gca	NN	_	_	_
291	_	_	SYM	_	_	_
292	000951875	000951875	CD	_	_	_
293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
294	genome	genome	NN	_	_	_
295	accession	accession	NN	_	_	_
296	:	:	:	_	_	_
297	GCA	gca	NN	_	_	_
298	_	_	SYM	_	_	_
299	000951915	000951915	CD	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	genome	genome	NN	_	_	_
302	accession	accession	NN	_	_	_
303	:	:	:	_	_	_
304	GCA	gca	NN	_	_	_
305	_	_	SYM	_	_	_
306	000965545	000965545	CD	_	_	_
307	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
308	genome	genome	NN	_	_	_
309	accession	accession	NN	_	_	_
310	:	:	:	_	_	_
311	GCA	gca	NN	_	_	_
312	_	_	SYM	_	_	_
313	000965555	000965555	CD	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	genome	genome	NN	_	_	_
316	accession	accession	NN	_	_	_
317	:	:	:	_	_	_
318	GCA	gca	NN	_	_	_
319	_	_	SYM	_	_	_
320	000965575	000965575	CD	_	_	_
321	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
322	genome	genome	NN	_	_	_
323	accession	accession	NN	_	_	_
324	:	:	:	_	_	_
325	GCA	gca	NN	_	_	_
326	_	_	SYM	_	_	_
327	000965625	000965625	CD	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	genome	genome	NN	_	_	_
330	accession	accession	NN	_	_	_
331	:	:	:	_	_	_
332	GCA	gca	NN	_	_	_
333	_	_	SYM	_	_	_
334	000965635	000965635	CD	_	_	_
335	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
336	genome	genome	NN	_	_	_
337	accession	accession	NN	_	_	_
338	:	:	:	_	_	_
339	GCA	gca	NN	_	_	_
340	_	_	SYM	_	_	_
341	000965655	000965655	CD	_	_	_
342	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
343	genome	genome	NN	_	_	_
344	accession	accession	NN	_	_	_
345	:	:	:	_	_	_
346	GCA	gca	NN	_	_	_
347	_	_	SYM	_	_	_
348	000965665	000965665	CD	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	genome	genome	NN	_	_	_
351	accession	accession	NN	_	_	_
352	:	:	:	_	_	_
353	GCA	gca	NN	_	_	_
354	_	_	SYM	_	_	_
355	000965705	000965705	CD	_	_	_
356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
357	genome	genome	NN	_	_	_
358	accession	accession	NN	_	_	_
359	:	:	:	_	_	_
360	GCA	gca	NN	_	_	_
361	_	_	SYM	_	_	_
362	000965715	000965715	CD	_	_	_
363	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
364	genome	genome	NN	_	_	_
365	accession	accession	NN	_	_	_
366	:	:	:	_	_	_
367	GCA	gca	NN	_	_	_
368	_	_	SYM	_	_	_
369	000966935	000966935	CD	_	_	_
370	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
371	genome	genome	NN	_	_	_
372	accession	accession	NN	_	_	_
373	:	:	:	_	_	_
374	PVRW00000000	pvrw00000000	NN	_	_	_
375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
376	group	group	NN	_	_	_
377	-LRB-	-lrb-	-LRB-	_	_	_
378	hus	hus	NN	_	_	_
379	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
380	induced	induce	VBD	_	_	_
381	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
382	Library	Library	NNP	_	_	_
383	preparation	preparation	NN	_	_	_
384	was	be	VBD	_	_	_
385	performed	perform	VBN	_	_	_
386	with	with	IN	_	_	_
387	TruSeq	TruSeq	NNP	_	_	_
388	Stranded	Stranded	NNP	_	_	_
389	Total	Total	NNP	_	_	_
390	RNA	rna	NN	_	_	_
391	HT	ht	NN	_	_	_
392	Sample	Sample	NNP	_	_	_
393	Prep	Prep	NNP	_	_	_
394	Kit	kit	NN	_	_	_
395	-LRB-	-lrb-	-LRB-	_	_	_
396	Illumina	Illumina	NNP	_	_	_
397	-RRB-	-rrb-	-RRB-	_	_	_
398	.	.	.	_	_	_

1	Libraries	library	NNS	_	_	_
2	were	be	VBD	_	_	_
3	sequenced	sequence	VBN	_	_	_
4	with	with	IN	_	_	_
5	50	50	CD	_	_	_
6	bp	bp	NN	_	_	_
7	single	single	JJ	_	_	_
8	read	read	NN	_	_	_
9	configuration	configuration	NN	_	_	_
10	on	on	IN	_	_	_
11	a	a	DT	_	_	_
12	HiSeq	hiseq	JJ	_	_	_
13	2500	2500	CD	_	_	_
14	system	system	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Illumina	Illumina	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Lowly	Lowly	NNP	_	_	_
3	expressed	express	VBD	_	_	_
4	genes	gene	NNS	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	<	<	JJR	_	_	_
7	1	1	CD	_	_	_
8	read	read	NN	_	_	_
9	per	per	IN	_	_	_
10	million	million	CD	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	were	be	VBD	_	_	_
13	removed	remove	VBN	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Normalization	normalization	NN	_	_	_
3	factors	factor	NNS	_	_	_
4	were	be	VBD	_	_	_
5	calculated	calculate	VBN	_	_	_
6	using	use	VBG	_	_	_
7	a	a	DT	_	_	_
8	non-linear	non-linear	JJ	_	_	_
9	Loess	loess	JJ	_	_	_
10	model	model	NN	_	_	_
11	using	use	VBG	_	_	_
12	csaw	csaw	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Bioconductor	bioconductor	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Reads	read	VBZ	_	_	_
18	aligning	align	VBG	_	_	_
19	to	to	TO	_	_	_
20	each	each	DT	_	_	_
21	protein-encoding	protein-encoding	JJ	_	_	_
22	gene	gene	NN	_	_	_
23	family	family	NN	_	_	_
24	with	with	IN	_	_	_
25	strand-specific	strand-specific	JJ	_	_	_
26	mapping	mapping	NN	_	_	_
27	quality	quality	NN	_	_	_
28	above	above	IN	_	_	_
29	23	23	CD	_	_	_
30	were	be	VBD	_	_	_
31	counted	count	VBN	_	_	_
32	using	use	VBG	_	_	_
33	HTSeq-count	htseq-count	JJ	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	Reads	read	NNS	_	_	_
36	were	be	VBD	_	_	_
37	end-to-end	end-to-end	JJ	_	_	_
38	aligned	align	VBN	_	_	_
39	,	,	,	_	_	_
40	with	with	IN	_	_	_
41	no	no	DT	_	_	_
42	mismatches	mismatch	NNS	_	_	_
43	allowed	allow	VBN	_	_	_
44	,	,	,	_	_	_
45	to	to	TO	_	_	_
46	the	the	DT	_	_	_
47	respective	respective	JJ	_	_	_
48	draft	draft	NN	_	_	_
49	genomes	genome	NNS	_	_	_
50	using	use	VBG	_	_	_
51	Bowtie2	bowtie2	NN	_	_	_
52	with	with	IN	_	_	_
53	default	default	NN	_	_	_
54	settings	setting	NNS	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBP	_	_	_
56	RNA-Seq	rna-seq	JJ	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	strain	strain	NN	_	_	_
59	:	:	:	_	_	_
60	FHI12	fhi12	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	strain	strain	NN	_	_	_
63	:	:	:	_	_	_
64	FHI24	fhi24	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	strain	strain	NN	_	_	_
67	:	:	:	_	_	_
68	FHI25	fhi25	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	strain	strain	NN	_	_	_
71	:	:	:	_	_	_
72	FHI27	fhi27	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	strain	strain	NN	_	_	_
75	:	:	:	_	_	_
76	FHI36	fhi36	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	strain	strain	NN	_	_	_
79	:	:	:	_	_	_
80	FHI4	fhi4	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	strain	strain	NN	_	_	_
83	:	:	:	_	_	_
84	FHI43	fhi43	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	strain	strain	NN	_	_	_
87	:	:	:	_	_	_
88	FHI48	fhi48	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	strain	strain	NN	_	_	_
91	:	:	:	_	_	_
92	FHI6	fhi6	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	strain	strain	NN	_	_	_
95	:	:	:	_	_	_
96	FHI63	fhi63	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	strain	strain	NN	_	_	_
99	:	:	:	_	_	_
100	FHI66	fhi66	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	strain	strain	NN	_	_	_
103	:	:	:	_	_	_
104	FHI7	fhi7	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	strain	strain	NN	_	_	_
107	:	:	:	_	_	_
108	FHI79	fhi79	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	strain	strain	NN	_	_	_
111	:	:	:	_	_	_
112	FHI8	fhi8	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	strain	strain	NN	_	_	_
115	:	:	:	_	_	_
116	FHI83	fhi83	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	strain	strain	NN	_	_	_
119	:	:	:	_	_	_
120	FHI9	fhi9	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	strain	strain	NN	_	_	_
123	:	:	:	_	_	_
124	FHI95	fhi95	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	strain	strain	NN	_	_	_
127	:	:	:	_	_	_
128	St.	St.	NNP	_	_	_
129	Olav104	Olav104	NNP	_	_	_
130	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
131	strain	strain	NN	_	_	_
132	:	:	:	_	_	_
133	St.	St.	NNP	_	_	_
134	Olav157	Olav157	NNP	_	_	_
135	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
136	strain	strain	NN	_	_	_
137	:	:	:	_	_	_
138	St.	St.	NNP	_	_	_
139	Olav164	Olav164	NNP	_	_	_
140	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
141	strain	strain	NN	_	_	_
142	:	:	:	_	_	_
143	St.	St.	NNP	_	_	_
144	Olav17	Olav17	NNP	_	_	_
145	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
146	strain	strain	NN	_	_	_
147	:	:	:	_	_	_
148	St.	St.	NNP	_	_	_
149	Olav172	Olav172	NNP	_	_	_
150	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
151	strain	strain	NN	_	_	_
152	:	:	:	_	_	_
153	St.	St.	NNP	_	_	_
154	Olav173	Olav173	NNP	_	_	_
155	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
156	strain	strain	NN	_	_	_
157	:	:	:	_	_	_
158	St.	St.	NNP	_	_	_
159	Olav174	Olav174	NNP	_	_	_
160	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
161	strain	strain	NN	_	_	_
162	:	:	:	_	_	_
163	St.	St.	NNP	_	_	_
164	Olav176	Olav176	NNP	_	_	_
165	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
166	strain	strain	NN	_	_	_
167	:	:	:	_	_	_
168	St.	St.	NNP	_	_	_
169	Olav178	Olav178	NNP	_	_	_
170	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
171	strain	strain	NN	_	_	_
172	:	:	:	_	_	_
173	St.	St.	NNP	_	_	_
174	Olav179	Olav179	NNP	_	_	_
175	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
176	strain	strain	NN	_	_	_
177	:	:	:	_	_	_
178	St.	St.	NNP	_	_	_
179	Olav39	Olav39	NNP	_	_	_
180	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
181	strain	strain	NN	_	_	_
182	:	:	:	_	_	_
183	St.	St.	NNP	_	_	_
184	Olav40	Olav40	NNP	_	_	_
185	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
186	strain	strain	NN	_	_	_
187	:	:	:	_	_	_
188	St.	St.	NNP	_	_	_
189	Olav63	Olav63	NNP	_	_	_
190	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
191	Supplementary	Supplementary	NNP	_	_	_
192	_	_	VBD	_	_	_
193	files	file	NNS	_	_	_
194	_	_	IN	_	_	_
195	format	format	NN	_	_	_
196	_	_	NN	_	_	_
197	and	and	CC	_	_	_
198	_	_	NN	_	_	_
199	content	content	NN	_	_	_
200	:	:	:	_	_	_
201	Processed	process	VBN	_	_	_
202	data	datum	NNS	_	_	_
203	files	file	NNS	_	_	_
204	contain	contain	VBP	_	_	_
205	raw	raw	JJ	_	_	_
206	counts	count	NNS	_	_	_
207	for	for	IN	_	_	_
208	CDS	cd	NNS	_	_	_
209	genomic	genomic	JJ	_	_	_
210	features	feature	NNS	_	_	_
211	,	,	,	_	_	_
212	locations	location	NNS	_	_	_
213	of	of	IN	_	_	_
214	genomic	genomic	JJ	_	_	_
215	features	feature	NNS	_	_	_
216	are	be	VBP	_	_	_
217	provided	provide	VBN	_	_	_
218	in	in	IN	_	_	_
219	associated	associate	VBN	_	_	_
220	.	.	.	_	_	_

1	gtf	gtf	NN	_	_	_
2	files	file	NNS	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	Tagwise	Tagwise	NNP	_	_	_
5	dispersion	dispersion	NN	_	_	_
6	was	be	VBD	_	_	_
7	estimated	estimate	VBN	_	_	_
8	using	use	VBG	_	_	_
9	the	the	DT	_	_	_
10	weighted	weighted	JJ	_	_	_
11	likelihood	likelihood	NN	_	_	_
12	empirical	empirical	JJ	_	_	_
13	Bayes	baye	NNS	_	_	_
14	method	method	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	The	the	DT	_	_	_
17	exponential	exponential	JJ	GrowthPhase	_	_
18	phase	phase	NN	GrowthPhase	_	_
19	culture	culture	NN	_	_	_
20	was	be	VBD	_	_	_
21	split	split	VBN	_	_	_
22	in	in	IN	_	_	_
23	two	two	CD	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	one	one	CD	_	_	_
27	part	part	NN	_	_	_
28	was	be	VBD	_	_	_
29	induced	induce	VBN	_	_	_
30	with	with	IN	_	_	_
31	mitomycin	mitomycin	NN	_	_	_
32	C	c	NN	_	_	_
33	at	at	IN	_	_	_
34	a	a	DT	_	_	_
35	final	final	JJ	_	_	_
36	concentration	concentration	NN	_	_	_
37	of	of	IN	_	_	_
38	0.25	0.25	CD	_	_	_
39	μg	μg	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	Total	total	JJ	_	_	_
42	RNA	rna	NN	_	_	_
43	was	be	VBD	_	_	_
44	isolated	isolate	VBN	_	_	_
45	from	from	IN	_	_	_
46	cell	cell	NN	_	_	_
47	pellets	pellet	NNS	_	_	_
48	using	use	VBG	_	_	_
49	Aurum	Aurum	NNP	_	_	_
50	total	total	JJ	_	_	_
51	RNA	rna	NN	_	_	_
52	mini	minus	NNS	_	_	_
53	kit	kit	NN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	Bio-Rad	Bio-Rad	NNP	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	according	accord	VBG	_	_	_
58	to	to	TO	_	_	_
59	the	the	DT	_	_	_
60	manufacturer	manufacturer	NN	_	_	_
61	's	's	POS	_	_	_
62	instructions	instruction	NNS	_	_	_
63	,	,	,	_	_	_
64	and	and	CC	_	_	_
65	RNA	rna	NN	_	_	_
66	quality	quality	NN	_	_	_
67	was	be	VBD	_	_	_
68	controlled	control	VBN	_	_	_
69	using	use	VBG	_	_	_
70	the	the	DT	_	_	_
71	RNA	rna	NN	_	_	_
72	6000	6000	CD	_	_	_
73	nano	nano	NN	_	_	_
74	kit	kit	NN	_	_	_
75	and	and	CC	_	_	_
76	2100	2100	CD	_	_	_
77	Bioanalyzer	Bioanalyzer	NNP	_	_	_
78	-LRB-	-lrb-	-LRB-	_	_	_
79	Agilent	Agilent	NNP	_	_	_
80	-RRB-	-rrb-	-RRB-	_	_	_
81	.	.	.	_	_	_

1	Ribosomal	ribosomal	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Ribo-Zero	Ribo-Zero	NNP	_	_	_
7	rRNA	rrna	NN	_	_	_
8	Removal	removal	NN	_	_	_
9	Kit	kit	NN	_	_	_
10	for	for	IN	_	_	_
11	Gram-Negative	gram-negative	JJ	_	_	_
12	Bacteria	bacterium	NNS	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Epicentre	Epicentre	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Alignment	alignment	NN	_	_	_
3	,	,	,	_	_	_
4	Quantiatino	quantiatino	NN	_	_	_
5	and	and	CC	_	_	_
6	Normalization	normalization	NN	_	_	_
7	,	,	,	_	_	_
8	Differential	differential	JJ	_	_	_
9	Expression	expression	NN	_	_	_
10	:	:	:	_	_	_
11	We	we	PRP	_	_	_
12	used	use	VBD	_	_	_
13	the	the	DT	_	_	_
14	SPARTA	SPARTA	NNP	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	version	version	NN	_	_	_
17	1	1	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	software	software	NN	_	_	_
20	package	package	NN	_	_	_
21	for	for	IN	_	_	_
22	alignment	alignment	NN	_	_	_
23	,	,	,	_	_	_
24	differential	differential	JJ	_	_	_
25	expression	expression	NN	_	_	_
26	analysis	analysis	NN	_	_	_
27	,	,	,	_	_	_
28	and	and	CC	_	_	_
29	post-analysis	post-analysis	JJ	_	_	_
30	diagnostics	diagnostic	NNS	_	_	_
31	.	.	.	_	_	_

1	SPARTA	SPARTA	NNP	_	_	_
2	is	be	VBZ	_	_	_
3	an	a	DT	_	_	_
4	RNA-Seq	rna-seq	NN	_	_	_
5	package	package	NN	_	_	_
6	specifically	specifically	RB	_	_	_
7	designed	design	VBN	_	_	_
8	for	for	IN	_	_	_
9	bacterial	bacterial	JJ	_	_	_
10	studies	study	NNS	_	_	_
11	.	.	.	_	_	_

1	It	it	PRP	_	_	_
2	uses	use	VBZ	_	_	_
3	the	the	DT	_	_	_
4	Bowtie	Bowtie	NNP	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	version	version	NN	_	_	_
7	1.1.1	1.1.1	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	short	short	JJ	_	_	_
10	read	read	NN	_	_	_
11	aligner	aligner	NN	_	_	_
12	,	,	,	_	_	_
13	HTSeq	htseq	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	version	version	NN	_	_	_
16	0.6.1	0.6.1	CD	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	to	to	TO	_	_	_
19	count	count	VB	_	_	_
20	gene	gene	NN	_	_	_
21	features	feature	NNS	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	edgeR	edger	NN	_	_	_
25	for	for	IN	_	_	_
26	differential	differential	JJ	_	_	_
27	expression	expression	NN	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Annotation	Annotation	NNP	_	_	_
3	:	:	:	_	_	_
4	The	the	DT	_	_	_
5	reference	reference	NN	_	_	_
6	genome	genome	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Escherichia	escherichia	FW	_	_	_
9	_	_	FW	_	_	_
10	coli	coli	FW	_	_	_
11	_	_	SYM	_	_	_
12	cft073.ASM744v1.dna.chromosome.Chromosome.fa	cft073.asm744v1.dna.chromosome.chromosome.fa	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	and	and	CC	_	_	_
15	annotations	annotation	NNS	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Escherichia	escherichia	FW	_	_	_
18	_	_	FW	_	_	_
19	coli	coli	FW	_	_	_
20	_	_	SYM	_	_	_
21	cft073.ASM744v1	cft073.asm744v1	NN	_	_	_
22	.32	.32	CD	_	_	_
23	.	.	.	_	_	_

1	gtf	gtf	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	were	be	VBD	_	_	_
4	downloaded	download	VBN	_	_	_
5	from	from	IN	_	_	_
6	EnsemblBacteria	EnsemblBacteria	NNP	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	Bacteria	bacterium	NNS	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
10	Cells	cell	NNS	_	_	_
11	were	be	VBD	_	_	_
12	then	then	RB	_	_	_
13	lysed	lyse	VBN	_	_	_
14	with	with	IN	_	_	_
15	0.2	0.2	CD	_	_	_
16	µM	µm	NN	_	_	_
17	of	of	IN	_	_	_
18	lysozyme	lysozyme	NN	_	_	_
19	in	in	IN	_	_	_
20	TE	TE	NNP	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	10	10	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	Tris-Cl	tris-cl	NN	_	_	_
25	,	,	,	_	_	_
26	1	1	CD	_	_	_
27	mM	mm	NN	KWSUPP	_	_
28	EDTA	edta	NN	_	_	_
29	,	,	,	_	_	_
30	pH	ph	NN	_	_	_
31	8.0	8.0	CD	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	for	for	IN	_	_	_
34	5	5	CD	_	_	_
35	min	min	NN	_	_	_
36	at	at	IN	_	_	_
37	room	room	NN	_	_	_
38	temperature	temperature	NN	_	_	_
39	,	,	,	_	_	_
40	and	and	CC	_	_	_
41	total	total	JJ	_	_	_
42	RNA	rna	NN	_	_	_
43	was	be	VBD	_	_	_
44	extracted	extract	VBN	_	_	_
45	using	use	VBG	_	_	_
46	the	the	DT	_	_	_
47	RNeasy	RNeasy	NNP	_	_	_
48	Mini	Mini	NNP	_	_	_
49	Kit	kit	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	Qiagen	qiagen	NN	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	contamination	contamination	NN	_	_	_
3	was	be	VBD	_	_	_
4	eliminated	eliminate	VBN	_	_	_
5	by	by	IN	_	_	_
6	treatment	treatment	NN	_	_	_
7	with	with	IN	_	_	_
8	TURBO	TURBO	NNP	_	_	_
9	DNase	dnase	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Thermo	Thermo	NNP	_	_	_
12	Fisher	Fisher	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	Depletion	depletion	NN	_	_	_
2	of	of	IN	_	_	_
3	ribosomal	ribosomal	JJ	_	_	_
4	RNA	rna	NN	_	_	_
5	was	be	VBD	_	_	_
6	accomplished	accomplish	VBN	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	Ribominus	Ribominus	NNP	_	_	_
10	Transcriptome	Transcriptome	NNP	_	_	_
11	Isolation	isolation	NN	_	_	_
12	Kit	kit	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Thermo	Thermo	NNP	_	_	_
15	Fisher	Fisher	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	followed	follow	VBN	_	_	_
18	by	by	IN	_	_	_
19	ethanol	ethanol	NN	_	_	_
20	precipitation	precipitation	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	CFT073	cft073	NN	_	_	_
3	+	+	CC	_	_	_
4	pBAD	pbad	NN	_	_	_
5	rep	rep	NN	GEN	_	_
6	1	1	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	CFT073	cft073	NN	_	_	_
9	+	+	CC	_	_	_
10	pBAD	pbad	NN	_	_	_
11	rep	rep	NN	GEN	_	_
12	2	2	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	CFT073	cft073	NN	_	_	_
15	+	+	CC	_	_	_
16	pBAD	pbad	NN	_	_	_
17	rep	rep	NN	GEN	_	_
18	3	3	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	CFT073	cft073	NN	_	_	_
21	+	+	CC	_	_	_
22	pBAD-tosR	pbad-tosr	NN	_	_	_
23	rep	rep	NN	GEN	_	_
24	1	1	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	CFT073	cft073	NN	_	_	_
27	+	+	CC	_	_	_
28	pBAD-tosR	pbad-tosr	NN	_	_	_
29	rep	rep	NN	GEN	_	_
30	2	2	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	CFT073	cft073	NN	_	_	_
33	+	+	CC	_	_	_
34	pBAD-tosR	pbad-tosr	NN	_	_	_
35	rep	rep	NN	GEN	_	_
36	3	3	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Depletion	depletion	NN	_	_	_
39	of	of	IN	_	_	_
40	ribosomal	ribosomal	JJ	_	_	_
41	RNA	rna	NN	_	_	_
42	was	be	VBD	_	_	_
43	accomplished	accomplish	VBN	_	_	_
44	with	with	IN	_	_	_
45	the	the	DT	_	_	_
46	Ribominus	Ribominus	NNP	_	_	_
47	Transcriptome	Transcriptome	NNP	_	_	_
48	Isolation	isolation	NN	_	_	_
49	Kit	kit	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	Thermo	Thermo	NNP	_	_	_
52	Fisher	Fisher	NNP	_	_	_
53	-RRB-	-rrb-	-RRB-	_	_	_
54	followed	follow	VBN	_	_	_
55	by	by	IN	_	_	_
56	ethanol	ethanol	NN	_	_	_
57	precipitation	precipitation	NN	_	_	_
58	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	stranded	stranded	JJ	_	_	_
3	library	library	NN	_	_	_
4	was	be	VBD	_	_	_
5	prepared	prepare	VBN	_	_	_
6	using	use	VBG	_	_	_
7	a	a	DT	_	_	_
8	ScriptSeq	ScriptSeq	NNP	_	_	_
9	kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Illumina	Illumina	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	using	use	VBG	_	_	_
14	manufacturer	manufacturer	NN	_	_	_
15	's	's	POS	_	_	_
16	recommended	recommend	VBN	_	_	_
17	protocols	protocol	NNS	_	_	_
18	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	sample	sample	NN	_	_	_
3	was	be	VBD	_	_	_
4	tagged	tag	VBN	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	six	six	CD	_	_	_
8	nucleotide	nucleotide	NN	_	_	_
9	barcode	barcode	NN	_	_	_
10	unique	unique	JJ	_	_	_
11	to	to	TO	_	_	_
12	each	each	DT	_	_	_
13	sample	sample	NN	_	_	_
14	to	to	TO	_	_	_
15	allow	allow	VB	_	_	_
16	multiplexing	multiplexing	NN	_	_	_
17	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	products	product	NNS	_	_	_
3	are	be	VBP	_	_	_
4	purified	purify	VBN	_	_	_
5	and	and	CC	_	_	_
6	enriched	enrich	VBN	_	_	_
7	by	by	IN	_	_	_
8	PCR	pcr	NN	_	_	_
9	to	to	TO	_	_	_
10	create	create	VB	_	_	_
11	the	the	DT	_	_	_
12	final	final	JJ	_	_	_
13	cDNA	cdna	NN	_	_	_
14	library	library	NN	_	_	_
15	.	.	.	_	_	_

1	Final	final	JJ	_	_	_
2	libraries	library	NNS	_	_	_
3	were	be	VBD	_	_	_
4	checked	check	VBN	_	_	_
5	for	for	IN	_	_	_
6	quality	quality	NN	_	_	_
7	and	and	CC	_	_	_
8	quantity	quantity	NN	_	_	_
9	by	by	IN	_	_	_
10	TapeStation	TapeStation	NNP	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Agilent	Agilent	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	and	and	CC	_	_	_
15	qPCR	qpcr	NN	_	_	_
16	using	use	VBG	_	_	_
17	Kapa	Kapa	NNP	_	_	_
18	's	's	POS	_	_	_
19	library	library	NN	_	_	_
20	quantification	quantification	NN	_	_	_
21	kit	kit	NN	_	_	_
22	for	for	IN	_	_	_
23	Illumina	Illumina	NNP	_	_	_
24	Sequencing	sequencing	NN	_	_	_
25	platforms	platform	NNS	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Kapa	Kapa	NNP	_	_	_
28	Biosystems	Biosystems	NNP	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	following	follow	VBG	_	_	_
31	the	the	DT	_	_	_
32	manufacturer	manufacturer	NN	_	_	_
33	's	's	POS	_	_	_
34	recommended	recommend	VBN	_	_	_
35	protocols	protocol	NNS	_	_	_
36	.	.	.	_	_	_

1	Six	six	CD	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	sequenced	sequence	VBN	_	_	_
5	per	per	IN	_	_	_
6	lane	lane	NN	_	_	_
7	on	on	IN	_	_	_
8	a	a	DT	_	_	_
9	50	50	CD	_	_	_
10	cycle	cycle	NN	_	_	_
11	single	single	JJ	_	_	_
12	end	end	NN	_	_	_
13	run	run	NN	_	_	_
14	on	on	IN	_	_	_
15	a	a	DT	_	_	_
16	HiSeq	hiseq	JJ	_	_	_
17	2500	2500	CD	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Illumina	Illumina	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	in	in	IN	_	_	_
22	high	high	JJ	_	_	_
23	output	output	NN	_	_	_
24	mode	mode	NN	_	_	_
25	using	use	VBG	_	_	_
26	version	version	NN	_	_	_
27	4	4	CD	_	_	_
28	reagents	reagent	NNS	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	CFT073	cft073	NN	_	_	_
5	carrying	carry	VBG	_	_	_
6	either	either	CC	_	_	_
7	pBAD	pbad	NN	_	_	_
8	or	or	CC	_	_	_
9	pBAD-tosR-his6	pbad-tosr-his6	NN	_	_	_
10	were	be	VBD	_	_	_
11	cultured	culture	VBN	_	_	_
12	overnight	overnight	JJ	_	_	_
13	in	in	IN	_	_	_
14	biological	biological	JJ	_	_	_
15	triplicates	triplicate	NNS	_	_	_
16	in	in	IN	_	_	_
17	LB	lb	NN	MED	_	_
18	medium	medium	NN	MED	_	_
19	containing	contain	VBG	_	_	_
20	ampicillin	ampicillin	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	100	100	CD	_	_	_
23	µg	µg	NN	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	Escherichia	escherichia	FW	Organism	_	_
26	coli	coli	FW	Organism	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Genome	Genome	NNP	_	_	_
29	_	_	NNP	_	_	_
30	build	build	VB	_	_	_
31	:	:	:	_	_	_
32	CFT073	CFT073	NNP	_	_	_
33	E.	E.	NNP	_	_	_
34	coli	coli	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	plasmid	plasmid	NN	_	_	_
37	:	:	:	_	_	_
38	pBAD	pbad	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	plasmid	plasmid	NN	_	_	_
41	:	:	:	_	_	_
42	pBAD-tosR	pbad-tosr	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	qC	qc	NN	_	_	_
45	:	:	:	_	_	_
46	We	we	PRP	_	_	_
47	checked	check	VBD	_	_	_
48	the	the	DT	_	_	_
49	quality	quality	NN	_	_	_
50	of	of	IN	_	_	_
51	the	the	DT	_	_	_
52	raw	raw	JJ	_	_	_
53	reads	read	VBZ	_	_	_
54	data	datum	NNS	_	_	_
55	for	for	IN	_	_	_
56	each	each	DT	_	_	_
57	sample	sample	NN	_	_	_
58	using	use	VBG	_	_	_
59	FastQC	fastqc	NN	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	version	version	NN	_	_	_
62	0.11.3	0.11.3	CD	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	to	to	TO	_	_	_
65	identify	identify	VB	_	_	_
66	features	feature	NNS	_	_	_
67	of	of	IN	_	_	_
68	the	the	DT	_	_	_
69	data	datum	NNS	_	_	_
70	that	that	WDT	_	_	_
71	may	may	MD	_	_	_
72	indicate	indicate	VB	_	_	_
73	quality	quality	NN	_	_	_
74	problems	problem	NNS	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	e.g.	e.g.	FW	_	_	_
77	low	low	JJ	_	_	_
78	quality	quality	NN	_	_	_
79	scores	score	NNS	_	_	_
80	,	,	,	_	_	_
81	over-represented	over-represented	JJ	_	_	_
82	sequences	sequence	NNS	_	_	_
83	,	,	,	_	_	_
84	inappropriate	inappropriate	JJ	_	_	_
85	GC	gc	NN	_	_	_
86	content	content	NN	_	_	_
87	,	,	,	_	_	_
88	etc.	etc.	FW	_	_	_
89	-RRB-	-rrb-	-RRB-	_	_	_
90	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	strain	strain	NN	_	_	_
5	:	:	:	_	_	_
6	CFT073	cft073	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Supplementary	supplementary	JJ	_	_	_
9	_	_	NN	_	_	_
10	files	file	NNS	_	_	_
11	_	_	IN	_	_	_
12	format	format	NN	_	_	_
13	_	_	NN	_	_	_
14	and	and	CC	_	_	_
15	_	_	NN	_	_	_
16	content	content	NN	_	_	_
17	:	:	:	_	_	_
18	.	.	.	_	_	_

1	xls	xl	NNS	_	_	_
2	,	,	,	_	_	_
3	spreadsheet	spreadsheet	NN	_	_	_
4	of	of	IN	_	_	_
5	normalized	normalize	VBN	_	_	_
6	read	read	NN	_	_	_
7	counts	count	NNS	_	_	_
8	for	for	IN	_	_	_
9	each	each	DT	_	_	_
10	gene	gene	NN	_	_	_
11	for	for	IN	_	_	_
12	each	each	DT	_	_	_
13	sample	sample	NN	_	_	_
14	,	,	,	_	_	_
15	differential	differential	JJ	_	_	_
16	expression	expression	NN	_	_	_
17	data	datum	NNS	_	_	_
18	,	,	,	_	_	_
19	and	and	CC	_	_	_
20	annotation	annotation	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
22	After	after	IN	_	_	_
23	chilling	chill	VBG	_	_	_
24	on	on	IN	_	_	_
25	ice	ice	NN	_	_	_
26	,	,	,	_	_	_
27	each	each	DT	_	_	_
28	100-ml	100-ml	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	was	be	VBD	_	_	_
31	mixed	mix	VBN	_	_	_
32	with	with	IN	_	_	_
33	25	25	CD	_	_	_
34	ml	ml	NN	_	_	_
35	ice-cold	ice-cold	JJ	_	_	_
36	ethanol	ethanol	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Bacterial	bacterial	JJ	_	_	_
39	cultures	culture	NNS	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
41	culture	culture	NN	_	_	_
42	temperature	temperature	NN	_	_	_
43	:	:	:	_	_	_
44	30	30	CD	_	_	_
45	°C	°c	NN	_	_	_
46	for	for	IN	_	_	_
47	60	60	CD	_	_	_
48	min	min	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	culture	culture	NN	_	_	_
51	temperature	temperature	NN	_	_	_
52	:	:	:	_	_	_
53	42	42	CD	_	_	_
54	°C	°c	NN	_	_	_
55	for	for	IN	_	_	_
56	60	60	CD	_	_	_
57	min	min	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	dnaB-Ts	dnab-t	NNS	_	_	_
60	_	_	VBP	_	_	_
61	30	30	CD	_	_	_
62	°C	°c	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	dnaB-Ts	dnab-t	NNS	_	_	_
65	_	_	VBP	_	_	_
66	42	42	CD	_	_	_
67	°C	°c	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	dnaB-Ts	dnab-t	NNS	_	_	_
70	Î	î	NN	_	_	_
71	''	''	''	_	_	_
72	ahpC	ahpc	NN	GEN	_	_
73	_	_	CD	_	_	_
74	30	30	CD	_	_	_
75	°C	°c	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	dnaB-Ts	dnab-t	NNS	_	_	_
78	Î	î	NN	_	_	_
79	''	''	''	_	_	_
80	ahpC	ahpc	NN	GEN	_	_
81	_	_	CD	_	_	_
82	42	42	CD	_	_	_
83	°C	°c	NN	_	_	_
84	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
85	Escherichia	escherichia	FW	Organism	_	_
86	coli	coli	FW	Organism	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	Genome	Genome	NNP	_	_	_
89	_	_	NNP	_	_	_
90	build	build	VB	_	_	_
91	:	:	:	_	_	_
92	E.coli	e.coli	NN	_	_	_
93	K12	k12	NN	_	_	_
94	BW25113	bw25113	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	Illumina	Illumina	NNP	_	_	_
97	Casava1	Casava1	NNP	_	_	_
98	.7	.7	CD	_	_	_
99	software	software	NN	_	_	_
100	used	use	VBN	_	_	_
101	for	for	IN	_	_	_
102	basecalling	basecalling	NN	_	_	_
103	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2	medium	medium	NN	_	_	_
3	:	:	:	_	_	_
4	SB	sb	NN	_	_	_
5	broth	broth	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Overnight	overnight	NN	_	_	_
8	cultures	culture	NNS	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	dnaB-Ts	dnab-ts	JJ	_	_	_
12	single	single	JJ	_	_	_
13	mutant	mutant	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	strain	strain	NN	_	_	_
16	2429	2429	CD	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	the	the	DT	_	_	_
20	dnaB-Ts	dnab-ts	JJ	_	_	_
21	ΔahpC	δahpc	NN	_	_	_
22	double	double	JJ	_	_	_
23	mutant	mutant	JJ	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	strain	strain	NN	_	_	_
26	3780	3780	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	were	be	VBD	_	_	_
29	diluted	dilute	VBN	_	_	_
30	100-fold	100-fold	RB	_	_	_
31	into	into	IN	_	_	_
32	fresh	fresh	JJ	_	_	_
33	SB	sb	NN	_	_	_
34	medium	medium	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	3.2	3.2	CD	_	_	_
37	%	%	NN	_	_	_
38	peptone	peptone	NN	_	_	_
39	,	,	,	_	_	_
40	2	2	CD	_	_	_
41	%	%	NN	_	_	_
42	yeast	yeast	NN	SUPP	_	_
43	extract	extract	NN	SUPP	_	_
44	and	and	CC	_	_	_
45	1	1	CD	_	_	_
46	%	%	NN	_	_	_
47	NaCl	nacl	NN	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	,	,	,	_	_	_
50	and	and	CC	_	_	_
51	they	they	PRP	_	_	_
52	were	be	VBD	_	_	_
53	then	then	RB	_	_	_
54	grown	grow	VBN	_	_	_
55	at	at	IN	_	_	_
56	30	30	CD	_	_	_
57	°C	°c	NN	_	_	_
58	to	to	TO	_	_	_
59	early-log	early-log	JJ	_	_	_
60	phase	phase	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	OD600	od600	NN	_	_	_
63	=	=	JJ	_	_	_
64	0.15	0.15	CD	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	.	.	.	_	_	_

1	Next	next	JJ	_	_	_
2	these	these	DT	_	_	_
3	log-phase	log-phase	JJ	_	_	_
4	cultures	culture	NNS	_	_	_
5	were	be	VBD	_	_	_
6	diluted	dilute	VBN	_	_	_
7	20-fold	20-fold	RB	_	_	_
8	into	into	IN	_	_	_
9	200	200	CD	_	_	_
10	ml	ml	NN	_	_	_
11	pre-warmed	pre-warmed	JJ	_	_	_
12	,	,	,	_	_	_
13	fresh	fresh	JJ	_	_	_
14	SB	sb	NN	_	_	_
15	medium	medium	NN	_	_	_
16	,	,	,	_	_	_
17	and	and	CC	_	_	_
18	they	they	PRP	_	_	_
19	were	be	VBD	_	_	_
20	grown	grow	VBN	_	_	_
21	at	at	IN	_	_	_
22	30	30	CD	_	_	_
23	°C	°c	NN	_	_	_
24	for	for	IN	_	_	_
25	another	another	DT	_	_	_
26	60	60	CD	_	_	_
27	min	min	NN	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Reads	read	VBZ	_	_	_
3	Per	per	IN	_	_	_
4	Kilobase	kilobase	NN	_	_	_
5	of	of	IN	_	_	_
6	exon	exon	NN	_	_	_
7	per	per	IN	_	_	_
8	Megabase	megabase	NN	_	_	_
9	of	of	IN	_	_	_
10	library	library	NN	_	_	_
11	size	size	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	RPKM	rpkm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	were	be	VBD	_	_	_
16	calculated	calculate	VBN	_	_	_
17	using	use	VBG	_	_	_
18	a	a	DT	_	_	_
19	protocol	protocol	NN	_	_	_
20	from	from	IN	_	_	_
21	Chepelev	Chepelev	NNP	_	_	_
22	et	et	FW	_	_	_
23	al.	al.	FW	_	_	_
24	,	,	,	_	_	_
25	Nucleic	Nucleic	NNP	_	_	_
26	Acids	Acids	NNP	_	_	_
27	Research	Research	NNP	_	_	_
28	,	,	,	_	_	_
29	2009	2009	CD	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	rRNA	rrna	NN	_	_	_
5	was	be	VBD	_	_	_
6	removed	remove	VBN	_	_	_
7	from	from	IN	_	_	_
8	total	total	JJ	_	_	_
9	RNA	rna	NN	_	_	_
10	by	by	IN	_	_	_
11	using	use	VBG	_	_	_
12	the	the	DT	_	_	_
13	Ribo-Zero	Ribo-Zero	NNP	_	_	_
14	rRNA	rrna	NN	_	_	_
15	removal	removal	NN	_	_	_
16	kit	kit	NN	_	_	_
17	.	.	.	_	_	_

1	Reverse	reverse	JJ	_	_	_
2	transcription	transcription	NN	_	_	_
3	and	and	CC	_	_	_
4	cDNA	cdna	NN	_	_	_
5	amplification	amplification	NN	_	_	_
6	were	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	with	with	IN	_	_	_
9	the	the	DT	_	_	_
10	SMART-Seq	smart-seq	NN	_	_	_
11	v4	v4	NN	_	_	_
12	Ultra	Ultra	NNP	_	_	_
13	Low	Low	NNP	_	_	_
14	Input	Input	NNP	_	_	_
15	RNA	rna	NN	_	_	_
16	Kit	kit	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Clontech	clontech	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	Libraries	library	NNS	_	_	_
2	were	be	VBD	_	_	_
3	constructed	construct	VBN	_	_	_
4	using	use	VBG	_	_	_
5	the	the	DT	_	_	_
6	Illumina	Illumina	NNP	_	_	_
7	Nextera	Nextera	NNP	_	_	_
8	XT	XT	NNP	_	_	_
9	kit	kit	NN	_	_	_
10	and	and	CC	_	_	_
11	analyzed	analyze	VBN	_	_	_
12	for	for	IN	_	_	_
13	concentration	concentration	NN	_	_	_
14	,	,	,	_	_	_
15	size	size	NN	_	_	_
16	distribution	distribution	NN	_	_	_
17	and	and	CC	_	_	_
18	quantification	quantification	NN	_	_	_
19	of	of	IN	_	_	_
20	viable	viable	JJ	_	_	_
21	sequencing	sequencing	NN	_	_	_
22	templates	template	NNS	_	_	_
23	via	via	IN	_	_	_
24	qPCR	qpcr	NN	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Samples	sample	NNS	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	200-ml	200-ml	JJ	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	of	of	IN	_	_	_
7	the	the	DT	_	_	_
8	above	above	JJ	_	_	_
9	cultures	culture	NNS	_	_	_
10	for	for	IN	_	_	_
11	each	each	DT	_	_	_
12	strain	strain	NN	_	_	_
13	were	be	VBD	_	_	_
14	split	split	VBN	_	_	_
15	into	into	IN	_	_	_
16	two	two	CD	_	_	_
17	aliquots	aliquot	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	each	each	DT	_	_	_
20	100	100	CD	_	_	_
21	ml	ml	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	,	,	,	_	_	_
24	and	and	CC	_	_	_
25	the	the	DT	_	_	_
26	aliquots	aliquot	NNS	_	_	_
27	were	be	VBD	_	_	_
28	then	then	RB	_	_	_
29	incubated	incubate	VBN	_	_	_
30	at	at	IN	_	_	_
31	30	30	CD	_	_	_
32	°C	°c	NN	_	_	_
33	or	or	CC	_	_	_
34	42	42	CD	_	_	_
35	°C	°c	NN	_	_	_
36	for	for	IN	_	_	_
37	another	another	DT	_	_	_
38	60	60	CD	_	_	_
39	min	min	NN	_	_	_
40	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Sequenced	sequence	VBD	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	trimmed	trim	VBN	_	_	_
6	for	for	IN	_	_	_
7	adaptor	adaptor	NN	_	_	_
8	sequence	sequence	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	masked	mask	VBN	_	_	_
12	for	for	IN	_	_	_
13	low-complexity	low-complexity	NN	_	_	_
14	or	or	CC	_	_	_
15	low-quality	low-quality	JJ	_	_	_
16	sequence	sequence	NN	_	_	_
17	,	,	,	_	_	_
18	then	then	RB	_	_	_
19	mapped	map	VBD	_	_	_
20	to	to	TO	_	_	_
21	E.coli	e.coli	VB	_	_	_
22	K2	k2	NN	_	_	_
23	BW25113	bw25113	NN	_	_	_
24	whole	whole	JJ	_	_	_
25	genome	genome	NN	_	_	_
26	using	use	VBG	_	_	_
27	bowtie	bowtie	NN	_	_	_
28	v0	v0	NN	_	_	_
29	.12.2	.12.2	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	strain	strain	NN	_	_	_
32	:	:	:	_	_	_
33	2429	2429	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	strain	strain	NN	_	_	_
36	:	:	:	_	_	_
37	3780	3780	CD	_	_	_
38	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
39	Supplementary	Supplementary	NNP	_	_	_
40	_	_	VBD	_	_	_
41	files	file	NNS	_	_	_
42	_	_	IN	_	_	_
43	format	format	NN	_	_	_
44	_	_	NN	_	_	_
45	and	and	CC	_	_	_
46	_	_	NN	_	_	_
47	content	content	NN	_	_	_
48	:	:	:	_	_	_
49	Tab-delimited	tab-delimited	JJ	_	_	_
50	text	text	NN	_	_	_
51	files	file	NNS	_	_	_
52	include	include	VBP	_	_	_
53	RPKM	rpkm	NN	_	_	_
54	values	value	NNS	_	_	_
55	for	for	IN	_	_	_
56	each	each	DT	_	_	_
57	sample	sample	NN	_	_	_
58	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	To	to	TO	_	_	_
3	generate	generate	VB	_	_	_
4	Illumina-compatible	illumina-compatible	JJ	_	_	_
5	sequencing	sequencing	NN	_	_	_
6	libraries	library	NNS	_	_	_
7	for	for	IN	_	_	_
8	each	each	DT	_	_	_
9	sample	sample	NN	_	_	_
10	,	,	,	_	_	_
11	molecular	molecular	JJ	_	_	_
12	indexes	index	NNS	_	_	_
13	were	be	VBD	_	_	_
14	added	add	VBN	_	_	_
15	to	to	TO	_	_	_
16	each	each	DT	_	_	_
17	library	library	NN	_	_	_
18	,	,	,	_	_	_
19	allowing	allow	VBG	_	_	_
20	samples	sample	NNS	_	_	_
21	to	to	TO	_	_	_
22	be	be	VB	_	_	_
23	pooled	pool	VBN	_	_	_
24	and	and	CC	_	_	_
25	sequenced	sequence	VBN	_	_	_
26	on	on	IN	_	_	_
27	the	the	DT	_	_	_
28	Illumina	Illumina	NNP	_	_	_
29	HiSeq	HiSeq	NNP	_	_	_
30	2500	2500	CD	_	_	_
31	with	with	IN	_	_	_
32	a	a	DT	_	_	_
33	1	1	CD	_	_	_
34	x	x	CC	_	_	_
35	50	50	CD	_	_	_
36	bp	bp	NN	_	_	_
37	single-end	single-end	JJ	_	_	_
38	configuration	configuration	NN	_	_	_
39	.	.	.	_	_	_

1	More	more	JJR	_	_	_
2	than	than	IN	_	_	_
3	250	250	CD	_	_	_
4	million	million	CD	_	_	_
5	reads	read	VBZ	_	_	_
6	were	be	VBD	_	_	_
7	generated	generate	VBN	_	_	_
8	per	per	IN	_	_	_
9	sample	sample	NN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	at	at	IN	_	_	_
13	least	least	JJS	_	_	_
14	80	80	CD	_	_	_
15	%	%	NN	_	_	_
16	bases	basis	NNS	_	_	_
17	had	have	VBD	_	_	_
18	quality	quality	NN	_	_	_
19	scores	score	NNS	_	_	_
20	above	above	IN	_	_	_
21	Q30	q30	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	1	1	CD	_	_	_
3	ml	ml	NN	_	_	_
4	aliquot	aliquot	NN	_	_	_
5	of	of	IN	_	_	_
6	culture	culture	NN	_	_	_
7	was	be	VBD	_	_	_
8	transferred	transfer	VBN	_	_	_
9	to	to	TO	_	_	_
10	pressure	pressure	VB	_	_	_
11	vessel	vessel	NN	_	_	_
12	and	and	CC	_	_	_
13	pressurized	pressurize	VBD	_	_	_
14	at	at	IN	_	_	_
15	1MPa	1mpa	NN	_	_	_
16	for	for	IN	_	_	_
17	15	15	CD	_	_	_
18	min	min	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	bacterial	bacterial	JJ	_	_	_
21	cells	cell	NNS	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	E.	e.	FW	_	_	_
24	coli	coli	FW	_	_	_
25	K-12	k-12	NN	_	_	_
26	MG	mg	NN	_	_	_
27	1655	1655	CD	_	_	_
28	was	be	VBD	_	_	_
29	grown	grow	VBN	_	_	_
30	in	in	IN	_	_	_
31	LB-Miller	lb-miller	NN	_	_	_
32	broth	broth	NN	_	_	_
33	at	at	IN	_	_	_
34	37	37	CD	_	_	_
35	°C	°c	NN	_	_	_
36	,160	,160	CD	_	_	_
37	rpm	rpm	NN	_	_	_
38	to	to	TO	_	_	_
39	an	a	DT	_	_	_
40	O.D.	o.d.	NN	_	_	_
41	600	600	CD	_	_	_
42	nm	nm	NN	_	_	_
43	of	of	IN	_	_	_
44	0	0	CD	_	_	_
45	.	.	.	_	_	_

1	7	7	CD	_	_	_
2	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3	Escherichia	escherichia	FW	Organism	_	_
4	coli	coli	FW	Organism	_	_
5	str	str	FW	_	_	_
6	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Gene	gene	NN	_	_	_
4	annotation	annotation	NN	_	_	_
5	was	be	VBD	_	_	_
6	obtained	obtain	VBN	_	_	_
7	from	from	IN	_	_	_
8	the	the	DT	_	_	_
9	EcoCyc	EcoCyc	NNP	_	_	_
10	E.	E.	NNP	_	_	_
11	coli	coli	NN	_	_	_
12	Database	database	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	https	http	NNS	_	_	_
15	:	:	:	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
17	Genome	Genome	NNP	_	_	_
18	_	_	NNP	_	_	_
19	build	build	VB	_	_	_
20	:	:	:	_	_	_
21	U00096	u00096	NN	_	_	_
22	.3	.3	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	MiSeq	miseq	NN	_	_	_
25	for	for	IN	_	_	_
26	base	base	NN	_	_	_
27	calling	call	VBG	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	RNA-Seq	rna-seq	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	stimulus	stimulus	NN	_	_	_
32	:	:	:	_	_	_
33	1	1	CD	_	_	_
34	MPa	mpa	NN	_	_	_
35	for	for	IN	_	_	_
36	15	15	CD	_	_	_
37	min	min	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	stimulus	stimulus	NN	_	_	_
40	:	:	:	_	_	_
41	Control	Control	NNP	_	_	_
42	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
43	strain	strain	NN	_	_	_
44	:	:	:	_	_	_
45	K-12	k-12	NN	_	_	_
46	substr	substr	NN	_	_	_
47	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Supplementary	supplementary	JJ	_	_	_
4	_	_	NN	_	_	_
5	files	file	NNS	_	_	_
6	_	_	IN	_	_	_
7	format	format	NN	_	_	_
8	_	_	NN	_	_	_
9	and	and	CC	_	_	_
10	_	_	NN	_	_	_
11	content	content	NN	_	_	_
12	:	:	:	_	_	_
13	Table	Table	NNP	_	_	_
14	of	of	IN	_	_	_
15	read	read	VBN	_	_	_
16	counts	count	NNS	_	_	_
17	with	with	IN	_	_	_
18	genes	gene	NNS	_	_	_
19	as	as	IN	_	_	_
20	rows	row	NNS	_	_	_
21	and	and	CC	_	_	_
22	samples	sample	NNS	_	_	_
23	as	as	IN	_	_	_
24	columns	column	NNS	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	counts	count	NNS	_	_	_
4	of	of	IN	_	_	_
5	reads	read	VBZ	_	_	_
6	150	150	CD	_	_	_
7	aligning	align	VBG	_	_	_
8	to	to	TO	_	_	_
9	genomic	genomic	JJ	_	_	_
10	features	feature	NNS	_	_	_
11	were	be	VBD	_	_	_
12	obtained	obtain	VBN	_	_	_
13	using	use	VBG	_	_	_
14	the	the	DT	_	_	_
15	`	`	``	_	_	_
16	feaureCounts	feaurecount	NNS	_	_	_
17	'	'	POS	_	_	_
18	function	function	NN	_	_	_
19	from	from	IN	_	_	_
20	the	the	DT	_	_	_
21	R	r	NN	_	_	_
22	package	package	NN	_	_	_
23	`	`	``	_	_	_
24	Rsubread	Rsubread	NNP	_	_	_
25	'	'	''	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	The	The	NNP	_	_	_
28	lysates	lysate	NNS	_	_	_
29	were	be	VBD	_	_	_
30	applied	apply	VBN	_	_	_
31	to	to	TO	_	_	_
32	gDNA	gdna	NN	_	_	_
33	removal	removal	NN	_	_	_
34	columns	column	NNS	_	_	_
35	and	and	CC	_	_	_
36	rRNA	rrna	NN	_	_	_
37	was	be	VBD	_	_	_
38	removed	remove	VBN	_	_	_
39	from	from	IN	_	_	_
40	total	total	JJ	_	_	_
41	RNA	rna	NN	_	_	_
42	using	use	VBG	_	_	_
43	a	a	DT	_	_	_
44	Ribo-Zero	Ribo-Zero	NNP	_	_	_
45	rRNA	rrna	NN	_	_	_
46	removal	removal	NN	_	_	_
47	kit	kit	NN	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	Illumina	Illumina	NNP	_	_	_
50	,	,	,	_	_	_
51	UK	UK	NNP	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	following	follow	VBG	_	_	_
54	the	the	DT	_	_	_
55	manufacture	manufacture	NN	_	_	_
56	's	's	POS	_	_	_
57	instruction	instruction	NN	_	_	_
58	for	for	IN	_	_	_
59	Gram-positive	gram-positive	JJ	_	_	_
60	bacteria	bacterium	NNS	_	_	_
61	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	sequencing	sequencing	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	prepared	prepare	VBN	_	_	_
6	from	from	IN	_	_	_
7	the	the	DT	_	_	_
8	enriched	enriched	JJ	_	_	_
9	mRNA	mrna	NN	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	NEBNext	nebnext	NN	_	_	_
13	Ultra	ultra	NN	_	_	_
14	RNA	rna	NN	_	_	_
15	library	library	NN	_	_	_
16	prep	prep	JJ	_	_	_
17	kit	kit	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	NEB	neb	NN	_	_	_
20	,	,	,	_	_	_
21	UK	UK	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	,	,	,	_	_	_
24	and	and	CC	_	_	_
25	independently	independently	RB	_	_	_
26	indexed	index	VBN	_	_	_
27	using	use	VBG	_	_	_
28	NEBNext	nebnext	NN	_	_	_
29	multi-plex	multi-plex	JJ	_	_	_
30	oligos	oligo	NNS	_	_	_
31	for	for	IN	_	_	_
32	Illumina	Illumina	NNP	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	NEB	NEB	NNP	_	_	_
35	,	,	,	_	_	_
36	UK	UK	NNP	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	libraries	library	NNS	_	_	_
3	were	be	VBD	_	_	_
4	pooled	pool	VBN	_	_	_
5	at	at	IN	_	_	_
6	equimolar	equimolar	JJ	_	_	_
7	ratios	ratio	NNS	_	_	_
8	before	before	IN	_	_	_
9	they	they	PRP	_	_	_
10	were	be	VBD	_	_	_
11	sequenced	sequence	VBN	_	_	_
12	using	use	VBG	_	_	_
13	MiSeq	MiSeq	NNP	_	_	_
14	Reagent	Reagent	NNP	_	_	_
15	Kit	kit	NN	_	_	_
16	v3	v3	NN	_	_	_
17	600	600	CD	_	_	_
18	cycles	cycle	NNS	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Illumina	Illumina	NNP	_	_	_
21	,	,	,	_	_	_
22	UK	UK	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	quality	quality	NN	_	_	_
4	of	of	IN	_	_	_
5	sequencing	sequencing	NN	_	_	_
6	data	datum	NNS	_	_	_
7	was	be	VBD	_	_	_
8	assessed	assess	VBN	_	_	_
9	using	use	VBG	_	_	_
10	FastQC	fastqc	NN	_	_	_
11	,	,	,	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	V11	v11	NN	_	_	_
14	.2	.2	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	before	before	IN	_	_	_
17	the	the	DT	_	_	_
18	reads	read	VBZ	_	_	_
19	were	be	VBD	_	_	_
20	trimmed	trim	VBN	_	_	_
21	using	use	VBG	_	_	_
22	Trimmomatic	trimmomatic	JJ	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	V0	v0	NN	_	_	_
25	.33	.33	CD	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	R	r	NN	_	_	_
4	package	package	NN	_	_	_
5	`	`	``	_	_	_
6	DESeq2	deseq2	NN	_	_	_
7	'	'	''	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Version	Version	NNP	_	_	_
10	1.12.4	1.12.4	CD	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	was	be	VBD	_	_	_
13	used	use	VBN	_	_	_
14	to	to	TO	_	_	_
15	calculate	calculate	VB	_	_	_
16	differential	differential	JJ	_	_	_
17	gene	gene	NN	_	_	_
18	expression	expression	NN	_	_	_
19	between	between	IN	_	_	_
20	the	the	DT	_	_	_
21	LP	lp	NN	_	_	_
22	group	group	NN	_	_	_
23	and	and	CC	_	_	_
24	the	the	DT	_	_	_
25	HP	HP	NNP	_	_	_
26	group	group	NN	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	trimmed	trimmed	RBR	_	_	_
4	reads	read	VBZ	_	_	_
5	were	be	VBD	_	_	_
6	aligned	align	VBN	_	_	_
7	against	against	IN	_	_	_
8	E.	E.	NNP	_	_	_
9	149	149	CD	_	_	_
10	coli	coli	NN	_	_	_
11	MG1655	mg1655	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	GenBank	genbank	NN	_	_	_
14	:	:	:	_	_	_
15	U00096	u00096	NN	_	_	_
16	.3	.3	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	using	use	VBG	_	_	_
19	bowtie2	bowtie2	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Version	version	NN	_	_	_
22	2.2.4	2.2.4	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	tissue	tissue	NN	_	_	_
26	:	:	:	_	_	_
27	bacterial	bacterial	JJ	_	_	_
28	cells	cell	NNS	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
30	Total	total	JJ	_	_	_
31	RNAs	rna	NNS	_	_	_
32	from	from	IN	_	_	_
33	two	two	CD	_	_	_
34	biological	biological	JJ	_	_	_
35	replicate	replicate	VB	_	_	_
36	,	,	,	_	_	_
37	each	each	DT	_	_	_
38	with	with	IN	_	_	_
39	two	two	CD	_	_	_
40	technical	technical	JJ	_	_	_
41	replicates	replicate	VBZ	_	_	_
42	were	be	VBD	_	_	_
43	extracted	extract	VBN	_	_	_
44	using	use	VBG	_	_	_
45	the	the	DT	_	_	_
46	Total	total	JJ	_	_	_
47	RNA	rna	NN	_	_	_
48	Purification	purification	NN	_	_	_
49	Kit	kit	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	Norgen	Norgen	NNP	_	_	_
52	Biotek	Biotek	NNP	_	_	_
53	,	,	,	_	_	_
54	UK	UK	NNP	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	according	accord	VBG	_	_	_
57	to	to	TO	_	_	_
58	the	the	DT	_	_	_
59	manufacturer	manufacturer	NN	_	_	_
60	's	's	POS	_	_	_
61	protocol	protocol	NN	_	_	_
62	with	with	IN	_	_	_
63	the	the	DT	_	_	_
64	addition	addition	NN	_	_	_
65	of	of	IN	_	_	_
66	1	1	CD	_	_	_
67	mg	mg	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	all	all	DT	_	_	_
70	cultures	culture	NNS	_	_	_
71	were	be	VBD	_	_	_
72	grown	grow	VBN	_	_	_
73	in	in	IN	_	_	_
74	10	10	CD	_	_	_
75	ml	ml	NN	_	_	_
76	LB	lb	NN	MED	_	_
77	broth	broth	NN	MED	_	_
78	at	at	IN	_	_	_
79	37C	37c	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	bacterial	bacterial	JJ	_	_	_
82	pellet	pellet	NN	_	_	_
83	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
84	Control	Control	NNP	_	_	_
85	_	_	NNP	_	_	_
86	1	1	CD	_	_	_
87	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
88	Control	Control	NNP	_	_	_
89	_	_	NNP	_	_	_
90	2	2	CD	_	_	_
91	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
92	Escherichia	escherichia	FW	Organism	_	_
93	coli	coli	FW	Organism	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	media	media	NNS	_	_	_
96	:	:	:	_	_	_
97	LB	lb	NN	MED	_	_
98	broth	broth	NN	MED	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	NN2	nn2	NN	_	_	_
101	_	_	CD	_	_	_
102	0018	0018	CD	_	_	_
103	_	_	NN	_	_	_
104	1	1	CD	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	NN2	nn2	NN	_	_	_
107	_	_	CD	_	_	_
108	0018	0018	CD	_	_	_
109	_	_	NN	_	_	_
110	2	2	CD	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	Omega17	omega17	NN	_	_	_
113	_	_	NN	_	_	_
114	1	1	CD	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	Omega17	omega17	NN	_	_	_
117	_	_	NN	_	_	_
118	2	2	CD	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	Omega76	omega76	NN	_	_	_
121	_	_	NN	_	_	_
122	1	1	CD	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	Omega76	omega76	NN	_	_	_
125	_	_	NN	_	_	_
126	2	2	CD	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	RNA	rna	NN	_	_	_
129	was	be	VBD	_	_	_
130	extracted	extract	VBN	_	_	_
131	using	use	VBG	_	_	_
132	Qiagen	Qiagen	NNP	_	_	_
133	's	's	POS	_	_	_
134	RNeasy	rneasy	NN	_	_	_
135	minikit	minikit	NN	_	_	_
136	Cat	cat	NN	_	_	_
137	#	#	#	_	_	_
138	74106	74106	CD	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
140	Samples	sample	NNS	_	_	_
141	were	be	VBD	_	_	_
142	background	background	NN	_	_	_
143	corrected	correct	VBN	_	_	_
144	using	use	VBG	_	_	_
145	the	the	DT	_	_	_
146	normexp	normexp	NN	_	_	_
147	-LRB-	-lrb-	-LRB-	_	_	_
148	-RRB-	-rrb-	-RRB-	_	_	_
149	function	function	NN	_	_	_
150	in	in	IN	_	_	_
151	the	the	DT	_	_	_
152	Limma	Limma	NNP	_	_	_
153	package	package	NN	_	_	_
154	in	in	IN	_	_	_
155	R	r	NN	_	_	_
156	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	was	be	VBD	_	_	_
3	followed	follow	VBN	_	_	_
4	by	by	IN	_	_	_
5	quantile	quantile	NN	_	_	_
6	normalization	normalization	NN	_	_	_
7	and	and	CC	_	_	_
8	log2	log2	NN	_	_	_
9	transformation	transformation	NN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	1	1	CD	_	_	_
3	ml	ml	NN	_	_	_
4	of	of	IN	_	_	_
5	overnight	overnight	JJ	_	_	_
6	culture	culture	NN	_	_	_
7	was	be	VBD	_	_	_
8	prepared	prepare	VBN	_	_	_
9	for	for	IN	_	_	_
10	E.	e.	FW	_	_	_
11	coli	coli	FW	_	_	_
12	DY	dy	NN	_	_	_
13	330	330	CD	_	_	_
14	GyrA-SPA	gyra-spa	NN	_	_	_
15	or	or	CC	_	_	_
16	E.	e.	FW	_	_	_
17	coli	coli	FW	_	_	_
18	DY	dy	NN	_	_	_
19	330	330	CD	_	_	_
20	GyrA-SPA	gyra-spa	NN	_	_	_
21	MuSGS	musgs	NN	_	_	_
22	by	by	IN	_	_	_
23	seeding	seed	VBG	_	_	_
24	2YT	2yt	JJ	_	_	_
25	medium	medium	NN	_	_	_
26	supplemented	supplement	VBN	_	_	_
27	with	with	IN	_	_	_
28	antibiotics	antibiotic	NNS	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	kanamycin	kanamycin	NN	_	_	_
31	50	50	CD	_	_	_
32	µg	µg	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
34	Cfx	Cfx	NNP	_	_	_
35	_	_	NNP	_	_	_
36	IN	in	IN	_	_	_
37	_	_	CD	_	_	_
38	10mkM	10mkm	NN	_	_	_
39	_	_	NN	_	_	_
40	3	3	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	Cfx	Cfx	NNP	_	_	_
43	_	_	NNP	_	_	_
44	IN	in	IN	_	_	_
45	_	_	SYM	_	_	_
46	Mu	mu	FW	_	_	_
47	_	_	FW	_	_	_
48	10mkM	10mkm	NN	_	_	_
49	_	_	NN	_	_	_
50	1	1	CD	_	_	_
51	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
52	Cfx	Cfx	NNP	_	_	_
53	_	_	NNP	_	_	_
54	IN	in	IN	_	_	_
55	_	_	SYM	_	_	_
56	Mu	mu	FW	_	_	_
57	_	_	FW	_	_	_
58	10mkM	10mkm	NN	_	_	_
59	_	_	NN	_	_	_
60	2	2	CD	_	_	_
61	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
62	Cfx	Cfx	NNP	_	_	_
63	_	_	NNP	_	_	_
64	IP	IP	NNP	_	_	_
65	_	_	NNP	_	_	_
66	10mkM	10mkM	NNP	_	_	_
67	_	_	SYM	_	_	_
68	3	3	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	Cfx	Cfx	NNP	_	_	_
71	_	_	NNP	_	_	_
72	IP	IP	NNP	_	_	_
73	_	_	SYM	_	_	_
74	Mu	mu	FW	_	_	_
75	_	_	FW	_	_	_
76	10mkM	10mkm	NN	_	_	_
77	_	_	NN	_	_	_
78	1	1	CD	_	_	_
79	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
80	Cfx	Cfx	NNP	_	_	_
81	_	_	NNP	_	_	_
82	IP	IP	NNP	_	_	_
83	_	_	SYM	_	_	_
84	Mu	mu	FW	_	_	_
85	_	_	FW	_	_	_
86	10mkM	10mkm	NN	_	_	_
87	_	_	NN	_	_	_
88	2	2	CD	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	ChIP-Seq	chip-seq	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	Ciprofloxacin	ciprofloxacin	NN	_	_	_
93	Rep	Rep	NNP	_	_	_
94	1	1	CD	_	_	_
95	+	+	CC	_	_	_
96	A-IP	a-ip	JJ	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	Ciprofloxacin	ciprofloxacin	NN	_	_	_
99	Rep	Rep	NNP	_	_	_
100	1	1	CD	_	_	_
101	+	+	CC	_	_	_
102	A+IP	A+IP	NNP	_	_	_
103	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
104	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
105	Rep	Rep	NNP	_	_	_
106	2	2	CD	_	_	_
107	+	+	CC	_	_	_
108	A-IP	a-ip	JJ	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	Ciprofloxacin	ciprofloxacin	NN	_	_	_
111	Rep	Rep	NNP	_	_	_
112	2	2	CD	_	_	_
113	+	+	CC	_	_	_
114	A+IP	A+IP	NNP	_	_	_
115	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
116	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
117	Rep	Rep	NNP	_	_	_
118	3	3	CD	_	_	_
119	+	+	CC	_	_	_
120	A-IP	a-ip	JJ	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	Ciprofloxacin	ciprofloxacin	NN	_	_	_
123	Rep	Rep	NNP	_	_	_
124	3	3	CD	_	_	_
125	+	+	CC	_	_	_
126	A+IP	a+ip	NN	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	Cultures	culture	NNS	_	_	_
129	-LRB-	-lrb-	-LRB-	_	_	_
130	+	+	CC	_	_	_
131	A	a	DT	_	_	_
132	and	and	CC	_	_	_
133	-	-	:	_	_	_
134	A	a	NN	_	_	_
135	-RRB-	-rrb-	-RRB-	_	_	_
136	were	be	VBD	_	_	_
137	incubated	incubate	VBN	_	_	_
138	at	at	IN	_	_	_
139	32	32	CD	_	_	_
140	°C	°c	NN	_	_	_
141	with	with	IN	_	_	_
142	shaking	shake	VBG	_	_	_
143	for	for	IN	_	_	_
144	additional	additional	JJ	_	_	_
145	15	15	CD	_	_	_
146	min	min	NN	_	_	_
147	,	,	,	_	_	_
148	then	then	RB	_	_	_
149	cells	cell	NNS	_	_	_
150	were	be	VBD	_	_	_
151	pelleted	pellete	VBN	_	_	_
152	by	by	IN	_	_	_
153	centrifugation	centrifugation	NN	_	_	_
154	at	at	IN	_	_	_
155	10	10	CD	_	_	_
156	°C	°c	NN	_	_	_
157	-LRB-	-lrb-	-LRB-	_	_	_
158	4500xg	4500xg	NN	_	_	_
159	-RRB-	-rrb-	-RRB-	_	_	_
160	and	and	CC	_	_	_
161	resuspended	resuspend	VBN	_	_	_
162	in	in	IN	_	_	_
163	10	10	CD	_	_	_
164	ml	ml	NN	_	_	_
165	of	of	IN	_	_	_
166	TES	tes	NN	_	_	_
167	buffer	buffer	NN	_	_	_
168	-LRB-	-lrb-	-LRB-	_	_	_
169	10	10	CD	_	_	_
170	mM	mm	NN	KWSUPP	_	_
171	Tris-Cl	tris-cl	NN	_	_	_
172	pH7	ph7	NN	_	_	_
173	.5	.5	CD	_	_	_
174	,	,	,	_	_	_
175	1	1	CD	_	_	_
176	mM	mm	NN	KWSUPP	_	_
177	EDTA	edta	NN	_	_	_
178	,	,	,	_	_	_
179	250	250	CD	_	_	_
180	mM	mm	NN	KWSUPP	_	_
181	NaCl	nacl	NN	_	_	_
182	-RRB-	-rrb-	-RRB-	_	_	_
183	.	.	.	_	_	_

1	Washing	wash	VBG	_	_	_
2	procedure	procedure	NN	_	_	_
3	was	be	VBD	_	_	_
4	repeated	repeat	VBN	_	_	_
5	twice	twice	RB	_	_	_
6	to	to	TO	_	_	_
7	remove	remove	VB	_	_	_
8	culture	culture	NN	_	_	_
9	liquid	liquid	NN	_	_	_
10	and	and	CC	_	_	_
11	excess	excess	NN	_	_	_
12	of	of	IN	_	_	_
13	gyrase	gyrase	NN	_	_	_
14	poison	poison	NN	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	from	from	IN	_	_	_
6	resulting	result	VBG	_	_	_
7	supernatant	supernatant	JJ	_	_	_
8	with	with	IN	_	_	_
9	phenol	phenol	NN	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Escherichia	escherichia	FW	Organism	_	_
12	coli	coli	FW	Organism	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	For	for	IN	_	_	_
15	proteolysis	proteolysis	NN	_	_	_
16	,	,	,	_	_	_
17	affinity	affinity	NN	_	_	_
18	gel	gel	NN	_	_	_
19	obtained	obtain	VBN	_	_	_
20	after	after	IN	_	_	_
21	the	the	DT	_	_	_
22	last	last	JJ	_	_	_
23	centrifugation	centrifugation	NN	_	_	_
24	step	step	NN	_	_	_
25	was	be	VBD	_	_	_
26	diluted	dilute	VBN	_	_	_
27	with	with	IN	_	_	_
28	TES	tes	NN	_	_	_
29	buffer	buffer	NN	_	_	_
30	up	up	IN	_	_	_
31	to	to	TO	_	_	_
32	final	final	JJ	_	_	_
33	volume	volume	NN	_	_	_
34	200	200	CD	_	_	_
35	μl	μl	NN	_	_	_
36	,	,	,	_	_	_
37	proteinase	proteinase	NN	_	_	_
38	K	k	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	Sigma-Aldrich	sigma-aldrich	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	was	be	VBD	_	_	_
43	added	add	VBN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	0.5	0.5	CD	_	_	_
46	mg	mg	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	Genome	Genome	NNP	_	_	_
49	_	_	NNP	_	_	_
50	build	build	VB	_	_	_
51	:	:	:	_	_	_
52	Escherichia	escherichia	FW	Organism	_	_
53	coli	coli	FW	Organism	_	_
54	W3110	w3110	NN	_	_	_
55	MuSGS	musgs	NN	_	_	_
56	-LRB-	-lrb-	-LRB-	_	_	_
57	on	on	IN	_	_	_
58	the	the	DT	_	_	_
59	basis	basis	NN	_	_	_
60	of	of	IN	_	_	_
61	NC	NC	NNP	_	_	_
62	_	_	SYM	_	_	_
63	007779.1	007779.1	CD	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	.	.	.	_	_	_

1	FASTA	fasta	NN	_	_	_
2	and	and	CC	_	_	_
3	GFF	gff	NN	_	_	_
4	are	be	VBP	_	_	_
5	included	include	VBN	_	_	_
6	on	on	IN	_	_	_
7	series	series	NN	_	_	_
8	record	record	NN	_	_	_
9	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Gyrase	gyrase	NN	_	_	_
3	Cleavage	cleavage	NN	_	_	_
4	Sites	site	NNS	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	GCSs	gcss	NNS	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	were	be	VBD	_	_	_
9	called	call	VBN	_	_	_
10	using	use	VBG	_	_	_
11	custom	custom	NN	_	_	_
12	script	script	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	GCSs_calling.py	gcss_calling.py	NN	_	_	_
15	,	,	,	_	_	_
16	github	github	NN	_	_	_
17	:	:	:	_	_	_
18	https	http	NNS	_	_	_
19	:	:	:	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Lysates	lysate	NNS	_	_	_
22	were	be	VBD	_	_	_
23	diluted	dilute	VBN	_	_	_
24	with	with	IN	_	_	_
25	1	1	CD	_	_	_
26	ml	ml	NN	_	_	_
27	of	of	IN	_	_	_
28	TES	tes	NN	_	_	_
29	buffer	buffer	NN	_	_	_
30	and	and	CC	_	_	_
31	100	100	CD	_	_	_
32	μl	μl	NN	_	_	_
33	of	of	IN	_	_	_
34	ANTI-FLAG	anti-flag	NN	_	_	_
35	®	®	CD	_	_	_
36	M2	m2	NN	_	_	_
37	affinity	affinity	NN	_	_	_
38	gel	gel	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	Sigma-Aldrich	sigma-aldrich	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	was	be	VBD	_	_	_
43	added	add	VBN	_	_	_
44	.	.	.	_	_	_

1	Immunoprecipitation	immunoprecipitation	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	for	for	IN	_	_	_
5	1.5-2	1.5-2	CD	_	_	_
6	hours	hour	NNS	_	_	_
7	at	at	IN	_	_	_
8	room	room	NN	_	_	_
9	temperature	temperature	NN	_	_	_
10	with	with	IN	_	_	_
11	moderate	moderate	JJ	_	_	_
12	mixing	mix	VBG	_	_	_
13	,	,	,	_	_	_
14	then	then	RB	_	_	_
15	affinity	affinity	NN	_	_	_
16	gel	gel	NN	_	_	_
17	was	be	VBD	_	_	_
18	washed	wash	VBN	_	_	_
19	4	4	CD	_	_	_
20	times	time	NNS	_	_	_
21	by	by	IN	_	_	_
22	repeating	repeat	VBG	_	_	_
23	steps	step	NNS	_	_	_
24	of	of	IN	_	_	_
25	centrifugation	centrifugation	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	1.5	1.5	CD	_	_	_
28	minute	minute	NN	_	_	_
29	,	,	,	_	_	_
30	1000xg	1000xg	NN	_	_	_
31	at	at	IN	_	_	_
32	room	room	NN	_	_	_
33	temperature	temperature	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	and	and	CC	_	_	_
36	resuspention	resuspention	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	x2	x2	NN	_	_	_
39	with	with	IN	_	_	_
40	1	1	CD	_	_	_
41	ml	ml	NN	_	_	_
42	of	of	IN	_	_	_
43	TESS	TESS	NNP	_	_	_
44	buffer	buffer	NN	_	_	_
45	,	,	,	_	_	_
46	x1	x1	NN	_	_	_
47	with	with	IN	_	_	_
48	1	1	CD	_	_	_
49	ml	ml	NN	_	_	_
50	of	of	IN	_	_	_
51	TES	tes	NN	_	_	_
52	buffer	buffer	NN	_	_	_
53	,	,	,	_	_	_
54	x1	x1	NN	_	_	_
55	with	with	IN	_	_	_
56	1	1	CD	_	_	_
57	ml	ml	NN	_	_	_
58	of	of	IN	_	_	_
59	TE	TE	NNP	_	_	_
60	buffer	buffer	NN	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Microcin	microcin	NN	_	_	_
3	B17	b17	NN	_	_	_
4	Rep	Rep	NNP	_	_	_
5	1	1	CD	_	_	_
6	+	+	CC	_	_	_
7	A-IP	a-ip	JJ	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Microcin	microcin	NN	_	_	_
10	B17	b17	NN	_	_	_
11	Rep	Rep	NNP	_	_	_
12	1	1	CD	_	_	_
13	+	+	CC	_	_	_
14	A+IP	A+IP	NNP	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	Microcin	Microcin	NNP	_	_	_
17	B17	B17	NNP	_	_	_
18	Rep	Rep	NNP	_	_	_
19	2	2	CD	_	_	_
20	+	+	CC	_	_	_
21	A-IP	a-ip	JJ	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Microcin	microcin	NN	_	_	_
24	B17	b17	NN	_	_	_
25	Rep	Rep	NNP	_	_	_
26	2	2	CD	_	_	_
27	+	+	CC	_	_	_
28	A+IP	A+IP	NNP	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	Microcin	Microcin	NNP	_	_	_
31	B17	B17	NNP	_	_	_
32	Rep	Rep	NNP	_	_	_
33	3	3	CD	_	_	_
34	+	+	CC	_	_	_
35	A-IP	a-ip	JJ	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Microcin	microcin	NN	_	_	_
38	B17	b17	NN	_	_	_
39	Rep	Rep	NNP	_	_	_
40	3	3	CD	_	_	_
41	+	+	CC	_	_	_
42	A+IP	A+IP	NNP	_	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	Microcin	Microcin	NNP	_	_	_
45	_	_	NNP	_	_	_
46	IN	in	IN	_	_	_
47	_	_	CD	_	_	_
48	50mkM	50mkm	NN	_	_	_
49	_	_	NN	_	_	_
50	3	3	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	Microcin	microcin	NN	_	_	_
53	_	_	CD	_	_	_
54	IN	in	IN	_	_	_
55	_	_	CD	_	_	_
56	Mu	mu	NN	_	_	_
57	_	_	CD	_	_	_
58	10mkM	10mkm	NN	_	_	_
59	_	_	NN	_	_	_
60	1	1	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Microcin	microcin	NN	_	_	_
63	_	_	CD	_	_	_
64	IN	in	IN	_	_	_
65	_	_	CD	_	_	_
66	Mu	mu	NN	_	_	_
67	_	_	NN	_	_	_
68	10mkM	10mkm	NN	_	_	_
69	_	_	NN	_	_	_
70	2	2	CD	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	Microcin	microcin	NN	_	_	_
73	_	_	CD	_	_	_
74	IP	IP	NNP	_	_	_
75	_	_	NNP	_	_	_
76	50mkM	50mkM	NNP	_	_	_
77	_	_	SYM	_	_	_
78	3	3	CD	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	MIcrocin	microcin	NN	_	_	_
81	_	_	CD	_	_	_
82	IP	IP	NNP	_	_	_
83	_	_	SYM	_	_	_
84	Mu	mu	FW	_	_	_
85	_	_	FW	_	_	_
86	10mkM	10mkm	NN	_	_	_
87	_	_	NN	_	_	_
88	1	1	CD	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	Microcin	microcin	NN	_	_	_
91	_	_	CD	_	_	_
92	IP	IP	NNP	_	_	_
93	_	_	SYM	_	_	_
94	Mu	mu	FW	_	_	_
95	_	_	FW	_	_	_
96	10mkM	10mkm	NN	_	_	_
97	_	_	NN	_	_	_
98	2	2	CD	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	musgs	musg	NNS	_	_	_
101	presence	presence	NN	_	_	_
102	:	:	:	_	_	_
103	-	-	:	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	musgs	musg	NNS	_	_	_
106	presence	presence	NN	_	_	_
107	:	:	:	_	_	_
108	MuSGS	musgs	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
110	Oxo	Oxo	NNP	_	_	_
111	_	_	NNP	_	_	_
112	IN	in	IN	_	_	_
113	_	_	CD	_	_	_
114	120mkM	120mkm	NN	_	_	_
115	_	_	NN	_	_	_
116	3	3	CD	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	Oxo	Oxo	NNP	_	_	_
119	_	_	NNP	_	_	_
120	IN	in	IN	_	_	_
121	_	_	SYM	_	_	_
122	Mu	mu	FW	_	_	_
123	_	_	FW	_	_	_
124	120mkM	120mkm	NN	_	_	_
125	_	_	NN	_	_	_
126	1	1	CD	_	_	_
127	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
128	Oxo	Oxo	NNP	_	_	_
129	_	_	NNP	_	_	_
130	IN	in	IN	_	_	_
131	_	_	SYM	_	_	_
132	Mu	mu	FW	_	_	_
133	_	_	FW	_	_	_
134	120mkM	120mkm	NN	_	_	_
135	_	_	NN	_	_	_
136	2	2	CD	_	_	_
137	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
138	Oxo	Oxo	NNP	_	_	_
139	_	_	NNP	_	_	_
140	IP	IP	NNP	_	_	_
141	_	_	SYM	_	_	_
142	120mkM	120mkm	NN	_	_	_
143	_	_	NN	_	_	_
144	3	3	CD	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	Oxo	Oxo	NNP	_	_	_
147	_	_	NNP	_	_	_
148	IP	IP	NNP	_	_	_
149	_	_	SYM	_	_	_
150	Mu	mu	FW	_	_	_
151	_	_	FW	_	_	_
152	120mkM	120mkm	NN	_	_	_
153	_	_	NN	_	_	_
154	1	1	CD	_	_	_
155	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
156	Oxo	Oxo	NNP	_	_	_
157	_	_	NNP	_	_	_
158	IP	IP	NNP	_	_	_
159	_	_	SYM	_	_	_
160	Mu	mu	FW	_	_	_
161	_	_	FW	_	_	_
162	120mkM	120mkm	NN	_	_	_
163	_	_	NN	_	_	_
164	2	2	CD	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	Oxolinic	oxolinic	JJ	_	_	_
167	acid	acid	NN	_	_	_
168	Rep	Rep	NNP	_	_	_
169	1	1	CD	_	_	_
170	+	+	CC	_	_	_
171	A-IP	a-ip	JJ	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	Oxolinic	oxolinic	JJ	_	_	_
174	acid	acid	NN	_	_	_
175	Rep	Rep	NNP	_	_	_
176	1	1	CD	_	_	_
177	+	+	CC	_	_	_
178	A+IP	A+IP	NNP	_	_	_
179	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
180	Oxolinic	oxolinic	JJ	_	_	_
181	acid	acid	NN	_	_	_
182	Rep	Rep	NNP	_	_	_
183	2	2	CD	_	_	_
184	+	+	CC	_	_	_
185	A-IP	a-ip	JJ	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	Oxolinic	oxolinic	JJ	_	_	_
188	acid	acid	NN	_	_	_
189	Rep	Rep	NNP	_	_	_
190	2	2	CD	_	_	_
191	+	+	CC	_	_	_
192	A+IP	A+IP	NNP	_	_	_
193	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
194	Oxolinic	oxolinic	JJ	_	_	_
195	acid	acid	NN	_	_	_
196	Rep	Rep	NNP	_	_	_
197	3	3	CD	_	_	_
198	+	+	CC	_	_	_
199	A-IP	a-ip	JJ	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	Oxolinic	oxolinic	JJ	_	_	_
202	acid	acid	NN	_	_	_
203	Rep	Rep	NNP	_	_	_
204	3	3	CD	_	_	_
205	+	+	CC	_	_	_
206	A+IP	A+IP	NNP	_	_	_
207	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
208	Raw	raw	NN	_	_	_
209	reads	read	VBZ	_	_	_
210	were	be	VBD	_	_	_
211	aligned	align	VBN	_	_	_
212	to	to	TO	_	_	_
213	the	the	DT	_	_	_
214	E.	e.	FW	_	_	_
215	coli	coli	FW	_	_	_
216	w3110	w3110	NN	_	_	_
217	MuSGS	musgs	NN	_	_	_
218	genome	genome	NN	_	_	_
219	-LRB-	-lrb-	-LRB-	_	_	_
220	containing	contain	VBG	_	_	_
221	a	a	DT	_	_	_
222	strong	strong	JJ	_	_	_
223	gyrase	gyrase	NN	_	_	_
224	binding	binding	NN	_	_	_
225	site	site	NN	_	_	_
226	from	from	IN	_	_	_
227	bacteriophage	bacteriophage	NN	_	_	_
228	Mu	mu	NN	_	_	_
229	-RRB-	-rrb-	-RRB-	_	_	_
230	with	with	IN	_	_	_
231	BWA	bwa	NN	_	_	_
232	MEM	mem	NN	_	_	_
233	-LRB-	-lrb-	-LRB-	_	_	_
234	default	default	NN	_	_	_
235	settings	setting	NNS	_	_	_
236	-RRB-	-rrb-	-RRB-	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
238	Resulting	result	VBG	_	_	_
239	SAM	SAM	NNP	_	_	_
240	files	file	NNS	_	_	_
241	were	be	VBD	_	_	_
242	processed	process	VBN	_	_	_
243	with	with	IN	_	_	_
244	custom	custom	NN	_	_	_
245	script	script	NN	_	_	_
246	-LRB-	-lrb-	-LRB-	_	_	_
247	SAM_to_coverage_and_N5E_N3E.py	sam_to_coverage_and_n5e_n3e.py	NN	_	_	_
248	,	,	,	_	_	_
249	github	github	NN	_	_	_
250	:	:	:	_	_	_
251	https	http	NNS	_	_	_
252	:	:	:	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
254	Rifampicine	Rifampicine	NNP	_	_	_
255	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
256	Rep	Rep	NNP	_	_	_
257	1	1	LS	_	_	_
258	-	-	:	_	_	_
259	A-IP	a-ip	NN	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	Rifampicine	Rifampicine	NNP	_	_	_
262	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
263	Rep	Rep	NNP	_	_	_
264	1	1	CD	_	_	_
265	+	+	CC	_	_	_
266	A-IP	a-ip	JJ	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	Rifampicine	Rifampicine	NNP	_	_	_
269	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
270	Rep	Rep	NNP	_	_	_
271	1	1	CD	_	_	_
272	+	+	CC	_	_	_
273	A+IP	A+IP	NNP	_	_	_
274	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
275	Rifampicine	Rifampicine	NNP	_	_	_
276	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
277	Rep	Rep	NNP	_	_	_
278	2	2	CD	_	_	_
279	+	+	CC	_	_	_
280	A-IP	a-ip	JJ	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	Rifampicine	Rifampicine	NNP	_	_	_
283	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
284	Rep	Rep	NNP	_	_	_
285	2	2	CD	_	_	_
286	+	+	CC	_	_	_
287	A+IP	A+IP	NNP	_	_	_
288	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
289	Rifampicine	Rifampicine	NNP	_	_	_
290	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
291	Rep	Rep	NNP	_	_	_
292	3	3	CD	_	_	_
293	+	+	CC	_	_	_
294	A-IP	a-ip	JJ	_	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	Rifampicine	Rifampicine	NNP	_	_	_
297	Ciprofloxacin	Ciprofloxacin	NNP	_	_	_
298	Rep	Rep	NNP	_	_	_
299	3	3	CD	_	_	_
300	+	+	CC	_	_	_
301	A+IP	A+IP	NNP	_	_	_
302	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
303	RifCfx	RifCfx	NNP	_	_	_
304	_	_	NNP	_	_	_
305	IN	in	IN	_	_	_
306	_	_	CD	_	_	_
307	Mu	mu	NN	_	_	_
308	_	_	NN	_	_	_
309	122mkM	122mkm	NN	_	_	_
310	_	_	CD	_	_	_
311	10mkM	10mkm	NN	_	_	_
312	_	_	NN	_	_	_
313	1	1	CD	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	RifCfx	rifcfx	NN	_	_	_
316	_	_	CD	_	_	_
317	IN	in	IN	_	_	_
318	_	_	CD	_	_	_
319	Mu	mu	NN	_	_	_
320	_	_	NN	_	_	_
321	122mkM	122mkm	NN	_	_	_
322	_	_	CD	_	_	_
323	10mkM	10mkm	NN	_	_	_
324	_	_	NN	_	_	_
325	2	2	CD	_	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	RifCfx	rifcfx	NN	_	_	_
328	_	_	CD	_	_	_
329	IN	in	IN	_	_	_
330	_	_	CD	_	_	_
331	Mu	mu	NN	_	_	_
332	_	_	NN	_	_	_
333	122mkM	122mkm	NN	_	_	_
334	_	_	CD	_	_	_
335	10mkM	10mkm	NN	_	_	_
336	_	_	NN	_	_	_
337	3	3	CD	_	_	_
338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
339	RifCfx	rifcfx	NN	_	_	_
340	_	_	CD	_	_	_
341	IP	IP	NNP	_	_	_
342	_	_	SYM	_	_	_
343	Mu	mu	FW	_	_	_
344	_	_	FW	_	_	_
345	122mkM	122mkm	NN	_	_	_
346	_	_	CD	_	_	_
347	10mkM	10mkm	NN	_	_	_
348	_	_	NN	_	_	_
349	1	1	CD	_	_	_
350	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
351	RifCfx	rifcfx	NN	_	_	_
352	_	_	CD	_	_	_
353	IP	IP	NNP	_	_	_
354	_	_	SYM	_	_	_
355	Mu	mu	FW	_	_	_
356	_	_	FW	_	_	_
357	122mkM	122mkm	NN	_	_	_
358	_	_	CD	_	_	_
359	10mkM	10mkm	NN	_	_	_
360	_	_	NN	_	_	_
361	2	2	CD	_	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
363	RifCfx	rifcfx	NN	_	_	_
364	_	_	CD	_	_	_
365	IP	IP	NNP	_	_	_
366	_	_	SYM	_	_	_
367	Mu	mu	FW	_	_	_
368	_	_	FW	_	_	_
369	122mkM	122mkm	NN	_	_	_
370	_	_	CD	_	_	_
371	10mkM	10mkm	NN	_	_	_
372	_	_	NN	_	_	_
373	3	3	CD	_	_	_
374	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
375	Rif	rif	NN	_	_	_
376	_	_	CD	_	_	_
377	IN	in	IN	_	_	_
378	_	_	CD	_	_	_
379	Mu	mu	NN	_	_	_
380	_	_	CD	_	_	_
381	122mkM	122mkm	NN	_	_	_
382	_	_	NN	_	_	_
383	1	1	CD	_	_	_
384	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
385	Sequencing	sequencing	NN	_	_	_
386	libraries	library	NNS	_	_	_
387	were	be	VBD	_	_	_
388	prepared	prepare	VBN	_	_	_
389	with	with	IN	_	_	_
390	Accel	Accel	NNP	_	_	_
391	NGS	NGS	NNP	_	_	_
392	1S	1s	NN	_	_	_
393	kit	kit	NN	_	_	_
394	-LRB-	-lrb-	-LRB-	_	_	_
395	Swift	Swift	NNP	_	_	_
396	Bioscience	Bioscience	NNP	_	_	_
397	-RRB-	-rrb-	-RRB-	_	_	_
398	in	in	IN	_	_	_
399	accordanse	accordanse	NN	_	_	_
400	with	with	IN	_	_	_
401	manufacturer	manufacturer	NN	_	_	_
402	's	's	POS	_	_	_
403	protocol	protocol	NN	_	_	_
404	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Starter	Starter	NNP	_	_	_
3	was	be	VBD	_	_	_
4	cultivated	cultivate	VBN	_	_	_
5	at	at	IN	_	_	_
6	32	32	CD	_	_	_
7	°C	°c	NN	_	_	_
8	with	with	IN	_	_	_
9	shaking	shake	VBG	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	180	180	CD	_	_	_
12	rpm	rpm	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	,	,	,	_	_	_
15	then	then	RB	_	_	_
16	was	be	VBD	_	_	_
17	inoculated	inoculate	VBN	_	_	_
18	into	into	IN	_	_	_
19	100	100	CD	_	_	_
20	ml	ml	NN	_	_	_
21	of	of	IN	_	_	_
22	2YT	2yt	NN	_	_	_
23	without	without	IN	_	_	_
24	antibiotics	antibiotic	NNS	_	_	_
25	and	and	CC	_	_	_
26	cultivation	cultivation	NN	_	_	_
27	was	be	VBD	_	_	_
28	proceeded	proceed	VBN	_	_	_
29	under	under	IN	_	_	_
30	the	the	DT	_	_	_
31	same	same	JJ	_	_	_
32	conditions	condition	NNS	_	_	_
33	until	until	IN	_	_	_
34	culture	culture	NN	_	_	_
35	reaching	reach	VBG	_	_	_
36	mid-logphase	mid-logphase	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	OD600	od600	NN	_	_	_
39	=	=	JJ	_	_	_
40	0.6-0.8	0.6-0.8	CD	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	DY330	dy330	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Supplementary	supplementary	JJ	_	_	_
7	_	_	NN	_	_	_
8	files	file	NNS	_	_	_
9	_	_	IN	_	_	_
10	format	format	NN	_	_	_
11	_	_	NN	_	_	_
12	and	and	CC	_	_	_
13	_	_	NN	_	_	_
14	content	content	NN	_	_	_
15	:	:	:	_	_	_
16	tar	tar	NN	GEN	_	_
17	archives	archive	NNS	_	_	_
18	contain	contain	VBP	_	_	_
19	the	the	DT	_	_	_
20	following	following	NN	_	_	_
21	:	:	:	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	tab-delimited	tab-delimited	JJ	_	_	_
24	text	text	NN	_	_	_
25	files	file	NNS	_	_	_
26	with	with	IN	_	_	_
27	GCSs	gcss	NNS	_	_	_
28	coordinates	coordinate	VBZ	_	_	_
29	,	,	,	_	_	_
30	N3E	n3e	NN	_	_	_
31	values	value	NNS	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	\	\	CD	_	_	_
34	height	height	NN	_	_	_
35	of	of	IN	_	_	_
36	the	the	DT	_	_	_
37	peak	peak	NN	_	_	_
38	\	\	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	and	and	CC	_	_	_
41	GCSs	gcss	NNS	_	_	_
42	scores	score	NNS	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	score	score	NN	_	_	_
45	of	of	IN	_	_	_
46	the	the	DT	_	_	_
47	sequence	sequence	NN	_	_	_
48	under	under	IN	_	_	_
49	the	the	DT	_	_	_
50	GCS	gc	NNS	_	_	_
51	obtained	obtain	VBN	_	_	_
52	after	after	IN	_	_	_
53	scanning	scan	VBG	_	_	_
54	the	the	DT	_	_	_
55	genome	genome	NN	_	_	_
56	with	with	IN	_	_	_
57	DNA-gyrase	dna-gyrase	NN	_	_	_
58	binding	binding	NN	_	_	_
59	motif	motif	NN	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	tagged	tag	VBD	_	_	_
63	gyrase	gyrase	NN	_	_	_
64	subunit	subunit	NN	_	_	_
65	:	:	:	_	_	_
66	GyrA-SPA	gyra-spa	JJ	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	text	text	NN	_	_	_
69	wig	wig	NN	_	_	_
70	files	file	NNS	_	_	_
71	contain	contain	VBP	_	_	_
72	coverage	coverage	NN	_	_	_
73	depth	depth	NN	_	_	_
74	data	datum	NNS	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	text	text	NN	_	_	_
77	wig	wig	NN	_	_	_
78	files	file	NNS	_	_	_
79	contain	contain	VBP	_	_	_
80	N3E	n3e	NN	_	_	_
81	values	value	NNS	_	_	_
82	-LRB-	-lrb-	-LRB-	_	_	_
83	number	number	NN	_	_	_
84	of	of	IN	_	_	_
85	DNA	dna	NN	_	_	_
86	fragments	fragment	NNS	_	_	_
87	3	3	CD	_	_	_
88	'	'	''	_	_	_
89	ends	end	VBZ	_	_	_
90	for	for	IN	_	_	_
91	each	each	DT	_	_	_
92	position	position	NN	_	_	_
93	of	of	IN	_	_	_
94	the	the	DT	_	_	_
95	genome	genome	NN	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	Un	un	NN	_	_	_
99	_	_	CD	_	_	_
100	IN	in	IN	_	_	_
101	_	_	CD	_	_	_
102	3	3	CD	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	Un	un	NN	_	_	_
105	_	_	CD	_	_	_
106	IN	in	IN	_	_	_
107	_	_	CD	_	_	_
108	Mu	mu	NN	_	_	_
109	_	_	NN	_	_	_
110	1	1	CD	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	Un	un	NN	_	_	_
113	_	_	CD	_	_	_
114	IN	in	IN	_	_	_
115	_	_	CD	_	_	_
116	Mu	mu	NN	_	_	_
117	_	_	NN	_	_	_
118	2	2	CD	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	Un	un	NN	_	_	_
121	_	_	CD	_	_	_
122	IP	IP	NNP	_	_	_
123	_	_	SYM	_	_	_
124	3	3	CD	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	Un	un	NN	_	_	_
127	_	_	CD	_	_	_
128	IP	IP	NNP	_	_	_
129	_	_	SYM	_	_	_
130	Mu	mu	FW	_	_	_
131	_	_	FW	_	_	_
132	1	1	CD	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	Un	un	NN	_	_	_
135	_	_	CD	_	_	_
136	IP	IP	NNP	_	_	_
137	_	_	SYM	_	_	_
138	Mu	mu	FW	_	_	_
139	_	_	FW	_	_	_
140	2	2	CD	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
142	Untreated	untreated	JJ	_	_	_
143	Rep	Rep	NNP	_	_	_
144	1	1	LS	_	_	_
145	-	-	:	_	_	_
146	A-IP	a-ip	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	Untreated	untreated	JJ	_	_	_
149	Rep	Rep	NNP	_	_	_
150	1	1	LS	_	_	_
151	-	-	:	_	_	_
152	A+IP	a+ip	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	Untreated	untreated	JJ	_	_	_
155	Rep	Rep	NNP	_	_	_
156	2	2	LS	_	_	_
157	-	-	:	_	_	_
158	A-IP	a-ip	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	Untreated	untreated	JJ	_	_	_
161	Rep	Rep	NNP	_	_	_
162	2	2	LS	_	_	_
163	-	-	:	_	_	_
164	A+IP	a+ip	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	Untreated	untreated	JJ	_	_	_
167	Rep	Rep	NNP	_	_	_
168	3	3	LS	_	_	_
169	-	-	:	_	_	_
170	A-IP	a-ip	NN	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	Untreated	untreated	JJ	_	_	_
173	Rep	Rep	NNP	_	_	_
174	3	3	LS	_	_	_
175	-	-	:	_	_	_
176	A+IP	a+ip	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
178	Washed	wash	VBD	_	_	_
179	pellets	pellet	NNS	_	_	_
180	were	be	VBD	_	_	_
181	resuspended	resuspend	VBN	_	_	_
182	in	in	IN	_	_	_
183	1	1	CD	_	_	_
184	ml	ml	NN	_	_	_
185	of	of	IN	_	_	_
186	TESS	TESS	NNP	_	_	_
187	buffer	buffer	NN	_	_	_
188	-LRB-	-lrb-	-LRB-	_	_	_
189	10	10	CD	_	_	_
190	mM	mm	NN	KWSUPP	_	_
191	Tris-Cl	tris-cl	NN	_	_	_
192	pH7	ph7	NN	_	_	_
193	.5	.5	CD	_	_	_
194	,	,	,	_	_	_
195	1	1	CD	_	_	_
196	mM	mm	NN	KWSUPP	_	_
197	EDTA	edta	NN	_	_	_
198	,	,	,	_	_	_
199	250	250	CD	_	_	_
200	mM	mm	NN	KWSUPP	_	_
201	NaCl	nacl	NN	_	_	_
202	,	,	,	_	_	_
203	0.02	0.02	CD	_	_	_
204	%	%	NN	_	_	_
205	SDS	sds	NN	_	_	_
206	,	,	,	_	_	_
207	0.2	0.2	CD	_	_	_
208	%	%	NN	_	_	_
209	Tween-20	tween-20	NN	_	_	_
210	-RRB-	-rrb-	-RRB-	_	_	_
211	with	with	IN	_	_	_
212	addition	addition	NN	_	_	_
213	of	of	IN	_	_	_
214	proteases	protease	NNS	_	_	_
215	inhibitors	inhibitor	NNS	_	_	_
216	cocktail	cocktail	NN	_	_	_
217	-LRB-	-lrb-	-LRB-	_	_	_
218	cOmplete	complete	JJ	_	_	_
219	ultra	ultra	NNS	_	_	_
220	EDTA	edta	NN	_	_	_
221	free	free	JJ	_	_	_
222	,	,	,	_	_	_
223	Roche	Roche	NNP	_	_	_
224	-RRB-	-rrb-	-RRB-	_	_	_
225	and	and	CC	_	_	_
226	RNAse	rnase	NN	_	_	_
227	A	a	NN	_	_	_
228	-LRB-	-lrb-	-LRB-	_	_	_
229	Thermo	Thermo	NNP	_	_	_
230	Scientific	Scientific	NNP	_	_	_
231	-RRB-	-rrb-	-RRB-	_	_	_
232	.	.	.	_	_	_

1	Resulting	result	VBG	_	_	_
2	suspensions	suspension	NNS	_	_	_
3	were	be	VBD	_	_	_
4	sonicated	sonicate	VBN	_	_	_
5	with	with	IN	_	_	_
6	parameters	parameter	NNS	_	_	_
7	optimized	optimize	VBN	_	_	_
8	to	to	TO	_	_	_
9	obtain	obtain	VB	_	_	_
10	DNA	dna	NN	_	_	_
11	fragments	fragment	NNS	_	_	_
12	between	between	IN	_	_	_
13	200	200	CD	_	_	_
14	and	and	CC	_	_	_
15	700	700	CD	_	_	_
16	bp	bp	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	SONOPULS	sonopuls	NN	_	_	_
19	HD	hd	NN	_	_	_
20	3100	3100	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

1	Lysates	lysate	NNS	_	_	_
2	were	be	VBD	_	_	_
3	diluted	dilute	VBN	_	_	_
4	with	with	IN	_	_	_
5	1	1	CD	_	_	_
6	ml	ml	NN	_	_	_
7	of	of	IN	_	_	_
8	TES	tes	NN	_	_	_
9	buffer	buffer	NN	_	_	_
10	and	and	CC	_	_	_
11	100	100	CD	_	_	_
12	μl	μl	NN	_	_	_
13	of	of	IN	_	_	_
14	ANTI-FLAG	anti-flag	NN	_	_	_
15	®	®	CD	_	_	_
16	M2	m2	NN	_	_	_
17	affinity	affinity	NN	_	_	_
18	gel	gel	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Sigma-Aldrich	sigma-aldrich	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	was	be	VBD	_	_	_
23	added	add	VBN	_	_	_
24	.	.	.	_	_	_

1	Immunoprecipitation	immunoprecipitation	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	for	for	IN	_	_	_
5	1.5-2	1.5-2	CD	_	_	_
6	hours	hour	NNS	_	_	_
7	at	at	IN	_	_	_
8	room	room	NN	_	_	_
9	temperature	temperature	NN	_	_	_
10	with	with	IN	_	_	_
11	moderate	moderate	JJ	_	_	_
12	mixing	mix	VBG	_	_	_
13	,	,	,	_	_	_
14	then	then	RB	_	_	_
15	affinity	affinity	NN	_	_	_
16	gel	gel	NN	_	_	_
17	was	be	VBD	_	_	_
18	washed	wash	VBN	_	_	_
19	4	4	CD	_	_	_
20	times	time	NNS	_	_	_
21	by	by	IN	_	_	_
22	repeating	repeat	VBG	_	_	_
23	steps	step	NNS	_	_	_
24	of	of	IN	_	_	_
25	centrifugation	centrifugation	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	1.5	1.5	CD	_	_	_
28	minute	minute	NN	_	_	_
29	,	,	,	_	_	_
30	1000xg	1000xg	NN	_	_	_
31	at	at	IN	_	_	_
32	room	room	NN	_	_	_
33	temperature	temperature	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	and	and	CC	_	_	_
36	resuspention	resuspention	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	x2	x2	NN	_	_	_
39	with	with	IN	_	_	_
40	1	1	CD	_	_	_
41	ml	ml	NN	_	_	_
42	of	of	IN	_	_	_
43	TESS	TESS	NNP	_	_	_
44	buffer	buffer	NN	_	_	_
45	,	,	,	_	_	_
46	x1	x1	NN	_	_	_
47	with	with	IN	_	_	_
48	1	1	CD	_	_	_
49	ml	ml	NN	_	_	_
50	of	of	IN	_	_	_
51	TES	tes	NN	_	_	_
52	buffer	buffer	NN	_	_	_
53	,	,	,	_	_	_
54	x1	x1	NN	_	_	_
55	with	with	IN	_	_	_
56	1	1	CD	_	_	_
57	ml	ml	NN	_	_	_
58	of	of	IN	_	_	_
59	TE	TE	NNP	_	_	_
60	buffer	buffer	NN	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	When	when	WRB	_	_	_
3	reaching	reach	VBG	_	_	_
4	the	the	DT	_	_	_
5	optical	optical	JJ	_	_	_
6	density	density	NN	_	_	_
7	indicated	indicate	VBD	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	OD600	od600	NN	_	_	_
10	=	=	JJ	_	_	_
11	0.6-0.8	0.6-0.8	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	the	the	DT	_	_	_
14	culture	culture	NN	_	_	_
15	was	be	VBD	_	_	_
16	bisected	bisect	VBN	_	_	_
17	and	and	CC	_	_	_
18	DNA	dna	NN	_	_	_
19	gyrase	gyrase	NN	_	_	_
20	poison	poison	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	ciprofloxacin	ciprofloxacin	NN	_	_	_
23	,	,	,	_	_	_
24	oxolinic	oxolinic	JJ	_	_	_
25	acid	acid	NN	_	_	_
26	or	or	CC	_	_	_
27	microcin	microcin	NN	_	_	_
28	B17	b17	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	was	be	VBD	_	_	_
31	added	add	VBN	_	_	_
32	to	to	TO	_	_	_
33	the	the	DT	_	_	_
34	first	first	JJ	_	_	_
35	half	half	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	+	+	CC	_	_	_
38	A	a	DT	_	_	_
39	samples	sample	NNS	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	,	,	,	_	_	_
42	while	while	IN	_	_	_
43	second	second	JJ	_	_	_
44	served	serve	VBD	_	_	_
45	as	as	IN	_	_	_
46	a	a	DT	_	_	_
47	control	control	NN	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	-	-	:	_	_	_
50	A	a	NN	_	_	_
51	samples	sample	NNS	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	After	after	IN	_	_	_
3	exposed	expose	VBN	_	_	_
4	under	under	IN	_	_	_
5	the	the	DT	_	_	_
6	red	red	JJ	_	_	_
7	light	light	NN	_	_	_
8	with	with	IN	_	_	_
9	a	a	DT	_	_	_
10	specific	specific	JJ	_	_	_
11	ON	ON	NNP	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	BW25113	bw25113	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	envz3600	envz3600	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	envz600	envz600	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	envz900	envz900	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	envzM1200	envzm1200	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	envzM2400	envzm2400	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	envzM3600	envzm3600	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	envzM600	envzm600	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	envzM900	envzm900	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Escherichia	escherichia	FW	Organism	_	_
32	coli	coli	FW	Organism	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	input	input	NN	_	_	_
35	signal	signal	NN	_	_	_
36	frequency	frequency	NN	_	_	_
37	:	:	:	_	_	_
38	1	1	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	In	in	IN	_	_	_
41	the	the	DT	_	_	_
42	15	15	CD	_	_	_
43	ml	ml	NN	_	_	_
44	centrifuge	centrifuge	NN	_	_	_
45	tube	tube	NN	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	Corning	Corning	NNP	_	_	_
48	,	,	,	_	_	_
49	430791	430791	CD	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	,	,	,	_	_	_
52	the	the	DT	_	_	_
53	overnight	overnight	JJ	_	_	_
54	culture	culture	NN	_	_	_
55	was	be	VBD	_	_	_
56	diluted	dilute	VBN	_	_	_
57	to	to	TO	_	_	_
58	2	2	CD	_	_	_
59	ml	ml	NN	_	_	_
60	in	in	IN	_	_	_
61	fresh	fresh	JJ	_	_	_
62	LB	lb	NN	MED	_	_
63	medium	medium	NN	MED	_	_
64	containing	contain	VBG	_	_	_
65	Ampicillin	ampicillin	NN	_	_	_
66	-LRB-	-lrb-	-LRB-	_	_	_
67	50	50	CD	_	_	_
68	ng	ng	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	PCA	pca	NN	_	_	_
71	analysis	analysis	NN	_	_	_
72	was	be	VBD	_	_	_
73	performed	perform	VBN	_	_	_
74	using	use	VBG	_	_	_
75	the	the	DT	_	_	_
76	top	top	JJ	_	_	_
77	500	500	CD	_	_	_
78	genes	gene	NNS	_	_	_
79	with	with	IN	_	_	_
80	the	the	DT	_	_	_
81	most	most	RBS	_	_	_
82	variations	variation	NNS	_	_	_
83	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	plasmid	plasmid	NN	_	_	_
3	:	:	:	_	_	_
4	pLCenvZM	plcenvzm	NN	_	_	_
5	,	,	,	_	_	_
6	pPCB	ppcb	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	mutation	mutation	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Plasmid	plasmid	NN	_	_	_
12	pLCenvZ	plcenvz	NN	_	_	_
13	or	or	CC	_	_	_
14	pLCenvZM	plcenvzm	NN	_	_	_
15	was	be	VBD	_	_	_
16	co-transformed	co-transform	VBN	_	_	_
17	with	with	IN	_	_	_
18	pPCB	ppcb	NN	_	_	_
19	into	into	IN	_	_	_
20	the	the	DT	_	_	_
21	competent	competent	JJ	_	_	_
22	cells	cell	NNS	_	_	_
23	of	of	IN	_	_	_
24	E.	e.	FW	_	_	_
25	coli	coli	FW	_	_	_
26	JW3367	jw3367	NN	_	_	_
27	and	and	CC	_	_	_
28	spread	spread	NN	_	_	_
29	on	on	IN	_	_	_
30	LB	LB	NNP	_	_	_
31	agar	agar	NN	_	_	_
32	plates	plate	NNS	_	_	_
33	containing	contain	VBG	_	_	_
34	Ampicillin	ampicillin	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	50	50	CD	_	_	_
37	ng	ng	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	plasmid	plasmid	NN	_	_	_
40	:	:	:	_	_	_
41	pLCenvZ	plcenvz	NN	_	_	_
42	,	,	,	_	_	_
43	pPCB	ppcb	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	wild	wild	JJ	_	_	_
46	type	type	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	Read	read	VB	_	_	_
50	counts	count	NNS	_	_	_
51	per	per	IN	_	_	_
52	gene	gene	NN	_	_	_
53	determined	determine	VBN	_	_	_
54	using	use	VBG	_	_	_
55	HTseq	htseq	NN	_	_	_
56	count	count	NN	_	_	_
57	before	before	IN	_	_	_
58	normalized	normalize	VBN	_	_	_
59	using	use	VBG	_	_	_
60	DESeq2	deseq2	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	RNA	rna	NN	_	_	_
63	libraries	library	NNS	_	_	_
64	were	be	VBD	_	_	_
65	prepared	prepare	VBN	_	_	_
66	for	for	IN	_	_	_
67	sequencing	sequencing	NN	_	_	_
68	using	use	VBG	_	_	_
69	standard	standard	JJ	_	_	_
70	Illumina	Illumina	NNP	_	_	_
71	protocols	protocol	NNS	_	_	_
72	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
73	RNA-Seq	RNA-Seq	NNP	_	_	_
74	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
75	Sequencing	sequencing	NN	_	_	_
76	reads	read	VBZ	_	_	_
77	were	be	VBD	_	_	_
78	mapped	map	VBN	_	_	_
79	to	to	TO	_	_	_
80	the	the	DT	_	_	_
81	E.	e.	FW	_	_	_
82	coli	coli	FW	_	_	_
83	genome	genome	NN	_	_	_
84	with	with	IN	_	_	_
85	bowtie2	bowtie2	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	strain	strain	NN	_	_	_
88	:	:	:	_	_	_
89	JW3367	jw3367	NN	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	Supplementary	supplementary	JJ	_	_	_
92	_	_	NN	_	_	_
93	files	file	NNS	_	_	_
94	_	_	IN	_	_	_
95	format	format	NN	_	_	_
96	_	_	NN	_	_	_
97	and	and	CC	_	_	_
98	_	_	NN	_	_	_
99	content	content	NN	_	_	_
100	:	:	:	_	_	_
101	The	the	DT	_	_	_
102	txt	txt	NN	_	_	_
103	file	file	NN	_	_	_
104	includes	include	VBZ	_	_	_
105	the	the	DT	_	_	_
106	gene	gene	NN	_	_	_
107	expression	expression	NN	_	_	_
108	profiles	profile	NNS	_	_	_
109	of	of	IN	_	_	_
110	all	all	PDT	_	_	_
111	the	the	DT	_	_	_
112	samples	sample	NNS	_	_	_
113	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	xlsx	xlsx	NN	_	_	_
3	file	file	NN	_	_	_
4	contains	contain	VBZ	_	_	_
5	the	the	DT	_	_	_
6	PC1	pc1	NN	_	_	_
7	and	and	CC	_	_	_
8	PC2	pc2	NN	_	_	_
9	values	value	NNS	_	_	_
10	of	of	IN	_	_	_
11	all	all	PDT	_	_	_
12	the	the	DT	_	_	_
13	samples	sample	NNS	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	BW25113	bw25113	NN	_	_	_
3	sdiA-empty	sdia-empty	JJ	_	_	_
4	vector	vector	NN	_	_	_
5	12h	12h	NN	_	_	_
6	biofilm	biofilm	NN	_	_	_
7	cells	cell	NNS	_	_	_
8	at	at	IN	_	_	_
9	30oC	30oC	NNP	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	BW25113	bw25113	NN	_	_	_
12	sdiA-SdiA1E11	sdia-sdia1e11	NN	_	_	_
13	12h	12h	NN	_	_	_
14	biofilm	biofilm	NN	_	_	_
15	cells	cell	NNS	_	_	_
16	at	at	IN	_	_	_
17	30oC	30oC	NNP	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	BW25113	bw25113	NN	_	_	_
20	sdiA-WTSdiA	sdia-wtsdia	NN	_	_	_
21	12h	12h	NN	_	_	_
22	biofilm	biofilm	NN	_	_	_
23	cells	cell	NNS	_	_	_
24	at	at	IN	_	_	_
25	30oC	30oC	NNP	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	Channel	Channel	NNP	_	_	_
28	1	1	CD	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	Escherichia	escherichia	FW	Organism	_	_
31	coli	coli	FW	Organism	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
33	MAS	mas	FW	_	_	_
34	5.0	5.0	CD	_	_	_
35	Expression	expression	NN	_	_	_
36	Analysis	analysis	NN	_	_	_
37	Default	Default	NNP	_	_	_
38	Setting	set	VBG	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	mutant	mutant	JJ	_	_	_
41	SdiA1E11	sdia1e11	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	RNA	rna	NN	_	_	_
44	extracted	extract	VBN	_	_	_
45	from	from	IN	_	_	_
46	biofilm	biofilm	NN	_	_	_
47	cells	cell	NNS	_	_	_
48	of	of	IN	_	_	_
49	K-12	k-12	NN	_	_	_
50	sdiA-no	sdia-no	JJ	_	_	_
51	SdiA	sdia	NN	TF	_	_
52	1	1	CD	_	_	_
53	after	after	IN	_	_	_
54	12h	12h	NN	_	_	_
55	of	of	IN	_	_	_
56	growth	growth	NN	_	_	_
57	in	in	IN	_	_	_
58	LB	lb	NN	_	_	_
59	+	+	CC	_	_	_
60	1	1	CD	_	_	_
61	mMIPTG	mmiptg	NN	_	_	_
62	and	and	CC	_	_	_
63	30	30	CD	_	_	_
64	microM	microm	NN	_	_	_
65	Cm	cm	NN	_	_	_
66	with	with	IN	_	_	_
67	glass	glass	NN	_	_	_
68	wool	wool	NN	_	_	_
69	at	at	IN	_	_	_
70	30oC	30oC	NNP	_	_	_
71	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
72	RNA	RNA	NNP	_	_	_
73	extracted	extract	VBN	_	_	_
74	from	from	IN	_	_	_
75	biofilm	biofilm	NN	_	_	_
76	cells	cell	NNS	_	_	_
77	of	of	IN	_	_	_
78	K-12	k-12	NN	_	_	_
79	sdiA-SdiA1E11	sdia-sdia1e11	NN	_	_	_
80	after	after	IN	_	_	_
81	12h	12h	NN	_	_	_
82	of	of	IN	_	_	_
83	growth	growth	NN	_	_	_
84	in	in	IN	_	_	_
85	LB	lb	NN	_	_	_
86	+	+	CC	_	_	_
87	1	1	CD	_	_	_
88	mMIPTG	mmiptg	NN	_	_	_
89	and	and	CC	_	_	_
90	30	30	CD	_	_	_
91	microM	microm	NN	_	_	_
92	Cm	cm	NN	_	_	_
93	with	with	IN	_	_	_
94	glass	glass	NN	_	_	_
95	wool	wool	NN	_	_	_
96	at	at	IN	_	_	_
97	30oC	30oC	NNP	_	_	_
98	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
99	RNA	RNA	NNP	_	_	_
100	extracted	extract	VBN	_	_	_
101	from	from	IN	_	_	_
102	biofilm	biofilm	NN	_	_	_
103	cells	cell	NNS	_	_	_
104	of	of	IN	_	_	_
105	K-12	k-12	NN	_	_	_
106	sdiA-WTSdiA	sdia-wtsdia	NN	_	_	_
107	after	after	IN	_	_	_
108	12h	12h	NN	_	_	_
109	of	of	IN	_	_	_
110	growth	growth	NN	_	_	_
111	in	in	IN	_	_	_
112	LB	lb	NN	_	_	_
113	+	+	CC	_	_	_
114	1	1	CD	_	_	_
115	mMIPTG	mmiptg	NN	_	_	_
116	and	and	CC	_	_	_
117	30	30	CD	_	_	_
118	microM	microm	NN	_	_	_
119	Cm	cm	NN	_	_	_
120	with	with	IN	_	_	_
121	glass	glass	NN	_	_	_
122	wool	wool	NN	_	_	_
123	at	at	IN	_	_	_
124	30oC	30oC	NNP	_	_	_
125	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
126	To	to	TO	_	_	_
127	lyse	lyse	VB	_	_	_
128	the	the	DT	_	_	_
129	cells	cell	NNS	_	_	_
130	,	,	,	_	_	_
131	1.0	1.0	CD	_	_	_
132	mL	ml	NN	_	_	_
133	RLT	rlt	NN	_	_	_
134	buffer	buffer	NN	_	_	_
135	-LRB-	-lrb-	-LRB-	_	_	_
136	Qiagen	Qiagen	NNP	_	_	_
137	,	,	,	_	_	_
138	Inc.	Inc.	NNP	_	_	_
139	,	,	,	_	_	_
140	Valencia	Valencia	NNP	_	_	_
141	,	,	,	_	_	_
142	CA	CA	NNP	_	_	_
143	-RRB-	-rrb-	-RRB-	_	_	_
144	and	and	CC	_	_	_
145	0.2	0.2	CD	_	_	_
146	mL	ml	NN	_	_	_
147	0.1	0.1	CD	_	_	_
148	mm	mm	NN	_	_	_
149	zirconia	zirconia	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	wild	wild	JJ	_	_	_
152	type	type	NN	_	_	_
153	SdiA	sdia	NN	TF	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	After	after	IN	_	_	_
156	50	50	CD	_	_	_
157	hours	hour	NNS	_	_	_
158	,	,	,	_	_	_
159	samples	sample	NNS	_	_	_
160	-LRB-	-lrb-	-LRB-	_	_	_
161	10	10	CD	_	_	_
162	ml	ml	NN	_	_	_
163	-RRB-	-rrb-	-RRB-	_	_	_
164	were	be	VBD	_	_	_
165	harvested	harvest	VBN	_	_	_
166	directly	directly	RB	_	_	_
167	into	into	IN	_	_	_
168	RNA	rna	NN	_	_	_
169	Protect	protect	VB	_	_	_
170	-LRB-	-lrb-	-LRB-	_	_	_
171	Qiagen	Qiagen	NNP	_	_	_
172	-RRB-	-rrb-	-RRB-	_	_	_
173	to	to	TO	_	_	_
174	stabilize	stabilize	VB	_	_	_
175	RNA	rna	NN	_	_	_
176	,	,	,	_	_	_
177	and	and	CC	_	_	_
178	total	total	JJ	_	_	_
179	RNA	rna	NN	_	_	_
180	was	be	VBD	_	_	_
181	purified	purify	VBN	_	_	_
182	using	use	VBG	_	_	_
183	Qiagen	Qiagen	NNP	_	_	_
184	's	's	POS	_	_	_
185	RNeasy	RNeasy	NNP	_	_	_
186	Mini	Mini	NNP	_	_	_
187	kit	kit	NN	_	_	_
188	as	as	IN	_	_	_
189	recommended	recommend	VBN	_	_	_
190	by	by	IN	_	_	_
191	the	the	DT	_	_	_
192	suppliers	supplier	NNS	_	_	_
193	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	quantified	quantify	VBN	_	_	_
4	using	use	VBG	_	_	_
5	a	a	DT	_	_	_
6	BioPhotometer	biophotometer	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Eppendorf	eppendorf	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Spots	spot	NNS	_	_	_
6	automatically	automatically	RB	_	_	_
7	flagged	flag	VBD	_	_	_
8	as	as	IN	_	_	_
9	bad	bad	JJ	_	_	_
10	,	,	,	_	_	_
11	negative	negative	JJ	_	_	_
12	or	or	CC	_	_	_
13	poor	poor	JJ	_	_	_
14	in	in	IN	_	_	_
15	the	the	DT	_	_	_
16	Imagene	imagene	NN	_	_	_
17	software	software	NN	_	_	_
18	were	be	VBD	_	_	_
19	removed	remove	VBN	_	_	_
20	before	before	IN	_	_	_
21	the	the	DT	_	_	_
22	statistical	statistical	JJ	_	_	_
23	analysis	analysis	NN	_	_	_
24	was	be	VBD	_	_	_
25	carried	carry	VBN	_	_	_
26	out	out	RP	_	_	_
27	in	in	IN	_	_	_
28	GeneSight	GeneSight	NNP	_	_	_
29	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	mean	mean	NN	_	_	_
3	values	value	NNS	_	_	_
4	from	from	IN	_	_	_
5	each	each	DT	_	_	_
6	channel	channel	NN	_	_	_
7	were	be	VBD	_	_	_
8	log2	log2	NN	_	_	_
9	transformed	transform	VBN	_	_	_
10	and	and	CC	_	_	_
11	normalised	normalise	VBN	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	Lowess	lowess	NN	_	_	_
15	method	method	NN	_	_	_
16	to	to	TO	_	_	_
17	remove	remove	VB	_	_	_
18	intensity-dependent	intensity-dependent	JJ	_	_	_
19	effects	effect	NNS	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	log2	log2	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	ratios	ratio	NNS	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	values	value	NNS	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	Cy3	cy3	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Steady-state	steady-state	JJ	_	_	_
5	continuously-cultured	continuously-cultured	JJ	_	_	_
6	control	control	NN	_	_	_
7	samples	sample	NNS	_	_	_
8	in	in	IN	_	_	_
9	the	the	DT	_	_	_
10	presence	presence	NN	_	_	_
11	of	of	IN	_	_	_
12	adequate	adequate	JJ	_	_	_
13	Zn	zn	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
15	Steady-state	steady-state	JJ	_	_	_
16	continuously-cultured	continuously-cultured	JJ	_	_	_
17	experiment	experiment	NN	_	_	_
18	samples	sample	NNS	_	_	_
19	in	in	IN	_	_	_
20	the	the	DT	_	_	_
21	total	total	JJ	_	_	_
22	absence	absence	NN	_	_	_
23	of	of	IN	_	_	_
24	Zn	zn	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
26	Steady-state	steady-state	JJ	_	_	_
27	continuously-cultured	continuously-cultured	JJ	_	_	_
28	experiment	experiment	NN	_	_	_
29	samples	sample	NNS	_	_	_
30	in	in	IN	_	_	_
31	total	total	JJ	_	_	_
32	absence	absence	NN	_	_	_
33	of	of	IN	_	_	_
34	Zn	zn	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
36	Steady-state	steady-state	JJ	_	_	_
37	continuously-cultured	continuously-cultured	JJ	_	_	_
38	MG1655	mg1655	NN	_	_	_
39	in	in	IN	_	_	_
40	the	the	DT	_	_	_
41	presence	presence	NN	_	_	_
42	of	of	IN	_	_	_
43	adequate	adequate	JJ	_	_	_
44	Zn	zn	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
46	Steady-state	steady-state	JJ	_	_	_
47	continuously-cultured	continuously-cultured	JJ	_	_	_
48	MG1655	mg1655	NN	_	_	_
49	in	in	IN	_	_	_
50	the	the	DT	_	_	_
51	total	total	JJ	_	_	_
52	absence	absence	NN	_	_	_
53	of	of	IN	_	_	_
54	Zn	zn	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	Transcriptional	transcriptional	JJ	_	_	_
57	profiling	profiling	NN	_	_	_
58	of	of	IN	_	_	_
59	Escherichia	escherichia	FW	Organism	_	_
60	coli	coli	FW	Organism	_	_
61	cultured	culture	VBN	_	_	_
62	under	under	IN	_	_	_
63	severe	severe	JJ	_	_	_
64	zinc	zinc	NN	_	_	_
65	limitation	limitation	NN	_	_	_
66	Chemostat	Chemostat	NNP	_	_	_
67	1A	1a	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	Transcriptional	transcriptional	JJ	_	_	_
70	profiling	profiling	NN	_	_	_
71	of	of	IN	_	_	_
72	Escherichia	escherichia	FW	Organism	_	_
73	coli	coli	FW	Organism	_	_
74	cultured	culture	VBN	_	_	_
75	under	under	IN	_	_	_
76	severe	severe	JJ	_	_	_
77	zinc	zinc	NN	_	_	_
78	limitation	limitation	NN	_	_	_
79	Chemostat	chemostat	NN	_	_	_
80	1B	1b	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	Transcriptional	transcriptional	JJ	_	_	_
83	profiling	profiling	NN	_	_	_
84	of	of	IN	_	_	_
85	Escherichia	escherichia	FW	Organism	_	_
86	coli	coli	FW	Organism	_	_
87	cultured	culture	VBN	_	_	_
88	under	under	IN	_	_	_
89	severe	severe	JJ	_	_	_
90	zinc	zinc	NN	_	_	_
91	limitation	limitation	NN	_	_	_
92	Chemostat	Chemostat	NNP	_	_	_
93	2A	2a	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	Transcriptional	transcriptional	JJ	_	_	_
96	profiling	profiling	NN	_	_	_
97	of	of	IN	_	_	_
98	Escherichia	escherichia	FW	Organism	_	_
99	coli	coli	FW	Organism	_	_
100	cultured	culture	VBN	_	_	_
101	under	under	IN	_	_	_
102	severe	severe	JJ	_	_	_
103	zinc	zinc	NN	_	_	_
104	limitation	limitation	NN	_	_	_
105	Chemostat	Chemostat	NNP	_	_	_
106	2B	2b	NN	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	Transcriptional	transcriptional	JJ	_	_	_
109	profiling	profiling	NN	_	_	_
110	of	of	IN	_	_	_
111	Escherichia	escherichia	FW	Organism	_	_
112	coli	coli	FW	Organism	_	_
113	cultured	culture	VBN	_	_	_
114	under	under	IN	_	_	_
115	severe	severe	JJ	_	_	_
116	zinc	zinc	NN	_	_	_
117	limitation	limitation	NN	_	_	_
118	Chemostat	Chemostat	NNP	_	_	_
119	3A	3a	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	Transcriptional	transcriptional	JJ	_	_	_
122	profiling	profiling	NN	_	_	_
123	of	of	IN	_	_	_
124	Escherichia	escherichia	FW	Organism	_	_
125	coli	coli	FW	Organism	_	_
126	cultured	culture	VBN	_	_	_
127	under	under	IN	_	_	_
128	severe	severe	JJ	_	_	_
129	zinc	zinc	NN	_	_	_
130	limitation	limitation	NN	_	_	_
131	Chemostat	Chemostat	NNP	_	_	_
132	3B	3b	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	1	1	CD	_	_	_
135	.	.	.	_	_	_

1	Holme	Holme	NNP	_	_	_
2	T	t	NN	_	_	_
3	,	,	,	_	_	_
4	Arvidson	Arvidson	NNP	_	_	_
5	S	S	NNP	_	_	_
6	,	,	,	_	_	_
7	Lindholm	Lindholm	NNP	_	_	_
8	B	B	NNP	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	Pavlu	Pavlu	NNP	_	_	_
12	B.	B.	NNP	_	_	_
13	1970	1970	CD	_	_	_
14	.	.	.	_	_	_

1	Enzymes	enzyme	NNS	_	_	_
2	:	:	:	_	_	_
3	Laboratory-scale	laboratory-scale	JJ	_	_	_
4	production	production	NN	_	_	_
5	.	.	.	_	_	_

1	Process	process	VB	_	_	_
2	Biochemistry	Biochemistry	NNP	_	_	_
3	62-66	62-66	CD	_	_	_
4	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	1	1	CD	_	_	_
3	.	.	.	_	_	_

1	Neubauer	Neubauer	NNP	_	_	_
2	,	,	,	_	_	_
3	A.	a.	NN	_	_	_
4	,	,	,	_	_	_
5	J.	J.	NNP	_	_	_
6	Soini	Soini	NNP	_	_	_
7	,	,	,	_	_	_
8	M.	M.	NNP	_	_	_
9	Bollok	Bollok	NNP	_	_	_
10	,	,	,	_	_	_
11	M.	M.	NNP	_	_	_
12	Zenker	Zenker	NNP	_	_	_
13	,	,	,	_	_	_
14	J.	J.	NNP	_	_	_
15	Sandqvist	Sandqvist	NNP	_	_	_
16	,	,	,	_	_	_
17	J.	J.	NNP	_	_	_
18	Myllyharju	Myllyharju	NNP	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	P.	P.	NNP	_	_	_
22	Neubauer	Neubauer	NNP	_	_	_
23	.	.	.	_	_	_

1	2007	2007	CD	_	_	_
2	.	.	.	_	_	_

1	Fermentation	fermentation	NN	_	_	_
2	process	process	NN	_	_	_
3	for	for	IN	_	_	_
4	tetrameric	tetrameric	JJ	_	_	_
5	human	human	JJ	_	_	_
6	collagen	collagen	NN	_	_	_
7	prolyl	prolyl	JJ	_	_	_
8	4-hydroxylase	4-hydroxylase	NN	_	_	_
9	in	in	IN	_	_	_
10	Escherichia	escherichia	FW	Organism	_	_
11	coli	coli	FW	Organism	_	_
12	:	:	:	_	_	_
13	improvement	improvement	NN	_	_	_
14	by	by	IN	_	_	_
15	gene	gene	NN	_	_	_
16	optimisation	optimisation	NN	_	_	_
17	of	of	IN	_	_	_
18	the	the	DT	_	_	_
19	PDI	PDI	NNP	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	E.coli	e.coli	NN	_	_	_
22	W3110	w3110	NN	_	_	_
23	,	,	,	_	_	_
24	15	15	CD	_	_	_
25	minutes	minute	NNS	_	_	_
26	after	after	IN	_	_	_
27	oxygen	oxygen	NN	_	_	_
28	downshift	downshift	NN	_	_	_
29	,	,	,	_	_	_
30	sample	sample	NN	_	_	_
31	S2	s2	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	E.coli	e.coli	NN	_	_	_
34	W3110	w3110	NN	_	_	_
35	,	,	,	_	_	_
36	15	15	CD	_	_	_
37	minutes	minute	NNS	_	_	_
38	before	before	IN	_	_	_
39	oxygen	oxygen	NN	_	_	_
40	downshift	downshift	NN	_	_	_
41	,	,	,	_	_	_
42	sample	sample	NN	_	_	_
43	S1	s1	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	E.coli	e.coli	NN	_	_	_
46	W3110	w3110	NN	_	_	_
47	,	,	,	_	_	_
48	45	45	CD	_	_	_
49	minutes	minute	NNS	_	_	_
50	after	after	IN	_	_	_
51	oxygen	oxygen	NN	_	_	_
52	downshift	downshift	NN	_	_	_
53	,	,	,	_	_	_
54	sample	sample	NN	_	_	_
55	S3	s3	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	E.coli	e.coli	NN	_	_	_
58	W3110	w3110	NN	_	_	_
59	,	,	,	_	_	_
60	75	75	CD	_	_	_
61	minutes	minute	NNS	_	_	_
62	after	after	IN	_	_	_
63	oxygen	oxygen	NN	_	_	_
64	downshift	downshift	NN	_	_	_
65	,	,	,	_	_	_
66	sample	sample	NN	_	_	_
67	S4	s4	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	E.coli	e.coli	NN	_	_	_
70	W3110	w3110	NN	_	_	_
71	,	,	,	_	_	_
72	fermentation	fermentation	NN	_	_	_
73	sample	sample	NN	_	_	_
74	taken	take	VBN	_	_	_
75	15	15	CD	_	_	_
76	minutes	minute	NNS	_	_	_
77	after	after	IN	_	_	_
78	oxygen	oxygen	NN	_	_	_
79	downshift	downshift	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	E.coli	e.coli	NN	_	_	_
82	W3110	w3110	NN	_	_	_
83	,	,	,	_	_	_
84	fermentation	fermentation	NN	_	_	_
85	sample	sample	NN	_	_	_
86	taken	take	VBN	_	_	_
87	15	15	CD	_	_	_
88	minutes	minute	NNS	_	_	_
89	before	before	IN	_	_	_
90	oxygen	oxygen	NN	_	_	_
91	downshift	downshift	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	E.coli	e.coli	NN	_	_	_
94	W3110	w3110	NN	_	_	_
95	,	,	,	_	_	_
96	fermentation	fermentation	NN	_	_	_
97	sample	sample	NN	_	_	_
98	taken	take	VBN	_	_	_
99	45	45	CD	_	_	_
100	minutes	minute	NNS	_	_	_
101	after	after	IN	_	_	_
102	oxygen	oxygen	NN	_	_	_
103	downshift	downshift	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	E.coli	e.coli	NN	_	_	_
106	W3110	w3110	NN	_	_	_
107	,	,	,	_	_	_
108	fermentation	fermentation	NN	_	_	_
109	sample	sample	NN	_	_	_
110	taken	take	VBN	_	_	_
111	75	75	CD	_	_	_
112	minutes	minute	NNS	_	_	_
113	after	after	IN	_	_	_
114	oxygen	oxygen	NN	_	_	_
115	downshift	downshift	NN	_	_	_
116	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
117	Escherichia	escherichia	FW	Organism	_	_
118	coli	coli	FW	Organism	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	GCOS	gcos	NN	_	_	_
121	1.0	1.0	CD	_	_	_
122	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
123	References	References	NNPS	_	_	_
124	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
125	References	References	NNPS	_	_	_
126	:	:	:	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
128	Samples	sample	NNS	_	_	_
129	for	for	IN	_	_	_
130	microarray	microarray	NN	_	_	_
131	analysis	analysis	NN	_	_	_
132	were	be	VBD	_	_	_
133	collected	collect	VBN	_	_	_
134	as	as	IN	_	_	_
135	described	describe	VBN	_	_	_
136	earlier	earlier	JJR	_	_	_
137	-LSB-	-lsb-	-LRB-	_	_	_
138	1	1	CD	_	_	_
139	-RSB-	-rsb-	-RRB-	_	_	_
140	,	,	,	_	_	_
141	-LRB-	-lrb-	-LRB-	_	_	_
142	Samples	sample	NNS	_	_	_
143	were	be	VBD	_	_	_
144	shortly	shortly	RB	_	_	_
145	mixed	mix	VBN	_	_	_
146	by	by	IN	_	_	_
147	vortexing	vortex	VBG	_	_	_
148	,	,	,	_	_	_
149	divided	divide	VBN	_	_	_
150	in	in	IN	_	_	_
151	0.5	0.5	CD	_	_	_
152	mL	ml	NN	_	_	_
153	aliquots	aliquot	NNS	_	_	_
154	and	and	CC	_	_	_
155	1	1	CD	_	_	_
156	.	.	.	_	_	_

1	centrifuged	centrifuge	VBN	_	_	_
2	for	for	IN	_	_	_
3	3	3	CD	_	_	_
4	min	min	NN	_	_	_
5	at	at	IN	_	_	_
6	16,100	16,100	CD	_	_	_
7	×	×	CD	_	_	_
8	g	g	NN	_	_	_
9	and	and	CC	_	_	_
10	+4	+4	NN	_	_	_
11	°C	°c	NN	_	_	_
12	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellets	pellet	NNS	_	_	_
3	were	be	VBD	_	_	_
4	resuspended	resuspend	VBN	_	_	_
5	in	in	IN	_	_	_
6	250	250	CD	_	_	_
7	µL	µl	NN	_	_	_
8	of	of	IN	_	_	_
9	RNALater	rnalater	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Ambion	Ambion	NNP	_	_	_
12	,	,	,	_	_	_
13	USA	USA	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	and	and	CC	_	_	_
16	stored	store	VBN	_	_	_
17	at	at	IN	_	_	_
18	-20	-20	CD	_	_	_
19	°C	°c	NN	_	_	_
20	until	until	IN	_	_	_
21	analysis	analysis	NN	_	_	_
22	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	extracted	extract	VBN	_	_	_
4	using	use	VBG	_	_	_
5	the	the	DT	_	_	_
6	total	total	JJ	_	_	_
7	RNA	rna	NN	_	_	_
8	kit	kit	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	A&A	A&A	NNP	_	_	_
11	Biotechnology	Biotechnology	NNP	_	_	_
12	,	,	,	_	_	_
13	Poland	Poland	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Strain	Strain	NNP	_	_	_
3	:	:	:	_	_	_
4	Escherichia	escherichia	FW	Organism	_	_
5	coli	coli	FW	Organism	_	_
6	W3110	w3110	NN	_	_	_
7	-LSB-	-lsb-	-LRB-	_	_	_
8	F	f	NN	_	_	_
9	--	--	:	_	_	_
10	IN	in	IN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	rrnD-rrnE	rrnd-rrne	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	1	1	CD	_	_	_
15	-RSB-	-rsb-	-RRB-	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
17	The	the	DT	_	_	_
18	cultivations	cultivation	NNS	_	_	_
19	were	be	VBD	_	_	_
20	performed	perform	VBN	_	_	_
21	in	in	IN	_	_	_
22	a	a	DT	_	_	_
23	Biostat	biostat	NN	_	_	_
24	C	c	NN	_	_	_
25	15	15	CD	_	_	_
26	L	l	NN	_	_	_
27	bioreactor	bioreactor	NN	_	_	_
28	with	with	IN	_	_	_
29	the	the	DT	_	_	_
30	DCU-3	dcu-3	NN	_	_	_
31	controlling	control	VBG	_	_	_
32	unit	unit	NN	_	_	_
33	and	and	CC	_	_	_
34	MFCS-win	mfcs-win	NN	_	_	_
35	supervisory	supervisory	JJ	_	_	_
36	system	system	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Sartorius	sartorius	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	with	with	IN	_	_	_
41	an	a	DT	_	_	_
42	initial	initial	JJ	_	_	_
43	working	work	VBG	_	_	_
44	volume	volume	NN	_	_	_
45	of	of	IN	_	_	_
46	8	8	CD	_	_	_
47	L	l	NN	_	_	_
48	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	mineral	mineral	NN	_	_	_
3	salt	salt	NN	_	_	_
4	medium	medium	NN	_	_	_
5	contained	contain	VBD	_	_	_
6	per	per	IN	_	_	_
7	liter	liter	NN	_	_	_
8	:	:	:	_	_	_
9	14.6	14.6	CD	_	_	_
10	g	g	NN	_	_	_
11	K2HPO4	k2hpo4	NN	_	_	_
12	,	,	,	_	_	_
13	3.6	3.6	CD	_	_	_
14	g	g	NN	_	_	_
15	NaH2PO4	nah2po4	NN	_	_	_
16	×	×	NN	_	_	_
17	2	2	CD	_	_	_
18	H2O	h2o	NN	_	_	_
19	,	,	,	_	_	_
20	2.0	2.0	CD	_	_	_
21	g	g	NN	_	_	_
22	Na2SO4	na2so4	NN	_	_	_
23	,	,	,	_	_	_
24	2.47	2.47	CD	_	_	_
25	g	g	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	NH4	nh4	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	2SO4	2so4	NN	_	_	_
30	,	,	,	_	_	_
31	0.5	0.5	CD	_	_	_
32	g	g	NN	_	_	_
33	NH4Cl	nh4cl	NN	_	_	_
34	,	,	,	_	_	_
35	1.0	1.0	CD	_	_	_
36	g	g	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	NH4	nh4	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	2-H-citrate	2-h-citrate	NN	_	_	_
41	,	,	,	_	_	_
42	2	2	CD	_	_	_
43	mM	mm	NN	KWSUPP	_	_
44	MgSO4	mgso4	NN	_	_	_
45	,	,	,	_	_	_
46	0.1	0.1	CD	_	_	_
47	g	g	NN	_	_	_
48	thiamine	thiamine	NN	SUPP	_	_
49	hydrochloride	hydrochloride	NN	SUPP	_	_
50	,	,	,	_	_	_
51	0.1	0.1	CD	_	_	_
52	mL	ml	NN	_	_	_
53	antifoam	antifoam	NN	_	_	_
54	204	204	CD	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	Sigma	Sigma	NNP	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	and	and	CC	_	_	_
59	2	2	CD	_	_	_
60	mL	ml	NN	_	_	_
61	trace	trace	NN	_	_	_
62	element	element	NN	_	_	_
63	solution	solution	NN	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	1	1	CD	_	_	_
66	-RRB-	-rrb-	-RRB-	_	_	_
67	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	initial	initial	JJ	_	_	_
3	glucose	glucose	NN	SUPP	_	_
4	concentration	concentration	NN	_	_	_
5	was	be	VBD	_	_	_
6	40	40	CD	_	_	_
7	g	g	NN	_	_	_
8	L-1	l-1	NN	_	_	_
9	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	feed	feed	NN	_	_	_
3	solution	solution	NN	_	_	_
4	contained	contain	VBD	_	_	_
5	650	650	CD	_	_	_
6	g	g	NN	_	_	_
7	L-1	l-1	NN	_	_	_
8	glucose	glucose	NN	SUPP	_	_
9	.	.	.	_	_	_

1	2	2	CD	_	_	_
2	mL	ml	NN	_	_	_
3	L-1	l-1	NN	_	_	_
4	of	of	IN	_	_	_
5	sterile	sterile	JJ	_	_	_
6	filtered	filter	VBN	_	_	_
7	1M	1m	NN	_	_	_
8	MgSO4	mgso4	NN	_	_	_
9	were	be	VBD	_	_	_
10	added	add	VBN	_	_	_
11	regularly	regularly	RB	_	_	_
12	per	per	IN	_	_	_
13	OD600	od600	NN	_	_	_
14	=	=	JJ	_	_	_
15	10	10	CD	_	_	_
16	increase	increase	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Two	two	CD	_	_	_
3	precultures	preculture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	in	in	IN	_	_	_
7	LB	lb	NN	MED	_	_
8	medium	medium	NN	MED	_	_
9	and	and	CC	_	_	_
10	mineral	mineral	NN	_	_	_
11	salt	salt	NN	_	_	_
12	medium	medium	NN	_	_	_
13	with	with	IN	_	_	_
14	10	10	CD	_	_	_
15	g	g	NN	_	_	_
16	L	l	NN	_	_	_
17	1	1	CD	_	_	_
18	of	of	IN	_	_	_
19	glucose	glucose	NN	SUPP	_	_
20	without	without	IN	_	_	_
21	antifoam	antifoam	JJ	_	_	_
22	agent	agent	NN	_	_	_
23	consecutively	consecutively	RB	_	_	_
24	at	at	IN	_	_	_
25	37	37	CD	_	_	_
26	°C	°c	NN	_	_	_
27	at	at	IN	_	_	_
28	a	a	DT	_	_	_
29	rotary	rotary	JJ	_	_	_
30	shaker	shaker	NN	_	_	_
31	at	at	IN	_	_	_
32	180	180	CD	_	_	_
33	rpm	rpm	NN	_	_	_
34	.	.	.	_	_	_

1	Main	Main	NNP	_	_	_
2	cultivations	cultivation	NNS	_	_	_
3	were	be	VBD	_	_	_
4	started	start	VBN	_	_	_
5	as	as	IN	_	_	_
6	batch	batch	NN	_	_	_
7	cultures	culture	NNS	_	_	_
8	at	at	IN	_	_	_
9	a	a	DT	_	_	_
10	temperature	temperature	NN	_	_	_
11	of	of	IN	_	_	_
12	37	37	CD	_	_	_
13	°C	°c	NN	_	_	_
14	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pH	ph	NN	_	_	_
3	was	be	VBD	_	_	_
4	kept	keep	VBN	_	_	_
5	at	at	IN	_	_	_
6	7.0	7.0	CD	_	_	_
7	by	by	IN	_	_	_
8	controlled	controlled	JJ	_	_	_
9	addition	addition	NN	_	_	_
10	of	of	IN	_	_	_
11	25	25	CD	_	_	_
12	%	%	NN	_	_	_
13	ammonia	ammonia	NN	_	_	_
14	solution	solution	NN	_	_	_
15	.	.	.	_	_	_

1	At	at	IN	_	_	_
2	the	the	DT	_	_	_
3	end	end	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	exponential	exponential	JJ	_	_	_
7	growth	growth	NN	_	_	_
8	phase	phase	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	cell	cell	NN	_	_	_
11	dry	dry	JJ	_	_	_
12	weight	weight	NN	_	_	_
13	about	about	IN	_	_	_
14	16	16	CD	_	_	_
15	g	g	NN	_	_	_
16	L-1	l-1	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	the	the	DT	_	_	_
19	stirrer	stirrer	NN	_	_	_
20	rate	rate	NN	_	_	_
21	was	be	VBD	_	_	_
22	lowered	lower	VBN	_	_	_
23	from	from	IN	_	_	_
24	1000	1000	CD	_	_	_
25	rpm	rpm	NN	_	_	_
26	to	to	TO	_	_	_
27	500	500	CD	_	_	_
28	rpm	rpm	NN	_	_	_
29	,	,	,	_	_	_
30	to	to	TO	_	_	_
31	provoke	provoke	VB	_	_	_
32	oxygen	oxygen	NN	_	_	_
33	limitation	limitation	NN	_	_	_
34	by	by	IN	_	_	_
35	decreased	decrease	VBN	_	_	_
36	oxygen	oxygen	NN	_	_	_
37	transfer	transfer	NN	_	_	_
38	.	.	.	_	_	_

1	Constant	constant	JJ	_	_	_
2	glucose	glucose	NN	SUPP	_	_
3	feed	feed	NN	_	_	_
4	of	of	IN	_	_	_
5	100	100	CD	_	_	_
6	g	g	NN	_	_	_
7	L-1	l-1	NN	_	_	_
8	h-1	h-1	NN	_	_	_
9	was	be	VBD	_	_	_
10	started	start	VBN	_	_	_
11	15	15	CD	_	_	_
12	min	min	NN	_	_	_
13	after	after	IN	_	_	_
14	the	the	DT	_	_	_
15	oxygen	oxygen	NN	_	_	_
16	drop	drop	NN	_	_	_
17	which	which	WDT	_	_	_
18	was	be	VBD	_	_	_
19	enough	enough	RB	_	_	_
20	to	to	TO	_	_	_
21	ensure	ensure	VB	_	_	_
22	glucose	glucose	NN	SUPP	_	_
23	excess	excess	NN	_	_	_
24	during	during	IN	_	_	_
25	the	the	DT	_	_	_
26	whole	whole	JJ	_	_	_
27	cultivation	cultivation	NN	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Background	background	NN	_	_	_
3	correction	correction	NN	_	_	_
4	,	,	,	_	_	_
5	normalization	normalization	NN	_	_	_
6	and	and	CC	_	_	_
7	calculation	calculation	NN	_	_	_
8	of	of	IN	_	_	_
9	the	the	DT	_	_	_
10	expression	expression	NN	_	_	_
11	measures	measure	NNS	_	_	_
12	were	be	VBD	_	_	_
13	performed	perform	VBN	_	_	_
14	using	use	VBG	_	_	_
15	RMA	RMA	NNP	_	_	_
16	procedure	procedure	NN	_	_	_
17	with	with	IN	_	_	_
18	the	the	DT	_	_	_
19	WebArray	WebArray	NNP	_	_	_
20	platform	platform	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	http	http	NN	_	_	_
23	:	:	:	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Cell	cell	NN	_	_	_
26	suspension	suspension	NN	_	_	_
27	was	be	VBD	_	_	_
28	ammended	ammend	VBN	_	_	_
29	with	with	IN	_	_	_
30	1.25	1.25	CD	_	_	_
31	M	m	NN	_	_	_
32	sucrose	sucrose	NN	_	_	_
33	to	to	TO	_	_	_
34	an	a	DT	_	_	_
35	osmotic	osmotic	JJ	_	_	_
36	pressure	pressure	NN	_	_	_
37	of	of	IN	_	_	_
38	2.7	2.7	CD	_	_	_
39	Os	os	NNS	_	_	_
40	kg-1	kg-1	NN	_	_	_
41	for	for	IN	_	_	_
42	10	10	CD	_	_	_
43	minutes	minute	NNS	_	_	_
44	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	biomass	biomass	NN	_	_	_
3	was	be	VBD	_	_	_
4	centrifuged	centrifuge	VBN	_	_	_
5	at	at	IN	_	_	_
6	4000	4000	CD	_	_	_
7	rpm	rpm	NN	_	_	_
8	and	and	CC	_	_	_
9	the	the	DT	_	_	_
10	pellet	pellet	NN	_	_	_
11	treated	treat	VBN	_	_	_
12	with	with	IN	_	_	_
13	RNAProtect	rnaprotect	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Qiagen	qiagen	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	following	follow	VBG	_	_	_
18	the	the	DT	_	_	_
19	manufacturer	manufacturer	NN	_	_	_
20	's	's	POS	_	_	_
21	protocol	protocol	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cell	cell	NN	_	_	_
3	suspension	suspension	NN	_	_	_
4	was	be	VBD	_	_	_
5	ammended	ammend	VBN	_	_	_
6	with	with	IN	_	_	_
7	1.37	1.37	CD	_	_	_
8	M	m	NN	_	_	_
9	NaCl	nacl	NN	_	_	_
10	to	to	TO	_	_	_
11	obtain	obtain	VB	_	_	_
12	an	a	DT	_	_	_
13	osmotic	osmotic	JJ	_	_	_
14	pressure	pressure	NN	_	_	_
15	of	of	IN	_	_	_
16	2.7	2.7	CD	_	_	_
17	Os	os	NNS	_	_	_
18	kg-1	kg-1	NN	_	_	_
19	for	for	IN	_	_	_
20	10	10	CD	_	_	_
21	minutes	minute	NNS	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	biomass	biomass	NN	_	_	_
3	was	be	VBD	_	_	_
4	centrifuged	centrifuge	VBN	_	_	_
5	at	at	IN	_	_	_
6	4000	4000	CD	_	_	_
7	rpm	rpm	NN	_	_	_
8	and	and	CC	_	_	_
9	the	the	DT	_	_	_
10	pellet	pellet	NN	_	_	_
11	treated	treat	VBN	_	_	_
12	with	with	IN	_	_	_
13	RNAProtect	rnaprotect	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Qiagen	qiagen	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	following	follow	VBG	_	_	_
18	the	the	DT	_	_	_
19	manufacturer	manufacturer	NN	_	_	_
20	's	's	POS	_	_	_
21	protocol	protocol	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	control	control	NN	_	_	_
5	,	,	,	_	_	_
6	biological	biological	JJ	_	_	_
7	replicate	replicate	VB	_	_	_
8	1	1	CD	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	E.	E.	NNP	_	_	_
11	coli	coli	NN	_	_	_
12	control	control	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	biological	biological	JJ	_	_	_
15	replicate	replicate	VBP	_	_	_
16	2	2	LS	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	E.	e.	FW	_	_	_
20	coli	coli	FW	_	_	_
21	Frag1	frag1	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	biological	biological	JJ	_	_	_
24	replicate	replicate	VBP	_	_	_
25	2	2	LS	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
28	E.	e.	FW	_	_	_
29	coli	coli	FW	_	_	_
30	Frag1	frag1	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	control	control	NN	_	_	_
33	sample	sample	NN	_	_	_
34	1	1	CD	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
37	E.	e.	FW	_	_	_
38	coli	coli	FW	_	_	_
39	Frag1	frag1	NN	_	_	_
40	,	,	,	_	_	_
41	hyperosmotic	hyperosmotic	JJ	_	_	_
42	NaCl	nacl	NN	_	_	_
43	treatment	treatment	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	biological	biological	JJ	_	_	_
46	replicate	replicate	VBP	_	_	_
47	1	1	LS	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	E.	e.	FW	_	_	_
51	coli	coli	FW	_	_	_
52	Frag1	frag1	NN	_	_	_
53	,	,	,	_	_	_
54	NaCl	nacl	NN	_	_	_
55	hyperosmotic	hyperosmotic	JJ	_	_	_
56	treatment	treatment	NN	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	biological	biological	JJ	_	_	_
59	replicate	replicate	VBP	_	_	_
60	2	2	LS	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	E.coli	e.coli	NN	_	_	_
64	Frag1	frag1	NN	_	_	_
65	,	,	,	_	_	_
66	sucrose	sucrose	NN	_	_	_
67	hyperosmotic	hyperosmotic	JJ	_	_	_
68	treatment	treatment	NN	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	biological	biological	JJ	_	_	_
71	replicate	replicate	VBP	_	_	_
72	1	1	LS	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
75	E.	e.	FW	_	_	_
76	coli	coli	FW	_	_	_
77	Frag1	frag1	NN	_	_	_
78	,	,	,	_	_	_
79	sucrose	sucrose	NN	_	_	_
80	hyperosmotic	hyperosmotic	JJ	_	_	_
81	treatment	treatment	NN	_	_	_
82	-LRB-	-lrb-	-LRB-	_	_	_
83	biological	biological	JJ	_	_	_
84	replicate	replicate	VBP	_	_	_
85	2	2	LS	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
88	E.	e.	FW	_	_	_
89	coli	coli	FW	_	_	_
90	NaCl	nacl	NN	_	_	_
91	hyperosmotic	hyperosmotic	JJ	_	_	_
92	treatment	treatment	NN	_	_	_
93	-LRB-	-lrb-	-LRB-	_	_	_
94	biological	biological	JJ	_	_	_
95	replicate	replicate	VBP	_	_	_
96	1	1	LS	_	_	_
97	-RRB-	-rrb-	-RRB-	_	_	_
98	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
99	E.	e.	FW	_	_	_
100	coli	coli	FW	_	_	_
101	NaCl	nacl	NN	_	_	_
102	hyperosmotic	hyperosmotic	JJ	_	_	_
103	treatment	treatment	NN	_	_	_
104	-LRB-	-lrb-	-LRB-	_	_	_
105	biological	biological	JJ	_	_	_
106	replicate	replicate	VBP	_	_	_
107	2	2	LS	_	_	_
108	-RRB-	-rrb-	-RRB-	_	_	_
109	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
110	E.	E.	NNP	_	_	_
111	coli	coli	NN	_	_	_
112	,	,	,	_	_	_
113	strain	strain	NN	_	_	_
114	Frag1	frag1	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	E.	e.	FW	_	_	_
117	coli	coli	FW	_	_	_
118	sucrose	sucrose	NN	_	_	_
119	hyperosmotic	hyperosmotic	JJ	_	_	_
120	treatment	treatment	NN	_	_	_
121	-LRB-	-lrb-	-LRB-	_	_	_
122	biological	biological	JJ	_	_	_
123	replicate	replicate	VBP	_	_	_
124	1	1	LS	_	_	_
125	-RRB-	-rrb-	-RRB-	_	_	_
126	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
127	E.	e.	FW	_	_	_
128	coli	coli	FW	_	_	_
129	sucrose	sucrose	NN	_	_	_
130	hyperosmotic	hyperosmotic	JJ	_	_	_
131	treatment	treatment	NN	_	_	_
132	-LRB-	-lrb-	-LRB-	_	_	_
133	biological	biological	JJ	_	_	_
134	replicate	replicate	VBP	_	_	_
135	2	2	LS	_	_	_
136	-RRB-	-rrb-	-RRB-	_	_	_
137	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
138	Escherichia	escherichia	FW	Organism	_	_
139	coli	coli	FW	Organism	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	Grown	grow	VBN	_	_	_
142	in	in	IN	_	_	_
143	Davis	Davis	NNP	_	_	_
144	's	's	POS	_	_	_
145	Mineral	Mineral	NNP	_	_	_
146	Salts	salt	NNS	_	_	_
147	medium	medium	NN	_	_	_
148	-LRB-	-lrb-	-LRB-	_	_	_
149	Gibco	Gibco	NNP	_	_	_
150	BRL	brl	NN	_	_	_
151	Life	Life	NNP	_	_	_
152	Technologies	Technologies	NNP	_	_	_
153	Inc.	Inc.	NNP	_	_	_
154	-RRB-	-rrb-	-RRB-	_	_	_
155	with	with	IN	_	_	_
156	0.1	0.1	CD	_	_	_
157	%	%	NN	_	_	_
158	D-glucose	d-glucose	NN	_	_	_
159	at	at	IN	_	_	_
160	25	25	CD	_	_	_
161	C	c	NN	_	_	_
162	-LRB-	-lrb-	-LRB-	_	_	_
163	100	100	CD	_	_	_
164	r.p.m.	r.p.m.	NN	_	_	_
165	shaking	shake	VBG	_	_	_
166	-RRB-	-rrb-	-RRB-	_	_	_
167	until	until	IN	_	_	_
168	an	a	DT	_	_	_
169	OD	od	NN	_	_	_
170	-LRB-	-lrb-	-LRB-	_	_	_
171	550	550	CD	_	_	_
172	nm	nm	NN	_	_	_
173	-RRB-	-rrb-	-RRB-	_	_	_
174	of	of	IN	_	_	_
175	0.6	0.6	CD	_	_	_
176	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	No	no	DT	_	_	_
3	treatment	treatment	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	control	control	NN	_	_	_
6	sample	sample	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	obtained	obtain	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	RNAeasy	rnaeasy	NN	_	_	_
8	MIDI	midi	NN	_	_	_
9	RNA	rna	NN	_	_	_
10	extraction	extraction	NN	_	_	_
11	kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Qiagen	qiagen	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	using	use	VBG	_	_	_
16	lysis	lysis	NN	_	_	_
17	buffer	buffer	NN	_	_	_
18	containing	contain	VBG	_	_	_
19	0.1	0.1	CD	_	_	_
20	%	%	NN	_	_	_
21	beta-mercaptoethanol	beta-mercaptoethanol	NN	_	_	_
22	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	extracted	extract	VBN	_	_	_
4	from	from	IN	_	_	_
5	lysates	lysate	NNS	_	_	_
6	and	and	CC	_	_	_
7	purified	purify	VBN	_	_	_
8	according	accord	VBG	_	_	_
9	to	to	TO	_	_	_
10	the	the	DT	_	_	_
11	manufacturer	manufacturer	NN	_	_	_
12	's	's	POS	_	_	_
13	standard	standard	JJ	_	_	_
14	protocol	protocol	NN	_	_	_
15	and	and	CC	_	_	_
16	subsequently	subsequently	RB	_	_	_
17	stored	store	VBN	_	_	_
18	at	at	IN	_	_	_
19	-80	-80	CD	_	_	_
20	°C	°c	NN	_	_	_
21	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	quality	quality	NN	_	_	_
3	was	be	VBD	_	_	_
4	assessed	assess	VBN	_	_	_
5	with	with	IN	_	_	_
6	electrophoresis	electrophoresis	NN	_	_	_
7	using	use	VBG	_	_	_
8	a	a	DT	_	_	_
9	RNA	rna	NN	_	_	_
10	bioanalyser	bioanalyser	NN	_	_	_
11	2100	2100	CD	_	_	_
12	and	and	CC	_	_	_
13	Lab	lab	NN	_	_	_
14	RNAChip	rnachip	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Agilent	Agilent	NNP	_	_	_
17	Technologies	Technologies	NNPS	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	before	before	IN	_	_	_
20	progression	progression	NN	_	_	_
21	to	to	TO	_	_	_
22	microarray	microarray	NN	_	_	_
23	hybridization	hybridization	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	15	15	CD	_	_	_
5	minute	minute	NN	_	_	_
6	5	5	CD	_	_	_
7	µM	µm	NN	_	_	_
8	cadmium	cadmium	NN	_	_	_
9	dye	dye	VB	_	_	_
10	swap	swap	NN	_	_	_
11	treatment	treatment	NN	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	E.	E.	NNP	_	_	_
14	coli	coli	NN	_	_	_
15	15	15	CD	_	_	_
16	minute	minute	NN	_	_	_
17	5	5	CD	_	_	_
18	µM	µm	NN	_	_	_
19	cadmium	cadmium	NN	_	_	_
20	treatment	treatment	NN	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	E.	E.	NNP	_	_	_
23	coli	coli	NN	_	_	_
24	15	15	CD	_	_	_
25	minute	minute	NN	_	_	_
26	pH	ph	NN	_	_	_
27	only	only	RB	_	_	_
28	dye	dye	VB	_	_	_
29	swap	swap	NN	_	_	_
30	treatment	treatment	NN	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	E.	E.	NNP	_	_	_
33	coli	coli	NN	_	_	_
34	15	15	CD	_	_	_
35	minute	minute	NN	_	_	_
36	pH	ph	NN	_	_	_
37	only	only	RB	_	_	_
38	treatment	treatment	NN	_	_	_
39	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
40	E.	E.	NNP	_	_	_
41	coli	coli	NN	_	_	_
42	,	,	,	_	_	_
43	15	15	CD	_	_	_
44	minutes	minute	NNS	_	_	_
45	,	,	,	_	_	_
46	5	5	CD	_	_	_
47	µM	µm	NN	_	_	_
48	cadmium	cadmium	NN	_	_	_
49	,	,	,	_	_	_
50	pH	ph	NN	_	_	_
51	5	5	CD	_	_	_
52	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
53	E.	E.	NNP	_	_	_
54	coli	coli	NN	_	_	_
55	,	,	,	_	_	_
56	15	15	CD	_	_	_
57	minutes	minute	NNS	_	_	_
58	,	,	,	_	_	_
59	5	5	CD	_	_	_
60	µM	µm	NN	_	_	_
61	cadmium	cadmium	NN	_	_	_
62	,	,	,	_	_	_
63	pH	ph	NN	_	_	_
64	7	7	CD	_	_	_
65	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
66	E.	E.	NNP	_	_	_
67	coli	coli	NN	_	_	_
68	,	,	,	_	_	_
69	15	15	CD	_	_	_
70	minutes	minute	NNS	_	_	_
71	,	,	,	_	_	_
72	no	no	DT	_	_	_
73	cadmium	cadmium	NN	_	_	_
74	,	,	,	_	_	_
75	pH	ph	NN	_	_	_
76	5	5	CD	_	_	_
77	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
78	E.	E.	NNP	_	_	_
79	coli	coli	NN	_	_	_
80	,	,	,	_	_	_
81	15	15	CD	_	_	_
82	minutes	minute	NNS	_	_	_
83	,	,	,	_	_	_
84	no	no	DT	_	_	_
85	cadmium	cadmium	NN	_	_	_
86	,	,	,	_	_	_
87	pH	ph	NN	_	_	_
88	7	7	CD	_	_	_
89	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
90	E.	E.	NNP	_	_	_
91	coli	coli	NN	_	_	_
92	5	5	CD	_	_	_
93	minute	minute	NN	_	_	_
94	5	5	CD	_	_	_
95	µM	µm	NN	_	_	_
96	cadmium	cadmium	NN	_	_	_
97	dye	dye	VB	_	_	_
98	swap	swap	NN	_	_	_
99	treatment	treatment	NN	_	_	_
100	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
101	E.	E.	NNP	_	_	_
102	coli	coli	NN	_	_	_
103	5	5	CD	_	_	_
104	minute	minute	NN	_	_	_
105	5	5	CD	_	_	_
106	µM	µm	NN	_	_	_
107	cadmium	cadmium	NN	_	_	_
108	treatment	treatment	NN	_	_	_
109	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
110	E.	E.	NNP	_	_	_
111	coli	coli	NN	_	_	_
112	5	5	CD	_	_	_
113	minute	minute	NN	_	_	_
114	pH	ph	NN	_	_	_
115	only	only	RB	_	_	_
116	dye	dye	VB	_	_	_
117	swap	swap	NN	_	_	_
118	treatment	treatment	NN	_	_	_
119	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
120	E.	E.	NNP	_	_	_
121	coli	coli	NN	_	_	_
122	5	5	CD	_	_	_
123	minute	minute	NN	_	_	_
124	pH	ph	NN	_	_	_
125	only	only	RB	_	_	_
126	treatment	treatment	NN	_	_	_
127	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
128	E.	E.	NNP	_	_	_
129	coli	coli	NN	_	_	_
130	,	,	,	_	_	_
131	5	5	CD	_	_	_
132	minutes	minute	NNS	_	_	_
133	,	,	,	_	_	_
134	5	5	CD	_	_	_
135	µM	µm	NN	_	_	_
136	cadmium	cadmium	NN	_	_	_
137	,	,	,	_	_	_
138	pH	ph	NN	_	_	_
139	5	5	CD	_	_	_
140	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
141	E.	E.	NNP	_	_	_
142	coli	coli	NN	_	_	_
143	,	,	,	_	_	_
144	5	5	CD	_	_	_
145	minutes	minute	NNS	_	_	_
146	,	,	,	_	_	_
147	5	5	CD	_	_	_
148	µM	µm	NN	_	_	_
149	cadmium	cadmium	NN	_	_	_
150	,	,	,	_	_	_
151	pH	ph	NN	_	_	_
152	7	7	CD	_	_	_
153	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
154	E.	E.	NNP	_	_	_
155	coli	coli	NN	_	_	_
156	,	,	,	_	_	_
157	5	5	CD	_	_	_
158	minutes	minute	NNS	_	_	_
159	,	,	,	_	_	_
160	no	no	DT	_	_	_
161	cadmium	cadmium	NN	_	_	_
162	,	,	,	_	_	_
163	pH	ph	NN	_	_	_
164	5	5	CD	_	_	_
165	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
166	E.	E.	NNP	_	_	_
167	coli	coli	NN	_	_	_
168	,	,	,	_	_	_
169	5	5	CD	_	_	_
170	minutes	minute	NNS	_	_	_
171	,	,	,	_	_	_
172	no	no	DT	_	_	_
173	cadmium	cadmium	NN	_	_	_
174	,	,	,	_	_	_
175	pH	ph	NN	_	_	_
176	7	7	CD	_	_	_
177	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
178	E.	E.	NNP	_	_	_
179	coli	coli	NN	_	_	_
180	was	be	VBD	_	_	_
181	grown	grow	VBN	_	_	_
182	in	in	IN	_	_	_
183	M9	m9	NN	_	_	_
184	medium	medium	NN	_	_	_
185	supplemented	supplement	VBN	_	_	_
186	with	with	IN	_	_	_
187	0.4	0.4	CD	_	_	_
188	%	%	NN	_	_	_
189	glucose	glucose	NN	SUPP	_	_
190	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	rotary	rotary	JJ	_	_	_
8	shaker	shaker	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	200	200	CD	_	_	_
11	rpm	rpm	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	until	until	IN	_	_	_
17	the	the	DT	_	_	_
18	contents	contents	NNS	_	_	_
19	of	of	IN	_	_	_
20	the	the	DT	_	_	_
21	flask	flask	NN	_	_	_
22	reached	reach	VBD	_	_	_
23	an	a	DT	_	_	_
24	OD600	od600	NN	_	_	_
25	of	of	IN	_	_	_
26	0.3	0.3	CD	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	mid-log	mid-log	JJ	_	_	_
29	phase	phase	NN	_	_	_
30	of	of	IN	_	_	_
31	growth	growth	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	divided	divide	VBN	_	_	_
5	into	into	IN	_	_	_
6	25	25	CD	_	_	_
7	mL	ml	NN	_	_	_
8	aliquots	aliquot	NNS	_	_	_
9	,	,	,	_	_	_
10	transferred	transfer	VBN	_	_	_
11	to	to	TO	_	_	_
12	50	50	CD	_	_	_
13	mL	ml	NN	_	_	_
14	conical	conical	JJ	_	_	_
15	tubes	tube	NNS	_	_	_
16	,	,	,	_	_	_
17	and	and	CC	_	_	_
18	centrifuged	centrifuge	VBD	_	_	_
19	at	at	IN	_	_	_
20	2540	2540	CD	_	_	_
21	x	x	CC	_	_	_
22	g	g	NN	_	_	_
23	for	for	IN	_	_	_
24	12	12	CD	_	_	_
25	minutes	minute	NNS	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	decanted	decant	VBN	_	_	_
5	,	,	,	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	cells	cell	NNS	_	_	_
9	were	be	VBD	_	_	_
10	resuspended	resuspend	VBN	_	_	_
11	in	in	IN	_	_	_
12	25	25	CD	_	_	_
13	mL	ml	NN	_	_	_
14	of	of	IN	_	_	_
15	M9	m9	NN	_	_	_
16	medium	medium	NN	_	_	_
17	at	at	IN	_	_	_
18	pH	ph	NN	_	_	_
19	7	7	CD	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	presence	presence	NN	_	_	_
23	of	of	IN	_	_	_
24	5.4	5.4	CD	_	_	_
25	µM	µm	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	1	1	CD	_	_	_
28	µg	µg	NN	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	E.	E.	NNP	_	_	_
31	coli	coli	NN	_	_	_
32	was	be	VBD	_	_	_
33	grown	grow	VBN	_	_	_
34	in	in	IN	_	_	_
35	M9	m9	NN	_	_	_
36	medium	medium	NN	_	_	_
37	supplemented	supplement	VBN	_	_	_
38	with	with	IN	_	_	_
39	0.4	0.4	CD	_	_	_
40	%	%	NN	_	_	_
41	glucose	glucose	NN	SUPP	_	_
42	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	rotary	rotary	JJ	_	_	_
8	shaker	shaker	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	200	200	CD	_	_	_
11	rpm	rpm	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	until	until	IN	_	_	_
17	the	the	DT	_	_	_
18	contents	contents	NNS	_	_	_
19	of	of	IN	_	_	_
20	the	the	DT	_	_	_
21	flask	flask	NN	_	_	_
22	reached	reach	VBD	_	_	_
23	an	a	DT	_	_	_
24	OD600	od600	NN	_	_	_
25	of	of	IN	_	_	_
26	0.3	0.3	CD	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	mid-log	mid-log	JJ	_	_	_
29	phase	phase	NN	_	_	_
30	of	of	IN	_	_	_
31	growth	growth	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	divided	divide	VBN	_	_	_
5	into	into	IN	_	_	_
6	25	25	CD	_	_	_
7	mL	ml	NN	_	_	_
8	aliquots	aliquot	NNS	_	_	_
9	,	,	,	_	_	_
10	transferred	transfer	VBN	_	_	_
11	to	to	TO	_	_	_
12	50	50	CD	_	_	_
13	mL	ml	NN	_	_	_
14	conical	conical	JJ	_	_	_
15	tubes	tube	NNS	_	_	_
16	,	,	,	_	_	_
17	and	and	CC	_	_	_
18	centrifuged	centrifuge	VBD	_	_	_
19	at	at	IN	_	_	_
20	2540	2540	CD	_	_	_
21	x	x	CC	_	_	_
22	g	g	NN	_	_	_
23	for	for	IN	_	_	_
24	12	12	CD	_	_	_
25	minutes	minute	NNS	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	decanted	decant	VBN	_	_	_
5	,	,	,	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	cells	cell	NNS	_	_	_
9	were	be	VBD	_	_	_
10	resuspended	resuspend	VBN	_	_	_
11	in	in	IN	_	_	_
12	25	25	CD	_	_	_
13	mL	ml	NN	_	_	_
14	of	of	IN	_	_	_
15	M9	m9	NN	_	_	_
16	medium	medium	NN	_	_	_
17	at	at	IN	_	_	_
18	pH	ph	NN	_	_	_
19	7	7	CD	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	incubated	incubate	VBN	_	_	_
5	at	at	IN	_	_	_
6	25	25	CD	_	_	_
7	°C	°c	NN	_	_	_
8	for	for	IN	_	_	_
9	15	15	CD	_	_	_
10	minutes	minute	NNS	_	_	_
11	with	with	IN	_	_	_
12	manual	manual	JJ	_	_	_
13	rotations	rotation	NNS	_	_	_
14	of	of	IN	_	_	_
15	the	the	DT	_	_	_
16	flasks	flask	NNS	_	_	_
17	once	once	RB	_	_	_
18	per	per	IN	_	_	_
19	minute	minute	NN	_	_	_
20	to	to	TO	_	_	_
21	resuspend	resuspend	VB	_	_	_
22	the	the	DT	_	_	_
23	cells	cell	NNS	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	was	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	M9	m9	NN	_	_	_
8	medium	medium	NN	_	_	_
9	supplemented	supplement	VBN	_	_	_
10	with	with	IN	_	_	_
11	0.4	0.4	CD	_	_	_
12	%	%	NN	_	_	_
13	glucose	glucose	NN	SUPP	_	_
14	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	rotary	rotary	JJ	_	_	_
8	shaker	shaker	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	200	200	CD	_	_	_
11	rpm	rpm	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	until	until	IN	_	_	_
17	the	the	DT	_	_	_
18	contents	contents	NNS	_	_	_
19	of	of	IN	_	_	_
20	the	the	DT	_	_	_
21	flask	flask	NN	_	_	_
22	reached	reach	VBD	_	_	_
23	an	a	DT	_	_	_
24	OD600	od600	NN	_	_	_
25	of	of	IN	_	_	_
26	0.3	0.3	CD	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	mid-log	mid-log	JJ	_	_	_
29	phase	phase	NN	_	_	_
30	of	of	IN	_	_	_
31	growth	growth	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	divided	divide	VBN	_	_	_
5	into	into	IN	_	_	_
6	25	25	CD	_	_	_
7	mL	ml	NN	_	_	_
8	aliquots	aliquot	NNS	_	_	_
9	,	,	,	_	_	_
10	transferred	transfer	VBN	_	_	_
11	to	to	TO	_	_	_
12	50	50	CD	_	_	_
13	mL	ml	NN	_	_	_
14	conical	conical	JJ	_	_	_
15	tubes	tube	NNS	_	_	_
16	,	,	,	_	_	_
17	and	and	CC	_	_	_
18	centrifuged	centrifuge	VBD	_	_	_
19	at	at	IN	_	_	_
20	2540	2540	CD	_	_	_
21	x	x	CC	_	_	_
22	g	g	NN	_	_	_
23	for	for	IN	_	_	_
24	12	12	CD	_	_	_
25	minutes	minute	NNS	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	decanted	decant	VBN	_	_	_
5	,	,	,	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	cells	cell	NNS	_	_	_
9	were	be	VBD	_	_	_
10	resuspended	resuspend	VBN	_	_	_
11	in	in	IN	_	_	_
12	25	25	CD	_	_	_
13	mL	ml	NN	_	_	_
14	of	of	IN	_	_	_
15	M9	m9	NN	_	_	_
16	medium	medium	NN	_	_	_
17	at	at	IN	_	_	_
18	pH	ph	NN	_	_	_
19	7	7	CD	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	incubated	incubate	VBN	_	_	_
5	at	at	IN	_	_	_
6	25	25	CD	_	_	_
7	°C	°c	NN	_	_	_
8	for	for	IN	_	_	_
9	5	5	CD	_	_	_
10	minutes	minute	NNS	_	_	_
11	with	with	IN	_	_	_
12	manual	manual	JJ	_	_	_
13	rotations	rotation	NNS	_	_	_
14	of	of	IN	_	_	_
15	the	the	DT	_	_	_
16	flasks	flask	NNS	_	_	_
17	once	once	RB	_	_	_
18	per	per	IN	_	_	_
19	minute	minute	NN	_	_	_
20	to	to	TO	_	_	_
21	resuspend	resuspend	VB	_	_	_
22	the	the	DT	_	_	_
23	cells	cell	NNS	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	was	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	M9	m9	NN	_	_	_
8	medium	medium	NN	_	_	_
9	supplemented	supplement	VBN	_	_	_
10	with	with	IN	_	_	_
11	0.4	0.4	CD	_	_	_
12	%	%	NN	_	_	_
13	glucose	glucose	NN	SUPP	_	_
14	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	rotary	rotary	JJ	_	_	_
8	shaker	shaker	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	200	200	CD	_	_	_
11	rpm	rpm	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	until	until	IN	_	_	_
17	the	the	DT	_	_	_
18	contents	contents	NNS	_	_	_
19	of	of	IN	_	_	_
20	the	the	DT	_	_	_
21	flask	flask	NN	_	_	_
22	reached	reach	VBD	_	_	_
23	an	a	DT	_	_	_
24	OD600	od600	NN	_	_	_
25	of	of	IN	_	_	_
26	0.3	0.3	CD	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	mid-log	mid-log	JJ	_	_	_
29	phase	phase	NN	_	_	_
30	of	of	IN	_	_	_
31	growth	growth	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	divided	divide	VBN	_	_	_
5	into	into	IN	_	_	_
6	25	25	CD	_	_	_
7	mL	ml	NN	_	_	_
8	aliquots	aliquot	NNS	_	_	_
9	,	,	,	_	_	_
10	transferred	transfer	VBN	_	_	_
11	to	to	TO	_	_	_
12	four	four	CD	_	_	_
13	50	50	CD	_	_	_
14	mL	ml	NN	_	_	_
15	conical	conical	JJ	_	_	_
16	tubes	tube	NNS	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	centrifuged	centrifuge	VBD	_	_	_
20	at	at	IN	_	_	_
21	2540	2540	CD	_	_	_
22	x	x	CC	_	_	_
23	g	g	NN	_	_	_
24	for	for	IN	_	_	_
25	12	12	CD	_	_	_
26	minutes	minute	NNS	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	decanted	decant	VBN	_	_	_
5	,	,	,	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	cells	cell	NNS	_	_	_
9	were	be	VBD	_	_	_
10	resuspended	resuspend	VBN	_	_	_
11	in	in	IN	_	_	_
12	25	25	CD	_	_	_
13	mL	ml	NN	_	_	_
14	of	of	IN	_	_	_
15	M9	m9	NN	_	_	_
16	medium	medium	NN	_	_	_
17	at	at	IN	_	_	_
18	pH	ph	NN	_	_	_
19	5	5	CD	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	presence	presence	NN	_	_	_
23	of	of	IN	_	_	_
24	5.4	5.4	CD	_	_	_
25	µM	µm	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	1	1	CD	_	_	_
28	µg	µg	NN	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	E.	E.	NNP	_	_	_
31	coli	coli	NN	_	_	_
32	was	be	VBD	_	_	_
33	grown	grow	VBN	_	_	_
34	in	in	IN	_	_	_
35	M9	m9	NN	_	_	_
36	medium	medium	NN	_	_	_
37	supplemented	supplement	VBN	_	_	_
38	with	with	IN	_	_	_
39	0.4	0.4	CD	_	_	_
40	%	%	NN	_	_	_
41	glucose	glucose	NN	SUPP	_	_
42	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	rotary	rotary	JJ	_	_	_
8	shaker	shaker	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	200	200	CD	_	_	_
11	rpm	rpm	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	until	until	IN	_	_	_
17	the	the	DT	_	_	_
18	contents	contents	NNS	_	_	_
19	of	of	IN	_	_	_
20	the	the	DT	_	_	_
21	flask	flask	NN	_	_	_
22	reached	reach	VBD	_	_	_
23	an	a	DT	_	_	_
24	OD600	od600	NN	_	_	_
25	of	of	IN	_	_	_
26	0.3	0.3	CD	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	mid-log	mid-log	JJ	_	_	_
29	phase	phase	NN	_	_	_
30	of	of	IN	_	_	_
31	growth	growth	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	divided	divide	VBN	_	_	_
5	into	into	IN	_	_	_
6	25	25	CD	_	_	_
7	mL	ml	NN	_	_	_
8	aliquots	aliquot	NNS	_	_	_
9	,	,	,	_	_	_
10	transferred	transfer	VBN	_	_	_
11	to	to	TO	_	_	_
12	four	four	CD	_	_	_
13	50	50	CD	_	_	_
14	mL	ml	NN	_	_	_
15	conical	conical	JJ	_	_	_
16	tubes	tube	NNS	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	centrifuged	centrifuge	VBD	_	_	_
20	at	at	IN	_	_	_
21	2540	2540	CD	_	_	_
22	x	x	CC	_	_	_
23	g	g	NN	_	_	_
24	for	for	IN	_	_	_
25	12	12	CD	_	_	_
26	minutes	minute	NNS	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	decanted	decant	VBN	_	_	_
5	,	,	,	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	cells	cell	NNS	_	_	_
9	were	be	VBD	_	_	_
10	resuspended	resuspend	VBN	_	_	_
11	in	in	IN	_	_	_
12	25	25	CD	_	_	_
13	mL	ml	NN	_	_	_
14	of	of	IN	_	_	_
15	M9	m9	NN	_	_	_
16	medium	medium	NN	_	_	_
17	at	at	IN	_	_	_
18	pH	ph	NN	_	_	_
19	5	5	CD	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	presence	presence	NN	_	_	_
23	of	of	IN	_	_	_
24	5.4	5.4	CD	_	_	_
25	µM	µm	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	1	1	CD	_	_	_
28	µg	µg	NN	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	E.	E.	NNP	_	_	_
31	coli	coli	NN	_	_	_
32	was	be	VBD	_	_	_
33	grown	grow	VBN	_	_	_
34	in	in	IN	_	_	_
35	M9	m9	NN	_	_	_
36	medium	medium	NN	_	_	_
37	supplemented	supplement	VBN	_	_	_
38	with	with	IN	_	_	_
39	0.4	0.4	CD	_	_	_
40	%	%	NN	_	_	_
41	glucose	glucose	NN	SUPP	_	_
42	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	rotary	rotary	JJ	_	_	_
8	shaker	shaker	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	200	200	CD	_	_	_
11	rpm	rpm	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	until	until	IN	_	_	_
17	the	the	DT	_	_	_
18	contents	contents	NNS	_	_	_
19	of	of	IN	_	_	_
20	the	the	DT	_	_	_
21	flask	flask	NN	_	_	_
22	reached	reach	VBD	_	_	_
23	an	a	DT	_	_	_
24	OD600	od600	NN	_	_	_
25	of	of	IN	_	_	_
26	0.3	0.3	CD	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	mid-log	mid-log	JJ	_	_	_
29	phase	phase	NN	_	_	_
30	of	of	IN	_	_	_
31	growth	growth	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	divided	divide	VBN	_	_	_
5	into	into	IN	_	_	_
6	25	25	CD	_	_	_
7	mL	ml	NN	_	_	_
8	aliquots	aliquot	NNS	_	_	_
9	,	,	,	_	_	_
10	transferred	transfer	VBN	_	_	_
11	to	to	TO	_	_	_
12	four	four	CD	_	_	_
13	50	50	CD	_	_	_
14	mL	ml	NN	_	_	_
15	conical	conical	JJ	_	_	_
16	tubes	tube	NNS	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	centrifuged	centrifuge	VBD	_	_	_
20	at	at	IN	_	_	_
21	2540	2540	CD	_	_	_
22	x	x	CC	_	_	_
23	g	g	NN	_	_	_
24	for	for	IN	_	_	_
25	12	12	CD	_	_	_
26	minutes	minute	NNS	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	decanted	decant	VBN	_	_	_
5	,	,	,	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	cells	cell	NNS	_	_	_
9	were	be	VBD	_	_	_
10	resuspended	resuspend	VBN	_	_	_
11	in	in	IN	_	_	_
12	25	25	CD	_	_	_
13	mL	ml	NN	_	_	_
14	of	of	IN	_	_	_
15	M9	m9	NN	_	_	_
16	medium	medium	NN	_	_	_
17	at	at	IN	_	_	_
18	pH	ph	NN	_	_	_
19	5	5	CD	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	incubated	incubate	VBN	_	_	_
5	at	at	IN	_	_	_
6	25	25	CD	_	_	_
7	°C	°c	NN	_	_	_
8	for	for	IN	_	_	_
9	15	15	CD	_	_	_
10	minutes	minute	NNS	_	_	_
11	with	with	IN	_	_	_
12	manual	manual	JJ	_	_	_
13	rotations	rotation	NNS	_	_	_
14	of	of	IN	_	_	_
15	the	the	DT	_	_	_
16	flasks	flask	NNS	_	_	_
17	once	once	RB	_	_	_
18	per	per	IN	_	_	_
19	minute	minute	NN	_	_	_
20	to	to	TO	_	_	_
21	resuspend	resuspend	VB	_	_	_
22	the	the	DT	_	_	_
23	cells	cell	NNS	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	was	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	M9	m9	NN	_	_	_
8	medium	medium	NN	_	_	_
9	supplemented	supplement	VBN	_	_	_
10	with	with	IN	_	_	_
11	0.4	0.4	CD	_	_	_
12	%	%	NN	_	_	_
13	glucose	glucose	NN	SUPP	_	_
14	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	rotary	rotary	JJ	_	_	_
8	shaker	shaker	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	200	200	CD	_	_	_
11	rpm	rpm	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	until	until	IN	_	_	_
17	the	the	DT	_	_	_
18	contents	contents	NNS	_	_	_
19	of	of	IN	_	_	_
20	the	the	DT	_	_	_
21	flask	flask	NN	_	_	_
22	reached	reach	VBD	_	_	_
23	an	a	DT	_	_	_
24	OD600	od600	NN	_	_	_
25	of	of	IN	_	_	_
26	0.3	0.3	CD	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	mid-log	mid-log	JJ	_	_	_
29	phase	phase	NN	_	_	_
30	of	of	IN	_	_	_
31	growth	growth	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	divided	divide	VBN	_	_	_
5	into	into	IN	_	_	_
6	25	25	CD	_	_	_
7	mL	ml	NN	_	_	_
8	aliquots	aliquot	NNS	_	_	_
9	,	,	,	_	_	_
10	transferred	transfer	VBN	_	_	_
11	to	to	TO	_	_	_
12	four	four	CD	_	_	_
13	50	50	CD	_	_	_
14	mL	ml	NN	_	_	_
15	conical	conical	JJ	_	_	_
16	tubes	tube	NNS	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	centrifuged	centrifuge	VBD	_	_	_
20	at	at	IN	_	_	_
21	2540	2540	CD	_	_	_
22	x	x	CC	_	_	_
23	g	g	NN	_	_	_
24	for	for	IN	_	_	_
25	12	12	CD	_	_	_
26	minutes	minute	NNS	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	decanted	decant	VBN	_	_	_
5	,	,	,	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	cells	cell	NNS	_	_	_
9	were	be	VBD	_	_	_
10	resuspended	resuspend	VBN	_	_	_
11	in	in	IN	_	_	_
12	25	25	CD	_	_	_
13	mL	ml	NN	_	_	_
14	of	of	IN	_	_	_
15	M9	m9	NN	_	_	_
16	medium	medium	NN	_	_	_
17	at	at	IN	_	_	_
18	pH	ph	NN	_	_	_
19	5	5	CD	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	incubated	incubate	VBN	_	_	_
5	at	at	IN	_	_	_
6	25	25	CD	_	_	_
7	°C	°c	NN	_	_	_
8	for	for	IN	_	_	_
9	5	5	CD	_	_	_
10	minutes	minute	NNS	_	_	_
11	with	with	IN	_	_	_
12	manual	manual	JJ	_	_	_
13	rotations	rotation	NNS	_	_	_
14	of	of	IN	_	_	_
15	the	the	DT	_	_	_
16	flasks	flask	NNS	_	_	_
17	once	once	RB	_	_	_
18	per	per	IN	_	_	_
19	minute	minute	NN	_	_	_
20	to	to	TO	_	_	_
21	resuspend	resuspend	VB	_	_	_
22	the	the	DT	_	_	_
23	cells	cell	NNS	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	was	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	M9	m9	NN	_	_	_
8	medium	medium	NN	_	_	_
9	supplemented	supplement	VBN	_	_	_
10	with	with	IN	_	_	_
11	0.4	0.4	CD	_	_	_
12	%	%	NN	_	_	_
13	glucose	glucose	NN	SUPP	_	_
14	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	rotary	rotary	JJ	_	_	_
8	shaker	shaker	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	200	200	CD	_	_	_
11	rpm	rpm	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	until	until	IN	_	_	_
17	the	the	DT	_	_	_
18	contents	contents	NNS	_	_	_
19	of	of	IN	_	_	_
20	the	the	DT	_	_	_
21	flask	flask	NN	_	_	_
22	reached	reach	VBD	_	_	_
23	an	a	DT	_	_	_
24	OD600	od600	NN	_	_	_
25	of	of	IN	_	_	_
26	0.3	0.3	CD	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	mid-log	mid-log	JJ	_	_	_
29	phase	phase	NN	_	_	_
30	of	of	IN	_	_	_
31	growth	growth	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	divided	divide	VBN	_	_	_
5	into	into	IN	_	_	_
6	25	25	CD	_	_	_
7	mL	ml	NN	_	_	_
8	aliquots	aliquot	NNS	_	_	_
9	,	,	,	_	_	_
10	transferred	transfer	VBN	_	_	_
11	to	to	TO	_	_	_
12	four	four	CD	_	_	_
13	50	50	CD	_	_	_
14	mL	ml	NN	_	_	_
15	conical	conical	JJ	_	_	_
16	tubes	tube	NNS	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	centrifuged	centrifuge	VBD	_	_	_
20	at	at	IN	_	_	_
21	2540	2540	CD	_	_	_
22	x	x	CC	_	_	_
23	g	g	NN	_	_	_
24	for	for	IN	_	_	_
25	12	12	CD	_	_	_
26	minutes	minute	NNS	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	decanted	decant	VBN	_	_	_
5	,	,	,	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	cells	cell	NNS	_	_	_
9	were	be	VBD	_	_	_
10	resuspended	resuspend	VBN	_	_	_
11	in	in	IN	_	_	_
12	25	25	CD	_	_	_
13	mL	ml	NN	_	_	_
14	of	of	IN	_	_	_
15	M9	m9	NN	_	_	_
16	medium	medium	NN	_	_	_
17	at	at	IN	_	_	_
18	pH	ph	NN	_	_	_
19	7	7	CD	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	presence	presence	NN	_	_	_
23	of	of	IN	_	_	_
24	5.4	5.4	CD	_	_	_
25	µM	µm	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	1	1	CD	_	_	_
28	µg	µg	NN	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	E.	E.	NNP	_	_	_
31	coli	coli	NN	_	_	_
32	was	be	VBD	_	_	_
33	grown	grow	VBN	_	_	_
34	in	in	IN	_	_	_
35	M9	m9	NN	_	_	_
36	medium	medium	NN	_	_	_
37	supplemented	supplement	VBN	_	_	_
38	with	with	IN	_	_	_
39	0.4	0.4	CD	_	_	_
40	%	%	NN	_	_	_
41	glucose	glucose	NN	SUPP	_	_
42	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	rotary	rotary	JJ	_	_	_
8	shaker	shaker	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	200	200	CD	_	_	_
11	rpm	rpm	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	until	until	IN	_	_	_
17	the	the	DT	_	_	_
18	contents	contents	NNS	_	_	_
19	of	of	IN	_	_	_
20	the	the	DT	_	_	_
21	flask	flask	NN	_	_	_
22	reached	reach	VBD	_	_	_
23	an	a	DT	_	_	_
24	OD600	od600	NN	_	_	_
25	of	of	IN	_	_	_
26	0.3	0.3	CD	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	mid-log	mid-log	JJ	_	_	_
29	phase	phase	NN	_	_	_
30	of	of	IN	_	_	_
31	growth	growth	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	divided	divide	VBN	_	_	_
5	into	into	IN	_	_	_
6	25	25	CD	_	_	_
7	mL	ml	NN	_	_	_
8	aliquots	aliquot	NNS	_	_	_
9	,	,	,	_	_	_
10	transferred	transfer	VBN	_	_	_
11	to	to	TO	_	_	_
12	four	four	CD	_	_	_
13	50	50	CD	_	_	_
14	mL	ml	NN	_	_	_
15	conical	conical	JJ	_	_	_
16	tubes	tube	NNS	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	centrifuged	centrifuge	VBD	_	_	_
20	at	at	IN	_	_	_
21	2540	2540	CD	_	_	_
22	x	x	CC	_	_	_
23	g	g	NN	_	_	_
24	for	for	IN	_	_	_
25	12	12	CD	_	_	_
26	minutes	minute	NNS	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	decanted	decant	VBN	_	_	_
5	,	,	,	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	cells	cell	NNS	_	_	_
9	were	be	VBD	_	_	_
10	resuspended	resuspend	VBN	_	_	_
11	in	in	IN	_	_	_
12	25	25	CD	_	_	_
13	mL	ml	NN	_	_	_
14	of	of	IN	_	_	_
15	M9	m9	NN	_	_	_
16	medium	medium	NN	_	_	_
17	at	at	IN	_	_	_
18	pH	ph	NN	_	_	_
19	7	7	CD	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	presence	presence	NN	_	_	_
23	of	of	IN	_	_	_
24	5.4	5.4	CD	_	_	_
25	µM	µm	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	1	1	CD	_	_	_
28	µg	µg	NN	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	Escherichia	escherichia	FW	Organism	_	_
31	coli	coli	FW	Organism	_	_
32	str	str	FW	_	_	_
33	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	MG1655	mg1655	NN	_	_	_
4	strain	strain	NN	_	_	_
5	of	of	IN	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	K-12	k-12	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	RNA	rna	NN	_	_	_
11	was	be	VBD	_	_	_
12	extracted	extract	VBN	_	_	_
13	and	and	CC	_	_	_
14	purified	purify	VBN	_	_	_
15	using	use	VBG	_	_	_
16	a	a	DT	_	_	_
17	Masterpure	masterpure	NN	_	_	_
18	RNA	rna	NN	_	_	_
19	purification	purification	NN	_	_	_
20	kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Epicentre	Epicentre	NNP	_	_	_
23	Technologies	Technologies	NNPS	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	and	and	CC	_	_	_
6	purified	purify	VBN	_	_	_
7	using	use	VBG	_	_	_
8	a	a	DT	_	_	_
9	Masterpure	masterpure	NN	_	_	_
10	RNA	rna	NN	_	_	_
11	purification	purification	NN	_	_	_
12	kit	kit	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Epicentre	Epicentre	NNP	_	_	_
15	Technologies	Technologies	NNPS	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Spot	Spot	NNP	_	_	_
3	intensities	intensity	NNS	_	_	_
4	and	and	CC	_	_	_
5	locations	location	NNS	_	_	_
6	were	be	VBD	_	_	_
7	determined	determine	VBN	_	_	_
8	using	use	VBG	_	_	_
9	TIGR	TIGR	NNP	_	_	_
10	Spotfinder	Spotfinder	NNP	_	_	_
11	,	,	,	_	_	_
12	Version	Version	NNP	_	_	_
13	3.1.1	3.1.1	CD	_	_	_
14	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	subsequent	subsequent	JJ	_	_	_
3	analyses	analysis	NNS	_	_	_
4	were	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	ma-anova	ma-anova	JJ	_	_	_
9	package	package	NN	_	_	_
10	in	in	IN	_	_	_
11	the	the	DT	_	_	_
12	open-source	open-source	JJ	_	_	_
13	statistical	statistical	JJ	_	_	_
14	software	software	NN	_	_	_
15	package	package	NN	_	_	_
16	,	,	,	_	_	_
17	R	r	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	www.r-project.org	www.r-project.org	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	,	,	,	_	_	_
22	Version	Version	NNP	_	_	_
23	2.4.1	2.4.1	CD	_	_	_
24	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	data	datum	NNS	_	_	_
3	were	be	VBD	_	_	_
4	normalized	normalize	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	regional	regional	JJ	_	_	_
8	lowess	lowess	NN	_	_	_
9	method	method	NN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Spot	Spot	NNP	_	_	_
3	intensities	intensity	NNS	_	_	_
4	and	and	CC	_	_	_
5	locations	location	NNS	_	_	_
6	were	be	VBD	_	_	_
7	determined	determine	VBN	_	_	_
8	using	use	VBG	_	_	_
9	TIGR	TIGR	NNP	_	_	_
10	Spotfinder	Spotfinder	NNP	_	_	_
11	,	,	,	_	_	_
12	Version	Version	NNP	_	_	_
13	3.1.1	3.1.1	CD	_	_	_
14	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	subsequent	subsequent	JJ	_	_	_
3	analyses	analysis	NNS	_	_	_
4	were	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	ma-anova	ma-anova	JJ	_	_	_
9	package	package	NN	_	_	_
10	in	in	IN	_	_	_
11	the	the	DT	_	_	_
12	open-source	open-source	JJ	_	_	_
13	statistical	statistical	JJ	_	_	_
14	software	software	NN	_	_	_
15	package	package	NN	_	_	_
16	,	,	,	_	_	_
17	R	r	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	www.r-project.org	www.r-project.org	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	,	,	,	_	_	_
22	Version	Version	NNP	_	_	_
23	2.4.1	2.4.1	CD	_	_	_
24	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	data	datum	NNS	_	_	_
3	were	be	VBD	_	_	_
4	normalized	normalize	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	regional	regional	JJ	_	_	_
8	lowess	lowess	NN	_	_	_
9	method	method	NN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	corresponding	correspond	VBG	_	_	_
4	to	to	TO	_	_	_
5	10	10	CD	_	_	_
6	ml	ml	NN	_	_	_
7	culture	culture	NN	_	_	_
8	volume	volume	NN	_	_	_
9	were	be	VBD	_	_	_
10	harvested	harvest	VBN	_	_	_
11	at	at	IN	_	_	_
12	0	0	CD	_	_	_
13	hrs	hr	NNS	_	_	_
14	using	use	VBG	_	_	_
15	centrifugation	centrifugation	NN	_	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cell	cell	NN	_	_	_
3	pellet	pellet	NN	_	_	_
4	was	be	VBD	_	_	_
5	immediately	immediately	RB	_	_	_
6	resuspended	resuspend	VBN	_	_	_
7	in	in	IN	_	_	_
8	RNAlater	rnalater	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Ambion	Ambion	NNP	_	_	_
11	,	,	,	_	_	_
12	Austin	Austin	NNP	_	_	_
13	,	,	,	_	_	_
14	TX	TX	NNP	_	_	_
15	,	,	,	_	_	_
16	USA	USA	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	stored	store	VBN	_	_	_
20	at	at	IN	_	_	_
21	-20	-20	CD	_	_	_
22	°C	°c	NN	_	_	_
23	until	until	IN	_	_	_
24	further	further	JJ	_	_	_
25	processing	processing	NN	_	_	_
26	.	.	.	_	_	_

1	Prior	prior	RB	_	_	_
2	to	to	TO	_	_	_
3	RNA	rna	NN	_	_	_
4	extraction	extraction	NN	_	_	_
5	using	use	VBG	_	_	_
6	MasterPure	masterpure	NN	_	_	_
7	RNA	rna	NN	_	_	_
8	purification	purification	NN	_	_	_
9	kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Epicentre	Epicentre	NNP	_	_	_
12	,	,	,	_	_	_
13	Madison	Madison	NNP	_	_	_
14	,	,	,	_	_	_
15	WI	WI	NNP	_	_	_
16	,	,	,	_	_	_
17	USA	USA	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	the	the	DT	_	_	_
20	pellet	pellet	NN	_	_	_
21	was	be	VBD	_	_	_
22	washed	wash	VBN	_	_	_
23	in	in	IN	_	_	_
24	cold	cold	JJ	_	_	_
25	phosphate-buffered	phosphate-buffered	JJ	_	_	_
26	saline	saline	NN	_	_	_
27	to	to	TO	_	_	_
28	remove	remove	VB	_	_	_
29	RNAlater	rnalater	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	corresponding	correspond	VBG	_	_	_
4	to	to	TO	_	_	_
5	10	10	CD	_	_	_
6	ml	ml	NN	_	_	_
7	culture	culture	NN	_	_	_
8	volume	volume	NN	_	_	_
9	were	be	VBD	_	_	_
10	harvested	harvest	VBN	_	_	_
11	at	at	IN	_	_	_
12	1.5	1.5	CD	_	_	_
13	hrs	hr	NNS	_	_	_
14	after	after	IN	_	_	_
15	induction	induction	NN	_	_	_
16	with	with	IN	_	_	_
17	0.1	0.1	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	IPTG	iptg	NN	_	_	_
20	using	use	VBG	_	_	_
21	centrifugation	centrifugation	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cell	cell	NN	_	_	_
3	pellet	pellet	NN	_	_	_
4	was	be	VBD	_	_	_
5	immediately	immediately	RB	_	_	_
6	resuspended	resuspend	VBN	_	_	_
7	in	in	IN	_	_	_
8	RNAlater	rnalater	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Ambion	Ambion	NNP	_	_	_
11	,	,	,	_	_	_
12	Austin	Austin	NNP	_	_	_
13	,	,	,	_	_	_
14	TX	TX	NNP	_	_	_
15	,	,	,	_	_	_
16	USA	USA	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	stored	store	VBN	_	_	_
20	at	at	IN	_	_	_
21	-20	-20	CD	_	_	_
22	°C	°c	NN	_	_	_
23	until	until	IN	_	_	_
24	further	further	JJ	_	_	_
25	processing	processing	NN	_	_	_
26	.	.	.	_	_	_

1	Prior	prior	RB	_	_	_
2	to	to	TO	_	_	_
3	RNA	rna	NN	_	_	_
4	extraction	extraction	NN	_	_	_
5	using	use	VBG	_	_	_
6	MasterPure	masterpure	NN	_	_	_
7	RNA	rna	NN	_	_	_
8	purification	purification	NN	_	_	_
9	kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Epicentre	Epicentre	NNP	_	_	_
12	,	,	,	_	_	_
13	Madison	Madison	NNP	_	_	_
14	,	,	,	_	_	_
15	WI	WI	NNP	_	_	_
16	,	,	,	_	_	_
17	USA	USA	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	the	the	DT	_	_	_
20	pellet	pellet	NN	_	_	_
21	was	be	VBD	_	_	_
22	washed	wash	VBN	_	_	_
23	in	in	IN	_	_	_
24	cold	cold	JJ	_	_	_
25	phosphate-buffered	phosphate-buffered	JJ	_	_	_
26	saline	saline	NN	_	_	_
27	to	to	TO	_	_	_
28	remove	remove	VB	_	_	_
29	RNAlater	rnalater	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	corresponding	correspond	VBG	_	_	_
4	to	to	TO	_	_	_
5	10	10	CD	_	_	_
6	ml	ml	NN	_	_	_
7	culture	culture	NN	_	_	_
8	volume	volume	NN	_	_	_
9	were	be	VBD	_	_	_
10	harvested	harvest	VBN	_	_	_
11	at	at	IN	_	_	_
12	1.5	1.5	CD	_	_	_
13	hrs	hr	NNS	_	_	_
14	after	after	IN	_	_	_
15	induction	induction	NN	_	_	_
16	with	with	IN	_	_	_
17	0	0	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	IPTG	iptg	NN	_	_	_
20	using	use	VBG	_	_	_
21	centrifugation	centrifugation	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cell	cell	NN	_	_	_
3	pellet	pellet	NN	_	_	_
4	was	be	VBD	_	_	_
5	immediately	immediately	RB	_	_	_
6	resuspended	resuspend	VBN	_	_	_
7	in	in	IN	_	_	_
8	RNAlater	rnalater	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Ambion	Ambion	NNP	_	_	_
11	,	,	,	_	_	_
12	Austin	Austin	NNP	_	_	_
13	,	,	,	_	_	_
14	TX	TX	NNP	_	_	_
15	,	,	,	_	_	_
16	USA	USA	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	stored	store	VBN	_	_	_
20	at	at	IN	_	_	_
21	-20	-20	CD	_	_	_
22	°C	°c	NN	_	_	_
23	until	until	IN	_	_	_
24	further	further	JJ	_	_	_
25	processing	processing	NN	_	_	_
26	.	.	.	_	_	_

1	Prior	prior	RB	_	_	_
2	to	to	TO	_	_	_
3	RNA	rna	NN	_	_	_
4	extraction	extraction	NN	_	_	_
5	using	use	VBG	_	_	_
6	MasterPure	masterpure	NN	_	_	_
7	RNA	rna	NN	_	_	_
8	purification	purification	NN	_	_	_
9	kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Epicentre	Epicentre	NNP	_	_	_
12	,	,	,	_	_	_
13	Madison	Madison	NNP	_	_	_
14	,	,	,	_	_	_
15	WI	WI	NNP	_	_	_
16	,	,	,	_	_	_
17	USA	USA	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	the	the	DT	_	_	_
20	pellet	pellet	NN	_	_	_
21	was	be	VBD	_	_	_
22	washed	wash	VBN	_	_	_
23	in	in	IN	_	_	_
24	cold	cold	JJ	_	_	_
25	phosphate-buffered	phosphate-buffered	JJ	_	_	_
26	saline	saline	NN	_	_	_
27	to	to	TO	_	_	_
28	remove	remove	VB	_	_	_
29	RNAlater	rnalater	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	corresponding	correspond	VBG	_	_	_
4	to	to	TO	_	_	_
5	10	10	CD	_	_	_
6	ml	ml	NN	_	_	_
7	culture	culture	NN	_	_	_
8	volume	volume	NN	_	_	_
9	were	be	VBD	_	_	_
10	harvested	harvest	VBN	_	_	_
11	at	at	IN	_	_	_
12	1.5	1.5	CD	_	_	_
13	hrs	hr	NNS	_	_	_
14	after	after	IN	_	_	_
15	induction	induction	NN	_	_	_
16	with	with	IN	_	_	_
17	1.0	1.0	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	IPTG	iptg	NN	_	_	_
20	using	use	VBG	_	_	_
21	centrifugation	centrifugation	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cell	cell	NN	_	_	_
3	pellet	pellet	NN	_	_	_
4	was	be	VBD	_	_	_
5	immediately	immediately	RB	_	_	_
6	resuspended	resuspend	VBN	_	_	_
7	in	in	IN	_	_	_
8	RNAlater	rnalater	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Ambion	Ambion	NNP	_	_	_
11	,	,	,	_	_	_
12	Austin	Austin	NNP	_	_	_
13	,	,	,	_	_	_
14	TX	TX	NNP	_	_	_
15	,	,	,	_	_	_
16	USA	USA	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	stored	store	VBN	_	_	_
20	at	at	IN	_	_	_
21	-20	-20	CD	_	_	_
22	°C	°c	NN	_	_	_
23	until	until	IN	_	_	_
24	further	further	JJ	_	_	_
25	processing	processing	NN	_	_	_
26	.	.	.	_	_	_

1	Prior	prior	RB	_	_	_
2	to	to	TO	_	_	_
3	RNA	rna	NN	_	_	_
4	extraction	extraction	NN	_	_	_
5	using	use	VBG	_	_	_
6	MasterPure	masterpure	NN	_	_	_
7	RNA	rna	NN	_	_	_
8	purification	purification	NN	_	_	_
9	kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Epicentre	Epicentre	NNP	_	_	_
12	,	,	,	_	_	_
13	Madison	Madison	NNP	_	_	_
14	,	,	,	_	_	_
15	WI	WI	NNP	_	_	_
16	,	,	,	_	_	_
17	USA	USA	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	the	the	DT	_	_	_
20	pellet	pellet	NN	_	_	_
21	was	be	VBD	_	_	_
22	washed	wash	VBN	_	_	_
23	in	in	IN	_	_	_
24	cold	cold	JJ	_	_	_
25	phosphate-buffered	phosphate-buffered	JJ	_	_	_
26	saline	saline	NN	_	_	_
27	to	to	TO	_	_	_
28	remove	remove	VB	_	_	_
29	RNAlater	rnalater	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	corresponding	correspond	VBG	_	_	_
4	to	to	TO	_	_	_
5	10	10	CD	_	_	_
6	ml	ml	NN	_	_	_
7	culture	culture	NN	_	_	_
8	volume	volume	NN	_	_	_
9	were	be	VBD	_	_	_
10	harvested	harvest	VBN	_	_	_
11	at	at	IN	_	_	_
12	3.5	3.5	CD	_	_	_
13	hrs	hr	NNS	_	_	_
14	after	after	IN	_	_	_
15	induction	induction	NN	_	_	_
16	with	with	IN	_	_	_
17	0.1	0.1	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	IPTG	iptg	NN	_	_	_
20	using	use	VBG	_	_	_
21	centrifugation	centrifugation	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cell	cell	NN	_	_	_
3	pellet	pellet	NN	_	_	_
4	was	be	VBD	_	_	_
5	immediately	immediately	RB	_	_	_
6	resuspended	resuspend	VBN	_	_	_
7	in	in	IN	_	_	_
8	RNAlater	rnalater	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Ambion	Ambion	NNP	_	_	_
11	,	,	,	_	_	_
12	Austin	Austin	NNP	_	_	_
13	,	,	,	_	_	_
14	TX	TX	NNP	_	_	_
15	,	,	,	_	_	_
16	USA	USA	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	stored	store	VBN	_	_	_
20	at	at	IN	_	_	_
21	-20	-20	CD	_	_	_
22	°C	°c	NN	_	_	_
23	until	until	IN	_	_	_
24	further	further	JJ	_	_	_
25	processing	processing	NN	_	_	_
26	.	.	.	_	_	_

1	Prior	prior	RB	_	_	_
2	to	to	TO	_	_	_
3	RNA	rna	NN	_	_	_
4	extraction	extraction	NN	_	_	_
5	using	use	VBG	_	_	_
6	MasterPure	masterpure	NN	_	_	_
7	RNA	rna	NN	_	_	_
8	purification	purification	NN	_	_	_
9	kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Epicentre	Epicentre	NNP	_	_	_
12	,	,	,	_	_	_
13	Madison	Madison	NNP	_	_	_
14	,	,	,	_	_	_
15	WI	WI	NNP	_	_	_
16	,	,	,	_	_	_
17	USA	USA	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	the	the	DT	_	_	_
20	pellet	pellet	NN	_	_	_
21	was	be	VBD	_	_	_
22	washed	wash	VBN	_	_	_
23	in	in	IN	_	_	_
24	cold	cold	JJ	_	_	_
25	phosphate-buffered	phosphate-buffered	JJ	_	_	_
26	saline	saline	NN	_	_	_
27	to	to	TO	_	_	_
28	remove	remove	VB	_	_	_
29	RNAlater	rnalater	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	corresponding	correspond	VBG	_	_	_
4	to	to	TO	_	_	_
5	10	10	CD	_	_	_
6	ml	ml	NN	_	_	_
7	culture	culture	NN	_	_	_
8	volume	volume	NN	_	_	_
9	were	be	VBD	_	_	_
10	harvested	harvest	VBN	_	_	_
11	at	at	IN	_	_	_
12	3.5	3.5	CD	_	_	_
13	hrs	hr	NNS	_	_	_
14	after	after	IN	_	_	_
15	induction	induction	NN	_	_	_
16	with	with	IN	_	_	_
17	0	0	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	IPTG	iptg	NN	_	_	_
20	using	use	VBG	_	_	_
21	centrifugation	centrifugation	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cell	cell	NN	_	_	_
3	pellet	pellet	NN	_	_	_
4	was	be	VBD	_	_	_
5	immediately	immediately	RB	_	_	_
6	resuspended	resuspend	VBN	_	_	_
7	in	in	IN	_	_	_
8	RNAlater	rnalater	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Ambion	Ambion	NNP	_	_	_
11	,	,	,	_	_	_
12	Austin	Austin	NNP	_	_	_
13	,	,	,	_	_	_
14	TX	TX	NNP	_	_	_
15	,	,	,	_	_	_
16	USA	USA	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	stored	store	VBN	_	_	_
20	at	at	IN	_	_	_
21	-20	-20	CD	_	_	_
22	°C	°c	NN	_	_	_
23	until	until	IN	_	_	_
24	further	further	JJ	_	_	_
25	processing	processing	NN	_	_	_
26	.	.	.	_	_	_

1	Prior	prior	RB	_	_	_
2	to	to	TO	_	_	_
3	RNA	rna	NN	_	_	_
4	extraction	extraction	NN	_	_	_
5	using	use	VBG	_	_	_
6	MasterPure	masterpure	NN	_	_	_
7	RNA	rna	NN	_	_	_
8	purification	purification	NN	_	_	_
9	kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Epicentre	Epicentre	NNP	_	_	_
12	,	,	,	_	_	_
13	Madison	Madison	NNP	_	_	_
14	,	,	,	_	_	_
15	WI	WI	NNP	_	_	_
16	,	,	,	_	_	_
17	USA	USA	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	the	the	DT	_	_	_
20	pellet	pellet	NN	_	_	_
21	was	be	VBD	_	_	_
22	washed	wash	VBN	_	_	_
23	in	in	IN	_	_	_
24	cold	cold	JJ	_	_	_
25	phosphate-buffered	phosphate-buffered	JJ	_	_	_
26	saline	saline	NN	_	_	_
27	to	to	TO	_	_	_
28	remove	remove	VB	_	_	_
29	RNAlater	rnalater	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	corresponding	correspond	VBG	_	_	_
4	to	to	TO	_	_	_
5	10	10	CD	_	_	_
6	ml	ml	NN	_	_	_
7	culture	culture	NN	_	_	_
8	volume	volume	NN	_	_	_
9	were	be	VBD	_	_	_
10	harvested	harvest	VBN	_	_	_
11	at	at	IN	_	_	_
12	3.5	3.5	CD	_	_	_
13	hrs	hr	NNS	_	_	_
14	after	after	IN	_	_	_
15	induction	induction	NN	_	_	_
16	with	with	IN	_	_	_
17	1.0	1.0	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	IPTG	iptg	NN	_	_	_
20	using	use	VBG	_	_	_
21	centrifugation	centrifugation	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cell	cell	NN	_	_	_
3	pellet	pellet	NN	_	_	_
4	was	be	VBD	_	_	_
5	immediately	immediately	RB	_	_	_
6	resuspended	resuspend	VBN	_	_	_
7	in	in	IN	_	_	_
8	RNAlater	rnalater	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Ambion	Ambion	NNP	_	_	_
11	,	,	,	_	_	_
12	Austin	Austin	NNP	_	_	_
13	,	,	,	_	_	_
14	TX	TX	NNP	_	_	_
15	,	,	,	_	_	_
16	USA	USA	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	stored	store	VBN	_	_	_
20	at	at	IN	_	_	_
21	-20	-20	CD	_	_	_
22	°C	°c	NN	_	_	_
23	until	until	IN	_	_	_
24	further	further	JJ	_	_	_
25	processing	processing	NN	_	_	_
26	.	.	.	_	_	_

1	Prior	prior	RB	_	_	_
2	to	to	TO	_	_	_
3	RNA	rna	NN	_	_	_
4	extraction	extraction	NN	_	_	_
5	using	use	VBG	_	_	_
6	MasterPure	masterpure	NN	_	_	_
7	RNA	rna	NN	_	_	_
8	purification	purification	NN	_	_	_
9	kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Epicentre	Epicentre	NNP	_	_	_
12	,	,	,	_	_	_
13	Madison	Madison	NNP	_	_	_
14	,	,	,	_	_	_
15	WI	WI	NNP	_	_	_
16	,	,	,	_	_	_
17	USA	USA	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	the	the	DT	_	_	_
20	pellet	pellet	NN	_	_	_
21	was	be	VBD	_	_	_
22	washed	wash	VBN	_	_	_
23	in	in	IN	_	_	_
24	cold	cold	JJ	_	_	_
25	phosphate-buffered	phosphate-buffered	JJ	_	_	_
26	saline	saline	NN	_	_	_
27	to	to	TO	_	_	_
28	remove	remove	VB	_	_	_
29	RNAlater	rnalater	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	E.coli	e.coli	NN	_	_	_
3	cells	cell	NNS	_	_	_
4	at	at	IN	_	_	_
5	1.5	1.5	CD	_	_	_
6	hrs	hr	NNS	_	_	_
7	after	after	IN	_	_	_
8	addition	addition	NN	_	_	_
9	of	of	IN	_	_	_
10	high	high	JJ	_	_	_
11	IPTG	iptg	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	1.0	1.0	CD	_	_	_
14	mM	mm	NN	KWSUPP	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	,	,	,	_	_	_
17	biological	biological	JJ	_	_	_
18	rep1	rep1	NN	_	_	_
19	,	,	,	_	_	_
20	technical	technical	JJ	_	_	_
21	rep	rep	NN	GEN	_	_
22	1	1	CD	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	E.coli	e.coli	NN	_	_	_
25	cells	cell	NNS	_	_	_
26	at	at	IN	_	_	_
27	1.5	1.5	CD	_	_	_
28	hrs	hr	NNS	_	_	_
29	after	after	IN	_	_	_
30	addition	addition	NN	_	_	_
31	of	of	IN	_	_	_
32	high	high	JJ	_	_	_
33	IPTG	iptg	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	1.0	1.0	CD	_	_	_
36	mM	mm	NN	KWSUPP	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	,	,	,	_	_	_
39	biological	biological	JJ	_	_	_
40	rep1	rep1	NN	_	_	_
41	,	,	,	_	_	_
42	technical	technical	JJ	_	_	_
43	rep2	rep2	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	E.coli	e.coli	NN	_	_	_
46	cells	cell	NNS	_	_	_
47	at	at	IN	_	_	_
48	1.5	1.5	CD	_	_	_
49	hrs	hr	NNS	_	_	_
50	after	after	IN	_	_	_
51	addition	addition	NN	_	_	_
52	of	of	IN	_	_	_
53	high	high	JJ	_	_	_
54	IPTG	iptg	NN	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	1.0	1.0	CD	_	_	_
57	mM	mm	NN	KWSUPP	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	,	,	,	_	_	_
60	biological	biological	JJ	_	_	_
61	rep2	rep2	NN	_	_	_
62	,	,	,	_	_	_
63	technical	technical	JJ	_	_	_
64	rep	rep	NN	GEN	_	_
65	1	1	CD	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	E.coli	e.coli	NN	_	_	_
68	cells	cell	NNS	_	_	_
69	at	at	IN	_	_	_
70	1.5	1.5	CD	_	_	_
71	hrs	hr	NNS	_	_	_
72	after	after	IN	_	_	_
73	addition	addition	NN	_	_	_
74	of	of	IN	_	_	_
75	high	high	JJ	_	_	_
76	IPTG	iptg	NN	_	_	_
77	-LRB-	-lrb-	-LRB-	_	_	_
78	1.0	1.0	CD	_	_	_
79	mM	mm	NN	KWSUPP	_	_
80	-RRB-	-rrb-	-RRB-	_	_	_
81	,	,	,	_	_	_
82	biological	biological	JJ	_	_	_
83	rep2	rep2	NN	_	_	_
84	,	,	,	_	_	_
85	technical	technical	JJ	_	_	_
86	rep2	rep2	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	E.coli	e.coli	NN	_	_	_
89	cells	cell	NNS	_	_	_
90	at	at	IN	_	_	_
91	1.5	1.5	CD	_	_	_
92	hrs	hr	NNS	_	_	_
93	after	after	IN	_	_	_
94	addition	addition	NN	_	_	_
95	of	of	IN	_	_	_
96	low	low	JJ	_	_	_
97	IPTG	iptg	NN	_	_	_
98	-LRB-	-lrb-	-LRB-	_	_	_
99	0.1	0.1	CD	_	_	_
100	mM	mm	NN	KWSUPP	_	_
101	-RRB-	-rrb-	-RRB-	_	_	_
102	,	,	,	_	_	_
103	biological	biological	JJ	_	_	_
104	rep1	rep1	NN	_	_	_
105	,	,	,	_	_	_
106	technical	technical	JJ	_	_	_
107	rep	rep	NN	GEN	_	_
108	1	1	CD	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	E.coli	e.coli	NN	_	_	_
111	cells	cell	NNS	_	_	_
112	at	at	IN	_	_	_
113	1.5	1.5	CD	_	_	_
114	hrs	hr	NNS	_	_	_
115	after	after	IN	_	_	_
116	addition	addition	NN	_	_	_
117	of	of	IN	_	_	_
118	low	low	JJ	_	_	_
119	IPTG	iptg	NN	_	_	_
120	-LRB-	-lrb-	-LRB-	_	_	_
121	0.1	0.1	CD	_	_	_
122	mM	mm	NN	KWSUPP	_	_
123	-RRB-	-rrb-	-RRB-	_	_	_
124	,	,	,	_	_	_
125	biological	biological	JJ	_	_	_
126	rep1	rep1	NN	_	_	_
127	,	,	,	_	_	_
128	technical	technical	JJ	_	_	_
129	rep2	rep2	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	E.coli	e.coli	NN	_	_	_
132	cells	cell	NNS	_	_	_
133	at	at	IN	_	_	_
134	1.5	1.5	CD	_	_	_
135	hrs	hr	NNS	_	_	_
136	after	after	IN	_	_	_
137	addition	addition	NN	_	_	_
138	of	of	IN	_	_	_
139	low	low	JJ	_	_	_
140	IPTG	iptg	NN	_	_	_
141	-LRB-	-lrb-	-LRB-	_	_	_
142	0.1	0.1	CD	_	_	_
143	mM	mm	NN	KWSUPP	_	_
144	-RRB-	-rrb-	-RRB-	_	_	_
145	,	,	,	_	_	_
146	biological	biological	JJ	_	_	_
147	rep2	rep2	NN	_	_	_
148	,	,	,	_	_	_
149	technical	technical	JJ	_	_	_
150	rep	rep	NN	GEN	_	_
151	1	1	CD	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	E.coli	e.coli	NN	_	_	_
154	cells	cell	NNS	_	_	_
155	at	at	IN	_	_	_
156	1.5	1.5	CD	_	_	_
157	hrs	hr	NNS	_	_	_
158	after	after	IN	_	_	_
159	addition	addition	NN	_	_	_
160	of	of	IN	_	_	_
161	low	low	JJ	_	_	_
162	IPTG	iptg	NN	_	_	_
163	-LRB-	-lrb-	-LRB-	_	_	_
164	0.1	0.1	CD	_	_	_
165	mM	mm	NN	KWSUPP	_	_
166	-RRB-	-rrb-	-RRB-	_	_	_
167	,	,	,	_	_	_
168	biological	biological	JJ	_	_	_
169	rep2	rep2	NN	_	_	_
170	,	,	,	_	_	_
171	technical	technical	JJ	_	_	_
172	rep2	rep2	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	E.coli	e.coli	NN	_	_	_
175	cells	cell	NNS	_	_	_
176	at	at	IN	_	_	_
177	1.5	1.5	CD	_	_	_
178	hrs	hr	NNS	_	_	_
179	after	after	IN	_	_	_
180	addition	addition	NN	_	_	_
181	of	of	IN	_	_	_
182	no	no	DT	_	_	_
183	IPTG	iptg	NN	_	_	_
184	-LRB-	-lrb-	-LRB-	_	_	_
185	0	0	CD	_	_	_
186	mM	mm	NN	KWSUPP	_	_
187	-RRB-	-rrb-	-RRB-	_	_	_
188	,	,	,	_	_	_
189	biological	biological	JJ	_	_	_
190	rep1	rep1	NN	_	_	_
191	,	,	,	_	_	_
192	technical	technical	JJ	_	_	_
193	rep	rep	NN	GEN	_	_
194	1	1	CD	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	E.coli	e.coli	NN	_	_	_
197	cells	cell	NNS	_	_	_
198	at	at	IN	_	_	_
199	1.5	1.5	CD	_	_	_
200	hrs	hr	NNS	_	_	_
201	after	after	IN	_	_	_
202	addition	addition	NN	_	_	_
203	of	of	IN	_	_	_
204	no	no	DT	_	_	_
205	IPTG	iptg	NN	_	_	_
206	-LRB-	-lrb-	-LRB-	_	_	_
207	0	0	CD	_	_	_
208	mM	mm	NN	KWSUPP	_	_
209	-RRB-	-rrb-	-RRB-	_	_	_
210	,	,	,	_	_	_
211	biological	biological	JJ	_	_	_
212	rep1	rep1	NN	_	_	_
213	,	,	,	_	_	_
214	technical	technical	JJ	_	_	_
215	rep2	rep2	NN	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	E.coli	e.coli	NN	_	_	_
218	cells	cell	NNS	_	_	_
219	at	at	IN	_	_	_
220	1.5	1.5	CD	_	_	_
221	hrs	hr	NNS	_	_	_
222	after	after	IN	_	_	_
223	addition	addition	NN	_	_	_
224	of	of	IN	_	_	_
225	no	no	DT	_	_	_
226	IPTG	iptg	NN	_	_	_
227	-LRB-	-lrb-	-LRB-	_	_	_
228	0	0	CD	_	_	_
229	mM	mm	NN	KWSUPP	_	_
230	-RRB-	-rrb-	-RRB-	_	_	_
231	,	,	,	_	_	_
232	biological	biological	JJ	_	_	_
233	rep2	rep2	NN	_	_	_
234	,	,	,	_	_	_
235	technical	technical	JJ	_	_	_
236	rep	rep	NN	GEN	_	_
237	1	1	CD	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	E.coli	e.coli	NN	_	_	_
240	cells	cell	NNS	_	_	_
241	at	at	IN	_	_	_
242	1.5	1.5	CD	_	_	_
243	hrs	hr	NNS	_	_	_
244	after	after	IN	_	_	_
245	addition	addition	NN	_	_	_
246	of	of	IN	_	_	_
247	no	no	DT	_	_	_
248	IPTG	iptg	NN	_	_	_
249	-LRB-	-lrb-	-LRB-	_	_	_
250	0	0	CD	_	_	_
251	mM	mm	NN	KWSUPP	_	_
252	-RRB-	-rrb-	-RRB-	_	_	_
253	,	,	,	_	_	_
254	biological	biological	JJ	_	_	_
255	rep2	rep2	NN	_	_	_
256	,	,	,	_	_	_
257	technical	technical	JJ	_	_	_
258	rep2	rep2	NN	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	E.coli	e.coli	NN	_	_	_
261	cells	cell	NNS	_	_	_
262	at	at	IN	_	_	_
263	1.5	1.5	CD	_	_	_
264	hrs	hr	NNS	_	_	_
265	after	after	IN	_	_	_
266	induction	induction	NN	_	_	_
267	with	with	IN	_	_	_
268	0.1	0.1	CD	_	_	_
269	mM	mm	NN	KWSUPP	_	_
270	IPTG	iptg	NN	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	E.coli	e.coli	NN	_	_	_
273	cells	cell	NNS	_	_	_
274	at	at	IN	_	_	_
275	1.5	1.5	CD	_	_	_
276	hrs	hr	NNS	_	_	_
277	after	after	IN	_	_	_
278	induction	induction	NN	_	_	_
279	with	with	IN	_	_	_
280	0	0	CD	_	_	_
281	mM	mm	NN	KWSUPP	_	_
282	IPTG	iptg	NN	_	_	_
283	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
284	E.coli	e.coli	NN	_	_	_
285	cells	cell	NNS	_	_	_
286	at	at	IN	_	_	_
287	1.5	1.5	CD	_	_	_
288	hrs	hr	NNS	_	_	_
289	after	after	IN	_	_	_
290	induction	induction	NN	_	_	_
291	with	with	IN	_	_	_
292	1.0	1.0	CD	_	_	_
293	mM	mm	NN	KWSUPP	_	_
294	IPTG	iptg	NN	_	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	E.coli	e.coli	NN	_	_	_
297	cells	cell	NNS	_	_	_
298	at	at	IN	_	_	_
299	3.5	3.5	CD	_	_	_
300	hrs	hr	NNS	_	_	_
301	after	after	IN	_	_	_
302	addition	addition	NN	_	_	_
303	of	of	IN	_	_	_
304	high	high	JJ	_	_	_
305	IPTG	iptg	NN	_	_	_
306	-LRB-	-lrb-	-LRB-	_	_	_
307	1.0	1.0	CD	_	_	_
308	mM	mm	NN	KWSUPP	_	_
309	-RRB-	-rrb-	-RRB-	_	_	_
310	,	,	,	_	_	_
311	biological	biological	JJ	_	_	_
312	rep1	rep1	NN	_	_	_
313	,	,	,	_	_	_
314	technical	technical	JJ	_	_	_
315	rep	rep	NN	GEN	_	_
316	1	1	CD	_	_	_
317	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
318	E.coli	e.coli	NN	_	_	_
319	cells	cell	NNS	_	_	_
320	at	at	IN	_	_	_
321	3.5	3.5	CD	_	_	_
322	hrs	hr	NNS	_	_	_
323	after	after	IN	_	_	_
324	addition	addition	NN	_	_	_
325	of	of	IN	_	_	_
326	high	high	JJ	_	_	_
327	IPTG	iptg	NN	_	_	_
328	-LRB-	-lrb-	-LRB-	_	_	_
329	1.0	1.0	CD	_	_	_
330	mM	mm	NN	KWSUPP	_	_
331	-RRB-	-rrb-	-RRB-	_	_	_
332	,	,	,	_	_	_
333	biological	biological	JJ	_	_	_
334	rep1	rep1	NN	_	_	_
335	,	,	,	_	_	_
336	technical	technical	JJ	_	_	_
337	rep2	rep2	NN	_	_	_
338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
339	E.coli	e.coli	NN	_	_	_
340	cells	cell	NNS	_	_	_
341	at	at	IN	_	_	_
342	3.5	3.5	CD	_	_	_
343	hrs	hr	NNS	_	_	_
344	after	after	IN	_	_	_
345	addition	addition	NN	_	_	_
346	of	of	IN	_	_	_
347	high	high	JJ	_	_	_
348	IPTG	iptg	NN	_	_	_
349	-LRB-	-lrb-	-LRB-	_	_	_
350	1.0	1.0	CD	_	_	_
351	mM	mm	NN	KWSUPP	_	_
352	-RRB-	-rrb-	-RRB-	_	_	_
353	,	,	,	_	_	_
354	biological	biological	JJ	_	_	_
355	rep2	rep2	NN	_	_	_
356	,	,	,	_	_	_
357	technical	technical	JJ	_	_	_
358	rep	rep	NN	GEN	_	_
359	1	1	CD	_	_	_
360	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
361	E.coli	e.coli	NN	_	_	_
362	cells	cell	NNS	_	_	_
363	at	at	IN	_	_	_
364	3.5	3.5	CD	_	_	_
365	hrs	hr	NNS	_	_	_
366	after	after	IN	_	_	_
367	addition	addition	NN	_	_	_
368	of	of	IN	_	_	_
369	high	high	JJ	_	_	_
370	IPTG	iptg	NN	_	_	_
371	-LRB-	-lrb-	-LRB-	_	_	_
372	1.0	1.0	CD	_	_	_
373	mM	mm	NN	KWSUPP	_	_
374	-RRB-	-rrb-	-RRB-	_	_	_
375	,	,	,	_	_	_
376	biological	biological	JJ	_	_	_
377	rep2	rep2	NN	_	_	_
378	,	,	,	_	_	_
379	technical	technical	JJ	_	_	_
380	rep2	rep2	NN	_	_	_
381	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
382	E.coli	e.coli	NN	_	_	_
383	cells	cell	NNS	_	_	_
384	at	at	IN	_	_	_
385	3.5	3.5	CD	_	_	_
386	hrs	hr	NNS	_	_	_
387	after	after	IN	_	_	_
388	addition	addition	NN	_	_	_
389	of	of	IN	_	_	_
390	low	low	JJ	_	_	_
391	IPTG	iptg	NN	_	_	_
392	-LRB-	-lrb-	-LRB-	_	_	_
393	0.1	0.1	CD	_	_	_
394	mM	mm	NN	KWSUPP	_	_
395	-RRB-	-rrb-	-RRB-	_	_	_
396	,	,	,	_	_	_
397	biological	biological	JJ	_	_	_
398	rep1	rep1	NN	_	_	_
399	,	,	,	_	_	_
400	technical	technical	JJ	_	_	_
401	rep	rep	NN	GEN	_	_
402	1	1	CD	_	_	_
403	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
404	E.coli	e.coli	NN	_	_	_
405	cells	cell	NNS	_	_	_
406	at	at	IN	_	_	_
407	3.5	3.5	CD	_	_	_
408	hrs	hr	NNS	_	_	_
409	after	after	IN	_	_	_
410	addition	addition	NN	_	_	_
411	of	of	IN	_	_	_
412	low	low	JJ	_	_	_
413	IPTG	iptg	NN	_	_	_
414	-LRB-	-lrb-	-LRB-	_	_	_
415	0.1	0.1	CD	_	_	_
416	mM	mm	NN	KWSUPP	_	_
417	-RRB-	-rrb-	-RRB-	_	_	_
418	,	,	,	_	_	_
419	biological	biological	JJ	_	_	_
420	rep1	rep1	NN	_	_	_
421	,	,	,	_	_	_
422	technical	technical	JJ	_	_	_
423	rep2	rep2	NN	_	_	_
424	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
425	E.coli	e.coli	NN	_	_	_
426	cells	cell	NNS	_	_	_
427	at	at	IN	_	_	_
428	3.5	3.5	CD	_	_	_
429	hrs	hr	NNS	_	_	_
430	after	after	IN	_	_	_
431	addition	addition	NN	_	_	_
432	of	of	IN	_	_	_
433	low	low	JJ	_	_	_
434	IPTG	iptg	NN	_	_	_
435	-LRB-	-lrb-	-LRB-	_	_	_
436	0.1	0.1	CD	_	_	_
437	mM	mm	NN	KWSUPP	_	_
438	-RRB-	-rrb-	-RRB-	_	_	_
439	,	,	,	_	_	_
440	biological	biological	JJ	_	_	_
441	rep2	rep2	NN	_	_	_
442	,	,	,	_	_	_
443	technical	technical	JJ	_	_	_
444	rep	rep	NN	GEN	_	_
445	1	1	CD	_	_	_
446	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
447	E.coli	e.coli	NN	_	_	_
448	cells	cell	NNS	_	_	_
449	at	at	IN	_	_	_
450	3.5	3.5	CD	_	_	_
451	hrs	hr	NNS	_	_	_
452	after	after	IN	_	_	_
453	addition	addition	NN	_	_	_
454	of	of	IN	_	_	_
455	low	low	JJ	_	_	_
456	IPTG	iptg	NN	_	_	_
457	-LRB-	-lrb-	-LRB-	_	_	_
458	0.1	0.1	CD	_	_	_
459	mM	mm	NN	KWSUPP	_	_
460	-RRB-	-rrb-	-RRB-	_	_	_
461	,	,	,	_	_	_
462	biological	biological	JJ	_	_	_
463	rep2	rep2	NN	_	_	_
464	,	,	,	_	_	_
465	technical	technical	JJ	_	_	_
466	rep2	rep2	NN	_	_	_
467	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
468	E.coli	e.coli	NN	_	_	_
469	cells	cell	NNS	_	_	_
470	at	at	IN	_	_	_
471	3.5	3.5	CD	_	_	_
472	hrs	hr	NNS	_	_	_
473	after	after	IN	_	_	_
474	addition	addition	NN	_	_	_
475	of	of	IN	_	_	_
476	no	no	DT	_	_	_
477	IPTG	iptg	NN	_	_	_
478	-LRB-	-lrb-	-LRB-	_	_	_
479	0	0	CD	_	_	_
480	mM	mm	NN	KWSUPP	_	_
481	-RRB-	-rrb-	-RRB-	_	_	_
482	,	,	,	_	_	_
483	biological	biological	JJ	_	_	_
484	rep1	rep1	NN	_	_	_
485	,	,	,	_	_	_
486	technical	technical	JJ	_	_	_
487	rep	rep	NN	GEN	_	_
488	1	1	CD	_	_	_
489	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
490	E.coli	e.coli	NN	_	_	_
491	cells	cell	NNS	_	_	_
492	at	at	IN	_	_	_
493	3.5	3.5	CD	_	_	_
494	hrs	hr	NNS	_	_	_
495	after	after	IN	_	_	_
496	addition	addition	NN	_	_	_
497	of	of	IN	_	_	_
498	no	no	DT	_	_	_
499	IPTG	iptg	NN	_	_	_
500	-LRB-	-lrb-	-LRB-	_	_	_
501	0	0	CD	_	_	_
502	mM	mm	NN	KWSUPP	_	_
503	-RRB-	-rrb-	-RRB-	_	_	_
504	,	,	,	_	_	_
505	biological	biological	JJ	_	_	_
506	rep1	rep1	NN	_	_	_
507	,	,	,	_	_	_
508	technical	technical	JJ	_	_	_
509	rep2	rep2	NN	_	_	_
510	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
511	E.coli	e.coli	NN	_	_	_
512	cells	cell	NNS	_	_	_
513	at	at	IN	_	_	_
514	3.5	3.5	CD	_	_	_
515	hrs	hr	NNS	_	_	_
516	after	after	IN	_	_	_
517	addition	addition	NN	_	_	_
518	of	of	IN	_	_	_
519	no	no	DT	_	_	_
520	IPTG	iptg	NN	_	_	_
521	-LRB-	-lrb-	-LRB-	_	_	_
522	0	0	CD	_	_	_
523	mM	mm	NN	KWSUPP	_	_
524	-RRB-	-rrb-	-RRB-	_	_	_
525	,	,	,	_	_	_
526	biological	biological	JJ	_	_	_
527	rep2	rep2	NN	_	_	_
528	,	,	,	_	_	_
529	technical	technical	JJ	_	_	_
530	rep	rep	NN	GEN	_	_
531	1	1	CD	_	_	_
532	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
533	E.coli	e.coli	NN	_	_	_
534	cells	cell	NNS	_	_	_
535	at	at	IN	_	_	_
536	3.5	3.5	CD	_	_	_
537	hrs	hr	NNS	_	_	_
538	after	after	IN	_	_	_
539	addition	addition	NN	_	_	_
540	of	of	IN	_	_	_
541	no	no	DT	_	_	_
542	IPTG	iptg	NN	_	_	_
543	-LRB-	-lrb-	-LRB-	_	_	_
544	0	0	CD	_	_	_
545	mM	mm	NN	KWSUPP	_	_
546	-RRB-	-rrb-	-RRB-	_	_	_
547	,	,	,	_	_	_
548	biological	biological	JJ	_	_	_
549	rep2	rep2	NN	_	_	_
550	,	,	,	_	_	_
551	technical	technical	JJ	_	_	_
552	rep2	rep2	NN	_	_	_
553	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
554	E.coli	e.coli	NN	_	_	_
555	cells	cell	NNS	_	_	_
556	at	at	IN	_	_	_
557	3.5	3.5	CD	_	_	_
558	hrs	hr	NNS	_	_	_
559	after	after	IN	_	_	_
560	induction	induction	NN	_	_	_
561	with	with	IN	_	_	_
562	0.1	0.1	CD	_	_	_
563	mM	mm	NN	KWSUPP	_	_
564	IPTG	iptg	NN	_	_	_
565	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
566	E.coli	e.coli	NN	_	_	_
567	cells	cell	NNS	_	_	_
568	at	at	IN	_	_	_
569	3.5	3.5	CD	_	_	_
570	hrs	hr	NNS	_	_	_
571	after	after	IN	_	_	_
572	induction	induction	NN	_	_	_
573	with	with	IN	_	_	_
574	0	0	CD	_	_	_
575	mM	mm	NN	KWSUPP	_	_
576	IPTG	iptg	NN	_	_	_
577	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
578	E.coli	e.coli	NN	_	_	_
579	cells	cell	NNS	_	_	_
580	at	at	IN	_	_	_
581	3.5	3.5	CD	_	_	_
582	hrs	hr	NNS	_	_	_
583	after	after	IN	_	_	_
584	induction	induction	NN	_	_	_
585	with	with	IN	_	_	_
586	1.0	1.0	CD	_	_	_
587	mM	mm	NN	KWSUPP	_	_
588	IPTG	iptg	NN	_	_	_
589	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
590	E.coli	e.coli	NN	_	_	_
591	cells	cell	NNS	_	_	_
592	at	at	IN	_	_	_
593	the	the	DT	_	_	_
594	time	time	NN	_	_	_
595	of	of	IN	_	_	_
596	IPTG	iptg	NN	_	_	_
597	induction	induction	NN	_	_	_
598	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
599	E.coli	e.coli	NN	_	_	_
600	cells	cell	NNS	_	_	_
601	at	at	IN	_	_	_
602	the	the	DT	_	_	_
603	time	time	NN	_	_	_
604	of	of	IN	_	_	_
605	IPTG	iptg	NN	_	_	_
606	induction	induction	NN	_	_	_
607	-LRB-	-lrb-	-LRB-	_	_	_
608	T	t	NN	_	_	_
609	=	=	JJ	_	_	_
610	0	0	CD	_	_	_
611	hrs	hr	NNS	_	_	_
612	-RRB-	-rrb-	-RRB-	_	_	_
613	,	,	,	_	_	_
614	biological	biological	JJ	_	_	_
615	rep1	rep1	NN	_	_	_
616	,	,	,	_	_	_
617	technical	technical	JJ	_	_	_
618	rep	rep	NN	GEN	_	_
619	1	1	CD	_	_	_
620	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
621	E.coli	e.coli	NN	_	_	_
622	cells	cell	NNS	_	_	_
623	at	at	IN	_	_	_
624	the	the	DT	_	_	_
625	time	time	NN	_	_	_
626	of	of	IN	_	_	_
627	IPTG	iptg	NN	_	_	_
628	induction	induction	NN	_	_	_
629	-LRB-	-lrb-	-LRB-	_	_	_
630	T	t	NN	_	_	_
631	=	=	JJ	_	_	_
632	0	0	CD	_	_	_
633	hrs	hr	NNS	_	_	_
634	-RRB-	-rrb-	-RRB-	_	_	_
635	,	,	,	_	_	_
636	biological	biological	JJ	_	_	_
637	rep1	rep1	NN	_	_	_
638	,	,	,	_	_	_
639	technical	technical	JJ	_	_	_
640	rep2	rep2	NN	_	_	_
641	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
642	E.coli	e.coli	NN	_	_	_
643	cells	cell	NNS	_	_	_
644	at	at	IN	_	_	_
645	the	the	DT	_	_	_
646	time	time	NN	_	_	_
647	of	of	IN	_	_	_
648	IPTG	iptg	NN	_	_	_
649	induction	induction	NN	_	_	_
650	-LRB-	-lrb-	-LRB-	_	_	_
651	T	t	NN	_	_	_
652	=	=	JJ	_	_	_
653	0	0	CD	_	_	_
654	hrs	hr	NNS	_	_	_
655	-RRB-	-rrb-	-RRB-	_	_	_
656	,	,	,	_	_	_
657	biological	biological	JJ	_	_	_
658	rep2	rep2	NN	_	_	_
659	,	,	,	_	_	_
660	technical	technical	JJ	_	_	_
661	rep	rep	NN	GEN	_	_
662	1	1	CD	_	_	_
663	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
664	E.coli	e.coli	NN	_	_	_
665	cells	cell	NNS	_	_	_
666	at	at	IN	_	_	_
667	the	the	DT	_	_	_
668	time	time	NN	_	_	_
669	of	of	IN	_	_	_
670	IPTG	iptg	NN	_	_	_
671	induction	induction	NN	_	_	_
672	-LRB-	-lrb-	-LRB-	_	_	_
673	T	t	NN	_	_	_
674	=	=	JJ	_	_	_
675	0	0	CD	_	_	_
676	hrs	hr	NNS	_	_	_
677	-RRB-	-rrb-	-RRB-	_	_	_
678	,	,	,	_	_	_
679	biological	biological	JJ	_	_	_
680	rep2	rep2	NN	_	_	_
681	,	,	,	_	_	_
682	technical	technical	JJ	_	_	_
683	rep2	rep2	NN	_	_	_
684	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
685	Escherichia	escherichia	FW	Organism	_	_
686	coli	coli	FW	Organism	_	_
687	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
688	The	the	DT	_	_	_
689	probe	probe	NN	_	_	_
690	intensity	intensity	NN	_	_	_
691	data	datum	NNS	_	_	_
692	was	be	VBD	_	_	_
693	analyzed	analyze	VBN	_	_	_
694	using	use	VBG	_	_	_
695	Genetraffic	genetraffic	JJ	_	_	_
696	software	software	NN	_	_	_
697	-LRB-	-lrb-	-LRB-	_	_	_
698	Iobion	Iobion	NNP	_	_	_
699	Informatics	Informatics	NNPS	_	_	_
700	LLC	LLC	NNP	_	_	_
701	,	,	,	_	_	_
702	La	La	NNP	_	_	_
703	Jolla	Jolla	NNP	_	_	_
704	,	,	,	_	_	_
705	CA	CA	NNP	_	_	_
706	,	,	,	_	_	_
707	USA	USA	NNP	_	_	_
708	-RRB-	-rrb-	-RRB-	_	_	_
709	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	probe	probe	NN	_	_	_
3	intensity	intensity	NN	_	_	_
4	data	datum	NNS	_	_	_
5	was	be	VBD	_	_	_
6	normalized	normalize	VBN	_	_	_
7	using	use	VBG	_	_	_
8	GC-RMA	gc-rma	NN	_	_	_
9	algorithm	algorithm	NN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	MasterPure	masterpure	NN	_	_	_
8	RNA	rna	NN	_	_	_
9	purification	purification	NN	_	_	_
10	kits	kit	NNS	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Epicentre	Epicentre	NNP	_	_	_
13	,	,	,	_	_	_
14	Madison	Madison	NNP	_	_	_
15	,	,	,	_	_	_
16	WI	WI	NNP	_	_	_
17	,	,	,	_	_	_
18	USA	USA	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	according	accord	VBG	_	_	_
21	to	to	TO	_	_	_
22	the	the	DT	_	_	_
23	manufacturer	manufacturer	NN	_	_	_
24	's	's	POS	_	_	_
25	protocol	protocol	NN	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	Acidic	Acidic	NNP	_	_	_
28	Hot	Hot	NNP	_	_	_
29	Phenol	Phenol	NNP	_	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
31	Cells	cell	NNS	_	_	_
32	were	be	VBD	_	_	_
33	grown	grow	VBN	_	_	_
34	in	in	IN	_	_	_
35	M63	m63	NN	_	_	_
36	glucose	glucose	NN	SUPP	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	0.2	0.2	CD	_	_	_
39	%	%	NN	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	minimal	minimal	JJ	_	_	_
42	media	media	NNS	_	_	_
43	at	at	IN	_	_	_
44	37oC	37oc	NN	_	_	_
45	at	at	IN	_	_	_
46	200	200	CD	_	_	_
47	rpm	rpm	NN	_	_	_
48	.	.	.	_	_	_

1	Overnight	overnight	JJ	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	inoculated	inoculate	VBN	_	_	_
5	with	with	IN	_	_	_
6	single	single	JJ	_	_	_
7	,	,	,	_	_	_
8	independent	independent	JJ	_	_	_
9	colonies	colony	NNS	_	_	_
10	in	in	IN	_	_	_
11	triplicate	triplicate	NN	_	_	_
12	,	,	,	_	_	_
13	incubated	incubate	VBN	_	_	_
14	aerobically	aerobically	RB	_	_	_
15	overnight	overnight	JJ	_	_	_
16	at	at	IN	_	_	_
17	37oC	37oc	NN	_	_	_
18	,	,	,	_	_	_
19	and	and	CC	_	_	_
20	sub-cultured	sub-cultured	JJ	_	_	_
21	to	to	TO	_	_	_
22	a	a	DT	_	_	_
23	starting	start	VBG	_	_	_
24	OD600	od600	NN	_	_	_
25	of	of	IN	_	_	_
26	0.0001	0.0001	CD	_	_	_
27	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	harvested	harvest	VBN	_	_	_
4	at	at	IN	_	_	_
5	an	a	DT	_	_	_
6	OD600	od600	NN	_	_	_
7	=	=	JJ	_	_	_
8	0.3	0.3	CD	_	_	_
9	after	after	IN	_	_	_
10	being	be	VBG	_	_	_
11	maintained	maintain	VBN	_	_	_
12	in	in	IN	_	_	_
13	exponential	exponential	JJ	GrowthPhase	_	_
14	phase	phase	NN	GrowthPhase	_	_
15	for	for	IN	_	_	_
16	at	at	IN	_	_	_
17	least	least	JJS	_	_	_
18	eight	eight	CD	_	_	_
19	generations	generation	NNS	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	M63	m63	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	0.2	0.2	CD	_	_	_
10	%	%	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	minimal	minimal	JJ	_	_	_
13	media	media	NNS	_	_	_
14	at	at	IN	_	_	_
15	37oC	37oc	NN	_	_	_
16	at	at	IN	_	_	_
17	200	200	CD	_	_	_
18	rpm	rpm	NN	_	_	_
19	.	.	.	_	_	_

1	Overnight	overnight	JJ	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	inoculated	inoculate	VBN	_	_	_
5	with	with	IN	_	_	_
6	single	single	JJ	_	_	_
7	,	,	,	_	_	_
8	independent	independent	JJ	_	_	_
9	colonies	colony	NNS	_	_	_
10	in	in	IN	_	_	_
11	triplicate	triplicate	NN	_	_	_
12	,	,	,	_	_	_
13	incubated	incubate	VBN	_	_	_
14	aerobically	aerobically	RB	_	_	_
15	overnight	overnight	JJ	_	_	_
16	at	at	IN	_	_	_
17	37oC	37oc	NN	_	_	_
18	,	,	,	_	_	_
19	and	and	CC	_	_	_
20	sub-cultured	sub-cultured	JJ	_	_	_
21	to	to	TO	_	_	_
22	a	a	DT	_	_	_
23	starting	start	VBG	_	_	_
24	OD600	od600	NN	_	_	_
25	of	of	IN	_	_	_
26	0.0001	0.0001	CD	_	_	_
27	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	harvested	harvest	VBN	_	_	_
4	at	at	IN	_	_	_
5	an	a	DT	_	_	_
6	OD600	od600	NN	_	_	_
7	=	=	JJ	_	_	_
8	1.5	1.5	CD	_	_	_
9	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	K12	k12	NN	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	M63	m63	NN	_	_	_
8	glucose	glucose	NN	SUPP	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	0.2	0.2	CD	_	_	_
11	%	%	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	minimal	minimal	JJ	_	_	_
14	media	media	NNS	_	_	_
15	,	,	,	_	_	_
16	sampled	sample	VBN	_	_	_
17	in	in	IN	_	_	_
18	exponential	exponential	JJ	GrowthPhase	_	_
19	phase	phase	NN	GrowthPhase	_	_
20	OD600	od600	NN	_	_	_
21	=	=	JJ	_	_	_
22	0.3	0.3	CD	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	E.	E.	NNP	_	_	_
25	coli	coli	NN	_	_	_
26	K12	k12	NN	_	_	_
27	grown	grow	VBN	_	_	_
28	in	in	IN	_	_	_
29	M63	m63	NN	_	_	_
30	glucose	glucose	NN	SUPP	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	0.2	0.2	CD	_	_	_
33	%	%	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	minimal	minimal	JJ	_	_	_
36	media	media	NNS	_	_	_
37	,	,	,	_	_	_
38	sampled	sample	VBN	_	_	_
39	in	in	IN	_	_	_
40	stationary	stationary	JJ	GrowthPhase	_	_
41	phase	phase	NN	GrowthPhase	_	_
42	OD600	od600	NN	_	_	_
43	=	=	JJ	_	_	_
44	1.5	1.5	CD	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	Escherichia	escherichia	FW	Organism	_	_
47	coli	coli	FW	Organism	_	_
48	K-12	k-12	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	Exp-rpoS-Rep1	exp-rpos-rep1	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	Exp-rpoS-Rep2	exp-rpos-rep2	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Exp-rpoS-Rep3	exp-rpos-rep3	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	Exp-WT-Rep1	exp-wt-rep1	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Exp-WT-Rep2	exp-wt-rep2	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	Exp-WT-Rep3	exp-wt-rep3	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	GCRMA	gcrma	NN	_	_	_
63	normalized	normalize	VBD	_	_	_
64	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
65	MG1655	MG1655	NNP	_	_	_
66	rpoS	rpos	NN	GEN	_	_
67	mutants	mutant	NNS	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	MG1655	mg1655	NN	_	_	_
70	wild	wild	JJ	_	_	_
71	type	type	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	Stat-rpoS-Rep1	stat-rpos-rep1	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	Stat-rpoS-Rep2	stat-rpos-rep2	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	Stat-rpoS-Rep3	stat-rpos-rep3	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	Stat-WT-Rep1	stat-wt-rep1	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	Stat-WT-Rep2	stat-wt-rep2	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	Stat-WT-Rep3	stat-wt-rep3	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	Ambion	Ambion	NNP	_	_	_
86	RiboPure	RiboPure	NNP	_	_	_
87	RNA	rna	NN	_	_	_
88	Isolation	isolation	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	Ambion	Ambion	NNP	_	_	_
91	RiboPure	RiboPure	NNP	_	_	_
92	RNA	rna	NN	_	_	_
93	Isolation	isolation	NN	_	_	_
94	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
95	Data	Data	NNP	_	_	_
96	has	have	VBZ	_	_	_
97	not	not	RB	_	_	_
98	been	be	VBN	_	_	_
99	processed	process	VBN	_	_	_
100	other	other	JJ	_	_	_
101	than	than	IN	_	_	_
102	those	those	DT	_	_	_
103	protocols	protocol	NNS	_	_	_
104	within	within	IN	_	_	_
105	GCOSv1	gcosv1	NN	_	_	_
106	.4	.4	CD	_	_	_
107	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
108	E.	E.	NNP	_	_	_
109	coli	coli	NN	_	_	_
110	8624	8624	CD	_	_	_
111	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
112	E.	E.	NNP	_	_	_
113	coli	coli	NN	_	_	_
114	8624	8624	CD	_	_	_
115	qseF	qsef	NN	_	_	_
116	deletion	deletion	NN	_	_	_
117	mutant	mutant	JJ	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	E.	e.	FW	_	_	_
120	coli	coli	FW	_	_	_
121	8624	8624	CD	_	_	_
122	WT	WT	NNP	_	_	_
123	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
124	Escherichia	escherichia	FW	Organism	_	_
125	coli	coli	FW	Organism	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	Escherichia	escherichia	FW	Organism	_	_
128	coli	coli	FW	Organism	_	_
129	8624	8624	CD	_	_	_
130	grown	grow	VBN	_	_	_
131	in	in	IN	_	_	_
132	DMEM	DMEM	NNP	_	_	_
133	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
134	Escherichia	escherichia	FW	Organism	_	_
135	coli	coli	FW	Organism	_	_
136	8624	8624	CD	_	_	_
137	qseF	qsef	NN	_	_	_
138	deletion	deletion	NN	_	_	_
139	mutant	mutant	JJ	_	_	_
140	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
141	Escherichia	escherichia	FW	Organism	_	_
142	coli	coli	FW	Organism	_	_
143	8624	8624	CD	_	_	_
144	qseF	qsef	NN	_	_	_
145	deletion	deletion	NN	_	_	_
146	mutant	mutant	JJ	_	_	_
147	grown	grow	VBN	_	_	_
148	in	in	IN	_	_	_
149	DMEM	DMEM	NNP	_	_	_
150	media	media	NNS	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	strain	strain	NN	_	_	_
153	:	:	:	_	_	_
154	Escherichia	escherichia	FW	Organism	_	_
155	coli	coli	FW	Organism	_	_
156	8624	8624	CD	_	_	_
157	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
158	Aerobic	Aerobic	NNP	_	_	_
159	E.	E.	NNP	_	_	_
160	coli	coli	NN	_	_	_
161	exposed	expose	VBN	_	_	_
162	to	to	TO	_	_	_
163	CO-RMs	co-rm	NNS	_	_	_
164	for	for	IN	_	_	_
165	15	15	CD	_	_	_
166	minutes	minute	NNS	_	_	_
167	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
168	Aerobic	Aerobic	NNP	_	_	_
169	E.	E.	NNP	_	_	_
170	coli	coli	NN	_	_	_
171	not	not	RB	_	_	_
172	exposed	expose	VBN	_	_	_
173	to	to	TO	_	_	_
174	CO-RMs	co-rm	NNS	_	_	_
175	for	for	IN	_	_	_
176	15	15	CD	_	_	_
177	minutes	minute	NNS	_	_	_
178	-LRB-	-lrb-	-LRB-	_	_	_
179	control	control	NN	_	_	_
180	cells	cell	NNS	_	_	_
181	-RRB-	-rrb-	-RRB-	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
183	Aerobic	aerobic	JJ	_	_	_
184	MG1655	mg1655	NN	_	_	_
185	exposed	expose	VBN	_	_	_
186	to	to	TO	_	_	_
187	CO-RMs	co-rm	NNS	_	_	_
188	for	for	IN	_	_	_
189	15	15	CD	_	_	_
190	minutes	minute	NNS	_	_	_
191	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
192	Aerobic	aerobic	JJ	_	_	_
193	MG1655	mg1655	NN	_	_	_
194	not	not	RB	_	_	_
195	exposed	expose	VBN	_	_	_
196	to	to	TO	_	_	_
197	CO-RMs	co-rm	NNS	_	_	_
198	for	for	IN	_	_	_
199	15	15	CD	_	_	_
200	minutes	minute	NNS	_	_	_
201	-LRB-	-lrb-	-LRB-	_	_	_
202	control	control	NN	_	_	_
203	cells	cell	NNS	_	_	_
204	-RRB-	-rrb-	-RRB-	_	_	_
205	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
206	Escherichia	escherichia	FW	Organism	_	_
207	coli	coli	FW	Organism	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	Escherichia	escherichia	FW	Organism	_	_
210	coli	coli	FW	Organism	_	_
211	after	after	IN	_	_	_
212	addition	addition	NN	_	_	_
213	of	of	IN	_	_	_
214	CO-RMs	co-rm	NNS	_	_	_
215	to	to	TO	_	_	_
216	aerobically	aerobically	RB	_	_	_
217	growing	grow	VBG	_	_	_
218	cells	cell	NNS	_	_	_
219	-	-	:	_	_	_
220	Sample	sample	NN	_	_	_
221	1a	1a	NN	_	_	_
222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
223	Escherichia	escherichia	FW	Organism	_	_
224	coli	coli	FW	Organism	_	_
225	after	after	IN	_	_	_
226	addition	addition	NN	_	_	_
227	of	of	IN	_	_	_
228	CO-RMs	co-rm	NNS	_	_	_
229	to	to	TO	_	_	_
230	aerobically	aerobically	RB	_	_	_
231	growing	grow	VBG	_	_	_
232	cells	cell	NNS	_	_	_
233	-	-	:	_	_	_
234	Sample	sample	NN	_	_	_
235	1b	1b	NN	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	Escherichia	escherichia	FW	Organism	_	_
238	coli	coli	FW	Organism	_	_
239	after	after	IN	_	_	_
240	addition	addition	NN	_	_	_
241	of	of	IN	_	_	_
242	CO-RMs	co-rm	NNS	_	_	_
243	to	to	TO	_	_	_
244	aerobically	aerobically	RB	_	_	_
245	growing	grow	VBG	_	_	_
246	cells	cell	NNS	_	_	_
247	-	-	:	_	_	_
248	Sample	sample	NN	_	_	_
249	2a	2a	NN	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	Escherichia	escherichia	FW	Organism	_	_
252	coli	coli	FW	Organism	_	_
253	after	after	IN	_	_	_
254	addition	addition	NN	_	_	_
255	of	of	IN	_	_	_
256	CO-RMs	co-rm	NNS	_	_	_
257	to	to	TO	_	_	_
258	aerobically	aerobically	RB	_	_	_
259	growing	grow	VBG	_	_	_
260	cells	cell	NNS	_	_	_
261	-	-	:	_	_	_
262	Sample	sample	NN	_	_	_
263	2b	2b	JJ	_	_	_
264	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
265	Escherichia	escherichia	FW	Organism	_	_
266	coli	coli	FW	Organism	_	_
267	after	after	IN	_	_	_
268	addition	addition	NN	_	_	_
269	of	of	IN	_	_	_
270	CO-RMs	co-rm	NNS	_	_	_
271	to	to	TO	_	_	_
272	aerobically	aerobically	RB	_	_	_
273	growing	grow	VBG	_	_	_
274	cells	cell	NNS	_	_	_
275	-	-	:	_	_	_
276	Sample	sample	NN	_	_	_
277	3a	3a	NN	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
279	Escherichia	escherichia	FW	Organism	_	_
280	coli	coli	FW	Organism	_	_
281	after	after	IN	_	_	_
282	addition	addition	NN	_	_	_
283	of	of	IN	_	_	_
284	CO-RMs	co-rm	NNS	_	_	_
285	to	to	TO	_	_	_
286	aerobically	aerobically	RB	_	_	_
287	growing	grow	VBG	_	_	_
288	cells	cell	NNS	_	_	_
289	-	-	:	_	_	_
290	Sample	sample	NN	_	_	_
291	3b	3b	NN	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	Escherichia	escherichia	FW	Organism	_	_
294	coli	coli	FW	Organism	_	_
295	after	after	IN	_	_	_
296	addition	addition	NN	_	_	_
297	of	of	IN	_	_	_
298	CO-RMs	co-rm	NNS	_	_	_
299	to	to	TO	_	_	_
300	aerobically	aerobically	RB	_	_	_
301	growing	grow	VBG	_	_	_
302	cells	cell	NNS	_	_	_
303	-	-	:	_	_	_
304	Sample	sample	NN	_	_	_
305	4a	4a	NN	_	_	_
306	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
307	Escherichia	escherichia	FW	Organism	_	_
308	coli	coli	FW	Organism	_	_
309	after	after	IN	_	_	_
310	addition	addition	NN	_	_	_
311	of	of	IN	_	_	_
312	CO-RMs	co-rm	NNS	_	_	_
313	to	to	TO	_	_	_
314	aerobically	aerobically	RB	_	_	_
315	growing	grow	VBG	_	_	_
316	cells	cell	NNS	_	_	_
317	-	-	:	_	_	_
318	Sample	sample	NN	_	_	_
319	4b	4b	NN	_	_	_
320	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
321	Samples	sample	NNS	_	_	_
322	-LRB-	-lrb-	-LRB-	_	_	_
323	30	30	CD	_	_	_
324	ml	ml	NN	_	_	_
325	-RRB-	-rrb-	-RRB-	_	_	_
326	were	be	VBD	_	_	_
327	harvested	harvest	VBN	_	_	_
328	directly	directly	RB	_	_	_
329	into	into	IN	_	_	_
330	cold	cold	JJ	_	_	_
331	phenol	phenol	NN	_	_	_
332	ethanol	ethanol	NN	_	_	_
333	-LRB-	-lrb-	-LRB-	_	_	_
334	187	187	CD	_	_	_
335	µl	µl	NN	_	_	_
336	phenol	phenol	NN	_	_	_
337	,	,	,	_	_	_
338	3.56	3.56	CD	_	_	_
339	ml	ml	NN	_	_	_
340	ethanol	ethanol	NN	_	_	_
341	-RRB-	-rrb-	-RRB-	_	_	_
342	to	to	TO	_	_	_
343	stabilize	stabilize	VB	_	_	_
344	RNA	rna	NN	_	_	_
345	,	,	,	_	_	_
346	and	and	CC	_	_	_
347	total	total	JJ	_	_	_
348	RNA	rna	NN	_	_	_
349	was	be	VBD	_	_	_
350	purified	purify	VBN	_	_	_
351	using	use	VBG	_	_	_
352	Qiagen	Qiagen	NNP	_	_	_
353	's	's	POS	_	_	_
354	RNeasy	RNeasy	NNP	_	_	_
355	Mini	Mini	NNP	_	_	_
356	kit	kit	NN	_	_	_
357	as	as	IN	_	_	_
358	recommended	recommend	VBN	_	_	_
359	by	by	IN	_	_	_
360	suppliers	supplier	NNS	_	_	_
361	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	quantified	quantify	VBN	_	_	_
4	using	use	VBG	_	_	_
5	a	a	DT	_	_	_
6	BioPhotometer	biophotometer	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Eppendorf	eppendorf	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Spots	spot	NNS	_	_	_
3	automatically	automatically	RB	_	_	_
4	flagged	flag	VBD	_	_	_
5	as	as	IN	_	_	_
6	bad	bad	JJ	_	_	_
7	,	,	,	_	_	_
8	negative	negative	JJ	_	_	_
9	or	or	CC	_	_	_
10	poor	poor	JJ	_	_	_
11	in	in	IN	_	_	_
12	the	the	DT	_	_	_
13	Imagene	imagene	NN	_	_	_
14	software	software	NN	_	_	_
15	were	be	VBD	_	_	_
16	removed	remove	VBN	_	_	_
17	before	before	IN	_	_	_
18	the	the	DT	_	_	_
19	statistical	statistical	JJ	_	_	_
20	analysis	analysis	NN	_	_	_
21	was	be	VBD	_	_	_
22	carried	carry	VBN	_	_	_
23	out	out	RP	_	_	_
24	in	in	IN	_	_	_
25	GeneSight	GeneSight	NNP	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	mean	mean	NN	_	_	_
3	values	value	NNS	_	_	_
4	from	from	IN	_	_	_
5	each	each	DT	_	_	_
6	channel	channel	NN	_	_	_
7	were	be	VBD	_	_	_
8	log2	log2	NN	_	_	_
9	transformed	transform	VBN	_	_	_
10	and	and	CC	_	_	_
11	normalised	normalise	VBN	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	Lowess	lowess	NN	_	_	_
15	method	method	NN	_	_	_
16	to	to	TO	_	_	_
17	remove	remove	VB	_	_	_
18	intensity-dependent	intensity-dependent	JJ	_	_	_
19	effects	effect	NNS	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	log2	log2	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	ratios	ratio	NNS	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	values	value	NNS	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	Cy3	cy3	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Anaerobic	anaerobic	JJ	_	_	_
5	E.	e.	FW	_	_	_
6	coli	coli	FW	_	_	_
7	exposed	expose	VBN	_	_	_
8	to	to	TO	_	_	_
9	CO-RMs	co-rm	NNS	_	_	_
10	for	for	IN	_	_	_
11	15	15	CD	_	_	_
12	minutes	minute	NNS	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Anaerobic	anaerobic	JJ	_	_	_
15	E.	e.	FW	_	_	_
16	coli	coli	FW	_	_	_
17	not	not	RB	_	_	_
18	exposed	expose	VBN	_	_	_
19	to	to	TO	_	_	_
20	CO-RMs	co-rm	NNS	_	_	_
21	for	for	IN	_	_	_
22	15	15	CD	_	_	_
23	minutes	minute	NNS	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	control	control	NN	_	_	_
26	cells	cell	NNS	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
29	Anaerobic	anaerobic	JJ	_	_	_
30	E.	e.	FW	_	_	_
31	coli	coli	FW	_	_	_
32	were	be	VBD	_	_	_
33	exposed	expose	VBN	_	_	_
34	to	to	TO	_	_	_
35	CO-RMs	co-rm	NNS	_	_	_
36	for	for	IN	_	_	_
37	15	15	CD	_	_	_
38	minutes	minute	NNS	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Anaerobic	anaerobic	JJ	_	_	_
41	MG1655	mg1655	NN	_	_	_
42	exposed	expose	VBN	_	_	_
43	to	to	TO	_	_	_
44	CO-RMs	co-rm	NNS	_	_	_
45	for	for	IN	_	_	_
46	15	15	CD	_	_	_
47	minutes	minute	NNS	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	Anaerobic	anaerobic	JJ	_	_	_
50	MG1655	mg1655	NN	_	_	_
51	not	not	RB	_	_	_
52	exposed	expose	VBN	_	_	_
53	to	to	TO	_	_	_
54	CO-RMs	co-rm	NNS	_	_	_
55	for	for	IN	_	_	_
56	15	15	CD	_	_	_
57	minutes	minute	NNS	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	control	control	NN	_	_	_
60	cells	cell	NNS	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
63	Anaerobic	anaerobic	JJ	_	_	_
64	MG1655	mg1655	NN	_	_	_
65	were	be	VBD	_	_	_
66	exposed	expose	VBN	_	_	_
67	to	to	TO	_	_	_
68	CO-RMs	co-rm	NNS	_	_	_
69	for	for	IN	_	_	_
70	15	15	CD	_	_	_
71	minutes	minute	NNS	_	_	_
72	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
73	Escherichia	escherichia	FW	Organism	_	_
74	coli	coli	FW	Organism	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	Escherichia	escherichia	FW	Organism	_	_
77	coli	coli	FW	Organism	_	_
78	after	after	IN	_	_	_
79	addition	addition	NN	_	_	_
80	of	of	IN	_	_	_
81	CO-RMs	co-rm	NNS	_	_	_
82	to	to	TO	_	_	_
83	anaerobically	anaerobically	RB	_	_	_
84	growing	grow	VBG	_	_	_
85	cells	cell	NNS	_	_	_
86	-	-	:	_	_	_
87	Sample	sample	NN	_	_	_
88	1a	1a	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	Escherichia	escherichia	FW	Organism	_	_
91	coli	coli	FW	Organism	_	_
92	after	after	IN	_	_	_
93	addition	addition	NN	_	_	_
94	of	of	IN	_	_	_
95	CO-RMs	co-rm	NNS	_	_	_
96	to	to	TO	_	_	_
97	anaerobically	anaerobically	RB	_	_	_
98	growing	grow	VBG	_	_	_
99	cells	cell	NNS	_	_	_
100	-	-	:	_	_	_
101	Sample	sample	NN	_	_	_
102	1b	1b	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	Escherichia	escherichia	FW	Organism	_	_
105	coli	coli	FW	Organism	_	_
106	after	after	IN	_	_	_
107	addition	addition	NN	_	_	_
108	of	of	IN	_	_	_
109	CO-RMs	co-rm	NNS	_	_	_
110	to	to	TO	_	_	_
111	anaerobically	anaerobically	RB	_	_	_
112	growing	grow	VBG	_	_	_
113	cells	cell	NNS	_	_	_
114	-	-	:	_	_	_
115	Sample	sample	NN	_	_	_
116	2a	2a	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	Escherichia	escherichia	FW	Organism	_	_
119	coli	coli	FW	Organism	_	_
120	after	after	IN	_	_	_
121	addition	addition	NN	_	_	_
122	of	of	IN	_	_	_
123	CO-RMs	co-rm	NNS	_	_	_
124	to	to	TO	_	_	_
125	anaerobically	anaerobically	RB	_	_	_
126	growing	grow	VBG	_	_	_
127	cells	cell	NNS	_	_	_
128	-	-	:	_	_	_
129	Sample	sample	NN	_	_	_
130	2b	2b	JJ	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	Escherichia	escherichia	FW	Organism	_	_
133	coli	coli	FW	Organism	_	_
134	after	after	IN	_	_	_
135	addition	addition	NN	_	_	_
136	of	of	IN	_	_	_
137	CO-RMs	co-rm	NNS	_	_	_
138	to	to	TO	_	_	_
139	anaerobically	anaerobically	RB	_	_	_
140	growing	grow	VBG	_	_	_
141	cells	cell	NNS	_	_	_
142	-	-	:	_	_	_
143	Sample	sample	NN	_	_	_
144	3a	3a	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	Escherichia	escherichia	FW	Organism	_	_
147	coli	coli	FW	Organism	_	_
148	after	after	IN	_	_	_
149	addition	addition	NN	_	_	_
150	of	of	IN	_	_	_
151	CO-RMs	co-rm	NNS	_	_	_
152	to	to	TO	_	_	_
153	anaerobically	anaerobically	RB	_	_	_
154	growing	grow	VBG	_	_	_
155	cells	cell	NNS	_	_	_
156	-	-	:	_	_	_
157	Sample	sample	NN	_	_	_
158	3b	3b	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	Escherichia	escherichia	FW	Organism	_	_
161	coli	coli	FW	Organism	_	_
162	after	after	IN	_	_	_
163	addition	addition	NN	_	_	_
164	of	of	IN	_	_	_
165	CO-RMs	co-rm	NNS	_	_	_
166	to	to	TO	_	_	_
167	anaerobically	anaerobically	RB	_	_	_
168	growing	grow	VBG	_	_	_
169	cells	cell	NNS	_	_	_
170	-	-	:	_	_	_
171	Sample	sample	NN	_	_	_
172	4a	4a	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	Escherichia	escherichia	FW	Organism	_	_
175	coli	coli	FW	Organism	_	_
176	after	after	IN	_	_	_
177	addition	addition	NN	_	_	_
178	of	of	IN	_	_	_
179	CO-RMs	co-rm	NNS	_	_	_
180	to	to	TO	_	_	_
181	anaerobically	anaerobically	RB	_	_	_
182	growing	grow	VBG	_	_	_
183	cells	cell	NNS	_	_	_
184	-	-	:	_	_	_
185	Sample	sample	NN	_	_	_
186	4b	4b	NN	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	Samples	sample	NNS	_	_	_
189	-LRB-	-lrb-	-LRB-	_	_	_
190	30	30	CD	_	_	_
191	ml	ml	NN	_	_	_
192	-RRB-	-rrb-	-RRB-	_	_	_
193	were	be	VBD	_	_	_
194	harvested	harvest	VBN	_	_	_
195	directly	directly	RB	_	_	_
196	into	into	IN	_	_	_
197	cold	cold	JJ	_	_	_
198	phenol	phenol	NN	_	_	_
199	ethanol	ethanol	NN	_	_	_
200	-LRB-	-lrb-	-LRB-	_	_	_
201	187	187	CD	_	_	_
202	µl	µl	NN	_	_	_
203	phenol	phenol	NN	_	_	_
204	,	,	,	_	_	_
205	3.56	3.56	CD	_	_	_
206	ml	ml	NN	_	_	_
207	ethanol	ethanol	NN	_	_	_
208	-RRB-	-rrb-	-RRB-	_	_	_
209	to	to	TO	_	_	_
210	stabilize	stabilize	VB	_	_	_
211	RNA	rna	NN	_	_	_
212	,	,	,	_	_	_
213	and	and	CC	_	_	_
214	total	total	JJ	_	_	_
215	RNA	rna	NN	_	_	_
216	was	be	VBD	_	_	_
217	purified	purify	VBN	_	_	_
218	using	use	VBG	_	_	_
219	Qiagen	Qiagen	NNP	_	_	_
220	's	's	POS	_	_	_
221	RNeasy	RNeasy	NNP	_	_	_
222	Mini	Mini	NNP	_	_	_
223	kit	kit	NN	_	_	_
224	as	as	IN	_	_	_
225	recommended	recommend	VBN	_	_	_
226	by	by	IN	_	_	_
227	suppliers	supplier	NNS	_	_	_
228	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	quantified	quantify	VBN	_	_	_
4	using	use	VBG	_	_	_
5	a	a	DT	_	_	_
6	BioPhotometer	biophotometer	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Eppendorf	eppendorf	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Spots	spot	NNS	_	_	_
3	automatically	automatically	RB	_	_	_
4	flagged	flag	VBD	_	_	_
5	as	as	IN	_	_	_
6	bad	bad	JJ	_	_	_
7	,	,	,	_	_	_
8	negative	negative	JJ	_	_	_
9	or	or	CC	_	_	_
10	poor	poor	JJ	_	_	_
11	in	in	IN	_	_	_
12	the	the	DT	_	_	_
13	Imagene	imagene	NN	_	_	_
14	software	software	NN	_	_	_
15	were	be	VBD	_	_	_
16	removed	remove	VBN	_	_	_
17	before	before	IN	_	_	_
18	the	the	DT	_	_	_
19	statistical	statistical	JJ	_	_	_
20	analysis	analysis	NN	_	_	_
21	was	be	VBD	_	_	_
22	carried	carry	VBN	_	_	_
23	out	out	RP	_	_	_
24	in	in	IN	_	_	_
25	GeneSight	GeneSight	NNP	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	mean	mean	NN	_	_	_
3	values	value	NNS	_	_	_
4	from	from	IN	_	_	_
5	each	each	DT	_	_	_
6	channel	channel	NN	_	_	_
7	were	be	VBD	_	_	_
8	log2	log2	NN	_	_	_
9	transformed	transform	VBN	_	_	_
10	and	and	CC	_	_	_
11	normalised	normalise	VBN	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	Lowess	lowess	NN	_	_	_
15	method	method	NN	_	_	_
16	to	to	TO	_	_	_
17	remove	remove	VB	_	_	_
18	intensity-dependent	intensity-dependent	JJ	_	_	_
19	effects	effect	NNS	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	log2	log2	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	ratios	ratio	NNS	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	values	value	NNS	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	Cy3	cy3	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Bexp	bexp	NN	_	_	_
5	_	_	CD	_	_	_
6	Bstat	Bstat	NNP	_	_	_
7	_	_	SYM	_	_	_
8	dyeswap1	dyeswap1	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Bexp	bexp	NN	_	_	_
11	_	_	CD	_	_	_
12	Bstat	Bstat	NNP	_	_	_
13	_	_	SYM	_	_	_
14	dyeswap2	dyeswap2	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Bexp	bexp	NN	_	_	_
17	_	_	CD	_	_	_
18	Bstat	Bstat	NNP	_	_	_
19	_	_	CD	_	_	_
20	rep1	rep1	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Bexp	bexp	NN	_	_	_
23	_	_	CD	_	_	_
24	Bstat	Bstat	NNP	_	_	_
25	_	_	CD	_	_	_
26	rep2	rep2	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Bexp	bexp	NN	_	_	_
29	_	_	CD	_	_	_
30	Kexp	Kexp	NNP	_	_	_
31	_	_	SYM	_	_	_
32	dyeswap1	dyeswap1	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Bexp	bexp	NN	_	_	_
35	_	_	CD	_	_	_
36	Kexp	Kexp	NNP	_	_	_
37	_	_	SYM	_	_	_
38	dyeswap2	dyeswap2	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Bexp	bexp	NN	_	_	_
41	_	_	CD	_	_	_
42	Kexp	Kexp	NNP	_	_	_
43	_	_	CD	_	_	_
44	rep1	rep1	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	Bexp	bexp	NN	_	_	_
47	_	_	CD	_	_	_
48	Kexp	Kexp	NNP	_	_	_
49	_	_	CD	_	_	_
50	rep2	rep2	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	Bexp	bexp	NN	_	_	_
53	_	_	CD	_	_	_
54	Kstat	Kstat	NNP	_	_	_
55	_	_	SYM	_	_	_
56	dyeswap1	dyeswap1	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Bexp	bexp	NN	_	_	_
59	_	_	CD	_	_	_
60	Kstat	Kstat	NNP	_	_	_
61	_	_	SYM	_	_	_
62	dyeswap2	dyeswap2	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	Bexp	bexp	NN	_	_	_
65	_	_	CD	_	_	_
66	Kstat	Kstat	NNP	_	_	_
67	_	_	CD	_	_	_
68	rep1	rep1	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	Bexp	bexp	NN	_	_	_
71	_	_	CD	_	_	_
72	Kstat	Kstat	NNP	_	_	_
73	_	_	SYM	_	_	_
74	rep2	rep2	CD	_	_	_
75	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
76	Escherichia	escherichia	FW	Organism	_	_
77	coli	coli	FW	Organism	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	Following	follow	VBG	_	_	_
80	background	background	NN	_	_	_
81	subtraction	subtraction	NN	_	_	_
82	,	,	,	_	_	_
83	spot	spot	NN	_	_	_
84	signal	signal	NN	_	_	_
85	intensities	intensity	NNS	_	_	_
86	were	be	VBD	_	_	_
87	calculated	calculate	VBN	_	_	_
88	as	as	IN	_	_	_
89	percentages	percentage	NNS	_	_	_
90	of	of	IN	_	_	_
91	total	total	JJ	_	_	_
92	signal	signal	NN	_	_	_
93	intensities	intensity	NNS	_	_	_
94	of	of	IN	_	_	_
95	Cy-3	cy-3	NN	_	_	_
96	or	or	CC	_	_	_
97	Cy-5	cy-5	NN	_	_	_
98	signals	signal	NNS	_	_	_
99	on	on	IN	_	_	_
100	each	each	DT	_	_	_
101	microarray	microarray	NN	_	_	_
102	,	,	,	_	_	_
103	as	as	IN	_	_	_
104	a	a	DT	_	_	_
105	means	means	NN	_	_	_
106	of	of	IN	_	_	_
107	normalization	normalization	NN	_	_	_
108	.	.	.	_	_	_

1	Spots	spot	NNS	_	_	_
2	with	with	IN	_	_	_
3	low	low	JJ	_	_	_
4	intensities	intensity	NNS	_	_	_
5	were	be	VBD	_	_	_
6	excluded	exclude	VBN	_	_	_
7	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	MG1655	mg1655	NN	_	_	_
3	,	,	,	_	_	_
4	exponential	exponential	JJ	GrowthPhase	_	_
5	phase	phase	NN	GrowthPhase	_	_
6	,	,	,	_	_	_
7	LB	lb	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	MG1655	mg1655	NN	_	_	_
10	,	,	,	_	_	_
11	stationary	stationary	JJ	GrowthPhase	_	_
12	phase	phase	NN	GrowthPhase	_	_
13	,	,	,	_	_	_
14	LB	lb	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	REL606	rel606	NN	_	_	_
17	,	,	,	_	_	_
18	exponential	exponential	JJ	GrowthPhase	_	_
19	phase	phase	NN	GrowthPhase	_	_
20	,	,	,	_	_	_
21	LB	lb	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	REL606	rel606	NN	_	_	_
24	,	,	,	_	_	_
25	stationary	stationary	JJ	GrowthPhase	_	_
26	phase	phase	NN	GrowthPhase	_	_
27	,	,	,	_	_	_
28	LB	lb	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Total	total	JJ	_	_	_
31	RNA	rna	NN	_	_	_
32	was	be	VBD	_	_	_
33	isolated	isolate	VBN	_	_	_
34	from	from	IN	_	_	_
35	cells	cell	NNS	_	_	_
36	grown	grow	VBN	_	_	_
37	in	in	IN	_	_	_
38	LB	lb	NN	MED	_	_
39	medium	medium	NN	MED	_	_
40	using	use	VBG	_	_	_
41	the	the	DT	_	_	_
42	Qiagen	Qiagen	NNP	_	_	_
43	RNeasy	RNeasy	NNP	_	_	_
44	column	column	NN	_	_	_
45	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Ecoli	Ecoli	NNP	_	_	_
3	_	_	SYM	_	_	_
4	ko	ko	FW	_	_	_
5	_	_	FW	_	_	_
6	arcA	arca	NN	GEN	_	_
7	_	_	NN	_	_	_
8	1	1	CD	_	_	_
9	%	%	NN	_	_	_
10	_	_	CD	_	_	_
11	isobutanol	isobutanol	NN	_	_	_
12	_	_	NN	_	_	_
13	Sample1	sample1	NN	_	_	_
14	_	_	CD	_	_	_
15	TechRep1	techrep1	NN	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Ecoli	Ecoli	NNP	_	_	_
18	_	_	SYM	_	_	_
19	ko	ko	FW	_	_	_
20	_	_	FW	_	_	_
21	arcA	arca	NN	GEN	_	_
22	_	_	NN	_	_	_
23	1	1	CD	_	_	_
24	%	%	NN	_	_	_
25	_	_	CD	_	_	_
26	isobutanol	isobutanol	NN	_	_	_
27	_	_	NN	_	_	_
28	Sample1	sample1	NN	_	_	_
29	_	_	CD	_	_	_
30	TechRep2	techrep2	NN	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	Ecoli	Ecoli	NNP	_	_	_
33	_	_	SYM	_	_	_
34	ko	ko	FW	_	_	_
35	_	_	FW	_	_	_
36	arcA	arca	NN	GEN	_	_
37	_	_	NN	_	_	_
38	1	1	CD	_	_	_
39	%	%	NN	_	_	_
40	_	_	CD	_	_	_
41	isobutanol	isobutanol	NN	_	_	_
42	_	_	NN	_	_	_
43	Sample2	sample2	NN	_	_	_
44	_	_	CD	_	_	_
45	TechRep1	techrep1	NN	_	_	_
46	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
47	Ecoli	Ecoli	NNP	_	_	_
48	_	_	SYM	_	_	_
49	ko	ko	FW	_	_	_
50	_	_	FW	_	_	_
51	arcA	arca	NN	GEN	_	_
52	_	_	NN	_	_	_
53	1	1	CD	_	_	_
54	%	%	NN	_	_	_
55	_	_	CD	_	_	_
56	isobutanol	isobutanol	NN	_	_	_
57	_	_	NN	_	_	_
58	Sample2	sample2	NN	_	_	_
59	_	_	CD	_	_	_
60	TechRep2	techrep2	NN	_	_	_
61	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
62	Ecoli	Ecoli	NNP	_	_	_
63	_	_	SYM	_	_	_
64	ko	ko	FW	_	_	_
65	_	_	FW	_	_	_
66	arcA	arca	NN	GEN	_	_
67	_	_	NN	_	_	_
68	1	1	CD	_	_	_
69	%	%	NN	_	_	_
70	_	_	CD	_	_	_
71	isobutanol	isobutanol	NN	_	_	_
72	_	_	NN	_	_	_
73	Sample3	sample3	NN	_	_	_
74	_	_	CD	_	_	_
75	TechRep1	techrep1	NN	_	_	_
76	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
77	Ecoli	Ecoli	NNP	_	_	_
78	_	_	SYM	_	_	_
79	ko	ko	FW	_	_	_
80	_	_	FW	_	_	_
81	arcA	arca	NN	GEN	_	_
82	_	_	NN	_	_	_
83	1	1	CD	_	_	_
84	%	%	NN	_	_	_
85	_	_	CD	_	_	_
86	isobutanol	isobutanol	NN	_	_	_
87	_	_	NN	_	_	_
88	Sample3	sample3	NN	_	_	_
89	_	_	CD	_	_	_
90	TechRep2	techrep2	NN	_	_	_
91	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
92	Ecoli	Ecoli	NNP	_	_	_
93	_	_	SYM	_	_	_
94	ko	ko	FW	_	_	_
95	_	_	FW	_	_	_
96	arcA	arca	NN	GEN	_	_
97	_	_	NN	_	_	_
98	1	1	CD	_	_	_
99	%	%	NN	_	_	_
100	_	_	CD	_	_	_
101	isobutanol	isobutanol	NN	_	_	_
102	_	_	NN	_	_	_
103	Sample4	sample4	NN	_	_	_
104	_	_	CD	_	_	_
105	TechRep1	techrep1	NN	_	_	_
106	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
107	Ecoli	Ecoli	NNP	_	_	_
108	_	_	SYM	_	_	_
109	ko	ko	FW	_	_	_
110	_	_	FW	_	_	_
111	arcA	arca	NN	GEN	_	_
112	_	_	NN	_	_	_
113	1	1	CD	_	_	_
114	%	%	NN	_	_	_
115	_	_	CD	_	_	_
116	isobutanol	isobutanol	NN	_	_	_
117	_	_	NN	_	_	_
118	Sample4	sample4	NN	_	_	_
119	_	_	CD	_	_	_
120	TechRep2	techrep2	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
122	Ecoli	ecoli	JJ	_	_	_
123	ko-arcA	ko-arca	NN	_	_	_
124	grown	grow	VBN	_	_	_
125	in	in	IN	_	_	_
126	MOPS	MOPS	NNP	MED	_	_
127	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
128	Ecoli	Ecoli	NNP	_	_	_
129	ko-arcA	ko-arcA	NNP	_	_	_
130	grown	grow	VBN	_	_	_
131	in	in	IN	_	_	_
132	MOPS	MOPS	NNP	MED	_	_
133	,	,	,	_	_	_
134	10	10	CD	_	_	_
135	minutes	minute	NNS	_	_	_
136	after	after	IN	_	_	_
137	1	1	CD	_	_	_
138	%	%	NN	_	_	_
139	isobutanol	isobutanol	NN	_	_	_
140	treatment	treatment	NN	_	_	_
141	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
142	Ecoli	Ecoli	NNP	_	_	_
143	_	_	SYM	_	_	_
144	ko	ko	FW	_	_	_
145	_	_	FW	_	_	_
146	fur	fur	NN	GEN	_	_
147	_	_	NN	_	_	_
148	1	1	CD	_	_	_
149	%	%	NN	_	_	_
150	_	_	CD	_	_	_
151	isobutanol	isobutanol	NN	_	_	_
152	_	_	NN	_	_	_
153	Sample1	sample1	NN	_	_	_
154	_	_	CD	_	_	_
155	TechRep1	techrep1	NN	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
157	Ecoli	ecolus	NNS	_	_	_
158	_	_	VBP	_	_	_
159	ko	ko	NN	_	_	_
160	_	_	NN	_	_	_
161	fur	fur	NN	GEN	_	_
162	_	_	NN	_	_	_
163	1	1	CD	_	_	_
164	%	%	NN	_	_	_
165	_	_	CD	_	_	_
166	isobutanol	isobutanol	NN	_	_	_
167	_	_	NN	_	_	_
168	Sample1	sample1	NN	_	_	_
169	_	_	CD	_	_	_
170	TechRep2	techrep2	NN	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	Ecoli	ecolus	NNS	_	_	_
173	_	_	VBP	_	_	_
174	ko	ko	NN	_	_	_
175	_	_	NN	_	_	_
176	fur	fur	NN	GEN	_	_
177	_	_	NN	_	_	_
178	1	1	CD	_	_	_
179	%	%	NN	_	_	_
180	_	_	CD	_	_	_
181	isobutanol	isobutanol	NN	_	_	_
182	_	_	SYM	_	_	_
183	Sample2	sample2	FW	_	_	_
184	_	_	FW	_	_	_
185	TechRep1	techrep1	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	Ecoli	ecolus	NNS	_	_	_
188	_	_	VBP	_	_	_
189	ko	ko	NN	_	_	_
190	_	_	NN	_	_	_
191	fur	fur	NN	GEN	_	_
192	_	_	NN	_	_	_
193	1	1	CD	_	_	_
194	%	%	NN	_	_	_
195	_	_	CD	_	_	_
196	isobutanol	isobutanol	NN	_	_	_
197	_	_	NN	_	_	_
198	Sample2	sample2	NN	_	_	_
199	_	_	CD	_	_	_
200	TechRep2	techrep2	NN	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	Ecoli	ecolus	NNS	_	_	_
203	_	_	VBP	_	_	_
204	ko	ko	NN	_	_	_
205	_	_	NN	_	_	_
206	fur	fur	NN	GEN	_	_
207	_	_	NN	_	_	_
208	1	1	CD	_	_	_
209	%	%	NN	_	_	_
210	_	_	CD	_	_	_
211	isobutanol	isobutanol	NN	_	_	_
212	_	_	SYM	_	_	_
213	Sample3	sample3	FW	_	_	_
214	_	_	FW	_	_	_
215	TechRep1	techrep1	NN	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	Ecoli	ecolus	NNS	_	_	_
218	_	_	VBP	_	_	_
219	ko	ko	NN	_	_	_
220	_	_	NN	_	_	_
221	fur	fur	NN	GEN	_	_
222	_	_	NN	_	_	_
223	1	1	CD	_	_	_
224	%	%	NN	_	_	_
225	_	_	CD	_	_	_
226	isobutanol	isobutanol	NN	_	_	_
227	_	_	SYM	_	_	_
228	Sample3	sample3	FW	_	_	_
229	_	_	FW	_	_	_
230	TechRep2	techrep2	NN	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	Ecoli	ecolus	NNS	_	_	_
233	_	_	VBP	_	_	_
234	ko	ko	NN	_	_	_
235	_	_	NN	_	_	_
236	fur	fur	NN	GEN	_	_
237	_	_	NN	_	_	_
238	1	1	CD	_	_	_
239	%	%	NN	_	_	_
240	_	_	CD	_	_	_
241	isobutanol	isobutanol	NN	_	_	_
242	_	_	NN	_	_	_
243	Sample4	sample4	NN	_	_	_
244	_	_	CD	_	_	_
245	TechRep1	techrep1	NN	_	_	_
246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
247	Ecoli	ecolus	NNS	_	_	_
248	_	_	VBP	_	_	_
249	ko	ko	NN	_	_	_
250	_	_	NN	_	_	_
251	fur	fur	NN	GEN	_	_
252	_	_	NN	_	_	_
253	1	1	CD	_	_	_
254	%	%	NN	_	_	_
255	_	_	CD	_	_	_
256	isobutanol	isobutanol	NN	_	_	_
257	_	_	NN	_	_	_
258	Sample4	sample4	NN	_	_	_
259	_	_	CD	_	_	_
260	TechRep2	techrep2	NN	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
262	Ecoli	ecoli	JJ	_	_	_
263	ko-fur	ko-fur	JJ	_	_	_
264	grown	grow	VBN	_	_	_
265	in	in	IN	_	_	_
266	MOPS	MOPS	NNP	MED	_	_
267	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
268	Ecoli	Ecoli	NNP	_	_	_
269	ko-fur	ko-fur	JJ	_	_	_
270	grown	grow	VBN	_	_	_
271	in	in	IN	_	_	_
272	MOPS	MOPS	NNP	MED	_	_
273	,	,	,	_	_	_
274	10	10	CD	_	_	_
275	minutes	minute	NNS	_	_	_
276	after	after	IN	_	_	_
277	1	1	CD	_	_	_
278	%	%	NN	_	_	_
279	isobutanol	isobutanol	NN	_	_	_
280	treatment	treatment	NN	_	_	_
281	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
282	Ecoli	Ecoli	NNP	_	_	_
283	ko-furgrown	ko-furgrown	NN	_	_	_
284	in	in	IN	_	_	_
285	MOPS	MOPS	NNP	MED	_	_
286	,	,	,	_	_	_
287	10	10	CD	_	_	_
288	minutes	minute	NNS	_	_	_
289	after	after	IN	_	_	_
290	1	1	CD	_	_	_
291	%	%	NN	_	_	_
292	isobutanol	isobutanol	NN	_	_	_
293	treatment	treatment	NN	_	_	_
294	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
295	Ecoli	Ecoli	NNP	_	_	_
296	_	_	SYM	_	_	_
297	ko	ko	FW	_	_	_
298	_	_	FW	_	_	_
299	ihfA	ihfa	NN	GEN	_	_
300	_	_	NN	_	_	_
301	1	1	CD	_	_	_
302	%	%	NN	_	_	_
303	_	_	CD	_	_	_
304	isobutanol	isobutanol	NN	_	_	_
305	_	_	NN	_	_	_
306	Sample1	sample1	NN	_	_	_
307	_	_	CD	_	_	_
308	TechRep1	techrep1	NN	_	_	_
309	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
310	Ecoli	Ecoli	NNP	_	_	_
311	_	_	SYM	_	_	_
312	ko	ko	FW	_	_	_
313	_	_	FW	_	_	_
314	ihfA	ihfa	NN	GEN	_	_
315	_	_	NN	_	_	_
316	1	1	CD	_	_	_
317	%	%	NN	_	_	_
318	_	_	CD	_	_	_
319	isobutanol	isobutanol	NN	_	_	_
320	_	_	NN	_	_	_
321	Sample1	sample1	NN	_	_	_
322	_	_	CD	_	_	_
323	TechRep2	techrep2	NN	_	_	_
324	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
325	Ecoli	Ecoli	NNP	_	_	_
326	_	_	SYM	_	_	_
327	ko	ko	FW	_	_	_
328	_	_	FW	_	_	_
329	ihfA	ihfa	NN	GEN	_	_
330	_	_	NN	_	_	_
331	1	1	CD	_	_	_
332	%	%	NN	_	_	_
333	_	_	CD	_	_	_
334	isobutanol	isobutanol	NN	_	_	_
335	_	_	NN	_	_	_
336	Sample2	sample2	NN	_	_	_
337	_	_	CD	_	_	_
338	TechRep1	techrep1	NN	_	_	_
339	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
340	Ecoli	Ecoli	NNP	_	_	_
341	_	_	SYM	_	_	_
342	ko	ko	FW	_	_	_
343	_	_	FW	_	_	_
344	ihfA	ihfa	NN	GEN	_	_
345	_	_	NN	_	_	_
346	1	1	CD	_	_	_
347	%	%	NN	_	_	_
348	_	_	CD	_	_	_
349	isobutanol	isobutanol	NN	_	_	_
350	_	_	NN	_	_	_
351	Sample2	sample2	NN	_	_	_
352	_	_	CD	_	_	_
353	TechRep2	techrep2	NN	_	_	_
354	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
355	Ecoli	Ecoli	NNP	_	_	_
356	_	_	SYM	_	_	_
357	ko	ko	FW	_	_	_
358	_	_	FW	_	_	_
359	ihfA	ihfa	NN	GEN	_	_
360	_	_	NN	_	_	_
361	1	1	CD	_	_	_
362	%	%	NN	_	_	_
363	_	_	CD	_	_	_
364	isobutanol	isobutanol	NN	_	_	_
365	_	_	NN	_	_	_
366	Sample3	sample3	NN	_	_	_
367	_	_	CD	_	_	_
368	TechRep1	techrep1	NN	_	_	_
369	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
370	Ecoli	Ecoli	NNP	_	_	_
371	_	_	SYM	_	_	_
372	ko	ko	FW	_	_	_
373	_	_	FW	_	_	_
374	ihfA	ihfa	NN	GEN	_	_
375	_	_	NN	_	_	_
376	1	1	CD	_	_	_
377	%	%	NN	_	_	_
378	_	_	CD	_	_	_
379	isobutanol	isobutanol	NN	_	_	_
380	_	_	NN	_	_	_
381	Sample3	sample3	NN	_	_	_
382	_	_	CD	_	_	_
383	TechRep2	techrep2	NN	_	_	_
384	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
385	Ecoli	Ecoli	NNP	_	_	_
386	_	_	SYM	_	_	_
387	ko	ko	FW	_	_	_
388	_	_	FW	_	_	_
389	ihfA	ihfa	NN	GEN	_	_
390	_	_	NN	_	_	_
391	1	1	CD	_	_	_
392	%	%	NN	_	_	_
393	_	_	CD	_	_	_
394	isobutanol	isobutanol	NN	_	_	_
395	_	_	NN	_	_	_
396	Sample4	sample4	NN	_	_	_
397	_	_	CD	_	_	_
398	TechRep1	techrep1	NN	_	_	_
399	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
400	Ecoli	Ecoli	NNP	_	_	_
401	_	_	SYM	_	_	_
402	ko	ko	FW	_	_	_
403	_	_	FW	_	_	_
404	ihfA	ihfa	NN	GEN	_	_
405	_	_	NN	_	_	_
406	1	1	CD	_	_	_
407	%	%	NN	_	_	_
408	_	_	CD	_	_	_
409	isobutanol	isobutanol	NN	_	_	_
410	_	_	NN	_	_	_
411	Sample4	sample4	NN	_	_	_
412	_	_	CD	_	_	_
413	TechRep2	techrep2	NN	_	_	_
414	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
415	Ecoli	ecoli	JJ	_	_	_
416	ko-ihfA	ko-ihfa	NN	_	_	_
417	grown	grow	VBN	_	_	_
418	in	in	IN	_	_	_
419	MOPS	MOPS	NNP	MED	_	_
420	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
421	Ecoli	Ecoli	NNP	_	_	_
422	ko-ihfA	ko-ihfA	NNP	_	_	_
423	grown	grow	VBN	_	_	_
424	in	in	IN	_	_	_
425	MOPS	MOPS	NNP	MED	_	_
426	,	,	,	_	_	_
427	10	10	CD	_	_	_
428	minutes	minute	NNS	_	_	_
429	after	after	IN	_	_	_
430	1	1	CD	_	_	_
431	%	%	NN	_	_	_
432	isobutanol	isobutanol	NN	_	_	_
433	treatment	treatment	NN	_	_	_
434	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
435	Ecoli	Ecoli	NNP	_	_	_
436	_	_	SYM	_	_	_
437	ko	ko	FW	_	_	_
438	_	_	FW	_	_	_
439	phoB	phob	NN	GEN	_	_
440	_	_	NN	_	_	_
441	1	1	CD	_	_	_
442	%	%	NN	_	_	_
443	_	_	CD	_	_	_
444	isobutanol	isobutanol	NN	_	_	_
445	_	_	NN	_	_	_
446	Sample1	sample1	NN	_	_	_
447	_	_	CD	_	_	_
448	TechRep1	techrep1	NN	_	_	_
449	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
450	Ecoli	Ecoli	NNP	_	_	_
451	_	_	SYM	_	_	_
452	ko	ko	FW	_	_	_
453	_	_	FW	_	_	_
454	phoB	phob	NN	GEN	_	_
455	_	_	NN	_	_	_
456	1	1	CD	_	_	_
457	%	%	NN	_	_	_
458	_	_	CD	_	_	_
459	isobutanol	isobutanol	NN	_	_	_
460	_	_	NN	_	_	_
461	Sample1	sample1	NN	_	_	_
462	_	_	CD	_	_	_
463	TechRep2	techrep2	NN	_	_	_
464	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
465	Ecoli	Ecoli	NNP	_	_	_
466	_	_	SYM	_	_	_
467	ko	ko	FW	_	_	_
468	_	_	FW	_	_	_
469	phoB	phob	NN	GEN	_	_
470	_	_	NN	_	_	_
471	1	1	CD	_	_	_
472	%	%	NN	_	_	_
473	_	_	CD	_	_	_
474	isobutanol	isobutanol	NN	_	_	_
475	_	_	NN	_	_	_
476	Sample2	sample2	NN	_	_	_
477	_	_	CD	_	_	_
478	TechRep1	techrep1	NN	_	_	_
479	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
480	Ecoli	Ecoli	NNP	_	_	_
481	_	_	SYM	_	_	_
482	ko	ko	FW	_	_	_
483	_	_	FW	_	_	_
484	phoB	phob	NN	GEN	_	_
485	_	_	NN	_	_	_
486	1	1	CD	_	_	_
487	%	%	NN	_	_	_
488	_	_	CD	_	_	_
489	isobutanol	isobutanol	NN	_	_	_
490	_	_	NN	_	_	_
491	Sample2	sample2	NN	_	_	_
492	_	_	CD	_	_	_
493	TechRep2	techrep2	NN	_	_	_
494	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
495	Ecoli	Ecoli	NNP	_	_	_
496	_	_	SYM	_	_	_
497	ko	ko	FW	_	_	_
498	_	_	FW	_	_	_
499	phoB	phob	NN	GEN	_	_
500	_	_	NN	_	_	_
501	1	1	CD	_	_	_
502	%	%	NN	_	_	_
503	_	_	CD	_	_	_
504	isobutanol	isobutanol	NN	_	_	_
505	_	_	NN	_	_	_
506	Sample3	sample3	NN	_	_	_
507	_	_	CD	_	_	_
508	TechRep1	techrep1	NN	_	_	_
509	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
510	Ecoli	Ecoli	NNP	_	_	_
511	_	_	SYM	_	_	_
512	ko	ko	FW	_	_	_
513	_	_	FW	_	_	_
514	phoB	phob	NN	GEN	_	_
515	_	_	NN	_	_	_
516	1	1	CD	_	_	_
517	%	%	NN	_	_	_
518	_	_	CD	_	_	_
519	isobutanol	isobutanol	NN	_	_	_
520	_	_	NN	_	_	_
521	Sample3	sample3	NN	_	_	_
522	_	_	CD	_	_	_
523	TechRep2	techrep2	NN	_	_	_
524	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
525	Ecoli	Ecoli	NNP	_	_	_
526	_	_	SYM	_	_	_
527	ko	ko	FW	_	_	_
528	_	_	FW	_	_	_
529	phoB	phob	NN	GEN	_	_
530	_	_	NN	_	_	_
531	1	1	CD	_	_	_
532	%	%	NN	_	_	_
533	_	_	CD	_	_	_
534	isobutanol	isobutanol	NN	_	_	_
535	_	_	NN	_	_	_
536	Sample4	sample4	NN	_	_	_
537	_	_	CD	_	_	_
538	TechRep1	techrep1	NN	_	_	_
539	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
540	Ecoli	Ecoli	NNP	_	_	_
541	_	_	SYM	_	_	_
542	ko	ko	FW	_	_	_
543	_	_	FW	_	_	_
544	phoB	phob	NN	GEN	_	_
545	_	_	NN	_	_	_
546	1	1	CD	_	_	_
547	%	%	NN	_	_	_
548	_	_	CD	_	_	_
549	isobutanol	isobutanol	NN	_	_	_
550	_	_	NN	_	_	_
551	Sample4	sample4	NN	_	_	_
552	_	_	CD	_	_	_
553	TechRep2	techrep2	NN	_	_	_
554	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
555	Ecoli	ecoli	JJ	_	_	_
556	ko-phoB	ko-phob	NN	_	_	_
557	grown	grow	VBN	_	_	_
558	in	in	IN	_	_	_
559	MOPS	MOPS	NNP	MED	_	_
560	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
561	Ecoli	Ecoli	NNP	_	_	_
562	ko-phoB	ko-phob	NN	_	_	_
563	grown	grow	VBN	_	_	_
564	in	in	IN	_	_	_
565	MOPS	MOPS	NNP	MED	_	_
566	,	,	,	_	_	_
567	10	10	CD	_	_	_
568	minutes	minute	NNS	_	_	_
569	after	after	IN	_	_	_
570	1	1	CD	_	_	_
571	%	%	NN	_	_	_
572	isobutanol	isobutanol	NN	_	_	_
573	treatment	treatment	NN	_	_	_
574	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
575	Ecoli	Ecoli	NNP	_	_	_
576	_	_	SYM	_	_	_
577	ko	ko	FW	_	_	_
578	_	_	FW	_	_	_
579	ubiE	ubie	NN	GEN	_	_
580	_	_	NN	_	_	_
581	1	1	CD	_	_	_
582	%	%	NN	_	_	_
583	_	_	CD	_	_	_
584	isobutanol	isobutanol	NN	_	_	_
585	_	_	NN	_	_	_
586	Sample1	sample1	NN	_	_	_
587	_	_	CD	_	_	_
588	TechRep1	techrep1	NN	_	_	_
589	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
590	Ecoli	Ecoli	NNP	_	_	_
591	_	_	SYM	_	_	_
592	ko	ko	FW	_	_	_
593	_	_	FW	_	_	_
594	ubiE	ubie	NN	GEN	_	_
595	_	_	NN	_	_	_
596	1	1	CD	_	_	_
597	%	%	NN	_	_	_
598	_	_	CD	_	_	_
599	isobutanol	isobutanol	NN	_	_	_
600	_	_	NN	_	_	_
601	Sample1	sample1	NN	_	_	_
602	_	_	CD	_	_	_
603	TechRep2	techrep2	NN	_	_	_
604	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
605	Ecoli	Ecoli	NNP	_	_	_
606	_	_	SYM	_	_	_
607	ko	ko	FW	_	_	_
608	_	_	FW	_	_	_
609	ubiE	ubie	NN	GEN	_	_
610	_	_	NN	_	_	_
611	1	1	CD	_	_	_
612	%	%	NN	_	_	_
613	_	_	CD	_	_	_
614	isobutanol	isobutanol	NN	_	_	_
615	_	_	SYM	_	_	_
616	Sample2	sample2	FW	_	_	_
617	_	_	FW	_	_	_
618	TechRep1	techrep1	NN	_	_	_
619	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
620	Ecoli	ecolus	NNS	_	_	_
621	_	_	VBP	_	_	_
622	ko	ko	NN	_	_	_
623	_	_	NN	_	_	_
624	ubiE	ubie	NN	GEN	_	_
625	_	_	NN	_	_	_
626	1	1	CD	_	_	_
627	%	%	NN	_	_	_
628	_	_	CD	_	_	_
629	isobutanol	isobutanol	NN	_	_	_
630	_	_	NN	_	_	_
631	Sample2	sample2	NN	_	_	_
632	_	_	CD	_	_	_
633	TechRep2	techrep2	NN	_	_	_
634	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
635	Ecoli	ecoli	JJ	_	_	_
636	ko-ubiE	ko-ubie	NN	_	_	_
637	grown	grow	VBN	_	_	_
638	in	in	IN	_	_	_
639	MOPS	MOPS	NNP	MED	_	_
640	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
641	Ecoli	Ecoli	NNP	_	_	_
642	ko-ubiE	ko-ubiE	NNP	_	_	_
643	grown	grow	VBN	_	_	_
644	in	in	IN	_	_	_
645	MOPS	MOPS	NNP	MED	_	_
646	,	,	,	_	_	_
647	10	10	CD	_	_	_
648	minutes	minute	NNS	_	_	_
649	after	after	IN	_	_	_
650	1	1	CD	_	_	_
651	%	%	NN	_	_	_
652	isobutanol	isobutanol	NN	_	_	_
653	treatment	treatment	NN	_	_	_
654	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
655	Ecoli	Ecoli	NNP	_	_	_
656	_	_	SYM	_	_	_
657	wildtype	wildtype	JJ	_	_	_
658	_	_	NN	_	_	_
659	1	1	CD	_	_	_
660	%	%	NN	_	_	_
661	_	_	CD	_	_	_
662	butanol	butanol	NN	_	_	_
663	_	_	SYM	_	_	_
664	Sample1	sample1	FW	_	_	_
665	_	_	FW	_	_	_
666	TechRep1	techrep1	NN	_	_	_
667	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
668	Ecoli	ecolus	NNS	_	_	_
669	_	_	VBP	_	_	_
670	wildtype	wildtype	JJ	_	_	_
671	_	_	NN	_	_	_
672	1	1	CD	_	_	_
673	%	%	NN	_	_	_
674	_	_	CD	_	_	_
675	butanol	butanol	NN	_	_	_
676	_	_	SYM	_	_	_
677	Sample1	sample1	FW	_	_	_
678	_	_	FW	_	_	_
679	TechRep2	techrep2	NN	_	_	_
680	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
681	Ecoli	ecolus	NNS	_	_	_
682	_	_	VBP	_	_	_
683	wildtype	wildtype	JJ	_	_	_
684	_	_	NN	_	_	_
685	1	1	CD	_	_	_
686	%	%	NN	_	_	_
687	_	_	CD	_	_	_
688	butanol	butanol	NN	_	_	_
689	_	_	SYM	_	_	_
690	Sample2	sample2	FW	_	_	_
691	_	_	FW	_	_	_
692	TechRep1	techrep1	NN	_	_	_
693	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
694	Ecoli	ecolus	NNS	_	_	_
695	_	_	VBP	_	_	_
696	wildtype	wildtype	JJ	_	_	_
697	_	_	NN	_	_	_
698	1	1	CD	_	_	_
699	%	%	NN	_	_	_
700	_	_	CD	_	_	_
701	butanol	butanol	NN	_	_	_
702	_	_	SYM	_	_	_
703	Sample2	sample2	FW	_	_	_
704	_	_	FW	_	_	_
705	TechRep2	techrep2	NN	_	_	_
706	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
707	Ecoli	ecolus	NNS	_	_	_
708	_	_	VBP	_	_	_
709	wildtype	wildtype	JJ	_	_	_
710	_	_	NN	_	_	_
711	1	1	CD	_	_	_
712	%	%	NN	_	_	_
713	_	_	CD	_	_	_
714	butanol	butanol	NN	_	_	_
715	_	_	SYM	_	_	_
716	Sample3	sample3	FW	_	_	_
717	_	_	FW	_	_	_
718	TechRep1	techrep1	NN	_	_	_
719	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
720	Ecoli	ecolus	NNS	_	_	_
721	_	_	VBP	_	_	_
722	wildtype	wildtype	JJ	_	_	_
723	_	_	NN	_	_	_
724	1	1	CD	_	_	_
725	%	%	NN	_	_	_
726	_	_	CD	_	_	_
727	butanol	butanol	NN	_	_	_
728	_	_	SYM	_	_	_
729	Sample3	sample3	FW	_	_	_
730	_	_	FW	_	_	_
731	TechRep2	techrep2	NN	_	_	_
732	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
733	Ecoli	ecolus	NNS	_	_	_
734	_	_	VBP	_	_	_
735	wildtype	wildtype	JJ	_	_	_
736	_	_	NN	_	_	_
737	1	1	CD	_	_	_
738	%	%	NN	_	_	_
739	_	_	CD	_	_	_
740	butanol	butanol	NN	_	_	_
741	_	_	SYM	_	_	_
742	Sample4	sample4	FW	_	_	_
743	_	_	FW	_	_	_
744	TechRep1	techrep1	NN	_	_	_
745	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
746	Ecoli	ecolus	NNS	_	_	_
747	_	_	VBP	_	_	_
748	wildtype	wildtype	JJ	_	_	_
749	_	_	NN	_	_	_
750	1	1	CD	_	_	_
751	%	%	NN	_	_	_
752	_	_	CD	_	_	_
753	butanol	butanol	NN	_	_	_
754	_	_	SYM	_	_	_
755	Sample4	sample4	FW	_	_	_
756	_	_	FW	_	_	_
757	TechRep2	techrep2	NN	_	_	_
758	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
759	Ecoli	ecolus	NNS	_	_	_
760	_	_	VBP	_	_	_
761	wildtype	wildtype	JJ	_	_	_
762	_	_	NN	_	_	_
763	1	1	CD	_	_	_
764	%	%	NN	_	_	_
765	_	_	CD	_	_	_
766	isobutanol	isobutanol	NN	_	_	_
767	_	_	NN	_	_	_
768	Sample1	sample1	NN	_	_	_
769	_	_	CD	_	_	_
770	TechRep1	techrep1	NN	_	_	_
771	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
772	Ecoli	ecolus	NNS	_	_	_
773	_	_	VBP	_	_	_
774	wildtype	wildtype	JJ	_	_	_
775	_	_	NN	_	_	_
776	1	1	CD	_	_	_
777	%	%	NN	_	_	_
778	_	_	CD	_	_	_
779	isobutanol	isobutanol	NN	_	_	_
780	_	_	NN	_	_	_
781	Sample1	sample1	NN	_	_	_
782	_	_	CD	_	_	_
783	TechRep2	techrep2	NN	_	_	_
784	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
785	Ecoli	ecolus	NNS	_	_	_
786	_	_	VBP	_	_	_
787	wildtype	wildtype	JJ	_	_	_
788	_	_	NN	_	_	_
789	1	1	CD	_	_	_
790	%	%	NN	_	_	_
791	_	_	CD	_	_	_
792	isobutanol	isobutanol	NN	_	_	_
793	_	_	SYM	_	_	_
794	Sample2	sample2	FW	_	_	_
795	_	_	FW	_	_	_
796	TechRep1	techrep1	NN	_	_	_
797	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
798	Ecoli	ecolus	NNS	_	_	_
799	_	_	VBP	_	_	_
800	wildtype	wildtype	JJ	_	_	_
801	_	_	NN	_	_	_
802	1	1	CD	_	_	_
803	%	%	NN	_	_	_
804	_	_	CD	_	_	_
805	isobutanol	isobutanol	NN	_	_	_
806	_	_	NN	_	_	_
807	Sample2	sample2	NN	_	_	_
808	_	_	CD	_	_	_
809	TechRep2	techrep2	NN	_	_	_
810	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
811	Ecoli	ecolus	NNS	_	_	_
812	_	_	VBP	_	_	_
813	wildtype	wildtype	JJ	_	_	_
814	_	_	NN	_	_	_
815	1	1	CD	_	_	_
816	%	%	NN	_	_	_
817	_	_	CD	_	_	_
818	isobutanol	isobutanol	NN	_	_	_
819	_	_	SYM	_	_	_
820	Sample3	sample3	FW	_	_	_
821	_	_	FW	_	_	_
822	TechRep1	techrep1	NN	_	_	_
823	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
824	Ecoli	ecolus	NNS	_	_	_
825	_	_	VBP	_	_	_
826	wildtype	wildtype	JJ	_	_	_
827	_	_	NN	_	_	_
828	1	1	CD	_	_	_
829	%	%	NN	_	_	_
830	_	_	CD	_	_	_
831	isobutanol	isobutanol	NN	_	_	_
832	_	_	SYM	_	_	_
833	Sample3	sample3	FW	_	_	_
834	_	_	FW	_	_	_
835	TechRep2	techrep2	NN	_	_	_
836	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
837	Ecoli	ecolus	NNS	_	_	_
838	_	_	VBP	_	_	_
839	wildtype	wildtype	JJ	_	_	_
840	_	_	NN	_	_	_
841	1	1	CD	_	_	_
842	%	%	NN	_	_	_
843	_	_	CD	_	_	_
844	isobutanol	isobutanol	NN	_	_	_
845	_	_	NN	_	_	_
846	Sample4	sample4	NN	_	_	_
847	_	_	CD	_	_	_
848	TechRep1	techrep1	NN	_	_	_
849	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
850	Ecoli	ecolus	NNS	_	_	_
851	_	_	VBP	_	_	_
852	wildtype	wildtype	JJ	_	_	_
853	_	_	NN	_	_	_
854	1	1	CD	_	_	_
855	%	%	NN	_	_	_
856	_	_	CD	_	_	_
857	isobutanol	isobutanol	NN	_	_	_
858	_	_	NN	_	_	_
859	Sample4	sample4	NN	_	_	_
860	_	_	CD	_	_	_
861	TechRep2	techrep2	NN	_	_	_
862	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
863	Ecoli	ecolus	NNS	_	_	_
864	_	_	VBP	_	_	_
865	wildtype	wildtype	JJ	_	_	_
866	_	_	NN	_	_	_
867	1	1	CD	_	_	_
868	%	%	NN	_	_	_
869	_	_	CD	_	_	_
870	isobutanol	isobutanol	NN	_	_	_
871	_	_	SYM	_	_	_
872	Sample5	sample5	FW	_	_	_
873	_	_	FW	_	_	_
874	TechRep1	techrep1	NN	_	_	_
875	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
876	Ecoli	ecolus	NNS	_	_	_
877	_	_	VBP	_	_	_
878	wildtype	wildtype	JJ	_	_	_
879	_	_	NN	_	_	_
880	1	1	CD	_	_	_
881	%	%	NN	_	_	_
882	_	_	CD	_	_	_
883	isobutanol	isobutanol	NN	_	_	_
884	_	_	SYM	_	_	_
885	Sample5	sample5	FW	_	_	_
886	_	_	FW	_	_	_
887	TechRep2	techrep2	NN	_	_	_
888	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
889	Ecoli	ecolus	NNS	_	_	_
890	_	_	VBP	_	_	_
891	wildtype	wildtype	JJ	_	_	_
892	_	_	NN	_	_	_
893	3	3	CD	_	_	_
894	%	%	NN	_	_	_
895	_	_	CD	_	_	_
896	ethanol	ethanol	NN	_	_	_
897	_	_	SYM	_	_	_
898	Sample1	sample1	FW	_	_	_
899	_	_	FW	_	_	_
900	TechRep1	techrep1	NN	_	_	_
901	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
902	Ecoli	ecolus	NNS	_	_	_
903	_	_	VBP	_	_	_
904	wildtype	wildtype	JJ	_	_	_
905	_	_	NN	_	_	_
906	3	3	CD	_	_	_
907	%	%	NN	_	_	_
908	_	_	CD	_	_	_
909	ethanol	ethanol	NN	_	_	_
910	_	_	NN	_	_	_
911	Sample1	sample1	NN	_	_	_
912	_	_	CD	_	_	_
913	TechRep2	techrep2	NN	_	_	_
914	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
915	Ecoli	ecolus	NNS	_	_	_
916	_	_	VBP	_	_	_
917	wildtype	wildtype	JJ	_	_	_
918	_	_	NN	_	_	_
919	3	3	CD	_	_	_
920	%	%	NN	_	_	_
921	_	_	CD	_	_	_
922	ethanol	ethanol	NN	_	_	_
923	_	_	SYM	_	_	_
924	Sample2	sample2	FW	_	_	_
925	_	_	FW	_	_	_
926	TechRep1	techrep1	NN	_	_	_
927	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
928	Ecoli	ecolus	NNS	_	_	_
929	_	_	VBP	_	_	_
930	wildtype	wildtype	JJ	_	_	_
931	_	_	NN	_	_	_
932	3	3	CD	_	_	_
933	%	%	NN	_	_	_
934	_	_	CD	_	_	_
935	ethanol	ethanol	NN	_	_	_
936	_	_	SYM	_	_	_
937	Sample2	sample2	FW	_	_	_
938	_	_	FW	_	_	_
939	TechRep2	techrep2	NN	_	_	_
940	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
941	Ecoli	ecolus	NNS	_	_	_
942	_	_	VBP	_	_	_
943	wildtype	wildtype	JJ	_	_	_
944	_	_	NN	_	_	_
945	3	3	CD	_	_	_
946	%	%	NN	_	_	_
947	_	_	CD	_	_	_
948	ethanol	ethanol	NN	_	_	_
949	_	_	SYM	_	_	_
950	Sample3	sample3	FW	_	_	_
951	_	_	FW	_	_	_
952	TechRep1	techrep1	NN	_	_	_
953	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
954	Ecoli	ecolus	NNS	_	_	_
955	_	_	VBP	_	_	_
956	wildtype	wildtype	JJ	_	_	_
957	_	_	NN	_	_	_
958	3	3	CD	_	_	_
959	%	%	NN	_	_	_
960	_	_	CD	_	_	_
961	ethanol	ethanol	NN	_	_	_
962	_	_	SYM	_	_	_
963	Sample3	sample3	FW	_	_	_
964	_	_	FW	_	_	_
965	TechRep2	techrep2	NN	_	_	_
966	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
967	Ecoli	ecolus	NNS	_	_	_
968	_	_	VBP	_	_	_
969	wildtype	wildtype	JJ	_	_	_
970	_	_	NN	_	_	_
971	3	3	CD	_	_	_
972	%	%	NN	_	_	_
973	_	_	CD	_	_	_
974	ethanol	ethanol	NN	_	_	_
975	_	_	SYM	_	_	_
976	Sample4	sample4	FW	_	_	_
977	_	_	FW	_	_	_
978	TechRep1	techrep1	NN	_	_	_
979	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
980	Ecoli	ecolus	NNS	_	_	_
981	_	_	VBP	_	_	_
982	wildtype	wildtype	JJ	_	_	_
983	_	_	NN	_	_	_
984	3	3	CD	_	_	_
985	%	%	NN	_	_	_
986	_	_	CD	_	_	_
987	ethanol	ethanol	NN	_	_	_
988	_	_	SYM	_	_	_
989	Sample4	sample4	FW	_	_	_
990	_	_	FW	_	_	_
991	TechRep2	techrep2	NN	_	_	_
992	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
993	Ecoli	ecolus	NNS	_	_	_
994	_	_	VBP	_	_	_
995	wildtype	wildtype	JJ	_	_	_
996	_	_	NN	_	_	_
997	calibration	calibration	NN	_	_	_
998	_	_	CD	_	_	_
999	Sample1	sample1	NN	_	_	_
1000	_	_	CD	_	_	_
1001	TechRep1	techrep1	NN	_	_	_
1002	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1003	Ecoli	ecolus	NNS	_	_	_
1004	_	_	VBP	_	_	_
1005	wildtype	wildtype	JJ	_	_	_
1006	_	_	NN	_	_	_
1007	calibration	calibration	NN	_	_	_
1008	_	_	CD	_	_	_
1009	Sample1	sample1	NN	_	_	_
1010	_	_	CD	_	_	_
1011	TechRep2	techrep2	NN	_	_	_
1012	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1013	Ecoli	ecolus	NNS	_	_	_
1014	_	_	VBP	_	_	_
1015	wildtype	wildtype	JJ	_	_	_
1016	_	_	NN	_	_	_
1017	calibration	calibration	NN	_	_	_
1018	_	_	SYM	_	_	_
1019	Sample2	sample2	FW	_	_	_
1020	_	_	FW	_	_	_
1021	TechRep1	techrep1	NN	_	_	_
1022	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1023	Ecoli	ecolus	NNS	_	_	_
1024	_	_	VBP	_	_	_
1025	wildtype	wildtype	JJ	_	_	_
1026	_	_	NN	_	_	_
1027	calibration	calibration	NN	_	_	_
1028	_	_	SYM	_	_	_
1029	Sample2	sample2	FW	_	_	_
1030	_	_	FW	_	_	_
1031	TechRep2	techrep2	NN	_	_	_
1032	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1033	Ecoli	ecoli	JJ	_	_	_
1034	wildtype	wildtype	JJ	_	_	_
1035	grown	grow	VBN	_	_	_
1036	in	in	IN	_	_	_
1037	MOPS	MOPS	NNP	MED	_	_
1038	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1039	Ecoli	Ecoli	NNP	_	_	_
1040	wildtype	wildtype	JJ	_	_	_
1041	grown	grow	VBN	_	_	_
1042	in	in	IN	_	_	_
1043	MOPS	MOPS	NNP	MED	_	_
1044	,	,	,	_	_	_
1045	10	10	CD	_	_	_
1046	minutes	minute	NNS	_	_	_
1047	after	after	IN	_	_	_
1048	1	1	CD	_	_	_
1049	%	%	NN	_	_	_
1050	butanol	butanol	NN	_	_	_
1051	treatment	treatment	NN	_	_	_
1052	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1053	Ecoli	Ecoli	NNP	_	_	_
1054	wildtype	wildtype	JJ	_	_	_
1055	grown	grow	VBN	_	_	_
1056	in	in	IN	_	_	_
1057	MOPS	MOPS	NNP	MED	_	_
1058	,	,	,	_	_	_
1059	10	10	CD	_	_	_
1060	minutes	minute	NNS	_	_	_
1061	after	after	IN	_	_	_
1062	1	1	CD	_	_	_
1063	%	%	NN	_	_	_
1064	isobutanol	isobutanol	NN	_	_	_
1065	treatment	treatment	NN	_	_	_
1066	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1067	Ecoli	Ecoli	NNP	_	_	_
1068	wildtype	wildtype	JJ	_	_	_
1069	grown	grow	VBN	_	_	_
1070	in	in	IN	_	_	_
1071	MOPS	MOPS	NNP	MED	_	_
1072	,	,	,	_	_	_
1073	10	10	CD	_	_	_
1074	minutes	minute	NNS	_	_	_
1075	after	after	IN	_	_	_
1076	3	3	CD	_	_	_
1077	%	%	NN	_	_	_
1078	ethanol	ethanol	NN	_	_	_
1079	treatment	treatment	NN	_	_	_
1080	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1081	Escherichia	escherichia	FW	Organism	_	_
1082	coli	coli	FW	Organism	_	_
1083	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1084	Qiagen	Qiagen	NNP	_	_	_
1085	RNeasy	RNeasy	NNP	_	_	_
1086	Midikit	Midikit	NNP	_	_	_
1087	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1088	Quantification	quantification	NN	_	_	_
1089	of	of	IN	_	_	_
1090	the	the	DT	_	_	_
1091	scans	scan	NNS	_	_	_
1092	were	be	VBD	_	_	_
1093	performed	perform	VBN	_	_	_
1094	with	with	IN	_	_	_
1095	ImaGene	imagene	NN	_	_	_
1096	-LRB-	-lrb-	-LRB-	_	_	_
1097	Version	version	NN	_	_	_
1098	6.0.1	6.0.1	CD	_	_	_
1099	;	;	:	_	_	_
1100	BioDiscovery	BioDiscovery	NNP	_	_	_
1101	;	;	:	_	_	_
1102	El	El	NNP	_	_	_
1103	Segundo	Segundo	NNP	_	_	_
1104	,	,	,	_	_	_
1105	CA	CA	NNP	_	_	_
1106	;	;	:	_	_	_
1107	www.biodiscovery.com	www.biodiscovery.com	NNP	_	_	_
1108	-RRB-	-rrb-	-RRB-	_	_	_
1109	;	;	:	_	_	_
1110	with	with	IN	_	_	_
1111	the	the	DT	_	_	_
1112	results	result	NNS	_	_	_
1113	presented	present	VBN	_	_	_
1114	in	in	IN	_	_	_
1115	the	the	DT	_	_	_
1116	associated	associate	VBN	_	_	_
1117	text	text	NN	_	_	_
1118	files	file	NNS	_	_	_
1119	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	normalized	normalize	VBN	_	_	_
3	data	datum	NNS	_	_	_
4	VALUE	value	NN	_	_	_
5	was	be	VBD	_	_	_
6	generated	generate	VBN	_	_	_
7	using	use	VBG	_	_	_
8	LOWESS	LOWESS	NNP	_	_	_
9	normalization	normalization	NN	_	_	_
10	with	with	IN	_	_	_
11	rank	rank	NN	_	_	_
12	invariant	invariant	JJ	_	_	_
13	selection	selection	NN	_	_	_
14	,	,	,	_	_	_
15	as	as	IN	_	_	_
16	implemented	implement	VBN	_	_	_
17	in	in	IN	_	_	_
18	lcDNA	lcdna	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	receptor.seas.ucla.edu	receptor.seas.ucla.edu	JJ	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	RNA	rna	NN	_	_	_
23	from	from	IN	_	_	_
24	1	1	CD	_	_	_
25	%	%	NN	_	_	_
26	isobutanol	isobutanol	NN	_	_	_
27	treated	treat	VBN	_	_	_
28	sample	sample	NN	_	_	_
29	and	and	CC	_	_	_
30	untreated	untreated	JJ	_	_	_
31	sample	sample	NN	_	_	_
32	were	be	VBD	_	_	_
33	mixed	mix	VBN	_	_	_
34	after	after	IN	_	_	_
35	RNA	rna	NN	_	_	_
36	purification	purification	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	strain	strain	NN	_	_	_
39	:	:	:	_	_	_
40	BW25113	bw25113	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	Strain	strain	NN	_	_	_
43	:	:	:	_	_	_
44	BW25113	bw25113	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	Strain	strain	NN	_	_	_
47	:	:	:	_	_	_
48	BW25113	bw25113	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	Treated	treat	VBN	_	_	_
51	with	with	IN	_	_	_
52	1	1	CD	_	_	_
53	%	%	NN	_	_	_
54	vol	vol	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	Treated	treat	VBN	_	_	_
57	with	with	IN	_	_	_
58	3	3	CD	_	_	_
59	%	%	NN	_	_	_
60	vol	vol	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	BW25113	bw25113	NN	_	_	_
63	,	,	,	_	_	_
64	H2O2	h2o2	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	BW25113	bw25113	NN	_	_	_
67	,	,	,	_	_	_
68	water	water	NN	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	negative	negative	JJ	_	_	_
71	control	control	NN	_	_	_
72	-RRB-	-rrb-	-RRB-	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	BW25113	bw25113	NN	_	_	_
75	ychH	ychh	NN	GEN	_	_
76	,	,	,	_	_	_
77	H2O2	h2o2	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	BW25113	bw25113	NN	_	_	_
80	ychH	ychh	NN	GEN	_	_
81	,	,	,	_	_	_
82	water	water	NN	_	_	_
83	-LRB-	-lrb-	-LRB-	_	_	_
84	negative	negative	JJ	_	_	_
85	control	control	NN	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	BW25113	bw25113	NN	_	_	_
89	ygiW	ygiw	NN	GEN	_	_
90	,	,	,	_	_	_
91	H2O2	h2o2	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	BW25113	bw25113	NN	_	_	_
94	ygiW	ygiw	NN	GEN	_	_
95	,	,	,	_	_	_
96	water	water	NN	_	_	_
97	-LRB-	-lrb-	-LRB-	_	_	_
98	negative	negative	JJ	_	_	_
99	control	control	NN	_	_	_
100	-RRB-	-rrb-	-RRB-	_	_	_
101	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
102	Channel	Channel	NNP	_	_	_
103	1	1	CD	_	_	_
104	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
105	Escherichia	escherichia	FW	Organism	_	_
106	coli	coli	FW	Organism	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
108	MAS	mas	FW	_	_	_
109	5.0	5.0	CD	_	_	_
110	Expression	expression	NN	_	_	_
111	Analysis	analysis	NN	_	_	_
112	Default	Default	NNP	_	_	_
113	Setting	set	VBG	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	RNA	rna	NN	_	_	_
116	extracted	extract	VBN	_	_	_
117	from	from	IN	_	_	_
118	cells	cell	NNS	_	_	_
119	of	of	IN	_	_	_
120	BW25113	bw25113	NN	_	_	_
121	at	at	IN	_	_	_
122	OD	od	NN	_	_	_
123	1.0	1.0	CD	_	_	_
124	after	after	IN	_	_	_
125	contacting	contact	VBG	_	_	_
126	for	for	IN	_	_	_
127	10	10	CD	_	_	_
128	min	min	NN	_	_	_
129	with	with	IN	_	_	_
130	2	2	CD	_	_	_
131	mM	mm	NN	KWSUPP	_	_
132	H2O2	h2o2	NN	_	_	_
133	in	in	IN	_	_	_
134	LB	lb	NN	_	_	_
135	at	at	IN	_	_	_
136	37oC	37oc	NN	_	_	_
137	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	extracted	extract	VBN	_	_	_
4	from	from	IN	_	_	_
5	cells	cell	NNS	_	_	_
6	of	of	IN	_	_	_
7	BW25113	bw25113	NN	_	_	_
8	at	at	IN	_	_	_
9	OD	od	NN	_	_	_
10	1.0	1.0	CD	_	_	_
11	after	after	IN	_	_	_
12	contacting	contact	VBG	_	_	_
13	for	for	IN	_	_	_
14	10	10	CD	_	_	_
15	min	min	NN	_	_	_
16	with	with	IN	_	_	_
17	water	water	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	negative	negative	JJ	_	_	_
20	control	control	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	in	in	IN	_	_	_
23	LB	lb	NN	_	_	_
24	at	at	IN	_	_	_
25	37oC	37oc	NN	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	extracted	extract	VBN	_	_	_
4	from	from	IN	_	_	_
5	cells	cell	NNS	_	_	_
6	of	of	IN	_	_	_
7	BW25113	bw25113	NN	_	_	_
8	ychH	ychh	NN	GEN	_	_
9	at	at	IN	_	_	_
10	OD	od	NN	_	_	_
11	1.0	1.0	CD	_	_	_
12	after	after	IN	_	_	_
13	contacting	contact	VBG	_	_	_
14	for	for	IN	_	_	_
15	10	10	CD	_	_	_
16	min	min	NN	_	_	_
17	with	with	IN	_	_	_
18	2	2	CD	_	_	_
19	mM	mm	NN	KWSUPP	_	_
20	H2O2	h2o2	NN	_	_	_
21	in	in	IN	_	_	_
22	LB	lb	NN	_	_	_
23	at	at	IN	_	_	_
24	37oC	37oc	NN	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	extracted	extract	VBN	_	_	_
4	from	from	IN	_	_	_
5	cells	cell	NNS	_	_	_
6	of	of	IN	_	_	_
7	BW25113	bw25113	NN	_	_	_
8	ychH	ychh	NN	GEN	_	_
9	at	at	IN	_	_	_
10	OD	od	NN	_	_	_
11	1.0	1.0	CD	_	_	_
12	after	after	IN	_	_	_
13	contacting	contact	VBG	_	_	_
14	for	for	IN	_	_	_
15	10	10	CD	_	_	_
16	min	min	NN	_	_	_
17	with	with	IN	_	_	_
18	water	water	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	negative	negative	JJ	_	_	_
21	control	control	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	in	in	IN	_	_	_
24	LB	lb	NN	_	_	_
25	at	at	IN	_	_	_
26	37oC	37oc	NN	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	extracted	extract	VBN	_	_	_
4	from	from	IN	_	_	_
5	cells	cell	NNS	_	_	_
6	of	of	IN	_	_	_
7	BW25113	bw25113	NN	_	_	_
8	ygiW	ygiw	NN	GEN	_	_
9	at	at	IN	_	_	_
10	OD	od	NN	_	_	_
11	1.0	1.0	CD	_	_	_
12	after	after	IN	_	_	_
13	contacting	contact	VBG	_	_	_
14	for	for	IN	_	_	_
15	10	10	CD	_	_	_
16	min	min	NN	_	_	_
17	with	with	IN	_	_	_
18	2	2	CD	_	_	_
19	mM	mm	NN	KWSUPP	_	_
20	H2O2	h2o2	NN	_	_	_
21	in	in	IN	_	_	_
22	LB	lb	NN	_	_	_
23	at	at	IN	_	_	_
24	37oC	37oc	NN	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	extracted	extract	VBN	_	_	_
4	from	from	IN	_	_	_
5	cells	cell	NNS	_	_	_
6	of	of	IN	_	_	_
7	BW25113	bw25113	NN	_	_	_
8	ygiW	ygiw	NN	GEN	_	_
9	at	at	IN	_	_	_
10	OD	od	NN	_	_	_
11	1.0	1.0	CD	_	_	_
12	after	after	IN	_	_	_
13	contacting	contact	VBG	_	_	_
14	for	for	IN	_	_	_
15	10	10	CD	_	_	_
16	min	min	NN	_	_	_
17	with	with	IN	_	_	_
18	water	water	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	negative	negative	JJ	_	_	_
21	control	control	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	in	in	IN	_	_	_
24	LB	lb	NN	_	_	_
25	at	at	IN	_	_	_
26	37oC	37oc	NN	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	extracted	extract	VBN	_	_	_
4	from	from	IN	_	_	_
5	cells	cell	NNS	_	_	_
6	of	of	IN	_	_	_
7	TG1	tg1	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	To	to	TO	_	_	_
10	lyse	lyse	VB	_	_	_
11	the	the	DT	_	_	_
12	cells	cell	NNS	_	_	_
13	,	,	,	_	_	_
14	1.0	1.0	CD	_	_	_
15	mL	ml	NN	_	_	_
16	RLT	rlt	NN	_	_	_
17	buffer	buffer	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	,	,	,	_	_	_
21	Inc.	Inc.	NNP	_	_	_
22	,	,	,	_	_	_
23	Valencia	Valencia	NNP	_	_	_
24	,	,	,	_	_	_
25	CA	CA	NNP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	and	and	CC	_	_	_
28	0.2	0.2	CD	_	_	_
29	mL	ml	NN	_	_	_
30	0.1	0.1	CD	_	_	_
31	mm	mm	NN	_	_	_
32	zirconia	zirconia	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Cell	cell	NN	_	_	_
35	pellets	pellet	NNS	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	from	from	IN	_	_	_
38	initial	initial	JJ	_	_	_
39	50	50	CD	_	_	_
40	ml	ml	NN	_	_	_
41	of	of	IN	_	_	_
42	culture	culture	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	were	be	VBD	_	_	_
45	thawed	thaw	VBN	_	_	_
46	and	and	CC	_	_	_
47	resuspended	resuspend	VBN	_	_	_
48	in	in	IN	_	_	_
49	250ul	250ul	NN	_	_	_
50	of	of	IN	_	_	_
51	IP	IP	NNP	_	_	_
52	buffer	buffer	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	100	100	CD	_	_	_
55	mM	mm	NN	KWSUPP	_	_
56	Tris	Tris	NNP	_	_	_
57	pH	ph	NN	_	_	_
58	8	8	CD	_	_	_
59	,	,	,	_	_	_
60	300	300	CD	_	_	_
61	mM	mm	NN	KWSUPP	_	_
62	NaCl	nacl	NN	_	_	_
63	,	,	,	_	_	_
64	2	2	CD	_	_	_
65	%	%	NN	_	_	_
66	TritonX-100	tritonx-100	NN	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	and	and	CC	_	_	_
69	sonicated	sonicate	VBN	_	_	_
70	using	use	VBG	_	_	_
71	a	a	DT	_	_	_
72	microtip	microtip	NN	_	_	_
73	sonicator	sonicator	NN	_	_	_
74	set	set	VBN	_	_	_
75	at	at	IN	_	_	_
76	10	10	CD	_	_	_
77	%	%	NN	_	_	_
78	output	output	NN	_	_	_
79	for	for	IN	_	_	_
80	20	20	CD	_	_	_
81	second	second	JJ	_	_	_
82	intervals	interval	NNS	_	_	_
83	with	with	IN	_	_	_
84	periods	period	NNS	_	_	_
85	of	of	IN	_	_	_
86	cooling	cool	VBG	_	_	_
87	in	in	IN	_	_	_
88	between	between	IN	_	_	_
89	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	treated	treat	VBN	_	_	_
5	for	for	IN	_	_	_
6	one	one	CD	_	_	_
7	hour	hour	NN	_	_	_
8	at	at	IN	_	_	_
9	4	4	CD	_	_	_
10	°C	°c	NN	_	_	_
11	with	with	IN	_	_	_
12	RNase	rnase	NN	_	_	_
13	A	a	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	2	2	CD	_	_	_
16	ng	ng	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Cells	cell	NNS	_	_	_
19	were	be	VBD	_	_	_
20	grown	grow	VBN	_	_	_
21	with	with	IN	_	_	_
22	vigorous	vigorous	JJ	_	_	_
23	shaking	shake	VBG	_	_	_
24	at	at	IN	_	_	_
25	37	37	CD	_	_	_
26	°C	°c	NN	_	_	_
27	to	to	TO	_	_	_
28	mid-log	mid-log	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	light	light	JJ	_	_	_
31	scattering	scattering	NN	_	_	_
32	at	at	IN	_	_	_
33	600	600	CD	_	_	_
34	nm	nm	NN	_	_	_
35	equivalent	equivalent	NN	_	_	_
36	to	to	TO	_	_	_
37	0.4	0.4	CD	_	_	_
38	OD	od	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	.	.	.	_	_	_

1	Sodium	sodium	NN	_	_	_
2	phosphate	phosphate	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Escherichia	escherichia	FW	Organism	_	_
7	coli	coli	FW	Organism	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
9	Genomic	genomic	JJ	_	_	_
10	DNA	dna	NN	_	_	_
11	control	control	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
13	Genomic	genomic	JJ	_	_	_
14	DNA	dna	NN	_	_	_
15	control	control	NN	_	_	_
16	from	from	IN	_	_	_
17	E.	e.	FW	_	_	_
18	coli	coli	FW	_	_	_
19	K-12	k-12	NN	_	_	_
20	MG1655	mg1655	NN	_	_	_
21	cells	cell	NNS	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
23	Genomic	genomic	JJ	_	_	_
24	DNA	dna	NN	_	_	_
25	control	control	NN	_	_	_
26	from	from	IN	_	_	_
27	E.	e.	FW	_	_	_
28	coli	coli	FW	_	_	_
29	K-12	k-12	NN	_	_	_
30	MG1655	mg1655	NN	_	_	_
31	cells	cell	NNS	_	_	_
32	treated	treat	VBN	_	_	_
33	with	with	IN	_	_	_
34	100ug	100ug	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
36	Genomic	genomic	JJ	_	_	_
37	DNA	dna	NN	_	_	_
38	control	control	NN	_	_	_
39	from	from	IN	_	_	_
40	E.	e.	FW	_	_	_
41	coli	coli	FW	_	_	_
42	K-12	k-12	NN	_	_	_
43	MG1655	mg1655	NN	_	_	_
44	cells	cell	NNS	_	_	_
45	treated	treat	VBN	_	_	_
46	with	with	IN	_	_	_
47	20ug	20ug	JJ	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
49	Genomic	genomic	JJ	_	_	_
50	DNA	dna	NN	_	_	_
51	control	control	NN	_	_	_
52	from	from	IN	_	_	_
53	E.	e.	FW	_	_	_
54	coli	coli	FW	_	_	_
55	K-12	k-12	NN	_	_	_
56	MG1655	mg1655	NN	_	_	_
57	HA3	ha3	NN	_	_	_
58	:	:	:	_	_	_
59	:	:	:	_	_	_
60	nusG	nusg	NN	GEN	_	_
61	cells	cell	NNS	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
63	Monoclonal	monoclonal	JJ	_	_	_
64	antibody	antibody	NN	_	_	_
65	for	for	IN	_	_	_
66	HA	HA	NNP	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	12CA5	12ca5	NN	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	Monoclonal	monoclonal	JJ	_	_	_
72	antibody	antibody	NN	_	_	_
73	for	for	IN	_	_	_
74	NusA	nusa	NN	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	1NA1	1na1	NN	_	_	_
77	-RRB-	-rrb-	-RRB-	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	Monoclonal	monoclonal	JJ	_	_	_
80	antibody	antibody	NN	_	_	_
81	for	for	IN	_	_	_
82	RNA	rna	NN	_	_	_
83	polymerase	polymerase	NN	_	_	_
84	Beta	beta	NN	_	_	_
85	'	'	''	_	_	_
86	subunit	subunit	NN	_	_	_
87	-LRB-	-lrb-	-LRB-	_	_	_
88	NT73	nt73	NN	_	_	_
89	-RRB-	-rrb-	-RRB-	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	Monoclonal	monoclonal	JJ	_	_	_
92	antibody	antibody	NN	_	_	_
93	for	for	IN	_	_	_
94	Sigma70	sigma70	NN	_	_	_
95	-LRB-	-lrb-	-LRB-	_	_	_
96	2G10	2g10	NN	_	_	_
97	-RRB-	-rrb-	-RRB-	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	NusA	nusa	NN	_	_	_
100	ChIP-chip	chip-chip	NN	_	_	_
101	in	in	IN	_	_	_
102	E.	e.	FW	_	_	_
103	coli	coli	FW	_	_	_
104	K-12	k-12	NN	_	_	_
105	MG1655	mg1655	NN	_	_	_
106	cells	cell	NNS	_	_	_
107	-LRB-	-lrb-	-LRB-	_	_	_
108	Dataset	Dataset	NNP	_	_	_
109	56226	56226	CD	_	_	_
110	-RRB-	-rrb-	-RRB-	_	_	_
111	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
112	NusA	nusa	NN	_	_	_
113	ChIP-chip	chip-chip	NN	_	_	_
114	in	in	IN	_	_	_
115	E.	e.	FW	_	_	_
116	coli	coli	FW	_	_	_
117	K-12	k-12	NN	_	_	_
118	MG1655	mg1655	NN	_	_	_
119	cells	cell	NNS	_	_	_
120	-LRB-	-lrb-	-LRB-	_	_	_
121	Dataset	Dataset	NNP	_	_	_
122	61392	61392	CD	_	_	_
123	-RRB-	-rrb-	-RRB-	_	_	_
124	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
125	NusA	nusa	NN	_	_	_
126	ChIP-chip	chip-chip	NN	_	_	_
127	in	in	IN	_	_	_
128	E.	e.	FW	_	_	_
129	coli	coli	FW	_	_	_
130	K-12	k-12	NN	_	_	_
131	MG1655	mg1655	NN	_	_	_
132	cells	cell	NNS	_	_	_
133	-LRB-	-lrb-	-LRB-	_	_	_
134	Dataset	Dataset	NNP	_	_	_
135	64131	64131	CD	_	_	_
136	-RRB-	-rrb-	-RRB-	_	_	_
137	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
138	NusA	nusa	NN	_	_	_
139	ChIP	chip	NN	_	_	_
140	in	in	IN	_	_	_
141	E.	e.	FW	_	_	_
142	coli	coli	FW	_	_	_
143	K-12	k-12	NN	_	_	_
144	MG1655	mg1655	NN	_	_	_
145	cells	cell	NNS	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
147	NusG	nusg	NN	_	_	_
148	ChIP-chip	chip-chip	NN	_	_	_
149	in	in	IN	_	_	_
150	E.	e.	FW	_	_	_
151	coli	coli	FW	_	_	_
152	K-12	k-12	NN	_	_	_
153	MG1655	mg1655	NN	_	_	_
154	cells	cell	NNS	_	_	_
155	-LRB-	-lrb-	-LRB-	_	_	_
156	Dataset	Dataset	NNP	_	_	_
157	70568	70568	CD	_	_	_
158	-RRB-	-rrb-	-RRB-	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	NusG	nusg	NN	_	_	_
161	ChIP-chip	chip-chip	NN	_	_	_
162	in	in	IN	_	_	_
163	E.	e.	FW	_	_	_
164	coli	coli	FW	_	_	_
165	K-12	k-12	NN	_	_	_
166	MG1655	mg1655	NN	_	_	_
167	HA3	ha3	NN	_	_	_
168	:	:	:	_	_	_
169	:	:	:	_	_	_
170	nusG	nusg	NN	GEN	_	_
171	cells	cell	NNS	_	_	_
172	-LRB-	-lrb-	-LRB-	_	_	_
173	Dataset	Dataset	NNP	_	_	_
174	62261	62261	CD	_	_	_
175	-RRB-	-rrb-	-RRB-	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	NusG	nusg	NN	_	_	_
178	ChIP-chip	chip-chip	NN	_	_	_
179	in	in	IN	_	_	_
180	E.	e.	FW	_	_	_
181	coli	coli	FW	_	_	_
182	K-12	k-12	NN	_	_	_
183	MG1655	mg1655	NN	_	_	_
184	HA3	ha3	NN	_	_	_
185	:	:	:	_	_	_
186	:	:	:	_	_	_
187	nusG	nusg	NN	GEN	_	_
188	cells	cell	NNS	_	_	_
189	-LRB-	-lrb-	-LRB-	_	_	_
190	Dataset	Dataset	NNP	_	_	_
191	62263	62263	CD	_	_	_
192	-RRB-	-rrb-	-RRB-	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	NusG	nusg	NN	_	_	_
195	ChIP	chip	NN	_	_	_
196	in	in	IN	_	_	_
197	E.	e.	FW	_	_	_
198	coli	coli	FW	_	_	_
199	K-12	k-12	NN	_	_	_
200	MG1655	mg1655	NN	_	_	_
201	cells	cell	NNS	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
203	NusG	nusg	NN	_	_	_
204	ChIP	chip	NN	_	_	_
205	in	in	IN	_	_	_
206	E.	e.	FW	_	_	_
207	coli	coli	FW	_	_	_
208	K-12	k-12	NN	_	_	_
209	MG1655	mg1655	NN	_	_	_
210	HA3	ha3	NN	_	_	_
211	:	:	:	_	_	_
212	:	:	:	_	_	_
213	nusG	nusg	NN	GEN	_	_
214	cells	cell	NNS	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
216	Polyclonal	polyclonal	JJ	_	_	_
217	antibody	antibody	NN	_	_	_
218	for	for	IN	_	_	_
219	NusG	nusg	NN	_	_	_
220	-LRB-	-lrb-	-LRB-	_	_	_
221	raised	raise	VBN	_	_	_
222	for	for	IN	_	_	_
223	this	this	DT	_	_	_
224	study	study	NN	_	_	_
225	-RRB-	-rrb-	-RRB-	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	Polyclonal	polyclonal	JJ	_	_	_
228	antibody	antibody	NN	_	_	_
229	for	for	IN	_	_	_
230	Rho	rho	NN	_	_	_
231	-LRB-	-lrb-	-LRB-	_	_	_
232	gift	gift	NN	_	_	_
233	from	from	IN	_	_	_
234	Jeff	Jeff	NNP	_	_	_
235	Roberts	Roberts	NNP	_	_	_
236	-RRB-	-rrb-	-RRB-	_	_	_
237	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
238	Rho	rho	NN	_	_	_
239	ChIP-chip	chip-chip	NN	_	_	_
240	in	in	IN	_	_	_
241	E.	e.	FW	_	_	_
242	coli	coli	FW	_	_	_
243	K-12	k-12	NN	_	_	_
244	MG1655	mg1655	NN	_	_	_
245	cells	cell	NNS	_	_	_
246	-LRB-	-lrb-	-LRB-	_	_	_
247	Dataset	Dataset	NNP	_	_	_
248	3421602	3421602	CD	_	_	_
249	-RRB-	-rrb-	-RRB-	_	_	_
250	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
251	Rho	rho	NN	_	_	_
252	ChIP-chip	chip-chip	NN	_	_	_
253	in	in	IN	_	_	_
254	E.	e.	FW	_	_	_
255	coli	coli	FW	_	_	_
256	K-12	k-12	NN	_	_	_
257	MG1655	mg1655	NN	_	_	_
258	cells	cell	NNS	_	_	_
259	-LRB-	-lrb-	-LRB-	_	_	_
260	Dataset	Dataset	NNP	_	_	_
261	70261	70261	CD	_	_	_
262	-RRB-	-rrb-	-RRB-	_	_	_
263	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
264	Rho	rho	NN	_	_	_
265	ChIP	chip	NN	_	_	_
266	in	in	IN	_	_	_
267	E.	e.	FW	_	_	_
268	coli	coli	FW	_	_	_
269	K-12	k-12	NN	_	_	_
270	MG1655	mg1655	NN	_	_	_
271	cells	cell	NNS	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	RNA	rna	NN	_	_	_
274	polymerase	polymerase	NN	_	_	_
275	-LRB-	-lrb-	-LRB-	_	_	_
276	Beta	beta	NN	_	_	_
277	'	'	''	_	_	_
278	-RRB-	-rrb-	-RRB-	_	_	_
279	ChIP-chip	chip-chip	NN	_	_	_
280	in	in	IN	_	_	_
281	E.	e.	FW	_	_	_
282	coli	coli	FW	_	_	_
283	K-12	k-12	NN	_	_	_
284	MG1655	mg1655	NN	_	_	_
285	cells	cell	NNS	_	_	_
286	-LRB-	-lrb-	-LRB-	_	_	_
287	Dataset	Dataset	NNP	_	_	_
288	100040	100040	CD	_	_	_
289	-RRB-	-rrb-	-RRB-	_	_	_
290	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
291	RNA	rna	NN	_	_	_
292	polymerase	polymerase	NN	_	_	_
293	-LRB-	-lrb-	-LRB-	_	_	_
294	Beta	beta	NN	_	_	_
295	'	'	''	_	_	_
296	-RRB-	-rrb-	-RRB-	_	_	_
297	ChIP-chip	chip-chip	NN	_	_	_
298	in	in	IN	_	_	_
299	E.	e.	FW	_	_	_
300	coli	coli	FW	_	_	_
301	K-12	k-12	NN	_	_	_
302	MG1655	mg1655	NN	_	_	_
303	cells	cell	NNS	_	_	_
304	-LRB-	-lrb-	-LRB-	_	_	_
305	Dataset	Dataset	NNP	_	_	_
306	56706	56706	CD	_	_	_
307	-RRB-	-rrb-	-RRB-	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	RNA	rna	NN	_	_	_
310	polymerase	polymerase	NN	_	_	_
311	-LRB-	-lrb-	-LRB-	_	_	_
312	Beta	beta	NN	_	_	_
313	'	'	''	_	_	_
314	-RRB-	-rrb-	-RRB-	_	_	_
315	ChIP-chip	chip-chip	NN	_	_	_
316	in	in	IN	_	_	_
317	E.	e.	FW	_	_	_
318	coli	coli	FW	_	_	_
319	K-12	k-12	NN	_	_	_
320	MG1655	mg1655	NN	_	_	_
321	cells	cell	NNS	_	_	_
322	-LRB-	-lrb-	-LRB-	_	_	_
323	Dataset	Dataset	NNP	_	_	_
324	62215	62215	CD	_	_	_
325	-RRB-	-rrb-	-RRB-	_	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	RNA	rna	NN	_	_	_
328	polymerase	polymerase	NN	_	_	_
329	-LRB-	-lrb-	-LRB-	_	_	_
330	Beta	beta	NN	_	_	_
331	'	'	''	_	_	_
332	-RRB-	-rrb-	-RRB-	_	_	_
333	ChIP-chip	chip-chip	NN	_	_	_
334	in	in	IN	_	_	_
335	E.	e.	FW	_	_	_
336	coli	coli	FW	_	_	_
337	K-12	k-12	NN	_	_	_
338	MG1655	mg1655	NN	_	_	_
339	cells	cell	NNS	_	_	_
340	treated	treat	VBN	_	_	_
341	with	with	IN	_	_	_
342	100ug	100ug	JJ	_	_	_
343	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
344	RNA	rna	NN	_	_	_
345	polymerase	polymerase	NN	_	_	_
346	-LRB-	-lrb-	-LRB-	_	_	_
347	Beta	beta	NN	_	_	_
348	'	'	''	_	_	_
349	-RRB-	-rrb-	-RRB-	_	_	_
350	ChIP-chip	chip-chip	NN	_	_	_
351	in	in	IN	_	_	_
352	E.	e.	FW	_	_	_
353	coli	coli	FW	_	_	_
354	K-12	k-12	NN	_	_	_
355	MG1655	mg1655	NN	_	_	_
356	cells	cell	NNS	_	_	_
357	treated	treat	VBN	_	_	_
358	with	with	IN	_	_	_
359	20ug	20ug	JJ	_	_	_
360	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
361	RNA	rna	NN	_	_	_
362	polymerase	polymerase	NN	_	_	_
363	-LRB-	-lrb-	-LRB-	_	_	_
364	Beta	beta	NN	_	_	_
365	'	'	''	_	_	_
366	-RRB-	-rrb-	-RRB-	_	_	_
367	ChIP	chip	NN	_	_	_
368	in	in	IN	_	_	_
369	E.	e.	FW	_	_	_
370	coli	coli	FW	_	_	_
371	K-12	k-12	NN	_	_	_
372	MG1655	mg1655	NN	_	_	_
373	cells	cell	NNS	_	_	_
374	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
375	RNA	rna	NN	_	_	_
376	polymerase	polymerase	NN	_	_	_
377	-LRB-	-lrb-	-LRB-	_	_	_
378	Beta	beta	NN	_	_	_
379	'	'	''	_	_	_
380	-RRB-	-rrb-	-RRB-	_	_	_
381	ChIP	chip	NN	_	_	_
382	in	in	IN	_	_	_
383	E.	e.	FW	_	_	_
384	coli	coli	FW	_	_	_
385	K-12	k-12	NN	_	_	_
386	MG1655	mg1655	NN	_	_	_
387	cells	cell	NNS	_	_	_
388	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
389	RNA	rna	NN	_	_	_
390	polymerase	polymerase	NN	_	_	_
391	-LRB-	-lrb-	-LRB-	_	_	_
392	Beta	beta	NN	_	_	_
393	'	'	''	_	_	_
394	-RRB-	-rrb-	-RRB-	_	_	_
395	ChIP	chip	NN	_	_	_
396	in	in	IN	_	_	_
397	E.	e.	FW	_	_	_
398	coli	coli	FW	_	_	_
399	K-12	k-12	NN	_	_	_
400	MG1655	mg1655	NN	_	_	_
401	cells	cell	NNS	_	_	_
402	treated	treat	VBN	_	_	_
403	with	with	IN	_	_	_
404	100ug	100ug	JJ	_	_	_
405	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
406	RNA	rna	NN	_	_	_
407	polymerase	polymerase	NN	_	_	_
408	-LRB-	-lrb-	-LRB-	_	_	_
409	Beta	beta	NN	_	_	_
410	'	'	''	_	_	_
411	-RRB-	-rrb-	-RRB-	_	_	_
412	ChIP	chip	NN	_	_	_
413	in	in	IN	_	_	_
414	E.	e.	FW	_	_	_
415	coli	coli	FW	_	_	_
416	K-12	k-12	NN	_	_	_
417	MG1655	mg1655	NN	_	_	_
418	cells	cell	NNS	_	_	_
419	treated	treat	VBN	_	_	_
420	with	with	IN	_	_	_
421	20ug	20ug	JJ	_	_	_
422	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
423	Sigma70	sigma70	NN	_	_	_
424	ChIP-chip	chip-chip	NN	_	_	_
425	in	in	IN	_	_	_
426	E.	e.	FW	_	_	_
427	coli	coli	FW	_	_	_
428	K-12	k-12	NN	_	_	_
429	MG1655	mg1655	NN	_	_	_
430	cells	cell	NNS	_	_	_
431	-LRB-	-lrb-	-LRB-	_	_	_
432	Dataset	Dataset	NNP	_	_	_
433	56859	56859	CD	_	_	_
434	-RRB-	-rrb-	-RRB-	_	_	_
435	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
436	Sigma70	sigma70	NN	_	_	_
437	ChIP-chip	chip-chip	NN	_	_	_
438	in	in	IN	_	_	_
439	E.	e.	FW	_	_	_
440	coli	coli	FW	_	_	_
441	K-12	k-12	NN	_	_	_
442	MG1655	mg1655	NN	_	_	_
443	cells	cell	NNS	_	_	_
444	-LRB-	-lrb-	-LRB-	_	_	_
445	Dataset	Dataset	NNP	_	_	_
446	62214	62214	CD	_	_	_
447	-RRB-	-rrb-	-RRB-	_	_	_
448	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
449	Sigma70	sigma70	NN	_	_	_
450	ChIP-chip	chip-chip	NN	_	_	_
451	in	in	IN	_	_	_
452	E.	e.	FW	_	_	_
453	coli	coli	FW	_	_	_
454	K-12	k-12	NN	_	_	_
455	MG1655	mg1655	NN	_	_	_
456	cells	cell	NNS	_	_	_
457	-LRB-	-lrb-	-LRB-	_	_	_
458	Dataset	Dataset	NNP	_	_	_
459	64194	64194	CD	_	_	_
460	-RRB-	-rrb-	-RRB-	_	_	_
461	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
462	Sigma70	sigma70	NN	_	_	_
463	ChIP-chip	chip-chip	NN	_	_	_
464	in	in	IN	_	_	_
465	E.	e.	FW	_	_	_
466	coli	coli	FW	_	_	_
467	K-12	k-12	NN	_	_	_
468	MG1655	mg1655	NN	_	_	_
469	cells	cell	NNS	_	_	_
470	treated	treat	VBN	_	_	_
471	with	with	IN	_	_	_
472	100ug	100ug	JJ	_	_	_
473	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
474	Sigma70	sigma70	NN	_	_	_
475	ChIP	chip	NN	_	_	_
476	in	in	IN	_	_	_
477	E.	e.	FW	_	_	_
478	coli	coli	FW	_	_	_
479	K-12	k-12	NN	_	_	_
480	MG1655	mg1655	NN	_	_	_
481	cells	cell	NNS	_	_	_
482	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
483	Sigma70	sigma70	NN	_	_	_
484	ChIP	chip	NN	_	_	_
485	in	in	IN	_	_	_
486	E.	e.	FW	_	_	_
487	coli	coli	FW	_	_	_
488	K-12	k-12	NN	_	_	_
489	MG1655	mg1655	NN	_	_	_
490	cells	cell	NNS	_	_	_
491	treated	treat	VBN	_	_	_
492	with	with	IN	_	_	_
493	100ug	100ug	JJ	_	_	_
494	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
495	Strain	strain	NN	_	_	_
496	MG1655	mg1655	NN	_	_	_
497	or	or	CC	_	_	_
498	isogenic	isogenic	JJ	_	_	_
499	strain	strain	NN	_	_	_
500	MG1655	mg1655	NN	_	_	_
501	HA3	ha3	NN	_	_	_
502	:	:	:	_	_	_
503	:	:	:	_	_	_
504	nusG	nusg	NN	GEN	_	_
505	cells	cell	NNS	_	_	_
506	were	be	VBD	_	_	_
507	grown	grow	VBN	_	_	_
508	in	in	IN	_	_	_
509	MOPS	mop	NNS	MED	_	_
510	minimal	minimal	JJ	_	_	_
511	medium	medium	NN	_	_	_
512	supplemented	supplement	VBN	_	_	_
513	with	with	IN	_	_	_
514	0.2	0.2	CD	_	_	_
515	%	%	NN	_	_	_
516	glucose	glucose	NN	SUPP	_	_
517	-LRB-	-lrb-	-LRB-	_	_	_
518	www.genome.wisc.edu	www.genome.wisc.edu	NN	_	_	_
519	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
520	VALUE	value	NN	_	_	_
521	=	=	JJ	_	_	_
522	log2	log2	NN	_	_	_
523	-LRB-	-lrb-	-LRB-	_	_	_
524	Cy3	cy3	NN	_	_	_
525	_	_	NN	_	_	_
526	signal	signal	NN	_	_	_
527	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
528	VALUE	value	NN	_	_	_
529	=	=	JJ	_	_	_
530	log2	log2	NN	_	_	_
531	-LRB-	-lrb-	-LRB-	_	_	_
532	Cy5	cy5	NN	_	_	_
533	_	_	NN	_	_	_
534	signal	signal	NN	_	_	_
535	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
536	E.coli	e.coli	NNS	_	_	_
537	_	_	VBP	_	_	_
538	15	15	CD	_	_	_
539	min	min	NN	_	_	_
540	_	_	CD	_	_	_
541	AE	ae	NN	_	_	_
542	_	_	NN	_	_	_
543	1	1	CD	_	_	_
544	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
545	E.coli	e.coli	NNS	_	_	_
546	_	_	VBP	_	_	_
547	15	15	CD	_	_	_
548	min	min	NN	_	_	_
549	_	_	CD	_	_	_
550	AE	ae	NN	_	_	_
551	_	_	NN	_	_	_
552	2	2	CD	_	_	_
553	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
554	E.coli	e.coli	NNS	_	_	_
555	_	_	VBP	_	_	_
556	15	15	CD	_	_	_
557	min	min	NN	_	_	_
558	_	_	NN	_	_	_
559	aerobic	aerobic	JJ	_	_	_
560	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
561	E.coli	e.coli	NNS	_	_	_
562	_	_	VBP	_	_	_
563	15	15	CD	_	_	_
564	min	min	NN	_	_	_
565	_	_	CD	_	_	_
566	ANA	ANA	NNP	_	_	_
567	_	_	SYM	_	_	_
568	1	1	CD	_	_	_
569	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
570	E.	e.	FW	_	_	_
571	coli	coli	FW	_	_	_
572	_	_	SYM	_	_	_
573	15	15	CD	_	_	_
574	min	min	NN	_	_	_
575	_	_	CD	_	_	_
576	ANA	ANA	NNP	_	_	_
577	_	_	NN	_	_	_
578	2	2	CD	_	_	_
579	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
580	E.	e.	FW	_	_	_
581	coli	coli	FW	_	_	_
582	_	_	SYM	_	_	_
583	15	15	CD	_	_	_
584	min	min	NN	_	_	_
585	_	_	NN	_	_	_
586	anaerobic	anaerobic	JJ	_	_	_
587	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
588	E.coli	e.coli	NNS	_	_	_
589	_	_	VBP	_	_	_
590	15	15	CD	_	_	_
591	min	min	NN	_	_	_
592	_	_	NN	_	_	_
593	anaerobic	anaerobic	JJ	_	_	_
594	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
595	E.coli	e.coli	NNS	_	_	_
596	_	_	VBP	_	_	_
597	15	15	CD	_	_	_
598	min	min	NN	_	_	_
599	_	_	CD	_	_	_
600	CORM-2	corm-2	NN	_	_	_
601	treated	treat	VBN	_	_	_
602	_	_	SYM	_	_	_
603	aerobic	aerobic	JJ	_	_	_
604	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
605	E.coli	e.coli	NNS	_	_	_
606	_	_	VBP	_	_	_
607	15	15	CD	_	_	_
608	min	min	NN	_	_	_
609	_	_	CD	_	_	_
610	CORM-2	corm-2	NN	_	_	_
611	treated	treat	VBN	_	_	_
612	_	_	SYM	_	_	_
613	anaerobic	anaerobic	JJ	_	_	_
614	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
615	E.coli	e.coli	NNS	_	_	_
616	_	_	VBP	_	_	_
617	15	15	CD	_	_	_
618	min	min	NN	_	_	_
619	_	_	CD	_	_	_
620	CORM	CORM	NNP	_	_	_
621	_	_	CD	_	_	_
622	AE	AE	NNP	_	_	_
623	_	_	SYM	_	_	_
624	1	1	CD	_	_	_
625	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
626	E.coli	e.coli	NNS	_	_	_
627	_	_	VBP	_	_	_
628	15	15	CD	_	_	_
629	min	min	NN	_	_	_
630	_	_	CD	_	_	_
631	CORM	CORM	NNP	_	_	_
632	_	_	CD	_	_	_
633	AE	AE	NNP	_	_	_
634	_	_	NN	_	_	_
635	2	2	CD	_	_	_
636	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
637	E.coli	e.coli	NNS	_	_	_
638	_	_	VBP	_	_	_
639	15	15	CD	_	_	_
640	min	min	NN	_	_	_
641	_	_	CD	_	_	_
642	CORM	CORM	NNP	_	_	_
643	_	_	NNP	_	_	_
644	ANA	ANA	NNP	_	_	_
645	_	_	SYM	_	_	_
646	1	1	CD	_	_	_
647	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
648	E.coli	e.coli	NNS	_	_	_
649	_	_	VBP	_	_	_
650	15	15	CD	_	_	_
651	min	min	NN	_	_	_
652	_	_	CD	_	_	_
653	CORM	CORM	NNP	_	_	_
654	_	_	NNP	_	_	_
655	ANA	ANA	NNP	_	_	_
656	_	_	NN	_	_	_
657	2	2	CD	_	_	_
658	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
659	Escherichia	escherichia	FW	Organism	_	_
660	coli	coli	FW	Organism	_	_
661	MG1655	mg1655	NN	_	_	_
662	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
663	Escherichia	escherichia	FW	Organism	_	_
664	coli	coli	FW	Organism	_	_
665	str	str	FW	_	_	_
666	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Scanned	scan	VBD	_	_	_
4	arrays	array	NNS	_	_	_
5	were	be	VBD	_	_	_
6	analyzed	analyze	VBN	_	_	_
7	with	with	IN	_	_	_
8	Affymetrix	Affymetrix	NNP	_	_	_
9	GCOS	GCOS	NNP	_	_	_
10	1.4	1.4	CD	_	_	_
11	software	software	NN	_	_	_
12	to	to	TO	_	_	_
13	obtain	obtain	VB	_	_	_
14	Detection	detection	NN	_	_	_
15	calls	call	NNS	_	_	_
16	and	and	CC	_	_	_
17	Expression	expression	NN	_	_	_
18	values	value	NNS	_	_	_
19	based	base	VBN	_	_	_
20	on	on	IN	_	_	_
21	MAS	MAS	NNP	_	_	_
22	5.0	5.0	CD	_	_	_
23	algorithms	algorithm	NNS	_	_	_
24	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	arrays	array	NNS	_	_	_
3	were	be	VBD	_	_	_
4	scaled	scale	VBN	_	_	_
5	to	to	TO	_	_	_
6	a	a	DT	_	_	_
7	target	target	NN	_	_	_
8	value	value	NN	_	_	_
9	of	of	IN	_	_	_
10	500	500	CD	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	hot-phenol	hot-phenol	NN	_	_	_
4	method	method	NN	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	to	to	TO	_	_	_
8	extract	extract	VB	_	_	_
9	total	total	JJ	_	_	_
10	RNA	rna	NN	_	_	_
11	from	from	IN	_	_	_
12	two	two	CD	_	_	_
13	independent	independent	JJ	_	_	_
14	cultures	culture	NNS	_	_	_
15	of	of	IN	_	_	_
16	cells	cell	NNS	_	_	_
17	grown	grow	VBN	_	_	_
18	aerobically	aerobically	RB	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	The	the	DT	_	_	_
21	hot-phenol	hot-phenol	NN	_	_	_
22	method	method	NN	_	_	_
23	was	be	VBD	_	_	_
24	used	use	VBN	_	_	_
25	to	to	TO	_	_	_
26	extract	extract	VB	_	_	_
27	total	total	JJ	_	_	_
28	RNA	rna	NN	_	_	_
29	from	from	IN	_	_	_
30	two	two	CD	_	_	_
31	independent	independent	JJ	_	_	_
32	cultures	culture	NNS	_	_	_
33	of	of	IN	_	_	_
34	cells	cell	NNS	_	_	_
35	grown	grow	VBN	_	_	_
36	aerobically	aerobically	RB	_	_	_
37	and	and	CC	_	_	_
38	treated	treat	VBN	_	_	_
39	with	with	IN	_	_	_
40	250	250	CD	_	_	_
41	μM	μm	NN	_	_	_
42	CORM-2	corm-2	NN	_	_	_
43	during	during	IN	_	_	_
44	15	15	CD	_	_	_
45	min	min	NN	_	_	_
46	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	hot-phenol	hot-phenol	NN	_	_	_
4	method	method	NN	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	to	to	TO	_	_	_
8	extract	extract	VB	_	_	_
9	total	total	JJ	_	_	_
10	RNA	rna	NN	_	_	_
11	from	from	IN	_	_	_
12	two	two	CD	_	_	_
13	independent	independent	JJ	_	_	_
14	cultures	culture	NNS	_	_	_
15	of	of	IN	_	_	_
16	cells	cell	NNS	_	_	_
17	grown	grow	VBN	_	_	_
18	anaerobically	anaerobically	RB	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	The	the	DT	_	_	_
21	hot-phenol	hot-phenol	NN	_	_	_
22	method	method	NN	_	_	_
23	was	be	VBD	_	_	_
24	used	use	VBN	_	_	_
25	to	to	TO	_	_	_
26	extract	extract	VB	_	_	_
27	total	total	JJ	_	_	_
28	RNA	rna	NN	_	_	_
29	from	from	IN	_	_	_
30	two	two	CD	_	_	_
31	independent	independent	JJ	_	_	_
32	cultures	culture	NNS	_	_	_
33	of	of	IN	_	_	_
34	cells	cell	NNS	_	_	_
35	grown	grow	VBN	_	_	_
36	anaerobically	anaerobically	RB	_	_	_
37	and	and	CC	_	_	_
38	treated	treat	VBN	_	_	_
39	with	with	IN	_	_	_
40	250	250	CD	_	_	_
41	μM	μm	NN	_	_	_
42	CORM-2	corm-2	NN	_	_	_
43	during	during	IN	_	_	_
44	15	15	CD	_	_	_
45	min	min	NN	_	_	_
46	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Acid	acid	NN	_	_	_
3	adaptation	adaptation	NN	_	_	_
4	was	be	VBD	_	_	_
5	done	do	VBN	_	_	_
6	in	in	IN	_	_	_
7	DMEM	dmem	NN	_	_	_
8	at	at	IN	_	_	_
9	pH	ph	NN	_	_	_
10	5.0	5.0	CD	_	_	_
11	at	at	IN	_	_	_
12	room	room	NN	_	_	_
13	temperature	temperature	NN	_	_	_
14	,	,	,	_	_	_
15	followed	follow	VBN	_	_	_
16	by	by	IN	_	_	_
17	acid-stress	acid-stress	NN	_	_	_
18	at	at	IN	_	_	_
19	pH	ph	NN	_	_	_
20	3.0	3.0	CD	_	_	_
21	for	for	IN	_	_	_
22	30	30	CD	_	_	_
23	minutes	minute	NNS	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Acid	acid	NN	_	_	_
26	shocking	shocking	JJ	_	_	_
27	was	be	VBD	_	_	_
28	done	do	VBN	_	_	_
29	in	in	IN	_	_	_
30	DMEM	dmem	NN	_	_	_
31	at	at	IN	_	_	_
32	pH	ph	NN	_	_	_
33	3.0	3.0	CD	_	_	_
34	at	at	IN	_	_	_
35	room	room	NN	_	_	_
36	temperature	temperature	NN	_	_	_
37	for	for	IN	_	_	_
38	30	30	CD	_	_	_
39	minutes	minute	NNS	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	Acid	acid	NN	_	_	_
42	shocking	shocking	JJ	_	_	_
43	was	be	VBD	_	_	_
44	done	do	VBN	_	_	_
45	in	in	IN	_	_	_
46	DMEM	dmem	NN	_	_	_
47	at	at	IN	_	_	_
48	pH	ph	NN	_	_	_
49	3.0	3.0	CD	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	unbuffered	unbuffered	JJ	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	at	at	IN	_	_	_
54	room	room	NN	_	_	_
55	temperature	temperature	NN	_	_	_
56	for	for	IN	_	_	_
57	15	15	CD	_	_	_
58	minutes	minute	NNS	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	Bacteria	bacterium	NNS	_	_	_
61	were	be	VBD	_	_	_
62	grown	grow	VBN	_	_	_
63	in	in	IN	_	_	_
64	LB	lb	NN	MED	_	_
65	broth	broth	NN	MED	_	_
66	overnight	overnight	JJ	_	_	_
67	and	and	CC	_	_	_
68	subcultured	subculture	VBN	_	_	_
69	in	in	IN	_	_	_
70	DMEM	DMEM	NNP	_	_	_
71	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
72	Bacteria	bacterium	NNS	_	_	_
73	were	be	VBD	_	_	_
74	grown	grow	VBN	_	_	_
75	in	in	IN	_	_	_
76	LB	lb	NN	MED	_	_
77	broth	broth	NN	MED	_	_
78	overnight	overnight	JJ	_	_	_
79	and	and	CC	_	_	_
80	subcultured	subculture	VBN	_	_	_
81	in	in	IN	_	_	_
82	DMEM	DMEM	NNP	_	_	_
83	prior	prior	RB	_	_	_
84	to	to	TO	_	_	_
85	acid	acid	NN	_	_	_
86	stress	stress	NN	_	_	_
87	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
88	Control	Control	NNP	_	_	_
89	treatment	treatment	NN	_	_	_
90	.	.	.	_	_	_

1	Bacteria	bacterium	NNS	_	_	_
2	were	be	VBD	_	_	_
3	grown	grow	VBN	_	_	_
4	in	in	IN	_	_	_
5	DMEM	DMEM	NNP	_	_	_
6	pH	ph	NN	_	_	_
7	7.4	7.4	CD	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	unstressed	unstressed	JJ	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Cy3	cy3	NN	_	_	_
13	labeled	label	VBN	_	_	_
14	EHEC	EHEC	NNP	_	_	_
15	grown	grow	VBN	_	_	_
16	in	in	IN	_	_	_
17	DMEM	DMEM	NNP	_	_	_
18	pH	ph	NN	_	_	_
19	7.4	7.4	CD	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Cy3	cy3	NN	_	_	_
22	labeled	label	VBN	_	_	_
23	EHEC	EHEC	NNP	_	_	_
24	grown	grow	VBN	_	_	_
25	in	in	IN	_	_	_
26	DMEM	DMEM	NNP	_	_	_
27	pH	ph	NN	_	_	_
28	7.4	7.4	CD	_	_	_
29	,	,	,	_	_	_
30	15	15	CD	_	_	_
31	minutes	minute	NNS	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	Cy5	cy5	NN	_	_	_
34	labeled	label	VBN	_	_	_
35	EHEC	ehec	NN	_	_	_
36	acid-adapted	acid-adapted	JJ	_	_	_
37	in	in	IN	_	_	_
38	DMEM	DMEM	NNP	_	_	_
39	pH	ph	NN	_	_	_
40	5	5	CD	_	_	_
41	,	,	,	_	_	_
42	followed	follow	VBN	_	_	_
43	by	by	IN	_	_	_
44	30	30	CD	_	_	_
45	minutes	minute	NNS	_	_	_
46	pH	ph	NN	_	_	_
47	3	3	CD	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	Cy5	cy5	NN	_	_	_
50	labeled	label	VBN	_	_	_
51	EHEC	EHEC	NNP	_	_	_
52	acid-stressed	acid-stressed	JJ	_	_	_
53	in	in	IN	_	_	_
54	DMEM	DMEM	NNP	_	_	_
55	pH	ph	NN	_	_	_
56	3	3	CD	_	_	_
57	,	,	,	_	_	_
58	15	15	CD	_	_	_
59	minutes	minute	NNS	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	Cy5	cy5	NN	_	_	_
62	labeled	label	VBN	_	_	_
63	EHEC	EHEC	NNP	_	_	_
64	acid-stressed	acid-stressed	JJ	_	_	_
65	in	in	IN	_	_	_
66	DMEM	DMEM	NNP	_	_	_
67	pH	ph	NN	_	_	_
68	3	3	CD	_	_	_
69	,	,	,	_	_	_
70	30minutes	30minutes	CD	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	EHEC	ehec	NN	_	_	_
73	strain	strain	NN	_	_	_
74	86-24	86-24	CD	_	_	_
75	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
76	Escherichia	escherichia	FW	Organism	_	_
77	coli	coli	FW	Organism	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	RNA	rna	NN	_	_	_
80	was	be	VBD	_	_	_
81	extracted	extract	VBN	_	_	_
82	using	use	VBG	_	_	_
83	Trizol	trizol	NN	_	_	_
84	-LRB-	-lrb-	-LRB-	_	_	_
85	Invitrogen	invitrogen	NN	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	Signal	signal	NN	_	_	_
89	intensities	intensity	NNS	_	_	_
90	were	be	VBD	_	_	_
91	averaged	average	VBN	_	_	_
92	among	among	IN	_	_	_
93	the	the	DT	_	_	_
94	technical	technical	JJ	_	_	_
95	replicates	replicate	VBZ	_	_	_
96	.	.	.	_	_	_

1	Two	two	CD	_	_	_
2	types	type	NNS	_	_	_
3	of	of	IN	_	_	_
4	data	data	NN	_	_	_
5	analysis	analysis	NN	_	_	_
6	were	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	:	:	:	_	_	_
9	to	to	TO	_	_	_
10	indentify	indentify	VB	_	_	_
11	density-dependent	density-dependent	JJ	_	_	_
12	changes	change	NNS	_	_	_
13	in	in	IN	_	_	_
14	gene	gene	NN	_	_	_
15	expression	expression	NN	_	_	_
16	,	,	,	_	_	_
17	single	single	JJ	_	_	_
18	averaged	average	VBD	_	_	_
19	normalized	normalize	VBN	_	_	_
20	signal	signal	NN	_	_	_
21	intensities	intensity	NNS	_	_	_
22	for	for	IN	_	_	_
23	each	each	DT	_	_	_
24	treatment	treatment	NN	_	_	_
25	point	point	NN	_	_	_
26	were	be	VBD	_	_	_
27	compared	compare	VBN	_	_	_
28	to	to	TO	_	_	_
29	the	the	DT	_	_	_
30	average	average	NN	_	_	_
31	of	of	IN	_	_	_
32	corresponding	corresponding	JJ	_	_	_
33	unstressed	unstressed	JJ	_	_	_
34	control	control	NN	_	_	_
35	signal	signal	NN	_	_	_
36	intensities	intensity	NNS	_	_	_
37	.	.	.	_	_	_

1	Genes	gene	NNS	_	_	_
2	which	which	WDT	_	_	_
3	showed	show	VBD	_	_	_
4	a	a	DT	_	_	_
5	relative	relative	JJ	_	_	_
6	signal	signal	NN	_	_	_
7	log2ratio	log2ratio	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	SLR	slr	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	value	value	NN	_	_	_
12	above	above	IN	_	_	_
13	1.0	1.0	CD	_	_	_
14	or	or	CC	_	_	_
15	below	below	IN	_	_	_
16	-1.0	-1.0	CD	_	_	_
17	were	be	VBD	_	_	_
18	selected	select	VBN	_	_	_
19	for	for	IN	_	_	_
20	further	further	JJ	_	_	_
21	analysis	analysis	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Signal	signal	NN	_	_	_
3	intensities	intensity	NNS	_	_	_
4	were	be	VBD	_	_	_
5	averaged	average	VBN	_	_	_
6	among	among	IN	_	_	_
7	the	the	DT	_	_	_
8	technical	technical	JJ	_	_	_
9	replicates	replicate	VBZ	_	_	_
10	.	.	.	_	_	_

1	Two	two	CD	_	_	_
2	types	type	NNS	_	_	_
3	of	of	IN	_	_	_
4	data	data	NN	_	_	_
5	analysis	analysis	NN	_	_	_
6	were	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	:	:	:	_	_	_
9	to	to	TO	_	_	_
10	indentify	indentify	VB	_	_	_
11	density-dependent	density-dependent	JJ	_	_	_
12	changes	change	NNS	_	_	_
13	in	in	IN	_	_	_
14	gene	gene	NN	_	_	_
15	expression	expression	NN	_	_	_
16	,	,	,	_	_	_
17	single	single	JJ	_	_	_
18	averaged	average	VBD	_	_	_
19	normalized	normalize	VBN	_	_	_
20	signal	signal	NN	_	_	_
21	intensities	intensity	NNS	_	_	_
22	for	for	IN	_	_	_
23	each	each	DT	_	_	_
24	treatment	treatment	NN	_	_	_
25	point	point	NN	_	_	_
26	were	be	VBD	_	_	_
27	compared	compare	VBN	_	_	_
28	to	to	TO	_	_	_
29	the	the	DT	_	_	_
30	average	average	NN	_	_	_
31	of	of	IN	_	_	_
32	corresponding	corresponding	JJ	_	_	_
33	unstressed	unstressed	JJ	_	_	_
34	control	control	NN	_	_	_
35	signal	signal	NN	_	_	_
36	intensities	intensity	NNS	_	_	_
37	.	.	.	_	_	_

1	Genes	gene	NNS	_	_	_
2	which	which	WDT	_	_	_
3	showed	show	VBD	_	_	_
4	a	a	DT	_	_	_
5	relative	relative	JJ	_	_	_
6	signal	signal	NN	_	_	_
7	log2ratio	log2ratio	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	SLR	slr	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	value	value	NN	_	_	_
12	above	above	IN	_	_	_
13	1.0	1.0	CD	_	_	_
14	or	or	CC	_	_	_
15	below	below	IN	_	_	_
16	-1.0	-1.0	CD	_	_	_
17	were	be	VBD	_	_	_
18	selected	select	VBN	_	_	_
19	for	for	IN	_	_	_
20	further	further	JJ	_	_	_
21	analysis	analysis	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Treatment	treatment	NN	_	_	_
3	1	1	CD	_	_	_
4	:	:	:	_	_	_
5	UA30	ua30	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	EHEC	ehec	NN	_	_	_
8	86-24	86-24	CD	_	_	_
9	exposed	expose	VBN	_	_	_
10	to	to	TO	_	_	_
11	pH	ph	NN	_	_	_
12	3	3	CD	_	_	_
13	for	for	IN	_	_	_
14	30	30	CD	_	_	_
15	min	min	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Treatment	treatment	NN	_	_	_
19	2	2	CD	_	_	_
20	:	:	:	_	_	_
21	AA30	aa30	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	EHEC	ehec	NN	_	_	_
24	86-24	86-24	CD	_	_	_
25	pH	ph	NN	_	_	_
26	5.0	5.0	CD	_	_	_
27	,	,	,	_	_	_
28	followed	follow	VBN	_	_	_
29	by	by	IN	_	_	_
30	30	30	CD	_	_	_
31	min	min	NN	_	_	_
32	pH	ph	NN	_	_	_
33	3.0	3.0	CD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
36	Treatment	treatment	NN	_	_	_
37	3	3	CD	_	_	_
38	:	:	:	_	_	_
39	UA15	ua15	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	EHEC	ehec	NN	_	_	_
42	86-24	86-24	CD	_	_	_
43	exposed	expose	VBN	_	_	_
44	to	to	TO	_	_	_
45	pH	ph	NN	_	_	_
46	3	3	CD	_	_	_
47	for	for	IN	_	_	_
48	15	15	CD	_	_	_
49	min	min	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	BW25113	bw25113	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	BW25113	bw25113	NN	_	_	_
55	mqsR	mqsr	NN	GEN	_	_
56	mutant	mutant	NN	_	_	_
57	at	at	IN	_	_	_
58	OD600	od600	NN	_	_	_
59	=	=	JJ	_	_	_
60	0.5	0.5	CD	_	_	_
61	LB	lb	NN	_	_	_
62	37C	37c	NN	_	_	_
63	suspension	suspension	NN	_	_	_
64	cell	cell	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	BW25113	bw25113	NN	_	_	_
67	wt	wt	JJ	_	_	_
68	at	at	IN	_	_	_
69	OD600	od600	NN	_	_	_
70	=	=	JJ	_	_	_
71	0.5	0.5	CD	_	_	_
72	LB	lb	NN	_	_	_
73	37C	37c	NN	_	_	_
74	suspension	suspension	NN	_	_	_
75	cell	cell	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	Chipchip	chipchip	NN	_	_	_
78	BW25113	bw25113	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	E.	e.	FW	_	_	_
81	coli	coli	FW	_	_	_
82	K-12	k-12	NN	_	_	_
83	BW25113	bw25113	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	E.	e.	FW	_	_	_
86	coli	coli	FW	_	_	_
87	K-12	k-12	NN	_	_	_
88	BW25113	bw25113	NN	_	_	_
89	mqsR	mqsr	NN	GEN	_	_
90	mutant	mutant	NN	_	_	_
91	at	at	IN	_	_	_
92	OD600	od600	NN	_	_	_
93	=	=	JJ	_	_	_
94	0.5	0.5	CD	_	_	_
95	LB	lb	NN	_	_	_
96	37C	37c	NN	_	_	_
97	suspension	suspension	NN	_	_	_
98	cell	cell	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	E.	e.	FW	_	_	_
101	coli	coli	FW	_	_	_
102	K-12	k-12	NN	_	_	_
103	BW25113	bw25113	NN	_	_	_
104	wt	wt	JJ	_	_	_
105	at	at	IN	_	_	_
106	OD600	od600	NN	_	_	_
107	=	=	JJ	_	_	_
108	0.5	0.5	CD	_	_	_
109	LB	lb	NN	_	_	_
110	37C	37c	NN	_	_	_
111	suspension	suspension	NN	_	_	_
112	cell	cell	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	Escherichia	escherichia	FW	Organism	_	_
115	coli	coli	FW	Organism	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	His-tagged	his-tagged	JJ	_	_	_
118	DNA	dna	NN	_	_	_
119	extracted	extract	VBN	_	_	_
120	from	from	IN	_	_	_
121	biofilm	biofilm	NN	_	_	_
122	cells	cell	NNS	_	_	_
123	of	of	IN	_	_	_
124	E.	e.	FW	_	_	_
125	coli	coli	FW	_	_	_
126	K-12	k-12	NN	_	_	_
127	wild	wild	JJ	_	_	_
128	type	type	NN	_	_	_
129	BW25113	bw25113	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	His-tagged	his-tagged	JJ	_	_	_
132	DNA	dna	NN	_	_	_
133	extracted	extract	VBN	_	_	_
134	from	from	IN	_	_	_
135	planktonic	planktonic	JJ	_	_	_
136	cells	cell	NNS	_	_	_
137	of	of	IN	_	_	_
138	E.	e.	FW	_	_	_
139	coli	coli	FW	_	_	_
140	K-12	k-12	NN	_	_	_
141	wild	wild	JJ	_	_	_
142	type	type	NN	_	_	_
143	BW25113	bw25113	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	MAS	mas	NN	_	_	_
146	5.0	5.0	CD	_	_	_
147	Expression	expression	NN	_	_	_
148	Analysis	analysis	NN	_	_	_
149	Default	Default	NNP	_	_	_
150	Setting	set	VBG	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	RNA	rna	NN	_	_	_
153	extracted	extract	VBN	_	_	_
154	from	from	IN	_	_	_
155	suspension	suspension	NN	_	_	_
156	cells	cell	NNS	_	_	_
157	of	of	IN	_	_	_
158	E.	e.	FW	_	_	_
159	coli	coli	FW	_	_	_
160	K-12	k-12	NN	_	_	_
161	BW25113	bw25113	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	RNA	rna	NN	_	_	_
164	extracted	extract	VBN	_	_	_
165	from	from	IN	_	_	_
166	suspension	suspension	NN	_	_	_
167	cells	cell	NNS	_	_	_
168	of	of	IN	_	_	_
169	E.	e.	FW	_	_	_
170	coli	coli	FW	_	_	_
171	K-12	k-12	NN	_	_	_
172	BW25113	bw25113	NN	_	_	_
173	mqsR	mqsr	NN	GEN	_	_
174	deleted	delete	VBN	_	_	_
175	mutant	mutant	JJ	_	_	_
176	after	after	IN	_	_	_
177	OD600	od600	NN	_	_	_
178	=	=	JJ	_	_	_
179	0.5	0.5	CD	_	_	_
180	of	of	IN	_	_	_
181	growth	growth	NN	_	_	_
182	in	in	IN	_	_	_
183	LB	lb	NN	_	_	_
184	at	at	IN	_	_	_
185	37oC	37oc	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	RNA	rna	NN	_	_	_
188	extracted	extract	VBN	_	_	_
189	from	from	IN	_	_	_
190	suspension	suspension	NN	_	_	_
191	cells	cell	NNS	_	_	_
192	of	of	IN	_	_	_
193	E.	e.	FW	_	_	_
194	coli	coli	FW	_	_	_
195	K-12	k-12	NN	_	_	_
196	BW25113	bw25113	NN	_	_	_
197	wild	wild	JJ	_	_	_
198	type	type	NN	_	_	_
199	after	after	IN	_	_	_
200	OD600	od600	NN	_	_	_
201	=	=	JJ	_	_	_
202	0.5	0.5	CD	_	_	_
203	of	of	IN	_	_	_
204	growth	growth	NN	_	_	_
205	in	in	IN	_	_	_
206	LB	lb	NN	_	_	_
207	at	at	IN	_	_	_
208	37oC	37oc	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
210	The	the	DT	_	_	_
211	overnight	overnight	JJ	_	_	_
212	culture	culture	NN	_	_	_
213	-LRB-	-lrb-	-LRB-	_	_	_
214	2.5	2.5	CD	_	_	_
215	ml	ml	NN	_	_	_
216	-RRB-	-rrb-	-RRB-	_	_	_
217	was	be	VBD	_	_	_
218	used	use	VBN	_	_	_
219	to	to	TO	_	_	_
220	inoculate	inoculate	VB	_	_	_
221	250	250	CD	_	_	_
222	ml	ml	NN	_	_	_
223	of	of	IN	_	_	_
224	fresh	fresh	JJ	_	_	_
225	LB	lb	NN	MED	_	_
226	medium	medium	NN	MED	_	_
227	with	with	IN	_	_	_
228	10	10	CD	_	_	_
229	g	g	NN	_	_	_
230	of	of	IN	_	_	_
231	submerged	submerged	JJ	_	_	_
232	glass	glass	NN	_	_	_
233	wool	wool	NN	_	_	_
234	-LRB-	-lrb-	-LRB-	_	_	_
235	Corning	Corning	NNP	_	_	_
236	Glass	Glass	NNP	_	_	_
237	Works	Works	NNP	_	_	_
238	,	,	,	_	_	_
239	Corning	Corning	NNP	_	_	_
240	,	,	,	_	_	_
241	NY	NY	NNP	_	_	_
242	-RRB-	-rrb-	-RRB-	_	_	_
243	for	for	IN	_	_	_
244	forming	form	VBG	_	_	_
245	biofilm	biofilm	NN	_	_	_
246	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	24	24	CD	_	_	_
5	h	h	NN	_	_	_
6	at	at	IN	_	_	_
7	37oC	37oc	NN	_	_	_
8	with	with	IN	_	_	_
9	shaking	shake	VBG	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	250	250	CD	_	_	_
12	rpm	rpm	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	,	,	,	_	_	_
15	the	the	DT	_	_	_
16	glass	glass	NN	_	_	_
17	wool	wool	NN	_	_	_
18	was	be	VBD	_	_	_
19	carefully	carefully	RB	_	_	_
20	and	and	CC	_	_	_
21	quickly	quickly	RB	_	_	_
22	removed	remove	VBD	_	_	_
23	and	and	CC	_	_	_
24	rinsed	rinse	VBD	_	_	_
25	with	with	IN	_	_	_
26	100	100	CD	_	_	_
27	ml	ml	NN	_	_	_
28	of	of	IN	_	_	_
29	sterile	sterile	JJ	_	_	_
30	0.85	0.85	CD	_	_	_
31	%	%	NN	_	_	_
32	NaCl	nacl	NN	_	_	_
33	solution	solution	NN	_	_	_
34	at	at	IN	_	_	_
35	0oC	0oc	NN	_	_	_
36	.	.	.	_	_	_

1	Biofilm	biofilm	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	sonicating	sonicate	VBG	_	_	_
7	the	the	DT	_	_	_
8	glass	glass	NN	_	_	_
9	wool	wool	NN	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	sterile	sterile	JJ	_	_	_
15	0.85	0.85	CD	_	_	_
16	%	%	NN	_	_	_
17	NaCl	nacl	NN	_	_	_
18	solution	solution	NN	_	_	_
19	at	at	IN	_	_	_
20	0oC	0oc	NN	_	_	_
21	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	overnight	overnight	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	to	to	TO	_	_	_
8	inoculate	inoculate	VB	_	_	_
9	25	25	CD	_	_	_
10	ml	ml	NN	_	_	_
11	of	of	IN	_	_	_
12	fresh	fresh	JJ	_	_	_
13	LB	lb	NN	MED	_	_
14	medium	medium	NN	MED	_	_
15	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	OD600	od600	NN	_	_	_
5	=	=	JJ	_	_	_
6	0.5	0.5	CD	_	_	_
7	at	at	IN	_	_	_
8	37oC	37oc	NN	_	_	_
9	under	under	IN	_	_	_
10	2	2	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	IPTG	iptg	NN	_	_	_
13	with	with	IN	_	_	_
14	shaking	shake	VBG	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	250	250	CD	_	_	_
17	rpm	rpm	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	the	the	DT	_	_	_
21	planktonic	planktonic	JJ	_	_	_
22	cells	cell	NNS	_	_	_
23	were	be	VBD	_	_	_
24	quickly	quickly	RB	_	_	_
25	removed	remove	VBN	_	_	_
26	and	and	CC	_	_	_
27	the	the	DT	_	_	_
28	total	total	JJ	_	_	_
29	RNA	rna	NN	_	_	_
30	was	be	VBD	_	_	_
31	isolated	isolate	VBN	_	_	_
32	with	with	IN	_	_	_
33	Qiagen	Qiagen	NNP	_	_	_
34	RNeasy	RNeasy	NNP	_	_	_
35	mini	minus	NNS	_	_	_
36	Kit	kit	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Cat	cat	NN	_	_	_
39	#	#	#	_	_	_
40	74104	74104	CD	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	overnight	overnight	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	to	to	TO	_	_	_
8	inoculate	inoculate	VB	_	_	_
9	25	25	CD	_	_	_
10	ml	ml	NN	_	_	_
11	of	of	IN	_	_	_
12	fresh	fresh	JJ	_	_	_
13	LB	lb	NN	MED	_	_
14	medium	medium	NN	MED	_	_
15	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	OD600	od600	NN	_	_	_
5	=	=	JJ	_	_	_
6	0.5	0.5	CD	_	_	_
7	at	at	IN	_	_	_
8	37oC	37oc	NN	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	250	250	CD	_	_	_
13	rpm	rpm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	the	the	DT	_	_	_
17	planktonic	planktonic	JJ	_	_	_
18	cells	cell	NNS	_	_	_
19	were	be	VBD	_	_	_
20	quickly	quickly	RB	_	_	_
21	removed	remove	VBN	_	_	_
22	and	and	CC	_	_	_
23	the	the	DT	_	_	_
24	total	total	JJ	_	_	_
25	RNA	rna	NN	_	_	_
26	was	be	VBD	_	_	_
27	isolated	isolate	VBN	_	_	_
28	with	with	IN	_	_	_
29	Qiagen	Qiagen	NNP	_	_	_
30	RNeasy	RNeasy	NNP	_	_	_
31	mini	minus	NNS	_	_	_
32	Kit	kit	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	Cat	cat	NN	_	_	_
35	#	#	#	_	_	_
36	74104	74104	CD	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	overnight	overnight	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	to	to	TO	_	_	_
8	inoculate	inoculate	VB	_	_	_
9	25	25	CD	_	_	_
10	ml	ml	NN	_	_	_
11	of	of	IN	_	_	_
12	fresh	fresh	JJ	_	_	_
13	LB	lb	NN	MED	_	_
14	medium	medium	NN	MED	_	_
15	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	OD600	od600	NN	_	_	_
5	=	=	JJ	_	_	_
6	0.8	0.8	CD	_	_	_
7	at	at	IN	_	_	_
8	37oC	37oc	NN	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	250	250	CD	_	_	_
13	rpm	rpm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	adding	add	VBG	_	_	_
17	0.5	0.5	CD	_	_	_
18	%	%	NN	_	_	_
19	L-arabinose	l-arabinose	NN	_	_	_
20	and	and	CC	_	_	_
21	incubated	incubate	VBN	_	_	_
22	for	for	IN	_	_	_
23	24	24	CD	_	_	_
24	h	h	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	10,000	10,000	CD	_	_	_
27	U	U	NNP	_	_	_
28	Pencillin	Pencillin	NNP	_	_	_
29	G	G	NNP	_	_	_
30	in	in	IN	_	_	_
31	media	media	NNS	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	72	72	CD	_	_	_
34	hr	hr	NN	_	_	_
35	colony	colony	NN	_	_	_
36	growth	growth	NN	_	_	_
37	equiv	equiv	NN	_	_	_
38	.	.	.	_	_	_

1	to	to	TO	_	_	_
2	wildtype	wildtype	JJ	_	_	_
3	colony	colony	NN	_	_	_
4	size	size	NN	_	_	_
5	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
6	Escherichia	escherichia	FW	Organism	_	_
7	coli	coli	FW	Organism	_	_
8	str	str	FW	_	_	_
9	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	W3110	w3110	CD	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	L-form	l-form	NN	_	_	_
4	,	,	,	_	_	_
5	brain	brain	NN	_	_	_
6	heart	heart	NN	_	_	_
7	infusion	infusion	NN	_	_	_
8	agar	agar	NN	_	_	_
9	+	+	CC	_	_	_
10	Sucrose	sucrose	NN	_	_	_
11	+	+	CC	_	_	_
12	MgSO4	mgso4	NN	_	_	_
13	+	+	CC	_	_	_
14	Pen	pen	NN	_	_	_
15	G	g	NN	_	_	_
16	,	,	,	_	_	_
17	rep	rep	NN	GEN	_	_
18	1	1	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	L-form	l-form	NN	_	_	_
21	,	,	,	_	_	_
22	brain	brain	NN	_	_	_
23	heart	heart	NN	_	_	_
24	infusion	infusion	NN	_	_	_
25	agar	agar	NN	_	_	_
26	+	+	CC	_	_	_
27	Sucrose	sucrose	NN	_	_	_
28	+	+	CC	_	_	_
29	MgSO4	mgso4	NN	_	_	_
30	+	+	CC	_	_	_
31	Pen	pen	NN	_	_	_
32	G	g	NN	_	_	_
33	,	,	,	_	_	_
34	rep	rep	NN	GEN	_	_
35	2	2	CD	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	L-form	l-form	NN	_	_	_
38	,	,	,	_	_	_
39	brain	brain	NN	_	_	_
40	heart	heart	NN	_	_	_
41	infusion	infusion	NN	_	_	_
42	agar	agar	NN	_	_	_
43	+	+	CC	_	_	_
44	Sucrose	sucrose	NN	_	_	_
45	+	+	CC	_	_	_
46	MgSO4	mgso4	NN	_	_	_
47	+	+	CC	_	_	_
48	Pen	pen	NN	_	_	_
49	G	g	NN	_	_	_
50	,	,	,	_	_	_
51	rep	rep	NN	GEN	_	_
52	3	3	CD	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	L-form	l-form	JJ	_	_	_
55	colony	colony	NN	_	_	_
56	morphology	morphology	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	MasterPure	masterpure	NN	_	_	_
59	RNA	rna	NN	_	_	_
60	purification	purification	NN	_	_	_
61	Kit	kit	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	overnight	overnight	JJ	_	_	_
64	colony	colony	NN	_	_	_
65	growth	growth	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	strain	strain	NN	_	_	_
68	:	:	:	_	_	_
69	L-form	l-form	JJ	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	strain	strain	NN	_	_	_
72	:	:	:	_	_	_
73	wildtype	wildtype	JJ	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
75	The	the	DT	_	_	_
76	data	datum	NNS	_	_	_
77	were	be	VBD	_	_	_
78	analyzed	analyze	VBN	_	_	_
79	with	with	IN	_	_	_
80	GCOS	gcos	NN	_	_	_
81	1.4	1.4	CD	_	_	_
82	software	software	NN	_	_	_
83	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	probe	probe	NN	_	_	_
3	sets	set	VBZ	_	_	_
4	scaling	scale	VBG	_	_	_
5	was	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	with	with	IN	_	_	_
8	a	a	DT	_	_	_
9	target	target	NN	_	_	_
10	signal	signal	NN	_	_	_
11	value	value	NN	_	_	_
12	of	of	IN	_	_	_
13	500	500	CD	_	_	_
14	.	.	.	_	_	_

1	No	no	DT	_	_	_
2	normalization	normalization	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	wildtype	wildtype	JJ	_	_	_
3	,	,	,	_	_	_
4	brain	brain	NN	_	_	_
5	heart	heart	NN	_	_	_
6	infusion	infusion	NN	_	_	_
7	agar	agar	NN	_	_	_
8	,	,	,	_	_	_
9	rep	rep	NN	GEN	_	_
10	1	1	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	wildtype	wildtype	JJ	_	_	_
13	,	,	,	_	_	_
14	brain	brain	NN	_	_	_
15	heart	heart	NN	_	_	_
16	infusion	infusion	NN	_	_	_
17	agar	agar	NN	_	_	_
18	,	,	,	_	_	_
19	rep	rep	NN	GEN	_	_
20	2	2	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	wildtype	wildtype	JJ	_	_	_
23	,	,	,	_	_	_
24	brain	brain	NN	_	_	_
25	heart	heart	NN	_	_	_
26	infusion	infusion	NN	_	_	_
27	agar	agar	NN	_	_	_
28	,	,	,	_	_	_
29	rep	rep	NN	GEN	_	_
30	3	3	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	wildtype	wildtype	JJ	_	_	_
33	,	,	,	_	_	_
34	brain	brain	NN	_	_	_
35	heart	heart	NN	_	_	_
36	infusion	infusion	NN	_	_	_
37	agar	agar	NN	_	_	_
38	+	+	CC	_	_	_
39	Sucrose	sucrose	NN	_	_	_
40	+	+	CC	_	_	_
41	MgSO4	mgso4	NN	_	_	_
42	,	,	,	_	_	_
43	rep	rep	NN	GEN	_	_
44	1	1	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	wildtype	wildtype	JJ	_	_	_
47	,	,	,	_	_	_
48	brain	brain	NN	_	_	_
49	heart	heart	NN	_	_	_
50	infusion	infusion	NN	_	_	_
51	agar	agar	NN	_	_	_
52	+	+	CC	_	_	_
53	Sucrose	sucrose	NN	_	_	_
54	+	+	CC	_	_	_
55	MgSO4	mgso4	NN	_	_	_
56	,	,	,	_	_	_
57	rep	rep	NN	GEN	_	_
58	2	2	CD	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	wildtype	wildtype	JJ	_	_	_
61	,	,	,	_	_	_
62	brain	brain	NN	_	_	_
63	heart	heart	NN	_	_	_
64	infusion	infusion	NN	_	_	_
65	agar	agar	NN	_	_	_
66	+	+	CC	_	_	_
67	Sucrose	sucrose	NN	_	_	_
68	+	+	CC	_	_	_
69	MgSO4	mgso4	NN	_	_	_
70	,	,	,	_	_	_
71	rep	rep	NN	GEN	_	_
72	3	3	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	wildtype	wildtype	JJ	_	_	_
75	colony	colony	NN	_	_	_
76	morphology	morphology	NN	_	_	_
77	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
78	Ambion	Ambion	NNP	_	_	_
79	RiboPure	RiboPure	NNP	_	_	_
80	RNA	rna	NN	_	_	_
81	Isolation	isolation	NN	_	_	_
82	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
83	Data	Data	NNP	_	_	_
84	included	include	VBD	_	_	_
85	in	in	IN	_	_	_
86	file	file	NN	_	_	_
87	has	have	VBZ	_	_	_
88	not	not	RB	_	_	_
89	been	be	VBN	_	_	_
90	processed	process	VBN	_	_	_
91	other	other	JJ	_	_	_
92	than	than	IN	_	_	_
93	those	those	DT	_	_	_
94	protocols	protocol	NNS	_	_	_
95	within	within	IN	_	_	_
96	GCOSv1	gcosv1	NN	_	_	_
97	.4	.4	CD	_	_	_
98	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
99	Escherichia	escherichia	FW	Organism	_	_
100	coli	coli	FW	Organism	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	Escherichia	escherichia	FW	Organism	_	_
103	coli	coli	FW	Organism	_	_
104	8624	8624	CD	_	_	_
105	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
106	Escherichia	escherichia	FW	Organism	_	_
107	coli	coli	FW	Organism	_	_
108	8624	8624	CD	_	_	_
109	grown	grow	VBN	_	_	_
110	in	in	IN	_	_	_
111	DMEM	dmem	NN	_	_	_
112	with	with	IN	_	_	_
113	AI3	ai3	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	Escherichia	escherichia	FW	Organism	_	_
116	coli	coli	FW	Organism	_	_
117	8624	8624	CD	_	_	_
118	grown	grow	VBN	_	_	_
119	in	in	IN	_	_	_
120	DMEM	dmem	NN	_	_	_
121	with	with	IN	_	_	_
122	Epinephrine	epinephrine	NN	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	Escherichia	escherichia	FW	Organism	_	_
125	coli	coli	FW	Organism	_	_
126	8624	8624	CD	_	_	_
127	grown	grow	VBN	_	_	_
128	in	in	IN	_	_	_
129	LB	LB	NNP	_	_	_
130	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
131	Escherichia	escherichia	FW	Organism	_	_
132	coli	coli	FW	Organism	_	_
133	8624	8624	CD	_	_	_
134	in	in	IN	_	_	_
135	LB	LB	NNP	_	_	_
136	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
137	Escherichia	escherichia	FW	Organism	_	_
138	coli	coli	FW	Organism	_	_
139	8624	8624	CD	_	_	_
140	kdpE	kdpe	NN	GEN	_	_
141	deletion	deletion	NN	_	_	_
142	mutant	mutant	JJ	_	_	_
143	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
144	Escherichia	escherichia	FW	Organism	_	_
145	coli	coli	FW	Organism	_	_
146	8624	8624	CD	_	_	_
147	kdpE	kdpe	NN	GEN	_	_
148	deletion	deletion	NN	_	_	_
149	mutant	mutant	JJ	_	_	_
150	grown	grow	VBN	_	_	_
151	in	in	IN	_	_	_
152	DMEM	DMEM	NNP	_	_	_
153	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
154	Escherichia	escherichia	FW	Organism	_	_
155	coli	coli	FW	Organism	_	_
156	8624	8624	CD	_	_	_
157	qseB	qseb	NN	GEN	_	_
158	deletion	deletion	NN	_	_	_
159	mutant	mutant	JJ	_	_	_
160	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
161	Escherichia	escherichia	FW	Organism	_	_
162	coli	coli	FW	Organism	_	_
163	8624	8624	CD	_	_	_
164	qseB	qseb	NN	GEN	_	_
165	deletion	deletion	NN	_	_	_
166	mutant	mutant	JJ	_	_	_
167	grown	grow	VBN	_	_	_
168	in	in	IN	_	_	_
169	DMEM	DMEM	NNP	_	_	_
170	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
171	Escherichia	escherichia	FW	Organism	_	_
172	coli	coli	FW	Organism	_	_
173	8624	8624	CD	_	_	_
174	qseC	qsec	NN	GEN	_	_
175	deletion	deletion	NN	_	_	_
176	mutant	mutant	JJ	_	_	_
177	grown	grow	VBN	_	_	_
178	in	in	IN	_	_	_
179	DMEM	DMEM	NNP	_	_	_
180	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
181	Escherichia	escherichia	FW	Organism	_	_
182	coli	coli	FW	Organism	_	_
183	8624	8624	CD	_	_	_
184	qseC	qsec	NN	GEN	_	_
185	deletion	deletion	NN	_	_	_
186	mutant	mutant	JJ	_	_	_
187	grown	grow	VBN	_	_	_
188	in	in	IN	_	_	_
189	DMEM	dmem	NN	_	_	_
190	with	with	IN	_	_	_
191	AI3	ai3	NN	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	Escherichia	escherichia	FW	Organism	_	_
194	coli	coli	FW	Organism	_	_
195	8624	8624	CD	_	_	_
196	qseC	qsec	NN	GEN	_	_
197	deletion	deletion	NN	_	_	_
198	mutant	mutant	JJ	_	_	_
199	grown	grow	VBN	_	_	_
200	in	in	IN	_	_	_
201	DMEM	dmem	NN	_	_	_
202	with	with	IN	_	_	_
203	Epinephrine	epinephrine	NN	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	Escherichia	escherichia	FW	Organism	_	_
206	coli	coli	FW	Organism	_	_
207	8624	8624	CD	_	_	_
208	qseC	qsec	NN	GEN	_	_
209	mutant	mutant	JJ	_	_	_
210	grown	grow	VBN	_	_	_
211	in	in	IN	_	_	_
212	LB	LB	NNP	_	_	_
213	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
214	Escherichia	escherichia	FW	Organism	_	_
215	coli	coli	FW	Organism	_	_
216	8624	8624	CD	_	_	_
217	qseC	qsec	NN	GEN	_	_
218	mutant	mutant	NN	_	_	_
219	in	in	IN	_	_	_
220	DMEM	DMEM	NNP	_	_	_
221	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
222	Escherichia	escherichia	FW	Organism	_	_
223	coli	coli	FW	Organism	_	_
224	8624	8624	CD	_	_	_
225	qseC	qsec	NN	GEN	_	_
226	mutant	mutant	NN	_	_	_
227	in	in	IN	_	_	_
228	DMEM	dmem	NN	_	_	_
229	with	with	IN	_	_	_
230	AI3	ai3	NN	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	Escherichia	escherichia	FW	Organism	_	_
233	coli	coli	FW	Organism	_	_
234	8624	8624	CD	_	_	_
235	qseC	qsec	NN	GEN	_	_
236	mutant	mutant	NN	_	_	_
237	in	in	IN	_	_	_
238	DMEM	dmem	NN	_	_	_
239	with	with	IN	_	_	_
240	epinephrine	epinephrine	NN	_	_	_
241	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
242	Escherichia	escherichia	FW	Organism	_	_
243	coli	coli	FW	Organism	_	_
244	8624	8624	CD	_	_	_
245	qseC	qsec	NN	GEN	_	_
246	mutant	mutant	NN	_	_	_
247	in	in	IN	_	_	_
248	LB	LB	NNP	_	_	_
249	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
250	grown	grow	VBN	_	_	_
251	to	to	TO	_	_	_
252	OD600	od600	NN	_	_	_
253	=	=	JJ	_	_	_
254	1.0	1.0	CD	_	_	_
255	in	in	IN	_	_	_
256	DMEM	DMEM	NNP	_	_	_
257	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
258	grown	grow	VBN	_	_	_
259	to	to	TO	_	_	_
260	OD600	od600	NN	_	_	_
261	=	=	JJ	_	_	_
262	1.0	1.0	CD	_	_	_
263	in	in	IN	_	_	_
264	DMEM	dmem	NN	_	_	_
265	with	with	IN	_	_	_
266	50	50	CD	_	_	_
267	uM	um	NN	_	_	_
268	epinephrine	epinephrine	NN	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	grown	grow	VBN	_	_	_
271	to	to	TO	_	_	_
272	OD600	od600	NN	_	_	_
273	=	=	JJ	_	_	_
274	1.0	1.0	CD	_	_	_
275	in	in	IN	_	_	_
276	DMEM	dmem	NN	_	_	_
277	with	with	IN	_	_	_
278	AI3	ai3	NN	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	grown	grow	VBN	_	_	_
281	to	to	TO	_	_	_
282	OD600	od600	NN	_	_	_
283	=	=	JJ	_	_	_
284	1.0	1.0	CD	_	_	_
285	in	in	IN	_	_	_
286	DMEM	dmem	NN	_	_	_
287	with	with	IN	_	_	_
288	AI3	ai3	NN	_	_	_
289	signaling	signaling	NN	_	_	_
290	molecule	molecule	NN	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	grown	grow	VBN	_	_	_
293	to	to	TO	_	_	_
294	OD600	od600	NN	_	_	_
295	=	=	JJ	_	_	_
296	1.0	1.0	CD	_	_	_
297	in	in	IN	_	_	_
298	DMEM	dmem	NN	_	_	_
299	with	with	IN	_	_	_
300	Epinephrine	epinephrine	NN	_	_	_
301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
302	grown	grow	VBN	_	_	_
303	to	to	TO	_	_	_
304	OD600	od600	NN	_	_	_
305	=	=	JJ	_	_	_
306	1.0	1.0	CD	_	_	_
307	in	in	IN	_	_	_
308	LB	LB	NNP	_	_	_
309	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
310	strain	strain	NN	_	_	_
311	:	:	:	_	_	_
312	Escherichia	escherichia	FW	Organism	_	_
313	coli	coli	FW	Organism	_	_
314	8624	8624	CD	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
316	strain	strain	NN	_	_	_
317	:	:	:	_	_	_
318	Escherichia	escherichia	FW	Organism	_	_
319	coli	coli	FW	Organism	_	_
320	strain	strain	NN	_	_	_
321	8624	8624	CD	_	_	_
322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
323	strain	strain	NN	_	_	_
324	:	:	:	_	_	_
325	Escherichia	escherichia	FW	Organism	_	_
326	coli	coli	FW	Organism	_	_
327	strain	strain	NN	_	_	_
328	8624	8624	CD	_	_	_
329	kdpE	kdpe	NN	GEN	_	_
330	mutant	mutant	JJ	_	_	_
331	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
332	strain	strain	NN	_	_	_
333	:	:	:	_	_	_
334	Escherichia	escherichia	FW	Organism	_	_
335	coli	coli	FW	Organism	_	_
336	strain	strain	NN	_	_	_
337	8624	8624	CD	_	_	_
338	qseB	qseb	NN	GEN	_	_
339	mutant	mutant	JJ	_	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
341	strain	strain	NN	_	_	_
342	:	:	:	_	_	_
343	Escherichia	escherichia	FW	Organism	_	_
344	coli	coli	FW	Organism	_	_
345	strain	strain	NN	_	_	_
346	8624	8624	CD	_	_	_
347	qseC	qseC	NNP	GEN	_	_
348	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
349	strain	strain	NN	_	_	_
350	:	:	:	_	_	_
351	Escherichia	escherichia	FW	Organism	_	_
352	coli	coli	FW	Organism	_	_
353	strain	strain	NN	_	_	_
354	8624	8624	CD	_	_	_
355	qseC	qsec	NN	GEN	_	_
356	mutant	mutant	JJ	_	_	_
357	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
358	E.	e.	FW	_	_	_
359	coli	coli	FW	_	_	_
360	strain	strain	NN	_	_	_
361	B-a	b-a	JJ	_	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
363	E.	e.	FW	_	_	_
364	coli	coli	FW	_	_	_
365	strain	strain	NN	_	_	_
366	B-b	b-b	JJ	_	_	_
367	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
368	E.	e.	FW	_	_	_
369	coli	coli	FW	_	_	_
370	strain	strain	NN	_	_	_
371	B	b	NN	_	_	_
372	DNA	dna	NN	_	_	_
373	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
374	E.	e.	FW	_	_	_
375	coli	coli	FW	_	_	_
376	strain	strain	NN	_	_	_
377	K12-a	k12-a	NN	_	_	_
378	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
379	E.	e.	FW	_	_	_
380	coli	coli	FW	_	_	_
381	strain	strain	NN	_	_	_
382	K12-b	k12-b	NN	_	_	_
383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
384	E.	e.	FW	_	_	_
385	coli	coli	FW	_	_	_
386	strain	strain	NN	_	_	_
387	K12-c	k12-c	NN	_	_	_
388	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
389	E.	e.	FW	_	_	_
390	coli	coli	FW	_	_	_
391	strain	strain	NN	_	_	_
392	K12-d	k12-d	JJ	_	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
394	E.	e.	FW	_	_	_
395	coli	coli	FW	_	_	_
396	strain	strain	NN	_	_	_
397	K12	k12	NN	_	_	_
398	DNA	dna	NN	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	Escherichia	escherichia	FW	Organism	_	_
401	coli	coli	FW	Organism	_	_
402	B	b	NN	_	_	_
403	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
404	Escherichia	escherichia	FW	Organism	_	_
405	coli	coli	FW	Organism	_	_
406	K-12	k-12	NN	_	_	_
407	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
408	Genomic	genomic	JJ	_	_	_
409	bacterial	bacterial	JJ	_	_	_
410	DNA	dna	NN	_	_	_
411	was	be	VBD	_	_	_
412	extracted	extract	VBN	_	_	_
413	following	follow	VBG	_	_	_
414	the	the	DT	_	_	_
415	protocol	protocol	NN	_	_	_
416	described	describe	VBN	_	_	_
417	in	in	IN	_	_	_
418	Maniatis	Maniatis	NNP	_	_	_
419	Sambrook	Sambrook	NNP	_	_	_
420	-LRB-	-lrb-	-LRB-	_	_	_
421	Sambrook	Sambrook	NNP	_	_	_
422	et	et	FW	_	_	_
423	al.	al.	FW	_	_	_
424	,	,	,	_	_	_
425	1989	1989	CD	_	_	_
426	-RRB-	-rrb-	-RRB-	_	_	_
427	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	sonicated	sonicate	VBN	_	_	_
4	in	in	IN	_	_	_
5	a	a	DT	_	_	_
6	Bioruptor	Bioruptor	NNP	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Diagenode	Diagenode	NNP	_	_	_
9	,	,	,	_	_	_
10	Liege	Liege	NNP	_	_	_
11	,	,	,	_	_	_
12	Belgium	Belgium	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	to	to	TO	_	_	_
15	obtain	obtain	VB	_	_	_
16	fragments	fragment	NNS	_	_	_
17	of	of	IN	_	_	_
18	approximately	approximately	RB	_	_	_
19	500	500	CD	_	_	_
20	bp	bp	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Signals	signal	NNS	_	_	_
3	of	of	IN	_	_	_
4	each	each	DT	_	_	_
5	slide	slide	NN	_	_	_
6	were	be	VBD	_	_	_
7	smoothed	smooth	VBN	_	_	_
8	using	use	VBG	_	_	_
9	the	the	DT	_	_	_
10	NMPP	nmpp	NN	_	_	_
11	program	program	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Wang	Wang	NNP	_	_	_
14	et	et	FW	_	_	_
15	al.	al.	FW	_	_	_
16	,	,	,	_	_	_
17	2006	2006	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	Normalisation	Normalisation	NNP	_	_	_
2	per	per	IN	_	_	_
3	chip	chip	NN	_	_	_
4	to	to	TO	_	_	_
5	50th	50th	JJ	_	_	_
6	percentile	percentile	NN	_	_	_
7	and	and	CC	_	_	_
8	further	further	JJ	_	_	_
9	analyses	analysis	NNS	_	_	_
10	were	be	VBD	_	_	_
11	performed	perform	VBN	_	_	_
12	in	in	IN	_	_	_
13	GeneSpring	GeneSpring	NNP	_	_	_
14	GX	GX	NNP	_	_	_
15	v7	v7	NN	_	_	_
16	.3.1	.3.1	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Agilent	Agilent	NNP	_	_	_
19	Technologies	Technologies	NNPS	_	_	_
20	,	,	,	_	_	_
21	Basel	Basel	NNP	_	_	_
22	,	,	,	_	_	_
23	Switzerland	Switzerland	NNP	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	B	b	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	strain	strain	NN	_	_	_
7	:	:	:	_	_	_
8	K-12	k-12	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Adenosine	adenosine	NN	_	_	_
11	addition	addition	NN	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	Alanine	Alanine	NNP	_	_	_
14	addition	addition	NN	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	Amino	amino	NN	_	_	_
17	acid	acid	NN	_	_	_
18	or	or	CC	_	_	_
19	nucleotide	nucleotide	NN	_	_	_
20	added	add	VBD	_	_	_
21	to	to	TO	_	_	_
22	final	final	JJ	_	_	_
23	concentration	concentration	NN	_	_	_
24	of	of	IN	_	_	_
25	1	1	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	not	not	RB	_	_	_
28	exceeding	exceed	VBG	_	_	_
29	1	1	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Arginine	arginine	NN	_	_	_
32	addition	addition	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Aspartate	aspartate	NN	_	_	_
35	addition	addition	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Cysteine	cysteine	NN	_	_	_
38	addition	addition	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Cytidine	cytidine	NN	_	_	_
41	addition	addition	NN	_	_	_
42	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
43	E.	E.	NNP	_	_	_
44	coli	coli	NN	_	_	_
45	cells	cell	NNS	_	_	_
46	0	0	CD	_	_	_
47	min	min	NN	_	_	_
48	before	before	IN	_	_	_
49	perturbation	perturbation	NN	_	_	_
50	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
51	E.	E.	NNP	_	_	_
52	coli	coli	NN	_	_	_
53	cells	cell	NNS	_	_	_
54	10	10	CD	_	_	_
55	min	min	NN	_	_	_
56	after	after	IN	_	_	_
57	specific	specific	JJ	_	_	_
58	perturbation	perturbation	NN	_	_	_
59	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
60	E.	E.	NNP	_	_	_
61	coli	coli	NN	_	_	_
62	cells	cell	NNS	_	_	_
63	grown	grow	VBN	_	_	_
64	to	to	TO	_	_	_
65	mid-exponential	mid-exponential	JJ	_	_	_
66	phase	phase	NN	_	_	_
67	after	after	IN	_	_	_
68	6-8	6-8	CD	_	_	_
69	generations	generation	NNS	_	_	_
70	after	after	IN	_	_	_
71	stationary	stationary	JJ	GrowthPhase	_	_
72	phase	phase	NN	GrowthPhase	_	_
73	in	in	IN	_	_	_
74	M9	m9	NN	MED	_	_
75	minimal	minimal	JJ	MED	_	_
76	medium	medium	NN	MED	_	_
77	+	+	CC	_	_	_
78	0.4	0.4	CD	_	_	_
79	%	%	NN	_	_	_
80	glucose	glucose	NN	SUPP	_	_
81	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Glutamate	glutamate	JJ	_	_	_
4	addition	addition	NN	_	_	_
5	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
6	Glutamine	Glutamine	NNP	_	_	_
7	addition	addition	NN	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	Glycine	Glycine	NNP	_	_	_
10	addition	addition	NN	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	Guanosine	Guanosine	NNP	_	_	_
13	addition	addition	NN	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	Histidine	Histidine	NNP	_	_	_
16	addition	addition	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Images	image	NNS	_	_	_
19	were	be	VBD	_	_	_
20	quantified	quantify	VBN	_	_	_
21	using	use	VBG	_	_	_
22	GenePix	GenePix	NNP	_	_	_
23	Pro	pro	FW	_	_	_
24	software	software	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Isoleucine	isoleucine	NN	_	_	_
27	addition	addition	NN	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	Lysine	Lysine	NNP	_	_	_
30	addition	addition	NN	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	Median	median	JJ	_	_	_
33	of	of	IN	_	_	_
34	intensity	intensity	NN	_	_	_
35	data	datum	NNS	_	_	_
36	was	be	VBD	_	_	_
37	extracted	extract	VBN	_	_	_
38	,	,	,	_	_	_
39	LOESS	LOESS	NNP	_	_	_
40	normalized	normalize	VBD	_	_	_
41	and	and	CC	_	_	_
42	an	a	DT	_	_	_
43	ANOVA	ANOVA	NNP	_	_	_
44	model	model	NN	_	_	_
45	was	be	VBD	_	_	_
46	fit	fit	VBN	_	_	_
47	using	use	VBG	_	_	_
48	the	the	DT	_	_	_
49	MAANOVA	MAANOVA	NNP	_	_	_
50	package	package	NN	_	_	_
51	in	in	IN	_	_	_
52	R	r	NN	_	_	_
53	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	Log	log	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	Cy5	cy5	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Methionine	methionine	NN	_	_	_
7	addition	addition	NN	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	Phenylalanine	Phenylalanine	NNP	_	_	_
10	addition	addition	NN	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	Proline	Proline	NNP	_	_	_
13	addition	addition	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Serine	serine	NN	_	_	_
16	addition	addition	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	stress	stress	NN	_	_	_
19	:	:	:	_	_	_
20	Adenosine	Adenosine	NNP	_	_	_
21	addition	addition	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	stress	stress	NN	_	_	_
24	:	:	:	_	_	_
25	Alanine	alanine	NN	_	_	_
26	addition	addition	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	stress	stress	NN	_	_	_
29	:	:	:	_	_	_
30	Arginine	arginine	NN	_	_	_
31	addition	addition	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	stress	stress	NN	_	_	_
34	:	:	:	_	_	_
35	Aspartate	Aspartate	NNP	_	_	_
36	addition	addition	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	stress	stress	NN	_	_	_
39	:	:	:	_	_	_
40	control	control	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	before	before	IN	_	_	_
43	perturbation	perturbation	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	stress	stress	NN	_	_	_
47	:	:	:	_	_	_
48	Cysteine	cysteine	NN	_	_	_
49	addition	addition	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	stress	stress	NN	_	_	_
52	:	:	:	_	_	_
53	Cytidine	cytidine	NN	_	_	_
54	addition	addition	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	stress	stress	NN	_	_	_
57	:	:	:	_	_	_
58	Glutamate	glutamate	JJ	_	_	_
59	addition	addition	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	stress	stress	NN	_	_	_
62	:	:	:	_	_	_
63	Glutamine	glutamine	NN	_	_	_
64	addition	addition	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	stress	stress	NN	_	_	_
67	:	:	:	_	_	_
68	Glycine	glycine	NN	_	_	_
69	addition	addition	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	stress	stress	NN	_	_	_
72	:	:	:	_	_	_
73	Guanosine	Guanosine	NNP	_	_	_
74	addition	addition	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	stress	stress	NN	_	_	_
77	:	:	:	_	_	_
78	Histidine	histidine	NN	_	_	_
79	addition	addition	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	stress	stress	NN	_	_	_
82	:	:	:	_	_	_
83	Isoleucine	isoleucine	NN	_	_	_
84	addition	addition	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	stress	stress	NN	_	_	_
87	:	:	:	_	_	_
88	Lysine	lysine	NN	_	_	_
89	addition	addition	NN	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	stress	stress	NN	_	_	_
92	:	:	:	_	_	_
93	Methionine	methionine	NN	_	_	_
94	addition	addition	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	stress	stress	NN	_	_	_
97	:	:	:	_	_	_
98	Phenylalanine	phenylalanine	NN	_	_	_
99	addition	addition	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	stress	stress	NN	_	_	_
102	:	:	:	_	_	_
103	Proline	Proline	NNP	_	_	_
104	addition	addition	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	stress	stress	NN	_	_	_
107	:	:	:	_	_	_
108	Serine	serine	NN	_	_	_
109	addition	addition	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	stress	stress	NN	_	_	_
112	:	:	:	_	_	_
113	Threonine	threonine	NN	_	_	_
114	addition	addition	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	stress	stress	NN	_	_	_
117	:	:	:	_	_	_
118	Thymidine	Thymidine	NNP	_	_	_
119	addition	addition	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	stress	stress	NN	_	_	_
122	:	:	:	_	_	_
123	Tryptophan	tryptophan	NN	_	_	_
124	addition	addition	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	stress	stress	NN	_	_	_
127	:	:	:	_	_	_
128	Uridine	uridine	NN	_	_	_
129	addition	addition	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	stress	stress	NN	_	_	_
132	:	:	:	_	_	_
133	Valine	Valine	NNP	_	_	_
134	addition	addition	NN	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	Threonine	threonine	NN	_	_	_
137	addition	addition	NN	_	_	_
138	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
139	Thymidine	Thymidine	NNP	_	_	_
140	addition	addition	NN	_	_	_
141	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
142	Total	Total	NNP	_	_	_
143	RNA	RNA	NNP	_	_	_
144	extracted	extract	VBN	_	_	_
145	using	use	VBG	_	_	_
146	Qiagen	Qiagen	NNP	_	_	_
147	RNEASY	RNEASY	NNP	_	_	_
148	kit	kit	NN	_	_	_
149	according	accord	VBG	_	_	_
150	to	to	TO	_	_	_
151	directions	direction	NNS	_	_	_
152	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
153	Tryptophan	Tryptophan	NNP	_	_	_
154	addition	addition	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	Uridine	uridine	NN	_	_	_
157	addition	addition	NN	_	_	_
158	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
159	Valine	Valine	NNP	_	_	_
160	addition	addition	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	antibody	antibody	NN	_	_	_
163	:	:	:	_	_	_
164	IgG	igg	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	antibody	antibody	NN	_	_	_
167	:	:	:	_	_	_
168	RNAP	rnap	NN	_	_	_
169	beta	beta	NN	_	_	_
170	subunit	subunit	NN	_	_	_
171	-LRB-	-lrb-	-LRB-	_	_	_
172	NT63	nt63	NN	_	_	_
173	-RRB-	-rrb-	-RRB-	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	Cells	cell	NNS	_	_	_
176	at	at	IN	_	_	_
177	appropriate	appropriate	JJ	_	_	_
178	cell	cell	NN	_	_	_
179	density	density	NN	_	_	_
180	were	be	VBD	_	_	_
181	cross-linked	cross-link	VBN	_	_	_
182	by	by	IN	_	_	_
183	1	1	CD	_	_	_
184	%	%	NN	_	_	_
185	formaldehyde	formaldehyde	NN	_	_	_
186	at	at	IN	_	_	_
187	room	room	NN	_	_	_
188	temperature	temperature	NN	_	_	_
189	for	for	IN	_	_	_
190	25	25	CD	_	_	_
191	min	min	NN	_	_	_
192	.	.	.	_	_	_

1	Following	follow	VBG	_	_	_
2	quenching	quench	VBG	_	_	_
3	the	the	DT	_	_	_
4	unused	unused	JJ	_	_	_
5	formaldehyde	formaldehyde	NN	_	_	_
6	with	with	IN	_	_	_
7	a	a	DT	_	_	_
8	final	final	JJ	_	_	_
9	concentration	concentration	NN	_	_	_
10	of	of	IN	_	_	_
11	125	125	CD	_	_	_
12	mM	mm	NN	KWSUPP	_	_
13	glycine	glycine	NN	_	_	_
14	at	at	IN	_	_	_
15	room	room	NN	_	_	_
16	temperature	temperature	NN	_	_	_
17	for	for	IN	_	_	_
18	5	5	CD	_	_	_
19	min	min	NN	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cross-linked	cross-linked	JJ	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	harvested	harvest	VBN	_	_	_
6	and	and	CC	_	_	_
7	washed	wash	VBN	_	_	_
8	three	three	CD	_	_	_
9	times	time	NNS	_	_	_
10	with	with	IN	_	_	_
11	50	50	CD	_	_	_
12	mL	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	ice-cold	ice-cold	JJ	_	_	_
15	TBS	tbs	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Tris	tris	NN	_	_	_
18	Buffered	buffer	VBN	_	_	_
19	Saline	saline	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	washed	wash	VBN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	re-suspended	re-suspended	JJ	_	_	_
6	in	in	IN	_	_	_
7	0.5	0.5	CD	_	_	_
8	mL	ml	NN	_	_	_
9	lysis	lysis	NN	_	_	_
10	buffer	buffer	NN	_	_	_
11	composed	compose	VBN	_	_	_
12	of	of	IN	_	_	_
13	50	50	CD	_	_	_
14	mM	mm	NN	KWSUPP	_	_
15	Tris-HCl	tris-hcl	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	pH	ph	NN	_	_	_
18	7.5	7.5	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	,	,	,	_	_	_
21	100	100	CD	_	_	_
22	mM	mm	NN	KWSUPP	_	_
23	NaCl	nacl	NN	_	_	_
24	,	,	,	_	_	_
25	1	1	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	EDTA	edta	NN	_	_	_
28	,	,	,	_	_	_
29	1	1	CD	_	_	_
30	ug	ug	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	condition	condition	NN	_	_	_
33	:	:	:	_	_	_
34	heat-shocked	heat-shocked	JJ	_	_	_
35	condition	condition	NN	_	_	_
36	without	without	IN	_	_	_
37	rifampicin	rifampicin	NN	SUPP	_	_
38	treatment	treatment	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	condition	condition	NN	_	_	_
41	:	:	:	_	_	_
42	mid-exponential	mid-exponential	JJ	_	_	_
43	condition	condition	NN	_	_	_
44	without	without	IN	_	_	_
45	rifampicin	rifampicin	NN	SUPP	_	_
46	treatment	treatment	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	condition	condition	NN	_	_	_
49	:	:	:	_	_	_
50	mid-exponential	mid-exponential	JJ	_	_	_
51	condition	condition	NN	_	_	_
52	with	with	IN	_	_	_
53	rifampicin	rifampicin	NN	SUPP	_	_
54	treatment	treatment	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	condition	condition	NN	_	_	_
57	:	:	:	_	_	_
58	nitrogen-limiting	nitrogen-limiting	JJ	_	_	_
59	condition	condition	NN	_	_	_
60	without	without	IN	_	_	_
61	rifampicin	rifampicin	NN	SUPP	_	_
62	treatment	treatment	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	condition	condition	NN	_	_	_
65	:	:	:	_	_	_
66	stationary	stationary	JJ	_	_	_
67	condition	condition	NN	_	_	_
68	without	without	IN	_	_	_
69	rifampicin	rifampicin	NN	SUPP	_	_
70	treatment	treatment	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	Cross-linked	cross-linked	JJ	_	_	_
73	and	and	CC	_	_	_
74	sonicated	sonicated	JJ	_	_	_
75	chromatin	chromatin	NN	_	_	_
76	complex	complex	NN	_	_	_
77	of	of	IN	_	_	_
78	RNAP	rnap	NN	_	_	_
79	beta-subunit	beta-subunit	NN	_	_	_
80	and	and	CC	_	_	_
81	DNA	dna	NN	_	_	_
82	was	be	VBD	_	_	_
83	immunoprecipitated	immunoprecipitate	VBN	_	_	_
84	by	by	IN	_	_	_
85	normal	normal	JJ	_	_	_
86	mouse	mouse	NN	_	_	_
87	IgG	igg	NN	_	_	_
88	-LRB-	-lrb-	-LRB-	_	_	_
89	Upstate	upstate	JJ	_	_	_
90	-RRB-	-rrb-	-RRB-	_	_	_
91	for	for	IN	_	_	_
92	the	the	DT	_	_	_
93	control	control	NN	_	_	_
94	-LRB-	-lrb-	-LRB-	_	_	_
95	mock-IP	mock-ip	NN	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cross-linked	cross-linked	JJ	_	_	_
3	and	and	CC	_	_	_
4	sonicated	sonicated	JJ	_	_	_
5	chromatin	chromatin	NN	_	_	_
6	complex	complex	NN	_	_	_
7	of	of	IN	_	_	_
8	RNAP	rnap	NN	_	_	_
9	beta-subunit	beta-subunit	NN	_	_	_
10	and	and	CC	_	_	_
11	DNA	dna	NN	_	_	_
12	was	be	VBD	_	_	_
13	immunoprecipitated	immunoprecipitate	VBN	_	_	_
14	by	by	IN	_	_	_
15	NT63	nt63	NN	_	_	_
16	mouse	mouse	NN	_	_	_
17	antibody	antibody	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	E.coli	e.coli	NNS	_	_	_
3	_	_	VBP	_	_	_
4	heat	heat	NN	_	_	_
5	_	_	NN	_	_	_
6	dynamic	dynamic	JJ	_	_	_
7	_	_	NN	_	_	_
8	1	1	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	E.coli	e.coli	NNS	_	_	_
11	_	_	VBP	_	_	_
12	heat	heat	NN	_	_	_
13	_	_	NN	_	_	_
14	dynamic	dynamic	JJ	_	_	_
15	_	_	NN	_	_	_
16	2	2	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	E.coli	e.coli	NNS	_	_	_
19	_	_	VBP	_	_	_
20	log	log	NN	_	_	_
21	_	_	NN	_	_	_
22	dynamic	dynamic	JJ	_	_	_
23	_	_	NN	_	_	_
24	1	1	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	E.coli	e.coli	NNS	_	_	_
27	_	_	VBP	_	_	_
28	log	log	NN	_	_	_
29	_	_	NN	_	_	_
30	dynamic	dynamic	JJ	_	_	_
31	_	_	NN	_	_	_
32	2	2	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	E.coli	e.coli	NNS	_	_	_
35	_	_	VBP	_	_	_
36	log	log	NN	_	_	_
37	_	_	NN	_	_	_
38	dynamic	dynamic	JJ	_	_	_
39	_	_	NN	_	_	_
40	3	3	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	E.coli	e.coli	NNS	_	_	_
43	_	_	VBP	_	_	_
44	log	log	NN	_	_	_
45	_	_	SYM	_	_	_
46	rif	rif	FW	_	_	_
47	_	_	FW	_	_	_
48	1	1	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	E.coli	e.coli	NNS	_	_	_
51	_	_	VBP	_	_	_
52	log	log	NN	_	_	_
53	_	_	CD	_	_	_
54	rif	rif	NN	_	_	_
55	_	_	NN	_	_	_
56	2	2	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	E.coli	e.coli	NNS	_	_	_
59	_	_	VBP	_	_	_
60	log	log	NN	_	_	_
61	_	_	SYM	_	_	_
62	rif	rif	FW	_	_	_
63	_	_	FW	_	_	_
64	3	3	CD	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	E.	e.	FW	_	_	_
67	coli	coli	FW	_	_	_
68	MG1655	mg1655	NN	_	_	_
69	strain	strain	NN	_	_	_
70	was	be	VBD	_	_	_
71	cultured	culture	VBN	_	_	_
72	in	in	IN	_	_	_
73	M9	m9	NN	_	_	_
74	complete	complete	JJ	_	_	_
75	medium	medium	NN	_	_	_
76	at	at	IN	_	_	_
77	37	37	CD	_	_	_
78	°C	°c	NN	_	_	_
79	with	with	IN	_	_	_
80	constant	constant	JJ	_	_	_
81	agitation	agitation	NN	_	_	_
82	and	and	CC	_	_	_
83	harvested	harvest	VBN	_	_	_
84	at	at	IN	_	_	_
85	mid-exponential	mid-exponential	JJ	_	_	_
86	phase	phase	NN	_	_	_
87	.	.	.	_	_	_

1	-LRB-	-lrb-	-LRB-	_	_	_
2	OD600nm	od600nm	NN	_	_	_
3	~	~	NN	_	_	_
4	0.6	0.6	CD	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	E.	e.	FW	_	_	_
8	coli	coli	FW	_	_	_
9	MG1655	mg1655	NN	_	_	_
10	strain	strain	NN	_	_	_
11	was	be	VBD	_	_	_
12	cultured	culture	VBN	_	_	_
13	in	in	IN	_	_	_
14	M9	m9	NN	_	_	_
15	complete	complete	JJ	_	_	_
16	medium	medium	NN	_	_	_
17	at	at	IN	_	_	_
18	37	37	CD	_	_	_
19	°C	°c	NN	_	_	_
20	with	with	IN	_	_	_
21	constant	constant	JJ	_	_	_
22	agitation	agitation	NN	_	_	_
23	and	and	CC	_	_	_
24	harvested	harvest	VBN	_	_	_
25	at	at	IN	_	_	_
26	stationary	stationary	JJ	GrowthPhase	_	_
27	phase	phase	NN	GrowthPhase	_	_
28	.	.	.	_	_	_

1	-LRB-	-lrb-	-LRB-	_	_	_
2	OD600nm	od600nm	NN	_	_	_
3	~	~	NN	_	_	_
4	1.5	1.5	CD	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	E.	e.	FW	_	_	_
8	coli	coli	FW	_	_	_
9	MG1655	mg1655	NN	_	_	_
10	strain	strain	NN	_	_	_
11	was	be	VBD	_	_	_
12	cultured	culture	VBN	_	_	_
13	in	in	IN	_	_	_
14	M9	m9	NN	_	_	_
15	complete	complete	JJ	_	_	_
16	medium	medium	NN	_	_	_
17	at	at	IN	_	_	_
18	37	37	CD	_	_	_
19	°C	°c	NN	_	_	_
20	with	with	IN	_	_	_
21	constant	constant	JJ	_	_	_
22	agitation	agitation	NN	_	_	_
23	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	heat-shock	heat-shock	NN	_	_	_
3	,	,	,	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	mix	mix	NN	_	_	_
7	with	with	IN	_	_	_
8	pre-warmed	pre-warmed	JJ	_	_	_
9	medium	medium	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	50	50	CD	_	_	_
12	°C	°c	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	and	and	CC	_	_	_
15	incubated	incubate	VBN	_	_	_
16	at	at	IN	_	_	_
17	45	45	CD	_	_	_
18	°C	°c	NN	_	_	_
19	for	for	IN	_	_	_
20	10	10	CD	_	_	_
21	min	min	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	strain	strain	NN	_	_	_
6	was	be	VBD	_	_	_
7	cultured	culture	VBN	_	_	_
8	in	in	IN	_	_	_
9	W2	w2	NN	_	_	_
10	minimal	minimal	JJ	_	_	_
11	medium	medium	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	for	for	IN	_	_	_
14	nitrogen-limiting	nitrogen-limiting	JJ	_	_	_
15	condition	condition	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	at	at	IN	_	_	_
18	37	37	CD	_	_	_
19	°C	°c	NN	_	_	_
20	with	with	IN	_	_	_
21	constant	constant	JJ	_	_	_
22	agitation	agitation	NN	_	_	_
23	and	and	CC	_	_	_
24	harvested	harvest	VBN	_	_	_
25	at	at	IN	_	_	_
26	mid-exponential	mid-exponential	JJ	_	_	_
27	phase	phase	NN	_	_	_
28	.	.	.	_	_	_

1	-LRB-	-lrb-	-LRB-	_	_	_
2	OD600nm	od600nm	NN	_	_	_
3	~	~	NN	_	_	_
4	0.6	0.6	CD	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	Powell	Powell	NNP	_	_	_
8	,	,	,	_	_	_
9	B.	B.	NNP	_	_	_
10	S.	S.	NNP	_	_	_
11	et	et	FW	_	_	_
12	al.	al.	FW	_	_	_
13	.	.	.	_	_	_

1	J	j	NN	_	_	_
2	of	of	IN	_	_	_
3	Biol	Biol	NNP	_	_	_
4	.	.	.	_	_	_

1	Chem	Chem	NNP	_	_	_
2	.270	.270	CD	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	9	9	CD	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	:	:	:	_	_	_
7	4822	4822	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	E.coli	e.coli	NNS	_	_	_
11	_	_	VBP	_	_	_
12	nitrogen	nitrogen	NN	_	_	_
13	_	_	NN	_	_	_
14	dynamic	dynamic	JJ	_	_	_
15	_	_	NN	_	_	_
16	1	1	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	E.coli	e.coli	NNS	_	_	_
19	_	_	VBP	_	_	_
20	nitrogen	nitrogen	NN	_	_	_
21	_	_	NN	_	_	_
22	dynamic	dynamic	JJ	_	_	_
23	_	_	NN	_	_	_
24	2	2	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	E.coli	e.coli	NNS	_	_	_
27	RNAP	rnap	NN	_	_	_
28	beta	beta	NN	_	_	_
29	subunit	subunit	NN	_	_	_
30	ChIP	chip	NN	_	_	_
31	DNA	dna	NN	_	_	_
32	from	from	IN	_	_	_
33	heat-shocked	heat-shocked	JJ	_	_	_
34	condition	condition	NN	_	_	_
35	without	without	IN	_	_	_
36	rifampicin	rifampicin	NN	SUPP	_	_
37	treatment	treatment	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	E.coli	e.coli	NNS	_	_	_
40	RNAP	rnap	NN	_	_	_
41	beta	beta	NN	_	_	_
42	subunit	subunit	NN	_	_	_
43	ChIP	chip	NN	_	_	_
44	DNA	dna	NN	_	_	_
45	from	from	IN	_	_	_
46	mid-exponential	mid-exponential	JJ	_	_	_
47	condition	condition	NN	_	_	_
48	without	without	IN	_	_	_
49	rifampicin	rifampicin	NN	SUPP	_	_
50	treatment	treatment	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	E.coli	e.coli	NNS	_	_	_
53	RNAP	rnap	NN	_	_	_
54	beta	beta	NN	_	_	_
55	subunit	subunit	NN	_	_	_
56	ChIP	chip	NN	_	_	_
57	DNA	dna	NN	_	_	_
58	from	from	IN	_	_	_
59	mid-exponential	mid-exponential	JJ	_	_	_
60	condition	condition	NN	_	_	_
61	with	with	IN	_	_	_
62	rifampicin	rifampicin	NN	SUPP	_	_
63	treatment	treatment	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	E.coli	e.coli	NNS	_	_	_
66	RNAP	rnap	NN	_	_	_
67	beta	beta	NN	_	_	_
68	subunit	subunit	NN	_	_	_
69	ChIP	chip	NN	_	_	_
70	DNA	dna	NN	_	_	_
71	from	from	IN	_	_	_
72	nitrogen-limiting	nitrogen-limiting	JJ	_	_	_
73	condition	condition	NN	_	_	_
74	without	without	IN	_	_	_
75	rifampicin	rifampicin	NN	SUPP	_	_
76	treatment	treatment	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	E.coli	e.coli	NNS	_	_	_
79	RNAP	rnap	NN	_	_	_
80	beta	beta	NN	_	_	_
81	subunit	subunit	NN	_	_	_
82	ChIP	chip	NN	_	_	_
83	DNA	dna	NN	_	_	_
84	from	from	IN	_	_	_
85	stationary	stationary	JJ	_	_	_
86	condition	condition	NN	_	_	_
87	without	without	IN	_	_	_
88	rifampicin	rifampicin	NN	SUPP	_	_
89	treatment	treatment	NN	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	E.coli	e.coli	NNS	_	_	_
92	_	_	VBP	_	_	_
93	stat	stat	NN	_	_	_
94	_	_	CD	_	_	_
95	dynamic	dynamic	JJ	_	_	_
96	_	_	NN	_	_	_
97	1	1	CD	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	E.coli	e.coli	NNS	_	_	_
100	_	_	VBP	_	_	_
101	stat	stat	NN	_	_	_
102	_	_	CD	_	_	_
103	dynamic	dynamic	JJ	_	_	_
104	_	_	NN	_	_	_
105	2	2	CD	_	_	_
106	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
107	Escherichia	escherichia	FW	Organism	_	_
108	coli	coli	FW	Organism	_	_
109	str	str	FW	_	_	_
110	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Input	input	NN	_	_	_
4	DNA	dna	NN	_	_	_
5	from	from	IN	_	_	_
6	heat-shocked	heat-shocked	JJ	_	_	_
7	condition	condition	NN	_	_	_
8	without	without	IN	_	_	_
9	rifampicin	rifampicin	NN	SUPP	_	_
10	treatment	treatment	NN	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	Input	Input	NNP	_	_	_
13	DNA	dna	NN	_	_	_
14	from	from	IN	_	_	_
15	mid-exponential	mid-exponential	JJ	_	_	_
16	condition	condition	NN	_	_	_
17	without	without	IN	_	_	_
18	rifampicin	rifampicin	NN	SUPP	_	_
19	treatment	treatment	NN	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	Input	Input	NNP	_	_	_
22	DNA	dna	NN	_	_	_
23	from	from	IN	_	_	_
24	mid-exponential	mid-exponential	JJ	_	_	_
25	condition	condition	NN	_	_	_
26	with	with	IN	_	_	_
27	rifampicin	rifampicin	NN	SUPP	_	_
28	treatment	treatment	NN	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	Input	Input	NNP	_	_	_
31	DNA	dna	NN	_	_	_
32	from	from	IN	_	_	_
33	nitrogen-limiting	nitrogen-limiting	JJ	_	_	_
34	condition	condition	NN	_	_	_
35	without	without	IN	_	_	_
36	rifampicin	rifampicin	NN	SUPP	_	_
37	treatment	treatment	NN	_	_	_
38	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
39	Input	Input	NNP	_	_	_
40	DNA	dna	NN	_	_	_
41	from	from	IN	_	_	_
42	stationary	stationary	JJ	_	_	_
43	condition	condition	NN	_	_	_
44	without	without	IN	_	_	_
45	rifampicin	rifampicin	NN	SUPP	_	_
46	treatment	treatment	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	reference	reference	NN	_	_	_
49	:	:	:	_	_	_
50	Input	input	NN	_	_	_
51	DNA	dna	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	strain	strain	NN	_	_	_
54	:	:	:	_	_	_
55	MG1655	mg1655	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
57	test	test	NN	_	_	_
58	:	:	:	_	_	_
59	ChIP	chip	NN	_	_	_
60	DNA	dna	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	The	the	DT	_	_	_
63	raw	raw	JJ	_	_	_
64	data	data	NN	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	.	.	.	_	_	_

1	pair	pair	NN	_	_	_
2	file	file	NN	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	was	be	VBD	_	_	_
5	subjected	subject	VBN	_	_	_
6	to	to	TO	_	_	_
7	per	per	IN	_	_	_
8	channel	channel	NN	_	_	_
9	quantile	quantile	NN	_	_	_
10	normalization	normalization	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Bolstad	Bolstad	NNP	_	_	_
13	et	et	FW	_	_	_
14	al.	al.	FW	_	_	_
15	.	.	.	_	_	_

1	Bioinformatics	bioinformatic	NNS	_	_	_
2	19	19	CD	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	2	2	CD	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	:	:	:	_	_	_
7	185	185	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	,	,	,	_	_	_
10	IP	IP	NNP	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	5	5	CD	_	_	_
13	ml	ml	NN	_	_	_
14	of	of	IN	_	_	_
15	the	the	DT	_	_	_
16	culture	culture	NN	_	_	_
17	was	be	VBD	_	_	_
18	mixed	mix	VBN	_	_	_
19	with	with	IN	_	_	_
20	1	1	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	bovine-biased-1	bovine-biased-1	NN	_	_	_
23	strain	strain	NN	_	_	_
24	grown	grow	VBN	_	_	_
25	to	to	TO	_	_	_
26	exponential	exponential	JJ	GrowthPhase	_	_
27	phase	phase	NN	GrowthPhase	_	_
28	of	of	IN	_	_	_
29	growth	growth	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	bovine-biased-2	bovine-biased-2	NN	_	_	_
32	strain	strain	NN	_	_	_
33	grown	grow	VBN	_	_	_
34	to	to	TO	_	_	_
35	exponential	exponential	JJ	GrowthPhase	_	_
36	phase	phase	NN	GrowthPhase	_	_
37	of	of	IN	_	_	_
38	growth	growth	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	bovine-biased-3	bovine-biased-3	NN	_	_	_
41	strain	strain	NN	_	_	_
42	grown	grow	VBN	_	_	_
43	to	to	TO	_	_	_
44	exponential	exponential	JJ	GrowthPhase	_	_
45	phase	phase	NN	GrowthPhase	_	_
46	of	of	IN	_	_	_
47	growth	growth	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	bovine-biased-4	bovine-biased-4	NN	_	_	_
50	strain	strain	NN	_	_	_
51	grown	grow	VBN	_	_	_
52	to	to	TO	_	_	_
53	exponential	exponential	JJ	GrowthPhase	_	_
54	phase	phase	NN	GrowthPhase	_	_
55	of	of	IN	_	_	_
56	growth	growth	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	clinical-1	clinical-1	NN	_	_	_
59	strain	strain	NN	_	_	_
60	grown	grow	VBN	_	_	_
61	to	to	TO	_	_	_
62	exponential	exponential	JJ	GrowthPhase	_	_
63	phase	phase	NN	GrowthPhase	_	_
64	of	of	IN	_	_	_
65	growth	growth	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	Clinical-1	clinical-1	NN	_	_	_
68	vs	vs	CC	_	_	_
69	Bovine-biased-1	bovine-biased-1	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	Clinical-1	clinical-1	NN	_	_	_
72	vs	vs	CC	_	_	_
73	Bovine-biased-2	bovine-biased-2	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	Clinical-1	clinical-1	NN	_	_	_
76	vs	vs	CC	_	_	_
77	Bovine-biased-3	bovine-biased-3	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	Clinical-1	clinical-1	NN	_	_	_
80	vs	vs	CC	_	_	_
81	Bovine-biased-4	bovine-biased-4	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	clinical-2	clinical-2	NN	_	_	_
84	strain	strain	NN	_	_	_
85	grown	grow	VBN	_	_	_
86	to	to	TO	_	_	_
87	exponential	exponential	JJ	GrowthPhase	_	_
88	phase	phase	NN	GrowthPhase	_	_
89	of	of	IN	_	_	_
90	growth	growth	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	Clinical-2	clinical-2	NN	_	_	_
93	vs	vs	CC	_	_	_
94	Bovine-biased-1	bovine-biased-1	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	Clinical-2	clinical-2	NN	_	_	_
97	vs	vs	CC	_	_	_
98	Bovine-biased-2	bovine-biased-2	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	Clinical-2	clinical-2	NN	_	_	_
101	vs	vs	CC	_	_	_
102	Bovine-biased-3	bovine-biased-3	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	Clinical-2	clinical-2	NN	_	_	_
105	vs	vs	CC	_	_	_
106	Bovine-biased-4	bovine-biased-4	NN	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	clinical-3	clinical-3	NN	_	_	_
109	strain	strain	NN	_	_	_
110	grown	grow	VBN	_	_	_
111	to	to	TO	_	_	_
112	exponential	exponential	JJ	GrowthPhase	_	_
113	phase	phase	NN	GrowthPhase	_	_
114	of	of	IN	_	_	_
115	growth	growth	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	Clinical-3	clinical-3	NN	_	_	_
118	vs	vs	CC	_	_	_
119	Bovine-biased-1	bovine-biased-1	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	Clinical-3	clinical-3	NN	_	_	_
122	vs	vs	CC	_	_	_
123	Bovine-biased-2	bovine-biased-2	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	Clinical-3	clinical-3	NN	_	_	_
126	vs	vs	CC	_	_	_
127	Bovine-biased-3	bovine-biased-3	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	Clinical-3	clinical-3	NN	_	_	_
130	vs	vs	CC	_	_	_
131	Bovine-biased-4	bovine-biased-4	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	clinical-4	clinical-4	NN	_	_	_
134	strain	strain	NN	_	_	_
135	grown	grow	VBN	_	_	_
136	to	to	TO	_	_	_
137	exponential	exponential	JJ	GrowthPhase	_	_
138	phase	phase	NN	GrowthPhase	_	_
139	of	of	IN	_	_	_
140	growth	growth	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	Clinical-4	clinical-4	NN	_	_	_
143	vs	vs	CC	_	_	_
144	Bovine-biased-1	bovine-biased-1	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	Clinical-4	clinical-4	NN	_	_	_
147	vs	vs	CC	_	_	_
148	Bovine-biased-2	bovine-biased-2	NN	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	Clinical-4	clinical-4	NN	_	_	_
151	vs	vs	CC	_	_	_
152	Bovine-biased-3	bovine-biased-3	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	Clinical-4	clinical-4	NN	_	_	_
155	vs	vs	CC	_	_	_
156	Bovine-biased-4	bovine-biased-4	NN	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
158	Escherichia	escherichia	FW	Organism	_	_
159	coli	coli	FW	Organism	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	replicate	replicate	VB	_	_	_
162	:	:	:	_	_	_
163	1	1	CD	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	replicate	replicate	VB	_	_	_
166	:	:	:	_	_	_
167	2	2	CD	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
169	replicate	replicate	VBP	_	_	_
170	:	:	:	_	_	_
171	3	3	CD	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	replicate	replicate	VB	_	_	_
174	:	:	:	_	_	_
175	4	4	CD	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	strain	strain	NN	_	_	_
178	:	:	:	_	_	_
179	e.	e.	FW	_	_	_
180	coli	coli	FW	_	_	_
181	o157	o157	FW	_	_	_
182	H7	h7	NN	_	_	_
183	strain	strain	NN	_	_	_
184	TW10915	tw10915	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	strain	strain	NN	_	_	_
187	:	:	:	_	_	_
188	e.	e.	FW	_	_	_
189	coli	coli	FW	_	_	_
190	o157	o157	FW	_	_	_
191	H7	h7	NN	_	_	_
192	strain	strain	NN	_	_	_
193	TW10916	tw10916	NN	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	strain	strain	NN	_	_	_
196	:	:	:	_	_	_
197	e.	e.	FW	_	_	_
198	coli	coli	FW	_	_	_
199	o157	o157	FW	_	_	_
200	H7	h7	NN	_	_	_
201	strain	strain	NN	_	_	_
202	TW10917	tw10917	NN	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	strain	strain	NN	_	_	_
205	:	:	:	_	_	_
206	e.	e.	FW	_	_	_
207	coli	coli	FW	_	_	_
208	o157	o157	FW	_	_	_
209	H7	h7	NN	_	_	_
210	strain	strain	NN	_	_	_
211	TW10938	tw10938	NN	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	strain	strain	NN	_	_	_
214	:	:	:	_	_	_
215	e.	e.	FW	_	_	_
216	coli	coli	FW	_	_	_
217	o157	o157	FW	_	_	_
218	H7	h7	NN	_	_	_
219	strain	strain	NN	_	_	_
220	TW10948	tw10948	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	strain	strain	NN	_	_	_
223	:	:	:	_	_	_
224	e.	e.	FW	_	_	_
225	coli	coli	FW	_	_	_
226	o157	o157	FW	_	_	_
227	H7	h7	NN	_	_	_
228	strain	strain	NN	_	_	_
229	TW10950	tw10950	NN	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
231	strain	strain	NN	_	_	_
232	:	:	:	_	_	_
233	e.	e.	FW	_	_	_
234	coli	coli	FW	_	_	_
235	o157	o157	FW	_	_	_
236	H7	h7	NN	_	_	_
237	strain	strain	NN	_	_	_
238	TW10957	tw10957	NN	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	strain	strain	NN	_	_	_
241	:	:	:	_	_	_
242	e.	e.	FW	_	_	_
243	coli	coli	FW	_	_	_
244	o157	o157	FW	_	_	_
245	H7	h7	NN	_	_	_
246	strain	strain	NN	_	_	_
247	TW10967	tw10967	NN	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
249	The	the	DT	_	_	_
250	microarray	microarray	NN	_	_	_
251	data	datum	NNS	_	_	_
252	were	be	VBD	_	_	_
253	analyzed	analyze	VBN	_	_	_
254	using	use	VBG	_	_	_
255	R	r	NN	_	_	_
256	-LRB-	-lrb-	-LRB-	_	_	_
257	v.	v.	CC	_	_	_
258	2.2.1	2.2.1	CD	_	_	_
259	-RRB-	-rrb-	-RRB-	_	_	_
260	and	and	CC	_	_	_
261	the	the	DT	_	_	_
262	MAANOVA	MAANOVA	NNP	_	_	_
263	-LRB-	-lrb-	-LRB-	_	_	_
264	v.	v.	CC	_	_	_
265	0.98.8	0.98.8	CD	_	_	_
266	-RRB-	-rrb-	-RRB-	_	_	_
267	package	package	NN	_	_	_
268	.	.	.	_	_	_

1	Raw	raw	NN	_	_	_
2	intensity	intensity	NN	_	_	_
3	values	value	NNS	_	_	_
4	from	from	IN	_	_	_
5	replicate	replicate	VBP	_	_	_
6	probes	probe	NNS	_	_	_
7	were	be	VBD	_	_	_
8	averaged	average	VBN	_	_	_
9	and	and	CC	_	_	_
10	log2	log2	NN	_	_	_
11	transformed	transform	VBN	_	_	_
12	after	after	IN	_	_	_
13	normalization	normalization	NN	_	_	_
14	with	with	IN	_	_	_
15	the	the	DT	_	_	_
16	pin-tip	pin-tip	JJ	_	_	_
17	LOWESS	lowess	NN	_	_	_
18	method	method	NN	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	normalized	normalize	VBN	_	_	_
3	intensity	intensity	NN	_	_	_
4	values	value	NNS	_	_	_
5	were	be	VBD	_	_	_
6	fitted	fit	VBN	_	_	_
7	to	to	TO	_	_	_
8	a	a	DT	_	_	_
9	mixed	mixed	JJ	_	_	_
10	model	model	NN	_	_	_
11	ANOVA	ANOVA	NNP	_	_	_
12	considering	consider	VBG	_	_	_
13	array	array	NN	_	_	_
14	and	and	CC	_	_	_
15	biological	biological	JJ	_	_	_
16	replicates	replicate	VBZ	_	_	_
17	as	as	IN	_	_	_
18	random	random	JJ	_	_	_
19	factors	factor	NNS	_	_	_
20	and	and	CC	_	_	_
21	dye	dye	VB	_	_	_
22	,	,	,	_	_	_
23	strain	strain	NN	_	_	_
24	as	as	IN	_	_	_
25	fixed	fixed	JJ	_	_	_
26	factors	factor	NNS	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	linear	linear	JJ	_	_	_
3	model	model	NN	_	_	_
4	tested	test	VBN	_	_	_
5	was	be	VBD	_	_	_
6	Y	y	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	intensity	intensity	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	=	=	JJ	_	_	_
11	array	array	NN	_	_	_
12	+	+	CC	_	_	_
13	dye	dye	VB	_	_	_
14	+	+	CC	_	_	_
15	strain	strain	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	clinical	clinical	JJ	_	_	_
18	or	or	CC	_	_	_
19	bovine-biased	bovine-biased	JJ	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	+	+	CC	_	_	_
22	sample	sample	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	biological	biological	JJ	_	_	_
25	replicate	replicate	VBP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	+	+	CC	_	_	_
28	error	error	NN	_	_	_
29	.	.	.	_	_	_

1	Significant	significant	JJ	_	_	_
2	differences	difference	NNS	_	_	_
3	in	in	IN	_	_	_
4	expression	expression	NN	_	_	_
5	due	due	JJ	_	_	_
6	to	to	TO	_	_	_
7	strain	strain	NN	_	_	_
8	were	be	VBD	_	_	_
9	determined	determine	VBN	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	Fs	f	NNS	_	_	_
13	test	test	NN	_	_	_
14	in	in	IN	_	_	_
15	MAANOVA	MAANOVA	NNP	_	_	_
16	which	which	WDT	_	_	_
17	uses	use	VBZ	_	_	_
18	a	a	DT	_	_	_
19	shrinkage	shrinkage	NN	_	_	_
20	estimator	estimator	NN	_	_	_
21	for	for	IN	_	_	_
22	gene-specific	gene-specific	JJ	_	_	_
23	variance	variance	NN	_	_	_
24	components	component	NNS	_	_	_
25	that	that	WDT	_	_	_
26	makes	make	VBZ	_	_	_
27	no	no	DT	_	_	_
28	assumption	assumption	NN	_	_	_
29	about	about	IN	_	_	_
30	the	the	DT	_	_	_
31	variances	variance	NNS	_	_	_
32	across	across	IN	_	_	_
33	genes	gene	NNS	_	_	_
34	with	with	IN	_	_	_
35	500	500	CD	_	_	_
36	random	random	JJ	_	_	_
37	permutations	permutation	NNS	_	_	_
38	to	to	TO	_	_	_
39	estimate	estimate	VB	_	_	_
40	the	the	DT	_	_	_
41	p-values	p-value	NNS	_	_	_
42	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	q-value	q-value	JJ	_	_	_
3	package	package	NN	_	_	_
4	in	in	IN	_	_	_
5	R	r	NN	_	_	_
6	was	be	VBD	_	_	_
7	used	use	VBN	_	_	_
8	for	for	IN	_	_	_
9	determining	determine	VBG	_	_	_
10	the	the	DT	_	_	_
11	false	false	JJ	_	_	_
12	discovery	discovery	NN	_	_	_
13	rate	rate	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	FDR	FDR	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	SAM	SAM	NNP	_	_	_
2	provided	provide	VBN	_	_	_
3	by	by	IN	_	_	_
4	TMEV	tmev	NN	_	_	_
5	was	be	VBD	_	_	_
6	also	also	RB	_	_	_
7	used	use	VBN	_	_	_
8	for	for	IN	_	_	_
9	data	data	NN	_	_	_
10	analysis	analysis	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	microarray	microarray	NN	_	_	_
4	data	datum	NNS	_	_	_
5	were	be	VBD	_	_	_
6	analyzed	analyze	VBN	_	_	_
7	using	use	VBG	_	_	_
8	R	r	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	v.	v.	CC	_	_	_
11	2.2.1	2.2.1	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	the	the	DT	_	_	_
15	MAANOVA	MAANOVA	NNP	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	v.	v.	CC	_	_	_
18	0.98.8	0.98.8	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	package	package	NN	_	_	_
21	.	.	.	_	_	_

1	Raw	raw	NN	_	_	_
2	intensity	intensity	NN	_	_	_
3	values	value	NNS	_	_	_
4	from	from	IN	_	_	_
5	replicate	replicate	VBP	_	_	_
6	probes	probe	NNS	_	_	_
7	were	be	VBD	_	_	_
8	averaged	average	VBN	_	_	_
9	and	and	CC	_	_	_
10	log2	log2	NN	_	_	_
11	transformed	transform	VBN	_	_	_
12	after	after	IN	_	_	_
13	normalization	normalization	NN	_	_	_
14	with	with	IN	_	_	_
15	the	the	DT	_	_	_
16	pin-tip	pin-tip	JJ	_	_	_
17	LOWESS	lowess	NN	_	_	_
18	method	method	NN	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	normalized	normalize	VBN	_	_	_
3	intensity	intensity	NN	_	_	_
4	values	value	NNS	_	_	_
5	were	be	VBD	_	_	_
6	fitted	fit	VBN	_	_	_
7	to	to	TO	_	_	_
8	a	a	DT	_	_	_
9	mixed	mixed	JJ	_	_	_
10	model	model	NN	_	_	_
11	ANOVA	ANOVA	NNP	_	_	_
12	considering	consider	VBG	_	_	_
13	array	array	NN	_	_	_
14	and	and	CC	_	_	_
15	biological	biological	JJ	_	_	_
16	replicates	replicate	VBZ	_	_	_
17	as	as	IN	_	_	_
18	random	random	JJ	_	_	_
19	factors	factor	NNS	_	_	_
20	and	and	CC	_	_	_
21	dye	dye	VB	_	_	_
22	,	,	,	_	_	_
23	strain	strain	NN	_	_	_
24	as	as	IN	_	_	_
25	fixed	fixed	JJ	_	_	_
26	factor	factor	NN	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	linear	linear	JJ	_	_	_
3	model	model	NN	_	_	_
4	tested	test	VBN	_	_	_
5	was	be	VBD	_	_	_
6	Y	y	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	intensity	intensity	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	=	=	JJ	_	_	_
11	array	array	NN	_	_	_
12	+	+	CC	_	_	_
13	dye	dye	VB	_	_	_
14	+	+	CC	_	_	_
15	strain	strain	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	clinical	clinical	JJ	_	_	_
18	or	or	CC	_	_	_
19	bovine-biased	bovine-biased	JJ	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	+	+	CC	_	_	_
22	sample	sample	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	biological	biological	JJ	_	_	_
25	replicate	replicate	VBP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	+	+	CC	_	_	_
28	error	error	NN	_	_	_
29	.	.	.	_	_	_

1	Significant	significant	JJ	_	_	_
2	differences	difference	NNS	_	_	_
3	in	in	IN	_	_	_
4	expression	expression	NN	_	_	_
5	due	due	JJ	_	_	_
6	to	to	TO	_	_	_
7	strain	strain	NN	_	_	_
8	were	be	VBD	_	_	_
9	determined	determine	VBN	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	Fs	f	NNS	_	_	_
13	test	test	NN	_	_	_
14	in	in	IN	_	_	_
15	MAANOVA	MAANOVA	NNP	_	_	_
16	which	which	WDT	_	_	_
17	uses	use	VBZ	_	_	_
18	a	a	DT	_	_	_
19	shrinkage	shrinkage	NN	_	_	_
20	estimator	estimator	NN	_	_	_
21	for	for	IN	_	_	_
22	gene-specific	gene-specific	JJ	_	_	_
23	variance	variance	NN	_	_	_
24	components	component	NNS	_	_	_
25	that	that	WDT	_	_	_
26	makes	make	VBZ	_	_	_
27	no	no	DT	_	_	_
28	assumption	assumption	NN	_	_	_
29	about	about	IN	_	_	_
30	the	the	DT	_	_	_
31	variances	variance	NNS	_	_	_
32	across	across	IN	_	_	_
33	genes	gene	NNS	_	_	_
34	with	with	IN	_	_	_
35	500	500	CD	_	_	_
36	random	random	JJ	_	_	_
37	permutations	permutation	NNS	_	_	_
38	to	to	TO	_	_	_
39	estimate	estimate	VB	_	_	_
40	the	the	DT	_	_	_
41	p-values	p-value	NNS	_	_	_
42	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	q-value	q-value	JJ	_	_	_
3	package	package	NN	_	_	_
4	in	in	IN	_	_	_
5	R	r	NN	_	_	_
6	was	be	VBD	_	_	_
7	used	use	VBN	_	_	_
8	for	for	IN	_	_	_
9	determining	determine	VBG	_	_	_
10	the	the	DT	_	_	_
11	false	false	JJ	_	_	_
12	discovery	discovery	NN	_	_	_
13	rate	rate	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	FDR	FDR	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	SAM	SAM	NNP	_	_	_
2	provided	provide	VBN	_	_	_
3	by	by	IN	_	_	_
4	TMEV	tmev	NN	_	_	_
5	was	be	VBD	_	_	_
6	also	also	RB	_	_	_
7	used	use	VBN	_	_	_
8	for	for	IN	_	_	_
9	data	data	NN	_	_	_
10	analysis	analysis	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	TW10915	tw10915	NN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	DMEM	DMEM	NNP	_	_	_
8	medium	medium	NN	_	_	_
9	upto	upto	NN	_	_	_
10	exponential	exponential	JJ	GrowthPhase	_	_
11	phase	phase	NN	GrowthPhase	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	OD600	od600	NN	_	_	_
14	~	~	NN	_	_	_
15	0.5	0.5	CD	_	_	_
16	,	,	,	_	_	_
17	2.5	2.5	CD	_	_	_
18	h	h	NN	_	_	_
19	after	after	IN	_	_	_
20	inoclulation	inoclulation	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	at	at	IN	_	_	_
23	37C	37c	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	TW10916	tw10916	NN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	DMEM	DMEM	NNP	_	_	_
8	medium	medium	NN	_	_	_
9	upto	upto	NN	_	_	_
10	exponential	exponential	JJ	GrowthPhase	_	_
11	phase	phase	NN	GrowthPhase	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	OD600	od600	NN	_	_	_
14	~	~	NN	_	_	_
15	0.5	0.5	CD	_	_	_
16	,	,	,	_	_	_
17	2.5	2.5	CD	_	_	_
18	h	h	NN	_	_	_
19	after	after	IN	_	_	_
20	inoclulation	inoclulation	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	at	at	IN	_	_	_
23	37C	37c	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	TW10917	tw10917	NN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	DMEM	DMEM	NNP	_	_	_
8	medium	medium	NN	_	_	_
9	upto	upto	NN	_	_	_
10	exponential	exponential	JJ	GrowthPhase	_	_
11	phase	phase	NN	GrowthPhase	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	OD600	od600	NN	_	_	_
14	~	~	NN	_	_	_
15	0.5	0.5	CD	_	_	_
16	,	,	,	_	_	_
17	2.5	2.5	CD	_	_	_
18	h	h	NN	_	_	_
19	after	after	IN	_	_	_
20	inoclulation	inoclulation	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	at	at	IN	_	_	_
23	37C	37c	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	TW10938	tw10938	NN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	DMEM	DMEM	NNP	_	_	_
8	medium	medium	NN	_	_	_
9	upto	upto	NN	_	_	_
10	exponential	exponential	JJ	GrowthPhase	_	_
11	phase	phase	NN	GrowthPhase	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	OD600	od600	NN	_	_	_
14	~	~	NN	_	_	_
15	0.5	0.5	CD	_	_	_
16	,	,	,	_	_	_
17	2.5	2.5	CD	_	_	_
18	h	h	NN	_	_	_
19	after	after	IN	_	_	_
20	inoclulation	inoclulation	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	at	at	IN	_	_	_
23	37C	37c	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	TW10948	tw10948	NN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	DMEM	DMEM	NNP	_	_	_
8	medium	medium	NN	_	_	_
9	upto	upto	NN	_	_	_
10	exponential	exponential	JJ	GrowthPhase	_	_
11	phase	phase	NN	GrowthPhase	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	OD600	od600	NN	_	_	_
14	~	~	NN	_	_	_
15	0.5	0.5	CD	_	_	_
16	,	,	,	_	_	_
17	2.5	2.5	CD	_	_	_
18	h	h	NN	_	_	_
19	after	after	IN	_	_	_
20	inoclulation	inoclulation	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	at	at	IN	_	_	_
23	37C	37c	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	TW10950	tw10950	NN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	DMEM	DMEM	NNP	_	_	_
8	medium	medium	NN	_	_	_
9	upto	upto	NN	_	_	_
10	exponential	exponential	JJ	GrowthPhase	_	_
11	phase	phase	NN	GrowthPhase	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	OD600	od600	NN	_	_	_
14	~	~	NN	_	_	_
15	0.5	0.5	CD	_	_	_
16	,	,	,	_	_	_
17	2.5	2.5	CD	_	_	_
18	h	h	NN	_	_	_
19	after	after	IN	_	_	_
20	inoclulation	inoclulation	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	at	at	IN	_	_	_
23	37C	37c	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	TW10957	tw10957	NN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	DMEM	DMEM	NNP	_	_	_
8	medium	medium	NN	_	_	_
9	upto	upto	NN	_	_	_
10	exponential	exponential	JJ	GrowthPhase	_	_
11	phase	phase	NN	GrowthPhase	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	OD600	od600	NN	_	_	_
14	~	~	NN	_	_	_
15	0.5	0.5	CD	_	_	_
16	,	,	,	_	_	_
17	2.5	2.5	CD	_	_	_
18	h	h	NN	_	_	_
19	after	after	IN	_	_	_
20	inoclulation	inoclulation	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	at	at	IN	_	_	_
23	37C	37c	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	TW10967	tw10967	NN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	DMEM	DMEM	NNP	_	_	_
8	medium	medium	NN	_	_	_
9	upto	upto	NN	_	_	_
10	exponential	exponential	JJ	GrowthPhase	_	_
11	phase	phase	NN	GrowthPhase	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	OD600	od600	NN	_	_	_
14	~	~	NN	_	_	_
15	0.5	0.5	CD	_	_	_
16	,	,	,	_	_	_
17	2.5	2.5	CD	_	_	_
18	h	h	NN	_	_	_
19	after	after	IN	_	_	_
20	inoclulation	inoclulation	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	at	at	IN	_	_	_
23	37C	37c	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Batch	batch	NN	_	_	_
3	cultures	culture	NNS	_	_	_
4	of	of	IN	_	_	_
5	E.	e.	FW	_	_	_
6	coli	coli	FW	_	_	_
7	MG1655	mg1655	NN	_	_	_
8	were	be	VBD	_	_	_
9	grown	grow	VBN	_	_	_
10	at	at	IN	_	_	_
11	37	37	CD	_	_	_
12	°C	°c	NN	_	_	_
13	with	with	IN	_	_	_
14	shaking	shake	VBG	_	_	_
15	in	in	IN	_	_	_
16	Luria-Bertani	luria-bertani	JJ	_	_	_
17	medium	medium	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	0.1	0.1	CD	_	_	_
20	%	%	NN	_	_	_
21	Bacto	bacto	NN	_	_	_
22	Tryptone	tryptone	NN	_	_	_
23	,	,	,	_	_	_
24	0.05	0.05	CD	_	_	_
25	%	%	NN	_	_	_
26	yeast	yeast	NN	SUPP	_	_
27	extract	extract	NN	SUPP	_	_
28	,	,	,	_	_	_
29	0.05	0.05	CD	_	_	_
30	%	%	NN	_	_	_
31	NaCl	nacl	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	For	for	IN	_	_	_
6	cross-linking	cross-linking	NN	_	_	_
7	,	,	,	_	_	_
8	30	30	CD	_	_	_
9	mL	ml	NN	_	_	_
10	of	of	IN	_	_	_
11	cells	cell	NNS	_	_	_
12	were	be	VBD	_	_	_
13	mixed	mix	VBN	_	_	_
14	with	with	IN	_	_	_
15	300	300	CD	_	_	_
16	uL	ul	NN	_	_	_
17	1M	1m	NN	_	_	_
18	sodium	sodium	NN	_	_	_
19	phosphates	phosphate	NNS	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	pH	ph	NN	_	_	_
22	7.6	7.6	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	and	and	CC	_	_	_
25	810	810	CD	_	_	_
26	uL	ul	NN	_	_	_
27	37	37	CD	_	_	_
28	%	%	NN	_	_	_
29	formaldehyde	formaldehyde	NN	_	_	_
30	.	.	.	_	_	_

1	Cross-linking	cross-linking	NN	_	_	_
2	was	be	VBD	_	_	_
3	quenched	quench	VBN	_	_	_
4	by	by	IN	_	_	_
5	addition	addition	NN	_	_	_
6	of	of	IN	_	_	_
7	2	2	CD	_	_	_
8	mL	ml	NN	_	_	_
9	2M	2m	NN	_	_	_
10	glycine	glycine	NN	_	_	_
11	.	.	.	_	_	_

1	Protein-DNA	protein-dna	JJ	_	_	_
2	complexes	complex	NNS	_	_	_
3	were	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	from	from	IN	_	_	_
6	cells	cell	NNS	_	_	_
7	grown	grow	VBN	_	_	_
8	to	to	TO	_	_	_
9	early	early	JJ	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	2.4	2.4	CD	_	_	_
12	x	x	CC	_	_	_
13	10	10	CD	_	_	_
14	^	^	NN	_	_	_
15	7	7	CD	_	_	_
16	CFU	CFU	NNP	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	Genomic	genomic	JJ	_	_	_
19	DNA	dna	NN	_	_	_
20	Extraction	extraction	NN	_	_	_
21	:	:	:	_	_	_
22	Genomic	genomic	JJ	_	_	_
23	DNA	dna	NN	_	_	_
24	was	be	VBD	_	_	_
25	extracted	extract	VBN	_	_	_
26	according	accord	VBG	_	_	_
27	to	to	TO	_	_	_
28	Current	current	JJ	_	_	_
29	Protocols	protocol	NNS	_	_	_
30	in	in	IN	_	_	_
31	Molecular	molecular	JJ	_	_	_
32	Biology	biology	NN	_	_	_
33	.	.	.	_	_	_

1	Protein-DNA	protein-dna	JJ	_	_	_
2	complex	complex	NN	_	_	_
3	isolation	isolation	NN	_	_	_
4	:	:	:	_	_	_
5	Protein-DNA	protein-dna	JJ	_	_	_
6	complexes	complex	NNS	_	_	_
7	were	be	VBD	_	_	_
8	isolated	isolate	VBN	_	_	_
9	by	by	IN	_	_	_
10	phenol	phenol	NN	_	_	_
11	extraction	extraction	NN	_	_	_
12	with	with	IN	_	_	_
13	150	150	CD	_	_	_
14	μL	μl	NN	_	_	_
15	10	10	CD	_	_	_
16	mM	mm	NN	KWSUPP	_	_
17	Tris	Tris	NNP	_	_	_
18	and	and	CC	_	_	_
19	500	500	CD	_	_	_
20	μL	μl	NN	_	_	_
21	25:24:1	25:24:1	CD	_	_	_
22	phenol	phenol	NN	_	_	_
23	:	:	:	_	_	_
24	chloroform	chloroform	NN	_	_	_
25	:	:	:	_	_	_
26	isoamyl	isoamyl	NN	_	_	_
27	alcohol	alcohol	NN	_	_	_
28	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	white	white	JJ	_	_	_
3	disk	disk	NN	_	_	_
4	was	be	VBD	_	_	_
5	readily	readily	RB	_	_	_
6	discernible	discernible	JJ	_	_	_
7	at	at	IN	_	_	_
8	the	the	DT	_	_	_
9	aqueous	aqueous	JJ	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	genomic	genomic	JJ	_	_	_
12	_	_	NN	_	_	_
13	ref1	ref1	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	genomic	genomic	JJ	_	_	_
16	_	_	NN	_	_	_
17	ref2	ref2	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	genomic	genomic	JJ	_	_	_
20	_	_	NN	_	_	_
21	ref3	ref3	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	genomic	genomic	JJ	_	_	_
24	_	_	NN	_	_	_
25	ref4	ref4	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	genomic	genomic	JJ	_	_	_
28	_	_	NN	_	_	_
29	ref5	ref5	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	genomic	genomic	JJ	_	_	_
32	_	_	NN	_	_	_
33	ref6	ref6	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
35	IPOD	ipod	VBD	_	_	_
36	_	_	RB	_	_	_
37	early	early	JJ	_	_	_
38	_	_	NN	_	_	_
39	log	log	NN	_	_	_
40	_	_	NN	_	_	_
41	1	1	CD	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	IPOD	ipod	NN	_	_	_
44	_	_	RB	_	_	_
45	early	early	JJ	_	_	_
46	_	_	NN	_	_	_
47	log	log	NN	_	_	_
48	_	_	NN	_	_	_
49	2	2	CD	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
51	IPOD	ipod	VBD	_	_	_
52	_	_	RB	_	_	_
53	late	late	JJ	_	_	_
54	_	_	NN	_	_	_
55	log	log	NN	_	_	_
56	_	_	NN	_	_	_
57	1	1	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	IPOD	ipod	NN	_	_	_
60	_	_	CD	_	_	_
61	late	late	JJ	_	_	_
62	_	_	NN	_	_	_
63	log	log	NN	_	_	_
64	_	_	NN	_	_	_
65	2	2	CD	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
67	IPOD	ipod	VBD	_	_	_
68	_	_	SYM	_	_	_
69	MDS42	mds42	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	MDS42	mds42	NN	_	_	_
72	DNA	dna	NN	_	_	_
73	isolated	isolate	VBN	_	_	_
74	from	from	IN	_	_	_
75	early-phase	early-phase	JJ	_	_	_
76	DNA-protein	dna-protein	JJ	_	_	_
77	complexes	complex	NNS	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	MG1655	mg1655	NN	_	_	_
80	DNA	dna	NN	_	_	_
81	isolated	isolate	VBN	_	_	_
82	from	from	IN	_	_	_
83	early-phase	early-phase	JJ	_	_	_
84	DNA-protein	dna-protein	JJ	_	_	_
85	complexes	complex	NNS	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	MG1655	mg1655	NN	_	_	_
88	DNA	dna	NN	_	_	_
89	isolated	isolate	VBN	_	_	_
90	from	from	IN	_	_	_
91	late-phase	late-phase	JJ	_	_	_
92	DNA-protein	dna-protein	JJ	_	_	_
93	complexes	complex	NNS	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	MG1655	mg1655	NN	_	_	_
96	genomic	genomic	JJ	_	_	_
97	DNA	dna	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	MG1655	mg1655	NN	_	_	_
100	RNA	rna	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	RNA	rna	NN	_	_	_
103	_	_	NN	_	_	_
104	1	1	CD	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	RNA	rna	NN	_	_	_
107	_	_	NN	_	_	_
108	2	2	CD	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	strain	strain	NN	_	_	_
111	:	:	:	_	_	_
112	MDS42	mds42	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	strain	strain	NN	_	_	_
115	:	:	:	_	_	_
116	MG1655	mg1655	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	We	we	PRP	_	_	_
119	developed	develop	VBD	_	_	_
120	in-house	in-house	JJ	_	_	_
121	computational	computational	JJ	_	_	_
122	and	and	CC	_	_	_
123	statistical	statistical	JJ	_	_	_
124	analysis	analysis	NN	_	_	_
125	tools	tool	NNS	_	_	_
126	for	for	IN	_	_	_
127	use	use	NN	_	_	_
128	with	with	IN	_	_	_
129	the	the	DT	_	_	_
130	E.	e.	FW	_	_	_
131	coli	coli	FW	_	_	_
132	tiling	tiling	NN	_	_	_
133	array	array	NN	_	_	_
134	.	.	.	_	_	_

1	We	we	PRP	_	_	_
2	used	use	VBD	_	_	_
3	a	a	DT	_	_	_
4	previous	previous	JJ	_	_	_
5	study	study	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	Choe	Choe	NNP	_	_	_
8	et	et	FW	_	_	_
9	al.	al.	FW	_	_	_
10	,	,	,	_	_	_
11	2005	2005	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	as	as	IN	_	_	_
14	a	a	DT	_	_	_
15	model	model	NN	_	_	_
16	for	for	IN	_	_	_
17	perfect	perfect	JJ	_	_	_
18	match	match	NN	_	_	_
19	adjustment	adjustment	NN	_	_	_
20	on	on	IN	_	_	_
21	single	single	JJ	_	_	_
22	arrays	array	NNS	_	_	_
23	.	.	.	_	_	_

1	Analysis	analysis	NN	_	_	_
2	scripts	script	NNS	_	_	_
3	were	be	VBD	_	_	_
4	written	write	VBN	_	_	_
5	in	in	IN	_	_	_
6	Perl	Perl	NNP	_	_	_
7	,	,	,	_	_	_
8	MatLab	MatLab	NNP	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	R	r	NN	_	_	_
12	to	to	TO	_	_	_
13	standardize	standardize	VB	_	_	_
14	the	the	DT	_	_	_
15	statistical	statistical	JJ	_	_	_
16	manipulations	manipulation	NNS	_	_	_
17	across	across	IN	_	_	_
18	all	all	DT	_	_	_
19	data	datum	NNS	_	_	_
20	sets	set	NNS	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	output	output	NN	_	_	_
3	file	file	NN	_	_	_
4	from	from	IN	_	_	_
5	the	the	DT	_	_	_
6	scanning	scanning	NN	_	_	_
7	process	process	NN	_	_	_
8	is	be	VBZ	_	_	_
9	a	a	DT	_	_	_
10	CEL	cel	NN	_	_	_
11	file	file	NN	_	_	_
12	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	raw	raw	JJ	_	_	_
3	CEL	cel	NN	_	_	_
4	data	datum	NNS	_	_	_
5	were	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	as	as	IN	_	_	_
8	the	the	DT	_	_	_
9	basis	basis	NN	_	_	_
10	for	for	IN	_	_	_
11	the	the	DT	_	_	_
12	manuscript	manuscript	NN	_	_	_
13	;	;	:	_	_	_
14	no	no	DT	_	_	_
15	processed	process	VBN	_	_	_
16	data	datum	NNS	_	_	_
17	are	be	VBP	_	_	_
18	available	available	JJ	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2	antibody	antibody	NN	_	_	_
3	:	:	:	_	_	_
4	Monoclonal	monoclonal	JJ	_	_	_
5	antibody	antibody	NN	_	_	_
6	for	for	IN	_	_	_
7	RNA	rna	NN	_	_	_
8	polymerase	polymerase	NN	_	_	_
9	Beta	beta	NN	_	_	_
10	'	'	''	_	_	_
11	subunit	subunit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	NT73	nt73	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	antibody	antibody	NN	_	_	_
17	:	:	:	_	_	_
18	Monoclonal	monoclonal	JJ	_	_	_
19	antibody	antibody	NN	_	_	_
20	for	for	IN	_	_	_
21	RNA	rna	NN	_	_	_
22	polymerase	polymerase	NN	_	_	_
23	Beta	beta	NN	_	_	_
24	subunit	subunit	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	W0002	w0002	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Cell	cell	NN	_	_	_
30	pellets	pellet	NNS	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	from	from	IN	_	_	_
33	initial	initial	JJ	_	_	_
34	50	50	CD	_	_	_
35	ml	ml	NN	_	_	_
36	of	of	IN	_	_	_
37	culture	culture	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	were	be	VBD	_	_	_
40	thawed	thaw	VBN	_	_	_
41	and	and	CC	_	_	_
42	resuspended	resuspend	VBN	_	_	_
43	in	in	IN	_	_	_
44	250ul	250ul	NN	_	_	_
45	of	of	IN	_	_	_
46	IP	IP	NNP	_	_	_
47	buffer	buffer	NN	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	100	100	CD	_	_	_
50	mM	mm	NN	KWSUPP	_	_
51	Tris	Tris	NNP	_	_	_
52	pH	ph	NN	_	_	_
53	8	8	CD	_	_	_
54	,	,	,	_	_	_
55	300	300	CD	_	_	_
56	mM	mm	NN	KWSUPP	_	_
57	NaCl	nacl	NN	_	_	_
58	,	,	,	_	_	_
59	2	2	CD	_	_	_
60	%	%	NN	_	_	_
61	TritonX-100	tritonx-100	NN	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	and	and	CC	_	_	_
64	sonicated	sonicate	VBN	_	_	_
65	using	use	VBG	_	_	_
66	a	a	DT	_	_	_
67	microtip	microtip	NN	_	_	_
68	sonicator	sonicator	NN	_	_	_
69	set	set	VBN	_	_	_
70	at	at	IN	_	_	_
71	10	10	CD	_	_	_
72	%	%	NN	_	_	_
73	output	output	NN	_	_	_
74	for	for	IN	_	_	_
75	20	20	CD	_	_	_
76	second	second	JJ	_	_	_
77	intervals	interval	NNS	_	_	_
78	with	with	IN	_	_	_
79	periods	period	NNS	_	_	_
80	of	of	IN	_	_	_
81	cooling	cool	VBG	_	_	_
82	in	in	IN	_	_	_
83	between	between	IN	_	_	_
84	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	treated	treat	VBN	_	_	_
5	for	for	IN	_	_	_
6	one	one	CD	_	_	_
7	hour	hour	NN	_	_	_
8	at	at	IN	_	_	_
9	4	4	CD	_	_	_
10	°C	°c	NN	_	_	_
11	with	with	IN	_	_	_
12	RNase	rnase	NN	_	_	_
13	A	a	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	2	2	CD	_	_	_
16	ng	ng	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Cells	cell	NNS	_	_	_
19	were	be	VBD	_	_	_
20	grown	grow	VBN	_	_	_
21	with	with	IN	_	_	_
22	vigorous	vigorous	JJ	_	_	_
23	shaking	shake	VBG	_	_	_
24	at	at	IN	_	_	_
25	37	37	CD	_	_	_
26	°C	°c	NN	_	_	_
27	to	to	TO	_	_	_
28	mid-log	mid-log	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	light	light	JJ	_	_	_
31	scattering	scattering	NN	_	_	_
32	at	at	IN	_	_	_
33	600	600	CD	_	_	_
34	nm	nm	NN	_	_	_
35	equivalent	equivalent	NN	_	_	_
36	to	to	TO	_	_	_
37	0.4	0.4	CD	_	_	_
38	OD	od	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	.	.	.	_	_	_

1	Sodium	sodium	NN	_	_	_
2	phosphate	phosphate	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Escherichia	escherichia	FW	Organism	_	_
7	coli	coli	FW	Organism	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
9	Genomic	genomic	JJ	_	_	_
10	DNA	dna	NN	_	_	_
11	control	control	NN	_	_	_
12	from	from	IN	_	_	_
13	E.	e.	FW	_	_	_
14	coli	coli	FW	_	_	_
15	K-12	k-12	NN	_	_	_
16	MG1655	mg1655	NN	_	_	_
17	cells	cell	NNS	_	_	_
18	treated	treat	VBN	_	_	_
19	with	with	IN	_	_	_
20	20ug	20ug	JJ	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
22	Genomic	genomic	JJ	_	_	_
23	DNA	dna	NN	_	_	_
24	control	control	NN	_	_	_
25	from	from	IN	_	_	_
26	E.	e.	FW	_	_	_
27	coli	coli	FW	_	_	_
28	K-12	k-12	NN	_	_	_
29	MG1655	mg1655	NN	_	_	_
30	cells	cell	NNS	_	_	_
31	,	,	,	_	_	_
32	untreated	untreated	JJ	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	reference	reference	NN	_	_	_
35	:	:	:	_	_	_
36	input	input	NN	_	_	_
37	Genomic	genomic	JJ	_	_	_
38	DNA	dna	NN	_	_	_
39	control	control	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	RNA	rna	NN	_	_	_
42	polymerase	polymerase	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	Beta	beta	NN	_	_	_
45	'	'	''	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	ChIP-chip	chip-chip	NN	_	_	_
48	in	in	IN	_	_	_
49	E.	e.	FW	_	_	_
50	coli	coli	FW	_	_	_
51	K-12	k-12	NN	_	_	_
52	MG1655	mg1655	NN	_	_	_
53	cells	cell	NNS	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	Dataset	Dataset	NNP	_	_	_
56	100040	100040	CD	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	RNA	rna	NN	_	_	_
60	polymerase	polymerase	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	Beta	beta	NN	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	ChIP-chip	chip-chip	NN	_	_	_
65	in	in	IN	_	_	_
66	E.	e.	FW	_	_	_
67	coli	coli	FW	_	_	_
68	K-12	k-12	NN	_	_	_
69	MG1655	mg1655	NN	_	_	_
70	cells	cell	NNS	_	_	_
71	-LRB-	-lrb-	-LRB-	_	_	_
72	Dataset	Dataset	NNP	_	_	_
73	3427302	3427302	CD	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	RNA	rna	NN	_	_	_
77	polymerase	polymerase	NN	_	_	_
78	-LRB-	-lrb-	-LRB-	_	_	_
79	Beta	beta	NN	_	_	_
80	'	'	''	_	_	_
81	-RRB-	-rrb-	-RRB-	_	_	_
82	ChIP-chip	chip-chip	NN	_	_	_
83	in	in	IN	_	_	_
84	E.	e.	FW	_	_	_
85	coli	coli	FW	_	_	_
86	K-12	k-12	NN	_	_	_
87	MG1655	mg1655	NN	_	_	_
88	cells	cell	NNS	_	_	_
89	treated	treat	VBN	_	_	_
90	with	with	IN	_	_	_
91	20ug	20ug	JJ	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	RNA	rna	NN	_	_	_
94	polymerase	polymerase	NN	_	_	_
95	-LRB-	-lrb-	-LRB-	_	_	_
96	Beta	beta	NN	_	_	_
97	-RRB-	-rrb-	-RRB-	_	_	_
98	ChIP-chip	chip-chip	NN	_	_	_
99	in	in	IN	_	_	_
100	E.	e.	FW	_	_	_
101	coli	coli	FW	_	_	_
102	K-12	k-12	NN	_	_	_
103	MG1655	mg1655	NN	_	_	_
104	cells	cell	NNS	_	_	_
105	treated	treat	VBN	_	_	_
106	with	with	IN	_	_	_
107	20ug	20ug	JJ	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	RNA	rna	NN	_	_	_
110	polymerase	polymerase	NN	_	_	_
111	-LRB-	-lrb-	-LRB-	_	_	_
112	Beta	beta	NN	_	_	_
113	'	'	''	_	_	_
114	-RRB-	-rrb-	-RRB-	_	_	_
115	ChIP	chip	NN	_	_	_
116	in	in	IN	_	_	_
117	E.	e.	FW	_	_	_
118	coli	coli	FW	_	_	_
119	K-12	k-12	NN	_	_	_
120	MG1655	mg1655	NN	_	_	_
121	cells	cell	NNS	_	_	_
122	treated	treat	VBN	_	_	_
123	with	with	IN	_	_	_
124	20ug	20ug	JJ	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	RNA	rna	NN	_	_	_
127	polymerase	polymerase	NN	_	_	_
128	-LRB-	-lrb-	-LRB-	_	_	_
129	Beta	beta	NN	_	_	_
130	-RRB-	-rrb-	-RRB-	_	_	_
131	ChIP	chip	NN	_	_	_
132	in	in	IN	_	_	_
133	E.	e.	FW	_	_	_
134	coli	coli	FW	_	_	_
135	K-12	k-12	NN	_	_	_
136	MG1655	mg1655	NN	_	_	_
137	cells	cell	NNS	_	_	_
138	treated	treat	VBN	_	_	_
139	with	with	IN	_	_	_
140	20ug	20ug	JJ	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	RNA	rna	NN	_	_	_
143	polymerase	polymerase	NN	_	_	_
144	-LRB-	-lrb-	-LRB-	_	_	_
145	Beta	beta	NN	_	_	_
146	'	'	''	_	_	_
147	-RRB-	-rrb-	-RRB-	_	_	_
148	ChIP	chip	NN	_	_	_
149	in	in	IN	_	_	_
150	E.	e.	FW	_	_	_
151	coli	coli	FW	_	_	_
152	K-12	k-12	NN	_	_	_
153	MG1655	mg1655	NN	_	_	_
154	cells	cell	NNS	_	_	_
155	,	,	,	_	_	_
156	untreated	untreated	JJ	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	RNA	rna	NN	_	_	_
159	polymerase	polymerase	NN	_	_	_
160	-LRB-	-lrb-	-LRB-	_	_	_
161	Beta	beta	NN	_	_	_
162	-RRB-	-rrb-	-RRB-	_	_	_
163	ChIP	chip	NN	_	_	_
164	in	in	IN	_	_	_
165	E.	e.	FW	_	_	_
166	coli	coli	FW	_	_	_
167	K-12	k-12	NN	_	_	_
168	MG1655	mg1655	NN	_	_	_
169	cells	cell	NNS	_	_	_
170	,	,	,	_	_	_
171	untreated	untreated	JJ	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	Strain	strain	NN	_	_	_
174	MG1655	mg1655	NN	_	_	_
175	cells	cell	NNS	_	_	_
176	were	be	VBD	_	_	_
177	grown	grow	VBN	_	_	_
178	in	in	IN	_	_	_
179	MOPS	mop	NNS	MED	_	_
180	minimal	minimal	JJ	_	_	_
181	medium	medium	NN	_	_	_
182	supplemented	supplement	VBN	_	_	_
183	with	with	IN	_	_	_
184	0.2	0.2	CD	_	_	_
185	%	%	NN	_	_	_
186	glucose	glucose	NN	SUPP	_	_
187	-LRB-	-lrb-	-LRB-	_	_	_
188	www.genome.wisc.edu	www.genome.wisc.edu	NN	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	The	the	DT	_	_	_
191	log2-ratio	log2-ratio	NN	_	_	_
192	is	be	VBZ	_	_	_
193	computed	compute	VBN	_	_	_
194	and	and	CC	_	_	_
195	scaled	scale	VBN	_	_	_
196	to	to	TO	_	_	_
197	center	center	VB	_	_	_
198	the	the	DT	_	_	_
199	ratio	ratio	NN	_	_	_
200	data	datum	NNS	_	_	_
201	around	around	IN	_	_	_
202	zero	zero	CD	_	_	_
203	.	.	.	_	_	_

1	Scaling	scaling	NN	_	_	_
2	is	be	VBZ	_	_	_
3	performed	perform	VBN	_	_	_
4	by	by	IN	_	_	_
5	subtracting	subtract	VBG	_	_	_
6	the	the	DT	_	_	_
7	bi-weight	bi-weight	JJ	_	_	_
8	mean	mean	NN	_	_	_
9	for	for	IN	_	_	_
10	the	the	DT	_	_	_
11	log2-ratio	log2-ratio	JJ	_	_	_
12	values	value	NNS	_	_	_
13	for	for	IN	_	_	_
14	all	all	DT	_	_	_
15	features	feature	NNS	_	_	_
16	on	on	IN	_	_	_
17	the	the	DT	_	_	_
18	array	array	NN	_	_	_
19	from	from	IN	_	_	_
20	each	each	DT	_	_	_
21	log2-ratio	log2-ratio	JJ	_	_	_
22	value	value	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	VALUE	value	NN	_	_	_
3	=	=	JJ	_	_	_
4	log2	log2	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	Cy5	cy5	NN	_	_	_
7	_	_	NN	_	_	_
8	signal	signal	NN	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	Escherichia	escherichia	FW	Organism	_	_
11	coli	coli	FW	Organism	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	Escherichia	escherichia	FW	Organism	_	_
14	coli	coli	FW	Organism	_	_
15	O157	o157	NN	_	_	_
16	:	:	:	_	_	_
17	H7	h7	NN	_	_	_
18	EDL933	edl933	NN	_	_	_
19	Inside	inside	IN	_	_	_
20	Acanthamoeba	acanthamoeba	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Escherichia	escherichia	FW	Organism	_	_
23	coli	coli	FW	Organism	_	_
24	O157	o157	NN	_	_	_
25	:	:	:	_	_	_
26	H7	h7	NN	_	_	_
27	EDL933	edl933	NN	_	_	_
28	Inside	inside	IN	_	_	_
29	Acanthamoeba	acanthamoeba	NN	_	_	_
30	vs.	vs.	CC	_	_	_
31	Control	control	NN	_	_	_
32	Slide	slide	NN	_	_	_
33	1	1	CD	_	_	_
34	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
35	Escherichia	escherichia	FW	Organism	_	_
36	coli	coli	FW	Organism	_	_
37	O157	o157	NN	_	_	_
38	:	:	:	_	_	_
39	H7	h7	NN	_	_	_
40	EDL933	edl933	NN	_	_	_
41	Inside	inside	IN	_	_	_
42	Acanthamoeba	acanthamoeba	NN	_	_	_
43	vs.	vs.	CC	_	_	_
44	Control	control	NN	_	_	_
45	Slide	slide	NN	_	_	_
46	2	2	CD	_	_	_
47	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
48	Escherichia	escherichia	FW	Organism	_	_
49	coli	coli	FW	Organism	_	_
50	O157	o157	NN	_	_	_
51	:	:	:	_	_	_
52	H7	h7	NN	_	_	_
53	EDL933	edl933	NN	_	_	_
54	Inside	inside	IN	_	_	_
55	Acanthamoeba	acanthamoeba	NN	_	_	_
56	vs.	vs.	CC	_	_	_
57	Control	control	NN	_	_	_
58	Slide	slide	NN	_	_	_
59	3	3	CD	_	_	_
60	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
61	Escherichia	escherichia	FW	Organism	_	_
62	coli	coli	FW	Organism	_	_
63	O157	o157	NN	_	_	_
64	:	:	:	_	_	_
65	H7	h7	NN	_	_	_
66	EDL933	edl933	NN	_	_	_
67	Inside	inside	IN	_	_	_
68	Acanthamoeba	acanthamoeba	NN	_	_	_
69	vs.	vs.	CC	_	_	_
70	Control	control	NN	_	_	_
71	Slide	slide	NN	_	_	_
72	4	4	CD	_	_	_
73	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
74	Escherichia	escherichia	FW	Organism	_	_
75	coli	coli	FW	Organism	_	_
76	O157	o157	NN	_	_	_
77	:	:	:	_	_	_
78	H7	h7	NN	_	_	_
79	EDL933	edl933	NN	_	_	_
80	Inside	inside	IN	_	_	_
81	Acanthamoeba	acanthamoeba	NN	_	_	_
82	vs.	vs.	CC	_	_	_
83	Control	control	NN	_	_	_
84	Slide	slide	NN	_	_	_
85	5	5	CD	_	_	_
86	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
87	Escherichia	escherichia	FW	Organism	_	_
88	coli	coli	FW	Organism	_	_
89	O157	o157	NN	_	_	_
90	:	:	:	_	_	_
91	H7	h7	NN	_	_	_
92	EDL933	edl933	NN	_	_	_
93	Inside	inside	IN	_	_	_
94	Acanthamoeba	acanthamoeba	NN	_	_	_
95	vs.	vs.	CC	_	_	_
96	Control	control	NN	_	_	_
97	Slide	slide	NN	_	_	_
98	6	6	CD	_	_	_
99	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
100	Escherichia	escherichia	FW	Organism	_	_
101	coli	coli	FW	Organism	_	_
102	O157	o157	NN	_	_	_
103	:	:	:	_	_	_
104	H7	h7	NN	_	_	_
105	EDL933	edl933	NN	_	_	_
106	Inside	inside	IN	_	_	_
107	Acanthamoeba	acanthamoeba	NN	_	_	_
108	vs.	vs.	CC	_	_	_
109	Control	control	NN	_	_	_
110	Slide	slide	NN	_	_	_
111	7	7	CD	_	_	_
112	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
113	Escherichia	escherichia	FW	Organism	_	_
114	coli	coli	FW	Organism	_	_
115	O157	o157	NN	_	_	_
116	:	:	:	_	_	_
117	H7	h7	NN	_	_	_
118	EDL933	edl933	NN	_	_	_
119	Inside	inside	IN	_	_	_
120	Acanthamoeba	acanthamoeba	NN	_	_	_
121	vs.	vs.	CC	_	_	_
122	Control	control	NN	_	_	_
123	Slide	slide	NN	_	_	_
124	8	8	CD	_	_	_
125	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
126	Escherichia	escherichia	FW	Organism	_	_
127	coli	coli	FW	Organism	_	_
128	O157	o157	NN	_	_	_
129	:	:	:	_	_	_
130	H7	h7	NN	_	_	_
131	EDL933	edl933	NN	_	_	_
132	Inside	inside	IN	_	_	_
133	Acanthamoeba	acanthamoeba	NN	_	_	_
134	vs.	vs.	CC	_	_	_
135	Control	control	NN	_	_	_
136	Slide	slide	NN	_	_	_
137	9	9	CD	_	_	_
138	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
139	Escherichia	escherichia	FW	Organism	_	_
140	coli	coli	FW	Organism	_	_
141	O157	o157	NN	_	_	_
142	:	:	:	_	_	_
143	H7	h7	NN	_	_	_
144	EDL933	edl933	NN	_	_	_
145	Outside	outside	JJ	_	_	_
146	Control	control	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	growth	growth	NN	_	_	_
149	condition	condition	NN	_	_	_
150	:	:	:	_	_	_
151	Inside	inside	IN	_	_	_
152	Acanthamoeba	acanthamoeba	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	growth	growth	NN	_	_	_
155	condition	condition	NN	_	_	_
156	:	:	:	_	_	_
157	Outside	outside	JJ	_	_	_
158	Control	control	NN	_	_	_
159	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
160	Mixed	Mixed	NNP	_	_	_
161	model	model	NN	_	_	_
162	analysis	analysis	NN	_	_	_
163	was	be	VBD	_	_	_
164	conducted	conduct	VBN	_	_	_
165	as	as	IN	_	_	_
166	previously	previously	RB	_	_	_
167	described	describe	VBN	_	_	_
168	-LRB-	-lrb-	-LRB-	_	_	_
169	Madsen	Madsen	NNP	_	_	_
170	,	,	,	_	_	_
171	et	et	FW	_	_	_
172	al.	al.	FW	_	_	_
173	,	,	,	_	_	_
174	2006	2006	CD	_	_	_
175	-RRB-	-rrb-	-RRB-	_	_	_
176	excluding	exclude	VBG	_	_	_
177	slide	slide	NN	_	_	_
178	region	region	NN	_	_	_
179	and	and	CC	_	_	_
180	slide-by-region	slide-by-region	NN	_	_	_
181	interaction	interaction	NN	_	_	_
182	effects	effect	NNS	_	_	_
183	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	value	value	NN	_	_	_
3	column	column	NN	_	_	_
4	was	be	VBD	_	_	_
5	not	not	RB	_	_	_
6	used	use	VBN	_	_	_
7	for	for	IN	_	_	_
8	analysis	analysis	NN	_	_	_
9	or	or	CC	_	_	_
10	in	in	IN	_	_	_
11	publication	publication	NN	_	_	_
12	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	normalized	normalize	VBN	_	_	_
3	values	value	NNS	_	_	_
4	for	for	IN	_	_	_
5	duplicate	duplicate	VBP	_	_	_
6	spots	spot	NNS	_	_	_
7	were	be	VBD	_	_	_
8	averaged	average	VBN	_	_	_
9	within	within	IN	_	_	_
10	each	each	DT	_	_	_
11	array	array	NN	_	_	_
12	to	to	TO	_	_	_
13	produce	produce	VB	_	_	_
14	one	one	CD	_	_	_
15	normalized	normalize	VBD	_	_	_
16	measure	measure	NN	_	_	_
17	of	of	IN	_	_	_
18	expression	expression	NN	_	_	_
19	for	for	IN	_	_	_
20	each	each	DT	_	_	_
21	of	of	IN	_	_	_
22	the	the	DT	_	_	_
23	probe	probe	NN	_	_	_
24	sequences	sequence	NNS	_	_	_
25	and	and	CC	_	_	_
26	each	each	DT	_	_	_
27	of	of	IN	_	_	_
28	the	the	DT	_	_	_
29	RNA	rna	NN	_	_	_
30	samples	sample	NNS	_	_	_
31	.	.	.	_	_	_

1	-LSB-	-lsb-	-LRB-	_	_	_
2	mean	mean	VB	_	_	_
3	log	log	NN	_	_	_
4	transformed	transform	VBN	_	_	_
5	median	median	JJ	_	_	_
6	centered	centered	JJ	_	_	_
7	lowess	lowess	NN	_	_	_
8	normalized	normalize	VBD	_	_	_
9	signal	signal	NN	_	_	_
10	intensity	intensity	NN	_	_	_
11	-RSB-	-rsb-	-RRB-	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	from	from	IN	_	_	_
17	samples	sample	NNS	_	_	_
18	using	use	VBG	_	_	_
19	the	the	DT	_	_	_
20	RNeasy	RNeasy	NNP	_	_	_
21	Mini	Mini	NNP	_	_	_
22	Kit	kit	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Qiagen	qiagen	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	Prior	prior	RB	_	_	_
2	to	to	TO	_	_	_
3	lysis	lysis	NN	_	_	_
4	all	all	DT	_	_	_
5	samples	sample	NNS	_	_	_
6	were	be	VBD	_	_	_
7	incubated	incubate	VBN	_	_	_
8	for	for	IN	_	_	_
9	30	30	CD	_	_	_
10	min	min	NN	_	_	_
11	on	on	IN	_	_	_
12	ice	ice	NN	_	_	_
13	in	in	IN	_	_	_
14	RNA	rna	NN	_	_	_
15	stop	stop	NN	_	_	_
16	solution	solution	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	0.1	0.1	CD	_	_	_
19	%	%	NN	_	_	_
20	SDS	sds	NN	_	_	_
21	,	,	,	_	_	_
22	1	1	CD	_	_	_
23	%	%	NN	_	_	_
24	Acidic	acidic	JJ	_	_	_
25	phenol	phenol	NN	_	_	_
26	,	,	,	_	_	_
27	19	19	CD	_	_	_
28	%	%	NN	_	_	_
29	ethanol	ethanol	NN	_	_	_
30	,	,	,	_	_	_
31	ice	ice	NN	_	_	_
32	cold	cold	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysis	lysis	NN	_	_	_
3	and	and	CC	_	_	_
4	digestion	digestion	NN	_	_	_
5	protocol	protocol	NN	_	_	_
6	was	be	VBD	_	_	_
7	followed	follow	VBN	_	_	_
8	with	with	IN	_	_	_
9	two	two	CD	_	_	_
10	50	50	CD	_	_	_
11	μl	μl	NN	_	_	_
12	ddH20	ddh20	NN	_	_	_
13	elutions	elution	NNS	_	_	_
14	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	sample	sample	NN	_	_	_
3	was	be	VBD	_	_	_
4	treated	treat	VBN	_	_	_
5	with	with	IN	_	_	_
6	2	2	CD	_	_	_
7	μl	μl	NN	_	_	_
8	of	of	IN	_	_	_
9	DNase	dnase	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Ambion	Ambion	NNP	_	_	_
12	,	,	,	_	_	_
13	Austin	Austin	NNP	_	_	_
14	,	,	,	_	_	_
15	TX	TX	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	at	at	IN	_	_	_
18	37	37	CD	_	_	_
19	°C	°c	NN	_	_	_
20	for	for	IN	_	_	_
21	30	30	CD	_	_	_
22	min	min	NN	_	_	_
23	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	purified	purify	VBN	_	_	_
4	and	and	CC	_	_	_
5	concentrated	concentrate	VBN	_	_	_
6	using	use	VBG	_	_	_
7	Microcon	Microcon	NNP	_	_	_
8	YM-30	ym-30	NN	_	_	_
9	columns	column	NNS	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Millipore	Millipore	NNP	_	_	_
12	,	,	,	_	_	_
13	Billerica	Billerica	NNP	_	_	_
14	,	,	,	_	_	_
15	MA	MA	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	the	the	DT	_	_	_
20	quantity	quantity	NN	_	_	_
21	and	and	CC	_	_	_
22	purity	purity	NN	_	_	_
23	were	be	VBD	_	_	_
24	determined	determine	VBN	_	_	_
25	using	use	VBG	_	_	_
26	an	a	DT	_	_	_
27	ND-1000	nd-1000	NN	_	_	_
28	spectrophotometer	spectrophotometer	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Nanodrop	Nanodrop	NNP	_	_	_
31	,	,	,	_	_	_
32	Wilmington	Wilmington	NNP	_	_	_
33	,	,	,	_	_	_
34	DE	de	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	determined	determine	VBN	_	_	_
4	to	to	TO	_	_	_
5	be	be	VB	_	_	_
6	free	free	JJ	_	_	_
7	of	of	IN	_	_	_
8	contaminating	contaminate	VBG	_	_	_
9	genomic	genomic	JJ	_	_	_
10	DNA	dna	NN	_	_	_
11	by	by	IN	_	_	_
12	absence	absence	NN	_	_	_
13	of	of	IN	_	_	_
14	a	a	DT	_	_	_
15	band	band	NN	_	_	_
16	on	on	IN	_	_	_
17	a	a	DT	_	_	_
18	DNA	dna	NN	_	_	_
19	electrophoresis	electrophoresis	NN	_	_	_
20	gel	gel	NN	_	_	_
21	after	after	IN	_	_	_
22	30	30	CD	_	_	_
23	rounds	round	NNS	_	_	_
24	of	of	IN	_	_	_
25	PCR	pcr	NN	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	BRP	BRP	NNP	_	_	_
3	Induction	induction	NN	_	_	_
4	10	10	CD	_	_	_
5	Minutes	Minutes	NNPS	_	_	_
6	against	against	IN	_	_	_
7	5	5	CD	_	_	_
8	Minutes	Minutes	NNPS	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	BRP	BRP	NNP	_	_	_
11	Induction	induction	NN	_	_	_
12	-10	-10	CD	_	_	_
13	minutes	minute	NNS	_	_	_
14	against	against	IN	_	_	_
15	60	60	CD	_	_	_
16	minutes	minute	NNS	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	BRP	BRP	NNP	_	_	_
19	Induction	induction	NN	_	_	_
20	20	20	CD	_	_	_
21	minutes	minute	NNS	_	_	_
22	against	against	IN	_	_	_
23	10	10	CD	_	_	_
24	minutes	minute	NNS	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	BRP	BRP	NNP	_	_	_
27	Induction	induction	NN	_	_	_
28	30	30	CD	_	_	_
29	minutes	minute	NNS	_	_	_
30	against	against	IN	_	_	_
31	20	20	CD	_	_	_
32	minutes	minute	NNS	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	BRP	BRP	NNP	_	_	_
35	Induction	induction	NN	_	_	_
36	45	45	CD	_	_	_
37	minutes	minute	NNS	_	_	_
38	against	against	IN	_	_	_
39	30	30	CD	_	_	_
40	minutes	minute	NNS	_	_	_
41	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
42	BRP	BRP	NNP	_	_	_
43	Induction	induction	NN	_	_	_
44	5	5	CD	_	_	_
45	minutes	minute	NNS	_	_	_
46	against	against	IN	_	_	_
47	2	2	CD	_	_	_
48	minutes	minute	NNS	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	BRP	BRP	NNP	_	_	_
51	Induction	induction	NN	_	_	_
52	60	60	CD	_	_	_
53	minutes	minute	NNS	_	_	_
54	against	against	IN	_	_	_
55	45	45	CD	_	_	_
56	minutes	minute	NNS	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	E.coli	e.coli	NN	_	_	_
59	0	0	CD	_	_	_
60	minutes	minute	NNS	_	_	_
61	after	after	IN	_	_	_
62	BRP	brp	NN	_	_	_
63	induction	induction	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	E.coli	e.coli	NN	_	_	_
66	-10	-10	CD	_	_	_
67	minutes	minute	NNS	_	_	_
68	after	after	IN	_	_	_
69	BRP	brp	NN	_	_	_
70	induction	induction	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	E.coli	e.coli	NN	_	_	_
73	10	10	CD	_	_	_
74	minutes	minute	NNS	_	_	_
75	after	after	IN	_	_	_
76	BRP	brp	NN	_	_	_
77	induction	induction	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	E.coli	e.coli	NN	_	_	_
80	20	20	CD	_	_	_
81	minutes	minute	NNS	_	_	_
82	after	after	IN	_	_	_
83	BRP	brp	NN	_	_	_
84	induction	induction	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	E.coli	e.coli	NN	_	_	_
87	2	2	CD	_	_	_
88	minutes	minute	NNS	_	_	_
89	after	after	IN	_	_	_
90	BRP	brp	NN	_	_	_
91	induction	induction	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	E.coli	e.coli	NN	_	_	_
94	30	30	CD	_	_	_
95	minutes	minute	NNS	_	_	_
96	after	after	IN	_	_	_
97	BRP	brp	NN	_	_	_
98	induction	induction	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	E.coli	e.coli	NN	_	_	_
101	45	45	CD	_	_	_
102	minutes	minute	NNS	_	_	_
103	after	after	IN	_	_	_
104	BRP	brp	NN	_	_	_
105	induction	induction	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	E.coli	e.coli	NNS	_	_	_
108	5	5	CD	_	_	_
109	minutes	minute	NNS	_	_	_
110	after	after	IN	_	_	_
111	BRP	brp	NN	_	_	_
112	induction	induction	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	E.coli	e.coli	NN	_	_	_
115	60	60	CD	_	_	_
116	minutes	minute	NNS	_	_	_
117	after	after	IN	_	_	_
118	BRP	BRP	NNP	_	_	_
119	induction	induction	NN	_	_	_
120	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
121	Escherichia	escherichia	FW	Organism	_	_
122	coli	coli	FW	Organism	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
124	Genomic	genomic	JJ	_	_	_
125	response	response	NN	_	_	_
126	analysis	analysis	NN	_	_	_
127	of	of	IN	_	_	_
128	E.coli	e.coli	NN	_	_	_
129	during	during	IN	_	_	_
130	coexpression	coexpression	NN	_	_	_
131	of	of	IN	_	_	_
132	a	a	DT	_	_	_
133	bacteriocin	bacteriocin	NN	_	_	_
134	release	release	NN	_	_	_
135	protein	protein	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	The	the	DT	_	_	_
138	scanning	scanning	NN	_	_	_
139	process	process	NN	_	_	_
140	of	of	IN	_	_	_
141	the	the	DT	_	_	_
142	hybridized	hybridize	VBN	_	_	_
143	chips	chip	NNS	_	_	_
144	included	include	VBD	_	_	_
145	a	a	DT	_	_	_
146	fourteen-fold	fourteen-fold	JJ	_	_	_
147	scan	scan	VB	_	_	_
148	of	of	IN	_	_	_
149	each	each	DT	_	_	_
150	chip	chip	NN	_	_	_
151	at	at	IN	_	_	_
152	different	different	JJ	_	_	_
153	settings	setting	NNS	_	_	_
154	,	,	,	_	_	_
155	altering	alter	VBG	_	_	_
156	both	both	CC	_	_	_
157	PMT	PMT	NNP	_	_	_
158	and	and	CC	_	_	_
159	laser	laser	NN	_	_	_
160	power	power	NN	_	_	_
161	settings	setting	NNS	_	_	_
162	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	following	follow	VBG	_	_	_
3	primary	primary	JJ	_	_	_
4	analysis	analysis	NN	_	_	_
5	served	serve	VBD	_	_	_
6	as	as	IN	_	_	_
7	a	a	DT	_	_	_
8	quantification	quantification	NN	_	_	_
9	method	method	NN	_	_	_
10	and	and	CC	_	_	_
11	is	be	VBZ	_	_	_
12	performed	perform	VBN	_	_	_
13	with	with	IN	_	_	_
14	the	the	DT	_	_	_
15	Gene	Gene	NNP	_	_	_
16	Pix	Pix	NNP	_	_	_
17	Pro	pro	FW	_	_	_
18	6.0	6.0	CD	_	_	_
19	™	™	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Molecular	molecular	JJ	_	_	_
22	Devices	Devices	NNPS	_	_	_
23	,	,	,	_	_	_
24	Sunnyvale	Sunnyvale	NNP	_	_	_
25	,	,	,	_	_	_
26	USA	USA	NNP	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	software	software	NN	_	_	_
29	tool	tool	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	secondary	secondary	JJ	_	_	_
4	analysis	analysis	NN	_	_	_
5	is	be	VBZ	_	_	_
6	subsequently	subsequently	RB	_	_	_
7	conducted	conduct	VBN	_	_	_
8	using	use	VBG	_	_	_
9	the	the	DT	_	_	_
10	data	datum	NNS	_	_	_
11	from	from	IN	_	_	_
12	the	the	DT	_	_	_
13	primary	primary	JJ	_	_	_
14	analysis	analysis	NN	_	_	_
15	.	.	.	_	_	_

1	Therefore	therefore	RB	_	_	_
2	,	,	,	_	_	_
3	data	datum	NNS	_	_	_
4	from	from	IN	_	_	_
5	different	different	JJ	_	_	_
6	scans	scan	NNS	_	_	_
7	is	be	VBZ	_	_	_
8	first	first	JJ	_	_	_
9	searched	search	VBD	_	_	_
10	for	for	IN	_	_	_
11	saturation	saturation	NN	_	_	_
12	effects	effect	NNS	_	_	_
13	,	,	,	_	_	_
14	which	which	WDT	_	_	_
15	are	be	VBP	_	_	_
16	eliminated	eliminate	VBN	_	_	_
17	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	locally	locally	RB	_	_	_
3	weighted	weighted	JJ	_	_	_
4	linear	linear	JJ	_	_	_
5	regression	regression	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	Lowess	lowess	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	has	have	VBZ	_	_	_
10	been	be	VBN	_	_	_
11	employed	employ	VBN	_	_	_
12	as	as	IN	_	_	_
13	a	a	DT	_	_	_
14	normalization	normalization	NN	_	_	_
15	method	method	NN	_	_	_
16	in	in	IN	_	_	_
17	order	order	NN	_	_	_
18	to	to	TO	_	_	_
19	account	account	VB	_	_	_
20	for	for	IN	_	_	_
21	intensity-dependent	intensity-dependent	JJ	_	_	_
22	effects	effect	NNS	_	_	_
23	.	.	.	_	_	_

1	Due	due	JJ	_	_	_
2	to	to	TO	_	_	_
3	the	the	DT	_	_	_
4	lacking	lack	VBG	_	_	_
5	gene	gene	NN	_	_	_
6	replicates	replicate	VBZ	_	_	_
7	on	on	IN	_	_	_
8	the	the	DT	_	_	_
9	commercial	commercial	JJ	_	_	_
10	whole	whole	JJ	_	_	_
11	genome	genome	NN	_	_	_
12	array	array	NN	_	_	_
13	,	,	,	_	_	_
14	a	a	DT	_	_	_
15	t-test	t-test	NN	_	_	_
16	could	could	MD	_	_	_
17	not	not	RB	_	_	_
18	be	be	VB	_	_	_
19	applied	apply	VBN	_	_	_
20	.	.	.	_	_	_

1	Instead	instead	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	quotients	quotient	NNS	_	_	_
5	of	of	IN	_	_	_
6	respectively	respectively	RB	_	_	_
7	two	two	CD	_	_	_
8	states	state	NNS	_	_	_
9	have	have	VBP	_	_	_
10	been	be	VBN	_	_	_
11	calculated	calculate	VBN	_	_	_
12	for	for	IN	_	_	_
13	the	the	DT	_	_	_
14	assessment	assessment	NN	_	_	_
15	of	of	IN	_	_	_
16	the	the	DT	_	_	_
17	regulation	regulation	NN	_	_	_
18	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	absolute	absolute	JJ	_	_	_
3	value	value	NN	_	_	_
4	of	of	IN	_	_	_
5	log-ratio	log-ratio	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	to	to	TO	_	_	_
8	base2	base2	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	higher	higher	JJR	_	_	_
11	than	than	IN	_	_	_
12	1	1	CD	_	_	_
13	is	be	VBZ	_	_	_
14	used	use	VBN	_	_	_
15	as	as	IN	_	_	_
16	criteria	criterion	NNS	_	_	_
17	for	for	IN	_	_	_
18	a	a	DT	_	_	_
19	regulated	regulate	VBN	_	_	_
20	gene	gene	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	strain	strain	NN	_	_	_
4	was	be	VBD	_	_	_
5	cultivated	cultivate	VBN	_	_	_
6	in	in	IN	_	_	_
7	5L	5l	NN	_	_	_
8	defined	define	VBN	_	_	_
9	medium	medium	NN	_	_	_
10	with	with	IN	_	_	_
11	glycerol	glycerol	NN	SUPP	_	_
12	as	as	IN	_	_	_
13	carbon	carbon	NN	_	_	_
14	source	source	NN	_	_	_
15	in	in	IN	_	_	_
16	a	a	DT	_	_	_
17	7L	7l	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	total	total	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	MBR-bioreactor	mbr-bioreactor	NN	_	_	_
22	.	.	.	_	_	_

1	When	when	WRB	_	_	_
2	the	the	DT	_	_	_
3	OD	od	NN	_	_	_
4	at	at	IN	_	_	_
5	600	600	CD	_	_	_
6	nm	nm	NN	_	_	_
7	reached	reach	VBD	_	_	_
8	a	a	DT	_	_	_
9	value	value	NN	_	_	_
10	of	of	IN	_	_	_
11	around	around	IN	_	_	_
12	5	5	CD	_	_	_
13	,	,	,	_	_	_
14	the	the	DT	_	_	_
15	BAD	BAD	NNP	_	_	_
16	--	--	:	_	_	_
17	promoter	promoter	NN	_	_	_
18	was	be	VBD	_	_	_
19	induced	induce	VBN	_	_	_
20	by	by	IN	_	_	_
21	adding	add	VBG	_	_	_
22	1g	1g	NN	_	_	_
23	per	per	IN	_	_	_
24	litre	litre	NN	_	_	_
25	and	and	CC	_	_	_
26	OD	od	NN	_	_	_
27	arabinose	arabinose	NN	_	_	_
28	to	to	TO	_	_	_
29	the	the	DT	_	_	_
30	medium	medium	NN	_	_	_
31	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	taken	take	VBN	_	_	_
4	at	at	IN	_	_	_
5	--	--	:	_	_	_
6	10	10	CD	_	_	_
7	,	,	,	_	_	_
8	0	0	CD	_	_	_
9	,	,	,	_	_	_
10	2	2	CD	_	_	_
11	,	,	,	_	_	_
12	5	5	CD	_	_	_
13	,	,	,	_	_	_
14	10	10	CD	_	_	_
15	,	,	,	_	_	_
16	20	20	CD	_	_	_
17	,	,	,	_	_	_
18	30	30	CD	_	_	_
19	,	,	,	_	_	_
20	45	45	CD	_	_	_
21	and	and	CC	_	_	_
22	60	60	CD	_	_	_
23	minutes	minute	NNS	_	_	_
24	related	related	JJ	_	_	_
25	to	to	TO	_	_	_
26	point	point	NN	_	_	_
27	of	of	IN	_	_	_
28	induction	induction	NN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	time	time	NN	_	_	_
3	point	point	NN	_	_	_
4	:	:	:	_	_	_
5	0	0	CD	_	_	_
6	minutes	minute	NNS	_	_	_
7	related	related	JJ	_	_	_
8	to	to	TO	_	_	_
9	point	point	NN	_	_	_
10	of	of	IN	_	_	_
11	BRP	brp	NN	_	_	_
12	induction	induction	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	time	time	NN	_	_	_
15	point	point	NN	_	_	_
16	:	:	:	_	_	_
17	-10	-10	CD	_	_	_
18	minutes	minute	NNS	_	_	_
19	related	related	JJ	_	_	_
20	to	to	TO	_	_	_
21	point	point	NN	_	_	_
22	of	of	IN	_	_	_
23	BRP	brp	NN	_	_	_
24	induction	induction	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	time	time	NN	_	_	_
27	point	point	NN	_	_	_
28	:	:	:	_	_	_
29	10	10	CD	_	_	_
30	minutes	minute	NNS	_	_	_
31	related	related	JJ	_	_	_
32	to	to	TO	_	_	_
33	point	point	NN	_	_	_
34	of	of	IN	_	_	_
35	BRP	brp	NN	_	_	_
36	induction	induction	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	time	time	NN	_	_	_
39	point	point	NN	_	_	_
40	:	:	:	_	_	_
41	20	20	CD	_	_	_
42	minutes	minute	NNS	_	_	_
43	related	related	JJ	_	_	_
44	to	to	TO	_	_	_
45	point	point	NN	_	_	_
46	of	of	IN	_	_	_
47	BRP	brp	NN	_	_	_
48	induction	induction	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	time	time	NN	_	_	_
51	point	point	NN	_	_	_
52	:	:	:	_	_	_
53	2	2	CD	_	_	_
54	minutes	minute	NNS	_	_	_
55	related	related	JJ	_	_	_
56	to	to	TO	_	_	_
57	point	point	NN	_	_	_
58	of	of	IN	_	_	_
59	BRP	brp	NN	_	_	_
60	induction	induction	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	time	time	NN	_	_	_
63	point	point	NN	_	_	_
64	:	:	:	_	_	_
65	30	30	CD	_	_	_
66	minutes	minute	NNS	_	_	_
67	related	related	JJ	_	_	_
68	to	to	TO	_	_	_
69	point	point	NN	_	_	_
70	of	of	IN	_	_	_
71	BRP	brp	NN	_	_	_
72	induction	induction	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	time	time	NN	_	_	_
75	point	point	NN	_	_	_
76	:	:	:	_	_	_
77	45	45	CD	_	_	_
78	minutes	minute	NNS	_	_	_
79	related	related	JJ	_	_	_
80	to	to	TO	_	_	_
81	point	point	NN	_	_	_
82	of	of	IN	_	_	_
83	BRP	brp	NN	_	_	_
84	induction	induction	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	time	time	NN	_	_	_
87	point	point	NN	_	_	_
88	:	:	:	_	_	_
89	5	5	CD	_	_	_
90	minutes	minute	NNS	_	_	_
91	related	related	JJ	_	_	_
92	to	to	TO	_	_	_
93	point	point	NN	_	_	_
94	of	of	IN	_	_	_
95	BRP	brp	NN	_	_	_
96	induction	induction	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	time	time	NN	_	_	_
99	point	point	NN	_	_	_
100	:	:	:	_	_	_
101	60	60	CD	_	_	_
102	minutes	minute	NNS	_	_	_
103	related	related	JJ	_	_	_
104	to	to	TO	_	_	_
105	point	point	NN	_	_	_
106	of	of	IN	_	_	_
107	BRP	BRP	NNP	_	_	_
108	induction	induction	NN	_	_	_
109	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
110	Total	Total	NNP	_	_	_
111	RNA	rna	NN	_	_	_
112	is	be	VBZ	_	_	_
113	extracted	extract	VBN	_	_	_
114	from	from	IN	_	_	_
115	10	10	CD	_	_	_
116	^	^	CD	_	_	_
117	9	9	CD	_	_	_
118	cells	cell	NNS	_	_	_
119	by	by	IN	_	_	_
120	phenol-chloroform	phenol-chloroform	JJ	_	_	_
121	extraction	extraction	NN	_	_	_
122	according	accord	VBG	_	_	_
123	to	to	TO	_	_	_
124	Sambrook	Sambrook	NNP	_	_	_
125	et	et	FW	_	_	_
126	al.	al.	FW	_	_	_
127	and	and	CC	_	_	_
128	ethanol	ethanol	NN	_	_	_
129	precipitation	precipitation	NN	_	_	_
130	with	with	IN	_	_	_
131	5M	5m	NN	_	_	_
132	NaCl	nacl	NN	_	_	_
133	.	.	.	_	_	_

1	Subsequently	subsequently	RB	_	_	_
2	a	a	DT	_	_	_
3	DNAse	dnase	NN	_	_	_
4	I	I	PRP	_	_	_
5	digest	digest	VBP	_	_	_
6	at	at	IN	_	_	_
7	37	37	CD	_	_	_
8	°C	°c	NN	_	_	_
9	for	for	IN	_	_	_
10	30	30	CD	_	_	_
11	minutes	minute	NNS	_	_	_
12	and	and	CC	_	_	_
13	an	a	DT	_	_	_
14	additional	additional	JJ	_	_	_
15	phenol-chloroform	phenol-chloroform	JJ	_	_	_
16	extraction	extraction	NN	_	_	_
17	step	step	NN	_	_	_
18	is	be	VBZ	_	_	_
19	performed	perform	VBN	_	_	_
20	.	.	.	_	_	_

1	Integrity	integrity	NN	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	total	total	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	is	be	VBZ	_	_	_
7	electrophoretically	electrophoretically	RB	_	_	_
8	confirmed	confirm	VBN	_	_	_
9	using	use	VBG	_	_	_
10	the	the	DT	_	_	_
11	Agilent	Agilent	NNP	_	_	_
12	2100	2100	CD	_	_	_
13	Bioanalyzer	Bioanalyzer	NNP	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	is	be	VBZ	_	_	_
5	extracted	extract	VBN	_	_	_
6	from	from	IN	_	_	_
7	10	10	CD	_	_	_
8	^	^	CD	_	_	_
9	9	9	CD	_	_	_
10	cells	cell	NNS	_	_	_
11	by	by	IN	_	_	_
12	phenol-chloroform	phenol-chloroform	JJ	_	_	_
13	extraction	extraction	NN	_	_	_
14	and	and	CC	_	_	_
15	ethanol	ethanol	NN	_	_	_
16	precipitation	precipitation	NN	_	_	_
17	with	with	IN	_	_	_
18	5M	5m	NN	_	_	_
19	NaCl	nacl	NN	_	_	_
20	.	.	.	_	_	_

1	Subsequently	subsequently	RB	_	_	_
2	a	a	DT	_	_	_
3	DNAse	dnase	NN	_	_	_
4	I	I	PRP	_	_	_
5	digest	digest	VBP	_	_	_
6	at	at	IN	_	_	_
7	37	37	CD	_	_	_
8	°C	°c	NN	_	_	_
9	for	for	IN	_	_	_
10	30	30	CD	_	_	_
11	minutes	minute	NNS	_	_	_
12	and	and	CC	_	_	_
13	an	a	DT	_	_	_
14	additional	additional	JJ	_	_	_
15	phenol-chloroform	phenol-chloroform	JJ	_	_	_
16	extraction	extraction	NN	_	_	_
17	step	step	NN	_	_	_
18	is	be	VBZ	_	_	_
19	performed	perform	VBN	_	_	_
20	.	.	.	_	_	_

1	Integrity	integrity	NN	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	total	total	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	is	be	VBZ	_	_	_
7	electrophoretically	electrophoretically	RB	_	_	_
8	confirmed	confirm	VBN	_	_	_
9	using	use	VBG	_	_	_
10	the	the	DT	_	_	_
11	Agilent	Agilent	NNP	_	_	_
12	2100	2100	CD	_	_	_
13	Bioanalyzer	Bioanalyzer	NNP	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	0	0	CD	_	_	_
3	min	min	NN	_	_	_
4	,	,	,	_	_	_
5	0.8	0.8	CD	_	_	_
6	%	%	NN	_	_	_
7	butanol	butanol	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	0min-1	0min-1	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	0min-2	0min-2	JJ	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	0min-3	0min-3	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	0	0	CD	_	_	_
16	min	min	NN	_	_	_
17	,	,	,	_	_	_
18	unstressed	unstressed	JJ	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	195	195	CD	_	_	_
21	min	min	NN	_	_	_
22	,	,	,	_	_	_
23	0.8	0.8	CD	_	_	_
24	%	%	NN	_	_	_
25	butanol	butanol	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	195min-1	195min-1	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
29	195min-2	195min-2	JJ	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	195min-3	195min-3	JJ	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	195	195	CD	_	_	_
34	min	min	NN	_	_	_
35	,	,	,	_	_	_
36	unstressed	unstressed	JJ	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	30	30	CD	_	_	_
39	min	min	NN	_	_	_
40	,	,	,	_	_	_
41	0.8	0.8	CD	_	_	_
42	%	%	NN	_	_	_
43	butanol	butanol	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	30min-1	30min-1	JJ	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	30min-2	30min-2	JJ	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	30min-3	30min-3	JJ	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	30	30	CD	_	_	_
52	min	min	NN	_	_	_
53	,	,	,	_	_	_
54	unstressed	unstressed	JJ	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	80	80	CD	_	_	_
57	min	min	NN	_	_	_
58	,	,	,	_	_	_
59	0.8	0.8	CD	_	_	_
60	%	%	NN	_	_	_
61	butanol	butanol	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	80min-1	80min-1	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	80min-2	80min-2	CD	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	80min-3	80min-3	CD	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	80	80	CD	_	_	_
70	min	min	NN	_	_	_
71	,	,	,	_	_	_
72	unstressed	unstressed	JJ	_	_	_
73	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
74	Biomass	Biomass	NNP	_	_	_
75	was	be	VBD	_	_	_
76	snap	snap	JJ	_	_	_
77	frozen	freeze	VBN	_	_	_
78	in	in	IN	_	_	_
79	liquid	liquid	JJ	_	_	_
80	nitrogen	nitrogen	NN	_	_	_
81	and	and	CC	_	_	_
82	stored	store	VBD	_	_	_
83	at	at	IN	_	_	_
84	-80	-80	CD	_	_	_
85	C	c	NN	_	_	_
86	prior	prior	JJ	_	_	_
87	to	to	TO	_	_	_
88	extraction	extraction	NN	_	_	_
89	with	with	IN	_	_	_
90	Qiagen	Qiagen	NNP	_	_	_
91	RNeasy	RNeasy	NNP	_	_	_
92	Midi	Midi	NNP	_	_	_
93	kits	kit	NNS	_	_	_
94	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	integrity	integrity	NN	_	_	_
3	was	be	VBD	_	_	_
4	verified	verify	VBN	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	2100	2100	CD	_	_	_
8	Bioanalyzer	Bioanalyzer	NNP	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Agilent	Agilent	NNP	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Feature	feature	NN	_	_	_
6	fluorescence	fluorescence	NN	_	_	_
7	intensities	intensity	NNS	_	_	_
8	-LSB-	-lsb-	-LRB-	_	_	_
9	F532	f532	NN	_	_	_
10	media-B532	media-b532	NN	_	_	_
11	and	and	CC	_	_	_
12	F635media-B635	f635media-b635	NN	_	_	_
13	-RSB-	-rsb-	-RRB-	_	_	_
14	were	be	VBD	_	_	_
15	extracted	extract	VBN	_	_	_
16	using	use	VBG	_	_	_
17	GenePix	GenePix	NNP	_	_	_
18	Pro	pro	FW	_	_	_
19	6.0	6.0	CD	_	_	_
20	.	.	.	_	_	_

1	Local	local	JJ	_	_	_
2	hybridization	hybridization	NN	_	_	_
3	and	and	CC	_	_	_
4	intensity-dependent	intensity-dependent	JJ	_	_	_
5	artifacts	artifact	NNS	_	_	_
6	were	be	VBD	_	_	_
7	removed	remove	VBN	_	_	_
8	with	with	IN	_	_	_
9	Lowess	lowess	NN	_	_	_
10	normalization	normalization	NN	_	_	_
11	using	use	VBG	_	_	_
12	Standardization	standardization	NN	_	_	_
13	and	and	CC	_	_	_
14	Normalization	normalization	NN	_	_	_
15	of	of	IN	_	_	_
16	Microarray	Microarray	NNP	_	_	_
17	Data	Data	NNP	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	SNOMAD	SNOMAD	NNP	_	_	_
20	,	,	,	_	_	_
21	http	http	NN	_	_	_
22	:	:	:	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	Individual	Individual	NNP	_	_	_
25	clones	clone	NNS	_	_	_
26	of	of	IN	_	_	_
27	E.	e.	FW	_	_	_
28	coli	coli	FW	_	_	_
29	DH1	dh1	NN	_	_	_
30	were	be	VBD	_	_	_
31	grown	grow	VBN	_	_	_
32	in	in	IN	_	_	_
33	M9	M9	NNP	_	_	_
34	MOPS	MOPS	NNP	MED	_	_
35	media	media	NNS	_	_	_
36	in	in	IN	_	_	_
37	300	300	CD	_	_	_
38	mL	ml	NN	_	_	_
39	media	media	NNS	_	_	_
40	in	in	IN	_	_	_
41	1	1	CD	_	_	_
42	L	l	NN	_	_	_
43	baffled	baffle	VBD	_	_	_
44	flasks	flask	NNS	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	strain	strain	NN	_	_	_
47	:	:	:	_	_	_
48	E.	e.	FW	_	_	_
49	coli	coli	FW	_	_	_
50	DH1	dh1	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	time	time	NN	_	_	_
53	:	:	:	_	_	_
54	0	0	CD	_	_	_
55	min	min	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	time	time	NN	_	_	_
58	:	:	:	_	_	_
59	195	195	CD	_	_	_
60	min	min	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	time	time	NN	_	_	_
63	:	:	:	_	_	_
64	30	30	CD	_	_	_
65	min	min	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	time	time	NN	_	_	_
68	:	:	:	_	_	_
69	80	80	CD	_	_	_
70	min	min	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	treatment	treatment	NN	_	_	_
73	:	:	:	_	_	_
74	0.8	0.8	CD	_	_	_
75	%	%	NN	_	_	_
76	n-butanol	n-butanol	NN	_	_	_
77	was	be	VBD	_	_	_
78	added	add	VBN	_	_	_
79	at	at	IN	_	_	_
80	time	time	NN	_	_	_
81	0	0	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	81-4420	81-4420	CD	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	83-2315	83-2315	CD	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	86-1390	86-1390	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	86-4220	86-4220	CD	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	87-4725	87-4725	CD	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	88-1861	88-1861	CD	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	88-4299	88-4299	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	89-56-196	89-56-196	CD	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	91-19-172	91-19-172	CD	_	_	_
100	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
101	Data	Data	NNP	_	_	_
102	obtained	obtain	VBN	_	_	_
103	from	from	IN	_	_	_
104	E.	e.	FW	_	_	_
105	coli	coli	FW	_	_	_
106	O157	o157	NN	_	_	_
107	:	:	:	_	_	_
108	H7	h7	NN	_	_	_
109	microarrays	microarray	NNS	_	_	_
110	were	be	VBD	_	_	_
111	normalized	normalize	VBN	_	_	_
112	using	use	VBG	_	_	_
113	the	the	DT	_	_	_
114	Ratio-based	ratio-based	JJ	_	_	_
115	and	and	CC	_	_	_
116	Lowess	lowess	JJ	_	_	_
117	methods	method	NNS	_	_	_
118	in	in	IN	_	_	_
119	Acuity	acuity	NN	_	_	_
120	3.1	3.1	CD	_	_	_
121	-LRB-	-lrb-	-LRB-	_	_	_
122	Axon	axon	NN	_	_	_
123	instruments	instrument	NNS	_	_	_
124	-RRB-	-rrb-	-RRB-	_	_	_
125	before	before	IN	_	_	_
126	analysis	analysis	NN	_	_	_
127	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	normalized	normalize	VBN	_	_	_
3	data	datum	NNS	_	_	_
4	for	for	IN	_	_	_
5	all	all	DT	_	_	_
6	strains	strain	NNS	_	_	_
7	were	be	VBD	_	_	_
8	converted	convert	VBN	_	_	_
9	into	into	IN	_	_	_
10	log2	log2	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Fluor	Fluor	NNP	_	_	_
13	647	647	CD	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
15	EDL	edl	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	O157	o157	NN	_	_	_
18	:	:	:	_	_	_
19	H7	h7	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Escherichia	escherichia	FW	Organism	_	_
23	coli	coli	FW	Organism	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Escherichia	escherichia	FW	Organism	_	_
26	coli	coli	FW	Organism	_	_
27	O157	o157	NN	_	_	_
28	:	:	:	_	_	_
29	H7	h7	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Escherichia	escherichia	FW	Organism	_	_
32	coli	coli	FW	Organism	_	_
33	O157	o157	NN	_	_	_
34	:	:	:	_	_	_
35	H7	h7	NN	_	_	_
36	str	str	NN	_	_	_
37	.	.	.	_	_	_

1	EDL933	edl933	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Escherichia	escherichia	FW	Organism	_	_
4	coli	coli	FW	Organism	_	_
5	O157	o157	NN	_	_	_
6	:	:	:	_	_	_
7	H7	h7	NN	_	_	_
8	str	str	NN	_	_	_
9	.	.	.	_	_	_

1	Sakai	Sakai	NNP	_	_	_
2	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3	Escherichia	escherichia	FW	Organism	_	_
4	coli	coli	FW	Organism	_	_
5	str	str	FW	_	_	_
6	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Overnight	overnight	JJ	_	_	_
4	bacterial	bacterial	JJ	_	_	_
5	culture	culture	NN	_	_	_
6	in	in	IN	_	_	_
7	BHI	BHI	NNP	_	_	_
8	broth	broth	NN	_	_	_
9	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	referece	referece	NN	_	_	_
3	:	:	:	_	_	_
4	The	the	DT	_	_	_
5	three	three	CD	_	_	_
6	genomes	genome	NNS	_	_	_
7	contributing	contribute	VBG	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	ORFs	orf	NNS	_	_	_
11	on	on	IN	_	_	_
12	the	the	DT	_	_	_
13	microarray	microarray	NN	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Sakai	Sakai	NNP	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	O157	O157	NNP	_	_	_
5	:	:	:	_	_	_
6	H7	h7	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	See	see	VB	_	_	_
10	the	the	DT	_	_	_
11	paper	paper	NN	_	_	_
12	Variation	variation	NN	_	_	_
13	in	in	IN	_	_	_
14	the	the	DT	_	_	_
15	Genomic	genomic	JJ	_	_	_
16	islands	island	NNS	_	_	_
17	of	of	IN	_	_	_
18	porcine	porcine	NN	_	_	_
19	enteropathogenic	enteropathogenic	JJ	_	_	_
20	Escherichia	escherichia	FW	Organism	_	_
21	coli	coli	FW	Organism	_	_
22	strains	strain	NNS	_	_	_
23	of	of	IN	_	_	_
24	serogroup	serogroup	NN	_	_	_
25	O45	o45	NN	_	_	_
26	revealed	reveal	VBN	_	_	_
27	by	by	IN	_	_	_
28	comparative	comparative	JJ	_	_	_
29	genomic	genomic	JJ	_	_	_
30	hybridization	hybridization	NN	_	_	_
31	and	and	CC	_	_	_
32	PCR	pcr	NN	_	_	_
33	by	by	IN	_	_	_
34	Bruant	Bruant	NNP	_	_	_
35	and	and	CC	_	_	_
36	Zhang	Zhang	NNP	_	_	_
37	et	et	FW	_	_	_
38	al.	al.	FW	_	_	_
39	2009	2009	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	strain	strain	NN	_	_	_
42	:	:	:	_	_	_
43	EHEC	ehec	NN	_	_	_
44	strain	strain	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	strain	strain	NN	_	_	_
47	:	:	:	_	_	_
48	Porcine	porcine	NN	_	_	_
49	EPEC	epec	NN	_	_	_
50	strain	strain	NN	_	_	_
51	O45	o45	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	strain	strain	NN	_	_	_
54	:	:	:	_	_	_
55	Rabbit	rabbit	NN	_	_	_
56	EPEC	epec	NN	_	_	_
57	strain	strain	NN	_	_	_
58	O103	o103	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
60	The	the	DT	_	_	_
61	cultures	culture	NNS	_	_	_
62	were	be	VBD	_	_	_
63	centrifuged	centrifuge	VBN	_	_	_
64	at	at	IN	_	_	_
65	8000	8000	CD	_	_	_
66	rpm	rpm	NN	_	_	_
67	for	for	IN	_	_	_
68	10	10	CD	_	_	_
69	minutes	minute	NNS	_	_	_
70	and	and	CC	_	_	_
71	the	the	DT	_	_	_
72	pellet	pellet	NN	_	_	_
73	was	be	VBD	_	_	_
74	dissolved	dissolve	VBN	_	_	_
75	in	in	IN	_	_	_
76	15	15	CD	_	_	_
77	mL	ml	NN	_	_	_
78	of	of	IN	_	_	_
79	10	10	CD	_	_	_
80	mM	mm	NN	KWSUPP	_	_
81	NaCl	nacl	NN	_	_	_
82	,	,	,	_	_	_
83	20	20	CD	_	_	_
84	mM	mm	NN	KWSUPP	_	_
85	Tris-HCl	tris-hcl	NN	_	_	_
86	-LRB-	-lrb-	-LRB-	_	_	_
87	pH	ph	NN	_	_	_
88	8.0	8.0	CD	_	_	_
89	-RRB-	-rrb-	-RRB-	_	_	_
90	,	,	,	_	_	_
91	1	1	CD	_	_	_
92	mM	mm	NN	KWSUPP	_	_
93	EDTA	edta	NN	_	_	_
94	,	,	,	_	_	_
95	100	100	CD	_	_	_
96	μg	μg	NN	_	_	_
97	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
98	Escherichia	escherichia	FW	Organism	_	_
99	coli	coli	FW	Organism	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	FRIK2000	frik2000	NN	_	_	_
102	Cy3	cy3	NN	_	_	_
103	rep1	rep1	NN	_	_	_
104	vs	vs	CC	_	_	_
105	EDL933	edl933	NN	_	_	_
106	pool	pool	NN	_	_	_
107	Cy5	cy5	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	FRIK2000	frik2000	CD	_	_	_
110	Cy3	cy3	NN	_	_	_
111	rep3	rep3	NN	_	_	_
112	vs	vs	CC	_	_	_
113	EDL933	edl933	NN	_	_	_
114	pool	pool	NN	_	_	_
115	Cy5	cy5	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	FRIK2000	frik2000	CD	_	_	_
118	Cy5	cy5	NN	_	_	_
119	rep2	rep2	NN	_	_	_
120	vs	vs	CC	_	_	_
121	EDL933	edl933	NN	_	_	_
122	pool	pool	NN	_	_	_
123	Cy3	cy3	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	FRIK2000	frik2000	CD	_	_	_
126	Cy5	cy5	NN	_	_	_
127	rep4	rep4	NN	_	_	_
128	vs	vs	CC	_	_	_
129	EDL933	edl933	NN	_	_	_
130	pool	pool	NN	_	_	_
131	Cy3	cy3	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	FRIK966	frik966	NN	_	_	_
134	Cy3	cy3	NN	_	_	_
135	rep1	rep1	NN	_	_	_
136	vs	vs	CC	_	_	_
137	EDL933	edl933	NN	_	_	_
138	pool	pool	NN	_	_	_
139	Cy5	cy5	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	FRIK966	frik966	NN	_	_	_
142	Cy3	cy3	NN	_	_	_
143	rep3	rep3	NN	_	_	_
144	vs	vs	CC	_	_	_
145	EDL933	edl933	NN	_	_	_
146	pool	pool	NN	_	_	_
147	Cy5	cy5	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	FRIK966	frik966	NN	_	_	_
150	Cy5	cy5	NN	_	_	_
151	rep2	rep2	NN	_	_	_
152	vs	vs	CC	_	_	_
153	EDL933	edl933	NN	_	_	_
154	pool	pool	NN	_	_	_
155	Cy3	cy3	NN	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
157	FRIK966	frik966	NN	_	_	_
158	Cy5	cy5	NN	_	_	_
159	rep4	rep4	NN	_	_	_
160	vs	vs	CC	_	_	_
161	EDL933	edl933	NN	_	_	_
162	pool	pool	NN	_	_	_
163	Cy3	cy3	NN	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	isolate	isolate	NN	_	_	_
166	:	:	:	_	_	_
167	bovine	bovine	JJ	_	_	_
168	isolate	isolate	NN	_	_	_
169	of	of	IN	_	_	_
170	e	e	SYM	_	_	_
171	coli	coli	FW	_	_	_
172	o157	o157	FW	_	_	_
173	:	:	:	_	_	_
174	H7	h7	NN	_	_	_
175	FRIK2000	frik2000	NN	_	_	_
176	lineage	lineage	NN	_	_	_
177	II	ii	CD	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	isolate	isolate	NN	_	_	_
180	:	:	:	_	_	_
181	bovine	bovine	JJ	_	_	_
182	isolate	isolate	NN	_	_	_
183	of	of	IN	_	_	_
184	e	e	SYM	_	_	_
185	coli	coli	FW	_	_	_
186	o157	o157	FW	_	_	_
187	:	:	:	_	_	_
188	H7	h7	NN	_	_	_
189	FRIK966	frik966	NN	_	_	_
190	lineage	lineage	NN	_	_	_
191	II	ii	CD	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	isolate	isolate	NN	_	_	_
194	:	:	:	_	_	_
195	clinical	clinical	JJ	_	_	_
196	isolate	isolate	JJ	_	_	_
197	e	e	SYM	_	_	_
198	coli	coli	FW	_	_	_
199	o157	o157	FW	_	_	_
200	:	:	:	_	_	_
201	H7	h7	NN	_	_	_
202	lineage	lineage	NN	_	_	_
203	I	I	PRP	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBP	_	_	_
205	late	late	JJ	_	_	_
206	log	log	NN	_	_	_
207	phase	phase	NN	_	_	_
208	grown	grow	VBN	_	_	_
209	e	e	SYM	_	_	_
210	coli	coli	NNS	_	_	_
211	966	966	CD	_	_	_
212	into	into	IN	_	_	_
213	RNAprotect	rnaprotect	NN	_	_	_
214	solution	solution	NN	_	_	_
215	,	,	,	_	_	_
216	RNA	rna	NN	_	_	_
217	extracted	extract	VBN	_	_	_
218	with	with	IN	_	_	_
219	qiagen	qiagen	NN	_	_	_
220	RNA	rna	NN	_	_	_
221	bacteria	bacterium	NNS	_	_	_
222	kits	kit	NNS	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	late	late	JJ	_	_	_
225	log	log	NN	_	_	_
226	phase	phase	NN	_	_	_
227	grown	grow	VBN	_	_	_
228	e	e	SYM	_	_	_
229	coli	coli	FW	_	_	_
230	EDL933	edl933	FW	_	_	_
231	into	into	IN	_	_	_
232	RNAprotect	rnaprotect	NN	_	_	_
233	solution	solution	NN	_	_	_
234	,	,	,	_	_	_
235	RNA	rna	NN	_	_	_
236	extracted	extract	VBN	_	_	_
237	with	with	IN	_	_	_
238	qiagen	qiagen	NN	_	_	_
239	RNA	rna	NN	_	_	_
240	bacteria	bacterium	NNS	_	_	_
241	kits	kit	NNS	_	_	_
242	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
243	Microarray	Microarray	NNP	_	_	_
244	data	data	NN	_	_	_
245	analyses	analysis	NNS	_	_	_
246	were	be	VBD	_	_	_
247	performed	perform	VBN	_	_	_
248	using	use	VBG	_	_	_
249	Acuity	acuity	NN	_	_	_
250	4.0	4.0	CD	_	_	_
251	software	software	NN	_	_	_
252	.	.	.	_	_	_

1	Slides	slide	NNS	_	_	_
2	were	be	VBD	_	_	_
3	normalized	normalize	VBN	_	_	_
4	using	use	VBG	_	_	_
5	standard	standard	JJ	_	_	_
6	ratio-based	ratio-based	JJ	_	_	_
7	methods	method	NNS	_	_	_
8	.	.	.	_	_	_

1	Data	datum	NNS	_	_	_
2	were	be	VBD	_	_	_
3	analyzed	analyze	VBN	_	_	_
4	based	base	VBN	_	_	_
5	upon	upon	IN	_	_	_
6	Log	log	NN	_	_	_
7	ratio	ratio	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	635	635	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	RNA	rna	NN	_	_	_
12	from	from	IN	_	_	_
13	late	late	JJ	_	_	_
14	log	log	NN	_	_	_
15	phase	phase	NN	_	_	_
16	E	e	NN	_	_	_
17	coli	coli	NN	_	_	_
18	EDL933	edl933	NN	_	_	_
19	pooled	pool	VBD	_	_	_
20	reference	reference	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	RNA	rna	NN	_	_	_
23	from	from	IN	_	_	_
24	late	late	JJ	_	_	_
25	log	log	NN	_	_	_
26	phase	phase	NN	_	_	_
27	E	e	NN	_	_	_
28	coli	coli	NN	_	_	_
29	FRIK2000	frik2000	NN	_	_	_
30	rep	rep	NN	GEN	_	_
31	1	1	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	RNA	rna	NN	_	_	_
34	from	from	IN	_	_	_
35	late	late	JJ	_	_	_
36	log	log	NN	_	_	_
37	phase	phase	NN	_	_	_
38	E	e	NN	_	_	_
39	coli	coli	NN	_	_	_
40	FRIK2000	frik2000	NN	_	_	_
41	rep	rep	NN	GEN	_	_
42	2	2	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	RNA	rna	NN	_	_	_
45	from	from	IN	_	_	_
46	late	late	JJ	_	_	_
47	log	log	NN	_	_	_
48	phase	phase	NN	_	_	_
49	E	e	NN	_	_	_
50	coli	coli	NN	_	_	_
51	FRIK2000	frik2000	NN	_	_	_
52	rep	rep	NN	GEN	_	_
53	3	3	CD	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	RNA	rna	NN	_	_	_
56	from	from	IN	_	_	_
57	late	late	JJ	_	_	_
58	log	log	NN	_	_	_
59	phase	phase	NN	_	_	_
60	E	e	NN	_	_	_
61	coli	coli	NN	_	_	_
62	FRIK2000	frik2000	NN	_	_	_
63	rep	rep	NN	GEN	_	_
64	4	4	CD	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	RNA	rna	NN	_	_	_
67	from	from	IN	_	_	_
68	late	late	JJ	_	_	_
69	log	log	NN	_	_	_
70	phase	phase	NN	_	_	_
71	E	e	NN	_	_	_
72	coli	coli	NN	_	_	_
73	FRIK966	frik966	NN	_	_	_
74	rep	rep	NN	GEN	_	_
75	1	1	CD	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	RNA	rna	NN	_	_	_
78	from	from	IN	_	_	_
79	late	late	JJ	_	_	_
80	log	log	NN	_	_	_
81	phase	phase	NN	_	_	_
82	E	e	NN	_	_	_
83	coli	coli	NN	_	_	_
84	FRIK966	frik966	NN	_	_	_
85	rep	rep	NN	GEN	_	_
86	2	2	CD	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	RNA	rna	NN	_	_	_
89	from	from	IN	_	_	_
90	late	late	JJ	_	_	_
91	log	log	NN	_	_	_
92	phase	phase	NN	_	_	_
93	E	e	NN	_	_	_
94	coli	coli	NN	_	_	_
95	FRIK966	frik966	NN	_	_	_
96	rep	rep	NN	GEN	_	_
97	3	3	CD	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	RNA	rna	NN	_	_	_
100	from	from	IN	_	_	_
101	late	late	JJ	_	_	_
102	log	log	NN	_	_	_
103	phase	phase	NN	_	_	_
104	E	e	NN	_	_	_
105	coli	coli	NN	_	_	_
106	FRIK966	frik966	NN	_	_	_
107	rep	rep	NN	GEN	_	_
108	4	4	CD	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	strain	strain	NN	_	_	_
111	:	:	:	_	_	_
112	EDL933	edl933	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	strain	strain	NN	_	_	_
115	:	:	:	_	_	_
116	FRIK2000	frik2000	CD	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	strain	strain	NN	_	_	_
119	:	:	:	_	_	_
120	FRIK966	frik966	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	e.coli	e.coli	NNS	_	_	_
123	,	,	,	_	_	_
124	37	37	CD	_	_	_
125	°C	°c	NN	_	_	_
126	,	,	,	_	_	_
127	60	60	CD	_	_	_
128	min	min	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	E.coli	e.coli	NNS	_	_	_
131	,	,	,	_	_	_
132	37	37	CD	_	_	_
133	°C	°c	NN	_	_	_
134	,	,	,	_	_	_
135	60	60	CD	_	_	_
136	min	min	NN	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	E.coli	e.coli	NN	_	_	_
139	,37	,37	CD	_	_	_
140	°C	°c	NN	_	_	_
141	,	,	,	_	_	_
142	60	60	CD	_	_	_
143	min	min	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	E.coli	e.coli	NN	_	_	_
146	，	，	NN	_	_	_
147	37	37	CD	_	_	_
148	°C	°c	NN	_	_	_
149	，	，	CD	_	_	_
150	60	60	CD	_	_	_
151	min	min	NN	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	e.coli	e.coli	NNS	_	_	_
154	,	,	,	_	_	_
155	43	43	CD	_	_	_
156	°C	°c	NN	_	_	_
157	,	,	,	_	_	_
158	60	60	CD	_	_	_
159	min	min	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	E.coli	e.coli	NNS	_	_	_
162	,	,	,	_	_	_
163	43	43	CD	_	_	_
164	°C	°c	NN	_	_	_
165	,	,	,	_	_	_
166	60	60	CD	_	_	_
167	min	min	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	E.coli	e.coli	NN	_	_	_
170	,43	,43	CD	_	_	_
171	°C	°c	NN	_	_	_
172	,	,	,	_	_	_
173	60	60	CD	_	_	_
174	min	min	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	E.coli	e.coli	NN	_	_	_
177	，	，	CD	_	_	_
178	43	43	CD	_	_	_
179	°C	°c	NN	_	_	_
180	，	，	CD	_	_	_
181	60	60	CD	_	_	_
182	min	min	NN	_	_	_
183	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
184	E.	E.	NNP	_	_	_
185	coli	coli	NN	_	_	_
186	heat	heat	NN	_	_	_
187	shock	shock	NN	_	_	_
188	gene	gene	NN	_	_	_
189	expression	expression	NN	_	_	_
190	data	datum	NNS	_	_	_
191	using	use	VBG	_	_	_
192	direct	direct	JJ	_	_	_
193	labeling	labeling	NN	_	_	_
194	method	method	NN	_	_	_
195	-LRB-	-lrb-	-LRB-	_	_	_
196	replicate-1	replicate-1	NN	_	_	_
197	-RRB-	-rrb-	-RRB-	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	E.	e.	FW	_	_	_
200	coli	coli	FW	_	_	_
201	heat	heat	NN	_	_	_
202	shock	shock	NN	_	_	_
203	gene	gene	NN	_	_	_
204	expression	expression	NN	_	_	_
205	data	datum	NNS	_	_	_
206	using	use	VBG	_	_	_
207	direct	direct	JJ	_	_	_
208	labeling	labeling	NN	_	_	_
209	method	method	NN	_	_	_
210	-LRB-	-lrb-	-LRB-	_	_	_
211	replicate-2	replicate-2	NN	_	_	_
212	-RRB-	-rrb-	-RRB-	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	E.	e.	FW	_	_	_
215	coli	coli	FW	_	_	_
216	heat	heat	NN	_	_	_
217	shock	shock	NN	_	_	_
218	gene	gene	NN	_	_	_
219	expression	expression	NN	_	_	_
220	data	datum	NNS	_	_	_
221	using	use	VBG	_	_	_
222	PAOD	paod	NN	_	_	_
223	method	method	NN	_	_	_
224	-LRB-	-lrb-	-LRB-	_	_	_
225	replicate-1	replicate-1	NN	_	_	_
226	-RRB-	-rrb-	-RRB-	_	_	_
227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
228	E.	e.	FW	_	_	_
229	coli	coli	FW	_	_	_
230	heat	heat	NN	_	_	_
231	shock	shock	NN	_	_	_
232	gene	gene	NN	_	_	_
233	expression	expression	NN	_	_	_
234	data	datum	NNS	_	_	_
235	using	use	VBG	_	_	_
236	PAOD	paod	NN	_	_	_
237	method	method	NN	_	_	_
238	-LRB-	-lrb-	-LRB-	_	_	_
239	replicate-2	replicate-2	NN	_	_	_
240	-RRB-	-rrb-	-RRB-	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	E.	e.	FW	_	_	_
243	coli	coli	FW	_	_	_
244	heat	heat	NN	_	_	_
245	shock	shock	NN	_	_	_
246	gene	gene	NN	_	_	_
247	expression	expression	NN	_	_	_
248	data	datum	NNS	_	_	_
249	using	use	VBG	_	_	_
250	random	random	JJ	_	_	_
251	priming	priming	NN	_	_	_
252	method	method	NN	_	_	_
253	-LRB-	-lrb-	-LRB-	_	_	_
254	replicate-1	replicate-1	NN	_	_	_
255	-RRB-	-rrb-	-RRB-	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
257	E.	e.	FW	_	_	_
258	coli	coli	FW	_	_	_
259	heat	heat	NN	_	_	_
260	shock	shock	NN	_	_	_
261	gene	gene	NN	_	_	_
262	expression	expression	NN	_	_	_
263	data	datum	NNS	_	_	_
264	using	use	VBG	_	_	_
265	random	random	JJ	_	_	_
266	priming	priming	NN	_	_	_
267	method	method	NN	_	_	_
268	-LRB-	-lrb-	-LRB-	_	_	_
269	replicate-2	replicate-2	NN	_	_	_
270	-RRB-	-rrb-	-RRB-	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	Escherichia	escherichia	FW	Organism	_	_
273	coli	coli	FW	Organism	_	_
274	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
275	strain	strain	NN	_	_	_
276	:	:	:	_	_	_
277	DH5α	dh5α	NN	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
279	The	the	DT	_	_	_
280	raw	raw	JJ	_	_	_
281	data	datum	NNS	_	_	_
282	were	be	VBD	_	_	_
283	normalized	normalize	VBN	_	_	_
284	using	use	VBG	_	_	_
285	a	a	DT	_	_	_
286	space	space	NN	_	_	_
287	and	and	CC	_	_	_
288	intensity-dependant	intensity-dependant	JJ	_	_	_
289	LOWESS	lowess	NN	_	_	_
290	program	program	NN	_	_	_
291	.	.	.	_	_	_

1	Data	datum	NNS	_	_	_
2	from	from	IN	_	_	_
3	faint	faint	JJ	_	_	_
4	spots	spot	NNS	_	_	_
5	were	be	VBD	_	_	_
6	removed	remove	VBN	_	_	_
7	,	,	,	_	_	_
8	in	in	IN	_	_	_
9	which	which	WDT	_	_	_
10	the	the	DT	_	_	_
11	intensity	intensity	NN	_	_	_
12	was	be	VBD	_	_	_
13	lower	lower	JJR	_	_	_
14	than	than	IN	_	_	_
15	the	the	DT	_	_	_
16	average	average	JJ	_	_	_
17	intensity	intensity	NN	_	_	_
18	plus	plus	CC	_	_	_
19	2	2	CD	_	_	_
20	standard	standard	JJ	_	_	_
21	deviations	deviation	NNS	_	_	_
22	of	of	IN	_	_	_
23	the	the	DT	_	_	_
24	negative	negative	JJ	_	_	_
25	controls	control	NNS	_	_	_
26	on	on	IN	_	_	_
27	the	the	DT	_	_	_
28	array	array	NN	_	_	_
29	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	experimental	experimental	JJ	_	_	_
4	and	and	CC	_	_	_
5	control	control	JJ	_	_	_
6	sample	sample	NN	_	_	_
7	,	,	,	_	_	_
8	amplification	amplification	NN	_	_	_
9	and	and	CC	_	_	_
10	hybridization	hybridization	NN	_	_	_
11	were	be	VBD	_	_	_
12	performed	perform	VBN	_	_	_
13	by	by	IN	_	_	_
14	a	a	DT	_	_	_
15	dye-swap	dye-swap	JJ	_	_	_
16	strategy	strategy	NN	_	_	_
17	in	in	IN	_	_	_
18	two	two	CD	_	_	_
19	independent	independent	JJ	_	_	_
20	experiments	experiment	NNS	_	_	_
21	.	.	.	_	_	_

1	Differentially	differentially	RB	_	_	_
2	expressed	express	VBN	_	_	_
3	genes	gene	NNS	_	_	_
4	were	be	VBD	_	_	_
5	identified	identify	VBN	_	_	_
6	with	with	IN	_	_	_
7	at	at	IN	_	_	_
8	least	least	JJS	_	_	_
9	2	2	CD	_	_	_
10	fold	fold	JJ	_	_	_
11	changes	change	NNS	_	_	_
12	and	and	CC	_	_	_
13	q	q	VB	_	_	_
14	<	<	JJR	_	_	_
15	0.001	0.001	CD	_	_	_
16	criteria	criterion	NNS	_	_	_
17	using	use	VBG	_	_	_
18	SAM	SAM	NNP	_	_	_
19	software	software	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	from	from	IN	_	_	_
7	E.coli	e.coli	JJ	_	_	_
8	cells	cell	NNS	_	_	_
9	using	use	VBG	_	_	_
10	NucleoSpin	NucleoSpin	NNP	_	_	_
11	®	®	SYM	_	_	_
12	RNA	rna	NN	_	_	_
13	II	ii	CD	_	_	_
14	kit	kit	NN	_	_	_
15	according	accord	VBG	_	_	_
16	to	to	TO	_	_	_
17	the	the	DT	_	_	_
18	manufacturers	manufacturer	NNS	_	_	_
19	'	'	POS	_	_	_
20	instructions	instruction	NNS	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Macherey	Macherey	NNP	_	_	_
23	Nagel	Nagel	NNP	_	_	_
24	,	,	,	_	_	_
25	Duren	Duren	NNP	_	_	_
26	,	,	,	_	_	_
27	Germany	Germany	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	examined	examine	VBN	_	_	_
5	in	in	IN	_	_	_
6	a	a	DT	_	_	_
7	1.5	1.5	CD	_	_	_
8	%	%	NN	_	_	_
9	denaturing	denature	VBG	_	_	_
10	agarose	agarose	NN	_	_	_
11	gel	gel	NN	_	_	_
12	,	,	,	_	_	_
13	quantitated	quantitate	VBN	_	_	_
14	by	by	IN	_	_	_
15	absorbance	absorbance	NN	_	_	_
16	at	at	IN	_	_	_
17	260	260	CD	_	_	_
18	nm	nm	NN	_	_	_
19	and	and	CC	_	_	_
20	stored	store	VBN	_	_	_
21	until	until	IN	_	_	_
22	further	further	JJ	_	_	_
23	use	use	NN	_	_	_
24	for	for	IN	_	_	_
25	microarray	microarray	NN	_	_	_
26	and	and	CC	_	_	_
27	RT-PCR	rt-pcr	NN	_	_	_
28	verification	verification	NN	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	Total	Total	NNP	_	_	_
31	RNA	rna	NN	_	_	_
32	was	be	VBD	_	_	_
33	isolated	isolate	VBN	_	_	_
34	from	from	IN	_	_	_
35	E.coli	e.coli	JJ	_	_	_
36	cells	cell	NNS	_	_	_
37	using	use	VBG	_	_	_
38	NucleoSpin	NucleoSpin	NNP	_	_	_
39	®	®	SYM	_	_	_
40	RNA	rna	NN	_	_	_
41	II	ii	CD	_	_	_
42	kit	kit	NN	_	_	_
43	according	accord	VBG	_	_	_
44	to	to	TO	_	_	_
45	the	the	DT	_	_	_
46	manufacturers	manufacturer	NNS	_	_	_
47	'	'	POS	_	_	_
48	instructions	instruction	NNS	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	Macherey	Macherey	NNP	_	_	_
51	Nagel	Nagel	NNP	_	_	_
52	,	,	,	_	_	_
53	Duren	Duren	NNP	_	_	_
54	,	,	,	_	_	_
55	Germany	Germany	NNP	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	examined	examine	VBN	_	_	_
5	in	in	IN	_	_	_
6	a	a	DT	_	_	_
7	1.5	1.5	CD	_	_	_
8	%	%	NN	_	_	_
9	denaturing	denature	VBG	_	_	_
10	agarose	agarose	NN	_	_	_
11	gel	gel	NN	_	_	_
12	,	,	,	_	_	_
13	quantitated	quantitate	VBN	_	_	_
14	by	by	IN	_	_	_
15	absorbance	absorbance	NN	_	_	_
16	at	at	IN	_	_	_
17	260	260	CD	_	_	_
18	nm	nm	NN	_	_	_
19	and	and	CC	_	_	_
20	stored	store	VBN	_	_	_
21	until	until	IN	_	_	_
22	further	further	JJ	_	_	_
23	use	use	NN	_	_	_
24	for	for	IN	_	_	_
25	microarray	microarray	NN	_	_	_
26	and	and	CC	_	_	_
27	RT-PCR	rt-pcr	NN	_	_	_
28	verification	verification	NN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	DNA	dna	NN	_	_	_
3	detected	detect	VBN	_	_	_
4	with	with	IN	_	_	_
5	GyrA	gyra	NN	_	_	_
6	immunoglobulin	immunoglobulin	NN	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	Escherichia	escherichia	FW	Organism	_	_
9	coli	coli	FW	Organism	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	gyrase	gyrase	NN	_	_	_
12	binding	binding	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	ChIP-chip	chip-chip	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	no.	no.	NN	_	_	_
17	1	1	CD	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	gyrase	gyrase	NN	_	_	_
20	binding	binding	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	ChIP-chip	chip-chip	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	no.	no.	NN	_	_	_
25	2	2	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	gyrase	gyrase	NN	_	_	_
28	binding	binding	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	ChIP-chip	chip-chip	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	no.	no.	RB	_	_	_
33	3	3	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	gyrase	gyrase	NN	_	_	_
36	binding	binding	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	ChIP-chip	chip-chip	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	no.	no.	RB	_	_	_
41	4	4	CD	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	gyrase	gyrase	NN	_	_	_
44	binding	binding	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	ChIP-chip	chip-chip	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	no.	no.	RB	_	_	_
49	5	5	CD	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	gyrase	gyrase	NN	_	_	_
52	binding	binding	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	ChIP-chip	chip-chip	NN	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	no.	no.	RB	_	_	_
57	6	6	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	gyrase	gyrase	NN	_	_	_
60	binding	binding	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	ChIP-chip	chip-chip	NN	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	no.	no.	NN	_	_	_
65	7	7	CD	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	gyrase	gyrase	NN	_	_	_
68	binding	binding	NN	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	ChIP-chip	chip-chip	NN	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	no.	no.	VBP	_	_	_
73	8	8	CD	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
75	Reference	Reference	NNP	_	_	_
76	Genomic	genomic	JJ	_	_	_
77	DNA	dna	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	Acidic	acidic	JJ	_	_	_
80	Hot	Hot	NNP	_	_	_
81	Phenol	Phenol	NNP	_	_	_
82	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
83	Cells	cell	NNS	_	_	_
84	were	be	VBD	_	_	_
85	grown	grow	VBN	_	_	_
86	in	in	IN	_	_	_
87	Luria	Luria	NNP	_	_	_
88	Bertani	Bertani	NNP	_	_	_
89	-LRB-	-lrb-	-LRB-	_	_	_
90	LB	LB	NNP	_	_	_
91	-RRB-	-rrb-	-RRB-	_	_	_
92	media	media	NNS	_	_	_
93	at	at	IN	_	_	_
94	37C	37c	NN	_	_	_
95	at	at	IN	_	_	_
96	200	200	CD	_	_	_
97	rpm	rpm	NN	_	_	_
98	.	.	.	_	_	_

1	Overnight	overnight	JJ	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	inoculated	inoculate	VBN	_	_	_
5	with	with	IN	_	_	_
6	single	single	JJ	_	_	_
7	,	,	,	_	_	_
8	independent	independent	JJ	_	_	_
9	colonies	colony	NNS	_	_	_
10	in	in	IN	_	_	_
11	triplicate	triplicate	NN	_	_	_
12	,	,	,	_	_	_
13	incubated	incubate	VBN	_	_	_
14	aerobically	aerobically	RB	_	_	_
15	overnight	overnight	JJ	_	_	_
16	at	at	IN	_	_	_
17	37oC	37oc	NN	_	_	_
18	,	,	,	_	_	_
19	and	and	CC	_	_	_
20	sub-cultured	sub-cultured	JJ	_	_	_
21	to	to	TO	_	_	_
22	a	a	DT	_	_	_
23	starting	start	VBG	_	_	_
24	OD600	od600	NN	_	_	_
25	of	of	IN	_	_	_
26	0.0001	0.0001	CD	_	_	_
27	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	harvested	harvest	VBN	_	_	_
4	at	at	IN	_	_	_
5	OD600	od600	NN	_	_	_
6	=	=	JJ	_	_	_
7	0.3	0.3	CD	_	_	_
8	in	in	IN	_	_	_
9	exponential	exponential	JJ	GrowthPhase	_	_
10	phase	phase	NN	GrowthPhase	_	_
11	and	and	CC	_	_	_
12	at	at	IN	_	_	_
13	OD600	od600	NN	_	_	_
14	=	=	JJ	_	_	_
15	1.5	1.5	CD	_	_	_
16	in	in	IN	_	_	_
17	stationary	stationary	JJ	GrowthPhase	_	_
18	phase	phase	NN	GrowthPhase	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	O157	o157	NN	_	_	_
5	:	:	:	_	_	_
6	H7	h7	NN	_	_	_
7	str	str	NN	_	_	_
8	.	.	.	_	_	_

1	EDL933	edl933	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Exponential	exponential	JJ	_	_	_
4	phase	phase	NN	_	_	_
5	culture	culture	NN	_	_	_
6	of	of	IN	_	_	_
7	EDL933	edl933	NN	_	_	_
8	rpoS	rpos	NN	GEN	_	_
9	mutants	mutant	NNS	_	_	_
10	in	in	IN	_	_	_
11	LB	lb	NN	_	_	_
12	at	at	IN	_	_	_
13	OD600	od600	NN	_	_	_
14	of	of	IN	_	_	_
15	0.3	0.3	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
17	Exponential	exponential	JJ	_	_	_
18	phase	phase	NN	_	_	_
19	culture	culture	NN	_	_	_
20	of	of	IN	_	_	_
21	EDL933	edl933	NN	_	_	_
22	wild	wild	JJ	_	_	_
23	type	type	NN	_	_	_
24	in	in	IN	_	_	_
25	LB	lb	NN	_	_	_
26	at	at	IN	_	_	_
27	OD600	od600	NN	_	_	_
28	of	of	IN	_	_	_
29	0.3	0.3	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Exp-rpoS-rep1	exp-rpos-rep1	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	Exp-rpoS-rep2	exp-rpos-rep2	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	Exp-rpoS-rep3	exp-rpos-rep3	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Exp-WT-rep1	exp-wt-rep1	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	Exp-WT-rep2	exp-wt-rep2	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	Exp-WT-rep3	exp-wt-rep3	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	GCRMA	gcrma	NN	_	_	_
44	method	method	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	genotype	genotype	NN	_	_	_
47	:	:	:	_	_	_
48	rpoS	rpos	NN	GEN	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	genotype	genotype	NN	_	_	_
51	:	:	:	_	_	_
52	WT	WT	NNP	_	_	_
53	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
54	growth	growth	NN	_	_	_
55	phase	phase	NN	_	_	_
56	:	:	:	_	_	_
57	Exponential	exponential	JJ	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	growth	growth	NN	_	_	_
60	phase	phase	NN	_	_	_
61	:	:	:	_	_	_
62	Stationary	stationary	JJ	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	Stationary	stationary	JJ	_	_	_
65	phase	phase	NN	_	_	_
66	culture	culture	NN	_	_	_
67	of	of	IN	_	_	_
68	EDL933	edl933	NN	_	_	_
69	rpoS	rpos	NN	GEN	_	_
70	mutants	mutant	NNS	_	_	_
71	in	in	IN	_	_	_
72	LB	lb	NN	_	_	_
73	at	at	IN	_	_	_
74	OD600	od600	NN	_	_	_
75	of	of	IN	_	_	_
76	1.5	1.5	CD	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
78	Stationary	stationary	JJ	_	_	_
79	phase	phase	NN	_	_	_
80	culture	culture	NN	_	_	_
81	of	of	IN	_	_	_
82	EDL933	edl933	NN	_	_	_
83	wild	wild	JJ	_	_	_
84	type	type	NN	_	_	_
85	in	in	IN	_	_	_
86	LB	lb	NN	_	_	_
87	at	at	IN	_	_	_
88	OD600	od600	NN	_	_	_
89	of	of	IN	_	_	_
90	1.5	1.5	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	Stat-rpoS-rep1	stat-rpos-rep1	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	Stat-rpoS-rep2	stat-rpos-rep2	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	Stat-rpoS-rep3	stat-rpos-rep3	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	Stat-WT-rep1	stat-wt-rep1	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	Stat-WT-rep2	stat-wt-rep2	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	Stat-WT-rep3	stat-wt-rep3	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	agent	agent	NN	_	_	_
105	:	:	:	_	_	_
106	no	no	DT	_	_	_
107	triclosan	triclosan	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	agent	agent	NN	_	_	_
110	:	:	:	_	_	_
111	triclosan	triclosan	NN	_	_	_
112	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
113	E.	E.	NNP	_	_	_
114	coli	coli	NN	_	_	_
115	imp	imp	NN	_	_	_
116	fabI	fabi	NN	GEN	_	_
117	-LRB-	-lrb-	-LRB-	_	_	_
118	G93V	g93v	NN	_	_	_
119	-RRB-	-rrb-	-RRB-	_	_	_
120	-LSB-	-lsb-	-LRB-	_	_	_
121	control	control	NN	_	_	_
122	-RSB-	-rsb-	-RRB-	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	E.	e.	FW	_	_	_
125	coli	coli	FW	_	_	_
126	imp	imp	FW	_	_	_
127	fabI	fabi	NN	GEN	_	_
128	-LRB-	-lrb-	-LRB-	_	_	_
129	G94V	g94v	NN	_	_	_
130	-RRB-	-rrb-	-RRB-	_	_	_
131	-LSB-	-lsb-	-LRB-	_	_	_
132	control	control	NN	_	_	_
133	-RSB-	-rsb-	-RRB-	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	Escherichia	escherichia	FW	Organism	_	_
136	coli	coli	FW	Organism	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	imp	imp	NN	_	_	_
139	mutation	mutation	NN	_	_	_
140	:	:	:	_	_	_
141	contains	contain	VBZ	_	_	_
142	a	a	DT	_	_	_
143	23	23	CD	_	_	_
144	codon	codon	NN	_	_	_
145	deletion	deletion	NN	_	_	_
146	allele	allele	NN	_	_	_
147	in	in	IN	_	_	_
148	imp	imp	NN	_	_	_
149	-LRB-	-lrb-	-LRB-	_	_	_
150	increased	increase	VBN	_	_	_
151	membrane	membrane	NN	_	_	_
152	permeability	permeability	NN	_	_	_
153	-RRB-	-rrb-	-RRB-	_	_	_
154	,	,	,	_	_	_
155	substitution	substitution	NN	_	_	_
156	of	of	IN	_	_	_
157	the	the	DT	_	_	_
158	93th	93th	JJ	_	_	_
159	codon	codon	NN	_	_	_
160	of	of	IN	_	_	_
161	fabI	fabi	NN	GEN	_	_
162	,	,	,	_	_	_
163	NTG	NTG	NNP	_	_	_
164	treatment	treatment	NN	_	_	_
165	;	;	:	_	_	_
166	fabI	fabi	NN	GEN	_	_
167	-LRB-	-lrb-	-LRB-	_	_	_
168	G93V	g93v	NN	_	_	_
169	-RRB-	-rrb-	-RRB-	_	_	_
170	,	,	,	_	_	_
171	substitution	substitution	NN	_	_	_
172	of	of	IN	_	_	_
173	Gly	gly	NN	_	_	_
174	-LRB-	-lrb-	-LRB-	_	_	_
175	the	the	DT	_	_	_
176	93th	93th	JJ	_	_	_
177	codon	codon	NN	_	_	_
178	-RRB-	-rrb-	-RRB-	_	_	_
179	of	of	IN	_	_	_
180	fabI	fabi	NN	GEN	_	_
181	with	with	IN	_	_	_
182	Val	val	NN	_	_	_
183	,	,	,	_	_	_
184	NTG	NTG	NNP	_	_	_
185	treatment	treatment	NN	_	_	_
186	to	to	TO	_	_	_
187	be	be	VB	_	_	_
188	high	high	JJ	_	_	_
189	resistance	resistance	NN	_	_	_
190	to	to	TO	_	_	_
191	triclosan	triclosan	NN	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	imp	imp	NN	_	_	_
194	mutation	mutation	NN	_	_	_
195	:	:	:	_	_	_
196	contains	contain	VBZ	_	_	_
197	a	a	DT	_	_	_
198	23	23	CD	_	_	_
199	codon	codon	NN	_	_	_
200	deletion	deletion	NN	_	_	_
201	allele	allele	NN	_	_	_
202	in	in	IN	_	_	_
203	imp	imp	NN	_	_	_
204	-LRB-	-lrb-	-LRB-	_	_	_
205	increased	increase	VBN	_	_	_
206	membrane	membrane	NN	_	_	_
207	permeability	permeability	NN	_	_	_
208	-RRB-	-rrb-	-RRB-	_	_	_
209	,	,	,	_	_	_
210	substitution	substitution	NN	_	_	_
211	of	of	IN	_	_	_
212	the	the	DT	_	_	_
213	94th	94th	JJ	_	_	_
214	codon	codon	NN	_	_	_
215	of	of	IN	_	_	_
216	fabI	fabi	NN	GEN	_	_
217	,	,	,	_	_	_
218	NTG	NTG	NNP	_	_	_
219	treatment	treatment	NN	_	_	_
220	;	;	:	_	_	_
221	fabI	fabi	NN	GEN	_	_
222	-LRB-	-lrb-	-LRB-	_	_	_
223	G93V	g93v	NN	_	_	_
224	-RRB-	-rrb-	-RRB-	_	_	_
225	,	,	,	_	_	_
226	substitution	substitution	NN	_	_	_
227	of	of	IN	_	_	_
228	Gly	gly	NN	_	_	_
229	-LRB-	-lrb-	-LRB-	_	_	_
230	the	the	DT	_	_	_
231	94th	94th	JJ	_	_	_
232	codon	codon	NN	_	_	_
233	-RRB-	-rrb-	-RRB-	_	_	_
234	of	of	IN	_	_	_
235	fabI	fabi	NN	GEN	_	_
236	with	with	IN	_	_	_
237	Val	val	NN	_	_	_
238	,	,	,	_	_	_
239	NTG	NTG	NNP	_	_	_
240	treatment	treatment	NN	_	_	_
241	to	to	TO	_	_	_
242	be	be	VB	_	_	_
243	high	high	JJ	_	_	_
244	resistance	resistance	NN	_	_	_
245	to	to	TO	_	_	_
246	triclosan	triclosan	NN	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	imp	imp	NN	_	_	_
249	mutation	mutation	NN	_	_	_
250	:	:	:	_	_	_
251	contains	contain	VBZ	_	_	_
252	a	a	DT	_	_	_
253	23	23	CD	_	_	_
254	codon	codon	NN	_	_	_
255	detion	detion	NN	_	_	_
256	allele	allele	NN	_	_	_
257	in	in	IN	_	_	_
258	imp	imp	NN	_	_	_
259	-LRB-	-lrb-	-LRB-	_	_	_
260	increased	increase	VBN	_	_	_
261	membrane	membrane	NN	_	_	_
262	permeability	permeability	NN	_	_	_
263	-RRB-	-rrb-	-RRB-	_	_	_
264	,	,	,	_	_	_
265	substitution	substitution	NN	_	_	_
266	of	of	IN	_	_	_
267	the	the	DT	_	_	_
268	93th	93th	JJ	_	_	_
269	codon	codon	NN	_	_	_
270	of	of	IN	_	_	_
271	fabI	fabi	NN	GEN	_	_
272	;	;	:	_	_	_
273	fabI	fabi	NN	GEN	_	_
274	-LRB-	-lrb-	-LRB-	_	_	_
275	G93V	g93v	NN	_	_	_
276	-RRB-	-rrb-	-RRB-	_	_	_
277	,	,	,	_	_	_
278	substitution	substitution	NN	_	_	_
279	of	of	IN	_	_	_
280	Gly	gly	NN	_	_	_
281	-LRB-	-lrb-	-LRB-	_	_	_
282	the	the	DT	_	_	_
283	93th	93th	JJ	_	_	_
284	codon	codon	NN	_	_	_
285	-RRB-	-rrb-	-RRB-	_	_	_
286	of	of	IN	_	_	_
287	fabI	fabi	NN	GEN	_	_
288	with	with	IN	_	_	_
289	Val	val	NN	_	_	_
290	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
291	imp	imp	NN	_	_	_
292	mutation	mutation	NN	_	_	_
293	:	:	:	_	_	_
294	contains	contain	VBZ	_	_	_
295	a	a	DT	_	_	_
296	23	23	CD	_	_	_
297	codon	codon	NN	_	_	_
298	detion	detion	NN	_	_	_
299	allele	allele	NN	_	_	_
300	in	in	IN	_	_	_
301	imp	imp	NN	_	_	_
302	-LRB-	-lrb-	-LRB-	_	_	_
303	increased	increase	VBN	_	_	_
304	membrane	membrane	NN	_	_	_
305	permeability	permeability	NN	_	_	_
306	-RRB-	-rrb-	-RRB-	_	_	_
307	,	,	,	_	_	_
308	substitution	substitution	NN	_	_	_
309	of	of	IN	_	_	_
310	the	the	DT	_	_	_
311	94th	94th	JJ	_	_	_
312	codon	codon	NN	_	_	_
313	of	of	IN	_	_	_
314	fabI	fabi	NN	GEN	_	_
315	;	;	:	_	_	_
316	fabI	fabi	NN	GEN	_	_
317	-LRB-	-lrb-	-LRB-	_	_	_
318	G93V	g93v	NN	_	_	_
319	-RRB-	-rrb-	-RRB-	_	_	_
320	,	,	,	_	_	_
321	substitution	substitution	NN	_	_	_
322	of	of	IN	_	_	_
323	Gly	gly	NN	_	_	_
324	-LRB-	-lrb-	-LRB-	_	_	_
325	the	the	DT	_	_	_
326	94th	94th	JJ	_	_	_
327	codon	codon	NN	_	_	_
328	-RRB-	-rrb-	-RRB-	_	_	_
329	of	of	IN	_	_	_
330	fabI	fabi	NN	GEN	_	_
331	with	with	IN	_	_	_
332	Val	val	NN	_	_	_
333	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
334	LOWESS	lowess	NN	_	_	_
335	normalized	normalize	VBD	_	_	_
336	,	,	,	_	_	_
337	background	background	NN	_	_	_
338	subtracted	subtract	VBD	_	_	_
339	data	datum	NNS	_	_	_
340	obtained	obtain	VBN	_	_	_
341	from	from	IN	_	_	_
342	log2	log2	NN	_	_	_
343	of	of	IN	_	_	_
344	processed	process	VBN	_	_	_
345	Red	red	JJ	_	_	_
346	signal	signal	NN	_	_	_
347	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
348	No	no	DT	_	_	_
349	triclosan	triclosan	NN	_	_	_
350	treatment	treatment	NN	_	_	_
351	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
352	NTG-treated	ntg-treated	JJ	_	_	_
353	E.	e.	FW	_	_	_
354	coli	coli	FW	_	_	_
355	imp	imp	FW	_	_	_
356	fabI	fabi	NN	GEN	_	_
357	-LRB-	-lrb-	-LRB-	_	_	_
358	G93V	g93v	NN	_	_	_
359	-RRB-	-rrb-	-RRB-	_	_	_
360	-LSB-	-lsb-	-LRB-	_	_	_
361	E.	e.	FW	_	_	_
362	coli	coli	FW	_	_	_
363	IFN4	ifn4	NN	_	_	_
364	-RSB-	-rsb-	-RRB-	_	_	_
365	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
366	NTG-treated	ntg-treated	JJ	_	_	_
367	E.	e.	FW	_	_	_
368	coli	coli	FW	_	_	_
369	imp	imp	FW	_	_	_
370	fabI	fabi	NN	GEN	_	_
371	-LRB-	-lrb-	-LRB-	_	_	_
372	G93V	g93v	NN	_	_	_
373	-RRB-	-rrb-	-RRB-	_	_	_
374	-LSB-	-lsb-	-LRB-	_	_	_
375	E.	e.	FW	_	_	_
376	coli	coli	FW	_	_	_
377	IFN5	ifn5	NN	_	_	_
378	-RSB-	-rsb-	-RRB-	_	_	_
379	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
380	ntg	ntg	NN	_	_	_
381	treatment	treatment	NN	_	_	_
382	:	:	:	_	_	_
383	yes	yes	UH	_	_	_
384	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
385	passage	passage	NN	_	_	_
386	:	:	:	_	_	_
387	4	4	CD	_	_	_
388	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
389	strain	strain	NN	_	_	_
390	:	:	:	_	_	_
391	E.	e.	FW	_	_	_
392	coli	coli	FW	_	_	_
393	imp	imp	FW	_	_	_
394	4231	4231	CD	_	_	_
395	-LRB-	-lrb-	-LRB-	_	_	_
396	G93V	g93v	NN	_	_	_
397	-RRB-	-rrb-	-RRB-	_	_	_
398	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
399	strain	strain	NN	_	_	_
400	:	:	:	_	_	_
401	E.	e.	FW	_	_	_
402	coli	coli	FW	_	_	_
403	imp	imp	FW	_	_	_
404	4231	4231	CD	_	_	_
405	-LRB-	-lrb-	-LRB-	_	_	_
406	G93V	g93v	NN	_	_	_
407	-RRB-	-rrb-	-RRB-	_	_	_
408	,	,	,	_	_	_
409	substitution	substitution	NN	_	_	_
410	of	of	IN	_	_	_
411	the	the	DT	_	_	_
412	93th	93th	JJ	_	_	_
413	codon	codon	NN	_	_	_
414	of	of	IN	_	_	_
415	fabI	fabI	NNP	GEN	_	_
416	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
417	strain	strain	NN	_	_	_
418	:	:	:	_	_	_
419	E.	e.	FW	_	_	_
420	coli	coli	FW	_	_	_
421	imp	imp	FW	_	_	_
422	4231	4231	CD	_	_	_
423	-LRB-	-lrb-	-LRB-	_	_	_
424	G93V	g93v	NN	_	_	_
425	-RRB-	-rrb-	-RRB-	_	_	_
426	,	,	,	_	_	_
427	substitution	substitution	NN	_	_	_
428	of	of	IN	_	_	_
429	the	the	DT	_	_	_
430	94th	94th	JJ	_	_	_
431	codon	codon	NN	_	_	_
432	of	of	IN	_	_	_
433	fabI	fabi	NN	GEN	_	_
434	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
435	The	the	DT	_	_	_
436	cells	cell	NNS	_	_	_
437	were	be	VBD	_	_	_
438	cultivated	cultivate	VBN	_	_	_
439	in	in	IN	_	_	_
440	100	100	CD	_	_	_
441	ml	ml	NN	_	_	_
442	LB	lb	NN	MED	_	_
443	broth	broth	NN	MED	_	_
444	containing	contain	VBG	_	_	_
445	2	2	CD	_	_	_
446	mg	mg	NN	_	_	_
447	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
448	Total	total	JJ	_	_	_
449	RNA	rna	NN	_	_	_
450	extracted	extract	VBN	_	_	_
451	using	use	VBG	_	_	_
452	RNAprotect	rnaprotect	NN	_	_	_
453	Bacterial	bacterial	JJ	_	_	_
454	Reagent	reagent	NN	_	_	_
455	-LRB-	-lrb-	-LRB-	_	_	_
456	Qiagen	qiagen	NN	_	_	_
457	-RRB-	-rrb-	-RRB-	_	_	_
458	and	and	CC	_	_	_
459	an	a	DT	_	_	_
460	RNeasy	RNeasy	NNP	_	_	_
461	Mini	Mini	NNP	_	_	_
462	kit	kit	NN	_	_	_
463	-LRB-	-lrb-	-LRB-	_	_	_
464	Qiagen	qiagen	NN	_	_	_
465	-RRB-	-rrb-	-RRB-	_	_	_
466	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Transcription	transcription	NN	_	_	_
3	profiles	profile	NNS	_	_	_
4	of	of	IN	_	_	_
5	NTG-treated	ntg-treated	JJ	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	imp	imp	FW	_	_	_
9	fabI	fabi	NN	GEN	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	G93V	g93v	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	its	its	PRP$	_	_	_
15	control	control	NN	_	_	_
16	strain	strain	NN	_	_	_
17	in	in	IN	_	_	_
18	the	the	DT	_	_	_
19	absence	absence	NN	_	_	_
20	of	of	IN	_	_	_
21	triclosan	triclosan	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Transcription	transcription	NN	_	_	_
24	profiles	profile	NNS	_	_	_
25	of	of	IN	_	_	_
26	NTG-treated	ntg-treated	JJ	_	_	_
27	E.	e.	FW	_	_	_
28	coli	coli	FW	_	_	_
29	imp	imp	FW	_	_	_
30	fabI	fabi	NN	GEN	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	G93V	g93v	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	and	and	CC	_	_	_
35	its	its	PRP$	_	_	_
36	control	control	NN	_	_	_
37	strain	strain	NN	_	_	_
38	in	in	IN	_	_	_
39	the	the	DT	_	_	_
40	presence	presence	NN	_	_	_
41	of	of	IN	_	_	_
42	triclosan	triclosan	NN	_	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	Treatment	treatment	NN	_	_	_
45	of	of	IN	_	_	_
46	sub-lethal	sub-lethal	JJ	_	_	_
47	triclosan	triclosan	NN	_	_	_
48	;	;	:	_	_	_
49	50	50	CD	_	_	_
50	mg	mg	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	5mL	5ml	NN	_	_	_
53	of	of	IN	_	_	_
54	culture	culture	NN	_	_	_
55	was	be	VBD	_	_	_
56	mixed	mix	VBN	_	_	_
57	with	with	IN	_	_	_
58	5mL	5ml	NN	_	_	_
59	of	of	IN	_	_	_
60	hot	hot	JJ	_	_	_
61	acid	acid	NN	_	_	_
62	phenol	phenol	NN	_	_	_
63	:	:	:	_	_	_
64	chloroform	chloroform	NN	_	_	_
65	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	held	hold	VBN	_	_	_
4	at	at	IN	_	_	_
5	65ºC	65ºc	NN	_	_	_
6	with	with	IN	_	_	_
7	periodic	periodic	JJ	_	_	_
8	shaking	shake	VBG	_	_	_
9	for	for	IN	_	_	_
10	at	at	IN	_	_	_
11	least	least	JJS	_	_	_
12	10	10	CD	_	_	_
13	minutes	minute	NNS	_	_	_
14	before	before	IN	_	_	_
15	centrifuging	centrifuge	VBG	_	_	_
16	at	at	IN	_	_	_
17	4000	4000	CD	_	_	_
18	rpm	rpm	NN	_	_	_
19	for	for	IN	_	_	_
20	20	20	CD	_	_	_
21	min	min	NN	_	_	_
22	.	.	.	_	_	_

1	Supernatant	supernatant	NN	_	_	_
2	was	be	VBD	_	_	_
3	extracted	extract	VBN	_	_	_
4	again	again	RB	_	_	_
5	with	with	IN	_	_	_
6	acid-phenol	acid-phenol	NN	_	_	_
7	:	:	:	_	_	_
8	chloroform	chloroform	NN	_	_	_
9	and	and	CC	_	_	_
10	then	then	RB	_	_	_
11	with	with	IN	_	_	_
12	chloroform	chloroform	NN	_	_	_
13	:	:	:	_	_	_
14	isoamyl	isoamyl	NN	_	_	_
15	alcohol	alcohol	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	24.1	24.1	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	precipitated	precipitated	JJ	_	_	_
4	overnight	overnight	JJ	_	_	_
5	at	at	IN	_	_	_
6	--	--	:	_	_	_
7	80ºC	80ºc	NN	_	_	_
8	in	in	IN	_	_	_
9	2.5	2.5	CD	_	_	_
10	V	v	NN	_	_	_
11	100	100	CD	_	_	_
12	%	%	NN	_	_	_
13	ethanol	ethanol	NN	_	_	_
14	and	and	CC	_	_	_
15	1	1	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	EcJR-8	ecjr-8	NN	_	_	_
18	grown	grow	VBN	_	_	_
19	to	to	TO	_	_	_
20	OD600	od600	NN	_	_	_
21	=	=	JJ	_	_	_
22	0.5	0.5	CD	_	_	_
23	in	in	IN	_	_	_
24	DMEM-MOPS	dmem-mops	NN	_	_	_
25	0.4	0.4	CD	_	_	_
26	%	%	NN	_	_	_
27	glucose	glucose	NN	SUPP	_	_
28	at	at	IN	_	_	_
29	a	a	DT	_	_	_
30	10:1	10:1	CD	_	_	_
31	flask-to-media	flask-to-media	NN	_	_	_
32	volume	volume	NN	_	_	_
33	in	in	IN	_	_	_
34	a	a	DT	_	_	_
35	rotary	rotary	JJ	_	_	_
36	shaker	shaker	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	180	180	CD	_	_	_
39	RPM	rpm	NN	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	EcJR-8	ecjr-8	NN	_	_	_
3	grown	grow	VBN	_	_	_
4	to	to	TO	_	_	_
5	OD600	od600	NN	_	_	_
6	=	=	JJ	_	_	_
7	1.8	1.8	CD	_	_	_
8	in	in	IN	_	_	_
9	DMEM-MOPS	dmem-mops	NN	_	_	_
10	0.4	0.4	CD	_	_	_
11	%	%	NN	_	_	_
12	glucose	glucose	NN	SUPP	_	_
13	at	at	IN	_	_	_
14	a	a	DT	_	_	_
15	10:1	10:1	CD	_	_	_
16	flask-to-media	flask-to-media	NN	_	_	_
17	volume	volume	NN	_	_	_
18	in	in	IN	_	_	_
19	a	a	DT	_	_	_
20	rotary	rotary	JJ	_	_	_
21	shaker	shaker	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	180	180	CD	_	_	_
24	RPM	rpm	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	O157	o157	NN	_	_	_
5	:	:	:	_	_	_
6	H7	h7	NN	_	_	_
7	str	str	NN	_	_	_
8	.	.	.	_	_	_

1	Sakai	Sakai	NNP	_	_	_
2	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3	genotype	genotype	NN	_	_	_
4	:	:	:	_	_	_
5	rpoN	rpon	NN	GEN	_	_
6	mutant	mutant	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	EcJR-8	ecjr-8	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	genotype	genotype	NN	_	_	_
12	:	:	:	_	_	_
13	wild	wild	JJ	_	_	_
14	type	type	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	growth	growth	NN	_	_	_
17	protocol	protocol	NN	_	_	_
18	:	:	:	_	_	_
19	logarithmic	logarithmic	JJ	_	_	_
20	phase	phase	NN	_	_	_
21	in	in	IN	_	_	_
22	DMEM-MOPS	dmem-mops	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	growth	growth	NN	_	_	_
25	protocol	protocol	NN	_	_	_
26	:	:	:	_	_	_
27	transition	transition	NN	_	_	_
28	phase	phase	NN	_	_	_
29	in	in	IN	_	_	_
30	DMEM-MOPS	dmem-mops	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Logarithmic	logarithmic	JJ	_	_	_
33	phase	phase	NN	_	_	_
34	sample	sample	NN	_	_	_
35	1	1	CD	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Logarithmic	logarithmic	JJ	_	_	_
38	phase	phase	NN	_	_	_
39	sample	sample	NN	_	_	_
40	2	2	CD	_	_	_
41	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
42	Logarithmic	logarithmic	JJ	_	_	_
43	phase	phase	NN	_	_	_
44	sample	sample	NN	_	_	_
45	3	3	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	Logarithmic	logarithmic	JJ	_	_	_
48	phase	phase	NN	_	_	_
49	sample	sample	NN	_	_	_
50	4	4	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	rpoN	rpon	NN	GEN	_	_
53	mutant	mutant	JJ	_	_	_
54	grown	grow	VBN	_	_	_
55	to	to	TO	_	_	_
56	logarithmic	logarithmic	JJ	_	_	_
57	phase	phase	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	rpoN	rpon	NN	GEN	_	_
60	mutant	mutant	JJ	_	_	_
61	grown	grow	VBN	_	_	_
62	to	to	TO	_	_	_
63	transition	transition	NN	_	_	_
64	phase	phase	NN	_	_	_
65	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
66	Sakai	Sakai	NNP	_	_	_
67	grown	grow	VBN	_	_	_
68	to	to	TO	_	_	_
69	OD600	od600	NN	_	_	_
70	=	=	JJ	_	_	_
71	1.8	1.8	CD	_	_	_
72	in	in	IN	_	_	_
73	DMEM-MOPS	dmem-mops	NN	_	_	_
74	0.4	0.4	CD	_	_	_
75	%	%	NN	_	_	_
76	glucose	glucose	NN	SUPP	_	_
77	at	at	IN	_	_	_
78	a	a	DT	_	_	_
79	10:1	10:1	CD	_	_	_
80	flask-to-media	flask-to-media	NN	_	_	_
81	volume	volume	NN	_	_	_
82	in	in	IN	_	_	_
83	a	a	DT	_	_	_
84	rotary	rotary	JJ	_	_	_
85	shaker	shaker	NN	_	_	_
86	-LRB-	-lrb-	-LRB-	_	_	_
87	180	180	CD	_	_	_
88	RPM	rpm	NN	_	_	_
89	-RRB-	-rrb-	-RRB-	_	_	_
90	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	microarray	microarray	NN	_	_	_
4	data	datum	NNS	_	_	_
5	were	be	VBD	_	_	_
6	analyzed	analyze	VBN	_	_	_
7	using	use	VBG	_	_	_
8	R	r	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	v.	v.	CC	_	_	_
11	2.2.1	2.2.1	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	the	the	DT	_	_	_
15	MAANOVA	MAANOVA	NNP	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	v.	v.	CC	_	_	_
18	0.98.8	0.98.8	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	package	package	NN	_	_	_
21	.	.	.	_	_	_

1	Raw	raw	NN	_	_	_
2	intensity	intensity	NN	_	_	_
3	values	value	NNS	_	_	_
4	from	from	IN	_	_	_
5	replicate	replicate	VBP	_	_	_
6	probes	probe	NNS	_	_	_
7	were	be	VBD	_	_	_
8	averaged	average	VBN	_	_	_
9	and	and	CC	_	_	_
10	log2	log2	NN	_	_	_
11	transformed	transform	VBN	_	_	_
12	after	after	IN	_	_	_
13	normalization	normalization	NN	_	_	_
14	with	with	IN	_	_	_
15	the	the	DT	_	_	_
16	pin-tip	pin-tip	JJ	_	_	_
17	LOWESS	lowess	NN	_	_	_
18	method	method	NN	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	normalized	normalize	VBN	_	_	_
3	intensity	intensity	NN	_	_	_
4	values	value	NNS	_	_	_
5	were	be	VBD	_	_	_
6	fitted	fit	VBN	_	_	_
7	to	to	TO	_	_	_
8	a	a	DT	_	_	_
9	mixed	mixed	JJ	_	_	_
10	model	model	NN	_	_	_
11	ANOVA	ANOVA	NNP	_	_	_
12	considering	consider	VBG	_	_	_
13	array	array	NN	_	_	_
14	and	and	CC	_	_	_
15	biological	biological	JJ	_	_	_
16	replicates	replicate	VBZ	_	_	_
17	as	as	IN	_	_	_
18	random	random	JJ	_	_	_
19	factors	factor	NNS	_	_	_
20	and	and	CC	_	_	_
21	dye	dye	VB	_	_	_
22	,	,	,	_	_	_
23	strain	strain	NN	_	_	_
24	and	and	CC	_	_	_
25	growth	growth	NN	_	_	_
26	phase	phase	NN	_	_	_
27	as	as	IN	_	_	_
28	fixed	fixed	JJ	_	_	_
29	factors	factor	NNS	_	_	_
30	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	linear	linear	JJ	_	_	_
3	model	model	NN	_	_	_
4	tested	test	VBN	_	_	_
5	was	be	VBD	_	_	_
6	Y	y	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	intensity	intensity	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	=	=	JJ	_	_	_
11	array	array	NN	_	_	_
12	+	+	CC	_	_	_
13	dye	dye	VB	_	_	_
14	+	+	CC	_	_	_
15	strain	strain	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	wild	wild	JJ	_	_	_
18	type	type	NN	_	_	_
19	or	or	CC	_	_	_
20	mutant	mutant	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	+	+	CC	_	_	_
23	growth	growth	NN	_	_	_
24	phase	phase	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	exponential	exponential	JJ	_	_	_
27	or	or	CC	_	_	_
28	stationary	stationary	JJ	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	+	+	CC	_	_	_
31	strain	strain	NN	_	_	_
32	*	*	SYM	_	_	_
33	growth	growth	NN	_	_	_
34	phase	phase	NN	_	_	_
35	+	+	CC	_	_	_
36	sample	sample	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	biological	biological	JJ	_	_	_
39	replicate	replicate	VBP	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	+	+	CC	_	_	_
42	error	error	NN	_	_	_
43	.	.	.	_	_	_

1	Significant	significant	JJ	_	_	_
2	differences	difference	NNS	_	_	_
3	in	in	IN	_	_	_
4	expression	expression	NN	_	_	_
5	due	due	JJ	_	_	_
6	to	to	TO	_	_	_
7	strain	strain	NN	_	_	_
8	,	,	,	_	_	_
9	growth	growth	NN	_	_	_
10	phase	phase	NN	_	_	_
11	and	and	CC	_	_	_
12	strain	strain	NN	_	_	_
13	*	*	SYM	_	_	_
14	growth	growth	NN	_	_	_
15	phase	phase	NN	_	_	_
16	were	be	VBD	_	_	_
17	determined	determine	VBN	_	_	_
18	using	use	VBG	_	_	_
19	the	the	DT	_	_	_
20	Fs	f	NNS	_	_	_
21	test	test	NN	_	_	_
22	in	in	IN	_	_	_
23	MAANOVA	MAANOVA	NNP	_	_	_
24	which	which	WDT	_	_	_
25	uses	use	VBZ	_	_	_
26	a	a	DT	_	_	_
27	shrinkage	shrinkage	NN	_	_	_
28	estimator	estimator	NN	_	_	_
29	for	for	IN	_	_	_
30	gene-specific	gene-specific	JJ	_	_	_
31	variance	variance	NN	_	_	_
32	components	component	NNS	_	_	_
33	that	that	WDT	_	_	_
34	makes	make	VBZ	_	_	_
35	no	no	DT	_	_	_
36	assumption	assumption	NN	_	_	_
37	about	about	IN	_	_	_
38	the	the	DT	_	_	_
39	variances	variance	NNS	_	_	_
40	across	across	IN	_	_	_
41	genes	gene	NNS	_	_	_
42	with	with	IN	_	_	_
43	500	500	CD	_	_	_
44	random	random	JJ	_	_	_
45	permutations	permutation	NNS	_	_	_
46	to	to	TO	_	_	_
47	estimate	estimate	VB	_	_	_
48	the	the	DT	_	_	_
49	p-values	p-value	NNS	_	_	_
50	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	q-value	q-value	JJ	_	_	_
3	package	package	NN	_	_	_
4	in	in	IN	_	_	_
5	R	r	NN	_	_	_
6	was	be	VBD	_	_	_
7	used	use	VBN	_	_	_
8	for	for	IN	_	_	_
9	determining	determine	VBG	_	_	_
10	the	the	DT	_	_	_
11	false	false	JJ	_	_	_
12	discovery	discovery	NN	_	_	_
13	rate	rate	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	FDR	FDR	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Transition	transition	NN	_	_	_
3	phase	phase	NN	_	_	_
4	sample	sample	NN	_	_	_
5	1	1	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Transition	transition	NN	_	_	_
8	phase	phase	NN	_	_	_
9	sample	sample	NN	_	_	_
10	2	2	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	Transition	transition	NN	_	_	_
13	phase	phase	NN	_	_	_
14	sample	sample	NN	_	_	_
15	3	3	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Transition	transition	NN	_	_	_
18	phase	phase	NN	_	_	_
19	sample	sample	NN	_	_	_
20	4	4	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
22	wild	wild	JJ	_	_	_
23	type	type	NN	_	_	_
24	grown	grow	VBN	_	_	_
25	to	to	TO	_	_	_
26	logarithmic	logarithmic	JJ	_	_	_
27	phase	phase	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	wild	wild	JJ	_	_	_
30	type	type	NN	_	_	_
31	grown	grow	VBN	_	_	_
32	to	to	TO	_	_	_
33	transition	transition	NN	_	_	_
34	phase	phase	NN	_	_	_
35	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
36	E.	E.	NNP	_	_	_
37	coli	coli	NN	_	_	_
38	,	,	,	_	_	_
39	1-h	1-h	NN	_	_	_
40	,	,	,	_	_	_
41	serine	serine	NN	_	_	_
42	hydroxamate	hydroxamate	NN	_	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	Escherichia	escherichia	FW	Organism	_	_
45	coli	coli	FW	Organism	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	Fifteen	fifteen	CD	_	_	_
48	mL	ml	NN	_	_	_
49	fermentation	fermentation	NN	_	_	_
50	broth	broth	NN	_	_	_
51	was	be	VBD	_	_	_
52	used	use	VBN	_	_	_
53	for	for	IN	_	_	_
54	each	each	DT	_	_	_
55	RNA	rna	NN	_	_	_
56	extraction	extraction	NN	_	_	_
57	.	.	.	_	_	_

1	Harvested	harvest	VBN	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	rapidly	rapidly	RB	_	_	_
5	cooled	cool	VBN	_	_	_
6	in	in	IN	_	_	_
7	a	a	DT	_	_	_
8	-80	-80	CD	_	_	_
9	°C	°c	NN	_	_	_
10	ethanol	ethanol	NN	_	_	_
11	bath	bath	NN	_	_	_
12	,	,	,	_	_	_
13	then	then	RB	_	_	_
14	centrifuged	centrifuge	VBD	_	_	_
15	at	at	IN	_	_	_
16	5000	5000	CD	_	_	_
17	g	g	NN	_	_	_
18	for	for	IN	_	_	_
19	seven	seven	CD	_	_	_
20	minutes	minute	NNS	_	_	_
21	at	at	IN	_	_	_
22	4	4	CD	_	_	_
23	°C	°c	NN	_	_	_
24	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	discarded	discard	VBN	_	_	_
5	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cell	cell	NN	_	_	_
3	pellet	pellet	NN	_	_	_
4	was	be	VBD	_	_	_
5	frozen	freeze	VBN	_	_	_
6	at	at	IN	_	_	_
7	-80	-80	CD	_	_	_
8	°C	°c	NN	_	_	_
9	.	.	.	_	_	_

1	Thawed	thaw	VBN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	on	on	IN	_	_	_
4	ice	ice	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	cell	cell	NN	_	_	_
7	pellets	pellet	NNS	_	_	_
8	were	be	VBD	_	_	_
9	suspended	suspend	VBN	_	_	_
10	in	in	IN	_	_	_
11	150	150	CD	_	_	_
12	mL	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	TE	TE	NNP	_	_	_
15	buffer	buffer	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	10	10	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	Tris-HCl	tris-hcl	NN	_	_	_
20	,	,	,	_	_	_
21	pH	ph	NN	_	_	_
22	7.6	7.6	CD	_	_	_
23	,	,	,	_	_	_
24	0.1	0.1	CD	_	_	_
25	mM	mm	NN	KWSUPP	_	_
26	EDTA	edta	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	containing	contain	VBG	_	_	_
29	0.75	0.75	CD	_	_	_
30	mg	mg	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Microarray	microarray	NN	_	_	_
33	suit	suit	NN	_	_	_
34	5.0	5.0	CD	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	Affymetrix	Affymetrix	NNP	_	_	_
37	Inc.	Inc.	NNP	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	was	be	VBD	_	_	_
40	used	use	VBN	_	_	_
41	to	to	TO	_	_	_
42	average	average	VB	_	_	_
43	the	the	DT	_	_	_
44	scans	scan	NNS	_	_	_
45	and	and	CC	_	_	_
46	process	process	NN	_	_	_
47	the	the	DT	_	_	_
48	data	datum	NNS	_	_	_
49	,	,	,	_	_	_
50	further	further	RB	_	_	_
51	data	data	NN	_	_	_
52	analysis	analysis	NN	_	_	_
53	was	be	VBD	_	_	_
54	conducted	conduct	VBN	_	_	_
55	using	use	VBG	_	_	_
56	Affymetrix	Affymetrix	NNP	_	_	_
57	®	®	NNP	_	_	_
58	Data	Data	NNP	_	_	_
59	Mining	Mining	NNP	_	_	_
60	Tool	Tool	NNP	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	DMT	DMT	NNP	_	_	_
63	3.0	3.0	CD	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	One	one	CD	_	_	_
3	set	set	NN	_	_	_
4	of	of	IN	_	_	_
5	fermentations	fermentation	NNS	_	_	_
6	were	be	VBD	_	_	_
7	exposed	expose	VBN	_	_	_
8	to	to	TO	_	_	_
9	5	5	CD	_	_	_
10	mM	mm	NN	KWSUPP	_	_
11	IPTG	iptg	NN	_	_	_
12	and	and	CC	_	_	_
13	one	one	CD	_	_	_
14	set	set	NN	_	_	_
15	was	be	VBD	_	_	_
16	not	not	RB	_	_	_
17	exposed	expose	VBN	_	_	_
18	to	to	TO	_	_	_
19	IPTG	IPTG	NNP	_	_	_
20	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	taken	take	VBN	_	_	_
4	0	0	CD	_	_	_
5	,	,	,	_	_	_
6	1	1	CD	_	_	_
7	,	,	,	_	_	_
8	and	and	CC	_	_	_
9	4	4	CD	_	_	_
10	hours	hour	NNS	_	_	_
11	post-synchronization	post-synchronization	JJ	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Time	time	NN	_	_	_
14	S0	s0	NN	_	_	_
15	,	,	,	_	_	_
16	S1	s1	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	S4	s4	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	plasmid	plasmid	NN	_	_	_
3	:	:	:	_	_	_
4	pPROEx-CAT	pproex-cat	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
6	Recombinant	recombinant	JJ	_	_	_
7	,	,	,	_	_	_
8	high	high	JJ	_	_	_
9	cell	cell	NN	_	_	_
10	density	density	NN	_	_	_
11	,	,	,	_	_	_
12	Time	Time	NNP	_	_	_
13	0	0	CD	_	_	_
14	,	,	,	_	_	_
15	no	no	DT	_	_	_
16	IPTG	iptg	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Recombinant	recombinant	JJ	_	_	_
19	,	,	,	_	_	_
20	high	high	JJ	_	_	_
21	cell	cell	NN	_	_	_
22	density	density	NN	_	_	_
23	,	,	,	_	_	_
24	Time	Time	NNP	_	_	_
25	1	1	CD	_	_	_
26	h	h	NN	_	_	_
27	,	,	,	_	_	_
28	5	5	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	IPTG	iptg	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Recombinant	recombinant	JJ	_	_	_
33	,	,	,	_	_	_
34	high	high	JJ	_	_	_
35	cell	cell	NN	_	_	_
36	density	density	NN	_	_	_
37	,	,	,	_	_	_
38	Time	Time	NNP	_	_	_
39	1	1	CD	_	_	_
40	h	h	NN	_	_	_
41	,	,	,	_	_	_
42	no	no	DT	_	_	_
43	IPTG	iptg	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	Recombinant	recombinant	JJ	_	_	_
46	,	,	,	_	_	_
47	high	high	JJ	_	_	_
48	cell	cell	NN	_	_	_
49	density	density	NN	_	_	_
50	,	,	,	_	_	_
51	Time	Time	NNP	_	_	_
52	4	4	CD	_	_	_
53	h	h	NN	_	_	_
54	,	,	,	_	_	_
55	no	no	DT	_	_	_
56	IPTG	iptg	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Recombinant	recombinant	JJ	_	_	_
59	,	,	,	_	_	_
60	high	high	JJ	_	_	_
61	cell	cell	NN	_	_	_
62	density	density	NN	_	_	_
63	,	,	,	_	_	_
64	Time	Time	NNP	_	_	_
65	S0	S0	NNP	_	_	_
66	,	,	,	_	_	_
67	no	no	DT	_	_	_
68	IPTG	iptg	NN	_	_	_
69	,	,	,	_	_	_
70	1	1	CD	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	Recombinant	recombinant	JJ	_	_	_
73	,	,	,	_	_	_
74	high	high	JJ	_	_	_
75	cell	cell	NN	_	_	_
76	density	density	NN	_	_	_
77	,	,	,	_	_	_
78	Time	Time	NNP	_	_	_
79	S0	S0	NNP	_	_	_
80	,	,	,	_	_	_
81	no	no	DT	_	_	_
82	IPTG	iptg	NN	_	_	_
83	,	,	,	_	_	_
84	2	2	CD	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
86	Recombinant	recombinant	JJ	_	_	_
87	,	,	,	_	_	_
88	high	high	JJ	_	_	_
89	cell	cell	NN	_	_	_
90	density	density	NN	_	_	_
91	,	,	,	_	_	_
92	Time	Time	NNP	_	_	_
93	S0	S0	NNP	_	_	_
94	,	,	,	_	_	_
95	no	no	DT	_	_	_
96	IPTG	iptg	NN	_	_	_
97	,	,	,	_	_	_
98	3	3	CD	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	Recombinant	recombinant	JJ	_	_	_
101	,	,	,	_	_	_
102	high	high	JJ	_	_	_
103	cell	cell	NN	_	_	_
104	density	density	NN	_	_	_
105	,	,	,	_	_	_
106	Time	Time	NNP	_	_	_
107	S1	s1	NN	_	_	_
108	,	,	,	_	_	_
109	IPTG	iptg	NN	_	_	_
110	,	,	,	_	_	_
111	1	1	CD	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	Recombinant	recombinant	JJ	_	_	_
114	,	,	,	_	_	_
115	high	high	JJ	_	_	_
116	cell	cell	NN	_	_	_
117	density	density	NN	_	_	_
118	,	,	,	_	_	_
119	Time	Time	NNP	_	_	_
120	S1	s1	NN	_	_	_
121	,	,	,	_	_	_
122	IPTG	iptg	NN	_	_	_
123	,	,	,	_	_	_
124	2	2	CD	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
126	Recombinant	recombinant	JJ	_	_	_
127	,	,	,	_	_	_
128	high	high	JJ	_	_	_
129	cell	cell	NN	_	_	_
130	density	density	NN	_	_	_
131	,	,	,	_	_	_
132	Time	Time	NNP	_	_	_
133	S1	s1	NN	_	_	_
134	,	,	,	_	_	_
135	IPTG	iptg	NN	_	_	_
136	,	,	,	_	_	_
137	3	3	CD	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	Recombinant	recombinant	JJ	_	_	_
140	,	,	,	_	_	_
141	high	high	JJ	_	_	_
142	cell	cell	NN	_	_	_
143	density	density	NN	_	_	_
144	,	,	,	_	_	_
145	Time	Time	NNP	_	_	_
146	S1	s1	NN	_	_	_
147	,	,	,	_	_	_
148	no	no	DT	_	_	_
149	IPTG	iptg	NN	_	_	_
150	,	,	,	_	_	_
151	1	1	CD	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	Recombinant	recombinant	JJ	_	_	_
154	,	,	,	_	_	_
155	high	high	JJ	_	_	_
156	cell	cell	NN	_	_	_
157	density	density	NN	_	_	_
158	,	,	,	_	_	_
159	Time	Time	NNP	_	_	_
160	S1	s1	NN	_	_	_
161	,	,	,	_	_	_
162	no	no	DT	_	_	_
163	IPTG	iptg	NN	_	_	_
164	,	,	,	_	_	_
165	2	2	CD	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
167	Recombinant	recombinant	JJ	_	_	_
168	,	,	,	_	_	_
169	high	high	JJ	_	_	_
170	cell	cell	NN	_	_	_
171	density	density	NN	_	_	_
172	,	,	,	_	_	_
173	Time	Time	NNP	_	_	_
174	S1	s1	NN	_	_	_
175	,	,	,	_	_	_
176	no	no	DT	_	_	_
177	IPTG	iptg	NN	_	_	_
178	,	,	,	_	_	_
179	3	3	CD	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	Recombinant	recombinant	JJ	_	_	_
182	,	,	,	_	_	_
183	high	high	JJ	_	_	_
184	cell	cell	NN	_	_	_
185	density	density	NN	_	_	_
186	,	,	,	_	_	_
187	Time	Time	NNP	_	_	_
188	S4	S4	NNP	_	_	_
189	,	,	,	_	_	_
190	no	no	DT	_	_	_
191	IPTG	iptg	NN	_	_	_
192	,	,	,	_	_	_
193	1	1	CD	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	Recombinant	recombinant	JJ	_	_	_
196	,	,	,	_	_	_
197	high	high	JJ	_	_	_
198	cell	cell	NN	_	_	_
199	density	density	NN	_	_	_
200	,	,	,	_	_	_
201	Time	Time	NNP	_	_	_
202	S4	S4	NNP	_	_	_
203	,	,	,	_	_	_
204	no	no	DT	_	_	_
205	IPTG	iptg	NN	_	_	_
206	,	,	,	_	_	_
207	2	2	CD	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
209	Recombinant	recombinant	JJ	_	_	_
210	,	,	,	_	_	_
211	high	high	JJ	_	_	_
212	cell	cell	NN	_	_	_
213	density	density	NN	_	_	_
214	,	,	,	_	_	_
215	Time	Time	NNP	_	_	_
216	S4	S4	NNP	_	_	_
217	,	,	,	_	_	_
218	no	no	DT	_	_	_
219	IPTG	iptg	NN	_	_	_
220	,	,	,	_	_	_
221	3	3	CD	_	_	_
222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
223	Serine	serine	NN	_	_	_
224	Hydroxamate	hydroxamate	NN	_	_	_
225	stressed	stress	VBD	_	_	_
226	,	,	,	_	_	_
227	replicate	replicate	VB	_	_	_
228	#	#	#	_	_	_
229	1	1	CD	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
231	Serine	serine	NN	_	_	_
232	Hydroxamate	hydroxamate	NN	_	_	_
233	stressed	stress	VBD	_	_	_
234	,	,	,	_	_	_
235	replicate	replicate	VB	_	_	_
236	#	#	#	_	_	_
237	2	2	CD	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	Serine	serine	NN	_	_	_
240	Hydroxamate	hydroxamate	NN	_	_	_
241	stressed	stress	VBD	_	_	_
242	,	,	,	_	_	_
243	replicate	replicate	VB	_	_	_
244	#	#	#	_	_	_
245	3	3	CD	_	_	_
246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
247	Serine	serine	NN	_	_	_
248	hydrxamate	hydrxamate	NN	_	_	_
249	-LRB-	-lrb-	-LRB-	_	_	_
250	100	100	CD	_	_	_
251	mg	mg	NN	_	_	_
252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
253	strain	strain	NN	_	_	_
254	:	:	:	_	_	_
255	MG1655	mg1655	NN	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
257	The	the	DT	_	_	_
258	strain	strain	NN	_	_	_
259	Escherichia	escherichia	FW	Organism	_	_
260	coli	coli	FW	Organism	_	_
261	MG1655	mg1655	NN	_	_	_
262	-LSB-	-lsb-	-LRB-	_	_	_
263	pPROEx-CAT	pproex-cat	NN	_	_	_
264	-RSB-	-rsb-	-RRB-	_	_	_
265	was	be	VBD	_	_	_
266	cultured	culture	VBN	_	_	_
267	in	in	IN	_	_	_
268	a	a	DT	_	_	_
269	fed-batch	fed-batch	JJ	_	_	_
270	fermenter	fermenter	NN	_	_	_
271	in	in	IN	_	_	_
272	LB	LB	NNP	MED	_	_
273	media	media	NNS	MED	_	_
274	w	w	NN	_	_	_
275	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
276	The	the	DT	_	_	_
277	strain	strain	NN	_	_	_
278	MG1655	mg1655	NN	_	_	_
279	-LSB-	-lsb-	-LRB-	_	_	_
280	pPROEx-CAT	pproex-cat	NN	_	_	_
281	-RSB-	-rsb-	-RRB-	_	_	_
282	was	be	VBD	_	_	_
283	cultured	culture	VBN	_	_	_
284	in	in	IN	_	_	_
285	a	a	DT	_	_	_
286	fed-batch	fed-batch	JJ	_	_	_
287	fermenter	fermenter	NN	_	_	_
288	in	in	IN	_	_	_
289	LB	LB	NNP	MED	_	_
290	media	media	NNS	MED	_	_
291	w	w	NN	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	1A	1a	NN	_	_	_
294	1y	1y	NN	_	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	1A	1a	NN	_	_	_
297	4y	4y	NN	_	_	_
298	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
299	1A	1a	NN	_	_	_
300	T0	t0	NN	_	_	_
301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
302	2A	2a	NN	_	_	_
303	1y	1y	NN	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	2A	2a	NN	_	_	_
306	4y	4y	NN	_	_	_
307	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
308	3A	3a	NN	_	_	_
309	1m	1m	NN	_	_	_
310	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
311	3A	3a	NN	_	_	_
312	1y	1y	NN	_	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
314	3A	3a	NN	_	_	_
315	4y	4y	NN	_	_	_
316	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
317	4A	4a	NN	_	_	_
318	1m	1m	NN	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
320	4A	4a	NN	_	_	_
321	1y	1y	NN	_	_	_
322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
323	4A	4a	NN	_	_	_
324	4y	4y	NN	_	_	_
325	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
326	5A	5a	NN	_	_	_
327	1m	1m	NN	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	6A	6a	NN	_	_	_
330	1m	1m	NN	_	_	_
331	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
332	9A	9a	NN	_	_	_
333	3y	3y	JJ	_	_	_
334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
335	9A	9a	NN	_	_	_
336	5y	5y	JJ	_	_	_
337	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
338	9A	9a	NN	_	_	_
339	T0	t0	NN	_	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
341	Alert	Alert	NNP	_	_	_
342	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
343	Archaea	Archaea	NNP	_	_	_
344	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
345	Bacteria	bacterium	NNS	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	Bio1	bio1	NN	_	_	_
348	1m	1m	NN	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	Bio1	bio1	NN	_	_	_
351	1y	1y	NN	_	_	_
352	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
353	Bio2	bio2	NN	_	_	_
354	1m	1m	NN	_	_	_
355	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
356	Bio2	bio2	NN	_	_	_
357	1y	1y	NN	_	_	_
358	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
359	Bio3	bio3	NN	_	_	_
360	1m	1m	NN	_	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
362	Bio3	bio3	NN	_	_	_
363	1y	1y	NN	_	_	_
364	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
365	Bio4	bio4	NN	_	_	_
366	1m	1m	NN	_	_	_
367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
368	Bio4	bio4	NN	_	_	_
369	1y	1y	NN	_	_	_
370	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
371	Bio-6	bio-6	NN	_	_	_
372	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
373	Bio	bio	NN	_	_	_
374	Contro	contro	NN	_	_	_
375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
376	bioremediation	bioremediation	NN	_	_	_
377	treatment	treatment	NN	_	_	_
378	:	:	:	_	_	_
379	Alert	Alert	NNP	_	_	_
380	-LRB-	-lrb-	-LRB-	_	_	_
381	ex	ex	FW	_	_	_
382	situ	situ	FW	_	_	_
383	-RRB-	-rrb-	-RRB-	_	_	_
384	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
385	bioremediation	bioremediation	NN	_	_	_
386	treatment	treatment	NN	_	_	_
387	:	:	:	_	_	_
388	Eureka	Eureka	NNP	_	_	_
389	-LRB-	-lrb-	-LRB-	_	_	_
390	in	in	FW	_	_	_
391	situ	situ	FW	_	_	_
392	-RRB-	-rrb-	-RRB-	_	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
394	BZNT	bznt	JJ	_	_	_
395	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
396	CompA	compa	NN	_	_	_
397	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
398	CompB	compb	NN	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	contamination	contamination	NN	_	_	_
401	status	status	NN	_	_	_
402	:	:	:	_	_	_
403	hydrocarbon	hydrocarbon	NN	_	_	_
404	contaminated	contaminate	VBN	_	_	_
405	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
406	Escherichia	escherichia	FW	Organism	_	_
407	coli	coli	FW	Organism	_	_
408	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
409	Eureka	eureka	FW	_	_	_
410	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
411	Lambda	Lambda	NNP	_	_	_
412	phage	phage	NN	_	_	_
413	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
414	NFNT	nfnt	JJ	_	_	_
415	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
416	phage	phage	NN	_	_	_
417	:	:	:	_	_	_
418	Lambda	Lambda	NNP	_	_	_
419	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
420	Poly	Poly	NNP	_	_	_
421	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
422	sample	sample	NN	_	_	_
423	:	:	:	_	_	_
424	1A	1a	NN	_	_	_
425	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
426	sample	sample	NN	_	_	_
427	:	:	:	_	_	_
428	23S	23s	NN	_	_	_
429	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
430	sample	sample	NN	_	_	_
431	:	:	:	_	_	_
432	2A	2a	NN	_	_	_
433	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
434	sample	sample	NN	_	_	_
435	:	:	:	_	_	_
436	32D	32d	NN	_	_	_
437	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
438	sample	sample	NN	_	_	_
439	:	:	:	_	_	_
440	33D	33d	NN	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
442	sample	sample	NN	_	_	_
443	:	:	:	_	_	_
444	35B	35b	NN	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	sample	sample	NN	_	_	_
447	:	:	:	_	_	_
448	3A	3a	NN	_	_	_
449	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
450	sample	sample	NN	_	_	_
451	:	:	:	_	_	_
452	4A	4a	NN	_	_	_
453	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
454	sample	sample	NN	_	_	_
455	:	:	:	_	_	_
456	5A	5a	NN	_	_	_
457	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
458	sample	sample	NN	_	_	_
459	:	:	:	_	_	_
460	#	#	#	_	_	_
461	6	6	CD	_	_	_
462	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
463	sample	sample	NN	_	_	_
464	:	:	:	_	_	_
465	6A	6a	NN	_	_	_
466	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
467	sample	sample	NN	_	_	_
468	:	:	:	_	_	_
469	9A	9a	NN	_	_	_
470	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
471	sample	sample	NN	_	_	_
472	:	:	:	_	_	_
473	Bio-1	bio-1	NN	_	_	_
474	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
475	sample	sample	NN	_	_	_
476	:	:	:	_	_	_
477	Bio-2	bio-2	NN	_	_	_
478	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
479	sample	sample	NN	_	_	_
480	:	:	:	_	_	_
481	Bio-3	bio-3	NN	_	_	_
482	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
483	sample	sample	NN	_	_	_
484	:	:	:	_	_	_
485	Bio-4	bio-4	NN	_	_	_
486	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
487	sample	sample	NN	_	_	_
488	:	:	:	_	_	_
489	Biopile	Biopile	NNP	_	_	_
490	control	control	NN	_	_	_
491	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
492	sample	sample	NN	_	_	_
493	:	:	:	_	_	_
494	BZ-NT	bz-nt	JJ	_	_	_
495	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
496	sample	sample	NN	_	_	_
497	:	:	:	_	_	_
498	Composite	Composite	NNP	_	_	_
499	A	A	NNP	_	_	_
500	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
501	sample	sample	NN	_	_	_
502	:	:	:	_	_	_
503	Composite	Composite	NNP	_	_	_
504	B	B	NNP	_	_	_
505	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
506	sample	sample	NN	_	_	_
507	:	:	:	_	_	_
508	LC-1	lc-1	NN	_	_	_
509	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
510	sample	sample	NN	_	_	_
511	:	:	:	_	_	_
512	NC	nc	NN	_	_	_
513	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
514	sample	sample	NN	_	_	_
515	:	:	:	_	_	_
516	NF-NT	nf-nt	JJ	_	_	_
517	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
518	sample	sample	NN	_	_	_
519	:	:	:	_	_	_
520	Polygons	polygon	NNS	_	_	_
521	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
522	sample	sample	NN	_	_	_
523	:	:	:	_	_	_
524	Vegetated	vegetated	JJ	_	_	_
525	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
526	Soil	soil	NN	_	_	_
527	DNA	dna	NN	_	_	_
528	was	be	VBD	_	_	_
529	extracted	extract	VBN	_	_	_
530	from	from	IN	_	_	_
531	a	a	DT	_	_	_
532	0.5	0.5	CD	_	_	_
533	g	g	NN	_	_	_
534	soil	soil	NN	_	_	_
535	sub-sample	sub-sample	NN	_	_	_
536	using	use	VBG	_	_	_
537	the	the	DT	_	_	_
538	MoBio	mobio	NN	_	_	_
539	DNA	dna	NN	_	_	_
540	Power	power	NN	_	_	_
541	Soil	soil	NN	_	_	_
542	kit	kit	NN	_	_	_
543	-LRB-	-lrb-	-LRB-	_	_	_
544	MoBio	mobio	NN	_	_	_
545	Laboratories	Laboratories	NNPS	_	_	_
546	,	,	,	_	_	_
547	Carlsbad	Carlsbad	NNP	_	_	_
548	,	,	,	_	_	_
549	CA	CA	NNP	_	_	_
550	-RRB-	-rrb-	-RRB-	_	_	_
551	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	intensity	intensity	NN	_	_	_
4	of	of	IN	_	_	_
5	each	each	DT	_	_	_
6	spot	spot	NN	_	_	_
7	was	be	VBD	_	_	_
8	measured	measure	VBN	_	_	_
9	with	with	IN	_	_	_
10	ScanArray	ScanArray	NNP	_	_	_
11	Express	Express	NNP	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	histogram	histogram	NN	_	_	_
15	quantitation	quantitation	NN	_	_	_
16	method	method	NN	_	_	_
17	;	;	:	_	_	_
18	the	the	DT	_	_	_
19	percentile	percentile	NN	_	_	_
20	ranges	range	VBZ	_	_	_
21	for	for	IN	_	_	_
22	histograms	histogram	NNS	_	_	_
23	were	be	VBD	_	_	_
24	80	80	CD	_	_	_
25	%	%	NN	_	_	_
26	for	for	IN	_	_	_
27	low	low	JJ	_	_	_
28	signal	signal	NN	_	_	_
29	range	range	NN	_	_	_
30	,	,	,	_	_	_
31	95	95	CD	_	_	_
32	%	%	NN	_	_	_
33	for	for	IN	_	_	_
34	high	high	JJ	_	_	_
35	signal	signal	NN	_	_	_
36	range	range	NN	_	_	_
37	,	,	,	_	_	_
38	5	5	CD	_	_	_
39	%	%	NN	_	_	_
40	for	for	IN	_	_	_
41	low	low	JJ	_	_	_
42	background	background	NN	_	_	_
43	range	range	NN	_	_	_
44	and	and	CC	_	_	_
45	20	20	CD	_	_	_
46	%	%	NN	_	_	_
47	for	for	IN	_	_	_
48	high	high	JJ	_	_	_
49	background	background	NN	_	_	_
50	range	range	NN	_	_	_
51	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	median	median	JJ	_	_	_
3	intensity	intensity	NN	_	_	_
4	minus	minus	CC	_	_	_
5	the	the	DT	_	_	_
6	median	median	JJ	_	_	_
7	background	background	NN	_	_	_
8	intensity	intensity	NN	_	_	_
9	was	be	VBD	_	_	_
10	used	use	VBN	_	_	_
11	for	for	IN	_	_	_
12	further	further	JJ	_	_	_
13	calculations	calculation	NNS	_	_	_
14	performed	perform	VBN	_	_	_
15	in	in	IN	_	_	_
16	Microsoft	Microsoft	NNP	_	_	_
17	Excel	Excel	NNP	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	background	background	NN	_	_	_
3	measurement	measurement	NN	_	_	_
4	refers	refer	VBZ	_	_	_
5	to	to	TO	_	_	_
6	the	the	DT	_	_	_
7	local	local	JJ	_	_	_
8	spot	spot	NN	_	_	_
9	background	background	NN	_	_	_
10	intensity	intensity	NN	_	_	_
11	.	.	.	_	_	_

1	Prior	prior	RB	_	_	_
2	to	to	TO	_	_	_
3	normalization	normalization	NN	_	_	_
4	,	,	,	_	_	_
5	all	all	DT	_	_	_
6	spots	spot	NNS	_	_	_
7	with	with	IN	_	_	_
8	a	a	DT	_	_	_
9	Signal-to-Noise	Signal-to-Noise	NNP	_	_	_
10	ratio	ratio	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	SNR	snr	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	lower	lower	JJR	_	_	_
15	than	than	IN	_	_	_
16	3	3	CD	_	_	_
17	were	be	VBD	_	_	_
18	removed	remove	VBN	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	SNR	snr	NN	_	_	_
3	was	be	VBD	_	_	_
4	calculated	calculate	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	following	follow	VBG	_	_	_
8	formula	formula	NN	_	_	_
9	:	:	:	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Median	median	JJ	_	_	_
12	Signal	signal	NN	_	_	_
13	--	--	:	_	_	_
14	Median	median	JJ	_	_	_
15	Background	background	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	year	year	NN	_	_	_
19	:	:	:	_	_	_
20	2000	2000	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	year	year	NN	_	_	_
23	:	:	:	_	_	_
24	2001	2001	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	year	year	NN	_	_	_
27	:	:	:	_	_	_
28	2003	2003	CD	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	year	year	NN	_	_	_
31	:	:	:	_	_	_
32	2004	2004	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	year	year	NN	_	_	_
35	:	:	:	_	_	_
36	2005	2005	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	year	year	NN	_	_	_
39	:	:	:	_	_	_
40	2006	2006	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	year	year	NN	_	_	_
43	:	:	:	_	_	_
44	2007	2007	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	year	year	NN	_	_	_
47	:	:	:	_	_	_
48	2008	2008	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	0.5	0.5	CD	_	_	_
51	%	%	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	w	w	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	0	0	CD	_	_	_
56	%	%	NN	_	_	_
57	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
58	_	_	NN	_	_	_
59	0	0	CD	_	_	_
60	min	min	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	0	0	CD	_	_	_
63	%	%	NN	_	_	_
64	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
65	_	_	CD	_	_	_
66	15	15	CD	_	_	_
67	min	min	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	0	0	CD	_	_	_
70	%	%	NN	_	_	_
71	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
72	_	_	CD	_	_	_
73	30	30	CD	_	_	_
74	min	min	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	0	0	CD	_	_	_
77	%	%	NN	_	_	_
78	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
79	_	_	CD	_	_	_
80	5	5	CD	_	_	_
81	min	min	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	0	0	CD	_	_	_
84	%	%	NN	_	_	_
85	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
86	_	_	CD	_	_	_
87	60	60	CD	_	_	_
88	min	min	NN	_	_	_
89	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
90	Affymetrix	Affymetrix	NNP	_	_	_
91	Microarray	Microarray	NNP	_	_	_
92	Suite	Suite	NNP	_	_	_
93	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
94	Cells	cell	NNS	_	_	_
95	were	be	VBD	_	_	_
96	incubated	incubate	VBN	_	_	_
97	at	at	IN	_	_	_
98	37C	37c	NN	_	_	_
99	prior	prior	RB	_	_	_
100	to	to	TO	_	_	_
101	extraction	extraction	NN	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	E.coliO157	e.colio157	NN	_	_	_
104	_	_	CD	_	_	_
105	0.5	0.5	CD	_	_	_
106	%	%	NN	_	_	_
107	-LRB-	-lrb-	-LRB-	_	_	_
108	w	w	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	E.coliO157	e.colio157	NN	_	_	_
111	_	_	CD	_	_	_
112	0	0	CD	_	_	_
113	%	%	NN	_	_	_
114	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
115	_	_	NN	_	_	_
116	0	0	CD	_	_	_
117	min	min	NN	_	_	_
118	_	_	CD	_	_	_
119	rep1	rep1	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	E.coliO157	e.colio157	NN	_	_	_
122	_	_	CD	_	_	_
123	0	0	CD	_	_	_
124	%	%	NN	_	_	_
125	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
126	_	_	NN	_	_	_
127	0	0	CD	_	_	_
128	min	min	NN	_	_	_
129	_	_	CD	_	_	_
130	rep2	rep2	NN	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	E.coliO157	e.colio157	NN	_	_	_
133	_	_	CD	_	_	_
134	0	0	CD	_	_	_
135	%	%	NN	_	_	_
136	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
137	_	_	CD	_	_	_
138	15	15	CD	_	_	_
139	min	min	NN	_	_	_
140	_	_	CD	_	_	_
141	rep1	rep1	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	E.coliO157	e.colio157	NN	_	_	_
144	_	_	CD	_	_	_
145	0	0	CD	_	_	_
146	%	%	NN	_	_	_
147	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
148	_	_	CD	_	_	_
149	15	15	CD	_	_	_
150	min	min	NN	_	_	_
151	_	_	CD	_	_	_
152	rep2	rep2	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	E.coliO157	e.colio157	NN	_	_	_
155	_	_	CD	_	_	_
156	0	0	CD	_	_	_
157	%	%	NN	_	_	_
158	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
159	_	_	CD	_	_	_
160	30	30	CD	_	_	_
161	min	min	NN	_	_	_
162	_	_	CD	_	_	_
163	rep1	rep1	NN	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	E.coliO157	e.colio157	NN	_	_	_
166	_	_	CD	_	_	_
167	0	0	CD	_	_	_
168	%	%	NN	_	_	_
169	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
170	_	_	CD	_	_	_
171	30	30	CD	_	_	_
172	min	min	NN	_	_	_
173	_	_	CD	_	_	_
174	rep2	rep2	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	E.coliO157	e.colio157	NN	_	_	_
177	_	_	CD	_	_	_
178	0	0	CD	_	_	_
179	%	%	NN	_	_	_
180	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
181	_	_	CD	_	_	_
182	5	5	CD	_	_	_
183	min	min	NN	_	_	_
184	_	_	CD	_	_	_
185	rep1	rep1	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	E.coliO157	e.colio157	NN	_	_	_
188	_	_	CD	_	_	_
189	0	0	CD	_	_	_
190	%	%	NN	_	_	_
191	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
192	_	_	CD	_	_	_
193	5	5	CD	_	_	_
194	min	min	NN	_	_	_
195	_	_	CD	_	_	_
196	rep2	rep2	NN	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	E.coliO157	e.colio157	NN	_	_	_
199	_	_	CD	_	_	_
200	0	0	CD	_	_	_
201	%	%	NN	_	_	_
202	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
203	_	_	CD	_	_	_
204	60	60	CD	_	_	_
205	min	min	NN	_	_	_
206	_	_	CD	_	_	_
207	rep1	rep1	NN	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	E.coliO157	e.colio157	NN	_	_	_
210	_	_	CD	_	_	_
211	0	0	CD	_	_	_
212	%	%	NN	_	_	_
213	sodiumbenzoate	sodiumbenzoate	NN	_	_	_
214	_	_	CD	_	_	_
215	60	60	CD	_	_	_
216	min	min	NN	_	_	_
217	_	_	CD	_	_	_
218	rep2	rep2	NN	_	_	_
219	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
220	Escherichia	escherichia	FW	Organism	_	_
221	coli	coli	FW	Organism	_	_
222	O157	o157	NN	_	_	_
223	:	:	:	_	_	_
224	H7	h7	NN	_	_	_
225	str	str	NN	_	_	_
226	.	.	.	_	_	_

1	EDL933	edl933	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	growth	growth	NN	_	_	_
4	phase	phase	NN	_	_	_
5	:	:	:	_	_	_
6	stationary	stationary	JJ	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	One	one	CD	_	_	_
9	hundred	hundred	CD	_	_	_
10	µl	µl	NN	_	_	_
11	tris-EDTA	tris-edta	NN	_	_	_
12	buffer	buffer	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	10	10	CD	_	_	_
15	mM	mm	NN	KWSUPP	_	_
16	Tris-Cl	tris-cl	NN	_	_	_
17	,	,	,	_	_	_
18	1	1	CD	_	_	_
19	mM	mm	NN	KWSUPP	_	_
20	EDTA	edta	NN	_	_	_
21	,	,	,	_	_	_
22	ph	ph	NN	_	_	_
23	8.0	8.0	CD	_	_	_
24	;	;	:	_	_	_
25	Promega	Promega	NNP	_	_	_
26	;	;	:	_	_	_
27	Madison	Madison	NNP	_	_	_
28	,	,	,	_	_	_
29	WI	WI	NNP	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	containing	contain	VBG	_	_	_
32	lysozyme	lysozyme	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	3	3	CD	_	_	_
35	mg	mg	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Stationary	stationary	JJ	_	_	_
38	phase	phase	NN	_	_	_
39	growth	growth	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	24	24	CD	_	_	_
42	hr	hr	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	~	~	NN	_	_	_
45	8	8	CD	_	_	_
46	log	log	NN	_	_	_
47	CFU	CFU	NNP	_	_	_
48	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
49	The	The	NNP	_	_	_
50	RNeasy	RNeasy	NNP	_	_	_
51	Mini	Mini	NNP	_	_	_
52	Purification	purification	NN	_	_	_
53	Kit	kit	NN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	Qiagen	qiagen	NN	_	_	_
56	;	;	:	_	_	_
57	Valencia	Valencia	NNP	_	_	_
58	,	,	,	_	_	_
59	CA	CA	NNP	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	was	be	VBD	_	_	_
62	used	use	VBN	_	_	_
63	to	to	TO	_	_	_
64	extract	extract	VB	_	_	_
65	total	total	JJ	_	_	_
66	RNA	rna	NN	_	_	_
67	from	from	IN	_	_	_
68	E.	e.	FW	_	_	_
69	coli	coli	FW	_	_	_
70	O157	o157	NN	_	_	_
71	:	:	:	_	_	_
72	H7	h7	NN	_	_	_
73	cultures	culture	NNS	_	_	_
74	.	.	.	_	_	_

1	RNAlater	rnalater	NN	_	_	_
2	Stabilization	stabilization	NN	_	_	_
3	Reagent	reagent	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	1.2	1.2	CD	_	_	_
6	ml	ml	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Qiagen	Qiagen	NNP	_	_	_
10	;	;	:	_	_	_
11	Valencia	Valencia	NNP	_	_	_
12	,	,	,	_	_	_
13	CA	CA	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	was	be	VBD	_	_	_
16	combined	combine	VBN	_	_	_
17	with	with	IN	_	_	_
18	0.6	0.6	CD	_	_	_
19	ml	ml	NN	_	_	_
20	E.	e.	FW	_	_	_
21	coli	coli	FW	_	_	_
22	O157	o157	NN	_	_	_
23	:	:	:	_	_	_
24	H7	h7	NN	_	_	_
25	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	10	10	CD	_	_	_
3	min	min	NN	_	_	_
4	at	at	IN	_	_	_
5	room	room	NN	_	_	_
6	temperature	temperature	NN	_	_	_
7	,	,	,	_	_	_
8	the	the	DT	_	_	_
9	mixture	mixture	NN	_	_	_
10	was	be	VBD	_	_	_
11	centrifuged	centrifuge	VBN	_	_	_
12	at	at	IN	_	_	_
13	8000	8000	CD	_	_	_
14	x	x	CC	_	_	_
15	g	g	NN	_	_	_
16	for	for	IN	_	_	_
17	10	10	CD	_	_	_
18	min	min	NN	_	_	_
19	under	under	IN	_	_	_
20	refrigeration	refrigeration	NN	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	decanted	decant	VBN	_	_	_
5	and	and	CC	_	_	_
6	the	the	DT	_	_	_
7	bacterial	bacterial	JJ	_	_	_
8	pellet	pellet	NN	_	_	_
9	was	be	VBD	_	_	_
10	stored	store	VBN	_	_	_
11	at	at	IN	_	_	_
12	-70	-70	CD	_	_	_
13	°C	°c	NN	_	_	_
14	until	until	IN	_	_	_
15	further	further	JJ	_	_	_
16	processed	process	VBN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	2-10	2-10	CD	_	_	_
19	h	h	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	0.5	0.5	CD	_	_	_
3	hour	hour	NN	_	_	_
4	expression	expression	NN	_	_	_
5	of	of	IN	_	_	_
6	synthetic	synthetic	JJ	_	_	_
7	protein	protein	NN	_	_	_
8	DX	dx	NN	_	_	_
9	in	in	IN	_	_	_
10	E.	e.	FW	_	_	_
11	coli	coli	FW	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	1.5	1.5	CD	_	_	_
14	hour	hour	NN	_	_	_
15	expression	expression	NN	_	_	_
16	of	of	IN	_	_	_
17	synthetic	synthetic	JJ	_	_	_
18	protein	protein	NN	_	_	_
19	DX	dx	NN	_	_	_
20	in	in	IN	_	_	_
21	E.	e.	FW	_	_	_
22	coli	coli	FW	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	1	1	CD	_	_	_
25	hour	hour	NN	_	_	_
26	expression	expression	NN	_	_	_
27	of	of	IN	_	_	_
28	synthetic	synthetic	JJ	_	_	_
29	protein	protein	NN	_	_	_
30	DX	dx	NN	_	_	_
31	in	in	IN	_	_	_
32	E.	e.	FW	_	_	_
33	coli	coli	FW	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	2	2	CD	_	_	_
36	hour	hour	NN	_	_	_
37	expression	expression	NN	_	_	_
38	of	of	IN	_	_	_
39	synthetic	synthetic	JJ	_	_	_
40	protein	protein	NN	_	_	_
41	DX	dx	NN	_	_	_
42	in	in	IN	_	_	_
43	E.	e.	FW	_	_	_
44	coli	coli	FW	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	3.5	3.5	CD	_	_	_
47	hour	hour	NN	_	_	_
48	expression	expression	NN	_	_	_
49	of	of	IN	_	_	_
50	synthetic	synthetic	JJ	_	_	_
51	protein	protein	NN	_	_	_
52	DX	dx	NN	_	_	_
53	in	in	IN	_	_	_
54	E.	e.	FW	_	_	_
55	coli	coli	FW	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	3	3	CD	_	_	_
58	hour	hour	NN	_	_	_
59	expression	expression	NN	_	_	_
60	of	of	IN	_	_	_
61	synthetic	synthetic	JJ	_	_	_
62	protein	protein	NN	_	_	_
63	DX	dx	NN	_	_	_
64	in	in	IN	_	_	_
65	E.	e.	FW	_	_	_
66	coli	coli	FW	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	4	4	CD	_	_	_
69	hour	hour	NN	_	_	_
70	expression	expression	NN	_	_	_
71	of	of	IN	_	_	_
72	synthetic	synthetic	JJ	_	_	_
73	protein	protein	NN	_	_	_
74	DX	dx	NN	_	_	_
75	in	in	IN	_	_	_
76	E.	e.	FW	_	_	_
77	coli	coli	FW	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	According	accord	VBG	_	_	_
80	to	to	TO	_	_	_
81	Invitrogen	Invitrogen	NNP	_	_	_
82	PureLink	PureLink	NNP	_	_	_
83	Micro-to-Midi	Micro-to-Midi	NNP	_	_	_
84	Total	Total	NNP	_	_	_
85	RNA	rna	NN	_	_	_
86	Purification	purification	NN	_	_	_
87	System	system	NN	_	_	_
88	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
89	Data	Data	NNP	_	_	_
90	was	be	VBD	_	_	_
91	processed	process	VBN	_	_	_
92	by	by	IN	_	_	_
93	MATLAB	MATLAB	NNP	_	_	_
94	to	to	TO	_	_	_
95	median	median	JJ	_	_	_
96	normalize	normalize	VB	_	_	_
97	each	each	DT	_	_	_
98	channel	channel	NN	_	_	_
99	and	and	CC	_	_	_
100	lowess	lowess	NN	_	_	_
101	normalize	normalize	VBP	_	_	_
102	the	the	DT	_	_	_
103	sample	sample	NN	_	_	_
104	set	set	NN	_	_	_
105	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	cells	cell	NNS	_	_	_
5	containing	contain	VBG	_	_	_
6	a	a	DT	_	_	_
7	pBAD18	pbad18	NN	_	_	_
8	vector	vector	NN	_	_	_
9	encoding	encode	VBG	_	_	_
10	synthetic	synthetic	JJ	_	_	_
11	protein	protein	NN	_	_	_
12	DX	DX	NNP	_	_	_
13	exposed	expose	VBN	_	_	_
14	to	to	TO	_	_	_
15	arabinose	arabinose	VB	_	_	_
16	inducer	inducer	NN	_	_	_
17	for	for	IN	_	_	_
18	0.5	0.5	CD	_	_	_
19	h.	h.	NN	_	_	_
20	RNA	rna	NN	_	_	_
21	extracted	extract	VBN	_	_	_
22	with	with	IN	_	_	_
23	Invitrogen	Invitrogen	NNP	_	_	_
24	PureLink	PureLink	NNP	_	_	_
25	kit	kit	NN	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Identical	identical	JJ	_	_	_
6	to	to	TO	_	_	_
7	Channel	Channel	NNP	_	_	_
8	1	1	CD	_	_	_
9	with	with	IN	_	_	_
10	no	no	DT	_	_	_
11	arabinose	arabinose	NN	_	_	_
12	added	add	VBD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	reference	reference	NN	_	_	_
15	:	:	:	_	_	_
16	E.	e.	FW	_	_	_
17	coli	coli	FW	_	_	_
18	TOP10	top10	NN	_	_	_
19	containing	contain	VBG	_	_	_
20	pBAD18	pbad18	NN	_	_	_
21	vector	vector	NN	_	_	_
22	with	with	IN	_	_	_
23	no	no	DT	_	_	_
24	arabinose	arabinose	NN	_	_	_
25	added	add	VBD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	RNA	rna	NN	_	_	_
28	from	from	IN	_	_	_
29	E.	e.	FW	_	_	_
30	coli	coli	FW	_	_	_
31	0.5	0.5	CD	_	_	_
32	hours	hour	NNS	_	_	_
33	after	after	IN	_	_	_
34	inoculation	inoculation	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	RNA	rna	NN	_	_	_
37	from	from	IN	_	_	_
38	E.	e.	FW	_	_	_
39	coli	coli	FW	_	_	_
40	1.5	1.5	CD	_	_	_
41	hours	hour	NNS	_	_	_
42	after	after	IN	_	_	_
43	inoculation	inoculation	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	RNA	rna	NN	_	_	_
46	from	from	IN	_	_	_
47	E.	e.	FW	_	_	_
48	coli	coli	FW	_	_	_
49	2	2	CD	_	_	_
50	hours	hour	NNS	_	_	_
51	after	after	IN	_	_	_
52	inoculation	inoculation	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	RNA	rna	NN	_	_	_
55	from	from	IN	_	_	_
56	E.	e.	FW	_	_	_
57	coli	coli	FW	_	_	_
58	3.5	3.5	CD	_	_	_
59	hours	hour	NNS	_	_	_
60	after	after	IN	_	_	_
61	inoculation	inoculation	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	RNA	rna	NN	_	_	_
64	from	from	IN	_	_	_
65	E.	e.	FW	_	_	_
66	coli	coli	FW	_	_	_
67	3	3	CD	_	_	_
68	hours	hour	NNS	_	_	_
69	after	after	IN	_	_	_
70	inoculation	inoculation	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	RNA	rna	NN	_	_	_
73	from	from	IN	_	_	_
74	E.	e.	FW	_	_	_
75	coli	coli	FW	_	_	_
76	4	4	CD	_	_	_
77	hours	hour	NNS	_	_	_
78	after	after	IN	_	_	_
79	inoculation	inoculation	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	RNA	rna	NN	_	_	_
82	from	from	IN	_	_	_
83	E.	e.	FW	_	_	_
84	coli	coli	FW	_	_	_
85	expressing	express	VBG	_	_	_
86	synthetic	synthetic	JJ	_	_	_
87	protein	protein	NN	_	_	_
88	DX	DX	NNP	_	_	_
89	for	for	IN	_	_	_
90	0.5	0.5	CD	_	_	_
91	hours	hour	NNS	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	RNA	rna	NN	_	_	_
94	from	from	IN	_	_	_
95	E.	e.	FW	_	_	_
96	coli	coli	FW	_	_	_
97	expressing	express	VBG	_	_	_
98	synthetic	synthetic	JJ	_	_	_
99	protein	protein	NN	_	_	_
100	DX	DX	NNP	_	_	_
101	for	for	IN	_	_	_
102	1.5	1.5	CD	_	_	_
103	hours	hour	NNS	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	RNA	rna	NN	_	_	_
106	from	from	IN	_	_	_
107	E.	e.	FW	_	_	_
108	coli	coli	FW	_	_	_
109	expressing	express	VBG	_	_	_
110	synthetic	synthetic	JJ	_	_	_
111	protein	protein	NN	_	_	_
112	DX	DX	NNP	_	_	_
113	for	for	IN	_	_	_
114	1	1	CD	_	_	_
115	hours	hour	NNS	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	RNA	rna	NN	_	_	_
118	from	from	IN	_	_	_
119	E.	e.	FW	_	_	_
120	coli	coli	FW	_	_	_
121	expressing	express	VBG	_	_	_
122	synthetic	synthetic	JJ	_	_	_
123	protein	protein	NN	_	_	_
124	DX	DX	NNP	_	_	_
125	for	for	IN	_	_	_
126	2	2	CD	_	_	_
127	hours	hour	NNS	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	RNA	rna	NN	_	_	_
130	from	from	IN	_	_	_
131	E.	e.	FW	_	_	_
132	coli	coli	FW	_	_	_
133	expressing	express	VBG	_	_	_
134	synthetic	synthetic	JJ	_	_	_
135	protein	protein	NN	_	_	_
136	DX	DX	NNP	_	_	_
137	for	for	IN	_	_	_
138	3.5	3.5	CD	_	_	_
139	hours	hour	NNS	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	RNA	rna	NN	_	_	_
142	from	from	IN	_	_	_
143	E.	e.	FW	_	_	_
144	coli	coli	FW	_	_	_
145	expressing	express	VBG	_	_	_
146	synthetic	synthetic	JJ	_	_	_
147	protein	protein	NN	_	_	_
148	DX	DX	NNP	_	_	_
149	for	for	IN	_	_	_
150	3	3	CD	_	_	_
151	hours	hour	NNS	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	RNA	rna	NN	_	_	_
154	from	from	IN	_	_	_
155	E.	e.	FW	_	_	_
156	coli	coli	FW	_	_	_
157	expressing	express	VBG	_	_	_
158	synthetic	synthetic	JJ	_	_	_
159	protein	protein	NN	_	_	_
160	DX	DX	NNP	_	_	_
161	for	for	IN	_	_	_
162	4	4	CD	_	_	_
163	hours	hour	NNS	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
165	test	test	NN	_	_	_
166	:	:	:	_	_	_
167	E.	e.	FW	_	_	_
168	coli	coli	FW	_	_	_
169	TOP10	top10	NN	_	_	_
170	containing	contain	VBG	_	_	_
171	pBAD18	pbad18	NN	_	_	_
172	vector	vector	NN	_	_	_
173	exposed	expose	VBN	_	_	_
174	to	to	TO	_	_	_
175	arabinose	arabinose	VB	_	_	_
176	inducer	inducer	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	cell	cell	NN	_	_	_
179	type	type	NN	_	_	_
180	:	:	:	_	_	_
181	biofilm	biofilm	NN	_	_	_
182	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
183	Escherichia	escherichia	FW	Organism	_	_
184	coli	coli	FW	Organism	_	_
185	K-12	k-12	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	growth	growth	NN	_	_	_
188	protocol	protocol	NN	_	_	_
189	:	:	:	_	_	_
190	biofilm	biofilm	NN	_	_	_
191	grown	grow	VBN	_	_	_
192	on	on	IN	_	_	_
193	glass	glass	NN	_	_	_
194	wool	wool	NN	_	_	_
195	,	,	,	_	_	_
196	37C	37c	NN	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	MAS	mas	NN	_	_	_
199	5.0	5.0	CD	_	_	_
200	Expression	expression	NN	_	_	_
201	Analysis	analysis	NN	_	_	_
202	Default	Default	NNP	_	_	_
203	Setting	Setting	NNP	_	_	_
204	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
205	medium	medium	NN	_	_	_
206	:	:	:	_	_	_
207	LB	lb	NN	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	pCA24N-hns	pca24n-hn	NNS	_	_	_
210	biofilm	biofilm	NN	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	pCA24N-hnsK57N	pca24n-hnsk57n	NN	_	_	_
213	biofilm	biofilm	NN	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	strain	strain	NN	_	_	_
216	:	:	:	_	_	_
217	BW25113	bw25113	NN	_	_	_
218	hha	hha	NN	GEN	_	_
219	hns	hn	VBZ	GEN	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	The	the	DT	_	_	_
222	overnight	overnight	JJ	_	_	_
223	culture	culture	NN	_	_	_
224	-LRB-	-lrb-	-LRB-	_	_	_
225	2.5	2.5	CD	_	_	_
226	ml	ml	NN	_	_	_
227	-RRB-	-rrb-	-RRB-	_	_	_
228	was	be	VBD	_	_	_
229	used	use	VBN	_	_	_
230	to	to	TO	_	_	_
231	inoculate	inoculate	VB	_	_	_
232	250	250	CD	_	_	_
233	ml	ml	NN	_	_	_
234	of	of	IN	_	_	_
235	fresh	fresh	JJ	_	_	_
236	LB	lb	NN	MED	_	_
237	medium	medium	NN	MED	_	_
238	with	with	IN	_	_	_
239	10	10	CD	_	_	_
240	g	g	NN	_	_	_
241	of	of	IN	_	_	_
242	submerged	submerged	JJ	_	_	_
243	glass	glass	NN	_	_	_
244	wool	wool	NN	_	_	_
245	-LRB-	-lrb-	-LRB-	_	_	_
246	Corning	Corning	NNP	_	_	_
247	Glass	Glass	NNP	_	_	_
248	Works	Works	NNP	_	_	_
249	,	,	,	_	_	_
250	Corning	Corning	NNP	_	_	_
251	,	,	,	_	_	_
252	NY	NY	NNP	_	_	_
253	-RRB-	-rrb-	-RRB-	_	_	_
254	for	for	IN	_	_	_
255	forming	form	VBG	_	_	_
256	biofilm	biofilm	NN	_	_	_
257	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	7	7	CD	_	_	_
5	h	h	NN	_	_	_
6	at	at	IN	_	_	_
7	37	37	CD	_	_	_
8	°C	°c	NN	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	250	250	CD	_	_	_
13	rpm	rpm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	the	the	DT	_	_	_
17	glass	glass	NN	_	_	_
18	wool	wool	NN	_	_	_
19	was	be	VBD	_	_	_
20	carefully	carefully	RB	_	_	_
21	and	and	CC	_	_	_
22	quickly	quickly	RB	_	_	_
23	removed	remove	VBD	_	_	_
24	and	and	CC	_	_	_
25	rinsed	rinse	VBD	_	_	_
26	with	with	IN	_	_	_
27	100	100	CD	_	_	_
28	ml	ml	NN	_	_	_
29	of	of	IN	_	_	_
30	sterile	sterile	JJ	_	_	_
31	0.85	0.85	CD	_	_	_
32	%	%	NN	_	_	_
33	NaCl	nacl	NN	_	_	_
34	solution	solution	NN	_	_	_
35	at	at	IN	_	_	_
36	0	0	CD	_	_	_
37	°C	°c	NN	_	_	_
38	.	.	.	_	_	_

1	Biofilm	biofilm	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	sonicating	sonicate	VBG	_	_	_
7	the	the	DT	_	_	_
8	glass	glass	NN	_	_	_
9	wool	wool	NN	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	sterile	sterile	JJ	_	_	_
15	0.85	0.85	CD	_	_	_
16	%	%	NN	_	_	_
17	NaCl	nacl	NN	_	_	_
18	solution	solution	NN	_	_	_
19	at	at	IN	_	_	_
20	0	0	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	time	time	NN	_	_	_
3	:	:	:	_	_	_
4	7	7	CD	_	_	_
5	hours	hour	NNS	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Adapted	adapt	VBN	_	_	_
8	E.	e.	FW	_	_	_
9	coli	coli	FW	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	DST160	dst160	NN	_	_	_
12	,	,	,	_	_	_
13	tolerant	tolerant	JJ	_	_	_
14	to	to	TO	_	_	_
15	high	high	JJ	_	_	_
16	succinic	succinic	JJ	_	_	_
17	acid	acid	NN	_	_	_
18	concentration	concentration	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	E.	e.	FW	_	_	_
22	coli	coli	FW	_	_	_
23	W3110	w3110	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	control	control	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Escherichia	escherichia	FW	Organism	_	_
29	coli	coli	FW	Organism	_	_
30	str	str	FW	_	_	_
31	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	W3110	w3110	CD	_	_	_
2	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3	High	High	NNP	_	_	_
4	succinic	succinic	JJ	_	_	_
5	acid	acid	NN	_	_	_
6	tolerance	tolerance	NN	_	_	_
7	E.coli	e.coli	NNS	_	_	_
8	_	_	VBP	_	_	_
9	rep	rep	NN	GEN	_	_
10	Dn	dn	NN	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	High	High	NNP	_	_	_
13	succinic	succinic	JJ	_	_	_
14	acid	acid	NN	_	_	_
15	tolerance	tolerance	NN	_	_	_
16	E.coli	e.coli	NNS	_	_	_
17	_	_	VBP	_	_	_
18	rep	rep	NN	GEN	_	_
19	Up	up	IN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	sample	sample	NN	_	_	_
22	type	type	NN	_	_	_
23	:	:	:	_	_	_
24	control	control	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
26	sample	sample	NN	_	_	_
27	type	type	NN	_	_	_
28	:	:	:	_	_	_
29	test	test	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Scanned	scan	VBD	_	_	_
32	images	image	NNS	_	_	_
33	were	be	VBD	_	_	_
34	analyzed	analyze	VBN	_	_	_
35	with	with	IN	_	_	_
36	GenePix	GenePix	NNP	_	_	_
37	Pro	pro	FW	_	_	_
38	3.0	3.0	CD	_	_	_
39	software	software	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	Axon	Axon	NNP	_	_	_
42	Instruments	Instruments	NNP	_	_	_
43	,	,	,	_	_	_
44	Union	Union	NNP	_	_	_
45	City	City	NNP	_	_	_
46	,	,	,	_	_	_
47	CA	CA	NNP	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	to	to	TO	_	_	_
50	obtain	obtain	VB	_	_	_
51	gene	gene	NN	_	_	_
52	expression	expression	NN	_	_	_
53	ratios	ratio	NNS	_	_	_
54	.	.	.	_	_	_

1	Logged	log	VBN	_	_	_
2	gene	gene	NN	_	_	_
3	expression	expression	NN	_	_	_
4	ratios	ratio	NNS	_	_	_
5	were	be	VBD	_	_	_
6	normalized	normalize	VBN	_	_	_
7	by	by	IN	_	_	_
8	LOWESS	lowess	NN	_	_	_
9	regression	regression	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Yang	Yang	NNP	_	_	_
12	et	et	FW	_	_	_
13	al.	al.	FW	_	_	_
14	,	,	,	_	_	_
15	2002	2002	CD	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	using	use	VBG	_	_	_
18	the	the	DT	_	_	_
19	GeneSpring	GeneSpring	NNP	_	_	_
20	GX	GX	NNP	_	_	_
21	7.3	7.3	CD	_	_	_
22	software	software	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Agilent	Agilent	NNP	_	_	_
25	Technologies	Technologies	NNPS	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	medium	medium	NN	_	_	_
4	for	for	IN	_	_	_
5	continuous	continuous	JJ	_	_	_
6	culture	culture	NN	_	_	_
7	contained	contain	VBD	_	_	_
8	3	3	CD	_	_	_
9	g	g	NN	_	_	_
10	glucose	glucose	NN	SUPP	_	_
11	medium	medium	NN	_	_	_
12	consisted	consist	VBD	_	_	_
13	with	with	IN	_	_	_
14	0.8	0.8	CD	_	_	_
15	g	g	NN	_	_	_
16	NH4Cl	nh4cl	NN	_	_	_
17	,	,	,	_	_	_
18	0.5	0.5	CD	_	_	_
19	g	g	NN	_	_	_
20	NaCl	nacl	NN	_	_	_
21	,	,	,	_	_	_
22	7.5	7.5	CD	_	_	_
23	g	g	NN	_	_	_
24	Na2HPO4	na2hpo4	NN	_	_	_
25	•	•	SYM	_	_	_
26	2H2O	2h2o	NN	_	_	_
27	,	,	,	_	_	_
28	3	3	CD	_	_	_
29	g	g	NN	_	_	_
30	KH2PO4	kh2po4	NN	_	_	_
31	with	with	IN	_	_	_
32	separately	separately	RB	_	_	_
33	added	add	VBN	_	_	_
34	trace	trace	NN	_	_	_
35	element	element	NN	_	_	_
36	of	of	IN	_	_	_
37	0.2	0.2	CD	_	_	_
38	g	g	NN	_	_	_
39	MgSO4	mgso4	NN	_	_	_
40	•	•	SYM	_	_	_
41	7H2O	7H2O	NNP	_	_	_
42	,	,	,	_	_	_
43	0.1	0.1	CD	_	_	_
44	g	g	NN	_	_	_
45	CaCl2	cacl2	NN	_	_	_
46	,	,	,	_	_	_
47	1	1	CD	_	_	_
48	mg	mg	NN	_	_	_
49	thiamine	thiamine	NN	SUPP	_	_
50	per	per	IN	_	_	_
51	liter	liter	NN	_	_	_
52	and	and	CC	_	_	_
53	the	the	DT	_	_	_
54	concentraiton	concentraiton	NN	_	_	_
55	of	of	IN	_	_	_
56	added	add	VBN	_	_	_
57	succinate	succinate	JJ	SUPP	_	_
58	gradually	gradually	RB	_	_	_
59	was	be	VBD	_	_	_
60	raised	raise	VBN	_	_	_
61	from	from	IN	_	_	_
62	30	30	CD	_	_	_
63	g	g	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
65	The	the	DT	_	_	_
66	medium	medium	NN	_	_	_
67	for	for	IN	_	_	_
68	continuous	continuous	JJ	_	_	_
69	culture	culture	NN	_	_	_
70	contained	contain	VBD	_	_	_
71	3	3	CD	_	_	_
72	g	g	NN	_	_	_
73	glucose	glucose	NN	SUPP	_	_
74	medium	medium	NN	_	_	_
75	consisted	consist	VBD	_	_	_
76	with	with	IN	_	_	_
77	0.8	0.8	CD	_	_	_
78	g	g	NN	_	_	_
79	NH4Cl	nh4cl	NN	_	_	_
80	,	,	,	_	_	_
81	0.5	0.5	CD	_	_	_
82	g	g	NN	_	_	_
83	NaCl	nacl	NN	_	_	_
84	,	,	,	_	_	_
85	7.5	7.5	CD	_	_	_
86	g	g	NN	_	_	_
87	Na2HPO4	na2hpo4	NN	_	_	_
88	•	•	SYM	_	_	_
89	2H2O	2h2o	NN	_	_	_
90	,	,	,	_	_	_
91	3	3	CD	_	_	_
92	g	g	NN	_	_	_
93	KH2PO4	kh2po4	NN	_	_	_
94	with	with	IN	_	_	_
95	separately	separately	RB	_	_	_
96	added	add	VBN	_	_	_
97	trace	trace	NN	_	_	_
98	element	element	NN	_	_	_
99	of	of	IN	_	_	_
100	0.2	0.2	CD	_	_	_
101	g	g	NN	_	_	_
102	MgSO4	mgso4	NN	_	_	_
103	•	•	SYM	_	_	_
104	7H2O	7H2O	NNP	_	_	_
105	,	,	,	_	_	_
106	0.1	0.1	CD	_	_	_
107	g	g	NN	_	_	_
108	CaCl2	cacl2	NN	_	_	_
109	,	,	,	_	_	_
110	1	1	CD	_	_	_
111	mg	mg	NN	_	_	_
112	thiamine	thiamine	NN	SUPP	_	_
113	per	per	IN	_	_	_
114	liter	liter	NN	_	_	_
115	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	fermentor	fermentor	NN	_	_	_
3	was	be	VBD	_	_	_
4	maintained	maintain	VBN	_	_	_
5	at	at	IN	_	_	_
6	37	37	CD	_	_	_
7	℃	℃	CD	_	_	_
8	,	,	,	_	_	_
9	350	350	CD	_	_	_
10	rpm	rpm	NN	_	_	_
11	with	with	IN	_	_	_
12	air	air	NN	_	_	_
13	gas	gas	NN	_	_	_
14	flushing	flushing	NN	_	_	_
15	and	and	CC	_	_	_
16	the	the	DT	_	_	_
17	feeding	feeding	NN	_	_	_
18	and	and	CC	_	_	_
19	outlet	outlet	NN	_	_	_
20	pumps	pump	NNS	_	_	_
21	were	be	VBD	_	_	_
22	maintained	maintain	VBN	_	_	_
23	at	at	IN	_	_	_
24	flow	flow	NN	_	_	_
25	rate	rate	NN	_	_	_
26	of	of	IN	_	_	_
27	0.1	0.1	CD	_	_	_
28	h-1	h-1	NN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	medium	medium	NN	_	_	_
4	for	for	IN	_	_	_
5	continuous	continuous	JJ	_	_	_
6	culture	culture	NN	_	_	_
7	contained	contain	VBD	_	_	_
8	3	3	CD	_	_	_
9	g	g	NN	_	_	_
10	glucose	glucose	NN	SUPP	_	_
11	medium	medium	NN	_	_	_
12	consisted	consist	VBD	_	_	_
13	with	with	IN	_	_	_
14	0.8	0.8	CD	_	_	_
15	g	g	NN	_	_	_
16	NH4Cl	nh4cl	NN	_	_	_
17	,	,	,	_	_	_
18	0.5	0.5	CD	_	_	_
19	g	g	NN	_	_	_
20	NaCl	nacl	NN	_	_	_
21	,	,	,	_	_	_
22	7.5	7.5	CD	_	_	_
23	g	g	NN	_	_	_
24	Na2HPO4	na2hpo4	NN	_	_	_
25	•	•	SYM	_	_	_
26	2H2O	2h2o	NN	_	_	_
27	,	,	,	_	_	_
28	3	3	CD	_	_	_
29	g	g	NN	_	_	_
30	KH2PO4	kh2po4	NN	_	_	_
31	with	with	IN	_	_	_
32	separately	separately	RB	_	_	_
33	added	add	VBN	_	_	_
34	trace	trace	NN	_	_	_
35	element	element	NN	_	_	_
36	of	of	IN	_	_	_
37	0.2	0.2	CD	_	_	_
38	g	g	NN	_	_	_
39	MgSO4	mgso4	NN	_	_	_
40	•	•	SYM	_	_	_
41	7H2O	7H2O	NNP	_	_	_
42	,	,	,	_	_	_
43	0.1	0.1	CD	_	_	_
44	g	g	NN	_	_	_
45	CaCl2	cacl2	NN	_	_	_
46	,	,	,	_	_	_
47	1	1	CD	_	_	_
48	mg	mg	NN	_	_	_
49	thiamine	thiamine	NN	SUPP	_	_
50	per	per	IN	_	_	_
51	liter	liter	NN	_	_	_
52	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	fermentor	fermentor	NN	_	_	_
3	was	be	VBD	_	_	_
4	maintained	maintain	VBN	_	_	_
5	at	at	IN	_	_	_
6	37	37	CD	_	_	_
7	℃	℃	CD	_	_	_
8	,	,	,	_	_	_
9	350	350	CD	_	_	_
10	rpm	rpm	NN	_	_	_
11	with	with	IN	_	_	_
12	air	air	NN	_	_	_
13	gas	gas	NN	_	_	_
14	flushing	flushing	NN	_	_	_
15	and	and	CC	_	_	_
16	the	the	DT	_	_	_
17	feeding	feeding	NN	_	_	_
18	and	and	CC	_	_	_
19	outlet	outlet	NN	_	_	_
20	pumps	pump	NNS	_	_	_
21	were	be	VBD	_	_	_
22	maintained	maintain	VBN	_	_	_
23	at	at	IN	_	_	_
24	flow	flow	NN	_	_	_
25	rate	rate	NN	_	_	_
26	of	of	IN	_	_	_
27	0.1	0.1	CD	_	_	_
28	h-1	h-1	NN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Transcriptome	transcriptome	NN	_	_	_
3	of	of	IN	_	_	_
4	cells	cell	NNS	_	_	_
5	was	be	VBD	_	_	_
6	prepared	prepare	VBN	_	_	_
7	using	use	VBG	_	_	_
8	a	a	DT	_	_	_
9	RNA	rna	NN	_	_	_
10	extraction	extraction	NN	_	_	_
11	kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	RNeasy	rneasy	NN	_	_	_
14	mini	minus	NNS	_	_	_
15	kit	kit	NN	_	_	_
16	;	;	:	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	,	,	,	_	_	_
19	Hilden	Hilden	NNP	_	_	_
20	,	,	,	_	_	_
21	Germany	Germany	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	Biofilms	Biofilms	NNPS	_	_	_
25	were	be	VBD	_	_	_
26	grown	grow	VBN	_	_	_
27	on	on	IN	_	_	_
28	nylon	nylon	NN	_	_	_
29	membranes	membrane	NNS	_	_	_
30	using	use	VBG	_	_	_
31	agar	agar	NN	_	_	_
32	as	as	IN	_	_	_
33	the	the	DT	_	_	_
34	source	source	NN	_	_	_
35	of	of	IN	_	_	_
36	nutrients	nutrient	NNS	_	_	_
37	and	and	CC	_	_	_
38	water	water	NN	_	_	_
39	.	.	.	_	_	_

1	Aliquots	aliquot	NNS	_	_	_
2	of	of	IN	_	_	_
3	10	10	CD	_	_	_
4	ml	ml	NN	_	_	_
5	Luria	Luria	NNP	_	_	_
6	agar	agar	NN	_	_	_
7	were	be	VBD	_	_	_
8	transferred	transfer	VBN	_	_	_
9	to	to	TO	_	_	_
10	petri	petri	VB	_	_	_
11	dishes	dish	NNS	_	_	_
12	to	to	TO	_	_	_
13	produce	produce	VB	_	_	_
14	layers	layer	NNS	_	_	_
15	of	of	IN	_	_	_
16	agar	agar	NN	_	_	_
17	approximately	approximately	RB	_	_	_
18	3	3	CD	_	_	_
19	mm	mm	NN	_	_	_
20	in	in	IN	_	_	_
21	depth	depth	NN	_	_	_
22	.	.	.	_	_	_

1	Nylon	nylon	NN	_	_	_
2	membrane	membrane	NN	_	_	_
3	filters	filter	NNS	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	47	47	CD	_	_	_
6	mm	mm	NN	_	_	_
7	diameter	diameter	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	with	with	IN	_	_	_
10	a	a	DT	_	_	_
11	0.2	0.2	CD	_	_	_
12	μm	μm	NN	_	_	_
13	pore	pore	NN	_	_	_
14	size	size	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Whatman	whatman	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	were	be	VBD	_	_	_
19	autoclaved	autoclave	VBN	_	_	_
20	in	in	IN	_	_	_
21	Milli-Q	milli-q	JJ	_	_	_
22	water	water	NN	_	_	_
23	,	,	,	_	_	_
24	dried	dry	VBD	_	_	_
25	and	and	CC	_	_	_
26	placed	place	VBD	_	_	_
27	on	on	IN	_	_	_
28	the	the	DT	_	_	_
29	agar	agar	NN	_	_	_
30	surface	surface	NN	_	_	_
31	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	100	100	CD	_	_	_
3	μl	μl	NN	_	_	_
4	aliquot	aliquot	NN	_	_	_
5	of	of	IN	_	_	_
6	an	a	DT	_	_	_
7	overnight	overnight	JJ	_	_	_
8	culture	culture	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	approximately	approximately	RB	_	_	_
11	108	108	CD	_	_	_
12	cells	cell	NNS	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	was	be	VBD	_	_	_
15	applied	apply	VBN	_	_	_
16	to	to	TO	_	_	_
17	the	the	DT	_	_	_
18	membrane	membrane	NN	_	_	_
19	as	as	IN	_	_	_
20	a	a	DT	_	_	_
21	single	single	JJ	_	_	_
22	spot	spot	NN	_	_	_
23	and	and	CC	_	_	_
24	allowed	allow	VBN	_	_	_
25	to	to	TO	_	_	_
26	dry	dry	JJ	_	_	_
27	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	of	of	IN	_	_	_
3	these	these	DT	_	_	_
4	steps	step	NNS	_	_	_
5	were	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	on	on	IN	_	_	_
8	a	a	DT	_	_	_
9	level	level	NN	_	_	_
10	table	table	NN	_	_	_
11	so	so	RB	_	_	_
12	as	as	IN	_	_	_
13	not	not	RB	_	_	_
14	to	to	TO	_	_	_
15	introduce	introduce	VB	_	_	_
16	unwanted	unwanted	JJ	_	_	_
17	gradients	gradient	NNS	_	_	_
18	.	.	.	_	_	_

1	Dishes	dish	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	inverted	inverted	JJ	_	_	_
5	and	and	CC	_	_	_
6	incubated	incubate	VBN	_	_	_
7	at	at	IN	_	_	_
8	37	37	CD	_	_	_
9	oC	oc	NN	_	_	_
10	for	for	IN	_	_	_
11	24	24	CD	_	_	_
12	h.	h.	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
14	Biofilms	biofilm	NNS	_	_	_
15	were	be	VBD	_	_	_
16	individually	individually	RB	_	_	_
17	removed	remove	VBN	_	_	_
18	from	from	IN	_	_	_
19	the	the	DT	_	_	_
20	incubator	incubator	NN	_	_	_
21	and	and	CC	_	_	_
22	,	,	,	_	_	_
23	using	use	VBG	_	_	_
24	a	a	DT	_	_	_
25	small	small	JJ	_	_	_
26	scalpel	scalpel	NN	_	_	_
27	blade	blade	NN	_	_	_
28	and	and	CC	_	_	_
29	sterile	sterile	JJ	_	_	_
30	forceps	forceps	NNS	_	_	_
31	,	,	,	_	_	_
32	the	the	DT	_	_	_
33	distinctive	distinctive	JJ	_	_	_
34	outer	outer	JJ	_	_	_
35	perimeter	perimeter	NN	_	_	_
36	of	of	IN	_	_	_
37	biofilm	biofilm	NN	_	_	_
38	growth	growth	NN	_	_	_
39	was	be	VBD	_	_	_
40	cut	cut	VBN	_	_	_
41	away	away	RB	_	_	_
42	from	from	IN	_	_	_
43	the	the	DT	_	_	_
44	rest	rest	NN	_	_	_
45	of	of	IN	_	_	_
46	the	the	DT	_	_	_
47	biofilm	biofilm	NN	_	_	_
48	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	two	two	CD	_	_	_
3	resulting	result	VBG	_	_	_
4	sections	section	NNS	_	_	_
5	of	of	IN	_	_	_
6	membrane	membrane	NN	_	_	_
7	were	be	VBD	_	_	_
8	submerged	submerge	VBN	_	_	_
9	in	in	IN	_	_	_
10	separate	separate	JJ	_	_	_
11	volumes	volume	NNS	_	_	_
12	of	of	IN	_	_	_
13	RNAprotect	rnaprotect	NN	_	_	_
14	Bacteria	bacterium	NNS	_	_	_
15	Reagent	reagent	NN	_	_	_
16	and	and	CC	_	_	_
17	vortexed	vortex	VBN	_	_	_
18	to	to	TO	_	_	_
19	release	release	VB	_	_	_
20	the	the	DT	_	_	_
21	cells	cell	NNS	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	sections	section	NNS	_	_	_
3	of	of	IN	_	_	_
4	membrane	membrane	NN	_	_	_
5	were	be	VBD	_	_	_
6	then	then	RB	_	_	_
7	removed	remove	VBN	_	_	_
8	from	from	IN	_	_	_
9	the	the	DT	_	_	_
10	resulting	result	VBG	_	_	_
11	suspension	suspension	NN	_	_	_
12	before	before	IN	_	_	_
13	RNA	rna	NN	_	_	_
14	extraction	extraction	NN	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	harvested	harvest	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	at	at	IN	_	_	_
8	5,000	5,000	CD	_	_	_
9	g	g	NN	_	_	_
10	for	for	IN	_	_	_
11	5	5	CD	_	_	_
12	min	min	NN	_	_	_
13	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	RNeasy	RNeasy	NNP	_	_	_
8	Mini	Mini	NNP	_	_	_
9	kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Qiagen	qiagen	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	according	accord	VBG	_	_	_
14	to	to	TO	_	_	_
15	the	the	DT	_	_	_
16	supplier	supplier	NN	_	_	_
17	's	's	POS	_	_	_
18	protocol	protocol	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	the	the	DT	_	_	_
21	composition	composition	NN	_	_	_
22	of	of	IN	_	_	_
23	the	the	DT	_	_	_
24	RNeasy	rneasy	NN	_	_	_
25	solutions	solution	NNS	_	_	_
26	are	be	VBP	_	_	_
27	unknown	unknown	JJ	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	decanted	decant	VBN	_	_	_
5	and	and	CC	_	_	_
6	200	200	CD	_	_	_
7	μl	μl	NN	_	_	_
8	of	of	IN	_	_	_
9	TE	TE	NNP	_	_	_
10	buffer	buffer	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	10	10	CD	_	_	_
13	mM	mm	NN	KWSUPP	_	_
14	Tris	Tris	NNP	_	_	_
15	,	,	,	_	_	_
16	1	1	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	EDTA	edta	NN	_	_	_
19	in	in	IN	_	_	_
20	DEPC-treated	depc-treated	JJ	_	_	_
21	water	water	NN	_	_	_
22	,	,	,	_	_	_
23	pH	ph	NN	_	_	_
24	8	8	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	plus	plus	CC	_	_	_
27	lysosyme	lysosyme	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Sigma	Sigma	NNP	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	was	be	VBD	_	_	_
32	used	use	VBN	_	_	_
33	to	to	TO	_	_	_
34	resuspend	resuspend	VB	_	_	_
35	the	the	DT	_	_	_
36	pellet	pellet	NN	_	_	_
37	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	was	be	VBD	_	_	_
3	mixed	mixed	JJ	_	_	_
4	vigorously	vigorously	RB	_	_	_
5	and	and	CC	_	_	_
6	incubated	incubate	VBN	_	_	_
7	with	with	IN	_	_	_
8	intermittent	intermittent	JJ	_	_	_
9	shaking	shake	VBG	_	_	_
10	for	for	IN	_	_	_
11	5	5	CD	_	_	_
12	min	min	NN	_	_	_
13	at	at	IN	_	_	_
14	room	room	NN	_	_	_
15	temperature	temperature	NN	_	_	_
16	.	.	.	_	_	_

1	Buffer	buffer	NN	_	_	_
2	RLT	rlt	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	700	700	CD	_	_	_
5	μl	μl	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	with	with	IN	_	_	_
8	β-mercaptoethanol	β-mercaptoethanol	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	10	10	CD	_	_	_
11	μl	μl	NN	_	_	_
12	of	of	IN	_	_	_
13	14.3	14.3	CD	_	_	_
14	M	m	NN	_	_	_
15	β-mercaptoethanol	β-mercaptoethanol	NN	_	_	_
16	per	per	IN	_	_	_
17	1	1	CD	_	_	_
18	ml	ml	NN	_	_	_
19	RTL	rtl	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	was	be	VBD	_	_	_
22	then	then	RB	_	_	_
23	added	add	VBN	_	_	_
24	to	to	TO	_	_	_
25	the	the	DT	_	_	_
26	solution	solution	NN	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	mixed	mix	VBN	_	_	_
6	with	with	IN	_	_	_
7	500	500	CD	_	_	_
8	μl	μl	NN	_	_	_
9	of	of	IN	_	_	_
10	absolute	absolute	JJ	_	_	_
11	ethanol	ethanol	NN	_	_	_
12	before	before	IN	_	_	_
13	applying	apply	VBG	_	_	_
14	the	the	DT	_	_	_
15	solution	solution	NN	_	_	_
16	to	to	TO	_	_	_
17	an	a	DT	_	_	_
18	RNeasy	rneasy	NN	_	_	_
19	Mini	Mini	NNP	_	_	_
20	column	column	NN	_	_	_
21	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	was	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	centrifuged	centrifuge	VBN	_	_	_
5	for	for	IN	_	_	_
6	15	15	CD	_	_	_
7	s	s	NNS	_	_	_
8	at	at	IN	_	_	_
9	8,000	8,000	CD	_	_	_
10	x	x	CC	_	_	_
11	g.	g.	NNP	_	_	_
12	Buffer	Buffer	NNP	_	_	_
13	RW1	rw1	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	700	700	CD	_	_	_
16	μl	μl	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	was	be	VBD	_	_	_
19	applied	apply	VBN	_	_	_
20	to	to	TO	_	_	_
21	the	the	DT	_	_	_
22	column	column	NN	_	_	_
23	and	and	CC	_	_	_
24	centrifuged	centrifuge	VBN	_	_	_
25	to	to	TO	_	_	_
26	wash	wash	VB	_	_	_
27	the	the	DT	_	_	_
28	RNA	rna	NN	_	_	_
29	.	.	.	_	_	_

1	At	at	IN	_	_	_
2	this	this	DT	_	_	_
3	point	point	NN	_	_	_
4	an	a	DT	_	_	_
5	RNase-free	rnase-free	JJ	_	_	_
6	DNase	dnase	NN	_	_	_
7	on-column	on-column	JJ	_	_	_
8	digest	digest	VB	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Qiagen	Qiagen	NNP	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	was	be	VBD	_	_	_
13	carried	carry	VBN	_	_	_
14	out	out	RP	_	_	_
15	,	,	,	_	_	_
16	before	before	IN	_	_	_
17	the	the	DT	_	_	_
18	wash	wash	NN	_	_	_
19	process	process	NN	_	_	_
20	was	be	VBD	_	_	_
21	repeated	repeat	VBN	_	_	_
22	twice	twice	RB	_	_	_
23	with	with	IN	_	_	_
24	500	500	CD	_	_	_
25	μl	μl	NN	_	_	_
26	of	of	IN	_	_	_
27	RPE	rpe	NN	_	_	_
28	buffer	buffer	NN	_	_	_
29	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	eluted	elute	VBN	_	_	_
5	twice	twice	RB	_	_	_
6	in	in	IN	_	_	_
7	one	one	CD	_	_	_
8	30	30	CD	_	_	_
9	μl	μl	NN	_	_	_
10	volume	volume	NN	_	_	_
11	of	of	IN	_	_	_
12	RNase-free	rnase-free	JJ	_	_	_
13	water	water	NN	_	_	_
14	and	and	CC	_	_	_
15	stored	store	VBD	_	_	_
16	at	at	IN	_	_	_
17	-70	-70	CD	_	_	_
18	oC	oc	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Colony	Colony	NNP	_	_	_
3	Biofilm	Biofilm	NNP	_	_	_
4	Replicate	replicate	VB	_	_	_
5	1	1	CD	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	Colony	Colony	NNP	_	_	_
8	Biofilm	Biofilm	NNP	_	_	_
9	Replicate	replicate	VB	_	_	_
10	2	2	CD	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	Colony	Colony	NNP	_	_	_
13	Biofilm	Biofilm	NNP	_	_	_
14	Replicate	replicate	VB	_	_	_
15	3	3	CD	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Colony	Colony	NNP	_	_	_
18	Biofilm	Biofilm	NNP	_	_	_
19	Replicate	replicate	VB	_	_	_
20	4	4	CD	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	Escherichia	escherichia	FW	Organism	_	_
23	coli	coli	FW	Organism	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Escherichia	escherichia	FW	Organism	_	_
26	coli	coli	FW	Organism	_	_
27	Colony	Colony	NNP	_	_	_
28	Biofilm	Biofilm	NNP	_	_	_
29	Interior	Interior	NNP	_	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
31	Escherichia	escherichia	FW	Organism	_	_
32	coli	coli	FW	Organism	_	_
33	Colony	Colony	NNP	_	_	_
34	Biofilm	Biofilm	NNP	_	_	_
35	Perimeter	Perimeter	NNP	_	_	_
36	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
37	strain	strain	NN	_	_	_
38	:	:	:	_	_	_
39	TG-1	tg-1	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	strain	strain	NN	_	_	_
42	:	:	:	_	_	_
43	TG-2	tg-2	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
45	The	the	DT	_	_	_
46	average	average	JJ	_	_	_
47	fluorescent	fluorescent	JJ	_	_	_
48	signal	signal	NN	_	_	_
49	intensity	intensity	NN	_	_	_
50	and	and	CC	_	_	_
51	local	local	JJ	_	_	_
52	background	background	NN	_	_	_
53	correction	correction	NN	_	_	_
54	for	for	IN	_	_	_
55	each	each	DT	_	_	_
56	spot	spot	NN	_	_	_
57	were	be	VBD	_	_	_
58	obtained	obtain	VBN	_	_	_
59	using	use	VBG	_	_	_
60	commercially	commercially	RB	_	_	_
61	available	available	JJ	_	_	_
62	software	software	NN	_	_	_
63	from	from	IN	_	_	_
64	Biodiscovery	Biodiscovery	NNP	_	_	_
65	Inc	Inc	NNP	_	_	_
66	-LRB-	-lrb-	-LRB-	_	_	_
67	Imagene	Imagene	NNP	_	_	_
68	,	,	,	_	_	_
69	version	version	NN	_	_	_
70	4.0	4.0	CD	_	_	_
71	and	and	CC	_	_	_
72	Genesight	Genesight	NNP	_	_	_
73	,	,	,	_	_	_
74	version	version	NN	_	_	_
75	3.5	3.5	CD	_	_	_
76	-RRB-	-rrb-	-RRB-	_	_	_
77	.	.	.	_	_	_

1	Spots	spot	NNS	_	_	_
2	with	with	IN	_	_	_
3	a	a	DT	_	_	_
4	signal	signal	NN	_	_	_
5	intensity	intensity	NN	_	_	_
6	lower	lower	JJR	_	_	_
7	than	than	IN	_	_	_
8	the	the	DT	_	_	_
9	background	background	NN	_	_	_
10	signal	signal	NN	_	_	_
11	or	or	CC	_	_	_
12	those	those	DT	_	_	_
13	with	with	IN	_	_	_
14	blemishes	blemish	NNS	_	_	_
15	were	be	VBD	_	_	_
16	omitted	omit	VBN	_	_	_
17	from	from	IN	_	_	_
18	subsequent	subsequent	JJ	_	_	_
19	analysis	analysis	NN	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	mean	mean	NN	_	_	_
3	values	value	NNS	_	_	_
4	from	from	IN	_	_	_
5	each	each	DT	_	_	_
6	channel	channel	NN	_	_	_
7	were	be	VBD	_	_	_
8	then	then	RB	_	_	_
9	log2	log2	NN	_	_	_
10	transformed	transform	VBN	_	_	_
11	and	and	CC	_	_	_
12	normalised	normalise	VBN	_	_	_
13	using	use	VBG	_	_	_
14	the	the	DT	_	_	_
15	LOWESS	lowess	NN	_	_	_
16	method	method	NN	_	_	_
17	to	to	TO	_	_	_
18	remove	remove	VB	_	_	_
19	intensity-dependent	intensity-dependent	JJ	_	_	_
20	effects	effect	NNS	_	_	_
21	in	in	IN	_	_	_
22	the	the	DT	_	_	_
23	log2	log2	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	ratios	ratio	NNS	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	values	value	NNS	_	_	_
28	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	Cy3	cy3	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	A-stat	a-stat	NN	_	_	_
5	gene	gene	NN	_	_	_
6	expression	expression	NN	_	_	_
7	changes	change	NNS	_	_	_
8	0.3	0.3	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	A-stat	a-stat	NN	_	_	_
11	gene	gene	NN	_	_	_
12	expression	expression	NN	_	_	_
13	changes	change	NNS	_	_	_
14	0.47	0.47	CD	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	Escherichia	escherichia	FW	Organism	_	_
17	coli	coli	FW	Organism	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Escherichia	escherichia	FW	Organism	_	_
20	coli	coli	FW	Organism	_	_
21	K12	k12	NN	_	_	_
22	MG1655	mg1655	NN	_	_	_
23	were	be	VBD	_	_	_
24	grown	grow	VBN	_	_	_
25	in	in	IN	_	_	_
26	M9	m9	NN	MED	_	_
27	minimal	minimal	JJ	MED	_	_
28	medium	medium	NN	MED	_	_
29	with	with	IN	_	_	_
30	10	10	CD	_	_	_
31	g	g	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	specific	specific	JJ	_	_	_
34	growth	growth	NN	_	_	_
35	rate	rate	NN	_	_	_
36	:	:	:	_	_	_
37	0.3	0.3	CD	_	_	_
38	h-1	h-1	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
40	Specific	specific	JJ	_	_	_
41	growth	growth	NN	_	_	_
42	rate	rate	NN	_	_	_
43	0.3	0.3	CD	_	_	_
44	h-1	h-1	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	specific	specific	JJ	_	_	_
47	growth	growth	NN	_	_	_
48	rate	rate	NN	_	_	_
49	:	:	:	_	_	_
50	0.47	0.47	CD	_	_	_
51	h-1	h-1	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
53	Specific	specific	JJ	_	_	_
54	growth	growth	NN	_	_	_
55	rate	rate	NN	_	_	_
56	0.47	0.47	CD	_	_	_
57	h-1	h-1	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	Spot	spot	NN	_	_	_
60	intensities	intensity	NNS	_	_	_
61	and	and	CC	_	_	_
62	corresponding	corresponding	JJ	_	_	_
63	background	background	NN	_	_	_
64	signals	signal	NNS	_	_	_
65	were	be	VBD	_	_	_
66	quantified	quantify	VBN	_	_	_
67	with	with	IN	_	_	_
68	Genepix	Genepix	NNP	_	_	_
69	Pro	pro	FW	_	_	_
70	-LRB-	-lrb-	-LRB-	_	_	_
71	version	version	NN	_	_	_
72	6	6	CD	_	_	_
73	;	;	:	_	_	_
74	Axon	Axon	NNP	_	_	_
75	Instruments	Instruments	NNPS	_	_	_
76	-LSB-	-lsb-	-LRB-	_	_	_
77	http	http	NN	_	_	_
78	:	:	:	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	strain	strain	NN	_	_	_
81	:	:	:	_	_	_
82	Escherichia	escherichia	FW	Organism	_	_
83	coli	coli	FW	Organism	_	_
84	K12	k12	NN	_	_	_
85	MG1655	mg1655	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	Total	total	JJ	_	_	_
88	RNA	rna	NN	_	_	_
89	was	be	VBD	_	_	_
90	extracted	extract	VBN	_	_	_
91	using	use	VBG	_	_	_
92	RNeasy	RNeasy	NNP	_	_	_
93	Mini	Mini	NNP	_	_	_
94	Kit	kit	NN	_	_	_
95	-LRB-	-lrb-	-LRB-	_	_	_
96	QIAGEN	QIAGEN	NNP	_	_	_
97	,	,	,	_	_	_
98	Valencia	Valencia	NNP	_	_	_
99	,	,	,	_	_	_
100	CA	CA	NNP	_	_	_
101	-RRB-	-rrb-	-RRB-	_	_	_
102	and	and	CC	_	_	_
103	the	the	DT	_	_	_
104	genomic	genomic	JJ	_	_	_
105	DNA	dna	NN	_	_	_
106	was	be	VBD	_	_	_
107	removed	remove	VBN	_	_	_
108	using	use	VBG	_	_	_
109	RNase-Free	rnase-free	JJ	_	_	_
110	DNase	dnase	NN	_	_	_
111	Set	set	VB	_	_	_
112	-LRB-	-lrb-	-LRB-	_	_	_
113	QIAGEN	QIAGEN	NNP	_	_	_
114	-RRB-	-rrb-	-RRB-	_	_	_
115	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	After	after	IN	_	_	_
3	collecting	collect	VBG	_	_	_
4	50	50	CD	_	_	_
5	ml	ml	NN	_	_	_
6	culture	culture	NN	_	_	_
7	as	as	IN	_	_	_
8	`	`	``	_	_	_
9	non	non	JJ	_	_	_
10	crosslinked	crosslink	VBN	_	_	_
11	'	'	''	_	_	_
12	sample	sample	NN	_	_	_
13	,	,	,	_	_	_
14	the	the	DT	_	_	_
15	rest	rest	NN	_	_	_
16	of	of	IN	_	_	_
17	the	the	DT	_	_	_
18	cells	cell	NNS	_	_	_
19	was	be	VBD	_	_	_
20	crosslinked.Crosslinked	crosslinked.crosslinked	VBN	_	_	_
21	and	and	CC	_	_	_
22	non	non	JJ	_	_	_
23	crosslinked	crosslink	VBN	_	_	_
24	cells	cell	NNS	_	_	_
25	were	be	VBD	_	_	_
26	washed	wash	VBN	_	_	_
27	and	and	CC	_	_	_
28	sonicated	sonicate	VBN	_	_	_
29	.	.	.	_	_	_

1	400	400	CD	_	_	_
2	µl	µl	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	sonicated	sonicated	JJ	_	_	_
6	extracts	extract	NNS	_	_	_
7	were	be	VBD	_	_	_
8	mixed	mix	VBN	_	_	_
9	with	with	IN	_	_	_
10	400	400	CD	_	_	_
11	µl	µl	NN	_	_	_
12	TE	te	NN	_	_	_
13	buffer	buffer	NN	_	_	_
14	and	and	CC	_	_	_
15	incubated	incubate	VBN	_	_	_
16	with	with	IN	_	_	_
17	2	2	CD	_	_	_
18	µl	µl	NN	_	_	_
19	RNase	rnase	NN	_	_	_
20	A	a	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	20	20	CD	_	_	_
23	mg	mg	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Cells	cell	NNS	_	_	_
26	were	be	VBD	_	_	_
27	grown	grow	VBN	_	_	_
28	at	at	IN	_	_	_
29	37	37	CD	_	_	_
30	°C	°c	NN	_	_	_
31	to	to	TO	_	_	_
32	an	a	DT	_	_	_
33	OD600	od600	NN	_	_	_
34	of	of	IN	_	_	_
35	about	about	IN	_	_	_
36	0.15	0.15	CD	_	_	_
37	in	in	IN	_	_	_
38	100	100	CD	_	_	_
39	ml	ml	NN	_	_	_
40	LB	lb	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	+	+	CC	_	_	_
43	0.2	0.2	CD	_	_	_
44	%	%	NN	_	_	_
45	glucose	glucose	NN	SUPP	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	at	at	IN	_	_	_
6	37	37	CD	_	_	_
7	°C	°c	NN	_	_	_
8	to	to	TO	_	_	_
9	an	a	DT	_	_	_
10	OD600	od600	NN	_	_	_
11	of	of	IN	_	_	_
12	about	about	IN	_	_	_
13	0.15	0.15	CD	_	_	_
14	in	in	IN	_	_	_
15	50	50	CD	_	_	_
16	ml	ml	NN	_	_	_
17	LB	lb	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	+	+	CC	_	_	_
20	0.2	0.2	CD	_	_	_
21	%	%	NN	_	_	_
22	glucose	glucose	NN	SUPP	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	before	before	IN	_	_	_
25	crosslinking	crosslink	VBG	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	65	65	CD	_	_	_
7	ml	ml	NN	_	_	_
8	LB	lb	NN	MED	_	_
9	medium	medium	NN	MED	_	_
10	at	at	IN	_	_	_
11	30	30	CD	_	_	_
12	°C	°c	NN	_	_	_
13	to	to	TO	_	_	_
14	an	a	DT	_	_	_
15	OD600	od600	NN	_	_	_
16	of	of	IN	_	_	_
17	about	about	IN	_	_	_
18	0.3	0.3	CD	_	_	_
19	.	.	.	_	_	_

1	Subsequently	subsequently	RB	_	_	_
2	30	30	CD	_	_	_
3	ml	ml	NN	_	_	_
4	of	of	IN	_	_	_
5	culture	culture	NN	_	_	_
6	were	be	VBD	_	_	_
7	transformed	transform	VBN	_	_	_
8	to	to	TO	_	_	_
9	a	a	DT	_	_	_
10	pre	pre	JJ	_	_	_
11	warmed	warm	VBN	_	_	_
12	flask	flask	NN	_	_	_
13	at	at	IN	_	_	_
14	43	43	CD	_	_	_
15	°C	°c	NN	_	_	_
16	and	and	CC	_	_	_
17	the	the	DT	_	_	_
18	remainder	remainder	NN	_	_	_
19	kept	keep	VBD	_	_	_
20	at	at	IN	_	_	_
21	30	30	CD	_	_	_
22	°C	°c	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	see	see	VB	_	_	_
25	control	control	JJ	_	_	_
26	sample	sample	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	65	65	CD	_	_	_
7	ml	ml	NN	_	_	_
8	LB	lb	NN	MED	_	_
9	medium	medium	NN	MED	_	_
10	at	at	IN	_	_	_
11	30	30	CD	_	_	_
12	°C	°c	NN	_	_	_
13	to	to	TO	_	_	_
14	an	a	DT	_	_	_
15	OD600	od600	NN	_	_	_
16	of	of	IN	_	_	_
17	about	about	IN	_	_	_
18	0.3	0.3	CD	_	_	_
19	.	.	.	_	_	_

1	Subsequently	subsequently	RB	_	_	_
2	30	30	CD	_	_	_
3	ml	ml	NN	_	_	_
4	of	of	IN	_	_	_
5	culture	culture	NN	_	_	_
6	were	be	VBD	_	_	_
7	transformed	transform	VBN	_	_	_
8	to	to	TO	_	_	_
9	a	a	DT	_	_	_
10	pre	pre	JJ	_	_	_
11	warmed	warm	VBN	_	_	_
12	flask	flask	NN	_	_	_
13	at	at	IN	_	_	_
14	43	43	CD	_	_	_
15	°C	°c	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	see	see	VB	_	_	_
18	heat	heat	NN	_	_	_
19	sample	sample	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	and	and	CC	_	_	_
22	the	the	DT	_	_	_
23	remainder	remainder	NN	_	_	_
24	kept	keep	VBD	_	_	_
25	at	at	IN	_	_	_
26	30	30	CD	_	_	_
27	°C	°c	NN	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	chip	chip	NN	_	_	_
3	antibody	antibody	NN	_	_	_
4	:	:	:	_	_	_
5	none	none	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	chip	chip	NN	_	_	_
8	antibody	antibody	NN	_	_	_
9	:	:	:	_	_	_
10	RNA	rna	NN	_	_	_
11	polymerase	polymerase	NN	_	_	_
12	subunit	subunit	NN	_	_	_
13	β	β	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
15	chip	chip	NN	_	_	_
16	antibody	antibody	NN	_	_	_
17	:	:	:	_	_	_
18	SeqA	seqa	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	chip	chip	NN	_	_	_
21	antibody	antibody	NN	_	_	_
22	:	:	:	_	_	_
23	σ32	σ32	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Crosslink	Crosslink	NNP	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	Crosslinked	Crosslinked	NNP	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	Cultures	culture	NNS	_	_	_
30	of	of	IN	_	_	_
31	E.	e.	FW	_	_	_
32	coli	coli	FW	_	_	_
33	MG1655	mg1655	NN	_	_	_
34	and	and	CC	_	_	_
35	its	its	PRP$	_	_	_
36	derivates	derivate	NNS	_	_	_
37	were	be	VBD	_	_	_
38	cross	cross	JJ	_	_	_
39	linked	link	VBN	_	_	_
40	by	by	IN	_	_	_
41	addition	addition	NN	_	_	_
42	of	of	IN	_	_	_
43	27	27	CD	_	_	_
44	µl	µl	NN	_	_	_
45	of	of	IN	_	_	_
46	formaldehyde	formaldehyde	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	37	37	CD	_	_	_
49	%	%	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	per	per	IN	_	_	_
52	ml	ml	NN	_	_	_
53	medium	medium	NN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	final	final	JJ	_	_	_
56	concentration	concentration	NN	_	_	_
57	1	1	CD	_	_	_
58	%	%	NN	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	.	.	.	_	_	_

1	Crosslinking	crosslinking	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	at	at	IN	_	_	_
5	slow	slow	JJ	_	_	_
6	shaking	shake	VBG	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	100	100	CD	_	_	_
9	rpm	rpm	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	for	for	IN	_	_	_
12	20	20	CD	_	_	_
13	min	min	NN	_	_	_
14	followed	follow	VBN	_	_	_
15	by	by	IN	_	_	_
16	quenching	quench	VBG	_	_	_
17	with	with	IN	_	_	_
18	0.2	0.2	CD	_	_	_
19	ml	ml	NN	_	_	_
20	of	of	IN	_	_	_
21	2.5	2.5	CD	_	_	_
22	M	m	NN	_	_	_
23	glycine	glycine	NN	_	_	_
24	per	per	IN	_	_	_
25	ml	ml	NN	_	_	_
26	medium	medium	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	final	final	JJ	_	_	_
29	concentration	concentration	NN	_	_	_
30	0.5	0.5	CD	_	_	_
31	M	m	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	collected	collect	VBN	_	_	_
4	by	by	IN	_	_	_
5	centrifugation	centrifugation	NN	_	_	_
6	and	and	CC	_	_	_
7	washed	wash	VBN	_	_	_
8	twice	twice	RB	_	_	_
9	with	with	IN	_	_	_
10	cold	cold	JJ	_	_	_
11	TBS	tbs	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	pH7	ph7	NN	_	_	_
14	.5	.5	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	resuspension	resuspension	NN	_	_	_
3	in	in	IN	_	_	_
4	1	1	CD	_	_	_
5	ml	ml	NN	_	_	_
6	lysis	lysis	NN	_	_	_
7	buffer	buffer	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	10mM	10mm	NN	_	_	_
10	Tris	tris	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	pH	ph	NN	_	_	_
13	8.0	8.0	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	20	20	CD	_	_	_
17	%	%	NN	_	_	_
18	sucrose	sucrose	NN	_	_	_
19	,	,	,	_	_	_
20	50mM	50mm	NN	_	_	_
21	NaCl	nacl	NN	_	_	_
22	,	,	,	_	_	_
23	10mM	10mm	NN	_	_	_
24	EDTA	edta	NN	_	_	_
25	,	,	,	_	_	_
26	10	10	CD	_	_	_
27	mg	mg	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Escherichia	escherichia	FW	Organism	_	_
30	coli	coli	FW	Organism	_	_
31	str	str	FW	_	_	_
32	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	fraction	fraction	NN	_	_	_
4	:	:	:	_	_	_
5	input	input	NN	_	_	_
6	DNA	dna	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	fraction	fraction	NN	_	_	_
9	:	:	:	_	_	_
10	input	input	NN	_	_	_
11	DNA	dna	NN	_	_	_
12	,	,	,	_	_	_
13	SeqA	seqa	NN	_	_	_
14	ChIP	chip	NN	_	_	_
15	supernatant	supernatant	JJ	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	fraction	fraction	NN	_	_	_
18	:	:	:	_	_	_
19	input	input	NN	_	_	_
20	DNA	dna	NN	_	_	_
21	,	,	,	_	_	_
22	σ32	σ32	NN	_	_	_
23	ChIP	chip	NN	_	_	_
24	supernatant	supernatant	JJ	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	genotype	genotype	NN	_	_	_
27	:	:	:	_	_	_
28	wildtype	wildtype	JJ	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	genotype	genotype	NN	_	_	_
31	:	:	:	_	_	_
32	ΔseqA	δseqa	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Input	input	NN	_	_	_
35	DNA	dna	NN	_	_	_
36	from	from	IN	_	_	_
37	E.	E.	NNP	_	_	_
38	Coli	Coli	NNP	_	_	_
39	MG1655	MG1655	NNP	_	_	_
40	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
41	Input	Input	NNP	_	_	_
42	DNA	dna	NN	_	_	_
43	from	from	IN	_	_	_
44	E.	E.	NNP	_	_	_
45	Coli	Coli	NNP	_	_	_
46	MG1655	MG1655	NNP	_	_	_
47	ΔseqA	ΔseqA	NNP	_	_	_
48	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
49	Input	Input	NNP	_	_	_
50	DNA	dna	NN	_	_	_
51	from	from	IN	_	_	_
52	SeqA	seqa	NN	_	_	_
53	ChIP	chip	NN	_	_	_
54	supernatant	supernatant	JJ	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	Input	input	NN	_	_	_
57	DNA	dna	NN	_	_	_
58	from	from	IN	_	_	_
59	ΔseqA-SeqA	δseqa-seqa	NN	_	_	_
60	ChIP	chip	NN	_	_	_
61	supernatant	supernatant	JJ	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	Input	input	NN	_	_	_
64	DNA	dna	NN	_	_	_
65	from	from	IN	_	_	_
66	σ32	σ32	NN	_	_	_
67	ChIP	chip	NN	_	_	_
68	supernatant	supernatant	JJ	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	Non-crosslinked	non-crosslinked	JJ	_	_	_
71	DNA	dna	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	RNAP	rnap	NN	_	_	_
74	ChIP	chip	NN	_	_	_
75	DNA	dna	NN	_	_	_
76	,	,	,	_	_	_
77	old	old	JJ	_	_	_
78	protocol	protocol	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	RNAP	rnap	NN	_	_	_
81	old	old	JJ	_	_	_
82	rep1	rep1	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	RNAP	rnap	NN	_	_	_
85	old	old	JJ	_	_	_
86	rep2	rep2	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	SeqA	seqa	NN	_	_	_
89	ChIP	chip	NN	_	_	_
90	DNA	dna	NN	_	_	_
91	,	,	,	_	_	_
92	new	new	JJ	_	_	_
93	protocol	protocol	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	SeqA	seqa	NN	_	_	_
96	ChIP	chip	NN	_	_	_
97	DNA	dna	NN	_	_	_
98	,	,	,	_	_	_
99	old	old	JJ	_	_	_
100	protocol	protocol	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	SeqA	seqa	NN	_	_	_
103	new	new	JJ	_	_	_
104	deltaSeqA	deltaseqa	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	SeqA	seqa	NN	_	_	_
107	new	new	JJ	_	_	_
108	rep1	rep1	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	SeqA	seqa	NN	_	_	_
111	new	new	JJ	_	_	_
112	rep2	rep2	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	SeqA	seqa	NN	_	_	_
115	old	old	JJ	_	_	_
116	deltaSeqA	deltaseqa	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	SeqA	seqa	NN	_	_	_
119	old	old	JJ	_	_	_
120	rep1	rep1	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	SeqA	seqa	NN	_	_	_
123	old	old	JJ	_	_	_
124	rep2	rep2	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	Spot	spot	NN	_	_	_
127	intensities	intensity	NNS	_	_	_
128	were	be	VBD	_	_	_
129	extracted	extract	VBN	_	_	_
130	using	use	VBG	_	_	_
131	the	the	DT	_	_	_
132	Feature	Feature	NNP	_	_	_
133	Extraction	extraction	NN	_	_	_
134	software	software	NN	_	_	_
135	10.5.1.1	10.5.1.1	CD	_	_	_
136	from	from	IN	_	_	_
137	Applied	Applied	NNP	_	_	_
138	Biosystems	Biosystems	NNPS	_	_	_
139	with	with	IN	_	_	_
140	a	a	DT	_	_	_
141	linear	linear	JJ	_	_	_
142	dye	dye	VB	_	_	_
143	normalization	normalization	NN	_	_	_
144	correction	correction	NN	_	_	_
145	method	method	NN	_	_	_
146	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	gProcessedSignal	gprocessedsignal	NN	_	_	_
3	and	and	CC	_	_	_
4	rProcessedSignal	rprocessedsignal	NN	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	for	for	IN	_	_	_
8	further	further	JJ	_	_	_
9	analysis	analysis	NN	_	_	_
10	with	with	IN	_	_	_
11	the	the	DT	_	_	_
12	statistics	statistics	NNS	_	_	_
13	software	software	NN	_	_	_
14	R.	R.	NNP	_	_	_
15	Ratios	Ratios	NNP	_	_	_
16	of	of	IN	_	_	_
17	g	g	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	sample	sample	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	to	to	TO	_	_	_
22	r	r	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	control	control	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	were	be	VBD	_	_	_
27	calculated	calculate	VBN	_	_	_
28	after	after	IN	_	_	_
29	background	background	NN	_	_	_
30	substraction	substraction	NN	_	_	_
31	and	and	CC	_	_	_
32	normalized	normalize	VBD	_	_	_
33	to	to	TO	_	_	_
34	the	the	DT	_	_	_
35	array	array	NN	_	_	_
36	wide	wide	JJ	_	_	_
37	average	average	NN	_	_	_
38	.	.	.	_	_	_

1	Data	datum	NNS	_	_	_
2	points	point	NNS	_	_	_
3	with	with	IN	_	_	_
4	a	a	DT	_	_	_
5	value	value	NN	_	_	_
6	below	below	IN	_	_	_
7	0	0	CD	_	_	_
8	after	after	IN	_	_	_
9	background	background	NN	_	_	_
10	subtraction	subtraction	NN	_	_	_
11	were	be	VBD	_	_	_
12	set	set	VBN	_	_	_
13	`	`	``	_	_	_
14	null	null	NN	_	_	_
15	'	'	''	_	_	_
16	.	.	.	_	_	_

1	Data	datum	NNS	_	_	_
2	points	point	NNS	_	_	_
3	form	form	VBP	_	_	_
4	non-unique	non-unique	JJ	_	_	_
5	regions	region	NNS	_	_	_
6	on	on	IN	_	_	_
7	the	the	DT	_	_	_
8	chromosome	chromosome	NN	_	_	_
9	were	be	VBD	_	_	_
10	excluded	exclude	VBN	_	_	_
11	from	from	IN	_	_	_
12	analysis	analysis	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	strain	strain	NN	_	_	_
7	:	:	:	_	_	_
8	MG1655	mg1655	NN	_	_	_
9	ΔseqA	δseqa	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	σ32	σ32	NN	_	_	_
12	30	30	CD	_	_	_
13	°C	°c	NN	_	_	_
14	rep1	rep1	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	σ32	σ32	NN	_	_	_
17	30	30	CD	_	_	_
18	°C	°c	NN	_	_	_
19	rep2	rep2	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	σ32	σ32	NN	_	_	_
22	30	30	CD	_	_	_
23	°C	°c	NN	_	_	_
24	short	short	JJ	_	_	_
25	RNase	rnase	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	σ32	σ32	NN	_	_	_
28	43	43	CD	_	_	_
29	°C	°c	NN	_	_	_
30	rep1	rep1	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	σ32	σ32	NN	_	_	_
33	43	43	CD	_	_	_
34	°C	°c	NN	_	_	_
35	rep2	rep2	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	σ32	σ32	NN	_	_	_
38	43	43	CD	_	_	_
39	°C	°c	NN	_	_	_
40	short	short	JJ	_	_	_
41	RNase	rnase	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	σ32	σ32	NN	_	_	_
44	ChIP	chip	NN	_	_	_
45	DNA	dna	NN	_	_	_
46	,	,	,	_	_	_
47	control	control	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	σ32	σ32	NN	_	_	_
50	ChIP	chip	NN	_	_	_
51	DNA	dna	NN	_	_	_
52	,	,	,	_	_	_
53	heat	heat	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	σ32	σ32	NN	_	_	_
56	ChIP	chip	NN	_	_	_
57	DNA	dna	NN	_	_	_
58	,	,	,	_	_	_
59	short	short	JJ	_	_	_
60	RNase	rnase	NN	_	_	_
61	digestion	digestion	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	At	at	IN	_	_	_
64	OD600	od600	NN	_	_	_
65	~	~	NN	_	_	_
66	0.3	0.3	CD	_	_	_
67	,	,	,	_	_	_
68	serine	serine	NN	_	_	_
69	hydroxamate	hydroxamate	NN	_	_	_
70	was	be	VBD	_	_	_
71	added	add	VBN	_	_	_
72	to	to	TO	_	_	_
73	a	a	DT	_	_	_
74	final	final	JJ	_	_	_
75	concentration	concentration	NN	_	_	_
76	of	of	IN	_	_	_
77	0.5	0.5	CD	_	_	_
78	mg	mg	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	Cells	cell	NNS	_	_	_
81	were	be	VBD	_	_	_
82	grown	grow	VBN	_	_	_
83	in	in	IN	_	_	_
84	M9	m9	NN	_	_	_
85	medium	medium	NN	_	_	_
86	supplemented	supplement	VBN	_	_	_
87	with	with	IN	_	_	_
88	0.2	0.2	CD	_	_	_
89	%	%	NN	_	_	_
90	glucose	glucose	NN	SUPP	_	_
91	and	and	CC	_	_	_
92	0.4	0.4	CD	_	_	_
93	%	%	NN	_	_	_
94	casamino	casamino	NN	_	_	_
95	acid	acid	NN	_	_	_
96	at	at	IN	_	_	_
97	37	37	CD	_	_	_
98	℃	℃	CD	_	_	_
99	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
100	Delta	Delta	NNP	_	_	_
101	dksA	dksA	NNP	GEN	_	_
102	Cells	cell	NNS	_	_	_
103	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
104	Delta	Delta	NNP	_	_	_
105	dksA	dksA	NNP	GEN	_	_
106	Cells	cell	NNS	_	_	_
107	Replicate	replicate	VB	_	_	_
108	1	1	CD	_	_	_
109	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
110	Delta	Delta	NNP	_	_	_
111	dksA	dksA	NNP	GEN	_	_
112	Cells	cell	NNS	_	_	_
113	Replicate	replicate	VB	_	_	_
114	2	2	CD	_	_	_
115	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
116	Delta	Delta	NNP	_	_	_
117	dksA	dksA	NNP	GEN	_	_
118	Cells	cell	NNS	_	_	_
119	Replicate	replicate	VB	_	_	_
120	3	3	CD	_	_	_
121	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
122	Escherichia	escherichia	FW	Organism	_	_
123	coli	coli	FW	Organism	_	_
124	str	str	FW	_	_	_
125	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	GenePix	GenePix	NNP	_	_	_
4	Pro	pro	FW	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	v	v	LS	_	_	_
7	6.1	6.1	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	was	be	VBD	_	_	_
10	used	use	VBN	_	_	_
11	for	for	IN	_	_	_
12	background	background	NN	_	_	_
13	subtraction	subtraction	NN	_	_	_
14	and	and	CC	_	_	_
15	normalization	normalization	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	growth	growth	NN	_	_	_
3	stage	stage	NN	_	_	_
4	:	:	:	_	_	_
5	log	log	NN	_	_	_
6	phase	phase	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	pooled	pool	VBD	_	_	_
9	reference	reference	NN	_	_	_
10	RNA	rna	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	RNA	rna	NN	_	_	_
13	was	be	VBD	_	_	_
14	extracted	extract	VBN	_	_	_
15	using	use	VBG	_	_	_
16	QIAGEN	QIAGEN	NNP	_	_	_
17	RNeasy	RNeasy	NNP	_	_	_
18	Mini	Mini	NNP	_	_	_
19	Kit	kit	NN	_	_	_
20	following	follow	VBG	_	_	_
21	manufacturer	manufacturer	NN	_	_	_
22	's	's	POS	_	_	_
23	instructions	instruction	NNS	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	SHX-treated	shx-treated	JJ	_	_	_
3	Delta	delta	NN	_	_	_
4	dksA	dksa	NN	GEN	_	_
5	Cells	cell	NNS	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	SHX-treated	shx-treated	JJ	_	_	_
8	Delta	delta	NN	_	_	_
9	dksA	dksa	NN	GEN	_	_
10	Cells	cell	NNS	_	_	_
11	Replicate	replicate	VB	_	_	_
12	1	1	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	SHX-treated	shx-treated	JJ	_	_	_
15	Delta	delta	NN	_	_	_
16	dksA	dksa	NN	GEN	_	_
17	Cells	cell	NNS	_	_	_
18	Replicate	replicate	VB	_	_	_
19	2	2	CD	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
21	SHX-treated	shx-treated	JJ	_	_	_
22	Delta	delta	NN	_	_	_
23	dksA	dksa	NN	GEN	_	_
24	Cells	cell	NNS	_	_	_
25	Replicate	replicate	VB	_	_	_
26	3	3	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	SHX-treated	shx-treated	JJ	_	_	_
29	Wild-type	wild-type	JJ	_	_	_
30	Cells	cell	NNS	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	SHX-treated	shx-treated	JJ	_	_	_
33	Wild-type	wild-type	JJ	_	_	_
34	Cells	cell	NNS	_	_	_
35	Replicate	replicate	VB	_	_	_
36	1	1	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	SHX-treated	shx-treated	JJ	_	_	_
39	Wild-type	wild-type	JJ	_	_	_
40	Cells	cell	NNS	_	_	_
41	Replicate	replicate	VB	_	_	_
42	2	2	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
44	SHX-treated	shx-treated	JJ	_	_	_
45	Wild-type	wild-type	JJ	_	_	_
46	Cells	cell	NNS	_	_	_
47	Replicate	replicate	VB	_	_	_
48	3	3	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	strain	strain	NN	_	_	_
51	:	:	:	_	_	_
52	MG1655	mg1655	NN	_	_	_
53	delta	delta	NN	_	_	_
54	lac	lac	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	strain	strain	NN	_	_	_
57	:	:	:	_	_	_
58	MG1655	mg1655	NN	_	_	_
59	delta	delta	NN	_	_	_
60	lac	lac	NN	_	_	_
61	delta	delta	NN	_	_	_
62	dksA	dksa	NN	GEN	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	strain	strain	NN	_	_	_
65	:	:	:	_	_	_
66	MG1655	mg1655	NN	_	_	_
67	delta	delta	NN	_	_	_
68	lac	lac	NN	_	_	_
69	+	+	CC	_	_	_
70	MG1655	mg1655	NN	_	_	_
71	delta	delta	NN	_	_	_
72	lac	lac	NN	_	_	_
73	delta	delta	NN	_	_	_
74	dksA	dksa	NN	GEN	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	treatment	treatment	NN	_	_	_
77	:	:	:	_	_	_
78	0.5	0.5	CD	_	_	_
79	mg	mg	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	treatment	treatment	NN	_	_	_
82	:	:	:	_	_	_
83	No	no	DT	_	_	_
84	treatment	treatment	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	treatment	treatment	NN	_	_	_
87	:	:	:	_	_	_
88	Pooled	pool	VBN	_	_	_
89	RNA	rna	NN	_	_	_
90	from	from	IN	_	_	_
91	mixture	mixture	NN	_	_	_
92	of	of	IN	_	_	_
93	the	the	DT	_	_	_
94	same	same	JJ	_	_	_
95	amount	amount	NN	_	_	_
96	of	of	IN	_	_	_
97	wt	wt	JJ	_	_	_
98	,	,	,	_	_	_
99	wt	wt	JJ	_	_	_
100	+	+	CC	_	_	_
101	SHX	shx	NN	_	_	_
102	,	,	,	_	_	_
103	dksA	dksa	NN	GEN	_	_
104	,	,	,	_	_	_
105	dksA	dksa	NN	GEN	_	_
106	+	+	CC	_	_	_
107	SHX	shx	NN	_	_	_
108	RNA	rna	NN	_	_	_
109	samples	sample	NNS	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	Wild-type	wild-type	JJ	_	_	_
112	Cells	cell	NNS	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
114	Wild-type	wild-type	JJ	_	_	_
115	Cells	cell	NNS	_	_	_
116	Replicate	replicate	VBP	_	_	_
117	1	1	CD	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	Wild-type	wild-type	JJ	_	_	_
120	Cells	cell	NNS	_	_	_
121	Replicate	replicate	VB	_	_	_
122	2	2	CD	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
124	Wild-type	wild-type	JJ	_	_	_
125	Cells	cell	NNS	_	_	_
126	Replicate	replicate	VB	_	_	_
127	3	3	CD	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	Biotinylated	biotinylate	VBN	_	_	_
130	GST	gst	NN	_	_	_
131	protein	protein	NN	_	_	_
132	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
133	Escherichia	escherichia	FW	Organism	_	_
134	coli	coli	FW	Organism	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	GSH-sepharose	gsh-sepharose	NN	_	_	_
137	4b	4b	NN	_	_	_
138	purification	purification	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	GST	gst	NN	_	_	_
141	control	control	NN	_	_	_
142	Protoarray	Protoarray	NNP	_	_	_
143	replicate	replicate	VB	_	_	_
144	1	1	CD	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	protein	protein	NN	_	_	_
147	:	:	:	_	_	_
148	GST	gst	NN	_	_	_
149	expressed	express	VBN	_	_	_
150	in	in	IN	_	_	_
151	E.	e.	FW	_	_	_
152	coli	coli	FW	_	_	_
153	BL21	bl21	NN	_	_	_
154	-LRB-	-lrb-	-LRB-	_	_	_
155	DE3	de3	NN	_	_	_
156	-RRB-	-rrb-	-RRB-	_	_	_
157	from	from	IN	_	_	_
158	pGEX-4T-3	pgex-4t-3	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	purification	purification	NN	_	_	_
161	:	:	:	_	_	_
162	Protein	protein	NN	_	_	_
163	purified	purify	VBN	_	_	_
164	using	use	VBG	_	_	_
165	GSH-sepharose	gsh-sepharose	JJ	_	_	_
166	4b	4b	NN	_	_	_
167	-LRB-	-lrb-	-LRB-	_	_	_
168	GE	GE	NNP	_	_	_
169	Life	Life	NNP	_	_	_
170	Sciences	Sciences	NNPS	_	_	_
171	-RRB-	-rrb-	-RRB-	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	Scanned	scan	VBN	_	_	_
174	spot	spot	NN	_	_	_
175	signals	signal	NNS	_	_	_
176	were	be	VBD	_	_	_
177	normalized	normalize	VBN	_	_	_
178	using	use	VBG	_	_	_
179	internal	internal	JJ	_	_	_
180	Protoarray	Protoarray	NNP	_	_	_
181	control	control	NN	_	_	_
182	proteins	protein	NNS	_	_	_
183	and	and	CC	_	_	_
184	Z	z	NN	_	_	_
185	scores	score	NNS	_	_	_
186	subsequently	subsequently	RB	_	_	_
187	determined	determine	VBD	_	_	_
188	based	base	VBN	_	_	_
189	on	on	IN	_	_	_
190	comparisons	comparison	NNS	_	_	_
191	of	of	IN	_	_	_
192	mean	mean	NN	_	_	_
193	signals	signal	NNS	_	_	_
194	for	for	IN	_	_	_
195	each	each	DT	_	_	_
196	spot	spot	NN	_	_	_
197	pair	pair	NN	_	_	_
198	to	to	TO	_	_	_
199	the	the	DT	_	_	_
200	mean	mean	NN	_	_	_
201	spot	spot	NN	_	_	_
202	intensity	intensity	NN	_	_	_
203	for	for	IN	_	_	_
204	the	the	DT	_	_	_
205	array	array	NN	_	_	_
206	.	.	.	_	_	_

1	Z	z	NN	_	_	_
2	scores	score	NNS	_	_	_
3	greater	greater	JJR	_	_	_
4	than	than	IN	_	_	_
5	3.0	3.0	CD	_	_	_
6	were	be	VBD	_	_	_
7	considered	consider	VBN	_	_	_
8	significant	significant	JJ	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	After	after	IN	_	_	_
11	the	the	DT	_	_	_
12	final	final	JJ	_	_	_
13	wash	wash	NN	_	_	_
14	&	&	CC	_	_	_
15	staining	staining	NN	_	_	_
16	step	step	NN	_	_	_
17	,	,	,	_	_	_
18	Affymetrix	Affymetrix	NNP	_	_	_
19	GeneChip	GeneChip	NNP	_	_	_
20	®	®	NNP	_	_	_
21	E.coli	E.coli	NNP	_	_	_
22	Genome	Genome	NNP	_	_	_
23	array	array	NN	_	_	_
24	was	be	VBD	_	_	_
25	scanned	scan	VBN	_	_	_
26	using	use	VBG	_	_	_
27	Affymetrix	Affymetrix	NNP	_	_	_
28	Model	Model	NNP	_	_	_
29	3000	3000	CD	_	_	_
30	G7	G7	NNP	_	_	_
31	scanner	scanner	NN	_	_	_
32	and	and	CC	_	_	_
33	the	the	DT	_	_	_
34	image	image	NN	_	_	_
35	data	datum	NNS	_	_	_
36	was	be	VBD	_	_	_
37	extracted	extract	VBN	_	_	_
38	through	through	IN	_	_	_
39	Affymetrix	Affymetrix	NNP	_	_	_
40	Commnad	Commnad	NNP	_	_	_
41	Console	Console	NNP	_	_	_
42	software	software	NN	_	_	_
43	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	raw	raw	JJ	_	_	_
3	.	.	.	_	_	_

1	cel	cel	NN	_	_	_
2	file	file	NN	_	_	_
3	generated	generate	VBN	_	_	_
4	through	through	IN	_	_	_
5	above	above	IN	_	_	_
6	procedure	procedure	NN	_	_	_
7	meant	mean	VBD	_	_	_
8	expression	expression	NN	_	_	_
9	intensity	intensity	NN	_	_	_
10	data	datum	NNS	_	_	_
11	and	and	CC	_	_	_
12	was	be	VBD	_	_	_
13	used	use	VBN	_	_	_
14	for	for	IN	_	_	_
15	the	the	DT	_	_	_
16	next	next	JJ	_	_	_
17	step	step	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	EDL	edl	NN	_	_	_
3	933	933	CD	_	_	_
4	at	at	IN	_	_	_
5	37oC	37oc	NN	_	_	_
6	at	at	IN	_	_	_
7	OD	od	NN	_	_	_
8	1.0	1.0	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
10	EDL	edl	NN	_	_	_
11	933	933	CD	_	_	_
12	with	with	IN	_	_	_
13	0.1	0.1	CD	_	_	_
14	mg	mg	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Escherichia	escherichia	FW	Organism	_	_
17	coli	coli	FW	Organism	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Expression	expression	NN	_	_	_
20	data	datum	NNS	_	_	_
21	were	be	VBD	_	_	_
22	normalized	normalize	VBN	_	_	_
23	using	use	VBG	_	_	_
24	the	the	DT	_	_	_
25	Affymetrix	Affymetrix	NNP	_	_	_
26	microarray	microarray	NN	_	_	_
27	suite	suite	NN	_	_	_
28	5	5	CD	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	MAS5	mas5	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	algorithm	algorithm	NN	_	_	_
33	implemented	implement	VBD	_	_	_
34	in	in	IN	_	_	_
35	Affymetrix	Affymetrix	NNP	_	_	_
36	expression	expression	NN	_	_	_
37	console	console	NN	_	_	_
38	software	software	NN	_	_	_
39	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	reduce	reduce	VB	_	_	_
3	noise	noise	NN	_	_	_
4	for	for	IN	_	_	_
5	the	the	DT	_	_	_
6	significance	significance	NN	_	_	_
7	analysis	analysis	NN	_	_	_
8	,	,	,	_	_	_
9	probe	probe	NN	_	_	_
10	sets	set	NNS	_	_	_
11	that	that	WDT	_	_	_
12	did	do	VBD	_	_	_
13	not	not	RB	_	_	_
14	show	show	VB	_	_	_
15	detection	detection	NN	_	_	_
16	call	call	NN	_	_	_
17	rate	rate	NN	_	_	_
18	at	at	IN	_	_	_
19	least	least	JJS	_	_	_
20	50	50	CD	_	_	_
21	%	%	NN	_	_	_
22	of	of	IN	_	_	_
23	the	the	DT	_	_	_
24	samples	sample	NNS	_	_	_
25	in	in	IN	_	_	_
26	the	the	DT	_	_	_
27	comparison	comparison	NN	_	_	_
28	were	be	VBD	_	_	_
29	filtered	filter	VBN	_	_	_
30	out	out	RP	_	_	_
31	.	.	.	_	_	_

1	Highly	highly	RB	_	_	_
2	expressed	express	VBN	_	_	_
3	genes	gene	NNS	_	_	_
4	that	that	WDT	_	_	_
5	showed	show	VBD	_	_	_
6	a	a	DT	_	_	_
7	2-fold	2-fold	JJ	_	_	_
8	change	change	NN	_	_	_
9	in	in	IN	_	_	_
10	expression	expression	NN	_	_	_
11	were	be	VBD	_	_	_
12	selected	select	VBN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	http	http	NN	_	_	_
4	:	:	:	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	strain	strain	NN	_	_	_
7	:	:	:	_	_	_
8	EDL	edl	NN	_	_	_
9	933	933	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
11	The	the	DT	_	_	_
12	web-based	web-based	JJ	_	_	_
13	tool	tool	NN	_	_	_
14	,	,	,	_	_	_
15	DAVID	DAVID	NNP	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	the	the	DT	_	_	_
18	Database	database	NN	_	_	_
19	for	for	IN	_	_	_
20	Annotation	Annotation	NNP	_	_	_
21	,	,	,	_	_	_
22	Visualization	visualization	NN	_	_	_
23	,	,	,	_	_	_
24	and	and	CC	_	_	_
25	Integrated	Integrated	NNP	_	_	_
26	Discovery	Discovery	NNP	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	was	be	VBD	_	_	_
29	used	use	VBN	_	_	_
30	to	to	TO	_	_	_
31	perform	perform	VB	_	_	_
32	the	the	DT	_	_	_
33	biological	biological	JJ	_	_	_
34	interpretation	interpretation	NN	_	_	_
35	of	of	IN	_	_	_
36	differentially	differentially	RB	_	_	_
37	expressed	express	VBN	_	_	_
38	genes	gene	NNS	_	_	_
39	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	,	,	,	_	_	_
3	these	these	DT	_	_	_
4	genes	gene	NNS	_	_	_
5	were	be	VBD	_	_	_
6	classified	classify	VBN	_	_	_
7	based	base	VBN	_	_	_
8	on	on	IN	_	_	_
9	the	the	DT	_	_	_
10	information	information	NN	_	_	_
11	of	of	IN	_	_	_
12	gene	gene	NN	_	_	_
13	function	function	NN	_	_	_
14	in	in	IN	_	_	_
15	Gene	Gene	NNP	_	_	_
16	ontology	ontology	NN	_	_	_
17	database	database	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	using	use	VBG	_	_	_
7	Ribopure	Ribopure	NNP	_	_	_
8	Bacteria	bacterium	NNS	_	_	_
9	Kit	kit	NN	_	_	_
10	as	as	IN	_	_	_
11	described	describe	VBN	_	_	_
12	by	by	IN	_	_	_
13	the	the	DT	_	_	_
14	manufacturer	manufacturer	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Ambion	Ambion	NNP	_	_	_
17	,	,	,	_	_	_
18	Huntingdon	Huntingdon	NNP	_	_	_
19	,	,	,	_	_	_
20	UK	UK	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	quality	quality	NN	_	_	_
3	was	be	VBD	_	_	_
4	assessed	assess	VBN	_	_	_
5	by	by	IN	_	_	_
6	Agilent	Agilent	NNP	_	_	_
7	2100	2100	CD	_	_	_
8	bioanalyser	bioanalyser	NN	_	_	_
9	using	use	VBG	_	_	_
10	the	the	DT	_	_	_
11	RNA	rna	NN	_	_	_
12	6000	6000	CD	_	_	_
13	Nano	Nano	NNP	_	_	_
14	Chip	chip	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Agilent	Agilent	NNP	_	_	_
17	Technologies	Technologies	NNPS	_	_	_
18	,	,	,	_	_	_
19	Amstelveen	Amstelveen	NNP	_	_	_
20	,	,	,	_	_	_
21	The	the	DT	_	_	_
22	Netherlands	Netherlands	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	quantity	quantity	NN	_	_	_
27	was	be	VBD	_	_	_
28	determined	determine	VBN	_	_	_
29	by	by	IN	_	_	_
30	ND-1000	nd-1000	NN	_	_	_
31	Spectrophotometer	spectrophotometer	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	NanoDrop	NanoDrop	NNP	_	_	_
34	Technologies	Technologies	NNPS	_	_	_
35	,	,	,	_	_	_
36	Inc.	Inc.	NNP	_	_	_
37	,	,	,	_	_	_
38	DE	de	NN	_	_	_
39	,	,	,	_	_	_
40	USA	USA	NNP	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	harvested	harvest	VBN	_	_	_
4	at	at	IN	_	_	_
5	mid-exponential	mid-exponential	JJ	_	_	_
6	phase	phase	NN	_	_	_
7	,	,	,	_	_	_
8	spun	spin	VBD	_	_	_
9	,	,	,	_	_	_
10	washed	wash	VBN	_	_	_
11	twice	twice	RB	_	_	_
12	with	with	IN	_	_	_
13	M9	m9	NN	_	_	_
14	medium	medium	NN	_	_	_
15	and	and	CC	_	_	_
16	shifted	shift	VBD	_	_	_
17	to	to	TO	_	_	_
18	limiting	limit	VBG	_	_	_
19	or	or	CC	_	_	_
20	no	no	DT	_	_	_
21	thymine	thymine	NN	_	_	_
22	medium	medium	NN	_	_	_
23	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	taken	take	VBN	_	_	_
3	at	at	IN	_	_	_
4	listed	list	VBN	_	_	_
5	intervals	interval	NNS	_	_	_
6	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	-	-	:	_	_	_
5	0	0	CD	_	_	_
6	min	min	NN	_	_	_
7	before	before	IN	_	_	_
8	nutrient	nutrient	NN	_	_	_
9	shift	shift	NN	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	E.	E.	NNP	_	_	_
12	coli	coli	NN	_	_	_
13	-	-	:	_	_	_
14	15	15	CD	_	_	_
15	min	min	NN	_	_	_
16	after	after	IN	_	_	_
17	shift	shift	NN	_	_	_
18	to	to	TO	_	_	_
19	limiting	limit	VBG	_	_	_
20	medium	medium	NN	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	E.	E.	NNP	_	_	_
23	coli	coli	NN	_	_	_
24	-	-	:	_	_	_
25	15	15	CD	_	_	_
26	min	min	NN	_	_	_
27	after	after	IN	_	_	_
28	shift	shift	NN	_	_	_
29	to	to	TO	_	_	_
30	thymineless	thymineless	JJ	_	_	_
31	medium	medium	NN	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	E.	E.	NNP	_	_	_
34	coli	coli	NN	_	_	_
35	-	-	:	_	_	_
36	30	30	CD	_	_	_
37	min	min	NN	_	_	_
38	after	after	IN	_	_	_
39	shift	shift	NN	_	_	_
40	to	to	TO	_	_	_
41	limiting	limit	VBG	_	_	_
42	medium	medium	NN	_	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	E.	E.	NNP	_	_	_
45	coli	coli	NN	_	_	_
46	-	-	:	_	_	_
47	30	30	CD	_	_	_
48	min	min	NN	_	_	_
49	after	after	IN	_	_	_
50	shift	shift	NN	_	_	_
51	to	to	TO	_	_	_
52	thymineless	thymineless	JJ	_	_	_
53	medium	medium	NN	_	_	_
54	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
55	E.	E.	NNP	_	_	_
56	coli	coli	NN	_	_	_
57	-	-	:	_	_	_
58	45	45	CD	_	_	_
59	min	min	NN	_	_	_
60	after	after	IN	_	_	_
61	shift	shift	NN	_	_	_
62	to	to	TO	_	_	_
63	limiting	limit	VBG	_	_	_
64	medium	medium	NN	_	_	_
65	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
66	E.	E.	NNP	_	_	_
67	coli	coli	NN	_	_	_
68	-	-	:	_	_	_
69	45	45	CD	_	_	_
70	min	min	NN	_	_	_
71	after	after	IN	_	_	_
72	shift	shift	NN	_	_	_
73	to	to	TO	_	_	_
74	thymineless	thymineless	JJ	_	_	_
75	medium	medium	NN	_	_	_
76	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
77	E.	E.	NNP	_	_	_
78	coli	coli	NN	_	_	_
79	-	-	:	_	_	_
80	60	60	CD	_	_	_
81	min	min	NN	_	_	_
82	after	after	IN	_	_	_
83	shift	shift	NN	_	_	_
84	to	to	TO	_	_	_
85	limiting	limit	VBG	_	_	_
86	medium	medium	NN	_	_	_
87	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
88	E.	E.	NNP	_	_	_
89	coli	coli	NN	_	_	_
90	-	-	:	_	_	_
91	60	60	CD	_	_	_
92	min	min	NN	_	_	_
93	after	after	IN	_	_	_
94	shift	shift	NN	_	_	_
95	to	to	TO	_	_	_
96	thymineless	thymineless	JJ	_	_	_
97	medium	medium	NN	_	_	_
98	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
99	E.	E.	NNP	_	_	_
100	coli	coli	NN	_	_	_
101	-	-	:	_	_	_
102	90	90	CD	_	_	_
103	min	min	NN	_	_	_
104	after	after	IN	_	_	_
105	shift	shift	NN	_	_	_
106	to	to	TO	_	_	_
107	limiting	limit	VBG	_	_	_
108	medium	medium	NN	_	_	_
109	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
110	E.	E.	NNP	_	_	_
111	coli	coli	NN	_	_	_
112	-	-	:	_	_	_
113	90	90	CD	_	_	_
114	min	min	NN	_	_	_
115	after	after	IN	_	_	_
116	shift	shift	NN	_	_	_
117	to	to	TO	_	_	_
118	thymineless	thymineless	JJ	_	_	_
119	medium	medium	NN	_	_	_
120	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
121	E.	E.	NNP	_	_	_
122	coli	coli	NN	_	_	_
123	MG1655	mg1655	NN	_	_	_
124	thyA	thya	NN	GEN	_	_
125	-	-	:	_	_	_
126	cells	cell	NNS	_	_	_
127	grown	grow	VBN	_	_	_
128	in	in	IN	_	_	_
129	M9	m9	NN	MED	_	_
130	minimal	minimal	JJ	MED	_	_
131	medium	medium	NN	MED	_	_
132	+	+	CC	_	_	_
133	0.2	0.2	CD	_	_	_
134	%	%	NN	_	_	_
135	glucose	glucose	NN	SUPP	_	_
136	and	and	CC	_	_	_
137	20	20	CD	_	_	_
138	ug	ug	NN	_	_	_
139	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
140	Escherichia	escherichia	FW	Organism	_	_
141	coli	coli	FW	Organism	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	Lowess	lowess	NN	_	_	_
144	normalized	normalize	VBD	_	_	_
145	data	datum	NNS	_	_	_
146	.	.	.	_	_	_

1	Resultant	resultant	JJ	_	_	_
2	data	datum	NNS	_	_	_
3	is	be	VBZ	_	_	_
4	log2	log2	NN	_	_	_
5	normalized	normalize	VBD	_	_	_
6	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	thyA	thya	NN	GEN	_	_
6	-	-	:	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	TLD-15-rep1	tld-15-rep1	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	TLD-15-rep2	tld-15-rep2	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	TLD-30-rep1	tld-30-rep1	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	TLD-30-rep2	tld-30-rep2	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	TLD-45-rep1	tld-45-rep1	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	TLD-45-rep2	tld-45-rep2	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	TLD-60-rep1	tld-60-rep1	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	TLD-60-rep2	tld-60-rep2	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	TLD-90-rep1	tld-90-rep1	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	TLD-90-rep2	tld-90-rep2	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	TLM-15	tlm-15	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	TLM-30	tlm-30	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	TLM-45	tlm-45	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	TLM-60	tlm-60	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	TLM-90	tlm-90	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Total	total	JJ	_	_	_
39	RNA	rna	NN	_	_	_
40	extracted	extract	VBN	_	_	_
41	using	use	VBG	_	_	_
42	QIAGEN	QIAGEN	NNP	_	_	_
43	RNeasy	RNeasy	NNP	_	_	_
44	kit	kit	NN	_	_	_
45	according	accord	VBG	_	_	_
46	to	to	TO	_	_	_
47	manufacturer	manufacturer	NN	_	_	_
48	's	's	POS	_	_	_
49	instructions	instruction	NNS	_	_	_
50	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
51	Channel	Channel	NNP	_	_	_
52	1	1	CD	_	_	_
53	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
54	E.	E.	NNP	_	_	_
55	coli	coli	NN	_	_	_
56	O157	o157	NN	_	_	_
57	:	:	:	_	_	_
58	H7	h7	NN	_	_	_
59	86-24	86-24	CD	_	_	_
60	in	in	IN	_	_	_
61	LB	lb	NN	_	_	_
62	at	at	IN	_	_	_
63	37oC	37oc	NN	_	_	_
64	at	at	IN	_	_	_
65	OD	od	NN	_	_	_
66	4.0	4.0	CD	_	_	_
67	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
68	E.	E.	NNP	_	_	_
69	coli	coli	NN	_	_	_
70	O157	o157	NN	_	_	_
71	:	:	:	_	_	_
72	H7	h7	NN	_	_	_
73	86-24	86-24	CD	_	_	_
74	was	be	VBD	_	_	_
75	inoculated	inoculate	VBN	_	_	_
76	in	in	IN	_	_	_
77	25	25	CD	_	_	_
78	ml	ml	NN	_	_	_
79	of	of	IN	_	_	_
80	LB	lb	NN	_	_	_
81	in	in	IN	_	_	_
82	250	250	CD	_	_	_
83	ml	ml	NN	_	_	_
84	shake	shake	NN	_	_	_
85	flasks	flask	NNS	_	_	_
86	with	with	IN	_	_	_
87	overnight	overnight	JJ	_	_	_
88	cultures	culture	NNS	_	_	_
89	that	that	WDT	_	_	_
90	were	be	VBD	_	_	_
91	diluted	dilute	VBN	_	_	_
92	1:100	1:100	CD	_	_	_
93	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	shaken	shake	VBN	_	_	_
4	at	at	IN	_	_	_
5	250	250	CD	_	_	_
6	rpm	rpm	NN	_	_	_
7	and	and	CC	_	_	_
8	37	37	CD	_	_	_
9	°C	°c	NN	_	_	_
10	for	for	IN	_	_	_
11	an	a	DT	_	_	_
12	absorbance	absorbance	NN	_	_	_
13	of	of	IN	_	_	_
14	4.0	4.0	CD	_	_	_
15	at	at	IN	_	_	_
16	600	600	CD	_	_	_
17	nm	nm	NN	_	_	_
18	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	immediately	immediately	RB	_	_	_
4	chilled	chill	VBN	_	_	_
5	with	with	IN	_	_	_
6	dry	dry	JJ	_	_	_
7	ice	ice	NN	_	_	_
8	and	and	CC	_	_	_
9	95	95	CD	_	_	_
10	%	%	NN	_	_	_
11	ethanol	ethanol	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	to	to	TO	_	_	_
14	prevent	prevent	VB	_	_	_
15	RNA	rna	NN	_	_	_
16	degradation	degradation	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	for	for	IN	_	_	_
19	30	30	CD	_	_	_
20	sec	sec	NN	_	_	_
21	before	before	IN	_	_	_
22	centrifugation	centrifugation	NN	_	_	_
23	at	at	IN	_	_	_
24	13,000	13,000	CD	_	_	_
25	g	g	NN	_	_	_
26	for	for	IN	_	_	_
27	2	2	CD	_	_	_
28	min	min	NN	_	_	_
29	;	;	:	_	_	_
30	cell	cell	NN	_	_	_
31	pellets	pellet	NNS	_	_	_
32	were	be	VBD	_	_	_
33	frozen	frozen	JJ	_	_	_
34	immediately	immediately	RB	_	_	_
35	with	with	IN	_	_	_
36	dry	dry	JJ	_	_	_
37	ice	ice	NN	_	_	_
38	and	and	CC	_	_	_
39	stored	store	VBD	_	_	_
40	-80	-80	CD	_	_	_
41	°C	°c	NN	_	_	_
42	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	isolated	isolate	VBN	_	_	_
4	using	use	VBG	_	_	_
5	Qiagen	Qiagen	NNP	_	_	_
6	RNeasy	RNeasy	NNP	_	_	_
7	mini	minus	NNS	_	_	_
8	Kit	kit	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Cat	cat	NN	_	_	_
11	#	#	#	_	_	_
12	74104	74104	CD	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	O157	o157	NN	_	_	_
5	:	:	:	_	_	_
6	H7	h7	NN	_	_	_
7	EDL933	edl933	NN	_	_	_
8	in	in	IN	_	_	_
9	LB	lb	NN	_	_	_
10	at	at	IN	_	_	_
11	37oC	37oc	NN	_	_	_
12	at	at	IN	_	_	_
13	OD	od	NN	_	_	_
14	4.0	4.0	CD	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	E.	E.	NNP	_	_	_
17	coli	coli	NN	_	_	_
18	O157	o157	NN	_	_	_
19	:	:	:	_	_	_
20	H7	h7	NN	_	_	_
21	EDL933	edl933	NN	_	_	_
22	was	be	VBD	_	_	_
23	inoculated	inoculate	VBN	_	_	_
24	in	in	IN	_	_	_
25	25	25	CD	_	_	_
26	ml	ml	NN	_	_	_
27	of	of	IN	_	_	_
28	LB	lb	NN	_	_	_
29	in	in	IN	_	_	_
30	250	250	CD	_	_	_
31	ml	ml	NN	_	_	_
32	shake	shake	NN	_	_	_
33	flasks	flask	NNS	_	_	_
34	with	with	IN	_	_	_
35	overnight	overnight	JJ	_	_	_
36	cultures	culture	NNS	_	_	_
37	that	that	WDT	_	_	_
38	were	be	VBD	_	_	_
39	diluted	dilute	VBN	_	_	_
40	1:100	1:100	CD	_	_	_
41	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	shaken	shake	VBN	_	_	_
4	at	at	IN	_	_	_
5	250	250	CD	_	_	_
6	rpm	rpm	NN	_	_	_
7	and	and	CC	_	_	_
8	37	37	CD	_	_	_
9	°C	°c	NN	_	_	_
10	for	for	IN	_	_	_
11	an	a	DT	_	_	_
12	absorbance	absorbance	NN	_	_	_
13	of	of	IN	_	_	_
14	4.0	4.0	CD	_	_	_
15	at	at	IN	_	_	_
16	600	600	CD	_	_	_
17	nm	nm	NN	_	_	_
18	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	immediately	immediately	RB	_	_	_
4	chilled	chill	VBN	_	_	_
5	with	with	IN	_	_	_
6	dry	dry	JJ	_	_	_
7	ice	ice	NN	_	_	_
8	and	and	CC	_	_	_
9	95	95	CD	_	_	_
10	%	%	NN	_	_	_
11	ethanol	ethanol	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	to	to	TO	_	_	_
14	prevent	prevent	VB	_	_	_
15	RNA	rna	NN	_	_	_
16	degradation	degradation	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	for	for	IN	_	_	_
19	30	30	CD	_	_	_
20	sec	sec	NN	_	_	_
21	before	before	IN	_	_	_
22	centrifugation	centrifugation	NN	_	_	_
23	at	at	IN	_	_	_
24	13,000	13,000	CD	_	_	_
25	g	g	NN	_	_	_
26	for	for	IN	_	_	_
27	2	2	CD	_	_	_
28	min	min	NN	_	_	_
29	;	;	:	_	_	_
30	cell	cell	NN	_	_	_
31	pellets	pellet	NNS	_	_	_
32	were	be	VBD	_	_	_
33	frozen	frozen	JJ	_	_	_
34	immediately	immediately	RB	_	_	_
35	with	with	IN	_	_	_
36	dry	dry	JJ	_	_	_
37	ice	ice	NN	_	_	_
38	and	and	CC	_	_	_
39	stored	store	VBD	_	_	_
40	-80	-80	CD	_	_	_
41	°C	°c	NN	_	_	_
42	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	isolated	isolate	VBN	_	_	_
4	using	use	VBG	_	_	_
5	Qiagen	Qiagen	NNP	_	_	_
6	RNeasy	RNeasy	NNP	_	_	_
7	mini	minus	NNS	_	_	_
8	Kit	kit	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Cat	cat	NN	_	_	_
11	#	#	#	_	_	_
12	74104	74104	CD	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
5	MAS	mas	FW	_	_	_
6	5.0	5.0	CD	_	_	_
7	Expression	expression	NN	_	_	_
8	Analysis	analysis	NN	_	_	_
9	Default	Default	NNP	_	_	_
10	Setting	set	VBG	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	strain	strain	NN	_	_	_
13	:	:	:	_	_	_
14	86-24	86-24	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	strain	strain	NN	_	_	_
17	:	:	:	_	_	_
18	EDL933	edl933	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	All	all	DT	_	_	_
21	cultures	culture	NNS	_	_	_
22	were	be	VBD	_	_	_
23	grown	grow	VBN	_	_	_
24	aerobically	aerobically	RB	_	_	_
25	in	in	IN	_	_	_
26	a	a	DT	_	_	_
27	thermostatically	thermostatically	RB	_	_	_
28	controlled	control	VBN	_	_	_
29	37oC	37oc	NN	_	_	_
30	culture	culture	NN	_	_	_
31	room	room	NN	_	_	_
32	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	150	150	CD	_	_	_
4	ml	ml	NN	_	_	_
5	culture	culture	NN	_	_	_
6	volume	volume	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	were	be	VBD	_	_	_
9	stirred	stir	VBN	_	_	_
10	by	by	IN	_	_	_
11	magnetic	magnetic	JJ	_	_	_
12	stirrers	stirrer	NNS	_	_	_
13	at	at	IN	_	_	_
14	330	330	CD	_	_	_
15	rpm	rpm	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Thermo	Thermo	NNP	_	_	_
18	Scientific	Scientific	NNP	_	_	_
19	Variomag	Variomag	NNP	_	_	_
20	Multipoint	Multipoint	NNP	_	_	_
21	6in	6in	JJ	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	1000	1000	CD	_	_	_
24	ml	ml	NN	_	_	_
25	Erlenmeyer	erlenmeyer	NN	_	_	_
26	flask	flask	NN	_	_	_
27	.	.	.	_	_	_

1	Starting	start	VBG	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	inoculated	inoculate	VBN	_	_	_
5	from	from	IN	_	_	_
6	a	a	DT	_	_	_
7	single	single	JJ	_	_	_
8	colony	colony	NN	_	_	_
9	and	and	CC	_	_	_
10	grown	grown	JJ	_	_	_
11	overnight	overnight	JJ	_	_	_
12	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	experimental	experimental	JJ	_	_	_
3	culture	culture	NN	_	_	_
4	was	be	VBD	_	_	_
5	then	then	RB	_	_	_
6	inoculated	inoculate	VBN	_	_	_
7	from	from	IN	_	_	_
8	such	such	JJ	_	_	_
9	an	a	DT	_	_	_
10	overnight	overnight	JJ	_	_	_
11	culture	culture	NN	_	_	_
12	at	at	IN	_	_	_
13	a	a	DT	_	_	_
14	dilution	dilution	NN	_	_	_
15	of	of	IN	_	_	_
16	1:20	1:20	CD	_	_	_
17	into	into	IN	_	_	_
18	150	150	CD	_	_	_
19	ml	ml	NN	_	_	_
20	fresh	fresh	JJ	_	_	_
21	MOPS	mop	NNS	MED	_	_
22	minimal	minimal	JJ	_	_	_
23	medium	medium	NN	_	_	_
24	in	in	IN	_	_	_
25	a	a	DT	_	_	_
26	1000	1000	CD	_	_	_
27	ml	ml	NN	_	_	_
28	flask	flask	NN	_	_	_
29	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	minimal	minimal	JJ	_	_	_
3	medium	medium	NN	_	_	_
4	used	use	VBN	_	_	_
5	for	for	IN	_	_	_
6	all	all	DT	_	_	_
7	experiments	experiment	NNS	_	_	_
8	was	be	VBD	_	_	_
9	a	a	DT	_	_	_
10	modification	modification	NN	_	_	_
11	of	of	IN	_	_	_
12	MOPS	mop	NNS	MED	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	morpholinopropane	morpholinopropane	NN	_	_	_
15	sulfonate	sulfonate	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	minimal	minimal	JJ	_	_	_
18	medium	medium	NN	_	_	_
19	obtained	obtain	VBN	_	_	_
20	from	from	IN	_	_	_
21	Teknova	Teknova	NNP	_	_	_
22	,	,	,	_	_	_
23	CA	CA	NNP	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	product	product	NN	_	_	_
26	number	number	NN	_	_	_
27	M2006	m2006	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	which	which	WDT	_	_	_
30	contains	contain	VBZ	_	_	_
31	86	86	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	NaCl	nacl	NN	_	_	_
34	,	,	,	_	_	_
35	9.5	9.5	CD	_	_	_
36	mM	mm	NN	KWSUPP	_	_
37	NH4Cl	nh4cl	NN	_	_	_
38	,	,	,	_	_	_
39	5	5	CD	_	_	_
40	mM	mm	NN	KWSUPP	_	_
41	K2HPO4	k2hpo4	NN	_	_	_
42	and	and	CC	_	_	_
43	0.2	0.2	CD	_	_	_
44	%	%	NN	_	_	_
45	glucose	glucose	NN	SUPP	_	_
46	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	coli	coli	NN	_	_	_
3	_	_	NN	_	_	_
4	coldstress	coldstress	VBP	_	_	_
5	_	_	SYM	_	_	_
6	timepoint1	timepoint1	CD	_	_	_
7	_	_	CD	_	_	_
8	rep1	rep1	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	coli	coli	NN	_	_	_
11	_	_	NN	_	_	_
12	coldstress	coldstress	VBP	_	_	_
13	_	_	SYM	_	_	_
14	timepoint1	timepoint1	CD	_	_	_
15	_	_	CD	_	_	_
16	rep2	rep2	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	coli	coli	NN	_	_	_
19	_	_	NN	_	_	_
20	coldstress	coldstress	VBP	_	_	_
21	_	_	SYM	_	_	_
22	timepoint1	timepoint1	CD	_	_	_
23	_	_	CD	_	_	_
24	rep3	rep3	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	coli	coli	NN	_	_	_
27	_	_	NN	_	_	_
28	coldstress	coldstress	VBP	_	_	_
29	_	_	SYM	_	_	_
30	timepoint2	timepoint2	CD	_	_	_
31	_	_	CD	_	_	_
32	rep1	rep1	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	coli	coli	NN	_	_	_
35	_	_	NN	_	_	_
36	coldstress	coldstress	VBP	_	_	_
37	_	_	SYM	_	_	_
38	timepoint2	timepoint2	CD	_	_	_
39	_	_	CD	_	_	_
40	rep2	rep2	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	coli	coli	NN	_	_	_
43	_	_	NN	_	_	_
44	coldstress	coldstress	VBP	_	_	_
45	_	_	SYM	_	_	_
46	timepoint2	timepoint2	CD	_	_	_
47	_	_	CD	_	_	_
48	rep3	rep3	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	coli	coli	NN	_	_	_
51	_	_	NN	_	_	_
52	coldstress	coldstress	VBP	_	_	_
53	_	_	SYM	_	_	_
54	timepoint3	timepoint3	CD	_	_	_
55	_	_	CD	_	_	_
56	rep1	rep1	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	coli	coli	NN	_	_	_
59	_	_	NN	_	_	_
60	coldstress	coldstress	VBP	_	_	_
61	_	_	SYM	_	_	_
62	timepoint3	timepoint3	CD	_	_	_
63	_	_	CD	_	_	_
64	rep2	rep2	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	coli	coli	NN	_	_	_
67	_	_	NN	_	_	_
68	coldstress	coldstress	VBP	_	_	_
69	_	_	SYM	_	_	_
70	timepoint3	timepoint3	CD	_	_	_
71	_	_	CD	_	_	_
72	rep3	rep3	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	coli	coli	NN	_	_	_
75	_	_	NN	_	_	_
76	coldstress	coldstress	VBP	_	_	_
77	_	_	SYM	_	_	_
78	timepoint4	timepoint4	CD	_	_	_
79	_	_	CD	_	_	_
80	rep1	rep1	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	coli	coli	NN	_	_	_
83	_	_	NN	_	_	_
84	coldstress	coldstress	VBP	_	_	_
85	_	_	SYM	_	_	_
86	timepoint4	timepoint4	CD	_	_	_
87	_	_	CD	_	_	_
88	rep2	rep2	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	coli	coli	NN	_	_	_
91	_	_	NN	_	_	_
92	coldstress	coldstress	VBP	_	_	_
93	_	_	SYM	_	_	_
94	timepoint4	timepoint4	CD	_	_	_
95	_	_	CD	_	_	_
96	rep3	rep3	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	coli	coli	NN	_	_	_
99	_	_	NN	_	_	_
100	coldstress	coldstress	VBP	_	_	_
101	_	_	SYM	_	_	_
102	timepoint5	timepoint5	CD	_	_	_
103	_	_	CD	_	_	_
104	rep1	rep1	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	coli	coli	NN	_	_	_
107	_	_	NN	_	_	_
108	coldstress	coldstress	VBP	_	_	_
109	_	_	SYM	_	_	_
110	timepoint5	timepoint5	CD	_	_	_
111	_	_	CD	_	_	_
112	rep2	rep2	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	coli	coli	NN	_	_	_
115	_	_	NN	_	_	_
116	coldstress	coldstress	VBP	_	_	_
117	_	_	SYM	_	_	_
118	timepoint5	timepoint5	CD	_	_	_
119	_	_	CD	_	_	_
120	rep3	rep3	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	coli	coli	NN	_	_	_
123	_	_	NN	_	_	_
124	coldstress	coldstress	VBP	_	_	_
125	_	_	SYM	_	_	_
126	timepoint6	timepoint6	CD	_	_	_
127	_	_	CD	_	_	_
128	rep1	rep1	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	coli	coli	NN	_	_	_
131	_	_	NN	_	_	_
132	coldstress	coldstress	VBP	_	_	_
133	_	_	SYM	_	_	_
134	timepoint6	timepoint6	CD	_	_	_
135	_	_	CD	_	_	_
136	rep2	rep2	NN	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	coli	coli	NN	_	_	_
139	_	_	NN	_	_	_
140	coldstress	coldstress	VBP	_	_	_
141	_	_	SYM	_	_	_
142	timepoint6	timepoint6	CD	_	_	_
143	_	_	CD	_	_	_
144	rep3	rep3	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	coli	coli	NN	_	_	_
147	_	_	NN	_	_	_
148	coldstress	coldstress	VBP	_	_	_
149	_	_	SYM	_	_	_
150	timepoint7	timepoint7	CD	_	_	_
151	_	_	CD	_	_	_
152	rep1	rep1	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	coli	coli	NN	_	_	_
155	_	_	NN	_	_	_
156	coldstress	coldstress	VBP	_	_	_
157	_	_	SYM	_	_	_
158	timepoint7	timepoint7	CD	_	_	_
159	_	_	CD	_	_	_
160	rep2	rep2	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	coli	coli	NN	_	_	_
163	_	_	NN	_	_	_
164	coldstress	coldstress	VBP	_	_	_
165	_	_	SYM	_	_	_
166	timepoint7	timepoint7	CD	_	_	_
167	_	_	CD	_	_	_
168	rep3	rep3	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	coli	coli	NN	_	_	_
171	_	_	NN	_	_	_
172	coldstress	coldstress	VBP	_	_	_
173	_	_	SYM	_	_	_
174	timepoint8	timepoint8	CD	_	_	_
175	_	_	CD	_	_	_
176	rep1	rep1	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	coli	coli	NN	_	_	_
179	_	_	NN	_	_	_
180	coldstress	coldstress	VBP	_	_	_
181	_	_	SYM	_	_	_
182	timepoint8	timepoint8	CD	_	_	_
183	_	_	CD	_	_	_
184	rep2	rep2	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	coli	coli	NN	_	_	_
187	_	_	NN	_	_	_
188	coldstress	coldstress	VBP	_	_	_
189	_	_	SYM	_	_	_
190	timepoint8	timepoint8	CD	_	_	_
191	_	_	CD	_	_	_
192	rep3	rep3	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	coli	coli	NN	_	_	_
195	_	_	NN	_	_	_
196	control	control	NN	_	_	_
197	_	_	CD	_	_	_
198	timepoint1	timepoint1	NN	_	_	_
199	_	_	CD	_	_	_
200	rep1	rep1	NN	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	coli	coli	NN	_	_	_
203	_	_	NN	_	_	_
204	control	control	NN	_	_	_
205	_	_	CD	_	_	_
206	timepoint1	timepoint1	NN	_	_	_
207	_	_	CD	_	_	_
208	rep2	rep2	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	coli	coli	NN	_	_	_
211	_	_	NN	_	_	_
212	control	control	NN	_	_	_
213	_	_	CD	_	_	_
214	timepoint1	timepoint1	NN	_	_	_
215	_	_	CD	_	_	_
216	rep3	rep3	NN	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	coli	coli	NN	_	_	_
219	_	_	NN	_	_	_
220	control	control	NN	_	_	_
221	_	_	CD	_	_	_
222	timepoint2	timepoint2	NN	_	_	_
223	_	_	CD	_	_	_
224	rep1	rep1	NN	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	coli	coli	NN	_	_	_
227	_	_	NN	_	_	_
228	control	control	NN	_	_	_
229	_	_	CD	_	_	_
230	timepoint2	timepoint2	NN	_	_	_
231	_	_	CD	_	_	_
232	rep2	rep2	NN	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	coli	coli	NN	_	_	_
235	_	_	NN	_	_	_
236	control	control	NN	_	_	_
237	_	_	CD	_	_	_
238	timepoint2	timepoint2	NN	_	_	_
239	_	_	CD	_	_	_
240	rep3	rep3	NN	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	coli	coli	NN	_	_	_
243	_	_	NN	_	_	_
244	control	control	NN	_	_	_
245	_	_	CD	_	_	_
246	timepoint3	timepoint3	NN	_	_	_
247	_	_	CD	_	_	_
248	rep1	rep1	NN	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	coli	coli	NN	_	_	_
251	_	_	NN	_	_	_
252	control	control	NN	_	_	_
253	_	_	CD	_	_	_
254	timepoint3	timepoint3	NN	_	_	_
255	_	_	CD	_	_	_
256	rep2	rep2	NN	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	coli	coli	NN	_	_	_
259	_	_	NN	_	_	_
260	control	control	NN	_	_	_
261	_	_	CD	_	_	_
262	timepoint3	timepoint3	NN	_	_	_
263	_	_	CD	_	_	_
264	rep3	rep3	NN	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	coli	coli	NN	_	_	_
267	_	_	NN	_	_	_
268	control	control	NN	_	_	_
269	_	_	CD	_	_	_
270	timepoint4	timepoint4	NN	_	_	_
271	_	_	CD	_	_	_
272	rep1	rep1	NN	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	coli	coli	NN	_	_	_
275	_	_	NN	_	_	_
276	control	control	NN	_	_	_
277	_	_	CD	_	_	_
278	timepoint4	timepoint4	NN	_	_	_
279	_	_	CD	_	_	_
280	rep2	rep2	NN	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	coli	coli	NN	_	_	_
283	_	_	NN	_	_	_
284	control	control	NN	_	_	_
285	_	_	CD	_	_	_
286	timepoint4	timepoint4	NN	_	_	_
287	_	_	CD	_	_	_
288	rep3	rep3	NN	_	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
290	coli	coli	NN	_	_	_
291	_	_	NN	_	_	_
292	control	control	NN	_	_	_
293	_	_	CD	_	_	_
294	timepoint5	timepoint5	NN	_	_	_
295	_	_	CD	_	_	_
296	rep1	rep1	NN	_	_	_
297	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
298	coli	coli	NN	_	_	_
299	_	_	NN	_	_	_
300	control	control	NN	_	_	_
301	_	_	CD	_	_	_
302	timepoint5	timepoint5	NN	_	_	_
303	_	_	CD	_	_	_
304	rep2	rep2	NN	_	_	_
305	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
306	coli	coli	NN	_	_	_
307	_	_	NN	_	_	_
308	control	control	NN	_	_	_
309	_	_	CD	_	_	_
310	timepoint5	timepoint5	NN	_	_	_
311	_	_	CD	_	_	_
312	rep3	rep3	NN	_	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
314	coli	coli	NN	_	_	_
315	_	_	NN	_	_	_
316	control	control	NN	_	_	_
317	_	_	CD	_	_	_
318	timepoint6	timepoint6	NN	_	_	_
319	_	_	CD	_	_	_
320	rep1	rep1	NN	_	_	_
321	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
322	coli	coli	NN	_	_	_
323	_	_	NN	_	_	_
324	control	control	NN	_	_	_
325	_	_	CD	_	_	_
326	timepoint6	timepoint6	NN	_	_	_
327	_	_	CD	_	_	_
328	rep2	rep2	NN	_	_	_
329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
330	coli	coli	NN	_	_	_
331	_	_	NN	_	_	_
332	control	control	NN	_	_	_
333	_	_	CD	_	_	_
334	timepoint6	timepoint6	NN	_	_	_
335	_	_	CD	_	_	_
336	rep3	rep3	NN	_	_	_
337	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
338	coli	coli	NN	_	_	_
339	_	_	NN	_	_	_
340	control	control	NN	_	_	_
341	_	_	CD	_	_	_
342	timepoint7	timepoint7	NN	_	_	_
343	_	_	CD	_	_	_
344	rep1	rep1	NN	_	_	_
345	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
346	coli	coli	NN	_	_	_
347	_	_	NN	_	_	_
348	control	control	NN	_	_	_
349	_	_	CD	_	_	_
350	timepoint7	timepoint7	NN	_	_	_
351	_	_	CD	_	_	_
352	rep2	rep2	NN	_	_	_
353	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
354	coli	coli	NN	_	_	_
355	_	_	NN	_	_	_
356	control	control	NN	_	_	_
357	_	_	CD	_	_	_
358	timepoint7	timepoint7	NN	_	_	_
359	_	_	CD	_	_	_
360	rep3	rep3	NN	_	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
362	coli	coli	NN	_	_	_
363	_	_	NN	_	_	_
364	control	control	NN	_	_	_
365	_	_	SYM	_	_	_
366	timepoint8	timepoint8	CD	_	_	_
367	_	_	CD	_	_	_
368	rep1	rep1	NN	_	_	_
369	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
370	coli	coli	NN	_	_	_
371	_	_	NN	_	_	_
372	control	control	NN	_	_	_
373	_	_	SYM	_	_	_
374	timepoint8	timepoint8	CD	_	_	_
375	_	_	CD	_	_	_
376	rep2	rep2	NN	_	_	_
377	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
378	coli	coli	NN	_	_	_
379	_	_	NN	_	_	_
380	control	control	NN	_	_	_
381	_	_	SYM	_	_	_
382	timepoint8	timepoint8	CD	_	_	_
383	_	_	CD	_	_	_
384	rep3	rep3	NN	_	_	_
385	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
386	coli	coli	NN	_	_	_
387	_	_	NN	_	_	_
388	heatstress	heatstress	VBP	_	_	_
389	_	_	SYM	_	_	_
390	timepoint1	timepoint1	CD	_	_	_
391	_	_	CD	_	_	_
392	rep1	rep1	NN	_	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
394	coli	coli	NN	_	_	_
395	_	_	NN	_	_	_
396	heatstress	heatstress	VBP	_	_	_
397	_	_	SYM	_	_	_
398	timepoint1	timepoint1	CD	_	_	_
399	_	_	CD	_	_	_
400	rep2	rep2	NN	_	_	_
401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
402	coli	coli	NN	_	_	_
403	_	_	NN	_	_	_
404	heatstress	heatstress	VBP	_	_	_
405	_	_	SYM	_	_	_
406	timepoint1	timepoint1	CD	_	_	_
407	_	_	CD	_	_	_
408	rep3	rep3	NN	_	_	_
409	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
410	coli	coli	NN	_	_	_
411	_	_	NN	_	_	_
412	heatstress	heatstress	VBP	_	_	_
413	_	_	SYM	_	_	_
414	timepoint2	timepoint2	CD	_	_	_
415	_	_	CD	_	_	_
416	rep1	rep1	NN	_	_	_
417	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
418	coli	coli	NN	_	_	_
419	_	_	NN	_	_	_
420	heatstress	heatstress	VBP	_	_	_
421	_	_	SYM	_	_	_
422	timepoint2	timepoint2	CD	_	_	_
423	_	_	CD	_	_	_
424	rep2	rep2	NN	_	_	_
425	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
426	coli	coli	NN	_	_	_
427	_	_	NN	_	_	_
428	heatstress	heatstress	VBP	_	_	_
429	_	_	SYM	_	_	_
430	timepoint2	timepoint2	CD	_	_	_
431	_	_	CD	_	_	_
432	rep3	rep3	NN	_	_	_
433	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
434	coli	coli	NN	_	_	_
435	_	_	NN	_	_	_
436	heatstress	heatstress	VBP	_	_	_
437	_	_	SYM	_	_	_
438	timepoint3	timepoint3	CD	_	_	_
439	_	_	CD	_	_	_
440	rep1	rep1	NN	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
442	coli	coli	NN	_	_	_
443	_	_	NN	_	_	_
444	heatstress	heatstress	VBP	_	_	_
445	_	_	SYM	_	_	_
446	timepoint3	timepoint3	CD	_	_	_
447	_	_	CD	_	_	_
448	rep2	rep2	NN	_	_	_
449	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
450	coli	coli	NN	_	_	_
451	_	_	NN	_	_	_
452	heatstress	heatstress	VBP	_	_	_
453	_	_	SYM	_	_	_
454	timepoint3	timepoint3	CD	_	_	_
455	_	_	CD	_	_	_
456	rep3	rep3	NN	_	_	_
457	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
458	coli	coli	NN	_	_	_
459	_	_	NN	_	_	_
460	heatstress	heatstress	VBP	_	_	_
461	_	_	SYM	_	_	_
462	timepoint4	timepoint4	CD	_	_	_
463	_	_	CD	_	_	_
464	rep1	rep1	NN	_	_	_
465	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
466	coli	coli	NN	_	_	_
467	_	_	NN	_	_	_
468	heatstress	heatstress	VBP	_	_	_
469	_	_	SYM	_	_	_
470	timepoint4	timepoint4	CD	_	_	_
471	_	_	CD	_	_	_
472	rep2	rep2	NN	_	_	_
473	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
474	coli	coli	NN	_	_	_
475	_	_	NN	_	_	_
476	heatstress	heatstress	VBP	_	_	_
477	_	_	SYM	_	_	_
478	timepoint4	timepoint4	CD	_	_	_
479	_	_	CD	_	_	_
480	rep3	rep3	NN	_	_	_
481	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
482	coli	coli	NN	_	_	_
483	_	_	NN	_	_	_
484	heatstress	heatstress	VBP	_	_	_
485	_	_	SYM	_	_	_
486	timepoint5	timepoint5	CD	_	_	_
487	_	_	CD	_	_	_
488	rep1	rep1	NN	_	_	_
489	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
490	coli	coli	NN	_	_	_
491	_	_	NN	_	_	_
492	heatstress	heatstress	VBP	_	_	_
493	_	_	SYM	_	_	_
494	timepoint5	timepoint5	CD	_	_	_
495	_	_	CD	_	_	_
496	rep2	rep2	NN	_	_	_
497	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
498	coli	coli	NN	_	_	_
499	_	_	NN	_	_	_
500	heatstress	heatstress	VBP	_	_	_
501	_	_	SYM	_	_	_
502	timepoint5	timepoint5	CD	_	_	_
503	_	_	CD	_	_	_
504	rep3	rep3	NN	_	_	_
505	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
506	coli	coli	NN	_	_	_
507	_	_	NN	_	_	_
508	heatstress	heatstress	VBP	_	_	_
509	_	_	SYM	_	_	_
510	timepoint6	timepoint6	CD	_	_	_
511	_	_	CD	_	_	_
512	rep1	rep1	NN	_	_	_
513	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
514	coli	coli	NN	_	_	_
515	_	_	NN	_	_	_
516	heatstress	heatstress	VBP	_	_	_
517	_	_	SYM	_	_	_
518	timepoint6	timepoint6	CD	_	_	_
519	_	_	CD	_	_	_
520	rep2	rep2	NN	_	_	_
521	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
522	coli	coli	NN	_	_	_
523	_	_	NN	_	_	_
524	heatstress	heatstress	VBP	_	_	_
525	_	_	SYM	_	_	_
526	timepoint6	timepoint6	CD	_	_	_
527	_	_	CD	_	_	_
528	rep3	rep3	NN	_	_	_
529	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
530	coli	coli	NN	_	_	_
531	_	_	NN	_	_	_
532	heatstress	heatstress	VBP	_	_	_
533	_	_	SYM	_	_	_
534	timepoint7	timepoint7	CD	_	_	_
535	_	_	CD	_	_	_
536	rep1	rep1	NN	_	_	_
537	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
538	coli	coli	NN	_	_	_
539	_	_	NN	_	_	_
540	heatstress	heatstress	VBP	_	_	_
541	_	_	SYM	_	_	_
542	timepoint7	timepoint7	CD	_	_	_
543	_	_	CD	_	_	_
544	rep2	rep2	NN	_	_	_
545	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
546	coli	coli	NN	_	_	_
547	_	_	NN	_	_	_
548	heatstress	heatstress	VBP	_	_	_
549	_	_	SYM	_	_	_
550	timepoint7	timepoint7	CD	_	_	_
551	_	_	CD	_	_	_
552	rep3	rep3	NN	_	_	_
553	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
554	coli	coli	NN	_	_	_
555	_	_	NN	_	_	_
556	heatstress	heatstress	VBP	_	_	_
557	_	_	SYM	_	_	_
558	timepoint8	timepoint8	CD	_	_	_
559	_	_	CD	_	_	_
560	rep1	rep1	NN	_	_	_
561	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
562	coli	coli	NN	_	_	_
563	_	_	NN	_	_	_
564	heatstress	heatstress	VBP	_	_	_
565	_	_	SYM	_	_	_
566	timepoint8	timepoint8	CD	_	_	_
567	_	_	CD	_	_	_
568	rep2	rep2	NN	_	_	_
569	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
570	coli	coli	NN	_	_	_
571	_	_	NN	_	_	_
572	heatstress	heatstress	VBP	_	_	_
573	_	_	SYM	_	_	_
574	timepoint8	timepoint8	CD	_	_	_
575	_	_	CD	_	_	_
576	rep3	rep3	NN	_	_	_
577	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
578	coli	coli	NN	_	_	_
579	_	_	NN	_	_	_
580	lactose	lactose	NN	_	_	_
581	_	_	CD	_	_	_
582	timepoint2	timepoint2	NN	_	_	_
583	_	_	CD	_	_	_
584	rep1	rep1	NN	_	_	_
585	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
586	coli	coli	NN	_	_	_
587	_	_	NN	_	_	_
588	lactose	lactose	NN	_	_	_
589	_	_	CD	_	_	_
590	timepoint2	timepoint2	NN	_	_	_
591	_	_	CD	_	_	_
592	rep2	rep2	NN	_	_	_
593	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
594	coli	coli	NN	_	_	_
595	_	_	NN	_	_	_
596	lactose	lactose	NN	_	_	_
597	_	_	CD	_	_	_
598	timepoint2	timepoint2	NN	_	_	_
599	_	_	CD	_	_	_
600	rep3	rep3	NN	_	_	_
601	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
602	coli	coli	NN	_	_	_
603	_	_	NN	_	_	_
604	lactose	lactose	NN	_	_	_
605	_	_	CD	_	_	_
606	timepoint3	timepoint3	NN	_	_	_
607	_	_	CD	_	_	_
608	rep1	rep1	NN	_	_	_
609	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
610	coli	coli	NN	_	_	_
611	_	_	NN	_	_	_
612	lactose	lactose	NN	_	_	_
613	_	_	CD	_	_	_
614	timepoint3	timepoint3	NN	_	_	_
615	_	_	CD	_	_	_
616	rep3	rep3	NN	_	_	_
617	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
618	coli	coli	NN	_	_	_
619	_	_	NN	_	_	_
620	lactose	lactose	NN	_	_	_
621	_	_	CD	_	_	_
622	timepoint4	timepoint4	NN	_	_	_
623	_	_	CD	_	_	_
624	rep1	rep1	NN	_	_	_
625	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
626	coli	coli	NN	_	_	_
627	_	_	NN	_	_	_
628	lactose	lactose	NN	_	_	_
629	_	_	CD	_	_	_
630	timepoint4	timepoint4	NN	_	_	_
631	_	_	CD	_	_	_
632	rep2	rep2	NN	_	_	_
633	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
634	coli	coli	NN	_	_	_
635	_	_	NN	_	_	_
636	lactose	lactose	NN	_	_	_
637	_	_	CD	_	_	_
638	timepoint4	timepoint4	NN	_	_	_
639	_	_	CD	_	_	_
640	rep3	rep3	NN	_	_	_
641	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
642	coli	coli	NN	_	_	_
643	_	_	NN	_	_	_
644	lactose	lactose	NN	_	_	_
645	_	_	CD	_	_	_
646	timepoint5	timepoint5	NN	_	_	_
647	_	_	CD	_	_	_
648	rep1	rep1	NN	_	_	_
649	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
650	coli	coli	NN	_	_	_
651	_	_	NN	_	_	_
652	lactose	lactose	NN	_	_	_
653	_	_	CD	_	_	_
654	timepoint5	timepoint5	NN	_	_	_
655	_	_	CD	_	_	_
656	rep2	rep2	NN	_	_	_
657	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
658	coli	coli	NN	_	_	_
659	_	_	NN	_	_	_
660	lactose	lactose	NN	_	_	_
661	_	_	CD	_	_	_
662	timepoint5	timepoint5	NN	_	_	_
663	_	_	CD	_	_	_
664	rep3	rep3	NN	_	_	_
665	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
666	coli	coli	NN	_	_	_
667	_	_	NN	_	_	_
668	lactose	lactose	NN	_	_	_
669	_	_	CD	_	_	_
670	timepoint6	timepoint6	NN	_	_	_
671	_	_	CD	_	_	_
672	rep1	rep1	NN	_	_	_
673	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
674	coli	coli	NN	_	_	_
675	_	_	NN	_	_	_
676	lactose	lactose	NN	_	_	_
677	_	_	CD	_	_	_
678	timepoint6	timepoint6	NN	_	_	_
679	_	_	CD	_	_	_
680	rep2	rep2	NN	_	_	_
681	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
682	coli	coli	NN	_	_	_
683	_	_	NN	_	_	_
684	lactose	lactose	NN	_	_	_
685	_	_	CD	_	_	_
686	timepoint6	timepoint6	NN	_	_	_
687	_	_	CD	_	_	_
688	rep3	rep3	NN	_	_	_
689	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
690	coli	coli	NN	_	_	_
691	_	_	NN	_	_	_
692	lactose	lactose	NN	_	_	_
693	_	_	CD	_	_	_
694	timepoint7	timepoint7	NN	_	_	_
695	_	_	CD	_	_	_
696	rep1	rep1	NN	_	_	_
697	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
698	coli	coli	NN	_	_	_
699	_	_	NN	_	_	_
700	lactose	lactose	NN	_	_	_
701	_	_	CD	_	_	_
702	timepoint7	timepoint7	NN	_	_	_
703	_	_	CD	_	_	_
704	rep2	rep2	NN	_	_	_
705	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
706	coli	coli	NN	_	_	_
707	_	_	NN	_	_	_
708	oxidativestress	oxidativestress	NN	_	_	_
709	_	_	CD	_	_	_
710	timepoint10	timepoint10	NN	_	_	_
711	_	_	CD	_	_	_
712	rep1	rep1	NN	_	_	_
713	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
714	coli	coli	NN	_	_	_
715	_	_	NN	_	_	_
716	oxidativestress	oxidativestress	NN	_	_	_
717	_	_	CD	_	_	_
718	timepoint10	timepoint10	NN	_	_	_
719	_	_	CD	_	_	_
720	rep2	rep2	NN	_	_	_
721	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
722	coli	coli	NN	_	_	_
723	_	_	NN	_	_	_
724	oxidativestress	oxidativestress	NN	_	_	_
725	_	_	CD	_	_	_
726	timepoint10	timepoint10	NN	_	_	_
727	_	_	CD	_	_	_
728	rep4	rep4	NN	_	_	_
729	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
730	coli	coli	NN	_	_	_
731	_	_	NN	_	_	_
732	oxidativestress	oxidativestress	NN	_	_	_
733	_	_	CD	_	_	_
734	timepoint11	timepoint11	NN	_	_	_
735	_	_	CD	_	_	_
736	rep1	rep1	NN	_	_	_
737	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
738	coli	coli	NN	_	_	_
739	_	_	NN	_	_	_
740	oxidativestress	oxidativestress	NN	_	_	_
741	_	_	CD	_	_	_
742	timepoint11	timepoint11	NN	_	_	_
743	_	_	CD	_	_	_
744	rep2	rep2	NN	_	_	_
745	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
746	coli	coli	NN	_	_	_
747	_	_	NN	_	_	_
748	oxidativestress	oxidativestress	NN	_	_	_
749	_	_	CD	_	_	_
750	timepoint11	timepoint11	NN	_	_	_
751	_	_	CD	_	_	_
752	rep4	rep4	NN	_	_	_
753	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
754	coli	coli	NN	_	_	_
755	_	_	NN	_	_	_
756	oxidativestress	oxidativestress	NN	_	_	_
757	_	_	CD	_	_	_
758	timepoint12	timepoint12	NN	_	_	_
759	_	_	CD	_	_	_
760	rep2	rep2	NN	_	_	_
761	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
762	coli	coli	NN	_	_	_
763	_	_	NN	_	_	_
764	oxidativestress	oxidativestress	NN	_	_	_
765	_	_	CD	_	_	_
766	timepoint1	timepoint1	NN	_	_	_
767	_	_	CD	_	_	_
768	rep1	rep1	NN	_	_	_
769	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
770	coli	coli	NN	_	_	_
771	_	_	NN	_	_	_
772	oxidativestress	oxidativestress	NN	_	_	_
773	_	_	CD	_	_	_
774	timepoint1	timepoint1	NN	_	_	_
775	_	_	CD	_	_	_
776	rep2	rep2	NN	_	_	_
777	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
778	coli	coli	NN	_	_	_
779	_	_	NN	_	_	_
780	oxidativestress	oxidativestress	NN	_	_	_
781	_	_	CD	_	_	_
782	timepoint1	timepoint1	NN	_	_	_
783	_	_	CD	_	_	_
784	rep4	rep4	NN	_	_	_
785	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
786	coli	coli	NN	_	_	_
787	_	_	NN	_	_	_
788	oxidativestress	oxidativestress	NN	_	_	_
789	_	_	CD	_	_	_
790	timepoint2	timepoint2	NN	_	_	_
791	_	_	CD	_	_	_
792	rep1	rep1	NN	_	_	_
793	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
794	coli	coli	NN	_	_	_
795	_	_	NN	_	_	_
796	oxidativestress	oxidativestress	NN	_	_	_
797	_	_	CD	_	_	_
798	timepoint2	timepoint2	NN	_	_	_
799	_	_	CD	_	_	_
800	rep2	rep2	NN	_	_	_
801	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
802	coli	coli	NN	_	_	_
803	_	_	NN	_	_	_
804	oxidativestress	oxidativestress	NN	_	_	_
805	_	_	CD	_	_	_
806	timepoint2	timepoint2	NN	_	_	_
807	_	_	CD	_	_	_
808	rep4	rep4	NN	_	_	_
809	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
810	coli	coli	NN	_	_	_
811	_	_	NN	_	_	_
812	oxidativestress	oxidativestress	NN	_	_	_
813	_	_	CD	_	_	_
814	timepoint3	timepoint3	NN	_	_	_
815	_	_	CD	_	_	_
816	rep1	rep1	NN	_	_	_
817	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
818	coli	coli	NN	_	_	_
819	_	_	NN	_	_	_
820	oxidativestress	oxidativestress	NN	_	_	_
821	_	_	CD	_	_	_
822	timepoint3	timepoint3	NN	_	_	_
823	_	_	CD	_	_	_
824	rep2	rep2	NN	_	_	_
825	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
826	coli	coli	NN	_	_	_
827	_	_	NN	_	_	_
828	oxidativestress	oxidativestress	NN	_	_	_
829	_	_	CD	_	_	_
830	timepoint3	timepoint3	NN	_	_	_
831	_	_	CD	_	_	_
832	rep4	rep4	NN	_	_	_
833	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
834	coli	coli	NN	_	_	_
835	_	_	NN	_	_	_
836	oxidativestress	oxidativestress	NN	_	_	_
837	_	_	CD	_	_	_
838	timepoint4	timepoint4	NN	_	_	_
839	_	_	CD	_	_	_
840	rep1	rep1	NN	_	_	_
841	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
842	coli	coli	NN	_	_	_
843	_	_	NN	_	_	_
844	oxidativestress	oxidativestress	NN	_	_	_
845	_	_	CD	_	_	_
846	timepoint4	timepoint4	NN	_	_	_
847	_	_	CD	_	_	_
848	rep2	rep2	NN	_	_	_
849	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
850	coli	coli	NN	_	_	_
851	_	_	NN	_	_	_
852	oxidativestress	oxidativestress	NN	_	_	_
853	_	_	CD	_	_	_
854	timepoint4	timepoint4	NN	_	_	_
855	_	_	CD	_	_	_
856	rep4	rep4	NN	_	_	_
857	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
858	coli	coli	NN	_	_	_
859	_	_	NN	_	_	_
860	oxidativestress	oxidativestress	NN	_	_	_
861	_	_	CD	_	_	_
862	timepoint5	timepoint5	NN	_	_	_
863	_	_	CD	_	_	_
864	rep1	rep1	NN	_	_	_
865	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
866	coli	coli	NN	_	_	_
867	_	_	NN	_	_	_
868	oxidativestress	oxidativestress	NN	_	_	_
869	_	_	CD	_	_	_
870	timepoint5	timepoint5	NN	_	_	_
871	_	_	CD	_	_	_
872	rep2	rep2	NN	_	_	_
873	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
874	coli	coli	NN	_	_	_
875	_	_	NN	_	_	_
876	oxidativestress	oxidativestress	NN	_	_	_
877	_	_	CD	_	_	_
878	timepoint5	timepoint5	NN	_	_	_
879	_	_	CD	_	_	_
880	rep4	rep4	NN	_	_	_
881	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
882	coli	coli	NN	_	_	_
883	_	_	NN	_	_	_
884	oxidativestress	oxidativestress	NN	_	_	_
885	_	_	CD	_	_	_
886	timepoint6	timepoint6	NN	_	_	_
887	_	_	CD	_	_	_
888	rep1	rep1	NN	_	_	_
889	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
890	coli	coli	NN	_	_	_
891	_	_	NN	_	_	_
892	oxidativestress	oxidativestress	NN	_	_	_
893	_	_	CD	_	_	_
894	timepoint6	timepoint6	NN	_	_	_
895	_	_	CD	_	_	_
896	rep2	rep2	NN	_	_	_
897	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
898	coli	coli	NN	_	_	_
899	_	_	NN	_	_	_
900	oxidativestress	oxidativestress	NN	_	_	_
901	_	_	CD	_	_	_
902	timepoint6	timepoint6	NN	_	_	_
903	_	_	CD	_	_	_
904	rep4	rep4	NN	_	_	_
905	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
906	coli	coli	NN	_	_	_
907	_	_	NN	_	_	_
908	oxidativestress	oxidativestress	NN	_	_	_
909	_	_	CD	_	_	_
910	timepoint7	timepoint7	NN	_	_	_
911	_	_	CD	_	_	_
912	rep1	rep1	NN	_	_	_
913	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
914	coli	coli	NN	_	_	_
915	_	_	NN	_	_	_
916	oxidativestress	oxidativestress	NN	_	_	_
917	_	_	CD	_	_	_
918	timepoint7	timepoint7	NN	_	_	_
919	_	_	CD	_	_	_
920	rep2	rep2	NN	_	_	_
921	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
922	coli	coli	NN	_	_	_
923	_	_	NN	_	_	_
924	oxidativestress	oxidativestress	NN	_	_	_
925	_	_	CD	_	_	_
926	timepoint7	timepoint7	NN	_	_	_
927	_	_	CD	_	_	_
928	rep4	rep4	NN	_	_	_
929	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
930	coli	coli	NN	_	_	_
931	_	_	NN	_	_	_
932	oxidativestress	oxidativestress	VBP	_	_	_
933	_	_	SYM	_	_	_
934	timepoint8	timepoint8	CD	_	_	_
935	_	_	CD	_	_	_
936	rep1	rep1	NN	_	_	_
937	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
938	coli	coli	NN	_	_	_
939	_	_	NN	_	_	_
940	oxidativestress	oxidativestress	VBP	_	_	_
941	_	_	SYM	_	_	_
942	timepoint8	timepoint8	CD	_	_	_
943	_	_	CD	_	_	_
944	rep2	rep2	NN	_	_	_
945	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
946	coli	coli	NN	_	_	_
947	_	_	NN	_	_	_
948	oxidativestress	oxidativestress	VBP	_	_	_
949	_	_	SYM	_	_	_
950	timepoint8	timepoint8	CD	_	_	_
951	_	_	CD	_	_	_
952	rep4	rep4	NN	_	_	_
953	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
954	coli	coli	NN	_	_	_
955	_	_	NN	_	_	_
956	oxidativestress	oxidativestress	NN	_	_	_
957	_	_	CD	_	_	_
958	timepoint9	timepoint9	NN	_	_	_
959	_	_	CD	_	_	_
960	rep1	rep1	NN	_	_	_
961	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
962	coli	coli	NN	_	_	_
963	_	_	NN	_	_	_
964	oxidativestress	oxidativestress	NN	_	_	_
965	_	_	CD	_	_	_
966	timepoint9	timepoint9	NN	_	_	_
967	_	_	CD	_	_	_
968	rep2	rep2	NN	_	_	_
969	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
970	coli	coli	NN	_	_	_
971	_	_	NN	_	_	_
972	oxidativestress	oxidativestress	NN	_	_	_
973	_	_	CD	_	_	_
974	timepoint9	timepoint9	NN	_	_	_
975	_	_	CD	_	_	_
976	rep4	rep4	NN	_	_	_
977	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
978	Escherichia	escherichia	FW	Organism	_	_
979	coli	coli	FW	Organism	_	_
980	_	_	FW	_	_	_
981	stress	stress	NN	_	_	_
982	experiment	experiment	NN	_	_	_
983	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
984	Escherichia	escherichia	FW	Organism	_	_
985	coli	coli	FW	Organism	_	_
986	str	str	FW	_	_	_
987	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	For	for	IN	_	_	_
4	further	further	JJ	_	_	_
5	analyses	analysis	NNS	_	_	_
6	the	the	DT	_	_	_
7	processed	process	VBN	_	_	_
8	signal	signal	NN	_	_	_
9	intensities	intensity	NNS	_	_	_
10	of	of	IN	_	_	_
11	all	all	DT	_	_	_
12	coding	code	VBG	_	_	_
13	regions	region	NNS	_	_	_
14	and	and	CC	_	_	_
15	RNA	rna	NN	_	_	_
16	genes	gene	NNS	_	_	_
17	were	be	VBD	_	_	_
18	extracted	extract	VBN	_	_	_
19	and	and	CC	_	_	_
20	used	use	VBN	_	_	_
21	.	.	.	_	_	_

1	Variance	variance	NN	_	_	_
2	stabilization	stabilization	NN	_	_	_
3	and	and	CC	_	_	_
4	normalization	normalization	NN	_	_	_
5	of	of	IN	_	_	_
6	the	the	DT	_	_	_
7	extracted	extract	VBN	_	_	_
8	intensities	intensity	NNS	_	_	_
9	were	be	VBD	_	_	_
10	performed	perform	VBN	_	_	_
11	with	with	IN	_	_	_
12	the	the	DT	_	_	_
13	vsn	vsn	NN	_	_	_
14	packages	package	NNS	_	_	_
15	of	of	IN	_	_	_
16	the	the	DT	_	_	_
17	R	r	NN	_	_	_
18	software	software	NN	_	_	_
19	environment	environment	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	R	r	NN	_	_	_
22	Development	development	NN	_	_	_
23	Core	core	NN	_	_	_
24	Team	Team	NNP	_	_	_
25	,	,	,	_	_	_
26	2007	2007	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	and	and	CC	_	_	_
29	back-transformed	back-transformed	JJ	_	_	_
30	to	to	TO	_	_	_
31	normal	normal	JJ	_	_	_
32	intensity	intensity	NN	_	_	_
33	scale	scale	NN	_	_	_
34	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	probeset	probeset	NN	_	_	_
4	,	,	,	_	_	_
5	e.g.	e.g.	FW	_	_	_
6	all	all	DT	_	_	_
7	probes	probe	NNS	_	_	_
8	representing	represent	VBG	_	_	_
9	for	for	IN	_	_	_
10	example	example	NN	_	_	_
11	,	,	,	_	_	_
12	a	a	DT	_	_	_
13	single	single	JJ	_	_	_
14	coding	coding	NN	_	_	_
15	gene	gene	NN	_	_	_
16	,	,	,	_	_	_
17	outliers	outlier	NNS	_	_	_
18	were	be	VBD	_	_	_
19	removed	remove	VBN	_	_	_
20	by	by	IN	_	_	_
21	boxplot	boxplot	NN	_	_	_
22	statistics	statistics	NNS	_	_	_
23	and	and	CC	_	_	_
24	the	the	DT	_	_	_
25	outlier-removed	outlier-removed	JJ	_	_	_
26	probe	probe	NN	_	_	_
27	intensities	intensity	NNS	_	_	_
28	were	be	VBD	_	_	_
29	averaged	average	VBN	_	_	_
30	in	in	IN	_	_	_
31	a	a	DT	_	_	_
32	robust	robust	JJ	_	_	_
33	way	way	NN	_	_	_
34	by	by	IN	_	_	_
35	computing	compute	VBG	_	_	_
36	the	the	DT	_	_	_
37	Tukey	tukey	NN	_	_	_
38	biweight	biweight	NN	_	_	_
39	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Oxidative	oxidative	JJ	_	_	_
3	stress	stress	NN	_	_	_
4	200	200	CD	_	_	_
5	ug	ug	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	RNA	rna	NN	_	_	_
8	was	be	VBD	_	_	_
9	extracted	extract	VBN	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	Qiagen	Qiagen	NNP	_	_	_
13	RNeasy	RNeasy	NNP	_	_	_
14	Mini	Mini	NNP	_	_	_
15	Kit	kit	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	74104	74104	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	and	and	CC	_	_	_
20	mechanical	mechanical	JJ	_	_	_
21	cell	cell	NN	_	_	_
22	disruption	disruption	NN	_	_	_
23	with	with	IN	_	_	_
24	glass	glass	NN	_	_	_
25	beads	bead	NNS	_	_	_
26	but	but	CC	_	_	_
27	without	without	IN	_	_	_
28	enzymatic	enzymatic	JJ	_	_	_
29	lysis	lysis	NN	_	_	_
30	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	was	be	VBD	_	_	_
3	carried	carry	VBN	_	_	_
4	out	out	RP	_	_	_
5	in	in	IN	_	_	_
6	the	the	DT	_	_	_
7	Qiagen	Qiagen	NNP	_	_	_
8	RNeasy	RNeasy	NNP	_	_	_
9	kit	kit	NN	_	_	_
10	lysis	lysis	NN	_	_	_
11	RLT	rlt	NN	_	_	_
12	buffer	buffer	NN	_	_	_
13	with	with	IN	_	_	_
14	beta-mercaptethanol	beta-mercaptethanol	NN	_	_	_
15	,	,	,	_	_	_
16	according	accord	VBG	_	_	_
17	to	to	TO	_	_	_
18	the	the	DT	_	_	_
19	manufacturer	manufacturer	NN	_	_	_
20	's	's	POS	_	_	_
21	recommendations	recommendation	NNS	_	_	_
22	.	.	.	_	_	_

1	Mechanical	mechanical	JJ	_	_	_
2	cell	cell	NN	_	_	_
3	disruption	disruption	NN	_	_	_
4	was	be	VBD	_	_	_
5	completed	complete	VBN	_	_	_
6	through	through	IN	_	_	_
7	shaking	shake	VBG	_	_	_
8	for	for	IN	_	_	_
9	five	five	CD	_	_	_
10	min	min	NN	_	_	_
11	using	use	VBG	_	_	_
12	a	a	DT	_	_	_
13	Retsch	Retsch	NNP	_	_	_
14	mill	mill	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Retsch	retsch	JJ	_	_	_
17	MM200	mm200	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	on	on	IN	_	_	_
20	maximum	maximum	NN	_	_	_
21	speed	speed	NN	_	_	_
22	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	subsequently	subsequently	RB	_	_	_
4	cleaned	clean	VBN	_	_	_
5	on-column	on-column	JJ	_	_	_
6	with	with	IN	_	_	_
7	an	a	DT	_	_	_
8	additional	additional	JJ	_	_	_
9	DNase	dnase	NN	_	_	_
10	treatment	treatment	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	Qiagen	NNP	_	_	_
13	79254	79254	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	quality	quality	NN	_	_	_
3	of	of	IN	_	_	_
4	extracted	extract	VBN	_	_	_
5	RNA	rna	NN	_	_	_
6	was	be	VBD	_	_	_
7	determined	determine	VBN	_	_	_
8	with	with	IN	_	_	_
9	an	a	DT	_	_	_
10	Agilent	Agilent	NNP	_	_	_
11	2100	2100	CD	_	_	_
12	bioanalyzer	bioanalyzer	NN	_	_	_
13	having	have	VBG	_	_	_
14	used	use	VBN	_	_	_
15	an	a	DT	_	_	_
16	Agilent	agilent	JJ	_	_	_
17	RNA	rna	NN	_	_	_
18	6000	6000	CD	_	_	_
19	Nano	Nano	NNP	_	_	_
20	Kit	kit	NN	_	_	_
21	according	accord	VBG	_	_	_
22	to	to	TO	_	_	_
23	the	the	DT	_	_	_
24	manufacturer	manufacturer	NN	_	_	_
25	's	's	POS	_	_	_
26	recommendations	recommendation	NNS	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	group	group	NN	_	_	_
4	:	:	:	_	_	_
5	cold	cold	JJ	_	_	_
6	stress	stress	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	treatment	treatment	NN	_	_	_
9	group	group	NN	_	_	_
10	:	:	:	_	_	_
11	control	control	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	treatment	treatment	NN	_	_	_
14	group	group	NN	_	_	_
15	:	:	:	_	_	_
16	heat	heat	NN	_	_	_
17	stress	stress	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	treatment	treatment	NN	_	_	_
20	group	group	NN	_	_	_
21	:	:	:	_	_	_
22	lactose	lactose	NN	_	_	_
23	shift	shift	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	treatment	treatment	NN	_	_	_
26	group	group	NN	_	_	_
27	:	:	:	_	_	_
28	oxidative	oxidative	JJ	_	_	_
29	stress	stress	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	treatment	treatment	NN	_	_	_
32	time	time	NN	_	_	_
33	:	:	:	_	_	_
34	T10	t10	NN	_	_	_
35	:	:	:	_	_	_
36	210	210	CD	_	_	_
37	min	min	NN	_	_	_
38	after	after	IN	_	_	_
39	stress	stress	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	treatment	treatment	NN	_	_	_
42	time	time	NN	_	_	_
43	:	:	:	_	_	_
44	T11	t11	NN	_	_	_
45	:	:	:	_	_	_
46	235	235	CD	_	_	_
47	min	min	NN	_	_	_
48	after	after	IN	_	_	_
49	stress	stress	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	treatment	treatment	NN	_	_	_
52	time	time	NN	_	_	_
53	:	:	:	_	_	_
54	T12	t12	NN	_	_	_
55	:	:	:	_	_	_
56	260	260	CD	_	_	_
57	min	min	NN	_	_	_
58	after	after	IN	_	_	_
59	stress	stress	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	treatment	treatment	NN	_	_	_
62	time	time	NN	_	_	_
63	:	:	:	_	_	_
64	T1	t1	NN	_	_	_
65	:	:	:	_	_	_
66	OD	od	NN	_	_	_
67	0.3	0.3	CD	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	treatment	treatment	NN	_	_	_
70	time	time	NN	_	_	_
71	:	:	:	_	_	_
72	T1	t1	NN	_	_	_
73	:	:	:	_	_	_
74	OD	od	NN	_	_	_
75	0.5	0.5	CD	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	treatment	treatment	NN	_	_	_
78	time	time	NN	_	_	_
79	:	:	:	_	_	_
80	T2	t2	NN	_	_	_
81	:	:	:	_	_	_
82	OD	od	NN	_	_	_
83	0.5	0.5	CD	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	treatment	treatment	NN	_	_	_
86	time	time	NN	_	_	_
87	:	:	:	_	_	_
88	T2	t2	NN	_	_	_
89	:	:	:	_	_	_
90	OD	od	NN	_	_	_
91	0.6	0.6	CD	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	treatment	treatment	NN	_	_	_
94	time	time	NN	_	_	_
95	:	:	:	_	_	_
96	T3	t3	NN	_	_	_
97	:	:	:	_	_	_
98	10	10	CD	_	_	_
99	min	min	NN	_	_	_
100	after	after	IN	_	_	_
101	reaching	reach	VBG	_	_	_
102	OD	od	NN	_	_	_
103	0.6	0.6	CD	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	treatment	treatment	NN	_	_	_
106	time	time	NN	_	_	_
107	:	:	:	_	_	_
108	T3	t3	NN	_	_	_
109	:	:	:	_	_	_
110	10	10	CD	_	_	_
111	min	min	NN	_	_	_
112	after	after	IN	_	_	_
113	stress	stress	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	treatment	treatment	NN	_	_	_
116	time	time	NN	_	_	_
117	:	:	:	_	_	_
118	T3	t3	NN	_	_	_
119	:	:	:	_	_	_
120	OD	od	NN	_	_	_
121	0.6	0.6	CD	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	treatment	treatment	NN	_	_	_
124	time	time	NN	_	_	_
125	:	:	:	_	_	_
126	T3	t3	NN	_	_	_
127	:	:	:	_	_	_
128	OD	od	NN	_	_	_
129	0.7	0.7	CD	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	treatment	treatment	NN	_	_	_
132	time	time	NN	_	_	_
133	:	:	:	_	_	_
134	T4	t4	NN	_	_	_
135	:	:	:	_	_	_
136	10	10	CD	_	_	_
137	min	min	NN	_	_	_
138	after	after	IN	_	_	_
139	growth	growth	NN	_	_	_
140	lag	lag	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	treatment	treatment	NN	_	_	_
143	time	time	NN	_	_	_
144	:	:	:	_	_	_
145	T4	t4	NN	_	_	_
146	:	:	:	_	_	_
147	10	10	CD	_	_	_
148	min	min	NN	_	_	_
149	after	after	IN	_	_	_
150	stress	stress	NN	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	treatment	treatment	NN	_	_	_
153	time	time	NN	_	_	_
154	:	:	:	_	_	_
155	T4	t4	NN	_	_	_
156	:	:	:	_	_	_
157	20	20	CD	_	_	_
158	min	min	NN	_	_	_
159	after	after	IN	_	_	_
160	reaching	reach	VBG	_	_	_
161	OD	od	NN	_	_	_
162	0.6	0.6	CD	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	treatment	treatment	NN	_	_	_
165	time	time	NN	_	_	_
166	:	:	:	_	_	_
167	T4	t4	NN	_	_	_
168	:	:	:	_	_	_
169	20	20	CD	_	_	_
170	min	min	NN	_	_	_
171	after	after	IN	_	_	_
172	stress	stress	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	treatment	treatment	NN	_	_	_
175	time	time	NN	_	_	_
176	:	:	:	_	_	_
177	T5	t5	NN	_	_	_
178	:	:	:	_	_	_
179	20	20	CD	_	_	_
180	min	min	NN	_	_	_
181	after	after	IN	_	_	_
182	growth	growth	NN	_	_	_
183	lag	lag	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	treatment	treatment	NN	_	_	_
186	time	time	NN	_	_	_
187	:	:	:	_	_	_
188	T5	t5	NN	_	_	_
189	:	:	:	_	_	_
190	20	20	CD	_	_	_
191	min	min	NN	_	_	_
192	after	after	IN	_	_	_
193	stress	stress	NN	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	treatment	treatment	NN	_	_	_
196	time	time	NN	_	_	_
197	:	:	:	_	_	_
198	T5	t5	NN	_	_	_
199	:	:	:	_	_	_
200	30	30	CD	_	_	_
201	min	min	NN	_	_	_
202	after	after	IN	_	_	_
203	reaching	reach	VBG	_	_	_
204	OD	od	NN	_	_	_
205	0.6	0.6	CD	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	treatment	treatment	NN	_	_	_
208	time	time	NN	_	_	_
209	:	:	:	_	_	_
210	T5	t5	NN	_	_	_
211	:	:	:	_	_	_
212	30	30	CD	_	_	_
213	min	min	NN	_	_	_
214	after	after	IN	_	_	_
215	stress	stress	NN	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	treatment	treatment	NN	_	_	_
218	time	time	NN	_	_	_
219	:	:	:	_	_	_
220	T6	t6	NN	_	_	_
221	:	:	:	_	_	_
222	30	30	CD	_	_	_
223	min	min	NN	_	_	_
224	after	after	IN	_	_	_
225	growth	growth	NN	_	_	_
226	lag	lag	NN	_	_	_
227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
228	treatment	treatment	NN	_	_	_
229	time	time	NN	_	_	_
230	:	:	:	_	_	_
231	T6	t6	NN	_	_	_
232	:	:	:	_	_	_
233	30	30	CD	_	_	_
234	min	min	NN	_	_	_
235	after	after	IN	_	_	_
236	stress	stress	NN	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	treatment	treatment	NN	_	_	_
239	time	time	NN	_	_	_
240	:	:	:	_	_	_
241	T6	t6	NN	_	_	_
242	:	:	:	_	_	_
243	40	40	CD	_	_	_
244	min	min	NN	_	_	_
245	after	after	IN	_	_	_
246	reaching	reach	VBG	_	_	_
247	OD	od	NN	_	_	_
248	0.6	0.6	CD	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	treatment	treatment	NN	_	_	_
251	time	time	NN	_	_	_
252	:	:	:	_	_	_
253	T6	t6	NN	_	_	_
254	:	:	:	_	_	_
255	40	40	CD	_	_	_
256	min	min	NN	_	_	_
257	after	after	IN	_	_	_
258	stress	stress	NN	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	treatment	treatment	NN	_	_	_
261	time	time	NN	_	_	_
262	:	:	:	_	_	_
263	T7	t7	NN	_	_	_
264	:	:	:	_	_	_
265	40	40	CD	_	_	_
266	min	min	NN	_	_	_
267	after	after	IN	_	_	_
268	growth	growth	NN	_	_	_
269	lag	lag	NN	_	_	_
270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
271	treatment	treatment	NN	_	_	_
272	time	time	NN	_	_	_
273	:	:	:	_	_	_
274	T7	t7	NN	_	_	_
275	:	:	:	_	_	_
276	40	40	CD	_	_	_
277	min	min	NN	_	_	_
278	after	after	IN	_	_	_
279	stress	stress	NN	_	_	_
280	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
281	treatment	treatment	NN	_	_	_
282	time	time	NN	_	_	_
283	:	:	:	_	_	_
284	T7	t7	NN	_	_	_
285	:	:	:	_	_	_
286	50	50	CD	_	_	_
287	min	min	NN	_	_	_
288	after	after	IN	_	_	_
289	reaching	reach	VBG	_	_	_
290	OD	od	NN	_	_	_
291	0.6	0.6	CD	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	treatment	treatment	NN	_	_	_
294	time	time	NN	_	_	_
295	:	:	:	_	_	_
296	T7	t7	NN	_	_	_
297	:	:	:	_	_	_
298	50	50	CD	_	_	_
299	min	min	NN	_	_	_
300	after	after	IN	_	_	_
301	stress	stress	NN	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
303	treatment	treatment	NN	_	_	_
304	time	time	NN	_	_	_
305	:	:	:	_	_	_
306	T8	t8	NN	_	_	_
307	:	:	:	_	_	_
308	90	90	CD	_	_	_
309	min	min	NN	_	_	_
310	after	after	IN	_	_	_
311	reaching	reach	VBG	_	_	_
312	OD	od	NN	_	_	_
313	0.6	0.6	CD	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	treatment	treatment	NN	_	_	_
316	time	time	NN	_	_	_
317	:	:	:	_	_	_
318	T8	t8	NN	_	_	_
319	:	:	:	_	_	_
320	90	90	CD	_	_	_
321	min	min	NN	_	_	_
322	after	after	IN	_	_	_
323	stress	stress	NN	_	_	_
324	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
325	treatment	treatment	NN	_	_	_
326	time	time	NN	_	_	_
327	:	:	:	_	_	_
328	T9	t9	NN	_	_	_
329	:	:	:	_	_	_
330	150	150	CD	_	_	_
331	min	min	NN	_	_	_
332	after	after	IN	_	_	_
333	stress	stress	NN	_	_	_
334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
335	bile	bile	NN	_	_	_
336	+1	+1	CD	_	_	_
337	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
338	bile	bile	NN	_	_	_
339	+2	+2	CD	_	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
341	bile	bile	NN	_	_	_
342	+3	+3	CD	_	_	_
343	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
344	ctrl1	ctrl1	NN	_	_	_
345	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
346	ctrl2	ctrl2	NN	_	_	_
347	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
348	ctrl3	ctrl3	NN	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	E.coli	e.coli	NN	_	_	_
351	O157	o157	NN	_	_	_
352	:	:	:	_	_	_
353	H7	h7	NN	_	_	_
354	in	in	IN	_	_	_
355	LB	lb	NN	_	_	_
356	at	at	IN	_	_	_
357	mid-log	mid-log	JJ	_	_	_
358	phase	phase	NN	_	_	_
359	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
360	Escherichia	escherichia	FW	Organism	_	_
361	coli	coli	FW	Organism	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
363	growth	growth	NN	_	_	_
364	media	media	NNS	_	_	_
365	:	:	:	_	_	_
366	LB	lb	NN	_	_	_
367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
368	growth	growth	NN	_	_	_
369	media	media	NNS	_	_	_
370	:	:	:	_	_	_
371	LB	lb	NN	_	_	_
372	;	;	:	_	_	_
373	0.8	0.8	CD	_	_	_
374	%	%	NN	_	_	_
375	bile	bile	NN	_	_	_
376	salts	salt	NNS	_	_	_
377	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
378	growth	growth	NN	_	_	_
379	phase	phase	NN	_	_	_
380	:	:	:	_	_	_
381	mid-log	mid-log	JJ	_	_	_
382	phase	phase	NN	_	_	_
383	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
384	Hot	hot	JJ	_	_	_
385	phenol	phenol	NN	_	_	_
386	extraction	extraction	NN	_	_	_
387	of	of	IN	_	_	_
388	total	total	JJ	_	_	_
389	RNA	rna	NN	_	_	_
390	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	O157	o157	NN	_	_	_
3	:	:	:	_	_	_
4	H7	h7	NN	_	_	_
5	cells	cell	NNS	_	_	_
6	were	be	VBD	_	_	_
7	grown	grow	VBN	_	_	_
8	to	to	TO	_	_	_
9	mid-log	mid-log	JJ	_	_	_
10	phase	phase	NN	_	_	_
11	in	in	IN	_	_	_
12	Luria	Luria	NNP	MED	_	_
13	broth	broth	NN	MED	_	_
14	with	with	IN	_	_	_
15	or	or	CC	_	_	_
16	without	without	IN	_	_	_
17	0.8	0.8	CD	_	_	_
18	%	%	NN	_	_	_
19	bile	bile	NN	_	_	_
20	salts	salt	NNS	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	strain	strain	NN	_	_	_
5	O157	o157	NN	_	_	_
6	:	:	:	_	_	_
7	H7	h7	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
9	The	the	DT	_	_	_
10	data	datum	NNS	_	_	_
11	were	be	VBD	_	_	_
12	imported	import	VBN	_	_	_
13	into	into	IN	_	_	_
14	FlexArray	FlexArray	NNP	_	_	_
15	using	use	VBG	_	_	_
16	gc-RMA	gc-rma	NN	_	_	_
17	preprocessing	preprocessing	NN	_	_	_
18	for	for	IN	_	_	_
19	analysis	analysis	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	8	8	CD	_	_	_
3	ml	ml	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	culture	culture	NN	_	_	_
7	was	be	VBD	_	_	_
8	mixed	mix	VBN	_	_	_
9	with	with	IN	_	_	_
10	1	1	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Escherichia	escherichia	FW	Organism	_	_
13	coli	coli	FW	Organism	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	serotype	serotype	NN	_	_	_
16	:	:	:	_	_	_
17	o157	o157	NN	_	_	_
18	:	:	:	_	_	_
19	H7	h7	NN	_	_	_
20	clade	clade	NN	_	_	_
21	2	2	CD	_	_	_
22	,	,	,	_	_	_
23	stx	stx	NN	_	_	_
24	1	1	CD	_	_	_
25	and	and	CC	_	_	_
26	2	2	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
28	serotype	serotype	NN	_	_	_
29	:	:	:	_	_	_
30	o157	o157	NN	_	_	_
31	:	:	:	_	_	_
32	H7	h7	NN	_	_	_
33	clade	clade	NN	_	_	_
34	2	2	CD	_	_	_
35	,	,	,	_	_	_
36	stx	stx	NN	_	_	_
37	2	2	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	serotype	serotype	NN	_	_	_
40	:	:	:	_	_	_
41	o157	o157	NN	_	_	_
42	:	:	:	_	_	_
43	H7	h7	NN	_	_	_
44	clade	clade	NN	_	_	_
45	8	8	CD	_	_	_
46	,	,	,	_	_	_
47	stx	stx	NN	_	_	_
48	2	2	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	serotype	serotype	NN	_	_	_
51	:	:	:	_	_	_
52	o157	o157	NN	_	_	_
53	:	:	:	_	_	_
54	H7	h7	NN	_	_	_
55	clade	clade	NN	_	_	_
56	8	8	CD	_	_	_
57	,	,	,	_	_	_
58	stx	stx	NN	_	_	_
59	2	2	CD	_	_	_
60	and	and	CC	_	_	_
61	2c	2c	JJ	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	strains	strain	NNS	_	_	_
64	TW014359	tw014359	NN	_	_	_
65	vs	vs	CC	_	_	_
66	TW04863	tw04863	NN	_	_	_
67	epithelial	epithelial	JJ	_	_	_
68	exposure	exposure	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	strains	strain	NNS	_	_	_
71	TW014359	tw014359	NN	_	_	_
72	vs	vs	CC	_	_	_
73	TW11037	tw11037	NN	_	_	_
74	epithelial	epithelial	JJ	_	_	_
75	exposure	exposure	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	strains	strain	NNS	_	_	_
78	TW02883	tw02883	NN	_	_	_
79	vs	vs	CC	_	_	_
80	TW11028	tw11028	NN	_	_	_
81	epithelial	epithelial	JJ	_	_	_
82	exposure	exposure	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	strains	strain	NNS	_	_	_
85	TW04863	tw04863	NN	_	_	_
86	vs	vs	CC	_	_	_
87	TW14279	tw14279	NN	_	_	_
88	epithelial	epithelial	JJ	_	_	_
89	exposure	exposure	NN	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	strains	strain	NNS	_	_	_
92	TW07591	tw07591	NN	_	_	_
93	vs	vs	CC	_	_	_
94	TW09098	tw09098	NN	_	_	_
95	epithelial	epithelial	JJ	_	_	_
96	exposure	exposure	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	strains	strain	NNS	_	_	_
99	TW07937	tw07937	NN	_	_	_
100	vs	vs	CC	_	_	_
101	TW11185	tw11185	NN	_	_	_
102	epithelial	epithelial	JJ	_	_	_
103	exposure	exposure	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	strains	strain	NNS	_	_	_
106	TW07961	tw07961	NN	_	_	_
107	vs	vs	CC	_	_	_
108	TW08610	tw08610	NN	_	_	_
109	epithelial	epithelial	JJ	_	_	_
110	exposure	exposure	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	strains	strain	NNS	_	_	_
113	TW07961	tw07961	NN	_	_	_
114	vs	vs	CC	_	_	_
115	TW11029	tw11029	NN	_	_	_
116	epithelial	epithelial	JJ	_	_	_
117	exposure	exposure	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	strains	strain	NNS	_	_	_
120	TW08030	tw08030	NN	_	_	_
121	vs	vs	CC	_	_	_
122	TW10045	tw10045	NN	_	_	_
123	epithelial	epithelial	JJ	_	_	_
124	exposure	exposure	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	strains	strain	NNS	_	_	_
127	TW08609	tw08609	NN	_	_	_
128	vs	vs	CC	_	_	_
129	TW08030	tw08030	NN	_	_	_
130	epithelial	epithelial	JJ	_	_	_
131	exposure	exposure	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	strains	strain	NNS	_	_	_
134	TW08609	tw08609	NN	_	_	_
135	vs	vs	CC	_	_	_
136	TW08623	tw08623	NN	_	_	_
137	epithelial	epithelial	JJ	_	_	_
138	exposure	exposure	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	strains	strain	NNS	_	_	_
141	TW08609	tw08609	NN	_	_	_
142	vs	vs	CC	_	_	_
143	TW11110	tw11110	NN	_	_	_
144	epithelial	epithelial	JJ	_	_	_
145	exposure	exposure	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	strains	strain	NNS	_	_	_
148	TW08610	tw08610	NN	_	_	_
149	vs	vs	CC	_	_	_
150	TW11110	tw11110	NN	_	_	_
151	epithelial	epithelial	JJ	_	_	_
152	exposure	exposure	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	strains	strain	NNS	_	_	_
155	TW08623	tw08623	NN	_	_	_
156	vs	vs	CC	_	_	_
157	TW02883	tw02883	NN	_	_	_
158	epithelial	epithelial	JJ	_	_	_
159	exposure	exposure	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	strains	strain	NNS	_	_	_
162	TW08623	tw08623	NN	_	_	_
163	vs	vs	CC	_	_	_
164	TW08030	tw08030	NN	_	_	_
165	epithelial	epithelial	JJ	_	_	_
166	exposure	exposure	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	strains	strain	NNS	_	_	_
169	TW08635	tw08635	NN	_	_	_
170	vs	vs	CC	_	_	_
171	TW09098	tw09098	NN	_	_	_
172	epithelial	epithelial	JJ	_	_	_
173	exposure	exposure	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	strains	strain	NNS	_	_	_
176	TW09098	tw09098	NN	_	_	_
177	vs	vs	CC	_	_	_
178	TW11308	tw11308	NN	_	_	_
179	epithelial	epithelial	JJ	_	_	_
180	exposure	exposure	NN	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	strains	strain	NNS	_	_	_
183	TW09189	tw09189	NN	_	_	_
184	vs	vs	CC	_	_	_
185	TW11032	tw11032	NN	_	_	_
186	epithelial	epithelial	JJ	_	_	_
187	exposure	exposure	NN	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	strains	strain	NNS	_	_	_
190	TW09189	tw09189	NN	_	_	_
191	vs	vs	CC	_	_	_
192	TW14279	tw14279	NN	_	_	_
193	epithelial	epithelial	JJ	_	_	_
194	exposure	exposure	NN	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	strains	strain	NNS	_	_	_
197	TW10012	tw10012	NN	_	_	_
198	vs	vs	CC	_	_	_
199	TW11037	tw11037	NN	_	_	_
200	epithelial	epithelial	JJ	_	_	_
201	exposure	exposure	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	strains	strain	NNS	_	_	_
204	TW10012	tw10012	NN	_	_	_
205	vs	vs	CC	_	_	_
206	TW14313	tw14313	NN	_	_	_
207	epithelial	epithelial	JJ	_	_	_
208	exposure	exposure	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	strains	strain	NNS	_	_	_
211	TW10045	tw10045	NN	_	_	_
212	vs	vs	CC	_	_	_
213	TW07937	tw07937	NN	_	_	_
214	epithelial	epithelial	JJ	_	_	_
215	exposure	exposure	NN	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	strains	strain	NNS	_	_	_
218	TW11028	tw11028	NN	_	_	_
219	vs	vs	CC	_	_	_
220	TW07937	tw07937	NN	_	_	_
221	epithelial	epithelial	JJ	_	_	_
222	exposure	exposure	NN	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	strains	strain	NNS	_	_	_
225	TW11028	tw11028	NN	_	_	_
226	vs	vs	CC	_	_	_
227	TW11308	tw11308	NN	_	_	_
228	epithelial	epithelial	JJ	_	_	_
229	exposure	exposure	NN	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
231	strains	strain	NNS	_	_	_
232	TW11029	tw11029	NN	_	_	_
233	vs	vs	CC	_	_	_
234	TW02883	tw02883	NN	_	_	_
235	epithelial	epithelial	JJ	_	_	_
236	exposure	exposure	NN	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	strains	strain	NNS	_	_	_
239	TW11029	tw11029	NN	_	_	_
240	vs	vs	CC	_	_	_
241	TW08610	tw08610	NN	_	_	_
242	epithelial	epithelial	JJ	_	_	_
243	exposure	exposure	NN	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	strains	strain	NNS	_	_	_
246	TW11032	tw11032	NN	_	_	_
247	vs	vs	CC	_	_	_
248	TW04863	tw04863	NN	_	_	_
249	epithelial	epithelial	JJ	_	_	_
250	exposure	exposure	NN	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	strains	strain	NNS	_	_	_
253	TW11032	tw11032	NN	_	_	_
254	vs	vs	CC	_	_	_
255	TW09189	tw09189	NN	_	_	_
256	epithelial	epithelial	JJ	_	_	_
257	exposure	exposure	NN	_	_	_
258	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
259	strains	strain	NNS	_	_	_
260	TW11037	tw11037	NN	_	_	_
261	vs	vs	CC	_	_	_
262	TW08635	tw08635	NN	_	_	_
263	epithelial	epithelial	JJ	_	_	_
264	exposure	exposure	NN	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	strains	strain	NNS	_	_	_
267	TW11110	tw11110	NN	_	_	_
268	vs	vs	CC	_	_	_
269	TW10012	tw10012	NN	_	_	_
270	epithelial	epithelial	JJ	_	_	_
271	exposure	exposure	NN	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	strains	strain	NNS	_	_	_
274	TW11185	tw11185	NN	_	_	_
275	vs	vs	CC	_	_	_
276	TW014313	tw014313	NN	_	_	_
277	epithelial	epithelial	JJ	_	_	_
278	exposure	exposure	NN	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	strains	strain	NNS	_	_	_
281	TW11185	tw11185	NN	_	_	_
282	vs	vs	CC	_	_	_
283	TW08635	tw08635	NN	_	_	_
284	epithelial	epithelial	JJ	_	_	_
285	exposure	exposure	NN	_	_	_
286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
287	strains	strain	NNS	_	_	_
288	TW11308	tw11308	NN	_	_	_
289	vs	vs	CC	_	_	_
290	TW07591	tw07591	NN	_	_	_
291	epithelial	epithelial	JJ	_	_	_
292	exposure	exposure	NN	_	_	_
293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
294	strains	strain	NNS	_	_	_
295	TW14279	tw14279	NN	_	_	_
296	vs	vs	CC	_	_	_
297	TW10045	tw10045	NN	_	_	_
298	epithelial	epithelial	JJ	_	_	_
299	exposure	exposure	NN	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	strains	strain	NNS	_	_	_
302	TW14313	tw14313	NN	_	_	_
303	vs	vs	CC	_	_	_
304	TW07591	tw07591	NN	_	_	_
305	epithelial	epithelial	JJ	_	_	_
306	exposure	exposure	NN	_	_	_
307	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
308	strains	strain	NNS	_	_	_
309	TW14359	tw14359	NN	_	_	_
310	vs	vs	CC	_	_	_
311	TW07961	tw07961	NN	_	_	_
312	epithelial	epithelial	JJ	_	_	_
313	exposure	exposure	NN	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	strain	strain	NN	_	_	_
316	TW02883	tw02883	NN	_	_	_
317	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
318	strain	strain	NN	_	_	_
319	TW02883	tw02883	NN	_	_	_
320	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
321	strain	strain	NN	_	_	_
322	TW04863	tw04863	NN	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	strain	strain	NN	_	_	_
325	TW07591	tw07591	NN	_	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	strain	strain	NN	_	_	_
328	TW07937	tw07937	NN	_	_	_
329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
330	strain	strain	NN	_	_	_
331	TW07961	tw07961	NN	_	_	_
332	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
333	strain	strain	NN	_	_	_
334	TW07961	tw07961	NN	_	_	_
335	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
336	strain	strain	NN	_	_	_
337	TW08030	tw08030	NN	_	_	_
338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
339	strain	strain	NN	_	_	_
340	TW08609	tw08609	NN	_	_	_
341	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
342	strain	strain	NN	_	_	_
343	TW08609	tw08609	NN	_	_	_
344	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
345	strain	strain	NN	_	_	_
346	TW08610	tw08610	NN	_	_	_
347	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
348	strain	strain	NN	_	_	_
349	TW08623	tw08623	NN	_	_	_
350	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
351	strain	strain	NN	_	_	_
352	TW08635	tw08635	NN	_	_	_
353	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
354	strain	strain	NN	_	_	_
355	TW08635	tw08635	NN	_	_	_
356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
357	strain	strain	NN	_	_	_
358	TW09098	tw09098	NN	_	_	_
359	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
360	strain	strain	NN	_	_	_
361	TW09098	tw09098	NN	_	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
363	strain	strain	NN	_	_	_
364	TW09189	tw09189	NN	_	_	_
365	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
366	strain	strain	NN	_	_	_
367	TW10012	tw10012	NN	_	_	_
368	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
369	strain	strain	NN	_	_	_
370	TW10045	tw10045	NN	_	_	_
371	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
372	strain	strain	NN	_	_	_
373	TW10045	tw10045	NN	_	_	_
374	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
375	strain	strain	NN	_	_	_
376	TW11028	tw11028	NN	_	_	_
377	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
378	strain	strain	NN	_	_	_
379	TW11029	tw11029	NN	_	_	_
380	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
381	strain	strain	NN	_	_	_
382	TW11029	tw11029	NN	_	_	_
383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
384	strain	strain	NN	_	_	_
385	TW11032	tw11032	NN	_	_	_
386	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
387	strain	strain	NN	_	_	_
388	TW11032	tw11032	NN	_	_	_
389	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
390	strain	strain	NN	_	_	_
391	TW11037	tw11037	NN	_	_	_
392	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
393	strain	strain	NN	_	_	_
394	TW11110	tw11110	NN	_	_	_
395	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
396	strain	strain	NN	_	_	_
397	TW11110	tw11110	NN	_	_	_
398	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
399	strain	strain	NN	_	_	_
400	TW11185	tw11185	NN	_	_	_
401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
402	strain	strain	NN	_	_	_
403	TW11185	tw11185	NN	_	_	_
404	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
405	strain	strain	NN	_	_	_
406	TW11308	tw11308	NN	_	_	_
407	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
408	strain	strain	NN	_	_	_
409	TW11308	tw11308	NN	_	_	_
410	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
411	strain	strain	NN	_	_	_
412	TW14279	tw14279	NN	_	_	_
413	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
414	strain	strain	NN	_	_	_
415	TW14279	tw14279	NN	_	_	_
416	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
417	strain	strain	NN	_	_	_
418	TW14313	tw14313	NN	_	_	_
419	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
420	strain	strain	NN	_	_	_
421	TW14359	tw14359	NN	_	_	_
422	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
423	Thirty-six	thirty-six	CD	_	_	_
424	dye-swap	dye-swap	JJ	_	_	_
425	hybridizations	hybridization	NNS	_	_	_
426	were	be	VBD	_	_	_
427	performed	perform	VBN	_	_	_
428	between	between	IN	_	_	_
429	four	four	CD	_	_	_
430	groups	group	NNS	_	_	_
431	with	with	IN	_	_	_
432	six	six	CD	_	_	_
433	strains	strain	NNS	_	_	_
434	per	per	IN	_	_	_
435	group	group	NN	_	_	_
436	,	,	,	_	_	_
437	according	accord	VBG	_	_	_
438	to	to	TO	_	_	_
439	a	a	DT	_	_	_
440	balanced	balanced	JJ	_	_	_
441	double	double	JJ	_	_	_
442	loop	loop	NN	_	_	_
443	design	design	NN	_	_	_
444	.	.	.	_	_	_

1	Strains	strain	NNS	_	_	_
2	were	be	VBD	_	_	_
3	grouped	group	VBN	_	_	_
4	based	base	VBN	_	_	_
5	on	on	IN	_	_	_
6	cladestx	cladestx	NN	_	_	_
7	profiles	profile	NNS	_	_	_
8	and	and	CC	_	_	_
9	each	each	DT	_	_	_
10	strain	strain	NN	_	_	_
11	was	be	VBD	_	_	_
12	considered	consider	VBN	_	_	_
13	an	a	DT	_	_	_
14	independent	independent	JJ	_	_	_
15	biological	biological	JJ	_	_	_
16	replicate	replicate	VB	_	_	_
17	of	of	IN	_	_	_
18	its	its	PRP$	_	_	_
19	group	group	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	n	n	NN	_	_	_
22	=	=	JJ	_	_	_
23	6	6	CD	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	six	six	CD	_	_	_
3	strains	strain	NNS	_	_	_
4	from	from	IN	_	_	_
5	each	each	DT	_	_	_
6	group	group	NN	_	_	_
7	were	be	VBD	_	_	_
8	randomly	randomly	RB	_	_	_
9	hybridized	hybridize	VBN	_	_	_
10	with	with	IN	_	_	_
11	six	six	CD	_	_	_
12	strains	strain	NNS	_	_	_
13	from	from	IN	_	_	_
14	every	every	DT	_	_	_
15	other	other	JJ	_	_	_
16	group	group	NN	_	_	_
17	;	;	:	_	_	_
18	each	each	DT	_	_	_
19	hybridization	hybridization	NN	_	_	_
20	compared	compare	VBN	_	_	_
21	a	a	DT	_	_	_
22	pair	pair	NN	_	_	_
23	of	of	IN	_	_	_
24	strains	strain	NNS	_	_	_
25	that	that	WDT	_	_	_
26	differed	differ	VBD	_	_	_
27	in	in	IN	_	_	_
28	either	either	CC	_	_	_
29	clade	clade	NN	_	_	_
30	or	or	CC	_	_	_
31	stx	stx	NN	_	_	_
32	profile	profile	NN	_	_	_
33	,	,	,	_	_	_
34	or	or	CC	_	_	_
35	both	both	DT	_	_	_
36	.	.	.	_	_	_

1	Subsequent	subsequent	JJ	_	_	_
2	to	to	TO	_	_	_
3	local	local	JJ	_	_	_
4	Lowess	Lowess	NNP	_	_	_
5	normalization	normalization	NN	_	_	_
6	,	,	,	_	_	_
7	averaging	averaging	NN	_	_	_
8	of	of	IN	_	_	_
9	replicate	replicate	VB	_	_	_
10	probes	probe	NNS	_	_	_
11	and	and	CC	_	_	_
12	log2	log2	NN	_	_	_
13	transformation	transformation	NN	_	_	_
14	,	,	,	_	_	_
15	the	the	DT	_	_	_
16	microarray	microarray	NN	_	_	_
17	data	datum	NNS	_	_	_
18	were	be	VBD	_	_	_
19	fitted	fit	VBN	_	_	_
20	to	to	TO	_	_	_
21	a	a	DT	_	_	_
22	2-factor	2-factor	NN	_	_	_
23	mixed	mixed	JJ	_	_	_
24	ANOVA	ANOVA	NNP	_	_	_
25	model	model	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	intensity	intensity	NN	_	_	_
28	=	=	JJ	_	_	_
29	Array	array	NN	_	_	_
30	+	+	CC	_	_	_
31	Dye	dye	NN	_	_	_
32	+	+	CC	_	_	_
33	Clade	clade	NN	_	_	_
34	+	+	CC	_	_	_
35	Stx	stx	NN	_	_	_
36	+	+	CC	_	_	_
37	Clade	clade	NN	_	_	_
38	:	:	:	_	_	_
39	Stx	stx	NN	_	_	_
40	+	+	CC	_	_	_
41	Sample	sample	NN	_	_	_
42	;	;	:	_	_	_
43	where	where	WRB	_	_	_
44	the	the	DT	_	_	_
45	biological	biological	JJ	_	_	_
46	replicate	replicate	VB	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	Sample	sample	NN	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	and	and	CC	_	_	_
51	array	array	NN	_	_	_
52	effects	effect	NNS	_	_	_
53	were	be	VBD	_	_	_
54	considered	consider	VBN	_	_	_
55	random	random	JJ	_	_	_
56	effects	effect	NNS	_	_	_
57	,	,	,	_	_	_
58	while	while	IN	_	_	_
59	all	all	DT	_	_	_
60	other	other	JJ	_	_	_
61	effects	effect	NNS	_	_	_
62	were	be	VBD	_	_	_
63	considered	consider	VBN	_	_	_
64	fixed	fixed	JJ	_	_	_
65	effects	effect	NNS	_	_	_
66	-RRB-	-rrb-	-RRB-	_	_	_
67	,	,	,	_	_	_
68	using	use	VBG	_	_	_
69	the	the	DT	_	_	_
70	MAANOVA	MAANOVA	NNP	_	_	_
71	package	package	NN	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	version	version	NN	_	_	_
74	0.98-8	0.98-8	CD	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	in	in	IN	_	_	_
77	R	r	NN	_	_	_
78	software	software	NN	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	version	version	NN	_	_	_
81	2.2.1	2.2.1	CD	_	_	_
82	-RRB-	-rrb-	-RRB-	_	_	_
83	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	model	model	NN	_	_	_
3	allows	allow	VBZ	_	_	_
4	independent	independent	JJ	_	_	_
5	consideration	consideration	NN	_	_	_
6	of	of	IN	_	_	_
7	the	the	DT	_	_	_
8	effect	effect	NN	_	_	_
9	of	of	IN	_	_	_
10	`	`	``	_	_	_
11	Clade	Clade	NNP	_	_	_
12	'	'	''	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	clade	clade	NN	_	_	_
15	divergence	divergence	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	and	and	CC	_	_	_
18	`	`	``	_	_	_
19	Stx	stx	FW	_	_	_
20	'	'	''	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	stx	stx	NN	_	_	_
23	type	type	NN	_	_	_
24	variation	variation	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	parameters	parameter	NNS	_	_	_
27	on	on	IN	_	_	_
28	differences	difference	NNS	_	_	_
29	in	in	IN	_	_	_
30	gene	gene	NN	_	_	_
31	expression	expression	NN	_	_	_
32	among	among	IN	_	_	_
33	O157	o157	NN	_	_	_
34	:	:	:	_	_	_
35	H7	h7	NN	_	_	_
36	strains	strain	NNS	_	_	_
37	,	,	,	_	_	_
38	as	as	RB	_	_	_
39	well	well	RB	_	_	_
40	as	as	IN	_	_	_
41	their	they	PRP$	_	_	_
42	interaction	interaction	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	combined	combine	VBN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	effect	effect	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	Clade	clade	NN	_	_	_
49	:	:	:	_	_	_
50	Stx	stx	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	.	.	.	_	_	_

1	Overall	overall	JJ	_	_	_
2	differences	difference	NNS	_	_	_
3	in	in	IN	_	_	_
4	gene	gene	NN	_	_	_
5	expression	expression	NN	_	_	_
6	between	between	IN	_	_	_
7	groups	group	NNS	_	_	_
8	were	be	VBD	_	_	_
9	determined	determine	VBN	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	Fs	f	NNS	_	_	_
13	test	test	NN	_	_	_
14	,	,	,	_	_	_
15	followed	follow	VBN	_	_	_
16	by	by	IN	_	_	_
17	pair-wise	pair-wise	JJ	_	_	_
18	contrasts	contrast	VBZ	_	_	_
19	to	to	TO	_	_	_
20	determine	determine	VB	_	_	_
21	significant	significant	JJ	_	_	_
22	differential	differential	JJ	_	_	_
23	expression	expression	NN	_	_	_
24	between	between	IN	_	_	_
25	each	each	DT	_	_	_
26	pair	pair	NN	_	_	_
27	of	of	IN	_	_	_
28	groups	group	NNS	_	_	_
29	.	.	.	_	_	_

1	Subsequently	subsequently	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	Fs	f	NNS	_	_	_
5	statistic	statistic	NN	_	_	_
6	was	be	VBD	_	_	_
7	estimated	estimate	VBN	_	_	_
8	for	for	IN	_	_	_
9	the	the	DT	_	_	_
10	`	`	``	_	_	_
11	Clade	clade	NN	_	_	_
12	'	'	''	_	_	_
13	effect	effect	NN	_	_	_
14	to	to	TO	_	_	_
15	determine	determine	VB	_	_	_
16	significant	significant	JJ	_	_	_
17	differences	difference	NNS	_	_	_
18	in	in	IN	_	_	_
19	gene	gene	NN	_	_	_
20	expression	expression	NN	_	_	_
21	between	between	IN	_	_	_
22	clades	clade	NNS	_	_	_
23	8	8	CD	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	n	n	NN	_	_	_
26	=	=	JJ	_	_	_
27	12	12	CD	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	and	and	CC	_	_	_
30	2	2	CD	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	n	n	NN	_	_	_
33	=	=	JJ	_	_	_
34	12	12	CD	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	,	,	,	_	_	_
37	regardless	regardless	RB	_	_	_
38	of	of	IN	_	_	_
39	stx	stx	NN	_	_	_
40	profile	profile	NN	_	_	_
41	.	.	.	_	_	_

1	Similarly	similarly	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	Fs	f	NNS	_	_	_
5	statistic	statistic	NN	_	_	_
6	was	be	VBD	_	_	_
7	estimated	estimate	VBN	_	_	_
8	for	for	IN	_	_	_
9	the	the	DT	_	_	_
10	`	`	``	_	_	_
11	Stx	stx	NN	_	_	_
12	'	'	''	_	_	_
13	effect	effect	NN	_	_	_
14	as	as	RB	_	_	_
15	well	well	RB	_	_	_
16	as	as	IN	_	_	_
17	the	the	DT	_	_	_
18	`	`	``	_	_	_
19	Clade	Clade	NNP	_	_	_
20	:	:	:	_	_	_
21	Stx	stx	NN	_	_	_
22	'	'	''	_	_	_
23	interaction	interaction	NN	_	_	_
24	effect	effect	NN	_	_	_
25	to	to	TO	_	_	_
26	examine	examine	VB	_	_	_
27	the	the	DT	_	_	_
28	combined	combined	JJ	_	_	_
29	effect	effect	NN	_	_	_
30	of	of	IN	_	_	_
31	clade	clade	NN	_	_	_
32	and	and	CC	_	_	_
33	stx	stx	NN	_	_	_
34	type	type	NN	_	_	_
35	on	on	IN	_	_	_
36	differences	difference	NNS	_	_	_
37	in	in	IN	_	_	_
38	gene	gene	NN	_	_	_
39	expression	expression	NN	_	_	_
40	among	among	IN	_	_	_
41	O157	o157	NN	_	_	_
42	:	:	:	_	_	_
43	H7	h7	NN	_	_	_
44	strains	strain	NNS	_	_	_
45	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	other	other	JJ	_	_	_
3	words	word	NNS	_	_	_
4	,	,	,	_	_	_
5	this	this	DT	_	_	_
6	analysis	analysis	NN	_	_	_
7	will	will	MD	_	_	_
8	determine	determine	VB	_	_	_
9	whether	whether	IN	_	_	_
10	the	the	DT	_	_	_
11	expression	expression	NN	_	_	_
12	of	of	IN	_	_	_
13	any	any	DT	_	_	_
14	given	give	VBN	_	_	_
15	gene	gene	NN	_	_	_
16	among	among	IN	_	_	_
17	groups	group	NNS	_	_	_
18	with	with	IN	_	_	_
19	different	different	JJ	_	_	_
20	stx	stx	NN	_	_	_
21	types	type	NNS	_	_	_
22	is	be	VBZ	_	_	_
23	also	also	RB	_	_	_
24	dependent	dependent	JJ	_	_	_
25	on	on	IN	_	_	_
26	clade	clade	NN	_	_	_
27	.	.	.	_	_	_

1	An	a	DT	_	_	_
2	interaction	interaction	NN	_	_	_
3	effect	effect	NN	_	_	_
4	would	would	MD	_	_	_
5	be	be	VB	_	_	_
6	observed	observe	VBN	_	_	_
7	if	if	IN	_	_	_
8	expression	expression	NN	_	_	_
9	estimates	estimate	NNS	_	_	_
10	between	between	IN	_	_	_
11	strain	strain	NN	_	_	_
12	groups	group	NNS	_	_	_
13	clade8stx2	clade8stx2	NN	_	_	_
14	and	and	CC	_	_	_
15	clade2stx2	clade2stx2	NN	_	_	_
16	are	be	VBP	_	_	_
17	different	different	JJ	_	_	_
18	from	from	IN	_	_	_
19	expression	expression	NN	_	_	_
20	estimates	estimate	NNS	_	_	_
21	between	between	IN	_	_	_
22	strain	strain	NN	_	_	_
23	groups	group	NNS	_	_	_
24	clade8stx2	clade8stx2	VBP	_	_	_
25	,2	,2	CD	_	_	_
26	c	c	NN	_	_	_
27	and	and	CC	_	_	_
28	clade2stx1	clade2stx1	NN	_	_	_
29	,2	,2	CD	_	_	_
30	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	every	every	DT	_	_	_
3	analysis	analysis	NN	_	_	_
4	,	,	,	_	_	_
5	1000	1000	CD	_	_	_
6	permutations	permutation	NNS	_	_	_
7	of	of	IN	_	_	_
8	the	the	DT	_	_	_
9	data	datum	NNS	_	_	_
10	were	be	VBD	_	_	_
11	performed	perform	VBN	_	_	_
12	to	to	TO	_	_	_
13	generate	generate	VB	_	_	_
14	P	p	NN	_	_	_
15	values	value	NNS	_	_	_
16	;	;	:	_	_	_
17	estimates	estimate	NNS	_	_	_
18	were	be	VBD	_	_	_
19	considered	consider	VBN	_	_	_
20	significant	significant	JJ	_	_	_
21	if	if	IN	_	_	_
22	the	the	DT	_	_	_
23	P	p	NN	_	_	_
24	value	value	NN	_	_	_
25	was	be	VBD	_	_	_
26	<	<	JJR	_	_	_
27	0.05	0.05	CD	_	_	_
28	after	after	IN	_	_	_
29	adjusting	adjust	VBG	_	_	_
30	for	for	IN	_	_	_
31	multiple	multiple	JJ	_	_	_
32	comparisons	comparison	NNS	_	_	_
33	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	SYM	_	_	_
5	-	-	:	_	_	_
6	Leu	leu	NN	_	_	_
7	t	t	NN	_	_	_
8	=	=	JJ	_	_	_
9	0	0	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	-	-	:	_	_	_
12	Leu	leu	NN	_	_	_
13	t	t	NN	_	_	_
14	=	=	JJ	_	_	_
15	0	0	CD	_	_	_
16	charged	charge	VBN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	SYM	_	_	_
18	-	-	:	_	_	_
19	Leu	leu	NN	_	_	_
20	t	t	NN	_	_	_
21	=	=	JJ	_	_	_
22	0	0	CD	_	_	_
23	total	total	JJ	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	-	-	:	_	_	_
26	Leu	leu	NN	_	_	_
27	t	t	NN	_	_	_
28	=	=	JJ	_	_	_
29	17	17	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	-	-	:	_	_	_
32	Leu	leu	NN	_	_	_
33	t	t	NN	_	_	_
34	=	=	JJ	_	_	_
35	17	17	CD	_	_	_
36	charged	charge	VBN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	SYM	_	_	_
38	-	-	:	_	_	_
39	Leu	leu	NN	_	_	_
40	t	t	NN	_	_	_
41	=	=	JJ	_	_	_
42	17	17	CD	_	_	_
43	total	total	JJ	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	-	-	:	_	_	_
46	Leu	leu	NN	_	_	_
47	t	t	NN	_	_	_
48	=	=	JJ	_	_	_
49	2	2	CD	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	-	-	:	_	_	_
52	Leu	leu	NN	_	_	_
53	t	t	NN	_	_	_
54	=	=	JJ	_	_	_
55	2	2	CD	_	_	_
56	charged	charge	VBN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	SYM	_	_	_
58	-	-	:	_	_	_
59	Leu	leu	NN	_	_	_
60	t	t	NN	_	_	_
61	=	=	JJ	_	_	_
62	2	2	CD	_	_	_
63	total	total	JJ	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	-	-	:	_	_	_
66	Leu	leu	NN	_	_	_
67	t	t	NN	_	_	_
68	=	=	JJ	_	_	_
69	32	32	CD	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	-	-	:	_	_	_
72	Leu	leu	NN	_	_	_
73	t	t	NN	_	_	_
74	=	=	JJ	_	_	_
75	32	32	CD	_	_	_
76	charged	charge	VBN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	SYM	_	_	_
78	-	-	:	_	_	_
79	Leu	leu	NN	_	_	_
80	t	t	NN	_	_	_
81	=	=	JJ	_	_	_
82	32	32	CD	_	_	_
83	total	total	JJ	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	-	-	:	_	_	_
86	Leu	leu	NN	_	_	_
87	t	t	NN	_	_	_
88	=	=	JJ	_	_	_
89	7	7	CD	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	-	-	:	_	_	_
92	Leu	leu	NN	_	_	_
93	t	t	NN	_	_	_
94	=	=	JJ	_	_	_
95	7	7	CD	_	_	_
96	charged	charge	VBN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	SYM	_	_	_
98	-	-	:	_	_	_
99	Leu	leu	NN	_	_	_
100	t	t	NN	_	_	_
101	=	=	JJ	_	_	_
102	7	7	CD	_	_	_
103	total	total	JJ	_	_	_
104	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
105	Bear	Bear	NNP	_	_	_
106	feces	fece	VBZ	_	_	_
107	isolate	isolate	JJ	_	_	_
108	B1	b1	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
110	Bear	Bear	NNP	_	_	_
111	feces	fece	VBZ	_	_	_
112	isolate	isolate	JJ	_	_	_
113	B3	b3	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
115	Bear	Bear	NNP	_	_	_
116	feces	fece	VBZ	_	_	_
117	isolate	isolate	JJ	_	_	_
118	B5	b5	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	Bear	Bear	NNP	_	_	_
121	III	III	NNP	_	_	_
122	versus	versus	CC	_	_	_
123	MG1655	MG1655	NNP	_	_	_
124	technical	technical	JJ	_	_	_
125	replicate	replicate	VB	_	_	_
126	1	1	CD	_	_	_
127	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
128	Bear	Bear	NNP	_	_	_
129	III	III	NNP	_	_	_
130	versus	versus	CC	_	_	_
131	MG1655	MG1655	NNP	_	_	_
132	technical	technical	JJ	_	_	_
133	replicate	replicate	VBP	_	_	_
134	2	2	CD	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
136	Bear	Bear	NNP	_	_	_
137	II	II	NNP	_	_	_
138	versus	versus	CC	_	_	_
139	MG1655	MG1655	NNP	_	_	_
140	technical	technical	JJ	_	_	_
141	replicate	replicate	VB	_	_	_
142	1	1	CD	_	_	_
143	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
144	Bear	Bear	NNP	_	_	_
145	II	II	NNP	_	_	_
146	versus	versus	CC	_	_	_
147	MG1655	MG1655	NNP	_	_	_
148	technical	technical	JJ	_	_	_
149	replicate	replicate	VB	_	_	_
150	2	2	CD	_	_	_
151	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
152	Bear	Bear	NNP	_	_	_
153	I	I	NNP	_	_	_
154	versus	versus	CC	_	_	_
155	MG1655	MG1655	NNP	_	_	_
156	technical	technical	JJ	_	_	_
157	replicate	replicate	VB	_	_	_
158	1	1	CD	_	_	_
159	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
160	Bear	Bear	NNP	_	_	_
161	I	I	NNP	_	_	_
162	versus	versus	CC	_	_	_
163	MG1655	MG1655	NNP	_	_	_
164	technical	technical	JJ	_	_	_
165	replicate	replicate	VBP	_	_	_
166	2	2	CD	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
168	Cattle	cattle	JJ	_	_	_
169	feces	fece	NNS	_	_	_
170	isolate	isolate	VBP	_	_	_
171	C1A	c1a	NN	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
173	Cattle	cattle	JJ	_	_	_
174	feces	fece	NNS	_	_	_
175	isolate	isolate	VBP	_	_	_
176	C4A	c4a	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
178	Cattle	cattle	JJ	_	_	_
179	feces	fece	NNS	_	_	_
180	isolate	isolate	VBP	_	_	_
181	C6D	c6d	NN	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
183	Cattle	Cattle	NNP	_	_	_
184	III	III	NNP	_	_	_
185	versus	versus	CC	_	_	_
186	MG1655	MG1655	NNP	_	_	_
187	technical	technical	JJ	_	_	_
188	replicate	replicate	VB	_	_	_
189	1	1	CD	_	_	_
190	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
191	Cattle	Cattle	NNP	_	_	_
192	III	III	NNP	_	_	_
193	versus	versus	CC	_	_	_
194	MG1655	MG1655	NNP	_	_	_
195	technical	technical	JJ	_	_	_
196	replicate	replicate	VB	_	_	_
197	2	2	CD	_	_	_
198	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
199	Cattle	Cattle	NNP	_	_	_
200	II	II	NNP	_	_	_
201	versus	versus	CC	_	_	_
202	MG1655	MG1655	NNP	_	_	_
203	technical	technical	JJ	_	_	_
204	replicate	replicate	VB	_	_	_
205	1	1	CD	_	_	_
206	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
207	Cattle	Cattle	NNP	_	_	_
208	II	II	NNP	_	_	_
209	versus	versus	CC	_	_	_
210	MG1655	MG1655	NNP	_	_	_
211	technical	technical	JJ	_	_	_
212	replicate	replicate	VB	_	_	_
213	2	2	CD	_	_	_
214	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
215	Cattle	Cattle	NNP	_	_	_
216	I	I	PRP	_	_	_
217	versus	versus	CC	_	_	_
218	MG1655	mg1655	NN	_	_	_
219	technical	technical	JJ	_	_	_
220	replicate	replicate	VB	_	_	_
221	1	1	CD	_	_	_
222	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
223	Cattle	Cattle	NNP	_	_	_
224	I	I	PRP	_	_	_
225	versus	versus	CC	_	_	_
226	MG1655	mg1655	NN	_	_	_
227	technical	technical	JJ	_	_	_
228	replicate	replicate	VB	_	_	_
229	2	2	CD	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
231	Deer	deer	NNS	_	_	_
232	feces	fece	NNS	_	_	_
233	isolate	isolate	VBP	_	_	_
234	D1	d1	NN	_	_	_
235	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
236	Deer	deer	NNS	_	_	_
237	feces	fece	NNS	_	_	_
238	isolate	isolate	NN	_	_	_
239	D3	d3	NN	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
241	Deer	deer	NNS	_	_	_
242	feces	fece	NNS	_	_	_
243	isolate	isolate	VBP	_	_	_
244	W6A	w6a	NN	_	_	_
245	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
246	Deer	deer	NNS	_	_	_
247	III	iii	CD	_	_	_
248	versus	versus	CC	_	_	_
249	MG1655	mg1655	CD	_	_	_
250	technical	technical	JJ	_	_	_
251	replicate	replicate	VB	_	_	_
252	1	1	CD	_	_	_
253	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
254	Deer	deer	NNS	_	_	_
255	III	iii	CD	_	_	_
256	versus	versus	CC	_	_	_
257	MG1655	mg1655	CD	_	_	_
258	technical	technical	JJ	_	_	_
259	replicate	replicate	VB	_	_	_
260	2	2	CD	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
262	Deer	deer	NNS	_	_	_
263	II	ii	CD	_	_	_
264	versus	versus	CC	_	_	_
265	MG1655	mg1655	CD	_	_	_
266	technical	technical	JJ	_	_	_
267	replicate	replicate	VB	_	_	_
268	1	1	CD	_	_	_
269	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
270	Deer	deer	NNS	_	_	_
271	II	ii	CD	_	_	_
272	versus	versus	CC	_	_	_
273	MG1655	mg1655	CD	_	_	_
274	technical	technical	JJ	_	_	_
275	replicate	replicate	VB	_	_	_
276	2	2	CD	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
278	Deer	deer	NNS	_	_	_
279	I	I	PRP	_	_	_
280	versus	versus	CC	_	_	_
281	MG1655	mg1655	NN	_	_	_
282	technical	technical	JJ	_	_	_
283	replicate	replicate	VB	_	_	_
284	1	1	CD	_	_	_
285	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
286	Deer	deer	NNS	_	_	_
287	I	I	PRP	_	_	_
288	versus	versus	CC	_	_	_
289	MG1655	mg1655	NN	_	_	_
290	technical	technical	JJ	_	_	_
291	replicate	replicate	VB	_	_	_
292	2	2	CD	_	_	_
293	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
294	E.	E.	NNP	_	_	_
295	coli	coli	NN	_	_	_
296	K12	k12	NN	_	_	_
297	MG1655	mg1655	NN	_	_	_
298	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
299	Escherichia	escherichia	FW	Organism	_	_
300	coli	coli	FW	Organism	_	_
301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
302	Escherichia	escherichia	FW	Organism	_	_
303	coli	coli	FW	Organism	_	_
304	str	str	FW	_	_	_
305	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
3	Genomic	genomic	JJ	_	_	_
4	DNA	dna	NN	_	_	_
5	was	be	VBD	_	_	_
6	extracted	extract	VBN	_	_	_
7	using	use	VBG	_	_	_
8	an	a	DT	_	_	_
9	SDS	sds	NN	_	_	_
10	lysis	lysis	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Human	human	JJ	_	_	_
13	III	iii	CD	_	_	_
14	versus	versus	CC	_	_	_
15	MG1655	mg1655	CD	_	_	_
16	technical	technical	JJ	_	_	_
17	replicate	replicate	VB	_	_	_
18	1	1	CD	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	Human	Human	NNP	_	_	_
21	III	III	NNP	_	_	_
22	versus	versus	CC	_	_	_
23	MG1655	MG1655	NNP	_	_	_
24	technical	technical	JJ	_	_	_
25	replicate	replicate	VB	_	_	_
26	2	2	CD	_	_	_
27	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
28	Human	Human	NNP	_	_	_
29	II	II	NNP	_	_	_
30	versus	versus	CC	_	_	_
31	MG1655	MG1655	NNP	_	_	_
32	technical	technical	JJ	_	_	_
33	replicate	replicate	VB	_	_	_
34	1	1	CD	_	_	_
35	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
36	Human	Human	NNP	_	_	_
37	II	II	NNP	_	_	_
38	versus	versus	CC	_	_	_
39	MG1655	MG1655	NNP	_	_	_
40	technical	technical	JJ	_	_	_
41	replicate	replicate	VBP	_	_	_
42	2	2	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
44	Human	human	JJ	_	_	_
45	I	I	PRP	_	_	_
46	versus	versus	CC	_	_	_
47	MG1655	mg1655	NN	_	_	_
48	technical	technical	JJ	_	_	_
49	replicate	replicate	VB	_	_	_
50	1	1	CD	_	_	_
51	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
52	Human	Human	NNP	_	_	_
53	I	I	PRP	_	_	_
54	versus	versus	CC	_	_	_
55	MG1655	mg1655	NN	_	_	_
56	technical	technical	JJ	_	_	_
57	replicate	replicate	VBP	_	_	_
58	2	2	CD	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
60	Human	human	JJ	_	_	_
61	sewage	sewage	NN	_	_	_
62	isolate	isolate	NN	_	_	_
63	H1	h1	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	Human	human	JJ	_	_	_
66	sewage	sewage	NN	_	_	_
67	isolate	isolate	NN	_	_	_
68	H2	h2	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	Human	human	JJ	_	_	_
71	sewage	sewage	NN	_	_	_
72	isolate	isolate	NN	_	_	_
73	H3	h3	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	Images	image	NNS	_	_	_
76	were	be	VBD	_	_	_
77	analyzed	analyze	VBN	_	_	_
78	using	use	VBG	_	_	_
79	a	a	DT	_	_	_
80	combination	combination	NN	_	_	_
81	of	of	IN	_	_	_
82	GenePix	GenePix	NNP	_	_	_
83	Pro	pro	FW	_	_	_
84	6.0	6.0	CD	_	_	_
85	,	,	,	_	_	_
86	the	the	DT	_	_	_
87	freely	freely	RB	_	_	_
88	available	available	JJ	_	_	_
89	TIGR	tigr	NN	_	_	_
90	TM4	tm4	NN	_	_	_
91	software	software	NN	_	_	_
92	suite	suite	NN	_	_	_
93	-LRB-	-lrb-	-LRB-	_	_	_
94	www.tm4.org	www.tm4.org	NN	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	and	and	CC	_	_	_
97	Microsoft	Microsoft	NNP	_	_	_
98	Excel	Excel	NNP	_	_	_
99	.	.	.	_	_	_

1	Spots	spot	NNS	_	_	_
2	with	with	IN	_	_	_
3	an	a	DT	_	_	_
4	intensity	intensity	NN	_	_	_
5	:	:	:	_	_	_
6	background	background	NN	_	_	_
7	ratio	ratio	NN	_	_	_
8	>	>	JJR	_	_	_
9	1.5	1.5	CD	_	_	_
10	and	and	CC	_	_	_
11	overall	overall	JJ	_	_	_
12	intensity	intensity	NN	_	_	_
13	>	>	JJR	_	_	_
14	350	350	CD	_	_	_
15	in	in	IN	_	_	_
16	the	the	DT	_	_	_
17	reference	reference	NN	_	_	_
18	channel	channel	NN	_	_	_
19	and	and	CC	_	_	_
20	an	a	DT	_	_	_
21	intensity	intensity	NN	_	_	_
22	:	:	:	_	_	_
23	background	background	NN	_	_	_
24	ratio	ratio	NN	_	_	_
25	of	of	IN	_	_	_
26	>	>	JJR	_	_	_
27	1.0	1.0	CD	_	_	_
28	in	in	IN	_	_	_
29	the	the	DT	_	_	_
30	experimental	experimental	JJ	_	_	_
31	channel	channel	NN	_	_	_
32	were	be	VBD	_	_	_
33	considered	consider	VBN	_	_	_
34	acceptable	acceptable	JJ	_	_	_
35	for	for	IN	_	_	_
36	downstream	downstream	JJ	_	_	_
37	processing	processing	NN	_	_	_
38	.	.	.	_	_	_

1	Local	local	JJ	_	_	_
2	background	background	NN	_	_	_
3	was	be	VBD	_	_	_
4	subtracted	subtract	VBN	_	_	_
5	for	for	IN	_	_	_
6	each	each	DT	_	_	_
7	spot	spot	NN	_	_	_
8	,	,	,	_	_	_
9	the	the	DT	_	_	_
10	corresponding	corresponding	JJ	_	_	_
11	log2	log2	NN	_	_	_
12	ratios	ratio	NNS	_	_	_
13	were	be	VBD	_	_	_
14	normalized	normalize	VBN	_	_	_
15	using	use	VBG	_	_	_
16	total	total	JJ	_	_	_
17	intensity	intensity	NN	_	_	_
18	normalization	normalization	NN	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	replicate	replicate	VB	_	_	_
22	spots	spot	NNS	_	_	_
23	were	be	VBD	_	_	_
24	averaged	average	VBN	_	_	_
25	using	use	VBG	_	_	_
26	TIGR	TIGR	NNP	_	_	_
27	MIDAS	MIDAS	NNP	_	_	_
28	.	.	.	_	_	_

1	Genes	gene	NNS	_	_	_
2	that	that	WDT	_	_	_
3	had	have	VBD	_	_	_
4	missing	missing	JJ	_	_	_
5	data	datum	NNS	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	i.e.	i.e.	FW	_	_	_
8	unacceptable	unacceptable	JJ	_	_	_
9	spots	spot	NNS	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	for	for	IN	_	_	_
12	more	more	JJR	_	_	_
13	than	than	IN	_	_	_
14	one-third	one-third	NN	_	_	_
15	of	of	IN	_	_	_
16	the	the	DT	_	_	_
17	samples	sample	NNS	_	_	_
18	were	be	VBD	_	_	_
19	excluded	exclude	VBN	_	_	_
20	from	from	IN	_	_	_
21	the	the	DT	_	_	_
22	downstream	downstream	JJ	_	_	_
23	analysis	analysis	NN	_	_	_
24	leaving	leave	VBG	_	_	_
25	3993	3993	CD	_	_	_
26	ORFs	orf	NNS	_	_	_
27	in	in	IN	_	_	_
28	the	the	DT	_	_	_
29	final	final	JJ	_	_	_
30	data	data	NN	_	_	_
31	set	set	NN	_	_	_
32	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	sample	sample	NN	_	_	_
3	was	be	VBD	_	_	_
4	hybridized	hybridize	VBN	_	_	_
5	twice	twice	RB	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	results	result	NNS	_	_	_
9	averaged	average	VBD	_	_	_
10	in	in	IN	_	_	_
11	Microsoft	Microsoft	NNP	_	_	_
12	Excel	Excel	NNP	_	_	_
13	after	after	IN	_	_	_
14	processing	process	VBG	_	_	_
15	with	with	IN	_	_	_
16	MIDAS	MIDAS	NNP	_	_	_
17	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	strict	strict	JJ	_	_	_
3	cutoff	cutoff	NN	_	_	_
4	of	of	IN	_	_	_
5	log2	log2	NN	_	_	_
6	ratio	ratio	NN	_	_	_
7	>	>	JJR	_	_	_
8	0.9	0.9	CD	_	_	_
9	or	or	CC	_	_	_
10	<	<	JJR	_	_	_
11	0.9	0.9	CD	_	_	_
12	was	be	VBD	_	_	_
13	applied	apply	VBN	_	_	_
14	for	for	IN	_	_	_
15	the	the	DT	_	_	_
16	determination	determination	NN	_	_	_
17	of	of	IN	_	_	_
18	gene	gene	NN	_	_	_
19	amplifications	amplification	NNS	_	_	_
20	and	and	CC	_	_	_
21	gene	gene	NN	_	_	_
22	absences	absence	NNS	_	_	_
23	,	,	,	_	_	_
24	respectively	respectively	RB	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	Bear	Bear	NNP	_	_	_
5	feces	fece	VBZ	_	_	_
6	isolate	isolate	JJ	_	_	_
7	B1	b1	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	strain	strain	NN	_	_	_
10	:	:	:	_	_	_
11	Bear	Bear	NNP	_	_	_
12	feces	fece	VBZ	_	_	_
13	isolate	isolate	JJ	_	_	_
14	B3	b3	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	strain	strain	NN	_	_	_
17	:	:	:	_	_	_
18	Bear	Bear	NNP	_	_	_
19	feces	fece	VBZ	_	_	_
20	isolate	isolate	JJ	_	_	_
21	B5	b5	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	strain	strain	NN	_	_	_
24	:	:	:	_	_	_
25	Cattle	Cattle	NNP	_	_	_
26	feces	fece	NNS	_	_	_
27	isolate	isolate	VBP	_	_	_
28	C1A	c1a	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	strain	strain	NN	_	_	_
31	:	:	:	_	_	_
32	Cattle	Cattle	NNP	_	_	_
33	feces	fece	NNS	_	_	_
34	isolate	isolate	VBP	_	_	_
35	C4A	c4a	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	strain	strain	NN	_	_	_
38	:	:	:	_	_	_
39	Cattle	Cattle	NNP	_	_	_
40	feces	fece	NNS	_	_	_
41	isolate	isolate	VBP	_	_	_
42	C6D	c6d	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	strain	strain	NN	_	_	_
45	:	:	:	_	_	_
46	Deer	deer	NNS	_	_	_
47	feces	fece	NNS	_	_	_
48	isolate	isolate	VBP	_	_	_
49	D1	d1	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	strain	strain	NN	_	_	_
52	:	:	:	_	_	_
53	Deer	deer	NNS	_	_	_
54	feces	fece	NNS	_	_	_
55	isolate	isolate	NN	_	_	_
56	D3	d3	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	strain	strain	NN	_	_	_
59	:	:	:	_	_	_
60	Deer	deer	NNS	_	_	_
61	feces	fece	NNS	_	_	_
62	isolate	isolate	VBP	_	_	_
63	W6A	w6a	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	strain	strain	NN	_	_	_
66	:	:	:	_	_	_
67	E.	e.	FW	_	_	_
68	coli	coli	FW	_	_	_
69	K12	k12	NN	_	_	_
70	MG1655	mg1655	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	strain	strain	NN	_	_	_
73	:	:	:	_	_	_
74	Human	human	JJ	_	_	_
75	sewage	sewage	NN	_	_	_
76	isolate	isolate	NN	_	_	_
77	H1	h1	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	strain	strain	NN	_	_	_
80	:	:	:	_	_	_
81	Human	human	JJ	_	_	_
82	sewage	sewage	NN	_	_	_
83	isolate	isolate	NN	_	_	_
84	H2	h2	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	strain	strain	NN	_	_	_
87	:	:	:	_	_	_
88	Human	human	JJ	_	_	_
89	sewage	sewage	NN	_	_	_
90	isolate	isolate	NN	_	_	_
91	H3	h3	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
93	At	at	IN	_	_	_
94	time	time	NN	_	_	_
95	point	point	NN	_	_	_
96	0	0	CD	_	_	_
97	,	,	,	_	_	_
98	rifampicin	rifampicin	NN	SUPP	_	_
99	was	be	VBD	_	_	_
100	added	add	VBN	_	_	_
101	to	to	TO	_	_	_
102	a	a	DT	_	_	_
103	final	final	JJ	_	_	_
104	concentration	concentration	NN	_	_	_
105	of	of	IN	_	_	_
106	500ug	500ug	JJ	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	E.coli	e.coli	NN	_	_	_
109	strain	strain	NN	_	_	_
110	,	,	,	_	_	_
111	DY330	dy330	NN	_	_	_
112	,	,	,	_	_	_
113	was	be	VBD	_	_	_
114	grown	grow	VBN	_	_	_
115	at	at	IN	_	_	_
116	30C	30C	NNP	_	_	_
117	in	in	IN	_	_	_
118	M9	M9	NNP	_	_	_
119	media	media	NNS	_	_	_
120	supplemented	supplement	VBN	_	_	_
121	with	with	IN	_	_	_
122	0.4	0.4	CD	_	_	_
123	%	%	NN	_	_	_
124	glucose	glucose	NN	SUPP	_	_
125	,	,	,	_	_	_
126	vitamins	vitamin	NNS	_	_	_
127	and	and	CC	_	_	_
128	amino	amino	NN	SUPP	_	_
129	acids	acid	NNS	SUPP	_	_
130	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	RNA-Seq	rna-seq	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	RNA	rna	NN	_	_	_
8	was	be	VBD	_	_	_
9	purified	purify	VBN	_	_	_
10	from	from	IN	_	_	_
11	lysates	lysate	NNS	_	_	_
12	by	by	IN	_	_	_
13	phenol	phenol	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Sequence	sequence	NN	_	_	_
16	reads	read	VBZ	_	_	_
17	were	be	VBD	_	_	_
18	obtained	obtain	VBN	_	_	_
19	and	and	CC	_	_	_
20	mapped	map	VBN	_	_	_
21	to	to	TO	_	_	_
22	the	the	DT	_	_	_
23	W3110	w3110	NN	_	_	_
24	genome	genome	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	NCBI	ncbi	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	using	use	VBG	_	_	_
29	the	the	DT	_	_	_
30	Illumina	Illumina	NNP	_	_	_
31	Genome	Genome	NNP	_	_	_
32	Analyzer	Analyzer	NNP	_	_	_
33	Pipeline	Pipeline	NNP	_	_	_
34	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	reads	read	VBZ	_	_	_
3	mapping	mapping	NN	_	_	_
4	with	with	IN	_	_	_
5	two	two	CD	_	_	_
6	or	or	CC	_	_	_
7	fewer	fewer	JJR	_	_	_
8	mismatches	mismatch	NNS	_	_	_
9	were	be	VBD	_	_	_
10	retained	retain	VBN	_	_	_
11	.	.	.	_	_	_

1	Repeated	repeated	JJ	_	_	_
2	sequences	sequence	NNS	_	_	_
3	were	be	VBD	_	_	_
4	ignored	ignore	VBN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	rRNA	rrna	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	counts	count	NNS	_	_	_
3	in	in	IN	_	_	_
4	each	each	DT	_	_	_
5	sample	sample	NN	_	_	_
6	was	be	VBD	_	_	_
7	normalized	normalize	VBN	_	_	_
8	by	by	IN	_	_	_
9	ssrA	ssra	NN	GEN	_	_
10	RNA	rna	NN	_	_	_
11	and	and	CC	_	_	_
12	then	then	RB	_	_	_
13	converted	convert	VBD	_	_	_
14	to	to	TO	_	_	_
15	logarithmic	logarithmic	JJ	_	_	_
16	values	value	NNS	_	_	_
17	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	value	value	NN	_	_	_
3	of	of	IN	_	_	_
4	1	1	CD	_	_	_
5	was	be	VBD	_	_	_
6	added	add	VBN	_	_	_
7	to	to	TO	_	_	_
8	every	every	DT	_	_	_
9	count	count	NN	_	_	_
10	before	before	IN	_	_	_
11	the	the	DT	_	_	_
12	logarithmic	logarithmic	JJ	_	_	_
13	conversion	conversion	NN	_	_	_
14	to	to	TO	_	_	_
15	avoid	avoid	VB	_	_	_
16	an	a	DT	_	_	_
17	undefined	undefined	JJ	_	_	_
18	logarithm	logarithm	NN	_	_	_
19	of	of	IN	_	_	_
20	0	0	CD	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	lifetime	lifetime	NN	_	_	_
3	was	be	VBD	_	_	_
4	determined	determine	VBN	_	_	_
5	from	from	IN	_	_	_
6	the	the	DT	_	_	_
7	inverse	inverse	NN	_	_	_
8	of	of	IN	_	_	_
9	the	the	DT	_	_	_
10	slope	slope	NN	_	_	_
11	of	of	IN	_	_	_
12	a	a	DT	_	_	_
13	linear	linear	JJ	_	_	_
14	fit	fit	NN	_	_	_
15	to	to	TO	_	_	_
16	the	the	DT	_	_	_
17	logarithmic	logarithmic	JJ	_	_	_
18	values	value	NNS	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	DY330	dy330	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	W3110	w3110	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	The	the	DT	_	_	_
10	measured	measure	VBN	_	_	_
11	lifetime	lifetime	NN	_	_	_
12	of	of	IN	_	_	_
13	mRNA	mrna	NN	_	_	_
14	is	be	VBZ	_	_	_
15	available	available	JJ	_	_	_
16	as	as	IN	_	_	_
17	a	a	DT	_	_	_
18	supplementary	supplementary	JJ	_	_	_
19	file	file	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	real_rna_life.txt	real_rna_life.txt	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	on	on	IN	_	_	_
24	the	the	DT	_	_	_
25	Series	Series	NNP	_	_	_
26	record	record	NN	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	fragmented	fragmented	JJ	_	_	_
6	using	use	VBG	_	_	_
7	Ambion	Ambion	NNP	_	_	_
8	's	's	POS	_	_	_
9	Fragmentation	fragmentation	NN	_	_	_
10	Reagent	reagent	NN	_	_	_
11	at	at	IN	_	_	_
12	70	70	CD	_	_	_
13	°C	°c	NN	_	_	_
14	for	for	IN	_	_	_
15	5	5	CD	_	_	_
16	min	min	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	collected	collect	VBN	_	_	_
20	by	by	IN	_	_	_
21	Zymo	Zymo	NNP	_	_	_
22	's	's	POS	_	_	_
23	RNA	rna	NN	_	_	_
24	columns	column	NNS	_	_	_
25	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	seq	seq	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	prepared	prepare	VBN	_	_	_
6	according	accord	VBG	_	_	_
7	to	to	TO	_	_	_
8	Illumna	Illumna	NNP	_	_	_
9	's	's	POS	_	_	_
10	protocol	protocol	NN	_	_	_
11	,	,	,	_	_	_
12	using	use	VBG	_	_	_
13	NEB	neb	NN	_	_	_
14	enzymes	enzyme	NNS	_	_	_
15	and	and	CC	_	_	_
16	barcoded	barcoded	JJ	_	_	_
17	adapters	adapter	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Integrated	Integrated	NNP	_	_	_
20	DNA	DNA	NNP	_	_	_
21	Technologies	Technologies	NNPS	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	libraries	library	NNS	_	_	_
3	were	be	VBD	_	_	_
4	pooled	pool	VBN	_	_	_
5	and	and	CC	_	_	_
6	sequenced	sequence	VBN	_	_	_
7	with	with	IN	_	_	_
8	an	a	DT	_	_	_
9	Illumina	Illumina	NNP	_	_	_
10	GA	GA	NNP	_	_	_
11	II	II	NNP	_	_	_
12	machine	machine	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Center	center	NN	_	_	_
15	for	for	IN	_	_	_
16	Systems	Systems	NNP	_	_	_
17	Biology	Biology	NNP	_	_	_
18	,	,	,	_	_	_
19	Harvard	Harvard	NNP	_	_	_
20	University	University	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	time	time	NN	_	_	_
3	point	point	NN	_	_	_
4	0	0	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
6	time	time	NN	_	_	_
7	point	point	NN	_	_	_
8	2	2	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
10	time	time	NN	_	_	_
11	point	point	NN	_	_	_
12	4	4	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	time	time	NN	_	_	_
15	point	point	NN	_	_	_
16	6	6	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	time	time	NN	_	_	_
19	point	point	NN	_	_	_
20	8	8	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	treatment	treatment	NN	_	_	_
23	group	group	NN	_	_	_
24	:	:	:	_	_	_
25	rifampicin	rifampicin	NN	SUPP	_	_
26	time	time	NN	_	_	_
27	point	point	NN	_	_	_
28	0	0	CD	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	treatment	treatment	NN	_	_	_
31	group	group	NN	_	_	_
32	:	:	:	_	_	_
33	rifampicin	rifampicin	NN	SUPP	_	_
34	time	time	NN	_	_	_
35	point	point	NN	_	_	_
36	2	2	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	treatment	treatment	NN	_	_	_
39	group	group	NN	_	_	_
40	:	:	:	_	_	_
41	rifampicin	rifampicin	NN	SUPP	_	_
42	time	time	NN	_	_	_
43	point	point	NN	_	_	_
44	4	4	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	treatment	treatment	NN	_	_	_
47	group	group	NN	_	_	_
48	:	:	:	_	_	_
49	rifampicin	rifampicin	NN	SUPP	_	_
50	time	time	NN	_	_	_
51	point	point	NN	_	_	_
52	6	6	CD	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	treatment	treatment	NN	_	_	_
55	group	group	NN	_	_	_
56	:	:	:	_	_	_
57	rifampicin	rifampicin	NN	SUPP	_	_
58	time	time	NN	_	_	_
59	point	point	NN	_	_	_
60	8	8	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	10	10	CD	_	_	_
63	min	min	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	10	10	CD	_	_	_
66	min	min	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	additional	additional	JJ	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	15	15	CD	_	_	_
72	min	min	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	15	15	CD	_	_	_
75	min	min	NN	_	_	_
76	-LRB-	-lrb-	-LRB-	_	_	_
77	additional	additional	JJ	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	5	5	CD	_	_	_
81	min	min	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	5	5	CD	_	_	_
84	min	min	NN	_	_	_
85	-LRB-	-lrb-	-LRB-	_	_	_
86	additional	additional	JJ	_	_	_
87	-RRB-	-rrb-	-RRB-	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	control	control	NN	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	control	control	NN	_	_	_
92	-LRB-	-lrb-	-LRB-	_	_	_
93	additional	additional	JJ	_	_	_
94	-RRB-	-rrb-	-RRB-	_	_	_
95	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
96	E.	E.	NNP	_	_	_
97	coli	coli	NN	_	_	_
98	cell	cell	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	Escherichia	escherichia	FW	Organism	_	_
101	coli	coli	FW	Organism	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	Cells	cell	NNS	_	_	_
104	grew	grow	VBD	_	_	_
105	in	in	IN	_	_	_
106	MOPS	MOPS	NNP	MED	_	_
107	minimal	minimal	JJ	_	_	_
108	medium	medium	NN	_	_	_
109	with	with	IN	_	_	_
110	0.4	0.4	CD	_	_	_
111	%	%	NN	_	_	_
112	glucose	glucose	NN	SUPP	_	_
113	and	and	CC	_	_	_
114	0.2	0.2	CD	_	_	_
115	mM	mm	NN	KWSUPP	_	_
116	K2HPO4	k2hpo4	NN	_	_	_
117	and	and	CC	_	_	_
118	harvested	harvest	VBN	_	_	_
119	at	at	IN	_	_	_
120	the	the	DT	_	_	_
121	OD600	od600	NN	_	_	_
122	value	value	NN	_	_	_
123	of	of	IN	_	_	_
124	1.0	1.0	CD	_	_	_
125	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	PhoB	phob	NN	TF	_	_
6	knock-out	knock-out	JJ	_	_	_
7	strain	strain	NN	_	_	_
8	grows	grow	VBZ	_	_	_
9	under	under	IN	_	_	_
10	phosphate	phosphate	NN	_	_	_
11	starvation	starvation	NN	_	_	_
12	condition	condition	NN	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	E.	E.	NNP	_	_	_
15	coli	coli	NN	_	_	_
16	MG1655	mg1655	NN	_	_	_
17	wildtype	wildtype	JJ	_	_	_
18	strain	strain	NN	_	_	_
19	grows	grow	VBZ	_	_	_
20	under	under	IN	_	_	_
21	phosphate	phosphate	NN	_	_	_
22	starvation	starvation	NN	_	_	_
23	condition	condition	NN	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	Escherichia	escherichia	FW	Organism	_	_
26	coli	coli	FW	Organism	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	genotype	genotype	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	PhoB	phob	NN	TF	_	_
31	knock-out	knock-out	JJ	_	_	_
32	strain	strain	NN	_	_	_
33	,	,	,	_	_	_
34	rep1	rep1	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	PhoB	phob	NN	TF	_	_
37	knock-out	knock-out	JJ	_	_	_
38	strain	strain	NN	_	_	_
39	,	,	,	_	_	_
40	rep2	rep2	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	strain	strain	NN	_	_	_
43	:	:	:	_	_	_
44	MG1655	mg1655	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
46	The	the	DT	_	_	_
47	data	datum	NNS	_	_	_
48	were	be	VBD	_	_	_
49	normalized	normalize	VBN	_	_	_
50	by	by	IN	_	_	_
51	RMA	rma	NN	_	_	_
52	method	method	NN	_	_	_
53	and	and	CC	_	_	_
54	then	then	RB	_	_	_
55	analyzed	analyze	VBN	_	_	_
56	by	by	IN	_	_	_
57	limma	limma	NN	_	_	_
58	package	package	NN	_	_	_
59	to	to	TO	_	_	_
60	identify	identify	VB	_	_	_
61	differentially	differentially	RB	_	_	_
62	expressed	express	VBN	_	_	_
63	genes	gene	NNS	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	bioconductor	bioconductor	NN	_	_	_
66	-RRB-	-rrb-	-RRB-	_	_	_
67	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Trizol	trizol	NN	_	_	_
3	extraction	extraction	NN	_	_	_
4	of	of	IN	_	_	_
5	total	total	JJ	_	_	_
6	RNA	rna	NN	_	_	_
7	was	be	VBD	_	_	_
8	performed	perform	VBN	_	_	_
9	according	accord	VBG	_	_	_
10	to	to	TO	_	_	_
11	the	the	DT	_	_	_
12	manufacturer	manufacturer	NN	_	_	_
13	's	's	POS	_	_	_
14	instructions	instruction	NNS	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Wildtype	wildtype	NN	_	_	_
3	strain	strain	NN	_	_	_
4	,	,	,	_	_	_
5	rep1	rep1	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	wildtype	wildtype	JJ	_	_	_
8	strain	strain	NN	_	_	_
9	,	,	,	_	_	_
10	rep2	rep2	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	E4	e4	NN	_	_	_
13	-	-	:	_	_	_
14	O2	o2	CD	_	_	_
15	1	1	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	E4	e4	NN	_	_	_
18	+	+	CC	_	_	_
19	O2	o2	CD	_	_	_
20	1	1	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	E4	e4	NN	_	_	_
23	-	-	:	_	_	_
24	O2	o2	CD	_	_	_
25	2	2	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	E4	e4	NN	_	_	_
28	+	+	CC	_	_	_
29	O2	o2	CD	_	_	_
30	2	2	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	E4	e4	NN	_	_	_
33	-	-	:	_	_	_
34	O2	o2	CD	_	_	_
35	3	3	CD	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	E4	e4	NN	_	_	_
38	+	+	CC	_	_	_
39	O2	o2	CD	_	_	_
40	3	3	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	E.	e.	FW	_	_	_
43	coli	coli	FW	_	_	_
44	MG1655	mg1655	NN	_	_	_
45	,	,	,	_	_	_
46	M9	m9	NN	_	_	_
47	media	media	NNS	_	_	_
48	with	with	IN	_	_	_
49	4	4	CD	_	_	_
50	g	g	NN	_	_	_
51	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
52	Escherichia	escherichia	FW	Organism	_	_
53	coli	coli	FW	Organism	_	_
54	str	str	FW	_	_	_
55	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	No	no	DT	_	_	_
4	specific	specific	JJ	_	_	_
5	treatment	treatment	NN	_	_	_
6	was	be	VBD	_	_	_
7	done	do	VBN	_	_	_
8	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	collected	collect	VBN	_	_	_
4	in	in	IN	_	_	_
5	the	the	DT	_	_	_
6	mid-log	mid-log	JJ	_	_	_
7	growth	growth	NN	_	_	_
8	phase	phase	NN	_	_	_
9	for	for	IN	_	_	_
10	expression	expression	NN	_	_	_
11	analysis	analysis	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	Respiratory	respiratory	JJ	_	_	_
14	defecient	defecient	JJ	_	_	_
15	E.	e.	FW	_	_	_
16	coli	coli	FW	_	_	_
17	mutant	mutant	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	ECOM4	ecom4	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	,	,	,	_	_	_
22	M9	m9	NN	_	_	_
23	media	media	NNS	_	_	_
24	with	with	IN	_	_	_
25	4	4	CD	_	_	_
26	g	g	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	strain	strain	NN	_	_	_
29	:	:	:	_	_	_
30	ECOM4	ecom4	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	strain	strain	NN	_	_	_
33	:	:	:	_	_	_
34	K-12	k-12	NN	_	_	_
35	MG1655	mg1655	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
37	The	the	DT	_	_	_
38	data	datum	NNS	_	_	_
39	were	be	VBD	_	_	_
40	analyzed	analyze	VBN	_	_	_
41	with	with	IN	_	_	_
42	ArrayStar	arraystar	NN	_	_	_
43	3	3	CD	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	DNASTAR	dnastar	NN	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	using	use	VBG	_	_	_
48	RMA	RMA	NNP	_	_	_
49	normalization	normalization	NN	_	_	_
50	method	method	NN	_	_	_
51	.	.	.	_	_	_

1	Genes	gene	NNS	_	_	_
2	with	with	IN	_	_	_
3	at	at	IN	_	_	_
4	least	least	JJS	_	_	_
5	two-fold	two-fold	JJ	_	_	_
6	expression	expression	NN	_	_	_
7	level	level	NN	_	_	_
8	change	change	NN	_	_	_
9	and	and	CC	_	_	_
10	FDR-adjusted	fdr-adjusted	JJ	_	_	_
11	P-value	p-value	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	T-test	t-test	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	of	of	IN	_	_	_
16	less	less	JJR	_	_	_
17	than	than	IN	_	_	_
18	0.05	0.05	CD	_	_	_
19	were	be	VBD	_	_	_
20	considered	consider	VBN	_	_	_
21	significant	significant	JJ	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	total	total	JJ	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extreacted	extreact	VBN	_	_	_
6	using	use	VBG	_	_	_
7	Quagen	quagen	JJ	_	_	_
8	RNA	rna	NN	_	_	_
9	mini	minus	NNS	_	_	_
10	kit	kit	NN	_	_	_
11	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	removed	remove	VBN	_	_	_
4	by	by	IN	_	_	_
5	DNase	dnase	NN	_	_	_
6	digestion	digestion	NN	_	_	_
7	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	quality	quality	NN	_	_	_
3	and	and	CC	_	_	_
4	concentration	concentration	NN	_	_	_
5	was	be	VBD	_	_	_
6	determined	determine	VBN	_	_	_
7	by	by	IN	_	_	_
8	analysis	analysis	NN	_	_	_
9	with	with	IN	_	_	_
10	an	a	DT	_	_	_
11	Thermo	Thermo	NNP	_	_	_
12	NanoDrop	NanoDrop	NNP	_	_	_
13	1000	1000	CD	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Wild	Wild	NNP	_	_	_
3	type	type	NN	_	_	_
4	and	and	CC	_	_	_
5	the	the	DT	_	_	_
6	mutant	mutant	NN	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	on	on	IN	_	_	_
10	minimal	minimal	JJ	_	_	_
11	M9	m9	NN	_	_	_
12	media	media	NNS	_	_	_
13	with	with	IN	_	_	_
14	4	4	CD	_	_	_
15	g	g	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	WT	wt	SYM	_	_	_
18	-	-	:	_	_	_
19	O2	o2	CD	_	_	_
20	1	1	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	WT	wt	NN	_	_	_
23	+	+	CC	_	_	_
24	O2	o2	CD	_	_	_
25	1	1	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	WT	wt	SYM	_	_	_
28	-	-	:	_	_	_
29	O2	o2	CD	_	_	_
30	2	2	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	WT	wt	NN	_	_	_
33	+	+	CC	_	_	_
34	O2	o2	CD	_	_	_
35	2	2	CD	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	WT	wt	SYM	_	_	_
38	-	-	:	_	_	_
39	O2	o2	CD	_	_	_
40	3	3	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	WT	wt	NN	_	_	_
43	+	+	CC	_	_	_
44	O2	o2	CD	_	_	_
45	3	3	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	Cells	cell	NNS	_	_	_
48	grew	grow	VBD	_	_	_
49	in	in	IN	_	_	_
50	MOPS	MOPS	NNP	MED	_	_
51	minimal	minimal	JJ	_	_	_
52	medium	medium	NN	_	_	_
53	with	with	IN	_	_	_
54	0.4	0.4	CD	_	_	_
55	%	%	NN	_	_	_
56	glucose	glucose	NN	SUPP	_	_
57	and	and	CC	_	_	_
58	0.2	0.2	CD	_	_	_
59	mM	mm	NN	KWSUPP	_	_
60	K2HPO4	k2hpo4	NN	_	_	_
61	and	and	CC	_	_	_
62	harvested	harvest	VBN	_	_	_
63	at	at	IN	_	_	_
64	the	the	DT	_	_	_
65	OD600	od600	NN	_	_	_
66	value	value	NN	_	_	_
67	of	of	IN	_	_	_
68	1.0	1.0	CD	_	_	_
69	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	ChIP	chip	NN	_	_	_
3	DNA	dna	NN	_	_	_
4	from	from	IN	_	_	_
5	MG1655	mg1655	NN	_	_	_
6	_	_	CD	_	_	_
7	PhoB	phob	NN	TF	_	_
8	_	_	CD	_	_	_
9	FLAG	flag	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	ChIP	chip	NN	_	_	_
12	DNA	dna	NN	_	_	_
13	from	from	IN	_	_	_
14	MG1655	mg1655	NN	_	_	_
15	wild	wild	JJ	_	_	_
16	type	type	NN	_	_	_
17	strain	strain	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Cultures	culture	NNS	_	_	_
20	were	be	VBD	_	_	_
21	grown	grow	VBN	_	_	_
22	to	to	TO	_	_	_
23	the	the	DT	_	_	_
24	OD600	od600	NN	_	_	_
25	value	value	NN	_	_	_
26	of	of	IN	_	_	_
27	1.0	1.0	CD	_	_	_
28	and	and	CC	_	_	_
29	treated	treat	VBN	_	_	_
30	with	with	IN	_	_	_
31	1	1	CD	_	_	_
32	%	%	NN	_	_	_
33	formaldehyde	formaldehyde	NN	_	_	_
34	for	for	IN	_	_	_
35	10	10	CD	_	_	_
36	min	min	NN	_	_	_
37	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	quench	quench	VB	_	_	_
3	the	the	DT	_	_	_
4	reaction	reaction	NN	_	_	_
5	,	,	,	_	_	_
6	glycine	glycine	NN	_	_	_
7	was	be	VBD	_	_	_
8	added	add	VBN	_	_	_
9	at	at	IN	_	_	_
10	the	the	DT	_	_	_
11	final	final	JJ	_	_	_
12	concentration	concentration	NN	_	_	_
13	of	of	IN	_	_	_
14	0.125	0.125	CD	_	_	_
15	M	m	NN	_	_	_
16	for	for	IN	_	_	_
17	5	5	CD	_	_	_
18	min	min	NN	_	_	_
19	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	washed	wash	VBN	_	_	_
4	twice	twice	RB	_	_	_
5	with	with	IN	_	_	_
6	lysis	lysis	NN	_	_	_
7	buffer	buffer	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	10	10	CD	_	_	_
10	mM	mm	NN	KWSUPP	_	_
11	Tris-HCl	tris-hcl	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	pH	ph	NN	_	_	_
14	7.4	7.4	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	,	,	,	_	_	_
17	0.1	0.1	CD	_	_	_
18	M	m	NN	_	_	_
19	NaCl	nacl	NN	_	_	_
20	,	,	,	_	_	_
21	1	1	CD	_	_	_
22	mM	mm	NN	KWSUPP	_	_
23	EDTA	edta	NN	_	_	_
24	and	and	CC	_	_	_
25	0.5	0.5	CD	_	_	_
26	%	%	NN	_	_	_
27	Tween-20	tween-20	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	washed	wash	VBN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	then	then	RB	_	_	_
6	lysed	lyse	VBN	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	lysis	lysis	NN	_	_	_
10	buffer	buffer	NN	_	_	_
11	containing	contain	VBG	_	_	_
12	8	8	CD	_	_	_
13	KU	KU	NNP	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	Escherichia	escherichia	FW	Organism	_	_
16	coli	coli	FW	Organism	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	genotype	genotype	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	PhoB	phob	NN	TF	_	_
21	_	_	CD	_	_	_
22	ChIP	chip	NN	_	_	_
23	,	,	,	_	_	_
24	rep1	rep1	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	PhoB	phob	NN	TF	_	_
27	_	_	CD	_	_	_
28	ChIP	chip	NN	_	_	_
29	,	,	,	_	_	_
30	rep2	rep2	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	PhoB	phob	NN	TF	_	_
33	_	_	CD	_	_	_
34	ChIP	chip	NN	_	_	_
35	,	,	,	_	_	_
36	rep3	rep3	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	strain	strain	NN	_	_	_
39	:	:	:	_	_	_
40	MG1655	mg1655	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
42	The	the	DT	_	_	_
43	R	r	NN	_	_	_
44	package	package	NN	_	_	_
45	,	,	,	_	_	_
46	Ringo	Ringo	NNP	_	_	_
47	,	,	,	_	_	_
48	was	be	VBD	_	_	_
49	used	use	VBN	_	_	_
50	to	to	TO	_	_	_
51	read	read	VB	_	_	_
52	the	the	DT	_	_	_
53	pair	pair	NN	_	_	_
54	files	file	NNS	_	_	_
55	and	and	CC	_	_	_
56	the	the	DT	_	_	_
57	limma	limma	NN	_	_	_
58	package	package	NN	_	_	_
59	for	for	IN	_	_	_
60	within	within	IN	_	_	_
61	-	-	:	_	_	_
62	and	and	CC	_	_	_
63	between-array	between-array	JJ	_	_	_
64	normalization	normalization	NN	_	_	_
65	.	.	.	_	_	_

1	ChIP-chip	ChIP-chip	NNP	_	_	_
2	data	datum	NNS	_	_	_
3	were	be	VBD	_	_	_
4	bi-weighted	bi-weighted	JJ	_	_	_
5	scaled	scale	VBN	_	_	_
6	within	within	IN	_	_	_
7	each	each	DT	_	_	_
8	array	array	NN	_	_	_
9	and	and	CC	_	_	_
10	aquantile	aquantile	NN	_	_	_
11	normalized	normalize	VBD	_	_	_
12	between	between	IN	_	_	_
13	arrays	array	NNS	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	0.15	0.15	CD	_	_	_
3	%	%	NN	_	_	_
4	Bile	Bile	NNP	_	_	_
5	Salt	Salt	NNP	_	_	_
6	Mix	Mix	NNP	_	_	_
7	Stress	stress	NN	_	_	_
8	,	,	,	_	_	_
9	90	90	CD	_	_	_
10	minutes	minute	NNS	_	_	_
11	,	,	,	_	_	_
12	static	static	JJ	_	_	_
13	,	,	,	_	_	_
14	5	5	CD	_	_	_
15	%	%	NN	_	_	_
16	CO2	co2	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	EHEC	ehec	NN	_	_	_
19	strain	strain	NN	_	_	_
20	:	:	:	_	_	_
21	86-24	86-24	CD	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	Bacteria	bacterium	NNS	_	_	_
25	were	be	VBD	_	_	_
26	grown	grow	VBN	_	_	_
27	in	in	IN	_	_	_
28	LB	lb	NN	MED	_	_
29	broth	broth	NN	MED	_	_
30	overnight	overnight	JJ	_	_	_
31	and	and	CC	_	_	_
32	subcultured	subculture	VBN	_	_	_
33	in	in	IN	_	_	_
34	DMEM	dmem	NN	_	_	_
35	to	to	TO	_	_	_
36	OD600	od600	NN	_	_	_
37	of	of	IN	_	_	_
38	0.4	0.4	CD	_	_	_
39	.	.	.	_	_	_

1	Bacteria	bacterium	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	spun	spin	VBN	_	_	_
5	down	down	RP	_	_	_
6	,	,	,	_	_	_
7	media	media	NNS	_	_	_
8	removed	remove	VBD	_	_	_
9	and	and	CC	_	_	_
10	repalced	repalce	VBD	_	_	_
11	with	with	IN	_	_	_
12	DMEM	dmem	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Bacteria	bacterium	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	LB	lb	NN	MED	_	_
7	broth	broth	NN	MED	_	_
8	overnight	overnight	JJ	_	_	_
9	and	and	CC	_	_	_
10	subcultured	subculture	VBN	_	_	_
11	in	in	IN	_	_	_
12	DMEM	dmem	NN	_	_	_
13	to	to	TO	_	_	_
14	OD600	od600	NN	_	_	_
15	of	of	IN	_	_	_
16	0.4	0.4	CD	_	_	_
17	.	.	.	_	_	_

1	Bacteria	bacterium	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	spun	spin	VBN	_	_	_
5	down	down	RP	_	_	_
6	,	,	,	_	_	_
7	media	media	NNS	_	_	_
8	removed	remove	VBD	_	_	_
9	and	and	CC	_	_	_
10	repalced	repalce	VBD	_	_	_
11	with	with	IN	_	_	_
12	DMEM	dmem	NN	_	_	_
13	plus	plus	CC	_	_	_
14	0.15	0.15	CD	_	_	_
15	%	%	NN	_	_	_
16	bile	bile	NN	_	_	_
17	salt	salt	NN	_	_	_
18	mix	mix	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Bile	Bile	NNP	_	_	_
3	salt	salt	NN	_	_	_
4	stress	stress	NN	_	_	_
5	was	be	VBD	_	_	_
6	done	do	VBN	_	_	_
7	in	in	IN	_	_	_
8	DMEM	dmem	NN	_	_	_
9	at	at	IN	_	_	_
10	pH	ph	NN	_	_	_
11	7.4	7.4	CD	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	unbuffered	unbuffered	JJ	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	at	at	IN	_	_	_
16	37C	37c	NN	_	_	_
17	,	,	,	_	_	_
18	5	5	CD	_	_	_
19	%	%	NN	_	_	_
20	CO2	co2	NN	_	_	_
21	,	,	,	_	_	_
22	static	static	JJ	_	_	_
23	incubation	incubation	NN	_	_	_
24	for	for	IN	_	_	_
25	90	90	CD	_	_	_
26	minutes	minute	NNS	_	_	_
27	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
28	Control	Control	NNP	_	_	_
29	treatment	treatment	NN	_	_	_
30	.	.	.	_	_	_

1	Bacteria	bacterium	NNS	_	_	_
2	were	be	VBD	_	_	_
3	grown	grow	VBN	_	_	_
4	in	in	IN	_	_	_
5	DMEM	DMEM	NNP	_	_	_
6	pH	ph	NN	_	_	_
7	7.4	7.4	CD	_	_	_
8	,	,	,	_	_	_
9	90	90	CD	_	_	_
10	minutes	minute	NNS	_	_	_
11	,	,	,	_	_	_
12	37C	37c	NN	_	_	_
13	,	,	,	_	_	_
14	5	5	CD	_	_	_
15	%	%	NN	_	_	_
16	CO2	co2	NN	_	_	_
17	,	,	,	_	_	_
18	static	static	JJ	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	unstressed	unstressed	JJ	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Cy3	cy3	NN	_	_	_
24	labeled	label	VBN	_	_	_
25	EHEC	EHEC	NNP	_	_	_
26	grown	grow	VBN	_	_	_
27	in	in	IN	_	_	_
28	DMEM	DMEM	NNP	_	_	_
29	pH	ph	NN	_	_	_
30	7.4	7.4	CD	_	_	_
31	,	,	,	_	_	_
32	90	90	CD	_	_	_
33	minutes	minute	NNS	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	Cy5	cy5	NN	_	_	_
36	labeled	label	VBN	_	_	_
37	EHEC	EHEC	NNP	_	_	_
38	bile	bile	NN	_	_	_
39	salt-stressed	salt-stressed	JJ	_	_	_
40	in	in	IN	_	_	_
41	DMEM	DMEM	NNP	_	_	_
42	,	,	,	_	_	_
43	90	90	CD	_	_	_
44	minutes	minute	NNS	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	ehec	ehec	NN	_	_	_
47	strain	strain	NN	_	_	_
48	:	:	:	_	_	_
49	86-24	86-24	CD	_	_	_
50	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
51	Escherichia	escherichia	FW	Organism	_	_
52	coli	coli	FW	Organism	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	RNA	rna	NN	_	_	_
55	was	be	VBD	_	_	_
56	extracted	extract	VBN	_	_	_
57	using	use	VBG	_	_	_
58	Trizol	trizol	NN	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	Invitrogen	invitrogen	NN	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	Signal	signal	NN	_	_	_
64	intensities	intensity	NNS	_	_	_
65	were	be	VBD	_	_	_
66	averaged	average	VBN	_	_	_
67	among	among	IN	_	_	_
68	the	the	DT	_	_	_
69	technical	technical	JJ	_	_	_
70	replicates	replicate	VBZ	_	_	_
71	.	.	.	_	_	_

1	Two	two	CD	_	_	_
2	types	type	NNS	_	_	_
3	of	of	IN	_	_	_
4	data	data	NN	_	_	_
5	analysis	analysis	NN	_	_	_
6	were	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	:	:	:	_	_	_
9	to	to	TO	_	_	_
10	indentify	indentify	VB	_	_	_
11	density-dependent	density-dependent	JJ	_	_	_
12	changes	change	NNS	_	_	_
13	in	in	IN	_	_	_
14	gene	gene	NN	_	_	_
15	expression	expression	NN	_	_	_
16	,	,	,	_	_	_
17	single	single	JJ	_	_	_
18	averaged	average	VBD	_	_	_
19	normalized	normalize	VBN	_	_	_
20	signal	signal	NN	_	_	_
21	intensities	intensity	NNS	_	_	_
22	for	for	IN	_	_	_
23	each	each	DT	_	_	_
24	treatment	treatment	NN	_	_	_
25	point	point	NN	_	_	_
26	were	be	VBD	_	_	_
27	compared	compare	VBN	_	_	_
28	to	to	TO	_	_	_
29	the	the	DT	_	_	_
30	average	average	NN	_	_	_
31	of	of	IN	_	_	_
32	corresponding	corresponding	JJ	_	_	_
33	unstressed	unstressed	JJ	_	_	_
34	control	control	NN	_	_	_
35	signal	signal	NN	_	_	_
36	intensities	intensity	NNS	_	_	_
37	.	.	.	_	_	_

1	Genes	gene	NNS	_	_	_
2	which	which	WDT	_	_	_
3	showed	show	VBD	_	_	_
4	a	a	DT	_	_	_
5	relative	relative	JJ	_	_	_
6	signal	signal	NN	_	_	_
7	log2ratio	log2ratio	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	SLR	slr	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	value	value	NN	_	_	_
12	above	above	IN	_	_	_
13	1.0	1.0	CD	_	_	_
14	or	or	CC	_	_	_
15	below	below	IN	_	_	_
16	-1.0	-1.0	CD	_	_	_
17	were	be	VBD	_	_	_
18	selected	select	VBN	_	_	_
19	for	for	IN	_	_	_
20	further	further	JJ	_	_	_
21	analysis	analysis	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	After	after	IN	_	_	_
3	quality	quality	NN	_	_	_
4	controls	control	NNS	_	_	_
5	of	of	IN	_	_	_
6	data	datum	NNS	_	_	_
7	distribution	distribution	NN	_	_	_
8	the	the	DT	_	_	_
9	raw	raw	JJ	_	_	_
10	data	data	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	CEL	cel	NN	_	_	_
13	files	file	NNS	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	were	be	VBD	_	_	_
16	used	use	VBN	_	_	_
17	to	to	TO	_	_	_
18	perform	perform	VB	_	_	_
19	,	,	,	_	_	_
20	normalization	normalization	NN	_	_	_
21	and	and	CC	_	_	_
22	probe	probe	NN	_	_	_
23	set	set	VBD	_	_	_
24	summarization	summarization	NN	_	_	_
25	through	through	IN	_	_	_
26	RMA	RMA	NNP	_	_	_
27	algorithm	algorithm	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Robust	robust	JJ	_	_	_
30	Multiarray	Multiarray	NNP	_	_	_
31	Analysis	analysis	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	by	by	IN	_	_	_
34	using	use	VBG	_	_	_
35	the	the	DT	_	_	_
36	Affymetrix	Affymetrix	NNP	_	_	_
37	Gene	Gene	NNP	_	_	_
38	Expression	expression	NN	_	_	_
39	Console	Console	NNP	_	_	_
40	Software	Software	NNP	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	www.affymetrix.com	www.affymetrix.com	NNP	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	.	.	.	_	_	_

1	Normalized	normalize	VBN	_	_	_
2	data	datum	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	uploaded	upload	VBN	_	_	_
6	into	into	IN	_	_	_
7	OneChannelGUI	OneChannelGUI	NNP	_	_	_
8	Software	Software	NNP	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	http	http	JJ	_	_	_
11	:	:	:	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	E.coli	e.coli	NNS	_	_	_
14	_	_	VBP	_	_	_
15	IVT-RNA	ivt-rna	NN	_	_	_
16	_	_	CD	_	_	_
17	sigma70-1	sigma70-1	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	E.coli	e.coli	NNS	_	_	_
20	_	_	VBP	_	_	_
21	IVT-RNA	ivt-rna	NN	_	_	_
22	_	_	CD	_	_	_
23	sigma70-2	sigma70-2	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	E.coli	e.coli	NNS	_	_	_
26	_	_	VBP	_	_	_
27	IVT-RNA	ivt-rna	NN	_	_	_
28	_	_	CD	_	_	_
29	sigmaS	sigmas	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	E.coli	e.coli	NNS	_	_	_
32	_	_	VBP	_	_	_
33	IVT-RNA	ivt-rna	NN	_	_	_
34	_	_	CD	_	_	_
35	sigmaS-2	sigmas-2	NN	_	_	_
36	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
37	E.	E.	NNP	_	_	_
38	coli	coli	NN	_	_	_
39	RNA	rna	NN	_	_	_
40	polymerase	polymerase	NN	_	_	_
41	core	core	NN	_	_	_
42	enzyme	enzyme	NN	_	_	_
43	was	be	VBD	_	_	_
44	purchased	purchase	VBN	_	_	_
45	from	from	IN	_	_	_
46	Epicentre	Epicentre	NNP	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	Madison	Madison	NNP	_	_	_
49	,	,	,	_	_	_
50	WI	WI	NNP	_	_	_
51	,	,	,	_	_	_
52	USA	USA	NNP	_	_	_
53	-RRB-	-rrb-	-RRB-	_	_	_
54	.	.	.	_	_	_

1	Histidine-tagged	histidine-tagged	JJ	_	_	_
2	σ	σ	NN	_	_	_
3	factors	factor	NNS	_	_	_
4	were	be	VBD	_	_	_
5	produced	produce	VBN	_	_	_
6	and	and	CC	_	_	_
7	purified	purify	VBN	_	_	_
8	as	as	IN	_	_	_
9	described	describe	VBN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Lacour	Lacour	NNP	_	_	_
12	et	et	FW	_	_	_
13	al.	al.	FW	_	_	_
14	,	,	,	_	_	_
15	2003	2003	CD	_	_	_
16	;	;	:	_	_	_
17	Checroun	Checroun	NNP	_	_	_
18	et	et	FW	_	_	_
19	al.	al.	FW	_	_	_
20	,	,	,	_	_	_
21	2004	2004	CD	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	;	;	:	_	_	_
24	proteins	protein	NNS	_	_	_
25	appeared	appear	VBD	_	_	_
26	pure	pure	JJ	_	_	_
27	from	from	IN	_	_	_
28	contaminants	contaminant	NNS	_	_	_
29	as	as	IN	_	_	_
30	determined	determine	VBN	_	_	_
31	by	by	IN	_	_	_
32	denaturing	denature	VBG	_	_	_
33	protein	protein	NN	_	_	_
34	gel	gel	NN	_	_	_
35	electrophoresis	electrophoresis	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	data	datum	NNS	_	_	_
38	not	not	RB	_	_	_
39	shown	show	VBN	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	reconstitution	reconstitution	NN	_	_	_
3	of	of	IN	_	_	_
4	RNA	rna	NN	_	_	_
5	polymerase	polymerase	NN	_	_	_
6	holoenzymes	holoenzyme	NNS	_	_	_
7	,	,	,	_	_	_
8	the	the	DT	_	_	_
9	core	core	NN	_	_	_
10	enzyme	enzyme	NN	_	_	_
11	was	be	VBD	_	_	_
12	incubated	incubate	VBN	_	_	_
13	for	for	IN	_	_	_
14	10	10	CD	_	_	_
15	minutes	minute	NNS	_	_	_
16	at	at	IN	_	_	_
17	37	37	CD	_	_	_
18	°C	°c	NN	_	_	_
19	with	with	IN	_	_	_
20	either	either	CC	_	_	_
21	σS	σs	NN	_	_	_
22	or	or	CC	_	_	_
23	σ70	σ70	NN	_	_	_
24	at	at	IN	_	_	_
25	a	a	DT	_	_	_
26	1:10	1:10	CD	_	_	_
27	ratio	ratio	NN	_	_	_
28	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	calculation	calculation	NN	_	_	_
3	of	of	IN	_	_	_
4	RNA	rna	NN	_	_	_
5	polymerase	polymerase	NN	_	_	_
6	concentrations	concentration	NNS	_	_	_
7	in	in	IN	_	_	_
8	transcription	transcription	NN	_	_	_
9	assays	assay	NNS	_	_	_
10	,	,	,	_	_	_
11	it	it	PRP	_	_	_
12	was	be	VBD	_	_	_
13	assumed	assume	VBN	_	_	_
14	that	that	IN	_	_	_
15	,	,	,	_	_	_
16	after	after	IN	_	_	_
17	reconstitution	reconstitution	NN	_	_	_
18	,	,	,	_	_	_
19	core	core	NN	_	_	_
20	enzyme	enzyme	NN	_	_	_
21	would	would	MD	_	_	_
22	be	be	VB	_	_	_
23	100	100	CD	_	_	_
24	%	%	NN	_	_	_
25	active	active	JJ	_	_	_
26	and	and	CC	_	_	_
27	fully	fully	RB	_	_	_
28	saturated	saturate	VBN	_	_	_
29	by	by	IN	_	_	_
30	either	either	CC	_	_	_
31	σ	σ	NN	_	_	_
32	factor	factor	NN	_	_	_
33	.	.	.	_	_	_

1	2	2	CD	_	_	_
2	ug	ug	NN	_	_	_
3	of	of	IN	_	_	_
4	genomic	genomic	JJ	_	_	_
5	DNA	dna	NN	_	_	_
6	from	from	IN	_	_	_
7	E.	e.	FW	_	_	_
8	coli	coli	FW	_	_	_
9	MG1655	mg1655	NN	_	_	_
10	digested	digest	VBN	_	_	_
11	with	with	IN	_	_	_
12	EcoRI	ecori	NN	_	_	_
13	were	be	VBD	_	_	_
14	used	use	VBN	_	_	_
15	in	in	IN	_	_	_
16	transcription	transcription	NN	_	_	_
17	assays	assay	NNS	_	_	_
18	for	for	IN	_	_	_
19	ROMA	roma	NN	_	_	_
20	experiments	experiment	NNS	_	_	_
21	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	polymerase	polymerase	NN	_	_	_
3	holoenzyme	holoenzyme	NN	_	_	_
4	concentrations	concentration	NNS	_	_	_
5	were	be	VBD	_	_	_
6	100	100	CD	_	_	_
7	nM	nm	NN	_	_	_
8	in	in	IN	_	_	_
9	50	50	CD	_	_	_
10	ul	ul	NN	_	_	_
11	reaction	reaction	NN	_	_	_
12	mixture	mixture	NN	_	_	_
13	.	.	.	_	_	_

1	Ten	ten	CD	_	_	_
2	independent	independent	JJ	_	_	_
3	run-off	run-off	JJ	_	_	_
4	transcription	transcription	NN	_	_	_
5	assays	assay	NNS	_	_	_
6	were	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	,	,	,	_	_	_
9	and	and	CC	_	_	_
10	transcripts	transcript	NNS	_	_	_
11	were	be	VBD	_	_	_
12	pooled	pool	VBN	_	_	_
13	together	together	RB	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	ca.	ca.	FW	_	_	_
16	1	1	CD	_	_	_
17	ug	ug	NN	_	_	_
18	total	total	JJ	_	_	_
19	RNA	rna	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	RNA	rna	NN	_	_	_
4	produced	produce	VBN	_	_	_
5	by	by	IN	_	_	_
6	in	in	FW	_	_	_
7	vitro	vitro	FW	_	_	_
8	transcription	transcription	NN	_	_	_
9	,	,	,	_	_	_
10	with	with	IN	_	_	_
11	RNA	rna	NN	_	_	_
12	polymerase	polymerase	NN	_	_	_
13	E	e	NN	_	_	_
14	σ70	σ70	NN	_	_	_
15	,	,	,	_	_	_
16	of	of	IN	_	_	_
17	2	2	CD	_	_	_
18	ug	ug	NN	_	_	_
19	of	of	IN	_	_	_
20	genomic	genomic	JJ	_	_	_
21	DNA	dna	NN	_	_	_
22	from	from	IN	_	_	_
23	E.	e.	FW	_	_	_
24	coli	coli	FW	_	_	_
25	MG1655	mg1655	NN	_	_	_
26	digested	digest	VBN	_	_	_
27	with	with	IN	_	_	_
28	EcoRI	ecori	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	RNA	rna	NN	_	_	_
31	produced	produce	VBN	_	_	_
32	by	by	IN	_	_	_
33	in	in	FW	_	_	_
34	vitro	vitro	FW	_	_	_
35	transcription	transcription	NN	_	_	_
36	,	,	,	_	_	_
37	with	with	IN	_	_	_
38	RNA	rna	NN	_	_	_
39	polymerase	polymerase	NN	_	_	_
40	E	e	NN	_	_	_
41	σS	σs	NN	_	_	_
42	,	,	,	_	_	_
43	of	of	IN	_	_	_
44	2	2	CD	_	_	_
45	ug	ug	NN	_	_	_
46	of	of	IN	_	_	_
47	genomic	genomic	JJ	_	_	_
48	DNA	dna	NN	_	_	_
49	from	from	IN	_	_	_
50	E.	e.	FW	_	_	_
51	coli	coli	FW	_	_	_
52	MG1655	mg1655	NN	_	_	_
53	digested	digest	VBN	_	_	_
54	with	with	IN	_	_	_
55	EcoRI	ecori	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	sample	sample	NN	_	_	_
58	type	type	NN	_	_	_
59	:	:	:	_	_	_
60	cDNA	cdna	NN	_	_	_
61	produced	produce	VBN	_	_	_
62	by	by	IN	_	_	_
63	RT	rt	NN	_	_	_
64	of	of	IN	_	_	_
65	RNA	rna	NN	_	_	_
66	deriving	derive	VBG	_	_	_
67	from	from	IN	_	_	_
68	vitro	vitro	FW	_	_	_
69	transcription	transcription	NN	_	_	_
70	,	,	,	_	_	_
71	with	with	IN	_	_	_
72	RNA	rna	NN	_	_	_
73	polymerase	polymerase	NN	_	_	_
74	E	e	NN	_	_	_
75	σ70	σ70	NN	_	_	_
76	,	,	,	_	_	_
77	of	of	IN	_	_	_
78	2	2	CD	_	_	_
79	ug	ug	NN	_	_	_
80	of	of	IN	_	_	_
81	genomic	genomic	JJ	_	_	_
82	DNA	dna	NN	_	_	_
83	from	from	IN	_	_	_
84	E.	e.	FW	_	_	_
85	coli	coli	FW	_	_	_
86	MG1655	mg1655	NN	_	_	_
87	digested	digest	VBN	_	_	_
88	with	with	IN	_	_	_
89	EcoRI	ecori	NN	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	sample	sample	NN	_	_	_
92	type	type	NN	_	_	_
93	:	:	:	_	_	_
94	cDNA	cdna	NN	_	_	_
95	produced	produce	VBN	_	_	_
96	by	by	IN	_	_	_
97	RT	rt	NN	_	_	_
98	of	of	IN	_	_	_
99	RNA	rna	NN	_	_	_
100	deriving	derive	VBG	_	_	_
101	from	from	IN	_	_	_
102	vitro	vitro	FW	_	_	_
103	transcription	transcription	NN	_	_	_
104	,	,	,	_	_	_
105	with	with	IN	_	_	_
106	RNA	rna	NN	_	_	_
107	polymerase	polymerase	NN	_	_	_
108	E	e	NN	_	_	_
109	σS	σs	NN	_	_	_
110	,	,	,	_	_	_
111	of	of	IN	_	_	_
112	2	2	CD	_	_	_
113	ug	ug	NN	_	_	_
114	of	of	IN	_	_	_
115	genomic	genomic	JJ	_	_	_
116	DNA	dna	NN	_	_	_
117	from	from	IN	_	_	_
118	E.	e.	FW	_	_	_
119	coli	coli	FW	_	_	_
120	MG1655	mg1655	NN	_	_	_
121	digested	digest	VBN	_	_	_
122	with	with	IN	_	_	_
123	EcoRI	ecori	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	Cells	cell	NNS	_	_	_
126	in	in	IN	_	_	_
127	RNAlater	rnalater	NN	_	_	_
128	were	be	VBD	_	_	_
129	aliquoted	aliquote	VBN	_	_	_
130	into	into	IN	_	_	_
131	two	two	CD	_	_	_
132	.	.	.	_	_	_

1	One	one	CD	_	_	_
2	served	serve	VBD	_	_	_
3	as	as	IN	_	_	_
4	non-sorted	non-sorted	JJ	_	_	_
5	cells	cell	NNS	_	_	_
6	and	and	CC	_	_	_
7	kept	keep	VBD	_	_	_
8	at	at	IN	_	_	_
9	4	4	CD	_	_	_
10	degree	degree	NN	_	_	_
11	C	c	NN	_	_	_
12	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	other	other	JJ	_	_	_
3	aliquot	aliquot	NN	_	_	_
4	was	be	VBD	_	_	_
5	homogenized	homogenize	VBN	_	_	_
6	with	with	IN	_	_	_
7	OMNI	OMNI	NNP	_	_	_
8	TH	th	NN	_	_	_
9	homogenizer	homogenizer	NN	_	_	_
10	for	for	IN	_	_	_
11	2	2	CD	_	_	_
12	min	min	NN	_	_	_
13	on	on	IN	_	_	_
14	ice	ice	NN	_	_	_
15	and	and	CC	_	_	_
16	further	further	JJ	_	_	_
17	aliquoted	aliquote	VBN	_	_	_
18	into	into	IN	_	_	_
19	small	small	JJ	_	_	_
20	vials	vial	NNS	_	_	_
21	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	in	in	IN	_	_	_
3	each	each	DT	_	_	_
4	vial	vial	NN	_	_	_
5	were	be	VBD	_	_	_
6	then	then	RB	_	_	_
7	re-suspended	re-suspended	JJ	_	_	_
8	in	in	IN	_	_	_
9	nuclease-free	nuclease-free	JJ	_	_	_
10	phosphate	phosphate	NN	_	_	_
11	buffered	buffer	VBN	_	_	_
12	saline	saline	NN	_	_	_
13	,	,	,	_	_	_
14	incubated	incubate	VBN	_	_	_
15	with	with	IN	_	_	_
16	anti-E	anti-e	JJ	_	_	_
17	.	.	.	_	_	_

1	coli	coli	NN	_	_	_
2	antibody	antibody	NN	_	_	_
3	and	and	CC	_	_	_
4	microbeads	microbead	NNS	_	_	_
5	,	,	,	_	_	_
6	followed	follow	VBN	_	_	_
7	by	by	IN	_	_	_
8	separation	separation	NN	_	_	_
9	on	on	IN	_	_	_
10	a	a	DT	_	_	_
11	MACS	macs	NN	_	_	_
12	separator	separator	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Miltenyi	Miltenyi	NNP	_	_	_
15	,	,	,	_	_	_
16	Auburn	Auburn	NNP	_	_	_
17	,	,	,	_	_	_
18	CA	CA	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	at	at	IN	_	_	_
21	4	4	CD	_	_	_
22	degree	degree	NN	_	_	_
23	C.	c.	NN	_	_	_
24	Sorted	sort	VBN	_	_	_
25	cells	cell	NNS	_	_	_
26	were	be	VBD	_	_	_
27	re-suspended	re-suspended	JJ	_	_	_
28	into	into	IN	_	_	_
29	RNAlater	rnalater	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	was	be	VBD	_	_	_
4	analyzed	analyze	VBN	_	_	_
5	in	in	IN	_	_	_
6	the	the	DT	_	_	_
7	software	software	NN	_	_	_
8	Acuity	acuity	NN	_	_	_
9	4.0	4.0	CD	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Molecular	molecular	JJ	_	_	_
12	Devices	Devices	NNPS	_	_	_
13	,	,	,	_	_	_
14	Sunnyvale	Sunnyvale	NNP	_	_	_
15	,	,	,	_	_	_
16	CA	CA	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

1	LOWESS	lowess	NN	_	_	_
2	normalization	normalization	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	with	with	IN	_	_	_
6	three	three	CD	_	_	_
7	iterations	iteration	NNS	_	_	_
8	using	use	VBG	_	_	_
9	a	a	DT	_	_	_
10	smoothing	smoothing	NN	_	_	_
11	factor	factor	NN	_	_	_
12	of	of	IN	_	_	_
13	0.4	0.4	CD	_	_	_
14	.	.	.	_	_	_

1	Hybridized	hybridize	VBN	_	_	_
2	spots	spot	NNS	_	_	_
3	having	have	VBG	_	_	_
4	a	a	DT	_	_	_
5	high	high	JJ	_	_	_
6	QC	qc	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	quality	quality	NN	_	_	_
9	control	control	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	value	value	NN	_	_	_
12	>	>	JJR	_	_	_
13	0.1	0.1	CD	_	_	_
14	,	,	,	_	_	_
15	good	good	JJ	_	_	_
16	flag	flag	NN	_	_	_
17	tags	tag	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	A	a	NN	_	_	_
20	,	,	,	_	_	_
21	B	b	NN	_	_	_
22	and	and	CC	_	_	_
23	C	c	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	in	in	IN	_	_	_
26	both	both	CC	_	_	_
27	Cy3	cy3	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
29	E.	e.	FW	_	_	_
30	coli	coli	FW	_	_	_
31	cells	cell	NNS	_	_	_
32	were	be	VBD	_	_	_
33	grown	grow	VBN	_	_	_
34	in	in	IN	_	_	_
35	annular	annular	JJ	_	_	_
36	reactor	reactor	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	BioSurface	BioSurface	NNP	_	_	_
39	Technologies	Technologies	NNPS	_	_	_
40	,	,	,	_	_	_
41	Bozeman	Bozeman	NNP	_	_	_
42	,	,	,	_	_	_
43	MT	MT	NNP	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	inoculated	inoculate	VBN	_	_	_
46	with	with	IN	_	_	_
47	1	1	CD	_	_	_
48	ml	ml	NN	_	_	_
49	overnight	overnight	JJ	_	_	_
50	cultures	culture	NNS	_	_	_
51	and	and	CC	_	_	_
52	supplied	supply	VBN	_	_	_
53	with	with	IN	_	_	_
54	fresh	fresh	JJ	_	_	_
55	10-fold	10-fold	JJ	_	_	_
56	diluted	diluted	JJ	_	_	_
57	Luria	Luria	NNP	MED	_	_
58	broth	broth	NN	MED	_	_
59	at	at	IN	_	_	_
60	100	100	CD	_	_	_
61	ml	ml	NN	_	_	_
62	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
63	Escherichia	escherichia	FW	Organism	_	_
64	coli	coli	FW	Organism	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	growth	growth	NN	_	_	_
67	mode	mode	NN	_	_	_
68	:	:	:	_	_	_
69	planktonic	planktonic	JJ	_	_	_
70	culture	culture	NN	_	_	_
71	in	in	IN	_	_	_
72	annular	annular	JJ	_	_	_
73	reactor	reactor	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	growth	growth	NN	_	_	_
76	time	time	NN	_	_	_
77	:	:	:	_	_	_
78	7-day	7-day	JJ	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	non-sorted	non-sorted	JJ	_	_	_
81	E.	e.	FW	_	_	_
82	coli	coli	FW	_	_	_
83	cells	cell	NNS	_	_	_
84	from	from	IN	_	_	_
85	culture	culture	NN	_	_	_
86	1	1	CD	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	non-sorted	non-sorted	JJ	_	_	_
89	E.	e.	FW	_	_	_
90	coli	coli	FW	_	_	_
91	cells	cell	NNS	_	_	_
92	from	from	IN	_	_	_
93	culture	culture	NN	_	_	_
94	2	2	CD	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	RNAlater	rnalater	NN	_	_	_
97	was	be	VBD	_	_	_
98	removed	remove	VBN	_	_	_
99	from	from	IN	_	_	_
100	cells	cell	NNS	_	_	_
101	by	by	IN	_	_	_
102	filtration	filtration	NN	_	_	_
103	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	from	from	IN	_	_	_
6	cells	cell	NNS	_	_	_
7	using	use	VBG	_	_	_
8	a	a	DT	_	_	_
9	hot	hot	JJ	_	_	_
10	SDS	sds	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	sorted	sort	VBD	_	_	_
13	E.	e.	FW	_	_	_
14	coli	coli	FW	_	_	_
15	cells	cell	NNS	_	_	_
16	from	from	IN	_	_	_
17	culture	culture	NN	_	_	_
18	1	1	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	sorted	sort	VBD	_	_	_
21	E.	e.	FW	_	_	_
22	coli	coli	FW	_	_	_
23	cells	cell	NNS	_	_	_
24	from	from	IN	_	_	_
25	culture	culture	NN	_	_	_
26	2	2	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	sorted	sort	VBD	_	_	_
29	vs.	vs.	CC	_	_	_
30	non-sorted	non-sorted	JJ	_	_	_
31	cells	cell	NNS	_	_	_
32	bioreplicate	bioreplicate	VBP	_	_	_
33	1	1	CD	_	_	_
34	technical	technical	JJ	_	_	_
35	replicate	replicate	VBP	_	_	_
36	1	1	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	sorted	sort	VBD	_	_	_
39	vs.	vs.	CC	_	_	_
40	non-sorted	non-sorted	JJ	_	_	_
41	cells	cell	NNS	_	_	_
42	bioreplicate	bioreplicate	VBP	_	_	_
43	1	1	CD	_	_	_
44	technical	technical	JJ	_	_	_
45	replicate	replicate	VB	_	_	_
46	2	2	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
48	sorted	sort	VBD	_	_	_
49	vs.	vs.	CC	_	_	_
50	non-sorted	non-sorted	JJ	_	_	_
51	cells	cell	NNS	_	_	_
52	bioreplicate	bioreplicate	VBP	_	_	_
53	2	2	CD	_	_	_
54	technical	technical	JJ	_	_	_
55	replicate	replicate	VBP	_	_	_
56	1	1	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	sorted	sort	VBD	_	_	_
59	vs.	vs.	CC	_	_	_
60	non-sorted	non-sorted	JJ	_	_	_
61	cells	cell	NNS	_	_	_
62	bioreplicate	bioreplicate	VBP	_	_	_
63	2	2	CD	_	_	_
64	technical	technical	JJ	_	_	_
65	replicate	replicate	VB	_	_	_
66	2	2	CD	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
68	strain	strain	NN	_	_	_
69	:	:	:	_	_	_
70	K-12	k-12	NN	_	_	_
71	PHL644	phl644	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	treatment	treatment	NN	_	_	_
74	:	:	:	_	_	_
75	non-sorted	non-sorted	JJ	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	treatment	treatment	NN	_	_	_
78	:	:	:	_	_	_
79	sorted	sort	VBN	_	_	_
80	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
81	Bacteria	bacterium	NNS	_	_	_
82	were	be	VBD	_	_	_
83	inoculated	inoculate	VBN	_	_	_
84	by	by	IN	_	_	_
85	direct	direct	JJ	_	_	_
86	injection	injection	NN	_	_	_
87	of	of	IN	_	_	_
88	the	the	DT	_	_	_
89	mouse	mouse	NN	_	_	_
90	bladder	bladder	NN	_	_	_
91	,	,	,	_	_	_
92	and	and	CC	_	_	_
93	kidney	kidney	NN	_	_	_
94	samples	sample	NNS	_	_	_
95	were	be	VBD	_	_	_
96	taken	take	VBN	_	_	_
97	at	at	IN	_	_	_
98	day	day	NN	_	_	_
99	2	2	CD	_	_	_
100	post-infection	post-infection	JJ	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
102	cDNA	cdna	NN	_	_	_
103	made	make	VBN	_	_	_
104	from	from	IN	_	_	_
105	strain	strain	NN	_	_	_
106	KMD	kmd	NN	_	_	_
107	extracted	extract	VBN	_	_	_
108	from	from	IN	_	_	_
109	mouse	mouse	NN	_	_	_
110	kidney	kidney	NN	_	_	_
111	on	on	IN	_	_	_
112	day	day	NN	_	_	_
113	2	2	CD	_	_	_
114	post	post	NN	_	_	_
115	infection	infection	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	cDNA	cdna	NN	_	_	_
118	made	make	VBN	_	_	_
119	from	from	IN	_	_	_
120	strain	strain	NN	_	_	_
121	PC1012	pc1012	NN	_	_	_
122	-LRB-	-lrb-	-LRB-	_	_	_
123	marArobsoxS	mararobsoxs	NN	_	_	_
124	-RRB-	-rrb-	-RRB-	_	_	_
125	extracted	extract	VBN	_	_	_
126	from	from	IN	_	_	_
127	mouse	mouse	NN	_	_	_
128	kidney	kidney	NN	_	_	_
129	on	on	IN	_	_	_
130	day	day	NN	_	_	_
131	2	2	CD	_	_	_
132	post	post	NN	_	_	_
133	infection	infection	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	Escherichia	escherichia	FW	Organism	_	_
136	coli	coli	FW	Organism	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	Infected	infected	JJ	_	_	_
139	kidney	kidney	NN	_	_	_
140	solutions	solution	NNS	_	_	_
141	were	be	VBD	_	_	_
142	centrifuged	centrifuge	VBN	_	_	_
143	at	at	IN	_	_	_
144	5000xg	5000xg	CD	_	_	_
145	for	for	IN	_	_	_
146	10	10	CD	_	_	_
147	min	min	NN	_	_	_
148	to	to	TO	_	_	_
149	separate	separate	JJ	_	_	_
150	bacteria	bacterium	NNS	_	_	_
151	-LRB-	-lrb-	-LRB-	_	_	_
152	pellet	pellet	NN	_	_	_
153	-RRB-	-rrb-	-RRB-	_	_	_
154	from	from	IN	_	_	_
155	kidney	kidney	NN	_	_	_
156	-LRB-	-lrb-	-LRB-	_	_	_
157	surface	surface	NN	_	_	_
158	of	of	IN	_	_	_
159	RNA-later	rna-later	NN	_	_	_
160	solution	solution	NN	_	_	_
161	-RRB-	-rrb-	-RRB-	_	_	_
162	cells	cell	NNS	_	_	_
163	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	kidney	kidney	NN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	evacuated	evacuate	VBN	_	_	_
6	from	from	IN	_	_	_
7	the	the	DT	_	_	_
8	top	top	NN	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	solution	solution	NN	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	the	the	DT	_	_	_
15	remaining	remain	VBG	_	_	_
16	solution	solution	NN	_	_	_
17	was	be	VBD	_	_	_
18	spun	spin	VBN	_	_	_
19	once	once	RB	_	_	_
20	more	more	RBR	_	_	_
21	at	at	IN	_	_	_
22	12000xg	12000xg	CD	_	_	_
23	for	for	IN	_	_	_
24	10	10	CD	_	_	_
25	min	min	NN	_	_	_
26	,	,	,	_	_	_
27	followed	follow	VBN	_	_	_
28	by	by	IN	_	_	_
29	disposal	disposal	NN	_	_	_
30	of	of	IN	_	_	_
31	the	the	DT	_	_	_
32	supernatant	supernatant	NN	_	_	_
33	.	.	.	_	_	_

1	Pelleted	pelleted	JJ	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	resuspended	resuspend	VBN	_	_	_
5	in	in	IN	_	_	_
6	TE	TE	NNP	_	_	_
7	buffer	buffer	NN	_	_	_
8	and	and	CC	_	_	_
9	treated	treat	VBN	_	_	_
10	with	with	IN	_	_	_
11	lysozyme	lysozyme	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Sigma	Sigma	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	at	at	IN	_	_	_
16	1	1	CD	_	_	_
17	mg	mg	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	KMD	kmd	NN	_	_	_
20	1	1	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	KMD	kmd	NN	_	_	_
23	2	2	CD	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	KMD	kmd	NN	_	_	_
26	3	3	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Mouse	mouse	NN	_	_	_
29	kidneys	kidney	NNS	_	_	_
30	were	be	VBD	_	_	_
31	homogonized	homogonize	VBN	_	_	_
32	in	in	IN	_	_	_
33	RNALater	rnalater	NN	_	_	_
34	solution	solution	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	Ambion	ambion	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	and	and	CC	_	_	_
39	bacterial	bacterial	JJ	_	_	_
40	titers	titer	NNS	_	_	_
41	were	be	VBD	_	_	_
42	taken	take	VBN	_	_	_
43	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	pooled	pool	VBN	_	_	_
4	,	,	,	_	_	_
5	and	and	CC	_	_	_
6	centrifuged	centrifuge	VBD	_	_	_
7	as	as	IN	_	_	_
8	described	describe	VBN	_	_	_
9	below	below	IN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	PC	pc	NN	_	_	_
12	1	1	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	PC	pc	NN	_	_	_
15	2	2	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	PC	pc	NN	_	_	_
18	3	3	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	strain	strain	NN	_	_	_
21	:	:	:	_	_	_
22	KMD	KMD	NNP	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
24	strain	strain	NN	_	_	_
25	:	:	:	_	_	_
26	PC1012	pc1012	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
28	The	the	DT	_	_	_
29	data	datum	NNS	_	_	_
30	were	be	VBD	_	_	_
31	analyzed	analyze	VBN	_	_	_
32	with	with	IN	_	_	_
33	Microarray	Microarray	NNP	_	_	_
34	Suite	Suite	NNP	_	_	_
35	version	version	NN	_	_	_
36	5.0	5.0	CD	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	MAS	mas	NN	_	_	_
39	5.0	5.0	CD	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	using	use	VBG	_	_	_
42	Affymetrix	Affymetrix	NNP	_	_	_
43	default	default	NN	_	_	_
44	analysis	analysis	NN	_	_	_
45	settings	setting	NNS	_	_	_
46	and	and	CC	_	_	_
47	global	global	JJ	_	_	_
48	scaling	scaling	NN	_	_	_
49	as	as	IN	_	_	_
50	normalization	normalization	NN	_	_	_
51	method	method	NN	_	_	_
52	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	trimmed	trim	VBN	_	_	_
3	mean	mean	NN	_	_	_
4	target	target	NN	_	_	_
5	intensity	intensity	NN	_	_	_
6	of	of	IN	_	_	_
7	each	each	DT	_	_	_
8	array	array	NN	_	_	_
9	was	be	VBD	_	_	_
10	arbitrarily	arbitrarily	RB	_	_	_
11	set	set	VBN	_	_	_
12	to	to	TO	_	_	_
13	100	100	CD	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	tissue	tissue	NN	_	_	_
3	source	source	NN	_	_	_
4	:	:	:	_	_	_
5	kidney	kidney	NN	_	_	_
6	from	from	IN	_	_	_
7	CD-1	cd-1	JJ	_	_	_
8	mice	mouse	NNS	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Cells	cell	NNS	_	_	_
11	aerobically	aerobically	RB	_	_	_
12	grown	grow	VBN	_	_	_
13	to	to	TO	_	_	_
14	mid-log	mid-log	JJ	_	_	_
15	phase	phase	NN	_	_	_
16	in	in	IN	_	_	_
17	MOPS	MOPS	NNP	MED	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Control	Control	NNP	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	Ecoli	Ecoli	NNP	_	_	_
22	_	_	NNP	_	_	_
23	WT	WT	NNP	_	_	_
24	_	_	NNP	_	_	_
25	100uM	100uM	NNP	_	_	_
26	_	_	SYM	_	_	_
27	KCN	KCN	NNP	_	_	_
28	_	_	SYM	_	_	_
29	Sample1	sample1	FW	_	_	_
30	_	_	FW	_	_	_
31	TechRep1	techrep1	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	Ecoli	ecolus	NNS	_	_	_
34	_	_	VBP	_	_	_
35	WT	wt	JJ	_	_	_
36	_	_	NN	_	_	_
37	100uM	100um	NN	_	_	_
38	_	_	CD	_	_	_
39	KCN	KCN	NNP	_	_	_
40	_	_	SYM	_	_	_
41	Sample1	sample1	FW	_	_	_
42	_	_	FW	_	_	_
43	TechRep2	techrep2	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	Ecoli	ecolus	NNS	_	_	_
46	_	_	VBP	_	_	_
47	WT	wt	JJ	_	_	_
48	_	_	NN	_	_	_
49	100uM	100um	NN	_	_	_
50	_	_	CD	_	_	_
51	KCN	KCN	NNP	_	_	_
52	_	_	SYM	_	_	_
53	Sample2	sample2	FW	_	_	_
54	_	_	FW	_	_	_
55	TechRep1	techrep1	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	Ecoli	ecolus	NNS	_	_	_
58	_	_	VBP	_	_	_
59	WT	wt	JJ	_	_	_
60	_	_	NN	_	_	_
61	100uM	100um	NN	_	_	_
62	_	_	CD	_	_	_
63	KCN	KCN	NNP	_	_	_
64	_	_	SYM	_	_	_
65	Sample2	sample2	FW	_	_	_
66	_	_	FW	_	_	_
67	TechRep2	techrep2	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	Ecoli	ecolus	NNS	_	_	_
70	_	_	VBP	_	_	_
71	WT	wt	JJ	_	_	_
72	_	_	NN	_	_	_
73	100uM	100um	NN	_	_	_
74	_	_	CD	_	_	_
75	KCN	KCN	NNP	_	_	_
76	_	_	SYM	_	_	_
77	Sample3	sample3	FW	_	_	_
78	_	_	FW	_	_	_
79	TechRep1	techrep1	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	Ecoli	ecolus	NNS	_	_	_
82	_	_	VBP	_	_	_
83	WT	wt	JJ	_	_	_
84	_	_	NN	_	_	_
85	100uM	100um	NN	_	_	_
86	_	_	CD	_	_	_
87	KCN	KCN	NNP	_	_	_
88	_	_	SYM	_	_	_
89	Sample3	sample3	FW	_	_	_
90	_	_	FW	_	_	_
91	TechRep2	techrep2	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	Ecoli	ecolus	NNS	_	_	_
94	_	_	VBP	_	_	_
95	WT	wt	JJ	_	_	_
96	_	_	NN	_	_	_
97	100uM	100um	NN	_	_	_
98	_	_	CD	_	_	_
99	KCN	KCN	NNP	_	_	_
100	_	_	SYM	_	_	_
101	Sample4	sample4	FW	_	_	_
102	_	_	FW	_	_	_
103	TechRep1	techrep1	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	Ecoli	ecolus	NNS	_	_	_
106	_	_	VBP	_	_	_
107	WT	wt	JJ	_	_	_
108	_	_	NN	_	_	_
109	100uM	100um	NN	_	_	_
110	_	_	CD	_	_	_
111	KCN	KCN	NNP	_	_	_
112	_	_	SYM	_	_	_
113	Sample4	sample4	FW	_	_	_
114	_	_	FW	_	_	_
115	TechRep2	techrep2	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	Escherichia	escherichia	FW	Organism	_	_
118	coli	coli	FW	Organism	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	Quantification	quantification	NN	_	_	_
121	of	of	IN	_	_	_
122	the	the	DT	_	_	_
123	scans	scan	NNS	_	_	_
124	were	be	VBD	_	_	_
125	performed	perform	VBN	_	_	_
126	with	with	IN	_	_	_
127	ImaGene	imagene	NN	_	_	_
128	-LRB-	-lrb-	-LRB-	_	_	_
129	Version	version	NN	_	_	_
130	6.0.1	6.0.1	CD	_	_	_
131	;	;	:	_	_	_
132	BioDiscovery	BioDiscovery	NNP	_	_	_
133	;	;	:	_	_	_
134	El	El	NNP	_	_	_
135	Segundo	Segundo	NNP	_	_	_
136	,	,	,	_	_	_
137	CA	CA	NNP	_	_	_
138	;	;	:	_	_	_
139	www.biodiscovery.com	www.biodiscovery.com	NNP	_	_	_
140	-RRB-	-rrb-	-RRB-	_	_	_
141	;	;	:	_	_	_
142	with	with	IN	_	_	_
143	the	the	DT	_	_	_
144	results	result	NNS	_	_	_
145	presented	present	VBN	_	_	_
146	in	in	IN	_	_	_
147	the	the	DT	_	_	_
148	associated	associate	VBN	_	_	_
149	text	text	NN	_	_	_
150	files	file	NNS	_	_	_
151	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	normalized	normalize	VBN	_	_	_
3	data	datum	NNS	_	_	_
4	VALUE	value	NN	_	_	_
5	was	be	VBD	_	_	_
6	generated	generate	VBN	_	_	_
7	using	use	VBG	_	_	_
8	LOWESS	LOWESS	NNP	_	_	_
9	normalization	normalization	NN	_	_	_
10	with	with	IN	_	_	_
11	rank	rank	NN	_	_	_
12	invariant	invariant	JJ	_	_	_
13	selection	selection	NN	_	_	_
14	,	,	,	_	_	_
15	as	as	IN	_	_	_
16	implemented	implement	VBN	_	_	_
17	in	in	IN	_	_	_
18	lcDNA	lcdna	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	receptor.seas.ucla.edu	receptor.seas.ucla.edu	JJ	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	RNA	rna	NN	_	_	_
23	extracted	extract	VBN	_	_	_
24	by	by	IN	_	_	_
25	hot	hot	JJ	_	_	_
26	phenol	phenol	NN	_	_	_
27	choloroform	choloroform	NN	_	_	_
28	folled	foll	VBN	_	_	_
29	by	by	IN	_	_	_
30	Qiagen	Qiagen	NNP	_	_	_
31	RNA	rna	NN	_	_	_
32	Midi	midi	NN	_	_	_
33	column	column	NN	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	BW25113	bw25113	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Treated	treat	VBN	_	_	_
7	with	with	IN	_	_	_
8	100	100	CD	_	_	_
9	uM	um	NN	_	_	_
10	KCN	kcn	NN	_	_	_
11	for	for	IN	_	_	_
12	5	5	CD	_	_	_
13	minutes	minute	NNS	_	_	_
14	before	before	IN	_	_	_
15	harvesting	harvest	VBG	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Untreated	untreated	JJ	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Astat	astat	NN	_	_	_
20	_	_	NN	_	_	_
21	chemostat	chemostat	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	A-stat	a-stat	NN	_	_	_
24	,	,	,	_	_	_
25	specific	specific	JJ	_	_	_
26	growth	growth	NN	_	_	_
27	rate	rate	NN	_	_	_
28	0.48	0.48	CD	_	_	_
29	1	1	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	chemostat	chemostat	NN	_	_	_
32	,	,	,	_	_	_
33	specific	specific	JJ	_	_	_
34	growth	growth	NN	_	_	_
35	rate	rate	NN	_	_	_
36	0.51	0.51	CD	_	_	_
37	1	1	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	cultivation	cultivation	NN	_	_	_
40	:	:	:	_	_	_
41	continuous	continuous	JJ	_	_	_
42	cultivation	cultivation	NN	_	_	_
43	,	,	,	_	_	_
44	A-stat	a-stat	JJ	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	cultivation	cultivation	NN	_	_	_
47	:	:	:	_	_	_
48	continuous	continuous	JJ	_	_	_
49	cultivation	cultivation	NN	_	_	_
50	,	,	,	_	_	_
51	chemostat	chemostat	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	eco	eco	NN	GEN	_	_
54	_	_	CD	_	_	_
55	0.21	0.21	CD	_	_	_
56	_	_	SYM	_	_	_
57	0.11	0.11	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	eco	eco	NN	GEN	_	_
60	_	_	CD	_	_	_
61	0.26	0.26	CD	_	_	_
62	_	_	SYM	_	_	_
63	0.11	0.11	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	eco	eco	NN	GEN	_	_
66	_	_	CD	_	_	_
67	0.31	0.31	CD	_	_	_
68	_	_	SYM	_	_	_
69	0.11	0.11	CD	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	eco	eco	NN	GEN	_	_
72	_	_	CD	_	_	_
73	0.36	0.36	CD	_	_	_
74	_	_	SYM	_	_	_
75	0.11	0.11	CD	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	eco	eco	NN	GEN	_	_
78	_	_	CD	_	_	_
79	0.40	0.40	CD	_	_	_
80	_	_	SYM	_	_	_
81	0.11	0.11	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	eco	eco	NN	GEN	_	_
84	_	_	CD	_	_	_
85	0.48	0.48	CD	_	_	_
86	_	_	SYM	_	_	_
87	0.11	0.11	CD	_	_	_
88	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
89	Escherichia	escherichia	FW	Organism	_	_
90	coli	coli	FW	Organism	_	_
91	K12	k12	NN	_	_	_
92	MG1655	mg1655	NN	_	_	_
93	was	be	VBD	_	_	_
94	cultivated	cultivate	VBN	_	_	_
95	using	use	VBG	_	_	_
96	M9	m9	NN	MED	_	_
97	minimal	minimal	JJ	MED	_	_
98	medium	medium	NN	MED	_	_
99	containing	contain	VBG	_	_	_
100	4.5	4.5	CD	_	_	_
101	g	g	NN	_	_	_
102	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
103	Escherichia	escherichia	FW	Organism	_	_
104	coli	coli	FW	Organism	_	_
105	str	str	FW	_	_	_
106	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Image	image	NN	_	_	_
4	was	be	VBD	_	_	_
5	analized	analize	VBN	_	_	_
6	with	with	IN	_	_	_
7	Genepix	Genepix	NNP	_	_	_
8	6	6	CD	_	_	_
9	pro	pro	JJ	_	_	_
10	followed	follow	VBN	_	_	_
11	by	by	IN	_	_	_
12	background	background	NN	_	_	_
13	substration	substration	NN	_	_	_
14	and	and	CC	_	_	_
15	global	global	JJ	_	_	_
16	LOWESS	lowess	NN	_	_	_
17	normalization	normalization	NN	_	_	_
18	in	in	IN	_	_	_
19	R	r	NN	_	_	_
20	environment	environment	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	KTH	kth	NN	_	_	_
23	package	package	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	.	.	.	_	_	_

1	Spots	spot	NNS	_	_	_
2	with	with	IN	_	_	_
3	signal	signal	NN	_	_	_
4	to	to	TO	_	_	_
5	noise	noise	NN	_	_	_
6	ratio	ratio	NN	_	_	_
7	lower	lower	JJR	_	_	_
8	that	that	IN	_	_	_
9	3	3	CD	_	_	_
10	and	and	CC	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	RNA	rna	NN	_	_	_
13	degradation	degradation	NN	_	_	_
14	was	be	VBD	_	_	_
15	stopped	stop	VBN	_	_	_
16	using	use	VBG	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	's	's	POS	_	_	_
19	RNAprotect	rnaprotect	NN	_	_	_
20	reagent	reagent	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	specific	specific	JJ	_	_	_
23	growth	growth	NN	_	_	_
24	rate	rate	NN	_	_	_
25	0.11	0.11	CD	_	_	_
26	1	1	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	specific	specific	JJ	_	_	_
29	growth	growth	NN	_	_	_
30	rate	rate	NN	_	_	_
31	0.21	0.21	CD	_	_	_
32	1	1	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	specific	specific	JJ	_	_	_
35	growth	growth	NN	_	_	_
36	rate	rate	NN	_	_	_
37	0.26	0.26	CD	_	_	_
38	1	1	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	specific	specific	JJ	_	_	_
41	growth	growth	NN	_	_	_
42	rate	rate	NN	_	_	_
43	0.31	0.31	CD	_	_	_
44	1	1	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	specific	specific	JJ	_	_	_
47	growth	growth	NN	_	_	_
48	rate	rate	NN	_	_	_
49	0.36	0.36	CD	_	_	_
50	1	1	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	specific	specific	JJ	_	_	_
53	growth	growth	NN	_	_	_
54	rate	rate	NN	_	_	_
55	0.40	0.40	CD	_	_	_
56	1	1	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	specific	specific	JJ	_	_	_
59	growth	growth	NN	_	_	_
60	rate	rate	NN	_	_	_
61	0.48	0.48	CD	_	_	_
62	1	1	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	Total	total	JJ	_	_	_
65	RNA	rna	NN	_	_	_
66	was	be	VBD	_	_	_
67	extracted	extract	VBN	_	_	_
68	with	with	IN	_	_	_
69	Qiagen	Qiagen	NNP	_	_	_
70	's	's	POS	_	_	_
71	Rneasy	Rneasy	NNP	_	_	_
72	Mini	Mini	NNP	_	_	_
73	Kit	kit	NN	_	_	_
74	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
75	Bordetella	bordetella	NN	_	_	_
76	sp.	sp.	NN	_	_	_
77	.	.	.	_	_	_

1	IITR-02	iitr-02	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	ECDH5	ecdh5	NN	_	_	_
4	_	_	CD	_	_	_
5	GD	gd	NN	_	_	_
6	_	_	CD	_	_	_
7	RP1	rp1	NN	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	Escherichia	escherichia	FW	Organism	_	_
10	coli	coli	FW	Organism	_	_
11	BL21	bl21	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	Escherichia	escherichia	FW	Organism	_	_
14	coli	coli	FW	Organism	_	_
15	DH5	dh5	NN	_	_	_
16	-LSB-	-lsb-	-LRB-	_	_	_
17	alpha	alpha	NN	_	_	_
18	-RSB-	-rsb-	-RRB-	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Escherichia	escherichia	FW	Organism	_	_
21	coli	coli	FW	Organism	_	_
22	K-12	k-12	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
24	Genomic	genomic	JJ	_	_	_
25	DNA	dna	NN	_	_	_
26	of	of	IN	_	_	_
27	all	all	DT	_	_	_
28	strains	strain	NNS	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	degraders	degrader	NNS	_	_	_
31	and	and	CC	_	_	_
32	non-degraders	non-degrader	NNS	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	isolated	isolate	VBN	_	_	_
35	individually	individually	RB	_	_	_
36	and	and	CC	_	_	_
37	mixed	mix	VBN	_	_	_
38	in	in	IN	_	_	_
39	equal	equal	JJ	_	_	_
40	ratio	ratio	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	500ng	500ng	CD	_	_	_
43	each	each	DT	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
46	Genomic	genomic	JJ	_	_	_
47	DNA	dna	NN	_	_	_
48	of	of	IN	_	_	_
49	Escherichia	escherichia	FW	Organism	_	_
50	coli	coli	FW	Organism	_	_
51	DH5α	dh5α	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
53	Genomic	genomic	JJ	_	_	_
54	DNA	dna	NN	_	_	_
55	of	of	IN	_	_	_
56	mixed	mixed	JJ	_	_	_
57	culture	culture	NN	_	_	_
58	containing	contain	VBG	_	_	_
59	only	only	RB	_	_	_
60	non-degraders	non-degraders	JJ	_	_	_
61	in	in	IN	_	_	_
62	equal	equal	JJ	_	_	_
63	ratio	ratio	NN	_	_	_
64	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
65	Genomic	genomic	JJ	_	_	_
66	DNA	dna	NN	_	_	_
67	of	of	IN	_	_	_
68	mixed	mixed	JJ	_	_	_
69	culture	culture	NN	_	_	_
70	-LRB-	-lrb-	-LRB-	_	_	_
71	Degraders	degrader	NNS	_	_	_
72	and	and	CC	_	_	_
73	non-degraders	non-degrader	NNS	_	_	_
74	in	in	IN	_	_	_
75	2:1	2:1	CD	_	_	_
76	ratio	ratio	NN	_	_	_
77	-RRB-	-rrb-	-RRB-	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
79	Genomic	genomic	JJ	_	_	_
80	DNA	dna	NN	_	_	_
81	of	of	IN	_	_	_
82	mixed	mixed	JJ	_	_	_
83	culture	culture	NN	_	_	_
84	-LRB-	-lrb-	-LRB-	_	_	_
85	Degraders	degrader	NNS	_	_	_
86	:	:	:	_	_	_
87	NM-05	nm-05	NN	_	_	_
88	,	,	,	_	_	_
89	IITR-02	iitr-02	NN	_	_	_
90	,	,	,	_	_	_
91	RHA1	rha1	NN	_	_	_
92	;	;	:	_	_	_
93	Non-degraders	non-degrader	NNS	_	_	_
94	:	:	:	_	_	_
95	DH5α	dh5α	NN	_	_	_
96	,	,	,	_	_	_
97	BL21	bl21	NN	_	_	_
98	and	and	CC	_	_	_
99	K12	k12	NN	_	_	_
100	in	in	IN	_	_	_
101	equal	equal	JJ	_	_	_
102	ratio	ratio	NN	_	_	_
103	-RRB-	-rrb-	-RRB-	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	Images	image	NNS	_	_	_
106	were	be	VBD	_	_	_
107	quantified	quantify	VBN	_	_	_
108	using	use	VBG	_	_	_
109	Agilent	Agilent	NNP	_	_	_
110	Feature	Feature	NNP	_	_	_
111	Extraction	Extraction	NNP	_	_	_
112	Software	Software	NNP	_	_	_
113	-LRB-	-lrb-	-LRB-	_	_	_
114	10.5.1.1	10.5.1.1	CD	_	_	_
115	-RRB-	-rrb-	-RRB-	_	_	_
116	and	and	CC	_	_	_
117	obtained	obtain	VBN	_	_	_
118	background	background	NN	_	_	_
119	subtracted	subtract	VBN	_	_	_
120	and	and	CC	_	_	_
121	spatially	spatially	RB	_	_	_
122	detrended	detrend	VBD	_	_	_
123	Processed	processed	JJ	_	_	_
124	Signal	signal	NN	_	_	_
125	intensities	intensity	NNS	_	_	_
126	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Images	image	NNS	_	_	_
3	were	be	VBD	_	_	_
4	quantified	quantify	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Agilent	Agilent	NNP	_	_	_
7	Feature	Feature	NNP	_	_	_
8	Extraction	Extraction	NNP	_	_	_
9	Software	Software	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	version	version	NN	_	_	_
12	9.5.1.1	9.5.1.1	CD	_	_	_
13	&	&	CC	_	_	_
14	10.5.1.1	10.5.1.1	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	and	and	CC	_	_	_
17	obtained	obtain	VBN	_	_	_
18	background	background	NN	_	_	_
19	subtracted	subtract	VBN	_	_	_
20	and	and	CC	_	_	_
21	spatially	spatially	RB	_	_	_
22	detrended	detrend	VBD	_	_	_
23	Processed	processed	JJ	_	_	_
24	Signal	signal	NN	_	_	_
25	intensities	intensity	NNS	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	isolation	isolation	NN	_	_	_
3	source	source	NN	_	_	_
4	:	:	:	_	_	_
5	Mixed	mixed	JJ	_	_	_
6	culture	culture	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	isolation	isolation	NN	_	_	_
9	source	source	NN	_	_	_
10	:	:	:	_	_	_
11	Pure	pure	JJ	_	_	_
12	culture	culture	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	MC	MC	NNP	_	_	_
15	_	_	NNP	_	_	_
16	Val	val	NN	_	_	_
17	_	_	SYM	_	_	_
18	G1	g1	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	MC	MC	NNP	_	_	_
21	_	_	NNP	_	_	_
22	Val	val	NN	_	_	_
23	_	_	SYM	_	_	_
24	G2	g2	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	MC	MC	NNP	_	_	_
27	_	_	NNP	_	_	_
28	Val	val	NN	_	_	_
29	_	_	SYM	_	_	_
30	G3	g3	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	MC	MC	NNP	_	_	_
33	_	_	NNP	_	_	_
34	Val	val	NN	_	_	_
35	_	_	CD	_	_	_
36	G5	g5	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Rhodococcus	rhodococcus	NN	_	_	_
39	jostii	jostii	NN	_	_	_
40	RHA1	rha1	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	Sphingomonas	sphingomonas	FW	_	_	_
43	sp.	sp.	FW	_	_	_
44	.	.	.	_	_	_

1	NM05	nm05	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	The	the	DT	_	_	_
4	genomic	genomic	JJ	_	_	_
5	DNA	dna	NN	_	_	_
6	from	from	IN	_	_	_
7	pure	pure	JJ	_	_	_
8	and	and	CC	_	_	_
9	mixed	mixed	JJ	_	_	_
10	bacterial	bacterial	JJ	_	_	_
11	cultures	culture	NNS	_	_	_
12	was	be	VBD	_	_	_
13	isolated	isolate	VBN	_	_	_
14	using	use	VBG	_	_	_
15	the	the	DT	_	_	_
16	Wizard	Wizard	NNP	_	_	_
17	genomic	genomic	JJ	_	_	_
18	DNA	dna	NN	_	_	_
19	isolation	isolation	NN	_	_	_
20	kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Promega	Promega	NNP	_	_	_
23	corporation	corporation	NN	_	_	_
24	,	,	,	_	_	_
25	Madison	Madison	NNP	_	_	_
26	,	,	,	_	_	_
27	USA	USA	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	as	as	IN	_	_	_
30	per	per	IN	_	_	_
31	manufacturer	manufacturer	NN	_	_	_
32	's	's	POS	_	_	_
33	instructions	instruction	NNS	_	_	_
34	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	concentration	concentration	NN	_	_	_
3	of	of	IN	_	_	_
4	DNA	dna	NN	_	_	_
5	was	be	VBD	_	_	_
6	analyzed	analyze	VBN	_	_	_
7	by	by	IN	_	_	_
8	Nanodrop	Nanodrop	NNP	_	_	_
9	spectrophotometer	spectrophotometer	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Nanodrop	Nanodrop	NNP	_	_	_
12	Technologies	Technologies	NNPS	_	_	_
13	Inc	Inc	NNP	_	_	_
14	,	,	,	_	_	_
15	Rockland	Rockland	NNP	_	_	_
16	,	,	,	_	_	_
17	USA	USA	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	quality	quality	NN	_	_	_
22	was	be	VBD	_	_	_
23	determined	determine	VBN	_	_	_
24	by	by	IN	_	_	_
25	analysis	analysis	NN	_	_	_
26	on	on	IN	_	_	_
27	DNA	dna	NN	_	_	_
28	12000	12000	CD	_	_	_
29	kit	kit	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Caliper	Caliper	NNP	_	_	_
32	Sciences	Sciences	NNPS	_	_	_
33	,	,	,	_	_	_
34	USA	USA	NNP	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	using	use	VBG	_	_	_
37	the	the	DT	_	_	_
38	Agilent	Agilent	NNP	_	_	_
39	2100	2100	CD	_	_	_
40	Bioanalyzer	Bioanalyzer	NNP	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	Agilent	Agilent	NNP	_	_	_
43	Technologies	Technologies	NNPS	_	_	_
44	,	,	,	_	_	_
45	Palo	Palo	NNP	_	_	_
46	Alto	Alto	NNP	_	_	_
47	,	,	,	_	_	_
48	CA	CA	NNP	_	_	_
49	,	,	,	_	_	_
50	USA	USA	NNP	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	Sphingomonas	sphingomonas	JJ	_	_	_
4	sp.	sp.	NN	_	_	_
5	strain	strain	NN	_	_	_
6	NM-05	nm-05	NN	_	_	_
7	used	use	VBN	_	_	_
8	in	in	IN	_	_	_
9	the	the	DT	_	_	_
10	study	study	NN	_	_	_
11	is	be	VBZ	_	_	_
12	a	a	DT	_	_	_
13	known	known	JJ	_	_	_
14	degrader	degrader	NN	_	_	_
15	of	of	IN	_	_	_
16	γ-hexachlorocyclohexane	γ-hexachlorocyclohexane	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	γ-HCH	γ-hch	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	and	and	CC	_	_	_
21	has	have	VBZ	_	_	_
22	been	be	VBN	_	_	_
23	isolated	isolate	VBN	_	_	_
24	from	from	IN	_	_	_
25	the	the	DT	_	_	_
26	vicinity	vicinity	NN	_	_	_
27	of	of	IN	_	_	_
28	an	a	DT	_	_	_
29	industry	industry	NN	_	_	_
30	India	India	NNP	_	_	_
31	Pesticide	Pesticide	NNP	_	_	_
32	Limited	Limited	NNP	_	_	_
33	,	,	,	_	_	_
34	Chinhat	Chinhat	NNP	_	_	_
35	industrial	industrial	JJ	_	_	_
36	area	area	NN	_	_	_
37	,	,	,	_	_	_
38	Lucknow	Lucknow	NNP	_	_	_
39	which	which	WDT	_	_	_
40	is	be	VBZ	_	_	_
41	involved	involve	VBN	_	_	_
42	in	in	IN	_	_	_
43	manufacturing	manufacture	VBG	_	_	_
44	chlorinated	chlorinate	VBN	_	_	_
45	pesticides	pesticide	NNS	_	_	_
46	for	for	IN	_	_	_
47	last	last	JJ	_	_	_
48	25	25	CD	_	_	_
49	years	year	NNS	_	_	_
50	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	strain	strain	NN	_	_	_
3	was	be	VBD	_	_	_
4	harvested	harvest	VBN	_	_	_
5	in	in	IN	_	_	_
6	mineral	mineral	NN	_	_	_
7	salt	salt	NN	_	_	_
8	medium	medium	NN	_	_	_
9	with	with	IN	_	_	_
10	0.34	0.34	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	γ-HCH	γ-hch	NN	_	_	_
13	as	as	IN	_	_	_
14	sole	sole	JJ	_	_	_
15	source	source	NN	_	_	_
16	of	of	IN	_	_	_
17	carbon	carbon	NN	_	_	_
18	and	and	CC	_	_	_
19	energy	energy	NN	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	strain	strain	NN	_	_	_
3	Bordetella	bordetella	NN	_	_	_
4	sp.	sp.	NN	_	_	_
5	strain	strain	NN	_	_	_
6	IITR-02	iitr-02	NN	_	_	_
7	used	use	VBN	_	_	_
8	in	in	IN	_	_	_
9	this	this	DT	_	_	_
10	study	study	NN	_	_	_
11	has	have	VBZ	_	_	_
12	been	be	VBN	_	_	_
13	isolated	isolate	VBN	_	_	_
14	from	from	IN	_	_	_
15	the	the	DT	_	_	_
16	vicinity	vicinity	NN	_	_	_
17	of	of	IN	_	_	_
18	the	the	DT	_	_	_
19	industry	industry	NN	_	_	_
20	India	India	NNP	_	_	_
21	Pesticide	Pesticide	NNP	_	_	_
22	Limited	Limited	NNP	_	_	_
23	,	,	,	_	_	_
24	Chinhat	Chinhat	NNP	_	_	_
25	,	,	,	_	_	_
26	Lucknow	Lucknow	NNP	_	_	_
27	and	and	CC	_	_	_
28	is	be	VBZ	_	_	_
29	found	find	VBN	_	_	_
30	to	to	TO	_	_	_
31	be	be	VB	_	_	_
32	a	a	DT	_	_	_
33	degrader	degrader	NN	_	_	_
34	of	of	IN	_	_	_
35	1,2	1,2	CD	_	_	_
36	-	-	:	_	_	_
37	,	,	,	_	_	_
38	1,4-dichloro	1,4-dichloro	NN	_	_	_
39	and	and	CC	_	_	_
40	1,2,3	1,2,3	SYM	_	_	_
41	-	-	:	_	_	_
42	and	and	CC	_	_	_
43	1,2,4-trichlorobenzene	1,2,4-trichlorobenzene	NN	_	_	_
44	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	strain	strain	NN	_	_	_
3	was	be	VBD	_	_	_
4	harvested	harvest	VBN	_	_	_
5	in	in	IN	_	_	_
6	mineral	mineral	NN	_	_	_
7	salt	salt	NN	_	_	_
8	medium	medium	NN	_	_	_
9	with	with	IN	_	_	_
10	3.2	3.2	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	of	of	IN	_	_	_
13	1,2,4-trichlorobenzene	1,2,4-trichlorobenzene	NN	_	_	_
14	as	as	IN	_	_	_
15	sole	sole	JJ	_	_	_
16	source	source	NN	_	_	_
17	of	of	IN	_	_	_
18	carbon	carbon	NN	_	_	_
19	and	and	CC	_	_	_
20	energy	energy	NN	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	bacterium	bacterium	NN	_	_	_
3	Rhodococcus	rhodococcus	NN	_	_	_
4	sp.	sp.	NN	_	_	_
5	strain	strain	NN	_	_	_
6	RHA1	rha1	NN	_	_	_
7	which	which	WDT	_	_	_
8	is	be	VBZ	_	_	_
9	a	a	DT	_	_	_
10	known	known	JJ	_	_	_
11	degrader	degrader	NN	_	_	_
12	of	of	IN	_	_	_
13	polychlorinated	polychlorinate	VBN	_	_	_
14	biphenyls	biphenyl	NNS	_	_	_
15	,	,	,	_	_	_
16	substituted	substitute	VBN	_	_	_
17	phenols	phenol	NNS	_	_	_
18	,	,	,	_	_	_
19	benzoates	benzoate	NNS	_	_	_
20	and	and	CC	_	_	_
21	phthalates	phthalate	NNS	_	_	_
22	was	be	VBD	_	_	_
23	grown	grow	VBN	_	_	_
24	on	on	IN	_	_	_
25	0.2	0.2	CD	_	_	_
26	%	%	NN	_	_	_
27	biphenyl	biphenyl	NN	_	_	_
28	and	and	CC	_	_	_
29	20mM	20mm	NN	_	_	_
30	of	of	IN	_	_	_
31	benzoate	benzoate	NN	_	_	_
32	as	as	IN	_	_	_
33	carbon	carbon	NN	_	_	_
34	sources	source	NNS	_	_	_
35	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	strain	strain	NN	_	_	_
3	Escherichia	escherichia	FW	Organism	_	_
4	coli	coli	FW	Organism	_	_
5	DH5α	dh5α	NN	_	_	_
6	and	and	CC	_	_	_
7	Escherichia	escherichia	FW	Organism	_	_
8	coli	coli	FW	Organism	_	_
9	BL21	bl21	NN	_	_	_
10	were	be	VBD	_	_	_
11	grown	grow	VBN	_	_	_
12	in	in	IN	_	_	_
13	Luria-Bertani	luria-bertani	JJ	_	_	_
14	medium	medium	NN	_	_	_
15	and	and	CC	_	_	_
16	strain	strain	NN	_	_	_
17	Escherichia	escherichia	FW	Organism	_	_
18	coli	coli	FW	Organism	_	_
19	K12	k12	NN	_	_	_
20	was	be	VBD	_	_	_
21	grown	grow	VBN	_	_	_
22	in	in	IN	_	_	_
23	nutrient	nutrient	NN	_	_	_
24	broth	broth	NN	_	_	_
25	to	to	TO	_	_	_
26	an	a	DT	_	_	_
27	OD560nm	od560nm	NN	_	_	_
28	of	of	IN	_	_	_
29	0.4	0.4	CD	_	_	_
30	at	at	IN	_	_	_
31	37	37	CD	_	_	_
32	degree	degree	NN	_	_	_
33	centigrade	centigrade	NN	_	_	_
34	with	with	IN	_	_	_
35	continuous	continuous	JJ	_	_	_
36	shaking	shake	VBG	_	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	Sphingomonas	sphingomonas	JJ	_	_	_
4	sp.	sp.	NN	_	_	_
5	strain	strain	NN	_	_	_
6	NM-05	nm-05	NN	_	_	_
7	used	use	VBN	_	_	_
8	in	in	IN	_	_	_
9	the	the	DT	_	_	_
10	study	study	NN	_	_	_
11	is	be	VBZ	_	_	_
12	a	a	DT	_	_	_
13	known	known	JJ	_	_	_
14	degrader	degrader	NN	_	_	_
15	of	of	IN	_	_	_
16	γ-hexachlorocyclohexane	γ-hexachlorocyclohexane	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	γ-HCH	γ-hch	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	and	and	CC	_	_	_
21	has	have	VBZ	_	_	_
22	been	be	VBN	_	_	_
23	isolated	isolate	VBN	_	_	_
24	from	from	IN	_	_	_
25	the	the	DT	_	_	_
26	vicinity	vicinity	NN	_	_	_
27	of	of	IN	_	_	_
28	an	a	DT	_	_	_
29	industry	industry	NN	_	_	_
30	India	India	NNP	_	_	_
31	Pesticide	Pesticide	NNP	_	_	_
32	Limited	Limited	NNP	_	_	_
33	,	,	,	_	_	_
34	Chinhat	Chinhat	NNP	_	_	_
35	industrial	industrial	JJ	_	_	_
36	area	area	NN	_	_	_
37	,	,	,	_	_	_
38	Lucknow	Lucknow	NNP	_	_	_
39	which	which	WDT	_	_	_
40	is	be	VBZ	_	_	_
41	involved	involve	VBN	_	_	_
42	in	in	IN	_	_	_
43	manufacturing	manufacture	VBG	_	_	_
44	chlorinated	chlorinate	VBN	_	_	_
45	pesticides	pesticide	NNS	_	_	_
46	for	for	IN	_	_	_
47	last	last	JJ	_	_	_
48	25	25	CD	_	_	_
49	years	year	NNS	_	_	_
50	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	strain	strain	NN	_	_	_
3	was	be	VBD	_	_	_
4	harvested	harvest	VBN	_	_	_
5	in	in	IN	_	_	_
6	mineral	mineral	NN	_	_	_
7	salt	salt	NN	_	_	_
8	medium	medium	NN	_	_	_
9	with	with	IN	_	_	_
10	0.34	0.34	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	γ-HCH	γ-hch	NN	_	_	_
13	as	as	IN	_	_	_
14	sole	sole	JJ	_	_	_
15	source	source	NN	_	_	_
16	of	of	IN	_	_	_
17	carbon	carbon	NN	_	_	_
18	and	and	CC	_	_	_
19	energy	energy	NN	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	strain	strain	NN	_	_	_
3	Escherichia	escherichia	FW	Organism	_	_
4	coli	coli	FW	Organism	_	_
5	DH-5α	dh-5α	NN	_	_	_
6	was	be	VBD	_	_	_
7	grown	grow	VBN	_	_	_
8	in	in	IN	_	_	_
9	Luria-Bertani	luria-bertani	JJ	_	_	_
10	medium	medium	NN	_	_	_
11	to	to	TO	_	_	_
12	an	a	DT	_	_	_
13	O.D.	o.d.	NN	_	_	_
14	of	of	IN	_	_	_
15	0.4	0.4	CD	_	_	_
16	at	at	IN	_	_	_
17	37	37	CD	_	_	_
18	degree	degree	NN	_	_	_
19	centigrade	centigrade	NN	_	_	_
20	with	with	IN	_	_	_
21	continuous	continuous	JJ	_	_	_
22	shaking	shake	VBG	_	_	_
23	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	soil	soil	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	The	the	DT	_	_	_
5	total	total	JJ	_	_	_
6	DNA	dna	NN	_	_	_
7	to	to	TO	_	_	_
8	be	be	VB	_	_	_
9	used	use	VBN	_	_	_
10	as	as	IN	_	_	_
11	target	target	NN	_	_	_
12	for	for	IN	_	_	_
13	microarray	microarray	NN	_	_	_
14	hybridization	hybridization	NN	_	_	_
15	was	be	VBD	_	_	_
16	isolated	isolate	VBN	_	_	_
17	from	from	IN	_	_	_
18	soil	soil	NN	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	Data	Data	NNP	_	_	_
21	from	from	IN	_	_	_
22	two	two	CD	_	_	_
23	independent	independent	JJ	_	_	_
24	experiments	experiment	NNS	_	_	_
25	were	be	VBD	_	_	_
26	normalized	normalize	VBN	_	_	_
27	and	and	CC	_	_	_
28	then	then	RB	_	_	_
29	analyzed	analyze	VBN	_	_	_
30	using	use	VBG	_	_	_
31	the	the	DT	_	_	_
32	GenePix	GenePix	NNP	_	_	_
33	Pro	pro	FW	_	_	_
34	3.0	3.0	CD	_	_	_
35	software	software	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	Axon	Axon	NNP	_	_	_
38	Instruments	Instruments	NNP	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	ptsN	ptsn	NN	GEN	_	_
5	mutant	mutant	JJ	_	_	_
6	strain	strain	NN	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	Escherichia	escherichia	FW	Organism	_	_
9	coli	coli	FW	Organism	_	_
10	str	str	FW	_	_	_
11	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Escherichia	escherichia	FW	Organism	_	_
4	coli	coli	FW	Organism	_	_
5	wild	wild	JJ	_	_	_
6	type	type	NN	_	_	_
7	strain	strain	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	genotype	genotype	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	ptsN	ptsn	NN	GEN	_	_
12	mutant	mutant	NN	_	_	_
13	replicate	replicate	VBP	_	_	_
14	1	1	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	ptsN	ptsn	NN	GEN	_	_
17	mutant	mutant	NN	_	_	_
18	replicate	replicate	VBP	_	_	_
19	2	2	CD	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
21	RNA	rna	NN	_	_	_
22	was	be	VBD	_	_	_
23	extracted	extract	VBN	_	_	_
24	from	from	IN	_	_	_
25	each	each	DT	_	_	_
26	sample	sample	NN	_	_	_
27	using	use	VBG	_	_	_
28	a	a	DT	_	_	_
29	QIAGEN	QIAGEN	NNP	_	_	_
30	RNA	rna	NN	_	_	_
31	extraction	extraction	NN	_	_	_
32	kit	kit	NN	_	_	_
33	according	accord	VBG	_	_	_
34	to	to	TO	_	_	_
35	the	the	DT	_	_	_
36	manufacturer	manufacturer	NN	_	_	_
37	's	's	POS	_	_	_
38	instruction	instruction	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
40	The	the	DT	_	_	_
41	E.	e.	FW	_	_	_
42	coli	coli	FW	_	_	_
43	K12	k12	NN	_	_	_
44	strain	strain	NN	_	_	_
45	MG1655	mg1655	NN	_	_	_
46	and	and	CC	_	_	_
47	its	its	PRP$	_	_	_
48	isogenic	isogenic	JJ	_	_	_
49	ptsN	ptsn	NN	GEN	_	_
50	mutant	mutant	NN	_	_	_
51	were	be	VBD	_	_	_
52	grown	grow	VBN	_	_	_
53	in	in	IN	_	_	_
54	M9	m9	NN	MED	_	_
55	minimal	minimal	JJ	MED	_	_
56	medium	medium	NN	MED	_	_
57	containing	contain	VBG	_	_	_
58	0.5	0.5	CD	_	_	_
59	%	%	NN	_	_	_
60	glucose	glucose	NN	SUPP	_	_
61	as	as	IN	_	_	_
62	carbon	carbon	NN	_	_	_
63	source	source	NN	_	_	_
64	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	from	from	IN	_	_	_
3	duplicate	duplicate	VBP	_	_	_
4	experiments	experiment	NNS	_	_	_
5	were	be	VBD	_	_	_
6	harvested	harvest	VBN	_	_	_
7	in	in	IN	_	_	_
8	exponential	exponential	JJ	_	_	_
9	growth	growth	NN	_	_	_
10	phase	phase	NN	_	_	_
11	when	when	WRB	_	_	_
12	cultures	culture	NNS	_	_	_
13	reached	reach	VBD	_	_	_
14	an	a	DT	_	_	_
15	A600	a600	NN	_	_	_
16	of	of	IN	_	_	_
17	0.4	0.4	CD	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	for	for	IN	_	_	_
4	inoculation	inoculation	NN	_	_	_
5	were	be	VBD	_	_	_
6	from	from	IN	_	_	_
7	overnight	overnight	JJ	_	_	_
8	planktonic	planktonic	JJ	_	_	_
9	culture	culture	NN	_	_	_
10	in	in	IN	_	_	_
11	10	10	CD	_	_	_
12	%	%	NN	_	_	_
13	Luria-Bertani	luria-bertani	JJ	_	_	_
14	broth	broth	NN	_	_	_
15	at	at	IN	_	_	_
16	30	30	CD	_	_	_
17	degree	degree	NN	_	_	_
18	Celsius	Celsius	NNP	_	_	_
19	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	washed	wash	VBN	_	_	_
4	in	in	IN	_	_	_
5	equal	equal	JJ	_	_	_
6	volume	volume	NN	_	_	_
7	of	of	IN	_	_	_
8	fresh	fresh	JJ	_	_	_
9	10	10	CD	_	_	_
10	%	%	NN	_	_	_
11	LB	lb	NN	MED	_	_
12	broth	broth	NN	MED	_	_
13	before	before	IN	_	_	_
14	inoculation	inoculation	NN	_	_	_
15	and	and	CC	_	_	_
16	were	be	VBD	_	_	_
17	inoculated	inoculate	VBN	_	_	_
18	into	into	IN	_	_	_
19	5	5	CD	_	_	_
20	ml	ml	NN	_	_	_
21	10	10	CD	_	_	_
22	%	%	NN	_	_	_
23	LB	lb	NN	_	_	_
24	in	in	IN	_	_	_
25	a	a	DT	_	_	_
26	disposable	disposable	JJ	_	_	_
27	petri	petri	JJ	_	_	_
28	dish	dish	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	60	60	CD	_	_	_
31	mm	mm	NN	_	_	_
32	x	x	CC	_	_	_
33	15	15	CD	_	_	_
34	mm	mm	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	.	.	.	_	_	_

1	50	50	CD	_	_	_
2	ul	ul	NN	_	_	_
3	E.	e.	FW	_	_	_
4	coli	coli	FW	_	_	_
5	culture	culture	NN	_	_	_
6	was	be	VBD	_	_	_
7	inoculated	inoculate	VBN	_	_	_
8	for	for	IN	_	_	_
9	mono-species	mono-species	NNS	_	_	_
10	pure	pure	JJ	_	_	_
11	culture	culture	NN	_	_	_
12	.	.	.	_	_	_

1	50	50	CD	_	_	_
2	ul	ul	NN	_	_	_
3	E.	e.	FW	_	_	_
4	coli	coli	FW	_	_	_
5	and	and	CC	_	_	_
6	10	10	CD	_	_	_
7	ul	ul	NN	_	_	_
8	S.	S.	NNP	_	_	_
9	maltophilia	maltophilia	NNP	_	_	_
10	were	be	VBD	_	_	_
11	mixed	mixed	JJ	_	_	_
12	and	and	CC	_	_	_
13	inoculated	inoculate	VBN	_	_	_
14	for	for	IN	_	_	_
15	mixed-species	mixed-species	JJ	_	_	_
16	culture	culture	NN	_	_	_
17	.	.	.	_	_	_

1	Petri	petri	JJ	_	_	_
2	dishes	dish	NNS	_	_	_
3	were	be	VBD	_	_	_
4	set	set	VBN	_	_	_
5	static	static	JJ	_	_	_
6	at	at	IN	_	_	_
7	room	room	NN	_	_	_
8	temperature	temperature	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	20	20	CD	_	_	_
11	C	c	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	for	for	IN	_	_	_
14	18	18	CD	_	_	_
15	h	h	NN	_	_	_
16	for	for	IN	_	_	_
17	biofilm	biofilm	NN	_	_	_
18	growth	growth	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2	culture	culture	NN	_	_	_
3	media	media	NNS	_	_	_
4	:	:	:	_	_	_
5	10	10	CD	_	_	_
6	%	%	NN	_	_	_
7	Luria	Luria	NNP	MED	_	_
8	broth	broth	NN	MED	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	culture	culture	NN	_	_	_
11	system	system	NN	_	_	_
12	:	:	:	_	_	_
13	static	static	JJ	_	_	_
14	petri	petri	JJ	_	_	_
15	dish	dish	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	disposable	disposable	JJ	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	culture	culture	NN	_	_	_
21	temperature	temperature	NN	_	_	_
22	:	:	:	_	_	_
23	room	room	NN	_	_	_
24	temperature	temperature	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	20	20	CD	_	_	_
27	C	c	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	culture	culture	NN	_	_	_
31	time	time	NN	_	_	_
32	:	:	:	_	_	_
33	18	18	CD	_	_	_
34	h	h	NN	_	_	_
35	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
36	Data	Data	NNP	_	_	_
37	was	be	VBD	_	_	_
38	analyzed	analyze	VBN	_	_	_
39	in	in	IN	_	_	_
40	the	the	DT	_	_	_
41	software	software	NN	_	_	_
42	Acuity	acuity	NN	_	_	_
43	4.0	4.0	CD	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	Molecular	molecular	JJ	_	_	_
46	Devices	Devices	NNPS	_	_	_
47	,	,	,	_	_	_
48	Sunnyvale	Sunnyvale	NNP	_	_	_
49	,	,	,	_	_	_
50	CA	CA	NNP	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	.	.	.	_	_	_

1	Hybridized	hybridize	VBN	_	_	_
2	spots	spot	NNS	_	_	_
3	for	for	IN	_	_	_
4	E.	e.	FW	_	_	_
5	coli	coli	FW	_	_	_
6	K12	k12	NN	_	_	_
7	having	have	VBG	_	_	_
8	a	a	DT	_	_	_
9	high	high	JJ	_	_	_
10	QC	qc	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	quality	quality	NN	_	_	_
13	control	control	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	value	value	NN	_	_	_
16	>	>	JJR	_	_	_
17	0.1	0.1	CD	_	_	_
18	,	,	,	_	_	_
19	good	good	JJ	_	_	_
20	flag	flag	NN	_	_	_
21	tags	tag	NNS	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	A	a	NN	_	_	_
24	,	,	,	_	_	_
25	B	b	NN	_	_	_
26	and	and	CC	_	_	_
27	C	c	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	in	in	IN	_	_	_
30	both	both	CC	_	_	_
31	Cy3	cy3	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
33	Escherichia	escherichia	FW	Organism	_	_
34	coli	coli	FW	Organism	_	_
35	K-12	k-12	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Escherichia	escherichia	FW	Organism	_	_
38	coli	coli	FW	Organism	_	_
39	_	_	SYM	_	_	_
40	MixedSpeciesBiofilm	MixedSpeciesBiofilm	NNP	_	_	_
41	_	_	CD	_	_	_
42	bioreplicate1	bioreplicate1	NN	_	_	_
43	_	_	NN	_	_	_
44	techreplicate	techreplicate	NN	_	_	_
45	_	_	NN	_	_	_
46	1	1	CD	_	_	_
47	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
48	Escherichia	escherichia	FW	Organism	_	_
49	coli	coli	FW	Organism	_	_
50	_	_	SYM	_	_	_
51	MixedSpeciesBiofilm	MixedSpeciesBiofilm	NNP	_	_	_
52	_	_	CD	_	_	_
53	bioreplicate1	bioreplicate1	NN	_	_	_
54	_	_	NN	_	_	_
55	techreplicate	techreplicate	NN	_	_	_
56	_	_	NN	_	_	_
57	2	2	CD	_	_	_
58	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
59	Escherichia	escherichia	FW	Organism	_	_
60	coli	coli	FW	Organism	_	_
61	_	_	SYM	_	_	_
62	MixedSpeciesBiofilm	MixedSpeciesBiofilm	NNP	_	_	_
63	_	_	CD	_	_	_
64	bioreplicate1	bioreplicate1	NN	_	_	_
65	_	_	NN	_	_	_
66	techreplicate	techreplicate	NN	_	_	_
67	_	_	NN	_	_	_
68	3	3	CD	_	_	_
69	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
70	Escherichia	escherichia	FW	Organism	_	_
71	coli	coli	FW	Organism	_	_
72	_	_	SYM	_	_	_
73	MixedSpeciesBiofilm	MixedSpeciesBiofilm	NNP	_	_	_
74	_	_	CD	_	_	_
75	bioreplicate2	bioreplicate2	NN	_	_	_
76	_	_	NN	_	_	_
77	techreplicate	techreplicate	NN	_	_	_
78	_	_	NN	_	_	_
79	1	1	CD	_	_	_
80	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
81	Escherichia	escherichia	FW	Organism	_	_
82	coli	coli	FW	Organism	_	_
83	_	_	SYM	_	_	_
84	MixedSpeciesBiofilm	MixedSpeciesBiofilm	NNP	_	_	_
85	_	_	CD	_	_	_
86	bioreplicate2	bioreplicate2	NN	_	_	_
87	_	_	NN	_	_	_
88	techreplicate	techreplicate	NN	_	_	_
89	_	_	NN	_	_	_
90	2	2	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	RNAlater	rnalater	NN	_	_	_
93	was	be	VBD	_	_	_
94	removed	remove	VBN	_	_	_
95	from	from	IN	_	_	_
96	cells	cell	NNS	_	_	_
97	by	by	IN	_	_	_
98	filtration	filtration	NN	_	_	_
99	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	from	from	IN	_	_	_
6	cells	cell	NNS	_	_	_
7	using	use	VBG	_	_	_
8	a	a	DT	_	_	_
9	hot	hot	JJ	_	_	_
10	SDS	sds	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	sorted	sort	VBD	_	_	_
13	E.	e.	FW	_	_	_
14	coli	coli	FW	_	_	_
15	cells	cell	NNS	_	_	_
16	from	from	IN	_	_	_
17	dual-species	dual-species	JJ	_	_	_
18	biofilms	biofilm	NNS	_	_	_
19	1	1	CD	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	sorted	sort	VBD	_	_	_
22	E.	e.	FW	_	_	_
23	coli	coli	FW	_	_	_
24	cells	cell	NNS	_	_	_
25	from	from	IN	_	_	_
26	dual-species	dual-species	JJ	_	_	_
27	biofilms	biofilm	NNS	_	_	_
28	2	2	CD	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
30	sorted	sort	VBD	_	_	_
31	E.	e.	FW	_	_	_
32	coli	coli	FW	_	_	_
33	cells	cell	NNS	_	_	_
34	from	from	IN	_	_	_
35	mono-species	mono-species	JJ	_	_	_
36	biofilms	biofilm	NNS	_	_	_
37	1	1	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	sorted	sort	VBD	_	_	_
40	E.	e.	FW	_	_	_
41	coli	coli	FW	_	_	_
42	cells	cell	NNS	_	_	_
43	from	from	IN	_	_	_
44	mono-species	mono-species	JJ	_	_	_
45	biofilms	biofilm	NNS	_	_	_
46	2	2	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	Suspended	suspend	VBN	_	_	_
49	cells	cell	NNS	_	_	_
50	were	be	VBD	_	_	_
51	then	then	RB	_	_	_
52	removed	remove	VBN	_	_	_
53	and	and	CC	_	_	_
54	biofilms	biofilm	NNS	_	_	_
55	were	be	VBD	_	_	_
56	washed	wash	VBN	_	_	_
57	3	3	CD	_	_	_
58	times	time	NNS	_	_	_
59	with	with	IN	_	_	_
60	1	1	CD	_	_	_
61	ml	ml	NN	_	_	_
62	10	10	CD	_	_	_
63	%	%	NN	_	_	_
64	LB	lb	NN	MED	_	_
65	broth	broth	NN	MED	_	_
66	.	.	.	_	_	_

1	Biofilms	biofilm	NNS	_	_	_
2	from	from	IN	_	_	_
3	each	each	DT	_	_	_
4	petri	petri	NN	_	_	_
5	dish	dish	NN	_	_	_
6	were	be	VBD	_	_	_
7	then	then	RB	_	_	_
8	scraped	scrape	VBN	_	_	_
9	into	into	IN	_	_	_
10	a	a	DT	_	_	_
11	vial	vial	NN	_	_	_
12	containing	contain	VBG	_	_	_
13	1	1	CD	_	_	_
14	ml	ml	NN	_	_	_
15	10	10	CD	_	_	_
16	%	%	NN	_	_	_
17	LB	lb	NN	_	_	_
18	.	.	.	_	_	_

1	Scraped	scraped	JJ	_	_	_
2	biofilms	biofilm	NNS	_	_	_
3	in	in	IN	_	_	_
4	each	each	DT	_	_	_
5	vial	vial	NN	_	_	_
6	were	be	VBD	_	_	_
7	concentrated	concentrate	VBN	_	_	_
8	from	from	IN	_	_	_
9	1	1	CD	_	_	_
10	ml	ml	NN	_	_	_
11	into	into	IN	_	_	_
12	50	50	CD	_	_	_
13	ul	ul	NN	_	_	_
14	by	by	IN	_	_	_
15	centrifugation	centrifugation	NN	_	_	_
16	.	.	.	_	_	_

1	500	500	CD	_	_	_
2	ul	ul	NN	_	_	_
3	RNAlater	rnalater	NN	_	_	_
4	was	be	VBD	_	_	_
5	added	add	VBN	_	_	_
6	and	and	CC	_	_	_
7	mixed	mix	VBN	_	_	_
8	well	well	RB	_	_	_
9	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	in	in	IN	_	_	_
3	RNAlater	rnalater	NN	_	_	_
4	were	be	VBD	_	_	_
5	kept	keep	VBN	_	_	_
6	in	in	IN	_	_	_
7	4C	4c	NN	_	_	_
8	fridge	fridge	NN	_	_	_
9	overnight	overnight	JJ	_	_	_
10	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	vial	vial	NN	_	_	_
3	was	be	VBD	_	_	_
4	homogenized	homogenize	VBN	_	_	_
5	with	with	IN	_	_	_
6	OMNI	OMNI	NNP	_	_	_
7	TH	th	NN	_	_	_
8	homogenizer	homogenizer	NN	_	_	_
9	for	for	IN	_	_	_
10	2	2	CD	_	_	_
11	min	min	NN	_	_	_
12	on	on	IN	_	_	_
13	ice	ice	NN	_	_	_
14	and	and	CC	_	_	_
15	further	further	JJ	_	_	_
16	aliquoted	aliquote	VBN	_	_	_
17	into	into	IN	_	_	_
18	small	small	JJ	_	_	_
19	vials	vial	NNS	_	_	_
20	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	in	in	IN	_	_	_
3	each	each	DT	_	_	_
4	vial	vial	NN	_	_	_
5	were	be	VBD	_	_	_
6	then	then	RB	_	_	_
7	re-suspended	re-suspended	JJ	_	_	_
8	in	in	IN	_	_	_
9	nuclease-free	nuclease-free	JJ	_	_	_
10	phosphate	phosphate	NN	_	_	_
11	buffered	buffer	VBN	_	_	_
12	saline	saline	NN	_	_	_
13	,	,	,	_	_	_
14	incubated	incubate	VBN	_	_	_
15	with	with	IN	_	_	_
16	anti-E	anti-e	JJ	_	_	_
17	.	.	.	_	_	_

1	coli	coli	NN	_	_	_
2	antibody	antibody	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	ViroStat	virostat	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	and	and	CC	_	_	_
7	microbeads	microbead	NNS	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Miltenyi	miltenyi	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	,	,	,	_	_	_
12	followed	follow	VBN	_	_	_
13	by	by	IN	_	_	_
14	separation	separation	NN	_	_	_
15	on	on	IN	_	_	_
16	a	a	DT	_	_	_
17	MACS	macs	NN	_	_	_
18	separator	separator	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Miltenyi	Miltenyi	NNP	_	_	_
21	,	,	,	_	_	_
22	Auburn	Auburn	NNP	_	_	_
23	,	,	,	_	_	_
24	CA	CA	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	at	at	IN	_	_	_
27	4	4	CD	_	_	_
28	degree	degree	NN	_	_	_
29	C.	c.	NN	_	_	_
30	Sorted	sort	VBN	_	_	_
31	cells	cell	NNS	_	_	_
32	were	be	VBD	_	_	_
33	re-suspended	re-suspended	JJ	_	_	_
34	into	into	IN	_	_	_
35	RNAlater	rnalater	NN	_	_	_
36	until	until	IN	_	_	_
37	RNA	rna	NN	_	_	_
38	extractions	extraction	NNS	_	_	_
39	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	with	with	IN	_	_	_
5	homogenization	homogenization	NN	_	_	_
6	and	and	CC	_	_	_
7	separation	separation	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Cells	cell	NNS	_	_	_
10	for	for	IN	_	_	_
11	inoculation	inoculation	NN	_	_	_
12	were	be	VBD	_	_	_
13	from	from	IN	_	_	_
14	overnight	overnight	JJ	_	_	_
15	planktonic	planktonic	JJ	_	_	_
16	culture	culture	NN	_	_	_
17	in	in	IN	_	_	_
18	10	10	CD	_	_	_
19	%	%	NN	_	_	_
20	Luria-Bertani	luria-bertani	JJ	_	_	_
21	broth	broth	NN	_	_	_
22	at	at	IN	_	_	_
23	30	30	CD	_	_	_
24	degree	degree	NN	_	_	_
25	Celsius	Celsius	NNP	_	_	_
26	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	washed	wash	VBN	_	_	_
4	in	in	IN	_	_	_
5	equal	equal	JJ	_	_	_
6	volume	volume	NN	_	_	_
7	of	of	IN	_	_	_
8	fresh	fresh	JJ	_	_	_
9	10	10	CD	_	_	_
10	%	%	NN	_	_	_
11	LB	lb	NN	MED	_	_
12	broth	broth	NN	MED	_	_
13	before	before	IN	_	_	_
14	inoculated	inoculate	VBN	_	_	_
15	into	into	IN	_	_	_
16	30	30	CD	_	_	_
17	ml	ml	NN	_	_	_
18	10	10	CD	_	_	_
19	%	%	NN	_	_	_
20	LB	lb	NN	_	_	_
21	in	in	IN	_	_	_
22	a	a	DT	_	_	_
23	flask	flask	NN	_	_	_
24	.	.	.	_	_	_

1	300	300	CD	_	_	_
2	ul	ul	NN	_	_	_
3	E.	e.	FW	_	_	_
4	coli	coli	FW	_	_	_
5	culture	culture	NN	_	_	_
6	was	be	VBD	_	_	_
7	inoculated	inoculate	VBN	_	_	_
8	for	for	IN	_	_	_
9	mono-species	mono-species	NNS	_	_	_
10	pure	pure	JJ	_	_	_
11	culture	culture	NN	_	_	_
12	.	.	.	_	_	_

1	150	150	CD	_	_	_
2	ul	ul	NN	_	_	_
3	E.	e.	FW	_	_	_
4	coli	coli	FW	_	_	_
5	and	and	CC	_	_	_
6	60	60	CD	_	_	_
7	ul	ul	NN	_	_	_
8	S.	S.	NNP	_	_	_
9	maltophilia	maltophilia	NNP	_	_	_
10	were	be	VBD	_	_	_
11	mixed	mixed	JJ	_	_	_
12	and	and	CC	_	_	_
13	inoculated	inoculate	VBN	_	_	_
14	for	for	IN	_	_	_
15	mixed-species	mixed-species	NNS	_	_	_
16	cultures	culture	NNS	_	_	_
17	.	.	.	_	_	_

1	Flasks	flask	NNS	_	_	_
2	were	be	VBD	_	_	_
3	set	set	VBN	_	_	_
4	on	on	IN	_	_	_
5	a	a	DT	_	_	_
6	shaker	shaker	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	250	250	CD	_	_	_
9	rpm	rpm	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	at	at	IN	_	_	_
12	room	room	NN	_	_	_
13	temperature	temperature	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	20	20	CD	_	_	_
16	C	c	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	for	for	IN	_	_	_
19	18	18	CD	_	_	_
20	h.	h.	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Cells	cell	NNS	_	_	_
23	were	be	VBD	_	_	_
24	harvested	harvest	VBN	_	_	_
25	and	and	CC	_	_	_
26	resuspended	resuspend	VBN	_	_	_
27	in	in	IN	_	_	_
28	RNAlater	rnalater	NN	_	_	_
29	and	and	CC	_	_	_
30	kept	keep	VBD	_	_	_
31	in	in	IN	_	_	_
32	4C	4c	NN	_	_	_
33	fridge	fridge	NN	_	_	_
34	overnight	overnight	JJ	_	_	_
35	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	aliquoted	aliquote	VBN	_	_	_
4	into	into	IN	_	_	_
5	vials	vial	NNS	_	_	_
6	containing	contain	VBG	_	_	_
7	around	around	IN	_	_	_
8	2x10	2x10	JJ	_	_	_
9	^	^	NN	_	_	_
10	8	8	CD	_	_	_
11	cells	cell	NNS	_	_	_
12	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	in	in	IN	_	_	_
3	each	each	DT	_	_	_
4	vial	vial	NN	_	_	_
5	were	be	VBD	_	_	_
6	then	then	RB	_	_	_
7	re-suspended	re-suspended	JJ	_	_	_
8	in	in	IN	_	_	_
9	nuclease-free	nuclease-free	JJ	_	_	_
10	phosphate	phosphate	NN	_	_	_
11	buffered	buffer	VBN	_	_	_
12	saline	saline	NN	_	_	_
13	,	,	,	_	_	_
14	incubated	incubate	VBN	_	_	_
15	with	with	IN	_	_	_
16	anti-E	anti-e	JJ	_	_	_
17	.	.	.	_	_	_

1	coli	coli	NN	_	_	_
2	antibody	antibody	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	ViroStat	virostat	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	and	and	CC	_	_	_
7	microbeads	microbead	NNS	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Miltenyi	miltenyi	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	,	,	,	_	_	_
12	followed	follow	VBN	_	_	_
13	by	by	IN	_	_	_
14	separation	separation	NN	_	_	_
15	on	on	IN	_	_	_
16	a	a	DT	_	_	_
17	MACS	macs	NN	_	_	_
18	separator	separator	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Miltenyi	Miltenyi	NNP	_	_	_
21	,	,	,	_	_	_
22	Auburn	Auburn	NNP	_	_	_
23	,	,	,	_	_	_
24	CA	CA	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	at	at	IN	_	_	_
27	4	4	CD	_	_	_
28	degree	degree	NN	_	_	_
29	C.	c.	NN	_	_	_
30	Sorted	sort	VBN	_	_	_
31	cells	cell	NNS	_	_	_
32	were	be	VBD	_	_	_
33	re-suspended	re-suspended	JJ	_	_	_
34	into	into	IN	_	_	_
35	RNAlater	rnalater	NN	_	_	_
36	until	until	IN	_	_	_
37	RNA	rna	NN	_	_	_
38	extraction	extraction	NN	_	_	_
39	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2	culture	culture	NN	_	_	_
3	media	media	NNS	_	_	_
4	:	:	:	_	_	_
5	10	10	CD	_	_	_
6	%	%	NN	_	_	_
7	Luria	Luria	NNP	MED	_	_
8	broth	broth	NN	MED	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	culture	culture	NN	_	_	_
11	system	system	NN	_	_	_
12	:	:	:	_	_	_
13	flask	flask	NN	_	_	_
14	with	with	IN	_	_	_
15	continous	continous	JJ	_	_	_
16	shaking	shake	VBG	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	250	250	CD	_	_	_
19	rpm	rpm	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	culture	culture	NN	_	_	_
23	system	system	NN	_	_	_
24	:	:	:	_	_	_
25	flask	flask	NN	_	_	_
26	with	with	IN	_	_	_
27	continuous	continuous	JJ	_	_	_
28	shaking	shake	VBG	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	250	250	CD	_	_	_
31	rpm	rpm	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	culture	culture	NN	_	_	_
35	temperature	temperature	NN	_	_	_
36	:	:	:	_	_	_
37	room	room	NN	_	_	_
38	temperature	temperature	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	20	20	CD	_	_	_
41	C	c	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	culture	culture	NN	_	_	_
45	time	time	NN	_	_	_
46	:	:	:	_	_	_
47	18	18	CD	_	_	_
48	h	h	NN	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	Data	Data	NNP	_	_	_
51	was	be	VBD	_	_	_
52	analyzed	analyze	VBN	_	_	_
53	in	in	IN	_	_	_
54	the	the	DT	_	_	_
55	software	software	NN	_	_	_
56	Acuity	acuity	NN	_	_	_
57	4.0	4.0	CD	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	Molecular	molecular	JJ	_	_	_
60	Devices	Devices	NNPS	_	_	_
61	,	,	,	_	_	_
62	Sunnyvale	Sunnyvale	NNP	_	_	_
63	,	,	,	_	_	_
64	CA	CA	NNP	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	.	.	.	_	_	_

1	Hybridized	hybridize	VBN	_	_	_
2	spots	spot	NNS	_	_	_
3	for	for	IN	_	_	_
4	E.	e.	FW	_	_	_
5	coli	coli	FW	_	_	_
6	K12	k12	NN	_	_	_
7	having	have	VBG	_	_	_
8	a	a	DT	_	_	_
9	high	high	JJ	_	_	_
10	QC	qc	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	quality	quality	NN	_	_	_
13	control	control	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	value	value	NN	_	_	_
16	>	>	JJR	_	_	_
17	0.1	0.1	CD	_	_	_
18	,	,	,	_	_	_
19	good	good	JJ	_	_	_
20	flag	flag	NN	_	_	_
21	tags	tag	NNS	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	A	a	NN	_	_	_
24	,	,	,	_	_	_
25	B	b	NN	_	_	_
26	and	and	CC	_	_	_
27	C	c	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	in	in	IN	_	_	_
30	both	both	CC	_	_	_
31	Cy3	cy3	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
33	Escherichia	escherichia	FW	Organism	_	_
34	coli	coli	FW	Organism	_	_
35	K-12	k-12	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Escherichia	escherichia	FW	Organism	_	_
38	coli	coli	FW	Organism	_	_
39	_	_	SYM	_	_	_
40	MixedSpeciesPlanktonic	MixedSpeciesPlanktonic	NNP	_	_	_
41	_	_	CD	_	_	_
42	bioreplicate1	bioreplicate1	NN	_	_	_
43	_	_	NN	_	_	_
44	techreplicate	techreplicate	NN	_	_	_
45	_	_	NN	_	_	_
46	1	1	CD	_	_	_
47	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
48	Escherichia	escherichia	FW	Organism	_	_
49	coli	coli	FW	Organism	_	_
50	_	_	SYM	_	_	_
51	MixedSpeciesPlanktonic	MixedSpeciesPlanktonic	NNP	_	_	_
52	_	_	CD	_	_	_
53	bioreplicate1	bioreplicate1	NN	_	_	_
54	_	_	NN	_	_	_
55	techreplicate	techreplicate	NN	_	_	_
56	_	_	NN	_	_	_
57	2	2	CD	_	_	_
58	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
59	Escherichia	escherichia	FW	Organism	_	_
60	coli	coli	FW	Organism	_	_
61	_	_	SYM	_	_	_
62	MixedSpeciesPlanktonic	MixedSpeciesPlanktonic	NNP	_	_	_
63	_	_	CD	_	_	_
64	bioreplicate2	bioreplicate2	NN	_	_	_
65	_	_	NN	_	_	_
66	techreplicate	techreplicate	NN	_	_	_
67	_	_	NN	_	_	_
68	1	1	CD	_	_	_
69	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
70	Escherichia	escherichia	FW	Organism	_	_
71	coli	coli	FW	Organism	_	_
72	_	_	SYM	_	_	_
73	MixedSpeciesPlanktonic	MixedSpeciesPlanktonic	NNP	_	_	_
74	_	_	CD	_	_	_
75	bioreplicate2	bioreplicate2	NN	_	_	_
76	_	_	NN	_	_	_
77	techreplicate	techreplicate	NN	_	_	_
78	_	_	NN	_	_	_
79	2	2	CD	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	RNAlater	rnalater	NN	_	_	_
82	was	be	VBD	_	_	_
83	removed	remove	VBN	_	_	_
84	from	from	IN	_	_	_
85	cells	cell	NNS	_	_	_
86	by	by	IN	_	_	_
87	filtration	filtration	NN	_	_	_
88	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	from	from	IN	_	_	_
6	cells	cell	NNS	_	_	_
7	using	use	VBG	_	_	_
8	a	a	DT	_	_	_
9	hot	hot	JJ	_	_	_
10	SDS	sds	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	sorted	sort	VBD	_	_	_
13	E.	e.	FW	_	_	_
14	coli	coli	FW	_	_	_
15	cells	cell	NNS	_	_	_
16	from	from	IN	_	_	_
17	dual-species	dual-species	JJ	_	_	_
18	planktonic	planktonic	JJ	_	_	_
19	culture	culture	NN	_	_	_
20	1	1	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	sorted	sort	VBD	_	_	_
23	E.	e.	FW	_	_	_
24	coli	coli	FW	_	_	_
25	cells	cell	NNS	_	_	_
26	from	from	IN	_	_	_
27	dual-species	dual-species	JJ	_	_	_
28	planktonic	planktonic	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	2	2	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
32	sorted	sort	VBD	_	_	_
33	E.	e.	FW	_	_	_
34	coli	coli	FW	_	_	_
35	cells	cell	NNS	_	_	_
36	from	from	IN	_	_	_
37	mono-species	mono-species	NNS	_	_	_
38	pure	pure	JJ	_	_	_
39	planktonic	planktonic	JJ	_	_	_
40	culture	culture	NN	_	_	_
41	1	1	CD	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	sorted	sort	VBD	_	_	_
44	E.	e.	FW	_	_	_
45	coli	coli	FW	_	_	_
46	cells	cell	NNS	_	_	_
47	from	from	IN	_	_	_
48	mono-species	mono-species	NNS	_	_	_
49	pure	pure	JJ	_	_	_
50	planktonic	planktonic	JJ	_	_	_
51	culture	culture	NN	_	_	_
52	2	2	CD	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	treatment	treatment	NN	_	_	_
55	:	:	:	_	_	_
56	with	with	IN	_	_	_
57	homogenization	homogenization	NN	_	_	_
58	and	and	CC	_	_	_
59	separation	separation	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	Cells	cell	NNS	_	_	_
62	for	for	IN	_	_	_
63	inoculation	inoculation	NN	_	_	_
64	were	be	VBD	_	_	_
65	from	from	IN	_	_	_
66	overnight	overnight	JJ	_	_	_
67	planktonic	planktonic	JJ	_	_	_
68	culture	culture	NN	_	_	_
69	in	in	IN	_	_	_
70	10	10	CD	_	_	_
71	%	%	NN	_	_	_
72	Luria-Bertani	luria-bertani	JJ	_	_	_
73	broth	broth	NN	_	_	_
74	at	at	IN	_	_	_
75	30	30	CD	_	_	_
76	degree	degree	NN	_	_	_
77	Celsius	Celsius	NNP	_	_	_
78	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	washed	wash	VBN	_	_	_
4	in	in	IN	_	_	_
5	equal	equal	JJ	_	_	_
6	volume	volume	NN	_	_	_
7	of	of	IN	_	_	_
8	fresh	fresh	JJ	_	_	_
9	10	10	CD	_	_	_
10	%	%	NN	_	_	_
11	LB	lb	NN	MED	_	_
12	broth	broth	NN	MED	_	_
13	before	before	IN	_	_	_
14	inoculation	inoculation	NN	_	_	_
15	.	.	.	_	_	_

1	Planktonic	planktonic	JJ	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	conducted	conduct	VBN	_	_	_
5	in	in	IN	_	_	_
6	flasks	flask	NNS	_	_	_
7	with	with	IN	_	_	_
8	30	30	CD	_	_	_
9	ml	ml	NN	_	_	_
10	10	10	CD	_	_	_
11	%	%	NN	_	_	_
12	LB	lb	NN	_	_	_
13	,	,	,	_	_	_
14	inoculated	inoculate	VBN	_	_	_
15	with	with	IN	_	_	_
16	300	300	CD	_	_	_
17	ul	ul	NN	_	_	_
18	E.	e.	FW	_	_	_
19	coli	coli	FW	_	_	_
20	overnight	overnight	JJ	_	_	_
21	culture	culture	NN	_	_	_
22	.	.	.	_	_	_

1	Flasks	flask	NNS	_	_	_
2	were	be	VBD	_	_	_
3	set	set	VBN	_	_	_
4	on	on	IN	_	_	_
5	a	a	DT	_	_	_
6	shaker	shaker	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	250	250	CD	_	_	_
9	rpm	rpm	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	at	at	IN	_	_	_
12	room	room	NN	_	_	_
13	temperature	temperature	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	20	20	CD	_	_	_
16	C	c	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	for	for	IN	_	_	_
19	18	18	CD	_	_	_
20	h.	h.	NN	_	_	_
21	Biofilms	biofilm	NNS	_	_	_
22	were	be	VBD	_	_	_
23	cultivated	cultivate	VBN	_	_	_
24	in	in	IN	_	_	_
25	static	static	JJ	_	_	_
26	disposable	disposable	JJ	_	_	_
27	petri	petri	NN	_	_	_
28	dishes	dish	NNS	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	60	60	CD	_	_	_
31	mm	mm	NN	_	_	_
32	x	x	CC	_	_	_
33	15	15	CD	_	_	_
34	mm	mm	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	with	with	IN	_	_	_
37	5	5	CD	_	_	_
38	ml	ml	NN	_	_	_
39	10	10	CD	_	_	_
40	%	%	NN	_	_	_
41	LB	lb	NN	_	_	_
42	,	,	,	_	_	_
43	inoculated	inoculate	VBN	_	_	_
44	with	with	IN	_	_	_
45	50	50	CD	_	_	_
46	ul	ul	NN	_	_	_
47	E.	e.	FW	_	_	_
48	coli	coli	FW	_	_	_
49	overnight	overnight	JJ	_	_	_
50	culture	culture	NN	_	_	_
51	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	petri	petri	JJ	_	_	_
3	dishes	dish	NNS	_	_	_
4	were	be	VBD	_	_	_
5	set	set	VBN	_	_	_
6	static	static	JJ	_	_	_
7	at	at	IN	_	_	_
8	room	room	NN	_	_	_
9	temperature	temperature	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	20	20	CD	_	_	_
12	C	c	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	for	for	IN	_	_	_
15	18	18	CD	_	_	_
16	h.	h.	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	culture	culture	NN	_	_	_
19	media	media	NNS	_	_	_
20	:	:	:	_	_	_
21	10	10	CD	_	_	_
22	%	%	NN	_	_	_
23	Luria	Luria	NNP	MED	_	_
24	broth	broth	NN	MED	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	culture	culture	NN	_	_	_
27	system	system	NN	_	_	_
28	:	:	:	_	_	_
29	flask	flask	NN	_	_	_
30	with	with	IN	_	_	_
31	continuous	continuous	JJ	_	_	_
32	shaking	shake	VBG	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	250	250	CD	_	_	_
35	rpm	rpm	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	culture	culture	NN	_	_	_
39	system	system	NN	_	_	_
40	:	:	:	_	_	_
41	static	static	JJ	_	_	_
42	petri	petri	JJ	_	_	_
43	dish	dish	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	disposable	disposable	JJ	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	culture	culture	NN	_	_	_
49	temperature	temperature	NN	_	_	_
50	:	:	:	_	_	_
51	room	room	NN	_	_	_
52	temperature	temperature	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	20	20	CD	_	_	_
55	C	c	NN	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	culture	culture	NN	_	_	_
59	time	time	NN	_	_	_
60	:	:	:	_	_	_
61	18	18	CD	_	_	_
62	h	h	NN	_	_	_
63	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
64	Data	Data	NNP	_	_	_
65	was	be	VBD	_	_	_
66	analyzed	analyze	VBN	_	_	_
67	in	in	IN	_	_	_
68	the	the	DT	_	_	_
69	software	software	NN	_	_	_
70	Acuity	acuity	NN	_	_	_
71	4.0	4.0	CD	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	Molecular	molecular	JJ	_	_	_
74	Devices	Devices	NNPS	_	_	_
75	,	,	,	_	_	_
76	Sunnyvale	Sunnyvale	NNP	_	_	_
77	,	,	,	_	_	_
78	CA	CA	NNP	_	_	_
79	-RRB-	-rrb-	-RRB-	_	_	_
80	.	.	.	_	_	_

1	Hybridized	hybridize	VBN	_	_	_
2	spots	spot	NNS	_	_	_
3	for	for	IN	_	_	_
4	E.	e.	FW	_	_	_
5	coli	coli	FW	_	_	_
6	K12	k12	NN	_	_	_
7	having	have	VBG	_	_	_
8	a	a	DT	_	_	_
9	high	high	JJ	_	_	_
10	QC	qc	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	quality	quality	NN	_	_	_
13	control	control	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	value	value	NN	_	_	_
16	>	>	JJR	_	_	_
17	0.1	0.1	CD	_	_	_
18	,	,	,	_	_	_
19	good	good	JJ	_	_	_
20	flag	flag	NN	_	_	_
21	tags	tag	NNS	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	A	a	NN	_	_	_
24	,	,	,	_	_	_
25	B	b	NN	_	_	_
26	and	and	CC	_	_	_
27	C	c	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	in	in	IN	_	_	_
30	both	both	CC	_	_	_
31	Cy3	cy3	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
33	E.	e.	FW	_	_	_
34	coli	coli	FW	_	_	_
35	cells	cell	NNS	_	_	_
36	from	from	IN	_	_	_
37	biofilm	biofilm	NN	_	_	_
38	1	1	CD	_	_	_
39	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
40	E.	E.	NNP	_	_	_
41	coli	coli	NN	_	_	_
42	cells	cell	NNS	_	_	_
43	from	from	IN	_	_	_
44	biofilm	biofilm	NN	_	_	_
45	2	2	CD	_	_	_
46	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
47	E.	E.	NNP	_	_	_
48	coli	coli	NN	_	_	_
49	cells	cell	NNS	_	_	_
50	from	from	IN	_	_	_
51	planktonic	planktonic	JJ	_	_	_
52	culture	culture	NN	_	_	_
53	1	1	CD	_	_	_
54	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
55	E.	E.	NNP	_	_	_
56	coli	coli	NN	_	_	_
57	cells	cell	NNS	_	_	_
58	from	from	IN	_	_	_
59	planktonic	planktonic	JJ	_	_	_
60	culture	culture	NN	_	_	_
61	2	2	CD	_	_	_
62	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
63	Escherichia	escherichia	FW	Organism	_	_
64	coli	coli	FW	Organism	_	_
65	_	_	SYM	_	_	_
66	Biofilm	Biofilm	NNP	_	_	_
67	_	_	SYM	_	_	_
68	bioreplicate1	bioreplicate1	CD	_	_	_
69	_	_	NN	_	_	_
70	techreplicate	techreplicate	NN	_	_	_
71	_	_	NN	_	_	_
72	1	1	CD	_	_	_
73	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
74	Escherichia	escherichia	FW	Organism	_	_
75	coli	coli	FW	Organism	_	_
76	_	_	SYM	_	_	_
77	Biofilm	Biofilm	NNP	_	_	_
78	_	_	SYM	_	_	_
79	bioreplicate1	bioreplicate1	CD	_	_	_
80	_	_	NN	_	_	_
81	techreplicate	techreplicate	NN	_	_	_
82	_	_	NN	_	_	_
83	2	2	CD	_	_	_
84	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
85	Escherichia	escherichia	FW	Organism	_	_
86	coli	coli	FW	Organism	_	_
87	_	_	SYM	_	_	_
88	Biofilm	Biofilm	NNP	_	_	_
89	_	_	SYM	_	_	_
90	bioreplicate2	bioreplicate2	CD	_	_	_
91	_	_	NN	_	_	_
92	techreplicate	techreplicate	NN	_	_	_
93	_	_	NN	_	_	_
94	1	1	CD	_	_	_
95	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
96	Escherichia	escherichia	FW	Organism	_	_
97	coli	coli	FW	Organism	_	_
98	_	_	SYM	_	_	_
99	Biofilm	Biofilm	NNP	_	_	_
100	_	_	SYM	_	_	_
101	bioreplicate2	bioreplicate2	CD	_	_	_
102	_	_	NN	_	_	_
103	techreplicate	techreplicate	NN	_	_	_
104	_	_	NN	_	_	_
105	2	2	CD	_	_	_
106	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
107	Escherichia	escherichia	FW	Organism	_	_
108	coli	coli	FW	Organism	_	_
109	K-12	k-12	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
111	Planktonic	planktonic	JJ	_	_	_
112	cultures	culture	NNS	_	_	_
113	of	of	IN	_	_	_
114	E.	e.	FW	_	_	_
115	coli	coli	FW	_	_	_
116	were	be	VBD	_	_	_
117	harvested	harvest	VBN	_	_	_
118	and	and	CC	_	_	_
119	resuspended	resuspend	VBN	_	_	_
120	in	in	IN	_	_	_
121	RNAlater	rnalater	NN	_	_	_
122	and	and	CC	_	_	_
123	kept	keep	VBD	_	_	_
124	in	in	IN	_	_	_
125	4C	4c	NN	_	_	_
126	fridge	fridge	NN	_	_	_
127	overnight	overnight	JJ	_	_	_
128	.	.	.	_	_	_

1	Suspended	suspend	VBN	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	from	from	IN	_	_	_
6	petri	petri	JJ	_	_	_
7	dishes	dish	NNS	_	_	_
8	and	and	CC	_	_	_
9	biofilms	biofilm	NNS	_	_	_
10	were	be	VBD	_	_	_
11	washed	wash	VBN	_	_	_
12	three	three	CD	_	_	_
13	times	time	NNS	_	_	_
14	with	with	IN	_	_	_
15	fresh	fresh	JJ	_	_	_
16	10	10	CD	_	_	_
17	%	%	NN	_	_	_
18	LB	lb	NN	_	_	_
19	before	before	IN	_	_	_
20	being	be	VBG	_	_	_
21	craped	crap	VBN	_	_	_
22	from	from	IN	_	_	_
23	the	the	DT	_	_	_
24	bottom	bottom	JJ	_	_	_
25	surface	surface	NN	_	_	_
26	of	of	IN	_	_	_
27	petri	petri	NN	_	_	_
28	dishes	dish	NNS	_	_	_
29	.	.	.	_	_	_

1	Biofilms	biofilm	NNS	_	_	_
2	were	be	VBD	_	_	_
3	also	also	RB	_	_	_
4	re-suspeded	re-suspeded	JJ	_	_	_
5	into	into	IN	_	_	_
6	RNAlater	rnalater	NN	_	_	_
7	and	and	CC	_	_	_
8	kept	keep	VBD	_	_	_
9	at	at	IN	_	_	_
10	4C	4c	NN	_	_	_
11	overnight	overnight	JJ	_	_	_
12	.	.	.	_	_	_

1	Both	both	DT	_	_	_
2	planktonic	planktonic	JJ	_	_	_
3	and	and	CC	_	_	_
4	biofilm	biofilm	NN	_	_	_
5	samples	sample	NNS	_	_	_
6	were	be	VBD	_	_	_
7	homogenized	homogenize	VBN	_	_	_
8	for	for	IN	_	_	_
9	2	2	CD	_	_	_
10	min	min	NN	_	_	_
11	on	on	IN	_	_	_
12	ice	ice	NN	_	_	_
13	with	with	IN	_	_	_
14	an	a	DT	_	_	_
15	Omni	Omni	NNP	_	_	_
16	TH	th	NN	_	_	_
17	homogenizer	homogenizer	NN	_	_	_
18	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	aliquoted	aliquote	VBN	_	_	_
5	into	into	IN	_	_	_
6	vials	vial	NNS	_	_	_
7	containing	contain	VBG	_	_	_
8	around	around	IN	_	_	_
9	2x10	2x10	JJ	_	_	_
10	^	^	NN	_	_	_
11	8	8	CD	_	_	_
12	cells	cell	NNS	_	_	_
13	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	in	in	IN	_	_	_
3	each	each	DT	_	_	_
4	vial	vial	NN	_	_	_
5	were	be	VBD	_	_	_
6	then	then	RB	_	_	_
7	re-suspended	re-suspended	JJ	_	_	_
8	in	in	IN	_	_	_
9	nuclease-free	nuclease-free	JJ	_	_	_
10	phosphate	phosphate	NN	_	_	_
11	buffered	buffer	VBN	_	_	_
12	saline	saline	NN	_	_	_
13	,	,	,	_	_	_
14	incubated	incubate	VBN	_	_	_
15	with	with	IN	_	_	_
16	anti-E	anti-e	JJ	_	_	_
17	.	.	.	_	_	_

1	coli	coli	NN	_	_	_
2	antibody	antibody	NN	_	_	_
3	and	and	CC	_	_	_
4	microbeads	microbead	NNS	_	_	_
5	,	,	,	_	_	_
6	followed	follow	VBN	_	_	_
7	by	by	IN	_	_	_
8	separation	separation	NN	_	_	_
9	on	on	IN	_	_	_
10	a	a	DT	_	_	_
11	MACS	macs	NN	_	_	_
12	separator	separator	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Miltenyi	Miltenyi	NNP	_	_	_
15	,	,	,	_	_	_
16	Auburn	Auburn	NNP	_	_	_
17	,	,	,	_	_	_
18	CA	CA	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	at	at	IN	_	_	_
21	4	4	CD	_	_	_
22	degree	degree	NN	_	_	_
23	C.	c.	NN	_	_	_
24	Sorted	sort	VBN	_	_	_
25	cells	cell	NNS	_	_	_
26	were	be	VBD	_	_	_
27	re-suspended	re-suspended	JJ	_	_	_
28	into	into	IN	_	_	_
29	RNAlater	rnalater	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNAlater	rnalater	NN	_	_	_
3	was	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	from	from	IN	_	_	_
6	cells	cell	NNS	_	_	_
7	by	by	IN	_	_	_
8	filtration	filtration	NN	_	_	_
9	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	from	from	IN	_	_	_
6	cells	cell	NNS	_	_	_
7	using	use	VBG	_	_	_
8	a	a	DT	_	_	_
9	hot	hot	JJ	_	_	_
10	SDS	sds	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	treatment	treatment	NN	_	_	_
13	:	:	:	_	_	_
14	with	with	IN	_	_	_
15	homogenization	homogenization	NN	_	_	_
16	and	and	CC	_	_	_
17	separation	separation	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
19	chip	chip	NN	_	_	_
20	antibody	antibody	NN	_	_	_
21	:	:	:	_	_	_
22	FLAG	flag	NN	_	_	_
23	antibody	antibody	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
25	chip	chip	NN	_	_	_
26	antibody	antibody	NN	_	_	_
27	:	:	:	_	_	_
28	RNAP	rnap	NN	_	_	_
29	beta	beta	NN	_	_	_
30	subunit	subunit	NN	_	_	_
31	antibody	antibody	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	ChIP-Seq	chip-seq	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	-LSB-	-lsb-	-LRB-	_	_	_
36	E-MTAB-332	e-mtab-332	NN	_	_	_
37	-RSB-	-rsb-	-RRB-	_	_	_
38	fis	fi	VBZ	GEN	_	_
39	early-exponential	early-exponential	JJ	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	-LSB-	-lsb-	-LRB-	_	_	_
42	E-MTAB-332	e-mtab-332	NN	_	_	_
43	-RSB-	-rsb-	-RRB-	_	_	_
44	fis	fi	VBZ	GEN	_	_
45	mid-exponential	mid-exponential	JJ	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	-LSB-	-lsb-	-LRB-	_	_	_
48	E-MTAB-332	e-mtab-332	NN	_	_	_
49	-RSB-	-rsb-	-RRB-	_	_	_
50	H-NS	h-ns	NN	_	_	_
51	early-exponential	early-exponential	JJ	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	-LSB-	-lsb-	-LRB-	_	_	_
54	E-MTAB-332	e-mtab-332	NN	_	_	_
55	-RSB-	-rsb-	-RRB-	_	_	_
56	H-NS	h-ns	NN	_	_	_
57	mid-exponential	mid-exponential	JJ	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	-LSB-	-lsb-	-LRB-	_	_	_
60	E-MTAB-332	e-mtab-332	NN	_	_	_
61	-RSB-	-rsb-	-RRB-	_	_	_
62	H-NS	h-ns	NN	_	_	_
63	stationary	stationary	JJ	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	-LSB-	-lsb-	-LRB-	_	_	_
66	E-MTAB-332	e-mtab-332	NN	_	_	_
67	-RSB-	-rsb-	-RRB-	_	_	_
68	H-NS	h-ns	NN	_	_	_
69	transition-to-stationary	transition-to-stationary	JJ	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	-LSB-	-lsb-	-LRB-	_	_	_
72	E-MTAB-332	e-mtab-332	NN	_	_	_
73	-RSB-	-rsb-	-RRB-	_	_	_
74	rpo	rpo	NN	_	_	_
75	delfis	delfi	VBZ	_	_	_
76	mid-exponential	mid-exponential	JJ	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	-LSB-	-lsb-	-LRB-	_	_	_
79	E-MTAB-332	e-mtab-332	NN	_	_	_
80	-RSB-	-rsb-	-RRB-	_	_	_
81	rpo	rpo	NN	_	_	_
82	delhns	delhn	VBZ	_	_	_
83	mid-exponential	mid-exponential	JJ	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	-LSB-	-lsb-	-LRB-	_	_	_
86	E-MTAB-332	e-mtab-332	NN	_	_	_
87	-RSB-	-rsb-	-RRB-	_	_	_
88	rpo	rpo	NN	_	_	_
89	wt	wt	JJ	_	_	_
90	mid-exponential	mid-exponential	JJ	_	_	_
91	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
92	Escherichia	escherichia	FW	Organism	_	_
93	coli	coli	FW	Organism	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	Fis	fis	NN	TF	_	_
96	,	,	,	_	_	_
97	EE	ee	NN	_	_	_
98	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
99	Fis	Fis	NNP	TF	_	_
100	,	,	,	_	_	_
101	ME	ME	NNP	_	_	_
102	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
103	genotype	genotype	NN	_	_	_
104	:	:	:	_	_	_
105	del-fis	del-fis	JJ	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	genotype	genotype	NN	_	_	_
108	:	:	:	_	_	_
109	del-hns	del-hns	JJ	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	genotype	genotype	NN	_	_	_
112	:	:	:	_	_	_
113	fis	fi	NNS	GEN	_	_
114	:	:	:	_	_	_
115	:	:	:	_	_	_
116	3xFLAG	3xflag	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	genotype	genotype	NN	_	_	_
119	:	:	:	_	_	_
120	hns	hn	NNS	GEN	_	_
121	:	:	:	_	_	_
122	:	:	:	_	_	_
123	3xFLAG	3xflag	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	genotype	genotype	NN	_	_	_
126	:	:	:	_	_	_
127	wild	wild	JJ	_	_	_
128	_	_	NN	_	_	_
129	type	type	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	growth	growth	NN	_	_	_
132	condition	condition	NN	_	_	_
133	:	:	:	_	_	_
134	early-exponential	early-exponential	JJ	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	growth	growth	NN	_	_	_
137	condition	condition	NN	_	_	_
138	:	:	:	_	_	_
139	mid-exponential	mid-exponential	JJ	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	growth	growth	NN	_	_	_
142	condition	condition	NN	_	_	_
143	:	:	:	_	_	_
144	stationary	stationary	JJ	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	growth	growth	NN	_	_	_
147	condition	condition	NN	_	_	_
148	:	:	:	_	_	_
149	transition-to-stationary	transition-to-stationary	JJ	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
151	grow	grow	VBP	_	_	_
152	|	|	SYM	_	_	_
153	The	the	DT	_	_	_
154	E.	e.	FW	_	_	_
155	coli	coli	FW	_	_	_
156	K-12	k-12	NN	_	_	_
157	MG1655	mg1655	NN	_	_	_
158	bacterial	bacterial	JJ	_	_	_
159	strains	strain	NNS	_	_	_
160	used	use	VBN	_	_	_
161	in	in	IN	_	_	_
162	this	this	DT	_	_	_
163	work	work	NN	_	_	_
164	are	be	VBP	_	_	_
165	the	the	DT	_	_	_
166	following	following	NN	_	_	_
167	:	:	:	_	_	_
168	E.	e.	FW	_	_	_
169	coli	coli	FW	_	_	_
170	MG1655	mg1655	NN	_	_	_
171	-LRB-	-lrb-	-LRB-	_	_	_
172	F	f	NN	_	_	_
173	-	-	:	_	_	_
174	lambda	lambda	NN	_	_	_
175	-	-	:	_	_	_
176	ilvG	ilvg	NN	_	_	_
177	-	-	:	_	_	_
178	rfb-50	rfb-50	NN	_	_	_
179	rph-1	rph-1	NN	_	_	_
180	-RRB-	-rrb-	-RRB-	_	_	_
181	;	;	:	_	_	_
182	MG1655	mg1655	NN	_	_	_
183	hns	hn	NNS	GEN	_	_
184	-LRB-	-lrb-	-LRB-	_	_	_
185	hns	hn	NNS	GEN	_	_
186	:	:	:	_	_	_
187	:	:	:	_	_	_
188	Kanr	kanr	NN	_	_	_
189	-RRB-	-rrb-	-RRB-	_	_	_
190	;	;	:	_	_	_
191	MG1655	mg1655	NN	_	_	_
192	fis	fis	NN	GEN	_	_
193	-LRB-	-lrb-	-LRB-	_	_	_
194	fis	fis	NN	GEN	_	_
195	:	:	:	_	_	_
196	:	:	:	_	_	_
197	Kanr	kanr	NN	_	_	_
198	-RRB-	-rrb-	-RRB-	_	_	_
199	;	;	:	_	_	_
200	MG1655	mg1655	NN	_	_	_
201	hns-FLAG	hns-flag	NN	_	_	_
202	-LRB-	-lrb-	-LRB-	_	_	_
203	hns	hn	NNS	GEN	_	_
204	:	:	:	_	_	_
205	:	:	:	_	_	_
206	3xFLAG	3xflag	NN	_	_	_
207	:	:	:	_	_	_
208	:	:	:	_	_	_
209	Kanr	kanr	NN	_	_	_
210	-RRB-	-rrb-	-RRB-	_	_	_
211	;	;	:	_	_	_
212	MG1655	mg1655	NN	_	_	_
213	fis-FLAG	fis-flag	NN	_	_	_
214	-LRB-	-lrb-	-LRB-	_	_	_
215	fis	fis	NN	GEN	_	_
216	:	:	:	_	_	_
217	:	:	:	_	_	_
218	3xFLAG	3xflag	NN	_	_	_
219	:	:	:	_	_	_
220	:	:	:	_	_	_
221	Kanr	kanr	NN	_	_	_
222	-RRB-	-rrb-	-RRB-	_	_	_
223	.	.	.	_	_	_

1	Luria-Bertani	luria-bertani	JJ	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	0.5	0.5	CD	_	_	_
4	%	%	NN	_	_	_
5	NaCl	nacl	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	broth	broth	NN	_	_	_
8	and	and	CC	_	_	_
9	agar	agar	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	15	15	CD	_	_	_
12	g	g	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	H-NS	h-ns	NN	_	_	_
15	,	,	,	_	_	_
16	EE	ee	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	H-NS	h-ns	NN	_	_	_
19	,	,	,	_	_	_
20	ME	me	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	H-NS	h-ns	NN	_	_	_
23	,	,	,	_	_	_
24	S	s	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	H-NS	h-ns	NN	_	_	_
27	,	,	,	_	_	_
28	TS	ts	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	material	material	NN	_	_	_
31	type	type	NN	_	_	_
32	:	:	:	_	_	_
33	whole	whole	JJ	_	_	_
34	_	_	JJ	_	_	_
35	organism	organism	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	nucleic	nucleic	JJ	_	_	_
38	_	_	NN	_	_	_
39	acid	acid	NN	_	_	_
40	_	_	NN	_	_	_
41	extraction	extraction	NN	_	_	_
42	|	|	SYM	_	_	_
43	ChIP	chip	NN	_	_	_
44	was	be	VBD	_	_	_
45	performed	perform	VBN	_	_	_
46	as	as	IN	_	_	_
47	previously	previously	RB	_	_	_
48	described	describe	VBN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	Grainger	Grainger	NNP	_	_	_
51	et	et	FW	_	_	_
52	al	al	FW	_	_	_
53	,	,	,	_	_	_
54	2004	2004	CD	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	with	with	IN	_	_	_
57	some	some	DT	_	_	_
58	modifications	modification	NNS	_	_	_
59	to	to	TO	_	_	_
60	the	the	DT	_	_	_
61	protdegree	protdegree	NN	_	_	_
62	Col.	Col.	NNP	_	_	_
63	Cells	cell	NNS	_	_	_
64	were	be	VBD	_	_	_
65	grown	grow	VBN	_	_	_
66	aerobically	aerobically	RB	_	_	_
67	at	at	IN	_	_	_
68	37degree	37degree	CD	_	_	_
69	C	c	NN	_	_	_
70	to	to	TO	_	_	_
71	the	the	DT	_	_	_
72	desired	desire	VBN	_	_	_
73	OD600	od600	NN	_	_	_
74	and	and	CC	_	_	_
75	formaldehyde	formaldehyde	NN	_	_	_
76	was	be	VBD	_	_	_
77	added	add	VBN	_	_	_
78	to	to	TO	_	_	_
79	a	a	DT	_	_	_
80	final	final	JJ	_	_	_
81	concentration	concentration	NN	_	_	_
82	of	of	IN	_	_	_
83	1	1	CD	_	_	_
84	%	%	NN	_	_	_
85	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	20	20	CD	_	_	_
3	min	min	NN	_	_	_
4	of	of	IN	_	_	_
5	incubation	incubation	NN	_	_	_
6	,	,	,	_	_	_
7	glycine	glycine	NN	_	_	_
8	was	be	VBD	_	_	_
9	added	add	VBN	_	_	_
10	to	to	TO	_	_	_
11	a	a	DT	_	_	_
12	final	final	JJ	_	_	_
13	concentration	concentration	NN	_	_	_
14	of	of	IN	_	_	_
15	0.5	0.5	CD	_	_	_
16	M	m	NN	_	_	_
17	to	to	TO	_	_	_
18	quench	quench	VB	_	_	_
19	the	the	DT	_	_	_
20	reaction	reaction	NN	_	_	_
21	and	and	CC	_	_	_
22	incubated	incubate	VBN	_	_	_
23	for	for	IN	_	_	_
24	a	a	DT	_	_	_
25	further	further	JJ	_	_	_
26	5	5	CD	_	_	_
27	min	min	NN	_	_	_
28	.	.	.	_	_	_

1	Cross-linked	cross-linked	JJ	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	harvested	harvest	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	and	and	CC	_	_	_
8	washed	wash	VBN	_	_	_
9	twice	twice	RB	_	_	_
10	with	with	IN	_	_	_
11	ice-cold	ice-cold	JJ	_	_	_
12	TBS	tbs	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	pH	ph	NN	_	_	_
15	7.5	7.5	CD	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	resuspended	resuspend	VBN	_	_	_
4	in	in	IN	_	_	_
5	1	1	CD	_	_	_
6	ml	ml	NN	_	_	_
7	of	of	IN	_	_	_
8	lysis	lysis	NN	_	_	_
9	buffer	buffer	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	10	10	CD	_	_	_
12	mM	mm	NN	KWSUPP	_	_
13	Tris	tris	NN	_	_	_
14	-LSB-	-lsb-	-LRB-	_	_	_
15	pH	ph	NN	_	_	_
16	8.0	8.0	CD	_	_	_
17	-RSB-	-rsb-	-RRB-	_	_	_
18	,	,	,	_	_	_
19	20	20	CD	_	_	_
20	%	%	NN	_	_	_
21	sucrose	sucrose	NN	_	_	_
22	,	,	,	_	_	_
23	50	50	CD	_	_	_
24	mM	mm	NN	KWSUPP	_	_
25	NaCl	nacl	NN	_	_	_
26	,	,	,	_	_	_
27	10	10	CD	_	_	_
28	mM	mm	NN	KWSUPP	_	_
29	EDTA	edta	NN	_	_	_
30	,	,	,	_	_	_
31	20	20	CD	_	_	_
32	mg	mg	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	rpo	rpo	NN	_	_	_
35	,	,	,	_	_	_
36	delfis	delfis	NN	_	_	_
37	,	,	,	_	_	_
38	ME	me	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	rpo	rpo	NN	_	_	_
41	,	,	,	_	_	_
42	delhns	delhn	NNS	_	_	_
43	,	,	,	_	_	_
44	ME	me	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	rpo	rpo	NN	_	_	_
47	,	,	,	_	_	_
48	wt	wt	JJ	_	_	_
49	,	,	,	_	_	_
50	ME	me	JJ	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	Sequences	sequence	NNS	_	_	_
53	obtained	obtain	VBN	_	_	_
54	from	from	IN	_	_	_
55	the	the	DT	_	_	_
56	Illumina	Illumina	NNP	_	_	_
57	Genome	Genome	NNP	_	_	_
58	Analyzer	Analyzer	NNP	_	_	_
59	were	be	VBD	_	_	_
60	mapped	map	VBN	_	_	_
61	to	to	TO	_	_	_
62	both	both	DT	_	_	_
63	strands	strand	NNS	_	_	_
64	of	of	IN	_	_	_
65	the	the	DT	_	_	_
66	E.	e.	FW	_	_	_
67	coli	coli	FW	_	_	_
68	K12	k12	NN	_	_	_
69	MG1655	mg1655	NN	_	_	_
70	genome	genome	NN	_	_	_
71	using	use	VBG	_	_	_
72	BLAT	BLAT	NNP	_	_	_
73	allowing	allow	VBG	_	_	_
74	no	no	DT	_	_	_
75	gaps	gap	NNS	_	_	_
76	and	and	CC	_	_	_
77	up	up	RB	_	_	_
78	to	to	TO	_	_	_
79	two	two	CD	_	_	_
80	mismatches	mismatch	NNS	_	_	_
81	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	alignment	alignment	NN	_	_	_
3	was	be	VBD	_	_	_
4	extended	extend	VBN	_	_	_
5	to	to	TO	_	_	_
6	200bp	200bp	VB	_	_	_
7	the	the	DT	_	_	_
8	approximate	approximate	JJ	_	_	_
9	average	average	JJ	_	_	_
10	length	length	NN	_	_	_
11	of	of	IN	_	_	_
12	DNA	dna	NN	_	_	_
13	fragments	fragment	NNS	_	_	_
14	on	on	IN	_	_	_
15	the	the	DT	_	_	_
16	3	3	CD	_	_	_
17	'	'	''	_	_	_
18	end	end	NN	_	_	_
19	.	.	.	_	_	_

1	Only	only	RB	_	_	_
2	reads	read	VBZ	_	_	_
3	which	which	WDT	_	_	_
4	mapped	map	VBD	_	_	_
5	to	to	TO	_	_	_
6	a	a	DT	_	_	_
7	single	single	JJ	_	_	_
8	region	region	NN	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	genome	genome	NN	_	_	_
12	were	be	VBD	_	_	_
13	considered	consider	VBN	_	_	_
14	for	for	IN	_	_	_
15	further	further	JJ	_	_	_
16	analysis	analysis	NN	_	_	_
17	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	base	base	NN	_	_	_
4	position	position	NN	_	_	_
5	on	on	IN	_	_	_
6	the	the	DT	_	_	_
7	genome	genome	NN	_	_	_
8	,	,	,	_	_	_
9	the	the	DT	_	_	_
10	number	number	NN	_	_	_
11	of	of	IN	_	_	_
12	reads	read	VBZ	_	_	_
13	that	that	IN	_	_	_
14	mapped	map	VBN	_	_	_
15	to	to	TO	_	_	_
16	that	that	DT	_	_	_
17	position	position	NN	_	_	_
18	was	be	VBD	_	_	_
19	calculated	calculate	VBN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	sequencing	sequencing	NN	_	_	_
3	|	|	SYM	_	_	_
4	Immunoprecipitated	immunoprecipitate	VBN	_	_	_
5	samples	sample	NNS	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	sheared	sheared	JJ	_	_	_
9	DNA	dna	NN	_	_	_
10	following	follow	VBG	_	_	_
11	the	the	DT	_	_	_
12	Bioruptor	Bioruptor	NNP	_	_	_
13	were	be	VBD	_	_	_
14	de-crosslinked	de-crosslinked	JJ	_	_	_
15	in	in	IN	_	_	_
16	0.5	0.5	CD	_	_	_
17	x	x	CC	_	_	_
18	elution	elution	NN	_	_	_
19	buffer	buffer	NN	_	_	_
20	containing	contain	VBG	_	_	_
21	0.8	0.8	CD	_	_	_
22	mg	mg	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	strainorline	strainorline	NN	_	_	_
25	:	:	:	_	_	_
26	K-12	k-12	NN	_	_	_
27	substr	substr	NN	_	_	_
28	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	at	at	IN	_	_	_
7	37oC	37oc	NN	_	_	_
8	without	without	IN	_	_	_
9	shaking	shake	VBG	_	_	_
10	in	in	IN	_	_	_
11	18	18	CD	_	_	_
12	mm	mm	NN	_	_	_
13	test	test	NN	_	_	_
14	tubes	tube	NNS	_	_	_
15	containing	contain	VBG	_	_	_
16	5	5	CD	_	_	_
17	ml	ml	NN	_	_	_
18	of	of	IN	_	_	_
19	the	the	DT	_	_	_
20	MOPS-based	mops-based	JJ	_	_	_
21	culture	culture	NN	_	_	_
22	medium	medium	NN	_	_	_
23	designed	design	VBN	_	_	_
24	by	by	IN	_	_	_
25	Neidhardt	Neidhardt	NNP	_	_	_
26	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	cecal	cecal	JJ	_	_	_
3	mucus	mucus	NN	_	_	_
4	was	be	VBD	_	_	_
5	prepared	prepare	VBN	_	_	_
6	from	from	IN	_	_	_
7	streptomycin-treated	streptomycin-treated	JJ	_	_	_
8	CD-1	cd-1	NN	_	_	_
9	mice	mouse	NNS	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	not	not	RB	_	_	_
12	colonized	colonize	VBN	_	_	_
13	with	with	IN	_	_	_
14	E.	e.	FW	_	_	_
15	coli	coli	FW	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	grown	grow	VBN	_	_	_
4	to	to	TO	_	_	_
5	A600	a600	NN	_	_	_
6	=	=	JJ	_	_	_
7	0.4	0.4	CD	_	_	_
8	in	in	IN	_	_	_
9	MOPS	MOPS	NNP	MED	_	_
10	medium	medium	NN	_	_	_
11	containing	contain	VBG	_	_	_
12	glucose	glucose	NN	SUPP	_	_
13	or	or	CC	_	_	_
14	mannose	mannose	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	0.2	0.2	CD	_	_	_
17	%	%	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	and	and	CC	_	_	_
20	also	also	RB	_	_	_
21	in	in	IN	_	_	_
22	10	10	CD	_	_	_
23	mg	mg	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Cultures	culture	NNS	_	_	_
26	were	be	VBD	_	_	_
27	diluted	dilute	VBN	_	_	_
28	into	into	IN	_	_	_
29	DNA-RNA	DNA-RNA	NNP	_	_	_
30	Protect	Protect	NNP	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Sierra	Sierra	NNP	_	_	_
33	Diagnostics	Diagnostics	NNPS	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	to	to	TO	_	_	_
36	inhibit	inhibit	VB	_	_	_
37	RNA	rna	NN	_	_	_
38	degradation	degradation	NN	_	_	_
39	and	and	CC	_	_	_
40	the	the	DT	_	_	_
41	RNA	rna	NN	_	_	_
42	was	be	VBD	_	_	_
43	purified	purify	VBN	_	_	_
44	using	use	VBG	_	_	_
45	RNeasy	rneasy	NN	_	_	_
46	minkits	minkit	NNS	_	_	_
47	with	with	IN	_	_	_
48	the	the	DT	_	_	_
49	optional	optional	JJ	_	_	_
50	DNase	dnase	NN	_	_	_
51	treatment	treatment	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	Qiagen	qiagen	NN	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	flhD	flhd	NN	GEN	_	_
5	,	,	,	_	_	_
6	A600	a600	NN	_	_	_
7	=	=	JJ	_	_	_
8	0.2	0.2	CD	_	_	_
9	on	on	IN	_	_	_
10	mucus	mucus	NN	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	E.	E.	NNP	_	_	_
13	coli	coli	NN	_	_	_
14	flhD	flhd	NN	GEN	_	_
15	,	,	,	_	_	_
16	A600	a600	NN	_	_	_
17	=	=	JJ	_	_	_
18	0.4	0.4	CD	_	_	_
19	on	on	IN	_	_	_
20	glucose	glucose	NN	SUPP	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	E.	e.	FW	_	_	_
23	coli	coli	FW	_	_	_
24	flhD	flhd	NN	GEN	_	_
25	,	,	,	_	_	_
26	A600	a600	NN	_	_	_
27	=	=	JJ	_	_	_
28	0.4	0.4	CD	_	_	_
29	on	on	IN	_	_	_
30	mannose	mannose	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	E.	e.	FW	_	_	_
33	coli	coli	FW	_	_	_
34	flhD	flhd	NN	GEN	_	_
35	,	,	,	_	_	_
36	A600	a600	NN	_	_	_
37	=	=	JJ	_	_	_
38	0.5	0.5	CD	_	_	_
39	on	on	IN	_	_	_
40	mucus	mucus	NN	_	_	_
41	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
42	E.	E.	NNP	_	_	_
43	coli	coli	NN	_	_	_
44	MG1655star	mg1655star	NN	_	_	_
45	,	,	,	_	_	_
46	A600	a600	NN	_	_	_
47	=	=	JJ	_	_	_
48	0.2	0.2	CD	_	_	_
49	on	on	IN	_	_	_
50	mucus	mucus	NN	_	_	_
51	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
52	E.	E.	NNP	_	_	_
53	coli	coli	NN	_	_	_
54	MG1655star	mg1655star	NN	_	_	_
55	,	,	,	_	_	_
56	A600	a600	NN	_	_	_
57	=	=	JJ	_	_	_
58	0.4	0.4	CD	_	_	_
59	on	on	IN	_	_	_
60	glucose	glucose	NN	SUPP	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	E.	e.	FW	_	_	_
63	coli	coli	FW	_	_	_
64	MG1655star	mg1655star	NN	_	_	_
65	,	,	,	_	_	_
66	A600	a600	NN	_	_	_
67	=	=	JJ	_	_	_
68	0.4	0.4	CD	_	_	_
69	on	on	IN	_	_	_
70	mannose	mannose	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	E.	e.	FW	_	_	_
73	coli	coli	FW	_	_	_
74	MG1655star	mg1655star	NN	_	_	_
75	,	,	,	_	_	_
76	A600	a600	NN	_	_	_
77	=	=	JJ	_	_	_
78	0.5	0.5	CD	_	_	_
79	on	on	IN	_	_	_
80	mucus	mucus	NN	_	_	_
81	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
82	E.	E.	NNP	_	_	_
83	coli	coli	NN	_	_	_
84	wild-type	wild-type	JJ	_	_	_
85	,	,	,	_	_	_
86	A600	a600	NN	_	_	_
87	=	=	JJ	_	_	_
88	0.2	0.2	CD	_	_	_
89	on	on	IN	_	_	_
90	mucus	mucus	NN	_	_	_
91	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
92	E.	E.	NNP	_	_	_
93	coli	coli	NN	_	_	_
94	wild-type	wild-type	JJ	_	_	_
95	,	,	,	_	_	_
96	A600	a600	NN	_	_	_
97	=	=	JJ	_	_	_
98	0.4	0.4	CD	_	_	_
99	on	on	IN	_	_	_
100	glucose	glucose	NN	SUPP	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	E.	e.	FW	_	_	_
103	coli	coli	FW	_	_	_
104	wild-type	wild-type	JJ	_	_	_
105	,	,	,	_	_	_
106	A600	a600	NN	_	_	_
107	=	=	JJ	_	_	_
108	0.4	0.4	CD	_	_	_
109	on	on	IN	_	_	_
110	mannose	mannose	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	E.	e.	FW	_	_	_
113	coli	coli	FW	_	_	_
114	wild-type	wild-type	JJ	_	_	_
115	,	,	,	_	_	_
116	A600	a600	NN	_	_	_
117	=	=	JJ	_	_	_
118	0.5	0.5	CD	_	_	_
119	on	on	IN	_	_	_
120	mucus	mucus	NN	_	_	_
121	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
122	Escherichia	escherichia	FW	Organism	_	_
123	coli	coli	FW	Organism	_	_
124	str	str	FW	_	_	_
125	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	flhD-glucose	flhd-glucose	JJ	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	flhD-mannose	flhd-mannose	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	flhD-mucus-P1	flhd-mucus-p1	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	flhD-mucus-P2	flhd-mucus-p2	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	genotype	genotype	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	MG1655star-glucose	mg1655star-glucose	JJ	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	MG1655star-mannose	mg1655star-mannose	JJ	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	MG1655star-mucus-P1	mg1655star-mucus-p1	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	MG1655star-mucus-P2	mg1655star-mucus-p2	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
21	RMA	rma	NN	_	_	_
22	with	with	IN	_	_	_
23	quartile	quartile	JJ	_	_	_
24	normalization	normalization	NN	_	_	_
25	according	accord	VBG	_	_	_
26	to	to	TO	_	_	_
27	method	method	NN	_	_	_
28	of	of	IN	_	_	_
29	Irizarry	Irizarry	NNP	_	_	_
30	et	et	FW	_	_	_
31	al	al	FW	_	_	_
32	,	,	,	_	_	_
33	2003	2003	CD	_	_	_
34	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	raw	raw	JJ	_	_	_
3	.	.	.	_	_	_

1	cel	cel	NN	_	_	_
2	files	file	NNS	_	_	_
3	were	be	VBD	_	_	_
4	processed	process	VBN	_	_	_
5	in	in	IN	_	_	_
6	RMA	RMA	NNP	_	_	_
7	using	use	VBG	_	_	_
8	Bioconductor	Bioconductor	NNP	_	_	_
9	R	R	NNP	_	_	_
10	package	package	NN	_	_	_
11	:	:	:	_	_	_
12	affy	affy	VB	_	_	_
13	Version	Version	NNP	_	_	_
14	:	:	:	_	_	_
15	1.8.1	1.8.1	CD	_	_	_
16	Date	date	NN	_	_	_
17	:	:	:	_	_	_
18	2005-09-03	2005-09-03	CD	_	_	_
19	,	,	,	_	_	_
20	with	with	IN	_	_	_
21	the	the	DT	_	_	_
22	option	option	NN	_	_	_
23	Filter.genes	filter.genes	NNS	_	_	_
24	containing	contain	VBG	_	_	_
25	a	a	DT	_	_	_
26	subset	subset	NN	_	_	_
27	of	of	IN	_	_	_
28	probesets	probeset	NNS	_	_	_
29	corresponding	correspond	VBG	_	_	_
30	to	to	TO	_	_	_
31	MG1655	mg1655	NN	_	_	_
32	genes	gene	NNS	_	_	_
33	and	and	CC	_	_	_
34	intergenic	intergenic	JJ	_	_	_
35	regions	region	NNS	_	_	_
36	listed	list	VBN	_	_	_
37	in	in	IN	_	_	_
38	the	the	DT	_	_	_
39	matrix	matrix	NN	_	_	_
40	data	datum	NNS	_	_	_
41	.	.	.	_	_	_

1	Replicates	replicate	VBZ	_	_	_
2	were	be	VBD	_	_	_
3	averaged	average	VBN	_	_	_
4	for	for	IN	_	_	_
5	ratio	ratio	NN	_	_	_
6	calculations	calculation	NNS	_	_	_
7	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	WT-glucose-Rep1	wt-glucose-rep1	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	WT-glucose-Rep2	wt-glucose-rep2	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	WT-mannose	wt-mannose	JJ	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	WT-mucus-P1	wt-mucus-p1	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	WT-mucus-P2	wt-mucus-p2	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	1	1	CD	_	_	_
13	.	.	.	_	_	_

1	Use	Use	NNP	_	_	_
2	Agilent	Agilent	NNP	_	_	_
3	software	software	NN	_	_	_
4	Feature	Feature	NNP	_	_	_
5	Extraction	Extraction	NNP	_	_	_
6	to	to	TO	_	_	_
7	analyze	analyze	VB	_	_	_
8	spotted	spotted	JJ	_	_	_
9	arrays	array	NNS	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	252978410001	252978410001	CD	_	_	_
3	_	_	NN	_	_	_
4	B7A	b7a	NN	_	_	_
5	_	_	CD	_	_	_
6	CY5	cy5	NN	_	_	_
7	_	_	NN	_	_	_
8	BCE001MS16	bce001ms16	NN	_	_	_
9	_	_	CD	_	_	_
10	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	252978410001	252978410001	CD	_	_	_
13	_	_	NN	_	_	_
14	B7A	b7a	NN	_	_	_
15	_	_	CD	_	_	_
16	CY5	cy5	NN	_	_	_
17	_	_	NN	_	_	_
18	BCE022DS6	bce022ds6	NN	_	_	_
19	_	_	CD	_	_	_
20	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	252978410001	252978410001	CD	_	_	_
23	_	_	NN	_	_	_
24	B7A	b7a	NN	_	_	_
25	_	_	CD	_	_	_
26	CY5	cy5	NN	_	_	_
27	_	_	CD	_	_	_
28	BCE063MS14	bce063ms14	NN	_	_	_
29	_	_	CD	_	_	_
30	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	252978410001	252978410001	CD	_	_	_
33	_	_	NN	_	_	_
34	B7A	b7a	NN	_	_	_
35	_	_	CD	_	_	_
36	CY5	cy5	NN	_	_	_
37	_	_	SYM	_	_	_
38	ETP98015	etp98015	CD	_	_	_
39	_	_	SYM	_	_	_
40	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	252978410002	252978410002	CD	_	_	_
43	_	_	NN	_	_	_
44	B7A	b7a	NN	_	_	_
45	_	_	CD	_	_	_
46	CY5	cy5	NN	_	_	_
47	_	_	NN	_	_	_
48	BCE007	bce007	NN	_	_	_
49	_	_	CD	_	_	_
50	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	252978410002	252978410002	CD	_	_	_
53	_	_	NN	_	_	_
54	B7A	b7a	NN	_	_	_
55	_	_	CD	_	_	_
56	CY5	cy5	NN	_	_	_
57	_	_	CD	_	_	_
58	BCE041	bce041	NN	_	_	_
59	_	_	CD	_	_	_
60	MS11	ms11	NN	_	_	_
61	_	_	CD	_	_	_
62	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	252978410002	252978410002	CD	_	_	_
65	_	_	NN	_	_	_
66	B7A	b7a	NN	_	_	_
67	_	_	CD	_	_	_
68	CY5	cy5	NN	_	_	_
69	_	_	NN	_	_	_
70	BCE063	bce063	NN	_	_	_
71	_	_	CD	_	_	_
72	DS4	ds4	NN	_	_	_
73	_	_	CD	_	_	_
74	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	252978410002	252978410002	CD	_	_	_
77	_	_	NN	_	_	_
78	B7A	b7a	NN	_	_	_
79	_	_	CD	_	_	_
80	CY5	cy5	NN	_	_	_
81	_	_	SYM	_	_	_
82	ETP98028	etp98028	CD	_	_	_
83	_	_	SYM	_	_	_
84	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	252978410003	252978410003	CD	_	_	_
87	_	_	NN	_	_	_
88	B7A	b7a	NN	_	_	_
89	_	_	CD	_	_	_
90	CY5	cy5	NN	_	_	_
91	_	_	CD	_	_	_
92	C35662	c35662	NN	_	_	_
93	_	_	CD	_	_	_
94	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	252978410003	252978410003	CD	_	_	_
97	_	_	NN	_	_	_
98	B7A	b7a	NN	_	_	_
99	_	_	CD	_	_	_
100	CY5	cy5	NN	_	_	_
101	_	_	CD	_	_	_
102	ETP05	etp05	NN	_	_	_
103	_	_	NN	_	_	_
104	007	007	CD	_	_	_
105	_	_	SYM	_	_	_
106	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	252978410003	252978410003	CD	_	_	_
109	_	_	NN	_	_	_
110	B7A	b7a	NN	_	_	_
111	_	_	CD	_	_	_
112	CY5	cy5	NN	_	_	_
113	_	_	CD	_	_	_
114	ETP05	etp05	NN	_	_	_
115	_	_	NN	_	_	_
116	017	017	CD	_	_	_
117	_	_	SYM	_	_	_
118	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	252978410003	252978410003	CD	_	_	_
121	_	_	NN	_	_	_
122	B7A	b7a	NN	_	_	_
123	_	_	CD	_	_	_
124	CY5	cy5	NN	_	_	_
125	_	_	CD	_	_	_
126	ETP98062	etp98062	NN	_	_	_
127	_	_	CD	_	_	_
128	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	252978410004	252978410004	CD	_	_	_
131	_	_	NN	_	_	_
132	B7A	b7a	NN	_	_	_
133	_	_	CD	_	_	_
134	CY5	cy5	NN	_	_	_
135	_	_	NN	_	_	_
136	BCE003	bce003	NN	_	_	_
137	_	_	CD	_	_	_
138	DS5	ds5	NN	_	_	_
139	_	_	CD	_	_	_
140	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	252978410004	252978410004	CD	_	_	_
143	_	_	NN	_	_	_
144	B7A	b7a	NN	_	_	_
145	_	_	CD	_	_	_
146	CY5	cy5	NN	_	_	_
147	_	_	CD	_	_	_
148	BCE058	bce058	NN	_	_	_
149	_	_	CD	_	_	_
150	MS13	ms13	NN	_	_	_
151	_	_	CD	_	_	_
152	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	252978410004	252978410004	CD	_	_	_
155	_	_	NN	_	_	_
156	B7A	b7a	NN	_	_	_
157	_	_	CD	_	_	_
158	CY5	cy5	NN	_	_	_
159	_	_	NN	_	_	_
160	BCE069	bce069	NN	_	_	_
161	_	_	CD	_	_	_
162	MS9	ms9	NN	_	_	_
163	_	_	CD	_	_	_
164	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	252978410004	252978410004	CD	_	_	_
167	_	_	NN	_	_	_
168	B7A	b7a	NN	_	_	_
169	_	_	CD	_	_	_
170	CY5	cy5	NN	_	_	_
171	_	_	NN	_	_	_
172	BCE129	bce129	NN	_	_	_
173	_	_	CD	_	_	_
174	DS2	ds2	NN	_	_	_
175	_	_	CD	_	_	_
176	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	252978410005	252978410005	CD	_	_	_
179	_	_	NN	_	_	_
180	B7A	b7a	NN	_	_	_
181	_	_	CD	_	_	_
182	CY5	cy5	NN	_	_	_
183	_	_	CD	_	_	_
184	BCE008	bce008	NN	_	_	_
185	_	_	CD	_	_	_
186	MS13	ms13	NN	_	_	_
187	_	_	CD	_	_	_
188	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	252978410005	252978410005	CD	_	_	_
191	_	_	NN	_	_	_
192	B7A	b7a	NN	_	_	_
193	_	_	CD	_	_	_
194	CY5	cy5	NN	_	_	_
195	_	_	NN	_	_	_
196	BCE013	bce013	NN	_	_	_
197	_	_	CD	_	_	_
198	DS1	ds1	NN	_	_	_
199	_	_	CD	_	_	_
200	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	252978410005	252978410005	CD	_	_	_
203	_	_	NN	_	_	_
204	B7A	b7a	NN	_	_	_
205	_	_	CD	_	_	_
206	CY5	cy5	NN	_	_	_
207	_	_	NN	_	_	_
208	BCE035	bce035	NN	_	_	_
209	_	_	CD	_	_	_
210	MS8	ms8	NN	_	_	_
211	_	_	CD	_	_	_
212	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	252978410005	252978410005	CD	_	_	_
215	_	_	NN	_	_	_
216	B7A	b7a	NN	_	_	_
217	_	_	CD	_	_	_
218	CY5	cy5	NN	_	_	_
219	_	_	NN	_	_	_
220	BCE039	bce039	NN	_	_	_
221	_	_	CD	_	_	_
222	DS2	ds2	NN	_	_	_
223	_	_	CD	_	_	_
224	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	252978410006	252978410006	CD	_	_	_
227	_	_	NN	_	_	_
228	B7A	b7a	NN	_	_	_
229	_	_	CD	_	_	_
230	CY5	cy5	NN	_	_	_
231	_	_	CD	_	_	_
232	ETP05	etp05	NN	_	_	_
233	_	_	NN	_	_	_
234	012	012	CD	_	_	_
235	_	_	SYM	_	_	_
236	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	252978410006	252978410006	CD	_	_	_
239	_	_	NN	_	_	_
240	B7A	b7a	NN	_	_	_
241	_	_	CD	_	_	_
242	CY5	cy5	NN	_	_	_
243	_	_	CD	_	_	_
244	ETP05	etp05	NN	_	_	_
245	_	_	NN	_	_	_
246	019	019	CD	_	_	_
247	_	_	SYM	_	_	_
248	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	252978410006	252978410006	CD	_	_	_
251	_	_	NN	_	_	_
252	B7A	b7a	NN	_	_	_
253	_	_	CD	_	_	_
254	CY5	cy5	NN	_	_	_
255	_	_	CD	_	_	_
256	ETP05	etp05	NN	_	_	_
257	_	_	NN	_	_	_
258	026	026	CD	_	_	_
259	_	_	SYM	_	_	_
260	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
262	252978410006	252978410006	CD	_	_	_
263	_	_	NN	_	_	_
264	B7A	b7a	NN	_	_	_
265	_	_	CD	_	_	_
266	CY5	cy5	NN	_	_	_
267	_	_	CD	_	_	_
268	ETP05	etp05	NN	_	_	_
269	_	_	NN	_	_	_
270	044	044	CD	_	_	_
271	_	_	SYM	_	_	_
272	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	252978410007	252978410007	CD	_	_	_
275	_	_	NN	_	_	_
276	B7A	b7a	NN	_	_	_
277	_	_	CD	_	_	_
278	CY5	cy5	NN	_	_	_
279	_	_	CD	_	_	_
280	BCE002	bce002	NN	_	_	_
281	_	_	CD	_	_	_
282	MS12	ms12	NN	_	_	_
283	_	_	CD	_	_	_
284	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
286	252978410007	252978410007	CD	_	_	_
287	_	_	NN	_	_	_
288	B7A	b7a	NN	_	_	_
289	_	_	CD	_	_	_
290	CY5	cy5	NN	_	_	_
291	_	_	CD	_	_	_
292	BCE021	bce021	NN	_	_	_
293	_	_	CD	_	_	_
294	DS7	ds7	NN	_	_	_
295	_	_	CD	_	_	_
296	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
297	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
298	252978410007	252978410007	CD	_	_	_
299	_	_	NN	_	_	_
300	B7A	b7a	NN	_	_	_
301	_	_	CD	_	_	_
302	CY5	cy5	NN	_	_	_
303	_	_	NN	_	_	_
304	BCE049	bce049	NN	_	_	_
305	_	_	CD	_	_	_
306	MS9	ms9	NN	_	_	_
307	_	_	CD	_	_	_
308	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
310	252978410007	252978410007	CD	_	_	_
311	_	_	NN	_	_	_
312	B7A	b7a	NN	_	_	_
313	_	_	CD	_	_	_
314	CY5	cy5	NN	_	_	_
315	_	_	CD	_	_	_
316	ETP98061	etp98061	NN	_	_	_
317	_	_	CD	_	_	_
318	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
320	252978410008	252978410008	CD	_	_	_
321	_	_	NN	_	_	_
322	B7A	b7a	NN	_	_	_
323	_	_	CD	_	_	_
324	CY5	cy5	NN	_	_	_
325	_	_	SYM	_	_	_
326	180050	180050	CD	_	_	_
327	_	_	SYM	_	_	_
328	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
330	252978410008	252978410008	CD	_	_	_
331	_	_	NN	_	_	_
332	B7A	b7a	NN	_	_	_
333	_	_	CD	_	_	_
334	CY5	cy5	NN	_	_	_
335	_	_	CD	_	_	_
336	ETP98103	etp98103	NN	_	_	_
337	_	_	CD	_	_	_
338	CY3.mev.refIsIB.ou	cy3.mev.refisib.ou	NN	_	_	_
339	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
340	252978410008	252978410008	CD	_	_	_
341	_	_	NN	_	_	_
342	B7A	b7a	NN	_	_	_
343	_	_	CD	_	_	_
344	CY5	cy5	NN	_	_	_
345	_	_	CD	_	_	_
346	ETP98111	etp98111	NN	_	_	_
347	_	_	CD	_	_	_
348	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	252978410008	252978410008	CD	_	_	_
351	_	_	NN	_	_	_
352	B7A	b7a	NN	_	_	_
353	_	_	CD	_	_	_
354	CY5	cy5	NN	_	_	_
355	_	_	CD	_	_	_
356	TW03741	tw03741	NN	_	_	_
357	_	_	CD	_	_	_
358	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
359	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
360	252978410009	252978410009	CD	_	_	_
361	_	_	NN	_	_	_
362	B7A	b7a	NN	_	_	_
363	_	_	CD	_	_	_
364	CY5	cy5	NN	_	_	_
365	_	_	CD	_	_	_
366	E1787	e1787	NN	_	_	_
367	_	_	CD	_	_	_
368	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
369	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
370	252978410009	252978410009	CD	_	_	_
371	_	_	NN	_	_	_
372	B7A	b7a	NN	_	_	_
373	_	_	CD	_	_	_
374	CY5	cy5	NN	_	_	_
375	_	_	CD	_	_	_
376	E747	e747	NN	_	_	_
377	_	_	NN	_	_	_
378	0	0	CD	_	_	_
379	_	_	SYM	_	_	_
380	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
381	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
382	252978410009	252978410009	CD	_	_	_
383	_	_	NN	_	_	_
384	B7A	b7a	NN	_	_	_
385	_	_	CD	_	_	_
386	CY5	cy5	NN	_	_	_
387	_	_	CD	_	_	_
388	F595C	f595c	NN	_	_	_
389	_	_	CD	_	_	_
390	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
392	252978410009	252978410009	CD	_	_	_
393	_	_	NN	_	_	_
394	B7A	b7a	NN	_	_	_
395	_	_	CD	_	_	_
396	CY5	cy5	NN	_	_	_
397	_	_	CD	_	_	_
398	WS3572A1.mev.refIsIB.out	ws3572a1.mev.refisib.out	NN	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	252978410010	252978410010	CD	_	_	_
401	_	_	NN	_	_	_
402	B7A	b7a	NN	_	_	_
403	_	_	CD	_	_	_
404	CY5	cy5	NN	_	_	_
405	_	_	NN	_	_	_
406	229	229	CD	_	_	_
407	_	_	NN	_	_	_
408	1	1	CD	_	_	_
409	_	_	NN	_	_	_
410	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
412	252978410010	252978410010	CD	_	_	_
413	_	_	NN	_	_	_
414	B7A	b7a	NN	_	_	_
415	_	_	CD	_	_	_
416	CY5	cy5	NN	_	_	_
417	_	_	CD	_	_	_
418	ICDDR	icddr	NN	_	_	_
419	_	_	NN	_	_	_
420	B	b	NN	_	_	_
421	_	_	CD	_	_	_
422	p13	p13	NN	_	_	_
423	_	_	CD	_	_	_
424	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
425	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
426	252978410010	252978410010	CD	_	_	_
427	_	_	NN	_	_	_
428	B7A	b7a	NN	_	_	_
429	_	_	CD	_	_	_
430	CY5	cy5	NN	_	_	_
431	_	_	CD	_	_	_
432	ICDDR	icddr	NN	_	_	_
433	_	_	NN	_	_	_
434	B	b	NN	_	_	_
435	_	_	CD	_	_	_
436	p1	p1	NN	_	_	_
437	_	_	CD	_	_	_
438	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
439	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
440	252978410010	252978410010	CD	_	_	_
441	_	_	NN	_	_	_
442	B7A	b7a	NN	_	_	_
443	_	_	CD	_	_	_
444	CY5	cy5	NN	_	_	_
445	_	_	CD	_	_	_
446	ICDDR	icddr	NN	_	_	_
447	_	_	NN	_	_	_
448	B	b	NN	_	_	_
449	_	_	CD	_	_	_
450	p4	p4	NN	_	_	_
451	_	_	CD	_	_	_
452	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
453	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
454	252978410011	252978410011	CD	_	_	_
455	_	_	NN	_	_	_
456	B7A	b7a	NN	_	_	_
457	_	_	CD	_	_	_
458	CY5	cy5	NN	_	_	_
459	_	_	CD	_	_	_
460	DS26	ds26	NN	_	_	_
461	_	_	NN	_	_	_
462	1	1	CD	_	_	_
463	_	_	NN	_	_	_
464	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
465	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
466	252978410011	252978410011	CD	_	_	_
467	_	_	NN	_	_	_
468	B7A	b7a	NN	_	_	_
469	_	_	CD	_	_	_
470	CY5	cy5	NN	_	_	_
471	_	_	CD	_	_	_
472	E1777	e1777	NN	_	_	_
473	_	_	CD	_	_	_
474	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
475	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
476	252978410011	252978410011	CD	_	_	_
477	_	_	NN	_	_	_
478	B7A	b7a	NN	_	_	_
479	_	_	CD	_	_	_
480	CY5	cy5	NN	_	_	_
481	_	_	CD	_	_	_
482	E9034A	e9034a	NN	_	_	_
483	_	_	CD	_	_	_
484	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
485	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
486	252978410011	252978410011	CD	_	_	_
487	_	_	NN	_	_	_
488	B7A	b7a	NN	_	_	_
489	_	_	CD	_	_	_
490	CY5	cy5	NN	_	_	_
491	_	_	CD	_	_	_
492	NN	NN	NNP	_	_	_
493	_	_	SYM	_	_	_
494	34	34	CD	_	_	_
495	_	_	NN	_	_	_
496	1	1	CD	_	_	_
497	_	_	NN	_	_	_
498	3	3	CD	_	_	_
499	_	_	NN	_	_	_
500	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
501	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
502	252978410012	252978410012	CD	_	_	_
503	_	_	NN	_	_	_
504	B7A	b7a	NN	_	_	_
505	_	_	CD	_	_	_
506	CY5	cy5	NN	_	_	_
507	_	_	NN	_	_	_
508	42	42	CD	_	_	_
509	_	_	NN	_	_	_
510	1	1	CD	_	_	_
511	_	_	NN	_	_	_
512	C1	c1	NN	_	_	_
513	_	_	CD	_	_	_
514	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
515	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
516	252978410012	252978410012	CD	_	_	_
517	_	_	NN	_	_	_
518	B7A	b7a	NN	_	_	_
519	_	_	CD	_	_	_
520	CY5	cy5	NN	_	_	_
521	_	_	CD	_	_	_
522	ETEC	ETEC	NNP	_	_	_
523	_	_	SYM	_	_	_
524	18	18	CD	_	_	_
525	_	_	NN	_	_	_
526	2	2	CD	_	_	_
527	_	_	CD	_	_	_
528	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
529	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
530	252978410012	252978410012	CD	_	_	_
531	_	_	NN	_	_	_
532	B7A	b7a	NN	_	_	_
533	_	_	CD	_	_	_
534	CY5	cy5	NN	_	_	_
535	_	_	CD	_	_	_
536	ICDDR	icddr	NN	_	_	_
537	_	_	NN	_	_	_
538	B	b	NN	_	_	_
539	_	_	CD	_	_	_
540	p12	p12	NN	_	_	_
541	_	_	CD	_	_	_
542	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
543	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
544	252978410012	252978410012	CD	_	_	_
545	_	_	NN	_	_	_
546	B7A	b7a	NN	_	_	_
547	_	_	CD	_	_	_
548	CY5	cy5	NN	_	_	_
549	_	_	CD	_	_	_
550	LSN02	lsn02	NN	_	_	_
551	_	_	CD	_	_	_
552	012560	012560	CD	_	_	_
553	_	_	NN	_	_	_
554	A	a	DT	_	_	_
555	_	_	SYM	_	_	_
556	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
557	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
558	252978410013	252978410013	CD	_	_	_
559	_	_	NN	_	_	_
560	B7A	b7a	NN	_	_	_
561	_	_	CD	_	_	_
562	CY5	cy5	NN	_	_	_
563	_	_	SYM	_	_	_
564	180600	180600	CD	_	_	_
565	_	_	SYM	_	_	_
566	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
567	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
568	252978410013	252978410013	CD	_	_	_
569	_	_	NN	_	_	_
570	B7A	b7a	NN	_	_	_
571	_	_	CD	_	_	_
572	CY5	cy5	NN	_	_	_
573	_	_	SYM	_	_	_
574	ETEC	etec	NNS	_	_	_
575	_	_	VBP	_	_	_
576	10	10	CD	_	_	_
577	_	_	SYM	_	_	_
578	1	1	CD	_	_	_
579	_	_	CD	_	_	_
580	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
581	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
582	252978410013	252978410013	CD	_	_	_
583	_	_	NN	_	_	_
584	B7A	b7a	NN	_	_	_
585	_	_	CD	_	_	_
586	CY5	cy5	NN	_	_	_
587	_	_	CD	_	_	_
588	TW3574	tw3574	NN	_	_	_
589	_	_	CD	_	_	_
590	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
591	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
592	252978410013	252978410013	CD	_	_	_
593	_	_	NN	_	_	_
594	B7A	b7a	NN	_	_	_
595	_	_	CD	_	_	_
596	CY5	cy5	NN	_	_	_
597	_	_	NN	_	_	_
598	TW3585	tw3585	NN	_	_	_
599	_	_	CD	_	_	_
600	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
601	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
602	252978410014	252978410014	CD	_	_	_
603	_	_	NN	_	_	_
604	B7A	b7a	NN	_	_	_
605	_	_	CD	_	_	_
606	CY5	cy5	NN	_	_	_
607	_	_	CD	_	_	_
608	E20738A	e20738a	NN	_	_	_
609	_	_	CD	_	_	_
610	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
611	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
612	252978410014	252978410014	CD	_	_	_
613	_	_	NN	_	_	_
614	B7A	b7a	NN	_	_	_
615	_	_	CD	_	_	_
616	CY5	cy5	NN	_	_	_
617	_	_	CD	_	_	_
618	PUTI	PUTI	NNP	_	_	_
619	_	_	SYM	_	_	_
620	O26	o26	CD	_	_	_
621	_	_	SYM	_	_	_
622	UMN	UMN	NNP	_	_	_
623	_	_	SYM	_	_	_
624	O26	o26	CD	_	_	_
625	_	_	SYM	_	_	_
626	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
627	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
628	252978410014	252978410014	CD	_	_	_
629	_	_	NN	_	_	_
630	B7A	b7a	NN	_	_	_
631	_	_	CD	_	_	_
632	CY5	cy5	NN	_	_	_
633	_	_	CD	_	_	_
634	sPRH450	sprh450	NN	_	_	_
635	_	_	CD	_	_	_
636	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
637	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
638	252978410015	252978410015	CD	_	_	_
639	_	_	NN	_	_	_
640	B7A	b7a	NN	_	_	_
641	_	_	CD	_	_	_
642	CY5	cy5	NN	_	_	_
643	_	_	CD	_	_	_
644	E1392	e1392	NN	_	_	_
645	_	_	CD	_	_	_
646	75	75	CD	_	_	_
647	_	_	SYM	_	_	_
648	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
649	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
650	252978410015	252978410015	CD	_	_	_
651	_	_	NN	_	_	_
652	B7A	b7a	NN	_	_	_
653	_	_	CD	_	_	_
654	CY5	cy5	NN	_	_	_
655	_	_	CD	_	_	_
656	ICDDR	icddr	NN	_	_	_
657	_	_	NN	_	_	_
658	B	b	NN	_	_	_
659	_	_	CD	_	_	_
660	p5	p5	NN	_	_	_
661	_	_	CD	_	_	_
662	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
663	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
664	252978410015	252978410015	CD	_	_	_
665	_	_	NN	_	_	_
666	B7A	b7a	NN	_	_	_
667	_	_	CD	_	_	_
668	CY5	cy5	NN	_	_	_
669	_	_	CD	_	_	_
670	ICDDR	icddr	NN	_	_	_
671	_	_	NN	_	_	_
672	B	b	NN	_	_	_
673	_	_	CD	_	_	_
674	p8	p8	NN	_	_	_
675	_	_	CD	_	_	_
676	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
677	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
678	252978410015	252978410015	CD	_	_	_
679	_	_	NN	_	_	_
680	B7A	b7a	NN	_	_	_
681	_	_	CD	_	_	_
682	CY5	cy5	NN	_	_	_
683	_	_	CD	_	_	_
684	sPRH613	sprh613	NN	_	_	_
685	_	_	CD	_	_	_
686	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
687	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
688	252978410016	252978410016	CD	_	_	_
689	_	_	NN	_	_	_
690	B7A	b7a	NN	_	_	_
691	_	_	CD	_	_	_
692	CY5	cy5	NN	_	_	_
693	_	_	CD	_	_	_
694	D02	d02	NN	_	_	_
695	_	_	NN	_	_	_
696	2	2	CD	_	_	_
697	_	_	CD	_	_	_
698	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
699	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
700	252978410016	252978410016	CD	_	_	_
701	_	_	NN	_	_	_
702	B7A	b7a	NN	_	_	_
703	_	_	CD	_	_	_
704	CY5	cy5	NN	_	_	_
705	_	_	NN	_	_	_
706	E1785	e1785	NN	_	_	_
707	_	_	CD	_	_	_
708	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
709	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
710	252978410016	252978410016	CD	_	_	_
711	_	_	NN	_	_	_
712	B7A	b7a	NN	_	_	_
713	_	_	CD	_	_	_
714	CY5	cy5	NN	_	_	_
715	_	_	SYM	_	_	_
716	ETP98068	etp98068	CD	_	_	_
717	_	_	SYM	_	_	_
718	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
719	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
720	252978410016	252978410016	CD	_	_	_
721	_	_	NN	_	_	_
722	B7A	b7a	NN	_	_	_
723	_	_	CD	_	_	_
724	CY5	cy5	NN	_	_	_
725	_	_	CD	_	_	_
726	ICDDR	icddr	NN	_	_	_
727	_	_	NN	_	_	_
728	B	b	NN	_	_	_
729	_	_	CD	_	_	_
730	p11	p11	NN	_	_	_
731	_	_	CD	_	_	_
732	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
733	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
734	252978410017	252978410017	CD	_	_	_
735	_	_	NN	_	_	_
736	B7A	b7a	NN	_	_	_
737	_	_	CD	_	_	_
738	CY5	cy5	NN	_	_	_
739	_	_	NN	_	_	_
740	C35776	c35776	NN	_	_	_
741	_	_	CD	_	_	_
742	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
743	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
744	252978410017	252978410017	CD	_	_	_
745	_	_	NN	_	_	_
746	B7A	b7a	NN	_	_	_
747	_	_	CD	_	_	_
748	CY5	cy5	NN	_	_	_
749	_	_	CD	_	_	_
750	E1788	e1788	NN	_	_	_
751	_	_	CD	_	_	_
752	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
753	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
754	252978410017	252978410017	CD	_	_	_
755	_	_	NN	_	_	_
756	B7A	b7a	NN	_	_	_
757	_	_	CD	_	_	_
758	CY5	cy5	NN	_	_	_
759	_	_	CD	_	_	_
760	ETEC	ETEC	NNP	_	_	_
761	_	_	NNP	_	_	_
762	JURUA	JURUA	NNP	_	_	_
763	_	_	VBD	_	_	_
764	18	18	CD	_	_	_
765	_	_	SYM	_	_	_
766	11	11	CD	_	_	_
767	_	_	SYM	_	_	_
768	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
769	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
770	252978410017	252978410017	CD	_	_	_
771	_	_	NN	_	_	_
772	B7A	b7a	NN	_	_	_
773	_	_	CD	_	_	_
774	CY5	cy5	NN	_	_	_
775	_	_	CD	_	_	_
776	ICDDR	icddr	NN	_	_	_
777	_	_	NN	_	_	_
778	B	b	NN	_	_	_
779	_	_	CD	_	_	_
780	p9	p9	NN	_	_	_
781	_	_	CD	_	_	_
782	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
783	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
784	252978410018	252978410018	CD	_	_	_
785	_	_	NN	_	_	_
786	B7A	b7a	NN	_	_	_
787	_	_	CD	_	_	_
788	CY5	cy5	NN	_	_	_
789	_	_	CD	_	_	_
790	ARG3	arg3	NN	_	_	_
791	_	_	CD	_	_	_
792	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
793	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
794	252978410018	252978410018	CD	_	_	_
795	_	_	NN	_	_	_
796	B7A	b7a	NN	_	_	_
797	_	_	CD	_	_	_
798	CY5	cy5	NN	_	_	_
799	_	_	CD	_	_	_
800	E1792	e1792	NN	_	_	_
801	_	_	CD	_	_	_
802	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
803	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
804	252978410018	252978410018	CD	_	_	_
805	_	_	NN	_	_	_
806	B7A	b7a	NN	_	_	_
807	_	_	CD	_	_	_
808	CY5	cy5	NN	_	_	_
809	_	_	NN	_	_	_
810	MG1655	mg1655	NN	_	_	_
811	_	_	CD	_	_	_
812	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
813	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
814	252978410018	252978410018	CD	_	_	_
815	_	_	NN	_	_	_
816	B7A	b7a	NN	_	_	_
817	_	_	CD	_	_	_
818	CY5	cy5	NN	_	_	_
819	_	_	CD	_	_	_
820	sPRH21	sprh21	NN	_	_	_
821	_	_	CD	_	_	_
822	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
823	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
824	252978410019	252978410019	CD	_	_	_
825	_	_	NN	_	_	_
826	B7A	b7a	NN	_	_	_
827	_	_	CD	_	_	_
828	CY5	cy5	NN	_	_	_
829	_	_	CD	_	_	_
830	E1786	e1786	NN	_	_	_
831	_	_	CD	_	_	_
832	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
833	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
834	252978410019	252978410019	CD	_	_	_
835	_	_	NN	_	_	_
836	B7A	b7a	NN	_	_	_
837	_	_	CD	_	_	_
838	CY5	cy5	NN	_	_	_
839	_	_	CD	_	_	_
840	WS0115A	ws0115a	NN	_	_	_
841	_	_	CD	_	_	_
842	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
843	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
844	252978410020	252978410020	CD	_	_	_
845	_	_	NN	_	_	_
846	B7A	b7a	NN	_	_	_
847	_	_	CD	_	_	_
848	CY5	cy5	NN	_	_	_
849	_	_	SYM	_	_	_
850	179550	179550	CD	_	_	_
851	_	_	SYM	_	_	_
852	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
853	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
854	252978410020	252978410020	CD	_	_	_
855	_	_	NN	_	_	_
856	B7A	b7a	NN	_	_	_
857	_	_	CD	_	_	_
858	CY5	cy5	NN	_	_	_
859	_	_	NN	_	_	_
860	BCE046	bce046	NN	_	_	_
861	_	_	CD	_	_	_
862	DS2	ds2	NN	_	_	_
863	_	_	CD	_	_	_
864	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
865	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
866	252978410020	252978410020	CD	_	_	_
867	_	_	NN	_	_	_
868	B7A	b7a	NN	_	_	_
869	_	_	CD	_	_	_
870	CY5	cy5	NN	_	_	_
871	_	_	NN	_	_	_
872	BCE046	bce046	NN	_	_	_
873	_	_	CD	_	_	_
874	DS7	ds7	NN	_	_	_
875	_	_	CD	_	_	_
876	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
877	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
878	252978410020	252978410020	CD	_	_	_
879	_	_	NN	_	_	_
880	B7A	b7a	NN	_	_	_
881	_	_	CD	_	_	_
882	CY5	cy5	NN	_	_	_
883	_	_	CD	_	_	_
884	ETP98114	etp98114	NN	_	_	_
885	_	_	CD	_	_	_
886	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
887	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
888	252978410021	252978410021	CD	_	_	_
889	_	_	NN	_	_	_
890	B7A	b7a	NN	_	_	_
891	_	_	CD	_	_	_
892	CY5	cy5	NN	_	_	_
893	_	_	SYM	_	_	_
894	1080200	1080200	CD	_	_	_
895	_	_	SYM	_	_	_
896	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
897	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
898	252978410021	252978410021	CD	_	_	_
899	_	_	NN	_	_	_
900	B7A	b7a	NN	_	_	_
901	_	_	CD	_	_	_
902	CY5	cy5	NN	_	_	_
903	_	_	CD	_	_	_
904	BCE008	bce008	NN	_	_	_
905	_	_	CD	_	_	_
906	MS1	ms1	NN	_	_	_
907	_	_	CD	_	_	_
908	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
909	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
910	252978410021	252978410021	CD	_	_	_
911	_	_	NN	_	_	_
912	B7A	b7a	NN	_	_	_
913	_	_	CD	_	_	_
914	CY5	cy5	NN	_	_	_
915	_	_	CD	_	_	_
916	BCE054	bce054	NN	_	_	_
917	_	_	CD	_	_	_
918	MS24	ms24	NN	_	_	_
919	_	_	CD	_	_	_
920	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
921	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
922	252978410021	252978410021	CD	_	_	_
923	_	_	NN	_	_	_
924	B7A	b7a	NN	_	_	_
925	_	_	CD	_	_	_
926	CY5	cy5	NN	_	_	_
927	_	_	CD	_	_	_
928	ETP05	etp05	NN	_	_	_
929	_	_	NN	_	_	_
930	046	046	CD	_	_	_
931	_	_	SYM	_	_	_
932	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
933	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
934	252978410022	252978410022	CD	_	_	_
935	_	_	NN	_	_	_
936	B7A	b7a	NN	_	_	_
937	_	_	CD	_	_	_
938	CY5	cy5	NN	_	_	_
939	_	_	NN	_	_	_
940	BCE062	bce062	NN	_	_	_
941	_	_	CD	_	_	_
942	DS2	ds2	NN	_	_	_
943	_	_	CD	_	_	_
944	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
945	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
946	252978410022	252978410022	CD	_	_	_
947	_	_	NN	_	_	_
948	B7A	b7a	NN	_	_	_
949	_	_	CD	_	_	_
950	CY5	cy5	NN	_	_	_
951	_	_	NN	_	_	_
952	BCE069	bce069	NN	_	_	_
953	_	_	CD	_	_	_
954	DS2	ds2	NN	_	_	_
955	_	_	CD	_	_	_
956	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
957	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
958	252978410022	252978410022	CD	_	_	_
959	_	_	NN	_	_	_
960	B7A	b7a	NN	_	_	_
961	_	_	CD	_	_	_
962	CY5	cy5	NN	_	_	_
963	_	_	SYM	_	_	_
964	ETP98038	etp98038	CD	_	_	_
965	_	_	SYM	_	_	_
966	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
967	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
968	252978410022	252978410022	CD	_	_	_
969	_	_	NN	_	_	_
970	B7A	b7a	NN	_	_	_
971	_	_	CD	_	_	_
972	CY5	cy5	NN	_	_	_
973	_	_	CD	_	_	_
974	ETP98042	etp98042	NN	_	_	_
975	_	_	CD	_	_	_
976	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
977	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
978	252978410023	252978410023	CD	_	_	_
979	_	_	NN	_	_	_
980	B7A	b7a	NN	_	_	_
981	_	_	CD	_	_	_
982	CY5	cy5	NN	_	_	_
983	_	_	SYM	_	_	_
984	173150	173150	CD	_	_	_
985	_	_	SYM	_	_	_
986	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
987	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
988	252978410023	252978410023	CD	_	_	_
989	_	_	NN	_	_	_
990	B7A	b7a	NN	_	_	_
991	_	_	CD	_	_	_
992	CY5	cy5	NN	_	_	_
993	_	_	SYM	_	_	_
994	174750	174750	CD	_	_	_
995	_	_	SYM	_	_	_
996	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
997	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
998	252978410023	252978410023	CD	_	_	_
999	_	_	NN	_	_	_
1000	B7A	b7a	NN	_	_	_
1001	_	_	CD	_	_	_
1002	CY5	cy5	NN	_	_	_
1003	_	_	SYM	_	_	_
1004	178850	178850	CD	_	_	_
1005	_	_	SYM	_	_	_
1006	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1007	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1008	252978410023	252978410023	CD	_	_	_
1009	_	_	NN	_	_	_
1010	B7A	b7a	NN	_	_	_
1011	_	_	CD	_	_	_
1012	CY5	cy5	NN	_	_	_
1013	_	_	SYM	_	_	_
1014	ETP98115	etp98115	CD	_	_	_
1015	_	_	SYM	_	_	_
1016	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1017	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1018	252978410024	252978410024	CD	_	_	_
1019	_	_	NN	_	_	_
1020	B7A	b7a	NN	_	_	_
1021	_	_	CD	_	_	_
1022	CY5	cy5	NN	_	_	_
1023	_	_	CD	_	_	_
1024	BCE018	bce018	NN	_	_	_
1025	_	_	CD	_	_	_
1026	DS6	ds6	NN	_	_	_
1027	_	_	CD	_	_	_
1028	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1029	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1030	252978410024	252978410024	CD	_	_	_
1031	_	_	NN	_	_	_
1032	B7A	b7a	NN	_	_	_
1033	_	_	CD	_	_	_
1034	CY5	cy5	NN	_	_	_
1035	_	_	CD	_	_	_
1036	BCE019	bce019	NN	_	_	_
1037	_	_	CD	_	_	_
1038	MS16	ms16	NN	_	_	_
1039	_	_	CD	_	_	_
1040	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1041	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1042	252978410024	252978410024	CD	_	_	_
1043	_	_	NN	_	_	_
1044	B7A	b7a	NN	_	_	_
1045	_	_	CD	_	_	_
1046	CY5	cy5	NN	_	_	_
1047	_	_	NN	_	_	_
1048	BCE046	bce046	NN	_	_	_
1049	_	_	CD	_	_	_
1050	MS16	ms16	NN	_	_	_
1051	_	_	CD	_	_	_
1052	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1053	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1054	252978410024	252978410024	CD	_	_	_
1055	_	_	NN	_	_	_
1056	B7A	b7a	NN	_	_	_
1057	_	_	CD	_	_	_
1058	CY5	cy5	NN	_	_	_
1059	_	_	NN	_	_	_
1060	BCE069	bce069	NN	_	_	_
1061	_	_	CD	_	_	_
1062	MS15	ms15	NN	_	_	_
1063	_	_	CD	_	_	_
1064	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1065	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1066	252978410025	252978410025	CD	_	_	_
1067	_	_	NN	_	_	_
1068	B7A	b7a	NN	_	_	_
1069	_	_	CD	_	_	_
1070	CY5	cy5	NN	_	_	_
1071	_	_	NN	_	_	_
1072	BCE007	bce007	NN	_	_	_
1073	_	_	CD	_	_	_
1074	MS11	ms11	NN	_	_	_
1075	_	_	CD	_	_	_
1076	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1077	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1078	252978410025	252978410025	CD	_	_	_
1079	_	_	NN	_	_	_
1080	B7A	b7a	NN	_	_	_
1081	_	_	CD	_	_	_
1082	CY5	cy5	NN	_	_	_
1083	_	_	NN	_	_	_
1084	BCE039	bce039	NN	_	_	_
1085	_	_	CD	_	_	_
1086	MS13	ms13	NN	_	_	_
1087	_	_	CD	_	_	_
1088	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1089	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1090	252978410025	252978410025	CD	_	_	_
1091	_	_	NN	_	_	_
1092	B7A	b7a	NN	_	_	_
1093	_	_	CD	_	_	_
1094	CY5	cy5	NN	_	_	_
1095	_	_	NN	_	_	_
1096	C35959	c35959	NN	_	_	_
1097	_	_	CD	_	_	_
1098	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1099	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1100	252978410025	252978410025	CD	_	_	_
1101	_	_	NN	_	_	_
1102	B7A	b7a	NN	_	_	_
1103	_	_	CD	_	_	_
1104	CY5	cy5	NN	_	_	_
1105	_	_	CD	_	_	_
1106	ETP05	etp05	NN	_	_	_
1107	_	_	NN	_	_	_
1108	050	050	CD	_	_	_
1109	_	_	SYM	_	_	_
1110	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1112	252978410026	252978410026	CD	_	_	_
1113	_	_	NN	_	_	_
1114	B7A	b7a	NN	_	_	_
1115	_	_	CD	_	_	_
1116	CY5	cy5	NN	_	_	_
1117	_	_	CD	_	_	_
1118	E24377A	e24377a	NN	_	_	_
1119	_	_	CD	_	_	_
1120	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1122	252978410026	252978410026	CD	_	_	_
1123	_	_	NN	_	_	_
1124	B7A	b7a	NN	_	_	_
1125	_	_	CD	_	_	_
1126	CY5	cy5	NN	_	_	_
1127	_	_	CD	_	_	_
1128	sPRH	sprh	NN	_	_	_
1129	_	_	NN	_	_	_
1130	418	418	CD	_	_	_
1131	_	_	SYM	_	_	_
1132	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1134	252978410026	252978410026	CD	_	_	_
1135	_	_	NN	_	_	_
1136	B7A	b7a	NN	_	_	_
1137	_	_	CD	_	_	_
1138	CY5	cy5	NN	_	_	_
1139	_	_	CD	_	_	_
1140	WS1896A	ws1896a	NN	_	_	_
1141	_	_	CD	_	_	_
1142	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1144	252978410026	252978410026	CD	_	_	_
1145	_	_	NN	_	_	_
1146	B7A	b7a	NN	_	_	_
1147	_	_	CD	_	_	_
1148	CY5	cy5	NN	_	_	_
1149	_	_	CD	_	_	_
1150	WS2068A	ws2068a	NN	_	_	_
1151	_	_	CD	_	_	_
1152	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1154	252978410027	252978410027	CD	_	_	_
1155	_	_	NN	_	_	_
1156	B7A	b7a	NN	_	_	_
1157	_	_	CD	_	_	_
1158	CY5	cy5	NN	_	_	_
1159	_	_	CD	_	_	_
1160	LSN03	lsn03	NN	_	_	_
1161	_	_	SYM	_	_	_
1162	016011	016011	CD	_	_	_
1163	_	_	CD	_	_	_
1164	A	a	DT	_	_	_
1165	_	_	NN	_	_	_
1166	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1168	252978410027	252978410027	CD	_	_	_
1169	_	_	NN	_	_	_
1170	B7A	b7a	NN	_	_	_
1171	_	_	CD	_	_	_
1172	CY5	cy5	NN	_	_	_
1173	_	_	CD	_	_	_
1174	sPRH	sprh	NN	_	_	_
1175	_	_	NN	_	_	_
1176	414	414	CD	_	_	_
1177	_	_	SYM	_	_	_
1178	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1180	252978410027	252978410027	CD	_	_	_
1181	_	_	NN	_	_	_
1182	B7A	b7a	NN	_	_	_
1183	_	_	CD	_	_	_
1184	CY5	cy5	NN	_	_	_
1185	_	_	CD	_	_	_
1186	sPRH	sprh	NN	_	_	_
1187	_	_	NN	_	_	_
1188	420	420	CD	_	_	_
1189	_	_	SYM	_	_	_
1190	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1192	252978410027	252978410027	CD	_	_	_
1193	_	_	NN	_	_	_
1194	B7A	b7a	NN	_	_	_
1195	_	_	CD	_	_	_
1196	ETEC20	etec20	NN	_	_	_
1197	_	_	SYM	_	_	_
1198	10	10	CD	_	_	_
1199	_	_	SYM	_	_	_
1200	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1202	252978410028	252978410028	CD	_	_	_
1203	_	_	NN	_	_	_
1204	B7A	b7a	NN	_	_	_
1205	_	_	CD	_	_	_
1206	CY5	cy5	NN	_	_	_
1207	_	_	CD	_	_	_
1208	ETP98073	etp98073	NN	_	_	_
1209	_	_	CD	_	_	_
1210	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1212	252978410028	252978410028	CD	_	_	_
1213	_	_	NN	_	_	_
1214	B7A	b7a	NN	_	_	_
1215	_	_	CD	_	_	_
1216	CY5	cy5	NN	_	_	_
1217	_	_	CD	_	_	_
1218	TW3439	tw3439	NN	_	_	_
1219	_	_	CD	_	_	_
1220	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1222	252978410028	252978410028	CD	_	_	_
1223	_	_	NN	_	_	_
1224	B7A	b7a	NN	_	_	_
1225	_	_	CD	_	_	_
1226	CY5	cy5	NN	_	_	_
1227	_	_	CD	_	_	_
1228	TW3576	tw3576	NN	_	_	_
1229	_	_	CD	_	_	_
1230	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1232	252978410028	252978410028	CD	_	_	_
1233	_	_	NN	_	_	_
1234	B7A	b7a	NN	_	_	_
1235	_	_	CD	_	_	_
1236	CY5	cy5	NN	_	_	_
1237	_	_	CD	_	_	_
1238	WS3080A	ws3080a	NN	_	_	_
1239	_	_	CD	_	_	_
1240	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1242	252978410029	252978410029	CD	_	_	_
1243	_	_	NN	_	_	_
1244	B7A	b7a	NN	_	_	_
1245	_	_	CD	_	_	_
1246	CY5	cy5	NN	_	_	_
1247	_	_	CD	_	_	_
1248	sPRH	sprh	NN	_	_	_
1249	_	_	NN	_	_	_
1250	403	403	CD	_	_	_
1251	_	_	SYM	_	_	_
1252	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1254	252978410029	252978410029	CD	_	_	_
1255	_	_	NN	_	_	_
1256	B7A	b7a	NN	_	_	_
1257	_	_	CD	_	_	_
1258	CY5	cy5	NN	_	_	_
1259	_	_	CD	_	_	_
1260	sPRH	sprh	NN	_	_	_
1261	_	_	NN	_	_	_
1262	443	443	CD	_	_	_
1263	_	_	SYM	_	_	_
1264	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1266	252978410029	252978410029	CD	_	_	_
1267	_	_	NN	_	_	_
1268	B7A	b7a	NN	_	_	_
1269	_	_	CD	_	_	_
1270	CY5	cy5	NN	_	_	_
1271	_	_	CD	_	_	_
1272	sPRH	sprh	NN	_	_	_
1273	_	_	NN	_	_	_
1274	604	604	CD	_	_	_
1275	_	_	SYM	_	_	_
1276	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1278	252978410029	252978410029	CD	_	_	_
1279	_	_	NN	_	_	_
1280	B7A	b7a	NN	_	_	_
1281	_	_	CD	_	_	_
1282	CY5	cy5	NN	_	_	_
1283	_	_	CD	_	_	_
1284	sPRH	sprh	NN	_	_	_
1285	_	_	NN	_	_	_
1286	606	606	CD	_	_	_
1287	_	_	SYM	_	_	_
1288	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1290	252978410030	252978410030	CD	_	_	_
1291	_	_	NN	_	_	_
1292	B7A	b7a	NN	_	_	_
1293	_	_	CD	_	_	_
1294	CY5	cy5	NN	_	_	_
1295	_	_	NN	_	_	_
1296	C36255	c36255	NN	_	_	_
1297	_	_	CD	_	_	_
1298	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1299	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1300	252978410030	252978410030	CD	_	_	_
1301	_	_	NN	_	_	_
1302	B7A	b7a	NN	_	_	_
1303	_	_	CD	_	_	_
1304	CY5	cy5	NN	_	_	_
1305	_	_	CD	_	_	_
1306	ETP05	etp05	NN	_	_	_
1307	_	_	NN	_	_	_
1308	008	008	CD	_	_	_
1309	_	_	SYM	_	_	_
1310	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1312	252978410030	252978410030	CD	_	_	_
1313	_	_	NN	_	_	_
1314	B7A	b7a	NN	_	_	_
1315	_	_	CD	_	_	_
1316	CY5	cy5	NN	_	_	_
1317	_	_	CD	_	_	_
1318	ETP98105	etp98105	NN	_	_	_
1319	_	_	CD	_	_	_
1320	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1321	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1322	252978410030	252978410030	CD	_	_	_
1323	_	_	NN	_	_	_
1324	B7A	b7a	NN	_	_	_
1325	_	_	CD	_	_	_
1326	ETP98066	etp98066	NN	_	_	_
1327	_	_	CD	_	_	_
1328	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1330	252978410031	252978410031	CD	_	_	_
1331	_	_	NN	_	_	_
1332	B7A	b7a	NN	_	_	_
1333	_	_	CD	_	_	_
1334	CY5	cy5	NN	_	_	_
1335	_	_	CD	_	_	_
1336	BCE054	bce054	NN	_	_	_
1337	_	_	CD	_	_	_
1338	DS4	ds4	NN	_	_	_
1339	_	_	CD	_	_	_
1340	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1341	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1342	252978410031	252978410031	CD	_	_	_
1343	_	_	NN	_	_	_
1344	B7A	b7a	NN	_	_	_
1345	_	_	CD	_	_	_
1346	CY5	cy5	NN	_	_	_
1347	_	_	CD	_	_	_
1348	BCE068	bce068	NN	_	_	_
1349	_	_	CD	_	_	_
1350	MS10	ms10	NN	_	_	_
1351	_	_	CD	_	_	_
1352	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1353	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1354	252978410031	252978410031	CD	_	_	_
1355	_	_	NN	_	_	_
1356	B7A	b7a	NN	_	_	_
1357	_	_	CD	_	_	_
1358	CY5	cy5	NN	_	_	_
1359	_	_	CD	_	_	_
1360	BCE068	bce068	NN	_	_	_
1361	_	_	CD	_	_	_
1362	MS23.mev.refIsIB.out	ms23.mev.refisib.out	NN	_	_	_
1363	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1364	252978410031	252978410031	CD	_	_	_
1365	_	_	NN	_	_	_
1366	B7A	b7a	NN	_	_	_
1367	_	_	CD	_	_	_
1368	CY5	cy5	NN	_	_	_
1369	_	_	CD	_	_	_
1370	ETP05	etp05	NN	_	_	_
1371	_	_	NN	_	_	_
1372	015	015	CD	_	_	_
1373	_	_	SYM	_	_	_
1374	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1376	252978410032	252978410032	CD	_	_	_
1377	_	_	NN	_	_	_
1378	B7A	b7a	NN	_	_	_
1379	_	_	CD	_	_	_
1380	CY5	cy5	NN	_	_	_
1381	_	_	CD	_	_	_
1382	BCE011	bce011	NN	_	_	_
1383	_	_	CD	_	_	_
1384	DS3	ds3	NN	_	_	_
1385	_	_	CD	_	_	_
1386	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1387	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1388	252978410032	252978410032	CD	_	_	_
1389	_	_	NN	_	_	_
1390	B7A	b7a	NN	_	_	_
1391	_	_	CD	_	_	_
1392	CY5	cy5	NN	_	_	_
1393	_	_	NN	_	_	_
1394	BCE049	bce049	NN	_	_	_
1395	_	_	CD	_	_	_
1396	DS3	ds3	NN	_	_	_
1397	_	_	CD	_	_	_
1398	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1400	252978410032	252978410032	CD	_	_	_
1401	_	_	NN	_	_	_
1402	B7A	b7a	NN	_	_	_
1403	_	_	CD	_	_	_
1404	CY5	cy5	NN	_	_	_
1405	_	_	NN	_	_	_
1406	BCE062	bce062	NN	_	_	_
1407	_	_	CD	_	_	_
1408	MS24	ms24	NN	_	_	_
1409	_	_	CD	_	_	_
1410	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1412	252978410032	252978410032	CD	_	_	_
1413	_	_	NN	_	_	_
1414	B7A	b7a	NN	_	_	_
1415	_	_	CD	_	_	_
1416	CY5	cy5	NN	_	_	_
1417	_	_	NN	_	_	_
1418	BCE066	bce066	NN	_	_	_
1419	_	_	CD	_	_	_
1420	DS5	ds5	NN	_	_	_
1421	_	_	CD	_	_	_
1422	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1423	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1424	252978410033	252978410033	CD	_	_	_
1425	_	_	NN	_	_	_
1426	B7A	b7a	NN	_	_	_
1427	_	_	CD	_	_	_
1428	CY5	cy5	NN	_	_	_
1429	_	_	NN	_	_	_
1430	BCE035	bce035	NN	_	_	_
1431	_	_	CD	_	_	_
1432	DS6	ds6	NN	_	_	_
1433	_	_	CD	_	_	_
1434	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1435	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1436	252978410033	252978410033	CD	_	_	_
1437	_	_	NN	_	_	_
1438	B7A	b7a	NN	_	_	_
1439	_	_	CD	_	_	_
1440	CY5	cy5	NN	_	_	_
1441	_	_	NN	_	_	_
1442	C35209	c35209	NN	_	_	_
1443	_	_	CD	_	_	_
1444	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1446	252978410033	252978410033	CD	_	_	_
1447	_	_	NN	_	_	_
1448	B7A	b7a	NN	_	_	_
1449	_	_	CD	_	_	_
1450	CY5	cy5	NN	_	_	_
1451	_	_	CD	_	_	_
1452	ETP	etp	NN	_	_	_
1453	_	_	SYM	_	_	_
1454	98004	98004	CD	_	_	_
1455	_	_	SYM	_	_	_
1456	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1457	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1458	252978410033	252978410033	CD	_	_	_
1459	_	_	NN	_	_	_
1460	B7A	b7a	NN	_	_	_
1461	_	_	CD	_	_	_
1462	CY5	cy5	NN	_	_	_
1463	_	_	CD	_	_	_
1464	ETP98056	etp98056	NN	_	_	_
1465	_	_	CD	_	_	_
1466	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1467	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1468	252978410034	252978410034	CD	_	_	_
1469	_	_	NN	_	_	_
1470	B7A	b7a	NN	_	_	_
1471	_	_	CD	_	_	_
1472	CY5	cy5	NN	_	_	_
1473	_	_	NN	_	_	_
1474	BCE005	bce005	NN	_	_	_
1475	_	_	CD	_	_	_
1476	MS23	ms23	NN	_	_	_
1477	_	_	CD	_	_	_
1478	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1479	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1480	252978410034	252978410034	CD	_	_	_
1481	_	_	NN	_	_	_
1482	B7A	b7a	NN	_	_	_
1483	_	_	CD	_	_	_
1484	CY5	cy5	NN	_	_	_
1485	_	_	CD	_	_	_
1486	BCE061	bce061	NN	_	_	_
1487	_	_	CD	_	_	_
1488	DS1	ds1	NN	_	_	_
1489	_	_	CD	_	_	_
1490	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1491	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1492	252978410034	252978410034	CD	_	_	_
1493	_	_	NN	_	_	_
1494	B7A	b7a	NN	_	_	_
1495	_	_	CD	_	_	_
1496	CY5	cy5	NN	_	_	_
1497	_	_	CD	_	_	_
1498	ETP05	etp05	NN	_	_	_
1499	_	_	NN	_	_	_
1500	038	038	CD	_	_	_
1501	_	_	SYM	_	_	_
1502	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1503	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1504	252978410034	252978410034	CD	_	_	_
1505	_	_	NN	_	_	_
1506	B7A	b7a	NN	_	_	_
1507	_	_	CD	_	_	_
1508	CY5	cy5	NN	_	_	_
1509	_	_	CD	_	_	_
1510	ETP98053	etp98053	NN	_	_	_
1511	_	_	CD	_	_	_
1512	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1513	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1514	252978410035	252978410035	CD	_	_	_
1515	_	_	NN	_	_	_
1516	B7A	b7a	NN	_	_	_
1517	_	_	CD	_	_	_
1518	CY5	cy5	NN	_	_	_
1519	_	_	NN	_	_	_
1520	BCE055	bce055	NN	_	_	_
1521	_	_	CD	_	_	_
1522	DS1	ds1	NN	_	_	_
1523	_	_	CD	_	_	_
1524	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1525	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1526	252978410035	252978410035	CD	_	_	_
1527	_	_	NN	_	_	_
1528	B7A	b7a	NN	_	_	_
1529	_	_	CD	_	_	_
1530	CY5	cy5	NN	_	_	_
1531	_	_	CD	_	_	_
1532	ETP05	etp05	NN	_	_	_
1533	_	_	NN	_	_	_
1534	016	016	CD	_	_	_
1535	_	_	SYM	_	_	_
1536	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1537	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1538	252978410035	252978410035	CD	_	_	_
1539	_	_	NN	_	_	_
1540	B7A	b7a	NN	_	_	_
1541	_	_	CD	_	_	_
1542	CY5	cy5	NN	_	_	_
1543	_	_	CD	_	_	_
1544	ETP05	etp05	NN	_	_	_
1545	_	_	NN	_	_	_
1546	020	020	CD	_	_	_
1547	_	_	SYM	_	_	_
1548	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1549	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1550	252978410035	252978410035	CD	_	_	_
1551	_	_	NN	_	_	_
1552	B7A	b7a	NN	_	_	_
1553	_	_	CD	_	_	_
1554	CY5	cy5	NN	_	_	_
1555	_	_	CD	_	_	_
1556	ETP05	etp05	NN	_	_	_
1557	_	_	NN	_	_	_
1558	039	039	CD	_	_	_
1559	_	_	SYM	_	_	_
1560	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1561	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1562	252978410058	252978410058	CD	_	_	_
1563	_	_	NN	_	_	_
1564	B7A	b7a	NN	_	_	_
1565	_	_	CD	_	_	_
1566	CY5	cy5	NN	_	_	_
1567	_	_	SYM	_	_	_
1568	178900	178900	CD	_	_	_
1569	_	_	SYM	_	_	_
1570	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1571	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1572	252978410058	252978410058	CD	_	_	_
1573	_	_	NN	_	_	_
1574	B7A	b7a	NN	_	_	_
1575	_	_	CD	_	_	_
1576	CY5	cy5	NN	_	_	_
1577	_	_	SYM	_	_	_
1578	179100	179100	CD	_	_	_
1579	_	_	SYM	_	_	_
1580	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1581	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1582	252978410058	252978410058	CD	_	_	_
1583	_	_	NN	_	_	_
1584	B7A	b7a	NN	_	_	_
1585	_	_	CD	_	_	_
1586	CY5	cy5	NN	_	_	_
1587	_	_	CD	_	_	_
1588	ETP05	etp05	NN	_	_	_
1589	_	_	NN	_	_	_
1590	009	009	CD	_	_	_
1591	_	_	SYM	_	_	_
1592	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1593	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1594	252978410058	252978410058	CD	_	_	_
1595	_	_	NN	_	_	_
1596	B7A	b7a	NN	_	_	_
1597	_	_	CD	_	_	_
1598	CY5	cy5	NN	_	_	_
1599	_	_	CD	_	_	_
1600	ETP05	etp05	NN	_	_	_
1601	_	_	NN	_	_	_
1602	010	010	CD	_	_	_
1603	_	_	SYM	_	_	_
1604	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1605	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1606	252978410059	252978410059	CD	_	_	_
1607	_	_	NN	_	_	_
1608	B7A	b7a	NN	_	_	_
1609	_	_	CD	_	_	_
1610	CY5	cy5	NN	_	_	_
1611	_	_	NN	_	_	_
1612	532	532	CD	_	_	_
1613	_	_	NN	_	_	_
1614	WS6866B1	ws6866b1	NN	_	_	_
1615	_	_	CD	_	_	_
1616	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1617	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1618	252978410059	252978410059	CD	_	_	_
1619	_	_	NN	_	_	_
1620	B7A	b7a	NN	_	_	_
1621	_	_	CD	_	_	_
1622	CY5	cy5	NN	_	_	_
1623	_	_	CD	_	_	_
1624	ETP05	etp05	NN	_	_	_
1625	_	_	NN	_	_	_
1626	047	047	CD	_	_	_
1627	_	_	SYM	_	_	_
1628	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1629	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1630	252978410059	252978410059	CD	_	_	_
1631	_	_	NN	_	_	_
1632	B7A	b7a	NN	_	_	_
1633	_	_	CD	_	_	_
1634	CY5	cy5	NN	_	_	_
1635	_	_	CD	_	_	_
1636	ETP98097	etp98097	NN	_	_	_
1637	_	_	CD	_	_	_
1638	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1639	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1640	252978410059	252978410059	CD	_	_	_
1641	_	_	NN	_	_	_
1642	B7A	b7a	NN	_	_	_
1643	_	_	CD	_	_	_
1644	CY5	cy5	NN	_	_	_
1645	_	_	CD	_	_	_
1646	ETP98112	etp98112	NN	_	_	_
1647	_	_	CD	_	_	_
1648	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1649	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1650	252978410060	252978410060	CD	_	_	_
1651	_	_	NN	_	_	_
1652	B7A	b7a	NN	_	_	_
1653	_	_	CD	_	_	_
1654	CY5	cy5	NN	_	_	_
1655	_	_	CD	_	_	_
1656	ARG2	arg2	NN	_	_	_
1657	_	_	CD	_	_	_
1658	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1659	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1660	252978410060	252978410060	CD	_	_	_
1661	_	_	NN	_	_	_
1662	B7A	b7a	NN	_	_	_
1663	_	_	CD	_	_	_
1664	CY5	cy5	NN	_	_	_
1665	_	_	CD	_	_	_
1666	C35134	c35134	NN	_	_	_
1667	_	_	CD	_	_	_
1668	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1669	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1670	252978410060	252978410060	CD	_	_	_
1671	_	_	NN	_	_	_
1672	B7A	b7a	NN	_	_	_
1673	_	_	CD	_	_	_
1674	CY5	cy5	NN	_	_	_
1675	_	_	CD	_	_	_
1676	E1791	e1791	NN	_	_	_
1677	_	_	CD	_	_	_
1678	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1679	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1680	252978410060	252978410060	CD	_	_	_
1681	_	_	NN	_	_	_
1682	B7A	b7a	NN	_	_	_
1683	_	_	CD	_	_	_
1684	CY5	cy5	NN	_	_	_
1685	_	_	NN	_	_	_
1686	WS3596	ws3596	NN	_	_	_
1687	_	_	CD	_	_	_
1688	A4	a4	NN	_	_	_
1689	_	_	CD	_	_	_
1690	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1691	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1692	252978410061	252978410061	CD	_	_	_
1693	_	_	NN	_	_	_
1694	B7A	b7a	NN	_	_	_
1695	_	_	CD	_	_	_
1696	CY5	cy5	NN	_	_	_
1697	_	_	SYM	_	_	_
1698	COCAR07	cocar07	CD	_	_	_
1699	_	_	SYM	_	_	_
1700	40	40	CD	_	_	_
1701	_	_	SYM	_	_	_
1702	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1703	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1704	252978410061	252978410061	CD	_	_	_
1705	_	_	NN	_	_	_
1706	B7A	b7a	NN	_	_	_
1707	_	_	CD	_	_	_
1708	CY5	cy5	NN	_	_	_
1709	_	_	SYM	_	_	_
1710	COSIN07	cosin07	CD	_	_	_
1711	_	_	SYM	_	_	_
1712	88	88	CD	_	_	_
1713	_	_	SYM	_	_	_
1714	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1715	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1716	252978410061	252978410061	CD	_	_	_
1717	_	_	NN	_	_	_
1718	B7A	b7a	NN	_	_	_
1719	_	_	CD	_	_	_
1720	CY5	cy5	NN	_	_	_
1721	_	_	SYM	_	_	_
1722	COSIN07	cosin07	CD	_	_	_
1723	_	_	SYM	_	_	_
1724	92	92	CD	_	_	_
1725	_	_	SYM	_	_	_
1726	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1727	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1728	252978410062	252978410062	CD	_	_	_
1729	_	_	NN	_	_	_
1730	B7A	b7a	NN	_	_	_
1731	_	_	CD	_	_	_
1732	CY5	cy5	NN	_	_	_
1733	_	_	CD	_	_	_
1734	DS168	ds168	NN	_	_	_
1735	_	_	NN	_	_	_
1736	1	1	CD	_	_	_
1737	_	_	NN	_	_	_
1738	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1739	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1740	252978410062	252978410062	CD	_	_	_
1741	_	_	NN	_	_	_
1742	B7A	b7a	NN	_	_	_
1743	_	_	CD	_	_	_
1744	CY5	cy5	NN	_	_	_
1745	_	_	CD	_	_	_
1746	PE360	pe360	NN	_	_	_
1747	_	_	CD	_	_	_
1748	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1749	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1750	252978410062	252978410062	CD	_	_	_
1751	_	_	NN	_	_	_
1752	B7A	b7a	NN	_	_	_
1753	_	_	CD	_	_	_
1754	CY5	cy5	NN	_	_	_
1755	_	_	CD	_	_	_
1756	WS4087	ws4087	NN	_	_	_
1757	_	_	CD	_	_	_
1758	A1	a1	NN	_	_	_
1759	_	_	CD	_	_	_
1760	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1761	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1762	252978410062	252978410062	CD	_	_	_
1763	_	_	NN	_	_	_
1764	B7A	b7a	NN	_	_	_
1765	_	_	CD	_	_	_
1766	CY5	cy5	NN	_	_	_
1767	_	_	NN	_	_	_
1768	WS7179	ws7179	NN	_	_	_
1769	_	_	CD	_	_	_
1770	A2	a2	NN	_	_	_
1771	_	_	CD	_	_	_
1772	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1773	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1774	252978410063	252978410063	CD	_	_	_
1775	_	_	NN	_	_	_
1776	B7A	b7a	NN	_	_	_
1777	_	_	CD	_	_	_
1778	CY5	cy5	NN	_	_	_
1779	_	_	CD	_	_	_
1780	B7A	b7a	NN	_	_	_
1781	_	_	CD	_	_	_
1782	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1783	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1784	252978410063	252978410063	CD	_	_	_
1785	_	_	NN	_	_	_
1786	B7A	b7a	NN	_	_	_
1787	_	_	CD	_	_	_
1788	CY5	cy5	NN	_	_	_
1789	_	_	SYM	_	_	_
1790	COSIN07	cosin07	CD	_	_	_
1791	_	_	SYM	_	_	_
1792	14	14	CD	_	_	_
1793	_	_	SYM	_	_	_
1794	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1795	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1796	252978410063	252978410063	CD	_	_	_
1797	_	_	NN	_	_	_
1798	B7A	b7a	NN	_	_	_
1799	_	_	CD	_	_	_
1800	CY5	cy5	NN	_	_	_
1801	_	_	CD	_	_	_
1802	sPRH372	sprh372	NN	_	_	_
1803	_	_	CD	_	_	_
1804	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1805	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1806	252978410063	252978410063	CD	_	_	_
1807	_	_	NN	_	_	_
1808	B7A	b7a	NN	_	_	_
1809	_	_	CD	_	_	_
1810	CY5	cy5	NN	_	_	_
1811	_	_	CD	_	_	_
1812	TW3452	tw3452	NN	_	_	_
1813	_	_	CD	_	_	_
1814	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1815	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1816	252978410064	252978410064	CD	_	_	_
1817	_	_	NN	_	_	_
1818	B7A	b7a	NN	_	_	_
1819	_	_	CD	_	_	_
1820	CY5	cy5	NN	_	_	_
1821	_	_	CD	_	_	_
1822	E1789	e1789	NN	_	_	_
1823	_	_	CD	_	_	_
1824	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1825	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1826	252978410064	252978410064	CD	_	_	_
1827	_	_	NN	_	_	_
1828	B7A	b7a	NN	_	_	_
1829	_	_	CD	_	_	_
1830	CY5	cy5	NN	_	_	_
1831	_	_	CD	_	_	_
1832	E1790	e1790	NN	_	_	_
1833	_	_	CD	_	_	_
1834	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1835	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1836	252978410064	252978410064	CD	_	_	_
1837	_	_	NN	_	_	_
1838	B7A	b7a	NN	_	_	_
1839	_	_	CD	_	_	_
1840	CY5	cy5	NN	_	_	_
1841	_	_	CD	_	_	_
1842	HS	hs	NN	_	_	_
1843	_	_	CD	_	_	_
1844	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1845	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1846	252978410064	252978410064	CD	_	_	_
1847	_	_	NN	_	_	_
1848	B7A	b7a	NN	_	_	_
1849	_	_	CD	_	_	_
1850	CY5	cy5	NN	_	_	_
1851	_	_	CD	_	_	_
1852	sPRH609	sprh609	NN	_	_	_
1853	_	_	CD	_	_	_
1854	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1855	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1856	252978410065	252978410065	CD	_	_	_
1857	_	_	NN	_	_	_
1858	B7A	b7a	NN	_	_	_
1859	_	_	CD	_	_	_
1860	CY5	cy5	NN	_	_	_
1861	_	_	NN	_	_	_
1862	350C1A	350c1a	NN	_	_	_
1863	_	_	CD	_	_	_
1864	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1865	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1866	252978410065	252978410065	CD	_	_	_
1867	_	_	NN	_	_	_
1868	B7A	b7a	NN	_	_	_
1869	_	_	CD	_	_	_
1870	CY5	cy5	NN	_	_	_
1871	_	_	CD	_	_	_
1872	E2528	e2528	NN	_	_	_
1873	_	_	CD	_	_	_
1874	C1	c1	NN	_	_	_
1875	_	_	CD	_	_	_
1876	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1877	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1878	252978410065	252978410065	CD	_	_	_
1879	_	_	NN	_	_	_
1880	B7A	b7a	NN	_	_	_
1881	_	_	CD	_	_	_
1882	CY5	cy5	NN	_	_	_
1883	_	_	CD	_	_	_
1884	E8775	e8775	NN	_	_	_
1885	_	_	CD	_	_	_
1886	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1887	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1888	252978410065	252978410065	CD	_	_	_
1889	_	_	NN	_	_	_
1890	B7A	b7a	NN	_	_	_
1891	_	_	CD	_	_	_
1892	CY5	cy5	NN	_	_	_
1893	_	_	CD	_	_	_
1894	M424	m424	NN	_	_	_
1895	_	_	CD	_	_	_
1896	C1	c1	NN	_	_	_
1897	_	_	CD	_	_	_
1898	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1899	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1900	252978410066	252978410066	CD	_	_	_
1901	_	_	NN	_	_	_
1902	B7A	b7a	NN	_	_	_
1903	_	_	CD	_	_	_
1904	CY5	cy5	NN	_	_	_
1905	_	_	SYM	_	_	_
1906	2230	2230	CD	_	_	_
1907	_	_	SYM	_	_	_
1908	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1909	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1910	252978410066	252978410066	CD	_	_	_
1911	_	_	NN	_	_	_
1912	B7A	b7a	NN	_	_	_
1913	_	_	CD	_	_	_
1914	CY5	cy5	NN	_	_	_
1915	_	_	CD	_	_	_
1916	ICDDR	icddr	NN	_	_	_
1917	_	_	CD	_	_	_
1918	P	p	NN	_	_	_
1919	_	_	NN	_	_	_
1920	2	2	CD	_	_	_
1921	_	_	CD	_	_	_
1922	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1923	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1924	252978410066	252978410066	CD	_	_	_
1925	_	_	NN	_	_	_
1926	B7A	b7a	NN	_	_	_
1927	_	_	CD	_	_	_
1928	CY5	cy5	NN	_	_	_
1929	_	_	CD	_	_	_
1930	WS1933D	ws1933d	NN	_	_	_
1931	_	_	CD	_	_	_
1932	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1933	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1934	252978410066	252978410066	CD	_	_	_
1935	_	_	NN	_	_	_
1936	B7A	b7a	NN	_	_	_
1937	_	_	CD	_	_	_
1938	CY5	cy5	NN	_	_	_
1939	_	_	CD	_	_	_
1940	WS6582	ws6582	NN	_	_	_
1941	_	_	CD	_	_	_
1942	A1	a1	NN	_	_	_
1943	_	_	CD	_	_	_
1944	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1945	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1946	252978410067	252978410067	CD	_	_	_
1947	_	_	NN	_	_	_
1948	B7A	b7a	NN	_	_	_
1949	_	_	CD	_	_	_
1950	CY5	cy5	NN	_	_	_
1951	_	_	CD	_	_	_
1952	B2C	b2c	NN	_	_	_
1953	_	_	CD	_	_	_
1954	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1955	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1956	252978410067	252978410067	CD	_	_	_
1957	_	_	NN	_	_	_
1958	B7A	b7a	NN	_	_	_
1959	_	_	CD	_	_	_
1960	CY5	cy5	NN	_	_	_
1961	_	_	SYM	_	_	_
1962	ETEC	etec	NNS	_	_	_
1963	_	_	VBP	_	_	_
1964	8	8	CD	_	_	_
1965	_	_	SYM	_	_	_
1966	11	11	CD	_	_	_
1967	_	_	SYM	_	_	_
1968	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1969	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1970	252978410067	252978410067	CD	_	_	_
1971	_	_	NN	_	_	_
1972	B7A	b7a	NN	_	_	_
1973	_	_	CD	_	_	_
1974	CY5	cy5	NN	_	_	_
1975	_	_	CD	_	_	_
1976	F5656	f5656	NN	_	_	_
1977	_	_	CD	_	_	_
1978	C1	c1	NN	_	_	_
1979	_	_	CD	_	_	_
1980	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1981	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1982	252978410067	252978410067	CD	_	_	_
1983	_	_	NN	_	_	_
1984	B7A	b7a	NN	_	_	_
1985	_	_	CD	_	_	_
1986	CY5	cy5	NN	_	_	_
1987	_	_	CD	_	_	_
1988	WS7162	ws7162	NN	_	_	_
1989	_	_	CD	_	_	_
1990	A1	a1	NN	_	_	_
1991	_	_	CD	_	_	_
1992	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
1993	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1994	252978410068	252978410068	CD	_	_	_
1995	_	_	NN	_	_	_
1996	B7A	b7a	NN	_	_	_
1997	_	_	CD	_	_	_
1998	CY5	cy5	NN	_	_	_
1999	_	_	NN	_	_	_
2000	CFT073	cft073	NN	_	_	_
2001	_	_	CD	_	_	_
2002	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2003	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2004	252978410068	252978410068	CD	_	_	_
2005	_	_	NN	_	_	_
2006	B7A	b7a	NN	_	_	_
2007	_	_	CD	_	_	_
2008	CY5	cy5	NN	_	_	_
2009	_	_	CD	_	_	_
2010	ICDDR	icddr	NN	_	_	_
2011	_	_	NN	_	_	_
2012	B	b	NN	_	_	_
2013	_	_	CD	_	_	_
2014	p	p	NN	_	_	_
2015	_	_	SYM	_	_	_
2016	10	10	CD	_	_	_
2017	_	_	SYM	_	_	_
2018	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2019	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2020	252978410068	252978410068	CD	_	_	_
2021	_	_	NN	_	_	_
2022	B7A	b7a	NN	_	_	_
2023	_	_	CD	_	_	_
2024	CY5	cy5	NN	_	_	_
2025	_	_	CD	_	_	_
2026	M408C1	m408c1	NN	_	_	_
2027	_	_	CD	_	_	_
2028	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2029	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2030	252978410068	252978410068	CD	_	_	_
2031	_	_	NN	_	_	_
2032	B7A	b7a	NN	_	_	_
2033	_	_	CD	_	_	_
2034	CY5	cy5	NN	_	_	_
2035	_	_	CD	_	_	_
2036	WS3294A	ws3294a	NN	_	_	_
2037	_	_	CD	_	_	_
2038	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2039	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2040	252978410069	252978410069	CD	_	_	_
2041	_	_	NN	_	_	_
2042	B7A	b7a	NN	_	_	_
2043	_	_	CD	_	_	_
2044	CY5	cy5	NN	_	_	_
2045	_	_	CD	_	_	_
2046	278485	278485	CD	_	_	_
2047	_	_	NN	_	_	_
2048	1	1	CD	_	_	_
2049	_	_	NN	_	_	_
2050	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2051	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2052	252978410069	252978410069	CD	_	_	_
2053	_	_	NN	_	_	_
2054	B7A	b7a	NN	_	_	_
2055	_	_	CD	_	_	_
2056	CY5	cy5	NN	_	_	_
2057	_	_	CD	_	_	_
2058	sPRH25	sprh25	NN	_	_	_
2059	_	_	CD	_	_	_
2060	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2061	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2062	252978410069	252978410069	CD	_	_	_
2063	_	_	NN	_	_	_
2064	B7A	b7a	NN	_	_	_
2065	_	_	CD	_	_	_
2066	CY5	cy5	NN	_	_	_
2067	_	_	CD	_	_	_
2068	sPRH421	sprh421	NN	_	_	_
2069	_	_	CD	_	_	_
2070	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2071	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2072	252978410069	252978410069	CD	_	_	_
2073	_	_	NN	_	_	_
2074	B7A	b7a	NN	_	_	_
2075	_	_	CD	_	_	_
2076	CY5	cy5	NN	_	_	_
2077	_	_	CD	_	_	_
2078	sPRH610	sprh610	NN	_	_	_
2079	_	_	CD	_	_	_
2080	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2081	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2082	252978410070	252978410070	CD	_	_	_
2083	_	_	NN	_	_	_
2084	B7A	b7a	NN	_	_	_
2085	_	_	CD	_	_	_
2086	CY5	cy5	NN	_	_	_
2087	_	_	CD	_	_	_
2088	ICDDR	icddr	NN	_	_	_
2089	_	_	NN	_	_	_
2090	B	b	NN	_	_	_
2091	_	_	CD	_	_	_
2092	p7	p7	NN	_	_	_
2093	_	_	CD	_	_	_
2094	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2095	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2096	252978410070	252978410070	CD	_	_	_
2097	_	_	NN	_	_	_
2098	B7A	b7a	NN	_	_	_
2099	_	_	CD	_	_	_
2100	CY5	cy5	NN	_	_	_
2101	_	_	CD	_	_	_
2102	NR	nr	NN	_	_	_
2103	_	_	SYM	_	_	_
2104	12	12	CD	_	_	_
2105	_	_	SYM	_	_	_
2106	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2108	252978410070	252978410070	CD	_	_	_
2109	_	_	NN	_	_	_
2110	B7A	b7a	NN	_	_	_
2111	_	_	CD	_	_	_
2112	CY5	cy5	NN	_	_	_
2113	_	_	CD	_	_	_
2114	sPRH20	sprh20	NN	_	_	_
2115	_	_	CD	_	_	_
2116	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2118	252978410070	252978410070	CD	_	_	_
2119	_	_	NN	_	_	_
2120	B7A	b7a	NN	_	_	_
2121	_	_	CD	_	_	_
2122	CY5	cy5	NN	_	_	_
2123	_	_	CD	_	_	_
2124	sPRH612	sprh612	NN	_	_	_
2125	_	_	CD	_	_	_
2126	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2128	252978410071	252978410071	CD	_	_	_
2129	_	_	NN	_	_	_
2130	B7A	b7a	NN	_	_	_
2131	_	_	CD	_	_	_
2132	CY5	cy5	NN	_	_	_
2133	_	_	NN	_	_	_
2134	292	292	CD	_	_	_
2135	_	_	NN	_	_	_
2136	1	1	CD	_	_	_
2137	_	_	NN	_	_	_
2138	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2140	252978410071	252978410071	CD	_	_	_
2141	_	_	NN	_	_	_
2142	B7A	b7a	NN	_	_	_
2143	_	_	CD	_	_	_
2144	CY5	cy5	NN	_	_	_
2145	_	_	CD	_	_	_
2146	COCAR07	cocar07	NN	_	_	_
2147	_	_	NN	_	_	_
2148	043	043	CD	_	_	_
2149	_	_	SYM	_	_	_
2150	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2152	252978410071	252978410071	CD	_	_	_
2153	_	_	NN	_	_	_
2154	B7A	b7a	NN	_	_	_
2155	_	_	CD	_	_	_
2156	CY5	cy5	NN	_	_	_
2157	_	_	SYM	_	_	_
2158	COSIN07	cosin07	CD	_	_	_
2159	_	_	SYM	_	_	_
2160	61	61	CD	_	_	_
2161	_	_	SYM	_	_	_
2162	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2164	252978410071	252978410071	CD	_	_	_
2165	_	_	NN	_	_	_
2166	B7A	b7a	NN	_	_	_
2167	_	_	CD	_	_	_
2168	CY5	cy5	NN	_	_	_
2169	_	_	CD	_	_	_
2170	O157	o157	NN	_	_	_
2171	_	_	CD	_	_	_
2172	h7	h7	NN	_	_	_
2173	_	_	CD	_	_	_
2174	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2176	252978410072	252978410072	CD	_	_	_
2177	_	_	NN	_	_	_
2178	B7A	b7a	NN	_	_	_
2179	_	_	CD	_	_	_
2180	CY5	cy5	NN	_	_	_
2181	_	_	SYM	_	_	_
2182	COSIN07	cosin07	CD	_	_	_
2183	_	_	SYM	_	_	_
2184	36	36	CD	_	_	_
2185	_	_	SYM	_	_	_
2186	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2188	252978410072	252978410072	CD	_	_	_
2189	_	_	NN	_	_	_
2190	B7A	b7a	NN	_	_	_
2191	_	_	CD	_	_	_
2192	CY5	cy5	NN	_	_	_
2193	_	_	CD	_	_	_
2194	ICDDR	icddr	NN	_	_	_
2195	_	_	NN	_	_	_
2196	B	b	NN	_	_	_
2197	_	_	CD	_	_	_
2198	p6	p6	NN	_	_	_
2199	_	_	CD	_	_	_
2200	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2202	252978410072	252978410072	CD	_	_	_
2203	_	_	NN	_	_	_
2204	B7A	b7a	NN	_	_	_
2205	_	_	CD	_	_	_
2206	CY5	cy5	NN	_	_	_
2207	_	_	CD	_	_	_
2208	O63	o63	NN	_	_	_
2209	_	_	CD	_	_	_
2210	nm	nm	NN	_	_	_
2211	_	_	NN	_	_	_
2212	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2214	252978410072	252978410072	CD	_	_	_
2215	_	_	NN	_	_	_
2216	B7A	b7a	NN	_	_	_
2217	_	_	CD	_	_	_
2218	CY5	cy5	NN	_	_	_
2219	_	_	CD	_	_	_
2220	sPRH605	sprh605	NN	_	_	_
2221	_	_	CD	_	_	_
2222	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2224	252978410073	252978410073	CD	_	_	_
2225	_	_	NN	_	_	_
2226	B7A	b7a	NN	_	_	_
2227	_	_	CD	_	_	_
2228	CY5	cy5	NN	_	_	_
2229	_	_	NN	_	_	_
2230	214	214	CD	_	_	_
2231	_	_	NN	_	_	_
2232	4	4	CD	_	_	_
2233	_	_	SYM	_	_	_
2234	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2235	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2236	252978410073	252978410073	CD	_	_	_
2237	_	_	NN	_	_	_
2238	B7A	b7a	NN	_	_	_
2239	_	_	CD	_	_	_
2240	CY5	cy5	NN	_	_	_
2241	_	_	CD	_	_	_
2242	E7476A	e7476a	NN	_	_	_
2243	_	_	CD	_	_	_
2244	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2245	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2246	252978410073	252978410073	CD	_	_	_
2247	_	_	NN	_	_	_
2248	B7A	b7a	NN	_	_	_
2249	_	_	CD	_	_	_
2250	CY5	cy5	NN	_	_	_
2251	_	_	NN	_	_	_
2252	WS1896	ws1896	NN	_	_	_
2253	_	_	CD	_	_	_
2254	A1	a1	NN	_	_	_
2255	_	_	CD	_	_	_
2256	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2258	252978410073	252978410073	CD	_	_	_
2259	_	_	NN	_	_	_
2260	B7A	b7a	NN	_	_	_
2261	_	_	CD	_	_	_
2262	CY5	cy5	NN	_	_	_
2263	_	_	CD	_	_	_
2264	WS2173A	ws2173a	NN	_	_	_
2265	_	_	CD	_	_	_
2266	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2268	252978410075	252978410075	CD	_	_	_
2269	_	_	NN	_	_	_
2270	B7A	b7a	NN	_	_	_
2271	_	_	CD	_	_	_
2272	CY5	cy5	NN	_	_	_
2273	_	_	CD	_	_	_
2274	ETP05	etp05	NN	_	_	_
2275	_	_	NN	_	_	_
2276	011	011	CD	_	_	_
2277	_	_	SYM	_	_	_
2278	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2280	252978410075	252978410075	CD	_	_	_
2281	_	_	NN	_	_	_
2282	B7A	b7a	NN	_	_	_
2283	_	_	CD	_	_	_
2284	CY5	cy5	NN	_	_	_
2285	_	_	CD	_	_	_
2286	ETP05	etp05	NN	_	_	_
2287	_	_	NN	_	_	_
2288	035	035	CD	_	_	_
2289	_	_	SYM	_	_	_
2290	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2292	252978410075	252978410075	CD	_	_	_
2293	_	_	NN	_	_	_
2294	B7A	b7a	NN	_	_	_
2295	_	_	CD	_	_	_
2296	CY5	cy5	NN	_	_	_
2297	_	_	SYM	_	_	_
2298	O78	o78	CD	_	_	_
2299	_	_	CD	_	_	_
2300	h11	h11	NN	_	_	_
2301	_	_	CD	_	_	_
2302	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2304	252978410075	252978410075	CD	_	_	_
2305	_	_	NN	_	_	_
2306	B7A	b7a	NN	_	_	_
2307	_	_	CD	_	_	_
2308	CY5	cy5	NN	_	_	_
2309	_	_	CD	_	_	_
2310	sPRH445	sprh445	NN	_	_	_
2311	_	_	CD	_	_	_
2312	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2313	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2314	252978410076	252978410076	CD	_	_	_
2315	_	_	NN	_	_	_
2316	B7A	b7a	NN	_	_	_
2317	_	_	CD	_	_	_
2318	CY5	cy5	NN	_	_	_
2319	_	_	SYM	_	_	_
2320	178200	178200	CD	_	_	_
2321	_	_	SYM	_	_	_
2322	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2324	252978410076	252978410076	CD	_	_	_
2325	_	_	NN	_	_	_
2326	B7A	b7a	NN	_	_	_
2327	_	_	CD	_	_	_
2328	CY5	cy5	NN	_	_	_
2329	_	_	NN	_	_	_
2330	C35213	c35213	NN	_	_	_
2331	_	_	CD	_	_	_
2332	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2333	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2334	252978410076	252978410076	CD	_	_	_
2335	_	_	NN	_	_	_
2336	B7A	b7a	NN	_	_	_
2337	_	_	CD	_	_	_
2338	CY5	cy5	NN	_	_	_
2339	_	_	NN	_	_	_
2340	C35605	c35605	NN	_	_	_
2341	_	_	CD	_	_	_
2342	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2343	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2344	252978410076	252978410076	CD	_	_	_
2345	_	_	NN	_	_	_
2346	B7A	b7a	NN	_	_	_
2347	_	_	CD	_	_	_
2348	CY5	cy5	NN	_	_	_
2349	_	_	CD	_	_	_
2350	ETP98109	etp98109	NN	_	_	_
2351	_	_	CD	_	_	_
2352	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2353	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2354	252978410077	252978410077	CD	_	_	_
2355	_	_	NN	_	_	_
2356	B7A	b7a	NN	_	_	_
2357	_	_	CD	_	_	_
2358	CY5	cy5	NN	_	_	_
2359	_	_	SYM	_	_	_
2360	174900	174900	CD	_	_	_
2361	_	_	SYM	_	_	_
2362	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2363	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2364	252978410077	252978410077	CD	_	_	_
2365	_	_	NN	_	_	_
2366	B7A	b7a	NN	_	_	_
2367	_	_	CD	_	_	_
2368	CY5	cy5	NN	_	_	_
2369	_	_	NN	_	_	_
2370	C34666	c34666	NN	_	_	_
2371	_	_	CD	_	_	_
2372	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2373	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2374	252978410077	252978410077	CD	_	_	_
2375	_	_	NN	_	_	_
2376	B7A	b7a	NN	_	_	_
2377	_	_	CD	_	_	_
2378	CY5	cy5	NN	_	_	_
2379	_	_	CD	_	_	_
2380	ETP05	etp05	NN	_	_	_
2381	_	_	NN	_	_	_
2382	002	002	CD	_	_	_
2383	_	_	SYM	_	_	_
2384	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2385	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2386	252978410077	252978410077	CD	_	_	_
2387	_	_	NN	_	_	_
2388	B7A	b7a	NN	_	_	_
2389	_	_	CD	_	_	_
2390	CY5	cy5	NN	_	_	_
2391	_	_	CD	_	_	_
2392	ETP05	etp05	NN	_	_	_
2393	_	_	NN	_	_	_
2394	003	003	CD	_	_	_
2395	_	_	SYM	_	_	_
2396	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2397	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2398	252978410078	252978410078	CD	_	_	_
2399	_	_	NN	_	_	_
2400	B7A	b7a	NN	_	_	_
2401	_	_	CD	_	_	_
2402	CY5	cy5	NN	_	_	_
2403	_	_	NN	_	_	_
2404	2	2	CD	_	_	_
2405	_	_	NN	_	_	_
2406	1	1	CD	_	_	_
2407	_	_	NN	_	_	_
2408	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2409	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2410	252978410078	252978410078	CD	_	_	_
2411	_	_	NN	_	_	_
2412	B7A	b7a	NN	_	_	_
2413	_	_	CD	_	_	_
2414	CY5	cy5	NN	_	_	_
2415	_	_	CD	_	_	_
2416	WS2741	ws2741	NN	_	_	_
2417	_	_	CD	_	_	_
2418	A1	a1	NN	_	_	_
2419	_	_	CD	_	_	_
2420	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2421	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2422	252978410078	252978410078	CD	_	_	_
2423	_	_	NN	_	_	_
2424	B7A	b7a	NN	_	_	_
2425	_	_	CD	_	_	_
2426	CY5	cy5	NN	_	_	_
2427	_	_	CD	_	_	_
2428	WS4264	ws4264	NN	_	_	_
2429	_	_	CD	_	_	_
2430	A1	a1	NN	_	_	_
2431	_	_	CD	_	_	_
2432	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2433	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2434	252978410078	252978410078	CD	_	_	_
2435	_	_	NN	_	_	_
2436	B7A	b7a	NN	_	_	_
2437	_	_	CD	_	_	_
2438	CY5	cy5	NN	_	_	_
2439	_	_	CD	_	_	_
2440	WS5874	ws5874	NN	_	_	_
2441	_	_	CD	_	_	_
2442	A1	a1	NN	_	_	_
2443	_	_	CD	_	_	_
2444	CY3.mev.refIsIB.out	cy3.mev.refisib.out	NN	_	_	_
2445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2446	2	2	CD	_	_	_
2447	.	.	.	_	_	_

1	Use	use	NN	_	_	_
2	TM4	tm4	NN	_	_	_
3	suite	suite	NN	_	_	_
4	software	software	NN	_	_	_
5	ExpressConverter	expressconverter	NN	_	_	_
6	to	to	TO	_	_	_
7	modify	modify	VB	_	_	_
8	Agilent	Agilent	NNP	_	_	_
9	Feature	Feature	NNP	_	_	_
10	Extraction	Extraction	NNP	_	_	_
11	file	file	NN	_	_	_
12	into	into	IN	_	_	_
13	*	*	NN	_	_	_
14	.	.	.	_	_	_

1	mev	mev	NN	_	_	_
2	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	3a	3a	NN	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	.	.	.	_	_	_

1	If	if	IN	_	_	_
2	both	both	DT	_	_	_
3	channels	channel	NNS	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	QUERY	query	NN	_	_	_
6	_	_	CD	_	_	_
7	MEDIAN	MEDIAN	NNP	_	_	_
8	_	_	CD	_	_	_
9	INTENSITY	intensity	NN	_	_	_
10	and	and	CC	_	_	_
11	REF	ref	NN	_	_	_
12	_	_	CD	_	_	_
13	MEDIAN	MEDIAN	NNP	_	_	_
14	_	_	CD	_	_	_
15	INTENSITY	intensity	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	are	be	VBP	_	_	_
18	zero	zero	CD	_	_	_
19	,	,	,	_	_	_
20	assign	assign	VBP	_	_	_
21	the	the	DT	_	_	_
22	value	value	NN	_	_	_
23	null	null	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	3b	3b	NN	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	.	.	.	_	_	_

1	If	if	IN	_	_	_
2	one	one	CD	_	_	_
3	channel	channel	NN	_	_	_
4	is	be	VBZ	_	_	_
5	zero	zero	CD	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	other	other	JJ	_	_	_
9	is	be	VBZ	_	_	_
10	not	not	RB	_	_	_
11	zero	zero	CD	_	_	_
12	,	,	,	_	_	_
13	substitute	substitute	VB	_	_	_
14	the	the	DT	_	_	_
15	zero	zero	CD	_	_	_
16	with	with	IN	_	_	_
17	one	one	CD	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	1	1	CD	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	and	and	CC	_	_	_
22	then	then	RB	_	_	_
23	,	,	,	_	_	_
24	assign	assign	VB	_	_	_
25	the	the	DT	_	_	_
26	log2	log2	NN	_	_	_
27	ratio	ratio	NN	_	_	_
28	of	of	IN	_	_	_
29	QUERY	QUERY	NNP	_	_	_
30	_	_	NNP	_	_	_
31	MEDIAN	MEDIAN	NNP	_	_	_
32	_	_	SYM	_	_	_
33	INTENSITY	intensity	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	3	3	CD	_	_	_
36	.	.	.	_	_	_

1	Calculate	calculate	VB	_	_	_
2	the	the	DT	_	_	_
3	value	value	NN	_	_	_
4	of	of	IN	_	_	_
5	log2	log2	NN	_	_	_
6	ratio	ratio	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Reference	Reference	NNP	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	3c	3c	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	.	.	.	_	_	_

1	If	if	IN	_	_	_
2	neither	neither	DT	_	_	_
3	channel	channel	NN	_	_	_
4	is	be	VBZ	_	_	_
5	zero	zero	CD	_	_	_
6	,	,	,	_	_	_
7	assign	assign	VB	_	_	_
8	the	the	DT	_	_	_
9	log2	log2	NN	_	_	_
10	ratio	ratio	NN	_	_	_
11	of	of	IN	_	_	_
12	QUERY	QUERY	NNP	_	_	_
13	_	_	NNP	_	_	_
14	MEDIAN	MEDIAN	NNP	_	_	_
15	_	_	SYM	_	_	_
16	INTENSITY	intensity	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	cells	cell	NNS	_	_	_
19	were	be	VBD	_	_	_
20	grown	grow	VBN	_	_	_
21	in	in	IN	_	_	_
22	LB	lb	NN	_	_	_
23	overnight	overnight	JJ	_	_	_
24	at	at	IN	_	_	_
25	37	37	CD	_	_	_
26	degrees	degree	NNS	_	_	_
27	celcius	celcius	NN	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
5	Genomic	genomic	JJ	_	_	_
6	DNA	dna	NN	_	_	_
7	purified	purify	VBN	_	_	_
8	from	from	IN	_	_	_
9	wild	wild	JJ	_	_	_
10	type	type	NN	_	_	_
11	bacteri	bacteri	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
13	Genomic	genomic	JJ	_	_	_
14	DNA	dna	NN	_	_	_
15	purified	purify	VBN	_	_	_
16	from	from	IN	_	_	_
17	wild	wild	JJ	_	_	_
18	type	type	NN	_	_	_
19	bacteria	bacterium	NNS	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
21	Genomic	genomic	JJ	_	_	_
22	DNA	dna	NN	_	_	_
23	was	be	VBD	_	_	_
24	isolated	isolate	VBN	_	_	_
25	by	by	IN	_	_	_
26	lysozyme	lysozyme	NN	_	_	_
27	and	and	CC	_	_	_
28	proteinase	proteinase	NN	_	_	_
29	K	k	NN	_	_	_
30	treatment	treatment	NN	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genomic	genomic	JJ	_	_	_
3	DNA	dna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	by	by	IN	_	_	_
7	lysozyme	lysozyme	NN	_	_	_
8	and	and	CC	_	_	_
9	proteinase	proteinase	NN	_	_	_
10	K	k	NN	_	_	_
11	treatment	treatment	NN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	mev	mev	NN	_	_	_
3	data	datum	NNS	_	_	_
4	obtained	obtain	VBN	_	_	_
5	from	from	IN	_	_	_
6	the	the	DT	_	_	_
7	feature	feature	NN	_	_	_
8	extraction	extraction	NN	_	_	_
9	file	file	NN	_	_	_
10	used	use	VBN	_	_	_
11	,	,	,	_	_	_
12	no	no	DT	_	_	_
13	further	further	JJ	_	_	_
14	normalization	normalization	NN	_	_	_
15	needed	need	VBD	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	None	None	NNP	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Procedures	procedure	NNS	_	_	_
20	to	to	TO	_	_	_
21	calculate	calculate	VB	_	_	_
22	the	the	DT	_	_	_
23	value	value	NN	_	_	_
24	of	of	IN	_	_	_
25	log2	log2	NN	_	_	_
26	ratio	ratio	NN	_	_	_
27	:	:	:	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	strain	strain	NN	_	_	_
30	:	:	:	_	_	_
31	173150	173150	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	strain	strain	NN	_	_	_
34	:	:	:	_	_	_
35	174750	174750	CD	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	strain	strain	NN	_	_	_
38	:	:	:	_	_	_
39	174900	174900	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	strain	strain	NN	_	_	_
42	:	:	:	_	_	_
43	178200	178200	CD	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	strain	strain	NN	_	_	_
46	:	:	:	_	_	_
47	178850	178850	CD	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	strain	strain	NN	_	_	_
50	:	:	:	_	_	_
51	178900	178900	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	strain	strain	NN	_	_	_
54	:	:	:	_	_	_
55	179100	179100	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	strain	strain	NN	_	_	_
58	:	:	:	_	_	_
59	179550	179550	CD	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	strain	strain	NN	_	_	_
62	:	:	:	_	_	_
63	180050	180050	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	strain	strain	NN	_	_	_
66	:	:	:	_	_	_
67	180200	180200	CD	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	strain	strain	NN	_	_	_
70	:	:	:	_	_	_
71	180600	180600	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	strain	strain	NN	_	_	_
74	:	:	:	_	_	_
75	2-1	2-1	CD	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	strain	strain	NN	_	_	_
78	:	:	:	_	_	_
79	214-4	214-4	CD	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	strain	strain	NN	_	_	_
82	:	:	:	_	_	_
83	2230	2230	CD	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	strain	strain	NN	_	_	_
86	:	:	:	_	_	_
87	229-1	229-1	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	strain	strain	NN	_	_	_
90	:	:	:	_	_	_
91	278485-1	278485-1	CD	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	strain	strain	NN	_	_	_
94	:	:	:	_	_	_
95	292-1	292-1	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	strain	strain	NN	_	_	_
98	:	:	:	_	_	_
99	350C1A	350c1a	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	strain	strain	NN	_	_	_
102	:	:	:	_	_	_
103	42-1	42-1	CD	_	_	_
104	C1	c1	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	strain	strain	NN	_	_	_
107	:	:	:	_	_	_
108	ARG-2	arg-2	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	strain	strain	NN	_	_	_
111	:	:	:	_	_	_
112	ARG-3	arg-3	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	strain	strain	NN	_	_	_
115	:	:	:	_	_	_
116	B2C	b2c	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	strain	strain	NN	_	_	_
119	:	:	:	_	_	_
120	B7A	b7a	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	strain	strain	NN	_	_	_
123	:	:	:	_	_	_
124	BCE001	bce001	NN	_	_	_
125	,	,	,	_	_	_
126	MS16	ms16	NN	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	strain	strain	NN	_	_	_
129	:	:	:	_	_	_
130	BCE002	bce002	NN	_	_	_
131	,	,	,	_	_	_
132	MS12	ms12	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	strain	strain	NN	_	_	_
135	:	:	:	_	_	_
136	BCE003	bce003	NN	_	_	_
137	,	,	,	_	_	_
138	DS5	ds5	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	strain	strain	NN	_	_	_
141	:	:	:	_	_	_
142	BCE005	bce005	NN	_	_	_
143	,	,	,	_	_	_
144	MS23	ms23	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	strain	strain	NN	_	_	_
147	:	:	:	_	_	_
148	BCE007	bce007	NN	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	strain	strain	NN	_	_	_
151	:	:	:	_	_	_
152	BCE007	bce007	NN	_	_	_
153	,	,	,	_	_	_
154	MS11	ms11	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	strain	strain	NN	_	_	_
157	:	:	:	_	_	_
158	BCE008	bce008	NN	_	_	_
159	_	_	CD	_	_	_
160	MS1	ms1	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	strain	strain	NN	_	_	_
163	:	:	:	_	_	_
164	BCE008	bce008	NN	_	_	_
165	,	,	,	_	_	_
166	MS13	ms13	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	strain	strain	NN	_	_	_
169	:	:	:	_	_	_
170	BCE011	bce011	NN	_	_	_
171	,	,	,	_	_	_
172	DS3	ds3	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	strain	strain	NN	_	_	_
175	:	:	:	_	_	_
176	BCE013	bce013	NN	_	_	_
177	,	,	,	_	_	_
178	DS1	ds1	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	strain	strain	NN	_	_	_
181	:	:	:	_	_	_
182	BCE018	bce018	NN	_	_	_
183	,	,	,	_	_	_
184	DS6	ds6	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	strain	strain	NN	_	_	_
187	:	:	:	_	_	_
188	BCE019	bce019	NN	_	_	_
189	,	,	,	_	_	_
190	MS16	ms16	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	strain	strain	NN	_	_	_
193	:	:	:	_	_	_
194	BCE021	bce021	NN	_	_	_
195	,	,	,	_	_	_
196	DS7	ds7	NN	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	strain	strain	NN	_	_	_
199	:	:	:	_	_	_
200	BCE022DS6	bce022ds6	NN	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	strain	strain	NN	_	_	_
203	:	:	:	_	_	_
204	BCE035	bce035	NN	_	_	_
205	,	,	,	_	_	_
206	DS6	ds6	NN	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	strain	strain	NN	_	_	_
209	:	:	:	_	_	_
210	BCE035	bce035	NN	_	_	_
211	,	,	,	_	_	_
212	MS8	ms8	NN	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	strain	strain	NN	_	_	_
215	:	:	:	_	_	_
216	BCE039	bce039	NN	_	_	_
217	,	,	,	_	_	_
218	DS2	ds2	NN	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	strain	strain	NN	_	_	_
221	:	:	:	_	_	_
222	BCE039	bce039	NN	_	_	_
223	,	,	,	_	_	_
224	MS13	ms13	NN	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	strain	strain	NN	_	_	_
227	:	:	:	_	_	_
228	BCE041	bce041	NN	_	_	_
229	,	,	,	_	_	_
230	MS11	ms11	NN	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	strain	strain	NN	_	_	_
233	:	:	:	_	_	_
234	BCE046	bce046	NN	_	_	_
235	,	,	,	_	_	_
236	DS2	ds2	NN	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	strain	strain	NN	_	_	_
239	:	:	:	_	_	_
240	BCE046	bce046	NN	_	_	_
241	,	,	,	_	_	_
242	DS7	ds7	NN	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	strain	strain	NN	_	_	_
245	:	:	:	_	_	_
246	BCE046	bce046	NN	_	_	_
247	,	,	,	_	_	_
248	MS16	ms16	NN	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	strain	strain	NN	_	_	_
251	:	:	:	_	_	_
252	BCE049	bce049	NN	_	_	_
253	,	,	,	_	_	_
254	DS3	ds3	NN	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	strain	strain	NN	_	_	_
257	:	:	:	_	_	_
258	BCE049	bce049	NN	_	_	_
259	,	,	,	_	_	_
260	MS9	ms9	NN	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
262	strain	strain	NN	_	_	_
263	:	:	:	_	_	_
264	BCE054	bce054	NN	_	_	_
265	,	,	,	_	_	_
266	DS4	ds4	NN	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	strain	strain	NN	_	_	_
269	:	:	:	_	_	_
270	BCE054	bce054	NN	_	_	_
271	,	,	,	_	_	_
272	MS24	ms24	NN	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	strain	strain	NN	_	_	_
275	:	:	:	_	_	_
276	BCE055	bce055	NN	_	_	_
277	,	,	,	_	_	_
278	DS1	ds1	NN	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	strain	strain	NN	_	_	_
281	:	:	:	_	_	_
282	BCE058	bce058	NN	_	_	_
283	,	,	,	_	_	_
284	MS13	ms13	NN	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
286	strain	strain	NN	_	_	_
287	:	:	:	_	_	_
288	BCE061	bce061	NN	_	_	_
289	,	,	,	_	_	_
290	DS1	ds1	NN	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	strain	strain	NN	_	_	_
293	:	:	:	_	_	_
294	BCE062	bce062	NN	_	_	_
295	,	,	,	_	_	_
296	DS2	ds2	NN	_	_	_
297	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
298	strain	strain	NN	_	_	_
299	:	:	:	_	_	_
300	BCE062	bce062	NN	_	_	_
301	,	,	,	_	_	_
302	MS24	ms24	NN	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
304	strain	strain	NN	_	_	_
305	:	:	:	_	_	_
306	BCE063	bce063	NN	_	_	_
307	,	,	,	_	_	_
308	DS4	ds4	NN	_	_	_
309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
310	strain	strain	NN	_	_	_
311	:	:	:	_	_	_
312	BCE063	bce063	NN	_	_	_
313	,	,	,	_	_	_
314	MS14	ms14	NN	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
316	strain	strain	NN	_	_	_
317	:	:	:	_	_	_
318	BCE066	bce066	NN	_	_	_
319	,	,	,	_	_	_
320	DS5	ds5	NN	_	_	_
321	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
322	strain	strain	NN	_	_	_
323	:	:	:	_	_	_
324	BCE068	bce068	NN	_	_	_
325	,	,	,	_	_	_
326	MS10	ms10	NN	_	_	_
327	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
328	strain	strain	NN	_	_	_
329	:	:	:	_	_	_
330	BCE068	bce068	NN	_	_	_
331	,	,	,	_	_	_
332	MS23	ms23	NN	_	_	_
333	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
334	strain	strain	NN	_	_	_
335	:	:	:	_	_	_
336	BCE069	bce069	NN	_	_	_
337	,	,	,	_	_	_
338	DS2	ds2	NN	_	_	_
339	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
340	strain	strain	NN	_	_	_
341	:	:	:	_	_	_
342	BCE069	bce069	NN	_	_	_
343	,	,	,	_	_	_
344	MS15	ms15	NN	_	_	_
345	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
346	strain	strain	NN	_	_	_
347	:	:	:	_	_	_
348	BCE069	bce069	NN	_	_	_
349	,	,	,	_	_	_
350	MS9	ms9	NN	_	_	_
351	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
352	strain	strain	NN	_	_	_
353	:	:	:	_	_	_
354	BCE129	bce129	NN	_	_	_
355	,	,	,	_	_	_
356	DS2	ds2	NN	_	_	_
357	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
358	strain	strain	NN	_	_	_
359	:	:	:	_	_	_
360	C-34666	c-34666	NN	_	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
362	strain	strain	NN	_	_	_
363	:	:	:	_	_	_
364	C-35134	c-35134	NN	_	_	_
365	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
366	strain	strain	NN	_	_	_
367	:	:	:	_	_	_
368	C-35209	c-35209	NN	_	_	_
369	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
370	strain	strain	NN	_	_	_
371	:	:	:	_	_	_
372	C-35213	c-35213	NN	_	_	_
373	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
374	strain	strain	NN	_	_	_
375	:	:	:	_	_	_
376	C-35605	c-35605	NN	_	_	_
377	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
378	strain	strain	NN	_	_	_
379	:	:	:	_	_	_
380	C-35662	c-35662	NN	_	_	_
381	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
382	strain	strain	NN	_	_	_
383	:	:	:	_	_	_
384	C-35776	c-35776	NN	_	_	_
385	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
386	strain	strain	NN	_	_	_
387	:	:	:	_	_	_
388	C-35959	c-35959	NN	_	_	_
389	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
390	strain	strain	NN	_	_	_
391	:	:	:	_	_	_
392	C-36255	c-36255	NN	_	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
394	strain	strain	NN	_	_	_
395	:	:	:	_	_	_
396	CFT073	cft073	NN	_	_	_
397	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
398	strain	strain	NN	_	_	_
399	:	:	:	_	_	_
400	cocar	cocar	NN	_	_	_
401	07-043	07-043	CD	_	_	_
402	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
403	strain	strain	NN	_	_	_
404	:	:	:	_	_	_
405	cocar	cocar	NN	_	_	_
406	07-40	07-40	CD	_	_	_
407	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
408	strain	strain	NN	_	_	_
409	:	:	:	_	_	_
410	cosin	cosin	NN	_	_	_
411	07-14	07-14	CD	_	_	_
412	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
413	strain	strain	NN	_	_	_
414	:	:	:	_	_	_
415	cosin	cosin	NN	_	_	_
416	07-36	07-36	CD	_	_	_
417	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
418	strain	strain	NN	_	_	_
419	:	:	:	_	_	_
420	cosin	cosin	NN	_	_	_
421	07-61	07-61	CD	_	_	_
422	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
423	strain	strain	NN	_	_	_
424	:	:	:	_	_	_
425	cosin	cosin	NN	_	_	_
426	07-88	07-88	CD	_	_	_
427	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
428	strain	strain	NN	_	_	_
429	:	:	:	_	_	_
430	cosin	cosin	NN	_	_	_
431	07-92	07-92	CD	_	_	_
432	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
433	strain	strain	NN	_	_	_
434	:	:	:	_	_	_
435	D02-2	d02-2	NN	_	_	_
436	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
437	strain	strain	NN	_	_	_
438	:	:	:	_	_	_
439	DS168-1	ds168-1	NN	_	_	_
440	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
441	strain	strain	NN	_	_	_
442	:	:	:	_	_	_
443	DS26-1	ds26-1	NN	_	_	_
444	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
445	strain	strain	NN	_	_	_
446	:	:	:	_	_	_
447	E1392	e1392	NN	_	_	_
448	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
449	strain	strain	NN	_	_	_
450	:	:	:	_	_	_
451	E1777	e1777	NN	_	_	_
452	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
453	strain	strain	NN	_	_	_
454	:	:	:	_	_	_
455	E1785	e1785	NN	_	_	_
456	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
457	strain	strain	NN	_	_	_
458	:	:	:	_	_	_
459	E1786	e1786	NN	_	_	_
460	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
461	strain	strain	NN	_	_	_
462	:	:	:	_	_	_
463	E1787	e1787	NN	_	_	_
464	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
465	strain	strain	NN	_	_	_
466	:	:	:	_	_	_
467	E1788	e1788	NN	_	_	_
468	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
469	strain	strain	NN	_	_	_
470	:	:	:	_	_	_
471	E1789	e1789	NN	_	_	_
472	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
473	strain	strain	NN	_	_	_
474	:	:	:	_	_	_
475	E1790	e1790	NN	_	_	_
476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
477	strain	strain	NN	_	_	_
478	:	:	:	_	_	_
479	E1791	e1791	NN	_	_	_
480	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
481	strain	strain	NN	_	_	_
482	:	:	:	_	_	_
483	E1792	e1792	NN	_	_	_
484	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
485	strain	strain	NN	_	_	_
486	:	:	:	_	_	_
487	E20738A	e20738a	NN	_	_	_
488	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
489	strain	strain	NN	_	_	_
490	:	:	:	_	_	_
491	E24377A	e24377a	NN	_	_	_
492	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
493	strain	strain	NN	_	_	_
494	:	:	:	_	_	_
495	E2528C1	e2528c1	NN	_	_	_
496	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
497	strain	strain	NN	_	_	_
498	:	:	:	_	_	_
499	E7473	e7473	NN	_	_	_
500	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
501	strain	strain	NN	_	_	_
502	:	:	:	_	_	_
503	E7476A	e7476a	NN	_	_	_
504	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
505	strain	strain	NN	_	_	_
506	:	:	:	_	_	_
507	E8775	e8775	NN	_	_	_
508	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
509	strain	strain	NN	_	_	_
510	:	:	:	_	_	_
511	E9034A	e9034a	NN	_	_	_
512	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
513	strain	strain	NN	_	_	_
514	:	:	:	_	_	_
515	ETEC	ETEC	NNP	_	_	_
516	10	10	CD	_	_	_
517	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
518	strain	strain	NN	_	_	_
519	:	:	:	_	_	_
520	ETEC	ETEC	NNP	_	_	_
521	18	18	CD	_	_	_
522	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
523	strain	strain	NN	_	_	_
524	:	:	:	_	_	_
525	ETEC	ETEC	NNP	_	_	_
526	20	20	CD	_	_	_
527	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
528	strain	strain	NN	_	_	_
529	:	:	:	_	_	_
530	ETEC	etec	NNS	_	_	_
531	8	8	CD	_	_	_
532	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
533	strain	strain	NN	_	_	_
534	:	:	:	_	_	_
535	ETEC	ETEC	NNP	_	_	_
536	Jurua	Jurua	NNP	_	_	_
537	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
538	strain	strain	NN	_	_	_
539	:	:	:	_	_	_
540	ETP05-002	etp05-002	NN	_	_	_
541	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
542	strain	strain	NN	_	_	_
543	:	:	:	_	_	_
544	ETP05-003	etp05-003	NN	_	_	_
545	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
546	strain	strain	NN	_	_	_
547	:	:	:	_	_	_
548	ETP05-007	etp05-007	NN	_	_	_
549	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
550	strain	strain	NN	_	_	_
551	:	:	:	_	_	_
552	ETP05-008	etp05-008	NN	_	_	_
553	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
554	strain	strain	NN	_	_	_
555	:	:	:	_	_	_
556	ETP05-009	etp05-009	NN	_	_	_
557	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
558	strain	strain	NN	_	_	_
559	:	:	:	_	_	_
560	ETP05-010	etp05-010	NN	_	_	_
561	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
562	strain	strain	NN	_	_	_
563	:	:	:	_	_	_
564	ETP05-011	etp05-011	NN	_	_	_
565	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
566	strain	strain	NN	_	_	_
567	:	:	:	_	_	_
568	ETP05-012	etp05-012	NN	_	_	_
569	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
570	strain	strain	NN	_	_	_
571	:	:	:	_	_	_
572	ETP05-015	etp05-015	NN	_	_	_
573	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
574	strain	strain	NN	_	_	_
575	:	:	:	_	_	_
576	ETP05-016	etp05-016	NN	_	_	_
577	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
578	strain	strain	NN	_	_	_
579	:	:	:	_	_	_
580	ETP05-017	etp05-017	NN	_	_	_
581	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
582	strain	strain	NN	_	_	_
583	:	:	:	_	_	_
584	ETP05-019	etp05-019	NN	_	_	_
585	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
586	strain	strain	NN	_	_	_
587	:	:	:	_	_	_
588	ETP05-020	etp05-020	NN	_	_	_
589	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
590	strain	strain	NN	_	_	_
591	:	:	:	_	_	_
592	ETP05-026	etp05-026	NN	_	_	_
593	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
594	strain	strain	NN	_	_	_
595	:	:	:	_	_	_
596	ETP05-035	etp05-035	NN	_	_	_
597	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
598	strain	strain	NN	_	_	_
599	:	:	:	_	_	_
600	ETP05-038	etp05-038	NN	_	_	_
601	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
602	strain	strain	NN	_	_	_
603	:	:	:	_	_	_
604	ETP05-039	etp05-039	NN	_	_	_
605	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
606	strain	strain	NN	_	_	_
607	:	:	:	_	_	_
608	ETP05-044	etp05-044	NN	_	_	_
609	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
610	strain	strain	NN	_	_	_
611	:	:	:	_	_	_
612	ETP05-046	etp05-046	NN	_	_	_
613	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
614	strain	strain	NN	_	_	_
615	:	:	:	_	_	_
616	ETP05-047	etp05-047	NN	_	_	_
617	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
618	strain	strain	NN	_	_	_
619	:	:	:	_	_	_
620	ETP05-050	etp05-050	NN	_	_	_
621	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
622	strain	strain	NN	_	_	_
623	:	:	:	_	_	_
624	ETP98004	etp98004	NN	_	_	_
625	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
626	strain	strain	NN	_	_	_
627	:	:	:	_	_	_
628	ETP98015	etp98015	NN	_	_	_
629	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
630	strain	strain	NN	_	_	_
631	:	:	:	_	_	_
632	ETP98028	etp98028	NN	_	_	_
633	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
634	strain	strain	NN	_	_	_
635	:	:	:	_	_	_
636	ETP98038	etp98038	NN	_	_	_
637	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
638	strain	strain	NN	_	_	_
639	:	:	:	_	_	_
640	ETP98042	etp98042	NN	_	_	_
641	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
642	strain	strain	NN	_	_	_
643	:	:	:	_	_	_
644	ETP98053	etp98053	NN	_	_	_
645	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
646	strain	strain	NN	_	_	_
647	:	:	:	_	_	_
648	ETP98056	etp98056	NN	_	_	_
649	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
650	strain	strain	NN	_	_	_
651	:	:	:	_	_	_
652	ETP98061	etp98061	NN	_	_	_
653	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
654	strain	strain	NN	_	_	_
655	:	:	:	_	_	_
656	ETP98062	etp98062	NN	_	_	_
657	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
658	strain	strain	NN	_	_	_
659	:	:	:	_	_	_
660	ETP98066	etp98066	NN	_	_	_
661	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
662	strain	strain	NN	_	_	_
663	:	:	:	_	_	_
664	ETP98068	etp98068	NN	_	_	_
665	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
666	strain	strain	NN	_	_	_
667	:	:	:	_	_	_
668	ETP98073	etp98073	NN	_	_	_
669	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
670	strain	strain	NN	_	_	_
671	:	:	:	_	_	_
672	ETP98097	etp98097	NN	_	_	_
673	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
674	strain	strain	NN	_	_	_
675	:	:	:	_	_	_
676	ETP98103	etp98103	NN	_	_	_
677	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
678	strain	strain	NN	_	_	_
679	:	:	:	_	_	_
680	ETP98105	etp98105	NN	_	_	_
681	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
682	strain	strain	NN	_	_	_
683	:	:	:	_	_	_
684	ETP98109	etp98109	NN	_	_	_
685	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
686	strain	strain	NN	_	_	_
687	:	:	:	_	_	_
688	ETP98111	etp98111	NN	_	_	_
689	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
690	strain	strain	NN	_	_	_
691	:	:	:	_	_	_
692	ETP98112	etp98112	NN	_	_	_
693	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
694	strain	strain	NN	_	_	_
695	:	:	:	_	_	_
696	ETP98114	etp98114	NN	_	_	_
697	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
698	strain	strain	NN	_	_	_
699	:	:	:	_	_	_
700	ETP98115	etp98115	NN	_	_	_
701	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
702	strain	strain	NN	_	_	_
703	:	:	:	_	_	_
704	F5656-C1	f5656-c1	NN	_	_	_
705	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
706	strain	strain	NN	_	_	_
707	:	:	:	_	_	_
708	F595C	f595c	NN	_	_	_
709	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
710	strain	strain	NN	_	_	_
711	:	:	:	_	_	_
712	HS	hs	NN	_	_	_
713	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
714	strain	strain	NN	_	_	_
715	:	:	:	_	_	_
716	ICDDR	icddr	NN	_	_	_
717	,	,	,	_	_	_
718	B	b	NN	_	_	_
719	_	_	NN	_	_	_
720	p1	p1	NN	_	_	_
721	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
722	strain	strain	NN	_	_	_
723	:	:	:	_	_	_
724	ICDDR	icddr	NN	_	_	_
725	,	,	,	_	_	_
726	B	b	NN	_	_	_
727	_	_	NN	_	_	_
728	p10	p10	NN	_	_	_
729	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
730	strain	strain	NN	_	_	_
731	:	:	:	_	_	_
732	ICDDR	icddr	NN	_	_	_
733	,	,	,	_	_	_
734	B	b	NN	_	_	_
735	_	_	NN	_	_	_
736	p11	p11	NN	_	_	_
737	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
738	strain	strain	NN	_	_	_
739	:	:	:	_	_	_
740	ICDDR	icddr	NN	_	_	_
741	,	,	,	_	_	_
742	B	b	NN	_	_	_
743	_	_	NN	_	_	_
744	p12	p12	NN	_	_	_
745	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
746	strain	strain	NN	_	_	_
747	:	:	:	_	_	_
748	ICDDR	icddr	NN	_	_	_
749	,	,	,	_	_	_
750	B	b	NN	_	_	_
751	_	_	NN	_	_	_
752	p13	p13	NN	_	_	_
753	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
754	strain	strain	NN	_	_	_
755	:	:	:	_	_	_
756	ICDDR	icddr	NN	_	_	_
757	,	,	,	_	_	_
758	B	b	NN	_	_	_
759	_	_	NN	_	_	_
760	p2	p2	NN	_	_	_
761	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
762	strain	strain	NN	_	_	_
763	:	:	:	_	_	_
764	ICDDR	icddr	NN	_	_	_
765	,	,	,	_	_	_
766	B	b	NN	_	_	_
767	_	_	NN	_	_	_
768	p4	p4	NN	_	_	_
769	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
770	strain	strain	NN	_	_	_
771	:	:	:	_	_	_
772	ICDDR	icddr	NN	_	_	_
773	,	,	,	_	_	_
774	B	b	NN	_	_	_
775	_	_	NN	_	_	_
776	p5	p5	NN	_	_	_
777	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
778	strain	strain	NN	_	_	_
779	:	:	:	_	_	_
780	ICDDR	icddr	NN	_	_	_
781	,	,	,	_	_	_
782	B	b	NN	_	_	_
783	_	_	CD	_	_	_
784	p6	p6	NN	_	_	_
785	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
786	strain	strain	NN	_	_	_
787	:	:	:	_	_	_
788	ICDDR	icddr	NN	_	_	_
789	,	,	,	_	_	_
790	B	b	NN	_	_	_
791	_	_	NN	_	_	_
792	p7	p7	NN	_	_	_
793	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
794	strain	strain	NN	_	_	_
795	:	:	:	_	_	_
796	ICDDR	icddr	NN	_	_	_
797	,	,	,	_	_	_
798	B	b	NN	_	_	_
799	_	_	CD	_	_	_
800	p8	p8	NN	_	_	_
801	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
802	strain	strain	NN	_	_	_
803	:	:	:	_	_	_
804	ICDDR	icddr	NN	_	_	_
805	,	,	,	_	_	_
806	B	b	NN	_	_	_
807	_	_	CD	_	_	_
808	p9	p9	NN	_	_	_
809	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
810	strain	strain	NN	_	_	_
811	:	:	:	_	_	_
812	LSN02-012560	lsn02-012560	NN	_	_	_
813	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
814	strain	strain	NN	_	_	_
815	:	:	:	_	_	_
816	LSN03-016011	lsn03-016011	NN	_	_	_
817	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
818	strain	strain	NN	_	_	_
819	:	:	:	_	_	_
820	M408C1	m408c1	NN	_	_	_
821	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
822	strain	strain	NN	_	_	_
823	:	:	:	_	_	_
824	M424C1	m424c1	NN	_	_	_
825	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
826	strain	strain	NN	_	_	_
827	:	:	:	_	_	_
828	MG1655	mg1655	NN	_	_	_
829	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
830	strain	strain	NN	_	_	_
831	:	:	:	_	_	_
832	NN-34-1-3	nn-34-1-3	NN	_	_	_
833	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
834	strain	strain	NN	_	_	_
835	:	:	:	_	_	_
836	NR-12	nr-12	NN	_	_	_
837	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
838	strain	strain	NN	_	_	_
839	:	:	:	_	_	_
840	O157	o157	NN	_	_	_
841	:	:	:	_	_	_
842	h7	h7	NN	_	_	_
843	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
844	strain	strain	NN	_	_	_
845	:	:	:	_	_	_
846	O63	o63	NN	_	_	_
847	:	:	:	_	_	_
848	nm	nm	NN	_	_	_
849	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
850	strain	strain	NN	_	_	_
851	:	:	:	_	_	_
852	O78	o78	NN	_	_	_
853	:	:	:	_	_	_
854	h11	h11	NN	_	_	_
855	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
856	strain	strain	NN	_	_	_
857	:	:	:	_	_	_
858	PE360	pe360	NN	_	_	_
859	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
860	strain	strain	NN	_	_	_
861	:	:	:	_	_	_
862	PUTI	puti	NN	_	_	_
863	O26	o26	NN	_	_	_
864	UMN	umn	NN	_	_	_
865	O26	o26	NN	_	_	_
866	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
867	strain	strain	NN	_	_	_
868	:	:	:	_	_	_
869	sPRH-20	sprh-20	NN	_	_	_
870	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
871	strain	strain	NN	_	_	_
872	:	:	:	_	_	_
873	sPRH-21	sprh-21	NN	_	_	_
874	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
875	strain	strain	NN	_	_	_
876	:	:	:	_	_	_
877	sPRH-25	sprh-25	NN	_	_	_
878	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
879	strain	strain	NN	_	_	_
880	:	:	:	_	_	_
881	sPRH-372	sprh-372	NN	_	_	_
882	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
883	strain	strain	NN	_	_	_
884	:	:	:	_	_	_
885	sPRH-403	sprh-403	NN	_	_	_
886	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
887	strain	strain	NN	_	_	_
888	:	:	:	_	_	_
889	sPRH-414	sprh-414	NN	_	_	_
890	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
891	strain	strain	NN	_	_	_
892	:	:	:	_	_	_
893	sPRH-418	sprh-418	NN	_	_	_
894	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
895	strain	strain	NN	_	_	_
896	:	:	:	_	_	_
897	sPRH-420	sprh-420	NN	_	_	_
898	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
899	strain	strain	NN	_	_	_
900	:	:	:	_	_	_
901	sPRH-421	sprh-421	NN	_	_	_
902	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
903	strain	strain	NN	_	_	_
904	:	:	:	_	_	_
905	sPRH-443	sprh-443	NN	_	_	_
906	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
907	strain	strain	NN	_	_	_
908	:	:	:	_	_	_
909	sPRH-445	sprh-445	NN	_	_	_
910	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
911	strain	strain	NN	_	_	_
912	:	:	:	_	_	_
913	sPRH-450	sprh-450	NN	_	_	_
914	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
915	strain	strain	NN	_	_	_
916	:	:	:	_	_	_
917	sPRH-604	sprh-604	NN	_	_	_
918	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
919	strain	strain	NN	_	_	_
920	:	:	:	_	_	_
921	sPRH-605	sprh-605	NN	_	_	_
922	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
923	strain	strain	NN	_	_	_
924	:	:	:	_	_	_
925	sPRH-606	sprh-606	NN	_	_	_
926	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
927	strain	strain	NN	_	_	_
928	:	:	:	_	_	_
929	sPRH-609	sprh-609	NN	_	_	_
930	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
931	strain	strain	NN	_	_	_
932	:	:	:	_	_	_
933	sPRH-610	sprh-610	NN	_	_	_
934	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
935	strain	strain	NN	_	_	_
936	:	:	:	_	_	_
937	sPRH-612	sprh-612	NN	_	_	_
938	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
939	strain	strain	NN	_	_	_
940	:	:	:	_	_	_
941	sPRH-613	sprh-613	NN	_	_	_
942	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
943	strain	strain	NN	_	_	_
944	:	:	:	_	_	_
945	TW03439	tw03439	NN	_	_	_
946	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
947	strain	strain	NN	_	_	_
948	:	:	:	_	_	_
949	TW03452	tw03452	NN	_	_	_
950	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
951	strain	strain	NN	_	_	_
952	:	:	:	_	_	_
953	TW03574	tw03574	NN	_	_	_
954	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
955	strain	strain	NN	_	_	_
956	:	:	:	_	_	_
957	TW03576	tw03576	NN	_	_	_
958	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
959	strain	strain	NN	_	_	_
960	:	:	:	_	_	_
961	TW03585	tw03585	NN	_	_	_
962	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
963	strain	strain	NN	_	_	_
964	:	:	:	_	_	_
965	TW03741	tw03741	NN	_	_	_
966	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
967	strain	strain	NN	_	_	_
968	:	:	:	_	_	_
969	WS	ws	NN	_	_	_
970	0115A	0115a	NN	_	_	_
971	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
972	strain	strain	NN	_	_	_
973	:	:	:	_	_	_
974	WS1896A	ws1896a	NN	_	_	_
975	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
976	strain	strain	NN	_	_	_
977	:	:	:	_	_	_
978	WS1896	ws1896	NN	_	_	_
979	A-1	a-1	NN	_	_	_
980	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
981	strain	strain	NN	_	_	_
982	:	:	:	_	_	_
983	WS	ws	NN	_	_	_
984	1933D	1933d	NN	_	_	_
985	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
986	strain	strain	NN	_	_	_
987	:	:	:	_	_	_
988	WS2068A	ws2068a	NN	_	_	_
989	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
990	strain	strain	NN	_	_	_
991	:	:	:	_	_	_
992	WS	ws	NN	_	_	_
993	2173A	2173a	NN	_	_	_
994	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
995	strain	strain	NN	_	_	_
996	:	:	:	_	_	_
997	WS2741	ws2741	NN	_	_	_
998	A-1	a-1	NN	_	_	_
999	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1000	strain	strain	NN	_	_	_
1001	:	:	:	_	_	_
1002	WS3080A	ws3080a	NN	_	_	_
1003	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1004	strain	strain	NN	_	_	_
1005	:	:	:	_	_	_
1006	WS	ws	NN	_	_	_
1007	3294A	3294a	NN	_	_	_
1008	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1009	strain	strain	NN	_	_	_
1010	:	:	:	_	_	_
1011	WS	w	NNS	_	_	_
1012	3572	3572	CD	_	_	_
1013	A-1	a-1	NN	_	_	_
1014	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1015	strain	strain	NN	_	_	_
1016	:	:	:	_	_	_
1017	WS	w	NNS	_	_	_
1018	3596	3596	CD	_	_	_
1019	A-4	a-4	NN	_	_	_
1020	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1021	strain	strain	NN	_	_	_
1022	:	:	:	_	_	_
1023	WS4087	ws4087	NN	_	_	_
1024	A-1	a-1	NN	_	_	_
1025	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1026	strain	strain	NN	_	_	_
1027	:	:	:	_	_	_
1028	WS4264	ws4264	NN	_	_	_
1029	A-1	a-1	NN	_	_	_
1030	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1031	strain	strain	NN	_	_	_
1032	:	:	:	_	_	_
1033	WS5874	ws5874	NN	_	_	_
1034	A-1	a-1	NN	_	_	_
1035	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1036	strain	strain	NN	_	_	_
1037	:	:	:	_	_	_
1038	WS6582	ws6582	NN	_	_	_
1039	A-1	a-1	NN	_	_	_
1040	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1041	strain	strain	NN	_	_	_
1042	:	:	:	_	_	_
1043	WS	ws	NN	_	_	_
1044	6866B-1	6866b-1	NN	_	_	_
1045	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1046	strain	strain	NN	_	_	_
1047	:	:	:	_	_	_
1048	WS	w	NNS	_	_	_
1049	7162	7162	CD	_	_	_
1050	A-1	a-1	NN	_	_	_
1051	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1052	strain	strain	NN	_	_	_
1053	:	:	:	_	_	_
1054	WS7179	ws7179	NN	_	_	_
1055	A-2	a-2	NN	_	_	_
1056	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1057	CFT073	cft073	NN	_	_	_
1058	in	in	IN	_	_	_
1059	LB	LB	NNP	_	_	_
1060	,	,	,	_	_	_
1061	after	after	IN	_	_	_
1062	5	5	CD	_	_	_
1063	hours	hour	NNS	_	_	_
1064	of	of	IN	_	_	_
1065	growth	growth	NN	_	_	_
1066	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	CFT073	cft073	NN	_	_	_
3	in	in	IN	_	_	_
4	LB+PAC	lb+pac	NN	_	_	_
5	s	s	NNS	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	100	100	CD	_	_	_
8	µg	µg	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	CFT073	cft073	NN	_	_	_
11	_	_	CD	_	_	_
12	LB+PAC	lb+pac	NN	_	_	_
13	s	s	NNS	_	_	_
14	_	_	VBP	_	_	_
15	rep1	rep1	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	CFT073	cft073	NN	_	_	_
18	_	_	CD	_	_	_
19	LB+PAC	lb+pac	NN	_	_	_
20	s	s	NNS	_	_	_
21	_	_	VBP	_	_	_
22	rep2	rep2	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	CFT073	cft073	NN	_	_	_
25	_	_	CD	_	_	_
26	LB+PAC	lb+pac	NN	_	_	_
27	s	s	NNS	_	_	_
28	_	_	VBP	_	_	_
29	rep3	rep3	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	CFT073	cft073	NN	_	_	_
32	_	_	CD	_	_	_
33	LB	lb	NN	_	_	_
34	_	_	CD	_	_	_
35	rep1	rep1	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	CFT073	cft073	NN	_	_	_
38	_	_	CD	_	_	_
39	LB	lb	NN	_	_	_
40	_	_	CD	_	_	_
41	rep2	rep2	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	CFT073	cft073	NN	_	_	_
44	_	_	CD	_	_	_
45	LB	lb	NN	_	_	_
46	_	_	CD	_	_	_
47	rep3	rep3	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	Cultures	culture	NNS	_	_	_
50	of	of	IN	_	_	_
51	E.	e.	FW	_	_	_
52	coli	coli	FW	_	_	_
53	CFT073	cft073	NN	_	_	_
54	were	be	VBD	_	_	_
55	maintained	maintain	VBN	_	_	_
56	at	at	IN	_	_	_
57	--	--	:	_	_	_
58	80ºC	80ºc	NN	_	_	_
59	in	in	IN	_	_	_
60	Luria-Bertani	luria-bertani	JJ	_	_	_
61	broth	broth	NN	_	_	_
62	with	with	IN	_	_	_
63	15	15	CD	_	_	_
64	%	%	NN	_	_	_
65	glycerol	glycerol	NN	SUPP	_	_
66	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	streaked	streak	VBN	_	_	_
4	onto	onto	IN	_	_	_
5	LB	LB	NNP	_	_	_
6	agar	agar	NN	_	_	_
7	plates	plate	NNS	_	_	_
8	and	and	CC	_	_	_
9	incubated	incubate	VBN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	37	37	CD	_	_	_
12	°C	°c	NN	_	_	_
13	,	,	,	_	_	_
14	24	24	CD	_	_	_
15	h	h	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	single	single	JJ	_	_	_
3	colony	colony	NN	_	_	_
4	was	be	VBD	_	_	_
5	inoculated	inoculate	VBN	_	_	_
6	into	into	IN	_	_	_
7	150	150	CD	_	_	_
8	mL	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	LB	lb	NN	MED	_	_
11	broth	broth	NN	MED	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	in	in	IN	_	_	_
14	a	a	DT	_	_	_
15	500	500	CD	_	_	_
16	mL	ml	NN	_	_	_
17	baffled	baffle	VBN	_	_	_
18	flask	flask	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	Three	three	CD	_	_	_
2	inoculated	inoculate	VBN	_	_	_
3	flasks	flask	NNS	_	_	_
4	contained	contain	VBD	_	_	_
5	LB	lb	NN	MED	_	_
6	broth	broth	NN	MED	_	_
7	alone	alone	RB	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	controls	control	NNS	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	three	three	CD	_	_	_
14	inoculated	inoculate	VBN	_	_	_
15	flasks	flask	NNS	_	_	_
16	were	be	VBD	_	_	_
17	supplemented	supplement	VBN	_	_	_
18	with	with	IN	_	_	_
19	cranberry	cranberry	NN	_	_	_
20	derived	derive	VBN	_	_	_
21	PAC	PAC	NNP	_	_	_
22	extract	extract	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	100	100	CD	_	_	_
25	µg	µg	NN	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	Escherichia	escherichia	FW	Organism	_	_
28	coli	coli	FW	Organism	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	growth	growth	NN	_	_	_
31	condition	condition	NN	_	_	_
32	:	:	:	_	_	_
33	LB	lb	NN	MED	_	_
34	broth	broth	NN	MED	_	_
35	alone	alone	RB	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	control	control	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	growth	growth	NN	_	_	_
41	condition	condition	NN	_	_	_
42	:	:	:	_	_	_
43	LB	lb	NN	MED	_	_
44	broth	broth	NN	MED	_	_
45	supplemented	supplement	VBN	_	_	_
46	with	with	IN	_	_	_
47	cranberry	cranberry	NN	_	_	_
48	PACs	pac	NNS	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	100	100	CD	_	_	_
51	µg	µg	NN	_	_	_
52	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
53	One	one	CD	_	_	_
54	volume	volume	NN	_	_	_
55	of	of	IN	_	_	_
56	bacterial	bacterial	JJ	_	_	_
57	culture	culture	NN	_	_	_
58	was	be	VBD	_	_	_
59	added	add	VBN	_	_	_
60	to	to	TO	_	_	_
61	two	two	CD	_	_	_
62	volumes	volume	NNS	_	_	_
63	of	of	IN	_	_	_
64	RNAprotect	rnaprotect	NN	_	_	_
65	Bacteria	bacterium	NNS	_	_	_
66	Reagent	reagent	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	Qiagen	qiagen	NN	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	and	and	CC	_	_	_
71	RNA	rna	NN	_	_	_
72	was	be	VBD	_	_	_
73	extracted	extract	VBN	_	_	_
74	using	use	VBG	_	_	_
75	RNeasy	RNeasy	NNP	_	_	_
76	mini	minus	NNS	_	_	_
77	kit	kit	NN	_	_	_
78	-LRB-	-lrb-	-LRB-	_	_	_
79	Qiagen	qiagen	NN	_	_	_
80	-RRB-	-rrb-	-RRB-	_	_	_
81	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	on-column	on-column	JJ	_	_	_
5	treated	treat	VBN	_	_	_
6	with	with	IN	_	_	_
7	DNase	dnase	NN	_	_	_
8	I.	i.	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	RNA	rna	NN	_	_	_
11	extraction	extraction	NN	_	_	_
12	was	be	VBD	_	_	_
13	performed	perform	VBN	_	_	_
14	according	accord	VBG	_	_	_
15	to	to	TO	_	_	_
16	the	the	DT	_	_	_
17	manufacturer	manufacturer	NN	_	_	_
18	's	's	POS	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Qiagen	Qiagen	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	instructions	instruction	NNS	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	CFT073	cft073	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
6	The	the	DT	_	_	_
7	data	datum	NNS	_	_	_
8	were	be	VBD	_	_	_
9	analyzed	analyze	VBN	_	_	_
10	with	with	IN	_	_	_
11	FlexArray	FlexArray	NNP	_	_	_
12	1.4.1	1.4.1	CD	_	_	_
13	software	software	NN	_	_	_
14	program	program	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	http	http	NN	_	_	_
17	:	:	:	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Comparison	comparison	NN	_	_	_
20	cya	cya	NN	_	_	_
21	mutant	mutant	NN	_	_	_
22	with	with	IN	_	_	_
23	wt	wt	JJ	_	_	_
24	under	under	IN	_	_	_
25	glucose-limited	glucose-limited	JJ	_	_	_
26	conditions	condition	NNS	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	replicate	replicate	VB	_	_	_
29	1	1	LS	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Comparison	comparison	NN	_	_	_
33	cya	cya	NN	_	_	_
34	mutant	mutant	NN	_	_	_
35	with	with	IN	_	_	_
36	wt	wt	JJ	_	_	_
37	under	under	IN	_	_	_
38	glucose-limited	glucose-limited	JJ	_	_	_
39	conditions	condition	NNS	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	replicate	replicate	VB	_	_	_
42	2	2	LS	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	Comparison	comparison	NN	_	_	_
46	cya	cya	NN	_	_	_
47	mutant	mutant	NN	_	_	_
48	with	with	IN	_	_	_
49	wt	wt	JJ	_	_	_
50	under	under	IN	_	_	_
51	glucose-limited	glucose-limited	JJ	_	_	_
52	conditions	condition	NNS	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	replicate	replicate	VB	_	_	_
55	3	3	LS	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Comparison	comparison	NN	_	_	_
59	rpoS	rpos	NN	GEN	_	_
60	mutant	mutant	NN	_	_	_
61	with	with	IN	_	_	_
62	wt	wt	JJ	_	_	_
63	under	under	IN	_	_	_
64	glucose-limited	glucose-limited	JJ	_	_	_
65	conditions	condition	NNS	_	_	_
66	-LRB-	-lrb-	-LRB-	_	_	_
67	replicate	replicate	VB	_	_	_
68	1	1	LS	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	Comparison	comparison	NN	_	_	_
72	rpoS	rpos	NN	GEN	_	_
73	mutant	mutant	NN	_	_	_
74	with	with	IN	_	_	_
75	wt	wt	JJ	_	_	_
76	under	under	IN	_	_	_
77	glucose-limited	glucose-limited	JJ	_	_	_
78	conditions	condition	NNS	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	replicate	replicate	VB	_	_	_
81	2	2	LS	_	_	_
82	-RRB-	-rrb-	-RRB-	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	Comparison	comparison	NN	_	_	_
85	rpoS	rpos	NN	GEN	_	_
86	mutant	mutant	NN	_	_	_
87	with	with	IN	_	_	_
88	wt	wt	JJ	_	_	_
89	under	under	IN	_	_	_
90	glucose-limited	glucose-limited	JJ	_	_	_
91	conditions	condition	NNS	_	_	_
92	-LRB-	-lrb-	-LRB-	_	_	_
93	replicate	replicate	VB	_	_	_
94	3	3	LS	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	condition	condition	NN	_	_	_
98	:	:	:	_	_	_
99	glucose	glucose	NN	SUPP	_	_
100	limited	limited	JJ	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	control	control	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	cya	cya	NN	_	_	_
105	mutant	mutant	JJ	_	_	_
106	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
107	Escherichia	escherichia	FW	Organism	_	_
108	coli	coli	FW	Organism	_	_
109	K-12	k-12	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	genotype	genotype	NN	_	_	_
112	:	:	:	_	_	_
113	cya	cya	NN	_	_	_
114	mutant	mutant	JJ	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	genotype	genotype	NN	_	_	_
117	:	:	:	_	_	_
118	rpoS	rpos	NN	GEN	_	_
119	mutant	mutant	JJ	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	genotype	genotype	NN	_	_	_
122	:	:	:	_	_	_
123	wild-type	wild-type	JJ	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	rpoS	rpos	NN	GEN	_	_
126	mutant	mutant	JJ	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	strain	strain	NN	_	_	_
129	:	:	:	_	_	_
130	MG1655	mg1655	NN	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
132	The	the	DT	_	_	_
133	data	datum	NNS	_	_	_
134	provided	provide	VBN	_	_	_
135	are	be	VBP	_	_	_
136	the	the	DT	_	_	_
137	original	original	JJ	_	_	_
138	data	datum	NNS	_	_	_
139	generated	generate	VBN	_	_	_
140	with	with	IN	_	_	_
141	the	the	DT	_	_	_
142	Jaguar	Jaguar	NNP	_	_	_
143	software	software	NN	_	_	_
144	from	from	IN	_	_	_
145	the	the	DT	_	_	_
146	microarray	microarray	NN	_	_	_
147	images	image	NNS	_	_	_
148	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	VALUEs	value	NNS	_	_	_
3	reported	report	VBD	_	_	_
4	represent	represent	VBP	_	_	_
5	normalized	normalize	VBN	_	_	_
6	log10	log10	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Cy5	cy5	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Total	total	JJ	_	_	_
11	RNA	rna	NN	_	_	_
12	was	be	VBD	_	_	_
13	isolated	isolate	VBN	_	_	_
14	as	as	IN	_	_	_
15	described	describe	VBN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Sambrook	Sambrook	NNP	_	_	_
18	et	et	FW	_	_	_
19	al.	al.	FW	_	_	_
20	,	,	,	_	_	_
21	1989	1989	CD	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	extracted	extract	VBN	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	checked	check	VBN	_	_	_
6	for	for	IN	_	_	_
7	purity	purity	NN	_	_	_
8	by	by	IN	_	_	_
9	gel	gel	NN	_	_	_
10	electrophoresis	electrophoresis	NN	_	_	_
11	and	and	CC	_	_	_
12	was	be	VBD	_	_	_
13	quantified	quantify	VBN	_	_	_
14	by	by	IN	_	_	_
15	measuring	measure	VBG	_	_	_
16	extinction	extinction	NN	_	_	_
17	spectrophotometrically	spectrophotometrically	RB	_	_	_
18	at	at	IN	_	_	_
19	260	260	CD	_	_	_
20	nm	nm	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	200µl	200µl	NN	_	_	_
3	of	of	IN	_	_	_
4	prepared	prepared	JJ	_	_	_
5	E.coli	e.coli	NN	_	_	_
6	O157	o157	NN	_	_	_
7	cells	cell	NNS	_	_	_
8	within	within	IN	_	_	_
9	LB	lb	NN	MED	_	_
10	broth	broth	NN	MED	_	_
11	is	be	VBZ	_	_	_
12	spreaded	spread	VBN	_	_	_
13	to	to	TO	_	_	_
14	LB	LB	NNP	_	_	_
15	agar	agar	NN	_	_	_
16	plate	plate	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	sterilized	sterilize	VBN	_	_	_
20	6	6	CD	_	_	_
21	mm	mm	NN	_	_	_
22	filtered	filter	VBD	_	_	_
23	paper	paper	NN	_	_	_
24	disk	disk	NN	_	_	_
25	was	be	VBD	_	_	_
26	placed	place	VBN	_	_	_
27	on	on	IN	_	_	_
28	the	the	DT	_	_	_
29	plate	plate	NN	_	_	_
30	tightly	tightly	RB	_	_	_
31	,	,	,	_	_	_
32	where	where	WRB	_	_	_
33	E.coli	e.coli	JJ	_	_	_
34	O157	o157	NN	_	_	_
35	is	be	VBZ	_	_	_
36	spreaded	spread	VBN	_	_	_
37	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	filtered	filter	VBN	_	_	_
3	fractions	fraction	NNS	_	_	_
4	are	be	VBP	_	_	_
5	injected	inject	VBN	_	_	_
6	to	to	TO	_	_	_
7	each	each	DT	_	_	_
8	paper	paper	NN	_	_	_
9	disk	disk	NN	_	_	_
10	and	and	CC	_	_	_
11	Distilled	Distilled	NNP	_	_	_
12	water	water	NN	_	_	_
13	and	and	CC	_	_	_
14	Ampicillin	ampicillin	NN	_	_	_
15	were	be	VBD	_	_	_
16	used	use	VBN	_	_	_
17	as	as	IN	_	_	_
18	negative	negative	JJ	_	_	_
19	-	-	:	_	_	_
20	and	and	CC	_	_	_
21	positive	positive	JJ	_	_	_
22	control	control	NN	_	_	_
23	each	each	DT	_	_	_
24	and	and	CC	_	_	_
25	then	then	RB	_	_	_
26	cultured	culture	VBN	_	_	_
27	at	at	IN	_	_	_
28	37	37	CD	_	_	_
29	℃	℃	NN	_	_	_
30	for	for	IN	_	_	_
31	24	24	CD	_	_	_
32	hours	hour	NNS	_	_	_
33	.	.	.	_	_	_

1	Finally	finally	RB	_	_	_
2	the	the	DT	_	_	_
3	diameter	diameter	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	cleared	clear	VBN	_	_	_
7	zone	zone	NN	_	_	_
8	arisen	arise	VBN	_	_	_
9	around	around	IN	_	_	_
10	the	the	DT	_	_	_
11	paper	paper	NN	_	_	_
12	disk	disk	NN	_	_	_
13	was	be	VBD	_	_	_
14	measured	measure	VBN	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	50µl	50µl	CD	_	_	_
3	of	of	IN	_	_	_
4	total	total	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	of	of	IN	_	_	_
7	the	the	DT	_	_	_
8	cells	cell	NNS	_	_	_
9	affected	affect	VBN	_	_	_
10	by	by	IN	_	_	_
11	the	the	DT	_	_	_
12	Chrysanthemum	Chrysanthemum	NNP	_	_	_
13	herba	herba	NN	_	_	_
14	methyl	methyl	NN	_	_	_
15	chloride	chloride	NN	_	_	_
16	fraction	fraction	NN	_	_	_
17	was	be	VBD	_	_	_
18	isolated	isolate	VBN	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	RNA	rna	NN	_	_	_
3	extraction	extraction	NN	_	_	_
4	procedure	procedure	NN	_	_	_
5	was	be	VBD	_	_	_
6	carried	carry	VBN	_	_	_
7	out	out	RP	_	_	_
8	using	use	VBG	_	_	_
9	the	the	DT	_	_	_
10	RNeasy	rneasy	NN	_	_	_
11	mini	minus	NNS	_	_	_
12	kit	kit	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Qiagen	Qiagen	NNP	_	_	_
15	,	,	,	_	_	_
16	Inc.	Inc.	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	according	accord	VBG	_	_	_
19	to	to	TO	_	_	_
20	the	the	DT	_	_	_
21	manufacturer	manufacturer	NN	_	_	_
22	's	's	POS	_	_	_
23	instructions	instruction	NNS	_	_	_
24	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	1	1	CD	_	_	_
4	ml	ml	NN	_	_	_
5	of	of	IN	_	_	_
6	bacterial	bacterial	JJ	_	_	_
7	culture	culture	NN	_	_	_
8	was	be	VBD	_	_	_
9	added	add	VBN	_	_	_
10	to	to	TO	_	_	_
11	2	2	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	RNA	rna	NN	_	_	_
15	protect	protect	VBP	_	_	_
16	bacteria	bacterium	NNS	_	_	_
17	reagent	reagent	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	,	,	,	_	_	_
21	Inc.	Inc.	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

1	Centrifugation	centrifugation	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	5000	5000	CD	_	_	_
4	g	g	NN	_	_	_
5	for	for	IN	_	_	_
6	10	10	CD	_	_	_
7	minutes	minute	NNS	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	mixture	mixture	NN	_	_	_
12	was	be	VBD	_	_	_
13	performed	perform	VBN	_	_	_
14	to	to	TO	_	_	_
15	precipitate	precipitate	VB	_	_	_
16	the	the	DT	_	_	_
17	cells	cell	NNS	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	harvested	harvest	VBN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	incubated	incubate	VBN	_	_	_
6	in	in	IN	_	_	_
7	TE	TE	NNP	_	_	_
8	buffer	buffer	NN	_	_	_
9	with	with	IN	_	_	_
10	1	1	CD	_	_	_
11	mg	mg	NN	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	Data	Data	NNP	_	_	_
14	analysis	analysis	NN	_	_	_
15	was	be	VBD	_	_	_
16	carried	carry	VBN	_	_	_
17	out	out	RP	_	_	_
18	using	use	VBG	_	_	_
19	the	the	DT	_	_	_
20	Agilent	Agilent	NNP	_	_	_
21	GeneSpring	GeneSpring	NNP	_	_	_
22	GX	GX	NNP	_	_	_
23	.	.	.	_	_	_

1	Robust	robust	JJ	_	_	_
2	Multi-array	multi-array	JJ	_	_	_
3	Average	average	JJ	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	RMA	rma	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	normalization	normalization	NN	_	_	_
8	performed	perform	VBN	_	_	_
9	using	use	VBG	_	_	_
10	of	of	IN	_	_	_
11	signal	signal	NN	_	_	_
12	intensity	intensity	NN	_	_	_
13	spot	spot	NN	_	_	_
14	data	datum	NNS	_	_	_
15	which	which	WDT	_	_	_
16	obtained	obtain	VBN	_	_	_
17	by	by	IN	_	_	_
18	scanning	scanning	NN	_	_	_
19	process	process	NN	_	_	_
20	and	and	CC	_	_	_
21	it	it	PRP	_	_	_
22	is	be	VBZ	_	_	_
23	indicated	indicate	VBN	_	_	_
24	as	as	IN	_	_	_
25	a	a	DT	_	_	_
26	scatter	scatter	NN	_	_	_
27	plot	plot	NN	_	_	_
28	data	datum	NNS	_	_	_
29	.	.	.	_	_	_

1	Distribution	distribution	NN	_	_	_
2	of	of	IN	_	_	_
3	all	all	DT	_	_	_
4	genes	gene	NNS	_	_	_
5	which	which	WDT	_	_	_
6	obtained	obtain	VBD	_	_	_
7	result	result	NN	_	_	_
8	of	of	IN	_	_	_
9	the	the	DT	_	_	_
10	experiment	experiment	NN	_	_	_
11	is	be	VBZ	_	_	_
12	indicated	indicate	VBN	_	_	_
13	as	as	IN	_	_	_
14	a	a	DT	_	_	_
15	histogram	histogram	NN	_	_	_
16	.	.	.	_	_	_

1	Accuracy	accuracy	NN	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	results	result	NNS	_	_	_
5	of	of	IN	_	_	_
6	the	the	DT	_	_	_
7	experiment	experiment	NN	_	_	_
8	was	be	VBD	_	_	_
9	determined	determine	VBN	_	_	_
10	through	through	IN	_	_	_
11	comparison	comparison	NN	_	_	_
12	of	of	IN	_	_	_
13	the	the	DT	_	_	_
14	histogram	histogram	NN	_	_	_
15	with	with	IN	_	_	_
16	the	the	DT	_	_	_
17	scatter	scatter	NN	_	_	_
18	plot	plot	NN	_	_	_
19	data	datum	NNS	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	EDL932	edl932	NN	_	_	_
3	exposure	exposure	NN	_	_	_
4	to	to	TO	_	_	_
5	CL	cl	NN	_	_	_
6	MC	MC	NNP	_	_	_
7	fraction	fraction	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	EDL932	edl932	NN	_	_	_
10	unexposed	unexposed	JJ	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	Escherichia	escherichia	FW	Organism	_	_
13	coli	coli	FW	Organism	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	O157	o157	NN	_	_	_
16	_	_	CD	_	_	_
17	CL	cl	NN	_	_	_
18	MC	MC	NNP	_	_	_
19	fraction	fraction	NN	_	_	_
20	vs	vs	CC	_	_	_
21	control	control	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	strain	strain	NN	_	_	_
24	:	:	:	_	_	_
25	E.coli	e.coli	NNS	_	_	_
26	O157	o157	NN	_	_	_
27	:	:	:	_	_	_
28	H7	h7	NN	_	_	_
29	EDL	edl	NN	_	_	_
30	932	932	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
32	The	the	DT	_	_	_
33	bacterial	bacterial	JJ	_	_	_
34	cells	cell	NNS	_	_	_
35	were	be	VBD	_	_	_
36	grown	grow	VBN	_	_	_
37	at	at	IN	_	_	_
38	37	37	CD	_	_	_
39	℃	℃	NN	_	_	_
40	for	for	IN	_	_	_
41	17	17	CD	_	_	_
42	hours	hour	NNS	_	_	_
43	on	on	IN	_	_	_
44	Luria-Bertani	Luria-Bertani	NNP	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	LB	LB	NNP	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	agar	agar	NN	_	_	_
49	plate	plate	NN	_	_	_
50	.	.	.	_	_	_

1	An	a	DT	_	_	_
2	isolated	isolate	VBN	_	_	_
3	colony	colony	NN	_	_	_
4	was	be	VBD	_	_	_
5	picked	pick	VBN	_	_	_
6	and	and	CC	_	_	_
7	inoculated	inoculate	VBN	_	_	_
8	into	into	IN	_	_	_
9	100	100	CD	_	_	_
10	ml	ml	NN	_	_	_
11	of	of	IN	_	_	_
12	sterilized	sterilize	VBN	_	_	_
13	LB	lb	NN	MED	_	_
14	broth	broth	NN	MED	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	10g	10g	CD	_	_	_
17	of	of	IN	_	_	_
18	tryptone	tryptone	NN	SUPP	_	_
19	,	,	,	_	_	_
20	5g	5g	NN	_	_	_
21	of	of	IN	_	_	_
22	yeast	yeast	NN	SUPP	_	_
23	extract	extract	NN	SUPP	_	_
24	and	and	CC	_	_	_
25	10g	10g	NN	_	_	_
26	of	of	IN	_	_	_
27	sodium	sodium	NN	SUPP	_	_
28	chloride	chloride	NN	SUPP	_	_
29	per	per	IN	_	_	_
30	liter	liter	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	and	and	CC	_	_	_
33	incubated	incubate	VBN	_	_	_
34	overnight	overnight	JJ	_	_	_
35	for	for	IN	_	_	_
36	17	17	CD	_	_	_
37	hours	hour	NNS	_	_	_
38	at	at	IN	_	_	_
39	37	37	CD	_	_	_
40	℃	℃	NN	_	_	_
41	with	with	IN	_	_	_
42	shaking	shake	VBG	_	_	_
43	at	at	IN	_	_	_
44	250	250	CD	_	_	_
45	rpm	rpm	NN	_	_	_
46	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	1:100	1:100	CD	_	_	_
3	dilution	dilution	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	culture	culture	NN	_	_	_
7	was	be	VBD	_	_	_
8	performed	perform	VBN	_	_	_
9	using	use	VBG	_	_	_
10	pre-warmed	pre-warmed	JJ	_	_	_
11	LB	lb	NN	MED	_	_
12	broth	broth	NN	MED	_	_
13	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	diluted	diluted	JJ	_	_	_
3	culture	culture	NN	_	_	_
4	was	be	VBD	_	_	_
5	incubated	incubate	VBN	_	_	_
6	at	at	IN	_	_	_
7	37	37	CD	_	_	_
8	℃	℃	NN	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	at	at	IN	_	_	_
12	250rpm	250rpm	NN	_	_	_
13	until	until	IN	_	_	_
14	a	a	DT	_	_	_
15	final	final	JJ	_	_	_
16	optical	optical	JJ	_	_	_
17	density	density	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	OD600	od600	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	of	of	IN	_	_	_
22	0.8	0.8	CD	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	early	early	JJ	_	_	_
25	logarithmic	logarithmic	JJ	_	_	_
26	phase	phase	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	was	be	VBD	_	_	_
29	attained	attain	VBN	_	_	_
30	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	further	further	JJ	_	_	_
3	1:10	1:10	CD	_	_	_
4	dilution	dilution	NN	_	_	_
5	was	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	using	use	VBG	_	_	_
8	LB	lb	NN	MED	_	_
9	broth	broth	NN	MED	_	_
10	and	and	CC	_	_	_
11	incubated	incubate	VBN	_	_	_
12	at	at	IN	_	_	_
13	37	37	CD	_	_	_
14	℃	℃	NN	_	_	_
15	with	with	IN	_	_	_
16	shaking	shake	VBG	_	_	_
17	at	at	IN	_	_	_
18	250	250	CD	_	_	_
19	rpm	rpm	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2	antibody	antibody	NN	_	_	_
3	:	:	:	_	_	_
4	9E10	9e10	NN	_	_	_
5	Myc	myc	NN	_	_	_
6	tag	tag	NN	GEN	_	_
7	antibody	antibody	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	antibody	antibody	NN	_	_	_
10	manufacturer	manufacturer	NN	_	_	_
11	:	:	:	_	_	_
12	Upstate	upstate	JJ	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	antibody	antibody	NN	_	_	_
15	:	:	:	_	_	_
16	normal	normal	JJ	_	_	_
17	mouse	mouse	NN	_	_	_
18	IgG	igg	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	ArgR	argr	NN	TF	_	_
21	_	_	CD	_	_	_
22	Arginine	arginine	NN	_	_	_
23	_	_	NN	_	_	_
24	1	1	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	ArgR	argr	NN	TF	_	_
27	_	_	CD	_	_	_
28	Arginine	arginine	NN	_	_	_
29	_	_	NN	_	_	_
30	2	2	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	ArgR	argr	NN	TF	_	_
33	_	_	CD	_	_	_
34	NH4Cl	nh4cl	NN	_	_	_
35	_	_	NN	_	_	_
36	1	1	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	ArgR	argr	NN	TF	_	_
39	_	_	CD	_	_	_
40	NH4Cl	nh4cl	NN	_	_	_
41	_	_	NN	_	_	_
42	2	2	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Cells	cell	NNS	_	_	_
45	at	at	IN	_	_	_
46	appropriate	appropriate	JJ	_	_	_
47	cell	cell	NN	_	_	_
48	density	density	NN	_	_	_
49	were	be	VBD	_	_	_
50	cross-linked	cross-link	VBN	_	_	_
51	by	by	IN	_	_	_
52	1	1	CD	_	_	_
53	%	%	NN	_	_	_
54	formaldehyde	formaldehyde	NN	_	_	_
55	at	at	IN	_	_	_
56	room	room	NN	_	_	_
57	temperature	temperature	NN	_	_	_
58	for	for	IN	_	_	_
59	25	25	CD	_	_	_
60	min	min	NN	_	_	_
61	.	.	.	_	_	_

1	Following	follow	VBG	_	_	_
2	quenching	quench	VBG	_	_	_
3	the	the	DT	_	_	_
4	unused	unused	JJ	_	_	_
5	formaldehyde	formaldehyde	NN	_	_	_
6	with	with	IN	_	_	_
7	a	a	DT	_	_	_
8	final	final	JJ	_	_	_
9	concentration	concentration	NN	_	_	_
10	of	of	IN	_	_	_
11	125	125	CD	_	_	_
12	mM	mm	NN	KWSUPP	_	_
13	glycine	glycine	NN	_	_	_
14	at	at	IN	_	_	_
15	room	room	NN	_	_	_
16	temperature	temperature	NN	_	_	_
17	for	for	IN	_	_	_
18	5	5	CD	_	_	_
19	min	min	NN	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cross-linked	cross-linked	JJ	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	harvested	harvest	VBN	_	_	_
6	and	and	CC	_	_	_
7	washed	wash	VBN	_	_	_
8	three	three	CD	_	_	_
9	times	time	NNS	_	_	_
10	with	with	IN	_	_	_
11	50	50	CD	_	_	_
12	mL	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	ice-cold	ice-cold	JJ	_	_	_
15	TBS	tbs	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Tris	tris	NN	_	_	_
18	Buffered	buffer	VBN	_	_	_
19	Saline	saline	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	washed	wash	VBN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	re-suspended	re-suspended	JJ	_	_	_
6	in	in	IN	_	_	_
7	0.5	0.5	CD	_	_	_
8	mL	ml	NN	_	_	_
9	lysis	lysis	NN	_	_	_
10	buffer	buffer	NN	_	_	_
11	composed	compose	VBN	_	_	_
12	of	of	IN	_	_	_
13	50	50	CD	_	_	_
14	mM	mm	NN	KWSUPP	_	_
15	Tris-HCl	tris-hcl	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	pH	ph	NN	_	_	_
18	7.5	7.5	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	,	,	,	_	_	_
21	100	100	CD	_	_	_
22	mM	mm	NN	KWSUPP	_	_
23	NaCl	nacl	NN	_	_	_
24	,	,	,	_	_	_
25	1	1	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	EDTA	edta	NN	_	_	_
28	,	,	,	_	_	_
29	1	1	CD	_	_	_
30	ug	ug	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Cross-linked	cross-linked	JJ	_	_	_
33	and	and	CC	_	_	_
34	sonicated	sonicated	JJ	_	_	_
35	chromatin	chromatin	NN	_	_	_
36	complex	complex	NN	_	_	_
37	of	of	IN	_	_	_
38	ArgR-8myc	argr-8myc	NN	_	_	_
39	and	and	CC	_	_	_
40	DNA	dna	NN	_	_	_
41	was	be	VBD	_	_	_
42	immunoprecipitated	immunoprecipitate	VBN	_	_	_
43	by	by	IN	_	_	_
44	9E10	9e10	NN	_	_	_
45	myc	myc	NN	_	_	_
46	antibody	antibody	NN	_	_	_
47	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cross-linked	cross-linked	JJ	_	_	_
3	and	and	CC	_	_	_
4	sonicated	sonicated	JJ	_	_	_
5	chromatin	chromatin	NN	_	_	_
6	complex	complex	NN	_	_	_
7	of	of	IN	_	_	_
8	ArgR-8myc	argr-8myc	NN	_	_	_
9	and	and	CC	_	_	_
10	DNA	dna	NN	_	_	_
11	was	be	VBD	_	_	_
12	immunoprecipitated	immunoprecipitate	VBN	_	_	_
13	by	by	IN	_	_	_
14	using	use	VBG	_	_	_
15	normal	normal	JJ	_	_	_
16	mouse	mouse	NN	_	_	_
17	IgG	igg	NN	_	_	_
18	for	for	IN	_	_	_
19	the	the	DT	_	_	_
20	control	control	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cross-linked	cross-linked	JJ	_	_	_
3	and	and	CC	_	_	_
4	sonicated	sonicated	JJ	_	_	_
5	chromatin	chromatin	NN	_	_	_
6	complex	complex	NN	_	_	_
7	of	of	IN	_	_	_
8	Lrp-8myc	lrp-8myc	JJ	_	_	_
9	and	and	CC	_	_	_
10	DNA	dna	NN	_	_	_
11	was	be	VBD	_	_	_
12	immunoprecipitated	immunoprecipitate	VBN	_	_	_
13	by	by	IN	_	_	_
14	9E10	9e10	NN	_	_	_
15	myc	myc	NN	_	_	_
16	antibody	antibody	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cross-linked	cross-linked	JJ	_	_	_
3	and	and	CC	_	_	_
4	sonicated	sonicated	JJ	_	_	_
5	chromatin	chromatin	NN	_	_	_
6	complex	complex	NN	_	_	_
7	of	of	IN	_	_	_
8	Lrp-8myc	lrp-8myc	JJ	_	_	_
9	and	and	CC	_	_	_
10	DNA	dna	NN	_	_	_
11	was	be	VBD	_	_	_
12	immunoprecipitated	immunoprecipitate	VBN	_	_	_
13	by	by	IN	_	_	_
14	using	use	VBG	_	_	_
15	normal	normal	JJ	_	_	_
16	mouse	mouse	NN	_	_	_
17	IgG	igg	NN	_	_	_
18	for	for	IN	_	_	_
19	the	the	DT	_	_	_
20	control	control	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cross-linked	cross-linked	JJ	_	_	_
3	and	and	CC	_	_	_
4	sonicated	sonicated	JJ	_	_	_
5	chromatin	chromatin	NN	_	_	_
6	complex	complex	NN	_	_	_
7	of	of	IN	_	_	_
8	TrpR-8myc	trpr-8myc	NN	_	_	_
9	and	and	CC	_	_	_
10	DNA	dna	NN	_	_	_
11	was	be	VBD	_	_	_
12	immunoprecipitated	immunoprecipitate	VBN	_	_	_
13	by	by	IN	_	_	_
14	9E10	9e10	NN	_	_	_
15	myc	myc	NN	_	_	_
16	antibody	antibody	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cross-linked	cross-linked	JJ	_	_	_
3	and	and	CC	_	_	_
4	sonicated	sonicated	JJ	_	_	_
5	chromatin	chromatin	NN	_	_	_
6	complex	complex	NN	_	_	_
7	of	of	IN	_	_	_
8	TrpR-8myc	trpr-8myc	NN	_	_	_
9	and	and	CC	_	_	_
10	DNA	dna	NN	_	_	_
11	was	be	VBD	_	_	_
12	immunoprecipitated	immunoprecipitate	VBN	_	_	_
13	by	by	IN	_	_	_
14	using	use	VBG	_	_	_
15	normal	normal	JJ	_	_	_
16	mouse	mouse	NN	_	_	_
17	IgG	igg	NN	_	_	_
18	for	for	IN	_	_	_
19	the	the	DT	_	_	_
20	control	control	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	Coli	Coli	NNP	_	_	_
4	ArgR	argr	NN	TF	_	_
5	ChIP	chip	NN	_	_	_
6	DNA	dna	NN	_	_	_
7	Arginine	arginine	NN	_	_	_
8	1	1	CD	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	E.	E.	NNP	_	_	_
11	Coli	Coli	NNP	_	_	_
12	ArgR	argr	NN	TF	_	_
13	ChIP	chip	NN	_	_	_
14	DNA	dna	NN	_	_	_
15	Arginine	arginine	NN	_	_	_
16	2	2	CD	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	E.	E.	NNP	_	_	_
19	Coli	Coli	NNP	_	_	_
20	ArgR	argr	NN	TF	_	_
21	ChIP	chip	NN	_	_	_
22	DNA	dna	NN	_	_	_
23	NH4Cl	nh4cl	NN	_	_	_
24	1	1	CD	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	E.	E.	NNP	_	_	_
27	Coli	Coli	NNP	_	_	_
28	ArgR	argr	NN	TF	_	_
29	ChIP	chip	NN	_	_	_
30	DNA	dna	NN	_	_	_
31	NH4Cl	nh4cl	NN	_	_	_
32	2	2	CD	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	E.	E.	NNP	_	_	_
35	Coli	Coli	NNP	_	_	_
36	Lrp	Lrp	NNP	TF	_	_
37	ChIP	chip	NN	_	_	_
38	DNA	dna	NN	_	_	_
39	Leucine	leucine	NN	_	_	_
40	1	1	CD	_	_	_
41	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
42	E.	E.	NNP	_	_	_
43	Coli	Coli	NNP	_	_	_
44	Lrp	Lrp	NNP	TF	_	_
45	ChIP	ChIP	NNP	_	_	_
46	DNA	DNA	NNP	_	_	_
47	Leucine	leucine	NN	_	_	_
48	2	2	CD	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	E.	E.	NNP	_	_	_
51	Coli	Coli	NNP	_	_	_
52	Lrp	Lrp	NNP	TF	_	_
53	ChIP	chip	NN	_	_	_
54	DNA	dna	NN	_	_	_
55	Leucine	leucine	NN	_	_	_
56	3	3	CD	_	_	_
57	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
58	E.	E.	NNP	_	_	_
59	Coli	Coli	NNP	_	_	_
60	Lrp	Lrp	NNP	TF	_	_
61	ChIP	ChIP	NNP	_	_	_
62	DNA	DNA	NNP	_	_	_
63	NH4Cl	nh4cl	NN	_	_	_
64	1	1	CD	_	_	_
65	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
66	E.	E.	NNP	_	_	_
67	Coli	Coli	NNP	_	_	_
68	Lrp	Lrp	NNP	TF	_	_
69	ChIP	ChIP	NNP	_	_	_
70	DNA	DNA	NNP	_	_	_
71	NH4Cl	nh4cl	NN	_	_	_
72	2	2	CD	_	_	_
73	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
74	E.	E.	NNP	_	_	_
75	Coli	Coli	NNP	_	_	_
76	Lrp	Lrp	NNP	TF	_	_
77	ChIP	ChIP	NNP	_	_	_
78	DNA	DNA	NNP	_	_	_
79	NH4Cl	nh4cl	NN	_	_	_
80	3	3	CD	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	E.	e.	FW	_	_	_
83	coli	coli	FW	_	_	_
84	strains	strain	NNS	_	_	_
85	harboring	harbor	VBG	_	_	_
86	ArgR-8myc	argr-8myc	NN	_	_	_
87	were	be	VBD	_	_	_
88	grown	grow	VBN	_	_	_
89	in	in	IN	_	_	_
90	glucose	glucose	NN	SUPP	_	_
91	-LRB-	-lrb-	-LRB-	_	_	_
92	2	2	CD	_	_	_
93	g	g	NN	_	_	_
94	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
95	E.	E.	NNP	_	_	_
96	coli	coli	NN	_	_	_
97	strains	strain	NNS	_	_	_
98	harboring	harbor	VBG	_	_	_
99	Lrp-8myc	lrp-8myc	JJ	_	_	_
100	were	be	VBD	_	_	_
101	grown	grow	VBN	_	_	_
102	in	in	IN	_	_	_
103	glucose	glucose	NN	SUPP	_	_
104	-LRB-	-lrb-	-LRB-	_	_	_
105	2	2	CD	_	_	_
106	g	g	NN	_	_	_
107	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
108	E.	E.	NNP	_	_	_
109	coli	coli	NN	_	_	_
110	strains	strain	NNS	_	_	_
111	harboring	harbor	VBG	_	_	_
112	TrpR-8myc	trpr-8myc	NN	_	_	_
113	were	be	VBD	_	_	_
114	grown	grow	VBN	_	_	_
115	in	in	IN	_	_	_
116	glucose	glucose	NN	SUPP	_	_
117	-LRB-	-lrb-	-LRB-	_	_	_
118	2	2	CD	_	_	_
119	g	g	NN	_	_	_
120	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
121	E.	E.	NNP	_	_	_
122	Coli	Coli	NNP	_	_	_
123	TrpR	trpr	NN	TF	_	_
124	ChIP	chip	NN	_	_	_
125	DNA	dna	NN	_	_	_
126	glucose	glucose	NN	SUPP	_	_
127	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
128	E.	E.	NNP	_	_	_
129	Coli	Coli	NNP	_	_	_
130	TrpR	trpr	NN	TF	_	_
131	ChIP	chip	NN	_	_	_
132	DNA	dna	NN	_	_	_
133	Tryptophan	tryptophan	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	Escherichia	escherichia	FW	Organism	_	_
136	coli	coli	FW	Organism	_	_
137	str	str	FW	_	_	_
138	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	genotype	genotype	NN	_	_	_
4	:	:	:	_	_	_
5	ArgR-8myc	argr-8myc	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	genotype	genotype	NN	_	_	_
8	:	:	:	_	_	_
9	Lrp-8myc	lrp-8myc	JJ	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	genotype	genotype	NN	_	_	_
12	:	:	:	_	_	_
13	TrpR-8myc	trpr-8myc	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
15	Lrp	lrp	VBP	TF	_	_
16	_	_	SYM	_	_	_
17	Leu	Leu	NNP	_	_	_
18	_	_	SYM	_	_	_
19	1	1	CD	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	Lrp	Lrp	NNP	TF	_	_
22	_	_	NNP	_	_	_
23	Leu	Leu	NNP	_	_	_
24	_	_	NNP	_	_	_
25	2	2	CD	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	Lrp	Lrp	NNP	TF	_	_
28	_	_	NNP	_	_	_
29	Leu	Leu	NNP	_	_	_
30	_	_	NNP	_	_	_
31	3	3	CD	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	Lrp	Lrp	NNP	TF	_	_
34	_	_	SYM	_	_	_
35	NH4Cl	nh4cl	NN	_	_	_
36	_	_	NN	_	_	_
37	1	1	CD	_	_	_
38	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
39	Lrp	Lrp	NNP	TF	_	_
40	_	_	SYM	_	_	_
41	NH4Cl	nh4cl	NN	_	_	_
42	_	_	NN	_	_	_
43	2	2	CD	_	_	_
44	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
45	Lrp	Lrp	NNP	TF	_	_
46	_	_	SYM	_	_	_
47	NH4Cl	nh4cl	NN	_	_	_
48	_	_	NN	_	_	_
49	3	3	CD	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	The	the	DT	_	_	_
52	raw	raw	JJ	_	_	_
53	data	data	NN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	.	.	.	_	_	_

1	pair	pair	NN	_	_	_
2	file	file	NN	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	was	be	VBD	_	_	_
5	subjected	subject	VBN	_	_	_
6	to	to	TO	_	_	_
7	per	per	IN	_	_	_
8	channel	channel	NN	_	_	_
9	quantile	quantile	NN	_	_	_
10	normalization	normalization	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Bolstad	Bolstad	NNP	_	_	_
13	et	et	FW	_	_	_
14	al.	al.	FW	_	_	_
15	.	.	.	_	_	_

1	Bioinformatics	bioinformatic	NNS	_	_	_
2	19	19	CD	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	2	2	CD	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	:	:	:	_	_	_
7	185	185	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	,	,	,	_	_	_
10	IP	IP	NNP	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	treatment	treatment	NN	_	_	_
13	:	:	:	_	_	_
14	glucose	glucose	NN	SUPP	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	2	2	CD	_	_	_
17	g	g	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	TrpR	trpr	NN	TF	_	_
20	_	_	NN	_	_	_
21	glucose	glucose	NN	SUPP	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	TrpR	trpr	NN	TF	_	_
24	_	_	CD	_	_	_
25	Trp	trp	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	agent	agent	NN	_	_	_
28	:	:	:	_	_	_
29	H2O	h2o	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	agent	agent	NN	_	_	_
32	:	:	:	_	_	_
33	ZnSO4	znso4	NN	_	_	_
34	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
35	E.	E.	NNP	_	_	_
36	coli	coli	NN	_	_	_
37	0	0	CD	_	_	_
38	mins	min	NNS	_	_	_
39	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
40	E.	e.	FW	_	_	_
41	coli	coli	FW	_	_	_
42	10	10	CD	_	_	_
43	mins	min	NNS	_	_	_
44	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
45	E.	E.	NNP	_	_	_
46	coli	coli	NN	_	_	_
47	2.5	2.5	CD	_	_	_
48	mins	min	NNS	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	E.	e.	FW	_	_	_
51	coli	coli	FW	_	_	_
52	30	30	CD	_	_	_
53	mins	min	NNS	_	_	_
54	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
55	E.	E.	NNP	_	_	_
56	coli	coli	NN	_	_	_
57	7	7	CD	_	_	_
58	mins	min	NNS	_	_	_
59	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
60	Escherichia	escherichia	FW	Organism	_	_
61	coli	coli	FW	Organism	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	Spots	spot	NNS	_	_	_
64	automatically	automatically	RB	_	_	_
65	flagged	flag	VBD	_	_	_
66	as	as	IN	_	_	_
67	bad	bad	JJ	_	_	_
68	,	,	,	_	_	_
69	negative	negative	JJ	_	_	_
70	or	or	CC	_	_	_
71	poor	poor	JJ	_	_	_
72	in	in	IN	_	_	_
73	the	the	DT	_	_	_
74	Imagene	imagene	NN	_	_	_
75	software	software	NN	_	_	_
76	were	be	VBD	_	_	_
77	removed	remove	VBN	_	_	_
78	before	before	IN	_	_	_
79	the	the	DT	_	_	_
80	statistical	statistical	JJ	_	_	_
81	analysis	analysis	NN	_	_	_
82	was	be	VBD	_	_	_
83	carried	carry	VBN	_	_	_
84	out	out	RP	_	_	_
85	in	in	IN	_	_	_
86	GeneSight	GeneSight	NNP	_	_	_
87	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	mean	mean	NN	_	_	_
3	values	value	NNS	_	_	_
4	from	from	IN	_	_	_
5	each	each	DT	_	_	_
6	channel	channel	NN	_	_	_
7	were	be	VBD	_	_	_
8	log2	log2	NN	_	_	_
9	transformed	transform	VBN	_	_	_
10	and	and	CC	_	_	_
11	normalised	normalise	VBN	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	Lowess	lowess	NN	_	_	_
15	method	method	NN	_	_	_
16	to	to	TO	_	_	_
17	remove	remove	VB	_	_	_
18	intensity-dependent	intensity-dependent	JJ	_	_	_
19	effects	effect	NNS	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	log2	log2	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	ratios	ratio	NNS	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	values	value	NNS	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	Cy3	cy3	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	strain	strain	NN	_	_	_
5	:	:	:	_	_	_
6	MG1655	mg1655	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	The	the	DT	_	_	_
9	average	average	JJ	_	_	_
10	signal	signal	NN	_	_	_
11	intensity	intensity	NN	_	_	_
12	and	and	CC	_	_	_
13	local	local	JJ	_	_	_
14	background	background	NN	_	_	_
15	correction	correction	NN	_	_	_
16	were	be	VBD	_	_	_
17	obtained	obtain	VBN	_	_	_
18	using	use	VBG	_	_	_
19	a	a	DT	_	_	_
20	commercially	commercially	RB	_	_	_
21	available	available	JJ	_	_	_
22	software	software	NN	_	_	_
23	package	package	NN	_	_	_
24	from	from	IN	_	_	_
25	Biodiscovery	Biodiscovery	NNP	_	_	_
26	,	,	,	_	_	_
27	Inc	Inc	NNP	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Imagene	Imagene	NNP	_	_	_
30	,	,	,	_	_	_
31	version	version	NN	_	_	_
32	4.0	4.0	CD	_	_	_
33	and	and	CC	_	_	_
34	GeneSight	GeneSight	NNP	_	_	_
35	,	,	,	_	_	_
36	version	version	NN	_	_	_
37	3.5	3.5	CD	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	time	time	NN	_	_	_
3	:	:	:	_	_	_
4	0	0	CD	_	_	_
5	mins	min	NNS	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJR	_	_	_
7	time	time	NN	_	_	_
8	:	:	:	_	_	_
9	10	10	CD	_	_	_
10	mins	min	NNS	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJR	_	_	_
12	time	time	NN	_	_	_
13	:	:	:	_	_	_
14	2.5	2.5	CD	_	_	_
15	mins	min	NNS	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJR	_	_	_
17	time	time	NN	_	_	_
18	:	:	:	_	_	_
19	30	30	CD	_	_	_
20	mins	min	NNS	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJR	_	_	_
22	time	time	NN	_	_	_
23	:	:	:	_	_	_
24	7	7	CD	_	_	_
25	mins	min	NNS	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	Transcriptional	transcriptional	JJ	_	_	_
28	profiling	profiling	NN	_	_	_
29	of	of	IN	_	_	_
30	Escherichia	escherichia	FW	Organism	_	_
31	coli	coli	FW	Organism	_	_
32	during	during	IN	_	_	_
33	a	a	DT	_	_	_
34	transition	transition	NN	_	_	_
35	from	from	IN	_	_	_
36	zinc	zinc	NN	_	_	_
37	starvation	starvation	NN	_	_	_
38	to	to	TO	_	_	_
39	surfeit	surfeit	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	0A1	0a1	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Transcriptional	transcriptional	JJ	_	_	_
45	profiling	profiling	NN	_	_	_
46	of	of	IN	_	_	_
47	Escherichia	escherichia	FW	Organism	_	_
48	coli	coli	FW	Organism	_	_
49	during	during	IN	_	_	_
50	a	a	DT	_	_	_
51	transition	transition	NN	_	_	_
52	from	from	IN	_	_	_
53	zinc	zinc	NN	_	_	_
54	starvation	starvation	NN	_	_	_
55	to	to	TO	_	_	_
56	surfeit	surfeit	NN	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	slide	slide	NN	_	_	_
59	0A2	0a2	NN	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Transcriptional	transcriptional	JJ	_	_	_
63	profiling	profiling	NN	_	_	_
64	of	of	IN	_	_	_
65	Escherichia	escherichia	FW	Organism	_	_
66	coli	coli	FW	Organism	_	_
67	during	during	IN	_	_	_
68	a	a	DT	_	_	_
69	transition	transition	NN	_	_	_
70	from	from	IN	_	_	_
71	zinc	zinc	NN	_	_	_
72	starvation	starvation	NN	_	_	_
73	to	to	TO	_	_	_
74	surfeit	surfeit	NN	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	slide	slide	NN	_	_	_
77	0B1	0b1	NN	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	Transcriptional	transcriptional	JJ	_	_	_
81	profiling	profiling	NN	_	_	_
82	of	of	IN	_	_	_
83	Escherichia	escherichia	FW	Organism	_	_
84	coli	coli	FW	Organism	_	_
85	during	during	IN	_	_	_
86	a	a	DT	_	_	_
87	transition	transition	NN	_	_	_
88	from	from	IN	_	_	_
89	zinc	zinc	NN	_	_	_
90	starvation	starvation	NN	_	_	_
91	to	to	TO	_	_	_
92	surfeit	surfeit	NN	_	_	_
93	-LRB-	-lrb-	-LRB-	_	_	_
94	slide	slide	NN	_	_	_
95	0B2	0b2	NN	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	Transcriptional	transcriptional	JJ	_	_	_
99	profiling	profiling	NN	_	_	_
100	of	of	IN	_	_	_
101	Escherichia	escherichia	FW	Organism	_	_
102	coli	coli	FW	Organism	_	_
103	during	during	IN	_	_	_
104	a	a	DT	_	_	_
105	transition	transition	NN	_	_	_
106	from	from	IN	_	_	_
107	zinc	zinc	NN	_	_	_
108	starvation	starvation	NN	_	_	_
109	to	to	TO	_	_	_
110	surfeit	surfeit	NN	_	_	_
111	-LRB-	-lrb-	-LRB-	_	_	_
112	slide	slide	NN	_	_	_
113	10A1	10a1	NN	_	_	_
114	-RRB-	-rrb-	-RRB-	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	Transcriptional	transcriptional	JJ	_	_	_
117	profiling	profiling	NN	_	_	_
118	of	of	IN	_	_	_
119	Escherichia	escherichia	FW	Organism	_	_
120	coli	coli	FW	Organism	_	_
121	during	during	IN	_	_	_
122	a	a	DT	_	_	_
123	transition	transition	NN	_	_	_
124	from	from	IN	_	_	_
125	zinc	zinc	NN	_	_	_
126	starvation	starvation	NN	_	_	_
127	to	to	TO	_	_	_
128	surfeit	surfeit	NN	_	_	_
129	-LRB-	-lrb-	-LRB-	_	_	_
130	slide	slide	NN	_	_	_
131	10A2	10a2	NN	_	_	_
132	-RRB-	-rrb-	-RRB-	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	Transcriptional	transcriptional	JJ	_	_	_
135	profiling	profiling	NN	_	_	_
136	of	of	IN	_	_	_
137	Escherichia	escherichia	FW	Organism	_	_
138	coli	coli	FW	Organism	_	_
139	during	during	IN	_	_	_
140	a	a	DT	_	_	_
141	transition	transition	NN	_	_	_
142	from	from	IN	_	_	_
143	zinc	zinc	NN	_	_	_
144	starvation	starvation	NN	_	_	_
145	to	to	TO	_	_	_
146	surfeit	surfeit	NN	_	_	_
147	-LRB-	-lrb-	-LRB-	_	_	_
148	slide	slide	NN	_	_	_
149	10A3	10a3	NN	_	_	_
150	-RRB-	-rrb-	-RRB-	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	Transcriptional	transcriptional	JJ	_	_	_
153	profiling	profiling	NN	_	_	_
154	of	of	IN	_	_	_
155	Escherichia	escherichia	FW	Organism	_	_
156	coli	coli	FW	Organism	_	_
157	during	during	IN	_	_	_
158	a	a	DT	_	_	_
159	transition	transition	NN	_	_	_
160	from	from	IN	_	_	_
161	zinc	zinc	NN	_	_	_
162	starvation	starvation	NN	_	_	_
163	to	to	TO	_	_	_
164	surfeit	surfeit	NN	_	_	_
165	-LRB-	-lrb-	-LRB-	_	_	_
166	slide	slide	NN	_	_	_
167	10B1	10b1	NN	_	_	_
168	-RRB-	-rrb-	-RRB-	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	Transcriptional	transcriptional	JJ	_	_	_
171	profiling	profiling	NN	_	_	_
172	of	of	IN	_	_	_
173	Escherichia	escherichia	FW	Organism	_	_
174	coli	coli	FW	Organism	_	_
175	during	during	IN	_	_	_
176	a	a	DT	_	_	_
177	transition	transition	NN	_	_	_
178	from	from	IN	_	_	_
179	zinc	zinc	NN	_	_	_
180	starvation	starvation	NN	_	_	_
181	to	to	TO	_	_	_
182	surfeit	surfeit	NN	_	_	_
183	-LRB-	-lrb-	-LRB-	_	_	_
184	slide	slide	NN	_	_	_
185	10B2	10b2	NN	_	_	_
186	-RRB-	-rrb-	-RRB-	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	Transcriptional	transcriptional	JJ	_	_	_
189	profiling	profiling	NN	_	_	_
190	of	of	IN	_	_	_
191	Escherichia	escherichia	FW	Organism	_	_
192	coli	coli	FW	Organism	_	_
193	during	during	IN	_	_	_
194	a	a	DT	_	_	_
195	transition	transition	NN	_	_	_
196	from	from	IN	_	_	_
197	zinc	zinc	NN	_	_	_
198	starvation	starvation	NN	_	_	_
199	to	to	TO	_	_	_
200	surfeit	surfeit	NN	_	_	_
201	-LRB-	-lrb-	-LRB-	_	_	_
202	slide	slide	NN	_	_	_
203	2.5	2.5	CD	_	_	_
204	A1	a1	NN	_	_	_
205	-RRB-	-rrb-	-RRB-	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	Transcriptional	transcriptional	JJ	_	_	_
208	profiling	profiling	NN	_	_	_
209	of	of	IN	_	_	_
210	Escherichia	escherichia	FW	Organism	_	_
211	coli	coli	FW	Organism	_	_
212	during	during	IN	_	_	_
213	a	a	DT	_	_	_
214	transition	transition	NN	_	_	_
215	from	from	IN	_	_	_
216	zinc	zinc	NN	_	_	_
217	starvation	starvation	NN	_	_	_
218	to	to	TO	_	_	_
219	surfeit	surfeit	NN	_	_	_
220	-LRB-	-lrb-	-LRB-	_	_	_
221	slide	slide	NN	_	_	_
222	2.5	2.5	CD	_	_	_
223	A2	a2	NN	_	_	_
224	-RRB-	-rrb-	-RRB-	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	Transcriptional	transcriptional	JJ	_	_	_
227	profiling	profiling	NN	_	_	_
228	of	of	IN	_	_	_
229	Escherichia	escherichia	FW	Organism	_	_
230	coli	coli	FW	Organism	_	_
231	during	during	IN	_	_	_
232	a	a	DT	_	_	_
233	transition	transition	NN	_	_	_
234	from	from	IN	_	_	_
235	zinc	zinc	NN	_	_	_
236	starvation	starvation	NN	_	_	_
237	to	to	TO	_	_	_
238	surfeit	surfeit	NN	_	_	_
239	-LRB-	-lrb-	-LRB-	_	_	_
240	slide	slide	NN	_	_	_
241	2.5	2.5	CD	_	_	_
242	B1	b1	NN	_	_	_
243	-RRB-	-rrb-	-RRB-	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	Transcriptional	transcriptional	JJ	_	_	_
246	profiling	profiling	NN	_	_	_
247	of	of	IN	_	_	_
248	Escherichia	escherichia	FW	Organism	_	_
249	coli	coli	FW	Organism	_	_
250	during	during	IN	_	_	_
251	a	a	DT	_	_	_
252	transition	transition	NN	_	_	_
253	from	from	IN	_	_	_
254	zinc	zinc	NN	_	_	_
255	starvation	starvation	NN	_	_	_
256	to	to	TO	_	_	_
257	surfeit	surfeit	NN	_	_	_
258	-LRB-	-lrb-	-LRB-	_	_	_
259	slide	slide	NN	_	_	_
260	2.5	2.5	CD	_	_	_
261	B2	b2	NN	_	_	_
262	-RRB-	-rrb-	-RRB-	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
264	Transcriptional	transcriptional	JJ	_	_	_
265	profiling	profiling	NN	_	_	_
266	of	of	IN	_	_	_
267	Escherichia	escherichia	FW	Organism	_	_
268	coli	coli	FW	Organism	_	_
269	during	during	IN	_	_	_
270	a	a	DT	_	_	_
271	transition	transition	NN	_	_	_
272	from	from	IN	_	_	_
273	zinc	zinc	NN	_	_	_
274	starvation	starvation	NN	_	_	_
275	to	to	TO	_	_	_
276	surfeit	surfeit	NN	_	_	_
277	-LRB-	-lrb-	-LRB-	_	_	_
278	slide	slide	NN	_	_	_
279	30A1	30a1	NN	_	_	_
280	-RRB-	-rrb-	-RRB-	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	Transcriptional	transcriptional	JJ	_	_	_
283	profiling	profiling	NN	_	_	_
284	of	of	IN	_	_	_
285	Escherichia	escherichia	FW	Organism	_	_
286	coli	coli	FW	Organism	_	_
287	during	during	IN	_	_	_
288	a	a	DT	_	_	_
289	transition	transition	NN	_	_	_
290	from	from	IN	_	_	_
291	zinc	zinc	NN	_	_	_
292	starvation	starvation	NN	_	_	_
293	to	to	TO	_	_	_
294	surfeit	surfeit	NN	_	_	_
295	-LRB-	-lrb-	-LRB-	_	_	_
296	slide	slide	NN	_	_	_
297	30A2	30a2	NN	_	_	_
298	-RRB-	-rrb-	-RRB-	_	_	_
299	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
300	Transcriptional	transcriptional	JJ	_	_	_
301	profiling	profiling	NN	_	_	_
302	of	of	IN	_	_	_
303	Escherichia	escherichia	FW	Organism	_	_
304	coli	coli	FW	Organism	_	_
305	during	during	IN	_	_	_
306	a	a	DT	_	_	_
307	transition	transition	NN	_	_	_
308	from	from	IN	_	_	_
309	zinc	zinc	NN	_	_	_
310	starvation	starvation	NN	_	_	_
311	to	to	TO	_	_	_
312	surfeit	surfeit	NN	_	_	_
313	-LRB-	-lrb-	-LRB-	_	_	_
314	slide	slide	NN	_	_	_
315	30B1	30b1	NN	_	_	_
316	-RRB-	-rrb-	-RRB-	_	_	_
317	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
318	Transcriptional	transcriptional	JJ	_	_	_
319	profiling	profiling	NN	_	_	_
320	of	of	IN	_	_	_
321	Escherichia	escherichia	FW	Organism	_	_
322	coli	coli	FW	Organism	_	_
323	during	during	IN	_	_	_
324	a	a	DT	_	_	_
325	transition	transition	NN	_	_	_
326	from	from	IN	_	_	_
327	zinc	zinc	NN	_	_	_
328	starvation	starvation	NN	_	_	_
329	to	to	TO	_	_	_
330	surfeit	surfeit	NN	_	_	_
331	-LRB-	-lrb-	-LRB-	_	_	_
332	slide	slide	NN	_	_	_
333	30B2	30b2	NN	_	_	_
334	-RRB-	-rrb-	-RRB-	_	_	_
335	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
336	Transcriptional	transcriptional	JJ	_	_	_
337	profiling	profiling	NN	_	_	_
338	of	of	IN	_	_	_
339	Escherichia	escherichia	FW	Organism	_	_
340	coli	coli	FW	Organism	_	_
341	during	during	IN	_	_	_
342	a	a	DT	_	_	_
343	transition	transition	NN	_	_	_
344	from	from	IN	_	_	_
345	zinc	zinc	NN	_	_	_
346	starvation	starvation	NN	_	_	_
347	to	to	TO	_	_	_
348	surfeit	surfeit	NN	_	_	_
349	-LRB-	-lrb-	-LRB-	_	_	_
350	slide	slide	NN	_	_	_
351	7A1	7a1	NN	_	_	_
352	-RRB-	-rrb-	-RRB-	_	_	_
353	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
354	Transcriptional	transcriptional	JJ	_	_	_
355	profiling	profiling	NN	_	_	_
356	of	of	IN	_	_	_
357	Escherichia	escherichia	FW	Organism	_	_
358	coli	coli	FW	Organism	_	_
359	during	during	IN	_	_	_
360	a	a	DT	_	_	_
361	transition	transition	NN	_	_	_
362	from	from	IN	_	_	_
363	zinc	zinc	NN	_	_	_
364	starvation	starvation	NN	_	_	_
365	to	to	TO	_	_	_
366	surfeit	surfeit	NN	_	_	_
367	-LRB-	-lrb-	-LRB-	_	_	_
368	slide	slide	NN	_	_	_
369	7A2	7a2	NN	_	_	_
370	-RRB-	-rrb-	-RRB-	_	_	_
371	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
372	Transcriptional	transcriptional	JJ	_	_	_
373	profiling	profiling	NN	_	_	_
374	of	of	IN	_	_	_
375	Escherichia	escherichia	FW	Organism	_	_
376	coli	coli	FW	Organism	_	_
377	during	during	IN	_	_	_
378	a	a	DT	_	_	_
379	transition	transition	NN	_	_	_
380	from	from	IN	_	_	_
381	zinc	zinc	NN	_	_	_
382	starvation	starvation	NN	_	_	_
383	to	to	TO	_	_	_
384	surfeit	surfeit	NN	_	_	_
385	-LRB-	-lrb-	-LRB-	_	_	_
386	slide	slide	NN	_	_	_
387	7B1	7b1	NN	_	_	_
388	-RRB-	-rrb-	-RRB-	_	_	_
389	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
390	Transcriptional	transcriptional	JJ	_	_	_
391	profiling	profiling	NN	_	_	_
392	of	of	IN	_	_	_
393	Escherichia	escherichia	FW	Organism	_	_
394	coli	coli	FW	Organism	_	_
395	during	during	IN	_	_	_
396	a	a	DT	_	_	_
397	transition	transition	NN	_	_	_
398	from	from	IN	_	_	_
399	zinc	zinc	NN	_	_	_
400	starvation	starvation	NN	_	_	_
401	to	to	TO	_	_	_
402	surfeit	surfeit	NN	_	_	_
403	-LRB-	-lrb-	-LRB-	_	_	_
404	slide	slide	NN	_	_	_
405	7B2	7b2	NN	_	_	_
406	-RRB-	-rrb-	-RRB-	_	_	_
407	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
408	Zn-depleted	zn-depleted	JJ	_	_	_
409	custom-built	custom-built	JJ	_	_	_
410	chemostats	chemostat	NNS	_	_	_
411	were	be	VBD	_	_	_
412	grown	grow	VBN	_	_	_
413	for	for	IN	_	_	_
414	50	50	CD	_	_	_
415	h	h	NN	_	_	_
416	.	.	.	_	_	_

1	At	at	IN	_	_	_
2	this	this	DT	_	_	_
3	point	point	NN	_	_	_
4	,	,	,	_	_	_
5	ZnSO4	znso4	NN	_	_	_
6	.7	.7	CD	_	_	_
7	H2O	h2o	NN	_	_	_
8	in	in	IN	_	_	_
9	water	water	NN	_	_	_
10	was	be	VBD	_	_	_
11	added	add	VBN	_	_	_
12	to	to	TO	_	_	_
13	a	a	DT	_	_	_
14	final	final	JJ	_	_	_
15	concentration	concentration	NN	_	_	_
16	of	of	IN	_	_	_
17	0.2	0.2	CD	_	_	_
18	M	m	NN	_	_	_
19	in	in	IN	_	_	_
20	the	the	DT	_	_	_
21	chemostat	chemostat	NN	_	_	_
22	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	10	10	CD	_	_	_
3	ml	ml	NN	_	_	_
4	sample	sample	NN	_	_	_
5	of	of	IN	_	_	_
6	culture	culture	NN	_	_	_
7	was	be	VBD	_	_	_
8	taken	take	VBN	_	_	_
9	using	use	VBG	_	_	_
10	a	a	DT	_	_	_
11	polypropylene	polypropylene	NN	_	_	_
12	pipette	pipette	NN	_	_	_
13	tip	tip	NN	_	_	_
14	immediately	immediately	RB	_	_	_
15	prior	prior	RB	_	_	_
16	to	to	TO	_	_	_
17	Zn	zn	NN	_	_	_
18	addition	addition	NN	_	_	_
19	and	and	CC	_	_	_
20	2.5	2.5	CD	_	_	_
21	,	,	,	_	_	_
22	7	7	CD	_	_	_
23	,	,	,	_	_	_
24	10	10	CD	_	_	_
25	and	and	CC	_	_	_
26	30	30	CD	_	_	_
27	min	min	NN	_	_	_
28	after	after	IN	_	_	_
29	addition	addition	NN	_	_	_
30	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	pipetted	pipet	VBN	_	_	_
5	directly	directly	RB	_	_	_
6	into	into	IN	_	_	_
7	RNAprotect	rnaprotect	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Qiagen	qiagen	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	to	to	TO	_	_	_
12	stabilize	stabilize	VB	_	_	_
13	RNA	rna	NN	_	_	_
14	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Qiagen	Qiagen	NNP	_	_	_
7	's	's	POS	_	_	_
8	RNeasy	RNeasy	NNP	_	_	_
9	Mini	Mini	NNP	_	_	_
10	kit	kit	NN	_	_	_
11	as	as	IN	_	_	_
12	recommended	recommend	VBN	_	_	_
13	by	by	IN	_	_	_
14	the	the	DT	_	_	_
15	suppliers	supplier	NNS	_	_	_
16	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	quantified	quantify	VBN	_	_	_
4	using	use	VBG	_	_	_
5	a	a	DT	_	_	_
6	BioPhotometer	biophotometer	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Eppendorf	eppendorf	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	control	control	NN	_	_	_
3	experiment	experiment	NN	_	_	_
4	was	be	VBD	_	_	_
5	carried	carry	VBN	_	_	_
6	out	out	RP	_	_	_
7	in	in	IN	_	_	_
8	which	which	WDT	_	_	_
9	water	water	NN	_	_	_
10	was	be	VBD	_	_	_
11	added	add	VBN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Butanol	Butanol	NNP	_	_	_
3	_	_	NNP	_	_	_
4	Challenge	Challenge	NNP	_	_	_
5	_	_	VBD	_	_	_
6	Step	step	NN	_	_	_
7	_	_	SYM	_	_	_
8	1-1	1-1	CD	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	Butanol	Butanol	NNP	_	_	_
11	_	_	NNP	_	_	_
12	Challenge	Challenge	NNP	_	_	_
13	_	_	VBD	_	_	_
14	Step	step	NN	_	_	_
15	_	_	NN	_	_	_
16	1-2	1-2	CD	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	Butanol	Butanol	NNP	_	_	_
19	_	_	NNP	_	_	_
20	Challenge	Challenge	NNP	_	_	_
21	_	_	VBD	_	_	_
22	Step	step	NN	_	_	_
23	_	_	SYM	_	_	_
24	2-1	2-1	CD	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	Butanol	Butanol	NNP	_	_	_
27	_	_	NNP	_	_	_
28	Challenge	Challenge	NNP	_	_	_
29	_	_	VBD	_	_	_
30	Step	step	NN	_	_	_
31	_	_	SYM	_	_	_
32	2-2	2-2	CD	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	Butanol	Butanol	NNP	_	_	_
35	_	_	NNP	_	_	_
36	Challenge	Challenge	NNP	_	_	_
37	_	_	VBD	_	_	_
38	Step	step	NN	_	_	_
39	_	_	SYM	_	_	_
40	3-1	3-1	CD	_	_	_
41	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
42	Butanol	Butanol	NNP	_	_	_
43	_	_	NNP	_	_	_
44	Challenge	Challenge	NNP	_	_	_
45	_	_	VBD	_	_	_
46	Step	step	NN	_	_	_
47	_	_	SYM	_	_	_
48	3-2	3-2	CD	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	Butanol	Butanol	NNP	_	_	_
51	_	_	NNP	_	_	_
52	Challenge	Challenge	NNP	_	_	_
53	_	_	VBD	_	_	_
54	Step	step	NN	_	_	_
55	_	_	SYM	_	_	_
56	4-1	4-1	CD	_	_	_
57	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
58	Butanol	Butanol	NNP	_	_	_
59	_	_	NNP	_	_	_
60	Challenge	Challenge	NNP	_	_	_
61	_	_	VBD	_	_	_
62	Step	step	NN	_	_	_
63	_	_	SYM	_	_	_
64	4-2	4-2	CD	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	cell	cell	NN	_	_	_
67	type	type	NN	_	_	_
68	:	:	:	_	_	_
69	bacterial	bacterial	JJ	_	_	_
70	liquid	liquid	JJ	_	_	_
71	culture	culture	NN	_	_	_
72	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
73	Control	Control	NNP	_	_	_
74	_	_	NNP	_	_	_
75	Step	step	VB	_	_	_
76	_	_	SYM	_	_	_
77	1-1	1-1	CD	_	_	_
78	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
79	Control	Control	NNP	_	_	_
80	_	_	NNP	_	_	_
81	Step	step	VB	_	_	_
82	_	_	SYM	_	_	_
83	1-2	1-2	CD	_	_	_
84	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
85	Control	Control	NNP	_	_	_
86	_	_	NNP	_	_	_
87	Step	step	VB	_	_	_
88	_	_	SYM	_	_	_
89	2-1	2-1	CD	_	_	_
90	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
91	Control	Control	NNP	_	_	_
92	_	_	NNP	_	_	_
93	Step	step	VB	_	_	_
94	_	_	SYM	_	_	_
95	2-2	2-2	CD	_	_	_
96	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
97	Control	Control	NNP	_	_	_
98	_	_	NNP	_	_	_
99	Step	step	VB	_	_	_
100	_	_	SYM	_	_	_
101	3-1	3-1	CD	_	_	_
102	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
103	Control	Control	NNP	_	_	_
104	_	_	NNP	_	_	_
105	Step	step	VB	_	_	_
106	_	_	SYM	_	_	_
107	3-2	3-2	CD	_	_	_
108	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
109	Control	Control	NNP	_	_	_
110	_	_	NNP	_	_	_
111	Step	step	VB	_	_	_
112	_	_	SYM	_	_	_
113	4-1	4-1	CD	_	_	_
114	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
115	Control	Control	NNP	_	_	_
116	_	_	NNP	_	_	_
117	Step	step	VB	_	_	_
118	_	_	SYM	_	_	_
119	4-2	4-2	CD	_	_	_
120	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
121	Escherichia	escherichia	FW	Organism	_	_
122	coli	coli	FW	Organism	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	extracted	extract	VBN	_	_	_
125	molecule	molecule	NN	_	_	_
126	:	:	:	_	_	_
127	plasmid	plasmid	NN	_	_	_
128	DNA	dna	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
130	Genomic	genomic	JJ	_	_	_
131	Library	Library	NNP	_	_	_
132	of	of	IN	_	_	_
133	E.	e.	FW	_	_	_
134	coli	coli	FW	_	_	_
135	was	be	VBD	_	_	_
136	enriched	enriched	JJ	_	_	_
137	via	via	IN	_	_	_
138	serial	serial	NN	_	_	_
139	transfers	transfer	NNS	_	_	_
140	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	M9	m9	NN	MED	_	_
7	minimal	minimal	JJ	MED	_	_
8	media	media	NNS	MED	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	5	5	CD	_	_	_
11	g	g	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	Non-challenged	non-challenged	JJ	_	_	_
14	Library	Library	NNP	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	other	other	JJ	_	_	_
17	extracted	extract	VBN	_	_	_
18	using	use	VBG	_	_	_
19	alkalyne	alkalyne	JJ	_	_	_
20	lysis	lysis	NN	_	_	_
21	preparation	preparation	NN	_	_	_
22	.	.	.	_	_	_

1	Plasmid	plasmid	NN	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	clean	clean	JJ	_	_	_
5	and	and	CC	_	_	_
6	concentrated	concentrate	VBD	_	_	_
7	using	use	VBG	_	_	_
8	Zymo	Zymo	NNP	_	_	_
9	Clean	Clean	NNP	_	_	_
10	&	&	CC	_	_	_
11	Concentrated	Concentrated	NNP	_	_	_
12	-5	-5	CD	_	_	_
13	kit	kit	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
15	The	the	DT	_	_	_
16	image	image	NN	_	_	_
17	analysis	analysis	NN	_	_	_
18	performed	perform	VBN	_	_	_
19	using	use	VBG	_	_	_
20	GenePix	GenePix	NNP	_	_	_
21	Pro	pro	FW	_	_	_
22	6.0	6.0	CD	_	_	_
23	Software	Software	NNP	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Molecular	molecular	JJ	_	_	_
26	Devices	Devices	NNPS	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	,	,	,	_	_	_
29	normalized	normalize	VBN	_	_	_
30	with	with	IN	_	_	_
31	MIDAS	midas	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	LOWESS	lowess	NN	_	_	_
34	method	method	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	,	,	,	_	_	_
37	with	with	IN	_	_	_
38	clustering	clustering	NN	_	_	_
39	analysis	analysis	NN	_	_	_
40	in	in	IN	_	_	_
41	MeV	mev	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	CAST	cast	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	Bacterial	bacterial	JJ	_	_	_
47	RNA	rna	NN	_	_	_
48	was	be	VBD	_	_	_
49	stabilized	stabilize	VBN	_	_	_
50	in	in	FW	_	_	_
51	vivo	vivo	FW	_	_	_
52	,	,	,	_	_	_
53	by	by	IN	_	_	_
54	using	use	VBG	_	_	_
55	RNA	rna	NN	_	_	_
56	protect	protect	VBP	_	_	_
57	Bacteria	bacterium	NNS	_	_	_
58	Reagent	reagent	NN	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	Qiagen	qiagen	NN	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	by	by	IN	_	_	_
6	using	use	VBG	_	_	_
7	RNeasy	RNeasy	NNP	_	_	_
8	Kits	kit	NNS	_	_	_
9	for	for	IN	_	_	_
10	RNA	rna	NN	_	_	_
11	purification	purification	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Qiagen	qiagen	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	as	as	IN	_	_	_
16	per	per	IN	_	_	_
17	the	the	DT	_	_	_
18	manufacturer	manufacturer	NN	_	_	_
19	's	's	POS	_	_	_
20	protocol	protocol	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	to	to	TO	_	_	_
6	an	a	DT	_	_	_
7	OD	od	NN	_	_	_
8	of	of	IN	_	_	_
9	0.4	0.4	CD	_	_	_
10	and	and	CC	_	_	_
11	then	then	RB	_	_	_
12	0.5	0.5	CD	_	_	_
13	mM	mm	NN	KWSUPP	_	_
14	IPTG	iptg	NN	_	_	_
15	was	be	VBD	_	_	_
16	added	add	VBN	_	_	_
17	to	to	TO	_	_	_
18	induce	induce	VB	_	_	_
19	the	the	DT	_	_	_
20	protein	protein	NN	_	_	_
21	expression	expression	NN	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	Data	Data	NNP	_	_	_
24	extraction	extraction	NN	_	_	_
25	from	from	IN	_	_	_
26	Images	image	NNS	_	_	_
27	was	be	VBD	_	_	_
28	done	do	VBN	_	_	_
29	using	use	VBG	_	_	_
30	Feature	Feature	NNP	_	_	_
31	Extraction	Extraction	NNP	_	_	_
32	software	software	NN	_	_	_
33	v	v	LS	_	_	_
34	9.5.1	9.5.1	CD	_	_	_
35	of	of	IN	_	_	_
36	Agilent	Agilent	NNP	_	_	_
37	.	.	.	_	_	_

1	Feature	feature	NN	_	_	_
2	extracted	extract	VBN	_	_	_
3	raw	raw	JJ	_	_	_
4	data	datum	NNS	_	_	_
5	was	be	VBD	_	_	_
6	analyzed	analyze	VBN	_	_	_
7	using	use	VBG	_	_	_
8	GeneSpring	GeneSpring	NNP	_	_	_
9	GX	GX	NNP	_	_	_
10	V	V	NNP	_	_	_
11	7.3.1	7.3.1	CD	_	_	_
12	software	software	NN	_	_	_
13	from	from	IN	_	_	_
14	Agilent	Agilent	NNP	_	_	_
15	.	.	.	_	_	_

1	Normalization	normalization	NN	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	data	datum	NNS	_	_	_
5	was	be	VBD	_	_	_
6	done	do	VBN	_	_	_
7	in	in	IN	_	_	_
8	GeneSpring	GeneSpring	NNP	_	_	_
9	GX	GX	NNP	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	recommended	recommend	VBN	_	_	_
13	one	one	CD	_	_	_
14	color	color	NN	_	_	_
15	Per	per	IN	_	_	_
16	Chip	chip	NN	_	_	_
17	and	and	CC	_	_	_
18	Per	per	IN	_	_	_
19	Gene	Gene	NNP	_	_	_
20	Data	Data	NNP	_	_	_
21	Transformation	transformation	NN	_	_	_
22	:	:	:	_	_	_
23	Set	set	VB	_	_	_
24	measurements	measurement	NNS	_	_	_
25	less	less	JJR	_	_	_
26	than	than	IN	_	_	_
27	0.01	0.01	CD	_	_	_
28	to	to	TO	_	_	_
29	0.01	0.01	CD	_	_	_
30	,	,	,	_	_	_
31	Per	per	IN	_	_	_
32	Chip	chip	NN	_	_	_
33	:	:	:	_	_	_
34	Normalize	normalize	VB	_	_	_
35	to	to	TO	_	_	_
36	50th	50th	JJ	_	_	_
37	percentile	percentile	NN	_	_	_
38	,	,	,	_	_	_
39	Per	per	IN	_	_	_
40	Gene	gene	NN	_	_	_
41	:	:	:	_	_	_
42	Normalize	normalize	VB	_	_	_
43	to	to	TO	_	_	_
44	Specific	specific	JJ	_	_	_
45	Samples	sample	NNS	_	_	_
46	.	.	.	_	_	_

1	Significant	significant	JJ	_	_	_
2	genes	gene	NNS	_	_	_
3	up	up	RB	_	_	_
4	and	and	CC	_	_	_
5	down	down	RB	_	_	_
6	regulated	regulate	VBN	_	_	_
7	showing	show	VBG	_	_	_
8	one	one	CD	_	_	_
9	fold	fold	NN	_	_	_
10	and	and	CC	_	_	_
11	above	above	IN	_	_	_
12	among	among	IN	_	_	_
13	the	the	DT	_	_	_
14	samples	sample	NNS	_	_	_
15	was	be	VBD	_	_	_
16	identified	identify	VBN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	BL21	bl21	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	DE3	de3	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	cells	cell	NNS	_	_	_
9	expressing	express	VBG	_	_	_
10	catalytically	catalytically	RB	_	_	_
11	inactive	inactive	JJ	_	_	_
12	mutant	mutant	NN	_	_	_
13	of	of	IN	_	_	_
14	M.HpyAVIB	m.hpyavib	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
16	E.	e.	FW	_	_	_
17	coli	coli	FW	_	_	_
18	BL21	bl21	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	DE3	de3	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	cells	cell	NNS	_	_	_
23	expressing	express	VBG	_	_	_
24	wild-type	wild-type	JJ	_	_	_
25	M.HpyAVIB	m.hpyavib	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	Escherichia	escherichia	FW	Organism	_	_
28	coli	coli	FW	Organism	_	_
29	BL21	bl21	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	DE3	de3	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	genotype	genotype	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	mutant	mutant	JJ	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	wild	wild	JJ	_	_	_
39	type	type	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	antibody	antibody	NN	_	_	_
42	:	:	:	_	_	_
43	normal	normal	JJ	_	_	_
44	mouse	mouse	NN	_	_	_
45	IgG	igg	NN	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	Upstate	upstate	JJ	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	Cells	cell	NNS	_	_	_
51	at	at	IN	_	_	_
52	appropriate	appropriate	JJ	_	_	_
53	cell	cell	NN	_	_	_
54	density	density	NN	_	_	_
55	were	be	VBD	_	_	_
56	cross-linked	cross-link	VBN	_	_	_
57	by	by	IN	_	_	_
58	1	1	CD	_	_	_
59	%	%	NN	_	_	_
60	formaldehyde	formaldehyde	NN	_	_	_
61	at	at	IN	_	_	_
62	room	room	NN	_	_	_
63	temperature	temperature	NN	_	_	_
64	for	for	IN	_	_	_
65	25	25	CD	_	_	_
66	min	min	NN	_	_	_
67	.	.	.	_	_	_

1	Following	follow	VBG	_	_	_
2	quenching	quench	VBG	_	_	_
3	the	the	DT	_	_	_
4	unused	unused	JJ	_	_	_
5	formaldehyde	formaldehyde	NN	_	_	_
6	with	with	IN	_	_	_
7	a	a	DT	_	_	_
8	final	final	JJ	_	_	_
9	concentration	concentration	NN	_	_	_
10	of	of	IN	_	_	_
11	125	125	CD	_	_	_
12	mM	mm	NN	KWSUPP	_	_
13	glycine	glycine	NN	_	_	_
14	at	at	IN	_	_	_
15	room	room	NN	_	_	_
16	temperature	temperature	NN	_	_	_
17	for	for	IN	_	_	_
18	5	5	CD	_	_	_
19	min	min	NN	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cross-linked	cross-linked	JJ	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	harvested	harvest	VBN	_	_	_
6	and	and	CC	_	_	_
7	washed	wash	VBN	_	_	_
8	three	three	CD	_	_	_
9	times	time	NNS	_	_	_
10	with	with	IN	_	_	_
11	50	50	CD	_	_	_
12	mL	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	ice-cold	ice-cold	JJ	_	_	_
15	TBS	tbs	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Tris	tris	NN	_	_	_
18	Buffered	buffer	VBN	_	_	_
19	Saline	saline	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	washed	wash	VBN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	re-suspended	re-suspended	JJ	_	_	_
6	in	in	IN	_	_	_
7	0.5	0.5	CD	_	_	_
8	mL	ml	NN	_	_	_
9	lysis	lysis	NN	_	_	_
10	buffer	buffer	NN	_	_	_
11	composed	compose	VBN	_	_	_
12	of	of	IN	_	_	_
13	50	50	CD	_	_	_
14	mM	mm	NN	KWSUPP	_	_
15	Tris-HCl	tris-hcl	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	pH	ph	NN	_	_	_
18	7.5	7.5	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	,	,	,	_	_	_
21	100	100	CD	_	_	_
22	mM	mm	NN	KWSUPP	_	_
23	NaCl	nacl	NN	_	_	_
24	,	,	,	_	_	_
25	1	1	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	EDTA	edta	NN	_	_	_
28	,	,	,	_	_	_
29	1	1	CD	_	_	_
30	ug	ug	NN	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	chip	chip	NN	_	_	_
33	antibody	antibody	NN	_	_	_
34	:	:	:	_	_	_
35	9E10	9e10	NN	_	_	_
36	Myc	myc	NN	_	_	_
37	tag	tag	NN	GEN	_	_
38	antibody	antibody	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Cross-linked	cross-linked	JJ	_	_	_
41	and	and	CC	_	_	_
42	sonicated	sonicated	JJ	_	_	_
43	chromatin	chromatin	NN	_	_	_
44	complex	complex	NN	_	_	_
45	of	of	IN	_	_	_
46	PurR-8myc	purr-8myc	NN	_	_	_
47	and	and	CC	_	_	_
48	DNA	dna	NN	_	_	_
49	was	be	VBD	_	_	_
50	immunoprecipitated	immunoprecipitate	VBN	_	_	_
51	by	by	IN	_	_	_
52	9E10	9e10	NN	_	_	_
53	myc	myc	NN	_	_	_
54	antibody	antibody	NN	_	_	_
55	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cross-linked	cross-linked	JJ	_	_	_
3	and	and	CC	_	_	_
4	sonicated	sonicated	JJ	_	_	_
5	chromatin	chromatin	NN	_	_	_
6	complex	complex	NN	_	_	_
7	of	of	IN	_	_	_
8	PurR-8myc	purr-8myc	NN	_	_	_
9	and	and	CC	_	_	_
10	DNA	dna	NN	_	_	_
11	was	be	VBD	_	_	_
12	immunoprecipitated	immunoprecipitate	VBN	_	_	_
13	by	by	IN	_	_	_
14	using	use	VBG	_	_	_
15	normal	normal	JJ	_	_	_
16	mouse	mouse	NN	_	_	_
17	IgG	igg	NN	_	_	_
18	for	for	IN	_	_	_
19	the	the	DT	_	_	_
20	control	control	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	Coli	Coli	NNP	_	_	_
4	PurR	purr	NN	TF	_	_
5	ChIP	chip	NN	_	_	_
6	DNA	dna	NN	_	_	_
7	Adenine	adenine	NN	_	_	_
8	1	1	CD	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	E.	E.	NNP	_	_	_
11	Coli	Coli	NNP	_	_	_
12	PurR	purr	NN	TF	_	_
13	ChIP	chip	NN	_	_	_
14	DNA	dna	NN	_	_	_
15	Adenine	adenine	NN	_	_	_
16	2	2	CD	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	E.	E.	NNP	_	_	_
19	Coli	Coli	NNP	_	_	_
20	PurR	purr	NN	TF	_	_
21	ChIP	chip	NN	_	_	_
22	DNA	dna	NN	_	_	_
23	glucose	glucose	NN	SUPP	_	_
24	1	1	CD	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	E.	E.	NNP	_	_	_
27	Coli	Coli	NNP	_	_	_
28	PurR	purr	NN	TF	_	_
29	ChIP	chip	NN	_	_	_
30	DNA	dna	NN	_	_	_
31	glucose	glucose	NN	SUPP	_	_
32	2	2	CD	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	E.	E.	NNP	_	_	_
35	Coli	Coli	NNP	_	_	_
36	PurR	purr	NN	TF	_	_
37	Input	input	NN	_	_	_
38	DNA	dna	NN	_	_	_
39	Adenine	adenine	NN	_	_	_
40	1	1	CD	_	_	_
41	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
42	E.	E.	NNP	_	_	_
43	Coli	Coli	NNP	_	_	_
44	PurR	purr	NN	TF	_	_
45	Input	input	NN	_	_	_
46	DNA	dna	NN	_	_	_
47	Adenine	adenine	NN	_	_	_
48	2	2	CD	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	E.	E.	NNP	_	_	_
51	Coli	Coli	NNP	_	_	_
52	PurR	PurR	NNP	TF	_	_
53	Input	Input	NNP	_	_	_
54	DNA	DNA	NNP	_	_	_
55	glucose	glucose	NN	SUPP	_	_
56	1	1	CD	_	_	_
57	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
58	E.	E.	NNP	_	_	_
59	Coli	Coli	NNP	_	_	_
60	PurR	PurR	NNP	TF	_	_
61	Input	Input	NNP	_	_	_
62	DNA	DNA	NNP	_	_	_
63	glucose	glucose	NN	SUPP	_	_
64	2	2	CD	_	_	_
65	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
66	E.	E.	NNP	_	_	_
67	coli	coli	NN	_	_	_
68	strains	strain	NNS	_	_	_
69	harboring	harbor	VBG	_	_	_
70	PurR-8myc	purr-8myc	NN	_	_	_
71	were	be	VBD	_	_	_
72	grown	grow	VBN	_	_	_
73	in	in	IN	_	_	_
74	minimal	minimal	JJ	_	_	_
75	M9	m9	NN	_	_	_
76	medium	medium	NN	_	_	_
77	supplemented	supplement	VBN	_	_	_
78	with	with	IN	_	_	_
79	glucose	glucose	NN	SUPP	_	_
80	-LRB-	-lrb-	-LRB-	_	_	_
81	2	2	CD	_	_	_
82	g	g	NN	_	_	_
83	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
84	Escherichia	escherichia	FW	Organism	_	_
85	coli	coli	FW	Organism	_	_
86	str	str	FW	_	_	_
87	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	genotype	genotype	NN	_	_	_
4	:	:	:	_	_	_
5	PurR-8myc	purr-8myc	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	growth	growth	NN	_	_	_
8	condition	condition	NN	_	_	_
9	:	:	:	_	_	_
10	Adenine	Adenine	NNP	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	growth	growth	NN	_	_	_
13	condition	condition	NN	_	_	_
14	:	:	:	_	_	_
15	glucose	glucose	NN	SUPP	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	PurR	purr	NN	TF	_	_
18	_	_	CD	_	_	_
19	Adenine	Adenine	NNP	_	_	_
20	_	_	SYM	_	_	_
21	1	1	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	PurR	purr	NN	TF	_	_
24	_	_	CD	_	_	_
25	Adenine	Adenine	NNP	_	_	_
26	_	_	NN	_	_	_
27	2	2	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
29	PurR	purr	NN	TF	_	_
30	_	_	CD	_	_	_
31	glucose	glucose	NN	SUPP	_	_
32	_	_	NN	_	_	_
33	1	1	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	PurR	purr	NN	TF	_	_
36	_	_	CD	_	_	_
37	glucose	glucose	NN	SUPP	_	_
38	_	_	NN	_	_	_
39	2	2	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
41	The	the	DT	_	_	_
42	raw	raw	JJ	_	_	_
43	data	data	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	.	.	.	_	_	_

1	pair	pair	NN	_	_	_
2	file	file	NN	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	was	be	VBD	_	_	_
5	subjected	subject	VBN	_	_	_
6	to	to	TO	_	_	_
7	per	per	IN	_	_	_
8	channel	channel	NN	_	_	_
9	quantile	quantile	NN	_	_	_
10	normalization	normalization	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Bolstad	Bolstad	NNP	_	_	_
13	et	et	FW	_	_	_
14	al.	al.	FW	_	_	_
15	.	.	.	_	_	_

1	Bioinformatics	bioinformatic	NNS	_	_	_
2	19	19	CD	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	2	2	CD	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	:	:	:	_	_	_
7	185	185	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	,	,	,	_	_	_
10	IP	IP	NNP	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	10	10	CD	_	_	_
13	_	_	SYM	_	_	_
14	HF	hf	NNS	_	_	_
15	_	_	VBP	_	_	_
16	HP	HP	NNP	_	_	_
17	_	_	SYM	_	_	_
18	noDP	nodp	NN	_	_	_
19	_	_	CD	_	_	_
20	noRh	norh	NN	_	_	_
21	-LSB-	-lsb-	-LRB-	_	_	_
22	COPRO-Seq	copro-seq	NN	_	_	_
23	-RSB-	-rsb-	-RRB-	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	12	12	CD	_	_	_
26	_	_	SYM	_	_	_
27	HF	hf	NNS	_	_	_
28	_	_	VBP	_	_	_
29	LP	lp	NN	_	_	_
30	_	_	SYM	_	_	_
31	noDP	nodp	NN	_	_	_
32	-LSB-	-lsb-	-LRB-	_	_	_
33	COPRO-Seq	copro-seq	NN	_	_	_
34	-RSB-	-rsb-	-RRB-	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	13	13	CD	_	_	_
37	_	_	SYM	_	_	_
38	HF	hf	NNS	_	_	_
39	_	_	VBP	_	_	_
40	LP	lp	NN	_	_	_
41	_	_	SYM	_	_	_
42	noDP	nodp	NN	_	_	_
43	-LSB-	-lsb-	-LRB-	_	_	_
44	COPRO-Seq	copro-seq	NN	_	_	_
45	-RSB-	-rsb-	-RRB-	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	14	14	CD	_	_	_
48	_	_	SYM	_	_	_
49	HF	hf	NNS	_	_	_
50	_	_	VBP	_	_	_
51	LP	lp	NN	_	_	_
52	_	_	SYM	_	_	_
53	noDP	nodp	NN	_	_	_
54	-LSB-	-lsb-	-LRB-	_	_	_
55	COPRO-Seq	copro-seq	NN	_	_	_
56	-RSB-	-rsb-	-RRB-	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	15	15	CD	_	_	_
59	_	_	SYM	_	_	_
60	HF	hf	NNS	_	_	_
61	_	_	VBP	_	_	_
62	LP	lp	NN	_	_	_
63	_	_	SYM	_	_	_
64	noDP	nodp	NN	_	_	_
65	-LSB-	-lsb-	-LRB-	_	_	_
66	COPRO-Seq	copro-seq	NN	_	_	_
67	-RSB-	-rsb-	-RRB-	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	17	17	CD	_	_	_
70	_	_	SYM	_	_	_
71	HF	hf	NNS	_	_	_
72	_	_	VBP	_	_	_
73	HP	HP	NNP	_	_	_
74	_	_	SYM	_	_	_
75	noDP	nodp	NN	_	_	_
76	-LSB-	-lsb-	-LRB-	_	_	_
77	COPRO-Seq	copro-seq	NN	_	_	_
78	-RSB-	-rsb-	-RRB-	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	18	18	CD	_	_	_
81	_	_	SYM	_	_	_
82	HF	hf	NNS	_	_	_
83	_	_	VBP	_	_	_
84	HP	HP	NNP	_	_	_
85	_	_	SYM	_	_	_
86	noDP	nodp	NN	_	_	_
87	-LSB-	-lsb-	-LRB-	_	_	_
88	COPRO-Seq	copro-seq	NN	_	_	_
89	-RSB-	-rsb-	-RRB-	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	19	19	CD	_	_	_
92	_	_	SYM	_	_	_
93	HF	hf	NNS	_	_	_
94	_	_	VBP	_	_	_
95	HP	HP	NNP	_	_	_
96	_	_	SYM	_	_	_
97	noDP	nodp	NN	_	_	_
98	-LSB-	-lsb-	-LRB-	_	_	_
99	COPRO-Seq	copro-seq	NN	_	_	_
100	-RSB-	-rsb-	-RRB-	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	1	1	CD	_	_	_
103	_	_	SYM	_	_	_
104	HF	hf	NNS	_	_	_
105	_	_	VBP	_	_	_
106	LP	lp	NN	_	_	_
107	_	_	CD	_	_	_
108	noDP	nodp	NN	_	_	_
109	_	_	CD	_	_	_
110	noRh	norh	NN	_	_	_
111	-LSB-	-lsb-	-LRB-	_	_	_
112	COPRO-Seq	copro-seq	NN	_	_	_
113	-RSB-	-rsb-	-RRB-	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	20	20	CD	_	_	_
116	_	_	SYM	_	_	_
117	HF	hf	NNS	_	_	_
118	_	_	VBP	_	_	_
119	HP	HP	NNP	_	_	_
120	_	_	SYM	_	_	_
121	noDP	nodp	NN	_	_	_
122	-LSB-	-lsb-	-LRB-	_	_	_
123	COPRO-Seq	copro-seq	NN	_	_	_
124	-RSB-	-rsb-	-RRB-	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	2	2	CD	_	_	_
127	_	_	SYM	_	_	_
128	HF	hf	NNS	_	_	_
129	_	_	VBP	_	_	_
130	LP	lp	NN	_	_	_
131	_	_	CD	_	_	_
132	noDP	nodp	NN	_	_	_
133	_	_	CD	_	_	_
134	noRh	norh	NN	_	_	_
135	-LSB-	-lsb-	-LRB-	_	_	_
136	COPRO-Seq	copro-seq	NN	_	_	_
137	-RSB-	-rsb-	-RRB-	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	3	3	CD	_	_	_
140	_	_	NN	_	_	_
141	HF	hf	NNS	_	_	_
142	_	_	VBP	_	_	_
143	LP	lp	NN	_	_	_
144	_	_	CD	_	_	_
145	noDP	nodp	NN	_	_	_
146	_	_	CD	_	_	_
147	noRh	norh	NN	_	_	_
148	-LSB-	-lsb-	-LRB-	_	_	_
149	COPRO-Seq	copro-seq	NN	_	_	_
150	-RSB-	-rsb-	-RRB-	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	5	5	CD	_	_	_
153	_	_	SYM	_	_	_
154	HF	hf	NNS	_	_	_
155	_	_	VBP	_	_	_
156	LP	lp	NN	_	_	_
157	_	_	CD	_	_	_
158	noDP	nodp	NN	_	_	_
159	_	_	CD	_	_	_
160	noRh	norh	NN	_	_	_
161	-LSB-	-lsb-	-LRB-	_	_	_
162	COPRO-Seq	copro-seq	NN	_	_	_
163	-RSB-	-rsb-	-RRB-	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	6	6	CD	_	_	_
166	_	_	SYM	_	_	_
167	HF	hf	NNS	_	_	_
168	_	_	VBP	_	_	_
169	HP	HP	NNP	_	_	_
170	_	_	SYM	_	_	_
171	noDP	nodp	NN	_	_	_
172	_	_	CD	_	_	_
173	noRh	norh	NN	_	_	_
174	-LSB-	-lsb-	-LRB-	_	_	_
175	COPRO-Seq	copro-seq	NN	_	_	_
176	-RSB-	-rsb-	-RRB-	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	7	7	CD	_	_	_
179	_	_	SYM	_	_	_
180	HF	hf	NNS	_	_	_
181	_	_	VBP	_	_	_
182	HP	HP	NNP	_	_	_
183	_	_	SYM	_	_	_
184	noDP	nodp	NN	_	_	_
185	_	_	CD	_	_	_
186	noRh	norh	NN	_	_	_
187	-LSB-	-lsb-	-LRB-	_	_	_
188	COPRO-Seq	copro-seq	NN	_	_	_
189	-RSB-	-rsb-	-RRB-	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
191	9	9	CD	_	_	_
192	_	_	SYM	_	_	_
193	HF	hf	NNS	_	_	_
194	_	_	VBP	_	_	_
195	HP	HP	NNP	_	_	_
196	_	_	SYM	_	_	_
197	noDP	nodp	NN	_	_	_
198	_	_	CD	_	_	_
199	noRh	norh	NN	_	_	_
200	-LSB-	-lsb-	-LRB-	_	_	_
201	COPRO-Seq	copro-seq	NN	_	_	_
202	-RSB-	-rsb-	-RRB-	_	_	_
203	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
204	After	after	IN	_	_	_
205	dividing	divide	VBG	_	_	_
206	sequence	sequence	NN	_	_	_
207	runs	run	NNS	_	_	_
208	by	by	IN	_	_	_
209	barcode	barcode	NN	_	_	_
210	,	,	,	_	_	_
211	we	we	PRP	_	_	_
212	mapped	map	VBD	_	_	_
213	the	the	DT	_	_	_
214	reads	read	VBZ	_	_	_
215	to	to	TO	_	_	_
216	the	the	DT	_	_	_
217	relevant	relevant	JJ	_	_	_
218	genomes	genome	NNS	_	_	_
219	using	use	VBG	_	_	_
220	the	the	DT	_	_	_
221	ssaha2	ssaha2	NN	_	_	_
222	algorithm	algorithm	NN	_	_	_
223	.	.	.	_	_	_

1	Minimum	Minimum	NNP	_	_	_
2	score	score	NN	_	_	_
3	thresholds	threshold	NNS	_	_	_
4	for	for	IN	_	_	_
5	ssaha	ssaha	NN	_	_	_
6	were	be	VBD	_	_	_
7	selected	select	VBN	_	_	_
8	based	base	VBN	_	_	_
9	on	on	IN	_	_	_
10	the	the	DT	_	_	_
11	distribution	distribution	NN	_	_	_
12	of	of	IN	_	_	_
13	scores	score	NNS	_	_	_
14	for	for	IN	_	_	_
15	all	all	DT	_	_	_
16	mapped	map	VBN	_	_	_
17	reads	read	VBZ	_	_	_
18	of	of	IN	_	_	_
19	a	a	DT	_	_	_
20	32nt	32nt	JJ	_	_	_
21	barcoded	barcoded	JJ	_	_	_
22	sample	sample	NN	_	_	_
23	and	and	CC	_	_	_
24	a	a	DT	_	_	_
25	36-nt	36-nt	JJ	_	_	_
26	non-barcoded	non-barcoded	JJ	_	_	_
27	sample	sample	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	29	29	CD	_	_	_
30	was	be	VBD	_	_	_
31	selected	select	VBN	_	_	_
32	as	as	IN	_	_	_
33	the	the	DT	_	_	_
34	minimum	minimum	JJ	_	_	_
35	score	score	NN	_	_	_
36	for	for	IN	_	_	_
37	32nt	32nt	JJ	_	_	_
38	barcoded	barcoded	JJ	_	_	_
39	samples	sample	NNS	_	_	_
40	;	;	:	_	_	_
41	33	33	CD	_	_	_
42	was	be	VBD	_	_	_
43	the	the	DT	_	_	_
44	minimum	minimum	JJ	_	_	_
45	score	score	NN	_	_	_
46	used	use	VBN	_	_	_
47	for	for	IN	_	_	_
48	36-nt	36-nt	JJ	_	_	_
49	non-barcoded	non-barcoded	JJ	_	_	_
50	samples	sample	NNS	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	.	.	.	_	_	_

1	Although	although	IN	_	_	_
2	an	a	DT	_	_	_
3	18-nt	18-nt	JJ	_	_	_
4	read	read	NN	_	_	_
5	is	be	VBZ	_	_	_
6	sufficient	sufficient	JJ	_	_	_
7	to	to	TO	_	_	_
8	map	map	VB	GEN	_	_
9	more	more	JJR	_	_	_
10	than	than	IN	_	_	_
11	90	90	CD	_	_	_
12	%	%	NN	_	_	_
13	of	of	IN	_	_	_
14	the	the	DT	_	_	_
15	sequencing	sequencing	NN	_	_	_
16	reads	read	VBZ	_	_	_
17	,	,	,	_	_	_
18	even	even	RB	_	_	_
19	at	at	IN	_	_	_
20	32-36nt	32-36nt	JJ	_	_	_
21	there	there	EX	_	_	_
22	is	be	VBZ	_	_	_
23	a	a	DT	_	_	_
24	large	large	JJ	_	_	_
25	fraction	fraction	NN	_	_	_
26	of	of	IN	_	_	_
27	the	the	DT	_	_	_
28	reads	read	VBZ	_	_	_
29	that	that	IN	_	_	_
30	map	map	NN	GEN	_	_
31	to	to	TO	_	_	_
32	multiple	multiple	JJ	_	_	_
33	locations	location	NNS	_	_	_
34	within	within	IN	_	_	_
35	a	a	DT	_	_	_
36	genome	genome	NN	_	_	_
37	or	or	CC	_	_	_
38	across	across	IN	_	_	_
39	genomes	genome	NNS	_	_	_
40	.	.	.	_	_	_

1	Reads	read	NNS	_	_	_
2	that	that	WDT	_	_	_
3	map	map	VBP	GEN	_	_
4	non-uniquely	non-uniquely	JJ	_	_	_
5	were	be	VBD	_	_	_
6	discarded	discard	VBN	_	_	_
7	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Bacteroides	Bacteroides	NNPS	_	_	_
3	caccae	caccae	FW	_	_	_
4	ATCC	atcc	NN	_	_	_
5	43185	43185	CD	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	Bacteroides	Bacteroides	NNPS	_	_	_
8	ovatus	ovatus	NN	_	_	_
9	ATCC	atcc	NN	_	_	_
10	8483	8483	CD	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	Bacteroides	Bacteroides	NNPS	_	_	_
13	thetaiotaomicron	thetaiotaomicron	RB	_	_	_
14	VPI-5482	vpi-5482	JJ	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Blautia	blautia	NN	_	_	_
17	hydrogenotrophica	hydrogenotrophica	NN	_	_	_
18	DSM	DSM	NNP	_	_	_
19	10507	10507	CD	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	-LSB-	-lsb-	-LRB-	_	_	_
22	Clostridium	clostridium	NN	_	_	_
23	-RSB-	-rsb-	-RRB-	_	_	_
24	symbiosum	symbiosum	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Collinsella	collinsella	NN	_	_	_
27	aerofaciens	aerofacien	NNS	_	_	_
28	ATCC	atcc	NN	_	_	_
29	25986	25986	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	D2	d2	NN	_	_	_
32	_	_	CD	_	_	_
33	14	14	CD	_	_	_
34	_	_	NN	_	_	_
35	m10	m10	NN	_	_	_
36	-LSB-	-lsb-	-LRB-	_	_	_
37	COPRO-Seq	copro-seq	NN	_	_	_
38	-RSB-	-rsb-	-RRB-	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	D2	d2	NN	_	_	_
41	_	_	CD	_	_	_
42	14	14	CD	_	_	_
43	_	_	SYM	_	_	_
44	m11	m11	NN	_	_	_
45	-LSB-	-lsb-	-LRB-	_	_	_
46	COPRO-Seq	copro-seq	NN	_	_	_
47	-RSB-	-rsb-	-RRB-	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	D2	d2	NN	_	_	_
50	_	_	CD	_	_	_
51	14	14	CD	_	_	_
52	_	_	SYM	_	_	_
53	m12	m12	NN	_	_	_
54	-LSB-	-lsb-	-LRB-	_	_	_
55	COPRO-Seq	copro-seq	NN	_	_	_
56	-RSB-	-rsb-	-RRB-	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	D2	d2	NN	_	_	_
59	_	_	CD	_	_	_
60	14	14	CD	_	_	_
61	_	_	SYM	_	_	_
62	m13	m13	NN	_	_	_
63	-LSB-	-lsb-	-LRB-	_	_	_
64	COPRO-Seq	copro-seq	NN	_	_	_
65	-RSB-	-rsb-	-RRB-	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	D2	d2	NN	_	_	_
68	_	_	CD	_	_	_
69	14	14	CD	_	_	_
70	_	_	SYM	_	_	_
71	m1	m1	NN	_	_	_
72	-LSB-	-lsb-	-LRB-	_	_	_
73	COPRO-Seq	copro-seq	NN	_	_	_
74	-RSB-	-rsb-	-RRB-	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	D2	d2	NN	_	_	_
77	_	_	CD	_	_	_
78	14	14	CD	_	_	_
79	_	_	NN	_	_	_
80	m2	m2	NN	_	_	_
81	-LSB-	-lsb-	-LRB-	_	_	_
82	COPRO-Seq	copro-seq	NN	_	_	_
83	-RSB-	-rsb-	-RRB-	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	D2	d2	NN	_	_	_
86	_	_	CD	_	_	_
87	14	14	CD	_	_	_
88	_	_	NN	_	_	_
89	m3	m3	NN	_	_	_
90	-LSB-	-lsb-	-LRB-	_	_	_
91	COPRO-Seq	copro-seq	NN	_	_	_
92	-RSB-	-rsb-	-RRB-	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	D2	d2	NN	_	_	_
95	_	_	CD	_	_	_
96	14	14	CD	_	_	_
97	_	_	NN	_	_	_
98	m4	m4	NN	_	_	_
99	-LSB-	-lsb-	-LRB-	_	_	_
100	COPRO-Seq	copro-seq	NN	_	_	_
101	-RSB-	-rsb-	-RRB-	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	D2	d2	NN	_	_	_
104	_	_	CD	_	_	_
105	14	14	CD	_	_	_
106	_	_	NN	_	_	_
107	m5	m5	NN	_	_	_
108	-LSB-	-lsb-	-LRB-	_	_	_
109	COPRO-Seq	copro-seq	NN	_	_	_
110	-RSB-	-rsb-	-RRB-	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	D2	d2	NN	_	_	_
113	_	_	CD	_	_	_
114	14	14	CD	_	_	_
115	_	_	NN	_	_	_
116	m7	m7	NN	_	_	_
117	-LSB-	-lsb-	-LRB-	_	_	_
118	COPRO-Seq	copro-seq	NN	_	_	_
119	-RSB-	-rsb-	-RRB-	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	D2	d2	NN	_	_	_
122	_	_	CD	_	_	_
123	14	14	CD	_	_	_
124	_	_	NN	_	_	_
125	m8	m8	NN	_	_	_
126	-LSB-	-lsb-	-LRB-	_	_	_
127	COPRO-Seq	copro-seq	NN	_	_	_
128	-RSB-	-rsb-	-RRB-	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	D2	d2	NN	_	_	_
131	_	_	CD	_	_	_
132	14	14	CD	_	_	_
133	_	_	NN	_	_	_
134	m9	m9	NN	_	_	_
135	-LSB-	-lsb-	-LRB-	_	_	_
136	COPRO-Seq	copro-seq	NN	_	_	_
137	-RSB-	-rsb-	-RRB-	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	D2	d2	NN	_	_	_
140	_	_	NN	_	_	_
141	1	1	CD	_	_	_
142	_	_	CD	_	_	_
143	m12	m12	NN	_	_	_
144	-LSB-	-lsb-	-LRB-	_	_	_
145	COPRO-Seq	copro-seq	NN	_	_	_
146	-RSB-	-rsb-	-RRB-	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	D2	d2	NN	_	_	_
149	_	_	NN	_	_	_
150	1	1	CD	_	_	_
151	_	_	CD	_	_	_
152	m13	m13	NN	_	_	_
153	-LSB-	-lsb-	-LRB-	_	_	_
154	COPRO-Seq	copro-seq	NN	_	_	_
155	-RSB-	-rsb-	-RRB-	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
157	D2	d2	NN	_	_	_
158	_	_	NN	_	_	_
159	1	1	CD	_	_	_
160	_	_	SYM	_	_	_
161	m1	m1	NN	_	_	_
162	-LSB-	-lsb-	-LRB-	_	_	_
163	COPRO-Seq	copro-seq	NN	_	_	_
164	-RSB-	-rsb-	-RRB-	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	D2	d2	NN	_	_	_
167	_	_	NN	_	_	_
168	1	1	CD	_	_	_
169	_	_	CD	_	_	_
170	m2	m2	NN	_	_	_
171	-LSB-	-lsb-	-LRB-	_	_	_
172	COPRO-Seq	copro-seq	NN	_	_	_
173	-RSB-	-rsb-	-RRB-	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	D2	d2	NN	_	_	_
176	_	_	NN	_	_	_
177	1	1	CD	_	_	_
178	_	_	CD	_	_	_
179	m3	m3	NN	_	_	_
180	-LSB-	-lsb-	-LRB-	_	_	_
181	COPRO-Seq	copro-seq	NN	_	_	_
182	-RSB-	-rsb-	-RRB-	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	D2	d2	NN	_	_	_
185	_	_	NN	_	_	_
186	1	1	CD	_	_	_
187	_	_	CD	_	_	_
188	m4	m4	NN	_	_	_
189	-LSB-	-lsb-	-LRB-	_	_	_
190	COPRO-Seq	copro-seq	NN	_	_	_
191	-RSB-	-rsb-	-RRB-	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	D2	d2	NN	_	_	_
194	_	_	NN	_	_	_
195	1	1	CD	_	_	_
196	_	_	CD	_	_	_
197	m5	m5	NN	_	_	_
198	-LSB-	-lsb-	-LRB-	_	_	_
199	COPRO-Seq	copro-seq	NN	_	_	_
200	-RSB-	-rsb-	-RRB-	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	D2	d2	NN	_	_	_
203	_	_	NN	_	_	_
204	1	1	CD	_	_	_
205	_	_	CD	_	_	_
206	m6	m6	NN	_	_	_
207	-LSB-	-lsb-	-LRB-	_	_	_
208	COPRO-Seq	copro-seq	NN	_	_	_
209	-RSB-	-rsb-	-RRB-	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	D2	d2	NN	_	_	_
212	_	_	NN	_	_	_
213	1	1	CD	_	_	_
214	_	_	CD	_	_	_
215	m7	m7	NN	_	_	_
216	-LSB-	-lsb-	-LRB-	_	_	_
217	COPRO-Seq	copro-seq	NN	_	_	_
218	-RSB-	-rsb-	-RRB-	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	D2	d2	NN	_	_	_
221	_	_	NN	_	_	_
222	1	1	CD	_	_	_
223	_	_	CD	_	_	_
224	m8	m8	NN	_	_	_
225	-LSB-	-lsb-	-LRB-	_	_	_
226	COPRO-Seq	copro-seq	NN	_	_	_
227	-RSB-	-rsb-	-RRB-	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	D2	d2	NN	_	_	_
230	_	_	NN	_	_	_
231	1	1	CD	_	_	_
232	_	_	CD	_	_	_
233	m9	m9	NN	_	_	_
234	-LSB-	-lsb-	-LRB-	_	_	_
235	COPRO-Seq	copro-seq	NN	_	_	_
236	-RSB-	-rsb-	-RRB-	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	D2	d2	NN	_	_	_
239	_	_	NN	_	_	_
240	2	2	CD	_	_	_
241	_	_	CD	_	_	_
242	m10	m10	NN	_	_	_
243	-LSB-	-lsb-	-LRB-	_	_	_
244	COPRO-Seq	copro-seq	NN	_	_	_
245	-RSB-	-rsb-	-RRB-	_	_	_
246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
247	D2	d2	NN	_	_	_
248	_	_	NN	_	_	_
249	2	2	CD	_	_	_
250	_	_	CD	_	_	_
251	m12	m12	NN	_	_	_
252	-LSB-	-lsb-	-LRB-	_	_	_
253	COPRO-Seq	copro-seq	NN	_	_	_
254	-RSB-	-rsb-	-RRB-	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	D2	d2	NN	_	_	_
257	_	_	NN	_	_	_
258	2	2	CD	_	_	_
259	_	_	CD	_	_	_
260	m13	m13	NN	_	_	_
261	-LSB-	-lsb-	-LRB-	_	_	_
262	COPRO-Seq	copro-seq	NN	_	_	_
263	-RSB-	-rsb-	-RRB-	_	_	_
264	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
265	D2	d2	NN	_	_	_
266	_	_	NN	_	_	_
267	2	2	CD	_	_	_
268	_	_	SYM	_	_	_
269	m1	m1	NN	_	_	_
270	-LSB-	-lsb-	-LRB-	_	_	_
271	COPRO-Seq	copro-seq	NN	_	_	_
272	-RSB-	-rsb-	-RRB-	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	D2	d2	NN	_	_	_
275	_	_	NN	_	_	_
276	2	2	CD	_	_	_
277	_	_	CD	_	_	_
278	m2	m2	NN	_	_	_
279	-LSB-	-lsb-	-LRB-	_	_	_
280	COPRO-Seq	copro-seq	NN	_	_	_
281	-RSB-	-rsb-	-RRB-	_	_	_
282	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
283	D2	d2	NN	_	_	_
284	_	_	NN	_	_	_
285	2	2	CD	_	_	_
286	_	_	CD	_	_	_
287	m3	m3	NN	_	_	_
288	-LSB-	-lsb-	-LRB-	_	_	_
289	COPRO-Seq	copro-seq	NN	_	_	_
290	-RSB-	-rsb-	-RRB-	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	D2	d2	NN	_	_	_
293	_	_	NN	_	_	_
294	2	2	CD	_	_	_
295	_	_	CD	_	_	_
296	m4	m4	NN	_	_	_
297	-LSB-	-lsb-	-LRB-	_	_	_
298	COPRO-Seq	copro-seq	NN	_	_	_
299	-RSB-	-rsb-	-RRB-	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	D2	d2	NN	_	_	_
302	_	_	NN	_	_	_
303	2	2	CD	_	_	_
304	_	_	CD	_	_	_
305	m5	m5	NN	_	_	_
306	-LSB-	-lsb-	-LRB-	_	_	_
307	COPRO-Seq	copro-seq	NN	_	_	_
308	-RSB-	-rsb-	-RRB-	_	_	_
309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
310	D2	d2	NN	_	_	_
311	_	_	NN	_	_	_
312	2	2	CD	_	_	_
313	_	_	CD	_	_	_
314	m6	m6	NN	_	_	_
315	-LSB-	-lsb-	-LRB-	_	_	_
316	COPRO-Seq	copro-seq	NN	_	_	_
317	-RSB-	-rsb-	-RRB-	_	_	_
318	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
319	D2	d2	NN	_	_	_
320	_	_	NN	_	_	_
321	2	2	CD	_	_	_
322	_	_	CD	_	_	_
323	m7	m7	NN	_	_	_
324	-LSB-	-lsb-	-LRB-	_	_	_
325	COPRO-Seq	copro-seq	NN	_	_	_
326	-RSB-	-rsb-	-RRB-	_	_	_
327	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
328	D2	d2	NN	_	_	_
329	_	_	NN	_	_	_
330	2	2	CD	_	_	_
331	_	_	CD	_	_	_
332	m8	m8	NN	_	_	_
333	-LSB-	-lsb-	-LRB-	_	_	_
334	COPRO-Seq	copro-seq	NN	_	_	_
335	-RSB-	-rsb-	-RRB-	_	_	_
336	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
337	D2	d2	NN	_	_	_
338	_	_	NN	_	_	_
339	2	2	CD	_	_	_
340	_	_	CD	_	_	_
341	m9	m9	NN	_	_	_
342	-LSB-	-lsb-	-LRB-	_	_	_
343	COPRO-Seq	copro-seq	NN	_	_	_
344	-RSB-	-rsb-	-RRB-	_	_	_
345	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
346	D2	d2	NN	_	_	_
347	_	_	CD	_	_	_
348	4	4	CD	_	_	_
349	_	_	NN	_	_	_
350	m10	m10	NN	_	_	_
351	-LSB-	-lsb-	-LRB-	_	_	_
352	COPRO-Seq	copro-seq	NN	_	_	_
353	-RSB-	-rsb-	-RRB-	_	_	_
354	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
355	D2	d2	NN	_	_	_
356	_	_	CD	_	_	_
357	4	4	CD	_	_	_
358	_	_	SYM	_	_	_
359	m11	m11	NN	_	_	_
360	-LSB-	-lsb-	-LRB-	_	_	_
361	COPRO-Seq	copro-seq	NN	_	_	_
362	-RSB-	-rsb-	-RRB-	_	_	_
363	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
364	D2	d2	NN	_	_	_
365	_	_	CD	_	_	_
366	4	4	CD	_	_	_
367	_	_	SYM	_	_	_
368	m12	m12	NN	_	_	_
369	-LSB-	-lsb-	-LRB-	_	_	_
370	COPRO-Seq	copro-seq	NN	_	_	_
371	-RSB-	-rsb-	-RRB-	_	_	_
372	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
373	D2	d2	NN	_	_	_
374	_	_	CD	_	_	_
375	4	4	CD	_	_	_
376	_	_	SYM	_	_	_
377	m13	m13	NN	_	_	_
378	-LSB-	-lsb-	-LRB-	_	_	_
379	COPRO-Seq	copro-seq	NN	_	_	_
380	-RSB-	-rsb-	-RRB-	_	_	_
381	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
382	D2	d2	NN	_	_	_
383	_	_	CD	_	_	_
384	4	4	CD	_	_	_
385	_	_	SYM	_	_	_
386	m1	m1	NN	_	_	_
387	-LSB-	-lsb-	-LRB-	_	_	_
388	COPRO-Seq	copro-seq	NN	_	_	_
389	-RSB-	-rsb-	-RRB-	_	_	_
390	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
391	D2	d2	NN	_	_	_
392	_	_	CD	_	_	_
393	4	4	CD	_	_	_
394	_	_	NN	_	_	_
395	m3	m3	NN	_	_	_
396	-LSB-	-lsb-	-LRB-	_	_	_
397	COPRO-Seq	copro-seq	NN	_	_	_
398	-RSB-	-rsb-	-RRB-	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	D2	d2	NN	_	_	_
401	_	_	CD	_	_	_
402	4	4	CD	_	_	_
403	_	_	NN	_	_	_
404	m4	m4	NN	_	_	_
405	-LSB-	-lsb-	-LRB-	_	_	_
406	COPRO-Seq	copro-seq	NN	_	_	_
407	-RSB-	-rsb-	-RRB-	_	_	_
408	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
409	D2	d2	NN	_	_	_
410	_	_	CD	_	_	_
411	4	4	CD	_	_	_
412	_	_	NN	_	_	_
413	m5	m5	NN	_	_	_
414	-LSB-	-lsb-	-LRB-	_	_	_
415	COPRO-Seq	copro-seq	NN	_	_	_
416	-RSB-	-rsb-	-RRB-	_	_	_
417	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
418	D2	d2	NN	_	_	_
419	_	_	CD	_	_	_
420	4	4	CD	_	_	_
421	_	_	NN	_	_	_
422	m6	m6	NN	_	_	_
423	-LSB-	-lsb-	-LRB-	_	_	_
424	COPRO-Seq	copro-seq	NN	_	_	_
425	-RSB-	-rsb-	-RRB-	_	_	_
426	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
427	D2	d2	NN	_	_	_
428	_	_	CD	_	_	_
429	4	4	CD	_	_	_
430	_	_	NN	_	_	_
431	m7	m7	NN	_	_	_
432	-LSB-	-lsb-	-LRB-	_	_	_
433	COPRO-Seq	copro-seq	NN	_	_	_
434	-RSB-	-rsb-	-RRB-	_	_	_
435	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
436	D2	d2	NN	_	_	_
437	_	_	CD	_	_	_
438	4	4	CD	_	_	_
439	_	_	NN	_	_	_
440	m8	m8	NN	_	_	_
441	-LSB-	-lsb-	-LRB-	_	_	_
442	COPRO-Seq	copro-seq	NN	_	_	_
443	-RSB-	-rsb-	-RRB-	_	_	_
444	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
445	D2	d2	NN	_	_	_
446	_	_	NN	_	_	_
447	4	4	CD	_	_	_
448	_	_	CD	_	_	_
449	m9	m9	NN	_	_	_
450	-LSB-	-lsb-	-LRB-	_	_	_
451	COPRO-Seq	copro-seq	NN	_	_	_
452	-RSB-	-rsb-	-RRB-	_	_	_
453	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
454	D2	d2	NN	_	_	_
455	_	_	NN	_	_	_
456	7	7	CD	_	_	_
457	_	_	NN	_	_	_
458	m10	m10	NN	_	_	_
459	-LSB-	-lsb-	-LRB-	_	_	_
460	COPRO-Seq	copro-seq	NN	_	_	_
461	-RSB-	-rsb-	-RRB-	_	_	_
462	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
463	D2	d2	NN	_	_	_
464	_	_	NN	_	_	_
465	7	7	CD	_	_	_
466	_	_	NN	_	_	_
467	m11	m11	NN	_	_	_
468	-LSB-	-lsb-	-LRB-	_	_	_
469	COPRO-Seq	copro-seq	NN	_	_	_
470	-RSB-	-rsb-	-RRB-	_	_	_
471	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
472	D2	d2	NN	_	_	_
473	_	_	NN	_	_	_
474	7	7	CD	_	_	_
475	_	_	NN	_	_	_
476	m12	m12	NN	_	_	_
477	-LSB-	-lsb-	-LRB-	_	_	_
478	COPRO-Seq	copro-seq	NN	_	_	_
479	-RSB-	-rsb-	-RRB-	_	_	_
480	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
481	D2	d2	NN	_	_	_
482	_	_	NN	_	_	_
483	7	7	CD	_	_	_
484	_	_	NN	_	_	_
485	m13	m13	NN	_	_	_
486	-LSB-	-lsb-	-LRB-	_	_	_
487	COPRO-Seq	copro-seq	NN	_	_	_
488	-RSB-	-rsb-	-RRB-	_	_	_
489	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
490	D2	d2	NN	_	_	_
491	_	_	NN	_	_	_
492	7	7	CD	_	_	_
493	_	_	SYM	_	_	_
494	m1	m1	NN	_	_	_
495	-LSB-	-lsb-	-LRB-	_	_	_
496	COPRO-Seq	copro-seq	NN	_	_	_
497	-RSB-	-rsb-	-RRB-	_	_	_
498	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
499	D2	d2	NN	_	_	_
500	_	_	NN	_	_	_
501	7	7	CD	_	_	_
502	_	_	NN	_	_	_
503	m3	m3	NN	_	_	_
504	-LSB-	-lsb-	-LRB-	_	_	_
505	COPRO-Seq	copro-seq	NN	_	_	_
506	-RSB-	-rsb-	-RRB-	_	_	_
507	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
508	D2	d2	NN	_	_	_
509	_	_	NN	_	_	_
510	7	7	CD	_	_	_
511	_	_	NN	_	_	_
512	m4	m4	NN	_	_	_
513	-LSB-	-lsb-	-LRB-	_	_	_
514	COPRO-Seq	copro-seq	NN	_	_	_
515	-RSB-	-rsb-	-RRB-	_	_	_
516	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
517	D2	d2	NN	_	_	_
518	_	_	NN	_	_	_
519	7	7	CD	_	_	_
520	_	_	NN	_	_	_
521	m5	m5	NN	_	_	_
522	-LSB-	-lsb-	-LRB-	_	_	_
523	COPRO-Seq	copro-seq	NN	_	_	_
524	-RSB-	-rsb-	-RRB-	_	_	_
525	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
526	D2	d2	NN	_	_	_
527	_	_	NN	_	_	_
528	7	7	CD	_	_	_
529	_	_	NN	_	_	_
530	m6	m6	NN	_	_	_
531	-LSB-	-lsb-	-LRB-	_	_	_
532	COPRO-Seq	copro-seq	NN	_	_	_
533	-RSB-	-rsb-	-RRB-	_	_	_
534	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
535	D2	d2	NN	_	_	_
536	_	_	NN	_	_	_
537	7	7	CD	_	_	_
538	_	_	NN	_	_	_
539	m8	m8	NN	_	_	_
540	-LSB-	-lsb-	-LRB-	_	_	_
541	COPRO-Seq	copro-seq	NN	_	_	_
542	-RSB-	-rsb-	-RRB-	_	_	_
543	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
544	D2	d2	NN	_	_	_
545	_	_	NN	_	_	_
546	7	7	CD	_	_	_
547	_	_	NN	_	_	_
548	m9	m9	NN	_	_	_
549	-LSB-	-lsb-	-LRB-	_	_	_
550	COPRO-Seq	copro-seq	NN	_	_	_
551	-RSB-	-rsb-	-RRB-	_	_	_
552	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
553	D3	d3	NN	_	_	_
554	_	_	CD	_	_	_
555	10	10	CD	_	_	_
556	_	_	SYM	_	_	_
557	m1	m1	NN	_	_	_
558	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
559	D3	d3	NN	_	_	_
560	_	_	CD	_	_	_
561	10	10	CD	_	_	_
562	_	_	NN	_	_	_
563	m10	m10	NN	_	_	_
564	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
565	D3	d3	NN	_	_	_
566	_	_	CD	_	_	_
567	10	10	CD	_	_	_
568	_	_	NN	_	_	_
569	m11	m11	NN	_	_	_
570	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
571	D3	d3	NN	_	_	_
572	_	_	CD	_	_	_
573	10	10	CD	_	_	_
574	_	_	NN	_	_	_
575	m12	m12	NN	_	_	_
576	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
577	D3	d3	NN	_	_	_
578	_	_	CD	_	_	_
579	10	10	CD	_	_	_
580	_	_	NN	_	_	_
581	m13	m13	NN	_	_	_
582	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
583	D3	d3	NN	_	_	_
584	_	_	CD	_	_	_
585	10	10	CD	_	_	_
586	_	_	NN	_	_	_
587	m2	m2	NN	_	_	_
588	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
589	D3	d3	NN	_	_	_
590	_	_	CD	_	_	_
591	10	10	CD	_	_	_
592	_	_	NN	_	_	_
593	m3	m3	NN	_	_	_
594	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
595	D3	d3	NN	_	_	_
596	_	_	CD	_	_	_
597	10	10	CD	_	_	_
598	_	_	NN	_	_	_
599	m4	m4	NN	_	_	_
600	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
601	D3	d3	NN	_	_	_
602	_	_	CD	_	_	_
603	10	10	CD	_	_	_
604	_	_	NN	_	_	_
605	m5	m5	NN	_	_	_
606	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
607	D3	d3	NN	_	_	_
608	_	_	CD	_	_	_
609	10	10	CD	_	_	_
610	_	_	NN	_	_	_
611	m6	m6	NN	_	_	_
612	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
613	D3	d3	NN	_	_	_
614	_	_	CD	_	_	_
615	10	10	CD	_	_	_
616	_	_	NN	_	_	_
617	m7	m7	NN	_	_	_
618	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
619	D3	d3	NN	_	_	_
620	_	_	CD	_	_	_
621	10	10	CD	_	_	_
622	_	_	NN	_	_	_
623	m8	m8	NN	_	_	_
624	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
625	D3	d3	NN	_	_	_
626	_	_	CD	_	_	_
627	10	10	CD	_	_	_
628	_	_	NN	_	_	_
629	m9	m9	NN	_	_	_
630	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
631	D3	d3	NN	_	_	_
632	_	_	CD	_	_	_
633	14	14	CD	_	_	_
634	_	_	NN	_	_	_
635	m10	m10	NN	_	_	_
636	-LSB-	-lsb-	-LRB-	_	_	_
637	COPRO-Seq	copro-seq	NN	_	_	_
638	-RSB-	-rsb-	-RRB-	_	_	_
639	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
640	D3	d3	NN	_	_	_
641	_	_	CD	_	_	_
642	14	14	CD	_	_	_
643	_	_	SYM	_	_	_
644	m11	m11	NN	_	_	_
645	-LSB-	-lsb-	-LRB-	_	_	_
646	COPRO-Seq	copro-seq	NN	_	_	_
647	-RSB-	-rsb-	-RRB-	_	_	_
648	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
649	D3	d3	NN	_	_	_
650	_	_	CD	_	_	_
651	14	14	CD	_	_	_
652	_	_	SYM	_	_	_
653	m12	m12	NN	_	_	_
654	-LSB-	-lsb-	-LRB-	_	_	_
655	COPRO-Seq	copro-seq	NN	_	_	_
656	-RSB-	-rsb-	-RRB-	_	_	_
657	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
658	D3	d3	NN	_	_	_
659	_	_	CD	_	_	_
660	14	14	CD	_	_	_
661	_	_	SYM	_	_	_
662	m13	m13	NN	_	_	_
663	-LSB-	-lsb-	-LRB-	_	_	_
664	COPRO-Seq	copro-seq	NN	_	_	_
665	-RSB-	-rsb-	-RRB-	_	_	_
666	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
667	D3	d3	NN	_	_	_
668	_	_	CD	_	_	_
669	14	14	CD	_	_	_
670	_	_	NN	_	_	_
671	m2	m2	NN	_	_	_
672	-LSB-	-lsb-	-LRB-	_	_	_
673	COPRO-Seq	copro-seq	NN	_	_	_
674	-RSB-	-rsb-	-RRB-	_	_	_
675	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
676	D3	d3	NN	_	_	_
677	_	_	CD	_	_	_
678	14	14	CD	_	_	_
679	_	_	NN	_	_	_
680	m3	m3	NN	_	_	_
681	-LSB-	-lsb-	-LRB-	_	_	_
682	COPRO-Seq	copro-seq	NN	_	_	_
683	-RSB-	-rsb-	-RRB-	_	_	_
684	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
685	D3	d3	NN	_	_	_
686	_	_	CD	_	_	_
687	14	14	CD	_	_	_
688	_	_	NN	_	_	_
689	m4	m4	NN	_	_	_
690	-LSB-	-lsb-	-LRB-	_	_	_
691	COPRO-Seq	copro-seq	NN	_	_	_
692	-RSB-	-rsb-	-RRB-	_	_	_
693	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
694	D3	d3	NN	_	_	_
695	_	_	CD	_	_	_
696	14	14	CD	_	_	_
697	_	_	NN	_	_	_
698	m5	m5	NN	_	_	_
699	-LSB-	-lsb-	-LRB-	_	_	_
700	COPRO-Seq	copro-seq	NN	_	_	_
701	-RSB-	-rsb-	-RRB-	_	_	_
702	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
703	D3	d3	NN	_	_	_
704	_	_	CD	_	_	_
705	14	14	CD	_	_	_
706	_	_	NN	_	_	_
707	m6	m6	NN	_	_	_
708	-LSB-	-lsb-	-LRB-	_	_	_
709	COPRO-Seq	copro-seq	NN	_	_	_
710	-RSB-	-rsb-	-RRB-	_	_	_
711	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
712	D3	d3	NN	_	_	_
713	_	_	CD	_	_	_
714	14	14	CD	_	_	_
715	_	_	NN	_	_	_
716	m7	m7	NN	_	_	_
717	-LSB-	-lsb-	-LRB-	_	_	_
718	COPRO-Seq	copro-seq	NN	_	_	_
719	-RSB-	-rsb-	-RRB-	_	_	_
720	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
721	D3	d3	NN	_	_	_
722	_	_	CD	_	_	_
723	14	14	CD	_	_	_
724	_	_	NN	_	_	_
725	m8	m8	NN	_	_	_
726	-LSB-	-lsb-	-LRB-	_	_	_
727	COPRO-Seq	copro-seq	NN	_	_	_
728	-RSB-	-rsb-	-RRB-	_	_	_
729	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
730	D3	d3	NN	_	_	_
731	_	_	CD	_	_	_
732	14	14	CD	_	_	_
733	_	_	NN	_	_	_
734	m9	m9	NN	_	_	_
735	-LSB-	-lsb-	-LRB-	_	_	_
736	COPRO-Seq	copro-seq	NN	_	_	_
737	-RSB-	-rsb-	-RRB-	_	_	_
738	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
739	D3	d3	NN	_	_	_
740	_	_	NN	_	_	_
741	1	1	CD	_	_	_
742	_	_	CD	_	_	_
743	m10	m10	NN	_	_	_
744	-LSB-	-lsb-	-LRB-	_	_	_
745	COPRO-Seq	copro-seq	NN	_	_	_
746	-RSB-	-rsb-	-RRB-	_	_	_
747	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
748	D3	d3	NN	_	_	_
749	_	_	NN	_	_	_
750	1	1	CD	_	_	_
751	_	_	CD	_	_	_
752	m11	m11	NN	_	_	_
753	-LSB-	-lsb-	-LRB-	_	_	_
754	COPRO-Seq	copro-seq	NN	_	_	_
755	-RSB-	-rsb-	-RRB-	_	_	_
756	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
757	D3	d3	NN	_	_	_
758	_	_	NN	_	_	_
759	1	1	CD	_	_	_
760	_	_	CD	_	_	_
761	m13	m13	NN	_	_	_
762	-LSB-	-lsb-	-LRB-	_	_	_
763	COPRO-Seq	copro-seq	NN	_	_	_
764	-RSB-	-rsb-	-RRB-	_	_	_
765	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
766	D3	d3	NN	_	_	_
767	_	_	NN	_	_	_
768	1	1	CD	_	_	_
769	_	_	SYM	_	_	_
770	m1	m1	NN	_	_	_
771	-LSB-	-lsb-	-LRB-	_	_	_
772	COPRO-Seq	copro-seq	NN	_	_	_
773	-RSB-	-rsb-	-RRB-	_	_	_
774	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
775	D3	d3	NN	_	_	_
776	_	_	NN	_	_	_
777	1	1	CD	_	_	_
778	_	_	CD	_	_	_
779	m2	m2	NN	_	_	_
780	-LSB-	-lsb-	-LRB-	_	_	_
781	COPRO-Seq	copro-seq	NN	_	_	_
782	-RSB-	-rsb-	-RRB-	_	_	_
783	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
784	D3	d3	NN	_	_	_
785	_	_	NN	_	_	_
786	1	1	CD	_	_	_
787	_	_	CD	_	_	_
788	m3	m3	NN	_	_	_
789	-LSB-	-lsb-	-LRB-	_	_	_
790	COPRO-Seq	copro-seq	NN	_	_	_
791	-RSB-	-rsb-	-RRB-	_	_	_
792	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
793	D3	d3	NN	_	_	_
794	_	_	NN	_	_	_
795	1	1	CD	_	_	_
796	_	_	CD	_	_	_
797	m4	m4	NN	_	_	_
798	-LSB-	-lsb-	-LRB-	_	_	_
799	COPRO-Seq	copro-seq	NN	_	_	_
800	-RSB-	-rsb-	-RRB-	_	_	_
801	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
802	D3	d3	NN	_	_	_
803	_	_	NN	_	_	_
804	1	1	CD	_	_	_
805	_	_	CD	_	_	_
806	m5	m5	NN	_	_	_
807	-LSB-	-lsb-	-LRB-	_	_	_
808	COPRO-Seq	copro-seq	NN	_	_	_
809	-RSB-	-rsb-	-RRB-	_	_	_
810	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
811	D3	d3	NN	_	_	_
812	_	_	NN	_	_	_
813	1	1	CD	_	_	_
814	_	_	CD	_	_	_
815	m6	m6	NN	_	_	_
816	-LSB-	-lsb-	-LRB-	_	_	_
817	COPRO-Seq	copro-seq	NN	_	_	_
818	-RSB-	-rsb-	-RRB-	_	_	_
819	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
820	D3	d3	NN	_	_	_
821	_	_	NN	_	_	_
822	1	1	CD	_	_	_
823	_	_	CD	_	_	_
824	m7	m7	NN	_	_	_
825	-LSB-	-lsb-	-LRB-	_	_	_
826	COPRO-Seq	copro-seq	NN	_	_	_
827	-RSB-	-rsb-	-RRB-	_	_	_
828	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
829	D3	d3	NN	_	_	_
830	_	_	NN	_	_	_
831	1	1	CD	_	_	_
832	_	_	CD	_	_	_
833	m8	m8	NN	_	_	_
834	-LSB-	-lsb-	-LRB-	_	_	_
835	COPRO-Seq	copro-seq	NN	_	_	_
836	-RSB-	-rsb-	-RRB-	_	_	_
837	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
838	D3	d3	NN	_	_	_
839	_	_	NN	_	_	_
840	2	2	CD	_	_	_
841	_	_	CD	_	_	_
842	m10	m10	NN	_	_	_
843	-LSB-	-lsb-	-LRB-	_	_	_
844	COPRO-Seq	copro-seq	NN	_	_	_
845	-RSB-	-rsb-	-RRB-	_	_	_
846	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
847	D3	d3	NN	_	_	_
848	_	_	NN	_	_	_
849	2	2	CD	_	_	_
850	_	_	CD	_	_	_
851	m11	m11	NN	_	_	_
852	-LSB-	-lsb-	-LRB-	_	_	_
853	COPRO-Seq	copro-seq	NN	_	_	_
854	-RSB-	-rsb-	-RRB-	_	_	_
855	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
856	D3	d3	NN	_	_	_
857	_	_	NN	_	_	_
858	2	2	CD	_	_	_
859	_	_	CD	_	_	_
860	m12	m12	NN	_	_	_
861	-LSB-	-lsb-	-LRB-	_	_	_
862	COPRO-Seq	copro-seq	NN	_	_	_
863	-RSB-	-rsb-	-RRB-	_	_	_
864	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
865	D3	d3	NN	_	_	_
866	_	_	NN	_	_	_
867	2	2	CD	_	_	_
868	_	_	CD	_	_	_
869	m13	m13	NN	_	_	_
870	-LSB-	-lsb-	-LRB-	_	_	_
871	COPRO-Seq	copro-seq	NN	_	_	_
872	-RSB-	-rsb-	-RRB-	_	_	_
873	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
874	D3	d3	NN	_	_	_
875	_	_	NN	_	_	_
876	2	2	CD	_	_	_
877	_	_	CD	_	_	_
878	m2	m2	NN	_	_	_
879	-LSB-	-lsb-	-LRB-	_	_	_
880	COPRO-Seq	copro-seq	NN	_	_	_
881	-RSB-	-rsb-	-RRB-	_	_	_
882	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
883	D3	d3	NN	_	_	_
884	_	_	NN	_	_	_
885	2	2	CD	_	_	_
886	_	_	CD	_	_	_
887	m4	m4	NN	_	_	_
888	-LSB-	-lsb-	-LRB-	_	_	_
889	COPRO-Seq	copro-seq	NN	_	_	_
890	-RSB-	-rsb-	-RRB-	_	_	_
891	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
892	D3	d3	NN	_	_	_
893	_	_	NN	_	_	_
894	2	2	CD	_	_	_
895	_	_	CD	_	_	_
896	m5	m5	NN	_	_	_
897	-LSB-	-lsb-	-LRB-	_	_	_
898	COPRO-Seq	copro-seq	NN	_	_	_
899	-RSB-	-rsb-	-RRB-	_	_	_
900	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
901	D3	d3	NN	_	_	_
902	_	_	NN	_	_	_
903	2	2	CD	_	_	_
904	_	_	CD	_	_	_
905	m6	m6	NN	_	_	_
906	-LSB-	-lsb-	-LRB-	_	_	_
907	COPRO-Seq	copro-seq	NN	_	_	_
908	-RSB-	-rsb-	-RRB-	_	_	_
909	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
910	D3	d3	NN	_	_	_
911	_	_	NN	_	_	_
912	2	2	CD	_	_	_
913	_	_	CD	_	_	_
914	m7	m7	NN	_	_	_
915	-LSB-	-lsb-	-LRB-	_	_	_
916	COPRO-Seq	copro-seq	NN	_	_	_
917	-RSB-	-rsb-	-RRB-	_	_	_
918	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
919	D3	d3	NN	_	_	_
920	_	_	CD	_	_	_
921	4	4	CD	_	_	_
922	_	_	NN	_	_	_
923	m10	m10	NN	_	_	_
924	-LSB-	-lsb-	-LRB-	_	_	_
925	COPRO-Seq	copro-seq	NN	_	_	_
926	-RSB-	-rsb-	-RRB-	_	_	_
927	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
928	D3	d3	NN	_	_	_
929	_	_	CD	_	_	_
930	4	4	CD	_	_	_
931	_	_	SYM	_	_	_
932	m11	m11	NN	_	_	_
933	-LSB-	-lsb-	-LRB-	_	_	_
934	COPRO-Seq	copro-seq	NN	_	_	_
935	-RSB-	-rsb-	-RRB-	_	_	_
936	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
937	D3	d3	NN	_	_	_
938	_	_	CD	_	_	_
939	4	4	CD	_	_	_
940	_	_	SYM	_	_	_
941	m12	m12	NN	_	_	_
942	-LSB-	-lsb-	-LRB-	_	_	_
943	COPRO-Seq	copro-seq	NN	_	_	_
944	-RSB-	-rsb-	-RRB-	_	_	_
945	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
946	D3	d3	NN	_	_	_
947	_	_	CD	_	_	_
948	4	4	CD	_	_	_
949	_	_	SYM	_	_	_
950	m13	m13	NN	_	_	_
951	-LSB-	-lsb-	-LRB-	_	_	_
952	COPRO-Seq	copro-seq	NN	_	_	_
953	-RSB-	-rsb-	-RRB-	_	_	_
954	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
955	D3	d3	NN	_	_	_
956	_	_	CD	_	_	_
957	4	4	CD	_	_	_
958	_	_	SYM	_	_	_
959	m1	m1	NN	_	_	_
960	-LSB-	-lsb-	-LRB-	_	_	_
961	COPRO-Seq	copro-seq	NN	_	_	_
962	-RSB-	-rsb-	-RRB-	_	_	_
963	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
964	D3	d3	NN	_	_	_
965	_	_	CD	_	_	_
966	4	4	CD	_	_	_
967	_	_	NN	_	_	_
968	m2	m2	NN	_	_	_
969	-LSB-	-lsb-	-LRB-	_	_	_
970	COPRO-Seq	copro-seq	NN	_	_	_
971	-RSB-	-rsb-	-RRB-	_	_	_
972	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
973	D3	d3	NN	_	_	_
974	_	_	CD	_	_	_
975	4	4	CD	_	_	_
976	_	_	NN	_	_	_
977	m3	m3	NN	_	_	_
978	-LSB-	-lsb-	-LRB-	_	_	_
979	COPRO-Seq	copro-seq	NN	_	_	_
980	-RSB-	-rsb-	-RRB-	_	_	_
981	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
982	D3	d3	NN	_	_	_
983	_	_	CD	_	_	_
984	4	4	CD	_	_	_
985	_	_	NN	_	_	_
986	m4	m4	NN	_	_	_
987	-LSB-	-lsb-	-LRB-	_	_	_
988	COPRO-Seq	copro-seq	NN	_	_	_
989	-RSB-	-rsb-	-RRB-	_	_	_
990	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
991	D3	d3	NN	_	_	_
992	_	_	CD	_	_	_
993	4	4	CD	_	_	_
994	_	_	NN	_	_	_
995	m5	m5	NN	_	_	_
996	-LSB-	-lsb-	-LRB-	_	_	_
997	COPRO-Seq	copro-seq	NN	_	_	_
998	-RSB-	-rsb-	-RRB-	_	_	_
999	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1000	D3	d3	NN	_	_	_
1001	_	_	CD	_	_	_
1002	4	4	CD	_	_	_
1003	_	_	NN	_	_	_
1004	m6	m6	NN	_	_	_
1005	-LSB-	-lsb-	-LRB-	_	_	_
1006	COPRO-Seq	copro-seq	NN	_	_	_
1007	-RSB-	-rsb-	-RRB-	_	_	_
1008	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1009	D3	d3	NN	_	_	_
1010	_	_	CD	_	_	_
1011	4	4	CD	_	_	_
1012	_	_	NN	_	_	_
1013	m7	m7	NN	_	_	_
1014	-LSB-	-lsb-	-LRB-	_	_	_
1015	COPRO-Seq	copro-seq	NN	_	_	_
1016	-RSB-	-rsb-	-RRB-	_	_	_
1017	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1018	D3	d3	NN	_	_	_
1019	_	_	CD	_	_	_
1020	4	4	CD	_	_	_
1021	_	_	NN	_	_	_
1022	m8	m8	NN	_	_	_
1023	-LSB-	-lsb-	-LRB-	_	_	_
1024	COPRO-Seq	copro-seq	NN	_	_	_
1025	-RSB-	-rsb-	-RRB-	_	_	_
1026	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1027	D3	d3	NN	_	_	_
1028	_	_	NN	_	_	_
1029	4	4	CD	_	_	_
1030	_	_	CD	_	_	_
1031	m9	m9	NN	_	_	_
1032	-LSB-	-lsb-	-LRB-	_	_	_
1033	COPRO-Seq	copro-seq	NN	_	_	_
1034	-RSB-	-rsb-	-RRB-	_	_	_
1035	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1036	D3	d3	NN	_	_	_
1037	_	_	NN	_	_	_
1038	7	7	CD	_	_	_
1039	_	_	NN	_	_	_
1040	m10	m10	NN	_	_	_
1041	-LSB-	-lsb-	-LRB-	_	_	_
1042	COPRO-Seq	copro-seq	NN	_	_	_
1043	-RSB-	-rsb-	-RRB-	_	_	_
1044	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1045	D3	d3	NN	_	_	_
1046	_	_	NN	_	_	_
1047	7	7	CD	_	_	_
1048	_	_	NN	_	_	_
1049	m11	m11	NN	_	_	_
1050	-LSB-	-lsb-	-LRB-	_	_	_
1051	COPRO-Seq	copro-seq	NN	_	_	_
1052	-RSB-	-rsb-	-RRB-	_	_	_
1053	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1054	D3	d3	NN	_	_	_
1055	_	_	NN	_	_	_
1056	7	7	CD	_	_	_
1057	_	_	NN	_	_	_
1058	m12	m12	NN	_	_	_
1059	-LSB-	-lsb-	-LRB-	_	_	_
1060	COPRO-Seq	copro-seq	NN	_	_	_
1061	-RSB-	-rsb-	-RRB-	_	_	_
1062	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1063	D3	d3	NN	_	_	_
1064	_	_	NN	_	_	_
1065	7	7	CD	_	_	_
1066	_	_	NN	_	_	_
1067	m13	m13	NN	_	_	_
1068	-LSB-	-lsb-	-LRB-	_	_	_
1069	COPRO-Seq	copro-seq	NN	_	_	_
1070	-RSB-	-rsb-	-RRB-	_	_	_
1071	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1072	D3	d3	NN	_	_	_
1073	_	_	NN	_	_	_
1074	7	7	CD	_	_	_
1075	_	_	SYM	_	_	_
1076	m1	m1	NN	_	_	_
1077	-LSB-	-lsb-	-LRB-	_	_	_
1078	COPRO-Seq	copro-seq	NN	_	_	_
1079	-RSB-	-rsb-	-RRB-	_	_	_
1080	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1081	D3	d3	NN	_	_	_
1082	_	_	NN	_	_	_
1083	7	7	CD	_	_	_
1084	_	_	NN	_	_	_
1085	m2	m2	NN	_	_	_
1086	-LSB-	-lsb-	-LRB-	_	_	_
1087	COPRO-Seq	copro-seq	NN	_	_	_
1088	-RSB-	-rsb-	-RRB-	_	_	_
1089	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1090	D3	d3	NN	_	_	_
1091	_	_	NN	_	_	_
1092	7	7	CD	_	_	_
1093	_	_	NN	_	_	_
1094	m3	m3	NN	_	_	_
1095	-LSB-	-lsb-	-LRB-	_	_	_
1096	COPRO-Seq	copro-seq	NN	_	_	_
1097	-RSB-	-rsb-	-RRB-	_	_	_
1098	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1099	D3	d3	NN	_	_	_
1100	_	_	NN	_	_	_
1101	7	7	CD	_	_	_
1102	_	_	NN	_	_	_
1103	m4	m4	NN	_	_	_
1104	-LSB-	-lsb-	-LRB-	_	_	_
1105	COPRO-Seq	copro-seq	NN	_	_	_
1106	-RSB-	-rsb-	-RRB-	_	_	_
1107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1108	D3	d3	NN	_	_	_
1109	_	_	NN	_	_	_
1110	7	7	CD	_	_	_
1111	_	_	NN	_	_	_
1112	m5	m5	NN	_	_	_
1113	-LSB-	-lsb-	-LRB-	_	_	_
1114	COPRO-Seq	copro-seq	NN	_	_	_
1115	-RSB-	-rsb-	-RRB-	_	_	_
1116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1117	D3	d3	NN	_	_	_
1118	_	_	NN	_	_	_
1119	7	7	CD	_	_	_
1120	_	_	NN	_	_	_
1121	m6	m6	NN	_	_	_
1122	-LSB-	-lsb-	-LRB-	_	_	_
1123	COPRO-Seq	copro-seq	NN	_	_	_
1124	-RSB-	-rsb-	-RRB-	_	_	_
1125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1126	D3	d3	NN	_	_	_
1127	_	_	NN	_	_	_
1128	7	7	CD	_	_	_
1129	_	_	NN	_	_	_
1130	m9	m9	NN	_	_	_
1131	-LSB-	-lsb-	-LRB-	_	_	_
1132	COPRO-Seq	copro-seq	NN	_	_	_
1133	-RSB-	-rsb-	-RRB-	_	_	_
1134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1135	D4	d4	NN	_	_	_
1136	_	_	CD	_	_	_
1137	10	10	CD	_	_	_
1138	_	_	SYM	_	_	_
1139	m1	m1	NN	_	_	_
1140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1141	D4	d4	NN	_	_	_
1142	_	_	CD	_	_	_
1143	10	10	CD	_	_	_
1144	_	_	NN	_	_	_
1145	m10	m10	NN	_	_	_
1146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1147	D4	d4	NN	_	_	_
1148	_	_	CD	_	_	_
1149	10	10	CD	_	_	_
1150	_	_	NN	_	_	_
1151	m11	m11	NN	_	_	_
1152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1153	D4	d4	NN	_	_	_
1154	_	_	CD	_	_	_
1155	10	10	CD	_	_	_
1156	_	_	NN	_	_	_
1157	m12	m12	NN	_	_	_
1158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1159	D4	d4	NN	_	_	_
1160	_	_	CD	_	_	_
1161	10	10	CD	_	_	_
1162	_	_	NN	_	_	_
1163	m13	m13	NN	_	_	_
1164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1165	D4	d4	NN	_	_	_
1166	_	_	CD	_	_	_
1167	10	10	CD	_	_	_
1168	_	_	NN	_	_	_
1169	m2	m2	NN	_	_	_
1170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1171	D4	d4	NN	_	_	_
1172	_	_	CD	_	_	_
1173	10	10	CD	_	_	_
1174	_	_	NN	_	_	_
1175	m3	m3	NN	_	_	_
1176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1177	D4	d4	NN	_	_	_
1178	_	_	CD	_	_	_
1179	10	10	CD	_	_	_
1180	_	_	NN	_	_	_
1181	m4	m4	NN	_	_	_
1182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1183	D4	d4	NN	_	_	_
1184	_	_	CD	_	_	_
1185	10	10	CD	_	_	_
1186	_	_	NN	_	_	_
1187	m5	m5	NN	_	_	_
1188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1189	D4	d4	NN	_	_	_
1190	_	_	CD	_	_	_
1191	10	10	CD	_	_	_
1192	_	_	NN	_	_	_
1193	m6	m6	NN	_	_	_
1194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1195	D4	d4	NN	_	_	_
1196	_	_	CD	_	_	_
1197	10	10	CD	_	_	_
1198	_	_	NN	_	_	_
1199	m7	m7	NN	_	_	_
1200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1201	D4	d4	NN	_	_	_
1202	_	_	CD	_	_	_
1203	10	10	CD	_	_	_
1204	_	_	NN	_	_	_
1205	m8	m8	NN	_	_	_
1206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1207	D4	d4	NN	_	_	_
1208	_	_	CD	_	_	_
1209	10	10	CD	_	_	_
1210	_	_	NN	_	_	_
1211	m9	m9	NN	_	_	_
1212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1213	D4	d4	NN	_	_	_
1214	_	_	CD	_	_	_
1215	14	14	CD	_	_	_
1216	_	_	NN	_	_	_
1217	m10	m10	NN	_	_	_
1218	-LSB-	-lsb-	-LRB-	_	_	_
1219	COPRO-Seq	copro-seq	NN	_	_	_
1220	-RSB-	-rsb-	-RRB-	_	_	_
1221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1222	D4	d4	NN	_	_	_
1223	_	_	CD	_	_	_
1224	14	14	CD	_	_	_
1225	_	_	SYM	_	_	_
1226	m11	m11	NN	_	_	_
1227	-LSB-	-lsb-	-LRB-	_	_	_
1228	COPRO-Seq	copro-seq	NN	_	_	_
1229	-RSB-	-rsb-	-RRB-	_	_	_
1230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1231	D4	d4	NN	_	_	_
1232	_	_	CD	_	_	_
1233	14	14	CD	_	_	_
1234	_	_	SYM	_	_	_
1235	m12	m12	NN	_	_	_
1236	-LSB-	-lsb-	-LRB-	_	_	_
1237	COPRO-Seq	copro-seq	NN	_	_	_
1238	-RSB-	-rsb-	-RRB-	_	_	_
1239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1240	D4	d4	NN	_	_	_
1241	_	_	CD	_	_	_
1242	14	14	CD	_	_	_
1243	_	_	SYM	_	_	_
1244	m13	m13	NN	_	_	_
1245	-LSB-	-lsb-	-LRB-	_	_	_
1246	COPRO-Seq	copro-seq	NN	_	_	_
1247	-RSB-	-rsb-	-RRB-	_	_	_
1248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1249	D4	d4	NN	_	_	_
1250	_	_	CD	_	_	_
1251	14	14	CD	_	_	_
1252	_	_	SYM	_	_	_
1253	m1	m1	NN	_	_	_
1254	-LSB-	-lsb-	-LRB-	_	_	_
1255	COPRO-Seq	copro-seq	NN	_	_	_
1256	-RSB-	-rsb-	-RRB-	_	_	_
1257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1258	D4	d4	NN	_	_	_
1259	_	_	CD	_	_	_
1260	14	14	CD	_	_	_
1261	_	_	NN	_	_	_
1262	m2	m2	NN	_	_	_
1263	-LSB-	-lsb-	-LRB-	_	_	_
1264	COPRO-Seq	copro-seq	NN	_	_	_
1265	-RSB-	-rsb-	-RRB-	_	_	_
1266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1267	D4	d4	NN	_	_	_
1268	_	_	CD	_	_	_
1269	14	14	CD	_	_	_
1270	_	_	NN	_	_	_
1271	m3	m3	NN	_	_	_
1272	-LSB-	-lsb-	-LRB-	_	_	_
1273	COPRO-Seq	copro-seq	NN	_	_	_
1274	-RSB-	-rsb-	-RRB-	_	_	_
1275	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1276	D4	d4	NN	_	_	_
1277	_	_	CD	_	_	_
1278	14	14	CD	_	_	_
1279	_	_	NN	_	_	_
1280	m5	m5	NN	_	_	_
1281	-LSB-	-lsb-	-LRB-	_	_	_
1282	COPRO-Seq	copro-seq	NN	_	_	_
1283	-RSB-	-rsb-	-RRB-	_	_	_
1284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1285	D4	d4	NN	_	_	_
1286	_	_	CD	_	_	_
1287	14	14	CD	_	_	_
1288	_	_	NN	_	_	_
1289	m6	m6	NN	_	_	_
1290	-LSB-	-lsb-	-LRB-	_	_	_
1291	COPRO-Seq	copro-seq	NN	_	_	_
1292	-RSB-	-rsb-	-RRB-	_	_	_
1293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1294	D4	d4	NN	_	_	_
1295	_	_	CD	_	_	_
1296	14	14	CD	_	_	_
1297	_	_	NN	_	_	_
1298	m7	m7	NN	_	_	_
1299	-LSB-	-lsb-	-LRB-	_	_	_
1300	COPRO-Seq	copro-seq	NN	_	_	_
1301	-RSB-	-rsb-	-RRB-	_	_	_
1302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1303	D4	d4	NN	_	_	_
1304	_	_	CD	_	_	_
1305	14	14	CD	_	_	_
1306	_	_	NN	_	_	_
1307	m8	m8	NN	_	_	_
1308	-LSB-	-lsb-	-LRB-	_	_	_
1309	COPRO-Seq	copro-seq	NN	_	_	_
1310	-RSB-	-rsb-	-RRB-	_	_	_
1311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1312	D4	d4	NN	_	_	_
1313	_	_	CD	_	_	_
1314	14	14	CD	_	_	_
1315	_	_	NN	_	_	_
1316	m9	m9	NN	_	_	_
1317	-LSB-	-lsb-	-LRB-	_	_	_
1318	COPRO-Seq	copro-seq	NN	_	_	_
1319	-RSB-	-rsb-	-RRB-	_	_	_
1320	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1321	D4	d4	NN	_	_	_
1322	_	_	NN	_	_	_
1323	1	1	CD	_	_	_
1324	_	_	CD	_	_	_
1325	m10	m10	NN	_	_	_
1326	-LSB-	-lsb-	-LRB-	_	_	_
1327	COPRO-Seq	copro-seq	NN	_	_	_
1328	-RSB-	-rsb-	-RRB-	_	_	_
1329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1330	D4	d4	NN	_	_	_
1331	_	_	NN	_	_	_
1332	1	1	CD	_	_	_
1333	_	_	CD	_	_	_
1334	m11	m11	NN	_	_	_
1335	-LSB-	-lsb-	-LRB-	_	_	_
1336	COPRO-Seq	copro-seq	NN	_	_	_
1337	-RSB-	-rsb-	-RRB-	_	_	_
1338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1339	D4	d4	NN	_	_	_
1340	_	_	NN	_	_	_
1341	1	1	CD	_	_	_
1342	_	_	CD	_	_	_
1343	m12	m12	NN	_	_	_
1344	-LSB-	-lsb-	-LRB-	_	_	_
1345	COPRO-Seq	copro-seq	NN	_	_	_
1346	-RSB-	-rsb-	-RRB-	_	_	_
1347	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1348	D4	d4	NN	_	_	_
1349	_	_	NN	_	_	_
1350	1	1	CD	_	_	_
1351	_	_	CD	_	_	_
1352	m13	m13	NN	_	_	_
1353	-LSB-	-lsb-	-LRB-	_	_	_
1354	COPRO-Seq	copro-seq	NN	_	_	_
1355	-RSB-	-rsb-	-RRB-	_	_	_
1356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1357	D4	d4	NN	_	_	_
1358	_	_	NN	_	_	_
1359	1	1	CD	_	_	_
1360	_	_	CD	_	_	_
1361	m7	m7	NN	_	_	_
1362	-LSB-	-lsb-	-LRB-	_	_	_
1363	COPRO-Seq	copro-seq	NN	_	_	_
1364	-RSB-	-rsb-	-RRB-	_	_	_
1365	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1366	D4	d4	NN	_	_	_
1367	_	_	NN	_	_	_
1368	1	1	CD	_	_	_
1369	_	_	CD	_	_	_
1370	m8	m8	NN	_	_	_
1371	-LSB-	-lsb-	-LRB-	_	_	_
1372	COPRO-Seq	copro-seq	NN	_	_	_
1373	-RSB-	-rsb-	-RRB-	_	_	_
1374	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1375	D4	d4	NN	_	_	_
1376	_	_	NN	_	_	_
1377	1	1	CD	_	_	_
1378	_	_	CD	_	_	_
1379	m9	m9	NN	_	_	_
1380	-LSB-	-lsb-	-LRB-	_	_	_
1381	COPRO-Seq	copro-seq	NN	_	_	_
1382	-RSB-	-rsb-	-RRB-	_	_	_
1383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1384	D4	d4	NN	_	_	_
1385	_	_	NN	_	_	_
1386	2	2	CD	_	_	_
1387	_	_	CD	_	_	_
1388	m10	m10	NN	_	_	_
1389	-LSB-	-lsb-	-LRB-	_	_	_
1390	COPRO-Seq	copro-seq	NN	_	_	_
1391	-RSB-	-rsb-	-RRB-	_	_	_
1392	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1393	D4	d4	NN	_	_	_
1394	_	_	NN	_	_	_
1395	2	2	CD	_	_	_
1396	_	_	CD	_	_	_
1397	m11	m11	NN	_	_	_
1398	-LSB-	-lsb-	-LRB-	_	_	_
1399	COPRO-Seq	copro-seq	NN	_	_	_
1400	-RSB-	-rsb-	-RRB-	_	_	_
1401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1402	D4	d4	NN	_	_	_
1403	_	_	NN	_	_	_
1404	2	2	CD	_	_	_
1405	_	_	CD	_	_	_
1406	m12	m12	NN	_	_	_
1407	-LSB-	-lsb-	-LRB-	_	_	_
1408	COPRO-Seq	copro-seq	NN	_	_	_
1409	-RSB-	-rsb-	-RRB-	_	_	_
1410	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1411	D4	d4	NN	_	_	_
1412	_	_	NN	_	_	_
1413	2	2	CD	_	_	_
1414	_	_	CD	_	_	_
1415	m13	m13	NN	_	_	_
1416	-LSB-	-lsb-	-LRB-	_	_	_
1417	COPRO-Seq	copro-seq	NN	_	_	_
1418	-RSB-	-rsb-	-RRB-	_	_	_
1419	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1420	D4	d4	NN	_	_	_
1421	_	_	NN	_	_	_
1422	2	2	CD	_	_	_
1423	_	_	CD	_	_	_
1424	m2	m2	NN	_	_	_
1425	-LSB-	-lsb-	-LRB-	_	_	_
1426	COPRO-Seq	copro-seq	NN	_	_	_
1427	-RSB-	-rsb-	-RRB-	_	_	_
1428	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1429	D4	d4	NN	_	_	_
1430	_	_	NN	_	_	_
1431	2	2	CD	_	_	_
1432	_	_	CD	_	_	_
1433	m3	m3	NN	_	_	_
1434	-LSB-	-lsb-	-LRB-	_	_	_
1435	COPRO-Seq	copro-seq	NN	_	_	_
1436	-RSB-	-rsb-	-RRB-	_	_	_
1437	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1438	D4	d4	NN	_	_	_
1439	_	_	NN	_	_	_
1440	2	2	CD	_	_	_
1441	_	_	CD	_	_	_
1442	m4	m4	NN	_	_	_
1443	-LSB-	-lsb-	-LRB-	_	_	_
1444	COPRO-Seq	copro-seq	NN	_	_	_
1445	-RSB-	-rsb-	-RRB-	_	_	_
1446	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1447	D4	d4	NN	_	_	_
1448	_	_	NN	_	_	_
1449	2	2	CD	_	_	_
1450	_	_	CD	_	_	_
1451	m5	m5	NN	_	_	_
1452	-LSB-	-lsb-	-LRB-	_	_	_
1453	COPRO-Seq	copro-seq	NN	_	_	_
1454	-RSB-	-rsb-	-RRB-	_	_	_
1455	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1456	D4	d4	NN	_	_	_
1457	_	_	NN	_	_	_
1458	2	2	CD	_	_	_
1459	_	_	CD	_	_	_
1460	m6	m6	NN	_	_	_
1461	-LSB-	-lsb-	-LRB-	_	_	_
1462	COPRO-Seq	copro-seq	NN	_	_	_
1463	-RSB-	-rsb-	-RRB-	_	_	_
1464	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1465	D4	d4	NN	_	_	_
1466	_	_	NN	_	_	_
1467	2	2	CD	_	_	_
1468	_	_	CD	_	_	_
1469	m7	m7	NN	_	_	_
1470	-LSB-	-lsb-	-LRB-	_	_	_
1471	COPRO-Seq	copro-seq	NN	_	_	_
1472	-RSB-	-rsb-	-RRB-	_	_	_
1473	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1474	D4	d4	NN	_	_	_
1475	_	_	NN	_	_	_
1476	2	2	CD	_	_	_
1477	_	_	CD	_	_	_
1478	m8	m8	NN	_	_	_
1479	-LSB-	-lsb-	-LRB-	_	_	_
1480	COPRO-Seq	copro-seq	NN	_	_	_
1481	-RSB-	-rsb-	-RRB-	_	_	_
1482	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1483	D4	d4	NN	_	_	_
1484	_	_	NN	_	_	_
1485	2	2	CD	_	_	_
1486	_	_	CD	_	_	_
1487	m9	m9	NN	_	_	_
1488	-LSB-	-lsb-	-LRB-	_	_	_
1489	COPRO-Seq	copro-seq	NN	_	_	_
1490	-RSB-	-rsb-	-RRB-	_	_	_
1491	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1492	D4	d4	NN	_	_	_
1493	_	_	CD	_	_	_
1494	4	4	CD	_	_	_
1495	_	_	NN	_	_	_
1496	m10	m10	NN	_	_	_
1497	-LSB-	-lsb-	-LRB-	_	_	_
1498	COPRO-Seq	copro-seq	NN	_	_	_
1499	-RSB-	-rsb-	-RRB-	_	_	_
1500	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1501	D4	d4	NN	_	_	_
1502	_	_	CD	_	_	_
1503	4	4	CD	_	_	_
1504	_	_	SYM	_	_	_
1505	m12	m12	NN	_	_	_
1506	-LSB-	-lsb-	-LRB-	_	_	_
1507	COPRO-Seq	copro-seq	NN	_	_	_
1508	-RSB-	-rsb-	-RRB-	_	_	_
1509	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1510	D4	d4	NN	_	_	_
1511	_	_	CD	_	_	_
1512	4	4	CD	_	_	_
1513	_	_	SYM	_	_	_
1514	m13	m13	NN	_	_	_
1515	-LSB-	-lsb-	-LRB-	_	_	_
1516	COPRO-Seq	copro-seq	NN	_	_	_
1517	-RSB-	-rsb-	-RRB-	_	_	_
1518	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1519	D4	d4	NN	_	_	_
1520	_	_	CD	_	_	_
1521	4	4	CD	_	_	_
1522	_	_	NN	_	_	_
1523	m2	m2	NN	_	_	_
1524	-LSB-	-lsb-	-LRB-	_	_	_
1525	COPRO-Seq	copro-seq	NN	_	_	_
1526	-RSB-	-rsb-	-RRB-	_	_	_
1527	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1528	D4	d4	NN	_	_	_
1529	_	_	CD	_	_	_
1530	4	4	CD	_	_	_
1531	_	_	NN	_	_	_
1532	m4	m4	NN	_	_	_
1533	-LSB-	-lsb-	-LRB-	_	_	_
1534	COPRO-Seq	copro-seq	NN	_	_	_
1535	-RSB-	-rsb-	-RRB-	_	_	_
1536	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1537	D4	d4	NN	_	_	_
1538	_	_	CD	_	_	_
1539	4	4	CD	_	_	_
1540	_	_	NN	_	_	_
1541	m5	m5	NN	_	_	_
1542	-LSB-	-lsb-	-LRB-	_	_	_
1543	COPRO-Seq	copro-seq	NN	_	_	_
1544	-RSB-	-rsb-	-RRB-	_	_	_
1545	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1546	D4	d4	NN	_	_	_
1547	_	_	CD	_	_	_
1548	4	4	CD	_	_	_
1549	_	_	NN	_	_	_
1550	m6	m6	NN	_	_	_
1551	-LSB-	-lsb-	-LRB-	_	_	_
1552	COPRO-Seq	copro-seq	NN	_	_	_
1553	-RSB-	-rsb-	-RRB-	_	_	_
1554	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1555	D4	d4	NN	_	_	_
1556	_	_	CD	_	_	_
1557	4	4	CD	_	_	_
1558	_	_	NN	_	_	_
1559	m7	m7	NN	_	_	_
1560	-LSB-	-lsb-	-LRB-	_	_	_
1561	COPRO-Seq	copro-seq	NN	_	_	_
1562	-RSB-	-rsb-	-RRB-	_	_	_
1563	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1564	D4	d4	NN	_	_	_
1565	_	_	CD	_	_	_
1566	4	4	CD	_	_	_
1567	_	_	NN	_	_	_
1568	m8	m8	NN	_	_	_
1569	-LSB-	-lsb-	-LRB-	_	_	_
1570	COPRO-Seq	copro-seq	NN	_	_	_
1571	-RSB-	-rsb-	-RRB-	_	_	_
1572	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1573	D4	d4	NN	_	_	_
1574	_	_	NN	_	_	_
1575	4	4	CD	_	_	_
1576	_	_	CD	_	_	_
1577	m9	m9	NN	_	_	_
1578	-LSB-	-lsb-	-LRB-	_	_	_
1579	COPRO-Seq	copro-seq	NN	_	_	_
1580	-RSB-	-rsb-	-RRB-	_	_	_
1581	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1582	D4	d4	NN	_	_	_
1583	_	_	NN	_	_	_
1584	7	7	CD	_	_	_
1585	_	_	SYM	_	_	_
1586	m1	m1	NN	_	_	_
1587	-LSB-	-lsb-	-LRB-	_	_	_
1588	COPRO-Seq	copro-seq	NN	_	_	_
1589	-RSB-	-rsb-	-RRB-	_	_	_
1590	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1591	D4	d4	NN	_	_	_
1592	_	_	NN	_	_	_
1593	7	7	CD	_	_	_
1594	_	_	NN	_	_	_
1595	m2	m2	NN	_	_	_
1596	-LSB-	-lsb-	-LRB-	_	_	_
1597	COPRO-Seq	copro-seq	NN	_	_	_
1598	-RSB-	-rsb-	-RRB-	_	_	_
1599	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1600	D4	d4	NN	_	_	_
1601	_	_	NN	_	_	_
1602	7	7	CD	_	_	_
1603	_	_	NN	_	_	_
1604	m3	m3	NN	_	_	_
1605	-LSB-	-lsb-	-LRB-	_	_	_
1606	COPRO-Seq	copro-seq	NN	_	_	_
1607	-RSB-	-rsb-	-RRB-	_	_	_
1608	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1609	D4	d4	NN	_	_	_
1610	_	_	NN	_	_	_
1611	7	7	CD	_	_	_
1612	_	_	NN	_	_	_
1613	m4	m4	NN	_	_	_
1614	-LSB-	-lsb-	-LRB-	_	_	_
1615	COPRO-Seq	copro-seq	NN	_	_	_
1616	-RSB-	-rsb-	-RRB-	_	_	_
1617	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1618	D4	d4	NN	_	_	_
1619	_	_	NN	_	_	_
1620	7	7	CD	_	_	_
1621	_	_	NN	_	_	_
1622	m5	m5	NN	_	_	_
1623	-LSB-	-lsb-	-LRB-	_	_	_
1624	COPRO-Seq	copro-seq	NN	_	_	_
1625	-RSB-	-rsb-	-RRB-	_	_	_
1626	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1627	D4	d4	NN	_	_	_
1628	_	_	NN	_	_	_
1629	7	7	CD	_	_	_
1630	_	_	NN	_	_	_
1631	m6	m6	NN	_	_	_
1632	-LSB-	-lsb-	-LRB-	_	_	_
1633	COPRO-Seq	copro-seq	NN	_	_	_
1634	-RSB-	-rsb-	-RRB-	_	_	_
1635	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1636	Desulfovibrio	desulfovibrio	NN	_	_	_
1637	piger	piger	NN	_	_	_
1638	GOR1	gor1	NN	_	_	_
1639	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1640	diet	diet	NN	_	_	_
1641	:	:	:	_	_	_
1642	Mouse	mouse	NN	_	_	_
1643	was	be	VBD	_	_	_
1644	fed	feed	VBN	_	_	_
1645	a	a	DT	_	_	_
1646	meal	meal	NN	_	_	_
1647	of	of	IN	_	_	_
1648	human	human	JJ	_	_	_
1649	pureed	pureed	NN	_	_	_
1650	food	food	NN	_	_	_
1651	in	in	IN	_	_	_
1652	the	the	DT	_	_	_
1653	following	follow	VBG	_	_	_
1654	concentrations	concentration	NNS	_	_	_
1655	-LRB-	-lrb-	-LRB-	_	_	_
1656	g	g	NN	_	_	_
1657	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1658	diet	diet	NN	_	_	_
1659	:	:	:	_	_	_
1660	Mouse	mouse	NN	_	_	_
1661	was	be	VBD	_	_	_
1662	fed	feed	VBN	_	_	_
1663	Harlan	Harlan	NNP	_	_	_
1664	Teklad	Teklad	NNP	_	_	_
1665	Diet	Diet	NNP	_	_	_
1666	TD	TD	NNP	_	_	_
1667	.09049	.09049	CD	_	_	_
1668	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1669	diet	diet	NN	_	_	_
1670	:	:	:	_	_	_
1671	Mouse	mouse	NN	_	_	_
1672	was	be	VBD	_	_	_
1673	fed	feed	VBN	_	_	_
1674	Harlan	Harlan	NNP	_	_	_
1675	Teklad	Teklad	NNP	_	_	_
1676	Diet	Diet	NNP	_	_	_
1677	TD	TD	NNP	_	_	_
1678	.09050	.09050	CD	_	_	_
1679	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1680	diet	diet	NN	_	_	_
1681	:	:	:	_	_	_
1682	Mouse	mouse	NN	_	_	_
1683	was	be	VBD	_	_	_
1684	fed	feed	VBN	_	_	_
1685	Harlan	Harlan	NNP	_	_	_
1686	Teklad	Teklad	NNP	_	_	_
1687	Diet	Diet	NNP	_	_	_
1688	TD	TD	NNP	_	_	_
1689	.09051	.09051	CD	_	_	_
1690	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1691	diet	diet	NN	_	_	_
1692	:	:	:	_	_	_
1693	Mouse	mouse	NN	_	_	_
1694	was	be	VBD	_	_	_
1695	fed	feed	VBN	_	_	_
1696	Harlan	Harlan	NNP	_	_	_
1697	Teklad	Teklad	NNP	_	_	_
1698	Diet	Diet	NNP	_	_	_
1699	TD	TD	NNP	_	_	_
1700	.09052	.09052	CD	_	_	_
1701	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1702	diet	diet	NN	_	_	_
1703	:	:	:	_	_	_
1704	Mouse	mouse	NN	_	_	_
1705	was	be	VBD	_	_	_
1706	fed	feed	VBN	_	_	_
1707	Harlan	Harlan	NNP	_	_	_
1708	Teklad	Teklad	NNP	_	_	_
1709	Diet	Diet	NNP	_	_	_
1710	TD	TD	NNP	_	_	_
1711	.09053	.09053	CD	_	_	_
1712	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1713	diet	diet	NN	_	_	_
1714	:	:	:	_	_	_
1715	Mouse	mouse	NN	_	_	_
1716	was	be	VBD	_	_	_
1717	fed	feed	VBN	_	_	_
1718	Harlan	Harlan	NNP	_	_	_
1719	Teklad	Teklad	NNP	_	_	_
1720	Diet	Diet	NNP	_	_	_
1721	TD	TD	NNP	_	_	_
1722	.09054	.09054	CD	_	_	_
1723	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1724	diet	diet	NN	_	_	_
1725	:	:	:	_	_	_
1726	Mouse	mouse	NN	_	_	_
1727	was	be	VBD	_	_	_
1728	fed	feed	VBN	_	_	_
1729	Harlan	Harlan	NNP	_	_	_
1730	Teklad	Teklad	NNP	_	_	_
1731	Diet	Diet	NNP	_	_	_
1732	TD	TD	NNP	_	_	_
1733	.09055	.09055	CD	_	_	_
1734	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1735	diet	diet	NN	_	_	_
1736	:	:	:	_	_	_
1737	Mouse	mouse	NN	_	_	_
1738	was	be	VBD	_	_	_
1739	fed	feed	VBN	_	_	_
1740	Harlan	Harlan	NNP	_	_	_
1741	Teklad	Teklad	NNP	_	_	_
1742	Diet	Diet	NNP	_	_	_
1743	TD	TD	NNP	_	_	_
1744	.09055	.09055	CD	_	_	_
1745	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	diet	diet	NN	_	_	_
3	:	:	:	_	_	_
4	Mouse	mouse	NN	_	_	_
5	was	be	VBD	_	_	_
6	fed	feed	VBN	_	_	_
7	Harlan	Harlan	NNP	_	_	_
8	Teklad	Teklad	NNP	_	_	_
9	Diet	Diet	NNP	_	_	_
10	TD	TD	NNP	_	_	_
11	.09056	.09056	CD	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
13	diet	diet	NN	_	_	_
14	:	:	:	_	_	_
15	Mouse	mouse	NN	_	_	_
16	was	be	VBD	_	_	_
17	fed	feed	VBN	_	_	_
18	Harlan	Harlan	NNP	_	_	_
19	Teklad	Teklad	NNP	_	_	_
20	Diet	Diet	NNP	_	_	_
21	TD	TD	NNP	_	_	_
22	.09057	.09057	CD	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
24	diet	diet	NN	_	_	_
25	:	:	:	_	_	_
26	Mouse	mouse	NN	_	_	_
27	was	be	VBD	_	_	_
28	fed	feed	VBN	_	_	_
29	Harlan	Harlan	NNP	_	_	_
30	Teklad	Teklad	NNP	_	_	_
31	Diet	Diet	NNP	_	_	_
32	TD	TD	NNP	_	_	_
33	.09057	.09057	CD	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	diet	diet	NN	_	_	_
3	:	:	:	_	_	_
4	Mouse	mouse	NN	_	_	_
5	was	be	VBD	_	_	_
6	fed	feed	VBN	_	_	_
7	Harlan	Harlan	NNP	_	_	_
8	Teklad	Teklad	NNP	_	_	_
9	Diet	Diet	NNP	_	_	_
10	TD	TD	NNP	_	_	_
11	.09058	.09058	CD	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
13	diet	diet	NN	_	_	_
14	:	:	:	_	_	_
15	Mouse	mouse	NN	_	_	_
16	was	be	VBD	_	_	_
17	fed	feed	VBN	_	_	_
18	Harlan	Harlan	NNP	_	_	_
19	Teklad	Teklad	NNP	_	_	_
20	Diet	Diet	NNP	_	_	_
21	TD	TD	NNP	_	_	_
22	.09059	.09059	CD	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
24	diet	diet	NN	_	_	_
25	:	:	:	_	_	_
26	Mouse	mouse	NN	_	_	_
27	was	be	VBD	_	_	_
28	fed	feed	VBN	_	_	_
29	Harlan	Harlan	NNP	_	_	_
30	Teklad	Teklad	NNP	_	_	_
31	Diet	Diet	NNP	_	_	_
32	TD	TD	NNP	_	_	_
33	.09620	.09620	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
35	diet	diet	NN	_	_	_
36	:	:	:	_	_	_
37	Mouse	mouse	NN	_	_	_
38	was	be	VBD	_	_	_
39	fed	feed	VBN	_	_	_
40	Harlan	Harlan	NNP	_	_	_
41	Teklad	Teklad	NNP	_	_	_
42	Diet	Diet	NNP	_	_	_
43	TD	TD	NNP	_	_	_
44	.09621	.09621	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
46	diet	diet	NN	_	_	_
47	:	:	:	_	_	_
48	Mouse	mouse	NN	_	_	_
49	was	be	VBD	_	_	_
50	fed	feed	VBN	_	_	_
51	Harlan	Harlan	NNP	_	_	_
52	Teklad	Teklad	NNP	_	_	_
53	Diet	Diet	NNP	_	_	_
54	TD	TD	NNP	_	_	_
55	.09622	.09622	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
57	diet	diet	NN	_	_	_
58	:	:	:	_	_	_
59	Mouse	mouse	NN	_	_	_
60	was	be	VBD	_	_	_
61	fed	feed	VBN	_	_	_
62	Harlan	Harlan	NNP	_	_	_
63	Teklad	Teklad	NNP	_	_	_
64	Diet	Diet	NNP	_	_	_
65	TD	TD	NNP	_	_	_
66	.09623	.09623	CD	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
68	diet	diet	NN	_	_	_
69	:	:	:	_	_	_
70	Mouse	mouse	NN	_	_	_
71	was	be	VBD	_	_	_
72	fed	feed	VBN	_	_	_
73	Harlan	Harlan	NNP	_	_	_
74	Teklad	Teklad	NNP	_	_	_
75	Diet	Diet	NNP	_	_	_
76	TD	TD	NNP	_	_	_
77	.09624	.09624	CD	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
79	diet	diet	NN	_	_	_
80	:	:	:	_	_	_
81	Mouse	mouse	NN	_	_	_
82	was	be	VBD	_	_	_
83	fed	feed	VBN	_	_	_
84	Harlan	Harlan	NNP	_	_	_
85	Teklad	Teklad	NNP	_	_	_
86	Diet	Diet	NNP	_	_	_
87	TD	TD	NNP	_	_	_
88	.09625	.09625	CD	_	_	_
89	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
90	Double	double	JJ	_	_	_
91	stranded	strand	VBN	_	_	_
92	cDNA	cdna	NN	_	_	_
93	was	be	VBD	_	_	_
94	generated	generate	VBN	_	_	_
95	using	use	VBG	_	_	_
96	Superscript	Superscript	NNP	_	_	_
97	II	II	NNP	_	_	_
98	-LRB-	-lrb-	-LRB-	_	_	_
99	Invitrogen	Invitrogen	NNP	_	_	_
100	-RRB-	-rrb-	-RRB-	_	_	_
101	to	to	TO	_	_	_
102	generate	generate	VB	_	_	_
103	the	the	DT	_	_	_
104	first	first	JJ	_	_	_
105	strand	strand	NN	_	_	_
106	followed	follow	VBN	_	_	_
107	by	by	IN	_	_	_
108	E.	e.	FW	_	_	_
109	coli	coli	FW	_	_	_
110	DNA	dna	NN	_	_	_
111	polymerase	polymerase	NN	_	_	_
112	,	,	,	_	_	_
113	RNaseH	rnaseh	NN	_	_	_
114	,	,	,	_	_	_
115	and	and	CC	_	_	_
116	E.coli	e.coli	NN	_	_	_
117	DNA	dna	NN	_	_	_
118	ligase	ligase	NN	_	_	_
119	-LRB-	-lrb-	-LRB-	_	_	_
120	NEB	neb	NN	_	_	_
121	-RRB-	-rrb-	-RRB-	_	_	_
122	to	to	TO	_	_	_
123	generate	generate	VB	_	_	_
124	the	the	DT	_	_	_
125	second	second	JJ	_	_	_
126	strand	strand	NN	_	_	_
127	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Double	double	JJ	_	_	_
3	stranded	strand	VBN	_	_	_
4	cDNA	cdna	NN	_	_	_
5	was	be	VBD	_	_	_
6	generated	generate	VBN	_	_	_
7	using	use	VBG	_	_	_
8	Superscript	Superscript	NNP	_	_	_
9	II	II	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Invitrogen	Invitrogen	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	to	to	TO	_	_	_
14	generate	generate	VB	_	_	_
15	the	the	DT	_	_	_
16	first	first	JJ	_	_	_
17	strand	strand	NN	_	_	_
18	followed	follow	VBN	_	_	_
19	by	by	IN	_	_	_
20	E.	e.	FW	_	_	_
21	coli	coli	FW	_	_	_
22	DNA	dna	NN	_	_	_
23	polymerase	polymerase	NN	_	_	_
24	,	,	,	_	_	_
25	RNaseH	rnaseh	NN	_	_	_
26	,	,	,	_	_	_
27	and	and	CC	_	_	_
28	E.coli	e.coli	NN	_	_	_
29	DNA	dna	NN	_	_	_
30	ligase	ligase	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	NEB	neb	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	to	to	TO	_	_	_
35	generate	generate	VB	_	_	_
36	the	the	DT	_	_	_
37	second	second	JJ	_	_	_
38	strand.isoamyl	strand.isoamyl	JJ	_	_	_
39	alcohol	alcohol	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	25:24:1	25:24:1	CD	_	_	_
42	,	,	,	_	_	_
43	pH	ph	NN	_	_	_
44	8.0	8.0	CD	_	_	_
45	;	;	:	_	_	_
46	Ambion	Ambion	NNP	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	and	and	CC	_	_	_
49	lysed	lyse	VBN	_	_	_
50	by	by	IN	_	_	_
51	using	use	VBG	_	_	_
52	a	a	DT	_	_	_
53	bead	bead	NN	_	_	_
54	beater	beater	NN	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	BioSpec	BioSpec	NNP	_	_	_
57	Products	Products	NNPS	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	.	.	.	_	_	_

1	Cellular	cellular	JJ	_	_	_
2	debris	debris	NN	_	_	_
3	was	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	8,000	8,000	CD	_	_	_
9	g	g	NN	_	_	_
10	;	;	:	_	_	_
11	3	3	CD	_	_	_
12	min	min	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	nucleic	nucleic	JJ	_	_	_
3	acids	acid	NNS	_	_	_
4	were	be	VBD	_	_	_
5	precipitated	precipitate	VBN	_	_	_
6	with	with	IN	_	_	_
7	isopropanol	isopropanol	NN	_	_	_
8	and	and	CC	_	_	_
9	sodium	sodium	NN	SUPP	_	_
10	acetate	acetate	NN	SUPP	_	_
11	and	and	CC	_	_	_
12	resuspended	resuspend	VBN	_	_	_
13	in	in	IN	_	_	_
14	100	100	CD	_	_	_
15	ul	ul	NN	_	_	_
16	TE	TE	NNP	_	_	_
17	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	resuspension	resuspension	NN	_	_	_
3	was	be	VBD	_	_	_
4	further	further	JJ	_	_	_
5	purified	purify	VBN	_	_	_
6	with	with	IN	_	_	_
7	a	a	DT	_	_	_
8	Qiagen	Qiagen	NNP	_	_	_
9	PCR	pcr	NN	_	_	_
10	column	column	NN	_	_	_
11	and	and	CC	_	_	_
12	eluted	elute	VBN	_	_	_
13	into	into	IN	_	_	_
14	30	30	CD	_	_	_
15	ul	ul	NN	_	_	_
16	of	of	IN	_	_	_
17	EB	EB	NNP	_	_	_
18	buffer	buffer	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	E11	e11	NN	_	_	_
3	_	_	NN	_	_	_
4	1	1	CD	_	_	_
5	_	_	SYM	_	_	_
6	m1	m1	NN	_	_	_
7	-LSB-	-lsb-	-LRB-	_	_	_
8	COPRO-Seq	copro-seq	NN	_	_	_
9	-RSB-	-rsb-	-RRB-	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	E11	e11	NN	_	_	_
12	_	_	NN	_	_	_
13	1	1	CD	_	_	_
14	_	_	CD	_	_	_
15	m3	m3	NN	_	_	_
16	-LSB-	-lsb-	-LRB-	_	_	_
17	COPRO-Seq	copro-seq	NN	_	_	_
18	-RSB-	-rsb-	-RRB-	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	E11	e11	NN	_	_	_
21	_	_	NN	_	_	_
22	1	1	CD	_	_	_
23	_	_	CD	_	_	_
24	m4	m4	NN	_	_	_
25	-LSB-	-lsb-	-LRB-	_	_	_
26	COPRO-Seq	copro-seq	NN	_	_	_
27	-RSB-	-rsb-	-RRB-	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	E11	e11	NN	_	_	_
30	_	_	NN	_	_	_
31	1	1	CD	_	_	_
32	_	_	CD	_	_	_
33	m5	m5	NN	_	_	_
34	-LSB-	-lsb-	-LRB-	_	_	_
35	COPRO-Seq	copro-seq	NN	_	_	_
36	-RSB-	-rsb-	-RRB-	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	E11	e11	NN	_	_	_
39	_	_	NN	_	_	_
40	1	1	CD	_	_	_
41	_	_	CD	_	_	_
42	m6	m6	NN	_	_	_
43	-LSB-	-lsb-	-LRB-	_	_	_
44	COPRO-Seq	copro-seq	NN	_	_	_
45	-RSB-	-rsb-	-RRB-	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	E11	e11	NN	_	_	_
48	_	_	NN	_	_	_
49	1	1	CD	_	_	_
50	_	_	CD	_	_	_
51	m7	m7	NN	_	_	_
52	-LSB-	-lsb-	-LRB-	_	_	_
53	COPRO-Seq	copro-seq	NN	_	_	_
54	-RSB-	-rsb-	-RRB-	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	E11	e11	NN	_	_	_
57	_	_	NN	_	_	_
58	1	1	CD	_	_	_
59	_	_	CD	_	_	_
60	m8	m8	NN	_	_	_
61	-LSB-	-lsb-	-LRB-	_	_	_
62	COPRO-Seq	copro-seq	NN	_	_	_
63	-RSB-	-rsb-	-RRB-	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	E1	e1	NN	_	_	_
66	_	_	VBD	_	_	_
67	14	14	CD	_	_	_
68	_	_	SYM	_	_	_
69	m1	m1	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	E1	e1	NN	_	_	_
72	_	_	VBD	_	_	_
73	14	14	CD	_	_	_
74	_	_	SYM	_	_	_
75	m1	m1	NN	_	_	_
76	-LSB-	-lsb-	-LRB-	_	_	_
77	COPRO-Seq	copro-seq	NN	_	_	_
78	-RSB-	-rsb-	-RRB-	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	E11	e11	NN	_	_	_
81	_	_	CD	_	_	_
82	4	4	CD	_	_	_
83	_	_	SYM	_	_	_
84	m1	m1	NN	_	_	_
85	-LSB-	-lsb-	-LRB-	_	_	_
86	COPRO-Seq	copro-seq	NN	_	_	_
87	-RSB-	-rsb-	-RRB-	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	E1	e1	NN	_	_	_
90	_	_	VBD	_	_	_
91	14	14	CD	_	_	_
92	_	_	CD	_	_	_
93	m2	m2	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	E1	e1	NN	_	_	_
96	_	_	VBD	_	_	_
97	14	14	CD	_	_	_
98	_	_	CD	_	_	_
99	m2	m2	NN	_	_	_
100	-LSB-	-lsb-	-LRB-	_	_	_
101	COPRO-Seq	copro-seq	NN	_	_	_
102	-RSB-	-rsb-	-RRB-	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	E1	e1	NN	_	_	_
105	_	_	VBD	_	_	_
106	14	14	CD	_	_	_
107	_	_	CD	_	_	_
108	m3	m3	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	E1	e1	NN	_	_	_
111	_	_	VBD	_	_	_
112	14	14	CD	_	_	_
113	_	_	CD	_	_	_
114	m3	m3	NN	_	_	_
115	-LSB-	-lsb-	-LRB-	_	_	_
116	COPRO-Seq	copro-seq	NN	_	_	_
117	-RSB-	-rsb-	-RRB-	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	E1	e1	NN	_	_	_
120	_	_	VBD	_	_	_
121	14	14	CD	_	_	_
122	_	_	CD	_	_	_
123	m4	m4	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	E1	e1	NN	_	_	_
126	_	_	VBD	_	_	_
127	14	14	CD	_	_	_
128	_	_	CD	_	_	_
129	m4	m4	NN	_	_	_
130	-LSB-	-lsb-	-LRB-	_	_	_
131	COPRO-Seq	copro-seq	NN	_	_	_
132	-RSB-	-rsb-	-RRB-	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	E11	e11	NN	_	_	_
135	_	_	CD	_	_	_
136	4	4	CD	_	_	_
137	_	_	NN	_	_	_
138	m4	m4	NN	_	_	_
139	-LSB-	-lsb-	-LRB-	_	_	_
140	COPRO-Seq	copro-seq	NN	_	_	_
141	-RSB-	-rsb-	-RRB-	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	E1	e1	NN	_	_	_
144	_	_	VBD	_	_	_
145	14	14	CD	_	_	_
146	_	_	CD	_	_	_
147	m5	m5	NN	_	_	_
148	-LSB-	-lsb-	-LRB-	_	_	_
149	COPRO-Seq	copro-seq	NN	_	_	_
150	-RSB-	-rsb-	-RRB-	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	E11	e11	NN	_	_	_
153	_	_	CD	_	_	_
154	4	4	CD	_	_	_
155	_	_	NN	_	_	_
156	m5	m5	NN	_	_	_
157	-LSB-	-lsb-	-LRB-	_	_	_
158	COPRO-Seq	copro-seq	NN	_	_	_
159	-RSB-	-rsb-	-RRB-	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	E1	e1	NN	_	_	_
162	_	_	VBD	_	_	_
163	14	14	CD	_	_	_
164	_	_	CD	_	_	_
165	m6	m6	NN	_	_	_
166	-LSB-	-lsb-	-LRB-	_	_	_
167	COPRO-Seq	copro-seq	NN	_	_	_
168	-RSB-	-rsb-	-RRB-	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	E1	e1	NN	_	_	_
171	_	_	VBD	_	_	_
172	14	14	CD	_	_	_
173	_	_	CD	_	_	_
174	m7	m7	NN	_	_	_
175	-LSB-	-lsb-	-LRB-	_	_	_
176	COPRO-Seq	copro-seq	NN	_	_	_
177	-RSB-	-rsb-	-RRB-	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	E11	e11	NN	_	_	_
180	_	_	CD	_	_	_
181	4	4	CD	_	_	_
182	_	_	NN	_	_	_
183	m7	m7	NN	_	_	_
184	-LSB-	-lsb-	-LRB-	_	_	_
185	COPRO-Seq	copro-seq	NN	_	_	_
186	-RSB-	-rsb-	-RRB-	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	E1	e1	NN	_	_	_
189	_	_	VBD	_	_	_
190	14	14	CD	_	_	_
191	_	_	CD	_	_	_
192	m8	m8	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	E1	e1	NN	_	_	_
195	_	_	VBD	_	_	_
196	14	14	CD	_	_	_
197	_	_	CD	_	_	_
198	m8	m8	NN	_	_	_
199	-LSB-	-lsb-	-LRB-	_	_	_
200	COPRO-Seq	copro-seq	NN	_	_	_
201	-RSB-	-rsb-	-RRB-	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	E11	e11	NN	_	_	_
204	_	_	CD	_	_	_
205	4	4	CD	_	_	_
206	_	_	NN	_	_	_
207	m8	m8	NN	_	_	_
208	-LSB-	-lsb-	-LRB-	_	_	_
209	COPRO-Seq	copro-seq	NN	_	_	_
210	-RSB-	-rsb-	-RRB-	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	E11	e11	NN	_	_	_
213	_	_	CD	_	_	_
214	6	6	CD	_	_	_
215	_	_	NN	_	_	_
216	m2	m2	NN	_	_	_
217	-LSB-	-lsb-	-LRB-	_	_	_
218	COPRO-Seq	copro-seq	NN	_	_	_
219	-RSB-	-rsb-	-RRB-	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	E11	e11	NN	_	_	_
222	_	_	CD	_	_	_
223	6	6	CD	_	_	_
224	_	_	NN	_	_	_
225	m3	m3	NN	_	_	_
226	-LSB-	-lsb-	-LRB-	_	_	_
227	COPRO-Seq	copro-seq	NN	_	_	_
228	-RSB-	-rsb-	-RRB-	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
230	E11	e11	NN	_	_	_
231	_	_	CD	_	_	_
232	6	6	CD	_	_	_
233	_	_	NN	_	_	_
234	m4	m4	NN	_	_	_
235	-LSB-	-lsb-	-LRB-	_	_	_
236	COPRO-Seq	copro-seq	NN	_	_	_
237	-RSB-	-rsb-	-RRB-	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	E11	e11	NN	_	_	_
240	_	_	CD	_	_	_
241	6	6	CD	_	_	_
242	_	_	NN	_	_	_
243	m5	m5	NN	_	_	_
244	-LSB-	-lsb-	-LRB-	_	_	_
245	COPRO-Seq	copro-seq	NN	_	_	_
246	-RSB-	-rsb-	-RRB-	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	E11	e11	NN	_	_	_
249	_	_	NN	_	_	_
250	7	7	CD	_	_	_
251	_	_	SYM	_	_	_
252	m1	m1	NN	_	_	_
253	-LSB-	-lsb-	-LRB-	_	_	_
254	COPRO-Seq	copro-seq	NN	_	_	_
255	-RSB-	-rsb-	-RRB-	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
257	E11	e11	NN	_	_	_
258	_	_	NN	_	_	_
259	7	7	CD	_	_	_
260	_	_	NN	_	_	_
261	m2	m2	NN	_	_	_
262	-LSB-	-lsb-	-LRB-	_	_	_
263	COPRO-Seq	copro-seq	NN	_	_	_
264	-RSB-	-rsb-	-RRB-	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	E11	e11	NN	_	_	_
267	_	_	NN	_	_	_
268	7	7	CD	_	_	_
269	_	_	NN	_	_	_
270	m3	m3	NN	_	_	_
271	-LSB-	-lsb-	-LRB-	_	_	_
272	COPRO-Seq	copro-seq	NN	_	_	_
273	-RSB-	-rsb-	-RRB-	_	_	_
274	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
275	E11	e11	NN	_	_	_
276	_	_	NN	_	_	_
277	7	7	CD	_	_	_
278	_	_	NN	_	_	_
279	m4	m4	NN	_	_	_
280	-LSB-	-lsb-	-LRB-	_	_	_
281	COPRO-Seq	copro-seq	NN	_	_	_
282	-RSB-	-rsb-	-RRB-	_	_	_
283	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
284	E11	e11	NN	_	_	_
285	_	_	NN	_	_	_
286	7	7	CD	_	_	_
287	_	_	NN	_	_	_
288	m6	m6	NN	_	_	_
289	-LSB-	-lsb-	-LRB-	_	_	_
290	COPRO-Seq	copro-seq	NN	_	_	_
291	-RSB-	-rsb-	-RRB-	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	E11	e11	NN	_	_	_
294	_	_	NN	_	_	_
295	7	7	CD	_	_	_
296	_	_	NN	_	_	_
297	m7	m7	NN	_	_	_
298	-LSB-	-lsb-	-LRB-	_	_	_
299	COPRO-Seq	copro-seq	NN	_	_	_
300	-RSB-	-rsb-	-RRB-	_	_	_
301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
302	E11	e11	NN	_	_	_
303	_	_	NN	_	_	_
304	7	7	CD	_	_	_
305	_	_	NN	_	_	_
306	m8	m8	NN	_	_	_
307	-LSB-	-lsb-	-LRB-	_	_	_
308	COPRO-Seq	copro-seq	NN	_	_	_
309	-RSB-	-rsb-	-RRB-	_	_	_
310	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
311	E1	e1	NN	_	_	_
312	_	_	VBD	_	_	_
313	1	1	CD	_	_	_
314	_	_	SYM	_	_	_
315	m1	m1	NN	_	_	_
316	-LSB-	-lsb-	-LRB-	_	_	_
317	COPRO-Seq	copro-seq	NN	_	_	_
318	-RSB-	-rsb-	-RRB-	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
320	E1	e1	NN	_	_	_
321	_	_	VBD	_	_	_
322	1	1	CD	_	_	_
323	_	_	CD	_	_	_
324	m2	m2	NN	_	_	_
325	-LSB-	-lsb-	-LRB-	_	_	_
326	COPRO-Seq	copro-seq	NN	_	_	_
327	-RSB-	-rsb-	-RRB-	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	E1	e1	NN	_	_	_
330	_	_	VBD	_	_	_
331	1	1	CD	_	_	_
332	_	_	CD	_	_	_
333	m4	m4	NN	_	_	_
334	-LSB-	-lsb-	-LRB-	_	_	_
335	COPRO-Seq	copro-seq	NN	_	_	_
336	-RSB-	-rsb-	-RRB-	_	_	_
337	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
338	E1	e1	NN	_	_	_
339	_	_	VBD	_	_	_
340	1	1	CD	_	_	_
341	_	_	CD	_	_	_
342	m5	m5	NN	_	_	_
343	-LSB-	-lsb-	-LRB-	_	_	_
344	COPRO-Seq	copro-seq	NN	_	_	_
345	-RSB-	-rsb-	-RRB-	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	E1	e1	NN	_	_	_
348	_	_	VBD	_	_	_
349	1	1	CD	_	_	_
350	_	_	CD	_	_	_
351	m7	m7	NN	_	_	_
352	-LSB-	-lsb-	-LRB-	_	_	_
353	COPRO-Seq	copro-seq	NN	_	_	_
354	-RSB-	-rsb-	-RRB-	_	_	_
355	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
356	E1	e1	NN	_	_	_
357	_	_	VBD	_	_	_
358	1	1	CD	_	_	_
359	_	_	CD	_	_	_
360	m8	m8	NN	_	_	_
361	-LSB-	-lsb-	-LRB-	_	_	_
362	COPRO-Seq	copro-seq	NN	_	_	_
363	-RSB-	-rsb-	-RRB-	_	_	_
364	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
365	E1	e1	NN	_	_	_
366	_	_	NN	_	_	_
367	2	2	CD	_	_	_
368	_	_	SYM	_	_	_
369	m1	m1	NN	_	_	_
370	-LSB-	-lsb-	-LRB-	_	_	_
371	COPRO-Seq	copro-seq	NN	_	_	_
372	-RSB-	-rsb-	-RRB-	_	_	_
373	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
374	E1	e1	NN	_	_	_
375	_	_	NN	_	_	_
376	2	2	CD	_	_	_
377	_	_	CD	_	_	_
378	m2	m2	NN	_	_	_
379	-LSB-	-lsb-	-LRB-	_	_	_
380	COPRO-Seq	copro-seq	NN	_	_	_
381	-RSB-	-rsb-	-RRB-	_	_	_
382	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
383	E1	e1	NN	_	_	_
384	_	_	NN	_	_	_
385	2	2	CD	_	_	_
386	_	_	CD	_	_	_
387	m3	m3	NN	_	_	_
388	-LSB-	-lsb-	-LRB-	_	_	_
389	COPRO-Seq	copro-seq	NN	_	_	_
390	-RSB-	-rsb-	-RRB-	_	_	_
391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
392	E1	e1	NN	_	_	_
393	_	_	NN	_	_	_
394	2	2	CD	_	_	_
395	_	_	CD	_	_	_
396	m4	m4	NN	_	_	_
397	-LSB-	-lsb-	-LRB-	_	_	_
398	COPRO-Seq	copro-seq	NN	_	_	_
399	-RSB-	-rsb-	-RRB-	_	_	_
400	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
401	E1	e1	NN	_	_	_
402	_	_	NN	_	_	_
403	2	2	CD	_	_	_
404	_	_	CD	_	_	_
405	m5	m5	NN	_	_	_
406	-LSB-	-lsb-	-LRB-	_	_	_
407	COPRO-Seq	copro-seq	NN	_	_	_
408	-RSB-	-rsb-	-RRB-	_	_	_
409	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
410	E1	e1	NN	_	_	_
411	_	_	NN	_	_	_
412	2	2	CD	_	_	_
413	_	_	CD	_	_	_
414	m6	m6	NN	_	_	_
415	-LSB-	-lsb-	-LRB-	_	_	_
416	COPRO-Seq	copro-seq	NN	_	_	_
417	-RSB-	-rsb-	-RRB-	_	_	_
418	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
419	E1	e1	NN	_	_	_
420	_	_	NN	_	_	_
421	2	2	CD	_	_	_
422	_	_	CD	_	_	_
423	m7	m7	NN	_	_	_
424	-LSB-	-lsb-	-LRB-	_	_	_
425	COPRO-Seq	copro-seq	NN	_	_	_
426	-RSB-	-rsb-	-RRB-	_	_	_
427	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
428	E1	e1	NN	_	_	_
429	_	_	NN	_	_	_
430	2	2	CD	_	_	_
431	_	_	CD	_	_	_
432	m8	m8	NN	_	_	_
433	-LSB-	-lsb-	-LRB-	_	_	_
434	COPRO-Seq	copro-seq	NN	_	_	_
435	-RSB-	-rsb-	-RRB-	_	_	_
436	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
437	E13	e13	NN	_	_	_
438	_	_	NN	_	_	_
439	1	1	CD	_	_	_
440	_	_	SYM	_	_	_
441	m1	m1	NN	_	_	_
442	-LSB-	-lsb-	-LRB-	_	_	_
443	COPRO-Seq	copro-seq	NN	_	_	_
444	-RSB-	-rsb-	-RRB-	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	E13	e13	NN	_	_	_
447	_	_	NN	_	_	_
448	1	1	CD	_	_	_
449	_	_	CD	_	_	_
450	m2	m2	NN	_	_	_
451	-LSB-	-lsb-	-LRB-	_	_	_
452	COPRO-Seq	copro-seq	NN	_	_	_
453	-RSB-	-rsb-	-RRB-	_	_	_
454	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
455	E13	e13	NN	_	_	_
456	_	_	NN	_	_	_
457	1	1	CD	_	_	_
458	_	_	CD	_	_	_
459	m3	m3	NN	_	_	_
460	-LSB-	-lsb-	-LRB-	_	_	_
461	COPRO-Seq	copro-seq	NN	_	_	_
462	-RSB-	-rsb-	-RRB-	_	_	_
463	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
464	E13	e13	NN	_	_	_
465	_	_	NN	_	_	_
466	1	1	CD	_	_	_
467	_	_	CD	_	_	_
468	m4	m4	NN	_	_	_
469	-LSB-	-lsb-	-LRB-	_	_	_
470	COPRO-Seq	copro-seq	NN	_	_	_
471	-RSB-	-rsb-	-RRB-	_	_	_
472	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
473	E13	e13	NN	_	_	_
474	_	_	NN	_	_	_
475	1	1	CD	_	_	_
476	_	_	CD	_	_	_
477	m5	m5	NN	_	_	_
478	-LSB-	-lsb-	-LRB-	_	_	_
479	COPRO-Seq	copro-seq	NN	_	_	_
480	-RSB-	-rsb-	-RRB-	_	_	_
481	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
482	E13	e13	NN	_	_	_
483	_	_	NN	_	_	_
484	1	1	CD	_	_	_
485	_	_	CD	_	_	_
486	m6	m6	NN	_	_	_
487	-LSB-	-lsb-	-LRB-	_	_	_
488	COPRO-Seq	copro-seq	NN	_	_	_
489	-RSB-	-rsb-	-RRB-	_	_	_
490	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
491	E13	e13	NN	_	_	_
492	_	_	NN	_	_	_
493	1	1	CD	_	_	_
494	_	_	CD	_	_	_
495	m7	m7	NN	_	_	_
496	-LSB-	-lsb-	-LRB-	_	_	_
497	COPRO-Seq	copro-seq	NN	_	_	_
498	-RSB-	-rsb-	-RRB-	_	_	_
499	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
500	E13	e13	NN	_	_	_
501	_	_	NN	_	_	_
502	1	1	CD	_	_	_
503	_	_	CD	_	_	_
504	m8	m8	NN	_	_	_
505	-LSB-	-lsb-	-LRB-	_	_	_
506	COPRO-Seq	copro-seq	NN	_	_	_
507	-RSB-	-rsb-	-RRB-	_	_	_
508	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
509	E13	e13	NN	_	_	_
510	_	_	CD	_	_	_
511	4	4	CD	_	_	_
512	_	_	SYM	_	_	_
513	m1	m1	NN	_	_	_
514	-LSB-	-lsb-	-LRB-	_	_	_
515	COPRO-Seq	copro-seq	NN	_	_	_
516	-RSB-	-rsb-	-RRB-	_	_	_
517	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
518	E13	e13	NN	_	_	_
519	_	_	CD	_	_	_
520	4	4	CD	_	_	_
521	_	_	NN	_	_	_
522	m3	m3	NN	_	_	_
523	-LSB-	-lsb-	-LRB-	_	_	_
524	COPRO-Seq	copro-seq	NN	_	_	_
525	-RSB-	-rsb-	-RRB-	_	_	_
526	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
527	E13	e13	NN	_	_	_
528	_	_	CD	_	_	_
529	4	4	CD	_	_	_
530	_	_	NN	_	_	_
531	m4	m4	NN	_	_	_
532	-LSB-	-lsb-	-LRB-	_	_	_
533	COPRO-Seq	copro-seq	NN	_	_	_
534	-RSB-	-rsb-	-RRB-	_	_	_
535	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
536	E13	e13	NN	_	_	_
537	_	_	CD	_	_	_
538	4	4	CD	_	_	_
539	_	_	NN	_	_	_
540	m5	m5	NN	_	_	_
541	-LSB-	-lsb-	-LRB-	_	_	_
542	COPRO-Seq	copro-seq	NN	_	_	_
543	-RSB-	-rsb-	-RRB-	_	_	_
544	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
545	E13	e13	NN	_	_	_
546	_	_	CD	_	_	_
547	4	4	CD	_	_	_
548	_	_	NN	_	_	_
549	m6	m6	NN	_	_	_
550	-LSB-	-lsb-	-LRB-	_	_	_
551	COPRO-Seq	copro-seq	NN	_	_	_
552	-RSB-	-rsb-	-RRB-	_	_	_
553	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
554	E13	e13	NN	_	_	_
555	_	_	CD	_	_	_
556	4	4	CD	_	_	_
557	_	_	NN	_	_	_
558	m7	m7	NN	_	_	_
559	-LSB-	-lsb-	-LRB-	_	_	_
560	COPRO-Seq	copro-seq	NN	_	_	_
561	-RSB-	-rsb-	-RRB-	_	_	_
562	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
563	E13	e13	NN	_	_	_
564	_	_	CD	_	_	_
565	4	4	CD	_	_	_
566	_	_	NN	_	_	_
567	m8	m8	NN	_	_	_
568	-LSB-	-lsb-	-LRB-	_	_	_
569	COPRO-Seq	copro-seq	NN	_	_	_
570	-RSB-	-rsb-	-RRB-	_	_	_
571	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
572	E13	e13	NN	_	_	_
573	_	_	CD	_	_	_
574	6	6	CD	_	_	_
575	_	_	NN	_	_	_
576	m1	m1	NN	_	_	_
577	-LSB-	-lsb-	-LRB-	_	_	_
578	COPRO-Seq	copro-seq	NN	_	_	_
579	-RSB-	-rsb-	-RRB-	_	_	_
580	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
581	E13	e13	NN	_	_	_
582	_	_	CD	_	_	_
583	6	6	CD	_	_	_
584	_	_	NN	_	_	_
585	m4	m4	NN	_	_	_
586	-LSB-	-lsb-	-LRB-	_	_	_
587	COPRO-Seq	copro-seq	NN	_	_	_
588	-RSB-	-rsb-	-RRB-	_	_	_
589	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
590	E13	e13	NN	_	_	_
591	_	_	CD	_	_	_
592	6	6	CD	_	_	_
593	_	_	NN	_	_	_
594	m5	m5	NN	_	_	_
595	-LSB-	-lsb-	-LRB-	_	_	_
596	COPRO-Seq	copro-seq	NN	_	_	_
597	-RSB-	-rsb-	-RRB-	_	_	_
598	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
599	E13	e13	NN	_	_	_
600	_	_	NN	_	_	_
601	7	7	CD	_	_	_
602	_	_	SYM	_	_	_
603	m1	m1	NN	_	_	_
604	-LSB-	-lsb-	-LRB-	_	_	_
605	COPRO-Seq	copro-seq	NN	_	_	_
606	-RSB-	-rsb-	-RRB-	_	_	_
607	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
608	E13	e13	NN	_	_	_
609	_	_	NN	_	_	_
610	7	7	CD	_	_	_
611	_	_	NN	_	_	_
612	m2	m2	NN	_	_	_
613	-LSB-	-lsb-	-LRB-	_	_	_
614	COPRO-Seq	copro-seq	NN	_	_	_
615	-RSB-	-rsb-	-RRB-	_	_	_
616	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
617	E13	e13	NN	_	_	_
618	_	_	NN	_	_	_
619	7	7	CD	_	_	_
620	_	_	NN	_	_	_
621	m4	m4	NN	_	_	_
622	-LSB-	-lsb-	-LRB-	_	_	_
623	COPRO-Seq	copro-seq	NN	_	_	_
624	-RSB-	-rsb-	-RRB-	_	_	_
625	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
626	E13	e13	NN	_	_	_
627	_	_	NN	_	_	_
628	7	7	CD	_	_	_
629	_	_	NN	_	_	_
630	m5	m5	NN	_	_	_
631	-LSB-	-lsb-	-LRB-	_	_	_
632	COPRO-Seq	copro-seq	NN	_	_	_
633	-RSB-	-rsb-	-RRB-	_	_	_
634	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
635	E13	e13	NN	_	_	_
636	_	_	NN	_	_	_
637	7	7	CD	_	_	_
638	_	_	NN	_	_	_
639	m6	m6	NN	_	_	_
640	-LSB-	-lsb-	-LRB-	_	_	_
641	COPRO-Seq	copro-seq	NN	_	_	_
642	-RSB-	-rsb-	-RRB-	_	_	_
643	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
644	E13	e13	NN	_	_	_
645	_	_	NN	_	_	_
646	7	7	CD	_	_	_
647	_	_	NN	_	_	_
648	m7	m7	NN	_	_	_
649	-LSB-	-lsb-	-LRB-	_	_	_
650	COPRO-Seq	copro-seq	NN	_	_	_
651	-RSB-	-rsb-	-RRB-	_	_	_
652	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
653	E13	e13	NN	_	_	_
654	_	_	NN	_	_	_
655	7	7	CD	_	_	_
656	_	_	NN	_	_	_
657	m8	m8	NN	_	_	_
658	-LSB-	-lsb-	-LRB-	_	_	_
659	COPRO-Seq	copro-seq	NN	_	_	_
660	-RSB-	-rsb-	-RRB-	_	_	_
661	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
662	E1	e1	NN	_	_	_
663	_	_	VBD	_	_	_
664	4	4	CD	_	_	_
665	_	_	SYM	_	_	_
666	m1	m1	NN	_	_	_
667	-LSB-	-lsb-	-LRB-	_	_	_
668	COPRO-Seq	copro-seq	NN	_	_	_
669	-RSB-	-rsb-	-RRB-	_	_	_
670	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
671	E1	e1	NN	_	_	_
672	_	_	VBD	_	_	_
673	4	4	CD	_	_	_
674	_	_	CD	_	_	_
675	m2	m2	NN	_	_	_
676	-LSB-	-lsb-	-LRB-	_	_	_
677	COPRO-Seq	copro-seq	NN	_	_	_
678	-RSB-	-rsb-	-RRB-	_	_	_
679	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
680	E1	e1	NN	_	_	_
681	_	_	VBD	_	_	_
682	4	4	CD	_	_	_
683	_	_	CD	_	_	_
684	m3	m3	NN	_	_	_
685	-LSB-	-lsb-	-LRB-	_	_	_
686	COPRO-Seq	copro-seq	NN	_	_	_
687	-RSB-	-rsb-	-RRB-	_	_	_
688	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
689	E1	e1	NN	_	_	_
690	_	_	VBD	_	_	_
691	4	4	CD	_	_	_
692	_	_	CD	_	_	_
693	m4	m4	NN	_	_	_
694	-LSB-	-lsb-	-LRB-	_	_	_
695	COPRO-Seq	copro-seq	NN	_	_	_
696	-RSB-	-rsb-	-RRB-	_	_	_
697	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
698	E1	e1	NN	_	_	_
699	_	_	VBD	_	_	_
700	4	4	CD	_	_	_
701	_	_	CD	_	_	_
702	m5	m5	NN	_	_	_
703	-LSB-	-lsb-	-LRB-	_	_	_
704	COPRO-Seq	copro-seq	NN	_	_	_
705	-RSB-	-rsb-	-RRB-	_	_	_
706	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
707	E1	e1	NN	_	_	_
708	_	_	VBD	_	_	_
709	4	4	CD	_	_	_
710	_	_	CD	_	_	_
711	m6	m6	NN	_	_	_
712	-LSB-	-lsb-	-LRB-	_	_	_
713	COPRO-Seq	copro-seq	NN	_	_	_
714	-RSB-	-rsb-	-RRB-	_	_	_
715	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
716	E1	e1	NN	_	_	_
717	_	_	VBD	_	_	_
718	4	4	CD	_	_	_
719	_	_	CD	_	_	_
720	m7	m7	NN	_	_	_
721	-LSB-	-lsb-	-LRB-	_	_	_
722	COPRO-Seq	copro-seq	NN	_	_	_
723	-RSB-	-rsb-	-RRB-	_	_	_
724	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
725	E1	e1	NN	_	_	_
726	_	_	VBD	_	_	_
727	4	4	CD	_	_	_
728	_	_	CD	_	_	_
729	m8	m8	NN	_	_	_
730	-LSB-	-lsb-	-LRB-	_	_	_
731	COPRO-Seq	copro-seq	NN	_	_	_
732	-RSB-	-rsb-	-RRB-	_	_	_
733	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
734	E15	e15	CD	_	_	_
735	_	_	NN	_	_	_
736	1	1	CD	_	_	_
737	_	_	SYM	_	_	_
738	m1	m1	NN	_	_	_
739	-LSB-	-lsb-	-LRB-	_	_	_
740	COPRO-Seq	copro-seq	NN	_	_	_
741	-RSB-	-rsb-	-RRB-	_	_	_
742	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
743	E15	e15	CD	_	_	_
744	_	_	NN	_	_	_
745	1	1	CD	_	_	_
746	_	_	CD	_	_	_
747	m2	m2	NN	_	_	_
748	-LSB-	-lsb-	-LRB-	_	_	_
749	COPRO-Seq	copro-seq	NN	_	_	_
750	-RSB-	-rsb-	-RRB-	_	_	_
751	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
752	E15	e15	CD	_	_	_
753	_	_	NN	_	_	_
754	1	1	CD	_	_	_
755	_	_	CD	_	_	_
756	m3	m3	NN	_	_	_
757	-LSB-	-lsb-	-LRB-	_	_	_
758	COPRO-Seq	copro-seq	NN	_	_	_
759	-RSB-	-rsb-	-RRB-	_	_	_
760	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
761	E15	e15	CD	_	_	_
762	_	_	NN	_	_	_
763	1	1	CD	_	_	_
764	_	_	CD	_	_	_
765	m4	m4	NN	_	_	_
766	-LSB-	-lsb-	-LRB-	_	_	_
767	COPRO-Seq	copro-seq	NN	_	_	_
768	-RSB-	-rsb-	-RRB-	_	_	_
769	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
770	E15	e15	CD	_	_	_
771	_	_	NN	_	_	_
772	1	1	CD	_	_	_
773	_	_	CD	_	_	_
774	m5	m5	NN	_	_	_
775	-LSB-	-lsb-	-LRB-	_	_	_
776	COPRO-Seq	copro-seq	NN	_	_	_
777	-RSB-	-rsb-	-RRB-	_	_	_
778	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
779	E15	e15	CD	_	_	_
780	_	_	NN	_	_	_
781	1	1	CD	_	_	_
782	_	_	CD	_	_	_
783	m7	m7	NN	_	_	_
784	-LSB-	-lsb-	-LRB-	_	_	_
785	COPRO-Seq	copro-seq	NN	_	_	_
786	-RSB-	-rsb-	-RRB-	_	_	_
787	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
788	E15	e15	CD	_	_	_
789	_	_	NN	_	_	_
790	1	1	CD	_	_	_
791	_	_	CD	_	_	_
792	m8	m8	NN	_	_	_
793	-LSB-	-lsb-	-LRB-	_	_	_
794	COPRO-Seq	copro-seq	NN	_	_	_
795	-RSB-	-rsb-	-RRB-	_	_	_
796	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
797	E15	e15	CD	_	_	_
798	_	_	NN	_	_	_
799	4	4	CD	_	_	_
800	_	_	SYM	_	_	_
801	m1	m1	NN	_	_	_
802	-LSB-	-lsb-	-LRB-	_	_	_
803	COPRO-Seq	copro-seq	NN	_	_	_
804	-RSB-	-rsb-	-RRB-	_	_	_
805	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
806	E15	e15	CD	_	_	_
807	_	_	NN	_	_	_
808	4	4	CD	_	_	_
809	_	_	NN	_	_	_
810	m2	m2	NN	_	_	_
811	-LSB-	-lsb-	-LRB-	_	_	_
812	COPRO-Seq	copro-seq	NN	_	_	_
813	-RSB-	-rsb-	-RRB-	_	_	_
814	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
815	E15	e15	CD	_	_	_
816	_	_	NN	_	_	_
817	4	4	CD	_	_	_
818	_	_	NN	_	_	_
819	m3	m3	NN	_	_	_
820	-LSB-	-lsb-	-LRB-	_	_	_
821	COPRO-Seq	copro-seq	NN	_	_	_
822	-RSB-	-rsb-	-RRB-	_	_	_
823	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
824	E15	e15	CD	_	_	_
825	_	_	NN	_	_	_
826	4	4	CD	_	_	_
827	_	_	NN	_	_	_
828	m4	m4	NN	_	_	_
829	-LSB-	-lsb-	-LRB-	_	_	_
830	COPRO-Seq	copro-seq	NN	_	_	_
831	-RSB-	-rsb-	-RRB-	_	_	_
832	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
833	E15	e15	CD	_	_	_
834	_	_	NN	_	_	_
835	4	4	CD	_	_	_
836	_	_	NN	_	_	_
837	m6	m6	NN	_	_	_
838	-LSB-	-lsb-	-LRB-	_	_	_
839	COPRO-Seq	copro-seq	NN	_	_	_
840	-RSB-	-rsb-	-RRB-	_	_	_
841	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
842	E15	e15	CD	_	_	_
843	_	_	NN	_	_	_
844	4	4	CD	_	_	_
845	_	_	NN	_	_	_
846	m7	m7	NN	_	_	_
847	-LSB-	-lsb-	-LRB-	_	_	_
848	COPRO-Seq	copro-seq	NN	_	_	_
849	-RSB-	-rsb-	-RRB-	_	_	_
850	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
851	E15	e15	CD	_	_	_
852	_	_	NN	_	_	_
853	4	4	CD	_	_	_
854	_	_	NN	_	_	_
855	m8	m8	NN	_	_	_
856	-LSB-	-lsb-	-LRB-	_	_	_
857	COPRO-Seq	copro-seq	NN	_	_	_
858	-RSB-	-rsb-	-RRB-	_	_	_
859	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
860	E15	e15	CD	_	_	_
861	_	_	SYM	_	_	_
862	6	6	CD	_	_	_
863	_	_	SYM	_	_	_
864	m1	m1	NN	_	_	_
865	-LSB-	-lsb-	-LRB-	_	_	_
866	COPRO-Seq	copro-seq	NN	_	_	_
867	-RSB-	-rsb-	-RRB-	_	_	_
868	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
869	E15	e15	CD	_	_	_
870	_	_	NN	_	_	_
871	6	6	CD	_	_	_
872	_	_	NN	_	_	_
873	m3	m3	NN	_	_	_
874	-LSB-	-lsb-	-LRB-	_	_	_
875	COPRO-Seq	copro-seq	NN	_	_	_
876	-RSB-	-rsb-	-RRB-	_	_	_
877	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
878	E15	e15	CD	_	_	_
879	_	_	NN	_	_	_
880	6	6	CD	_	_	_
881	_	_	NN	_	_	_
882	m5	m5	NN	_	_	_
883	-LSB-	-lsb-	-LRB-	_	_	_
884	COPRO-Seq	copro-seq	NN	_	_	_
885	-RSB-	-rsb-	-RRB-	_	_	_
886	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
887	E15	e15	CD	_	_	_
888	_	_	NN	_	_	_
889	6	6	CD	_	_	_
890	_	_	NN	_	_	_
891	m6	m6	NN	_	_	_
892	-LSB-	-lsb-	-LRB-	_	_	_
893	COPRO-Seq	copro-seq	NN	_	_	_
894	-RSB-	-rsb-	-RRB-	_	_	_
895	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
896	E15	e15	CD	_	_	_
897	_	_	NN	_	_	_
898	6	6	CD	_	_	_
899	_	_	NN	_	_	_
900	m7	m7	NN	_	_	_
901	-LSB-	-lsb-	-LRB-	_	_	_
902	COPRO-Seq	copro-seq	NN	_	_	_
903	-RSB-	-rsb-	-RRB-	_	_	_
904	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
905	E15	e15	CD	_	_	_
906	_	_	NN	_	_	_
907	6	6	CD	_	_	_
908	_	_	NN	_	_	_
909	m8	m8	NN	_	_	_
910	-LSB-	-lsb-	-LRB-	_	_	_
911	COPRO-Seq	copro-seq	NN	_	_	_
912	-RSB-	-rsb-	-RRB-	_	_	_
913	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
914	E15	e15	CD	_	_	_
915	_	_	NN	_	_	_
916	7	7	CD	_	_	_
917	_	_	SYM	_	_	_
918	m1	m1	NN	_	_	_
919	-LSB-	-lsb-	-LRB-	_	_	_
920	COPRO-Seq	copro-seq	NN	_	_	_
921	-RSB-	-rsb-	-RRB-	_	_	_
922	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
923	E15	e15	CD	_	_	_
924	_	_	NN	_	_	_
925	7	7	CD	_	_	_
926	_	_	NN	_	_	_
927	m3	m3	NN	_	_	_
928	-LSB-	-lsb-	-LRB-	_	_	_
929	COPRO-Seq	copro-seq	NN	_	_	_
930	-RSB-	-rsb-	-RRB-	_	_	_
931	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
932	E15	e15	CD	_	_	_
933	_	_	NN	_	_	_
934	7	7	CD	_	_	_
935	_	_	NN	_	_	_
936	m4	m4	NN	_	_	_
937	-LSB-	-lsb-	-LRB-	_	_	_
938	COPRO-Seq	copro-seq	NN	_	_	_
939	-RSB-	-rsb-	-RRB-	_	_	_
940	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
941	E15	e15	CD	_	_	_
942	_	_	NN	_	_	_
943	7	7	CD	_	_	_
944	_	_	NN	_	_	_
945	m5	m5	NN	_	_	_
946	-LSB-	-lsb-	-LRB-	_	_	_
947	COPRO-Seq	copro-seq	NN	_	_	_
948	-RSB-	-rsb-	-RRB-	_	_	_
949	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
950	E15	e15	CD	_	_	_
951	_	_	NN	_	_	_
952	7	7	CD	_	_	_
953	_	_	NN	_	_	_
954	m7	m7	NN	_	_	_
955	-LSB-	-lsb-	-LRB-	_	_	_
956	COPRO-Seq	copro-seq	NN	_	_	_
957	-RSB-	-rsb-	-RRB-	_	_	_
958	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
959	E15	e15	CD	_	_	_
960	_	_	NN	_	_	_
961	7	7	CD	_	_	_
962	_	_	NN	_	_	_
963	m8	m8	NN	_	_	_
964	-LSB-	-lsb-	-LRB-	_	_	_
965	COPRO-Seq	copro-seq	NN	_	_	_
966	-RSB-	-rsb-	-RRB-	_	_	_
967	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
968	E17	e17	NN	_	_	_
969	_	_	NN	_	_	_
970	1	1	CD	_	_	_
971	_	_	SYM	_	_	_
972	m1	m1	NN	_	_	_
973	-LSB-	-lsb-	-LRB-	_	_	_
974	COPRO-Seq	copro-seq	NN	_	_	_
975	-RSB-	-rsb-	-RRB-	_	_	_
976	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
977	E17	e17	NN	_	_	_
978	_	_	NN	_	_	_
979	1	1	CD	_	_	_
980	_	_	CD	_	_	_
981	m2	m2	NN	_	_	_
982	-LSB-	-lsb-	-LRB-	_	_	_
983	COPRO-Seq	copro-seq	NN	_	_	_
984	-RSB-	-rsb-	-RRB-	_	_	_
985	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
986	E17	e17	NN	_	_	_
987	_	_	NN	_	_	_
988	1	1	CD	_	_	_
989	_	_	CD	_	_	_
990	m3	m3	NN	_	_	_
991	-LSB-	-lsb-	-LRB-	_	_	_
992	COPRO-Seq	copro-seq	NN	_	_	_
993	-RSB-	-rsb-	-RRB-	_	_	_
994	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
995	E17	e17	NN	_	_	_
996	_	_	NN	_	_	_
997	1	1	CD	_	_	_
998	_	_	CD	_	_	_
999	m4	m4	NN	_	_	_
1000	-LSB-	-lsb-	-LRB-	_	_	_
1001	COPRO-Seq	copro-seq	NN	_	_	_
1002	-RSB-	-rsb-	-RRB-	_	_	_
1003	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1004	E17	e17	NN	_	_	_
1005	_	_	NN	_	_	_
1006	1	1	CD	_	_	_
1007	_	_	CD	_	_	_
1008	m5	m5	NN	_	_	_
1009	-LSB-	-lsb-	-LRB-	_	_	_
1010	COPRO-Seq	copro-seq	NN	_	_	_
1011	-RSB-	-rsb-	-RRB-	_	_	_
1012	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1013	E17	e17	NN	_	_	_
1014	_	_	NN	_	_	_
1015	1	1	CD	_	_	_
1016	_	_	CD	_	_	_
1017	m6	m6	NN	_	_	_
1018	-LSB-	-lsb-	-LRB-	_	_	_
1019	COPRO-Seq	copro-seq	NN	_	_	_
1020	-RSB-	-rsb-	-RRB-	_	_	_
1021	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1022	E17	e17	NN	_	_	_
1023	_	_	NN	_	_	_
1024	1	1	CD	_	_	_
1025	_	_	CD	_	_	_
1026	m7	m7	NN	_	_	_
1027	-LSB-	-lsb-	-LRB-	_	_	_
1028	COPRO-Seq	copro-seq	NN	_	_	_
1029	-RSB-	-rsb-	-RRB-	_	_	_
1030	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1031	E17	e17	NN	_	_	_
1032	_	_	NN	_	_	_
1033	1	1	CD	_	_	_
1034	_	_	CD	_	_	_
1035	m8	m8	NN	_	_	_
1036	-LSB-	-lsb-	-LRB-	_	_	_
1037	COPRO-Seq	copro-seq	NN	_	_	_
1038	-RSB-	-rsb-	-RRB-	_	_	_
1039	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1040	E17	e17	NN	_	_	_
1041	_	_	CD	_	_	_
1042	4	4	CD	_	_	_
1043	_	_	SYM	_	_	_
1044	m1	m1	NN	_	_	_
1045	-LSB-	-lsb-	-LRB-	_	_	_
1046	COPRO-Seq	copro-seq	NN	_	_	_
1047	-RSB-	-rsb-	-RRB-	_	_	_
1048	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1049	E17	e17	NN	_	_	_
1050	_	_	CD	_	_	_
1051	4	4	CD	_	_	_
1052	_	_	NN	_	_	_
1053	m2	m2	NN	_	_	_
1054	-LSB-	-lsb-	-LRB-	_	_	_
1055	COPRO-Seq	copro-seq	NN	_	_	_
1056	-RSB-	-rsb-	-RRB-	_	_	_
1057	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1058	E17	e17	NN	_	_	_
1059	_	_	CD	_	_	_
1060	4	4	CD	_	_	_
1061	_	_	NN	_	_	_
1062	m3	m3	NN	_	_	_
1063	-LSB-	-lsb-	-LRB-	_	_	_
1064	COPRO-Seq	copro-seq	NN	_	_	_
1065	-RSB-	-rsb-	-RRB-	_	_	_
1066	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1067	E17	e17	NN	_	_	_
1068	_	_	CD	_	_	_
1069	4	4	CD	_	_	_
1070	_	_	NN	_	_	_
1071	m4	m4	NN	_	_	_
1072	-LSB-	-lsb-	-LRB-	_	_	_
1073	COPRO-Seq	copro-seq	NN	_	_	_
1074	-RSB-	-rsb-	-RRB-	_	_	_
1075	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1076	E17	e17	NN	_	_	_
1077	_	_	CD	_	_	_
1078	4	4	CD	_	_	_
1079	_	_	NN	_	_	_
1080	m5	m5	NN	_	_	_
1081	-LSB-	-lsb-	-LRB-	_	_	_
1082	COPRO-Seq	copro-seq	NN	_	_	_
1083	-RSB-	-rsb-	-RRB-	_	_	_
1084	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1085	E17	e17	NN	_	_	_
1086	_	_	CD	_	_	_
1087	4	4	CD	_	_	_
1088	_	_	NN	_	_	_
1089	m6	m6	NN	_	_	_
1090	-LSB-	-lsb-	-LRB-	_	_	_
1091	COPRO-Seq	copro-seq	NN	_	_	_
1092	-RSB-	-rsb-	-RRB-	_	_	_
1093	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1094	E17	e17	NN	_	_	_
1095	_	_	CD	_	_	_
1096	4	4	CD	_	_	_
1097	_	_	NN	_	_	_
1098	m7	m7	NN	_	_	_
1099	-LSB-	-lsb-	-LRB-	_	_	_
1100	COPRO-Seq	copro-seq	NN	_	_	_
1101	-RSB-	-rsb-	-RRB-	_	_	_
1102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1103	E17	e17	NN	_	_	_
1104	_	_	CD	_	_	_
1105	4	4	CD	_	_	_
1106	_	_	NN	_	_	_
1107	m8	m8	NN	_	_	_
1108	-LSB-	-lsb-	-LRB-	_	_	_
1109	COPRO-Seq	copro-seq	NN	_	_	_
1110	-RSB-	-rsb-	-RRB-	_	_	_
1111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1112	E17	e17	NN	_	_	_
1113	_	_	CD	_	_	_
1114	6	6	CD	_	_	_
1115	_	_	NN	_	_	_
1116	m1	m1	NN	_	_	_
1117	-LSB-	-lsb-	-LRB-	_	_	_
1118	COPRO-Seq	copro-seq	NN	_	_	_
1119	-RSB-	-rsb-	-RRB-	_	_	_
1120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1121	E17	e17	NN	_	_	_
1122	_	_	CD	_	_	_
1123	6	6	CD	_	_	_
1124	_	_	NN	_	_	_
1125	m3	m3	NN	_	_	_
1126	-LSB-	-lsb-	-LRB-	_	_	_
1127	COPRO-Seq	copro-seq	NN	_	_	_
1128	-RSB-	-rsb-	-RRB-	_	_	_
1129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1130	E17	e17	NN	_	_	_
1131	_	_	CD	_	_	_
1132	6	6	CD	_	_	_
1133	_	_	NN	_	_	_
1134	m4	m4	NN	_	_	_
1135	-LSB-	-lsb-	-LRB-	_	_	_
1136	COPRO-Seq	copro-seq	NN	_	_	_
1137	-RSB-	-rsb-	-RRB-	_	_	_
1138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1139	E17	e17	NN	_	_	_
1140	_	_	CD	_	_	_
1141	6	6	CD	_	_	_
1142	_	_	NN	_	_	_
1143	m5	m5	NN	_	_	_
1144	-LSB-	-lsb-	-LRB-	_	_	_
1145	COPRO-Seq	copro-seq	NN	_	_	_
1146	-RSB-	-rsb-	-RRB-	_	_	_
1147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1148	E17	e17	NN	_	_	_
1149	_	_	CD	_	_	_
1150	6	6	CD	_	_	_
1151	_	_	NN	_	_	_
1152	m6	m6	NN	_	_	_
1153	-LSB-	-lsb-	-LRB-	_	_	_
1154	COPRO-Seq	copro-seq	NN	_	_	_
1155	-RSB-	-rsb-	-RRB-	_	_	_
1156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1157	E17	e17	NN	_	_	_
1158	_	_	CD	_	_	_
1159	6	6	CD	_	_	_
1160	_	_	NN	_	_	_
1161	m7	m7	NN	_	_	_
1162	-LSB-	-lsb-	-LRB-	_	_	_
1163	COPRO-Seq	copro-seq	NN	_	_	_
1164	-RSB-	-rsb-	-RRB-	_	_	_
1165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1166	E17	e17	NN	_	_	_
1167	_	_	CD	_	_	_
1168	6	6	CD	_	_	_
1169	_	_	NN	_	_	_
1170	m8	m8	NN	_	_	_
1171	-LSB-	-lsb-	-LRB-	_	_	_
1172	COPRO-Seq	copro-seq	NN	_	_	_
1173	-RSB-	-rsb-	-RRB-	_	_	_
1174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1175	E17	e17	NN	_	_	_
1176	_	_	NN	_	_	_
1177	7	7	CD	_	_	_
1178	_	_	SYM	_	_	_
1179	m1	m1	NN	_	_	_
1180	-LSB-	-lsb-	-LRB-	_	_	_
1181	COPRO-Seq	copro-seq	NN	_	_	_
1182	-RSB-	-rsb-	-RRB-	_	_	_
1183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1184	E17	e17	NN	_	_	_
1185	_	_	NN	_	_	_
1186	7	7	CD	_	_	_
1187	_	_	NN	_	_	_
1188	m2	m2	NN	_	_	_
1189	-LSB-	-lsb-	-LRB-	_	_	_
1190	COPRO-Seq	copro-seq	NN	_	_	_
1191	-RSB-	-rsb-	-RRB-	_	_	_
1192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1193	E17	e17	NN	_	_	_
1194	_	_	NN	_	_	_
1195	7	7	CD	_	_	_
1196	_	_	NN	_	_	_
1197	m3	m3	NN	_	_	_
1198	-LSB-	-lsb-	-LRB-	_	_	_
1199	COPRO-Seq	copro-seq	NN	_	_	_
1200	-RSB-	-rsb-	-RRB-	_	_	_
1201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1202	E17	e17	NN	_	_	_
1203	_	_	NN	_	_	_
1204	7	7	CD	_	_	_
1205	_	_	NN	_	_	_
1206	m4	m4	NN	_	_	_
1207	-LSB-	-lsb-	-LRB-	_	_	_
1208	COPRO-Seq	copro-seq	NN	_	_	_
1209	-RSB-	-rsb-	-RRB-	_	_	_
1210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1211	E17	e17	NN	_	_	_
1212	_	_	NN	_	_	_
1213	7	7	CD	_	_	_
1214	_	_	NN	_	_	_
1215	m6	m6	NN	_	_	_
1216	-LSB-	-lsb-	-LRB-	_	_	_
1217	COPRO-Seq	copro-seq	NN	_	_	_
1218	-RSB-	-rsb-	-RRB-	_	_	_
1219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1220	E17	e17	NN	_	_	_
1221	_	_	NN	_	_	_
1222	7	7	CD	_	_	_
1223	_	_	NN	_	_	_
1224	m7	m7	NN	_	_	_
1225	-LSB-	-lsb-	-LRB-	_	_	_
1226	COPRO-Seq	copro-seq	NN	_	_	_
1227	-RSB-	-rsb-	-RRB-	_	_	_
1228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1229	E1	e1	NN	_	_	_
1230	_	_	NN	_	_	_
1231	7	7	CD	_	_	_
1232	_	_	SYM	_	_	_
1233	m1	m1	NN	_	_	_
1234	-LSB-	-lsb-	-LRB-	_	_	_
1235	COPRO-Seq	copro-seq	NN	_	_	_
1236	-RSB-	-rsb-	-RRB-	_	_	_
1237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1238	E1	e1	NN	_	_	_
1239	_	_	NN	_	_	_
1240	7	7	CD	_	_	_
1241	_	_	NN	_	_	_
1242	m2	m2	NN	_	_	_
1243	-LSB-	-lsb-	-LRB-	_	_	_
1244	COPRO-Seq	copro-seq	NN	_	_	_
1245	-RSB-	-rsb-	-RRB-	_	_	_
1246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1247	E1	e1	NN	_	_	_
1248	_	_	NN	_	_	_
1249	7	7	CD	_	_	_
1250	_	_	NN	_	_	_
1251	m3	m3	NN	_	_	_
1252	-LSB-	-lsb-	-LRB-	_	_	_
1253	COPRO-Seq	copro-seq	NN	_	_	_
1254	-RSB-	-rsb-	-RRB-	_	_	_
1255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1256	E1	e1	NN	_	_	_
1257	_	_	NN	_	_	_
1258	7	7	CD	_	_	_
1259	_	_	NN	_	_	_
1260	m4	m4	NN	_	_	_
1261	-LSB-	-lsb-	-LRB-	_	_	_
1262	COPRO-Seq	copro-seq	NN	_	_	_
1263	-RSB-	-rsb-	-RRB-	_	_	_
1264	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1265	E1	e1	NN	_	_	_
1266	_	_	NN	_	_	_
1267	7	7	CD	_	_	_
1268	_	_	NN	_	_	_
1269	m5	m5	NN	_	_	_
1270	-LSB-	-lsb-	-LRB-	_	_	_
1271	COPRO-Seq	copro-seq	NN	_	_	_
1272	-RSB-	-rsb-	-RRB-	_	_	_
1273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1274	E1	e1	NN	_	_	_
1275	_	_	NN	_	_	_
1276	7	7	CD	_	_	_
1277	_	_	NN	_	_	_
1278	m6	m6	NN	_	_	_
1279	-LSB-	-lsb-	-LRB-	_	_	_
1280	COPRO-Seq	copro-seq	NN	_	_	_
1281	-RSB-	-rsb-	-RRB-	_	_	_
1282	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1283	E1	e1	NN	_	_	_
1284	_	_	NN	_	_	_
1285	7	7	CD	_	_	_
1286	_	_	NN	_	_	_
1287	m7	m7	NN	_	_	_
1288	-LSB-	-lsb-	-LRB-	_	_	_
1289	COPRO-Seq	copro-seq	NN	_	_	_
1290	-RSB-	-rsb-	-RRB-	_	_	_
1291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1292	E1	e1	NN	_	_	_
1293	_	_	NN	_	_	_
1294	7	7	CD	_	_	_
1295	_	_	NN	_	_	_
1296	m8	m8	NN	_	_	_
1297	-LSB-	-lsb-	-LRB-	_	_	_
1298	COPRO-Seq	copro-seq	NN	_	_	_
1299	-RSB-	-rsb-	-RRB-	_	_	_
1300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1301	E19	e19	NN	_	_	_
1302	_	_	NN	_	_	_
1303	1	1	CD	_	_	_
1304	_	_	SYM	_	_	_
1305	m1	m1	NN	_	_	_
1306	-LSB-	-lsb-	-LRB-	_	_	_
1307	COPRO-Seq	copro-seq	NN	_	_	_
1308	-RSB-	-rsb-	-RRB-	_	_	_
1309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1310	E19	e19	NN	_	_	_
1311	_	_	NN	_	_	_
1312	1	1	CD	_	_	_
1313	_	_	CD	_	_	_
1314	m2	m2	NN	_	_	_
1315	-LSB-	-lsb-	-LRB-	_	_	_
1316	COPRO-Seq	copro-seq	NN	_	_	_
1317	-RSB-	-rsb-	-RRB-	_	_	_
1318	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1319	E19	e19	NN	_	_	_
1320	_	_	NN	_	_	_
1321	1	1	CD	_	_	_
1322	_	_	CD	_	_	_
1323	m3	m3	NN	_	_	_
1324	-LSB-	-lsb-	-LRB-	_	_	_
1325	COPRO-Seq	copro-seq	NN	_	_	_
1326	-RSB-	-rsb-	-RRB-	_	_	_
1327	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1328	E19	e19	NN	_	_	_
1329	_	_	NN	_	_	_
1330	1	1	CD	_	_	_
1331	_	_	CD	_	_	_
1332	m4	m4	NN	_	_	_
1333	-LSB-	-lsb-	-LRB-	_	_	_
1334	COPRO-Seq	copro-seq	NN	_	_	_
1335	-RSB-	-rsb-	-RRB-	_	_	_
1336	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1337	E19	e19	NN	_	_	_
1338	_	_	NN	_	_	_
1339	1	1	CD	_	_	_
1340	_	_	CD	_	_	_
1341	m5	m5	NN	_	_	_
1342	-LSB-	-lsb-	-LRB-	_	_	_
1343	COPRO-Seq	copro-seq	NN	_	_	_
1344	-RSB-	-rsb-	-RRB-	_	_	_
1345	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1346	E19	e19	NN	_	_	_
1347	_	_	NN	_	_	_
1348	1	1	CD	_	_	_
1349	_	_	CD	_	_	_
1350	m6	m6	NN	_	_	_
1351	-LSB-	-lsb-	-LRB-	_	_	_
1352	COPRO-Seq	copro-seq	NN	_	_	_
1353	-RSB-	-rsb-	-RRB-	_	_	_
1354	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1355	E19	e19	NN	_	_	_
1356	_	_	NN	_	_	_
1357	1	1	CD	_	_	_
1358	_	_	CD	_	_	_
1359	m7	m7	NN	_	_	_
1360	-LSB-	-lsb-	-LRB-	_	_	_
1361	COPRO-Seq	copro-seq	NN	_	_	_
1362	-RSB-	-rsb-	-RRB-	_	_	_
1363	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1364	E19	e19	NN	_	_	_
1365	_	_	NN	_	_	_
1366	1	1	CD	_	_	_
1367	_	_	CD	_	_	_
1368	m8	m8	NN	_	_	_
1369	-LSB-	-lsb-	-LRB-	_	_	_
1370	COPRO-Seq	copro-seq	NN	_	_	_
1371	-RSB-	-rsb-	-RRB-	_	_	_
1372	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1373	E19	e19	NN	_	_	_
1374	_	_	CD	_	_	_
1375	4	4	CD	_	_	_
1376	_	_	NN	_	_	_
1377	m2	m2	NN	_	_	_
1378	-LSB-	-lsb-	-LRB-	_	_	_
1379	COPRO-Seq	copro-seq	NN	_	_	_
1380	-RSB-	-rsb-	-RRB-	_	_	_
1381	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1382	E19	e19	NN	_	_	_
1383	_	_	CD	_	_	_
1384	4	4	CD	_	_	_
1385	_	_	NN	_	_	_
1386	m3	m3	NN	_	_	_
1387	-LSB-	-lsb-	-LRB-	_	_	_
1388	COPRO-Seq	copro-seq	NN	_	_	_
1389	-RSB-	-rsb-	-RRB-	_	_	_
1390	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1391	E19	e19	NN	_	_	_
1392	_	_	CD	_	_	_
1393	4	4	CD	_	_	_
1394	_	_	NN	_	_	_
1395	m4	m4	NN	_	_	_
1396	-LSB-	-lsb-	-LRB-	_	_	_
1397	COPRO-Seq	copro-seq	NN	_	_	_
1398	-RSB-	-rsb-	-RRB-	_	_	_
1399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1400	E19	e19	NN	_	_	_
1401	_	_	CD	_	_	_
1402	4	4	CD	_	_	_
1403	_	_	NN	_	_	_
1404	m5	m5	NN	_	_	_
1405	-LSB-	-lsb-	-LRB-	_	_	_
1406	COPRO-Seq	copro-seq	NN	_	_	_
1407	-RSB-	-rsb-	-RRB-	_	_	_
1408	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1409	E19	e19	NN	_	_	_
1410	_	_	CD	_	_	_
1411	4	4	CD	_	_	_
1412	_	_	NN	_	_	_
1413	m6	m6	NN	_	_	_
1414	-LSB-	-lsb-	-LRB-	_	_	_
1415	COPRO-Seq	copro-seq	NN	_	_	_
1416	-RSB-	-rsb-	-RRB-	_	_	_
1417	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1418	E19	e19	NN	_	_	_
1419	_	_	CD	_	_	_
1420	4	4	CD	_	_	_
1421	_	_	NN	_	_	_
1422	m7	m7	NN	_	_	_
1423	-LSB-	-lsb-	-LRB-	_	_	_
1424	COPRO-Seq	copro-seq	NN	_	_	_
1425	-RSB-	-rsb-	-RRB-	_	_	_
1426	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1427	E19	e19	NN	_	_	_
1428	_	_	CD	_	_	_
1429	4	4	CD	_	_	_
1430	_	_	NN	_	_	_
1431	m8	m8	NN	_	_	_
1432	-LSB-	-lsb-	-LRB-	_	_	_
1433	COPRO-Seq	copro-seq	NN	_	_	_
1434	-RSB-	-rsb-	-RRB-	_	_	_
1435	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1436	E19	e19	NN	_	_	_
1437	_	_	CD	_	_	_
1438	6	6	CD	_	_	_
1439	_	_	NN	_	_	_
1440	m1	m1	NN	_	_	_
1441	-LSB-	-lsb-	-LRB-	_	_	_
1442	COPRO-Seq	copro-seq	NN	_	_	_
1443	-RSB-	-rsb-	-RRB-	_	_	_
1444	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1445	E19	e19	NN	_	_	_
1446	_	_	CD	_	_	_
1447	6	6	CD	_	_	_
1448	_	_	NN	_	_	_
1449	m2	m2	NN	_	_	_
1450	-LSB-	-lsb-	-LRB-	_	_	_
1451	COPRO-Seq	copro-seq	NN	_	_	_
1452	-RSB-	-rsb-	-RRB-	_	_	_
1453	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1454	E19	e19	NN	_	_	_
1455	_	_	CD	_	_	_
1456	6	6	CD	_	_	_
1457	_	_	NN	_	_	_
1458	m3	m3	NN	_	_	_
1459	-LSB-	-lsb-	-LRB-	_	_	_
1460	COPRO-Seq	copro-seq	NN	_	_	_
1461	-RSB-	-rsb-	-RRB-	_	_	_
1462	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1463	E19	e19	NN	_	_	_
1464	_	_	CD	_	_	_
1465	6	6	CD	_	_	_
1466	_	_	NN	_	_	_
1467	m4	m4	NN	_	_	_
1468	-LSB-	-lsb-	-LRB-	_	_	_
1469	COPRO-Seq	copro-seq	NN	_	_	_
1470	-RSB-	-rsb-	-RRB-	_	_	_
1471	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1472	E19	e19	NN	_	_	_
1473	_	_	CD	_	_	_
1474	6	6	CD	_	_	_
1475	_	_	NN	_	_	_
1476	m5	m5	NN	_	_	_
1477	-LSB-	-lsb-	-LRB-	_	_	_
1478	COPRO-Seq	copro-seq	NN	_	_	_
1479	-RSB-	-rsb-	-RRB-	_	_	_
1480	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1481	E19	e19	NN	_	_	_
1482	_	_	CD	_	_	_
1483	6	6	CD	_	_	_
1484	_	_	NN	_	_	_
1485	m6	m6	NN	_	_	_
1486	-LSB-	-lsb-	-LRB-	_	_	_
1487	COPRO-Seq	copro-seq	NN	_	_	_
1488	-RSB-	-rsb-	-RRB-	_	_	_
1489	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1490	E19	e19	NN	_	_	_
1491	_	_	CD	_	_	_
1492	6	6	CD	_	_	_
1493	_	_	NN	_	_	_
1494	m7	m7	NN	_	_	_
1495	-LSB-	-lsb-	-LRB-	_	_	_
1496	COPRO-Seq	copro-seq	NN	_	_	_
1497	-RSB-	-rsb-	-RRB-	_	_	_
1498	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1499	E19	e19	NN	_	_	_
1500	_	_	CD	_	_	_
1501	6	6	CD	_	_	_
1502	_	_	NN	_	_	_
1503	m8	m8	NN	_	_	_
1504	-LSB-	-lsb-	-LRB-	_	_	_
1505	COPRO-Seq	copro-seq	NN	_	_	_
1506	-RSB-	-rsb-	-RRB-	_	_	_
1507	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1508	E19	e19	NN	_	_	_
1509	_	_	NN	_	_	_
1510	7	7	CD	_	_	_
1511	_	_	SYM	_	_	_
1512	m1	m1	NN	_	_	_
1513	-LSB-	-lsb-	-LRB-	_	_	_
1514	COPRO-Seq	copro-seq	NN	_	_	_
1515	-RSB-	-rsb-	-RRB-	_	_	_
1516	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1517	E19	e19	NN	_	_	_
1518	_	_	NN	_	_	_
1519	7	7	CD	_	_	_
1520	_	_	NN	_	_	_
1521	m2	m2	NN	_	_	_
1522	-LSB-	-lsb-	-LRB-	_	_	_
1523	COPRO-Seq	copro-seq	NN	_	_	_
1524	-RSB-	-rsb-	-RRB-	_	_	_
1525	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1526	E19	e19	NN	_	_	_
1527	_	_	NN	_	_	_
1528	7	7	CD	_	_	_
1529	_	_	NN	_	_	_
1530	m3	m3	NN	_	_	_
1531	-LSB-	-lsb-	-LRB-	_	_	_
1532	COPRO-Seq	copro-seq	NN	_	_	_
1533	-RSB-	-rsb-	-RRB-	_	_	_
1534	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1535	E19	e19	NN	_	_	_
1536	_	_	NN	_	_	_
1537	7	7	CD	_	_	_
1538	_	_	NN	_	_	_
1539	m4	m4	NN	_	_	_
1540	-LSB-	-lsb-	-LRB-	_	_	_
1541	COPRO-Seq	copro-seq	NN	_	_	_
1542	-RSB-	-rsb-	-RRB-	_	_	_
1543	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1544	E19	e19	NN	_	_	_
1545	_	_	NN	_	_	_
1546	7	7	CD	_	_	_
1547	_	_	NN	_	_	_
1548	m5	m5	NN	_	_	_
1549	-LSB-	-lsb-	-LRB-	_	_	_
1550	COPRO-Seq	copro-seq	NN	_	_	_
1551	-RSB-	-rsb-	-RRB-	_	_	_
1552	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1553	E19	e19	NN	_	_	_
1554	_	_	NN	_	_	_
1555	7	7	CD	_	_	_
1556	_	_	NN	_	_	_
1557	m6	m6	NN	_	_	_
1558	-LSB-	-lsb-	-LRB-	_	_	_
1559	COPRO-Seq	copro-seq	NN	_	_	_
1560	-RSB-	-rsb-	-RRB-	_	_	_
1561	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1562	E19	e19	NN	_	_	_
1563	_	_	NN	_	_	_
1564	7	7	CD	_	_	_
1565	_	_	NN	_	_	_
1566	m7	m7	NN	_	_	_
1567	-LSB-	-lsb-	-LRB-	_	_	_
1568	COPRO-Seq	copro-seq	NN	_	_	_
1569	-RSB-	-rsb-	-RRB-	_	_	_
1570	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1571	E19	e19	NN	_	_	_
1572	_	_	NN	_	_	_
1573	7	7	CD	_	_	_
1574	_	_	NN	_	_	_
1575	m8	m8	NN	_	_	_
1576	-LSB-	-lsb-	-LRB-	_	_	_
1577	COPRO-Seq	copro-seq	NN	_	_	_
1578	-RSB-	-rsb-	-RRB-	_	_	_
1579	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1580	E2	e2	NN	_	_	_
1581	_	_	CD	_	_	_
1582	14	14	CD	_	_	_
1583	_	_	SYM	_	_	_
1584	m1	m1	NN	_	_	_
1585	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1586	E2	e2	NN	_	_	_
1587	_	_	CD	_	_	_
1588	14	14	CD	_	_	_
1589	_	_	SYM	_	_	_
1590	m1	m1	NN	_	_	_
1591	-LSB-	-lsb-	-LRB-	_	_	_
1592	COPRO-Seq	copro-seq	NN	_	_	_
1593	-RSB-	-rsb-	-RRB-	_	_	_
1594	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1595	E2	e2	NN	_	_	_
1596	_	_	CD	_	_	_
1597	14	14	CD	_	_	_
1598	_	_	NN	_	_	_
1599	m2	m2	NN	_	_	_
1600	-LSB-	-lsb-	-LRB-	_	_	_
1601	COPRO-Seq	copro-seq	NN	_	_	_
1602	-RSB-	-rsb-	-RRB-	_	_	_
1603	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1604	E2	e2	NN	_	_	_
1605	_	_	CD	_	_	_
1606	14	14	CD	_	_	_
1607	_	_	NN	_	_	_
1608	m3	m3	NN	_	_	_
1609	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1610	E2	e2	NN	_	_	_
1611	_	_	CD	_	_	_
1612	14	14	CD	_	_	_
1613	_	_	NN	_	_	_
1614	m3	m3	NN	_	_	_
1615	-LSB-	-lsb-	-LRB-	_	_	_
1616	COPRO-Seq	copro-seq	NN	_	_	_
1617	-RSB-	-rsb-	-RRB-	_	_	_
1618	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1619	E2	e2	NN	_	_	_
1620	_	_	CD	_	_	_
1621	14	14	CD	_	_	_
1622	_	_	NN	_	_	_
1623	m4	m4	NN	_	_	_
1624	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1625	E2	e2	NN	_	_	_
1626	_	_	CD	_	_	_
1627	14	14	CD	_	_	_
1628	_	_	NN	_	_	_
1629	m4	m4	NN	_	_	_
1630	-LSB-	-lsb-	-LRB-	_	_	_
1631	COPRO-Seq	copro-seq	NN	_	_	_
1632	-RSB-	-rsb-	-RRB-	_	_	_
1633	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1634	E2	e2	NN	_	_	_
1635	_	_	CD	_	_	_
1636	14	14	CD	_	_	_
1637	_	_	NN	_	_	_
1638	m5	m5	NN	_	_	_
1639	-LSB-	-lsb-	-LRB-	_	_	_
1640	COPRO-Seq	copro-seq	NN	_	_	_
1641	-RSB-	-rsb-	-RRB-	_	_	_
1642	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1643	E2	e2	NN	_	_	_
1644	_	_	CD	_	_	_
1645	14	14	CD	_	_	_
1646	_	_	NN	_	_	_
1647	m6	m6	NN	_	_	_
1648	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1649	E2	e2	NN	_	_	_
1650	_	_	CD	_	_	_
1651	14	14	CD	_	_	_
1652	_	_	NN	_	_	_
1653	m6	m6	NN	_	_	_
1654	-LSB-	-lsb-	-LRB-	_	_	_
1655	COPRO-Seq	copro-seq	NN	_	_	_
1656	-RSB-	-rsb-	-RRB-	_	_	_
1657	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1658	E2	e2	NN	_	_	_
1659	_	_	CD	_	_	_
1660	14	14	CD	_	_	_
1661	_	_	NN	_	_	_
1662	m7	m7	NN	_	_	_
1663	-LSB-	-lsb-	-LRB-	_	_	_
1664	COPRO-Seq	copro-seq	NN	_	_	_
1665	-RSB-	-rsb-	-RRB-	_	_	_
1666	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1667	E2	e2	NN	_	_	_
1668	_	_	CD	_	_	_
1669	14	14	CD	_	_	_
1670	_	_	NN	_	_	_
1671	m8	m8	NN	_	_	_
1672	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1673	E2	e2	NN	_	_	_
1674	_	_	NN	_	_	_
1675	1	1	CD	_	_	_
1676	_	_	SYM	_	_	_
1677	m1	m1	NN	_	_	_
1678	-LSB-	-lsb-	-LRB-	_	_	_
1679	COPRO-Seq	copro-seq	NN	_	_	_
1680	-RSB-	-rsb-	-RRB-	_	_	_
1681	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1682	E2	e2	NN	_	_	_
1683	_	_	NN	_	_	_
1684	1	1	CD	_	_	_
1685	_	_	CD	_	_	_
1686	m2	m2	NN	_	_	_
1687	-LSB-	-lsb-	-LRB-	_	_	_
1688	COPRO-Seq	copro-seq	NN	_	_	_
1689	-RSB-	-rsb-	-RRB-	_	_	_
1690	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1691	E2	e2	NN	_	_	_
1692	_	_	NN	_	_	_
1693	1	1	CD	_	_	_
1694	_	_	CD	_	_	_
1695	m3	m3	NN	_	_	_
1696	-LSB-	-lsb-	-LRB-	_	_	_
1697	COPRO-Seq	copro-seq	NN	_	_	_
1698	-RSB-	-rsb-	-RRB-	_	_	_
1699	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1700	E2	e2	NN	_	_	_
1701	_	_	NN	_	_	_
1702	1	1	CD	_	_	_
1703	_	_	CD	_	_	_
1704	m4	m4	NN	_	_	_
1705	-LSB-	-lsb-	-LRB-	_	_	_
1706	COPRO-Seq	copro-seq	NN	_	_	_
1707	-RSB-	-rsb-	-RRB-	_	_	_
1708	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1709	E2	e2	NN	_	_	_
1710	_	_	NN	_	_	_
1711	1	1	CD	_	_	_
1712	_	_	CD	_	_	_
1713	m5	m5	NN	_	_	_
1714	-LSB-	-lsb-	-LRB-	_	_	_
1715	COPRO-Seq	copro-seq	NN	_	_	_
1716	-RSB-	-rsb-	-RRB-	_	_	_
1717	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1718	E2	e2	NN	_	_	_
1719	_	_	NN	_	_	_
1720	1	1	CD	_	_	_
1721	_	_	CD	_	_	_
1722	m6	m6	NN	_	_	_
1723	-LSB-	-lsb-	-LRB-	_	_	_
1724	COPRO-Seq	copro-seq	NN	_	_	_
1725	-RSB-	-rsb-	-RRB-	_	_	_
1726	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1727	E2	e2	NN	_	_	_
1728	_	_	NN	_	_	_
1729	1	1	CD	_	_	_
1730	_	_	CD	_	_	_
1731	m7	m7	NN	_	_	_
1732	-LSB-	-lsb-	-LRB-	_	_	_
1733	COPRO-Seq	copro-seq	NN	_	_	_
1734	-RSB-	-rsb-	-RRB-	_	_	_
1735	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1736	E2	e2	NN	_	_	_
1737	_	_	NN	_	_	_
1738	1	1	CD	_	_	_
1739	_	_	CD	_	_	_
1740	m8	m8	NN	_	_	_
1741	-LSB-	-lsb-	-LRB-	_	_	_
1742	COPRO-Seq	copro-seq	NN	_	_	_
1743	-RSB-	-rsb-	-RRB-	_	_	_
1744	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1745	E2	e2	NN	_	_	_
1746	_	_	NN	_	_	_
1747	2	2	CD	_	_	_
1748	_	_	SYM	_	_	_
1749	m1	m1	NN	_	_	_
1750	-LSB-	-lsb-	-LRB-	_	_	_
1751	COPRO-Seq	copro-seq	NN	_	_	_
1752	-RSB-	-rsb-	-RRB-	_	_	_
1753	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1754	E2	e2	NN	_	_	_
1755	_	_	NN	_	_	_
1756	2	2	CD	_	_	_
1757	_	_	CD	_	_	_
1758	m2	m2	NN	_	_	_
1759	-LSB-	-lsb-	-LRB-	_	_	_
1760	COPRO-Seq	copro-seq	NN	_	_	_
1761	-RSB-	-rsb-	-RRB-	_	_	_
1762	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1763	E2	e2	NN	_	_	_
1764	_	_	NN	_	_	_
1765	2	2	CD	_	_	_
1766	_	_	CD	_	_	_
1767	m3	m3	NN	_	_	_
1768	-LSB-	-lsb-	-LRB-	_	_	_
1769	COPRO-Seq	copro-seq	NN	_	_	_
1770	-RSB-	-rsb-	-RRB-	_	_	_
1771	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1772	E2	e2	NN	_	_	_
1773	_	_	NN	_	_	_
1774	2	2	CD	_	_	_
1775	_	_	CD	_	_	_
1776	m4	m4	NN	_	_	_
1777	-LSB-	-lsb-	-LRB-	_	_	_
1778	COPRO-Seq	copro-seq	NN	_	_	_
1779	-RSB-	-rsb-	-RRB-	_	_	_
1780	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1781	E2	e2	NN	_	_	_
1782	_	_	NN	_	_	_
1783	2	2	CD	_	_	_
1784	_	_	CD	_	_	_
1785	m5	m5	NN	_	_	_
1786	-LSB-	-lsb-	-LRB-	_	_	_
1787	COPRO-Seq	copro-seq	NN	_	_	_
1788	-RSB-	-rsb-	-RRB-	_	_	_
1789	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1790	E2	e2	NN	_	_	_
1791	_	_	NN	_	_	_
1792	2	2	CD	_	_	_
1793	_	_	CD	_	_	_
1794	m6	m6	NN	_	_	_
1795	-LSB-	-lsb-	-LRB-	_	_	_
1796	COPRO-Seq	copro-seq	NN	_	_	_
1797	-RSB-	-rsb-	-RRB-	_	_	_
1798	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1799	E2	e2	NN	_	_	_
1800	_	_	NN	_	_	_
1801	2	2	CD	_	_	_
1802	_	_	CD	_	_	_
1803	m7	m7	NN	_	_	_
1804	-LSB-	-lsb-	-LRB-	_	_	_
1805	COPRO-Seq	copro-seq	NN	_	_	_
1806	-RSB-	-rsb-	-RRB-	_	_	_
1807	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1808	E2	e2	NN	_	_	_
1809	_	_	NN	_	_	_
1810	2	2	CD	_	_	_
1811	_	_	CD	_	_	_
1812	m8	m8	NN	_	_	_
1813	-LSB-	-lsb-	-LRB-	_	_	_
1814	COPRO-Seq	copro-seq	NN	_	_	_
1815	-RSB-	-rsb-	-RRB-	_	_	_
1816	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1817	E2	e2	NN	_	_	_
1818	_	_	CD	_	_	_
1819	4	4	CD	_	_	_
1820	_	_	SYM	_	_	_
1821	m1	m1	NN	_	_	_
1822	-LSB-	-lsb-	-LRB-	_	_	_
1823	COPRO-Seq	copro-seq	NN	_	_	_
1824	-RSB-	-rsb-	-RRB-	_	_	_
1825	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1826	E2	e2	NN	_	_	_
1827	_	_	CD	_	_	_
1828	4	4	CD	_	_	_
1829	_	_	NN	_	_	_
1830	m2	m2	NN	_	_	_
1831	-LSB-	-lsb-	-LRB-	_	_	_
1832	COPRO-Seq	copro-seq	NN	_	_	_
1833	-RSB-	-rsb-	-RRB-	_	_	_
1834	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1835	E2	e2	NN	_	_	_
1836	_	_	CD	_	_	_
1837	4	4	CD	_	_	_
1838	_	_	NN	_	_	_
1839	m3	m3	NN	_	_	_
1840	-LSB-	-lsb-	-LRB-	_	_	_
1841	COPRO-Seq	copro-seq	NN	_	_	_
1842	-RSB-	-rsb-	-RRB-	_	_	_
1843	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1844	E2	e2	NN	_	_	_
1845	_	_	CD	_	_	_
1846	4	4	CD	_	_	_
1847	_	_	NN	_	_	_
1848	m4	m4	NN	_	_	_
1849	-LSB-	-lsb-	-LRB-	_	_	_
1850	COPRO-Seq	copro-seq	NN	_	_	_
1851	-RSB-	-rsb-	-RRB-	_	_	_
1852	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1853	E2	e2	NN	_	_	_
1854	_	_	CD	_	_	_
1855	4	4	CD	_	_	_
1856	_	_	NN	_	_	_
1857	m5	m5	NN	_	_	_
1858	-LSB-	-lsb-	-LRB-	_	_	_
1859	COPRO-Seq	copro-seq	NN	_	_	_
1860	-RSB-	-rsb-	-RRB-	_	_	_
1861	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1862	E2	e2	NN	_	_	_
1863	_	_	CD	_	_	_
1864	4	4	CD	_	_	_
1865	_	_	NN	_	_	_
1866	m6	m6	NN	_	_	_
1867	-LSB-	-lsb-	-LRB-	_	_	_
1868	COPRO-Seq	copro-seq	NN	_	_	_
1869	-RSB-	-rsb-	-RRB-	_	_	_
1870	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1871	E2	e2	NN	_	_	_
1872	_	_	CD	_	_	_
1873	4	4	CD	_	_	_
1874	_	_	NN	_	_	_
1875	m7	m7	NN	_	_	_
1876	-LSB-	-lsb-	-LRB-	_	_	_
1877	COPRO-Seq	copro-seq	NN	_	_	_
1878	-RSB-	-rsb-	-RRB-	_	_	_
1879	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1880	E2	e2	NN	_	_	_
1881	_	_	CD	_	_	_
1882	4	4	CD	_	_	_
1883	_	_	NN	_	_	_
1884	m8	m8	NN	_	_	_
1885	-LSB-	-lsb-	-LRB-	_	_	_
1886	COPRO-Seq	copro-seq	NN	_	_	_
1887	-RSB-	-rsb-	-RRB-	_	_	_
1888	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1889	E2	e2	NN	_	_	_
1890	_	_	NN	_	_	_
1891	7	7	CD	_	_	_
1892	_	_	SYM	_	_	_
1893	m1	m1	NN	_	_	_
1894	-LSB-	-lsb-	-LRB-	_	_	_
1895	COPRO-Seq	copro-seq	NN	_	_	_
1896	-RSB-	-rsb-	-RRB-	_	_	_
1897	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1898	E2	e2	NN	_	_	_
1899	_	_	NN	_	_	_
1900	7	7	CD	_	_	_
1901	_	_	NN	_	_	_
1902	m2	m2	NN	_	_	_
1903	-LSB-	-lsb-	-LRB-	_	_	_
1904	COPRO-Seq	copro-seq	NN	_	_	_
1905	-RSB-	-rsb-	-RRB-	_	_	_
1906	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1907	E2	e2	NN	_	_	_
1908	_	_	NN	_	_	_
1909	7	7	CD	_	_	_
1910	_	_	NN	_	_	_
1911	m3	m3	NN	_	_	_
1912	-LSB-	-lsb-	-LRB-	_	_	_
1913	COPRO-Seq	copro-seq	NN	_	_	_
1914	-RSB-	-rsb-	-RRB-	_	_	_
1915	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1916	E2	e2	NN	_	_	_
1917	_	_	NN	_	_	_
1918	7	7	CD	_	_	_
1919	_	_	NN	_	_	_
1920	m4	m4	NN	_	_	_
1921	-LSB-	-lsb-	-LRB-	_	_	_
1922	COPRO-Seq	copro-seq	NN	_	_	_
1923	-RSB-	-rsb-	-RRB-	_	_	_
1924	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1925	E2	e2	NN	_	_	_
1926	_	_	NN	_	_	_
1927	7	7	CD	_	_	_
1928	_	_	NN	_	_	_
1929	m5	m5	NN	_	_	_
1930	-LSB-	-lsb-	-LRB-	_	_	_
1931	COPRO-Seq	copro-seq	NN	_	_	_
1932	-RSB-	-rsb-	-RRB-	_	_	_
1933	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1934	E2	e2	NN	_	_	_
1935	_	_	NN	_	_	_
1936	7	7	CD	_	_	_
1937	_	_	NN	_	_	_
1938	m6	m6	NN	_	_	_
1939	-LSB-	-lsb-	-LRB-	_	_	_
1940	COPRO-Seq	copro-seq	NN	_	_	_
1941	-RSB-	-rsb-	-RRB-	_	_	_
1942	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1943	E2	e2	NN	_	_	_
1944	_	_	NN	_	_	_
1945	7	7	CD	_	_	_
1946	_	_	NN	_	_	_
1947	m7	m7	NN	_	_	_
1948	-LSB-	-lsb-	-LRB-	_	_	_
1949	COPRO-Seq	copro-seq	NN	_	_	_
1950	-RSB-	-rsb-	-RRB-	_	_	_
1951	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1952	E2	e2	NN	_	_	_
1953	_	_	NN	_	_	_
1954	7	7	CD	_	_	_
1955	_	_	NN	_	_	_
1956	m8	m8	NN	_	_	_
1957	-LSB-	-lsb-	-LRB-	_	_	_
1958	COPRO-Seq	copro-seq	NN	_	_	_
1959	-RSB-	-rsb-	-RRB-	_	_	_
1960	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1961	E3	e3	NN	_	_	_
1962	_	_	CD	_	_	_
1963	14	14	CD	_	_	_
1964	_	_	SYM	_	_	_
1965	m1	m1	NN	_	_	_
1966	-LSB-	-lsb-	-LRB-	_	_	_
1967	COPRO-Seq	copro-seq	NN	_	_	_
1968	-RSB-	-rsb-	-RRB-	_	_	_
1969	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1970	E3	e3	NN	_	_	_
1971	_	_	CD	_	_	_
1972	14	14	CD	_	_	_
1973	_	_	NN	_	_	_
1974	m2	m2	NN	_	_	_
1975	-LSB-	-lsb-	-LRB-	_	_	_
1976	COPRO-Seq	copro-seq	NN	_	_	_
1977	-RSB-	-rsb-	-RRB-	_	_	_
1978	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1979	E3	e3	NN	_	_	_
1980	_	_	CD	_	_	_
1981	14	14	CD	_	_	_
1982	_	_	NN	_	_	_
1983	m3	m3	NN	_	_	_
1984	-LSB-	-lsb-	-LRB-	_	_	_
1985	COPRO-Seq	copro-seq	NN	_	_	_
1986	-RSB-	-rsb-	-RRB-	_	_	_
1987	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1988	E3	e3	NN	_	_	_
1989	_	_	CD	_	_	_
1990	14	14	CD	_	_	_
1991	_	_	NN	_	_	_
1992	m4	m4	NN	_	_	_
1993	-LSB-	-lsb-	-LRB-	_	_	_
1994	COPRO-Seq	copro-seq	NN	_	_	_
1995	-RSB-	-rsb-	-RRB-	_	_	_
1996	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1997	E3	e3	NN	_	_	_
1998	_	_	CD	_	_	_
1999	14	14	CD	_	_	_
2000	_	_	NN	_	_	_
2001	m6	m6	NN	_	_	_
2002	-LSB-	-lsb-	-LRB-	_	_	_
2003	COPRO-Seq	copro-seq	NN	_	_	_
2004	-RSB-	-rsb-	-RRB-	_	_	_
2005	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2006	E3	e3	NN	_	_	_
2007	_	_	CD	_	_	_
2008	14	14	CD	_	_	_
2009	_	_	NN	_	_	_
2010	m7	m7	NN	_	_	_
2011	-LSB-	-lsb-	-LRB-	_	_	_
2012	COPRO-Seq	copro-seq	NN	_	_	_
2013	-RSB-	-rsb-	-RRB-	_	_	_
2014	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2015	E3	e3	NN	_	_	_
2016	_	_	CD	_	_	_
2017	14	14	CD	_	_	_
2018	_	_	NN	_	_	_
2019	m8	m8	NN	_	_	_
2020	-LSB-	-lsb-	-LRB-	_	_	_
2021	COPRO-Seq	copro-seq	NN	_	_	_
2022	-RSB-	-rsb-	-RRB-	_	_	_
2023	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2024	E3	e3	NN	_	_	_
2025	_	_	NN	_	_	_
2026	1	1	CD	_	_	_
2027	_	_	SYM	_	_	_
2028	m1	m1	NN	_	_	_
2029	-LSB-	-lsb-	-LRB-	_	_	_
2030	COPRO-Seq	copro-seq	NN	_	_	_
2031	-RSB-	-rsb-	-RRB-	_	_	_
2032	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2033	E3	e3	NN	_	_	_
2034	_	_	NN	_	_	_
2035	1	1	CD	_	_	_
2036	_	_	CD	_	_	_
2037	m2	m2	NN	_	_	_
2038	-LSB-	-lsb-	-LRB-	_	_	_
2039	COPRO-Seq	copro-seq	NN	_	_	_
2040	-RSB-	-rsb-	-RRB-	_	_	_
2041	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2042	E3	e3	NN	_	_	_
2043	_	_	NN	_	_	_
2044	1	1	CD	_	_	_
2045	_	_	CD	_	_	_
2046	m3	m3	NN	_	_	_
2047	-LSB-	-lsb-	-LRB-	_	_	_
2048	COPRO-Seq	copro-seq	NN	_	_	_
2049	-RSB-	-rsb-	-RRB-	_	_	_
2050	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2051	E3	e3	NN	_	_	_
2052	_	_	NN	_	_	_
2053	1	1	CD	_	_	_
2054	_	_	CD	_	_	_
2055	m4	m4	NN	_	_	_
2056	-LSB-	-lsb-	-LRB-	_	_	_
2057	COPRO-Seq	copro-seq	NN	_	_	_
2058	-RSB-	-rsb-	-RRB-	_	_	_
2059	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2060	E3	e3	NN	_	_	_
2061	_	_	NN	_	_	_
2062	1	1	CD	_	_	_
2063	_	_	CD	_	_	_
2064	m5	m5	NN	_	_	_
2065	-LSB-	-lsb-	-LRB-	_	_	_
2066	COPRO-Seq	copro-seq	NN	_	_	_
2067	-RSB-	-rsb-	-RRB-	_	_	_
2068	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2069	E3	e3	NN	_	_	_
2070	_	_	NN	_	_	_
2071	1	1	CD	_	_	_
2072	_	_	CD	_	_	_
2073	m6	m6	NN	_	_	_
2074	-LSB-	-lsb-	-LRB-	_	_	_
2075	COPRO-Seq	copro-seq	NN	_	_	_
2076	-RSB-	-rsb-	-RRB-	_	_	_
2077	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2078	E3	e3	NN	_	_	_
2079	_	_	NN	_	_	_
2080	1	1	CD	_	_	_
2081	_	_	CD	_	_	_
2082	m7	m7	NN	_	_	_
2083	-LSB-	-lsb-	-LRB-	_	_	_
2084	COPRO-Seq	copro-seq	NN	_	_	_
2085	-RSB-	-rsb-	-RRB-	_	_	_
2086	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2087	E3	e3	NN	_	_	_
2088	_	_	NN	_	_	_
2089	1	1	CD	_	_	_
2090	_	_	CD	_	_	_
2091	m8	m8	NN	_	_	_
2092	-LSB-	-lsb-	-LRB-	_	_	_
2093	COPRO-Seq	copro-seq	NN	_	_	_
2094	-RSB-	-rsb-	-RRB-	_	_	_
2095	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2096	E3	e3	NN	_	_	_
2097	_	_	NN	_	_	_
2098	2	2	CD	_	_	_
2099	_	_	SYM	_	_	_
2100	m1	m1	NN	_	_	_
2101	-LSB-	-lsb-	-LRB-	_	_	_
2102	COPRO-Seq	copro-seq	NN	_	_	_
2103	-RSB-	-rsb-	-RRB-	_	_	_
2104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2105	E3	e3	NN	_	_	_
2106	_	_	NN	_	_	_
2107	2	2	CD	_	_	_
2108	_	_	CD	_	_	_
2109	m2	m2	NN	_	_	_
2110	-LSB-	-lsb-	-LRB-	_	_	_
2111	COPRO-Seq	copro-seq	NN	_	_	_
2112	-RSB-	-rsb-	-RRB-	_	_	_
2113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2114	E3	e3	NN	_	_	_
2115	_	_	NN	_	_	_
2116	2	2	CD	_	_	_
2117	_	_	CD	_	_	_
2118	m3	m3	NN	_	_	_
2119	-LSB-	-lsb-	-LRB-	_	_	_
2120	COPRO-Seq	copro-seq	NN	_	_	_
2121	-RSB-	-rsb-	-RRB-	_	_	_
2122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2123	E3	e3	NN	_	_	_
2124	_	_	NN	_	_	_
2125	2	2	CD	_	_	_
2126	_	_	CD	_	_	_
2127	m4	m4	NN	_	_	_
2128	-LSB-	-lsb-	-LRB-	_	_	_
2129	COPRO-Seq	copro-seq	NN	_	_	_
2130	-RSB-	-rsb-	-RRB-	_	_	_
2131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2132	E3	e3	NN	_	_	_
2133	_	_	NN	_	_	_
2134	2	2	CD	_	_	_
2135	_	_	CD	_	_	_
2136	m5	m5	NN	_	_	_
2137	-LSB-	-lsb-	-LRB-	_	_	_
2138	COPRO-Seq	copro-seq	NN	_	_	_
2139	-RSB-	-rsb-	-RRB-	_	_	_
2140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2141	E3	e3	NN	_	_	_
2142	_	_	NN	_	_	_
2143	2	2	CD	_	_	_
2144	_	_	CD	_	_	_
2145	m6	m6	NN	_	_	_
2146	-LSB-	-lsb-	-LRB-	_	_	_
2147	COPRO-Seq	copro-seq	NN	_	_	_
2148	-RSB-	-rsb-	-RRB-	_	_	_
2149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2150	E3	e3	NN	_	_	_
2151	_	_	NN	_	_	_
2152	2	2	CD	_	_	_
2153	_	_	CD	_	_	_
2154	m7	m7	NN	_	_	_
2155	-LSB-	-lsb-	-LRB-	_	_	_
2156	COPRO-Seq	copro-seq	NN	_	_	_
2157	-RSB-	-rsb-	-RRB-	_	_	_
2158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2159	E3	e3	NN	_	_	_
2160	_	_	NN	_	_	_
2161	2	2	CD	_	_	_
2162	_	_	CD	_	_	_
2163	m8	m8	NN	_	_	_
2164	-LSB-	-lsb-	-LRB-	_	_	_
2165	COPRO-Seq	copro-seq	NN	_	_	_
2166	-RSB-	-rsb-	-RRB-	_	_	_
2167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2168	E3	e3	NN	_	_	_
2169	_	_	CD	_	_	_
2170	4	4	CD	_	_	_
2171	_	_	NN	_	_	_
2172	m2	m2	NN	_	_	_
2173	-LSB-	-lsb-	-LRB-	_	_	_
2174	COPRO-Seq	copro-seq	NN	_	_	_
2175	-RSB-	-rsb-	-RRB-	_	_	_
2176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2177	E3	e3	NN	_	_	_
2178	_	_	CD	_	_	_
2179	4	4	CD	_	_	_
2180	_	_	NN	_	_	_
2181	m3	m3	NN	_	_	_
2182	-LSB-	-lsb-	-LRB-	_	_	_
2183	COPRO-Seq	copro-seq	NN	_	_	_
2184	-RSB-	-rsb-	-RRB-	_	_	_
2185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2186	E3	e3	NN	_	_	_
2187	_	_	CD	_	_	_
2188	4	4	CD	_	_	_
2189	_	_	NN	_	_	_
2190	m4	m4	NN	_	_	_
2191	-LSB-	-lsb-	-LRB-	_	_	_
2192	COPRO-Seq	copro-seq	NN	_	_	_
2193	-RSB-	-rsb-	-RRB-	_	_	_
2194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2195	E3	e3	NN	_	_	_
2196	_	_	CD	_	_	_
2197	4	4	CD	_	_	_
2198	_	_	NN	_	_	_
2199	m5	m5	NN	_	_	_
2200	-LSB-	-lsb-	-LRB-	_	_	_
2201	COPRO-Seq	copro-seq	NN	_	_	_
2202	-RSB-	-rsb-	-RRB-	_	_	_
2203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2204	E3	e3	NN	_	_	_
2205	_	_	CD	_	_	_
2206	4	4	CD	_	_	_
2207	_	_	NN	_	_	_
2208	m6	m6	NN	_	_	_
2209	-LSB-	-lsb-	-LRB-	_	_	_
2210	COPRO-Seq	copro-seq	NN	_	_	_
2211	-RSB-	-rsb-	-RRB-	_	_	_
2212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2213	E3	e3	NN	_	_	_
2214	_	_	CD	_	_	_
2215	4	4	CD	_	_	_
2216	_	_	NN	_	_	_
2217	m7	m7	NN	_	_	_
2218	-LSB-	-lsb-	-LRB-	_	_	_
2219	COPRO-Seq	copro-seq	NN	_	_	_
2220	-RSB-	-rsb-	-RRB-	_	_	_
2221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2222	E3	e3	NN	_	_	_
2223	_	_	CD	_	_	_
2224	4	4	CD	_	_	_
2225	_	_	NN	_	_	_
2226	m8	m8	NN	_	_	_
2227	-LSB-	-lsb-	-LRB-	_	_	_
2228	COPRO-Seq	copro-seq	NN	_	_	_
2229	-RSB-	-rsb-	-RRB-	_	_	_
2230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2231	E3	e3	NN	_	_	_
2232	_	_	NN	_	_	_
2233	7	7	CD	_	_	_
2234	_	_	SYM	_	_	_
2235	m1	m1	NN	_	_	_
2236	-LSB-	-lsb-	-LRB-	_	_	_
2237	COPRO-Seq	copro-seq	NN	_	_	_
2238	-RSB-	-rsb-	-RRB-	_	_	_
2239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2240	E3	e3	NN	_	_	_
2241	_	_	NN	_	_	_
2242	7	7	CD	_	_	_
2243	_	_	NN	_	_	_
2244	m2	m2	NN	_	_	_
2245	-LSB-	-lsb-	-LRB-	_	_	_
2246	COPRO-Seq	copro-seq	NN	_	_	_
2247	-RSB-	-rsb-	-RRB-	_	_	_
2248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2249	E3	e3	NN	_	_	_
2250	_	_	NN	_	_	_
2251	7	7	CD	_	_	_
2252	_	_	NN	_	_	_
2253	m3	m3	NN	_	_	_
2254	-LSB-	-lsb-	-LRB-	_	_	_
2255	COPRO-Seq	copro-seq	NN	_	_	_
2256	-RSB-	-rsb-	-RRB-	_	_	_
2257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2258	E3	e3	NN	_	_	_
2259	_	_	NN	_	_	_
2260	7	7	CD	_	_	_
2261	_	_	NN	_	_	_
2262	m4	m4	NN	_	_	_
2263	-LSB-	-lsb-	-LRB-	_	_	_
2264	COPRO-Seq	copro-seq	NN	_	_	_
2265	-RSB-	-rsb-	-RRB-	_	_	_
2266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2267	E3	e3	NN	_	_	_
2268	_	_	NN	_	_	_
2269	7	7	CD	_	_	_
2270	_	_	NN	_	_	_
2271	m5	m5	NN	_	_	_
2272	-LSB-	-lsb-	-LRB-	_	_	_
2273	COPRO-Seq	copro-seq	NN	_	_	_
2274	-RSB-	-rsb-	-RRB-	_	_	_
2275	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2276	E3	e3	NN	_	_	_
2277	_	_	NN	_	_	_
2278	7	7	CD	_	_	_
2279	_	_	NN	_	_	_
2280	m6	m6	NN	_	_	_
2281	-LSB-	-lsb-	-LRB-	_	_	_
2282	COPRO-Seq	copro-seq	NN	_	_	_
2283	-RSB-	-rsb-	-RRB-	_	_	_
2284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2285	E3	e3	NN	_	_	_
2286	_	_	NN	_	_	_
2287	7	7	CD	_	_	_
2288	_	_	NN	_	_	_
2289	m7	m7	NN	_	_	_
2290	-LSB-	-lsb-	-LRB-	_	_	_
2291	COPRO-Seq	copro-seq	NN	_	_	_
2292	-RSB-	-rsb-	-RRB-	_	_	_
2293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2294	E3	e3	NN	_	_	_
2295	_	_	NN	_	_	_
2296	7	7	CD	_	_	_
2297	_	_	NN	_	_	_
2298	m8	m8	NN	_	_	_
2299	-LSB-	-lsb-	-LRB-	_	_	_
2300	COPRO-Seq	copro-seq	NN	_	_	_
2301	-RSB-	-rsb-	-RRB-	_	_	_
2302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2303	E9	e9	NN	_	_	_
2304	_	_	NN	_	_	_
2305	1	1	CD	_	_	_
2306	_	_	SYM	_	_	_
2307	m1	m1	NN	_	_	_
2308	-LSB-	-lsb-	-LRB-	_	_	_
2309	COPRO-Seq	copro-seq	NN	_	_	_
2310	-RSB-	-rsb-	-RRB-	_	_	_
2311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2312	E9	e9	NN	_	_	_
2313	_	_	NN	_	_	_
2314	1	1	CD	_	_	_
2315	_	_	CD	_	_	_
2316	m2	m2	NN	_	_	_
2317	-LSB-	-lsb-	-LRB-	_	_	_
2318	COPRO-Seq	copro-seq	NN	_	_	_
2319	-RSB-	-rsb-	-RRB-	_	_	_
2320	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2321	E9	e9	NN	_	_	_
2322	_	_	NN	_	_	_
2323	1	1	CD	_	_	_
2324	_	_	CD	_	_	_
2325	m3	m3	NN	_	_	_
2326	-LSB-	-lsb-	-LRB-	_	_	_
2327	COPRO-Seq	copro-seq	NN	_	_	_
2328	-RSB-	-rsb-	-RRB-	_	_	_
2329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2330	E9	e9	NN	_	_	_
2331	_	_	NN	_	_	_
2332	1	1	CD	_	_	_
2333	_	_	CD	_	_	_
2334	m4	m4	NN	_	_	_
2335	-LSB-	-lsb-	-LRB-	_	_	_
2336	COPRO-Seq	copro-seq	NN	_	_	_
2337	-RSB-	-rsb-	-RRB-	_	_	_
2338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2339	E9	e9	NN	_	_	_
2340	_	_	NN	_	_	_
2341	1	1	CD	_	_	_
2342	_	_	CD	_	_	_
2343	m5	m5	NN	_	_	_
2344	-LSB-	-lsb-	-LRB-	_	_	_
2345	COPRO-Seq	copro-seq	NN	_	_	_
2346	-RSB-	-rsb-	-RRB-	_	_	_
2347	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2348	E9	e9	NN	_	_	_
2349	_	_	NN	_	_	_
2350	1	1	CD	_	_	_
2351	_	_	CD	_	_	_
2352	m6	m6	NN	_	_	_
2353	-LSB-	-lsb-	-LRB-	_	_	_
2354	COPRO-Seq	copro-seq	NN	_	_	_
2355	-RSB-	-rsb-	-RRB-	_	_	_
2356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2357	E9	e9	NN	_	_	_
2358	_	_	NN	_	_	_
2359	1	1	CD	_	_	_
2360	_	_	CD	_	_	_
2361	m7	m7	NN	_	_	_
2362	-LSB-	-lsb-	-LRB-	_	_	_
2363	COPRO-Seq	copro-seq	NN	_	_	_
2364	-RSB-	-rsb-	-RRB-	_	_	_
2365	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2366	E9	e9	NN	_	_	_
2367	_	_	NN	_	_	_
2368	1	1	CD	_	_	_
2369	_	_	CD	_	_	_
2370	m8	m8	NN	_	_	_
2371	-LSB-	-lsb-	-LRB-	_	_	_
2372	COPRO-Seq	copro-seq	NN	_	_	_
2373	-RSB-	-rsb-	-RRB-	_	_	_
2374	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2375	E9	e9	NN	_	_	_
2376	_	_	CD	_	_	_
2377	4	4	CD	_	_	_
2378	_	_	SYM	_	_	_
2379	m1	m1	NN	_	_	_
2380	-LSB-	-lsb-	-LRB-	_	_	_
2381	COPRO-Seq	copro-seq	NN	_	_	_
2382	-RSB-	-rsb-	-RRB-	_	_	_
2383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2384	E9	e9	NN	_	_	_
2385	_	_	CD	_	_	_
2386	4	4	CD	_	_	_
2387	_	_	NN	_	_	_
2388	m2	m2	NN	_	_	_
2389	-LSB-	-lsb-	-LRB-	_	_	_
2390	COPRO-Seq	copro-seq	NN	_	_	_
2391	-RSB-	-rsb-	-RRB-	_	_	_
2392	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2393	E9	e9	NN	_	_	_
2394	_	_	CD	_	_	_
2395	4	4	CD	_	_	_
2396	_	_	NN	_	_	_
2397	m3	m3	NN	_	_	_
2398	-LSB-	-lsb-	-LRB-	_	_	_
2399	COPRO-Seq	copro-seq	NN	_	_	_
2400	-RSB-	-rsb-	-RRB-	_	_	_
2401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2402	E9	e9	NN	_	_	_
2403	_	_	CD	_	_	_
2404	4	4	CD	_	_	_
2405	_	_	NN	_	_	_
2406	m4	m4	NN	_	_	_
2407	-LSB-	-lsb-	-LRB-	_	_	_
2408	COPRO-Seq	copro-seq	NN	_	_	_
2409	-RSB-	-rsb-	-RRB-	_	_	_
2410	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2411	E9	e9	NN	_	_	_
2412	_	_	CD	_	_	_
2413	4	4	CD	_	_	_
2414	_	_	NN	_	_	_
2415	m5	m5	NN	_	_	_
2416	-LSB-	-lsb-	-LRB-	_	_	_
2417	COPRO-Seq	copro-seq	NN	_	_	_
2418	-RSB-	-rsb-	-RRB-	_	_	_
2419	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2420	E9	e9	NN	_	_	_
2421	_	_	CD	_	_	_
2422	4	4	CD	_	_	_
2423	_	_	NN	_	_	_
2424	m6	m6	NN	_	_	_
2425	-LSB-	-lsb-	-LRB-	_	_	_
2426	COPRO-Seq	copro-seq	NN	_	_	_
2427	-RSB-	-rsb-	-RRB-	_	_	_
2428	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2429	E9	e9	NN	_	_	_
2430	_	_	CD	_	_	_
2431	4	4	CD	_	_	_
2432	_	_	NN	_	_	_
2433	m7	m7	NN	_	_	_
2434	-LSB-	-lsb-	-LRB-	_	_	_
2435	COPRO-Seq	copro-seq	NN	_	_	_
2436	-RSB-	-rsb-	-RRB-	_	_	_
2437	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2438	E9	e9	NN	_	_	_
2439	_	_	CD	_	_	_
2440	4	4	CD	_	_	_
2441	_	_	NN	_	_	_
2442	m8	m8	NN	_	_	_
2443	-LSB-	-lsb-	-LRB-	_	_	_
2444	COPRO-Seq	copro-seq	NN	_	_	_
2445	-RSB-	-rsb-	-RRB-	_	_	_
2446	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2447	E9	e9	NN	_	_	_
2448	_	_	CD	_	_	_
2449	6	6	CD	_	_	_
2450	_	_	NN	_	_	_
2451	m2	m2	NN	_	_	_
2452	-LSB-	-lsb-	-LRB-	_	_	_
2453	COPRO-Seq	copro-seq	NN	_	_	_
2454	-RSB-	-rsb-	-RRB-	_	_	_
2455	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2456	E9	e9	NN	_	_	_
2457	_	_	CD	_	_	_
2458	6	6	CD	_	_	_
2459	_	_	NN	_	_	_
2460	m3	m3	NN	_	_	_
2461	-LSB-	-lsb-	-LRB-	_	_	_
2462	COPRO-Seq	copro-seq	NN	_	_	_
2463	-RSB-	-rsb-	-RRB-	_	_	_
2464	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2465	E9	e9	NN	_	_	_
2466	_	_	CD	_	_	_
2467	6	6	CD	_	_	_
2468	_	_	NN	_	_	_
2469	m4	m4	NN	_	_	_
2470	-LSB-	-lsb-	-LRB-	_	_	_
2471	COPRO-Seq	copro-seq	NN	_	_	_
2472	-RSB-	-rsb-	-RRB-	_	_	_
2473	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2474	E9	e9	NN	_	_	_
2475	_	_	CD	_	_	_
2476	6	6	CD	_	_	_
2477	_	_	NN	_	_	_
2478	m5	m5	NN	_	_	_
2479	-LSB-	-lsb-	-LRB-	_	_	_
2480	COPRO-Seq	copro-seq	NN	_	_	_
2481	-RSB-	-rsb-	-RRB-	_	_	_
2482	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2483	E9	e9	NN	_	_	_
2484	_	_	CD	_	_	_
2485	6	6	CD	_	_	_
2486	_	_	NN	_	_	_
2487	m7	m7	NN	_	_	_
2488	-LSB-	-lsb-	-LRB-	_	_	_
2489	COPRO-Seq	copro-seq	NN	_	_	_
2490	-RSB-	-rsb-	-RRB-	_	_	_
2491	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2492	E9	e9	NN	_	_	_
2493	_	_	NN	_	_	_
2494	7	7	CD	_	_	_
2495	_	_	NN	_	_	_
2496	m2	m2	NN	_	_	_
2497	-LSB-	-lsb-	-LRB-	_	_	_
2498	COPRO-Seq	copro-seq	NN	_	_	_
2499	-RSB-	-rsb-	-RRB-	_	_	_
2500	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2501	E9	e9	NN	_	_	_
2502	_	_	NN	_	_	_
2503	7	7	CD	_	_	_
2504	_	_	NN	_	_	_
2505	m3	m3	NN	_	_	_
2506	-LSB-	-lsb-	-LRB-	_	_	_
2507	COPRO-Seq	copro-seq	NN	_	_	_
2508	-RSB-	-rsb-	-RRB-	_	_	_
2509	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2510	E9	e9	NN	_	_	_
2511	_	_	NN	_	_	_
2512	7	7	CD	_	_	_
2513	_	_	NN	_	_	_
2514	m4	m4	NN	_	_	_
2515	-LSB-	-lsb-	-LRB-	_	_	_
2516	COPRO-Seq	copro-seq	NN	_	_	_
2517	-RSB-	-rsb-	-RRB-	_	_	_
2518	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2519	E9	e9	NN	_	_	_
2520	_	_	NN	_	_	_
2521	7	7	CD	_	_	_
2522	_	_	NN	_	_	_
2523	m5	m5	NN	_	_	_
2524	-LSB-	-lsb-	-LRB-	_	_	_
2525	COPRO-Seq	copro-seq	NN	_	_	_
2526	-RSB-	-rsb-	-RRB-	_	_	_
2527	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2528	E9	e9	NN	_	_	_
2529	_	_	NN	_	_	_
2530	7	7	CD	_	_	_
2531	_	_	NN	_	_	_
2532	m6	m6	NN	_	_	_
2533	-LSB-	-lsb-	-LRB-	_	_	_
2534	COPRO-Seq	copro-seq	NN	_	_	_
2535	-RSB-	-rsb-	-RRB-	_	_	_
2536	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2537	E9	e9	NN	_	_	_
2538	_	_	NN	_	_	_
2539	7	7	CD	_	_	_
2540	_	_	NN	_	_	_
2541	m7	m7	NN	_	_	_
2542	-LSB-	-lsb-	-LRB-	_	_	_
2543	COPRO-Seq	copro-seq	NN	_	_	_
2544	-RSB-	-rsb-	-RRB-	_	_	_
2545	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2546	E9	e9	NN	_	_	_
2547	_	_	NN	_	_	_
2548	7	7	CD	_	_	_
2549	_	_	NN	_	_	_
2550	m8	m8	NN	_	_	_
2551	-LSB-	-lsb-	-LRB-	_	_	_
2552	COPRO-Seq	copro-seq	NN	_	_	_
2553	-RSB-	-rsb-	-RRB-	_	_	_
2554	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2555	Escherichia	escherichia	FW	Organism	_	_
2556	coli	coli	FW	Organism	_	_
2557	str	str	FW	_	_	_
2558	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	-LSB-	-lsb-	-LRB-	_	_	_
4	Eubacterium	eubacterium	NN	_	_	_
5	-RSB-	-rsb-	-RRB-	_	_	_
6	rectale	rectale	JJ	_	_	_
7	ATCC	atcc	NN	_	_	_
8	33656	33656	CD	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	Fecal	fecal	JJ	_	_	_
11	samples	sample	NNS	_	_	_
12	obtained	obtain	VBN	_	_	_
13	from	from	IN	_	_	_
14	mice	mouse	NNS	_	_	_
15	were	be	VBD	_	_	_
16	immediately	immediately	RB	_	_	_
17	frozen	freeze	VBN	_	_	_
18	in	in	IN	_	_	_
19	liquid	liquid	JJ	_	_	_
20	nitrogen	nitrogen	NN	_	_	_
21	and	and	CC	_	_	_
22	stored	store	VBD	_	_	_
23	at	at	IN	_	_	_
24	-80	-80	CD	_	_	_
25	°C	°c	NN	_	_	_
26	until	until	IN	_	_	_
27	processing	processing	NN	_	_	_
28	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	samples	sample	NNS	_	_	_
5	were	be	VBD	_	_	_
6	suspended	suspend	VBN	_	_	_
7	in	in	IN	_	_	_
8	a	a	DT	_	_	_
9	solution	solution	NN	_	_	_
10	containing	contain	VBG	_	_	_
11	500	500	CD	_	_	_
12	ul	ul	NN	_	_	_
13	of	of	IN	_	_	_
14	acid-washed	acid-washed	JJ	_	_	_
15	glass	glass	NN	_	_	_
16	beads	bead	NNS	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Sigma-Aldrich	Sigma-Aldrich	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	,	,	,	_	_	_
21	500	500	CD	_	_	_
22	ul	ul	NN	_	_	_
23	of	of	IN	_	_	_
24	extraction	extraction	NN	_	_	_
25	buffer	buffer	NN	_	_	_
26	A	a	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	200	200	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	Tris	tris	NN	_	_	_
31	-LSB-	-lsb-	-LRB-	_	_	_
32	pH	ph	NN	_	_	_
33	8	8	CD	_	_	_
34	-RSB-	-rsb-	-RRB-	_	_	_
35	,	,	,	_	_	_
36	200	200	CD	_	_	_
37	mM	mm	NN	KWSUPP	_	_
38	NaCl	nacl	NN	_	_	_
39	,	,	,	_	_	_
40	20	20	CD	_	_	_
41	mM	mm	NN	KWSUPP	_	_
42	EDTA	edta	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	,	,	,	_	_	_
45	200	200	CD	_	_	_
46	ul	ul	NN	_	_	_
47	of	of	IN	_	_	_
48	20	20	CD	_	_	_
49	%	%	NN	_	_	_
50	SDS	sds	NN	_	_	_
51	,	,	,	_	_	_
52	and	and	CC	_	_	_
53	500	500	CD	_	_	_
54	ul	ul	NN	_	_	_
55	of	of	IN	_	_	_
56	a	a	DT	_	_	_
57	mixture	mixture	NN	_	_	_
58	of	of	IN	_	_	_
59	phenol	phenol	NN	_	_	_
60	:	:	:	_	_	_
61	chloroform	chloroform	NN	_	_	_
62	:	:	:	_	_	_
63	isoamyl	isoamyl	NN	_	_	_
64	alcohol	alcohol	NN	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	25:24:1	25:24:1	CD	_	_	_
67	,	,	,	_	_	_
68	pH	ph	NN	_	_	_
69	8.0	8.0	CD	_	_	_
70	;	;	:	_	_	_
71	Ambion	Ambion	NNP	_	_	_
72	-RRB-	-rrb-	-RRB-	_	_	_
73	and	and	CC	_	_	_
74	lysed	lyse	VBN	_	_	_
75	by	by	IN	_	_	_
76	using	use	VBG	_	_	_
77	a	a	DT	_	_	_
78	bead	bead	NN	_	_	_
79	beater	beater	NN	_	_	_
80	-LRB-	-lrb-	-LRB-	_	_	_
81	BioSpec	BioSpec	NNP	_	_	_
82	Products	Products	NNPS	_	_	_
83	-RRB-	-rrb-	-RRB-	_	_	_
84	.	.	.	_	_	_

1	Cellular	cellular	JJ	_	_	_
2	debris	debris	NN	_	_	_
3	was	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	8,000	8,000	CD	_	_	_
9	g	g	NN	_	_	_
10	;	;	:	_	_	_
11	3	3	CD	_	_	_
12	min	min	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	nucleic	nucleic	JJ	_	_	_
3	acids	acid	NNS	_	_	_
4	were	be	VBD	_	_	_
5	precipitated	precipitate	VBN	_	_	_
6	with	with	IN	_	_	_
7	isopropanol	isopropanol	NN	_	_	_
8	and	and	CC	_	_	_
9	sodium	sodium	NN	SUPP	_	_
10	acetate	acetate	NN	SUPP	_	_
11	and	and	CC	_	_	_
12	resuspended	resuspend	VBN	_	_	_
13	in	in	IN	_	_	_
14	100	100	CD	_	_	_
15	ul	ul	NN	_	_	_
16	TE	TE	NNP	_	_	_
17	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	resuspension	resuspension	NN	_	_	_
3	was	be	VBD	_	_	_
4	further	further	JJ	_	_	_
5	purified	purify	VBN	_	_	_
6	with	with	IN	_	_	_
7	a	a	DT	_	_	_
8	Qiagen	Qiagen	NNP	_	_	_
9	PCR	pcr	NN	_	_	_
10	column	column	NN	_	_	_
11	and	and	CC	_	_	_
12	eluted	elute	VBN	_	_	_
13	into	into	IN	_	_	_
14	30	30	CD	_	_	_
15	ul	ul	NN	_	_	_
16	of	of	IN	_	_	_
17	EB	EB	NNP	_	_	_
18	buffer	buffer	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Fecal	fecal	JJ	_	_	_
3	samples	sample	NNS	_	_	_
4	obtained	obtain	VBN	_	_	_
5	from	from	IN	_	_	_
6	mice	mouse	NNS	_	_	_
7	were	be	VBD	_	_	_
8	immediately	immediately	RB	_	_	_
9	frozen	freeze	VBN	_	_	_
10	in	in	IN	_	_	_
11	liquid	liquid	JJ	_	_	_
12	nitrogen	nitrogen	NN	_	_	_
13	and	and	CC	_	_	_
14	stored	store	VBD	_	_	_
15	at	at	IN	_	_	_
16	-80	-80	CD	_	_	_
17	°C	°c	NN	_	_	_
18	until	until	IN	_	_	_
19	processing	processing	NN	_	_	_
20	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	samples	sample	NNS	_	_	_
5	were	be	VBD	_	_	_
6	treated	treat	VBN	_	_	_
7	with	with	IN	_	_	_
8	RNAProtect	rnaprotect	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Qiagen	qiagen	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	and	and	CC	_	_	_
13	suspended	suspend	VBN	_	_	_
14	in	in	IN	_	_	_
15	a	a	DT	_	_	_
16	solution	solution	NN	_	_	_
17	containing	contain	VBG	_	_	_
18	500	500	CD	_	_	_
19	μl	μl	NN	_	_	_
20	of	of	IN	_	_	_
21	acid-washed	acid-washed	JJ	_	_	_
22	glass	glass	NN	_	_	_
23	beads	bead	NNS	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Sigma-Aldrich	Sigma-Aldrich	NNP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	,	,	,	_	_	_
28	500	500	CD	_	_	_
29	μl	μl	NN	_	_	_
30	of	of	IN	_	_	_
31	extraction	extraction	NN	_	_	_
32	buffer	buffer	NN	_	_	_
33	A	a	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	200	200	CD	_	_	_
36	mM	mm	NN	KWSUPP	_	_
37	NaCl	nacl	NN	_	_	_
38	,	,	,	_	_	_
39	20	20	CD	_	_	_
40	mM	mm	NN	KWSUPP	_	_
41	EDTA	edta	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	,	,	,	_	_	_
44	210	210	CD	_	_	_
45	μl	μl	NN	_	_	_
46	of	of	IN	_	_	_
47	20	20	CD	_	_	_
48	%	%	NN	_	_	_
49	SDS	sds	NN	_	_	_
50	,	,	,	_	_	_
51	and	and	CC	_	_	_
52	500	500	CD	_	_	_
53	μl	μl	NN	_	_	_
54	of	of	IN	_	_	_
55	a	a	DT	_	_	_
56	mixture	mixture	NN	_	_	_
57	of	of	IN	_	_	_
58	phenol	phenol	NN	_	_	_
59	:	:	:	_	_	_
60	chloroform	chloroform	NN	_	_	_
61	:	:	:	_	_	_
62	isoamyl	isoamyl	NN	_	_	_
63	alcohol	alcohol	NN	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	125:24:1	125:24:1	CD	_	_	_
66	,	,	,	_	_	_
67	pH	ph	NN	_	_	_
68	4.5	4.5	CD	_	_	_
69	;	;	:	_	_	_
70	Ambion	Ambion	NNP	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	and	and	CC	_	_	_
73	lysed	lyse	VBN	_	_	_
74	by	by	IN	_	_	_
75	using	use	VBG	_	_	_
76	a	a	DT	_	_	_
77	bead	bead	NN	_	_	_
78	beater	beater	NN	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	BioSpec	BioSpec	NNP	_	_	_
81	Products	Products	NNPS	_	_	_
82	-RRB-	-rrb-	-RRB-	_	_	_
83	.	.	.	_	_	_

1	Cellular	cellular	JJ	_	_	_
2	debris	debris	NN	_	_	_
3	was	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	8,000	8,000	CD	_	_	_
9	×	×	CD	_	_	_
10	g	g	NN	_	_	_
11	;	;	:	_	_	_
12	3	3	CD	_	_	_
13	min	min	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	nucleic	nucleic	JJ	_	_	_
3	acids	acid	NNS	_	_	_
4	were	be	VBD	_	_	_
5	precipitated	precipitate	VBN	_	_	_
6	with	with	IN	_	_	_
7	isopropanol	isopropanol	NN	_	_	_
8	and	and	CC	_	_	_
9	sodium	sodium	NN	SUPP	_	_
10	acetate	acetate	NN	SUPP	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	pH	ph	NN	_	_	_
13	5.5	5.5	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Fecal	fecal	JJ	_	_	_
3	samples	sample	NNS	_	_	_
4	obtained	obtain	VBN	_	_	_
5	from	from	IN	_	_	_
6	mice	mouse	NNS	_	_	_
7	were	be	VBD	_	_	_
8	span	span	NN	_	_	_
9	frozen	freeze	VBN	_	_	_
10	in	in	IN	_	_	_
11	liquid	liquid	JJ	_	_	_
12	nitrogen	nitrogen	NN	_	_	_
13	and	and	CC	_	_	_
14	stored	store	VBD	_	_	_
15	at	at	IN	_	_	_
16	-80	-80	CD	_	_	_
17	¬	¬	CD	_	_	_
18	∞	∞	NN	_	_	_
19	C	c	NN	_	_	_
20	and	and	CC	_	_	_
21	maintained	maintain	VBD	_	_	_
22	at	at	IN	_	_	_
23	this	this	DT	_	_	_
24	temperature	temperature	NN	_	_	_
25	prior	prior	RB	_	_	_
26	to	to	TO	_	_	_
27	processing	processing	NN	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Libraries	Libraries	NNPS	_	_	_
3	were	be	VBD	_	_	_
4	prepared	prepared	JJ	_	_	_
5	according	accord	VBG	_	_	_
6	to	to	TO	_	_	_
7	Illumina	Illumina	NNP	_	_	_
8	's	's	POS	_	_	_
9	instructions	instruction	NNS	_	_	_
10	accompanying	accompany	VBG	_	_	_
11	the	the	DT	_	_	_
12	genomic	genomic	JJ	_	_	_
13	DNA	dna	NN	_	_	_
14	Sample	sample	NN	_	_	_
15	Kit	kit	NN	_	_	_
16	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	cDNA	cdna	NN	_	_	_
4	was	be	VBD	_	_	_
5	sonicated	sonicate	VBN	_	_	_
6	in	in	IN	_	_	_
7	a	a	DT	_	_	_
8	biorupter	biorupter	NN	_	_	_
9	sonicator	sonicator	NN	_	_	_
10	,	,	,	_	_	_
11	cleaned	clean	VBD	_	_	_
12	up	up	RP	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Libraries	Libraries	NNPS	_	_	_
15	were	be	VBD	_	_	_
16	prepared	prepared	JJ	_	_	_
17	according	accord	VBG	_	_	_
18	to	to	TO	_	_	_
19	Illumina	Illumina	NNP	_	_	_
20	's	's	POS	_	_	_
21	instructions	instruction	NNS	_	_	_
22	accompanying	accompany	VBG	_	_	_
23	the	the	DT	_	_	_
24	genomic	genomic	JJ	_	_	_
25	DNA	dna	NN	_	_	_
26	Sample	sample	NN	_	_	_
27	Kit	kit	NN	_	_	_
28	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	gDNA	gdna	NN	_	_	_
4	was	be	VBD	_	_	_
5	sonicated	sonicate	VBN	_	_	_
6	in	in	IN	_	_	_
7	a	a	DT	_	_	_
8	biorupter	biorupter	NN	_	_	_
9	sonicator	sonicator	NN	_	_	_
10	,	,	,	_	_	_
11	cleaned	clean	VBD	_	_	_
12	up	up	RP	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Marvinbryantia	Marvinbryantia	NNP	_	_	_
15	formatexigens	formatexigen	NNS	_	_	_
16	DSM	DSM	NNP	_	_	_
17	14469	14469	CD	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
19	mouse	mouse	NN	_	_	_
20	feces	fece	VBZ	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	OTHER	OTHER	NNP	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	RNA-Seq	rna-seq	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	rRNA	rrna	NN	_	_	_
27	depletion	depletion	NN	_	_	_
28	:	:	:	_	_	_
29	Genomic	genomic	JJ	_	_	_
30	DNA	dna	NN	_	_	_
31	was	be	VBD	_	_	_
32	removed	remove	VBN	_	_	_
33	with	with	IN	_	_	_
34	TURBO	TURBO	NNP	_	_	_
35	DNAse	dnase	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	Ambion	ambion	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	,	,	,	_	_	_
40	and	and	CC	_	_	_
41	then	then	RB	_	_	_
42	total	total	JJ	_	_	_
43	RNA	rna	NN	_	_	_
44	was	be	VBD	_	_	_
45	run	run	VBN	_	_	_
46	over	over	IN	_	_	_
47	two	two	CD	_	_	_
48	MEGAClear	megaclear	NN	_	_	_
49	columns	column	NNS	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	Ambion	Ambion	NNP	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	to	to	TO	_	_	_
54	deplete	deplete	VB	_	_	_
55	tRNAs	trna	NNS	_	_	_
56	and	and	CC	_	_	_
57	5S	5s	NN	_	_	_
58	rRNA	rrna	NN	_	_	_
59	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	between	between	IN	_	_	_
3	the	the	DT	_	_	_
4	two	two	CD	_	_	_
5	column	column	NN	_	_	_
6	purifications	purification	NNS	_	_	_
7	,	,	,	_	_	_
8	a	a	DT	_	_	_
9	second	second	JJ	_	_	_
10	DNAse	dnase	NN	_	_	_
11	digestion	digestion	NN	_	_	_
12	was	be	VBD	_	_	_
13	performed	perform	VBN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Baseline-ZERO	baseline-zero	JJ	_	_	_
16	Epicenter	epicenter	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

1	16S	16s	NN	_	_	_
2	and	and	CC	_	_	_
3	23S	23s	NN	_	_	_
4	rRNA	rrna	NN	_	_	_
5	were	be	VBD	_	_	_
6	depleted	deplete	VBN	_	_	_
7	using	use	VBG	_	_	_
8	MICROBExpress	microbexpress	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Ambion	ambion	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	and	and	CC	_	_	_
13	custom	custom	NN	_	_	_
14	depletion	depletion	NN	_	_	_
15	oligos	oligo	NNS	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Rey	Rey	NNP	_	_	_
18	et.al	et.al	NNP	_	_	_
19	.	.	.	_	_	_

1	2010	2010	CD	_	_	_
2	;	;	:	_	_	_
3	JBC	JBC	NNP	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	sample	sample	NN	_	_	_
3	source	source	NN	_	_	_
4	:	:	:	_	_	_
5	Fecal	fecal	JJ	_	_	_
6	pellet	pellet	NN	_	_	_
7	from	from	IN	_	_	_
8	a	a	DT	_	_	_
9	mouse	mouse	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	c57Bl6	c57bl6	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	colonized	colonize	VBN	_	_	_
14	with	with	IN	_	_	_
15	10-gut	10-gut	JJ	_	_	_
16	bacteria	bacterium	NNS	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	sample	sample	NN	_	_	_
19	source	source	NN	_	_	_
20	:	:	:	_	_	_
21	Fecal	fecal	JJ	_	_	_
22	pellet	pellet	NN	_	_	_
23	from	from	IN	_	_	_
24	a	a	DT	_	_	_
25	mouse	mouse	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	c57Bl6	c57bl6	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	colonized	colonize	VBN	_	_	_
30	with	with	IN	_	_	_
31	10-gut	10-gut	JJ	_	_	_
32	bacteria	bacterium	NNS	_	_	_
33	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	was	be	VBD	_	_	_
3	fed	feed	VBN	_	_	_
4	Harlan	Harlan	NNP	_	_	_
5	Teklad	Teklad	NNP	_	_	_
6	Diet	Diet	NNP	_	_	_
7	TD	TD	NNP	_	_	_
8	.09049	.09049	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	sample	sample	NN	_	_	_
11	source	source	NN	_	_	_
12	:	:	:	_	_	_
13	Fecal	fecal	JJ	_	_	_
14	pellet	pellet	NN	_	_	_
15	from	from	IN	_	_	_
16	a	a	DT	_	_	_
17	mouse	mouse	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	c57Bl6	c57bl6	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	colonized	colonize	VBN	_	_	_
22	with	with	IN	_	_	_
23	10-gut	10-gut	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	was	be	VBD	_	_	_
3	fed	feed	VBN	_	_	_
4	Harlan	Harlan	NNP	_	_	_
5	Teklad	Teklad	NNP	_	_	_
6	Diet	Diet	NNP	_	_	_
7	TD	TD	NNP	_	_	_
8	.09050	.09050	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	sample	sample	NN	_	_	_
11	source	source	NN	_	_	_
12	:	:	:	_	_	_
13	Fecal	fecal	JJ	_	_	_
14	pellet	pellet	NN	_	_	_
15	from	from	IN	_	_	_
16	a	a	DT	_	_	_
17	mouse	mouse	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	c57Bl6	c57bl6	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	colonized	colonize	VBN	_	_	_
22	with	with	IN	_	_	_
23	10-gut	10-gut	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	was	be	VBD	_	_	_
3	fed	feed	VBN	_	_	_
4	Harlan	Harlan	NNP	_	_	_
5	Teklad	Teklad	NNP	_	_	_
6	Diet	Diet	NNP	_	_	_
7	TD	TD	NNP	_	_	_
8	.09051	.09051	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	sample	sample	NN	_	_	_
11	source	source	NN	_	_	_
12	:	:	:	_	_	_
13	Fecal	fecal	JJ	_	_	_
14	pellet	pellet	NN	_	_	_
15	from	from	IN	_	_	_
16	a	a	DT	_	_	_
17	mouse	mouse	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	c57Bl6	c57bl6	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	colonized	colonize	VBN	_	_	_
22	with	with	IN	_	_	_
23	10-gut	10-gut	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	was	be	VBD	_	_	_
3	fed	feed	VBN	_	_	_
4	Harlan	Harlan	NNP	_	_	_
5	Teklad	Teklad	NNP	_	_	_
6	Diet	Diet	NNP	_	_	_
7	TD	TD	NNP	_	_	_
8	.09052	.09052	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	sample	sample	NN	_	_	_
11	source	source	NN	_	_	_
12	:	:	:	_	_	_
13	Fecal	fecal	JJ	_	_	_
14	pellet	pellet	NN	_	_	_
15	from	from	IN	_	_	_
16	a	a	DT	_	_	_
17	mouse	mouse	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	c57Bl6	c57bl6	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	colonized	colonize	VBN	_	_	_
22	with	with	IN	_	_	_
23	10-gut	10-gut	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	was	be	VBD	_	_	_
3	fed	feed	VBN	_	_	_
4	Harlan	Harlan	NNP	_	_	_
5	Teklad	Teklad	NNP	_	_	_
6	Diet	Diet	NNP	_	_	_
7	TD	TD	NNP	_	_	_
8	.09053	.09053	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	sample	sample	NN	_	_	_
11	source	source	NN	_	_	_
12	:	:	:	_	_	_
13	Fecal	fecal	JJ	_	_	_
14	pellet	pellet	NN	_	_	_
15	from	from	IN	_	_	_
16	a	a	DT	_	_	_
17	mouse	mouse	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	c57Bl6	c57bl6	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	colonized	colonize	VBN	_	_	_
22	with	with	IN	_	_	_
23	10-gut	10-gut	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	was	be	VBD	_	_	_
3	fed	feed	VBN	_	_	_
4	Harlan	Harlan	NNP	_	_	_
5	Teklad	Teklad	NNP	_	_	_
6	Diet	Diet	NNP	_	_	_
7	TD	TD	NNP	_	_	_
8	.09054	.09054	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	sample	sample	NN	_	_	_
11	source	source	NN	_	_	_
12	:	:	:	_	_	_
13	Fecal	fecal	JJ	_	_	_
14	pellet	pellet	NN	_	_	_
15	from	from	IN	_	_	_
16	a	a	DT	_	_	_
17	mouse	mouse	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	c57Bl6	c57bl6	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	colonized	colonize	VBN	_	_	_
22	with	with	IN	_	_	_
23	10-gut	10-gut	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	was	be	VBD	_	_	_
3	fed	feed	VBN	_	_	_
4	Harlan	Harlan	NNP	_	_	_
5	Teklad	Teklad	NNP	_	_	_
6	Diet	Diet	NNP	_	_	_
7	TD	TD	NNP	_	_	_
8	.09055	.09055	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	sample	sample	NN	_	_	_
11	source	source	NN	_	_	_
12	:	:	:	_	_	_
13	Fecal	fecal	JJ	_	_	_
14	pellet	pellet	NN	_	_	_
15	from	from	IN	_	_	_
16	a	a	DT	_	_	_
17	mouse	mouse	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	c57Bl6	c57bl6	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	colonized	colonize	VBN	_	_	_
22	with	with	IN	_	_	_
23	10-gut	10-gut	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	was	be	VBD	_	_	_
3	fed	feed	VBN	_	_	_
4	Harlan	Harlan	NNP	_	_	_
5	Teklad	Teklad	NNP	_	_	_
6	Diet	Diet	NNP	_	_	_
7	TD	TD	NNP	_	_	_
8	.09056	.09056	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	sample	sample	NN	_	_	_
11	source	source	NN	_	_	_
12	:	:	:	_	_	_
13	Fecal	fecal	JJ	_	_	_
14	pellet	pellet	NN	_	_	_
15	from	from	IN	_	_	_
16	a	a	DT	_	_	_
17	mouse	mouse	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	c57Bl6	c57bl6	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	colonized	colonize	VBN	_	_	_
22	with	with	IN	_	_	_
23	10-gut	10-gut	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	was	be	VBD	_	_	_
3	fed	feed	VBN	_	_	_
4	Harlan	Harlan	NNP	_	_	_
5	Teklad	Teklad	NNP	_	_	_
6	Diet	Diet	NNP	_	_	_
7	TD	TD	NNP	_	_	_
8	.09057	.09057	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	sample	sample	NN	_	_	_
11	source	source	NN	_	_	_
12	:	:	:	_	_	_
13	Fecal	fecal	JJ	_	_	_
14	pellet	pellet	NN	_	_	_
15	from	from	IN	_	_	_
16	a	a	DT	_	_	_
17	mouse	mouse	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	c57Bl6	c57bl6	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	colonized	colonize	VBN	_	_	_
22	with	with	IN	_	_	_
23	10-gut	10-gut	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	was	be	VBD	_	_	_
3	fed	feed	VBN	_	_	_
4	Harlan	Harlan	NNP	_	_	_
5	Teklad	Teklad	NNP	_	_	_
6	Diet	Diet	NNP	_	_	_
7	TD	TD	NNP	_	_	_
8	.09058	.09058	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	sample	sample	NN	_	_	_
11	source	source	NN	_	_	_
12	:	:	:	_	_	_
13	Fecal	fecal	JJ	_	_	_
14	pellet	pellet	NN	_	_	_
15	from	from	IN	_	_	_
16	a	a	DT	_	_	_
17	mouse	mouse	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	c57Bl6	c57bl6	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	colonized	colonize	VBN	_	_	_
22	with	with	IN	_	_	_
23	10-gut	10-gut	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	was	be	VBD	_	_	_
3	fed	feed	VBN	_	_	_
4	Harlan	Harlan	NNP	_	_	_
5	Teklad	Teklad	NNP	_	_	_
6	Diet	Diet	NNP	_	_	_
7	TD	TD	NNP	_	_	_
8	.09059	.09059	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	sample	sample	NN	_	_	_
11	source	source	NN	_	_	_
12	:	:	:	_	_	_
13	Fecal	fecal	JJ	_	_	_
14	pellet	pellet	NN	_	_	_
15	from	from	IN	_	_	_
16	a	a	DT	_	_	_
17	mouse	mouse	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	c57Bl6	c57bl6	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	colonized	colonize	VBN	_	_	_
22	with	with	IN	_	_	_
23	10-gut	10-gut	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	was	be	VBD	_	_	_
3	fed	feed	VBN	_	_	_
4	Harlan	Harlan	NNP	_	_	_
5	Teklad	Teklad	NNP	_	_	_
6	Diet	Diet	NNP	_	_	_
7	TD	TD	NNP	_	_	_
8	.09620	.09620	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	sample	sample	NN	_	_	_
11	source	source	NN	_	_	_
12	:	:	:	_	_	_
13	Fecal	fecal	JJ	_	_	_
14	pellet	pellet	NN	_	_	_
15	from	from	IN	_	_	_
16	a	a	DT	_	_	_
17	mouse	mouse	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	c57Bl6	c57bl6	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	colonized	colonize	VBN	_	_	_
22	with	with	IN	_	_	_
23	10-gut	10-gut	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	was	be	VBD	_	_	_
3	fed	feed	VBN	_	_	_
4	Harlan	Harlan	NNP	_	_	_
5	Teklad	Teklad	NNP	_	_	_
6	Diet	Diet	NNP	_	_	_
7	TD	TD	NNP	_	_	_
8	.09621	.09621	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	sample	sample	NN	_	_	_
11	source	source	NN	_	_	_
12	:	:	:	_	_	_
13	Fecal	fecal	JJ	_	_	_
14	pellet	pellet	NN	_	_	_
15	from	from	IN	_	_	_
16	a	a	DT	_	_	_
17	mouse	mouse	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	c57Bl6	c57bl6	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	colonized	colonize	VBN	_	_	_
22	with	with	IN	_	_	_
23	10-gut	10-gut	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	was	be	VBD	_	_	_
3	fed	feed	VBN	_	_	_
4	Harlan	Harlan	NNP	_	_	_
5	Teklad	Teklad	NNP	_	_	_
6	Diet	Diet	NNP	_	_	_
7	TD	TD	NNP	_	_	_
8	.09622	.09622	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	sample	sample	NN	_	_	_
11	source	source	NN	_	_	_
12	:	:	:	_	_	_
13	Fecal	fecal	JJ	_	_	_
14	pellet	pellet	NN	_	_	_
15	from	from	IN	_	_	_
16	a	a	DT	_	_	_
17	mouse	mouse	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	c57Bl6	c57bl6	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	colonized	colonize	VBN	_	_	_
22	with	with	IN	_	_	_
23	10-gut	10-gut	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	was	be	VBD	_	_	_
3	fed	feed	VBN	_	_	_
4	Harlan	Harlan	NNP	_	_	_
5	Teklad	Teklad	NNP	_	_	_
6	Diet	Diet	NNP	_	_	_
7	TD	TD	NNP	_	_	_
8	.09623	.09623	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	sample	sample	NN	_	_	_
11	source	source	NN	_	_	_
12	:	:	:	_	_	_
13	Fecal	fecal	JJ	_	_	_
14	pellet	pellet	NN	_	_	_
15	from	from	IN	_	_	_
16	a	a	DT	_	_	_
17	mouse	mouse	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	c57Bl6	c57bl6	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	colonized	colonize	VBN	_	_	_
22	with	with	IN	_	_	_
23	10-gut	10-gut	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	was	be	VBD	_	_	_
3	fed	feed	VBN	_	_	_
4	Harlan	Harlan	NNP	_	_	_
5	Teklad	Teklad	NNP	_	_	_
6	Diet	Diet	NNP	_	_	_
7	TD	TD	NNP	_	_	_
8	.09624	.09624	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	sample	sample	NN	_	_	_
11	source	source	NN	_	_	_
12	:	:	:	_	_	_
13	Fecal	fecal	JJ	_	_	_
14	pellet	pellet	NN	_	_	_
15	from	from	IN	_	_	_
16	a	a	DT	_	_	_
17	mouse	mouse	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	c57Bl6	c57bl6	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	colonized	colonize	VBN	_	_	_
22	with	with	IN	_	_	_
23	10-gut	10-gut	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	.	.	.	_	_	_

1	Mouse	mouse	NN	_	_	_
2	was	be	VBD	_	_	_
3	fed	feed	VBN	_	_	_
4	Harlan	Harlan	NNP	_	_	_
5	Teklad	Teklad	NNP	_	_	_
6	Diet	Diet	NNP	_	_	_
7	TD	TD	NNP	_	_	_
8	.09625	.09625	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	sample	sample	NN	_	_	_
11	source	source	NN	_	_	_
12	:	:	:	_	_	_
13	Fecal	fecal	JJ	_	_	_
14	pellet	pellet	NN	_	_	_
15	from	from	IN	_	_	_
16	a	a	DT	_	_	_
17	mouse	mouse	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	c57Bl6	c57bl6	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	colonized	colonize	VBN	_	_	_
22	with	with	IN	_	_	_
23	8-gut	8-gut	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	sample	sample	NN	_	_	_
27	source	source	NN	_	_	_
28	:	:	:	_	_	_
29	Fecal	fecal	JJ	_	_	_
30	pellet	pellet	NN	_	_	_
31	from	from	IN	_	_	_
32	a	a	DT	_	_	_
33	mouse	mouse	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	c57Bl6	c57bl6	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	colonized	colonize	VBN	_	_	_
38	with	with	IN	_	_	_
39	9-gut	9-gut	JJ	_	_	_
40	bacteria	bacterium	NNS	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	time	time	NN	_	_	_
43	:	:	:	_	_	_
44	Sample	sample	NN	_	_	_
45	was	be	VBD	_	_	_
46	taken	take	VBN	_	_	_
47	after	after	IN	_	_	_
48	mouse	mouse	NN	_	_	_
49	was	be	VBD	_	_	_
50	on	on	IN	_	_	_
51	the	the	DT	_	_	_
52	diet	diet	NN	_	_	_
53	for	for	IN	_	_	_
54	14	14	CD	_	_	_
55	days	day	NNS	_	_	_
56	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	time	time	NN	_	_	_
3	:	:	:	_	_	_
4	Sample	sample	NN	_	_	_
5	was	be	VBD	_	_	_
6	taken	take	VBN	_	_	_
7	after	after	IN	_	_	_
8	mouse	mouse	NN	_	_	_
9	was	be	VBD	_	_	_
10	on	on	IN	_	_	_
11	the	the	DT	_	_	_
12	diet	diet	NN	_	_	_
13	for	for	IN	_	_	_
14	1	1	CD	_	_	_
15	days	day	NNS	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	time	time	NN	_	_	_
3	:	:	:	_	_	_
4	Sample	sample	NN	_	_	_
5	was	be	VBD	_	_	_
6	taken	take	VBN	_	_	_
7	after	after	IN	_	_	_
8	mouse	mouse	NN	_	_	_
9	was	be	VBD	_	_	_
10	on	on	IN	_	_	_
11	the	the	DT	_	_	_
12	diet	diet	NN	_	_	_
13	for	for	IN	_	_	_
14	2	2	CD	_	_	_
15	days	day	NNS	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	time	time	NN	_	_	_
3	:	:	:	_	_	_
4	Sample	sample	NN	_	_	_
5	was	be	VBD	_	_	_
6	taken	take	VBN	_	_	_
7	after	after	IN	_	_	_
8	mouse	mouse	NN	_	_	_
9	was	be	VBD	_	_	_
10	on	on	IN	_	_	_
11	the	the	DT	_	_	_
12	diet	diet	NN	_	_	_
13	for	for	IN	_	_	_
14	4	4	CD	_	_	_
15	days	day	NNS	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	time	time	NN	_	_	_
3	:	:	:	_	_	_
4	Sample	sample	NN	_	_	_
5	was	be	VBD	_	_	_
6	taken	take	VBN	_	_	_
7	after	after	IN	_	_	_
8	mouse	mouse	NN	_	_	_
9	was	be	VBD	_	_	_
10	on	on	IN	_	_	_
11	the	the	DT	_	_	_
12	diet	diet	NN	_	_	_
13	for	for	IN	_	_	_
14	6	6	CD	_	_	_
15	days	day	NNS	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	time	time	NN	_	_	_
3	:	:	:	_	_	_
4	Sample	sample	NN	_	_	_
5	was	be	VBD	_	_	_
6	taken	take	VBN	_	_	_
7	after	after	IN	_	_	_
8	mouse	mouse	NN	_	_	_
9	was	be	VBD	_	_	_
10	on	on	IN	_	_	_
11	the	the	DT	_	_	_
12	diet	diet	NN	_	_	_
13	for	for	IN	_	_	_
14	7	7	CD	_	_	_
15	days	day	NNS	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	AW1	aw1	NN	_	_	_
3	.7	.7	CD	_	_	_
4	,	,	,	_	_	_
5	steady-state	steady-state	JJ	_	_	_
6	continuous	continuous	JJ	_	_	_
7	cultured	culture	VBN	_	_	_
8	experimental	experimental	JJ	_	_	_
9	samples	sample	NNS	_	_	_
10	at	at	IN	_	_	_
11	37	37	CD	_	_	_
12	°C	°c	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	AW1	aw1	NN	_	_	_
15	.7	.7	CD	_	_	_
16	,	,	,	_	_	_
17	steady-state	steady-state	JJ	_	_	_
18	continuous	continuous	JJ	_	_	_
19	cultured	culture	VBN	_	_	_
20	experimental	experimental	JJ	_	_	_
21	samples	sample	NNS	_	_	_
22	at	at	IN	_	_	_
23	37	37	CD	_	_	_
24	°C	°c	NN	_	_	_
25	and	and	CC	_	_	_
26	then	then	RB	_	_	_
27	15	15	CD	_	_	_
28	minutes	minute	NNS	_	_	_
29	heatshock	heatshock	NN	_	_	_
30	at	at	IN	_	_	_
31	50	50	CD	_	_	_
32	°C	°c	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Cultures	culture	NNS	_	_	_
35	were	be	VBD	_	_	_
36	inoculated	inoculate	VBN	_	_	_
37	from	from	IN	_	_	_
38	a	a	DT	_	_	_
39	single	single	JJ	_	_	_
40	colony	colony	NN	_	_	_
41	,	,	,	_	_	_
42	incubated	incubate	VBN	_	_	_
43	overnight	overnight	RB	_	_	_
44	,	,	,	_	_	_
45	sub-cultured	sub-cultured	JJ	_	_	_
46	with	with	IN	_	_	_
47	a	a	DT	_	_	_
48	1	1	CD	_	_	_
49	%	%	NN	_	_	_
50	inoculum	inoculum	NN	_	_	_
51	,	,	,	_	_	_
52	and	and	CC	_	_	_
53	grown	grow	VBN	_	_	_
54	to	to	TO	_	_	_
55	the	the	DT	_	_	_
56	late	late	JJ	_	_	_
57	exponential	exponential	JJ	_	_	_
58	growth	growth	NN	_	_	_
59	phase	phase	NN	_	_	_
60	,	,	,	_	_	_
61	corresponding	correspond	VBG	_	_	_
62	to	to	TO	_	_	_
63	an	a	DT	_	_	_
64	OD600	od600	NN	_	_	_
65	nm	nm	NN	_	_	_
66	of	of	IN	_	_	_
67	0.6	0.6	CD	_	_	_
68	--	--	:	_	_	_
69	0.7	0.7	CD	_	_	_
70	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
5	First	First	NNP	_	_	_
6	biological	biological	JJ	_	_	_
7	repeat	repeat	NN	_	_	_
8	37	37	CD	_	_	_
9	°C	°c	NN	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	First	First	NNP	_	_	_
12	biological	biological	JJ	_	_	_
13	repeat	repeat	NN	_	_	_
14	50	50	CD	_	_	_
15	°C	°c	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	For	for	IN	_	_	_
18	RNA	rna	NN	_	_	_
19	isolation	isolation	NN	_	_	_
20	,	,	,	_	_	_
21	0.5	0.5	CD	_	_	_
22	mL	ml	NN	_	_	_
23	of	of	IN	_	_	_
24	the	the	DT	_	_	_
25	cultures	culture	NNS	_	_	_
26	were	be	VBD	_	_	_
27	mixed	mix	VBN	_	_	_
28	with	with	IN	_	_	_
29	1	1	CD	_	_	_
30	mL	ml	NN	_	_	_
31	RNA	rna	NN	_	_	_
32	protect	protect	VBP	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	Qiagen	Qiagen	NNP	_	_	_
35	,	,	,	_	_	_
36	Ontario	Ontario	NNP	_	_	_
37	,	,	,	_	_	_
38	Canada	Canada	NNP	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	and	and	CC	_	_	_
41	RNA	rna	NN	_	_	_
42	was	be	VBD	_	_	_
43	isolated	isolate	VBN	_	_	_
44	using	use	VBG	_	_	_
45	the	the	DT	_	_	_
46	RNeasy	RNeasy	NNP	_	_	_
47	Mini	Mini	NNP	_	_	_
48	kit	kit	NN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	Qiagen	qiagen	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	quantified	quantify	VBN	_	_	_
4	with	with	IN	_	_	_
5	a	a	DT	_	_	_
6	Nanodrop	Nanodrop	NNP	_	_	_
7	Spectrophotometer	Spectrophotometer	NNP	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Thermo	Thermo	NNP	_	_	_
10	scientific	scientific	JJ	_	_	_
11	,	,	,	_	_	_
12	Wilmington	Wilmington	NNP	_	_	_
13	,	,	,	_	_	_
14	USA	USA	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	and	and	CC	_	_	_
17	RNA	rna	NN	_	_	_
18	quality	quality	NN	_	_	_
19	was	be	VBD	_	_	_
20	determined	determine	VBN	_	_	_
21	with	with	IN	_	_	_
22	a	a	DT	_	_	_
23	Bioanalyzer	Bioanalyzer	NNP	_	_	_
24	2100	2100	CD	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	Agilent	Agilent	NNP	_	_	_
27	Technologies	Technologies	NNPS	_	_	_
28	,	,	,	_	_	_
29	Santa	Santa	NNP	_	_	_
30	Clara	Clara	NNP	_	_	_
31	,	,	,	_	_	_
32	USA	USA	NNP	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	samples	sample	NNS	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	approximately	approximately	RB	_	_	_
5	30	30	CD	_	_	_
6	µg	µg	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	were	be	VBD	_	_	_
9	treated	treat	VBN	_	_	_
10	with	with	IN	_	_	_
11	1U	1u	NN	_	_	_
12	RNase	rnase	NN	_	_	_
13	free	free	JJ	_	_	_
14	DNase	dnase	NN	_	_	_
15	I	i	CD	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Ambion	Ambion	NNP	_	_	_
18	,	,	,	_	_	_
19	Ontario	Ontario	NNP	_	_	_
20	,	,	,	_	_	_
21	Canada	Canada	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	at	at	IN	_	_	_
24	37	37	CD	_	_	_
25	°C	°c	NN	_	_	_
26	for	for	IN	_	_	_
27	30	30	CD	_	_	_
28	min	min	NN	_	_	_
29	and	and	CC	_	_	_
30	1U	1u	NN	_	_	_
31	RNase	rnase	NN	_	_	_
32	inhibitor	inhibitor	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	Ambion	ambion	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	was	be	VBD	_	_	_
37	added	add	VBN	_	_	_
38	prior	prior	RB	_	_	_
39	to	to	TO	_	_	_
40	storage	storage	NN	_	_	_
41	at	at	IN	_	_	_
42	4	4	CD	_	_	_
43	°C	°c	NN	_	_	_
44	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	reverse-transcribed	reverse-transcribed	JJ	_	_	_
4	using	use	VBG	_	_	_
5	the	the	DT	_	_	_
6	Array	array	NN	_	_	_
7	900MPX	900mpx	NN	_	_	_
8	Expression	expression	NN	_	_	_
9	Array	array	NN	_	_	_
10	Detection	detection	NN	_	_	_
11	Kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Genisphere	Genisphere	NNP	_	_	_
14	,	,	,	_	_	_
15	Hatfield	Hatfield	NNP	_	_	_
16	,	,	,	_	_	_
17	USA	USA	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	according	accord	VBG	_	_	_
20	to	to	TO	_	_	_
21	the	the	DT	_	_	_
22	instructions	instruction	NNS	_	_	_
23	of	of	IN	_	_	_
24	the	the	DT	_	_	_
25	manufacturer	manufacturer	NN	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cDNA	cdna	NN	_	_	_
3	was	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	MinElute	MinElute	NNP	_	_	_
8	PCR	pcr	NN	_	_	_
9	Purification	purification	NN	_	_	_
10	Kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Quiagen	quiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	,	,	,	_	_	_
15	and	and	CC	_	_	_
16	the	the	DT	_	_	_
17	purified	purify	VBN	_	_	_
18	DNA	dna	NN	_	_	_
19	was	be	VBD	_	_	_
20	used	use	VBN	_	_	_
21	for	for	IN	_	_	_
22	microarray	microarray	NN	_	_	_
23	and	and	CC	_	_	_
24	qPCR	qpcr	NN	_	_	_
25	experiments	experiment	NNS	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	GGG10	ggg10	NN	_	_	_
3	,	,	,	_	_	_
4	steady-state	steady-state	JJ	_	_	_
5	continuous	continuous	JJ	_	_	_
6	cultured	culture	VBN	_	_	_
7	experimental	experimental	JJ	_	_	_
8	samples	sample	NNS	_	_	_
9	at	at	IN	_	_	_
10	37	37	CD	_	_	_
11	°C	°c	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	GGG10	ggg10	NN	_	_	_
14	,	,	,	_	_	_
15	steady-state	steady-state	JJ	_	_	_
16	continuous	continuous	JJ	_	_	_
17	cultured	culture	VBN	_	_	_
18	experimental	experimental	JJ	_	_	_
19	samples	sample	NNS	_	_	_
20	at	at	IN	_	_	_
21	37	37	CD	_	_	_
22	°C	°c	NN	_	_	_
23	and	and	CC	_	_	_
24	then	then	RB	_	_	_
25	15	15	CD	_	_	_
26	minutes	minute	NNS	_	_	_
27	heatshock	heatshock	NN	_	_	_
28	at	at	IN	_	_	_
29	50	50	CD	_	_	_
30	°C	°c	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	heat	heat	NN	_	_	_
33	sensitivity	sensitivity	NN	_	_	_
34	:	:	:	_	_	_
35	resistant	resistant	JJ	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	heat	heat	NN	_	_	_
38	sensitivity	sensitivity	NN	_	_	_
39	:	:	:	_	_	_
40	sensitive	sensitive	JJ	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
42	Raw	raw	NN	_	_	_
43	data	datum	NNS	_	_	_
44	were	be	VBD	_	_	_
45	normalized	normalize	VBN	_	_	_
46	and	and	CC	_	_	_
47	log2	log2	NN	_	_	_
48	transformed	transform	VBN	_	_	_
49	with	with	IN	_	_	_
50	the	the	DT	_	_	_
51	Acuity	acuity	NN	_	_	_
52	4.0	4.0	CD	_	_	_
53	software	software	NN	_	_	_
54	package	package	NN	_	_	_
55	,	,	,	_	_	_
56	and	and	CC	_	_	_
57	data	datum	NNS	_	_	_
58	with	with	IN	_	_	_
59	low	low	JJ	_	_	_
60	fluorescence	fluorescence	NN	_	_	_
61	intensities	intensity	NNS	_	_	_
62	were	be	VBD	_	_	_
63	eliminated	eliminate	VBN	_	_	_
64	.	.	.	_	_	_

1	Genes	gene	NNS	_	_	_
2	were	be	VBD	_	_	_
3	considered	consider	VBN	_	_	_
4	to	to	TO	_	_	_
5	be	be	VB	_	_	_
6	differentially	differentially	RB	_	_	_
7	expressed	express	VBN	_	_	_
8	if	if	IN	_	_	_
9	the	the	DT	_	_	_
10	absolute	absolute	JJ	_	_	_
11	values	value	NNS	_	_	_
12	of	of	IN	_	_	_
13	log2	log2	NN	_	_	_
14	mean	mean	NN	_	_	_
15	expression	expression	NN	_	_	_
16	ratios	ratio	NNS	_	_	_
17	were	be	VBD	_	_	_
18	≥	≥	CD	_	_	_
19	1	1	CD	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	from	from	IN	_	_	_
6	late	late	JJ	_	_	_
7	exponential	exponential	JJ	_	_	_
8	cultures	culture	NNS	_	_	_
9	,	,	,	_	_	_
10	or	or	CC	_	_	_
11	from	from	IN	_	_	_
12	late	late	JJ	_	_	_
13	exponential	exponential	JJ	_	_	_
14	cells	cell	NNS	_	_	_
15	heat-shocked	heat-shock	VBN	_	_	_
16	by	by	IN	_	_	_
17	exposure	exposure	NN	_	_	_
18	to	to	TO	_	_	_
19	50	50	CD	_	_	_
20	°C	°c	NN	_	_	_
21	for	for	IN	_	_	_
22	15	15	CD	_	_	_
23	min	min	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Second	Second	NNP	_	_	_
3	biological	biological	JJ	_	_	_
4	repeat	repeat	NN	_	_	_
5	37	37	CD	_	_	_
6	°C	°c	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Second	second	JJ	_	_	_
9	biological	biological	JJ	_	_	_
10	repeat	repeat	NN	_	_	_
11	50	50	CD	_	_	_
12	°C	°c	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	strain	strain	NN	_	_	_
15	:	:	:	_	_	_
16	AW1	aw1	NN	_	_	_
17	.7	.7	CD	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	strain	strain	NN	_	_	_
20	:	:	:	_	_	_
21	GGG10	ggg10	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	The	the	DT	_	_	_
24	data	datum	NNS	_	_	_
25	did	do	VBD	_	_	_
26	not	not	RB	_	_	_
27	undergo	undergo	VB	_	_	_
28	normalization	normalization	NN	_	_	_
29	across	across	IN	_	_	_
30	samples	sample	NNS	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Third	Third	NNP	_	_	_
3	biological	biological	JJ	_	_	_
4	repeat	repeat	NN	_	_	_
5	37	37	CD	_	_	_
6	°C	°c	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Third	third	JJ	_	_	_
9	biological	biological	JJ	_	_	_
10	repeat	repeat	NN	_	_	_
11	50	50	CD	_	_	_
12	°C	°c	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	treatment	treatment	NN	_	_	_
15	:	:	:	_	_	_
16	37	37	CD	_	_	_
17	°C	°c	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	treatment	treatment	NN	_	_	_
20	:	:	:	_	_	_
21	50	50	CD	_	_	_
22	°C	°c	NN	_	_	_
23	heatshock	heatshock	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	agent	agent	NN	_	_	_
26	:	:	:	_	_	_
27	0.05	0.05	CD	_	_	_
28	mg	mg	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	agent	agent	NN	_	_	_
31	:	:	:	_	_	_
32	control	control	NN	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	E.	E.	NNP	_	_	_
35	coli	coli	NN	_	_	_
36	O157	o157	NN	_	_	_
37	:	:	:	_	_	_
38	H7	h7	NN	_	_	_
39	EDL933	edl933	NN	_	_	_
40	in	in	IN	_	_	_
41	LB	lb	NN	_	_	_
42	at	at	IN	_	_	_
43	37oC	37oc	NN	_	_	_
44	at	at	IN	_	_	_
45	7	7	CD	_	_	_
46	hrs	hr	NNS	_	_	_
47	incubation	incubation	NN	_	_	_
48	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
49	E.	E.	NNP	_	_	_
50	coli	coli	NN	_	_	_
51	O157	o157	NN	_	_	_
52	:	:	:	_	_	_
53	H7	h7	NN	_	_	_
54	EDL933	edl933	NN	_	_	_
55	in	in	IN	_	_	_
56	LB	lb	NN	_	_	_
57	at	at	IN	_	_	_
58	37oC	37oc	NN	_	_	_
59	at	at	IN	_	_	_
60	7	7	CD	_	_	_
61	hrs	hr	NNS	_	_	_
62	incubation	incubation	NN	_	_	_
63	with	with	IN	_	_	_
64	phloretin	phloretin	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	E.	e.	FW	_	_	_
67	coli	coli	FW	_	_	_
68	O157	o157	NN	_	_	_
69	:	:	:	_	_	_
70	H7	h7	NN	_	_	_
71	EDL933	edl933	NN	_	_	_
72	was	be	VBD	_	_	_
73	inoculated	inoculate	VBN	_	_	_
74	in	in	IN	_	_	_
75	25	25	CD	_	_	_
76	ml	ml	NN	_	_	_
77	of	of	IN	_	_	_
78	LB	lb	NN	_	_	_
79	in	in	IN	_	_	_
80	250	250	CD	_	_	_
81	ml	ml	NN	_	_	_
82	shake	shake	NN	_	_	_
83	flasks	flask	NNS	_	_	_
84	with	with	IN	_	_	_
85	overnight	overnight	JJ	_	_	_
86	cultures	culture	NNS	_	_	_
87	that	that	WDT	_	_	_
88	were	be	VBD	_	_	_
89	diluted	dilute	VBN	_	_	_
90	1:100	1:100	CD	_	_	_
91	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	shaken	shake	VBN	_	_	_
4	at	at	IN	_	_	_
5	100	100	CD	_	_	_
6	rpm	rpm	NN	_	_	_
7	and	and	CC	_	_	_
8	37	37	CD	_	_	_
9	°C	°c	NN	_	_	_
10	for	for	IN	_	_	_
11	7	7	CD	_	_	_
12	hrs	hr	NNS	_	_	_
13	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	immediately	immediately	RB	_	_	_
4	chilled	chill	VBN	_	_	_
5	with	with	IN	_	_	_
6	dry	dry	JJ	_	_	_
7	ice	ice	NN	_	_	_
8	and	and	CC	_	_	_
9	95	95	CD	_	_	_
10	%	%	NN	_	_	_
11	ethanol	ethanol	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	to	to	TO	_	_	_
14	prevent	prevent	VB	_	_	_
15	RNA	rna	NN	_	_	_
16	degradation	degradation	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	for	for	IN	_	_	_
19	30	30	CD	_	_	_
20	sec	sec	NN	_	_	_
21	before	before	IN	_	_	_
22	centrifugation	centrifugation	NN	_	_	_
23	in	in	IN	_	_	_
24	50	50	CD	_	_	_
25	ml	ml	NN	_	_	_
26	centrifuge	centrifuge	NN	_	_	_
27	tubes	tube	NNS	_	_	_
28	at	at	IN	_	_	_
29	13,000	13,000	CD	_	_	_
30	g	g	NN	_	_	_
31	for	for	IN	_	_	_
32	2	2	CD	_	_	_
33	min	min	NN	_	_	_
34	;	;	:	_	_	_
35	cell	cell	NN	_	_	_
36	pellets	pellet	NNS	_	_	_
37	were	be	VBD	_	_	_
38	frozen	frozen	JJ	_	_	_
39	immediately	immediately	RB	_	_	_
40	with	with	IN	_	_	_
41	dry	dry	JJ	_	_	_
42	ice	ice	NN	_	_	_
43	and	and	CC	_	_	_
44	stored	store	VBD	_	_	_
45	-80	-80	CD	_	_	_
46	°C	°c	NN	_	_	_
47	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	isolated	isolate	VBN	_	_	_
4	using	use	VBG	_	_	_
5	Qiagen	Qiagen	NNP	_	_	_
6	RNeasy	RNeasy	NNP	_	_	_
7	mini	minus	NNS	_	_	_
8	Kit	kit	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Cat	cat	NN	_	_	_
11	#	#	#	_	_	_
12	74104	74104	CD	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	with	with	IN	_	_	_
15	Qiagen	Qiagen	NNP	_	_	_
16	RNase-free	RNase-free	NNP	_	_	_
17	DNase	dnase	NN	_	_	_
18	I	i	CD	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Cat	cat	NN	_	_	_
21	#	#	#	_	_	_
22	79254	79254	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
5	MAS	mas	FW	_	_	_
6	5.0	5.0	CD	_	_	_
7	Expression	expression	NN	_	_	_
8	Analysis	analysis	NN	_	_	_
9	Default	Default	NNP	_	_	_
10	Setting	Setting	NNP	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	rna	rna	NN	GEN	_	_
13	extracted	extract	VBN	_	_	_
14	from	from	IN	_	_	_
15	e.	e.	FW	_	_	_
16	coli	coli	FW	_	_	_
17	o157	o157	NN	_	_	_
18	:	:	:	_	_	_
19	H7	h7	NN	_	_	_
20	EDL933	edl933	NN	_	_	_
21	cells	cell	NNS	_	_	_
22	grown	grow	VBN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	7	7	CD	_	_	_
25	hrs	hr	NNS	_	_	_
26	incubation	incubation	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	in	in	IN	_	_	_
29	LB	lb	NN	_	_	_
30	at	at	IN	_	_	_
31	37ºC	37ºc	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	rna	rna	NN	GEN	_	_
34	extracted	extract	VBN	_	_	_
35	from	from	IN	_	_	_
36	e.	e.	FW	_	_	_
37	coli	coli	FW	_	_	_
38	o157	o157	NN	_	_	_
39	:	:	:	_	_	_
40	H7	h7	NN	_	_	_
41	EDL933	edl933	NN	_	_	_
42	cells	cell	NNS	_	_	_
43	grown	grow	VBN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	7	7	CD	_	_	_
46	hrs	hr	NNS	_	_	_
47	incubation	incubation	NN	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	in	in	IN	_	_	_
50	LB	lb	NN	_	_	_
51	at	at	IN	_	_	_
52	37ºC	37ºc	NN	_	_	_
53	with	with	IN	_	_	_
54	0.05	0.05	CD	_	_	_
55	mg	mg	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	agent	agent	NN	_	_	_
58	:	:	:	_	_	_
59	0.5	0.5	CD	_	_	_
60	%	%	NN	_	_	_
61	honey	honey	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	agent	agent	NN	_	_	_
64	:	:	:	_	_	_
65	control	control	NN	_	_	_
66	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
67	E.	E.	NNP	_	_	_
68	coli	coli	NN	_	_	_
69	O157	o157	NN	_	_	_
70	:	:	:	_	_	_
71	H7	h7	NN	_	_	_
72	EDL933	edl933	NN	_	_	_
73	in	in	IN	_	_	_
74	LB	lb	NN	_	_	_
75	at	at	IN	_	_	_
76	37oC	37oc	NN	_	_	_
77	for	for	IN	_	_	_
78	7	7	CD	_	_	_
79	hrs	hr	NNS	_	_	_
80	incubation	incubation	NN	_	_	_
81	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
82	E.	E.	NNP	_	_	_
83	coli	coli	NN	_	_	_
84	O157	o157	NN	_	_	_
85	:	:	:	_	_	_
86	H7	h7	NN	_	_	_
87	EDL933	edl933	NN	_	_	_
88	in	in	IN	_	_	_
89	LB	lb	NN	_	_	_
90	at	at	IN	_	_	_
91	37oC	37oc	NN	_	_	_
92	for	for	IN	_	_	_
93	7	7	CD	_	_	_
94	hrs	hr	NNS	_	_	_
95	incubation	incubation	NN	_	_	_
96	with	with	IN	_	_	_
97	honey	honey	NN	_	_	_
98	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
99	E.	E.	NNP	_	_	_
100	coli	coli	NN	_	_	_
101	O157	o157	NN	_	_	_
102	:	:	:	_	_	_
103	H7	h7	NN	_	_	_
104	EDL933	edl933	NN	_	_	_
105	was	be	VBD	_	_	_
106	inoculated	inoculate	VBN	_	_	_
107	in	in	IN	_	_	_
108	250	250	CD	_	_	_
109	ml	ml	NN	_	_	_
110	of	of	IN	_	_	_
111	LB	lb	NN	_	_	_
112	in	in	IN	_	_	_
113	1000	1000	CD	_	_	_
114	ml	ml	NN	_	_	_
115	shake	shake	NN	_	_	_
116	flasks	flask	NNS	_	_	_
117	with	with	IN	_	_	_
118	overnight	overnight	JJ	_	_	_
119	cultures	culture	NNS	_	_	_
120	that	that	WDT	_	_	_
121	were	be	VBD	_	_	_
122	diluted	dilute	VBN	_	_	_
123	1:100	1:100	CD	_	_	_
124	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	shaken	shake	VBN	_	_	_
4	with	with	IN	_	_	_
5	10	10	CD	_	_	_
6	g	g	NN	_	_	_
7	of	of	IN	_	_	_
8	glass	glass	NN	_	_	_
9	wool	wool	NN	_	_	_
10	at	at	IN	_	_	_
11	100	100	CD	_	_	_
12	rpm	rpm	NN	_	_	_
13	and	and	CC	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	for	for	IN	_	_	_
17	7	7	CD	_	_	_
18	hrs	hr	NNS	_	_	_
19	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	immediately	immediately	RB	_	_	_
4	chilled	chill	VBN	_	_	_
5	with	with	IN	_	_	_
6	dry	dry	JJ	_	_	_
7	ice	ice	NN	_	_	_
8	and	and	CC	_	_	_
9	95	95	CD	_	_	_
10	%	%	NN	_	_	_
11	ethanol	ethanol	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	to	to	TO	_	_	_
14	prevent	prevent	VB	_	_	_
15	RNA	rna	NN	_	_	_
16	degradation	degradation	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	for	for	IN	_	_	_
19	30	30	CD	_	_	_
20	sec	sec	NN	_	_	_
21	before	before	IN	_	_	_
22	centrifugation	centrifugation	NN	_	_	_
23	in	in	IN	_	_	_
24	50	50	CD	_	_	_
25	ml	ml	NN	_	_	_
26	centrifuge	centrifuge	NN	_	_	_
27	tubes	tube	NNS	_	_	_
28	at	at	IN	_	_	_
29	13,000	13,000	CD	_	_	_
30	g	g	NN	_	_	_
31	for	for	IN	_	_	_
32	2	2	CD	_	_	_
33	min	min	NN	_	_	_
34	;	;	:	_	_	_
35	cell	cell	NN	_	_	_
36	pellets	pellet	NNS	_	_	_
37	were	be	VBD	_	_	_
38	frozen	frozen	JJ	_	_	_
39	immediately	immediately	RB	_	_	_
40	with	with	IN	_	_	_
41	dry	dry	JJ	_	_	_
42	ice	ice	NN	_	_	_
43	and	and	CC	_	_	_
44	stored	store	VBD	_	_	_
45	-80	-80	CD	_	_	_
46	°C	°c	NN	_	_	_
47	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	isolated	isolate	VBN	_	_	_
4	using	use	VBG	_	_	_
5	Qiagen	Qiagen	NNP	_	_	_
6	RNeasy	RNeasy	NNP	_	_	_
7	mini	minus	NNS	_	_	_
8	Kit	kit	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Cat	cat	NN	_	_	_
11	#	#	#	_	_	_
12	74104	74104	CD	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	with	with	IN	_	_	_
15	Qiagen	Qiagen	NNP	_	_	_
16	RNase-free	RNase-free	NNP	_	_	_
17	DNase	dnase	NN	_	_	_
18	I	i	CD	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Cat	cat	NN	_	_	_
21	#	#	#	_	_	_
22	79254	79254	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
5	MAS	mas	FW	_	_	_
6	5.0	5.0	CD	_	_	_
7	Expression	expression	NN	_	_	_
8	Analysis	analysis	NN	_	_	_
9	Default	Default	NNP	_	_	_
10	Setting	Setting	NNP	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	rna	rna	NN	GEN	_	_
13	extracted	extract	VBN	_	_	_
14	from	from	IN	_	_	_
15	e.	e.	FW	_	_	_
16	coli	coli	FW	_	_	_
17	o157	o157	NN	_	_	_
18	:	:	:	_	_	_
19	H7	h7	NN	_	_	_
20	EDL933	edl933	NN	_	_	_
21	cells	cell	NNS	_	_	_
22	grown	grow	VBN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	7	7	CD	_	_	_
25	hrs	hr	NNS	_	_	_
26	incubation	incubation	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	in	in	IN	_	_	_
29	LB	lb	NN	_	_	_
30	at	at	IN	_	_	_
31	37ºC	37ºc	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	rna	rna	NN	GEN	_	_
34	extracted	extract	VBN	_	_	_
35	from	from	IN	_	_	_
36	e.	e.	FW	_	_	_
37	coli	coli	FW	_	_	_
38	o157	o157	NN	_	_	_
39	:	:	:	_	_	_
40	H7	h7	NN	_	_	_
41	EDL933	edl933	NN	_	_	_
42	cells	cell	NNS	_	_	_
43	grown	grow	VBN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	7	7	CD	_	_	_
46	hrs	hr	NNS	_	_	_
47	incubation	incubation	NN	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	in	in	IN	_	_	_
50	LB	lb	NN	_	_	_
51	at	at	IN	_	_	_
52	37ºC	37ºc	NN	_	_	_
53	with	with	IN	_	_	_
54	0.5	0.5	CD	_	_	_
55	%	%	NN	_	_	_
56	honey	honey	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Cells	cell	NNS	_	_	_
59	were	be	VBD	_	_	_
60	transferred	transfer	VBN	_	_	_
61	to	to	TO	_	_	_
62	the	the	DT	_	_	_
63	fresh	fresh	JJ	_	_	_
64	minimal	minimal	JJ	_	_	_
65	media	media	NNS	_	_	_
66	,	,	,	_	_	_
67	mM63	mm63	NN	_	_	_
68	,	,	,	_	_	_
69	in	in	IN	_	_	_
70	the	the	DT	_	_	_
71	presence	presence	NN	_	_	_
72	or	or	CC	_	_	_
73	absence	absence	NN	_	_	_
74	of	of	IN	_	_	_
75	histidine	histidine	NN	_	_	_
76	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	initial	initial	JJ	_	_	_
3	cell	cell	NN	_	_	_
4	concentrations	concentration	NNS	_	_	_
5	were	be	VBD	_	_	_
6	controlled	control	VBN	_	_	_
7	as	as	IN	_	_	_
8	104-105	104-105	CD	_	_	_
9	cells	cell	NNS	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Control	Control	NNP	_	_	_
12	strain	strain	NN	_	_	_
13	exponentially	exponentially	RB	_	_	_
14	grown	grow	VBN	_	_	_
15	in	in	IN	_	_	_
16	the	the	DT	_	_	_
17	absence	absence	NN	_	_	_
18	of	of	IN	_	_	_
19	histidine	histidine	NN	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	Control	Control	NNP	_	_	_
22	strain	strain	NN	_	_	_
23	exponentially	exponentially	RB	_	_	_
24	grown	grow	VBN	_	_	_
25	in	in	IN	_	_	_
26	the	the	DT	_	_	_
27	presence	presence	NN	_	_	_
28	of	of	IN	_	_	_
29	histidine	histidine	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	1	1	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	Escherichia	escherichia	FW	Organism	_	_
36	coli	coli	FW	Organism	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	genotype	genotype	NN	_	_	_
39	:	:	:	_	_	_
40	DH1	dh1	NN	_	_	_
41	ΔhisC	δhisc	NN	_	_	_
42	:	:	:	_	_	_
43	:	:	:	_	_	_
44	cat	cat	NN	_	_	_
45	ΔintC	δintc	NN	_	_	_
46	:	:	:	_	_	_
47	:	:	:	_	_	_
48	Ptrc-rfp-tetR-zeocinr	Ptrc-rfp-tetR-zeocinr	NNP	_	_	_
49	ΔgalK	ΔgalK	NNP	_	_	_
50	:	:	:	_	_	_
51	:	:	:	_	_	_
52	PtetA-gfp-hisC-kanr	PtetA-gfp-hisC-kanr	NNP	_	_	_
53	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
54	genotype	genotype	NN	_	_	_
55	:	:	:	_	_	_
56	DH1	dh1	NN	_	_	_
57	ΔhisC	δhisc	NN	_	_	_
58	:	:	:	_	_	_
59	:	:	:	_	_	_
60	cat	cat	NN	_	_	_
61	ΔintC	δintc	NN	_	_	_
62	:	:	:	_	_	_
63	:	:	:	_	_	_
64	Ptrc-rfp-tetR-zeocinr	Ptrc-rfp-tetR-zeocinr	NNP	_	_	_
65	ΔgalK	ΔgalK	NNP	_	_	_
66	:	:	:	_	_	_
67	:	:	:	_	_	_
68	PtetA-gfp-kanr	PtetA-gfp-kanr	NNP	_	_	_
69	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
70	HisC	hisc	NN	_	_	_
71	rewired	rewire	VBD	_	_	_
72	strain	strain	NN	_	_	_
73	exponentially	exponentially	RB	_	_	_
74	grown	grow	VBN	_	_	_
75	in	in	IN	_	_	_
76	the	the	DT	_	_	_
77	absence	absence	NN	_	_	_
78	of	of	IN	_	_	_
79	histidine	histidine	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	HisC	hisc	NN	_	_	_
82	rewired	rewire	VBD	_	_	_
83	strain	strain	NN	_	_	_
84	exponentially	exponentially	RB	_	_	_
85	grown	grow	VBN	_	_	_
86	in	in	IN	_	_	_
87	the	the	DT	_	_	_
88	presence	presence	NN	_	_	_
89	of	of	IN	_	_	_
90	histidine	histidine	NN	_	_	_
91	-LRB-	-lrb-	-LRB-	_	_	_
92	1	1	CD	_	_	_
93	mM	mm	NN	KWSUPP	_	_
94	-RRB-	-rrb-	-RRB-	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	log10	log10	NN	_	_	_
97	mRNA	mrna	NN	_	_	_
98	concentration	concentration	NN	_	_	_
99	-LRB-	-lrb-	-LRB-	_	_	_
100	pM	pm	NN	_	_	_
101	-RRB-	-rrb-	-RRB-	_	_	_
102	data	datum	NNS	_	_	_
103	are	be	VBP	_	_	_
104	provided	provide	VBN	_	_	_
105	as	as	IN	_	_	_
106	a	a	DT	_	_	_
107	supplementary	supplementary	JJ	_	_	_
108	file	file	NN	_	_	_
109	on	on	IN	_	_	_
110	the	the	DT	_	_	_
111	SERIES	series	NN	_	_	_
112	record	record	NN	_	_	_
113	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Microarray	Microarray	NNP	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	processed	process	VBN	_	_	_
6	using	use	VBG	_	_	_
7	custom	custom	NN	_	_	_
8	scripts	script	NNS	_	_	_
9	written	write	VBN	_	_	_
10	in	in	IN	_	_	_
11	R	r	NN	_	_	_
12	based	base	VBN	_	_	_
13	on	on	IN	_	_	_
14	the	the	DT	_	_	_
15	finite	finite	JJ	_	_	_
16	hybridisation	hybridisation	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	FH	fh	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	model	model	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Ono	Ono	NNP	_	_	_
23	et	et	FW	_	_	_
24	al	al	FW	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	2008	2008	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	An	a	DT	_	_	_
29	improved	improve	VBN	_	_	_
30	physico-chemical	physico-chemical	JJ	_	_	_
31	model	model	NN	_	_	_
32	of	of	IN	_	_	_
33	hybridization	hybridization	NN	_	_	_
34	on	on	IN	_	_	_
35	high-density	high-density	JJ	_	_	_
36	oligonucleotide	oligonucleotide	NN	_	_	_
37	microarrays	microarray	NNS	_	_	_
38	.	.	.	_	_	_

1	Bioinformatics	bioinformatic	NNS	_	_	_
2	24	24	CD	_	_	_
3	:	:	:	_	_	_
4	1278-1285	1278-1285	CD	_	_	_
5	.	.	.	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_

1	and	and	CC	_	_	_
2	the	the	DT	_	_	_
3	thermodynamic	thermodynamic	JJ	_	_	_
4	model	model	NN	_	_	_
5	of	of	IN	_	_	_
6	non-specific	non-specific	JJ	_	_	_
7	binding	binding	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	NSB	nsb	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	on	on	IN	_	_	_
12	short	short	JJ	_	_	_
13	nucleotide	nucleotide	NN	_	_	_
14	microarrays	microarray	NNS	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Furusawa	Furusawa	NNP	_	_	_
17	et	et	FW	_	_	_
18	al	al	FW	_	_	_
19	,	,	,	_	_	_
20	2009	2009	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	OSU11	osu11	NN	_	_	_
3	,	,	,	_	_	_
4	nurishment	nurishment	NN	_	_	_
5	,	,	,	_	_	_
6	biological	biological	JJ	_	_	_
7	rep	rep	NN	GEN	_	_
8	1	1	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	OSU11	osu11	NN	_	_	_
11	,	,	,	_	_	_
12	nurishment	nurishment	NN	_	_	_
13	,	,	,	_	_	_
14	biological	biological	JJ	_	_	_
15	rep	rep	NN	GEN	_	_
16	2	2	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	OSU11	osu11	NN	_	_	_
19	,	,	,	_	_	_
20	nurishment	nurishment	NN	_	_	_
21	,	,	,	_	_	_
22	biological	biological	JJ	_	_	_
23	rep	rep	NN	GEN	_	_
24	3	3	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	OSU11	osu11	NN	_	_	_
27	,	,	,	_	_	_
28	starved	starve	VBN	_	_	_
29	,	,	,	_	_	_
30	biological	biological	JJ	_	_	_
31	rep	rep	NN	GEN	_	_
32	1	1	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	OSU11	osu11	NN	_	_	_
35	,	,	,	_	_	_
36	starved	starve	VBN	_	_	_
37	,	,	,	_	_	_
38	biological	biological	JJ	_	_	_
39	rep	rep	NN	GEN	_	_
40	2	2	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	OSU11	osu11	NN	_	_	_
43	,	,	,	_	_	_
44	starved	starve	VBN	_	_	_
45	,	,	,	_	_	_
46	biological	biological	JJ	_	_	_
47	rep	rep	NN	GEN	_	_
48	3	3	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	OSU12-hisC	osu12-hisc	NN	_	_	_
51	,	,	,	_	_	_
52	nurishment	nurishment	NN	_	_	_
53	,	,	,	_	_	_
54	biological	biological	JJ	_	_	_
55	rep	rep	NN	GEN	_	_
56	1	1	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	OSU12-hisC	osu12-hisc	NN	_	_	_
59	,	,	,	_	_	_
60	nurishment	nurishment	NN	_	_	_
61	,	,	,	_	_	_
62	biological	biological	JJ	_	_	_
63	rep	rep	NN	GEN	_	_
64	2	2	CD	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	OSU12-hisC	osu12-hisc	NN	_	_	_
67	,	,	,	_	_	_
68	nurishment	nurishment	NN	_	_	_
69	,	,	,	_	_	_
70	biological	biological	JJ	_	_	_
71	rep	rep	NN	GEN	_	_
72	3	3	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	OSU12-hisC	osu12-hisc	NN	_	_	_
75	,	,	,	_	_	_
76	starved	starve	VBN	_	_	_
77	,	,	,	_	_	_
78	biological	biological	JJ	_	_	_
79	rep	rep	NN	GEN	_	_
80	1	1	CD	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	OSU12-hisC	osu12-hisc	NN	_	_	_
83	,	,	,	_	_	_
84	starved	starve	VBN	_	_	_
85	,	,	,	_	_	_
86	biological	biological	JJ	_	_	_
87	rep	rep	NN	GEN	_	_
88	2	2	CD	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	OSU12-hisC	osu12-hisc	NN	_	_	_
91	,	,	,	_	_	_
92	starved	starve	VBN	_	_	_
93	,	,	,	_	_	_
94	biological	biological	JJ	_	_	_
95	rep	rep	NN	GEN	_	_
96	3	3	CD	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	platform	platform	NN	_	_	_
99	_	_	CD	_	_	_
100	id	id	NN	_	_	_
101	design	design	NN	_	_	_
102	:	:	:	_	_	_
103	EcFS	ecfs	NN	_	_	_
104	_	_	NN	_	_	_
105	1	1	CD	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	platform	platform	NN	_	_	_
108	_	_	CD	_	_	_
109	id	id	NN	_	_	_
110	design	design	NN	_	_	_
111	:	:	:	_	_	_
112	EcFS	ecfs	NN	_	_	_
113	_	_	NN	_	_	_
114	2	2	CD	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
116	The	the	DT	_	_	_
117	cell	cell	NN	_	_	_
118	culture	culture	NN	_	_	_
119	was	be	VBD	_	_	_
120	put	put	VBN	_	_	_
121	into	into	IN	_	_	_
122	cold	cold	JJ	_	_	_
123	phenol-ethanol	phenol-ethanol	JJ	_	_	_
124	solution	solution	NN	_	_	_
125	-LRB-	-lrb-	-LRB-	_	_	_
126	1	1	CD	_	_	_
127	g	g	NN	_	_	_
128	of	of	IN	_	_	_
129	phenol	phenol	NN	_	_	_
130	in	in	IN	_	_	_
131	10	10	CD	_	_	_
132	mL	ml	NN	_	_	_
133	of	of	IN	_	_	_
134	ethanol	ethanol	NN	_	_	_
135	-RRB-	-rrb-	-RRB-	_	_	_
136	prepared	prepare	VBN	_	_	_
137	in	in	IN	_	_	_
138	advance	advance	NN	_	_	_
139	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	collected	collect	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	at	at	IN	_	_	_
8	16,000	16,000	CD	_	_	_
9	×	×	CD	_	_	_
10	g	g	NN	_	_	_
11	for	for	IN	_	_	_
12	5	5	CD	_	_	_
13	min	min	NN	_	_	_
14	at	at	IN	_	_	_
15	4	4	CD	_	_	_
16	°C	°c	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	the	the	DT	_	_	_
20	pelleted	pelleted	JJ	_	_	_
21	cells	cell	NNS	_	_	_
22	were	be	VBD	_	_	_
23	stored	store	VBN	_	_	_
24	at	at	IN	_	_	_
25	--	--	:	_	_	_
26	80	80	CD	_	_	_
27	°C	°c	NN	_	_	_
28	prior	prior	RB	_	_	_
29	to	to	TO	_	_	_
30	use	use	VB	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNAs	rna	NNS	_	_	_
4	were	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	an	a	DT	_	_	_
8	RNeasy	rneasy	NN	_	_	_
9	mini	minus	NNS	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	qiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	in	in	IN	_	_	_
15	accordance	accordance	NN	_	_	_
16	with	with	IN	_	_	_
17	the	the	DT	_	_	_
18	manufacturer	manufacturer	NN	_	_	_
19	's	's	POS	_	_	_
20	instructions	instruction	NNS	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	10	10	CD	_	_	_
3	ml	ml	NN	_	_	_
4	of	of	IN	_	_	_
5	cell	cell	NN	_	_	_
6	culture	culture	NN	_	_	_
7	was	be	VBD	_	_	_
8	mixed	mix	VBN	_	_	_
9	with	with	IN	_	_	_
10	5	5	CD	_	_	_
11	ml	ml	NN	_	_	_
12	ice	ice	NN	_	_	_
13	cold	cold	JJ	_	_	_
14	killing	killing	NN	_	_	_
15	buffer	buffer	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	20mM	20mm	NN	_	_	_
18	Tris	tris	NN	_	_	_
19	and	and	CC	_	_	_
20	5mM	5mm	NN	_	_	_
21	MgCl2	mgcl2	NN	_	_	_
22	and	and	CC	_	_	_
23	20mM	20mm	NN	_	_	_
24	NaN3	nan3	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	and	and	CC	_	_	_
27	cells	cell	NNS	_	_	_
28	collected	collect	VBN	_	_	_
29	by	by	IN	_	_	_
30	centrifugation	centrifugation	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	8000g	8000g	CD	_	_	_
33	,	,	,	_	_	_
34	4C	4c	NN	_	_	_
35	,	,	,	_	_	_
36	3	3	CD	_	_	_
37	min	min	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	discarded	discard	VBN	_	_	_
5	and	and	CC	_	_	_
6	the	the	DT	_	_	_
7	pellet	pellet	NN	_	_	_
8	resuspended	resuspend	VBN	_	_	_
9	in	in	IN	_	_	_
10	300μL	300μL	NNP	_	_	_
11	TE	TE	NNP	_	_	_
12	with	with	IN	_	_	_
13	40	40	CD	_	_	_
14	μl	μl	NN	_	_	_
15	10	10	CD	_	_	_
16	%	%	NN	_	_	_
17	SDS	sds	NN	_	_	_
18	and	and	CC	_	_	_
19	3	3	CD	_	_	_
20	μl	μl	NN	_	_	_
21	0.5	0.5	CD	_	_	_
22	M	m	NN	_	_	_
23	EDTA	edta	NN	_	_	_
24	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	5	5	CD	_	_	_
5	min	min	NN	_	_	_
6	at	at	IN	_	_	_
7	65	65	CD	_	_	_
8	°C	°c	NN	_	_	_
9	750μl	750μl	CD	_	_	_
10	isopropanole	isopropanole	NN	_	_	_
11	was	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	before	before	IN	_	_	_
14	centrifugation	centrifugation	NN	_	_	_
15	at	at	IN	_	_	_
16	15600	15600	CD	_	_	_
17	rcf	rcf	NN	_	_	_
18	for	for	IN	_	_	_
19	5	5	CD	_	_	_
20	min	min	NN	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	was	be	VBD	_	_	_
4	resuspended	resuspend	VBN	_	_	_
5	in	in	IN	_	_	_
6	500μL	500μl	NN	_	_	_
7	TE	te	NN	_	_	_
8	and	and	CC	_	_	_
9	2μL	2μl	NN	_	_	_
10	RNase	rnase	NN	_	_	_
11	A	a	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	25	25	CD	_	_	_
14	mg	mg	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	500	500	CD	_	_	_
17	ng	ng	NN	_	_	_
18	chrom	chrom	NN	_	_	_
19	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	digested	digest	VBN	_	_	_
4	with	with	IN	_	_	_
5	10U	10u	NN	_	_	_
6	of	of	IN	_	_	_
7	MseI	msei	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	NEB	neb	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	in	in	IN	_	_	_
12	10μL	10μl	NN	_	_	_
13	volume	volume	NN	_	_	_
14	for	for	IN	_	_	_
15	3h	3h	NN	_	_	_
16	at	at	IN	_	_	_
17	37	37	CD	_	_	_
18	°C	°c	NN	_	_	_
19	and	and	CC	_	_	_
20	heat	heat	NN	_	_	_
21	inactivated	inactivate	VBD	_	_	_
22	for	for	IN	_	_	_
23	20	20	CD	_	_	_
24	min	min	NN	_	_	_
25	at	at	IN	_	_	_
26	65	65	CD	_	_	_
27	°C	°c	NN	_	_	_
28	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	prepare	prepare	VB	_	_	_
3	adapters	adapter	NNS	_	_	_
4	100pmol	100pmol	CD	_	_	_
5	of	of	IN	_	_	_
6	MseIlong	MseIlong	NNP	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	AGTGGGATTCCGCATGCTAGT	AGTGGGATTCCGCATGCTAGT	NNP	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	and	and	CC	_	_	_
11	MseIshortnewNo	mseishortnewno	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	TAACTAGCATGC	taactagcatgc	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	were	be	VBD	_	_	_
16	annealed	anneal	VBN	_	_	_
17	in	in	IN	_	_	_
18	8µl	8µl	JJ	_	_	_
19	ddH2O	ddh2o	NN	_	_	_
20	by	by	IN	_	_	_
21	heating	heat	VBG	_	_	_
22	to	to	TO	_	_	_
23	95	95	CD	_	_	_
24	°C	°c	NN	_	_	_
25	for	for	IN	_	_	_
26	3	3	CD	_	_	_
27	min	min	NN	_	_	_
28	and	and	CC	_	_	_
29	than	than	IN	_	_	_
30	cooling	cool	VBG	_	_	_
31	to	to	TO	_	_	_
32	70	70	CD	_	_	_
33	°C	°c	NN	_	_	_
34	and	and	CC	_	_	_
35	subsequently	subsequently	RB	_	_	_
36	to	to	TO	_	_	_
37	15	15	CD	_	_	_
38	°C	°c	NN	_	_	_
39	with	with	IN	_	_	_
40	1	1	CD	_	_	_
41	°C	°c	NN	_	_	_
42	per	per	IN	_	_	_
43	min	min	NN	_	_	_
44	.	.	.	_	_	_

1	At	at	IN	_	_	_
2	15	15	CD	_	_	_
3	°C	°c	NN	_	_	_
4	10µl	10µl	JJ	_	_	_
5	MseI	msei	NN	_	_	_
6	digested	digest	VBD	_	_	_
7	DNA	dna	NN	_	_	_
8	,	,	,	_	_	_
9	2µl	2µl	JJ	_	_	_
10	ligase	ligase	NN	_	_	_
11	buffer	buffer	NN	_	_	_
12	and	and	CC	_	_	_
13	400U	400u	NN	_	_	_
14	T4-ligase	t4-ligase	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	NEB	neb	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	were	be	VBD	_	_	_
19	added	add	VBN	_	_	_
20	and	and	CC	_	_	_
21	ligated	ligate	VBN	_	_	_
22	over	over	IN	_	_	_
23	night	night	NN	_	_	_
24	.	.	.	_	_	_

1	Ligase	ligase	NN	_	_	_
2	was	be	VBD	_	_	_
3	inactivated	inactivate	VBN	_	_	_
4	at	at	IN	_	_	_
5	65	65	CD	_	_	_
6	°C	°c	NN	_	_	_
7	for	for	IN	_	_	_
8	10	10	CD	_	_	_
9	min	min	NN	_	_	_
10	.	.	.	_	_	_

1	One	one	CD	_	_	_
2	halve	halve	VBP	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	ligation	ligation	NN	_	_	_
6	mix	mix	NN	_	_	_
7	was	be	VBD	_	_	_
8	digested	digest	VBN	_	_	_
9	with	with	IN	_	_	_
10	20	20	CD	_	_	_
11	U	U	NNP	_	_	_
12	DpnI	DpnI	NNP	_	_	_
13	for	for	IN	_	_	_
14	2h	2h	NN	_	_	_
15	at	at	IN	_	_	_
16	37	37	CD	_	_	_
17	°C	°c	NN	_	_	_
18	in	in	IN	_	_	_
19	a	a	DT	_	_	_
20	volume	volume	NN	_	_	_
21	of	of	IN	_	_	_
22	50µl	50µl	JJ	_	_	_
23	and	and	CC	_	_	_
24	the	the	DT	_	_	_
25	other	other	JJ	_	_	_
26	halve	halve	VBP	_	_	_
27	treated	treated	JJ	_	_	_
28	similar	similar	JJ	_	_	_
29	with	with	IN	_	_	_
30	water	water	NN	_	_	_
31	instead	instead	RB	_	_	_
32	of	of	IN	_	_	_
33	DpnI	dpni	NN	_	_	_
34	as	as	IN	_	_	_
35	control	control	NN	_	_	_
36	.	.	.	_	_	_

1	5µl	5µl	NN	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	DNA	dna	NN	_	_	_
5	was	be	VBD	_	_	_
6	amplified	amplify	VBN	_	_	_
7	in	in	IN	_	_	_
8	a	a	DT	_	_	_
9	50	50	CD	_	_	_
10	µl	µl	NN	_	_	_
11	PCR	pcr	NN	_	_	_
12	reaction	reaction	NN	_	_	_
13	with	with	IN	_	_	_
14	0.2	0.2	CD	_	_	_
15	mM	mm	NN	KWSUPP	_	_
16	dNTPs	dntp	NNS	_	_	_
17	,	,	,	_	_	_
18	0.5	0.5	CD	_	_	_
19	µM	µm	NN	_	_	_
20	primer	primer	NN	_	_	_
21	MseIlong	MseIlong	NNP	_	_	_
22	,	,	,	_	_	_
23	10µl	10µl	JJ	_	_	_
24	Phusion	Phusion	NNP	_	_	_
25	HF	hf	NN	_	_	_
26	buffer	buffer	NN	_	_	_
27	and	and	CC	_	_	_
28	1U	1u	NN	_	_	_
29	Phusion	phusion	NN	_	_	_
30	DNA	dna	NN	_	_	_
31	polymerase	polymerase	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	Finnzymes	finnzyme	NNS	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	with	with	IN	_	_	_
36	the	the	DT	_	_	_
37	program	program	NN	_	_	_
38	30sec	30sec	CD	_	_	_
39	98	98	CD	_	_	_
40	°C	°c	NN	_	_	_
41	,	,	,	_	_	_
42	20x	20x	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	30sec	30sec	CD	_	_	_
45	98	98	CD	_	_	_
46	°C	°c	NN	_	_	_
47	,	,	,	_	_	_
48	30	30	CD	_	_	_
49	sec	sec	NN	_	_	_
50	62	62	CD	_	_	_
51	°C	°c	NN	_	_	_
52	,	,	,	_	_	_
53	60sec	60sec	JJ	_	_	_
54	72	72	CD	_	_	_
55	°C	°c	NN	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	,	,	,	_	_	_
58	10	10	CD	_	_	_
59	min	min	NN	_	_	_
60	72	72	CD	_	_	_
61	°C	°c	NN	_	_	_
62	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	purified	purify	VBN	_	_	_
4	with	with	IN	_	_	_
5	a	a	DT	_	_	_
6	Qiagen	Qiagen	NNP	_	_	_
7	PCR	pcr	NN	_	_	_
8	cleanup	cleanup	NN	_	_	_
9	kit	kit	NN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cell	cell	NN	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	cross	cross	JJ	_	_	_
6	linked	link	VBN	_	_	_
7	by	by	IN	_	_	_
8	addition	addition	NN	_	_	_
9	of	of	IN	_	_	_
10	27	27	CD	_	_	_
11	µl	µl	NN	_	_	_
12	of	of	IN	_	_	_
13	formaldehyde	formaldehyde	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	37	37	CD	_	_	_
16	%	%	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	per	per	IN	_	_	_
19	ml	ml	NN	_	_	_
20	medium	medium	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	final	final	JJ	_	_	_
23	concentration	concentration	NN	_	_	_
24	1	1	CD	_	_	_
25	%	%	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

1	Crosslinking	crosslinking	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	at	at	IN	_	_	_
5	slow	slow	JJ	_	_	_
6	shaking	shake	VBG	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	100	100	CD	_	_	_
9	rpm	rpm	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	for	for	IN	_	_	_
12	20	20	CD	_	_	_
13	min	min	NN	_	_	_
14	followed	follow	VBN	_	_	_
15	by	by	IN	_	_	_
16	quenching	quench	VBG	_	_	_
17	with	with	IN	_	_	_
18	0.2	0.2	CD	_	_	_
19	ml	ml	NN	_	_	_
20	of	of	IN	_	_	_
21	2.5	2.5	CD	_	_	_
22	M	m	NN	_	_	_
23	glycine	glycine	NN	_	_	_
24	per	per	IN	_	_	_
25	ml	ml	NN	_	_	_
26	medium	medium	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	final	final	JJ	_	_	_
29	concentration	concentration	NN	_	_	_
30	0.5	0.5	CD	_	_	_
31	M	m	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	collected	collect	VBN	_	_	_
4	from	from	IN	_	_	_
5	15	15	CD	_	_	_
6	ml	ml	NN	_	_	_
7	by	by	IN	_	_	_
8	centrifugation	centrifugation	NN	_	_	_
9	and	and	CC	_	_	_
10	washed	wash	VBN	_	_	_
11	twice	twice	RB	_	_	_
12	with	with	IN	_	_	_
13	cold	cold	JJ	_	_	_
14	TBS	tbs	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	pH7	ph7	NN	_	_	_
17	.5	.5	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	wa	wa	NN	_	_	_
4	resuspended	resuspend	VBN	_	_	_
5	in	in	IN	_	_	_
6	300μL	300μL	NNP	_	_	_
7	TE	TE	NNP	_	_	_
8	with	with	IN	_	_	_
9	40	40	CD	_	_	_
10	μl	μl	NN	_	_	_
11	10	10	CD	_	_	_
12	%	%	NN	_	_	_
13	SDS	sds	NN	_	_	_
14	and	and	CC	_	_	_
15	3	3	CD	_	_	_
16	μl	μl	NN	_	_	_
17	0.5	0.5	CD	_	_	_
18	M	m	NN	_	_	_
19	EDTA	edta	NN	_	_	_
20	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	5	5	CD	_	_	_
5	min	min	NN	_	_	_
6	at	at	IN	_	_	_
7	65	65	CD	_	_	_
8	°C	°c	NN	_	_	_
9	750μl	750μl	CD	_	_	_
10	isopropanole	isopropanole	NN	_	_	_
11	was	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	before	before	IN	_	_	_
14	centrifugation	centrifugation	NN	_	_	_
15	at	at	IN	_	_	_
16	15600	15600	CD	_	_	_
17	rcf	rcf	NN	_	_	_
18	for	for	IN	_	_	_
19	5	5	CD	_	_	_
20	min	min	NN	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	was	be	VBD	_	_	_
4	resuspended	resuspend	VBN	_	_	_
5	in	in	IN	_	_	_
6	500μL	500μl	NN	_	_	_
7	TE	te	NN	_	_	_
8	and	and	CC	_	_	_
9	3μL	3μl	NN	_	_	_
10	RNase	rnase	NN	_	_	_
11	A	a	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	25	25	CD	_	_	_
14	mg	mg	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Cells	cell	NNS	_	_	_
17	were	be	VBD	_	_	_
18	grown	grow	VBN	_	_	_
19	at	at	IN	_	_	_
20	30	30	CD	_	_	_
21	°C	°c	NN	_	_	_
22	to	to	TO	_	_	_
23	an	a	DT	_	_	_
24	OD450	od450	NN	_	_	_
25	of	of	IN	_	_	_
26	about	about	IN	_	_	_
27	0.07	0.07	CD	_	_	_
28	in	in	IN	_	_	_
29	AB	AB	NNP	_	_	_
30	glucose	glucose	NN	SUPP	_	_
31	CAA	CAA	NNP	_	_	_
32	medium	medium	NN	_	_	_
33	,	,	,	_	_	_
34	shifted	shift	VBD	_	_	_
35	to	to	TO	_	_	_
36	39	39	CD	_	_	_
37	°C	°c	NN	_	_	_
38	for	for	IN	_	_	_
39	70	70	CD	_	_	_
40	min	min	NN	_	_	_
41	and	and	CC	_	_	_
42	back	back	RB	_	_	_
43	to	to	TO	_	_	_
44	30	30	CD	_	_	_
45	°C	°c	NN	_	_	_
46	for	for	IN	_	_	_
47	0	0	CD	_	_	_
48	min	min	NN	_	_	_
49	before	before	IN	_	_	_
50	crosslinking	crosslink	VBG	_	_	_
51	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	at	at	IN	_	_	_
6	30	30	CD	_	_	_
7	°C	°c	NN	_	_	_
8	to	to	TO	_	_	_
9	an	a	DT	_	_	_
10	OD450	od450	NN	_	_	_
11	of	of	IN	_	_	_
12	about	about	IN	_	_	_
13	0.07	0.07	CD	_	_	_
14	in	in	IN	_	_	_
15	AB	AB	NNP	_	_	_
16	glucose	glucose	NN	SUPP	_	_
17	CAA	CAA	NNP	_	_	_
18	medium	medium	NN	_	_	_
19	,	,	,	_	_	_
20	shifted	shift	VBD	_	_	_
21	to	to	TO	_	_	_
22	39	39	CD	_	_	_
23	°C	°c	NN	_	_	_
24	for	for	IN	_	_	_
25	70	70	CD	_	_	_
26	min	min	NN	_	_	_
27	and	and	CC	_	_	_
28	back	back	RB	_	_	_
29	to	to	TO	_	_	_
30	30	30	CD	_	_	_
31	°C	°c	NN	_	_	_
32	for	for	IN	_	_	_
33	15	15	CD	_	_	_
34	min	min	NN	_	_	_
35	before	before	IN	_	_	_
36	crosslinking	crosslink	VBG	_	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	at	at	IN	_	_	_
6	30	30	CD	_	_	_
7	°C	°c	NN	_	_	_
8	to	to	TO	_	_	_
9	an	a	DT	_	_	_
10	OD450	od450	NN	_	_	_
11	of	of	IN	_	_	_
12	about	about	IN	_	_	_
13	0.07	0.07	CD	_	_	_
14	in	in	IN	_	_	_
15	AB	AB	NNP	_	_	_
16	glucose	glucose	NN	SUPP	_	_
17	CAA	CAA	NNP	_	_	_
18	medium	medium	NN	_	_	_
19	,	,	,	_	_	_
20	shifted	shift	VBD	_	_	_
21	to	to	TO	_	_	_
22	39	39	CD	_	_	_
23	°C	°c	NN	_	_	_
24	for	for	IN	_	_	_
25	70	70	CD	_	_	_
26	min	min	NN	_	_	_
27	and	and	CC	_	_	_
28	back	back	RB	_	_	_
29	to	to	TO	_	_	_
30	30	30	CD	_	_	_
31	°C	°c	NN	_	_	_
32	for	for	IN	_	_	_
33	16	16	CD	_	_	_
34	min	min	NN	_	_	_
35	before	before	IN	_	_	_
36	crosslinking	crosslink	VBG	_	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	at	at	IN	_	_	_
6	30	30	CD	_	_	_
7	°C	°c	NN	_	_	_
8	to	to	TO	_	_	_
9	an	a	DT	_	_	_
10	OD450	od450	NN	_	_	_
11	of	of	IN	_	_	_
12	about	about	IN	_	_	_
13	0.07	0.07	CD	_	_	_
14	in	in	IN	_	_	_
15	AB	AB	NNP	_	_	_
16	glucose	glucose	NN	SUPP	_	_
17	CAA	CAA	NNP	_	_	_
18	medium	medium	NN	_	_	_
19	,	,	,	_	_	_
20	shifted	shift	VBD	_	_	_
21	to	to	TO	_	_	_
22	39	39	CD	_	_	_
23	°C	°c	NN	_	_	_
24	for	for	IN	_	_	_
25	70	70	CD	_	_	_
26	min	min	NN	_	_	_
27	and	and	CC	_	_	_
28	back	back	RB	_	_	_
29	to	to	TO	_	_	_
30	30	30	CD	_	_	_
31	°C	°c	NN	_	_	_
32	for	for	IN	_	_	_
33	17	17	CD	_	_	_
34	min	min	NN	_	_	_
35	before	before	IN	_	_	_
36	crosslinking	crosslink	VBG	_	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	at	at	IN	_	_	_
6	30	30	CD	_	_	_
7	°C	°c	NN	_	_	_
8	to	to	TO	_	_	_
9	an	a	DT	_	_	_
10	OD450	od450	NN	_	_	_
11	of	of	IN	_	_	_
12	about	about	IN	_	_	_
13	0.07	0.07	CD	_	_	_
14	in	in	IN	_	_	_
15	AB	AB	NNP	_	_	_
16	glucose	glucose	NN	SUPP	_	_
17	CAA	CAA	NNP	_	_	_
18	medium	medium	NN	_	_	_
19	,	,	,	_	_	_
20	shifted	shift	VBD	_	_	_
21	to	to	TO	_	_	_
22	39	39	CD	_	_	_
23	°C	°c	NN	_	_	_
24	for	for	IN	_	_	_
25	70	70	CD	_	_	_
26	min	min	NN	_	_	_
27	and	and	CC	_	_	_
28	back	back	RB	_	_	_
29	to	to	TO	_	_	_
30	30	30	CD	_	_	_
31	°C	°c	NN	_	_	_
32	for	for	IN	_	_	_
33	35	35	CD	_	_	_
34	min	min	NN	_	_	_
35	before	before	IN	_	_	_
36	crosslinking	crosslink	VBG	_	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	at	at	IN	_	_	_
6	30	30	CD	_	_	_
7	°C	°c	NN	_	_	_
8	to	to	TO	_	_	_
9	an	a	DT	_	_	_
10	OD450	od450	NN	_	_	_
11	of	of	IN	_	_	_
12	about	about	IN	_	_	_
13	0.07	0.07	CD	_	_	_
14	in	in	IN	_	_	_
15	AB	AB	NNP	_	_	_
16	glucose	glucose	NN	SUPP	_	_
17	CAA	CAA	NNP	_	_	_
18	medium	medium	NN	_	_	_
19	,	,	,	_	_	_
20	shifted	shift	VBD	_	_	_
21	to	to	TO	_	_	_
22	39	39	CD	_	_	_
23	°C	°c	NN	_	_	_
24	for	for	IN	_	_	_
25	70	70	CD	_	_	_
26	min	min	NN	_	_	_
27	and	and	CC	_	_	_
28	back	back	RB	_	_	_
29	to	to	TO	_	_	_
30	30	30	CD	_	_	_
31	°C	°c	NN	_	_	_
32	for	for	IN	_	_	_
33	50	50	CD	_	_	_
34	min	min	NN	_	_	_
35	before	before	IN	_	_	_
36	crosslinking	crosslink	VBG	_	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	at	at	IN	_	_	_
6	30	30	CD	_	_	_
7	°C	°c	NN	_	_	_
8	to	to	TO	_	_	_
9	an	a	DT	_	_	_
10	OD450	od450	NN	_	_	_
11	of	of	IN	_	_	_
12	about	about	IN	_	_	_
13	0.07	0.07	CD	_	_	_
14	in	in	IN	_	_	_
15	AB	AB	NNP	_	_	_
16	glucose	glucose	NN	SUPP	_	_
17	CAA	CAA	NNP	_	_	_
18	medium	medium	NN	_	_	_
19	,	,	,	_	_	_
20	shifted	shift	VBD	_	_	_
21	to	to	TO	_	_	_
22	39	39	CD	_	_	_
23	°C	°c	NN	_	_	_
24	for	for	IN	_	_	_
25	70	70	CD	_	_	_
26	min	min	NN	_	_	_
27	and	and	CC	_	_	_
28	back	back	RB	_	_	_
29	to	to	TO	_	_	_
30	30	30	CD	_	_	_
31	°C	°c	NN	_	_	_
32	for	for	IN	_	_	_
33	5	5	CD	_	_	_
34	min	min	NN	_	_	_
35	before	before	IN	_	_	_
36	crosslinking	crosslink	VBG	_	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	at	at	IN	_	_	_
6	37	37	CD	_	_	_
7	°C	°c	NN	_	_	_
8	to	to	TO	_	_	_
9	an	a	DT	_	_	_
10	OD450	od450	NN	_	_	_
11	of	of	IN	_	_	_
12	about	about	IN	_	_	_
13	0.15	0.15	CD	_	_	_
14	in	in	IN	_	_	_
15	100	100	CD	_	_	_
16	ml	ml	NN	_	_	_
17	AB	AB	NNP	_	_	_
18	acetate	acetate	NN	SUPP	_	_
19	medium	medium	NN	_	_	_
20	before	before	IN	_	_	_
21	crosslinking	crosslink	VBG	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	at	at	IN	_	_	_
6	37	37	CD	_	_	_
7	°C	°c	NN	_	_	_
8	to	to	TO	_	_	_
9	an	a	DT	_	_	_
10	OD600	od600	NN	_	_	_
11	of	of	IN	_	_	_
12	about	about	IN	_	_	_
13	0.15	0.15	CD	_	_	_
14	in	in	IN	_	_	_
15	50	50	CD	_	_	_
16	ml	ml	NN	_	_	_
17	LB	lb	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	+	+	CC	_	_	_
20	0.2	0.2	CD	_	_	_
21	%	%	NN	_	_	_
22	glucose	glucose	NN	SUPP	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	before	before	IN	_	_	_
25	crosslinking	crosslink	VBG	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	chip	chip	NN	_	_	_
3	antibody	antibody	NN	_	_	_
4	:	:	:	_	_	_
5	SeqA	seqa	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Cultures	culture	NNS	_	_	_
8	of	of	IN	_	_	_
9	E.	e.	FW	_	_	_
10	coli	coli	FW	_	_	_
11	MG1655	mg1655	NN	_	_	_
12	and	and	CC	_	_	_
13	its	its	PRP$	_	_	_
14	derivates	derivate	NNS	_	_	_
15	were	be	VBD	_	_	_
16	cross	cross	JJ	_	_	_
17	linked	link	VBN	_	_	_
18	by	by	IN	_	_	_
19	addition	addition	NN	_	_	_
20	of	of	IN	_	_	_
21	27	27	CD	_	_	_
22	µl	µl	NN	_	_	_
23	of	of	IN	_	_	_
24	formaldehyde	formaldehyde	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	37	37	CD	_	_	_
27	%	%	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	per	per	IN	_	_	_
30	ml	ml	NN	_	_	_
31	medium	medium	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	final	final	JJ	_	_	_
34	concentration	concentration	NN	_	_	_
35	1	1	CD	_	_	_
36	%	%	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	.	.	.	_	_	_

1	Crosslinking	crosslinking	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	at	at	IN	_	_	_
5	slow	slow	JJ	_	_	_
6	shaking	shake	VBG	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	100	100	CD	_	_	_
9	rpm	rpm	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	for	for	IN	_	_	_
12	20	20	CD	_	_	_
13	min	min	NN	_	_	_
14	followed	follow	VBN	_	_	_
15	by	by	IN	_	_	_
16	quenching	quench	VBG	_	_	_
17	with	with	IN	_	_	_
18	0.2	0.2	CD	_	_	_
19	ml	ml	NN	_	_	_
20	of	of	IN	_	_	_
21	2.5	2.5	CD	_	_	_
22	M	m	NN	_	_	_
23	glycine	glycine	NN	_	_	_
24	per	per	IN	_	_	_
25	ml	ml	NN	_	_	_
26	medium	medium	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	final	final	JJ	_	_	_
29	concentration	concentration	NN	_	_	_
30	0.5	0.5	CD	_	_	_
31	M	m	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	collected	collect	VBN	_	_	_
4	by	by	IN	_	_	_
5	centrifugation	centrifugation	NN	_	_	_
6	and	and	CC	_	_	_
7	washed	wash	VBN	_	_	_
8	twice	twice	RB	_	_	_
9	with	with	IN	_	_	_
10	cold	cold	JJ	_	_	_
11	TBS	tbs	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	pH7	ph7	NN	_	_	_
14	.5	.5	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	resuspension	resuspension	NN	_	_	_
3	in	in	IN	_	_	_
4	1	1	CD	_	_	_
5	ml	ml	NN	_	_	_
6	lysis	lysis	NN	_	_	_
7	buffer	buffer	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	10mM	10mm	NN	_	_	_
10	Tris	tris	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	pH	ph	NN	_	_	_
13	8.0	8.0	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	20	20	CD	_	_	_
17	%	%	NN	_	_	_
18	sucrose	sucrose	NN	_	_	_
19	,	,	,	_	_	_
20	50mM	50mm	NN	_	_	_
21	NaCl	nacl	NN	_	_	_
22	,	,	,	_	_	_
23	10mM	10mm	NN	_	_	_
24	EDTA	edta	NN	_	_	_
25	,	,	,	_	_	_
26	10	10	CD	_	_	_
27	mg	mg	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Escherichia	escherichia	FW	Organism	_	_
30	coli	coli	FW	Organism	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Escherichia	escherichia	FW	Organism	_	_
33	coli	coli	FW	Organism	_	_
34	str	str	FW	_	_	_
35	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	genotype	genotype	NN	_	_	_
4	:	:	:	_	_	_
5	dnaC2	dnac2	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	genotype	genotype	NN	_	_	_
8	:	:	:	_	_	_
9	dnaC2	dnac2	NN	_	_	_
10	,	,	,	_	_	_
11	pMQ430	pmq430	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	genotype	genotype	NN	_	_	_
14	:	:	:	_	_	_
15	GATC-cluster	gatc-cluster	NN	_	_	_
16	:	:	:	_	_	_
17	:	:	:	_	_	_
18	hisA	hisA	NNP	GEN	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	genotype	genotype	NN	_	_	_
21	:	:	:	_	_	_
22	GATC-cluster	gatc-cluster	NN	_	_	_
23	:	:	:	_	_	_
24	:	:	:	_	_	_
25	srlA	srla	NN	GEN	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	genotype	genotype	NN	_	_	_
28	:	:	:	_	_	_
29	GATC-cluster	gatc-cluster	NN	_	_	_
30	:	:	:	_	_	_
31	:	:	:	_	_	_
32	ter	ter	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	genotype	genotype	NN	_	_	_
35	:	:	:	_	_	_
36	GATC-cluster	gatc-cluster	NN	_	_	_
37	:	:	:	_	_	_
38	:	:	:	_	_	_
39	tnaA	tnaa	NN	GEN	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	genotype	genotype	NN	_	_	_
42	:	:	:	_	_	_
43	wildtype	wildtype	JJ	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	input	input	NN	_	_	_
46	DNA	dna	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	Methylation	methylation	NN	_	_	_
49	in	in	IN	_	_	_
50	0	0	CD	_	_	_
51	min	min	NN	_	_	_
52	dnaC2	dnac2	NN	_	_	_
53	rep1	rep1	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	Methylation	methylation	NN	_	_	_
56	in	in	IN	_	_	_
57	0	0	CD	_	_	_
58	min	min	NN	_	_	_
59	dnaC2	dnac2	NN	_	_	_
60	rep2	rep2	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Methylation	methylation	NN	_	_	_
63	in	in	IN	_	_	_
64	15	15	CD	_	_	_
65	min	min	NN	_	_	_
66	dnaC2	dnac2	NN	_	_	_
67	rep1	rep1	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	Methylation	methylation	NN	_	_	_
70	in	in	IN	_	_	_
71	15	15	CD	_	_	_
72	min	min	NN	_	_	_
73	dnaC2	dnac2	NN	_	_	_
74	rep2	rep2	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	SeqA	seqa	NN	_	_	_
77	ChIP	chip	NN	_	_	_
78	DNA	dna	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	SeqA	seqa	NN	_	_	_
81	in	in	IN	_	_	_
82	0	0	CD	_	_	_
83	min	min	NN	_	_	_
84	dnaC2	dnac2	NN	_	_	_
85	rep1	rep1	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	SeqA	seqa	NN	_	_	_
88	in	in	IN	_	_	_
89	0	0	CD	_	_	_
90	min	min	NN	_	_	_
91	dnaC2	dnac2	NN	_	_	_
92	rep2	rep2	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	SeqA	seqa	NN	_	_	_
95	in	in	IN	_	_	_
96	15	15	CD	_	_	_
97	min	min	NN	_	_	_
98	dnaC2	dnac2	NN	_	_	_
99	LB	lb	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	SeqA	seqa	NN	_	_	_
102	in	in	IN	_	_	_
103	15	15	CD	_	_	_
104	min	min	NN	_	_	_
105	dnaC2	dnac2	NN	_	_	_
106	LB	lb	NN	_	_	_
107	dam	dam	NN	GEN	_	_
108	+	+	CC	_	_	_
109	+	+	CC	_	_	_
110	rep1	rep1	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	SeqA	seqa	NN	_	_	_
113	in	in	IN	_	_	_
114	15	15	CD	_	_	_
115	min	min	NN	_	_	_
116	dnaC2	dnac2	NN	_	_	_
117	LB	lb	NN	_	_	_
118	dam	dam	NN	GEN	_	_
119	+	+	CC	_	_	_
120	+	+	CC	_	_	_
121	rep2	rep2	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	SeqA	seqa	NN	_	_	_
124	in	in	IN	_	_	_
125	15	15	CD	_	_	_
126	min	min	NN	_	_	_
127	dnaC2	dnac2	NN	_	_	_
128	rep1	rep1	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	SeqA	seqa	NN	_	_	_
131	in	in	IN	_	_	_
132	15	15	CD	_	_	_
133	min	min	NN	_	_	_
134	dnaC2	dnac2	NN	_	_	_
135	rep2	rep2	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	SeqA	seqa	NN	_	_	_
138	in	in	IN	_	_	_
139	15	15	CD	_	_	_
140	min	min	NN	_	_	_
141	dnaC2	dnac2	NN	_	_	_
142	rep3	rep3	NN	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	SeqA	seqa	NN	_	_	_
145	in	in	IN	_	_	_
146	16	16	CD	_	_	_
147	min	min	NN	_	_	_
148	dnaC2	dnac2	NN	_	_	_
149	rep1	rep1	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	SeqA	seqa	NN	_	_	_
152	in	in	IN	_	_	_
153	16	16	CD	_	_	_
154	min	min	NN	_	_	_
155	dnaC2	dnac2	NN	_	_	_
156	rep2	rep2	NN	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	SeqA	seqa	NN	_	_	_
159	in	in	IN	_	_	_
160	17	17	CD	_	_	_
161	min	min	NN	_	_	_
162	dnaC2	dnac2	NN	_	_	_
163	rep1	rep1	NN	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	SeqA	seqa	NN	_	_	_
166	in	in	IN	_	_	_
167	17	17	CD	_	_	_
168	min	min	NN	_	_	_
169	dnaC2	dnac2	NN	_	_	_
170	rep2	rep2	NN	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	SeqA	seqa	NN	_	_	_
173	in	in	IN	_	_	_
174	35	35	CD	_	_	_
175	min	min	NN	_	_	_
176	dnaC2	dnac2	NN	_	_	_
177	rep1	rep1	NN	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	SeqA	seqa	NN	_	_	_
180	in	in	IN	_	_	_
181	35	35	CD	_	_	_
182	min	min	NN	_	_	_
183	dnaC2	dnac2	NN	_	_	_
184	rep2	rep2	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	SeqA	seqa	NN	_	_	_
187	in	in	IN	_	_	_
188	50	50	CD	_	_	_
189	min	min	NN	_	_	_
190	dnaC2	dnac2	NN	_	_	_
191	rep1	rep1	NN	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	SeqA	seqa	NN	_	_	_
194	in	in	IN	_	_	_
195	50	50	CD	_	_	_
196	min	min	NN	_	_	_
197	dnaC2	dnac2	NN	_	_	_
198	rep2	rep2	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	SeqA	seqa	NN	_	_	_
201	in	in	IN	_	_	_
202	5	5	CD	_	_	_
203	min	min	NN	_	_	_
204	dnaC2	dnac2	NN	_	_	_
205	rep1	rep1	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	SeqA	seqa	NN	_	_	_
208	in	in	IN	_	_	_
209	5	5	CD	_	_	_
210	min	min	NN	_	_	_
211	dnaC2	dnac2	NN	_	_	_
212	rep2	rep2	NN	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	SeqA	seqa	NN	_	_	_
215	in	in	IN	_	_	_
216	AB	AB	NNP	_	_	_
217	acetate	acetate	NN	SUPP	_	_
218	rep1	rep1	NN	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	SeqA	seqa	NN	_	_	_
221	in	in	IN	_	_	_
222	AB	AB	NNP	_	_	_
223	acetate	acetate	NN	SUPP	_	_
224	rep2	rep2	NN	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	SeqA	seqa	NN	_	_	_
227	in	in	IN	_	_	_
228	hisA	hisA	NNP	GEN	_	_
229	GATC	GATC	NNP	_	_	_
230	cluster	cluster	NN	_	_	_
231	rep1	rep1	NN	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	SeqA	seqa	NN	_	_	_
234	in	in	IN	_	_	_
235	hisA	hisA	NNP	GEN	_	_
236	GATC	GATC	NNP	_	_	_
237	cluster	cluster	NN	_	_	_
238	rep2	rep2	NN	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	SeqA	seqa	NN	_	_	_
241	in	in	IN	_	_	_
242	srlA	srla	NN	GEN	_	_
243	GATC	gatc	NN	_	_	_
244	cluster	cluster	NN	_	_	_
245	rep1	rep1	NN	_	_	_
246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
247	SeqA	seqa	NN	_	_	_
248	in	in	IN	_	_	_
249	srlA	srla	NN	GEN	_	_
250	GATC	gatc	NN	_	_	_
251	cluster	cluster	NN	_	_	_
252	rep2	rep2	NN	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
254	SeqA	seqa	NN	_	_	_
255	in	in	IN	_	_	_
256	ter	ter	NN	_	_	_
257	GATC	gatc	NN	_	_	_
258	cluster	cluster	NN	_	_	_
259	rep1	rep1	NN	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	SeqA	seqa	NN	_	_	_
262	in	in	IN	_	_	_
263	ter	ter	NN	_	_	_
264	GATC	gatc	NN	_	_	_
265	cluster	cluster	NN	_	_	_
266	rep2	rep2	NN	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	SeqA	seqa	NN	_	_	_
269	in	in	IN	_	_	_
270	tnaA	tnaa	NN	GEN	_	_
271	GATC	gatc	NN	_	_	_
272	cluster	cluster	NN	_	_	_
273	rep1	rep1	NN	_	_	_
274	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
275	SeqA	seqa	NN	_	_	_
276	in	in	IN	_	_	_
277	tnaA	tnaa	NN	GEN	_	_
278	GATC	gatc	NN	_	_	_
279	cluster	cluster	NN	_	_	_
280	rep2	rep2	NN	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	Spot	spot	NN	_	_	_
283	intensities	intensity	NNS	_	_	_
284	were	be	VBD	_	_	_
285	extracted	extract	VBN	_	_	_
286	using	use	VBG	_	_	_
287	the	the	DT	_	_	_
288	Feature	Feature	NNP	_	_	_
289	Extraction	extraction	NN	_	_	_
290	software	software	NN	_	_	_
291	10.5.1.1	10.5.1.1	CD	_	_	_
292	from	from	IN	_	_	_
293	Applied	Applied	NNP	_	_	_
294	Biosystems	Biosystems	NNPS	_	_	_
295	with	with	IN	_	_	_
296	a	a	DT	_	_	_
297	linear	linear	JJ	_	_	_
298	dye	dye	VB	_	_	_
299	normalization	normalization	NN	_	_	_
300	correction	correction	NN	_	_	_
301	method	method	NN	_	_	_
302	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	gProcessedSignal	gprocessedsignal	NN	_	_	_
3	and	and	CC	_	_	_
4	rProcessedSignal	rprocessedsignal	NN	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	for	for	IN	_	_	_
8	further	further	JJ	_	_	_
9	analysis	analysis	NN	_	_	_
10	with	with	IN	_	_	_
11	the	the	DT	_	_	_
12	statistics	statistics	NNS	_	_	_
13	software	software	NN	_	_	_
14	R.	R.	NNP	_	_	_
15	Ratios	Ratios	NNP	_	_	_
16	of	of	IN	_	_	_
17	g	g	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	sample	sample	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	to	to	TO	_	_	_
22	r	r	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	control	control	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	were	be	VBD	_	_	_
27	calculated	calculate	VBN	_	_	_
28	after	after	IN	_	_	_
29	background	background	NN	_	_	_
30	substraction	substraction	NN	_	_	_
31	and	and	CC	_	_	_
32	normalized	normalize	VBD	_	_	_
33	to	to	TO	_	_	_
34	the	the	DT	_	_	_
35	array	array	NN	_	_	_
36	wide	wide	JJ	_	_	_
37	average	average	NN	_	_	_
38	.	.	.	_	_	_

1	Data	datum	NNS	_	_	_
2	points	point	NNS	_	_	_
3	with	with	IN	_	_	_
4	a	a	DT	_	_	_
5	value	value	NN	_	_	_
6	below	below	IN	_	_	_
7	0	0	CD	_	_	_
8	after	after	IN	_	_	_
9	background	background	NN	_	_	_
10	subtraction	subtraction	NN	_	_	_
11	were	be	VBD	_	_	_
12	set	set	VBN	_	_	_
13	`	`	``	_	_	_
14	null	null	NN	_	_	_
15	'	'	''	_	_	_
16	.	.	.	_	_	_

1	Data	datum	NNS	_	_	_
2	points	point	NNS	_	_	_
3	form	form	VBP	_	_	_
4	non-unique	non-unique	JJ	_	_	_
5	regions	region	NNS	_	_	_
6	on	on	IN	_	_	_
7	the	the	DT	_	_	_
8	chromosome	chromosome	NN	_	_	_
9	were	be	VBD	_	_	_
10	excluded	exclude	VBN	_	_	_
11	from	from	IN	_	_	_
12	analysis	analysis	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Spot	Spot	NNP	_	_	_
3	intensities	intensity	NNS	_	_	_
4	were	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	Feature	Feature	NNP	_	_	_
9	Extraction	extraction	NN	_	_	_
10	software	software	NN	_	_	_
11	10.5.1.1	10.5.1.1	CD	_	_	_
12	from	from	IN	_	_	_
13	Applied	Applied	NNP	_	_	_
14	Biosystems	Biosystems	NNPS	_	_	_
15	with	with	IN	_	_	_
16	a	a	DT	_	_	_
17	linear	linear	JJ	_	_	_
18	dye	dye	VB	_	_	_
19	normalization	normalization	NN	_	_	_
20	correction	correction	NN	_	_	_
21	method	method	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	gProcessedSignal	gprocessedsignal	NN	_	_	_
3	and	and	CC	_	_	_
4	rProcessedSignal	rprocessedsignal	NN	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	for	for	IN	_	_	_
8	further	further	JJ	_	_	_
9	analysis	analysis	NN	_	_	_
10	with	with	IN	_	_	_
11	the	the	DT	_	_	_
12	statistics	statistics	NNS	_	_	_
13	software	software	NN	_	_	_
14	R.	R.	NNP	_	_	_
15	Ratios	Ratios	NNP	_	_	_
16	of	of	IN	_	_	_
17	g	g	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	sample	sample	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	to	to	TO	_	_	_
22	r	r	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	control	control	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	were	be	VBD	_	_	_
27	calculated	calculate	VBN	_	_	_
28	after	after	IN	_	_	_
29	background	background	NN	_	_	_
30	substraction	substraction	NN	_	_	_
31	.	.	.	_	_	_

1	Data	datum	NNS	_	_	_
2	points	point	NNS	_	_	_
3	with	with	IN	_	_	_
4	a	a	DT	_	_	_
5	value	value	NN	_	_	_
6	below	below	IN	_	_	_
7	0	0	CD	_	_	_
8	after	after	IN	_	_	_
9	background	background	NN	_	_	_
10	subtraction	subtraction	NN	_	_	_
11	were	be	VBD	_	_	_
12	set	set	VBN	_	_	_
13	`	`	``	_	_	_
14	null	null	NN	_	_	_
15	'	'	''	_	_	_
16	.	.	.	_	_	_

1	Data	datum	NNS	_	_	_
2	points	point	NNS	_	_	_
3	form	form	VBP	_	_	_
4	non-unique	non-unique	JJ	_	_	_
5	regions	region	NNS	_	_	_
6	on	on	IN	_	_	_
7	the	the	DT	_	_	_
8	chromosome	chromosome	NN	_	_	_
9	were	be	VBD	_	_	_
10	excluded	exclude	VBN	_	_	_
11	from	from	IN	_	_	_
12	analysis	analysis	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	strain	strain	NN	_	_	_
7	:	:	:	_	_	_
8	MG1655dnaC2	mg1655dnac2	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	strain	strain	NN	_	_	_
11	:	:	:	_	_	_
12	TB16	tb16	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	strain	strain	NN	_	_	_
15	:	:	:	_	_	_
16	TWx30	twx30	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	strain	strain	NN	_	_	_
19	:	:	:	_	_	_
20	TWx31	twx31	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	strain	strain	NN	_	_	_
23	:	:	:	_	_	_
24	TWx34	twx34	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	strain	strain	NN	_	_	_
27	:	:	:	_	_	_
28	TWx48	twx48	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	treatment	treatment	NN	_	_	_
31	:	:	:	_	_	_
32	control	control	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	treatment	treatment	NN	_	_	_
35	:	:	:	_	_	_
36	DpnI	dpni	NN	_	_	_
37	digested	digest	VBD	_	_	_
38	DNA	dna	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	untreated	untreated	JJ	_	_	_
41	control	control	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
43	285c	285c	JJ	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	All	all	DT	_	_	_
46	strains	strain	NNS	_	_	_
47	were	be	VBD	_	_	_
48	grown	grow	VBN	_	_	_
49	in	in	IN	_	_	_
50	M9	m9	NN	MED	_	_
51	minimal	minimal	JJ	MED	_	_
52	media	media	NNS	MED	_	_
53	supplemented	supplement	VBN	_	_	_
54	with	with	IN	_	_	_
55	25	25	CD	_	_	_
56	ug	ug	NN	_	_	_
57	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
58	Control	Control	NNP	_	_	_
59	samples	sample	NNS	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	285c	285c	JJ	_	_	_
62	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
63	Data	datum	NNS	_	_	_
64	were	be	VBD	_	_	_
65	normalized	normalize	VBN	_	_	_
66	using	use	VBG	_	_	_
67	LOWESS	lowess	NN	_	_	_
68	-LRB-	-lrb-	-LRB-	_	_	_
69	MIDAS	midas	NN	_	_	_
70	-RRB-	-rrb-	-RRB-	_	_	_
71	and	and	CC	_	_	_
72	analyzed	analyze	VBN	_	_	_
73	for	for	IN	_	_	_
74	statistical	statistical	JJ	_	_	_
75	significance	significance	NN	_	_	_
76	using	use	VBG	_	_	_
77	the	the	DT	_	_	_
78	Rank	Rank	NNP	_	_	_
79	Product	Product	NNP	_	_	_
80	method	method	NN	_	_	_
81	in	in	IN	_	_	_
82	the	the	DT	_	_	_
83	MultiExperimentViewer	MultiExperimentViewer	NNP	_	_	_
84	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
85	Escherichia	escherichia	FW	Organism	_	_
86	coli	coli	FW	Organism	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	genotype	genotype	NN	_	_	_
89	:	:	:	_	_	_
90	285c	285c	JJ	_	_	_
91	rpoD	rpod	NN	GEN	_	_
92	mutation	mutation	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	Sigma70	sigma70	NN	_	_	_
95	LB	lb	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	Sigma70	sigma70	NN	_	_	_
98	LB-1	lb-1	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	Sigma70	sigma70	NN	_	_	_
101	LB-2	lb-2	NN	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	Sigma70	sigma70	NN	_	_	_
104	LB-3	lb-3	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	Sigma70	sigma70	NN	_	_	_
107	LP	lp	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	Sigma70	sigma70	NN	_	_	_
110	LP-1	lp-1	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	Sigma70	sigma70	NN	_	_	_
113	LP-2	lp-2	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	Sigma70	sigma70	NN	_	_	_
116	LP-3	lp-3	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
118	The	the	DT	_	_	_
119	Zymo	Zymo	NNP	_	_	_
120	Fungal	fungal	JJ	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	transformation	transformation	NN	_	_	_
123	:	:	:	_	_	_
124	empty	empty	JJ	_	_	_
125	vector	vector	NN	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	transformation	transformation	NN	_	_	_
128	:	:	:	_	_	_
129	pSigma70-LB	psigma70-lb	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	transformation	transformation	NN	_	_	_
132	:	:	:	_	_	_
133	pSigma70-LP	psigma70-lp	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	treatment	treatment	NN	_	_	_
136	:	:	:	_	_	_
137	30	30	CD	_	_	_
138	C	c	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	treatment	treatment	NN	_	_	_
141	:	:	:	_	_	_
142	42	42	CD	_	_	_
143	C	c	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	Cells	cell	NNS	_	_	_
146	from	from	IN	_	_	_
147	single	single	JJ	_	_	_
148	colonies	colony	NNS	_	_	_
149	were	be	VBD	_	_	_
150	grown	grow	VBN	_	_	_
151	on	on	IN	_	_	_
152	LB	LB	NNP	_	_	_
153	agar	agar	NN	_	_	_
154	and	and	CC	_	_	_
155	then	then	RB	_	_	_
156	inoculated	inoculate	VBN	_	_	_
157	into	into	IN	_	_	_
158	liquid	liquid	JJ	_	_	_
159	LB	lb	NN	_	_	_
160	and	and	CC	_	_	_
161	grown	grow	VBN	_	_	_
162	to	to	TO	_	_	_
163	saturation	saturation	NN	_	_	_
164	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	50	50	CD	_	_	_
3	µl	µl	NN	_	_	_
4	was	be	VBD	_	_	_
5	inoculated	inoculate	VBN	_	_	_
6	into	into	IN	_	_	_
7	5	5	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	K-medium	k-medium	NN	_	_	_
11	and	and	CC	_	_	_
12	grown	grow	VBN	_	_	_
13	to	to	TO	_	_	_
14	saturation	saturation	NN	_	_	_
15	again	again	RB	_	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	inoculated	inoculate	VBN	_	_	_
6	into	into	IN	_	_	_
7	the	the	DT	_	_	_
8	separate	separate	JJ	_	_	_
9	media	media	NNS	_	_	_
10	as	as	IN	_	_	_
11	follows	follow	VBZ	_	_	_
12	:	:	:	_	_	_
13	25	25	CD	_	_	_
14	μl	μl	NN	_	_	_
15	into	into	IN	_	_	_
16	K-medium	k-medium	NN	_	_	_
17	,	,	,	_	_	_
18	50	50	CD	_	_	_
19	µl	µl	NN	_	_	_
20	into	into	IN	_	_	_
21	K-medium	k-medium	NN	_	_	_
22	+	+	CC	_	_	_
23	0.3	0.3	CD	_	_	_
24	M	m	NN	_	_	_
25	NaCl	nacl	NN	_	_	_
26	,	,	,	_	_	_
27	75	75	CD	_	_	_
28	µl	µl	NN	_	_	_
29	into	into	IN	_	_	_
30	K-medium	k-medium	NN	_	_	_
31	+	+	CC	_	_	_
32	0.6	0.6	CD	_	_	_
33	M	m	NN	_	_	_
34	urea	urea	NN	_	_	_
35	;	;	:	_	_	_
36	the	the	DT	_	_	_
37	final	final	JJ	_	_	_
38	volume	volume	NN	_	_	_
39	was	be	VBD	_	_	_
40	5	5	CD	_	_	_
41	ml	ml	NN	_	_	_
42	in	in	IN	_	_	_
43	all	all	DT	_	_	_
44	cases	case	NNS	_	_	_
45	.	.	.	_	_	_

1	These	these	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	overnight	overnight	RB	_	_	_
6	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	incubated	incubate	VBN	_	_	_
5	in	in	IN	_	_	_
6	250	250	CD	_	_	_
7	ml	ml	NN	_	_	_
8	Erlenmeyer	erlenmeyer	NN	_	_	_
9	flasks	flask	NNS	_	_	_
10	in	in	IN	_	_	_
11	the	the	DT	_	_	_
12	three	three	CD	_	_	_
13	media	media	NNS	_	_	_
14	in	in	IN	_	_	_
15	a	a	DT	_	_	_
16	water	water	NN	_	_	_
17	bath	bath	NN	_	_	_
18	at	at	IN	_	_	_
19	30ºC	30ºC	NNP	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	CFT073	cft073	NN	_	_	_
3	in	in	IN	_	_	_
4	K-med	k-med	JJ	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	CFT073	cft073	NN	_	_	_
7	in	in	IN	_	_	_
8	NaCl	nacl	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	CFT073	cft073	NN	_	_	_
11	in	in	IN	_	_	_
12	urea	urea	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	CFT073	cft073	NN	_	_	_
15	K-med	k-med	JJ	_	_	_
16	biological	biological	JJ	_	_	_
17	rep	rep	NN	GEN	_	_
18	1	1	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	CFT073	cft073	NN	_	_	_
21	K-med	k-med	JJ	_	_	_
22	biological	biological	JJ	_	_	_
23	rep	rep	NN	GEN	_	_
24	2	2	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	CFT073	cft073	NN	_	_	_
27	K-med	k-med	JJ	_	_	_
28	biological	biological	JJ	_	_	_
29	rep	rep	NN	GEN	_	_
30	3	3	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	CFT073	cft073	NN	_	_	_
33	NaCl	nacl	NN	_	_	_
34	biological	biological	JJ	_	_	_
35	rep	rep	NN	GEN	_	_
36	1	1	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	CFT073	cft073	NN	_	_	_
39	NaCl	nacl	NN	_	_	_
40	biological	biological	JJ	_	_	_
41	rep	rep	NN	GEN	_	_
42	2	2	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	CFT073	cft073	NN	_	_	_
45	NaCl	nacl	NN	_	_	_
46	biological	biological	JJ	_	_	_
47	rep	rep	NN	GEN	_	_
48	3	3	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	CFT073	cft073	NN	_	_	_
51	urea	urea	NN	_	_	_
52	biological	biological	JJ	_	_	_
53	rep	rep	NN	GEN	_	_
54	1	1	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	CFT073	cft073	NN	_	_	_
57	urea	urea	NN	_	_	_
58	biological	biological	JJ	_	_	_
59	rep	rep	NN	GEN	_	_
60	2	2	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	CFT073	cft073	NN	_	_	_
63	urea	urea	NN	_	_	_
64	biological	biological	JJ	_	_	_
65	rep	rep	NN	GEN	_	_
66	3	3	CD	_	_	_
67	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
68	Escherichia	escherichia	FW	Organism	_	_
69	coli	coli	FW	Organism	_	_
70	CFT073	cft073	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	GCOS	gcos	NN	_	_	_
73	was	be	VBD	_	_	_
74	used	use	VBN	_	_	_
75	to	to	TO	_	_	_
76	obtain	obtain	VB	_	_	_
77	detection	detection	NN	_	_	_
78	calls	call	NNS	_	_	_
79	for	for	IN	_	_	_
80	each	each	DT	_	_	_
81	microarray	microarray	NN	_	_	_
82	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	statistical	statistical	JJ	_	_	_
3	difference	difference	NN	_	_	_
4	for	for	IN	_	_	_
5	mRNA	mrna	NN	_	_	_
6	expression	expression	NN	_	_	_
7	were	be	VBD	_	_	_
8	analyzed	analyze	VBN	_	_	_
9	using	use	VBG	_	_	_
10	CarmaWeb	CarmaWeb	NNP	_	_	_
11	.	.	.	_	_	_

1	Affymetrix	Affymetrix	NNP	_	_	_
2	GeneChip	GeneChip	NNP	_	_	_
3	analysis	analysis	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	using	use	VBG	_	_	_
7	MAS	MAS	NNP	_	_	_
8	for	for	IN	_	_	_
9	background	background	NN	_	_	_
10	correction	correction	NN	_	_	_
11	,	,	,	_	_	_
12	VSN	VSN	NNP	_	_	_
13	for	for	IN	_	_	_
14	normalization	normalization	NN	_	_	_
15	,	,	,	_	_	_
16	MAS	MAS	NNP	_	_	_
17	for	for	IN	_	_	_
18	PM	PM	NNP	_	_	_
19	correction	correction	NN	_	_	_
20	and	and	CC	_	_	_
21	Medianpolish	medianpolish	NN	_	_	_
22	for	for	IN	_	_	_
23	Expression	expression	NN	_	_	_
24	.	.	.	_	_	_

1	VSN	VSN	NNP	_	_	_
2	normalized	normalize	VBD	_	_	_
3	data	datum	NNS	_	_	_
4	not	not	RB	_	_	_
5	provided	provide	VBN	_	_	_
6	by	by	IN	_	_	_
7	submitter	submitter	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	growth	growth	NN	_	_	_
3	condition	condition	NN	_	_	_
4	:	:	:	_	_	_
5	25	25	CD	_	_	_
6	μl	μl	NN	_	_	_
7	into	into	IN	_	_	_
8	K-medium	k-medium	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	growth	growth	NN	_	_	_
11	condition	condition	NN	_	_	_
12	:	:	:	_	_	_
13	50	50	CD	_	_	_
14	µl	µl	NN	_	_	_
15	into	into	IN	_	_	_
16	K-medium	k-medium	NN	_	_	_
17	+	+	CC	_	_	_
18	0.3	0.3	CD	_	_	_
19	M	m	NN	_	_	_
20	NaCl	nacl	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	growth	growth	NN	_	_	_
23	condition	condition	NN	_	_	_
24	:	:	:	_	_	_
25	75	75	CD	_	_	_
26	µl	µl	NN	_	_	_
27	into	into	IN	_	_	_
28	K-medium	k-medium	NN	_	_	_
29	+	+	CC	_	_	_
30	0.6	0.6	CD	_	_	_
31	M	m	NN	_	_	_
32	urea	urea	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Total	total	JJ	_	_	_
35	RNA	rna	NN	_	_	_
36	was	be	VBD	_	_	_
37	extracted	extract	VBN	_	_	_
38	by	by	IN	_	_	_
39	the	the	DT	_	_	_
40	hot	hot	JJ	_	_	_
41	phenol	phenol	NN	_	_	_
42	--	--	:	_	_	_
43	chloroform	chloroform	NN	_	_	_
44	method	method	NN	_	_	_
45	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	When	when	WRB	_	_	_
3	the	the	DT	_	_	_
4	samples	sample	NNS	_	_	_
5	had	have	VBD	_	_	_
6	reached	reach	VBN	_	_	_
7	an	a	DT	_	_	_
8	OD600	od600	NN	_	_	_
9	of	of	IN	_	_	_
10	0.4-0.5	0.4-0.5	CD	_	_	_
11	,	,	,	_	_	_
12	25	25	CD	_	_	_
13	ml	ml	NN	_	_	_
14	of	of	IN	_	_	_
15	each	each	DT	_	_	_
16	culture	culture	NN	_	_	_
17	was	be	VBD	_	_	_
18	added	add	VBN	_	_	_
19	to	to	TO	_	_	_
20	a	a	DT	_	_	_
21	2.5	2.5	CD	_	_	_
22	ml	ml	NN	_	_	_
23	mixture	mixture	NN	_	_	_
24	of	of	IN	_	_	_
25	cold	cold	JJ	_	_	_
26	95	95	CD	_	_	_
27	%	%	NN	_	_	_
28	ethanol	ethanol	NN	_	_	_
29	and	and	CC	_	_	_
30	5	5	CD	_	_	_
31	%	%	NN	_	_	_
32	phenol	phenol	NN	_	_	_
33	to	to	TO	_	_	_
34	preserve	preserve	VB	_	_	_
35	the	the	DT	_	_	_
36	mRNA	mrna	NN	_	_	_
37	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	cooled	cool	VBN	_	_	_
5	rapidly	rapidly	RB	_	_	_
6	on	on	IN	_	_	_
7	ice	ice	NN	_	_	_
8	and	and	CC	_	_	_
9	immediately	immediately	RB	_	_	_
10	harvested	harvest	VBN	_	_	_
11	by	by	IN	_	_	_
12	centrifugation	centrifugation	NN	_	_	_
13	at	at	IN	_	_	_
14	4	4	CD	_	_	_
15	°C	°c	NN	_	_	_
16	,	,	,	_	_	_
17	and	and	CC	_	_	_
18	the	the	DT	_	_	_
19	pellet	pellet	NN	_	_	_
20	was	be	VBD	_	_	_
21	frozen	freeze	VBN	_	_	_
22	on	on	IN	_	_	_
23	dry	dry	JJ	_	_	_
24	ice	ice	NN	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	1	1	CD	_	_	_
3	.	.	.	_	_	_

1	library	library	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	maanova	maanova	NN	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	2	2	CD	_	_	_
7	.	.	.	_	_	_

1	Read	Read	NNP	_	_	_
2	data	datum	NNS	_	_	_
3	:	:	:	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
5	3	3	CD	_	_	_
6	.	.	.	_	_	_

1	Log	log	VB	_	_	_
2	transformation	transformation	NN	_	_	_
3	:	:	:	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	4	4	CD	_	_	_
6	.	.	.	_	_	_

1	Normalization	normalization	NN	_	_	_
2	by	by	IN	_	_	_
3	Glowess	glowess	NN	_	_	_
4	method	method	NN	_	_	_
5	:	:	:	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	5	5	CD	_	_	_
8	.	.	.	_	_	_

1	Save	save	VB	_	_	_
2	the	the	DT	_	_	_
3	plot	plot	NN	_	_	_
4	files	file	VBZ	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	6	6	CD	_	_	_
7	.	.	.	_	_	_

1	close	close	RB	_	_	_
2	the	the	DT	_	_	_
3	graph	graph	NN	_	_	_
4	:	:	:	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	7	7	CD	_	_	_
7	.	.	.	_	_	_

1	output	output	NN	_	_	_
2	:	:	:	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
4	Add	add	VBP	_	_	_
5	100	100	CD	_	_	_
6	μl	μl	NN	_	_	_
7	1	1	CD	_	_	_
8	mg	mg	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Bacterial	bacterial	JJ	_	_	_
11	lysis	lysis	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	Column	column	NN	_	_	_
14	purification	purification	NN	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	Data	Data	NNP	_	_	_
17	=	=	JJ	_	_	_
18	read.madata	read.madata	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	\	\	CD	_	_	_
21	NormInput.txt	norminput.txt	NN	_	_	_
22	\	\	NN	_	_	_
23	,	,	,	_	_	_
24	designfile	designfile	NN	_	_	_
25	=	=	JJ	_	_	_
26	\	\	CD	_	_	_
27	Designfile1.txt	designfile1.txt	NN	_	_	_
28	\	\	NN	_	_	_
29	,	,	,	_	_	_
30	header	header	NN	_	_	_
31	=	=	JJ	_	_	_
32	TRUE	true	JJ	_	_	_
33	,	,	,	_	_	_
34	spotflag	spotflag	NN	_	_	_
35	=	=	JJ	_	_	_
36	TRUE	true	JJ	_	_	_
37	,	,	,	_	_	_
38	metarow	metarow	NN	_	_	_
39	=	=	JJ	_	_	_
40	1	1	CD	_	_	_
41	,	,	,	_	_	_
42	metacol	metacol	NN	_	_	_
43	=	=	JJ	_	_	_
44	2	2	CD	_	_	_
45	,	,	,	_	_	_
46	row	row	NN	_	_	_
47	=	=	JJ	_	_	_
48	3	3	CD	_	_	_
49	,	,	,	_	_	_
50	col	col	NN	_	_	_
51	=	=	JJ	_	_	_
52	4	4	CD	_	_	_
53	,	,	,	_	_	_
54	geneID	geneid	NN	_	_	_
55	=	=	JJ	_	_	_
56	5	5	CD	_	_	_
57	,	,	,	_	_	_
58	pmt	pmt	NN	_	_	_
59	=	=	JJ	_	_	_
60	6	6	CD	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
63	Data	Data	NNP	_	_	_
64	selection	selection	NN	_	_	_
65	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
66	E.	E.	NNP	_	_	_
67	coli	coli	NN	_	_	_
68	K12	k12	NN	_	_	_
69	cells	cell	NNS	_	_	_
70	,	,	,	_	_	_
71	M9	m9	NN	_	_	_
72	,	,	,	_	_	_
73	8	8	CD	_	_	_
74	h	h	NN	_	_	_
75	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
76	E.	E.	NNP	_	_	_
77	coli	coli	NN	_	_	_
78	K12	k12	NN	_	_	_
79	_	_	CD	_	_	_
80	WT	WT	NNP	_	_	_
81	_	_	NNP	_	_	_
82	M9	M9	NNP	_	_	_
83	_	_	SYM	_	_	_
84	rep1	rep1	CD	_	_	_
85	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
86	E.	E.	NNP	_	_	_
87	coli	coli	NN	_	_	_
88	K12	k12	NN	_	_	_
89	_	_	CD	_	_	_
90	WT	WT	NNP	_	_	_
91	_	_	NNP	_	_	_
92	M9	M9	NNP	_	_	_
93	_	_	SYM	_	_	_
94	rep2	rep2	CD	_	_	_
95	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
96	E.	E.	NNP	_	_	_
97	coli	coli	NN	_	_	_
98	K12	k12	NN	_	_	_
99	ybjN	ybjn	NN	GEN	_	_
100	mutant	mutant	JJ	_	_	_
101	cells	cell	NNS	_	_	_
102	,	,	,	_	_	_
103	M9	m9	NN	_	_	_
104	,	,	,	_	_	_
105	8	8	CD	_	_	_
106	h	h	NN	_	_	_
107	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
108	E.	E.	NNP	_	_	_
109	coli	coli	NN	_	_	_
110	K12	k12	NN	_	_	_
111	_	_	CD	_	_	_
112	ybjN	ybjn	NN	GEN	_	_
113	_	_	CD	_	_	_
114	MUTANT	mutant	JJ	_	_	_
115	_	_	NN	_	_	_
116	M9	m9	NN	_	_	_
117	_	_	CD	_	_	_
118	rep1	rep1	NN	_	_	_
119	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
120	E.	E.	NNP	_	_	_
121	coli	coli	NN	_	_	_
122	K12	k12	NN	_	_	_
123	_	_	CD	_	_	_
124	ybjN	ybjn	NN	GEN	_	_
125	_	_	CD	_	_	_
126	MUTANT	mutant	JJ	_	_	_
127	_	_	NN	_	_	_
128	M9	m9	NN	_	_	_
129	_	_	CD	_	_	_
130	rep2	rep2	NN	_	_	_
131	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
132	E.	E.	NNP	_	_	_
133	coli	coli	NN	_	_	_
134	K12	k12	NN	_	_	_
135	_	_	CD	_	_	_
136	ybjN	ybjn	NN	GEN	_	_
137	_	_	CD	_	_	_
138	MUTANT	mutant	JJ	_	_	_
139	_	_	NN	_	_	_
140	M9	m9	NN	_	_	_
141	_	_	CD	_	_	_
142	rep3	rep3	NN	_	_	_
143	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
144	E.	E.	NNP	_	_	_
145	coli	coli	NN	_	_	_
146	K12	k12	NN	_	_	_
147	ybjN	ybjn	NN	GEN	_	_
148	over-expression	over-expression	NN	_	_	_
149	cells	cell	NNS	_	_	_
150	,	,	,	_	_	_
151	M9	m9	NN	_	_	_
152	,	,	,	_	_	_
153	8	8	CD	_	_	_
154	h	h	NN	_	_	_
155	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
156	E.	E.	NNP	_	_	_
157	coli	coli	NN	_	_	_
158	K12	k12	NN	_	_	_
159	_	_	CD	_	_	_
160	ybjN	ybjn	NN	GEN	_	_
161	_	_	NN	_	_	_
162	OVER-EXPRESSION	over-expression	NN	_	_	_
163	_	_	CD	_	_	_
164	M9	m9	NN	_	_	_
165	_	_	CD	_	_	_
166	rep1	rep1	NN	_	_	_
167	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
168	E.	E.	NNP	_	_	_
169	coli	coli	NN	_	_	_
170	K12	k12	NN	_	_	_
171	_	_	CD	_	_	_
172	ybjN	ybjn	NN	GEN	_	_
173	_	_	NN	_	_	_
174	OVER-EXPRESSION	over-expression	NN	_	_	_
175	_	_	CD	_	_	_
176	M9	m9	NN	_	_	_
177	_	_	CD	_	_	_
178	rep2	rep2	NN	_	_	_
179	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
180	E.	E.	NNP	_	_	_
181	coli	coli	NN	_	_	_
182	K12	k12	NN	_	_	_
183	_	_	CD	_	_	_
184	ybjN	ybjn	NN	GEN	_	_
185	_	_	NN	_	_	_
186	OVER-EXPRESSION	over-expression	NN	_	_	_
187	_	_	CD	_	_	_
188	M9	m9	NN	_	_	_
189	_	_	CD	_	_	_
190	rep3	rep3	NN	_	_	_
191	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
192	Escherichia	escherichia	FW	Organism	_	_
193	coli	coli	FW	Organism	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	genotype	genotype	NN	_	_	_
196	:	:	:	_	_	_
197	wild	wild	JJ	_	_	_
198	type	type	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	genotype	genotype	NN	_	_	_
201	:	:	:	_	_	_
202	ybjN	ybjn	NN	GEN	_	_
203	mutant	mutant	JJ	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	genotype	genotype	NN	_	_	_
206	:	:	:	_	_	_
207	ybjN	ybjn	NN	GEN	_	_
208	over-expression	over-expression	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
210	go	go	VBP	_	_	_
211	to	to	TO	_	_	_
212	the	the	DT	_	_	_
213	directory	directory	NN	_	_	_
214	:	:	:	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	graphics.off	graphics.off	NN	_	_	_
217	-LRB-	-lrb-	-LRB-	_	_	_
218	-RRB-	-rrb-	-RRB-	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
220	Grow	grow	VBP	_	_	_
221	bacteria	bacterium	NNS	_	_	_
222	overnight	overnight	JJ	_	_	_
223	in	in	IN	_	_	_
224	LB	lb	NN	MED	_	_
225	medium	medium	NN	MED	_	_
226	,	,	,	_	_	_
227	reinoculate	reinoculate	NN	_	_	_
228	in	in	IN	_	_	_
229	M9	m9	NN	MED	_	_
230	minimal	minimal	JJ	MED	_	_
231	medium	medium	NN	MED	_	_
232	at	at	IN	_	_	_
233	an	a	DT	_	_	_
234	initial	initial	JJ	_	_	_
235	OD600	od600	NN	_	_	_
236	of	of	IN	_	_	_
237	0.005	0.005	CD	_	_	_
238	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	eight	eight	CD	_	_	_
3	hours	hour	NNS	_	_	_
4	growth	growth	NN	_	_	_
5	at	at	IN	_	_	_
6	34	34	CD	_	_	_
7	°C	°c	NN	_	_	_
8	in	in	IN	_	_	_
9	M9	m9	NN	_	_	_
10	medium	medium	NN	_	_	_
11	,	,	,	_	_	_
12	2	2	CD	_	_	_
13	mL	ml	NN	_	_	_
14	of	of	IN	_	_	_
15	RNA	rna	NN	_	_	_
16	Protect	protect	VB	_	_	_
17	Reagent	reagent	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Qiagen	qiagen	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	was	be	VBD	_	_	_
22	added	add	VBN	_	_	_
23	to	to	TO	_	_	_
24	1	1	CD	_	_	_
25	ml	ml	NN	_	_	_
26	bacterial	bacterial	JJ	_	_	_
27	cultures	culture	NNS	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	at	at	IN	_	_	_
30	OD600	od600	NN	_	_	_
31	of	of	IN	_	_	_
32	about	about	IN	_	_	_
33	0.5-0.8	0.5-0.8	CD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	to	to	TO	_	_	_
36	stabilize	stabilize	VB	_	_	_
37	RNA	rna	NN	_	_	_
38	.	.	.	_	_	_

1	Centrifuge	Centrifuge	NNP	_	_	_
2	for	for	IN	_	_	_
3	10	10	CD	_	_	_
4	min	min	NN	_	_	_
5	at	at	IN	_	_	_
6	4000	4000	CD	_	_	_
7	g.	g.	NNP	_	_	_
8	Decant	Decant	NNP	_	_	_
9	the	the	DT	_	_	_
10	supernatant	supernatant	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	growing	grow	VBG	_	_	_
3	condition	condition	NN	_	_	_
4	:	:	:	_	_	_
5	M9	m9	NN	MED	_	_
6	minimal	minimal	JJ	MED	_	_
7	medium	medium	NN	MED	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	LogData	logdata	NN	_	_	_
10	=	=	JJ	_	_	_
11	createData	createdata	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Data	data	NN	_	_	_
14	,	,	,	_	_	_
15	n.rep	n.rep	NN	_	_	_
16	=	=	JJ	_	_	_
17	1	1	CD	_	_	_
18	,	,	,	_	_	_
19	log.trans	log.trans	VBZ	_	_	_
20	=	=	JJ	_	_	_
21	TRUE	true	JJ	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	Microarray	microarray	NN	_	_	_
25	data	datum	NNS	_	_	_
26	normalization	normalization	NN	_	_	_
27	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
28	Microarray	Microarray	NNP	_	_	_
29	normalization	normalization	NN	_	_	_
30	is	be	VBZ	_	_	_
31	carried	carry	VBN	_	_	_
32	out	out	RP	_	_	_
33	using	use	VBG	_	_	_
34	maanova	maanova	NN	_	_	_
35	function	function	NN	_	_	_
36	in	in	IN	_	_	_
37	R	r	NN	_	_	_
38	program	program	NN	_	_	_
39	version	version	NN	_	_	_
40	2.2.1	2.2.1	CD	_	_	_
41	.	.	.	_	_	_

1	Eight	eight	CD	_	_	_
2	arrays	array	NNS	_	_	_
3	in	in	IN	_	_	_
4	one	one	CD	_	_	_
5	slide	slide	NN	_	_	_
6	were	be	VBD	_	_	_
7	globally	globally	RB	_	_	_
8	normalized	normalize	VBN	_	_	_
9	using	use	VBG	_	_	_
10	glowess	glowess	NN	_	_	_
11	method	method	NN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	NormalData	normaldata	NN	_	_	_
3	=	=	JJ	_	_	_
4	transform.madata	transform.madata	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	LogData	LogData	NNP	_	_	_
7	,	,	,	_	_	_
8	method	method	NN	_	_	_
9	=	=	JJ	_	_	_
10	c	c	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	\	\	CD	_	_	_
13	glowess	glowess	NN	_	_	_
14	\	\	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	norm.temp	norm.temp	NN	_	_	_
19	<	<	JJR	_	_	_
20	-	-	:	_	_	_
21	cbind	cbind	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	NormalData	NormalData	NNP	_	_	_
24	$	$	$	_	_	_
25	metarow	metarow	JJ	_	_	_
26	,	,	,	_	_	_
27	NormalData	NormalData	NNP	_	_	_
28	$	$	$	_	_	_
29	metacol	metacol	JJ	_	_	_
30	,	,	,	_	_	_
31	NormalData	NormalData	NNP	_	_	_
32	$	$	$	_	_	_
33	row	row	NN	_	_	_
34	,	,	,	_	_	_
35	NormalData	NormalData	NNP	_	_	_
36	$	$	$	_	_	_
37	col	col	CD	_	_	_
38	,	,	,	_	_	_
39	NormalData	NormalData	NNP	_	_	_
40	$	$	$	_	_	_
41	geneID	geneid	JJ	_	_	_
42	,	,	,	_	_	_
43	NormalData	NormalData	NNP	_	_	_
44	$	$	$	_	_	_
45	data	datum	NNS	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
48	postscript	postscript	NN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	file	file	NN	_	_	_
51	=	=	JJ	_	_	_
52	\	\	CD	_	_	_
53	PlotGLOWESS.ps	plotglowess.ps	NNS	_	_	_
54	\	\	NN	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	postscript	postscript	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	file	file	NN	_	_	_
60	=	=	JJ	_	_	_
61	\	\	CD	_	_	_
62	PlotRawData.ps	plotrawdata.ps	NNS	_	_	_
63	\	\	CD	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	riplot	riplot	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	LogData	LogData	NNP	_	_	_
69	,	,	,	_	_	_
70	onScreen	onscreen	NN	_	_	_
71	=	=	JJ	_	_	_
72	FALSE	false	NN	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	riplot	riplot	NN	_	_	_
76	-LRB-	-lrb-	-LRB-	_	_	_
77	NormalData	NormalData	NNP	_	_	_
78	,	,	,	_	_	_
79	onScreen	onscreen	NN	_	_	_
80	=	=	JJ	_	_	_
81	FALSE	false	NN	_	_	_
82	-RRB-	-rrb-	-RRB-	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	Sample	sample	NN	_	_	_
85	collection	collection	NN	_	_	_
86	from	from	IN	_	_	_
87	M9	m9	NN	_	_	_
88	medium	medium	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	setwd	setwd	NN	_	_	_
91	-LRB-	-lrb-	-LRB-	_	_	_
92	\	\	CD	_	_	_
93	C	c	NN	_	_	_
94	:	:	:	_	_	_
95	\	\	SYM	_	_	_
96	Documents	document	NNS	_	_	_
97	and	and	CC	_	_	_
98	Settings	setting	NNS	_	_	_
99	\	\	VBP	_	_	_
100	Wang	Wang	NNP	_	_	_
101	\	\	NNP	_	_	_
102	Desktop	Desktop	NNP	_	_	_
103	\	\	NNP	_	_	_
104	Erwinia	Erwinia	NNP	_	_	_
105	in	in	FW	_	_	_
106	vivo	vivo	FW	_	_	_
107	\	\	SYM	_	_	_
108	rcsC	rcsC	NNP	GEN	_	_
109	MBMA	MBMA	NNP	_	_	_
110	\	\	NN	_	_	_
111	-RRB-	-rrb-	-RRB-	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	Stage	stage	NN	_	_	_
114	:	:	:	_	_	_
115	logarithm	logarithm	NN	_	_	_
116	phase	phase	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
118	Statistical	statistical	JJ	_	_	_
119	comparisons	comparison	NNS	_	_	_
120	were	be	VBD	_	_	_
121	performed	perform	VBN	_	_	_
122	using	use	VBG	_	_	_
123	multiple	multiple	JJ	_	_	_
124	testing	testing	NN	_	_	_
125	procedures	procedure	NNS	_	_	_
126	to	to	TO	_	_	_
127	evaluate	evaluate	VB	_	_	_
128	statistical	statistical	JJ	_	_	_
129	significance	significance	NN	_	_	_
130	for	for	IN	_	_	_
131	differentially	differentially	RB	_	_	_
132	expressed	express	VBN	_	_	_
133	genes	gene	NNS	_	_	_
134	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	modified	modify	VBN	_	_	_
3	t-test	t-test	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	p-value	p-value	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	was	be	VBD	_	_	_
8	computed	compute	VBN	_	_	_
9	to	to	TO	_	_	_
10	measure	measure	VB	_	_	_
11	the	the	DT	_	_	_
12	significance	significance	NN	_	_	_
13	associated	associate	VBN	_	_	_
14	with	with	IN	_	_	_
15	each	each	DT	_	_	_
16	differential	differential	JJ	_	_	_
17	expression	expression	NN	_	_	_
18	value	value	NN	_	_	_
19	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	gene	gene	NN	_	_	_
3	expression	expression	NN	_	_	_
4	value	value	NN	_	_	_
5	was	be	VBD	_	_	_
6	decided	decide	VBN	_	_	_
7	to	to	TO	_	_	_
8	be	be	VB	_	_	_
9	significantly	significantly	RB	_	_	_
10	different	different	JJ	_	_	_
11	in	in	IN	_	_	_
12	the	the	DT	_	_	_
13	mutant	mutant	JJ	_	_	_
14	and	and	CC	_	_	_
15	over-expression	over-expression	NN	_	_	_
16	strains	strain	NNS	_	_	_
17	when	when	WRB	_	_	_
18	the	the	DT	_	_	_
19	p-value	p-value	NN	_	_	_
20	was	be	VBD	_	_	_
21	less	less	JJR	_	_	_
22	than	than	IN	_	_	_
23	0.05	0.05	CD	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	except	except	IN	_	_	_
26	otherwise	otherwise	RB	_	_	_
27	mentioned	mention	VBN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	and	and	CC	_	_	_
30	the	the	DT	_	_	_
31	expression	expression	NN	_	_	_
32	ratio	ratio	NN	_	_	_
33	was	be	VBD	_	_	_
34	≥	≥	CD	_	_	_
35	2.0	2.0	CD	_	_	_
36	or	or	CC	_	_	_
37	≤	≤	CD	_	_	_
38	0.5	0.5	CD	_	_	_
39	.	.	.	_	_	_

1	Gene	Gene	NNP	_	_	_
2	functions	function	NNS	_	_	_
3	were	be	VBD	_	_	_
4	assigned	assign	VBN	_	_	_
5	using	use	VBG	_	_	_
6	data	datum	NNS	_	_	_
7	from	from	IN	_	_	_
8	EcoCyc	ecocyc	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	http	http	NN	_	_	_
11	:	:	:	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	strain	strain	NN	_	_	_
14	:	:	:	_	_	_
15	K12	k12	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Total	total	JJ	_	_	_
18	RNA	rna	NN	_	_	_
19	isolation	isolation	NN	_	_	_
20	was	be	VBD	_	_	_
21	performed	perform	VBN	_	_	_
22	using	use	VBG	_	_	_
23	the	the	DT	_	_	_
24	RNeasy	RNeasy	NNP	_	_	_
25	Protect	Protect	NNP	_	_	_
26	Bacteria	bacterium	NNS	_	_	_
27	system	system	NN	_	_	_
28	from	from	IN	_	_	_
29	Qiagen	Qiagen	NNP	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Transfer	transfer	NN	_	_	_
3	700	700	CD	_	_	_
4	μl	μl	NN	_	_	_
5	lysate	lysate	NN	_	_	_
6	into	into	IN	_	_	_
7	RNeasy	RNeasy	NNP	_	_	_
8	Mini	Mini	NNP	_	_	_
9	column	column	NN	_	_	_
10	place	place	NN	_	_	_
11	in	in	IN	_	_	_
12	a	a	DT	_	_	_
13	2	2	CD	_	_	_
14	ml	ml	NN	_	_	_
15	collection	collection	NN	_	_	_
16	tube	tube	NN	_	_	_
17	and	and	CC	_	_	_
18	centrifuge	centrifuge	NN	_	_	_
19	for	for	IN	_	_	_
20	30	30	CD	_	_	_
21	s	s	NNS	_	_	_
22	at	at	IN	_	_	_
23	highest	highest	JJS	_	_	_
24	speed	speed	NN	_	_	_
25	.	.	.	_	_	_

1	Add	add	VB	_	_	_
2	350	350	CD	_	_	_
3	μl	μl	NN	_	_	_
4	Buffer	buffer	NN	_	_	_
5	RW1	rw1	NN	_	_	_
6	to	to	TO	_	_	_
7	the	the	DT	_	_	_
8	column	column	NN	_	_	_
9	and	and	CC	_	_	_
10	centrifuge	centrifuge	NN	_	_	_
11	for	for	IN	_	_	_
12	30	30	CD	_	_	_
13	s.	s.	NN	_	_	_
14	Discard	Discard	NNP	_	_	_
15	flow-through	flow-through	JJ	_	_	_
16	and	and	CC	_	_	_
17	reuse	reuse	VB	_	_	_
18	the	the	DT	_	_	_
19	collection	collection	NN	_	_	_
20	tube	tube	NN	_	_	_
21	.	.	.	_	_	_

1	Add	add	VB	_	_	_
2	10	10	CD	_	_	_
3	μl	μl	NN	_	_	_
4	DNase	dnase	NN	_	_	_
5	stock	stock	NN	_	_	_
6	solution	solution	NN	_	_	_
7	to	to	TO	_	_	_
8	70	70	CD	_	_	_
9	μ	μ	NN	_	_	_
10	l	l	NN	_	_	_
11	RDD	RDD	NNP	_	_	_
12	Buffer	Buffer	NNP	_	_	_
13	.	.	.	_	_	_

1	Add	add	VB	_	_	_
2	the	the	DT	_	_	_
3	DNase	dnase	NN	_	_	_
4	I	i	CD	_	_	_
5	solution	solution	NN	_	_	_
6	into	into	IN	_	_	_
7	the	the	DT	_	_	_
8	column	column	NN	_	_	_
9	and	and	CC	_	_	_
10	incubate	incubate	VB	_	_	_
11	at	at	IN	_	_	_
12	RT	rt	NN	_	_	_
13	for	for	IN	_	_	_
14	15	15	CD	_	_	_
15	min	min	NN	_	_	_
16	.	.	.	_	_	_

1	Add	add	VB	_	_	_
2	350	350	CD	_	_	_
3	μl	μl	NN	_	_	_
4	Buffer	buffer	NN	_	_	_
5	RW1	rw1	NN	_	_	_
6	to	to	TO	_	_	_
7	the	the	DT	_	_	_
8	column	column	NN	_	_	_
9	and	and	CC	_	_	_
10	wait	wait	VB	_	_	_
11	for	for	IN	_	_	_
12	5	5	CD	_	_	_
13	min	min	NN	_	_	_
14	,	,	,	_	_	_
15	centrifuge	centrifuge	NN	_	_	_
16	for	for	IN	_	_	_
17	30	30	CD	_	_	_
18	s.	s.	NN	_	_	_
19	Discard	Discard	NNP	_	_	_
20	the	the	DT	_	_	_
21	flow-through	flow-through	JJ	_	_	_
22	and	and	CC	_	_	_
23	collection	collection	NN	_	_	_
24	tubes	tube	NNS	_	_	_
25	.	.	.	_	_	_

1	Place	place	VB	_	_	_
2	the	the	DT	_	_	_
3	RNeasy	RNeasy	NNP	_	_	_
4	Mini	Mini	NNP	_	_	_
5	spin	spin	VB	_	_	_
6	column	column	NN	_	_	_
7	in	in	IN	_	_	_
8	a	a	DT	_	_	_
9	new	new	JJ	_	_	_
10	2	2	CD	_	_	_
11	ml	ml	NN	_	_	_
12	collection	collection	NN	_	_	_
13	tube	tube	NN	_	_	_
14	.	.	.	_	_	_

1	Add	add	VB	_	_	_
2	500	500	CD	_	_	_
3	μl	μl	NN	_	_	_
4	Buffer	buffer	NN	_	_	_
5	RPE	rpe	NN	_	_	_
6	to	to	TO	_	_	_
7	the	the	DT	_	_	_
8	column	column	NN	_	_	_
9	.	.	.	_	_	_

1	Centrifuge	Centrifuge	NNP	_	_	_
2	for	for	IN	_	_	_
3	30	30	CD	_	_	_
4	s.	s.	NN	_	_	_
5	Place	place	NN	_	_	_
6	the	the	DT	_	_	_
7	column	column	NN	_	_	_
8	in	in	IN	_	_	_
9	a	a	DT	_	_	_
10	new	new	JJ	_	_	_
11	1.5	1.5	CD	_	_	_
12	ml	ml	NN	_	_	_
13	tube	tube	NN	_	_	_
14	,	,	,	_	_	_
15	and	and	CC	_	_	_
16	centrifuge	centrifuge	NN	_	_	_
17	for	for	IN	_	_	_
18	1	1	CD	_	_	_
19	min	min	NN	_	_	_
20	to	to	TO	_	_	_
21	eliminate	eliminate	VB	_	_	_
22	any	any	DT	_	_	_
23	residue	residue	NN	_	_	_
24	ethanol	ethanol	NN	_	_	_
25	.	.	.	_	_	_

1	Place	place	VB	_	_	_
2	the	the	DT	_	_	_
3	column	column	NN	_	_	_
4	in	in	IN	_	_	_
5	a	a	DT	_	_	_
6	new	new	JJ	_	_	_
7	collection	collection	NN	_	_	_
8	tube	tube	NN	_	_	_
9	.	.	.	_	_	_

1	Add	add	VB	_	_	_
2	50	50	CD	_	_	_
3	μl	μl	NN	_	_	_
4	RNase	rnase	NN	_	_	_
5	free	free	JJ	_	_	_
6	water	water	NN	_	_	_
7	,	,	,	_	_	_
8	centrifuge	centrifuge	NN	_	_	_
9	for	for	IN	_	_	_
10	1	1	CD	_	_	_
11	min	min	NN	_	_	_
12	.	.	.	_	_	_

1	Store	store	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	samples	sample	NNS	_	_	_
4	at	at	IN	_	_	_
5	-20	-20	CD	_	_	_
6	°C	°c	NN	_	_	_
7	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	write.table	write.table	JJ	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	norm.temp	norm.temp	JJ	_	_	_
5	,	,	,	_	_	_
6	file	file	NN	_	_	_
7	=	=	JJ	_	_	_
8	\	\	CD	_	_	_
9	Normal	normal	JJ	_	_	_
10	_	_	NN	_	_	_
11	Data.csv	data.csv	NN	_	_	_
12	\	\	NN	_	_	_
13	,	,	,	_	_	_
14	sep	sep	NN	_	_	_
15	=\	=\	NN	_	_	_
16	,	,	,	_	_	_
17	\	\	NN	_	_	_
18	,	,	,	_	_	_
19	row.names	row.names	NN	_	_	_
20	=	=	JJ	_	_	_
21	FALSE	false	NN	_	_	_
22	,	,	,	_	_	_
23	col.names	col.names	NNS	_	_	_
24	=	=	JJ	_	_	_
25	TRUE	true	JJ	_	_	_
26	,	,	,	_	_	_
27	quote	quote	NN	_	_	_
28	=	=	JJ	_	_	_
29	FALSE	false	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Average	average	JJ	_	_	_
33	Normalization	normalization	NN	_	_	_
34	using	use	VBG	_	_	_
35	GeneChip	GeneChip	NNP	_	_	_
36	Operating	Operating	NNP	_	_	_
37	Software	Software	NNP	_	_	_
38	Version	Version	NNP	_	_	_
39	1.4	1.4	CD	_	_	_
40	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
41	Control	Control	NNP	_	_	_
42	Strain	Strain	NNP	_	_	_
43	at	at	IN	_	_	_
44	specific	specific	JJ	_	_	_
45	growth	growth	NN	_	_	_
46	rate	rate	NN	_	_	_
47	0.5h-1	0.5h-1	JJ	_	_	_
48	0h	0h	NN	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	Control	Control	NNP	_	_	_
51	Strain	Strain	NNP	_	_	_
52	at	at	IN	_	_	_
53	specific	specific	JJ	_	_	_
54	growth	growth	NN	_	_	_
55	rate	rate	NN	_	_	_
56	0.5h-1	0.5h-1	JJ	_	_	_
57	10h	10h	CD	_	_	_
58	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
59	Control	Control	NNP	_	_	_
60	Strain	Strain	NNP	_	_	_
61	at	at	IN	_	_	_
62	specific	specific	JJ	_	_	_
63	growth	growth	NN	_	_	_
64	rate	rate	NN	_	_	_
65	0.5h-1	0.5h-1	JJ	_	_	_
66	16h	16h	NN	_	_	_
67	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
68	Control	Control	NNP	_	_	_
69	Strain	Strain	NNP	_	_	_
70	at	at	IN	_	_	_
71	specific	specific	JJ	_	_	_
72	growth	growth	NN	_	_	_
73	rate	rate	NN	_	_	_
74	0.5h-1	0.5h-1	JJ	_	_	_
75	20h	20h	JJ	_	_	_
76	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
77	Control	Control	NNP	_	_	_
78	Strain	Strain	NNP	_	_	_
79	at	at	IN	_	_	_
80	specific	specific	JJ	_	_	_
81	growth	growth	NN	_	_	_
82	rate	rate	NN	_	_	_
83	0.5h-1	0.5h-1	JJ	_	_	_
84	6h	6h	JJ	_	_	_
85	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
86	Control	Control	NNP	_	_	_
87	Strain	Strain	NNP	_	_	_
88	at	at	IN	_	_	_
89	specific	specific	JJ	_	_	_
90	growth	growth	NN	_	_	_
91	rate	rate	NN	_	_	_
92	0.5h-1	0.5h-1	JJ	_	_	_
93	8h	8h	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	Culture	culture	NN	_	_	_
96	samples	sample	NNS	_	_	_
97	frozen	freeze	VBN	_	_	_
98	in	in	IN	_	_	_
99	liquid	liquid	JJ	_	_	_
100	methanol	methanol	NN	_	_	_
101	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
102	Escherichia	escherichia	FW	Organism	_	_
103	coli	coli	FW	Organism	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	Fed	Fed	NNP	_	_	_
106	batch	batch	NN	_	_	_
107	high	high	JJ	_	_	_
108	cell	cell	NN	_	_	_
109	density	density	NN	_	_	_
110	cultivation	cultivation	NN	_	_	_
111	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
112	Indole	Indole	NNP	_	_	_
113	treated	treat	VBN	_	_	_
114	at	at	IN	_	_	_
115	specific	specific	JJ	_	_	_
116	growth	growth	NN	_	_	_
117	rate	rate	NN	_	_	_
118	0.5h-1	0.5h-1	JJ	_	_	_
119	0h	0h	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	Indole	indole	FW	_	_	_
122	treated	treat	VBN	_	_	_
123	at	at	IN	_	_	_
124	specific	specific	JJ	_	_	_
125	growth	growth	NN	_	_	_
126	rate	rate	NN	_	_	_
127	0.5h-1	0.5h-1	JJ	_	_	_
128	10h	10h	JJ	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	Indole	indole	FW	_	_	_
131	treated	treat	VBN	_	_	_
132	at	at	IN	_	_	_
133	specific	specific	JJ	_	_	_
134	growth	growth	NN	_	_	_
135	rate	rate	NN	_	_	_
136	0.5h-1	0.5h-1	JJ	_	_	_
137	16h	16h	JJ	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	Indole	indole	FW	_	_	_
140	treated	treat	VBN	_	_	_
141	at	at	IN	_	_	_
142	specific	specific	JJ	_	_	_
143	growth	growth	NN	_	_	_
144	rate	rate	NN	_	_	_
145	0.5h-1	0.5h-1	JJ	_	_	_
146	5h	5h	JJ	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	Indole	indole	FW	_	_	_
149	treated	treat	VBN	_	_	_
150	at	at	IN	_	_	_
151	specific	specific	JJ	_	_	_
152	growth	growth	NN	_	_	_
153	rate	rate	NN	_	_	_
154	0.5h-1	0.5h-1	JJ	_	_	_
155	8h	8h	NN	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
157	Qiagen	qiagen	NN	_	_	_
158	RNA	rna	NN	_	_	_
159	extraction	extraction	NN	_	_	_
160	kit	kit	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	specific	specific	JJ	_	_	_
163	growth	growth	NN	_	_	_
164	rate	rate	NN	_	_	_
165	:	:	:	_	_	_
166	0.5h-1	0.5h-1	JJ	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	strain	strain	NN	_	_	_
169	:	:	:	_	_	_
170	W3110hns	w3110hn	NNS	_	_	_
171	∆	∆	VBP	_	_	_
172	93-1	93-1	CD	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
174	time	time	NN	_	_	_
175	post-induction	post-induction	JJ	_	_	_
176	:	:	:	_	_	_
177	0h	0h	NN	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	time	time	NN	_	_	_
180	post-induction	post-induction	JJ	_	_	_
181	:	:	:	_	_	_
182	10h	10h	CD	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
184	time	time	NN	_	_	_
185	post-induction	post-induction	JJ	_	_	_
186	:	:	:	_	_	_
187	16h	16h	JJ	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
189	time	time	NN	_	_	_
190	post-induction	post-induction	JJ	_	_	_
191	:	:	:	_	_	_
192	20h	20h	JJ	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
194	time	time	NN	_	_	_
195	post-induction	post-induction	JJ	_	_	_
196	:	:	:	_	_	_
197	5h	5h	JJ	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
199	time	time	NN	_	_	_
200	post-induction	post-induction	JJ	_	_	_
201	:	:	:	_	_	_
202	6h	6h	JJ	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
204	time	time	NN	_	_	_
205	post-induction	post-induction	JJ	_	_	_
206	:	:	:	_	_	_
207	8h	8h	NN	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	treatment	treatment	NN	_	_	_
210	group	group	NN	_	_	_
211	:	:	:	_	_	_
212	control	control	NN	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	treatment	treatment	NN	_	_	_
215	group	group	NN	_	_	_
216	:	:	:	_	_	_
217	indole	indole	NN	_	_	_
218	treated	treat	VBN	_	_	_
219	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
220	Briefly	briefly	RB	_	_	_
221	,	,	,	_	_	_
222	total	total	JJ	_	_	_
223	RNA	rna	NN	_	_	_
224	were	be	VBD	_	_	_
225	isolated	isolate	VBN	_	_	_
226	from	from	IN	_	_	_
227	cell	cell	NN	_	_	_
228	culture	culture	NN	_	_	_
229	with	with	IN	_	_	_
230	Total	total	JJ	_	_	_
231	RNA	rna	NN	_	_	_
232	Extraction	extraction	NN	_	_	_
233	Kit	kit	NN	_	_	_
234	-LRB-	-lrb-	-LRB-	_	_	_
235	RBC	rbc	NN	_	_	_
236	Bioscience	bioscience	NN	_	_	_
237	-RRB-	-rrb-	-RRB-	_	_	_
238	according	accord	VBG	_	_	_
239	to	to	TO	_	_	_
240	manufacturer	manufacturer	NN	_	_	_
241	's	's	POS	_	_	_
242	specifications	specification	NNS	_	_	_
243	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	degraded	degrade	VBN	_	_	_
4	by	by	IN	_	_	_
5	DNAse	dnase	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	Promega	promega	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	control	control	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
4	double	double	JJ	_	_	_
5	mutant	mutant	JJ	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	PPK1	ppk1	NN	_	_	_
8	and	and	CC	_	_	_
9	PPX	ppx	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Escherichia	escherichia	FW	Organism	_	_
13	coli	coli	FW	Organism	_	_
14	K-12	k-12	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	exopolyphosphatase	exopolyphosphatase	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	PPX	ppx	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	mutant	mutant	JJ	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	genotype	genotype	NN	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	Microarray	Microarray	NNP	_	_	_
25	data	data	NN	_	_	_
26	analysis	analysis	NN	_	_	_
27	was	be	VBD	_	_	_
28	performed	perform	VBN	_	_	_
29	with	with	IN	_	_	_
30	free	free	JJ	_	_	_
31	software	software	NN	_	_	_
32	genArise	genarise	NN	_	_	_
33	,	,	,	_	_	_
34	developed	develop	VBN	_	_	_
35	in	in	IN	_	_	_
36	the	the	DT	_	_	_
37	Computing	Computing	NNP	_	_	_
38	Unit	unit	NN	_	_	_
39	of	of	IN	_	_	_
40	Cellular	cellular	JJ	_	_	_
41	Physiology	Physiology	NNP	_	_	_
42	Institute	Institute	NNP	_	_	_
43	of	of	IN	_	_	_
44	UNAM	UNAM	NNP	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	http	http	JJ	_	_	_
47	:	:	:	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	polyphosphate	polyphosphate	NN	_	_	_
50	kinase	kinase	NN	_	_	_
51	1	1	CD	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	PPK1	ppk1	NN	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	mutant	mutant	JJ	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	PPK1-PPX	ppk1-ppx	NN	_	_	_
58	double	double	JJ	_	_	_
59	mutant	mutant	JJ	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	single	single	JJ	_	_	_
62	mutant	mutant	NN	_	_	_
63	in	in	IN	_	_	_
64	exopolyphosphatase	exopolyphosphatase	NN	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	PPX	ppx	NN	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	single	single	JJ	_	_	_
70	mutant	mutant	NN	_	_	_
71	in	in	IN	_	_	_
72	polyphosphate	polyphosphate	NN	_	_	_
73	kinase	kinase	NN	_	_	_
74	1	1	CD	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	PPK1	ppk1	NN	_	_	_
77	-RRB-	-rrb-	-RRB-	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	zi	zi	NN	_	_	_
80	=	=	JJ	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	Ri	Ri	NNP	_	_	_
83	--	--	:	_	_	_
84	mean	mean	NN	_	_	_
85	-LRB-	-lrb-	-LRB-	_	_	_
86	R	r	NN	_	_	_
87	-RRB-	-rrb-	-RRB-	_	_	_
88	-RRB-	-rrb-	-RRB-	_	_	_
89	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
90	E.	e.	FW	_	_	_
91	coli	coli	FW	_	_	_
92	K-12	k-12	NN	_	_	_
93	strain	strain	NN	_	_	_
94	BW25113	bw25113	NN	_	_	_
95	was	be	VBD	_	_	_
96	evolved	evolve	VBN	_	_	_
97	in	in	IN	_	_	_
98	chemostats	chemostat	NNS	_	_	_
99	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	M9	m9	NN	MED	_	_
7	minimal	minimal	JJ	MED	_	_
8	media	media	NNS	MED	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	5	5	CD	_	_	_
11	g	g	NN	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	Escherichia	escherichia	FW	Organism	_	_
14	coli	coli	FW	Organism	_	_
15	K-12	k-12	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	growth	growth	NN	_	_	_
18	medium	medium	NN	_	_	_
19	:	:	:	_	_	_
20	liquid	liquid	JJ	_	_	_
21	culture	culture	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	P2-08	p2-08	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	P2-08	p2-08	NN	_	_	_
26	_	_	CD	_	_	_
27	R1	r1	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	P2-08	p2-08	NN	_	_	_
30	_	_	CD	_	_	_
31	R2	r2	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	P2-08	p2-08	NN	_	_	_
34	_	_	CD	_	_	_
35	R3	r3	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	P2-51	p2-51	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	P2-51	p2-51	NN	_	_	_
40	_	_	CD	_	_	_
41	R1	r1	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	P2-51	p2-51	NN	_	_	_
44	_	_	CD	_	_	_
45	R2	r2	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	P2-51	p2-51	NN	_	_	_
48	_	_	CD	_	_	_
49	R3	r3	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	P2-58	p2-58	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	P2-58	p2-58	NN	_	_	_
54	_	_	CD	_	_	_
55	R1	r1	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	P2-58	p2-58	NN	_	_	_
58	_	_	CD	_	_	_
59	R2	r2	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	P2-58	p2-58	NN	_	_	_
62	_	_	CD	_	_	_
63	R3	r3	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	P2-66	p2-66	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	P2-66	p2-66	NN	_	_	_
68	_	_	CD	_	_	_
69	R1	r1	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	P2-66	p2-66	NN	_	_	_
72	_	_	CD	_	_	_
73	R2	r2	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	P2-66	p2-66	NN	_	_	_
76	_	_	CD	_	_	_
77	R3	r3	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	P2-77	p2-77	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	P2-77	p2-77	NN	_	_	_
82	_	_	CD	_	_	_
83	R1	r1	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	P2-77	p2-77	NN	_	_	_
86	_	_	CD	_	_	_
87	R2	r2	NN	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	P2-77	p2-77	NN	_	_	_
90	_	_	CD	_	_	_
91	R3	r3	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	PF2-04	pf2-04	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	PF2-04	pf2-04	NN	_	_	_
96	_	_	CD	_	_	_
97	R1	r1	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	PF2-04	pf2-04	NN	_	_	_
100	_	_	CD	_	_	_
101	R2	r2	NN	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	PF2-04	pf2-04	NN	_	_	_
104	_	_	CD	_	_	_
105	R3	r3	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	PF2-08	pf2-08	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	PF2-08	pf2-08	NN	_	_	_
110	_	_	CD	_	_	_
111	R1	r1	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	PF2-08	pf2-08	NN	_	_	_
114	_	_	CD	_	_	_
115	R2	r2	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	PF2-08	pf2-08	NN	_	_	_
118	_	_	CD	_	_	_
119	R3	r3	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	PF2-12	pf2-12	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	PF2-12	pf2-12	NN	_	_	_
124	_	_	CD	_	_	_
125	R1	r1	NN	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	PF2-12	pf2-12	NN	_	_	_
128	_	_	CD	_	_	_
129	R2	r2	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	PF2-12	pf2-12	NN	_	_	_
132	_	_	CD	_	_	_
133	R3	r3	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	RNA	rna	NN	_	_	_
136	was	be	VBD	_	_	_
137	extracted	extract	VBN	_	_	_
138	using	use	VBG	_	_	_
139	the	the	DT	_	_	_
140	RNeasy	RNeasy	NNP	_	_	_
141	Mini	Mini	NNP	_	_	_
142	Kit	kit	NN	_	_	_
143	-LRB-	-lrb-	-LRB-	_	_	_
144	QIAGEN	qiagen	NN	_	_	_
145	-RRB-	-rrb-	-RRB-	_	_	_
146	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	SuperScript	SuperScript	NNP	_	_	_
3	indirect	indirect	JJ	_	_	_
4	cDNA	cdna	NN	_	_	_
5	labeling	labeling	NN	_	_	_
6	system	system	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Invitrogen	invitrogen	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	was	be	VBD	_	_	_
11	used	use	VBN	_	_	_
12	to	to	TO	_	_	_
13	generate	generate	VB	_	_	_
14	cDNA	cdna	NN	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	BW25113	bw25113	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
6	The	the	DT	_	_	_
7	image	image	NN	_	_	_
8	analysis	analysis	NN	_	_	_
9	was	be	VBD	_	_	_
10	performed	perform	VBN	_	_	_
11	using	use	VBG	_	_	_
12	GenePix	GenePix	NNP	_	_	_
13	Pro	pro	FW	_	_	_
14	6.0	6.0	CD	_	_	_
15	Software	Software	NNP	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Molecular	molecular	JJ	_	_	_
18	Devices	Devices	NNPS	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	Data	datum	NNS	_	_	_
2	were	be	VBD	_	_	_
3	normalized	normalize	VBN	_	_	_
4	with	with	IN	_	_	_
5	MIDAS	midas	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	LOWESS	lowess	NN	_	_	_
8	method	method	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	,	,	,	_	_	_
11	with	with	IN	_	_	_
12	clustering	clustering	NN	_	_	_
13	analysis	analysis	NN	_	_	_
14	in	in	IN	_	_	_
15	MeV	mev	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	CAST	cast	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	wild-type	wild-type	JJ	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	wt	wt	JJ	_	_	_
5	or	or	CC	_	_	_
6	mutant	mutant	JJ	_	_	_
7	:	:	:	_	_	_
8	P2-08	p2-08	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	wt	wt	JJ	_	_	_
11	or	or	CC	_	_	_
12	mutant	mutant	JJ	_	_	_
13	:	:	:	_	_	_
14	P2-51	p2-51	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	wt	wt	JJ	_	_	_
17	or	or	CC	_	_	_
18	mutant	mutant	JJ	_	_	_
19	:	:	:	_	_	_
20	P2-58	p2-58	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	wt	wt	JJ	_	_	_
23	or	or	CC	_	_	_
24	mutant	mutant	JJ	_	_	_
25	:	:	:	_	_	_
26	P2-66	p2-66	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	wt	wt	JJ	_	_	_
29	or	or	CC	_	_	_
30	mutant	mutant	JJ	_	_	_
31	:	:	:	_	_	_
32	P2-77	p2-77	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	wt	wt	JJ	_	_	_
35	or	or	CC	_	_	_
36	mutant	mutant	JJ	_	_	_
37	:	:	:	_	_	_
38	PF2-04	pf2-04	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	wt	wt	JJ	_	_	_
41	or	or	CC	_	_	_
42	mutant	mutant	JJ	_	_	_
43	:	:	:	_	_	_
44	PF2-08	pf2-08	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	wt	wt	JJ	_	_	_
47	or	or	CC	_	_	_
48	mutant	mutant	JJ	_	_	_
49	:	:	:	_	_	_
50	PF2-12	pf2-12	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	wt	wt	JJ	_	_	_
53	or	or	CC	_	_	_
54	mutant	mutant	JJ	_	_	_
55	:	:	:	_	_	_
56	WT	WT	NNP	_	_	_
57	@	@	SYM	_	_	_
58	0.8	0.8	CD	_	_	_
59	%	%	NN	_	_	_
60	But	but	CC	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	cpxA-ala-1	cpxa-ala-1	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	cpxA-ala-2	cpxa-ala-2	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	cpxA	cpxa	NN	GEN	_	_
67	mutant	mutant	NN	_	_	_
68	in	in	IN	_	_	_
69	Ala	Ala	NNP	_	_	_
70	media	media	NNS	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	cpxA	cpxa	NN	GEN	_	_
73	mutant	mutant	NN	_	_	_
74	in	in	IN	_	_	_
75	Gln	gln	NN	_	_	_
76	media	media	NNS	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	cysQ-gln-1	cysq-gln-1	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	cysQ-gln-2	cysq-gln-2	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	cysQ	cysq	NN	GEN	_	_
83	mutantin	mutantin	NN	_	_	_
84	Ala	ala	NN	_	_	_
85	media	media	NNS	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	cysQ	cysq	NN	GEN	_	_
88	mutantin	mutantin	NN	_	_	_
89	Gln	gln	NN	_	_	_
90	media	media	NNS	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	dnaJ-ala-1	dnaj-ala-1	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	dnaJ-ala-2	dnaj-ala-2	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	dnaJ-gln-1	dnaj-gln-1	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	dnaJ-gln-2	dnaj-gln-2	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	dnaJ	dnaj	NN	GEN	_	_
101	mutant	mutant	NN	_	_	_
102	in	in	IN	_	_	_
103	Ala	Ala	NNP	_	_	_
104	media	media	NNS	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	dnaJ	dnaj	NN	GEN	_	_
107	mutant	mutant	NN	_	_	_
108	in	in	IN	_	_	_
109	Gln	gln	NN	_	_	_
110	media	media	NNS	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	Escherichia	escherichia	FW	Organism	_	_
113	coli	coli	FW	Organism	_	_
114	str	str	FW	_	_	_
115	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	gcvT-ala-1	gcvt-ala-1	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	gcvT-ala-2	gcvt-ala-2	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	gcvT	gcvt	NN	GEN	_	_
8	mutant	mutant	NN	_	_	_
9	in	in	IN	_	_	_
10	Ala	Ala	NNP	_	_	_
11	media	media	NNS	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	gcvT	gcvt	NN	GEN	_	_
14	mutant	mutant	NN	_	_	_
15	in	in	IN	_	_	_
16	Gln	gln	NN	_	_	_
17	media	media	NNS	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	genotype	genotype	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	hfq-gln-1	hfq-gln-1	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	hfq-gln-2	hfq-gln-2	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	hfq	hfq	NN	GEN	_	_
26	mutant	mutant	NN	_	_	_
27	in	in	IN	_	_	_
28	Ala	Ala	NNP	_	_	_
29	media	media	NNS	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	hfq	hfq	NN	GEN	_	_
32	mutant	mutant	NN	_	_	_
33	in	in	IN	_	_	_
34	Gln	gln	NN	_	_	_
35	media	media	NNS	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Irp	irp	NN	_	_	_
38	mutant	mutant	NN	_	_	_
39	in	in	IN	_	_	_
40	Ala	Ala	NNP	_	_	_
41	media	media	NNS	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	Irp	irp	NN	_	_	_
44	mutant	mutant	NN	_	_	_
45	in	in	IN	_	_	_
46	Gln	gln	NN	_	_	_
47	media	media	NNS	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	LB-grown	lb-grown	JJ	_	_	_
50	overnight	overnight	JJ	_	_	_
51	cultures	culture	NNS	_	_	_
52	were	be	VBD	_	_	_
53	pelleted	pellete	VBN	_	_	_
54	by	by	IN	_	_	_
55	centrifugation	centrifugation	NN	_	_	_
56	,	,	,	_	_	_
57	washed	wash	VBN	_	_	_
58	,	,	,	_	_	_
59	and	and	CC	_	_	_
60	resuspended	resuspend	VBN	_	_	_
61	in	in	IN	_	_	_
62	M9-glutamine	m9-glutamine	NN	_	_	_
63	of	of	IN	_	_	_
64	M9-alanine	m9-alanine	NN	_	_	_
65	media	media	NNS	_	_	_
66	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	shaken	shake	VBN	_	_	_
4	at	at	IN	_	_	_
5	250	250	CD	_	_	_
6	rpm	rpm	NN	_	_	_
7	at	at	IN	_	_	_
8	37C	37c	NN	_	_	_
9	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	taken	take	VBN	_	_	_
4	in	in	IN	_	_	_
5	mid-exponential	mid-exponential	JJ	_	_	_
6	phase	phase	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	OD600	od600	NN	_	_	_
9	=	=	JJ	_	_	_
10	0.15	0.15	CD	_	_	_
11	for	for	IN	_	_	_
12	glutamine	glutamine	NN	_	_	_
13	and	and	CC	_	_	_
14	OD600	od600	NN	_	_	_
15	=	=	JJ	_	_	_
16	0.2	0.2	CD	_	_	_
17	for	for	IN	_	_	_
18	alanine	alanine	NN	_	_	_
19	on	on	IN	_	_	_
20	an	a	DT	_	_	_
21	Ultraspec	ultraspec	JJ	_	_	_
22	3100	3100	CD	_	_	_
23	pro	pro	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	after	after	IN	_	_	_
26	~	~	NN	_	_	_
27	5	5	CD	_	_	_
28	generations	generation	NNS	_	_	_
29	of	of	IN	_	_	_
30	growth	growth	NN	_	_	_
31	in	in	IN	_	_	_
32	the	the	DT	_	_	_
33	media	media	NNS	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	lrp-gln-1	lrp-gln-1	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	lrp-gln-2	lrp-gln-2	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	pgi-ala-1	pgi-ala-1	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	pgi-ala-2	pgi-ala-2	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	pgi	pgi	NN	GEN	_	_
11	mutantin	mutantin	NN	_	_	_
12	Ala	ala	NN	_	_	_
13	media	media	NNS	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	pgi	pgi	NN	GEN	_	_
16	mutantin	mutantin	NN	_	_	_
17	Gln	gln	NN	_	_	_
18	media	media	NNS	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	strain	strain	NN	_	_	_
21	:	:	:	_	_	_
22	AH28	ah28	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	strain	strain	NN	_	_	_
25	:	:	:	_	_	_
26	ZD1	zd1	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	strain	strain	NN	_	_	_
29	:	:	:	_	_	_
30	ZD26	zd26	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	strain	strain	NN	_	_	_
33	:	:	:	_	_	_
34	ZD51	zd51	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	strain	strain	NN	_	_	_
37	:	:	:	_	_	_
38	ZD56	zd56	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	strain	strain	NN	_	_	_
41	:	:	:	_	_	_
42	ZD59	zd59	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	strain	strain	NN	_	_	_
45	:	:	:	_	_	_
46	ZD60	zd60	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	strain	strain	NN	_	_	_
49	:	:	:	_	_	_
50	ZD8	zd8	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
52	The	the	DT	_	_	_
53	`	`	``	_	_	_
54	LogRatio	LogRatio	NNP	_	_	_
55	'	'	''	_	_	_
56	value	value	NN	_	_	_
57	was	be	VBD	_	_	_
58	used	use	VBN	_	_	_
59	in	in	IN	_	_	_
60	subsequent	subsequent	JJ	_	_	_
61	analyses	analysis	NNS	_	_	_
62	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	values	value	NNS	_	_	_
3	for	for	IN	_	_	_
4	the	the	DT	_	_	_
5	same	same	JJ	_	_	_
6	ORF	orf	NN	_	_	_
7	were	be	VBD	_	_	_
8	averaged	average	VBN	_	_	_
9	as	as	IN	_	_	_
10	were	be	VBD	_	_	_
11	the	the	DT	_	_	_
12	values	value	NNS	_	_	_
13	from	from	IN	_	_	_
14	the	the	DT	_	_	_
15	two	two	CD	_	_	_
16	biological	biological	JJ	_	_	_
17	replicates	replicate	VBZ	_	_	_
18	performed	perform	VBN	_	_	_
19	for	for	IN	_	_	_
20	each	each	DT	_	_	_
21	comparison	comparison	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	When	when	WRB	_	_	_
3	the	the	DT	_	_	_
4	cultures	culture	NNS	_	_	_
5	reached	reach	VBD	_	_	_
6	the	the	DT	_	_	_
7	desired	desire	VBN	_	_	_
8	density	density	NN	_	_	_
9	,	,	,	_	_	_
10	2	2	CD	_	_	_
11	ml	ml	NN	_	_	_
12	of	of	IN	_	_	_
13	culture	culture	NN	_	_	_
14	was	be	VBD	_	_	_
15	added	add	VBN	_	_	_
16	to	to	TO	_	_	_
17	4	4	CD	_	_	_
18	ml	ml	NN	_	_	_
19	of	of	IN	_	_	_
20	RNAprotect	rnaprotect	NN	_	_	_
21	Bacteria	bacterium	NNS	_	_	_
22	Reagent	reagent	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Qiagen	qiagen	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	mixture	mixture	NN	_	_	_
3	was	be	VBD	_	_	_
4	incubated	incubate	VBN	_	_	_
5	at	at	IN	_	_	_
6	room	room	NN	_	_	_
7	temperature	temperature	NN	_	_	_
8	for	for	IN	_	_	_
9	5	5	CD	_	_	_
10	min	min	NN	_	_	_
11	and	and	CC	_	_	_
12	then	then	RB	_	_	_
13	centrifuged	centrifuge	VBD	_	_	_
14	at	at	IN	_	_	_
15	5000	5000	CD	_	_	_
16	g	g	NN	_	_	_
17	for	for	IN	_	_	_
18	10	10	CD	_	_	_
19	min	min	NN	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	and	and	CC	_	_	_
6	the	the	DT	_	_	_
7	pellets	pellet	NNS	_	_	_
8	were	be	VBD	_	_	_
9	stored	store	VBN	_	_	_
10	at	at	IN	_	_	_
11	-80	-80	CD	_	_	_
12	C.	c.	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	using	use	VBG	_	_	_
17	the	the	DT	_	_	_
18	Norgen	Norgen	NNP	_	_	_
19	Total	Total	NNP	_	_	_
20	RNA	rna	NN	_	_	_
21	Purification	purification	NN	_	_	_
22	Kit	kit	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Product	product	NN	_	_	_
25	#	#	#	_	_	_
26	17200	17200	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	according	accord	VBG	_	_	_
29	to	to	TO	_	_	_
30	the	the	DT	_	_	_
31	manufacturer	manufacturer	NN	_	_	_
32	's	's	POS	_	_	_
33	directions	direction	NNS	_	_	_
34	except	except	IN	_	_	_
35	in	in	IN	_	_	_
36	the	the	DT	_	_	_
37	last	last	JJ	_	_	_
38	step	step	NN	_	_	_
39	the	the	DT	_	_	_
40	RNA	rna	NN	_	_	_
41	was	be	VBD	_	_	_
42	eluted	elute	VBN	_	_	_
43	in	in	IN	_	_	_
44	35	35	CD	_	_	_
45	uL	ul	NN	_	_	_
46	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	wild-type	wild-type	JJ	_	_	_
3	in	in	IN	_	_	_
4	ala	ala	NN	_	_	_
5	media	media	NNS	_	_	_
6	_	_	NN	_	_	_
7	1	1	CD	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	wild-type	wild-type	JJ	_	_	_
10	in	in	IN	_	_	_
11	ala	ala	NN	_	_	_
12	media	media	NNS	_	_	_
13	_	_	NN	_	_	_
14	2	2	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
16	wild-type	wild-type	JJ	_	_	_
17	in	in	IN	_	_	_
18	gln	gln	NN	_	_	_
19	media	media	NNS	_	_	_
20	_	_	NN	_	_	_
21	1	1	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	wild-type	wild-type	JJ	_	_	_
24	in	in	IN	_	_	_
25	gln	gln	NN	_	_	_
26	media	media	NNS	_	_	_
27	_	_	NN	_	_	_
28	2	2	CD	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	E.	E.	NNP	_	_	_
31	coli	coli	NN	_	_	_
32	O157	o157	NN	_	_	_
33	:	:	:	_	_	_
34	H7	h7	NN	_	_	_
35	EDL933	edl933	NN	_	_	_
36	in	in	IN	_	_	_
37	LB	lb	NN	_	_	_
38	at	at	IN	_	_	_
39	37oC	37oc	NN	_	_	_
40	for	for	IN	_	_	_
41	7	7	CD	_	_	_
42	hrs	hr	NNS	_	_	_
43	incubation	incubation	NN	_	_	_
44	with	with	IN	_	_	_
45	DMSO	dmso	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
47	E.	e.	FW	_	_	_
48	coli	coli	FW	_	_	_
49	O157	o157	NN	_	_	_
50	:	:	:	_	_	_
51	H7	h7	NN	_	_	_
52	EDL933	edl933	NN	_	_	_
53	in	in	IN	_	_	_
54	LB	lb	NN	_	_	_
55	at	at	IN	_	_	_
56	37oC	37oc	NN	_	_	_
57	for	for	IN	_	_	_
58	7	7	CD	_	_	_
59	hrs	hr	NNS	_	_	_
60	incubation	incubation	NN	_	_	_
61	with	with	IN	_	_	_
62	indole-3-acetaldehyde	indole-3-acetaldehyde	JJ	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
64	E.	e.	FW	_	_	_
65	coli	coli	FW	_	_	_
66	O157	o157	NN	_	_	_
67	:	:	:	_	_	_
68	H7	h7	NN	_	_	_
69	EDL933	edl933	NN	_	_	_
70	was	be	VBD	_	_	_
71	inoculated	inoculate	VBN	_	_	_
72	in	in	IN	_	_	_
73	100	100	CD	_	_	_
74	ml	ml	NN	_	_	_
75	of	of	IN	_	_	_
76	LB	lb	NN	_	_	_
77	in	in	IN	_	_	_
78	250	250	CD	_	_	_
79	ml	ml	NN	_	_	_
80	shake	shake	NN	_	_	_
81	flasks	flask	NNS	_	_	_
82	with	with	IN	_	_	_
83	overnight	overnight	JJ	_	_	_
84	cultures	culture	NNS	_	_	_
85	that	that	WDT	_	_	_
86	were	be	VBD	_	_	_
87	diluted	dilute	VBN	_	_	_
88	1:100	1:100	CD	_	_	_
89	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	shaken	shake	VBN	_	_	_
4	with	with	IN	_	_	_
5	4	4	CD	_	_	_
6	g	g	NN	_	_	_
7	of	of	IN	_	_	_
8	glass	glass	NN	_	_	_
9	wool	wool	NN	_	_	_
10	at	at	IN	_	_	_
11	250	250	CD	_	_	_
12	rpm	rpm	NN	_	_	_
13	and	and	CC	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	for	for	IN	_	_	_
17	7	7	CD	_	_	_
18	hrs	hr	NNS	_	_	_
19	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	immediately	immediately	RB	_	_	_
4	chilled	chill	VBN	_	_	_
5	with	with	IN	_	_	_
6	dry	dry	JJ	_	_	_
7	ice	ice	NN	_	_	_
8	and	and	CC	_	_	_
9	95	95	CD	_	_	_
10	%	%	NN	_	_	_
11	ethanol	ethanol	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	to	to	TO	_	_	_
14	prevent	prevent	VB	_	_	_
15	RNA	rna	NN	_	_	_
16	degradation	degradation	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	for	for	IN	_	_	_
19	30	30	CD	_	_	_
20	sec	sec	NN	_	_	_
21	before	before	IN	_	_	_
22	centrifugation	centrifugation	NN	_	_	_
23	in	in	IN	_	_	_
24	50	50	CD	_	_	_
25	ml	ml	NN	_	_	_
26	centrifuge	centrifuge	NN	_	_	_
27	tubes	tube	NNS	_	_	_
28	at	at	IN	_	_	_
29	13,000	13,000	CD	_	_	_
30	g	g	NN	_	_	_
31	for	for	IN	_	_	_
32	2	2	CD	_	_	_
33	min	min	NN	_	_	_
34	;	;	:	_	_	_
35	cell	cell	NN	_	_	_
36	pellets	pellet	NNS	_	_	_
37	were	be	VBD	_	_	_
38	frozen	frozen	JJ	_	_	_
39	immediately	immediately	RB	_	_	_
40	with	with	IN	_	_	_
41	dry	dry	JJ	_	_	_
42	ice	ice	NN	_	_	_
43	and	and	CC	_	_	_
44	stored	store	VBD	_	_	_
45	-80	-80	CD	_	_	_
46	°C	°c	NN	_	_	_
47	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	isolated	isolate	VBN	_	_	_
4	using	use	VBG	_	_	_
5	Qiagen	Qiagen	NNP	_	_	_
6	RNeasy	RNeasy	NNP	_	_	_
7	mini	minus	NNS	_	_	_
8	Kit	kit	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Cat	cat	NN	_	_	_
11	#	#	#	_	_	_
12	74104	74104	CD	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	with	with	IN	_	_	_
15	Qiagen	Qiagen	NNP	_	_	_
16	RNase-free	RNase-free	NNP	_	_	_
17	DNase	dnase	NN	_	_	_
18	I	i	CD	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Cat	cat	NN	_	_	_
21	#	#	#	_	_	_
22	79254	79254	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
5	MAS	mas	FW	_	_	_
6	5.0	5.0	CD	_	_	_
7	Expression	expression	NN	_	_	_
8	Analysis	analysis	NN	_	_	_
9	Default	Default	NNP	_	_	_
10	Setting	set	VBG	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	RNA	rna	NN	_	_	_
13	extracted	extract	VBN	_	_	_
14	from	from	IN	_	_	_
15	e.	e.	FW	_	_	_
16	coli	coli	FW	_	_	_
17	o157	o157	NN	_	_	_
18	:	:	:	_	_	_
19	H7	h7	NN	_	_	_
20	EDL933	edl933	NN	_	_	_
21	cells	cell	NNS	_	_	_
22	grown	grow	VBN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	7	7	CD	_	_	_
25	hrs	hr	NNS	_	_	_
26	incubation	incubation	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	in	in	IN	_	_	_
29	LB	lb	NN	_	_	_
30	at	at	IN	_	_	_
31	37ºC	37ºc	NN	_	_	_
32	with	with	IN	_	_	_
33	0.1	0.1	CD	_	_	_
34	mg	mg	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	RNA	rna	NN	_	_	_
37	extracted	extract	VBN	_	_	_
38	from	from	IN	_	_	_
39	e.	e.	FW	_	_	_
40	coli	coli	FW	_	_	_
41	o157	o157	NN	_	_	_
42	:	:	:	_	_	_
43	H7	h7	NN	_	_	_
44	EDL933	edl933	NN	_	_	_
45	cells	cell	NNS	_	_	_
46	grown	grow	VBN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	7	7	CD	_	_	_
49	hrs	hr	NNS	_	_	_
50	incubation	incubation	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	in	in	IN	_	_	_
53	LB	lb	NN	_	_	_
54	at	at	IN	_	_	_
55	37ºC	37ºc	NN	_	_	_
56	with	with	IN	_	_	_
57	DMSO	dmso	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
59	serotype	serotype	NN	_	_	_
60	:	:	:	_	_	_
61	O157	o157	NN	_	_	_
62	:	:	:	_	_	_
63	H7	h7	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	strain	strain	NN	_	_	_
66	:	:	:	_	_	_
67	EDL933	edl933	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	Cells	cell	NNS	_	_	_
70	in	in	IN	_	_	_
71	log	log	NN	_	_	_
72	phase	phase	NN	_	_	_
73	under	under	IN	_	_	_
74	ethanol	ethanol	NN	_	_	_
75	stress	stress	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	Cells	cell	NNS	_	_	_
78	were	be	VBD	_	_	_
79	grown	grow	VBN	_	_	_
80	at	at	IN	_	_	_
81	37	37	CD	_	_	_
82	°C	°c	NN	_	_	_
83	in	in	IN	_	_	_
84	Luria-Bertani	Luria-Bertani	NNP	_	_	_
85	-LRB-	-lrb-	-LRB-	_	_	_
86	LB	LB	NNP	_	_	_
87	-RRB-	-rrb-	-RRB-	_	_	_
88	medium	medium	NN	_	_	_
89	containing	contain	VBG	_	_	_
90	50	50	CD	_	_	_
91	μg	μg	NN	_	_	_
92	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
93	Data	Data	NNP	_	_	_
94	were	be	VBD	_	_	_
95	analyzed	analyze	VBN	_	_	_
96	using	use	VBG	_	_	_
97	GeneChip	GeneChip	NNP	_	_	_
98	Operating	Operating	NNP	_	_	_
99	Software	Software	NNP	_	_	_
100	Version	Version	NNP	_	_	_
101	1.4	1.4	CD	_	_	_
102	-LRB-	-lrb-	-LRB-	_	_	_
103	Affymetrix	Affymetrix	NNP	_	_	_
104	-RRB-	-rrb-	-RRB-	_	_	_
105	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
106	Escherichia	escherichia	FW	Organism	_	_
107	coli	coli	FW	Organism	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	genotype	genotype	NN	_	_	_
110	:	:	:	_	_	_
111	ethanol-tolerant	ethanol-tolerant	JJ	_	_	_
112	mutant	mutant	JJ	_	_	_
113	E1	e1	NN	_	_	_
114	of	of	IN	_	_	_
115	IrrE	irre	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	genotype	genotype	NN	_	_	_
118	:	:	:	_	_	_
119	wild	wild	JJ	_	_	_
120	type	type	NN	_	_	_
121	IrrE	irre	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	mutant	mutant	JJ	_	_	_
124	E1	e1	NN	_	_	_
125	,	,	,	_	_	_
126	biological	biological	JJ	_	_	_
127	rep1	rep1	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	mutant	mutant	JJ	_	_	_
130	E1	e1	NN	_	_	_
131	,	,	,	_	_	_
132	biological	biological	JJ	_	_	_
133	rep2	rep2	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	mutant	mutant	JJ	_	_	_
136	E1	e1	NN	_	_	_
137	,	,	,	_	_	_
138	biological	biological	JJ	_	_	_
139	rep3	rep3	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	strain	strain	NN	_	_	_
142	:	:	:	_	_	_
143	DH5a	dh5a	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
145	The	the	DT	_	_	_
146	cells	cell	NNS	_	_	_
147	were	be	VBD	_	_	_
148	centrifuged	centrifuge	VBN	_	_	_
149	when	when	WRB	_	_	_
150	they	they	PRP	_	_	_
151	reached	reach	VBD	_	_	_
152	the	the	DT	_	_	_
153	log	log	NN	_	_	_
154	phase	phase	NN	_	_	_
155	,	,	,	_	_	_
156	and	and	CC	_	_	_
157	then	then	RB	_	_	_
158	rapidly	rapidly	RB	_	_	_
159	chilled	chill	VBD	_	_	_
160	and	and	CC	_	_	_
161	stored	store	VBD	_	_	_
162	in	in	IN	_	_	_
163	liquid	liquid	JJ	_	_	_
164	nitrogen	nitrogen	NN	_	_	_
165	until	until	IN	_	_	_
166	used	use	VBN	_	_	_
167	for	for	IN	_	_	_
168	the	the	DT	_	_	_
169	DNA	dna	NN	_	_	_
170	microarray	microarray	NN	_	_	_
171	assay	assay	NN	_	_	_
172	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
173	Total	Total	NNP	_	_	_
174	RNA	rna	NN	_	_	_
175	was	be	VBD	_	_	_
176	isolated	isolate	VBN	_	_	_
177	from	from	IN	_	_	_
178	the	the	DT	_	_	_
179	cells	cell	NNS	_	_	_
180	stored	store	VBN	_	_	_
181	in	in	IN	_	_	_
182	liquid	liquid	JJ	_	_	_
183	nitrogen	nitrogen	NN	_	_	_
184	using	use	VBG	_	_	_
185	TRIzol	trizol	NN	_	_	_
186	Reagent	reagent	NN	_	_	_
187	-LRB-	-lrb-	-LRB-	_	_	_
188	Invitrogen	Invitrogen	NNP	_	_	_
189	Life	Life	NNP	_	_	_
190	Technologies	Technologies	NNPS	_	_	_
191	,	,	,	_	_	_
192	Carlsbad	Carlsbad	NNP	_	_	_
193	,	,	,	_	_	_
194	CA	CA	NNP	_	_	_
195	,	,	,	_	_	_
196	USA	USA	NNP	_	_	_
197	-RRB-	-rrb-	-RRB-	_	_	_
198	and	and	CC	_	_	_
199	RNeasy	rneasy	NN	_	_	_
200	MinElute	MinElute	NNP	_	_	_
201	Cleanup	Cleanup	NNP	_	_	_
202	Kits	kit	NNS	_	_	_
203	-LRB-	-lrb-	-LRB-	_	_	_
204	Qiagen	Qiagen	NNP	_	_	_
205	,	,	,	_	_	_
206	Valencia	Valencia	NNP	_	_	_
207	,	,	,	_	_	_
208	CA	CA	NNP	_	_	_
209	,	,	,	_	_	_
210	USA	USA	NNP	_	_	_
211	-RRB-	-rrb-	-RRB-	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	wild	wild	JJ	_	_	_
214	type	type	NN	_	_	_
215	E0	e0	NN	_	_	_
216	,	,	,	_	_	_
217	biological	biological	JJ	_	_	_
218	rep1	rep1	NN	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	wild	wild	JJ	_	_	_
221	type	type	NN	_	_	_
222	E0	e0	NN	_	_	_
223	,	,	,	_	_	_
224	biological	biological	JJ	_	_	_
225	rep2	rep2	NN	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	wild	wild	JJ	_	_	_
228	type	type	NN	_	_	_
229	E0	e0	NN	_	_	_
230	,	,	,	_	_	_
231	biological	biological	JJ	_	_	_
232	rep3	rep3	NN	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	E.	e.	FW	_	_	_
235	coli	coli	FW	_	_	_
236	cultutures	cultuture	NNS	_	_	_
237	were	be	VBD	_	_	_
238	grown	grow	VBN	_	_	_
239	in	in	IN	_	_	_
240	M9	m9	NN	_	_	_
241	media	media	NNS	_	_	_
242	using	use	VBG	_	_	_
243	standard	standard	JJ	_	_	_
244	protocol	protocol	NN	_	_	_
245	,	,	,	_	_	_
246	to	to	TO	_	_	_
247	log	log	VB	_	_	_
248	phase	phase	NN	_	_	_
249	-LRB-	-lrb-	-LRB-	_	_	_
250	OD600	od600	NN	_	_	_
251	of	of	IN	_	_	_
252	0.7-0.8	0.7-0.8	CD	_	_	_
253	-RRB-	-rrb-	-RRB-	_	_	_
254	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
255	Escherichia	escherichia	FW	Organism	_	_
256	coli	coli	FW	Organism	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	genotype	genotype	NN	_	_	_
259	:	:	:	_	_	_
260	gss	gss	NN	GEN	_	_
261	mutant	mutant	JJ	_	_	_
262	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
263	genotype	genotype	NN	_	_	_
264	:	:	:	_	_	_
265	wild	wild	JJ	_	_	_
266	type	type	NN	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	gss-1	gss-1	NN	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	gss-2	gss-2	NN	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	gss-3	gss-3	NN	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	MAS	mas	NN	_	_	_
275	5.0	5.0	CD	_	_	_
276	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
277	No	no	DT	_	_	_
278	treatment	treatment	NN	_	_	_
279	,	,	,	_	_	_
280	just	just	RB	_	_	_
281	comparison	comparison	NN	_	_	_
282	of	of	IN	_	_	_
283	RNAs	rna	NNS	_	_	_
284	from	from	IN	_	_	_
285	wild	wild	JJ	_	_	_
286	type	type	NN	_	_	_
287	and	and	CC	_	_	_
288	mutant	mutant	NN	_	_	_
289	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Trizol	trizol	NN	_	_	_
3	extraction	extraction	NN	_	_	_
4	of	of	IN	_	_	_
5	total	total	JJ	_	_	_
6	RNA	rna	NN	_	_	_
7	was	be	VBD	_	_	_
8	performed	perform	VBN	_	_	_
9	according	accord	VBG	_	_	_
10	to	to	TO	_	_	_
11	the	the	DT	_	_	_
12	manufacturer	manufacturer	NN	_	_	_
13	's	's	POS	_	_	_
14	instructions	instruction	NNS	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	WT-1	wt-1	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	WT-2	wt-2	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	WT-3	wt-3	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Affymetrix	Affymetrix	NNP	_	_	_
9	GeneChip	GeneChip	NNP	_	_	_
10	Operating	Operating	NNP	_	_	_
11	Software	Software	NNP	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	GCOS	GCOS	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	Version	Version	NNP	_	_	_
16	1.4	1.4	CD	_	_	_
17	Details	detail	NNS	_	_	_
18	:	:	:	_	_	_
19	Intra-chip	intra-chip	JJ	_	_	_
20	normalizations	normalization	NNS	_	_	_
21	were	be	VBD	_	_	_
22	performed	perform	VBN	_	_	_
23	using	use	VBG	_	_	_
24	Affymetrix	Affymetrix	NNP	_	_	_
25	Gene	Gene	NNP	_	_	_
26	Chip	Chip	NNP	_	_	_
27	Operating	Operating	NNP	_	_	_
28	Software	Software	NNP	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	GCOS	GCOS	NNP	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	.	.	.	_	_	_

1	Default	Default	NNP	_	_	_
2	statistical	statistical	JJ	_	_	_
3	parameters	parameter	NNS	_	_	_
4	were	be	VBD	_	_	_
5	used	use	VBN	_	_	_
6	to	to	TO	_	_	_
7	normalize	normalize	VB	_	_	_
8	each	each	DT	_	_	_
9	chip	chip	NN	_	_	_
10	to	to	TO	_	_	_
11	the	the	DT	_	_	_
12	same	same	JJ	_	_	_
13	target	target	NN	_	_	_
14	intensity	intensity	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	1500	1500	CD	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	as	as	IN	_	_	_
19	described	describe	VBN	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	Affymetrix	Affymetrix	NNP	_	_	_
23	GeneChip	GeneChip	NNP	_	_	_
24	Expression	expression	NN	_	_	_
25	Analysis	analysis	NN	_	_	_
26	manual	manual	NN	_	_	_
27	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	nine	nine	CD	_	_	_
3	possible	possible	JJ	_	_	_
4	inter-chip	inter-chip	NN	_	_	_
5	comparisons	comparison	NNS	_	_	_
6	were	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	in	in	IN	_	_	_
9	GCOS	gcos	NN	_	_	_
10	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	data	datum	NNS	_	_	_
3	were	be	VBD	_	_	_
4	subsequently	subsequently	RB	_	_	_
5	exported	export	VBN	_	_	_
6	to	to	TO	_	_	_
7	a	a	DT	_	_	_
8	Microsoft	Microsoft	NNP	_	_	_
9	Excel	Excel	NNP	_	_	_
10	spreadsheet	spreadsheet	NN	_	_	_
11	for	for	IN	_	_	_
12	manipulation	manipulation	NN	_	_	_
13	.	.	.	_	_	_

1	Consensus	consensus	NN	_	_	_
2	``	``	``	_	_	_
3	detection	detection	NN	_	_	_
4	p-value	p-value	NN	_	_	_
5	''	''	''	_	_	_
6	,	,	,	_	_	_
7	``	``	``	_	_	_
8	change	change	NN	_	_	_
9	p-value	p-value	NN	_	_	_
10	''	''	''	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	``	``	``	_	_	_
14	signal	signal	NN	_	_	_
15	log	log	NN	_	_	_
16	ratios	ratio	NNS	_	_	_
17	''	''	''	_	_	_
18	were	be	VBD	_	_	_
19	calculated	calculate	VBN	_	_	_
20	,	,	,	_	_	_
21	and	and	CC	_	_	_
22	the	the	DT	_	_	_
23	default	default	NN	_	_	_
24	E.	e.	FW	_	_	_
25	coli	coli	FW	_	_	_
26	array	array	NN	_	_	_
27	p-value	p-value	NN	_	_	_
28	cutoff	cutoff	NN	_	_	_
29	parameters	parameter	NNS	_	_	_
30	were	be	VBD	_	_	_
31	applied	apply	VBN	_	_	_
32	to	to	TO	_	_	_
33	these	these	DT	_	_	_
34	consensus	consensus	NN	_	_	_
35	values	value	NNS	_	_	_
36	to	to	TO	_	_	_
37	estimate	estimate	VB	_	_	_
38	the	the	DT	_	_	_
39	transcript	transcript	NN	_	_	_
40	change	change	NN	_	_	_
41	between	between	IN	_	_	_
42	two	two	CD	_	_	_
43	conditions	condition	NNS	_	_	_
44	and	and	CC	_	_	_
45	the	the	DT	_	_	_
46	transcript	transcript	NN	_	_	_
47	presence	presence	NN	_	_	_
48	under	under	IN	_	_	_
49	each	each	DT	_	_	_
50	condition	condition	NN	_	_	_
51	.	.	.	_	_	_

1	Background-subtracted	background-subtracted	JJ	_	_	_
2	data	datum	NNS	_	_	_
3	sets	set	NNS	_	_	_
4	were	be	VBD	_	_	_
5	used	use	VBN	_	_	_
6	to	to	TO	_	_	_
7	calculate	calculate	VB	_	_	_
8	up-regulated	up-regulate	VBN	_	_	_
9	and	and	CC	_	_	_
10	down-regulated	down-regulate	VBN	_	_	_
11	genes	gene	NNS	_	_	_
12	based	base	VBN	_	_	_
13	on	on	IN	_	_	_
14	fold	fold	JJ	_	_	_
15	changes	change	NNS	_	_	_
16	of	of	IN	_	_	_
17	greater	greater	JJR	_	_	_
18	than	than	IN	_	_	_
19	2	2	CD	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	E.coli	e.coli	NN	_	_	_
3	cells	cell	NNS	_	_	_
4	grown	grow	VBN	_	_	_
5	with	with	IN	_	_	_
6	aeration	aeration	NN	_	_	_
7	in	in	IN	_	_	_
8	LB	LB	NNP	MED	_	_
9	media	media	NNS	MED	_	_
10	at	at	IN	_	_	_
11	37º	37º	CD	_	_	_
12	C	c	NN	_	_	_
13	until	until	IN	_	_	_
14	early	early	JJ	_	_	_
15	log	log	NN	_	_	_
16	phase	phase	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	0.4	0.4	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	and	and	CC	_	_	_
21	were	be	VBD	_	_	_
22	treated	treat	VBN	_	_	_
23	with	with	IN	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	E.	E.	NNP	_	_	_
26	coli	coli	NN	_	_	_
27	K12	k12	NN	_	_	_
28	strain	strain	NN	_	_	_
29	JM109	jm109	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Escherichia	escherichia	FW	Organism	_	_
32	coli	coli	FW	Organism	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	JM109-1	jm109-1	NN	_	_	_
35	,	,	,	_	_	_
36	biological	biological	JJ	_	_	_
37	rep1	rep1	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	JM109-2	jm109-2	NN	_	_	_
40	,	,	,	_	_	_
41	biological	biological	JJ	_	_	_
42	rep2	rep2	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	JM109-3	jm109-3	NN	_	_	_
45	,	,	,	_	_	_
46	biological	biological	JJ	_	_	_
47	rep3	rep3	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	JM109	jm109	NN	_	_	_
50	GLY-1	gly-1	NN	_	_	_
51	,	,	,	_	_	_
52	biological	biological	JJ	_	_	_
53	rep1	rep1	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	JM109	jm109	NN	_	_	_
56	GLY-2	gly-2	NN	_	_	_
57	,	,	,	_	_	_
58	biological	biological	JJ	_	_	_
59	rep2	rep2	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	JM109	jm109	NN	_	_	_
62	GLY-3	gly-3	NN	_	_	_
63	,	,	,	_	_	_
64	biological	biological	JJ	_	_	_
65	rep3	rep3	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	Total	total	JJ	_	_	_
68	RNA	rna	NN	_	_	_
69	was	be	VBD	_	_	_
70	extracted	extract	VBN	_	_	_
71	using	use	VBG	_	_	_
72	the	the	DT	_	_	_
73	commercial	commercial	JJ	_	_	_
74	product	product	NN	_	_	_
75	TRIzol	trizol	NN	_	_	_
76	Reagent	reagent	NN	_	_	_
77	-LRB-	-lrb-	-LRB-	_	_	_
78	Invitrogen	Invitrogen	NNP	_	_	_
79	,	,	,	_	_	_
80	Carlsbad	Carlsbad	NNP	_	_	_
81	,	,	,	_	_	_
82	CA	CA	NNP	_	_	_
83	-RRB-	-rrb-	-RRB-	_	_	_
84	.	.	.	_	_	_

1	Disrupt	disrupt	VB	_	_	_
2	about	about	IN	_	_	_
3	107cells	107cell	NNS	_	_	_
4	with	with	IN	_	_	_
5	a	a	DT	_	_	_
6	homogenizer	homogenizer	NN	_	_	_
7	with	with	IN	_	_	_
8	1	1	CD	_	_	_
9	ml	ml	NN	_	_	_
10	TRIzol	trizol	NN	_	_	_
11	Reafent	reafent	NN	_	_	_
12	on	on	IN	_	_	_
13	ice	ice	NN	_	_	_
14	.	.	.	_	_	_

1	Store	Store	NNP	_	_	_
2	the	the	DT	_	_	_
3	homogenate	homogenate	NN	_	_	_
4	for	for	IN	_	_	_
5	5	5	CD	_	_	_
6	minutes	minute	NNS	_	_	_
7	at	at	IN	_	_	_
8	room	room	NN	_	_	_
9	temperature	temperature	NN	_	_	_
10	to	to	TO	_	_	_
11	permit	permit	VB	_	_	_
12	the	the	DT	_	_	_
13	complete	complete	JJ	_	_	_
14	dissociation	dissociation	NN	_	_	_
15	of	of	IN	_	_	_
16	nucleoprotein	nucleoprotein	NN	_	_	_
17	complexes	complex	NNS	_	_	_
18	.	.	.	_	_	_

1	Next	next	RB	_	_	_
2	,	,	,	_	_	_
3	supplement	supplement	VBP	_	_	_
4	the	the	DT	_	_	_
5	homogenate	homogenate	NN	_	_	_
6	with	with	IN	_	_	_
7	0.2	0.2	CD	_	_	_
8	ml	ml	NN	_	_	_
9	chloroform	chloroform	NN	_	_	_
10	per	per	IN	_	_	_
11	1	1	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	TRI	TRI	NNP	_	_	_
15	Reagent	Reagent	NNP	_	_	_
16	,	,	,	_	_	_
17	cover	cover	VBP	_	_	_
18	the	the	DT	_	_	_
19	samples	sample	NNS	_	_	_
20	tightly	tightly	RB	_	_	_
21	and	and	CC	_	_	_
22	shake	shake	VB	_	_	_
23	vigorously	vigorously	RB	_	_	_
24	for	for	IN	_	_	_
25	15	15	CD	_	_	_
26	seconds	seconds	NNS	_	_	_
27	.	.	.	_	_	_

1	Store	Store	NNP	_	_	_
2	the	the	DT	_	_	_
3	resulting	result	VBG	_	_	_
4	mixture	mixture	NN	_	_	_
5	at	at	IN	_	_	_
6	room	room	NN	_	_	_
7	temperature	temperature	NN	_	_	_
8	for	for	IN	_	_	_
9	2-15	2-15	CD	_	_	_
10	minutes	minute	NNS	_	_	_
11	and	and	CC	_	_	_
12	centrifuge	centrifuge	NN	_	_	_
13	at	at	IN	_	_	_
14	12,000	12,000	CD	_	_	_
15	g	g	NN	_	_	_
16	for	for	IN	_	_	_
17	15	15	CD	_	_	_
18	minutes	minute	NNS	_	_	_
19	at	at	IN	_	_	_
20	4	4	CD	_	_	_
21	C.	C.	NNP	_	_	_
22	Following	follow	VBG	_	_	_
23	centrifugation	centrifugation	NN	_	_	_
24	,	,	,	_	_	_
25	the	the	DT	_	_	_
26	mixture	mixture	NN	_	_	_
27	separates	separate	VBZ	_	_	_
28	into	into	IN	_	_	_
29	a	a	DT	_	_	_
30	lower	lower	JJR	_	_	_
31	red	red	JJ	_	_	_
32	phenol-chloroform	phenol-chloroform	NN	_	_	_
33	phase	phase	NN	_	_	_
34	,	,	,	_	_	_
35	interphase	interphase	NN	_	_	_
36	and	and	CC	_	_	_
37	the	the	DT	_	_	_
38	colorless	colorless	JJ	_	_	_
39	upper	upper	JJ	_	_	_
40	aqueous	aqueous	JJ	_	_	_
41	phase	phase	NN	_	_	_
42	.	.	.	_	_	_

1	Transfer	transfer	NN	_	_	_
2	the	the	DT	_	_	_
3	aqueous	aqueous	JJ	_	_	_
4	phase	phase	NN	_	_	_
5	to	to	TO	_	_	_
6	a	a	DT	_	_	_
7	fresh	fresh	JJ	_	_	_
8	tube	tube	NN	_	_	_
9	.	.	.	_	_	_

1	Precipitate	precipitate	VB	_	_	_
2	RNA	rna	NN	_	_	_
3	from	from	IN	_	_	_
4	the	the	DT	_	_	_
5	aqueous	aqueous	JJ	_	_	_
6	phase	phase	NN	_	_	_
7	by	by	IN	_	_	_
8	mixing	mix	VBG	_	_	_
9	with	with	IN	_	_	_
10	isopropanol	isopropanol	NN	_	_	_
11	.	.	.	_	_	_

1	Use	Use	NNP	_	_	_
2	0.5	0.5	CD	_	_	_
3	ml	ml	NN	_	_	_
4	of	of	IN	_	_	_
5	isopropanol	isopropanol	NN	_	_	_
6	per	per	IN	_	_	_
7	1	1	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	TRI	TRI	NNP	_	_	_
11	Reagent	Reagent	NNP	_	_	_
12	used	use	VBD	_	_	_
13	for	for	IN	_	_	_
14	the	the	DT	_	_	_
15	initial	initial	JJ	_	_	_
16	homogenization	homogenization	NN	_	_	_
17	.	.	.	_	_	_

1	Store	Store	NNP	_	_	_
2	samples	sample	NNS	_	_	_
3	at	at	IN	_	_	_
4	room	room	NN	_	_	_
5	temperature	temperature	NN	_	_	_
6	for	for	IN	_	_	_
7	5-10	5-10	CD	_	_	_
8	minutes	minute	NNS	_	_	_
9	and	and	CC	_	_	_
10	centrifuge	centrifuge	NN	_	_	_
11	at	at	IN	_	_	_
12	12,000	12,000	CD	_	_	_
13	g	g	NN	_	_	_
14	for	for	IN	_	_	_
15	8	8	CD	_	_	_
16	minutes	minute	NNS	_	_	_
17	at	at	IN	_	_	_
18	4	4	CD	_	_	_
19	-	-	:	_	_	_
20	25	25	CD	_	_	_
21	C.	C.	NNP	_	_	_
22	Remove	remove	VB	_	_	_
23	the	the	DT	_	_	_
24	supernatant	supernatant	NN	_	_	_
25	and	and	CC	_	_	_
26	wash	wash	VB	_	_	_
27	the	the	DT	_	_	_
28	RNA	rna	NN	_	_	_
29	pellet	pellet	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	by	by	IN	_	_	_
32	vortexing	vortex	VBG	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	with	with	IN	_	_	_
35	75	75	CD	_	_	_
36	%	%	NN	_	_	_
37	ethanol	ethanol	NN	_	_	_
38	and	and	CC	_	_	_
39	subsequent	subsequent	JJ	_	_	_
40	centrifugation	centrifugation	NN	_	_	_
41	at	at	IN	_	_	_
42	7,500	7,500	CD	_	_	_
43	g	g	NN	_	_	_
44	for	for	IN	_	_	_
45	5	5	CD	_	_	_
46	minutes	minute	NNS	_	_	_
47	at	at	IN	_	_	_
48	4	4	CD	_	_	_
49	-	-	:	_	_	_
50	25	25	CD	_	_	_
51	C.	C.	NNP	_	_	_
52	Add	add	VB	_	_	_
53	at	at	IN	_	_	_
54	least	least	JJS	_	_	_
55	1	1	CD	_	_	_
56	ml	ml	NN	_	_	_
57	of	of	IN	_	_	_
58	75	75	CD	_	_	_
59	%	%	NN	_	_	_
60	ethanol	ethanol	NN	_	_	_
61	per	per	IN	_	_	_
62	1	1	CD	_	_	_
63	ml	ml	NN	_	_	_
64	TRI	TRI	NNP	_	_	_
65	Reagent	Reagent	NNP	_	_	_
66	used	use	VBD	_	_	_
67	for	for	IN	_	_	_
68	the	the	DT	_	_	_
69	initial	initial	JJ	_	_	_
70	homogenization	homogenization	NN	_	_	_
71	.	.	.	_	_	_

1	Remove	remove	VB	_	_	_
2	the	the	DT	_	_	_
3	ethanol	ethanol	NN	_	_	_
4	wash	wash	NN	_	_	_
5	and	and	CC	_	_	_
6	briefly	briefly	NN	_	_	_
7	air-dry	air-dry	VB	_	_	_
8	the	the	DT	_	_	_
9	RNA	rna	NN	_	_	_
10	pellet	pellet	NN	_	_	_
11	for	for	IN	_	_	_
12	3	3	LS	_	_	_
13	-	-	:	_	_	_
14	5	5	CD	_	_	_
15	min	min	NN	_	_	_
16	.	.	.	_	_	_

1	Dissolve	dissolve	VB	_	_	_
2	RNA	rna	NN	_	_	_
3	in	in	IN	_	_	_
4	DEPC-treated	depc-treated	JJ	_	_	_
5	water	water	NN	_	_	_
6	by	by	IN	_	_	_
7	passing	pass	VBG	_	_	_
8	solution	solution	NN	_	_	_
9	a	a	DT	_	_	_
10	few	few	JJ	_	_	_
11	times	time	NNS	_	_	_
12	through	through	IN	_	_	_
13	a	a	DT	_	_	_
14	pipette	pipette	NN	_	_	_
15	tip	tip	NN	_	_	_
16	.	.	.	_	_	_

1	Using	use	VBG	_	_	_
2	an	a	DT	_	_	_
3	on-column	on-column	JJ	_	_	_
4	DNase	dnase	NN	_	_	_
5	digestion	digestion	NN	_	_	_
6	with	with	IN	_	_	_
7	RNase-free	rnase-free	JJ	_	_	_
8	DNase	dnase	NN	_	_	_
9	I	i	CD	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Qiagen	qiagen	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	to	to	TO	_	_	_
14	purify	purify	VB	_	_	_
15	the	the	DT	_	_	_
16	total	total	JJ	_	_	_
17	RNA	rna	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	200	200	CD	_	_	_
5	mM	mm	NN	KWSUPP	_	_
6	glyphosate	glyphosate	NN	_	_	_
7	shock	shock	NN	_	_	_
8	for	for	IN	_	_	_
9	1	1	CD	_	_	_
10	h	h	NN	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	Treatment	Treatment	NNP	_	_	_
13	protocol	protocol	NN	_	_	_
14	-	-	:	_	_	_
15	E.coli	e.coli	NN	_	_	_
16	cells	cell	NNS	_	_	_
17	grown	grow	VBN	_	_	_
18	in	in	IN	_	_	_
19	LB	LB	NNP	MED	_	_
20	media	media	NNS	MED	_	_
21	with	with	IN	_	_	_
22	at	at	IN	_	_	_
23	37C	37c	NN	_	_	_
24	until	until	IN	_	_	_
25	early	early	JJ	_	_	_
26	log	log	NN	_	_	_
27	phase	phase	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	0.4	0.4	CD	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	,	,	,	_	_	_
32	then	then	RB	_	_	_
33	were	be	VBD	_	_	_
34	treated	treat	VBN	_	_	_
35	with	with	IN	_	_	_
36	200	200	CD	_	_	_
37	mM	mm	NN	KWSUPP	_	_
38	glyphosate	glyphosate	NN	_	_	_
39	for	for	IN	_	_	_
40	1	1	CD	_	_	_
41	h	h	NN	_	_	_
42	,	,	,	_	_	_
43	after	after	IN	_	_	_
44	that	that	IN	_	_	_
45	the	the	DT	_	_	_
46	cells	cell	NNS	_	_	_
47	were	be	VBD	_	_	_
48	harvested	harvest	VBN	_	_	_
49	to	to	TO	_	_	_
50	extract	extract	NN	_	_	_
51	RNA	rna	NN	_	_	_
52	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	without	without	IN	_	_	_
5	salt	salt	NN	_	_	_
6	shock	shock	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	BW25113	bw25113	NN	_	_	_
9	mqsR	mqsr	NN	GEN	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	cell	cell	NN	_	_	_
12	type	type	NN	_	_	_
13	:	:	:	_	_	_
14	Planktonic	planktonic	JJ	_	_	_
15	cells	cell	NNS	_	_	_
16	harvested	harvest	VBN	_	_	_
17	at	at	IN	_	_	_
18	a	a	DT	_	_	_
19	turbidity	turbidity	NN	_	_	_
20	of	of	IN	_	_	_
21	0.5	0.5	CD	_	_	_
22	at	at	IN	_	_	_
23	600	600	CD	_	_	_
24	nm	nm	NN	_	_	_
25	,	,	,	_	_	_
26	adjusted	adjust	VBN	_	_	_
27	to	to	TO	_	_	_
28	the	the	DT	_	_	_
29	turbidity	turbidity	NN	_	_	_
30	at	at	IN	_	_	_
31	1	1	CD	_	_	_
32	,	,	,	_	_	_
33	and	and	CC	_	_	_
34	then	then	RB	_	_	_
35	exposed	expose	VBN	_	_	_
36	to	to	TO	_	_	_
37	20	20	CD	_	_	_
38	μg	μg	NN	_	_	_
39	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
40	Escherichia	escherichia	FW	Organism	_	_
41	coli	coli	FW	Organism	_	_
42	K-12	k-12	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	genotype	genotype	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	MAS	mas	NN	_	_	_
47	5.0	5.0	CD	_	_	_
48	Expression	expression	NN	_	_	_
49	Analysis	analysis	NN	_	_	_
50	Default	Default	NNP	_	_	_
51	Setting	Setting	NNP	_	_	_
52	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
53	medium	medium	NN	_	_	_
54	:	:	:	_	_	_
55	LB	lb	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	strains	strain	NNS	_	_	_
58	:	:	:	_	_	_
59	K-12	k-12	NN	_	_	_
60	BW25113	bw25113	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	temp	temp	NN	_	_	_
63	:	:	:	_	_	_
64	37ºC	37ºc	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
66	The	the	DT	_	_	_
67	overnight	overnight	JJ	_	_	_
68	culture	culture	NN	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	0.25	0.25	CD	_	_	_
71	ml	ml	NN	_	_	_
72	-RRB-	-rrb-	-RRB-	_	_	_
73	was	be	VBD	_	_	_
74	used	use	VBN	_	_	_
75	to	to	TO	_	_	_
76	inoculate	inoculate	VB	_	_	_
77	25	25	CD	_	_	_
78	ml	ml	NN	_	_	_
79	of	of	IN	_	_	_
80	fresh	fresh	JJ	_	_	_
81	LB	lb	NN	MED	_	_
82	medium	medium	NN	MED	_	_
83	.	.	.	_	_	_

1	Planktonic	planktonic	JJ	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	to	to	TO	_	_	_
6	a	a	DT	_	_	_
7	turbidity	turbidity	NN	_	_	_
8	of	of	IN	_	_	_
9	0.5	0.5	CD	_	_	_
10	at	at	IN	_	_	_
11	600	600	CD	_	_	_
12	nm	nm	NN	_	_	_
13	in	in	IN	_	_	_
14	LB	lb	NN	MED	_	_
15	medium	medium	NN	MED	_	_
16	with	with	IN	_	_	_
17	1	1	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	IPTG	iptg	NN	_	_	_
20	at	at	IN	_	_	_
21	37	37	CD	_	_	_
22	°C	°c	NN	_	_	_
23	,	,	,	_	_	_
24	adjusted	adjust	VBN	_	_	_
25	the	the	DT	_	_	_
26	turbidity	turbidity	NN	_	_	_
27	to	to	TO	_	_	_
28	1	1	CD	_	_	_
29	,	,	,	_	_	_
30	and	and	CC	_	_	_
31	exposed	expose	VBN	_	_	_
32	to	to	TO	_	_	_
33	20	20	CD	_	_	_
34	μg	μg	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
36	The	the	DT	_	_	_
37	overnight	overnight	JJ	_	_	_
38	culture	culture	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	0.25	0.25	CD	_	_	_
41	mL	ml	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	was	be	VBD	_	_	_
44	used	use	VBN	_	_	_
45	to	to	TO	_	_	_
46	inoculate	inoculate	VB	_	_	_
47	25	25	CD	_	_	_
48	mL	ml	NN	_	_	_
49	of	of	IN	_	_	_
50	fresh	fresh	JJ	_	_	_
51	LB	lb	NN	MED	_	_
52	medium	medium	NN	MED	_	_
53	.	.	.	_	_	_

1	Planktonic	planktonic	JJ	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	to	to	TO	_	_	_
6	a	a	DT	_	_	_
7	turbidity	turbidity	NN	_	_	_
8	of	of	IN	_	_	_
9	0.5	0.5	CD	_	_	_
10	at	at	IN	_	_	_
11	600	600	CD	_	_	_
12	nm	nm	NN	_	_	_
13	in	in	IN	_	_	_
14	LB	lb	NN	MED	_	_
15	medium	medium	NN	MED	_	_
16	with	with	IN	_	_	_
17	1	1	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	IPTG	iptg	NN	_	_	_
20	at	at	IN	_	_	_
21	37	37	CD	_	_	_
22	°C	°c	NN	_	_	_
23	,	,	,	_	_	_
24	adjusted	adjust	VBN	_	_	_
25	the	the	DT	_	_	_
26	turbidity	turbidity	NN	_	_	_
27	to	to	TO	_	_	_
28	1	1	CD	_	_	_
29	,	,	,	_	_	_
30	and	and	CC	_	_	_
31	exposed	expose	VBN	_	_	_
32	to	to	TO	_	_	_
33	20	20	CD	_	_	_
34	μg	μg	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	time	time	NN	_	_	_
37	:	:	:	_	_	_
38	1	1	CD	_	_	_
39	h	h	NN	_	_	_
40	with	with	IN	_	_	_
41	20	20	CD	_	_	_
42	μg	μg	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	EM1456	em1456	NN	_	_	_
45	wild-type	wild-type	JJ	_	_	_
46	pNM12	pnm12	NN	_	_	_
47	#	#	#	_	_	_
48	1	1	CD	_	_	_
49	+	+	CC	_	_	_
50	arabinose	arabinose	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	Escherichia	escherichia	FW	Organism	_	_
53	coli	coli	FW	Organism	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	experiment	experiment	NN	_	_	_
56	#	#	#	_	_	_
57	115	115	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	experiment	experiment	NN	_	_	_
60	#	#	#	_	_	_
61	116	116	CD	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	experiment	experiment	NN	_	_	_
64	#	#	#	_	_	_
65	203	203	CD	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	experiment	experiment	NN	_	_	_
68	#	#	#	_	_	_
69	204	204	CD	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	experiment	experiment	NN	_	_	_
72	#	#	#	_	_	_
73	205	205	CD	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	experiment	experiment	NN	_	_	_
76	#	#	#	_	_	_
77	206	206	CD	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	experiment	experiment	NN	_	_	_
80	#	#	#	_	_	_
81	303	303	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	experiment	experiment	NN	_	_	_
84	#	#	#	_	_	_
85	305	305	CD	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	experiment	experiment	NN	_	_	_
88	#	#	#	_	_	_
89	306	306	CD	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	fur	fur	NN	GEN	_	_
92	mutant	mutant	JJ	_	_	_
93	pBAD-ryhB	pbad-ryhb	NN	_	_	_
94	#	#	#	_	_	_
95	1	1	CD	_	_	_
96	+	+	CC	_	_	_
97	arabinose	arabinose	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	fur	fur	NN	GEN	_	_
100	mutant	mutant	JJ	_	_	_
101	pBAD-ryhB	pbad-ryhb	NN	_	_	_
102	#	#	#	_	_	_
103	2	2	CD	_	_	_
104	+	+	CC	_	_	_
105	arabinose	arabinose	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	fur	fur	NN	GEN	_	_
108	mutant	mutant	JJ	_	_	_
109	pNM12	pnm12	NN	_	_	_
110	#	#	#	_	_	_
111	1	1	CD	_	_	_
112	+	+	CC	_	_	_
113	arabinose	arabinose	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	fur	fur	NN	GEN	_	_
116	mutant	mutant	JJ	_	_	_
117	pNM12	pnm12	NN	_	_	_
118	#	#	#	_	_	_
119	2	2	CD	_	_	_
120	+	+	CC	_	_	_
121	arabinose	arabinose	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	Microarray	microarray	NN	_	_	_
124	suite	suite	NN	_	_	_
125	5.0	5.0	CD	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	Strain	strain	NN	_	_	_
128	EM1453	em1453	NN	_	_	_
129	wild-type	wild-type	JJ	_	_	_
130	pBAD-ryhB	pbad-ryhb	NN	_	_	_
131	#	#	#	_	_	_
132	1	1	CD	_	_	_
133	+	+	CC	_	_	_
134	arabinose	arabinose	NN	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
136	wild-type	wild-type	JJ	_	_	_
137	pBAD-ryhB	pbad-ryhb	NN	_	_	_
138	#	#	#	_	_	_
139	1	1	CD	_	_	_
140	+	+	CC	_	_	_
141	arabinose	arabinose	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
143	wild-type	wild-type	JJ	_	_	_
144	pBAD-ryhB	pbad-ryhb	NN	_	_	_
145	#	#	#	_	_	_
146	1	1	CD	_	_	_
147	+	+	CC	_	_	_
148	FeSO4	feso4	NN	_	_	_
149	+	+	CC	_	_	_
150	arabinose	arabinose	NN	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
152	wild-type	wild-type	JJ	_	_	_
153	pBAD-ryhB	pbad-ryhb	NN	_	_	_
154	#	#	#	_	_	_
155	2	2	CD	_	_	_
156	+	+	CC	_	_	_
157	arabinose	arabinose	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
159	wild-type	wild-type	JJ	_	_	_
160	pBAD-ryhB	pbad-ryhb	NN	_	_	_
161	#	#	#	_	_	_
162	2	2	CD	_	_	_
163	+	+	CC	_	_	_
164	FeSO4	feso4	NN	_	_	_
165	+	+	CC	_	_	_
166	arabinose	arabinose	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
168	wild-type	wild-type	JJ	_	_	_
169	pNM12	pnm12	NN	_	_	_
170	#	#	#	_	_	_
171	1	1	CD	_	_	_
172	+	+	CC	_	_	_
173	arabinose	arabinose	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
175	wild-type	wild-type	JJ	_	_	_
176	pNM12	pnm12	NN	_	_	_
177	#	#	#	_	_	_
178	1	1	CD	_	_	_
179	+	+	CC	_	_	_
180	FeSO4	feso4	NN	_	_	_
181	+	+	CC	_	_	_
182	arabinose	arabinose	NN	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
184	wild-type	wild-type	JJ	_	_	_
185	pNM12	pnm12	NN	_	_	_
186	#	#	#	_	_	_
187	2	2	CD	_	_	_
188	+	+	CC	_	_	_
189	arabinose	arabinose	NN	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
191	wild-type	wild-type	JJ	_	_	_
192	pNM12	pnm12	NN	_	_	_
193	#	#	#	_	_	_
194	2	2	CD	_	_	_
195	+	+	CC	_	_	_
196	FeSO4	feso4	NN	_	_	_
197	+	+	CC	_	_	_
198	arabinose	arabinose	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	Escherichia	escherichia	FW	Organism	_	_
201	coli	coli	FW	Organism	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	N3433	n3433	NN	_	_	_
204	-LRB-	-lrb-	-LRB-	_	_	_
205	rne	rne	NN	GEN	_	_
206	deletion	deletion	NN	_	_	_
207	-RRB-	-rrb-	-RRB-	_	_	_
208	pBADRNE	pbadrne	NN	_	_	_
209	in	in	IN	_	_	_
210	LB	lb	NN	_	_	_
211	at	at	IN	_	_	_
212	30	30	CD	_	_	_
213	degrees	degree	NNS	_	_	_
214	C	c	NN	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	N3433	n3433	NN	_	_	_
217	-LRB-	-lrb-	-LRB-	_	_	_
218	rne	rne	NN	GEN	_	_
219	deletion	deletion	NN	_	_	_
220	-RRB-	-rrb-	-RRB-	_	_	_
221	pBAD-RNE	pbad-rne	NN	_	_	_
222	w	w	NN	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	N3433	n3433	NN	_	_	_
225	-LRB-	-lrb-	-LRB-	_	_	_
226	rne	rne	NN	GEN	_	_
227	deletion	deletion	NN	_	_	_
228	-RRB-	-rrb-	-RRB-	_	_	_
229	pNRNE5	pnrne5	NN	_	_	_
230	at	at	IN	_	_	_
231	30	30	CD	_	_	_
232	degrees	degree	NNS	_	_	_
233	C	c	NN	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	N3433	n3433	NN	_	_	_
236	-LRB-	-lrb-	-LRB-	_	_	_
237	rne	rne	NN	GEN	_	_
238	deletion	deletion	NN	_	_	_
239	-RRB-	-rrb-	-RRB-	_	_	_
240	pRNG3	prng3	NN	_	_	_
241	at	at	IN	_	_	_
242	30	30	CD	_	_	_
243	degrees	degree	NNS	_	_	_
244	C	c	NN	_	_	_
245	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
246	N3433	n3433	NN	_	_	_
247	-LRB-	-lrb-	-LRB-	_	_	_
248	rng	rng	NN	GEN	_	_
249	deletion	deletion	NN	_	_	_
250	-RRB-	-rrb-	-RRB-	_	_	_
251	in	in	IN	_	_	_
252	LB	lb	NN	_	_	_
253	at	at	IN	_	_	_
254	30	30	CD	_	_	_
255	degrees	degree	NNS	_	_	_
256	C	c	NN	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	N3433	n3433	NN	_	_	_
259	-LRB-	-lrb-	-LRB-	_	_	_
260	rng	rng	NN	GEN	_	_
261	deletion	deletion	NN	_	_	_
262	-RRB-	-rrb-	-RRB-	_	_	_
263	LB	lb	NN	_	_	_
264	at	at	IN	_	_	_
265	30	30	CD	_	_	_
266	C	c	NN	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	N3433	n3433	NN	_	_	_
269	-LRB-	-lrb-	-LRB-	_	_	_
270	wt	wt	JJ	_	_	_
271	-RRB-	-rrb-	-RRB-	_	_	_
272	in	in	IN	_	_	_
273	LB	lb	NN	_	_	_
274	at	at	IN	_	_	_
275	30	30	CD	_	_	_
276	degrees	degree	NNS	_	_	_
277	C	c	NN	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
279	N3433	n3433	NN	_	_	_
280	-LRB-	-lrb-	-LRB-	_	_	_
281	wt	wt	JJ	_	_	_
282	-RRB-	-rrb-	-RRB-	_	_	_
283	pPM30	ppm30	NN	_	_	_
284	in	in	IN	_	_	_
285	LB	lb	NN	_	_	_
286	at	at	IN	_	_	_
287	30	30	CD	_	_	_
288	degrees	degree	NNS	_	_	_
289	C	c	NN	_	_	_
290	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
291	N3433	n3433	NN	_	_	_
292	-LRB-	-lrb-	-LRB-	_	_	_
293	wt	wt	JJ	_	_	_
294	-RRB-	-rrb-	-RRB-	_	_	_
295	pRNG3	prng3	NN	_	_	_
296	in	in	IN	_	_	_
297	LB	lb	NN	_	_	_
298	at	at	IN	_	_	_
299	30	30	CD	_	_	_
300	degrees	degree	NNS	_	_	_
301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
302	N3433	n3433	NN	_	_	_
303	-LRB-	-lrb-	-LRB-	_	_	_
304	wt	wt	JJ	_	_	_
305	-RRB-	-rrb-	-RRB-	_	_	_
306	vs	vs	CC	_	_	_
307	N3433	n3433	NN	_	_	_
308	-LRB-	-lrb-	-LRB-	_	_	_
309	rne	rne	NN	GEN	_	_
310	deletion	deletion	NN	_	_	_
311	-RRB-	-rrb-	-RRB-	_	_	_
312	pBADRNE	pbadrne	NN	_	_	_
313	in	in	IN	_	_	_
314	LB	lb	NN	_	_	_
315	at	at	IN	_	_	_
316	30	30	CD	_	_	_
317	degrees	degree	NNS	_	_	_
318	C	c	NN	_	_	_
319	Trial	trial	NN	_	_	_
320	B	b	NN	_	_	_
321	*	*	SYM	_	_	_
322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
323	N3433	n3433	NN	_	_	_
324	-LRB-	-lrb-	-LRB-	_	_	_
325	wt	wt	JJ	_	_	_
326	-RRB-	-rrb-	-RRB-	_	_	_
327	vs	vs	CC	_	_	_
328	N3433	n3433	NN	_	_	_
329	-LRB-	-lrb-	-LRB-	_	_	_
330	rne	rne	NN	GEN	_	_
331	deletion	deletion	NN	_	_	_
332	-RRB-	-rrb-	-RRB-	_	_	_
333	pBAD-RNE	pbad-rne	NN	_	_	_
334	w	w	NN	_	_	_
335	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
336	N3433	n3433	NN	_	_	_
337	-LRB-	-lrb-	-LRB-	_	_	_
338	wt	wt	JJ	_	_	_
339	-RRB-	-rrb-	-RRB-	_	_	_
340	vs	vs	CC	_	_	_
341	N3433	n3433	NN	_	_	_
342	-LRB-	-lrb-	-LRB-	_	_	_
343	rne	rne	NN	GEN	_	_
344	deletion	deletion	NN	_	_	_
345	-RRB-	-rrb-	-RRB-	_	_	_
346	pNRNE5	pnrne5	NN	_	_	_
347	at	at	IN	_	_	_
348	30	30	CD	_	_	_
349	degrees	degree	NNS	_	_	_
350	C	c	NN	_	_	_
351	Trial	trial	NN	_	_	_
352	A	a	NN	_	_	_
353	*	*	SYM	_	_	_
354	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
355	N3433	n3433	NN	_	_	_
356	-LRB-	-lrb-	-LRB-	_	_	_
357	wt	wt	JJ	_	_	_
358	-RRB-	-rrb-	-RRB-	_	_	_
359	vs	vs	CC	_	_	_
360	N3433	n3433	NN	_	_	_
361	-LRB-	-lrb-	-LRB-	_	_	_
362	rne	rne	NN	GEN	_	_
363	deletion	deletion	NN	_	_	_
364	-RRB-	-rrb-	-RRB-	_	_	_
365	pNRNE5	pnrne5	NN	_	_	_
366	at	at	IN	_	_	_
367	30	30	CD	_	_	_
368	degrees	degree	NNS	_	_	_
369	C	c	NN	_	_	_
370	Trial	trial	NN	_	_	_
371	B	b	NN	_	_	_
372	*	*	SYM	_	_	_
373	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
374	N3433	n3433	NN	_	_	_
375	-LRB-	-lrb-	-LRB-	_	_	_
376	wt	wt	JJ	_	_	_
377	-RRB-	-rrb-	-RRB-	_	_	_
378	vs	vs	CC	_	_	_
379	N3433	n3433	NN	_	_	_
380	-LRB-	-lrb-	-LRB-	_	_	_
381	rne	rne	NN	GEN	_	_
382	deletion	deletion	NN	_	_	_
383	-RRB-	-rrb-	-RRB-	_	_	_
384	pRNG3	prng3	NN	_	_	_
385	at	at	IN	_	_	_
386	30	30	CD	_	_	_
387	degrees	degree	NNS	_	_	_
388	C	c	NN	_	_	_
389	Trial	trial	NN	_	_	_
390	A	a	NN	_	_	_
391	*	*	SYM	_	_	_
392	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
393	N3433	n3433	NN	_	_	_
394	-LRB-	-lrb-	-LRB-	_	_	_
395	wt	wt	JJ	_	_	_
396	-RRB-	-rrb-	-RRB-	_	_	_
397	vs	vs	CC	_	_	_
398	N3433	n3433	NN	_	_	_
399	-LRB-	-lrb-	-LRB-	_	_	_
400	rne	rne	NN	GEN	_	_
401	deletion	deletion	NN	_	_	_
402	-RRB-	-rrb-	-RRB-	_	_	_
403	pRNG3	prng3	NN	_	_	_
404	at	at	IN	_	_	_
405	30	30	CD	_	_	_
406	degrees	degree	NNS	_	_	_
407	C	c	NN	_	_	_
408	Trial	trial	NN	_	_	_
409	B	b	NN	_	_	_
410	*	*	SYM	_	_	_
411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
412	N3433	n3433	NN	_	_	_
413	-LRB-	-lrb-	-LRB-	_	_	_
414	wt	wt	JJ	_	_	_
415	-RRB-	-rrb-	-RRB-	_	_	_
416	vs	vs	CC	_	_	_
417	N3433	n3433	NN	_	_	_
418	-LRB-	-lrb-	-LRB-	_	_	_
419	rng	rng	NN	GEN	_	_
420	deletion	deletion	NN	_	_	_
421	-RRB-	-rrb-	-RRB-	_	_	_
422	in	in	IN	_	_	_
423	LB	lb	NN	_	_	_
424	at	at	IN	_	_	_
425	30	30	CD	_	_	_
426	degrees	degree	NNS	_	_	_
427	C	c	NN	_	_	_
428	Trial	trial	NN	_	_	_
429	B	b	NN	_	_	_
430	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
431	N3433	n3433	NN	_	_	_
432	-LRB-	-lrb-	-LRB-	_	_	_
433	wt	wt	JJ	_	_	_
434	-RRB-	-rrb-	-RRB-	_	_	_
435	vs	vs	CC	_	_	_
436	N3433	n3433	NN	_	_	_
437	-LRB-	-lrb-	-LRB-	_	_	_
438	rng	rng	NN	GEN	_	_
439	deletion	deletion	NN	_	_	_
440	-RRB-	-rrb-	-RRB-	_	_	_
441	LB	lb	NN	_	_	_
442	at	at	IN	_	_	_
443	30	30	CD	_	_	_
444	C	c	NN	_	_	_
445	Trial	trial	NN	_	_	_
446	A	a	NN	_	_	_
447	*	*	SYM	_	_	_
448	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
449	N3433	n3433	NN	_	_	_
450	-LRB-	-lrb-	-LRB-	_	_	_
451	wt	wt	JJ	_	_	_
452	-RRB-	-rrb-	-RRB-	_	_	_
453	vs	vs	CC	_	_	_
454	N3433	n3433	NN	_	_	_
455	-LRB-	-lrb-	-LRB-	_	_	_
456	wt	wt	JJ	_	_	_
457	-RRB-	-rrb-	-RRB-	_	_	_
458	pRNG3	prng3	NN	_	_	_
459	in	in	IN	_	_	_
460	LB	lb	NN	_	_	_
461	at	at	IN	_	_	_
462	30	30	CD	_	_	_
463	degrees	degree	NNS	_	_	_
464	Trial	trial	NN	_	_	_
465	A	a	DT	_	_	_
466	*	*	SYM	_	_	_
467	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
468	N3433	n3433	NN	_	_	_
469	-LRB-	-lrb-	-LRB-	_	_	_
470	wt	wt	JJ	_	_	_
471	-RRB-	-rrb-	-RRB-	_	_	_
472	vs	vs	CC	_	_	_
473	N3433	n3433	NN	_	_	_
474	-LRB-	-lrb-	-LRB-	_	_	_
475	wt	wt	JJ	_	_	_
476	-RRB-	-rrb-	-RRB-	_	_	_
477	pRNG3	prng3	NN	_	_	_
478	in	in	IN	_	_	_
479	LB	lb	NN	_	_	_
480	at	at	IN	_	_	_
481	30	30	CD	_	_	_
482	degrees	degree	NNS	_	_	_
483	Trial	trial	NN	_	_	_
484	B	b	NN	_	_	_
485	*	*	SYM	_	_	_
486	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
487	VALUE	VALUE	NNP	_	_	_
488	is	be	VBZ	_	_	_
489	Log	log	NN	_	_	_
490	-LRB-	-lrb-	-LRB-	_	_	_
491	base	base	NN	_	_	_
492	2	2	CD	_	_	_
493	-RRB-	-rrb-	-RRB-	_	_	_
494	of	of	IN	_	_	_
495	the	the	DT	_	_	_
496	ratio	ratio	NN	_	_	_
497	of	of	IN	_	_	_
498	the	the	DT	_	_	_
499	median	median	NN	_	_	_
500	of	of	IN	_	_	_
501	Channel	Channel	NNP	_	_	_
502	2	2	CD	_	_	_
503	-LRB-	-lrb-	-LRB-	_	_	_
504	usually	usually	RB	_	_	_
505	635	635	CD	_	_	_
506	nm	nm	NN	_	_	_
507	-RRB-	-rrb-	-RRB-	_	_	_
508	to	to	TO	_	_	_
509	Channel	Channel	NNP	_	_	_
510	1	1	CD	_	_	_
511	-LRB-	-lrb-	-LRB-	_	_	_
512	usually	usually	RB	_	_	_
513	532	532	CD	_	_	_
514	nm	nm	NN	_	_	_
515	-RRB-	-rrb-	-RRB-	_	_	_
516	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
517	A10	a10	NN	_	_	_
518	:	:	:	_	_	_
519	LJ110	lj110	NN	_	_	_
520	del	del	FW	_	_	_
521	pdhr	pdhr	FW	_	_	_
522	MMAcetat	mmacetat	NN	_	_	_
523	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
524	A11	a11	NN	_	_	_
525	:	:	:	_	_	_
526	LJ110	lj110	NN	_	_	_
527	pTM30	ptm30	NN	_	_	_
528	MMAcetat	mmacetat	NN	_	_	_
529	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
530	A12	a12	NN	_	_	_
531	:	:	:	_	_	_
532	LJ110	lj110	NN	_	_	_
533	pTM30pdhr	ptm30pdhr	NN	_	_	_
534	MMAcetat	mmacetat	NN	_	_	_
535	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
536	A1	a1	NN	_	_	_
537	:	:	:	_	_	_
538	LJ110	lj110	NN	_	_	_
539	LBo	lbo	NN	_	_	_
540	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
541	A2	a2	NN	_	_	_
542	:	:	:	_	_	_
543	LJ110	lj110	NN	_	_	_
544	del	del	FW	_	_	_
545	pdhr	pdhr	FW	_	_	_
546	LBo	lbo	FW	_	_	_
547	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
548	A3	a3	NN	_	_	_
549	:	:	:	_	_	_
550	LJ110	lj110	NN	_	_	_
551	pTM30	ptm30	NN	_	_	_
552	LBo	lbo	NN	_	_	_
553	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
554	A4	a4	NN	_	_	_
555	:	:	:	_	_	_
556	LJ110	lj110	NN	_	_	_
557	pTM30pdhr	ptm30pdhr	NN	_	_	_
558	LBo	lbo	NN	_	_	_
559	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
560	A5	a5	NN	_	_	_
561	:	:	:	_	_	_
562	LJ110	lj110	NN	_	_	_
563	MMPyruvat	mmpyruvat	NN	_	_	_
564	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
565	A6	a6	NN	_	_	_
566	:	:	:	_	_	_
567	LJ110	lj110	NN	_	_	_
568	del	del	FW	_	_	_
569	pdhr	pdhr	FW	_	_	_
570	MMPyruvat	mmpyruvat	NN	_	_	_
571	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
572	A7	a7	NN	_	_	_
573	:	:	:	_	_	_
574	LJ110	lj110	NN	_	_	_
575	pTM30	ptm30	NN	_	_	_
576	MMPyruvat	mmpyruvat	NN	_	_	_
577	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
578	A8	a8	NN	_	_	_
579	:	:	:	_	_	_
580	LJ110	lj110	NN	_	_	_
581	pTM30pdhr	ptm30pdhr	NN	_	_	_
582	MMPyruvat	mmpyruvat	NN	_	_	_
583	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
584	A9	a9	NN	_	_	_
585	:	:	:	_	_	_
586	LJ110	lj110	NN	_	_	_
587	MMAcetat	mmacetat	NN	_	_	_
588	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
589	B10	b10	NN	_	_	_
590	:	:	:	_	_	_
591	LJ110	lj110	NN	_	_	_
592	del	del	FW	_	_	_
593	pdhr	pdhr	FW	_	_	_
594	MMAcetat	mmacetat	NN	_	_	_
595	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
596	B11	b11	NN	_	_	_
597	:	:	:	_	_	_
598	LJ110	lj110	NN	_	_	_
599	pTM30	ptm30	NN	_	_	_
600	MMAcetat	mmacetat	NN	_	_	_
601	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
602	B12	b12	NN	_	_	_
603	:	:	:	_	_	_
604	LJ110	lj110	NN	_	_	_
605	pTM30pdhr	ptm30pdhr	NN	_	_	_
606	MMAcetat	mmacetat	NN	_	_	_
607	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
608	B1	b1	NN	_	_	_
609	:	:	:	_	_	_
610	LJ110	lj110	NN	_	_	_
611	LBo	lbo	NN	_	_	_
612	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
613	B2	b2	NN	_	_	_
614	:	:	:	_	_	_
615	LJ110	lj110	NN	_	_	_
616	del	del	FW	_	_	_
617	pdhr	pdhr	FW	_	_	_
618	LBo	lbo	FW	_	_	_
619	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
620	B3	b3	NN	_	_	_
621	:	:	:	_	_	_
622	LJ110	lj110	NN	_	_	_
623	pTM30	ptm30	NN	_	_	_
624	LBo	lbo	NN	_	_	_
625	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
626	B4	b4	NN	_	_	_
627	:	:	:	_	_	_
628	LJ110	lj110	NN	_	_	_
629	pTM30pdhr	ptm30pdhr	NN	_	_	_
630	LBo	lbo	NN	_	_	_
631	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
632	B5	b5	NN	_	_	_
633	:	:	:	_	_	_
634	LJ110	lj110	NN	_	_	_
635	MMPyruvat	mmpyruvat	NN	_	_	_
636	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
637	B6	b6	NN	_	_	_
638	:	:	:	_	_	_
639	LJ110	lj110	NN	_	_	_
640	del	del	FW	_	_	_
641	pdhr	pdhr	FW	_	_	_
642	MMPyruvat	mmpyruvat	NN	_	_	_
643	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
644	B7	b7	NN	_	_	_
645	:	:	:	_	_	_
646	LJ110	lj110	NN	_	_	_
647	pTM30	ptm30	NN	_	_	_
648	MMPyruvat	mmpyruvat	NN	_	_	_
649	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
650	B8	b8	NN	_	_	_
651	:	:	:	_	_	_
652	LJ110	lj110	NN	_	_	_
653	pTM30pdhr	ptm30pdhr	NN	_	_	_
654	MMPyruvat	mmpyruvat	NN	_	_	_
655	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
656	B9	b9	NN	_	_	_
657	:	:	:	_	_	_
658	LJ110	lj110	NN	_	_	_
659	MMAcetat	mmacetat	NN	_	_	_
660	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
661	background	background	NN	_	_	_
662	strain	strain	NN	_	_	_
663	:	:	:	_	_	_
664	LJ110	lj110	NN	_	_	_
665	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
666	Escherichia	escherichia	FW	Organism	_	_
667	coli	coli	FW	Organism	_	_
668	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
669	Expression	expression	NN	_	_	_
670	values	value	NNS	_	_	_
671	were	be	VBD	_	_	_
672	calculated	calculate	VBN	_	_	_
673	by	by	IN	_	_	_
674	the	the	DT	_	_	_
675	software	software	NN	_	_	_
676	package	package	NN	_	_	_
677	Feature	Feature	NNP	_	_	_
678	Extraction	Extraction	NNP	_	_	_
679	10.5.1.1	10.5.1.1	CD	_	_	_
680	using	use	VBG	_	_	_
681	protocol	protocol	NN	_	_	_
682	GE1	ge1	NN	_	_	_
683	_	_	NN	_	_	_
684	105	105	CD	_	_	_
685	_	_	SYM	_	_	_
686	Dec08	dec08	NN	_	_	_
687	-LRB-	-lrb-	-LRB-	_	_	_
688	Agilent	Agilent	NNP	_	_	_
689	Technologies	Technologies	NNPS	_	_	_
690	;	;	:	_	_	_
691	Waldbronn	Waldbronn	NNP	_	_	_
692	,	,	,	_	_	_
693	Germany	Germany	NNP	_	_	_
694	-RRB-	-rrb-	-RRB-	_	_	_
695	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
696	genetic	genetic	JJ	_	_	_
697	modification	modification	NN	_	_	_
698	:	:	:	_	_	_
699	empty	empty	JJ	_	_	_
700	plasmid	plasmid	NN	_	_	_
701	-LRB-	-lrb-	-LRB-	_	_	_
702	LJ110	lj110	NN	_	_	_
703	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
704	genetic	genetic	JJ	_	_	_
705	modification	modification	NN	_	_	_
706	:	:	:	_	_	_
707	PdhR	pdhr	NN	TF	_	_
708	knockout	knockout	NN	_	_	_
709	mutant	mutant	NN	_	_	_
710	-LRB-	-lrb-	-LRB-	_	_	_
711	LJ110deltapdhR	lj110deltapdhr	NN	_	_	_
712	-RRB-	-rrb-	-RRB-	_	_	_
713	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
714	genetic	genetic	JJ	_	_	_
715	modification	modification	NN	_	_	_
716	:	:	:	_	_	_
717	PdhR	pdhr	NN	TF	_	_
718	overexpression	overexpression	NN	_	_	_
719	strain	strain	NN	_	_	_
720	-LRB-	-lrb-	-LRB-	_	_	_
721	LJ110	lj110	NN	_	_	_
722	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
723	genetic	genetic	JJ	_	_	_
724	modification	modification	NN	_	_	_
725	:	:	:	_	_	_
726	wild	wild	JJ	_	_	_
727	type	type	NN	_	_	_
728	LJ110	lj110	CD	_	_	_
729	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
730	LJ110	lj110	NN	_	_	_
731	del	del	FW	_	_	_
732	pdhr	pdhr	FW	_	_	_
733	LBo	lbo	FW	_	_	_
734	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
735	LJ110	lj110	NN	_	_	_
736	del	del	FW	_	_	_
737	pdhr	pdhr	FW	_	_	_
738	MMAcetat	mmacetat	NN	_	_	_
739	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
740	LJ110	lj110	NN	_	_	_
741	del	del	FW	_	_	_
742	pdhr	pdhr	FW	_	_	_
743	MMPyruvat	mmpyruvat	NN	_	_	_
744	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
745	LJ110	lj110	NN	_	_	_
746	LBo	lbo	NN	_	_	_
747	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
748	LJ110	lj110	NN	_	_	_
749	MMAcetat	mmacetat	NN	_	_	_
750	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
751	LJ110	lj110	NN	_	_	_
752	MMPyruvat	mmpyruvat	NN	_	_	_
753	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
754	LJ110	lj110	NN	_	_	_
755	pTM30	ptm30	NN	_	_	_
756	LBo	lbo	NN	_	_	_
757	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
758	LJ110	lj110	NN	_	_	_
759	pTM30	ptm30	NN	_	_	_
760	MMAcetat	mmacetat	NN	_	_	_
761	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
762	LJ110	lj110	NN	_	_	_
763	pTM30	ptm30	NN	_	_	_
764	MMPyruvat	mmpyruvat	NN	_	_	_
765	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
766	LJ110	lj110	NN	_	_	_
767	pTM30pdhr	ptm30pdhr	NN	_	_	_
768	LBo	lbo	NN	_	_	_
769	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
770	LJ110	lj110	NN	_	_	_
771	pTM30pdhr	ptm30pdhr	NN	_	_	_
772	MMAcetat	mmacetat	NN	_	_	_
773	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
774	LJ110	lj110	NN	_	_	_
775	pTM30pdhr	ptm30pdhr	NN	_	_	_
776	MMPyruvat	mmpyruvat	NN	_	_	_
777	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
778	MMAcetat	mmacetat	NN	_	_	_
779	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
780	MMPyruvat	mmpyruvat	NN	_	_	_
781	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
782	RNAeasy	rnaeasy	NN	_	_	_
783	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
784	CRE	cre	NN	_	_	_
785	Multi	multi	JJ	_	_	_
786	0uM	0um	NN	_	_	_
787	Rep1	rep1	NN	_	_	_
788	Plasmid	plasmid	NN	_	_	_
789	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
790	CRE	cre	NN	_	_	_
791	Multi	multi	JJ	_	_	_
792	0uM	0um	NN	_	_	_
793	Rep2	rep2	NN	_	_	_
794	Plasmid	plasmid	NN	_	_	_
795	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
796	CRE	cre	NN	_	_	_
797	Multi	multi	JJ	_	_	_
798	100uM	100um	NN	_	_	_
799	Rep1	rep1	NN	_	_	_
800	Plasmid	plasmid	NN	_	_	_
801	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
802	CRE	cre	NN	_	_	_
803	Multi	multi	JJ	_	_	_
804	100uM	100um	NN	_	_	_
805	Rep2	rep2	NN	_	_	_
806	Plasmid	plasmid	NN	_	_	_
807	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
808	CRE	cre	NN	_	_	_
809	Single	single	JJ	_	_	_
810	100uM	100um	NN	_	_	_
811	Rep1	rep1	NN	_	_	_
812	Plasmid	plasmid	NN	_	_	_
813	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
814	CRE	cre	NN	_	_	_
815	Single	single	JJ	_	_	_
816	100uM	100um	NN	_	_	_
817	Rep2	rep2	NN	_	_	_
818	Plasmid	plasmid	NN	_	_	_
819	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
820	Escherichia	escherichia	FW	Organism	_	_
821	coli	coli	FW	Organism	_	_
822	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
823	HEK293T	hek293t	NN	_	_	_
824	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
825	IFNB	ifnb	NN	_	_	_
826	Multi	multi	JJ	_	_	_
827	SeV0	sev0	NN	_	_	_
828	Rep1	rep1	NN	_	_	_
829	Plasmid	plasmid	NN	_	_	_
830	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
831	IFNB	ifnb	NN	_	_	_
832	Multi	multi	JJ	_	_	_
833	SeV10	sev10	NN	_	_	_
834	Rep1	rep1	NN	_	_	_
835	Plasmid	plasmid	NN	_	_	_
836	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
837	IFNB	ifnb	NN	_	_	_
838	Single	single	JJ	_	_	_
839	SeV10	sev10	NN	_	_	_
840	Rep1	rep1	NN	_	_	_
841	Plasmid	plasmid	NN	_	_	_
842	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
843	Plasmid	plasmid	NN	_	_	_
844	pool	pool	NN	_	_	_
845	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
846	reporter	reporter	NN	_	_	_
847	:	:	:	_	_	_
848	CRE	cre	NN	_	_	_
849	multi-hit	multi-hit	JJ	_	_	_
850	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
851	reporter	reporter	NN	_	_	_
852	:	:	:	_	_	_
853	CRE	cre	NN	_	_	_
854	single-hit	single-hit	JJ	_	_	_
855	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
856	reporter	reporter	NN	_	_	_
857	:	:	:	_	_	_
858	IFNB	ifnb	NN	_	_	_
859	multi-hit	multi-hit	JJ	_	_	_
860	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
861	reporter	reporter	NN	_	_	_
862	:	:	:	_	_	_
863	IFNB	ifnb	NN	_	_	_
864	single-hit	single-hit	JJ	_	_	_
865	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
866	RNA-Seq	rna-seq	NN	_	_	_
867	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
868	sample	sample	NN	_	_	_
869	type	type	NN	_	_	_
870	:	:	:	_	_	_
871	plasmid	plasmid	NN	_	_	_
872	pool	pool	NN	_	_	_
873	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
874	To	to	TO	_	_	_
875	infer	infer	VB	_	_	_
876	the	the	DT	_	_	_
877	tag	tag	NN	GEN	_	_
878	copy	copy	NN	_	_	_
879	numbers	number	NNS	_	_	_
880	in	in	IN	_	_	_
881	each	each	DT	_	_	_
882	Tag-Seq	Tag-Seq	NNP	_	_	_
883	library	library	NN	_	_	_
884	,	,	,	_	_	_
885	all	all	DT	_	_	_
886	sequence	sequence	NN	_	_	_
887	reads	read	VBZ	_	_	_
888	were	be	VBD	_	_	_
889	examined	examine	VBN	_	_	_
890	,	,	,	_	_	_
891	regardless	regardless	RB	_	_	_
892	of	of	IN	_	_	_
893	their	they	PRP$	_	_	_
894	quality	quality	NN	_	_	_
895	scores	score	NNS	_	_	_
896	.	.	.	_	_	_

1	If	if	IN	_	_	_
2	the	the	DT	_	_	_
3	first	first	JJ	_	_	_
4	ten	ten	CD	_	_	_
5	nucleotides	nucleotide	NNS	_	_	_
6	of	of	IN	_	_	_
7	a	a	DT	_	_	_
8	read	read	NN	_	_	_
9	perfectly	perfectly	RB	_	_	_
10	matched	match	VBD	_	_	_
11	one	one	CD	_	_	_
12	of	of	IN	_	_	_
13	the	the	DT	_	_	_
14	13,000	13,000	CD	_	_	_
15	or	or	CC	_	_	_
16	27,000	27,000	CD	_	_	_
17	designed	design	VBN	_	_	_
18	tags	tag	NNS	_	_	_
19	and	and	CC	_	_	_
20	the	the	DT	_	_	_
21	remaining	remain	VBG	_	_	_
22	nucleotides	nucleotide	NNS	_	_	_
23	matched	match	VBD	_	_	_
24	the	the	DT	_	_	_
25	expected	expect	VBN	_	_	_
26	upstream	upstream	JJ	_	_	_
27	MPRA	MPRA	NNP	_	_	_
28	construct	construct	NN	_	_	_
29	sequence	sequence	NN	_	_	_
30	,	,	,	_	_	_
31	this	this	DT	_	_	_
32	was	be	VBD	_	_	_
33	counted	count	VBN	_	_	_
34	as	as	IN	_	_	_
35	one	one	CD	_	_	_
36	occurrence	occurrence	NN	_	_	_
37	of	of	IN	_	_	_
38	that	that	DT	_	_	_
39	tag	tag	NN	GEN	_	_
40	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	reads	read	VBZ	_	_	_
3	that	that	IN	_	_	_
4	did	do	VBD	_	_	_
5	not	not	RB	_	_	_
6	meet	meet	VB	_	_	_
7	this	this	DT	_	_	_
8	criterion	criterion	NN	_	_	_
9	were	be	VBD	_	_	_
10	discarded	discard	VBN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	from	from	IN	_	_	_
7	cell	cell	NN	_	_	_
8	lysates	lysate	NNS	_	_	_
9	using	use	VBG	_	_	_
10	RNeasy	RNeasy	NNP	_	_	_
11	kits	kit	NNS	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Qiagen	Qiagen	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	mRNA	mrna	NN	_	_	_
2	was	be	VBD	_	_	_
3	extracted	extract	VBN	_	_	_
4	from	from	IN	_	_	_
5	total	total	JJ	_	_	_
6	RNA	rna	NN	_	_	_
7	using	use	VBG	_	_	_
8	MicroPoly	MicroPoly	NNP	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	A	A	NNP	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	Puristâ	Puristâ	NNP	_	_	_
13	``	``	``	_	_	_
14	¢	¢	$	_	_	_
15	kits	kit	NNS	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Ambion	Ambion	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	and	and	CC	_	_	_
20	treated	treat	VBN	_	_	_
21	with	with	IN	_	_	_
22	DNase	dnase	NN	_	_	_
23	I	i	CD	_	_	_
24	using	use	VBG	_	_	_
25	the	the	DT	_	_	_
26	Turbo	Turbo	NNP	_	_	_
27	DNA-freeâ	DNA-freeâ	NNP	_	_	_
28	``	``	``	_	_	_
29	¢	¢	$	_	_	_
30	kit	kit	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Ambion	ambion	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	First-strand	first-strand	JJ	_	_	_
2	cDNA	cdna	NN	_	_	_
3	was	be	VBD	_	_	_
4	synthesized	synthesize	VBN	_	_	_
5	from	from	IN	_	_	_
6	400-700	400-700	CD	_	_	_
7	ng	ng	NN	_	_	_
8	mRNA	mrna	NN	_	_	_
9	using	use	VBG	_	_	_
10	High	high	JJ	_	_	_
11	Capacity	capacity	NN	_	_	_
12	RNA-to-cDNA	rna-to-cdna	NN	_	_	_
13	kits	kit	NNS	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Applied	Applied	NNP	_	_	_
16	Biosystems	Biosystems	NNPS	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

1	Tag-Seq	tag-seq	JJ	_	_	_
2	sequencing	sequencing	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	generated	generate	VBN	_	_	_
6	directly	directly	RB	_	_	_
7	from	from	IN	_	_	_
8	12	12	CD	_	_	_
9	%	%	NN	_	_	_
10	of	of	IN	_	_	_
11	a	a	DT	_	_	_
12	cDNA	cdna	NN	_	_	_
13	reaction	reaction	NN	_	_	_
14	or	or	CC	_	_	_
15	50	50	CD	_	_	_
16	ng	ng	NN	_	_	_
17	plasmid	plasmid	NN	_	_	_
18	DNA	dna	NN	_	_	_
19	by	by	IN	_	_	_
20	26	26	CD	_	_	_
21	cycle	cycle	NN	_	_	_
22	PCR	pcr	NN	_	_	_
23	using	use	VBG	_	_	_
24	Pfu	pfu	NN	_	_	_
25	Ultra	Ultra	NNP	_	_	_
26	HS	hs	NN	_	_	_
27	DNA	dna	NN	_	_	_
28	polymerase	polymerase	NN	_	_	_
29	2x	2x	NN	_	_	_
30	master	master	NN	_	_	_
31	mix	mix	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	Agilent	agilent	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	and	and	CC	_	_	_
36	primers	primer	NNS	_	_	_
37	AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT	AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT	NNP	_	_	_
38	and	and	CC	_	_	_
39	CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCGAGGTGCCTAAAGG	CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCGAGGTGCCTAAAGG	NNP	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	where	where	WRB	_	_	_
42	XXXXXXXX	XXXXXXXX	NNP	_	_	_
43	is	be	VBZ	_	_	_
44	a	a	DT	_	_	_
45	library-specific	library-specific	JJ	_	_	_
46	index	index	NN	_	_	_
47	sequence	sequence	NN	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	resultant	resultant	JJ	_	_	_
3	PCR	pcr	NN	_	_	_
4	products	product	NNS	_	_	_
5	were	be	VBD	_	_	_
6	size-selected	size-selected	JJ	_	_	_
7	using	use	VBG	_	_	_
8	2	2	CD	_	_	_
9	%	%	NN	_	_	_
10	agarose	agarose	NN	_	_	_
11	E-Gel	e-gel	NN	_	_	_
12	EX	ex	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Invitrogen	invitrogen	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	N	n	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	0	0	CD	_	_	_
7	min	min	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	10	10	CD	_	_	_
10	min	min	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	30	30	CD	_	_	_
13	min	min	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	60	60	CD	_	_	_
16	min	min	NN	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	Agilent	Agilent	NNP	_	_	_
19	Feature	Feature	NNP	_	_	_
20	Extraction	Extraction	NNP	_	_	_
21	Software	Software	NNP	_	_	_
22	v.	v.	CC	_	_	_
23	9.5.3.1	9.5.3.1	CD	_	_	_
24	was	be	VBD	_	_	_
25	used	use	VBN	_	_	_
26	for	for	IN	_	_	_
27	background	background	NN	_	_	_
28	subtraction	subtraction	NN	_	_	_
29	and	and	CC	_	_	_
30	LOWESS	lowess	NN	_	_	_
31	normalization	normalization	NN	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	0	0	CD	_	_	_
5	min	min	NN	_	_	_
6	vs	vs	CC	_	_	_
7	10	10	CD	_	_	_
8	min	min	NN	_	_	_
9	Rep1	rep1	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Escherichia	escherichia	FW	Organism	_	_
12	coli	coli	FW	Organism	_	_
13	10	10	CD	_	_	_
14	min	min	NN	_	_	_
15	vs	vs	CC	_	_	_
16	0	0	CD	_	_	_
17	min	min	NN	_	_	_
18	Rep2	rep2	JJ	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Escherichia	escherichia	FW	Organism	_	_
21	coli	coli	FW	Organism	_	_
22	30	30	CD	_	_	_
23	min	min	NN	_	_	_
24	vs	vs	CC	_	_	_
25	60	60	CD	_	_	_
26	min	min	NN	_	_	_
27	Rep1	rep1	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Escherichia	escherichia	FW	Organism	_	_
30	coli	coli	FW	Organism	_	_
31	60	60	CD	_	_	_
32	min	min	NN	_	_	_
33	vs	vs	CC	_	_	_
34	30	30	CD	_	_	_
35	min	min	NN	_	_	_
36	Rep2	rep2	JJ	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Escherichia	escherichia	FW	Organism	_	_
39	coli	coli	FW	Organism	_	_
40	K-12	k-12	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
42	One	one	CD	_	_	_
43	conditions	condition	NNS	_	_	_
44	:	:	:	_	_	_
45	5	5	CD	_	_	_
46	%	%	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	v	v	LS	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
50	Overnight	overnight	JJ	_	_	_
51	culture	culture	NN	_	_	_
52	of	of	IN	_	_	_
53	E.	e.	FW	_	_	_
54	coli	coli	FW	_	_	_
55	BW25113	bw25113	NN	_	_	_
56	in	in	IN	_	_	_
57	LB	lb	NN	_	_	_
58	was	be	VBD	_	_	_
59	diluted	dilute	VBN	_	_	_
60	in	in	IN	_	_	_
61	M9	m9	NN	MED	_	_
62	minimal	minimal	JJ	MED	_	_
63	medium	medium	NN	MED	_	_
64	with	with	IN	_	_	_
65	supplements	supplement	NNS	_	_	_
66	to	to	TO	_	_	_
67	OD600	od600	NN	_	_	_
68	=	=	JJ	_	_	_
69	0.02	0.02	CD	_	_	_
70	and	and	CC	_	_	_
71	was	be	VBD	_	_	_
72	incubated	incubate	VBN	_	_	_
73	at	at	IN	_	_	_
74	37	37	CD	_	_	_
75	Ceilsus	ceilsus	NN	_	_	_
76	degree	degree	NN	_	_	_
77	with	with	IN	_	_	_
78	shaking	shake	VBG	_	_	_
79	at	at	IN	_	_	_
80	250rpm	250rpm	NN	_	_	_
81	until	until	IN	_	_	_
82	its	its	PRP$	_	_	_
83	OD600	od600	NN	_	_	_
84	reached	reach	VBD	_	_	_
85	0.1	0.1	CD	_	_	_
86	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	K-12	k-12	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	time	time	NN	_	_	_
7	:	:	:	_	_	_
8	0	0	CD	_	_	_
9	min	min	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	time	time	NN	_	_	_
12	:	:	:	_	_	_
13	10	10	CD	_	_	_
14	min	min	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	time	time	NN	_	_	_
17	:	:	:	_	_	_
18	30	30	CD	_	_	_
19	min	min	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	time	time	NN	_	_	_
22	:	:	:	_	_	_
23	60	60	CD	_	_	_
24	min	min	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Total	total	JJ	_	_	_
27	RNA	rna	NN	_	_	_
28	was	be	VBD	_	_	_
29	extracted	extract	VBN	_	_	_
30	from	from	IN	_	_	_
31	5	5	CD	_	_	_
32	ml	ml	NN	_	_	_
33	cell	cell	NN	_	_	_
34	culture	culture	NN	_	_	_
35	at	at	IN	_	_	_
36	0	0	CD	_	_	_
37	,	,	,	_	_	_
38	10	10	CD	_	_	_
39	,	,	,	_	_	_
40	30	30	CD	_	_	_
41	and	and	CC	_	_	_
42	60	60	CD	_	_	_
43	min	min	NN	_	_	_
44	incubation	incubation	NN	_	_	_
45	after	after	IN	_	_	_
46	addition	addition	NN	_	_	_
47	of	of	IN	_	_	_
48	5	5	CD	_	_	_
49	%	%	NN	_	_	_
50	isooctane	isooctane	NN	_	_	_
51	using	use	VBG	_	_	_
52	RNeasy	rneasy	NN	_	_	_
53	mini	minus	NNS	_	_	_
54	kit	kit	NN	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	Qiagen	Qiagen	NNP	_	_	_
57	,	,	,	_	_	_
58	Inc.	Inc.	NNP	_	_	_
59	,	,	,	_	_	_
60	Valencia	Valencia	NNP	_	_	_
61	,	,	,	_	_	_
62	CA	CA	NNP	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	according	accord	VBG	_	_	_
65	to	to	TO	_	_	_
66	the	the	DT	_	_	_
67	manufacturer	manufacturer	NN	_	_	_
68	's	's	POS	_	_	_
69	protocol	protocol	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	treatment	treatment	NN	_	_	_
72	:	:	:	_	_	_
73	5	5	CD	_	_	_
74	percent	percent	NN	_	_	_
75	isooctane	isooctane	NN	_	_	_
76	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
77	Escherichia	escherichia	FW	Organism	_	_
78	coli	coli	FW	Organism	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	normalized	normalize	VBD	_	_	_
81	using	use	VBG	_	_	_
82	lcDNA	lcdna	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	ppsA	ppsa	NN	GEN	_	_
85	mutant	mutant	JJ	_	_	_
86	15	15	CD	_	_	_
87	min	min	NN	_	_	_
88	-LRB-	-lrb-	-LRB-	_	_	_
89	1	1	CD	_	_	_
90	-RRB-	-rrb-	-RRB-	_	_	_
91	slide	slide	NN	_	_	_
92	1	1	CD	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	ppsA	ppsa	NN	GEN	_	_
95	mutant	mutant	JJ	_	_	_
96	15	15	CD	_	_	_
97	min	min	NN	_	_	_
98	-LRB-	-lrb-	-LRB-	_	_	_
99	1	1	CD	_	_	_
100	-RRB-	-rrb-	-RRB-	_	_	_
101	slide	slide	NN	_	_	_
102	2	2	CD	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	ppsA	ppsa	NN	GEN	_	_
105	mutant	mutant	NN	_	_	_
106	1	1	CD	_	_	_
107	hour	hour	NN	_	_	_
108	-LRB-	-lrb-	-LRB-	_	_	_
109	1	1	CD	_	_	_
110	-RRB-	-rrb-	-RRB-	_	_	_
111	slide	slide	NN	_	_	_
112	1	1	CD	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	ppsA	ppsa	NN	GEN	_	_
115	mutant	mutant	NN	_	_	_
116	1	1	CD	_	_	_
117	hour	hour	NN	_	_	_
118	-LRB-	-lrb-	-LRB-	_	_	_
119	1	1	CD	_	_	_
120	-RRB-	-rrb-	-RRB-	_	_	_
121	slide	slide	NN	_	_	_
122	2	2	CD	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	ppsA	ppsa	NN	GEN	_	_
125	mutant	mutant	NN	_	_	_
126	1	1	CD	_	_	_
127	hour	hour	NN	_	_	_
128	-LRB-	-lrb-	-LRB-	_	_	_
129	2	2	CD	_	_	_
130	-RRB-	-rrb-	-RRB-	_	_	_
131	slide	slide	NN	_	_	_
132	1	1	CD	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	ppsA	ppsa	NN	GEN	_	_
135	mutant	mutant	NN	_	_	_
136	1	1	CD	_	_	_
137	hour	hour	NN	_	_	_
138	-LRB-	-lrb-	-LRB-	_	_	_
139	2	2	CD	_	_	_
140	-RRB-	-rrb-	-RRB-	_	_	_
141	slide	slide	NN	_	_	_
142	2	2	CD	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	ppsA	ppsa	NN	GEN	_	_
145	mutant	mutant	NN	_	_	_
146	1	1	CD	_	_	_
147	hour	hour	NN	_	_	_
148	-LRB-	-lrb-	-LRB-	_	_	_
149	3	3	CD	_	_	_
150	-RRB-	-rrb-	-RRB-	_	_	_
151	slide	slide	NN	_	_	_
152	1	1	CD	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	ppsA	ppsa	NN	GEN	_	_
155	mutant	mutant	NN	_	_	_
156	1	1	CD	_	_	_
157	hour	hour	NN	_	_	_
158	-LRB-	-lrb-	-LRB-	_	_	_
159	3	3	CD	_	_	_
160	-RRB-	-rrb-	-RRB-	_	_	_
161	slide	slide	NN	_	_	_
162	2	2	CD	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	ppsA	ppsa	NN	GEN	_	_
165	mutant	mutant	NN	_	_	_
166	2	2	CD	_	_	_
167	hour	hour	NN	_	_	_
168	-LRB-	-lrb-	-LRB-	_	_	_
169	1	1	CD	_	_	_
170	-RRB-	-rrb-	-RRB-	_	_	_
171	slide	slide	NN	_	_	_
172	1	1	CD	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	ppsA	ppsa	NN	GEN	_	_
175	mutant	mutant	NN	_	_	_
176	2	2	CD	_	_	_
177	hour	hour	NN	_	_	_
178	-LRB-	-lrb-	-LRB-	_	_	_
179	1	1	CD	_	_	_
180	-RRB-	-rrb-	-RRB-	_	_	_
181	slide	slide	NN	_	_	_
182	2	2	CD	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	ppsA	ppsa	NN	GEN	_	_
185	mutant	mutant	NN	_	_	_
186	2	2	CD	_	_	_
187	hour	hour	NN	_	_	_
188	-LRB-	-lrb-	-LRB-	_	_	_
189	2	2	CD	_	_	_
190	-RRB-	-rrb-	-RRB-	_	_	_
191	slide	slide	NN	_	_	_
192	1	1	CD	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	ppsA	ppsa	NN	GEN	_	_
195	mutant	mutant	NN	_	_	_
196	2	2	CD	_	_	_
197	hour	hour	NN	_	_	_
198	-LRB-	-lrb-	-LRB-	_	_	_
199	2	2	CD	_	_	_
200	-RRB-	-rrb-	-RRB-	_	_	_
201	slide	slide	NN	_	_	_
202	2	2	CD	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	ppsA	ppsa	NN	GEN	_	_
205	mutant	mutant	NN	_	_	_
206	2	2	CD	_	_	_
207	hour	hour	NN	_	_	_
208	-LRB-	-lrb-	-LRB-	_	_	_
209	3	3	CD	_	_	_
210	-RRB-	-rrb-	-RRB-	_	_	_
211	slide	slide	NN	_	_	_
212	1	1	CD	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	ppsA	ppsa	NN	GEN	_	_
215	mutant	mutant	NN	_	_	_
216	2	2	CD	_	_	_
217	hour	hour	NN	_	_	_
218	-LRB-	-lrb-	-LRB-	_	_	_
219	3	3	CD	_	_	_
220	-RRB-	-rrb-	-RRB-	_	_	_
221	slide	slide	NN	_	_	_
222	2	2	CD	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	ppsA	ppsa	NN	GEN	_	_
225	mutant	mutant	JJ	_	_	_
226	30	30	CD	_	_	_
227	min	min	NN	_	_	_
228	-LRB-	-lrb-	-LRB-	_	_	_
229	1	1	CD	_	_	_
230	-RRB-	-rrb-	-RRB-	_	_	_
231	slide	slide	NN	_	_	_
232	1	1	CD	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	ppsA	ppsa	NN	GEN	_	_
235	mutant	mutant	JJ	_	_	_
236	30	30	CD	_	_	_
237	min	min	NN	_	_	_
238	-LRB-	-lrb-	-LRB-	_	_	_
239	1	1	CD	_	_	_
240	-RRB-	-rrb-	-RRB-	_	_	_
241	slide	slide	NN	_	_	_
242	2	2	CD	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	ppsA	ppsa	NN	GEN	_	_
245	mutant	mutant	JJ	_	_	_
246	3	3	CD	_	_	_
247	hour	hour	NN	_	_	_
248	-LRB-	-lrb-	-LRB-	_	_	_
249	1	1	CD	_	_	_
250	-RRB-	-rrb-	-RRB-	_	_	_
251	slide	slide	NN	_	_	_
252	1	1	CD	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
254	ppsA	ppsa	NN	GEN	_	_
255	mutant	mutant	JJ	_	_	_
256	3	3	CD	_	_	_
257	hour	hour	NN	_	_	_
258	-LRB-	-lrb-	-LRB-	_	_	_
259	1	1	CD	_	_	_
260	-RRB-	-rrb-	-RRB-	_	_	_
261	slide	slide	NN	_	_	_
262	2	2	CD	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
264	ppsA	ppsa	NN	GEN	_	_
265	mutant	mutant	JJ	_	_	_
266	3	3	CD	_	_	_
267	hour	hour	NN	_	_	_
268	-LRB-	-lrb-	-LRB-	_	_	_
269	2	2	CD	_	_	_
270	-RRB-	-rrb-	-RRB-	_	_	_
271	slide	slide	NN	_	_	_
272	1	1	CD	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	ppsA	ppsa	NN	GEN	_	_
275	mutant	mutant	JJ	_	_	_
276	3	3	CD	_	_	_
277	hour	hour	NN	_	_	_
278	-LRB-	-lrb-	-LRB-	_	_	_
279	2	2	CD	_	_	_
280	-RRB-	-rrb-	-RRB-	_	_	_
281	slide	slide	NN	_	_	_
282	2	2	CD	_	_	_
283	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
284	ppsA	ppsa	NN	GEN	_	_
285	mutant	mutant	JJ	_	_	_
286	3	3	CD	_	_	_
287	hour	hour	NN	_	_	_
288	-LRB-	-lrb-	-LRB-	_	_	_
289	3	3	CD	_	_	_
290	-RRB-	-rrb-	-RRB-	_	_	_
291	slide	slide	NN	_	_	_
292	1	1	CD	_	_	_
293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
294	ppsA	ppsa	NN	GEN	_	_
295	mutant	mutant	JJ	_	_	_
296	3	3	CD	_	_	_
297	hour	hour	NN	_	_	_
298	-LRB-	-lrb-	-LRB-	_	_	_
299	3	3	CD	_	_	_
300	-RRB-	-rrb-	-RRB-	_	_	_
301	slide	slide	NN	_	_	_
302	2	2	CD	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
304	ppsA	ppsa	NN	GEN	_	_
305	mutant	mutant	JJ	_	_	_
306	4	4	CD	_	_	_
307	hour	hour	NN	_	_	_
308	-LRB-	-lrb-	-LRB-	_	_	_
309	1	1	CD	_	_	_
310	-RRB-	-rrb-	-RRB-	_	_	_
311	slide	slide	NN	_	_	_
312	1	1	CD	_	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
314	ppsA	ppsa	NN	GEN	_	_
315	mutant	mutant	JJ	_	_	_
316	4	4	CD	_	_	_
317	hour	hour	NN	_	_	_
318	-LRB-	-lrb-	-LRB-	_	_	_
319	1	1	CD	_	_	_
320	-RRB-	-rrb-	-RRB-	_	_	_
321	slide	slide	NN	_	_	_
322	2	2	CD	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	ppsA	ppsa	NN	GEN	_	_
325	mutant	mutant	JJ	_	_	_
326	4	4	CD	_	_	_
327	hour	hour	NN	_	_	_
328	-LRB-	-lrb-	-LRB-	_	_	_
329	2	2	CD	_	_	_
330	-RRB-	-rrb-	-RRB-	_	_	_
331	slide	slide	NN	_	_	_
332	1	1	CD	_	_	_
333	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
334	ppsA	ppsa	NN	GEN	_	_
335	mutant	mutant	JJ	_	_	_
336	4	4	CD	_	_	_
337	hour	hour	NN	_	_	_
338	-LRB-	-lrb-	-LRB-	_	_	_
339	2	2	CD	_	_	_
340	-RRB-	-rrb-	-RRB-	_	_	_
341	slide	slide	NN	_	_	_
342	2	2	CD	_	_	_
343	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
344	ppsA	ppsa	NN	GEN	_	_
345	mutant	mutant	JJ	_	_	_
346	4	4	CD	_	_	_
347	hour	hour	NN	_	_	_
348	-LRB-	-lrb-	-LRB-	_	_	_
349	3	3	CD	_	_	_
350	-RRB-	-rrb-	-RRB-	_	_	_
351	slide	slide	NN	_	_	_
352	1	1	CD	_	_	_
353	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
354	ppsA	ppsa	NN	GEN	_	_
355	mutant	mutant	JJ	_	_	_
356	4	4	CD	_	_	_
357	hour	hour	NN	_	_	_
358	-LRB-	-lrb-	-LRB-	_	_	_
359	3	3	CD	_	_	_
360	-RRB-	-rrb-	-RRB-	_	_	_
361	slide	slide	NN	_	_	_
362	2	2	CD	_	_	_
363	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
364	ppsA	ppsa	NN	GEN	_	_
365	mutant	mutant	JJ	_	_	_
366	5	5	CD	_	_	_
367	hour	hour	NN	_	_	_
368	-LRB-	-lrb-	-LRB-	_	_	_
369	1	1	CD	_	_	_
370	-RRB-	-rrb-	-RRB-	_	_	_
371	slide	slide	NN	_	_	_
372	1	1	CD	_	_	_
373	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
374	ppsA	ppsa	NN	GEN	_	_
375	mutant	mutant	JJ	_	_	_
376	5	5	CD	_	_	_
377	hour	hour	NN	_	_	_
378	-LRB-	-lrb-	-LRB-	_	_	_
379	1	1	CD	_	_	_
380	-RRB-	-rrb-	-RRB-	_	_	_
381	slide	slide	NN	_	_	_
382	2	2	CD	_	_	_
383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
384	ppsA	ppsa	NN	GEN	_	_
385	mutant	mutant	JJ	_	_	_
386	5	5	CD	_	_	_
387	hour	hour	NN	_	_	_
388	-LRB-	-lrb-	-LRB-	_	_	_
389	2	2	CD	_	_	_
390	-RRB-	-rrb-	-RRB-	_	_	_
391	slide	slide	NN	_	_	_
392	1	1	CD	_	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
394	ppsA	ppsa	NN	GEN	_	_
395	mutant	mutant	JJ	_	_	_
396	5	5	CD	_	_	_
397	hour	hour	NN	_	_	_
398	-LRB-	-lrb-	-LRB-	_	_	_
399	2	2	CD	_	_	_
400	-RRB-	-rrb-	-RRB-	_	_	_
401	slide	slide	NN	_	_	_
402	2	2	CD	_	_	_
403	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
404	ppsA	ppsa	NN	GEN	_	_
405	mutant	mutant	JJ	_	_	_
406	5	5	CD	_	_	_
407	min	min	NN	_	_	_
408	-LRB-	-lrb-	-LRB-	_	_	_
409	1	1	CD	_	_	_
410	-RRB-	-rrb-	-RRB-	_	_	_
411	slide	slide	NN	_	_	_
412	1	1	CD	_	_	_
413	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
414	ppsA	ppsa	NN	GEN	_	_
415	mutant	mutant	JJ	_	_	_
416	5	5	CD	_	_	_
417	min	min	NN	_	_	_
418	-LRB-	-lrb-	-LRB-	_	_	_
419	1	1	CD	_	_	_
420	-RRB-	-rrb-	-RRB-	_	_	_
421	slide	slide	NN	_	_	_
422	2	2	CD	_	_	_
423	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
424	ppsA	ppsa	NN	GEN	_	_
425	mutant	mutant	JJ	_	_	_
426	6	6	CD	_	_	_
427	hour	hour	NN	_	_	_
428	-LRB-	-lrb-	-LRB-	_	_	_
429	1	1	CD	_	_	_
430	-RRB-	-rrb-	-RRB-	_	_	_
431	slide	slide	NN	_	_	_
432	1	1	CD	_	_	_
433	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
434	ppsA	ppsa	NN	GEN	_	_
435	mutant	mutant	JJ	_	_	_
436	6	6	CD	_	_	_
437	hour	hour	NN	_	_	_
438	-LRB-	-lrb-	-LRB-	_	_	_
439	1	1	CD	_	_	_
440	-RRB-	-rrb-	-RRB-	_	_	_
441	slide	slide	NN	_	_	_
442	2	2	CD	_	_	_
443	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
444	ppsA	ppsa	NN	GEN	_	_
445	mutant	mutant	JJ	_	_	_
446	6	6	CD	_	_	_
447	hour	hour	NN	_	_	_
448	-LRB-	-lrb-	-LRB-	_	_	_
449	2	2	CD	_	_	_
450	-RRB-	-rrb-	-RRB-	_	_	_
451	slide	slide	NN	_	_	_
452	1	1	CD	_	_	_
453	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
454	ppsA	ppsa	NN	GEN	_	_
455	mutant	mutant	JJ	_	_	_
456	6	6	CD	_	_	_
457	hour	hour	NN	_	_	_
458	-LRB-	-lrb-	-LRB-	_	_	_
459	2	2	CD	_	_	_
460	-RRB-	-rrb-	-RRB-	_	_	_
461	slide	slide	NN	_	_	_
462	2	2	CD	_	_	_
463	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
464	reference	reference	NN	_	_	_
465	sample	sample	NN	_	_	_
466	harvested	harvest	VBN	_	_	_
467	immediately	immediately	RB	_	_	_
468	prior	prior	RB	_	_	_
469	to	to	TO	_	_	_
470	glucose	glucose	NN	SUPP	_	_
471	to	to	TO	_	_	_
472	acetate	acetate	NN	SUPP	_	_
473	shift	shift	NN	_	_	_
474	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
475	strain	strain	NN	_	_	_
476	BW25113	bw25113	NN	_	_	_
477	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
478	Strain	strain	NN	_	_	_
479	BW25113	bw25113	NN	_	_	_
480	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
481	Strain	strain	NN	_	_	_
482	BW25113	bw25113	NN	_	_	_
483	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
484	strain	strain	NN	_	_	_
485	BW25113	bw25113	NN	_	_	_
486	ppsA	ppsa	NN	GEN	_	_
487	deletion	deletion	NN	_	_	_
488	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
489	time	time	NN	_	_	_
490	course	course	NN	_	_	_
491	sample	sample	NN	_	_	_
492	harvested	harvest	VBN	_	_	_
493	after	after	IN	_	_	_
494	15	15	CD	_	_	_
495	min	min	NN	_	_	_
496	of	of	IN	_	_	_
497	glucose	glucose	NN	SUPP	_	_
498	to	to	TO	_	_	_
499	acetate	acetate	NN	SUPP	_	_
500	shift	shift	NN	_	_	_
501	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
502	time	time	NN	_	_	_
503	course	course	NN	_	_	_
504	sample	sample	NN	_	_	_
505	harvested	harvest	VBN	_	_	_
506	after	after	IN	_	_	_
507	1	1	CD	_	_	_
508	hour	hour	NN	_	_	_
509	of	of	IN	_	_	_
510	glucose	glucose	NN	SUPP	_	_
511	to	to	TO	_	_	_
512	acetate	acetate	NN	SUPP	_	_
513	shift	shift	NN	_	_	_
514	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
515	time	time	NN	_	_	_
516	course	course	NN	_	_	_
517	sample	sample	NN	_	_	_
518	harvested	harvest	VBN	_	_	_
519	after	after	IN	_	_	_
520	2	2	CD	_	_	_
521	hour	hour	NN	_	_	_
522	of	of	IN	_	_	_
523	glucose	glucose	NN	SUPP	_	_
524	to	to	TO	_	_	_
525	acetate	acetate	NN	SUPP	_	_
526	shift	shift	NN	_	_	_
527	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
528	time	time	NN	_	_	_
529	course	course	NN	_	_	_
530	sample	sample	NN	_	_	_
531	harvested	harvest	VBN	_	_	_
532	after	after	IN	_	_	_
533	30	30	CD	_	_	_
534	min	min	NN	_	_	_
535	of	of	IN	_	_	_
536	glucose	glucose	NN	SUPP	_	_
537	to	to	TO	_	_	_
538	acetate	acetate	NN	SUPP	_	_
539	shift	shift	NN	_	_	_
540	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
541	time	time	NN	_	_	_
542	course	course	NN	_	_	_
543	sample	sample	NN	_	_	_
544	harvested	harvest	VBN	_	_	_
545	after	after	IN	_	_	_
546	3	3	CD	_	_	_
547	hour	hour	NN	_	_	_
548	of	of	IN	_	_	_
549	glucose	glucose	NN	SUPP	_	_
550	to	to	TO	_	_	_
551	acetate	acetate	NN	SUPP	_	_
552	shift	shift	NN	_	_	_
553	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
554	time	time	NN	_	_	_
555	course	course	NN	_	_	_
556	sample	sample	NN	_	_	_
557	harvested	harvest	VBN	_	_	_
558	after	after	IN	_	_	_
559	4	4	CD	_	_	_
560	hour	hour	NN	_	_	_
561	of	of	IN	_	_	_
562	glucose	glucose	NN	SUPP	_	_
563	to	to	TO	_	_	_
564	acetate	acetate	NN	SUPP	_	_
565	shift	shift	NN	_	_	_
566	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
567	time	time	NN	_	_	_
568	course	course	NN	_	_	_
569	sample	sample	NN	_	_	_
570	harvested	harvest	VBN	_	_	_
571	after	after	IN	_	_	_
572	5	5	CD	_	_	_
573	hour	hour	NN	_	_	_
574	of	of	IN	_	_	_
575	glucose	glucose	NN	SUPP	_	_
576	to	to	TO	_	_	_
577	acetate	acetate	NN	SUPP	_	_
578	shift	shift	NN	_	_	_
579	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
580	time	time	NN	_	_	_
581	course	course	NN	_	_	_
582	sample	sample	NN	_	_	_
583	harvested	harvest	VBN	_	_	_
584	after	after	IN	_	_	_
585	5	5	CD	_	_	_
586	min	min	NN	_	_	_
587	of	of	IN	_	_	_
588	glucose	glucose	NN	SUPP	_	_
589	to	to	TO	_	_	_
590	acetate	acetate	NN	SUPP	_	_
591	shift	shift	NN	_	_	_
592	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
593	time	time	NN	_	_	_
594	course	course	NN	_	_	_
595	sample	sample	NN	_	_	_
596	harvested	harvest	VBN	_	_	_
597	after	after	IN	_	_	_
598	6	6	CD	_	_	_
599	hour	hour	NN	_	_	_
600	of	of	IN	_	_	_
601	glucose	glucose	NN	SUPP	_	_
602	to	to	TO	_	_	_
603	acetate	acetate	NN	SUPP	_	_
604	shift	shift	NN	_	_	_
605	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
606	wild-type	wild-type	JJ	_	_	_
607	15	15	CD	_	_	_
608	min	min	NN	_	_	_
609	-LRB-	-lrb-	-LRB-	_	_	_
610	1	1	CD	_	_	_
611	-RRB-	-rrb-	-RRB-	_	_	_
612	slide	slide	NN	_	_	_
613	1	1	CD	_	_	_
614	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
615	wild-type	wild-type	JJ	_	_	_
616	15	15	CD	_	_	_
617	min	min	NN	_	_	_
618	-LRB-	-lrb-	-LRB-	_	_	_
619	1	1	CD	_	_	_
620	-RRB-	-rrb-	-RRB-	_	_	_
621	slide	slide	NN	_	_	_
622	2	2	CD	_	_	_
623	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
624	wild-type	wild-type	JJ	_	_	_
625	15	15	CD	_	_	_
626	min	min	NN	_	_	_
627	-LRB-	-lrb-	-LRB-	_	_	_
628	2	2	CD	_	_	_
629	-RRB-	-rrb-	-RRB-	_	_	_
630	slide	slide	NN	_	_	_
631	1	1	CD	_	_	_
632	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
633	wild-type	wild-type	JJ	_	_	_
634	15	15	CD	_	_	_
635	min	min	NN	_	_	_
636	-LRB-	-lrb-	-LRB-	_	_	_
637	2	2	CD	_	_	_
638	-RRB-	-rrb-	-RRB-	_	_	_
639	slide	slide	NN	_	_	_
640	2	2	CD	_	_	_
641	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
642	wild-type	wild-type	JJ	_	_	_
643	1	1	CD	_	_	_
644	hour	hour	NN	_	_	_
645	-LRB-	-lrb-	-LRB-	_	_	_
646	1	1	CD	_	_	_
647	-RRB-	-rrb-	-RRB-	_	_	_
648	slide	slide	NN	_	_	_
649	1	1	CD	_	_	_
650	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
651	wild-type	wild-type	JJ	_	_	_
652	1	1	CD	_	_	_
653	hour	hour	NN	_	_	_
654	-LRB-	-lrb-	-LRB-	_	_	_
655	1	1	CD	_	_	_
656	-RRB-	-rrb-	-RRB-	_	_	_
657	slide	slide	NN	_	_	_
658	2	2	CD	_	_	_
659	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
660	wild-type	wild-type	JJ	_	_	_
661	1	1	CD	_	_	_
662	hour	hour	NN	_	_	_
663	-LRB-	-lrb-	-LRB-	_	_	_
664	2	2	CD	_	_	_
665	-RRB-	-rrb-	-RRB-	_	_	_
666	slide	slide	NN	_	_	_
667	2	2	CD	_	_	_
668	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
669	wild-type	wild-type	JJ	_	_	_
670	1	1	CD	_	_	_
671	hour	hour	NN	_	_	_
672	-LRB-	-lrb-	-LRB-	_	_	_
673	3	3	CD	_	_	_
674	-RRB-	-rrb-	-RRB-	_	_	_
675	slide	slide	NN	_	_	_
676	1	1	CD	_	_	_
677	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
678	wild-type	wild-type	JJ	_	_	_
679	1	1	CD	_	_	_
680	hour	hour	NN	_	_	_
681	-LRB-	-lrb-	-LRB-	_	_	_
682	3	3	CD	_	_	_
683	-RRB-	-rrb-	-RRB-	_	_	_
684	slide	slide	NN	_	_	_
685	2	2	CD	_	_	_
686	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
687	wild-type	wild-type	JJ	_	_	_
688	2	2	CD	_	_	_
689	hour	hour	NN	_	_	_
690	-LRB-	-lrb-	-LRB-	_	_	_
691	1	1	CD	_	_	_
692	-RRB-	-rrb-	-RRB-	_	_	_
693	slide	slide	NN	_	_	_
694	1	1	CD	_	_	_
695	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
696	wild-type	wild-type	JJ	_	_	_
697	2	2	CD	_	_	_
698	hour	hour	NN	_	_	_
699	-LRB-	-lrb-	-LRB-	_	_	_
700	1	1	CD	_	_	_
701	-RRB-	-rrb-	-RRB-	_	_	_
702	slide	slide	NN	_	_	_
703	2	2	CD	_	_	_
704	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
705	wild-type	wild-type	JJ	_	_	_
706	2	2	CD	_	_	_
707	hour	hour	NN	_	_	_
708	-LRB-	-lrb-	-LRB-	_	_	_
709	2	2	CD	_	_	_
710	-RRB-	-rrb-	-RRB-	_	_	_
711	slide	slide	NN	_	_	_
712	1	1	CD	_	_	_
713	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
714	wild-type	wild-type	JJ	_	_	_
715	2	2	CD	_	_	_
716	hour	hour	NN	_	_	_
717	-LRB-	-lrb-	-LRB-	_	_	_
718	2	2	CD	_	_	_
719	-RRB-	-rrb-	-RRB-	_	_	_
720	slide	slide	NN	_	_	_
721	2	2	CD	_	_	_
722	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
723	wild-type	wild-type	JJ	_	_	_
724	2	2	CD	_	_	_
725	hour	hour	NN	_	_	_
726	-LRB-	-lrb-	-LRB-	_	_	_
727	3	3	CD	_	_	_
728	-RRB-	-rrb-	-RRB-	_	_	_
729	slide	slide	NN	_	_	_
730	1	1	CD	_	_	_
731	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
732	wild-type	wild-type	JJ	_	_	_
733	2	2	CD	_	_	_
734	hour	hour	NN	_	_	_
735	-LRB-	-lrb-	-LRB-	_	_	_
736	3	3	CD	_	_	_
737	-RRB-	-rrb-	-RRB-	_	_	_
738	slide	slide	NN	_	_	_
739	2	2	CD	_	_	_
740	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
741	wild-type	wild-type	JJ	_	_	_
742	30	30	CD	_	_	_
743	min	min	NN	_	_	_
744	-LRB-	-lrb-	-LRB-	_	_	_
745	1	1	CD	_	_	_
746	-RRB-	-rrb-	-RRB-	_	_	_
747	slide	slide	NN	_	_	_
748	1	1	CD	_	_	_
749	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
750	wild-type	wild-type	JJ	_	_	_
751	30	30	CD	_	_	_
752	min	min	NN	_	_	_
753	-LRB-	-lrb-	-LRB-	_	_	_
754	1	1	CD	_	_	_
755	-RRB-	-rrb-	-RRB-	_	_	_
756	slide	slide	NN	_	_	_
757	2	2	CD	_	_	_
758	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
759	wild-type	wild-type	JJ	_	_	_
760	30	30	CD	_	_	_
761	min	min	NN	_	_	_
762	-LRB-	-lrb-	-LRB-	_	_	_
763	2	2	CD	_	_	_
764	-RRB-	-rrb-	-RRB-	_	_	_
765	slide	slide	NN	_	_	_
766	1	1	CD	_	_	_
767	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
768	wild-type	wild-type	JJ	_	_	_
769	30	30	CD	_	_	_
770	min	min	NN	_	_	_
771	-LRB-	-lrb-	-LRB-	_	_	_
772	2	2	CD	_	_	_
773	-RRB-	-rrb-	-RRB-	_	_	_
774	slide	slide	NN	_	_	_
775	2	2	CD	_	_	_
776	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
777	wild-type	wild-type	JJ	_	_	_
778	3	3	CD	_	_	_
779	hour	hour	NN	_	_	_
780	-LRB-	-lrb-	-LRB-	_	_	_
781	1	1	CD	_	_	_
782	-RRB-	-rrb-	-RRB-	_	_	_
783	slide	slide	NN	_	_	_
784	1	1	CD	_	_	_
785	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
786	wild-type	wild-type	JJ	_	_	_
787	3	3	CD	_	_	_
788	hour	hour	NN	_	_	_
789	-LRB-	-lrb-	-LRB-	_	_	_
790	1	1	CD	_	_	_
791	-RRB-	-rrb-	-RRB-	_	_	_
792	slide	slide	NN	_	_	_
793	2	2	CD	_	_	_
794	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
795	wild-type	wild-type	JJ	_	_	_
796	3	3	CD	_	_	_
797	hour	hour	NN	_	_	_
798	-LRB-	-lrb-	-LRB-	_	_	_
799	2	2	CD	_	_	_
800	-RRB-	-rrb-	-RRB-	_	_	_
801	slide	slide	NN	_	_	_
802	1	1	CD	_	_	_
803	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
804	wild-type	wild-type	JJ	_	_	_
805	3	3	CD	_	_	_
806	hour	hour	NN	_	_	_
807	-LRB-	-lrb-	-LRB-	_	_	_
808	2	2	CD	_	_	_
809	-RRB-	-rrb-	-RRB-	_	_	_
810	slide	slide	NN	_	_	_
811	2	2	CD	_	_	_
812	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
813	wild-type	wild-type	JJ	_	_	_
814	3	3	CD	_	_	_
815	hour	hour	NN	_	_	_
816	-LRB-	-lrb-	-LRB-	_	_	_
817	3	3	CD	_	_	_
818	-RRB-	-rrb-	-RRB-	_	_	_
819	slide	slide	NN	_	_	_
820	1	1	CD	_	_	_
821	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
822	wild-type	wild-type	JJ	_	_	_
823	3	3	CD	_	_	_
824	hour	hour	NN	_	_	_
825	-LRB-	-lrb-	-LRB-	_	_	_
826	3	3	CD	_	_	_
827	-RRB-	-rrb-	-RRB-	_	_	_
828	slide	slide	NN	_	_	_
829	2	2	CD	_	_	_
830	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
831	wild-type	wild-type	JJ	_	_	_
832	4	4	CD	_	_	_
833	hour	hour	NN	_	_	_
834	-LRB-	-lrb-	-LRB-	_	_	_
835	1	1	CD	_	_	_
836	-RRB-	-rrb-	-RRB-	_	_	_
837	slide	slide	NN	_	_	_
838	1	1	CD	_	_	_
839	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
840	wild-type	wild-type	JJ	_	_	_
841	4	4	CD	_	_	_
842	hour	hour	NN	_	_	_
843	-LRB-	-lrb-	-LRB-	_	_	_
844	1	1	CD	_	_	_
845	-RRB-	-rrb-	-RRB-	_	_	_
846	slide	slide	NN	_	_	_
847	2	2	CD	_	_	_
848	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
849	wild-type	wild-type	JJ	_	_	_
850	4	4	CD	_	_	_
851	hour	hour	NN	_	_	_
852	-LRB-	-lrb-	-LRB-	_	_	_
853	2	2	CD	_	_	_
854	-RRB-	-rrb-	-RRB-	_	_	_
855	slide	slide	NN	_	_	_
856	1	1	CD	_	_	_
857	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
858	wild-type	wild-type	JJ	_	_	_
859	4	4	CD	_	_	_
860	hour	hour	NN	_	_	_
861	-LRB-	-lrb-	-LRB-	_	_	_
862	2	2	CD	_	_	_
863	-RRB-	-rrb-	-RRB-	_	_	_
864	slide	slide	NN	_	_	_
865	2	2	CD	_	_	_
866	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
867	wild-type	wild-type	JJ	_	_	_
868	4	4	CD	_	_	_
869	hour	hour	NN	_	_	_
870	-LRB-	-lrb-	-LRB-	_	_	_
871	3	3	CD	_	_	_
872	-RRB-	-rrb-	-RRB-	_	_	_
873	slide	slide	NN	_	_	_
874	1	1	CD	_	_	_
875	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
876	wild-type	wild-type	JJ	_	_	_
877	4	4	CD	_	_	_
878	hour	hour	NN	_	_	_
879	-LRB-	-lrb-	-LRB-	_	_	_
880	3	3	CD	_	_	_
881	-RRB-	-rrb-	-RRB-	_	_	_
882	slide	slide	NN	_	_	_
883	2	2	CD	_	_	_
884	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
885	wild-type	wild-type	JJ	_	_	_
886	5	5	CD	_	_	_
887	hour	hour	NN	_	_	_
888	-LRB-	-lrb-	-LRB-	_	_	_
889	1	1	CD	_	_	_
890	-RRB-	-rrb-	-RRB-	_	_	_
891	slide	slide	NN	_	_	_
892	1	1	CD	_	_	_
893	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
894	wild-type	wild-type	JJ	_	_	_
895	5	5	CD	_	_	_
896	hour	hour	NN	_	_	_
897	-LRB-	-lrb-	-LRB-	_	_	_
898	1	1	CD	_	_	_
899	-RRB-	-rrb-	-RRB-	_	_	_
900	slide	slide	NN	_	_	_
901	2	2	CD	_	_	_
902	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
903	wild-type	wild-type	JJ	_	_	_
904	5	5	CD	_	_	_
905	hour	hour	NN	_	_	_
906	-LRB-	-lrb-	-LRB-	_	_	_
907	2	2	CD	_	_	_
908	-RRB-	-rrb-	-RRB-	_	_	_
909	slide	slide	NN	_	_	_
910	1	1	CD	_	_	_
911	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
912	wild-type	wild-type	JJ	_	_	_
913	5	5	CD	_	_	_
914	hour	hour	NN	_	_	_
915	-LRB-	-lrb-	-LRB-	_	_	_
916	2	2	CD	_	_	_
917	-RRB-	-rrb-	-RRB-	_	_	_
918	slide	slide	NN	_	_	_
919	2	2	CD	_	_	_
920	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
921	wild-type	wild-type	JJ	_	_	_
922	5	5	CD	_	_	_
923	min	min	NN	_	_	_
924	-LRB-	-lrb-	-LRB-	_	_	_
925	1	1	CD	_	_	_
926	-RRB-	-rrb-	-RRB-	_	_	_
927	slide	slide	NN	_	_	_
928	1	1	CD	_	_	_
929	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
930	wild-type	wild-type	JJ	_	_	_
931	5	5	CD	_	_	_
932	min	min	NN	_	_	_
933	-LRB-	-lrb-	-LRB-	_	_	_
934	1	1	CD	_	_	_
935	-RRB-	-rrb-	-RRB-	_	_	_
936	slide	slide	NN	_	_	_
937	2	2	CD	_	_	_
938	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
939	wild-type	wild-type	JJ	_	_	_
940	5	5	CD	_	_	_
941	min	min	NN	_	_	_
942	-LRB-	-lrb-	-LRB-	_	_	_
943	2	2	CD	_	_	_
944	-RRB-	-rrb-	-RRB-	_	_	_
945	slide	slide	NN	_	_	_
946	1	1	CD	_	_	_
947	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
948	wild-type	wild-type	JJ	_	_	_
949	5	5	CD	_	_	_
950	min	min	NN	_	_	_
951	-LRB-	-lrb-	-LRB-	_	_	_
952	2	2	CD	_	_	_
953	-RRB-	-rrb-	-RRB-	_	_	_
954	slide	slide	NN	_	_	_
955	2	2	CD	_	_	_
956	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
957	wild-type	wild-type	JJ	_	_	_
958	6	6	CD	_	_	_
959	hour	hour	NN	_	_	_
960	-LRB-	-lrb-	-LRB-	_	_	_
961	1	1	CD	_	_	_
962	-RRB-	-rrb-	-RRB-	_	_	_
963	slide	slide	NN	_	_	_
964	1	1	CD	_	_	_
965	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
966	wild-type	wild-type	JJ	_	_	_
967	6	6	CD	_	_	_
968	hour	hour	NN	_	_	_
969	-LRB-	-lrb-	-LRB-	_	_	_
970	1	1	CD	_	_	_
971	-RRB-	-rrb-	-RRB-	_	_	_
972	slide	slide	NN	_	_	_
973	2	2	CD	_	_	_
974	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
975	wild-type	wild-type	JJ	_	_	_
976	6	6	CD	_	_	_
977	hour	hour	NN	_	_	_
978	-LRB-	-lrb-	-LRB-	_	_	_
979	2	2	CD	_	_	_
980	-RRB-	-rrb-	-RRB-	_	_	_
981	slide	slide	NN	_	_	_
982	1	1	CD	_	_	_
983	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
984	wild-type	wild-type	JJ	_	_	_
985	6	6	CD	_	_	_
986	hour	hour	NN	_	_	_
987	-LRB-	-lrb-	-LRB-	_	_	_
988	2	2	CD	_	_	_
989	-RRB-	-rrb-	-RRB-	_	_	_
990	slide	slide	NN	_	_	_
991	2	2	CD	_	_	_
992	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
993	After	after	IN	_	_	_
994	6	6	CD	_	_	_
995	hours	hour	NNS	_	_	_
996	of	of	IN	_	_	_
997	growth	growth	NN	_	_	_
998	both	both	CC	_	_	_
999	control	control	NN	_	_	_
1000	and	and	CC	_	_	_
1001	test	test	NN	_	_	_
1002	strains	strain	NNS	_	_	_
1003	were	be	VBD	_	_	_
1004	induced	induce	VBN	_	_	_
1005	with	with	IN	_	_	_
1006	0.5	0.5	CD	_	_	_
1007	mM	mm	NN	KWSUPP	_	_
1008	IPTG	iptg	NN	_	_	_
1009	and	and	CC	_	_	_
1010	harvested	harvest	VBN	_	_	_
1011	2	2	CD	_	_	_
1012	hours	hour	NNS	_	_	_
1013	post-induction	post-induction	JJ	_	_	_
1014	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	EGS084	egs084	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	EGS084	egs084	NN	_	_	_
5	_	_	NN	_	_	_
6	control	control	NN	_	_	_
7	_	_	CD	_	_	_
8	rep	rep	NN	GEN	_	_
9	_	_	NN	_	_	_
10	1	1	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	EGS084	egs084	NN	_	_	_
13	_	_	NN	_	_	_
14	control	control	NN	_	_	_
15	_	_	CD	_	_	_
16	rep	rep	NN	GEN	_	_
17	_	_	NN	_	_	_
18	2	2	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	EGS084	egs084	NN	_	_	_
21	_	_	NN	_	_	_
22	control	control	NN	_	_	_
23	_	_	CD	_	_	_
24	rep	rep	NN	GEN	_	_
25	_	_	NN	_	_	_
26	3	3	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	EGS084	egs084	NN	_	_	_
29	_	_	NN	_	_	_
30	control	control	NN	_	_	_
31	_	_	CD	_	_	_
32	rep	rep	NN	GEN	_	_
33	_	_	NN	_	_	_
34	4	4	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	EGS084	egs084	NN	_	_	_
37	_	_	NN	_	_	_
38	control	control	NN	_	_	_
39	_	_	CD	_	_	_
40	rep	rep	NN	GEN	_	_
41	_	_	SYM	_	_	_
42	5	5	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	EGS084	egs084	NN	_	_	_
45	_	_	NN	_	_	_
46	control	control	NN	_	_	_
47	_	_	CD	_	_	_
48	rep	rep	NN	GEN	_	_
49	_	_	NN	_	_	_
50	6	6	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	EGS212	egs212	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	EGS212	egs212	NN	_	_	_
55	_	_	CD	_	_	_
56	MlfabH	mlfabh	NN	_	_	_
57	_	_	CD	_	_	_
58	rep	rep	NN	GEN	_	_
59	_	_	NN	_	_	_
60	1	1	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	EGS212	egs212	NN	_	_	_
63	_	_	CD	_	_	_
64	MlfabH	mlfabh	NN	_	_	_
65	_	_	CD	_	_	_
66	rep	rep	NN	GEN	_	_
67	_	_	NN	_	_	_
68	2	2	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	EGS212	egs212	NN	_	_	_
71	_	_	CD	_	_	_
72	MlfabH	mlfabh	NN	_	_	_
73	_	_	CD	_	_	_
74	rep	rep	NN	GEN	_	_
75	_	_	NN	_	_	_
76	3	3	CD	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	EGS212	egs212	NN	_	_	_
79	_	_	CD	_	_	_
80	MlfabH	mlfabh	NN	_	_	_
81	_	_	CD	_	_	_
82	rep	rep	NN	GEN	_	_
83	_	_	NN	_	_	_
84	4	4	CD	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	EGS212	egs212	NN	_	_	_
87	_	_	CD	_	_	_
88	MlfabH	mlfabh	NN	_	_	_
89	_	_	NN	_	_	_
90	rep	rep	NN	GEN	_	_
91	_	_	CD	_	_	_
92	5	5	CD	_	_	_
93	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
94	Escherichia	escherichia	FW	Organism	_	_
95	coli	coli	FW	Organism	_	_
96	DH1	dh1	NN	_	_	_
97	∆	∆	CD	_	_	_
98	fadE	fade	NN	GEN	_	_
99	control	control	NN	_	_	_
100	and	and	CC	_	_	_
101	test	test	NN	_	_	_
102	strains	strain	NNS	_	_	_
103	were	be	VBD	_	_	_
104	seeded	seed	VBN	_	_	_
105	with	with	IN	_	_	_
106	OD600nm	od600nm	NN	_	_	_
107	0.03	0.03	CD	_	_	_
108	overnight	overnight	JJ	_	_	_
109	cultures	culture	NNS	_	_	_
110	into	into	IN	_	_	_
111	15	15	CD	_	_	_
112	ml	ml	NN	_	_	_
113	tryptic	tryptic	JJ	_	_	_
114	soy	soy	NN	_	_	_
115	broth	broth	NN	_	_	_
116	media	media	NNS	_	_	_
117	and	and	CC	_	_	_
118	grown	grow	VBN	_	_	_
119	at	at	IN	_	_	_
120	37	37	CD	_	_	_
121	°C	°c	NN	_	_	_
122	with	with	IN	_	_	_
123	200rpm	200rpm	JJ	_	_	_
124	agitation	agitation	NN	_	_	_
125	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	K-12	k-12	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	genotype	genotype	NN	_	_	_
7	:	:	:	_	_	_
8	∆	∆	CD	_	_	_
9	fadE	fade	NN	GEN	_	_
10	with	with	IN	_	_	_
11	overexpression	overexpression	NN	_	_	_
12	of	of	IN	_	_	_
13	`	`	``	_	_	_
14	tesA	tesa	NN	GEN	_	_
15	and	and	CC	_	_	_
16	MlfabH	mlfabh	NN	_	_	_
17	via	via	IN	_	_	_
18	an	a	DT	_	_	_
19	IPTG-inudcible	iptg-inudcible	JJ	_	_	_
20	promoter	promoter	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	genotype	genotype	NN	_	_	_
23	:	:	:	_	_	_
24	∆	∆	CD	_	_	_
25	fadE	fade	NN	GEN	_	_
26	with	with	IN	_	_	_
27	overexpression	overexpression	NN	_	_	_
28	of	of	IN	_	_	_
29	`	`	``	_	_	_
30	tesA	tesa	NN	GEN	_	_
31	via	via	IN	_	_	_
32	an	a	DT	_	_	_
33	IPTG-inudcible	iptg-inudcible	JJ	_	_	_
34	promoter	promoter	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	phenotype	phenotype	NN	_	_	_
37	:	:	:	_	_	_
38	normal	normal	JJ	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	phenotype	phenotype	NN	_	_	_
41	:	:	:	_	_	_
42	small	small	JJ	_	_	_
43	improvement	improvement	NN	_	_	_
44	in	in	IN	_	_	_
45	methyl	methyl	NN	_	_	_
46	ketone	ketone	NN	_	_	_
47	production	production	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	substrain	substrain	NN	_	_	_
50	:	:	:	_	_	_
51	DH1	dh1	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
53	The	the	DT	_	_	_
54	raw	raw	JJ	_	_	_
55	data	data	NN	_	_	_
56	-LRB-	-lrb-	-LRB-	_	_	_
57	.	.	.	_	_	_

1	pair	pair	NN	_	_	_
2	file	file	NN	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	was	be	VBD	_	_	_
5	subjected	subject	VBN	_	_	_
6	to	to	TO	_	_	_
7	RMA	rma	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Robust	robust	JJ	_	_	_
10	Multi-Array	multi-array	JJ	_	_	_
11	Analysis	analysis	NN	_	_	_
12	;	;	:	_	_	_
13	Irizarry	Irizarry	NNP	_	_	_
14	et	et	FW	_	_	_
15	al.	al.	FW	_	_	_
16	.	.	.	_	_	_

1	Biostatistics	biostatistic	NNS	_	_	_
2	4	4	CD	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	2	2	CD	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	:	:	:	_	_	_
7	249	249	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	,	,	,	_	_	_
10	quantile	quantile	JJ	_	_	_
11	normalization	normalization	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Bolstad	Bolstad	NNP	_	_	_
14	et	et	FW	_	_	_
15	al.	al.	FW	_	_	_
16	.	.	.	_	_	_

1	Bioinformatics	bioinformatic	NNS	_	_	_
2	19	19	CD	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	2	2	CD	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	:	:	:	_	_	_
7	185	185	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	background	background	NN	_	_	_
12	correction	correction	NN	_	_	_
13	as	as	IN	_	_	_
14	implemented	implement	VBN	_	_	_
15	in	in	IN	_	_	_
16	the	the	DT	_	_	_
17	NimbleScan	NimbleScan	NNP	_	_	_
18	software	software	NN	_	_	_
19	package	package	NN	_	_	_
20	,	,	,	_	_	_
21	version	version	NN	_	_	_
22	2.4.27	2.4.27	CD	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Roche	Roche	NNP	_	_	_
25	NimbleGen	NimbleGen	NNP	_	_	_
26	,	,	,	_	_	_
27	Inc.	Inc.	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	RNeasy	RNeasy	NNP	_	_	_
9	Mini	Mini	NNP	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	Qiagen	NNP	_	_	_
13	Inc.	Inc.	NNP	_	_	_
14	,	,	,	_	_	_
15	Valencia	Valencia	NNP	_	_	_
16	,	,	,	_	_	_
17	CA	CA	NNP	_	_	_
18	,	,	,	_	_	_
19	USA	USA	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	and	and	CC	_	_	_
22	the	the	DT	_	_	_
23	RNAprotect	rnaprotect	NN	_	_	_
24	reagent	reagent	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	Qiagen	qiagen	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	and	and	CC	_	_	_
29	DNA	dna	NN	_	_	_
30	was	be	VBD	_	_	_
31	removed	remove	VBN	_	_	_
32	by	by	IN	_	_	_
33	on-column	on-column	JJ	_	_	_
34	DNase	dnase	NN	_	_	_
35	digestion	digestion	NN	_	_	_
36	with	with	IN	_	_	_
37	the	the	DT	_	_	_
38	RNase-Free	rnase-free	JJ	_	_	_
39	DNase	dnase	NN	_	_	_
40	set	set	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	Qiagen	qiagen	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	concentration	concentration	NN	_	_	_
3	was	be	VBD	_	_	_
4	determined	determine	VBN	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	Nanodrop	Nanodrop	NNP	_	_	_
8	ND-1000	nd-1000	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Thermo	Thermo	NNP	_	_	_
11	Scientific	Scientific	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	RNA	rna	NN	_	_	_
15	quality	quality	NN	_	_	_
16	was	be	VBD	_	_	_
17	determined	determine	VBN	_	_	_
18	by	by	IN	_	_	_
19	analysis	analysis	NN	_	_	_
20	with	with	IN	_	_	_
21	an	a	DT	_	_	_
22	Agilent	Agilent	NNP	_	_	_
23	2100	2100	CD	_	_	_
24	bioanalyzer	bioanalyzer	NN	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	10	10	CD	_	_	_
6	min	min	NN	_	_	_
7	after	after	IN	_	_	_
8	TMP	tmp	NN	_	_	_
9	+	+	CC	_	_	_
10	adenine	adenine	NN	_	_	_
11	+	+	CC	_	_	_
12	glycine	glycine	NN	_	_	_
13	+	+	CC	_	_	_
14	methionine	methionine	NN	SUPP	_	_
15	treatment	treatment	NN	_	_	_
16	in	in	IN	_	_	_
17	M9	m9	NN	_	_	_
18	media	media	NNS	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	E.	e.	FW	_	_	_
21	coli	coli	FW	_	_	_
22	MG1655	mg1655	NN	_	_	_
23	10	10	CD	_	_	_
24	min	min	NN	_	_	_
25	after	after	IN	_	_	_
26	TMP	tmp	NN	_	_	_
27	+	+	CC	_	_	_
28	adenine	adenine	NN	_	_	_
29	treatment	treatment	NN	_	_	_
30	in	in	IN	_	_	_
31	M9	m9	NN	_	_	_
32	media	media	NNS	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	E.	e.	FW	_	_	_
35	coli	coli	FW	_	_	_
36	MG1655	mg1655	NN	_	_	_
37	10	10	CD	_	_	_
38	min	min	NN	_	_	_
39	after	after	IN	_	_	_
40	TMP	tmp	NN	_	_	_
41	+	+	CC	_	_	_
42	glycine	glycine	NN	_	_	_
43	+	+	CC	_	_	_
44	methionine	methionine	NN	SUPP	_	_
45	treatment	treatment	NN	_	_	_
46	in	in	IN	_	_	_
47	M9	m9	NN	_	_	_
48	media	media	NNS	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	E.	e.	FW	_	_	_
51	coli	coli	FW	_	_	_
52	MG1655	mg1655	NN	_	_	_
53	10	10	CD	_	_	_
54	min	min	NN	_	_	_
55	after	after	IN	_	_	_
56	TMP	tmp	NN	_	_	_
57	+	+	CC	_	_	_
58	thymine	thymine	NN	_	_	_
59	+	+	CC	_	_	_
60	adenine	adenine	NN	_	_	_
61	+	+	CC	_	_	_
62	glycine	glycine	NN	_	_	_
63	+	+	CC	_	_	_
64	methionine	methionine	NN	SUPP	_	_
65	treatment	treatment	NN	_	_	_
66	in	in	IN	_	_	_
67	M9	m9	NN	_	_	_
68	media	media	NNS	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	E.	e.	FW	_	_	_
71	coli	coli	FW	_	_	_
72	MG1655	mg1655	NN	_	_	_
73	10	10	CD	_	_	_
74	min	min	NN	_	_	_
75	after	after	IN	_	_	_
76	TMP	tmp	NN	_	_	_
77	treatment	treatment	NN	_	_	_
78	in	in	IN	_	_	_
79	LB	LB	NNP	MED	_	_
80	media	media	NNS	MED	_	_
81	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
82	E.	e.	FW	_	_	_
83	coli	coli	FW	_	_	_
84	MG1655	mg1655	NN	_	_	_
85	10	10	CD	_	_	_
86	min	min	NN	_	_	_
87	after	after	IN	_	_	_
88	TMP	tmp	NN	_	_	_
89	treatment	treatment	NN	_	_	_
90	in	in	IN	_	_	_
91	M9	m9	NN	_	_	_
92	media	media	NNS	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	E.	e.	FW	_	_	_
95	coli	coli	FW	_	_	_
96	MG1655	mg1655	NN	_	_	_
97	120	120	CD	_	_	_
98	min	min	NN	_	_	_
99	after	after	IN	_	_	_
100	TMP	tmp	NN	_	_	_
101	+	+	CC	_	_	_
102	adenine	adenine	NN	_	_	_
103	+	+	CC	_	_	_
104	glycine	glycine	NN	_	_	_
105	+	+	CC	_	_	_
106	methionine	methionine	NN	SUPP	_	_
107	treatment	treatment	NN	_	_	_
108	in	in	IN	_	_	_
109	M9	m9	NN	_	_	_
110	media	media	NNS	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	E.	e.	FW	_	_	_
113	coli	coli	FW	_	_	_
114	MG1655	mg1655	NN	_	_	_
115	120	120	CD	_	_	_
116	min	min	NN	_	_	_
117	after	after	IN	_	_	_
118	TMP	tmp	NN	_	_	_
119	+	+	CC	_	_	_
120	adenine	adenine	NN	_	_	_
121	treatment	treatment	NN	_	_	_
122	in	in	IN	_	_	_
123	M9	m9	NN	_	_	_
124	media	media	NNS	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	E.	e.	FW	_	_	_
127	coli	coli	FW	_	_	_
128	MG1655	mg1655	NN	_	_	_
129	120	120	CD	_	_	_
130	min	min	NN	_	_	_
131	after	after	IN	_	_	_
132	TMP	tmp	NN	_	_	_
133	+	+	CC	_	_	_
134	glycine	glycine	NN	_	_	_
135	+	+	CC	_	_	_
136	methionine	methionine	NN	SUPP	_	_
137	treatment	treatment	NN	_	_	_
138	in	in	IN	_	_	_
139	M9	m9	NN	_	_	_
140	media	media	NNS	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	E.	e.	FW	_	_	_
143	coli	coli	FW	_	_	_
144	MG1655	mg1655	NN	_	_	_
145	120	120	CD	_	_	_
146	min	min	NN	_	_	_
147	after	after	IN	_	_	_
148	TMP	tmp	NN	_	_	_
149	+	+	CC	_	_	_
150	thymine	thymine	NN	_	_	_
151	+	+	CC	_	_	_
152	adenine	adenine	NN	_	_	_
153	+	+	CC	_	_	_
154	glycine	glycine	NN	_	_	_
155	+	+	CC	_	_	_
156	methionine	methionine	NN	SUPP	_	_
157	treatment	treatment	NN	_	_	_
158	in	in	IN	_	_	_
159	M9	m9	NN	_	_	_
160	media	media	NNS	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	E.	e.	FW	_	_	_
163	coli	coli	FW	_	_	_
164	MG1655	mg1655	NN	_	_	_
165	120	120	CD	_	_	_
166	min	min	NN	_	_	_
167	after	after	IN	_	_	_
168	TMP	tmp	NN	_	_	_
169	treatment	treatment	NN	_	_	_
170	in	in	IN	_	_	_
171	LB	LB	NNP	MED	_	_
172	media	media	NNS	MED	_	_
173	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
174	E.	e.	FW	_	_	_
175	coli	coli	FW	_	_	_
176	MG1655	mg1655	NN	_	_	_
177	120	120	CD	_	_	_
178	min	min	NN	_	_	_
179	after	after	IN	_	_	_
180	TMP	tmp	NN	_	_	_
181	treatment	treatment	NN	_	_	_
182	in	in	IN	_	_	_
183	M9	m9	NN	_	_	_
184	media	media	NNS	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	E.	e.	FW	_	_	_
187	coli	coli	FW	_	_	_
188	MG1655	mg1655	NN	_	_	_
189	30	30	CD	_	_	_
190	min	min	NN	_	_	_
191	after	after	IN	_	_	_
192	TMP	tmp	NN	_	_	_
193	+	+	CC	_	_	_
194	adenine	adenine	NN	_	_	_
195	+	+	CC	_	_	_
196	glycine	glycine	NN	_	_	_
197	+	+	CC	_	_	_
198	methionine	methionine	NN	SUPP	_	_
199	treatment	treatment	NN	_	_	_
200	in	in	IN	_	_	_
201	M9	m9	NN	_	_	_
202	media	media	NNS	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	E.	e.	FW	_	_	_
205	coli	coli	FW	_	_	_
206	MG1655	mg1655	NN	_	_	_
207	30	30	CD	_	_	_
208	min	min	NN	_	_	_
209	after	after	IN	_	_	_
210	TMP	tmp	NN	_	_	_
211	+	+	CC	_	_	_
212	adenine	adenine	NN	_	_	_
213	treatment	treatment	NN	_	_	_
214	in	in	IN	_	_	_
215	M9	m9	NN	_	_	_
216	media	media	NNS	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	E.	e.	FW	_	_	_
219	coli	coli	FW	_	_	_
220	MG1655	mg1655	NN	_	_	_
221	30	30	CD	_	_	_
222	min	min	NN	_	_	_
223	after	after	IN	_	_	_
224	TMP	tmp	NN	_	_	_
225	+	+	CC	_	_	_
226	glycine	glycine	NN	_	_	_
227	+	+	CC	_	_	_
228	methionine	methionine	NN	SUPP	_	_
229	treatment	treatment	NN	_	_	_
230	in	in	IN	_	_	_
231	M9	m9	NN	_	_	_
232	media	media	NNS	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	E.	e.	FW	_	_	_
235	coli	coli	FW	_	_	_
236	MG1655	mg1655	NN	_	_	_
237	30	30	CD	_	_	_
238	min	min	NN	_	_	_
239	after	after	IN	_	_	_
240	TMP	tmp	NN	_	_	_
241	+	+	CC	_	_	_
242	thymine	thymine	NN	_	_	_
243	+	+	CC	_	_	_
244	adenine	adenine	NN	_	_	_
245	+	+	CC	_	_	_
246	glycine	glycine	NN	_	_	_
247	+	+	CC	_	_	_
248	methionine	methionine	NN	SUPP	_	_
249	treatment	treatment	NN	_	_	_
250	in	in	IN	_	_	_
251	M9	m9	NN	_	_	_
252	media	media	NNS	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
254	E.	e.	FW	_	_	_
255	coli	coli	FW	_	_	_
256	MG1655	mg1655	NN	_	_	_
257	30	30	CD	_	_	_
258	min	min	NN	_	_	_
259	after	after	IN	_	_	_
260	TMP	tmp	NN	_	_	_
261	treatment	treatment	NN	_	_	_
262	in	in	IN	_	_	_
263	LB	LB	NNP	MED	_	_
264	media	media	NNS	MED	_	_
265	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
266	E.	e.	FW	_	_	_
267	coli	coli	FW	_	_	_
268	MG1655	mg1655	NN	_	_	_
269	30	30	CD	_	_	_
270	min	min	NN	_	_	_
271	after	after	IN	_	_	_
272	TMP	tmp	NN	_	_	_
273	treatment	treatment	NN	_	_	_
274	in	in	IN	_	_	_
275	M9	m9	NN	_	_	_
276	media	media	NNS	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	E.	e.	FW	_	_	_
279	coli	coli	FW	_	_	_
280	MG1655	mg1655	NN	_	_	_
281	60	60	CD	_	_	_
282	min	min	NN	_	_	_
283	after	after	IN	_	_	_
284	TMP	tmp	NN	_	_	_
285	+	+	CC	_	_	_
286	adenine	adenine	NN	_	_	_
287	+	+	CC	_	_	_
288	glycine	glycine	NN	_	_	_
289	+	+	CC	_	_	_
290	methionine	methionine	NN	SUPP	_	_
291	treatment	treatment	NN	_	_	_
292	in	in	IN	_	_	_
293	M9	m9	NN	_	_	_
294	media	media	NNS	_	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	E.	e.	FW	_	_	_
297	coli	coli	FW	_	_	_
298	MG1655	mg1655	NN	_	_	_
299	60	60	CD	_	_	_
300	min	min	NN	_	_	_
301	after	after	IN	_	_	_
302	TMP	tmp	NN	_	_	_
303	+	+	CC	_	_	_
304	adenine	adenine	NN	_	_	_
305	treatment	treatment	NN	_	_	_
306	in	in	IN	_	_	_
307	M9	m9	NN	_	_	_
308	media	media	NNS	_	_	_
309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
310	E.	e.	FW	_	_	_
311	coli	coli	FW	_	_	_
312	MG1655	mg1655	NN	_	_	_
313	60	60	CD	_	_	_
314	min	min	NN	_	_	_
315	after	after	IN	_	_	_
316	TMP	tmp	NN	_	_	_
317	+	+	CC	_	_	_
318	glycine	glycine	NN	_	_	_
319	+	+	CC	_	_	_
320	methionine	methionine	NN	SUPP	_	_
321	treatment	treatment	NN	_	_	_
322	in	in	IN	_	_	_
323	M9	m9	NN	_	_	_
324	media	media	NNS	_	_	_
325	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
326	E.	e.	FW	_	_	_
327	coli	coli	FW	_	_	_
328	MG1655	mg1655	NN	_	_	_
329	60	60	CD	_	_	_
330	min	min	NN	_	_	_
331	after	after	IN	_	_	_
332	TMP	tmp	NN	_	_	_
333	+	+	CC	_	_	_
334	thymine	thymine	NN	_	_	_
335	+	+	CC	_	_	_
336	adenine	adenine	NN	_	_	_
337	+	+	CC	_	_	_
338	glycine	glycine	NN	_	_	_
339	+	+	CC	_	_	_
340	methionine	methionine	NN	SUPP	_	_
341	treatment	treatment	NN	_	_	_
342	in	in	IN	_	_	_
343	M9	m9	NN	_	_	_
344	media	media	NNS	_	_	_
345	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
346	E.	e.	FW	_	_	_
347	coli	coli	FW	_	_	_
348	MG1655	mg1655	NN	_	_	_
349	60	60	CD	_	_	_
350	min	min	NN	_	_	_
351	after	after	IN	_	_	_
352	TMP	tmp	NN	_	_	_
353	treatment	treatment	NN	_	_	_
354	in	in	IN	_	_	_
355	LB	LB	NNP	MED	_	_
356	media	media	NNS	MED	_	_
357	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
358	E.	e.	FW	_	_	_
359	coli	coli	FW	_	_	_
360	MG1655	mg1655	NN	_	_	_
361	60	60	CD	_	_	_
362	min	min	NN	_	_	_
363	after	after	IN	_	_	_
364	TMP	tmp	NN	_	_	_
365	treatment	treatment	NN	_	_	_
366	in	in	IN	_	_	_
367	M9	m9	NN	_	_	_
368	media	media	NNS	_	_	_
369	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
370	E.	e.	FW	_	_	_
371	coli	coli	FW	_	_	_
372	MG1655	mg1655	NN	_	_	_
373	90	90	CD	_	_	_
374	min	min	NN	_	_	_
375	after	after	IN	_	_	_
376	TMP	tmp	NN	_	_	_
377	+	+	CC	_	_	_
378	adenine	adenine	NN	_	_	_
379	+	+	CC	_	_	_
380	glycine	glycine	NN	_	_	_
381	+	+	CC	_	_	_
382	methionine	methionine	NN	SUPP	_	_
383	treatment	treatment	NN	_	_	_
384	in	in	IN	_	_	_
385	M9	m9	NN	_	_	_
386	media	media	NNS	_	_	_
387	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
388	E.	e.	FW	_	_	_
389	coli	coli	FW	_	_	_
390	MG1655	mg1655	NN	_	_	_
391	90	90	CD	_	_	_
392	min	min	NN	_	_	_
393	after	after	IN	_	_	_
394	TMP	tmp	NN	_	_	_
395	treatment	treatment	NN	_	_	_
396	in	in	IN	_	_	_
397	M9	m9	NN	_	_	_
398	media	media	NNS	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	E.	e.	FW	_	_	_
401	coli	coli	FW	_	_	_
402	MG1655	mg1655	NN	_	_	_
403	mid-log	mid-log	JJ	_	_	_
404	phase	phase	NN	_	_	_
405	in	in	IN	_	_	_
406	LB	LB	NNP	MED	_	_
407	media	media	NNS	MED	_	_
408	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
409	E.	e.	FW	_	_	_
410	coli	coli	FW	_	_	_
411	MG1655	mg1655	NN	_	_	_
412	mid-log	mid-log	JJ	_	_	_
413	phase	phase	NN	_	_	_
414	in	in	IN	_	_	_
415	M9	m9	NN	_	_	_
416	media	media	NNS	_	_	_
417	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
418	Escherichia	escherichia	FW	Organism	_	_
419	coli	coli	FW	Organism	_	_
420	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
421	LBTMP50	lbtmp50	NN	_	_	_
422	_	_	CD	_	_	_
423	10	10	CD	_	_	_
424	min	min	NN	_	_	_
425	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
426	LBTMP50	lbtmp50	NN	_	_	_
427	_	_	NN	_	_	_
428	120	120	CD	_	_	_
429	min	min	NN	_	_	_
430	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
431	LBTMP50	lbtmp50	NN	_	_	_
432	_	_	CD	_	_	_
433	30	30	CD	_	_	_
434	min	min	NN	_	_	_
435	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
436	LBTMP50	lbtmp50	NN	_	_	_
437	_	_	CD	_	_	_
438	60	60	CD	_	_	_
439	min	min	NN	_	_	_
440	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
441	M9TMP5	m9tmp5	NN	_	_	_
442	_	_	CD	_	_	_
443	10	10	CD	_	_	_
444	min	min	NN	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	M9TMP5	m9tmp5	NN	_	_	_
447	_	_	NN	_	_	_
448	120	120	CD	_	_	_
449	min	min	NN	_	_	_
450	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
451	M9TMP5	m9tmp5	NN	_	_	_
452	_	_	CD	_	_	_
453	30	30	CD	_	_	_
454	min	min	NN	_	_	_
455	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
456	M9TMP5	m9tmp5	NN	_	_	_
457	_	_	CD	_	_	_
458	60	60	CD	_	_	_
459	min	min	NN	_	_	_
460	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
461	M9TMP5	m9tmp5	NN	_	_	_
462	_	_	CD	_	_	_
463	90	90	CD	_	_	_
464	min	min	NN	_	_	_
465	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
466	M9TMP5	m9tmp5	NN	_	_	_
467	_	_	CD	_	_	_
468	AdAA	adaa	NN	_	_	_
469	_	_	NN	_	_	_
470	10	10	CD	_	_	_
471	min	min	NN	_	_	_
472	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
473	M9TMP5	m9tmp5	NN	_	_	_
474	_	_	CD	_	_	_
475	AdAA	adaa	NN	_	_	_
476	_	_	NN	_	_	_
477	120	120	CD	_	_	_
478	min	min	NN	_	_	_
479	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
480	M9TMP5	m9tmp5	NN	_	_	_
481	_	_	CD	_	_	_
482	AdAA	adaa	NN	_	_	_
483	_	_	CD	_	_	_
484	30	30	CD	_	_	_
485	min	min	NN	_	_	_
486	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
487	M9TMP5	m9tmp5	NN	_	_	_
488	_	_	CD	_	_	_
489	AdAA	adaa	NN	_	_	_
490	_	_	NN	_	_	_
491	60	60	CD	_	_	_
492	min	min	NN	_	_	_
493	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
494	M9TMP5	m9tmp5	NN	_	_	_
495	_	_	CD	_	_	_
496	AdAA	adaa	NN	_	_	_
497	_	_	NN	_	_	_
498	90	90	CD	_	_	_
499	min	min	NN	_	_	_
500	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
501	M9	m9	NN	_	_	_
502	_	_	CD	_	_	_
503	TMP5	tmp5	NN	_	_	_
504	_	_	NN	_	_	_
505	THY	thy	NN	_	_	_
506	_	_	CD	_	_	_
507	Ad	ad	NN	_	_	_
508	_	_	SYM	_	_	_
509	AA	aa	SYM	_	_	_
510	_	_	SYM	_	_	_
511	10	10	CD	_	_	_
512	min	min	NN	_	_	_
513	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
514	M9	m9	NN	_	_	_
515	_	_	CD	_	_	_
516	TMP5	tmp5	NN	_	_	_
517	_	_	CD	_	_	_
518	THY	THY	NNP	_	_	_
519	_	_	SYM	_	_	_
520	Ad	ad	FW	_	_	_
521	_	_	FW	_	_	_
522	AA	aa	NN	_	_	_
523	_	_	NN	_	_	_
524	120	120	CD	_	_	_
525	min	min	NN	_	_	_
526	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
527	M9	m9	NN	_	_	_
528	_	_	CD	_	_	_
529	TMP5	tmp5	NN	_	_	_
530	_	_	CD	_	_	_
531	THY	THY	NNP	_	_	_
532	_	_	SYM	_	_	_
533	Ad	ad	FW	_	_	_
534	_	_	FW	_	_	_
535	AA	aa	NN	_	_	_
536	_	_	SYM	_	_	_
537	30	30	CD	_	_	_
538	min	min	NN	_	_	_
539	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
540	M9	m9	NN	_	_	_
541	_	_	CD	_	_	_
542	TMP5	tmp5	NN	_	_	_
543	_	_	CD	_	_	_
544	THY	THY	NNP	_	_	_
545	_	_	SYM	_	_	_
546	Ad	ad	FW	_	_	_
547	_	_	FW	_	_	_
548	AA	aa	NN	_	_	_
549	_	_	NN	_	_	_
550	60	60	CD	_	_	_
551	min	min	NN	_	_	_
552	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
553	M9TMP	m9tmp	NN	_	_	_
554	_	_	CD	_	_	_
555	AA	aa	NN	_	_	_
556	_	_	NN	_	_	_
557	10	10	CD	_	_	_
558	min	min	NN	_	_	_
559	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
560	M9TMP	m9tmp	NN	_	_	_
561	_	_	CD	_	_	_
562	AA	aa	NN	_	_	_
563	_	_	NN	_	_	_
564	120	120	CD	_	_	_
565	min	min	NN	_	_	_
566	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
567	M9TMP	m9tmp	NN	_	_	_
568	_	_	CD	_	_	_
569	AA	aa	NN	_	_	_
570	_	_	SYM	_	_	_
571	30	30	CD	_	_	_
572	min	min	NN	_	_	_
573	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
574	M9TMP	m9tmp	NN	_	_	_
575	_	_	CD	_	_	_
576	AA	aa	NN	_	_	_
577	_	_	NN	_	_	_
578	60	60	CD	_	_	_
579	min	min	NN	_	_	_
580	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
581	M9TMP	m9tmp	NN	_	_	_
582	_	_	CD	_	_	_
583	Ad	ad	NN	_	_	_
584	_	_	SYM	_	_	_
585	10	10	CD	_	_	_
586	min	min	NN	_	_	_
587	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
588	M9TMP	m9tmp	NN	_	_	_
589	_	_	CD	_	_	_
590	Ad	ad	NN	_	_	_
591	_	_	NN	_	_	_
592	120	120	CD	_	_	_
593	min	min	NN	_	_	_
594	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
595	M9TMP	m9tmp	NN	_	_	_
596	_	_	CD	_	_	_
597	Ad	ad	NN	_	_	_
598	_	_	SYM	_	_	_
599	30	30	CD	_	_	_
600	min	min	NN	_	_	_
601	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
602	M9TMP	m9tmp	NN	_	_	_
603	_	_	CD	_	_	_
604	Ad	ad	NN	_	_	_
605	_	_	SYM	_	_	_
606	60	60	CD	_	_	_
607	min	min	NN	_	_	_
608	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
609	Overnight	Overnight	NNP	_	_	_
610	cultures	culture	NNS	_	_	_
611	were	be	VBD	_	_	_
612	resuspended	resuspend	VBN	_	_	_
613	in	in	IN	_	_	_
614	fresh	fresh	JJ	_	_	_
615	medium	medium	NN	_	_	_
616	and	and	CC	_	_	_
617	TMP	tmp	NN	_	_	_
618	was	be	VBD	_	_	_
619	added	add	VBN	_	_	_
620	when	when	WRB	_	_	_
621	the	the	DT	_	_	_
622	optical	optical	JJ	_	_	_
623	density	density	NN	_	_	_
624	-LRB-	-lrb-	-LRB-	_	_	_
625	O.D.	o.d.	NN	_	_	_
626	600	600	CD	_	_	_
627	nm	nm	NN	_	_	_
628	-RRB-	-rrb-	-RRB-	_	_	_
629	of	of	IN	_	_	_
630	the	the	DT	_	_	_
631	culture	culture	NN	_	_	_
632	reached	reach	VBD	_	_	_
633	0.3-0.4	0.3-0.4	CD	_	_	_
634	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	fluorescence	fluorescence	NN	_	_	_
4	intensity	intensity	NN	_	_	_
5	data	datum	NNS	_	_	_
6	were	be	VBD	_	_	_
7	normalized	normalize	VBN	_	_	_
8	in	in	IN	_	_	_
9	R	r	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	http	http	NN	_	_	_
12	:	:	:	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	strain	strain	NN	_	_	_
15	:	:	:	_	_	_
16	MG1655	mg1655	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Time-point	time-point	NN	_	_	_
19	samples	sample	NNS	_	_	_
20	were	be	VBD	_	_	_
21	taken	take	VBN	_	_	_
22	every	every	DT	_	_	_
23	15-30	15-30	CD	_	_	_
24	minutes	minute	NNS	_	_	_
25	from	from	IN	_	_	_
26	15	15	CD	_	_	_
27	minutes	minute	NNS	_	_	_
28	to	to	TO	_	_	_
29	2	2	CD	_	_	_
30	hours	hour	NNS	_	_	_
31	post	post	NN	_	_	_
32	treatment	treatment	NN	_	_	_
33	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	samples	sample	NNS	_	_	_
5	were	be	VBD	_	_	_
6	purified	purify	VBN	_	_	_
7	using	use	VBG	_	_	_
8	the	the	DT	_	_	_
9	Qiagen	Qiagen	NNP	_	_	_
10	RNeasy	RNeasy	NNP	_	_	_
11	kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Chatsworth	Chatsworth	NNP	_	_	_
14	,	,	,	_	_	_
15	CA	CA	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	according	accord	VBG	_	_	_
18	to	to	TO	_	_	_
19	the	the	DT	_	_	_
20	manufacturer	manufacturer	NN	_	_	_
21	's	's	POS	_	_	_
22	protocol	protocol	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	20	20	CD	_	_	_
3	ug	ug	NN	_	_	_
4	of	of	IN	_	_	_
5	Total	total	JJ	_	_	_
6	RNA	rna	NN	_	_	_
7	from	from	IN	_	_	_
8	MG1655	mg1655	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Repaired	repair	VBN	_	_	_
11	NCM	NCM	NNP	_	_	_
12	3416	3416	CD	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	in	in	IN	_	_	_
15	LB	lb	NN	_	_	_
16	at	at	IN	_	_	_
17	30	30	CD	_	_	_
18	degrees	degree	NNS	_	_	_
19	OD	od	NN	_	_	_
20	600	600	CD	_	_	_
21	=	=	JJ	_	_	_
22	0.8	0.8	CD	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	20	20	CD	_	_	_
25	ug	ug	NN	_	_	_
26	of	of	IN	_	_	_
27	Total	total	JJ	_	_	_
28	RNA	rna	NN	_	_	_
29	from	from	IN	_	_	_
30	MG1655	mg1655	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Repaired	repair	VBN	_	_	_
33	NCM	NCM	NNP	_	_	_
34	3416	3416	CD	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	in	in	IN	_	_	_
37	M9	m9	NN	_	_	_
38	at	at	IN	_	_	_
39	30	30	CD	_	_	_
40	degrees	degree	NNS	_	_	_
41	OD	od	NN	_	_	_
42	600	600	CD	_	_	_
43	=	=	JJ	_	_	_
44	0.8	0.8	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	2	2	CD	_	_	_
47	ug	ug	NN	_	_	_
48	of	of	IN	_	_	_
49	Genomic	genomic	JJ	_	_	_
50	MG	mg	NN	_	_	_
51	1655	1655	CD	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	Repaired	repair	VBN	_	_	_
54	NCM	NCM	NNP	_	_	_
55	3416	3416	CD	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	DNA	dna	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	2	2	CD	_	_	_
60	ug	ug	NN	_	_	_
61	of	of	IN	_	_	_
62	MG1655	mg1655	NN	_	_	_
63	-LRB-	-lrb-	-LRB-	_	_	_
64	Repaired	repair	VBN	_	_	_
65	NCM	NCM	NNP	_	_	_
66	3416	3416	CD	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	Genomic	genomic	JJ	_	_	_
69	DNA	dna	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	Escherichia	escherichia	FW	Organism	_	_
72	coli	coli	FW	Organism	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	Transcript	transcript	NN	_	_	_
75	Abundance	abundance	NN	_	_	_
76	in	in	IN	_	_	_
77	LB	lb	NN	_	_	_
78	at	at	IN	_	_	_
79	30	30	CD	_	_	_
80	degrees	degree	NNS	_	_	_
81	OD600	od600	NN	_	_	_
82	=	=	JJ	_	_	_
83	0.8	0.8	CD	_	_	_
84	Trial	trial	NN	_	_	_
85	A	a	DT	_	_	_
86	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
87	Transcript	Transcript	NNP	_	_	_
88	Abundance	Abundance	NNP	_	_	_
89	in	in	IN	_	_	_
90	LB	LB	NNP	_	_	_
91	at	at	IN	_	_	_
92	30	30	CD	_	_	_
93	degrees	degree	NNS	_	_	_
94	OD600	od600	NN	_	_	_
95	=	=	JJ	_	_	_
96	0.8	0.8	CD	_	_	_
97	Trial	trial	NN	_	_	_
98	B	b	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	Transcript	transcript	NN	_	_	_
101	Abundance	abundance	NN	_	_	_
102	in	in	IN	_	_	_
103	M9	m9	NN	_	_	_
104	at	at	IN	_	_	_
105	30	30	CD	_	_	_
106	degrees	degree	NNS	_	_	_
107	OD600	od600	NN	_	_	_
108	=	=	JJ	_	_	_
109	0.8	0.8	CD	_	_	_
110	Trial	trial	NN	_	_	_
111	A	a	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	Transcript	transcript	NN	_	_	_
114	Abundance	abundance	NN	_	_	_
115	in	in	IN	_	_	_
116	M9	m9	NN	_	_	_
117	at	at	IN	_	_	_
118	30	30	CD	_	_	_
119	degrees	degree	NNS	_	_	_
120	OD600	od600	NN	_	_	_
121	=	=	JJ	_	_	_
122	0.8	0.8	CD	_	_	_
123	Trial	trial	NN	_	_	_
124	B	b	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	VALUE	value	NN	_	_	_
127	is	be	VBZ	_	_	_
128	Log	log	NN	_	_	_
129	-LRB-	-lrb-	-LRB-	_	_	_
130	base	base	NN	_	_	_
131	2	2	CD	_	_	_
132	-RRB-	-rrb-	-RRB-	_	_	_
133	of	of	IN	_	_	_
134	the	the	DT	_	_	_
135	ratio	ratio	NN	_	_	_
136	of	of	IN	_	_	_
137	the	the	DT	_	_	_
138	median	median	NN	_	_	_
139	of	of	IN	_	_	_
140	Channel	Channel	NNP	_	_	_
141	2	2	CD	_	_	_
142	-LRB-	-lrb-	-LRB-	_	_	_
143	usually	usually	RB	_	_	_
144	635	635	CD	_	_	_
145	nm	nm	NN	_	_	_
146	-RRB-	-rrb-	-RRB-	_	_	_
147	to	to	TO	_	_	_
148	Channel	Channel	NNP	_	_	_
149	1	1	CD	_	_	_
150	-LRB-	-lrb-	-LRB-	_	_	_
151	usually	usually	RB	_	_	_
152	532	532	CD	_	_	_
153	nm	nm	NN	_	_	_
154	-RRB-	-rrb-	-RRB-	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	2	2	CD	_	_	_
157	'	'	''	_	_	_
158	RNA	rna	NN	_	_	_
159	Decay	decay	NN	_	_	_
160	of	of	IN	_	_	_
161	MG1655	mg1655	NN	_	_	_
162	-LRB-	-lrb-	-LRB-	_	_	_
163	Repaired	repair	VBN	_	_	_
164	NCM	NCM	NNP	_	_	_
165	3416	3416	CD	_	_	_
166	-RRB-	-rrb-	-RRB-	_	_	_
167	in	in	IN	_	_	_
168	LB	lb	NN	_	_	_
169	at	at	IN	_	_	_
170	30	30	CD	_	_	_
171	C	c	NN	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	2	2	CD	_	_	_
174	'	'	''	_	_	_
175	RNA	rna	NN	_	_	_
176	Decay	decay	NN	_	_	_
177	of	of	IN	_	_	_
178	MG1655	mg1655	NN	_	_	_
179	-LRB-	-lrb-	-LRB-	_	_	_
180	Repaired	repair	VBN	_	_	_
181	NCM	NCM	NNP	_	_	_
182	3416	3416	CD	_	_	_
183	-RRB-	-rrb-	-RRB-	_	_	_
184	in	in	IN	_	_	_
185	M9	m9	NN	_	_	_
186	+	+	CC	_	_	_
187	0.2	0.2	CD	_	_	_
188	%	%	NN	_	_	_
189	Glucose	glucose	NN	_	_	_
190	Trial	trial	NN	_	_	_
191	A	a	NN	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	2	2	CD	_	_	_
194	'	'	''	_	_	_
195	RNA	rna	NN	_	_	_
196	Decay	decay	NN	_	_	_
197	of	of	IN	_	_	_
198	MG1655	mg1655	NN	_	_	_
199	-LRB-	-lrb-	-LRB-	_	_	_
200	Repaired	repair	VBN	_	_	_
201	NCM	NCM	NNP	_	_	_
202	3416	3416	CD	_	_	_
203	-RRB-	-rrb-	-RRB-	_	_	_
204	in	in	IN	_	_	_
205	M9	m9	NN	_	_	_
206	+	+	CC	_	_	_
207	0.2	0.2	CD	_	_	_
208	%	%	NN	_	_	_
209	Glucose	glucose	NN	_	_	_
210	Trial	trial	NN	_	_	_
211	B	b	NN	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	4	4	CD	_	_	_
214	'	'	''	_	_	_
215	RNA	rna	NN	_	_	_
216	Decay	decay	NN	_	_	_
217	of	of	IN	_	_	_
218	MG1655	mg1655	NN	_	_	_
219	-LRB-	-lrb-	-LRB-	_	_	_
220	Repaired	repair	VBN	_	_	_
221	NCM	NCM	NNP	_	_	_
222	3416	3416	CD	_	_	_
223	-RRB-	-rrb-	-RRB-	_	_	_
224	in	in	IN	_	_	_
225	LB	lb	NN	_	_	_
226	at	at	IN	_	_	_
227	30	30	CD	_	_	_
228	C	c	NN	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
230	4	4	CD	_	_	_
231	'	'	''	_	_	_
232	RNA	rna	NN	_	_	_
233	Decay	decay	NN	_	_	_
234	of	of	IN	_	_	_
235	MG1655	mg1655	NN	_	_	_
236	-LRB-	-lrb-	-LRB-	_	_	_
237	Repaired	repair	VBN	_	_	_
238	NCM	NCM	NNP	_	_	_
239	3416	3416	CD	_	_	_
240	-RRB-	-rrb-	-RRB-	_	_	_
241	in	in	IN	_	_	_
242	M9	m9	NN	_	_	_
243	+	+	CC	_	_	_
244	0.2	0.2	CD	_	_	_
245	%	%	NN	_	_	_
246	Glucose	glucose	NN	_	_	_
247	Trial	trial	NN	_	_	_
248	A	a	NN	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	4	4	CD	_	_	_
251	'	'	''	_	_	_
252	RNA	rna	NN	_	_	_
253	Decay	decay	NN	_	_	_
254	of	of	IN	_	_	_
255	MG1655	mg1655	NN	_	_	_
256	-LRB-	-lrb-	-LRB-	_	_	_
257	Repaired	repair	VBN	_	_	_
258	NCM	NCM	NNP	_	_	_
259	3416	3416	CD	_	_	_
260	-RRB-	-rrb-	-RRB-	_	_	_
261	in	in	IN	_	_	_
262	M9	m9	NN	_	_	_
263	+	+	CC	_	_	_
264	0.2	0.2	CD	_	_	_
265	%	%	NN	_	_	_
266	Glucose	glucose	NN	_	_	_
267	Trial	trial	NN	_	_	_
268	B	b	NN	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	6	6	CD	_	_	_
271	'	'	''	_	_	_
272	RNA	rna	NN	_	_	_
273	Decay	decay	NN	_	_	_
274	of	of	IN	_	_	_
275	MG1655	mg1655	NN	_	_	_
276	-LRB-	-lrb-	-LRB-	_	_	_
277	Repaired	repair	VBN	_	_	_
278	NCM	NCM	NNP	_	_	_
279	3416	3416	CD	_	_	_
280	-RRB-	-rrb-	-RRB-	_	_	_
281	in	in	IN	_	_	_
282	LB	lb	NN	_	_	_
283	at	at	IN	_	_	_
284	30	30	CD	_	_	_
285	C	c	NN	_	_	_
286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
287	6	6	CD	_	_	_
288	'	'	''	_	_	_
289	RNA	rna	NN	_	_	_
290	Decay	decay	NN	_	_	_
291	of	of	IN	_	_	_
292	MG1655	mg1655	NN	_	_	_
293	-LRB-	-lrb-	-LRB-	_	_	_
294	Repaired	repair	VBN	_	_	_
295	NCM	NCM	NNP	_	_	_
296	3416	3416	CD	_	_	_
297	-RRB-	-rrb-	-RRB-	_	_	_
298	in	in	IN	_	_	_
299	M9	m9	NN	_	_	_
300	+	+	CC	_	_	_
301	0.2	0.2	CD	_	_	_
302	%	%	NN	_	_	_
303	Glucose	glucose	NN	_	_	_
304	Trial	trial	NN	_	_	_
305	A	a	NN	_	_	_
306	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
307	6	6	CD	_	_	_
308	'	'	''	_	_	_
309	RNA	rna	NN	_	_	_
310	Decay	decay	NN	_	_	_
311	of	of	IN	_	_	_
312	MG1655	mg1655	NN	_	_	_
313	-LRB-	-lrb-	-LRB-	_	_	_
314	Repaired	repair	VBN	_	_	_
315	NCM	NCM	NNP	_	_	_
316	3416	3416	CD	_	_	_
317	-RRB-	-rrb-	-RRB-	_	_	_
318	in	in	IN	_	_	_
319	M9	m9	NN	_	_	_
320	+	+	CC	_	_	_
321	0.2	0.2	CD	_	_	_
322	%	%	NN	_	_	_
323	Glucose	glucose	NN	_	_	_
324	Trial	trial	NN	_	_	_
325	B	b	NN	_	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	8	8	CD	_	_	_
328	'	'	''	_	_	_
329	RNA	rna	NN	_	_	_
330	Decay	decay	NN	_	_	_
331	of	of	IN	_	_	_
332	MG1655	mg1655	NN	_	_	_
333	-LRB-	-lrb-	-LRB-	_	_	_
334	Repaired	repair	VBN	_	_	_
335	MCM	mcm	NN	_	_	_
336	3416	3416	CD	_	_	_
337	-RRB-	-rrb-	-RRB-	_	_	_
338	in	in	IN	_	_	_
339	M9	m9	NN	_	_	_
340	+	+	CC	_	_	_
341	0.2	0.2	CD	_	_	_
342	%	%	NN	_	_	_
343	Glucose	glucose	NN	_	_	_
344	Trial	trial	NN	_	_	_
345	A	a	NN	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	8	8	CD	_	_	_
348	'	'	''	_	_	_
349	RNA	rna	NN	_	_	_
350	Decay	decay	NN	_	_	_
351	of	of	IN	_	_	_
352	MG1655	mg1655	NN	_	_	_
353	-LRB-	-lrb-	-LRB-	_	_	_
354	Repaired	repair	VBN	_	_	_
355	NCM	NCM	NNP	_	_	_
356	3416	3416	CD	_	_	_
357	-RRB-	-rrb-	-RRB-	_	_	_
358	in	in	IN	_	_	_
359	LB	lb	NN	_	_	_
360	at	at	IN	_	_	_
361	30	30	CD	_	_	_
362	C	c	NN	_	_	_
363	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
364	8	8	CD	_	_	_
365	'	'	''	_	_	_
366	RNA	rna	NN	_	_	_
367	Decay	decay	NN	_	_	_
368	of	of	IN	_	_	_
369	MG1655	mg1655	NN	_	_	_
370	-LRB-	-lrb-	-LRB-	_	_	_
371	Repaired	repair	VBN	_	_	_
372	NCM	NCM	NNP	_	_	_
373	3416	3416	CD	_	_	_
374	-RRB-	-rrb-	-RRB-	_	_	_
375	in	in	IN	_	_	_
376	M9	m9	NN	_	_	_
377	+	+	CC	_	_	_
378	0.2	0.2	CD	_	_	_
379	%	%	NN	_	_	_
380	Glucose	glucose	NN	_	_	_
381	Trial	trial	NN	_	_	_
382	B	b	NN	_	_	_
383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
384	Escherichia	escherichia	FW	Organism	_	_
385	coli	coli	FW	Organism	_	_
386	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
387	MG1655	mg1655	NN	_	_	_
388	2	2	CD	_	_	_
389	'	'	''	_	_	_
390	post	post	JJ	_	_	_
391	rif	rif	NN	_	_	_
392	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
393	MG1655	mg1655	NN	_	_	_
394	4	4	CD	_	_	_
395	'	'	''	_	_	_
396	post	post	JJ	_	_	_
397	rif	rif	NN	_	_	_
398	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
399	MG1655	mg1655	NN	_	_	_
400	6	6	CD	_	_	_
401	'	'	''	_	_	_
402	post	post	JJ	_	_	_
403	rif	rif	NN	_	_	_
404	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
405	MG1655	mg1655	NN	_	_	_
406	8	8	CD	_	_	_
407	'	'	''	_	_	_
408	post	post	JJ	_	_	_
409	rif	rif	NN	_	_	_
410	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
411	MG1655	mg1655	NN	_	_	_
412	at	at	IN	_	_	_
413	30	30	CD	_	_	_
414	Degrees	degree	NNS	_	_	_
415	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
416	MG1655	mg1655	NN	_	_	_
417	-LRB-	-lrb-	-LRB-	_	_	_
418	Repaired	repair	VBN	_	_	_
419	MCM	mcm	NN	_	_	_
420	3416	3416	CD	_	_	_
421	-RRB-	-rrb-	-RRB-	_	_	_
422	in	in	IN	_	_	_
423	M9	m9	NN	_	_	_
424	+	+	CC	_	_	_
425	0.2	0.2	CD	_	_	_
426	%	%	NN	_	_	_
427	Glucose	glucose	NN	_	_	_
428	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
429	MG1655	mg1655	NN	_	_	_
430	-LRB-	-lrb-	-LRB-	_	_	_
431	Repaired	repair	VBN	_	_	_
432	MCM	mcm	NN	_	_	_
433	3416	3416	CD	_	_	_
434	-RRB-	-rrb-	-RRB-	_	_	_
435	in	in	IN	_	_	_
436	M9	m9	NN	_	_	_
437	+	+	CC	_	_	_
438	0.2	0.2	CD	_	_	_
439	%	%	NN	_	_	_
440	Glucose	glucose	NN	_	_	_
441	8	8	CD	_	_	_
442	'	'	''	_	_	_
443	post	post	JJ	_	_	_
444	rif	rif	NN	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	MG1655	mg1655	NN	_	_	_
447	-LRB-	-lrb-	-LRB-	_	_	_
448	Repaired	repair	VBN	_	_	_
449	NCM	NCM	NNP	_	_	_
450	3416	3416	CD	_	_	_
451	-RRB-	-rrb-	-RRB-	_	_	_
452	in	in	IN	_	_	_
453	M9	m9	NN	_	_	_
454	+	+	CC	_	_	_
455	0.2	0.2	CD	_	_	_
456	%	%	NN	_	_	_
457	Glucose	glucose	NN	_	_	_
458	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
459	MG1655	mg1655	NN	_	_	_
460	-LRB-	-lrb-	-LRB-	_	_	_
461	Repaired	repair	VBN	_	_	_
462	NCM	NCM	NNP	_	_	_
463	3416	3416	CD	_	_	_
464	-RRB-	-rrb-	-RRB-	_	_	_
465	in	in	IN	_	_	_
466	M9	m9	NN	_	_	_
467	+	+	CC	_	_	_
468	0.2	0.2	CD	_	_	_
469	%	%	NN	_	_	_
470	Glucose	glucose	NN	_	_	_
471	2	2	CD	_	_	_
472	'	'	''	_	_	_
473	post	post	JJ	_	_	_
474	rif	rif	NN	_	_	_
475	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
476	MG1655	mg1655	NN	_	_	_
477	-LRB-	-lrb-	-LRB-	_	_	_
478	Repaired	repair	VBN	_	_	_
479	NCM	NCM	NNP	_	_	_
480	3416	3416	CD	_	_	_
481	-RRB-	-rrb-	-RRB-	_	_	_
482	in	in	IN	_	_	_
483	M9	m9	NN	_	_	_
484	+	+	CC	_	_	_
485	0.2	0.2	CD	_	_	_
486	%	%	NN	_	_	_
487	Glucose	glucose	NN	_	_	_
488	4	4	CD	_	_	_
489	'	'	''	_	_	_
490	post	post	JJ	_	_	_
491	rif	rif	NN	_	_	_
492	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
493	MG1655	mg1655	NN	_	_	_
494	-LRB-	-lrb-	-LRB-	_	_	_
495	Repaired	repair	VBN	_	_	_
496	NCM	NCM	NNP	_	_	_
497	3416	3416	CD	_	_	_
498	-RRB-	-rrb-	-RRB-	_	_	_
499	in	in	IN	_	_	_
500	M9	m9	NN	_	_	_
501	+	+	CC	_	_	_
502	0.2	0.2	CD	_	_	_
503	%	%	NN	_	_	_
504	Glucose	glucose	NN	_	_	_
505	6	6	CD	_	_	_
506	'	'	''	_	_	_
507	post	post	JJ	_	_	_
508	rif	rif	NN	_	_	_
509	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
510	MG1655	mg1655	NN	_	_	_
511	-LRB-	-lrb-	-LRB-	_	_	_
512	Repaired	repair	VBN	_	_	_
513	NCM	NCM	NNP	_	_	_
514	3416	3416	CD	_	_	_
515	-RRB-	-rrb-	-RRB-	_	_	_
516	in	in	IN	_	_	_
517	M9	m9	NN	_	_	_
518	+	+	CC	_	_	_
519	0.2	0.2	CD	_	_	_
520	%	%	NN	_	_	_
521	Glucose	glucose	NN	_	_	_
522	8	8	CD	_	_	_
523	'	'	''	_	_	_
524	post	post	JJ	_	_	_
525	rif	rif	NN	_	_	_
526	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
527	VALUE	value	NN	_	_	_
528	is	be	VBZ	_	_	_
529	Log	log	NN	_	_	_
530	-LRB-	-lrb-	-LRB-	_	_	_
531	base	base	NN	_	_	_
532	2	2	CD	_	_	_
533	-RRB-	-rrb-	-RRB-	_	_	_
534	of	of	IN	_	_	_
535	the	the	DT	_	_	_
536	ratio	ratio	NN	_	_	_
537	of	of	IN	_	_	_
538	the	the	DT	_	_	_
539	mean	mean	NN	_	_	_
540	of	of	IN	_	_	_
541	Channel	Channel	NNP	_	_	_
542	2	2	CD	_	_	_
543	-LRB-	-lrb-	-LRB-	_	_	_
544	usually	usually	RB	_	_	_
545	635	635	CD	_	_	_
546	nm	nm	NN	_	_	_
547	-RRB-	-rrb-	-RRB-	_	_	_
548	to	to	TO	_	_	_
549	Channel	Channel	NNP	_	_	_
550	1	1	CD	_	_	_
551	-LRB-	-lrb-	-LRB-	_	_	_
552	usually	usually	RB	_	_	_
553	532	532	CD	_	_	_
554	nm	nm	NN	_	_	_
555	-RRB-	-rrb-	-RRB-	_	_	_
556	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
557	Escherichia	escherichia	FW	Organism	_	_
558	coli	coli	FW	Organism	_	_
559	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
560	lrp	lrp	NN	GEN	_	_
561	-	-	:	_	_	_
562	+	+	CC	_	_	_
563	Leu	Leu	NNP	_	_	_
564	vs.	vs.	FW	_	_	_
565	lrp	lrp	SYM	GEN	_	_
566	-	-	:	_	_	_
567	-	-	:	_	_	_
568	Leu	leu	NN	_	_	_
569	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
570	lrp	lrp	NN	GEN	_	_
571	-	-	:	_	_	_
572	-	-	:	_	_	_
573	Leu	leu	NN	_	_	_
574	vs.	vs.	CC	_	_	_
575	wt	wt	JJ	_	_	_
576	-	-	:	_	_	_
577	Leu	leu	NN	_	_	_
578	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
579	lrp	lrp	NN	GEN	_	_
580	-	-	:	_	_	_
581	+	+	CC	_	_	_
582	Leu	Leu	NNP	_	_	_
583	vs.	vs.	FW	_	_	_
584	wt	wt	JJ	_	_	_
585	-	-	:	_	_	_
586	Leu	leu	NN	_	_	_
587	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
588	VALUE	value	NN	_	_	_
589	is	be	VBZ	_	_	_
590	Log	log	NN	_	_	_
591	-LRB-	-lrb-	-LRB-	_	_	_
592	base	base	NN	_	_	_
593	2	2	CD	_	_	_
594	-RRB-	-rrb-	-RRB-	_	_	_
595	of	of	IN	_	_	_
596	the	the	DT	_	_	_
597	ratio	ratio	NN	_	_	_
598	of	of	IN	_	_	_
599	the	the	DT	_	_	_
600	median	median	NN	_	_	_
601	of	of	IN	_	_	_
602	Channel	Channel	NNP	_	_	_
603	2	2	CD	_	_	_
604	-LRB-	-lrb-	-LRB-	_	_	_
605	usually	usually	RB	_	_	_
606	635	635	CD	_	_	_
607	nm	nm	NN	_	_	_
608	-RRB-	-rrb-	-RRB-	_	_	_
609	to	to	TO	_	_	_
610	Channel	Channel	NNP	_	_	_
611	1	1	CD	_	_	_
612	-LRB-	-lrb-	-LRB-	_	_	_
613	usually	usually	RB	_	_	_
614	532	532	CD	_	_	_
615	nm	nm	NN	_	_	_
616	-RRB-	-rrb-	-RRB-	_	_	_
617	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
618	\	\	CD	_	_	_
619	W3110	w3110	NN	_	_	_
620	lrp	lrp	NN	GEN	_	_
621	-	-	:	_	_	_
622	at	at	IN	_	_	_
623	OD420	od420	NN	_	_	_
624	~	~	NN	_	_	_
625	0.3	0.3	CD	_	_	_
626	in	in	IN	_	_	_
627	MOPS	mop	NNS	MED	_	_
628	-LRB-	-lrb-	-LRB-	_	_	_
629	ile	ile	FW	_	_	_
630	,	,	,	_	_	_
631	val	val	NN	_	_	_
632	,	,	,	_	_	_
633	thi	thi	NN	_	_	_
634	-RRB-	-rrb-	-RRB-	_	_	_
635	,	,	,	_	_	_
636	20	20	CD	_	_	_
637	ug	ug	NN	_	_	_
638	total	total	NN	_	_	_
639	,	,	,	_	_	_
640	10	10	CD	_	_	_
641	ug	ug	NN	_	_	_
642	pdN6	pdn6	NN	_	_	_
643	\	\	SYM	_	_	_
644	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
645	\	\	SYM	_	_	_
646	W3110	w3110	CD	_	_	_
647	lrp	lrp	SYM	GEN	_	_
648	-	-	:	_	_	_
649	at	at	IN	_	_	_
650	OD420	od420	NN	_	_	_
651	~	~	NN	_	_	_
652	0.3	0.3	CD	_	_	_
653	in	in	IN	_	_	_
654	MOPS	mop	NNS	MED	_	_
655	-LRB-	-lrb-	-LRB-	_	_	_
656	ile	ile	FW	_	_	_
657	,	,	,	_	_	_
658	val	val	NN	_	_	_
659	,	,	,	_	_	_
660	thi	thi	NN	_	_	_
661	-RRB-	-rrb-	-RRB-	_	_	_
662	+	+	CC	_	_	_
663	Leu	leu	NN	_	_	_
664	,	,	,	_	_	_
665	20	20	CD	_	_	_
666	ug	ug	NN	_	_	_
667	total	total	JJ	_	_	_
668	RNA	rna	NN	_	_	_
669	,10	,10	CD	_	_	_
670	ug	ug	NN	_	_	_
671	pdN6	pdn6	NN	_	_	_
672	\	\	SYM	_	_	_
673	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
674	\	\	SYM	_	_	_
675	W3110	w3110	CD	_	_	_
676	lrp	lrp	SYM	GEN	_	_
677	-	-	:	_	_	_
678	at	at	IN	_	_	_
679	OD420	od420	NN	_	_	_
680	~	~	NN	_	_	_
681	0.3	0.3	CD	_	_	_
682	in	in	IN	_	_	_
683	MOPS	mop	NNS	MED	_	_
684	-LRB-	-lrb-	-LRB-	_	_	_
685	ile	ile	FW	_	_	_
686	,	,	,	_	_	_
687	val	val	NN	_	_	_
688	,	,	,	_	_	_
689	thi	thi	NN	_	_	_
690	-RRB-	-rrb-	-RRB-	_	_	_
691	plus	plus	CC	_	_	_
692	Leu	leu	NN	_	_	_
693	,	,	,	_	_	_
694	20	20	CD	_	_	_
695	ug	ug	NN	_	_	_
696	total	total	JJ	_	_	_
697	RNA	rna	NN	_	_	_
698	,	,	,	_	_	_
699	10	10	CD	_	_	_
700	ug	ug	NN	_	_	_
701	pdN6	pdn6	NN	_	_	_
702	\	\	SYM	_	_	_
703	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
704	\	\	SYM	_	_	_
705	W3110	w3110	CD	_	_	_
706	lrp	lrp	SYM	GEN	_	_
707	-	-	:	_	_	_
708	in	in	IN	_	_	_
709	MOPS	mop	NNS	MED	_	_
710	-LRB-	-lrb-	-LRB-	_	_	_
711	ile	ile	FW	_	_	_
712	,	,	,	_	_	_
713	val	val	NN	_	_	_
714	,	,	,	_	_	_
715	thi	thi	NN	_	_	_
716	-RRB-	-rrb-	-RRB-	_	_	_
717	to	to	TO	_	_	_
718	OD420	od420	NN	_	_	_
719	~	~	NN	_	_	_
720	0.3	0.3	CD	_	_	_
721	,	,	,	_	_	_
722	20	20	CD	_	_	_
723	ug	ug	NN	_	_	_
724	total	total	JJ	_	_	_
725	RNA	rna	NN	_	_	_
726	,	,	,	_	_	_
727	10	10	CD	_	_	_
728	ug	ug	NN	_	_	_
729	pdN6	pdn6	NN	_	_	_
730	\	\	SYM	_	_	_
731	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
732	\	\	SYM	_	_	_
733	W3110	w3110	CD	_	_	_
734	wt	wt	JJ	_	_	_
735	in	in	IN	_	_	_
736	MOPS	mop	NNS	MED	_	_
737	-LRB-	-lrb-	-LRB-	_	_	_
738	ile	ile	FW	_	_	_
739	,	,	,	_	_	_
740	val	val	NN	_	_	_
741	,	,	,	_	_	_
742	thi	thi	NN	_	_	_
743	-RRB-	-rrb-	-RRB-	_	_	_
744	at	at	IN	_	_	_
745	OD420	od420	CD	_	_	_
746	~	~	NN	_	_	_
747	0.3	0.3	CD	_	_	_
748	,	,	,	_	_	_
749	20	20	CD	_	_	_
750	ug	ug	NN	_	_	_
751	total	total	JJ	_	_	_
752	,10	,10	CD	_	_	_
753	ug	ug	NN	_	_	_
754	pdN6	pdn6	NN	_	_	_
755	\	\	SYM	_	_	_
756	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
757	\	\	SYM	_	_	_
758	W3110	w3110	CD	_	_	_
759	wt	wt	JJ	_	_	_
760	OD420	od420	NN	_	_	_
761	~	~	NN	_	_	_
762	0.3	0.3	CD	_	_	_
763	in	in	IN	_	_	_
764	MOPS	mop	NNS	MED	_	_
765	-LRB-	-lrb-	-LRB-	_	_	_
766	ile	ile	FW	_	_	_
767	,	,	,	_	_	_
768	val	val	NN	_	_	_
769	,	,	,	_	_	_
770	thi	thi	NN	_	_	_
771	-RRB-	-rrb-	-RRB-	_	_	_
772	+	+	CC	_	_	_
773	Leu	leu	NN	_	_	_
774	,	,	,	_	_	_
775	20	20	CD	_	_	_
776	ug	ug	NN	_	_	_
777	total	total	JJ	_	_	_
778	RNA	rna	NN	_	_	_
779	,	,	,	_	_	_
780	10	10	CD	_	_	_
781	ug	ug	NN	_	_	_
782	pdN6	pdn6	NN	_	_	_
783	\	\	CD	_	_	_
784	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
785	wt	wt	JJ	_	_	_
786	+	+	CC	_	_	_
787	Leu	leu	NN	_	_	_
788	vs.	vs.	CC	_	_	_
789	wt	wt	JJ	_	_	_
790	-	-	:	_	_	_
791	Leu	leu	NN	_	_	_
792	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
793	accession	accession	NN	_	_	_
794	:	:	:	_	_	_
795	U00006	U00006	NNP	_	_	_
796	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
797	Eco	Eco	NNP	_	_	_
798	50ng	50ng	SYM	_	_	_
799	-	-	:	_	_	_
800	0	0	CD	_	_	_
801	%	%	NN	_	_	_
802	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
803	Eco	eco	NN	_	_	_
804	50ng	50ng	SYM	_	_	_
805	-	-	:	_	_	_
806	10	10	CD	_	_	_
807	%	%	NN	_	_	_
808	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
809	Eco	eco	NN	_	_	_
810	50ng	50ng	SYM	_	_	_
811	-	-	:	_	_	_
812	15	15	CD	_	_	_
813	%	%	NN	_	_	_
814	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
815	Eco	eco	NN	_	_	_
816	50ng	50ng	SYM	_	_	_
817	-	-	:	_	_	_
818	20	20	CD	_	_	_
819	%	%	NN	_	_	_
820	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
821	Eco	eco	NN	_	_	_
822	50ng	50ng	SYM	_	_	_
823	-	-	:	_	_	_
824	25	25	CD	_	_	_
825	%	%	NN	_	_	_
826	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
827	Eco	eco	NN	_	_	_
828	50ng	50ng	SYM	_	_	_
829	-	-	:	_	_	_
830	32.5	32.5	CD	_	_	_
831	%	%	NN	_	_	_
832	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
833	Eco	eco	NN	_	_	_
834	50ng	50ng	SYM	_	_	_
835	-	-	:	_	_	_
836	45	45	CD	_	_	_
837	%	%	NN	_	_	_
838	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
839	Eco	eco	NN	_	_	_
840	50ng	50ng	SYM	_	_	_
841	-	-	:	_	_	_
842	5	5	CD	_	_	_
843	%	%	NN	_	_	_
844	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
845	Eco	eco	NN	_	_	_
846	5ng	5ng	SYM	_	_	_
847	-	-	:	_	_	_
848	0	0	CD	_	_	_
849	%	%	NN	_	_	_
850	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
851	Eco	eco	NN	_	_	_
852	5ng	5ng	SYM	_	_	_
853	-	-	:	_	_	_
854	10	10	CD	_	_	_
855	%	%	NN	_	_	_
856	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
857	Eco	eco	NN	_	_	_
858	5ng	5ng	SYM	_	_	_
859	-	-	:	_	_	_
860	15	15	CD	_	_	_
861	%	%	NN	_	_	_
862	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
863	Eco	eco	NN	_	_	_
864	5ng	5ng	SYM	_	_	_
865	-	-	:	_	_	_
866	20	20	CD	_	_	_
867	%	%	NN	_	_	_
868	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
869	Eco	eco	NN	_	_	_
870	5ng	5ng	SYM	_	_	_
871	-	-	:	_	_	_
872	25	25	CD	_	_	_
873	%	%	NN	_	_	_
874	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
875	Eco	eco	NN	_	_	_
876	5ng	5ng	SYM	_	_	_
877	-	-	:	_	_	_
878	32.5	32.5	CD	_	_	_
879	%	%	NN	_	_	_
880	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
881	Eco	eco	NN	_	_	_
882	5ng	5ng	SYM	_	_	_
883	-	-	:	_	_	_
884	45	45	CD	_	_	_
885	%	%	NN	_	_	_
886	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
887	Eco	eco	NN	_	_	_
888	5ng	5ng	SYM	_	_	_
889	-	-	:	_	_	_
890	5	5	CD	_	_	_
891	%	%	NN	_	_	_
892	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
893	E.	E.	NNP	_	_	_
894	coli	coli	NN	_	_	_
895	was	be	VBD	_	_	_
896	grown	grow	VBN	_	_	_
897	to	to	TO	_	_	_
898	mid-log	mid-log	JJ	_	_	_
899	phase	phase	NN	_	_	_
900	-LRB-	-lrb-	-LRB-	_	_	_
901	O.D.	o.d.	NN	_	_	_
902	600nm	600nm	CD	_	_	_
903	0.3-0.4	0.3-0.4	CD	_	_	_
904	-RRB-	-rrb-	-RRB-	_	_	_
905	in	in	IN	_	_	_
906	Lennox	Lennox	NNP	_	_	_
907	LB	LB	NNP	MED	_	_
908	broth	broth	NN	MED	_	_
909	-LRB-	-lrb-	-LRB-	_	_	_
910	Becton	Becton	NNP	_	_	_
911	Dickinson	Dickinson	NNP	_	_	_
912	,	,	,	_	_	_
913	Franklin	Franklin	NNP	_	_	_
914	Lakes	Lakes	NNP	_	_	_
915	,	,	,	_	_	_
916	NJ	NJ	NNP	_	_	_
917	-RRB-	-rrb-	-RRB-	_	_	_
918	at	at	IN	_	_	_
919	37	37	CD	_	_	_
920	°C	°c	NN	_	_	_
921	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	K-12	k-12	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Escherichia	escherichia	FW	Organism	_	_
7	coli	coli	FW	Organism	_	_
8	K12	k12	NN	_	_	_
9	wild-type	wild-type	JJ	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Genomic	genomic	JJ	_	_	_
12	DNA	dna	NN	_	_	_
13	was	be	VBD	_	_	_
14	extracted	extract	VBN	_	_	_
15	using	use	VBG	_	_	_
16	Ultra	Ultra	NNP	_	_	_
17	Clean	Clean	NNP	_	_	_
18	Soil	Soil	NNP	_	_	_
19	DNA	dna	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	MoBio	mobio	NN	_	_	_
22	Laboratories	Laboratories	NNPS	_	_	_
23	,	,	,	_	_	_
24	Solana	Solana	NNP	_	_	_
25	Beach	Beach	NNP	_	_	_
26	,	,	,	_	_	_
27	CA	CA	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	genotype	genotype	NN	_	_	_
3	:	:	:	_	_	_
4	Wild	Wild	NNP	_	_	_
5	Type	type	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	hybridization	hybridization	NN	_	_	_
8	buffer	buffer	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	formamide	formamide	NN	_	_	_
11	content	content	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	:	:	:	_	_	_
14	0	0	CD	_	_	_
15	%	%	NN	_	_	_
16	formamide	formamide	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	hybridization	hybridization	NN	_	_	_
19	buffer	buffer	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	formamide	formamide	NN	_	_	_
22	content	content	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	:	:	:	_	_	_
25	10	10	CD	_	_	_
26	%	%	NN	_	_	_
27	formamide	formamide	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	hybridization	hybridization	NN	_	_	_
30	buffer	buffer	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	formamide	formamide	NN	_	_	_
33	content	content	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	:	:	:	_	_	_
36	15	15	CD	_	_	_
37	%	%	NN	_	_	_
38	formamide	formamide	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	hybridization	hybridization	NN	_	_	_
41	buffer	buffer	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	formamide	formamide	NN	_	_	_
44	content	content	NN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	:	:	:	_	_	_
47	20	20	CD	_	_	_
48	%	%	NN	_	_	_
49	formamide	formamide	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	hybridization	hybridization	NN	_	_	_
52	buffer	buffer	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	formamide	formamide	NN	_	_	_
55	content	content	NN	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	:	:	:	_	_	_
58	25	25	CD	_	_	_
59	%	%	NN	_	_	_
60	formamide	formamide	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	hybridization	hybridization	NN	_	_	_
63	buffer	buffer	NN	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	formamide	formamide	NN	_	_	_
66	content	content	NN	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	:	:	:	_	_	_
69	32.5	32.5	CD	_	_	_
70	%	%	NN	_	_	_
71	formamide	formamide	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	hybridization	hybridization	NN	_	_	_
74	buffer	buffer	NN	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	formamide	formamide	NN	_	_	_
77	content	content	NN	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	:	:	:	_	_	_
80	45	45	CD	_	_	_
81	%	%	NN	_	_	_
82	formamide	formamide	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	hybridization	hybridization	NN	_	_	_
85	buffer	buffer	NN	_	_	_
86	-LRB-	-lrb-	-LRB-	_	_	_
87	formamide	formamide	NN	_	_	_
88	content	content	NN	_	_	_
89	-RRB-	-rrb-	-RRB-	_	_	_
90	:	:	:	_	_	_
91	5	5	CD	_	_	_
92	%	%	NN	_	_	_
93	formamide	formamide	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	hybridization	hybridization	NN	_	_	_
96	buffer	buffer	NN	_	_	_
97	-LRB-	-lrb-	-LRB-	_	_	_
98	total	total	JJ	_	_	_
99	rna	rna	NN	GEN	_	_
100	-RRB-	-rrb-	-RRB-	_	_	_
101	:	:	:	_	_	_
102	50	50	CD	_	_	_
103	ng	ng	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	hybridization	hybridization	NN	_	_	_
106	buffer	buffer	NN	_	_	_
107	-LRB-	-lrb-	-LRB-	_	_	_
108	total	total	JJ	_	_	_
109	rna	rna	NN	GEN	_	_
110	-RRB-	-rrb-	-RRB-	_	_	_
111	:	:	:	_	_	_
112	5	5	CD	_	_	_
113	ng	ng	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	phenotype	phenotype	NN	_	_	_
116	:	:	:	_	_	_
117	normal	normal	JJ	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
119	Raw	raw	NN	_	_	_
120	data	datum	NNS	_	_	_
121	-LRB-	-lrb-	-LRB-	_	_	_
122	.	.	.	_	_	_

1	pair	pair	NN	_	_	_
2	files	file	NNS	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	was	be	VBD	_	_	_
5	analyzed	analyze	VBN	_	_	_
6	using	use	VBG	_	_	_
7	Matlab	Matlab	NNP	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	The	the	DT	_	_	_
10	MathWorks	MathWorks	NNPS	_	_	_
11	,	,	,	_	_	_
12	Natick	Natick	NNP	_	_	_
13	,	,	,	_	_	_
14	MA	MA	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	probe	probe	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	average	average	JJ	_	_	_
7	intensity	intensity	NN	_	_	_
8	of	of	IN	_	_	_
9	three	three	CD	_	_	_
10	replicates	replicate	VBZ	_	_	_
11	were	be	VBD	_	_	_
12	calculated	calculate	VBN	_	_	_
13	after	after	IN	_	_	_
14	the	the	DT	_	_	_
15	elimination	elimination	NN	_	_	_
16	of	of	IN	_	_	_
17	outliers	outlier	NNS	_	_	_
18	based	base	VBN	_	_	_
19	on	on	IN	_	_	_
20	a	a	DT	_	_	_
21	standard	standard	JJ	_	_	_
22	deviation	deviation	NN	_	_	_
23	test	test	NN	_	_	_
24	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	average	average	NN	_	_	_
3	of	of	IN	_	_	_
4	control	control	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	Nonsense	nonsense	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	probes	probe	NNS	_	_	_
9	was	be	VBD	_	_	_
10	subtracted	subtract	VBN	_	_	_
11	from	from	IN	_	_	_
12	all	all	DT	_	_	_
13	averages	average	NNS	_	_	_
14	to	to	TO	_	_	_
15	obtain	obtain	VB	_	_	_
16	background-corrected	background-corrected	JJ	_	_	_
17	results	result	NNS	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	R.	R.	NNP	_	_	_
3	sphaeroides	sphaeroide	NNS	_	_	_
4	was	be	VBD	_	_	_
5	phototrophically	phototrophically	RB	_	_	_
6	grown	grow	VBN	_	_	_
7	to	to	TO	_	_	_
8	mid-log	mid-log	JJ	_	_	_
9	phase	phase	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	100-150	100-150	CD	_	_	_
12	kletts	klett	NNS	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	in	in	IN	_	_	_
15	Sistrom	Sistrom	NNP	_	_	_
16	's	's	POS	_	_	_
17	minimal	minimal	JJ	_	_	_
18	medium	medium	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Sistrom	sistrom	NN	_	_	_
21	,	,	,	_	_	_
22	W.	W.	NNP	_	_	_
23	1960	1960	CD	_	_	_
24	.	.	.	_	_	_

1	Journal	Journal	NNP	_	_	_
2	of	of	IN	_	_	_
3	General	General	NNP	_	_	_
4	Microbiology	Microbiology	NNP	_	_	_
5	.	.	.	_	_	_

1	22:778-785	22:778-785	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	amended	amend	VBN	_	_	_
4	with	with	IN	_	_	_
5	33.9	33.9	CD	_	_	_
6	mM	mm	NN	KWSUPP	_	_
7	succinate	succinate	NN	SUPP	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	the	the	DT	_	_	_
7	minimal	minimal	JJ	_	_	_
8	media	media	NNS	_	_	_
9	,	,	,	_	_	_
10	M63	m63	NN	_	_	_
11	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	final	final	JJ	_	_	_
3	cell	cell	NN	_	_	_
4	concentrations	concentration	NNS	_	_	_
5	were	be	VBD	_	_	_
6	controlled	control	VBN	_	_	_
7	~	~	NN	_	_	_
8	108	108	CD	_	_	_
9	cells	cell	NNS	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Escherichia	escherichia	FW	Organism	_	_
12	coli	coli	FW	Organism	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	growth	growth	NN	_	_	_
15	protocol	protocol	NN	_	_	_
16	:	:	:	_	_	_
17	heat	heat	NN	_	_	_
18	shock	shock	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	growth	growth	NN	_	_	_
21	protocol	protocol	NN	_	_	_
22	:	:	:	_	_	_
23	steady	steady	JJ	_	_	_
24	growth	growth	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	heat	heat	NN	_	_	_
27	shock	shock	NN	_	_	_
28	response	response	NN	_	_	_
29	in	in	IN	_	_	_
30	the	the	DT	_	_	_
31	minimal	minimal	JJ	_	_	_
32	medium	medium	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	MDS42	mds42	NN	_	_	_
35	,	,	,	_	_	_
36	biological	biological	JJ	_	_	_
37	rep	rep	NN	GEN	_	_
38	1	1	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	MDS42	mds42	NN	_	_	_
41	,	,	,	_	_	_
42	biological	biological	JJ	_	_	_
43	rep	rep	NN	GEN	_	_
44	2	2	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	MDS42	mds42	NN	_	_	_
47	,	,	,	_	_	_
48	biological	biological	JJ	_	_	_
49	rep	rep	NN	GEN	_	_
50	3	3	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	MDS42	mds42	NN	_	_	_
53	,	,	,	_	_	_
54	biological	biological	JJ	_	_	_
55	rep	rep	NN	GEN	_	_
56	4	4	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	MDS42	mds42	NN	_	_	_
59	,	,	,	_	_	_
60	biological	biological	JJ	_	_	_
61	rep	rep	NN	GEN	_	_
62	5	5	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	MDS42	mds42	NN	_	_	_
65	,	,	,	_	_	_
66	biological	biological	JJ	_	_	_
67	rep	rep	NN	GEN	_	_
68	6	6	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	MDS42	mds42	NN	_	_	_
71	,	,	,	_	_	_
72	biological	biological	JJ	_	_	_
73	rep	rep	NN	GEN	_	_
74	7	7	CD	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	MDS42	mds42	NN	_	_	_
77	exponentially	exponentially	RB	_	_	_
78	grown	grow	VBN	_	_	_
79	in	in	IN	_	_	_
80	the	the	DT	_	_	_
81	minimal	minimal	JJ	_	_	_
82	medium	medium	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	MDS42	mds42	NN	_	_	_
85	,	,	,	_	_	_
86	heat	heat	NN	_	_	_
87	shock	shock	NN	_	_	_
88	,	,	,	_	_	_
89	biological	biological	JJ	_	_	_
90	rep	rep	NN	GEN	_	_
91	1	1	CD	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	MDS42	mds42	NN	_	_	_
94	,	,	,	_	_	_
95	heat	heat	NN	_	_	_
96	shock	shock	NN	_	_	_
97	,	,	,	_	_	_
98	biological	biological	JJ	_	_	_
99	rep	rep	NN	GEN	_	_
100	2	2	CD	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	MDS42	mds42	NN	_	_	_
103	,	,	,	_	_	_
104	heat	heat	NN	_	_	_
105	shock	shock	NN	_	_	_
106	,	,	,	_	_	_
107	biological	biological	JJ	_	_	_
108	rep	rep	NN	GEN	_	_
109	3	3	CD	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	MG1655	mg1655	NN	_	_	_
112	,	,	,	_	_	_
113	biological	biological	JJ	_	_	_
114	rep	rep	NN	GEN	_	_
115	1	1	CD	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	MG1655	mg1655	NN	_	_	_
118	,	,	,	_	_	_
119	biological	biological	JJ	_	_	_
120	rep	rep	NN	GEN	_	_
121	2	2	CD	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	MG1655	mg1655	NN	_	_	_
124	,	,	,	_	_	_
125	biological	biological	JJ	_	_	_
126	rep	rep	NN	GEN	_	_
127	3	3	CD	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	MG1655	mg1655	NN	_	_	_
130	,	,	,	_	_	_
131	biological	biological	JJ	_	_	_
132	rep	rep	NN	GEN	_	_
133	4	4	CD	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	MG1655	mg1655	NN	_	_	_
136	,	,	,	_	_	_
137	biological	biological	JJ	_	_	_
138	rep	rep	NN	GEN	_	_
139	5	5	CD	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	MG1655	mg1655	NN	_	_	_
142	,	,	,	_	_	_
143	biological	biological	JJ	_	_	_
144	rep	rep	NN	GEN	_	_
145	6	6	CD	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	MG1655	mg1655	NN	_	_	_
148	,	,	,	_	_	_
149	biological	biological	JJ	_	_	_
150	rep	rep	NN	GEN	_	_
151	7	7	CD	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	MG1655	mg1655	NN	_	_	_
154	exponentially	exponentially	RB	_	_	_
155	grown	grow	VBN	_	_	_
156	in	in	IN	_	_	_
157	the	the	DT	_	_	_
158	minimal	minimal	JJ	_	_	_
159	medium	medium	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	MG1655	mg1655	NN	_	_	_
162	,	,	,	_	_	_
163	heat	heat	NN	_	_	_
164	shock	shock	NN	_	_	_
165	,	,	,	_	_	_
166	biological	biological	JJ	_	_	_
167	rep	rep	NN	GEN	_	_
168	1	1	CD	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	MG1655	mg1655	NN	_	_	_
171	,	,	,	_	_	_
172	heat	heat	NN	_	_	_
173	shock	shock	NN	_	_	_
174	,	,	,	_	_	_
175	biological	biological	JJ	_	_	_
176	rep	rep	NN	GEN	_	_
177	2	2	CD	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	MG1655	mg1655	NN	_	_	_
180	,	,	,	_	_	_
181	heat	heat	NN	_	_	_
182	shock	shock	NN	_	_	_
183	,	,	,	_	_	_
184	biological	biological	JJ	_	_	_
185	rep	rep	NN	GEN	_	_
186	3	3	CD	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	Microarray	microarray	NN	_	_	_
189	data	datum	NNS	_	_	_
190	were	be	VBD	_	_	_
191	processed	process	VBN	_	_	_
192	using	use	VBG	_	_	_
193	custom	custom	NN	_	_	_
194	scripts	script	NNS	_	_	_
195	written	write	VBN	_	_	_
196	in	in	IN	_	_	_
197	R	r	NN	_	_	_
198	based	base	VBN	_	_	_
199	on	on	IN	_	_	_
200	the	the	DT	_	_	_
201	finite	finite	JJ	_	_	_
202	hybridisation	hybridisation	NN	_	_	_
203	-LRB-	-lrb-	-LRB-	_	_	_
204	FH	fh	NN	_	_	_
205	-RRB-	-rrb-	-RRB-	_	_	_
206	model	model	NN	_	_	_
207	-LRB-	-lrb-	-LRB-	_	_	_
208	Ono	Ono	NNP	_	_	_
209	et	et	FW	_	_	_
210	al	al	FW	_	_	_
211	,	,	,	_	_	_
212	2008	2008	CD	_	_	_
213	-RRB-	-rrb-	-RRB-	_	_	_
214	and	and	CC	_	_	_
215	the	the	DT	_	_	_
216	thermodynamic	thermodynamic	JJ	_	_	_
217	model	model	NN	_	_	_
218	of	of	IN	_	_	_
219	non-specific	non-specific	JJ	_	_	_
220	binding	binding	NN	_	_	_
221	-LRB-	-lrb-	-LRB-	_	_	_
222	NSB	nsb	NN	_	_	_
223	-RRB-	-rrb-	-RRB-	_	_	_
224	on	on	IN	_	_	_
225	short	short	JJ	_	_	_
226	nucleotide	nucleotide	NN	_	_	_
227	microarrays	microarray	NNS	_	_	_
228	-LRB-	-lrb-	-LRB-	_	_	_
229	Furusawa	Furusawa	NNP	_	_	_
230	et	et	FW	_	_	_
231	al	al	FW	_	_	_
232	,	,	,	_	_	_
233	2009	2009	CD	_	_	_
234	-RRB-	-rrb-	-RRB-	_	_	_
235	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MDS42	mds42	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	genome	genome	NN	_	_	_
7	reduced	reduce	VBN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	strain	strain	NN	_	_	_
11	:	:	:	_	_	_
12	MG1655	mg1655	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	parent	parent	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	The	the	DT	_	_	_
18	cell	cell	NN	_	_	_
19	culture	culture	NN	_	_	_
20	was	be	VBD	_	_	_
21	put	put	VBN	_	_	_
22	into	into	IN	_	_	_
23	cold	cold	JJ	_	_	_
24	phenol-ethanol	phenol-ethanol	JJ	_	_	_
25	solution	solution	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	1	1	CD	_	_	_
28	g	g	NN	_	_	_
29	of	of	IN	_	_	_
30	phenol	phenol	NN	_	_	_
31	in	in	IN	_	_	_
32	10	10	CD	_	_	_
33	mL	ml	NN	_	_	_
34	of	of	IN	_	_	_
35	ethanol	ethanol	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	prepared	prepare	VBN	_	_	_
38	in	in	IN	_	_	_
39	advance	advance	NN	_	_	_
40	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	collected	collect	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	at	at	IN	_	_	_
8	16,000	16,000	CD	_	_	_
9	×	×	CD	_	_	_
10	g	g	NN	_	_	_
11	for	for	IN	_	_	_
12	5	5	CD	_	_	_
13	min	min	NN	_	_	_
14	at	at	IN	_	_	_
15	4	4	CD	_	_	_
16	°C	°c	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	the	the	DT	_	_	_
20	pelleted	pelleted	JJ	_	_	_
21	cells	cell	NNS	_	_	_
22	were	be	VBD	_	_	_
23	stored	store	VBN	_	_	_
24	at	at	IN	_	_	_
25	--	--	:	_	_	_
26	80	80	CD	_	_	_
27	°C	°c	NN	_	_	_
28	prior	prior	RB	_	_	_
29	to	to	TO	_	_	_
30	use	use	VB	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	log10	log10	NN	_	_	_
4	mRNA	mrna	NN	_	_	_
5	concentration	concentration	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	pM	pm	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	data	datum	NNS	_	_	_
10	are	be	VBP	_	_	_
11	provided	provide	VBN	_	_	_
12	as	as	IN	_	_	_
13	a	a	DT	_	_	_
14	supplementary	supplementary	JJ	_	_	_
15	file	file	NN	_	_	_
16	on	on	IN	_	_	_
17	the	the	DT	_	_	_
18	SERIES	series	NN	_	_	_
19	record	record	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNAs	rna	NNS	_	_	_
4	were	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	an	a	DT	_	_	_
8	RNeasy	rneasy	NN	_	_	_
9	mini	minus	NNS	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	qiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	in	in	IN	_	_	_
15	accordance	accordance	NN	_	_	_
16	with	with	IN	_	_	_
17	the	the	DT	_	_	_
18	manufacturer	manufacturer	NN	_	_	_
19	's	's	POS	_	_	_
20	instructions	instruction	NNS	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	An	a	DT	_	_	_
3	overnight	overnight	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	diluted	dilute	VBN	_	_	_
7	to	to	TO	_	_	_
8	an	a	DT	_	_	_
9	OD600	od600	NN	_	_	_
10	of	of	IN	_	_	_
11	0.02	0.02	CD	_	_	_
12	in	in	IN	_	_	_
13	LB	LB	NNP	MED	_	_
14	media	media	NNS	MED	_	_
15	supplemented	supplement	VBN	_	_	_
16	with	with	IN	_	_	_
17	100	100	CD	_	_	_
18	µg	µg	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Cells	cell	NNS	_	_	_
21	were	be	VBD	_	_	_
22	flash	flash	NN	_	_	_
23	frozen	freeze	VBN	_	_	_
24	in	in	IN	_	_	_
25	liquid	liquid	JJ	_	_	_
26	nitrogen	nitrogen	NN	_	_	_
27	after	after	IN	_	_	_
28	the	the	DT	_	_	_
29	media	media	NNS	_	_	_
30	was	be	VBD	_	_	_
31	rapidly	rapidly	RB	_	_	_
32	filtered	filter	VBN	_	_	_
33	.	.	.	_	_	_

1	Frozen	frozen	JJ	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	pulverized	pulverize	VBN	_	_	_
5	by	by	IN	_	_	_
6	mixer	mixer	NN	_	_	_
7	milling	milling	NN	_	_	_
8	and	and	CC	_	_	_
9	thawed	thaw	VBN	_	_	_
10	in	in	IN	_	_	_
11	20	20	CD	_	_	_
12	mM	mm	NN	KWSUPP	_	_
13	EDC	edc	NN	_	_	_
14	,	,	,	_	_	_
15	pH	ph	NN	_	_	_
16	5.8	5.8	CD	_	_	_
17	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	crosslinking	crosslinking	NN	_	_	_
3	reaction	reaction	NN	_	_	_
4	was	be	VBD	_	_	_
5	quenched	quench	VBN	_	_	_
6	with	with	IN	_	_	_
7	250	250	CD	_	_	_
8	mM	mm	NN	KWSUPP	_	_
9	glycine	glycine	NN	_	_	_
10	,	,	,	_	_	_
11	100	100	CD	_	_	_
12	mM	mm	NN	KWSUPP	_	_
13	Tris	Tris	NNP	_	_	_
14	Cl	Cl	NNP	_	_	_
15	8.0	8.0	CD	_	_	_
16	,	,	,	_	_	_
17	and	and	CC	_	_	_
18	4	4	CD	_	_	_
19	mM	mm	NN	KWSUPP	_	_
20	NaHCO3	nahco3	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	flash	flash	NN	_	_	_
5	frozen	freeze	VBN	_	_	_
6	in	in	IN	_	_	_
7	liquid	liquid	JJ	_	_	_
8	nitrogen	nitrogen	NN	_	_	_
9	after	after	IN	_	_	_
10	the	the	DT	_	_	_
11	media	media	NNS	_	_	_
12	was	be	VBD	_	_	_
13	rapidly	rapidly	RB	_	_	_
14	filtered	filter	VBN	_	_	_
15	.	.	.	_	_	_

1	Frozen	frozen	JJ	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	pulverized	pulverize	VBN	_	_	_
5	by	by	IN	_	_	_
6	mixer	mixer	NN	_	_	_
7	milling	milling	NN	_	_	_
8	and	and	CC	_	_	_
9	thawed	thaw	VBN	_	_	_
10	in	in	IN	_	_	_
11	2.5	2.5	CD	_	_	_
12	mM	mm	NN	KWSUPP	_	_
13	DSP	DSP	NNP	_	_	_
14	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	crosslinking	crosslinking	NN	_	_	_
3	reaction	reaction	NN	_	_	_
4	was	be	VBD	_	_	_
5	quenched	quench	VBN	_	_	_
6	with	with	IN	_	_	_
7	100	100	CD	_	_	_
8	mM	mm	NN	KWSUPP	_	_
9	Tris	Tris	NNP	_	_	_
10	Cl	Cl	NNP	_	_	_
11	8.3	8.3	CD	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Clarified	clarify	VBD	_	_	_
3	extracts	extract	NNS	_	_	_
4	were	be	VBD	_	_	_
5	treated	treat	VBN	_	_	_
6	with	with	IN	_	_	_
7	microccocal	microccocal	JJ	_	_	_
8	nuclease	nuclease	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	45	45	CD	_	_	_
11	enzyme	enzyme	NN	_	_	_
12	units	unit	NNS	_	_	_
13	per	per	IN	_	_	_
14	absorbance	absorbance	NN	_	_	_
15	unit	unit	NN	_	_	_
16	of	of	IN	_	_	_
17	lysate	lysate	NN	_	_	_
18	at	at	IN	_	_	_
19	260	260	CD	_	_	_
20	nm	nm	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	,	,	,	_	_	_
23	purified	purify	VBN	_	_	_
24	through	through	IN	_	_	_
25	a	a	DT	_	_	_
26	sucrose	sucrose	NN	_	_	_
27	cushion	cushion	NN	_	_	_
28	,	,	,	_	_	_
29	and	and	CC	_	_	_
30	affinity	affinity	NN	_	_	_
31	purified	purify	VBN	_	_	_
32	via	via	IN	_	_	_
33	TF	tf	NN	_	_	_
34	.	.	.	_	_	_

1	Ribosome-protected	ribosome-protected	JJ	_	_	_
2	footprints	footprint	NNS	_	_	_
3	were	be	VBD	_	_	_
4	size	size	NN	_	_	_
5	selected	select	VBN	_	_	_
6	and	and	CC	_	_	_
7	converted	convert	VBN	_	_	_
8	into	into	IN	_	_	_
9	a	a	DT	_	_	_
10	cDNA	cdna	NN	_	_	_
11	library	library	NN	_	_	_
12	for	for	IN	_	_	_
13	sequencing	sequencing	NN	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Clarified	clarify	VBD	_	_	_
3	extracts	extract	NNS	_	_	_
4	were	be	VBD	_	_	_
5	treated	treat	VBN	_	_	_
6	with	with	IN	_	_	_
7	microccocal	microccocal	JJ	_	_	_
8	nuclease	nuclease	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	45	45	CD	_	_	_
11	enzyme	enzyme	NN	_	_	_
12	units	unit	NNS	_	_	_
13	per	per	IN	_	_	_
14	absorbance	absorbance	NN	_	_	_
15	unit	unit	NN	_	_	_
16	of	of	IN	_	_	_
17	lysate	lysate	NN	_	_	_
18	at	at	IN	_	_	_
19	260	260	CD	_	_	_
20	nm	nm	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	,	,	,	_	_	_
23	purified	purify	VBN	_	_	_
24	through	through	IN	_	_	_
25	a	a	DT	_	_	_
26	sucrose	sucrose	NN	_	_	_
27	gradient	gradient	NN	_	_	_
28	.	.	.	_	_	_

1	Ribosome-protected	ribosome-protected	JJ	_	_	_
2	footprints	footprint	NNS	_	_	_
3	were	be	VBD	_	_	_
4	size	size	NN	_	_	_
5	selected	select	VBN	_	_	_
6	and	and	CC	_	_	_
7	converted	convert	VBN	_	_	_
8	into	into	IN	_	_	_
9	a	a	DT	_	_	_
10	cDNA	cdna	NN	_	_	_
11	library	library	NN	_	_	_
12	for	for	IN	_	_	_
13	sequencing	sequencing	NN	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	DSP1	dsp1	NN	_	_	_
3	_	_	CD	_	_	_
4	AP	ap	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	DSP1	dsp1	NN	_	_	_
7	_	_	CD	_	_	_
8	Total	total	JJ	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	DSP2	dsp2	NN	_	_	_
11	_	_	CD	_	_	_
12	AP	ap	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	DSP2	dsp2	NN	_	_	_
15	_	_	CD	_	_	_
16	Total	total	JJ	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	DSP3	dsp3	NN	_	_	_
19	_	_	CD	_	_	_
20	AP	ap	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	DSP3	dsp3	NN	_	_	_
23	_	_	CD	_	_	_
24	Total	total	JJ	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	EDC1	edc1	NN	_	_	_
27	_	_	CD	_	_	_
28	AP	ap	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	EDC1	edc1	NN	_	_	_
31	_	_	CD	_	_	_
32	Total	total	JJ	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	Escherichia	escherichia	FW	Organism	_	_
35	coli	coli	FW	Organism	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	genotype	genotype	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	growth	growth	NN	_	_	_
40	stage	stage	NN	_	_	_
41	:	:	:	_	_	_
42	mid-log	mid-log	JJ	_	_	_
43	phase	phase	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	Harvested	harvest	VBN	_	_	_
46	by	by	IN	_	_	_
47	chloramphenicol	chloramphenicol	NN	_	_	_
48	pre-treatment	pre-treatment	NN	_	_	_
49	and	and	CC	_	_	_
50	centrifugation	centrifugation	NN	_	_	_
51	;	;	:	_	_	_
52	DSP	DSP	NNP	_	_	_
53	treated	treat	VBN	_	_	_
54	ex	ex	FW	_	_	_
55	vivo	vivo	FW	_	_	_
56	;	;	:	_	_	_
57	Affinity	affinity	NN	_	_	_
58	purified	purify	VBN	_	_	_
59	TF	tf	NN	_	_	_
60	crosslinked	crosslink	VBD	_	_	_
61	RNC	rnc	NN	_	_	_
62	footprints	footprint	NNS	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	Harvested	harvest	VBN	_	_	_
65	by	by	IN	_	_	_
66	chloramphenicol	chloramphenicol	NN	_	_	_
67	pre-treatment	pre-treatment	NN	_	_	_
68	and	and	CC	_	_	_
69	centrifugation	centrifugation	NN	_	_	_
70	;	;	:	_	_	_
71	DSP	DSP	NNP	_	_	_
72	treated	treat	VBN	_	_	_
73	ex	ex	FW	_	_	_
74	vivo	vivo	FW	_	_	_
75	;	;	:	_	_	_
76	Total	total	JJ	_	_	_
77	footprints	footprint	NNS	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	Harvested	harvest	VBN	_	_	_
80	by	by	IN	_	_	_
81	rapid	rapid	JJ	_	_	_
82	filtration	filtration	NN	_	_	_
83	;	;	:	_	_	_
84	DSP	DSP	NNP	_	_	_
85	treated	treat	VBN	_	_	_
86	ex	ex	FW	_	_	_
87	vivo	vivo	FW	_	_	_
88	;	;	:	_	_	_
89	Affinity	affinity	NN	_	_	_
90	purified	purify	VBN	_	_	_
91	TF	tf	NN	_	_	_
92	crosslinked	crosslink	VBD	_	_	_
93	RNC	rnc	NN	_	_	_
94	footprints	footprint	NNS	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	Harvested	harvest	VBN	_	_	_
97	by	by	IN	_	_	_
98	rapid	rapid	JJ	_	_	_
99	filtration	filtration	NN	_	_	_
100	;	;	:	_	_	_
101	DSP	DSP	NNP	_	_	_
102	treated	treat	VBN	_	_	_
103	ex	ex	FW	_	_	_
104	vivo	vivo	FW	_	_	_
105	;	;	:	_	_	_
106	Total	total	JJ	_	_	_
107	footprints	footprint	NNS	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	Harvested	harvest	VBN	_	_	_
110	by	by	IN	_	_	_
111	rapid	rapid	JJ	_	_	_
112	filtration	filtration	NN	_	_	_
113	;	;	:	_	_	_
114	EDC	edc	NN	_	_	_
115	treated	treat	VBN	_	_	_
116	ex	ex	FW	_	_	_
117	vivo	vivo	FW	_	_	_
118	;	;	:	_	_	_
119	Affinity	affinity	NN	_	_	_
120	purified	purify	VBN	_	_	_
121	TF	tf	NN	_	_	_
122	crosslinked	crosslink	VBD	_	_	_
123	RNC	rnc	NN	_	_	_
124	footprints	footprint	NNS	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	Harvested	harvest	VBN	_	_	_
127	by	by	IN	_	_	_
128	rapid	rapid	JJ	_	_	_
129	filtration	filtration	NN	_	_	_
130	;	;	:	_	_	_
131	EDC	edc	NN	_	_	_
132	treated	treat	VBN	_	_	_
133	ex	ex	FW	_	_	_
134	vivo	vivo	FW	_	_	_
135	;	;	:	_	_	_
136	Total	total	JJ	_	_	_
137	footprints	footprint	NNS	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
139	library	library	NN	_	_	_
140	strategy	strategy	NN	_	_	_
141	:	:	:	_	_	_
142	Ribosome	Ribosome	NNP	_	_	_
143	profiling	profile	VBG	_	_	_
144	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
145	library	library	NN	_	_	_
146	strategy	strategy	NN	_	_	_
147	:	:	:	_	_	_
148	Selective	selective	JJ	_	_	_
149	ribosome	ribosome	NN	_	_	_
150	profiling	profile	VBG	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	RNA-Seq	rna-seq	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	strain	strain	NN	_	_	_
155	:	:	:	_	_	_
156	MC4100	mc4100	NN	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
158	The	the	DT	_	_	_
159	.	.	.	_	_	_

1	align	align	VB	_	_	_
2	files	file	NNS	_	_	_
3	have	have	VBP	_	_	_
4	been	be	VBN	_	_	_
5	processed	process	VBN	_	_	_
6	using	use	VBG	_	_	_
7	tagalign	tagalign	NN	_	_	_
8	.	.	.	_	_	_

1	Reads	read	NNS	_	_	_
2	were	be	VBD	_	_	_
3	aligned	align	VBN	_	_	_
4	to	to	TO	_	_	_
5	the	the	DT	_	_	_
6	reference	reference	NN	_	_	_
7	genome	genome	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Bowtie	Bowtie	NNP	_	_	_
10	v.	v.	CC	_	_	_
11	0.12.0	0.12.0	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	by	by	IN	_	_	_
14	the	the	DT	_	_	_
15	first	first	JJ	_	_	_
16	25	25	CD	_	_	_
17	nt	nt	NNS	_	_	_
18	and	and	CC	_	_	_
19	extended	extend	VBN	_	_	_
20	to	to	TO	_	_	_
21	account	account	VB	_	_	_
22	for	for	IN	_	_	_
23	the	the	DT	_	_	_
24	linker	linker	NN	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	culture	culture	NN	_	_	_
4	was	be	VBD	_	_	_
5	incubated	incubate	VBN	_	_	_
6	with	with	IN	_	_	_
7	100	100	CD	_	_	_
8	µg	µg	NN	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	E.	E.	NNP	_	_	_
11	coli	coli	NN	_	_	_
12	K12	k12	NN	_	_	_
13	interacted	interact	VBD	_	_	_
14	with	with	IN	_	_	_
15	lettuce	lettuce	NN	_	_	_
16	rhizosphere	rhizosphere	NN	_	_	_
17	rep1	rep1	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	E.	e.	FW	_	_	_
20	coli	coli	FW	_	_	_
21	K12	k12	NN	_	_	_
22	interacted	interact	VBD	_	_	_
23	with	with	IN	_	_	_
24	lettuce	lettuce	NN	_	_	_
25	rhizosphere	rhizosphere	NN	_	_	_
26	rep2	rep2	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	E.	e.	FW	_	_	_
29	coli	coli	FW	_	_	_
30	K12	k12	NN	_	_	_
31	interacted	interact	VBD	_	_	_
32	with	with	IN	_	_	_
33	lettuce	lettuce	NN	_	_	_
34	rhizosphere	rhizosphere	NN	_	_	_
35	rep3	rep3	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	E.	e.	FW	_	_	_
38	coli	coli	FW	_	_	_
39	K12	k12	NN	_	_	_
40	interacted	interact	VBD	_	_	_
41	with	with	IN	_	_	_
42	lettuce	lettuce	NN	_	_	_
43	rhizosphere	rhizosphere	NN	_	_	_
44	rep4	rep4	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	E.	e.	FW	_	_	_
47	coli	coli	FW	_	_	_
48	K12	k12	NN	_	_	_
49	interacted	interact	VBD	_	_	_
50	with	with	IN	_	_	_
51	lettuce	lettuce	NN	_	_	_
52	rhizosphere	rhizosphere	NN	_	_	_
53	rep5	rep5	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	E.	e.	FW	_	_	_
56	coli	coli	FW	_	_	_
57	K12	k12	NN	_	_	_
58	interacted	interact	VBD	_	_	_
59	with	with	IN	_	_	_
60	lettuce	lettuce	NN	_	_	_
61	rhizosphere	rhizosphere	NN	_	_	_
62	rep6	rep6	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	Escherichia	escherichia	FW	Organism	_	_
65	coli	coli	FW	Organism	_	_
66	MG1655	mg1655	NN	_	_	_
67	cells	cell	NNS	_	_	_
68	grown	grow	VBN	_	_	_
69	in	in	IN	_	_	_
70	the	the	DT	_	_	_
71	hydroponic	hydroponic	JJ	_	_	_
72	system	system	NN	_	_	_
73	without	without	IN	_	_	_
74	interacting	interact	VBG	_	_	_
75	with	with	IN	_	_	_
76	the	the	DT	_	_	_
77	lettuce	lettuce	NN	_	_	_
78	rhizosphere	rhizosphere	NN	_	_	_
79	for	for	IN	_	_	_
80	3	3	CD	_	_	_
81	days	day	NNS	_	_	_
82	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
83	Escherichia	escherichia	FW	Organism	_	_
84	coli	coli	FW	Organism	_	_
85	MG1655	mg1655	NN	_	_	_
86	cells	cell	NNS	_	_	_
87	interacted	interact	VBD	_	_	_
88	with	with	IN	_	_	_
89	the	the	DT	_	_	_
90	lettuce	lettuce	NN	_	_	_
91	rhizosphere	rhizosphere	NN	_	_	_
92	for	for	IN	_	_	_
93	3	3	CD	_	_	_
94	days	day	NNS	_	_	_
95	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
96	Escherichia	escherichia	FW	Organism	_	_
97	coli	coli	FW	Organism	_	_
98	MG1655	mg1655	NN	_	_	_
99	were	be	VBD	_	_	_
100	grown	grow	VBN	_	_	_
101	in	in	IN	_	_	_
102	10	10	CD	_	_	_
103	ml	ml	NN	_	_	_
104	of	of	IN	_	_	_
105	LB	lb	NN	MED	_	_
106	medium	medium	NN	MED	_	_
107	until	until	IN	_	_	_
108	stationary	stationary	JJ	GrowthPhase	_	_
109	phase	phase	NN	GrowthPhase	_	_
110	,	,	,	_	_	_
111	collected	collect	VBN	_	_	_
112	by	by	IN	_	_	_
113	centrifugation	centrifugation	NN	_	_	_
114	at	at	IN	_	_	_
115	8,000	8,000	CD	_	_	_
116	×	×	CD	_	_	_
117	g	g	NN	_	_	_
118	for	for	IN	_	_	_
119	10	10	CD	_	_	_
120	min	min	NN	_	_	_
121	,	,	,	_	_	_
122	and	and	CC	_	_	_
123	washed	wash	VBN	_	_	_
124	twice	twice	RB	_	_	_
125	with	with	IN	_	_	_
126	sterilized	sterilize	VBN	_	_	_
127	,	,	,	_	_	_
128	plant	plant	NN	_	_	_
129	growth	growth	NN	_	_	_
130	medium	medium	NN	_	_	_
131	-LRB-	-lrb-	-LRB-	_	_	_
132	Caspersen	Caspersen	NNP	_	_	_
133	et	et	FW	_	_	_
134	al.	al.	FW	_	_	_
135	1999	1999	CD	_	_	_
136	-RRB-	-rrb-	-RRB-	_	_	_
137	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	resultant	resultant	JJ	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	re-suspended	re-suspended	JJ	_	_	_
6	in	in	IN	_	_	_
7	10	10	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	same	same	JJ	_	_	_
12	plant	plant	NN	_	_	_
13	growth	growth	NN	_	_	_
14	medium	medium	NN	_	_	_
15	to	to	TO	_	_	_
16	a	a	DT	_	_	_
17	final	final	JJ	_	_	_
18	concentration	concentration	NN	_	_	_
19	of	of	IN	_	_	_
20	approximately	approximately	RB	_	_	_
21	10E9	10e9	JJ	_	_	_
22	cells	cell	NNS	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	Escherichia	escherichia	FW	Organism	_	_
25	coli	coli	FW	Organism	_	_
26	str	str	FW	_	_	_
27	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Following	follow	VBG	_	_	_
4	incubation	incubation	NN	_	_	_
5	,	,	,	_	_	_
6	roots	root	NNS	_	_	_
7	had	have	VBD	_	_	_
8	been	be	VBN	_	_	_
9	gently	gently	RB	_	_	_
10	rinsed	rinse	VBN	_	_	_
11	to	to	TO	_	_	_
12	remove	remove	VB	_	_	_
13	loosely	loosely	RB	_	_	_
14	attached	attach	VBN	_	_	_
15	bacteria	bacterium	NNS	_	_	_
16	and	and	CC	_	_	_
17	roots	root	NNS	_	_	_
18	were	be	VBD	_	_	_
19	cut	cut	VBN	_	_	_
20	directly	directly	RB	_	_	_
21	into	into	IN	_	_	_
22	100	100	CD	_	_	_
23	ml	ml	NN	_	_	_
24	ice	ice	NN	_	_	_
25	cold	cold	JJ	_	_	_
26	stop	stop	NN	_	_	_
27	solution	solution	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	5	5	CD	_	_	_
30	%	%	NN	_	_	_
31	H2O-saturated	h2o-saturated	JJ	_	_	_
32	phenol	phenol	NN	_	_	_
33	,	,	,	_	_	_
34	pH	ph	NN	_	_	_
35	4.3	4.3	CD	_	_	_
36	,	,	,	_	_	_
37	in	in	IN	_	_	_
38	95	95	CD	_	_	_
39	%	%	NN	_	_	_
40	ethanol	ethanol	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	.	.	.	_	_	_

1	Root	root	NN	_	_	_
2	extracts	extract	NNS	_	_	_
3	were	be	VBD	_	_	_
4	filtered	filter	VBN	_	_	_
5	using	use	VBG	_	_	_
6	0.5	0.5	CD	_	_	_
7	µm	µm	NN	_	_	_
8	filters	filter	NNS	_	_	_
9	to	to	TO	_	_	_
10	separate	separate	JJ	_	_	_
11	bacteria	bacterium	NNS	_	_	_
12	cells	cell	NNS	_	_	_
13	from	from	IN	_	_	_
14	plant	plant	NN	_	_	_
15	cells	cell	NNS	_	_	_
16	in	in	IN	_	_	_
17	order	order	NN	_	_	_
18	to	to	TO	_	_	_
19	prevent	prevent	VB	_	_	_
20	interference	interference	NN	_	_	_
21	of	of	IN	_	_	_
22	the	the	DT	_	_	_
23	cDNA	cdna	NN	_	_	_
24	labeling	labeling	NN	_	_	_
25	.	.	.	_	_	_

1	Qiagen	Qiagen	NNP	_	_	_
2	RNA	rna	NN	_	_	_
3	protect	protect	VB	_	_	_
4	solution	solution	NN	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	to	to	TO	_	_	_
8	stabilize	stabilize	VB	_	_	_
9	RNA	rna	NN	_	_	_
10	during	during	IN	_	_	_
11	extraction	extraction	NN	_	_	_
12	.	.	.	_	_	_

1	Bacteria	bacterium	NNS	_	_	_
2	had	have	VBD	_	_	_
3	been	be	VBN	_	_	_
4	collected	collect	VBN	_	_	_
5	by	by	IN	_	_	_
6	shaking	shake	VBG	_	_	_
7	and	and	CC	_	_	_
8	washing	wash	VBG	_	_	_
9	and	and	CC	_	_	_
10	stored	store	VBN	_	_	_
11	in	in	IN	_	_	_
12	-80	-80	CD	_	_	_
13	°C	°c	NN	_	_	_
14	until	until	IN	_	_	_
15	using	use	VBG	_	_	_
16	for	for	IN	_	_	_
17	RNA	rna	NN	_	_	_
18	isolation	isolation	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Signal	signal	NN	_	_	_
3	intensities	intensity	NNS	_	_	_
4	were	be	VBD	_	_	_
5	normalized	normalize	VBN	_	_	_
6	for	for	IN	_	_	_
7	spot	spot	NN	_	_	_
8	and	and	CC	_	_	_
9	slide	slide	NN	_	_	_
10	abnormalities	abnormality	NNS	_	_	_
11	with	with	IN	_	_	_
12	the	the	DT	_	_	_
13	spatial	spatial	JJ	_	_	_
14	Lowess	lowess	NN	_	_	_
15	algorithm	algorithm	NN	_	_	_
16	and	and	CC	_	_	_
17	analyzed	analyze	VBN	_	_	_
18	by	by	IN	_	_	_
19	mixed-effect	mixed-effect	JJ	_	_	_
20	ANOVA	ANOVA	NNP	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	MAANOVA	MAANOVA	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Kerr	Kerr	NNP	_	_	_
26	et	et	FW	_	_	_
27	al.	al.	FW	_	_	_
28	2000	2000	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	Both	both	DT	_	_	_
2	Lowess	lowess	NN	_	_	_
3	and	and	CC	_	_	_
4	MAANOVA	maanova	NN	_	_	_
5	are	be	VBP	_	_	_
6	part	part	NN	_	_	_
7	of	of	IN	_	_	_
8	the	the	DT	_	_	_
9	R	r	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Standard	standard	JJ	_	_	_
12	hot-phenol	hot-phenol	NN	_	_	_
13	method	method	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	treatment	treatment	NN	_	_	_
16	:	:	:	_	_	_
17	control	control	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	treatment	treatment	NN	_	_	_
20	:	:	:	_	_	_
21	exposed	expose	VBN	_	_	_
22	to	to	TO	_	_	_
23	the	the	DT	_	_	_
24	lettuce	lettuce	NN	_	_	_
25	rhizosphere	rhizosphere	NN	_	_	_
26	for	for	IN	_	_	_
27	3	3	CD	_	_	_
28	days	day	NNS	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Cells	cell	NNS	_	_	_
31	were	be	VBD	_	_	_
32	harvested	harvest	VBN	_	_	_
33	using	use	VBG	_	_	_
34	RNAprotect	rnaprotect	NN	_	_	_
35	Bacteria	bacterium	NNS	_	_	_
36	Reagent	reagent	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Qiagen	Qiagen	NNP	_	_	_
39	,	,	,	_	_	_
40	Hilden	Hilden	NNP	_	_	_
41	,	,	,	_	_	_
42	Germany	Germany	NNP	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	for	for	IN	_	_	_
45	stabilization	stabilization	NN	_	_	_
46	of	of	IN	_	_	_
47	RNA	rna	NN	_	_	_
48	.	.	.	_	_	_

1	Stabilized	stabilize	VBN	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	used	use	VBN	_	_	_
5	for	for	IN	_	_	_
6	RNA	rna	NN	_	_	_
7	isolation	isolation	NN	_	_	_
8	using	use	VBG	_	_	_
9	the	the	DT	_	_	_
10	RNeasy	rneasy	NN	_	_	_
11	MiniKit	minikit	NN	_	_	_
12	system	system	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Qiagen	Qiagen	NNP	_	_	_
15	,	,	,	_	_	_
16	Hilden	Hilden	NNP	_	_	_
17	,	,	,	_	_	_
18	Germany	Germany	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	brief	brief	NN	_	_	_
3	,	,	,	_	_	_
4	1	1	CD	_	_	_
5	ml	ml	NN	_	_	_
6	of	of	IN	_	_	_
7	each	each	DT	_	_	_
8	culture	culture	NN	_	_	_
9	was	be	VBD	_	_	_
10	used	use	VBN	_	_	_
11	and	and	CC	_	_	_
12	processed	process	VBN	_	_	_
13	according	accord	VBG	_	_	_
14	to	to	TO	_	_	_
15	the	the	DT	_	_	_
16	manufacturer	manufacturer	NN	_	_	_
17	's	's	POS	_	_	_
18	instructions	instruction	NNS	_	_	_
19	including	include	VBG	_	_	_
20	an	a	DT	_	_	_
21	on-column	on-column	JJ	_	_	_
22	DNaseI	dnasei	NN	_	_	_
23	treatment	treatment	NN	_	_	_
24	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	quality	quality	NN	_	_	_
3	was	be	VBD	_	_	_
4	assayed	assay	VBN	_	_	_
5	by	by	IN	_	_	_
6	denaturing	denature	VBG	_	_	_
7	urea-PAGE	urea-page	NN	_	_	_
8	and	and	CC	_	_	_
9	by	by	IN	_	_	_
10	measuring	measure	VBG	_	_	_
11	the	the	DT	_	_	_
12	ratio	ratio	NN	_	_	_
13	of	of	IN	_	_	_
14	absorption	absorption	NN	_	_	_
15	at	at	IN	_	_	_
16	260	260	CD	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	Data	datum	NNS	_	_	_
19	were	be	VBD	_	_	_
20	processed	process	VBN	_	_	_
21	using	use	VBG	_	_	_
22	Affymetrix	Affymetrix	NNP	_	_	_
23	apt-probeset-summarize	apt-probeset-summarize	JJ	_	_	_
24	software	software	NN	_	_	_
25	version	version	NN	_	_	_
26	1.10	1.10	CD	_	_	_
27	and	and	CC	_	_	_
28	RMA	RMA	NNP	_	_	_
29	algorithm	algorithm	NN	_	_	_
30	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	normalized	normalize	VBN	_	_	_
4	using	use	VBG	_	_	_
5	the	the	DT	_	_	_
6	standard	standard	JJ	_	_	_
7	normalization	normalization	NN	_	_	_
8	probes	probe	NNS	_	_	_
9	present	present	JJ	_	_	_
10	on	on	IN	_	_	_
11	the	the	DT	_	_	_
12	Affymetrix	Affymetrix	NNP	_	_	_
13	GeneChip	GeneChip	NNP	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	K-12	k-12	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Exponential	exponential	JJ	_	_	_
7	cultures	culture	NNS	_	_	_
8	of	of	IN	_	_	_
9	transformants	transformant	NNS	_	_	_
10	were	be	VBD	_	_	_
11	inoculated	inoculate	VBN	_	_	_
12	from	from	IN	_	_	_
13	fresh	fresh	JJ	_	_	_
14	overnight	overnight	JJ	_	_	_
15	cultures	culture	NNS	_	_	_
16	in	in	IN	_	_	_
17	LB	lb	NN	MED	_	_
18	medium	medium	NN	MED	_	_
19	supplemented	supplement	VBN	_	_	_
20	with	with	IN	_	_	_
21	25	25	CD	_	_	_
22	µg	µg	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	genotype	genotype	NN	_	_	_
25	:	:	:	_	_	_
26	Δ	δ	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	genotype	genotype	NN	_	_	_
32	:	:	:	_	_	_
33	Δ	δ	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	ΔleuO	δleuo	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	genotype	genotype	NN	_	_	_
40	:	:	:	_	_	_
41	Δ	δ	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	ΔrcsB	δrcsb	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	K12	k12	NN	_	_	_
48	Δ	δ	NN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	+	+	CC	_	_	_
53	ctrl	ctrl	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	K12	k12	NN	_	_	_
56	Δ	δ	NN	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	+	+	CC	_	_	_
61	ctrl	ctrl	NN	_	_	_
62	,	,	,	_	_	_
63	biological	biological	JJ	_	_	_
64	replicate	replicate	VB	_	_	_
65	1	1	CD	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	K12	k12	NN	_	_	_
68	Δ	δ	NN	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	+	+	CC	_	_	_
73	ctrl	ctrl	NN	_	_	_
74	,	,	,	_	_	_
75	biological	biological	JJ	_	_	_
76	replicate	replicate	VB	_	_	_
77	2	2	CD	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
79	K12	k12	NN	_	_	_
80	Δ	δ	NN	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
83	-RRB-	-rrb-	-RRB-	_	_	_
84	+	+	CC	_	_	_
85	ctrl	ctrl	NN	_	_	_
86	,	,	,	_	_	_
87	biological	biological	JJ	_	_	_
88	replicate	replicate	VB	_	_	_
89	3	3	CD	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	K12	k12	NN	_	_	_
92	Δ	δ	NN	_	_	_
93	-LRB-	-lrb-	-LRB-	_	_	_
94	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	+	+	CC	_	_	_
97	ctrl	ctrl	NN	_	_	_
98	,	,	,	_	_	_
99	biological	biological	JJ	_	_	_
100	replicate	replicate	VB	_	_	_
101	4	4	CD	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
103	K12	k12	NN	_	_	_
104	Δ	δ	NN	_	_	_
105	-LRB-	-lrb-	-LRB-	_	_	_
106	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
107	-RRB-	-rrb-	-RRB-	_	_	_
108	+	+	CC	_	_	_
109	pBglJ	pbglj	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	K12Δ	k12δ	NN	_	_	_
112	-LRB-	-lrb-	-LRB-	_	_	_
113	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
114	-RRB-	-rrb-	-RRB-	_	_	_
115	+	+	CC	_	_	_
116	pBglJ	pbglj	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	K12	k12	NN	_	_	_
119	Δ	δ	NN	_	_	_
120	-LRB-	-lrb-	-LRB-	_	_	_
121	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
122	-RRB-	-rrb-	-RRB-	_	_	_
123	+	+	CC	_	_	_
124	pBglJ	pbglj	NN	_	_	_
125	,	,	,	_	_	_
126	biological	biological	JJ	_	_	_
127	replicate	replicate	VB	_	_	_
128	1	1	CD	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	K12	k12	NN	_	_	_
131	Δ	δ	NN	_	_	_
132	-LRB-	-lrb-	-LRB-	_	_	_
133	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
134	-RRB-	-rrb-	-RRB-	_	_	_
135	+	+	CC	_	_	_
136	pBglJ	pbglj	NN	_	_	_
137	,	,	,	_	_	_
138	biological	biological	JJ	_	_	_
139	replicate	replicate	VB	_	_	_
140	2	2	CD	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
142	K12Δ	k12δ	NN	_	_	_
143	-LRB-	-lrb-	-LRB-	_	_	_
144	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
145	-RRB-	-rrb-	-RRB-	_	_	_
146	+	+	CC	_	_	_
147	pBglJ	pbglj	NN	_	_	_
148	,	,	,	_	_	_
149	biological	biological	JJ	_	_	_
150	replicate	replicate	VB	_	_	_
151	3	3	CD	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	K12	k12	NN	_	_	_
154	Δ	δ	NN	_	_	_
155	-LRB-	-lrb-	-LRB-	_	_	_
156	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
157	-RRB-	-rrb-	-RRB-	_	_	_
158	+	+	CC	_	_	_
159	pBglJ	pbglj	NN	_	_	_
160	,	,	,	_	_	_
161	biological	biological	JJ	_	_	_
162	replicate	replicate	VB	_	_	_
163	4	4	CD	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
165	K12	k12	NN	_	_	_
166	Δ	δ	NN	_	_	_
167	-LRB-	-lrb-	-LRB-	_	_	_
168	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
169	-RRB-	-rrb-	-RRB-	_	_	_
170	+	+	CC	_	_	_
171	pLeuO	pleuo	NN	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	K12	k12	NN	_	_	_
174	Δ	δ	NN	_	_	_
175	-LRB-	-lrb-	-LRB-	_	_	_
176	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
177	-RRB-	-rrb-	-RRB-	_	_	_
178	+	+	CC	_	_	_
179	pLeuO	pleuo	NN	_	_	_
180	,	,	,	_	_	_
181	biological	biological	JJ	_	_	_
182	replicate	replicate	VB	_	_	_
183	1	1	CD	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	K12	k12	NN	_	_	_
186	Δ	δ	NN	_	_	_
187	-LRB-	-lrb-	-LRB-	_	_	_
188	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
189	-RRB-	-rrb-	-RRB-	_	_	_
190	+	+	CC	_	_	_
191	pLeuO	pleuo	NN	_	_	_
192	,	,	,	_	_	_
193	biological	biological	JJ	_	_	_
194	replicate	replicate	VB	_	_	_
195	2	2	CD	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
197	K12	k12	NN	_	_	_
198	Δ	δ	NN	_	_	_
199	-LRB-	-lrb-	-LRB-	_	_	_
200	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
201	-RRB-	-rrb-	-RRB-	_	_	_
202	+	+	CC	_	_	_
203	pLeuO	pleuo	NN	_	_	_
204	,	,	,	_	_	_
205	biological	biological	JJ	_	_	_
206	replicate	replicate	VB	_	_	_
207	3	3	CD	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	K12	k12	NN	_	_	_
210	Δ	δ	NN	_	_	_
211	-LRB-	-lrb-	-LRB-	_	_	_
212	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
213	-RRB-	-rrb-	-RRB-	_	_	_
214	+	+	CC	_	_	_
215	pLeuO	pleuo	NN	_	_	_
216	,	,	,	_	_	_
217	biological	biological	JJ	_	_	_
218	replicate	replicate	VB	_	_	_
219	4	4	CD	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
221	K12	k12	NN	_	_	_
222	Δ	δ	NN	_	_	_
223	-LRB-	-lrb-	-LRB-	_	_	_
224	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
225	-RRB-	-rrb-	-RRB-	_	_	_
226	ΔleuO	δleuo	NN	_	_	_
227	+	+	CC	_	_	_
228	ctrl	ctrl	NN	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
230	K12	k12	NN	_	_	_
231	Δ	δ	NN	_	_	_
232	-LRB-	-lrb-	-LRB-	_	_	_
233	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
234	-RRB-	-rrb-	-RRB-	_	_	_
235	ΔleuO	δleuo	NN	_	_	_
236	+	+	CC	_	_	_
237	ctrl	ctrl	NN	_	_	_
238	,	,	,	_	_	_
239	biological	biological	JJ	_	_	_
240	replicate	replicate	VB	_	_	_
241	1	1	CD	_	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
243	K12	k12	NN	_	_	_
244	Δ	δ	NN	_	_	_
245	-LRB-	-lrb-	-LRB-	_	_	_
246	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
247	-RRB-	-rrb-	-RRB-	_	_	_
248	ΔleuO	δleuo	NN	_	_	_
249	+	+	CC	_	_	_
250	ctrl	ctrl	NN	_	_	_
251	,	,	,	_	_	_
252	biological	biological	JJ	_	_	_
253	replicate	replicate	VB	_	_	_
254	2	2	CD	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
256	K12	k12	NN	_	_	_
257	Δ	δ	NN	_	_	_
258	-LRB-	-lrb-	-LRB-	_	_	_
259	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
260	-RRB-	-rrb-	-RRB-	_	_	_
261	ΔleuO	δleuo	NN	_	_	_
262	+	+	CC	_	_	_
263	ctrl	ctrl	NN	_	_	_
264	,	,	,	_	_	_
265	biological	biological	JJ	_	_	_
266	replicate	replicate	VB	_	_	_
267	3	3	CD	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	K12	k12	NN	_	_	_
270	Δ	δ	NN	_	_	_
271	-LRB-	-lrb-	-LRB-	_	_	_
272	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
273	-RRB-	-rrb-	-RRB-	_	_	_
274	ΔleuO	δleuo	NN	_	_	_
275	+	+	CC	_	_	_
276	ctrl	ctrl	NN	_	_	_
277	,	,	,	_	_	_
278	biological	biological	JJ	_	_	_
279	replicate	replicate	VB	_	_	_
280	4	4	CD	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
282	K12	k12	NN	_	_	_
283	Δ	δ	NN	_	_	_
284	-LRB-	-lrb-	-LRB-	_	_	_
285	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
286	-RRB-	-rrb-	-RRB-	_	_	_
287	ΔleuO	δleuo	NN	_	_	_
288	+	+	CC	_	_	_
289	pBglJ	pbglj	NN	_	_	_
290	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
291	K12	k12	NN	_	_	_
292	Δ	δ	NN	_	_	_
293	-LRB-	-lrb-	-LRB-	_	_	_
294	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
295	-RRB-	-rrb-	-RRB-	_	_	_
296	ΔleuO	δleuo	NN	_	_	_
297	+	+	CC	_	_	_
298	pBglJ	pbglj	NN	_	_	_
299	,	,	,	_	_	_
300	biological	biological	JJ	_	_	_
301	replicate	replicate	VB	_	_	_
302	1	1	CD	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
304	K12	k12	NN	_	_	_
305	Δ	δ	NN	_	_	_
306	-LRB-	-lrb-	-LRB-	_	_	_
307	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
308	-RRB-	-rrb-	-RRB-	_	_	_
309	ΔleuO	δleuo	NN	_	_	_
310	+	+	CC	_	_	_
311	pBglJ	pbglj	NN	_	_	_
312	,	,	,	_	_	_
313	biological	biological	JJ	_	_	_
314	replicate	replicate	VB	_	_	_
315	2	2	CD	_	_	_
316	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
317	K12	k12	NN	_	_	_
318	Δ	δ	NN	_	_	_
319	-LRB-	-lrb-	-LRB-	_	_	_
320	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
321	-RRB-	-rrb-	-RRB-	_	_	_
322	ΔleuO	δleuo	NN	_	_	_
323	+	+	CC	_	_	_
324	pBglJ	pbglj	NN	_	_	_
325	,	,	,	_	_	_
326	biological	biological	JJ	_	_	_
327	replicate	replicate	VB	_	_	_
328	3	3	CD	_	_	_
329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
330	K12	k12	NN	_	_	_
331	Δ	δ	NN	_	_	_
332	-LRB-	-lrb-	-LRB-	_	_	_
333	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
334	-RRB-	-rrb-	-RRB-	_	_	_
335	ΔleuO	δleuo	NN	_	_	_
336	+	+	CC	_	_	_
337	pBglJ	pbglj	NN	_	_	_
338	,	,	,	_	_	_
339	biological	biological	JJ	_	_	_
340	replicate	replicate	VB	_	_	_
341	4	4	CD	_	_	_
342	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
343	K12	k12	NN	_	_	_
344	Δ	δ	NN	_	_	_
345	-LRB-	-lrb-	-LRB-	_	_	_
346	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
347	-RRB-	-rrb-	-RRB-	_	_	_
348	ΔrcsB	δrcsb	NN	_	_	_
349	+	+	CC	_	_	_
350	ctrl	ctrl	NN	_	_	_
351	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
352	K12	k12	NN	_	_	_
353	Δ	δ	NN	_	_	_
354	-LRB-	-lrb-	-LRB-	_	_	_
355	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
356	-RRB-	-rrb-	-RRB-	_	_	_
357	ΔrcsB	δrcsb	NN	_	_	_
358	+	+	CC	_	_	_
359	ctrl	ctrl	NN	_	_	_
360	,	,	,	_	_	_
361	biological	biological	JJ	_	_	_
362	replicate	replicate	VB	_	_	_
363	1	1	CD	_	_	_
364	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
365	K12	k12	NN	_	_	_
366	Δ	δ	NN	_	_	_
367	-LRB-	-lrb-	-LRB-	_	_	_
368	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
369	-RRB-	-rrb-	-RRB-	_	_	_
370	ΔrcsB	δrcsb	NN	_	_	_
371	+	+	CC	_	_	_
372	ctrl	ctrl	NN	_	_	_
373	,	,	,	_	_	_
374	biological	biological	JJ	_	_	_
375	replicate	replicate	VB	_	_	_
376	2	2	CD	_	_	_
377	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
378	K12	k12	NN	_	_	_
379	Δ	δ	NN	_	_	_
380	-LRB-	-lrb-	-LRB-	_	_	_
381	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
382	-RRB-	-rrb-	-RRB-	_	_	_
383	ΔrcsB	δrcsb	NN	_	_	_
384	+	+	CC	_	_	_
385	ctrl	ctrl	NN	_	_	_
386	,	,	,	_	_	_
387	biological	biological	JJ	_	_	_
388	replicate	replicate	VB	_	_	_
389	3	3	CD	_	_	_
390	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
391	K12	k12	NN	_	_	_
392	Δ	δ	NN	_	_	_
393	-LRB-	-lrb-	-LRB-	_	_	_
394	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
395	-RRB-	-rrb-	-RRB-	_	_	_
396	ΔrcsB	δrcsb	NN	_	_	_
397	+	+	CC	_	_	_
398	ctrl	ctrl	NN	_	_	_
399	,	,	,	_	_	_
400	biological	biological	JJ	_	_	_
401	replicate	replicate	VB	_	_	_
402	4	4	CD	_	_	_
403	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
404	K12	k12	NN	_	_	_
405	Δ	δ	NN	_	_	_
406	-LRB-	-lrb-	-LRB-	_	_	_
407	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
408	-RRB-	-rrb-	-RRB-	_	_	_
409	ΔrcsB	δrcsb	NN	_	_	_
410	+	+	CC	_	_	_
411	pBglJ	pbglj	NN	_	_	_
412	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
413	K12	k12	NN	_	_	_
414	Δ	δ	NN	_	_	_
415	-LRB-	-lrb-	-LRB-	_	_	_
416	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
417	-RRB-	-rrb-	-RRB-	_	_	_
418	ΔrcsB	δrcsb	NN	_	_	_
419	+	+	CC	_	_	_
420	pBglJ	pbglj	NN	_	_	_
421	,	,	,	_	_	_
422	biological	biological	JJ	_	_	_
423	replicate	replicate	VB	_	_	_
424	1	1	CD	_	_	_
425	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
426	K12	k12	NN	_	_	_
427	Δ	δ	NN	_	_	_
428	-LRB-	-lrb-	-LRB-	_	_	_
429	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
430	-RRB-	-rrb-	-RRB-	_	_	_
431	ΔrcsB	δrcsb	NN	_	_	_
432	+	+	CC	_	_	_
433	pBglJ	pbglj	NN	_	_	_
434	,	,	,	_	_	_
435	biological	biological	JJ	_	_	_
436	replicate	replicate	VB	_	_	_
437	2	2	CD	_	_	_
438	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
439	K12	k12	NN	_	_	_
440	Δ	δ	NN	_	_	_
441	-LRB-	-lrb-	-LRB-	_	_	_
442	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
443	-RRB-	-rrb-	-RRB-	_	_	_
444	ΔrcsB	δrcsb	NN	_	_	_
445	+	+	CC	_	_	_
446	pBglJ	pbglj	NN	_	_	_
447	,	,	,	_	_	_
448	biological	biological	JJ	_	_	_
449	replicate	replicate	VB	_	_	_
450	3	3	CD	_	_	_
451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
452	K12	k12	NN	_	_	_
453	Δ	δ	NN	_	_	_
454	-LRB-	-lrb-	-LRB-	_	_	_
455	yjjP-yjjQ-bglJ	yjjp-yjjq-bglj	NN	_	_	_
456	-RRB-	-rrb-	-RRB-	_	_	_
457	ΔrcsB	δrcsb	NN	_	_	_
458	+	+	CC	_	_	_
459	pBglJ	pbglj	NN	_	_	_
460	,	,	,	_	_	_
461	biological	biological	JJ	_	_	_
462	replicate	replicate	VB	_	_	_
463	4	4	CD	_	_	_
464	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
465	overexpression	overexpression	NN	_	_	_
466	:	:	:	_	_	_
467	-	-	:	_	_	_
468	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
469	overexpression	overexpression	NN	_	_	_
470	:	:	:	_	_	_
471	BglJ	bglj	NN	_	_	_
472	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
473	overexpression	overexpression	NN	_	_	_
474	:	:	:	_	_	_
475	LeuO	leuo	NN	TF	_	_
476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
477	plasmid	plasmid	NN	_	_	_
478	:	:	:	_	_	_
479	pKEDR13	pkedr13	NN	_	_	_
480	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
481	plasmid	plasmid	NN	_	_	_
482	:	:	:	_	_	_
483	pKESK22	pkesk22	NN	_	_	_
484	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
485	plasmid	plasmid	NN	_	_	_
486	:	:	:	_	_	_
487	pKETS1	pkets1	NN	_	_	_
488	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
489	sample	sample	NN	_	_	_
490	id	id	NN	_	_	_
491	:	:	:	_	_	_
492	1a	1a	NN	_	_	_
493	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
494	sample	sample	NN	_	_	_
495	id	id	NN	_	_	_
496	:	:	:	_	_	_
497	1b	1b	CD	_	_	_
498	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
499	sample	sample	NN	_	_	_
500	id	id	NN	_	_	_
501	:	:	:	_	_	_
502	1c	1c	NN	_	_	_
503	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
504	sample	sample	NN	_	_	_
505	id	id	NN	_	_	_
506	:	:	:	_	_	_
507	1d	1d	CD	_	_	_
508	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
509	sample	sample	NN	_	_	_
510	id	id	NN	_	_	_
511	:	:	:	_	_	_
512	2a	2a	NN	_	_	_
513	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
514	sample	sample	NN	_	_	_
515	id	id	NN	_	_	_
516	:	:	:	_	_	_
517	2b	2b	JJ	_	_	_
518	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
519	sample	sample	NN	_	_	_
520	id	id	NN	_	_	_
521	:	:	:	_	_	_
522	2c	2c	JJ	_	_	_
523	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
524	sample	sample	NN	_	_	_
525	id	id	NN	_	_	_
526	:	:	:	_	_	_
527	2d	2d	JJ	_	_	_
528	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
529	sample	sample	NN	_	_	_
530	id	id	NN	_	_	_
531	:	:	:	_	_	_
532	3a	3a	NN	_	_	_
533	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
534	sample	sample	NN	_	_	_
535	id	id	NN	_	_	_
536	:	:	:	_	_	_
537	3b	3b	CD	_	_	_
538	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
539	sample	sample	NN	_	_	_
540	id	id	NN	_	_	_
541	:	:	:	_	_	_
542	3c	3c	NN	_	_	_
543	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
544	sample	sample	NN	_	_	_
545	id	id	NN	_	_	_
546	:	:	:	_	_	_
547	3d	3d	JJ	_	_	_
548	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
549	sample	sample	NN	_	_	_
550	id	id	NN	_	_	_
551	:	:	:	_	_	_
552	4a	4a	NN	_	_	_
553	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
554	sample	sample	NN	_	_	_
555	id	id	NN	_	_	_
556	:	:	:	_	_	_
557	4b	4b	NN	_	_	_
558	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
559	sample	sample	NN	_	_	_
560	id	id	NN	_	_	_
561	:	:	:	_	_	_
562	4c	4c	NN	_	_	_
563	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
564	sample	sample	NN	_	_	_
565	id	id	NN	_	_	_
566	:	:	:	_	_	_
567	4d	4d	NN	_	_	_
568	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
569	sample	sample	NN	_	_	_
570	id	id	NN	_	_	_
571	:	:	:	_	_	_
572	5a	5a	NN	_	_	_
573	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
574	sample	sample	NN	_	_	_
575	id	id	NN	_	_	_
576	:	:	:	_	_	_
577	5b	5b	NN	_	_	_
578	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
579	sample	sample	NN	_	_	_
580	id	id	NN	_	_	_
581	:	:	:	_	_	_
582	5c	5c	NN	_	_	_
583	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
584	sample	sample	NN	_	_	_
585	id	id	NN	_	_	_
586	:	:	:	_	_	_
587	5d	5d	JJ	_	_	_
588	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
589	sample	sample	NN	_	_	_
590	id	id	NN	_	_	_
591	:	:	:	_	_	_
592	6a	6a	FW	_	_	_
593	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
594	sample	sample	NN	_	_	_
595	id	id	NN	_	_	_
596	:	:	:	_	_	_
597	6b	6b	JJ	_	_	_
598	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
599	sample	sample	NN	_	_	_
600	id	id	NN	_	_	_
601	:	:	:	_	_	_
602	6c	6c	JJ	_	_	_
603	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
604	sample	sample	NN	_	_	_
605	id	id	NN	_	_	_
606	:	:	:	_	_	_
607	6d	6d	JJ	_	_	_
608	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
609	sample	sample	NN	_	_	_
610	id	id	NN	_	_	_
611	:	:	:	_	_	_
612	7a	7a	NN	_	_	_
613	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
614	sample	sample	NN	_	_	_
615	id	id	NN	_	_	_
616	:	:	:	_	_	_
617	7b	7b	CD	_	_	_
618	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
619	sample	sample	NN	_	_	_
620	id	id	NN	_	_	_
621	:	:	:	_	_	_
622	7c	7c	CD	_	_	_
623	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
624	sample	sample	NN	_	_	_
625	id	id	NN	_	_	_
626	:	:	:	_	_	_
627	7d	7d	CD	_	_	_
628	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
629	strain	strain	NN	_	_	_
630	:	:	:	_	_	_
631	T175	t175	NN	_	_	_
632	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
633	strain	strain	NN	_	_	_
634	:	:	:	_	_	_
635	T177	t177	NN	_	_	_
636	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
637	strain	strain	NN	_	_	_
638	:	:	:	_	_	_
639	T75	t75	NN	_	_	_
640	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
641	control	control	NN	_	_	_
642	,	,	,	_	_	_
643	biological	biological	JJ	_	_	_
644	rep1	rep1	NN	_	_	_
645	C1	c1	NN	_	_	_
646	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
647	control	control	NN	_	_	_
648	,	,	,	_	_	_
649	biological	biological	JJ	_	_	_
650	rep1	rep1	NN	_	_	_
651	C2	c2	NN	_	_	_
652	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
653	control	control	NN	_	_	_
654	,	,	,	_	_	_
655	biological	biological	JJ	_	_	_
656	rep1	rep1	NN	_	_	_
657	C3	c3	NN	_	_	_
658	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
659	control	control	NN	_	_	_
660	,	,	,	_	_	_
661	biological	biological	JJ	_	_	_
662	rep2	rep2	NN	_	_	_
663	C4	c4	NN	_	_	_
664	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
665	control	control	NN	_	_	_
666	,	,	,	_	_	_
667	biological	biological	JJ	_	_	_
668	rep2	rep2	NN	_	_	_
669	C5	c5	NN	_	_	_
670	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
671	control	control	NN	_	_	_
672	,	,	,	_	_	_
673	biological	biological	JJ	_	_	_
674	rep2	rep2	NN	_	_	_
675	C6	c6	NN	_	_	_
676	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
677	E.coli	e.coli	NNS	_	_	_
678	,	,	,	_	_	_
679	grown	grow	VBN	_	_	_
680	in	in	IN	_	_	_
681	LB	lb	NN	_	_	_
682	+	+	CC	_	_	_
683	glycerol	glycerol	NN	SUPP	_	_
684	to0	to0	NN	_	_	_
685	.8	.8	CD	_	_	_
686	OD	od	NN	_	_	_
687	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
688	E.coli	e.coli	NNS	_	_	_
689	,	,	,	_	_	_
690	grown	grow	VBN	_	_	_
691	in	in	IN	_	_	_
692	LB	lb	NN	_	_	_
693	to0	to0	NN	_	_	_
694	.8	.8	CD	_	_	_
695	OD	od	NN	_	_	_
696	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
697	Escherichia	escherichia	FW	Organism	_	_
698	coli	coli	FW	Organism	_	_
699	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
700	Escherichia	escherichia	FW	Organism	_	_
701	coli	coli	FW	Organism	_	_
702	was	be	VBD	_	_	_
703	grown	grow	VBN	_	_	_
704	aerobically	aerobically	RB	_	_	_
705	in	in	IN	_	_	_
706	Luria-Bertani	Luria-Bertani	NNP	_	_	_
707	-LRB-	-lrb-	-LRB-	_	_	_
708	LB	LB	NNP	_	_	_
709	-RRB-	-rrb-	-RRB-	_	_	_
710	broth	broth	NN	_	_	_
711	at	at	IN	_	_	_
712	30	30	CD	_	_	_
713	°C	°c	NN	_	_	_
714	in	in	IN	_	_	_
715	an	a	DT	_	_	_
716	incubator	incubator	NN	_	_	_
717	shaker	shaker	NN	_	_	_
718	at	at	IN	_	_	_
719	150	150	CD	_	_	_
720	r.p.m.	r.p.m.	NN	_	_	_
721	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
722	Experimental	experimental	JJ	_	_	_
723	,	,	,	_	_	_
724	biological	biological	JJ	_	_	_
725	rep1	rep1	NN	_	_	_
726	G1	g1	NN	_	_	_
727	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
728	Experimental	experimental	JJ	_	_	_
729	,	,	,	_	_	_
730	biological	biological	JJ	_	_	_
731	rep1	rep1	NN	_	_	_
732	G2	g2	NN	_	_	_
733	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
734	Experimental	experimental	JJ	_	_	_
735	,	,	,	_	_	_
736	biological	biological	JJ	_	_	_
737	rep1	rep1	NN	_	_	_
738	G3	g3	NN	_	_	_
739	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
740	Experimental	experimental	JJ	_	_	_
741	,	,	,	_	_	_
742	biological	biological	JJ	_	_	_
743	rep2	rep2	NN	_	_	_
744	G4	g4	NN	_	_	_
745	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
746	Experimental	experimental	JJ	_	_	_
747	,	,	,	_	_	_
748	biological	biological	JJ	_	_	_
749	rep2	rep2	NN	_	_	_
750	G5	g5	NN	_	_	_
751	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
752	Experimental	experimental	JJ	_	_	_
753	,	,	,	_	_	_
754	biological	biological	JJ	_	_	_
755	rep2	rep2	NN	_	_	_
756	G6	g6	NN	_	_	_
757	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
758	growth	growth	NN	_	_	_
759	medium	medium	NN	_	_	_
760	:	:	:	_	_	_
761	LB	lb	NN	_	_	_
762	+	+	CC	_	_	_
763	glycerol	glycerol	NN	SUPP	_	_
764	medium	medium	NN	_	_	_
765	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
766	growth	growth	NN	_	_	_
767	medium	medium	NN	_	_	_
768	:	:	:	_	_	_
769	LB	lb	NN	MED	_	_
770	medium	medium	NN	MED	_	_
771	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
772	RNA	rna	NN	_	_	_
773	was	be	VBD	_	_	_
774	isolated	isolate	VBN	_	_	_
775	from	from	IN	_	_	_
776	the	the	DT	_	_	_
777	culture	culture	NN	_	_	_
778	by	by	IN	_	_	_
779	using	use	VBG	_	_	_
780	the	the	DT	_	_	_
781	Qiagen	Qiagen	NNP	_	_	_
782	RNeasy	RNeasy	NNP	_	_	_
783	mini-prep	mini-prep	NN	_	_	_
784	kit.cDNA	kit.cdna	NN	_	_	_
785	was	be	VBD	_	_	_
786	synthesized	synthesize	VBN	_	_	_
787	using	use	VBG	_	_	_
788	5-10	5-10	CD	_	_	_
789	µg	µg	NN	_	_	_
790	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
791	strain	strain	NN	_	_	_
792	:	:	:	_	_	_
793	Escherichia	escherichia	FW	Organism	_	_
794	coli	coli	FW	Organism	_	_
795	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
796	The	the	DT	_	_	_
797	intensity	intensity	NN	_	_	_
798	cell	cell	NN	_	_	_
799	files	file	NNS	_	_	_
800	were	be	VBD	_	_	_
801	then	then	RB	_	_	_
802	imported	import	VBN	_	_	_
803	,	,	,	_	_	_
804	normalized	normalize	VBN	_	_	_
805	for	for	IN	_	_	_
806	background	background	NN	_	_	_
807	correction	correction	NN	_	_	_
808	using	use	VBG	_	_	_
809	PLIER	plier	NN	_	_	_
810	and	and	CC	_	_	_
811	data	datum	NNS	_	_	_
812	analysed	analyse	VBN	_	_	_
813	using	use	VBG	_	_	_
814	Gene	Gene	NNP	_	_	_
815	Spring	Spring	NNP	_	_	_
816	11.5	11.5	CD	_	_	_
817	software	software	NN	_	_	_
818	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	To	to	TO	_	_	_
3	study	study	VB	_	_	_
4	gene	gene	NN	_	_	_
5	expression	expression	NN	_	_	_
6	in	in	IN	_	_	_
7	the	the	DT	_	_	_
8	presence	presence	NN	_	_	_
9	and	and	CC	_	_	_
10	absence	absence	NN	_	_	_
11	of	of	IN	_	_	_
12	glycerol	glycerol	NN	SUPP	_	_
13	,	,	,	_	_	_
14	LB	lb	NN	_	_	_
15	was	be	VBD	_	_	_
16	supplemented	supplement	VBN	_	_	_
17	with	with	IN	_	_	_
18	10	10	CD	_	_	_
19	%	%	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	v	v	LS	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	At	at	IN	_	_	_
24	OD450	od450	NN	_	_	_
25	=	=	JJ	_	_	_
26	0.3	0.3	CD	_	_	_
27	,	,	,	_	_	_
28	cultures	culture	NNS	_	_	_
29	induced	induce	VBN	_	_	_
30	with	with	IN	_	_	_
31	1	1	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	IPTG	iptg	NN	_	_	_
34	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	harvested	harvest	VBD	_	_	_
3	0	0	CD	_	_	_
4	min	min	NN	_	_	_
5	after	after	IN	_	_	_
6	induction	induction	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	At	at	IN	_	_	_
9	OD450	od450	NN	_	_	_
10	=	=	JJ	_	_	_
11	0.3	0.3	CD	_	_	_
12	,	,	,	_	_	_
13	cultures	culture	NNS	_	_	_
14	induced	induce	VBN	_	_	_
15	with	with	IN	_	_	_
16	1	1	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	IPTG	iptg	NN	_	_	_
19	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	harvested	harvest	VBD	_	_	_
3	10	10	CD	_	_	_
4	min	min	NN	_	_	_
5	after	after	IN	_	_	_
6	induction	induction	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	At	at	IN	_	_	_
9	OD450	od450	NN	_	_	_
10	=	=	JJ	_	_	_
11	0.3	0.3	CD	_	_	_
12	,	,	,	_	_	_
13	cultures	culture	NNS	_	_	_
14	induced	induce	VBN	_	_	_
15	with	with	IN	_	_	_
16	1	1	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	IPTG	iptg	NN	_	_	_
19	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	harvested	harvest	VBN	_	_	_
3	15	15	CD	_	_	_
4	min	min	NN	_	_	_
5	after	after	IN	_	_	_
6	induction	induction	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	At	at	IN	_	_	_
9	OD450	od450	NN	_	_	_
10	=	=	JJ	_	_	_
11	0.3	0.3	CD	_	_	_
12	,	,	,	_	_	_
13	cultures	culture	NNS	_	_	_
14	induced	induce	VBN	_	_	_
15	with	with	IN	_	_	_
16	1	1	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	IPTG	iptg	NN	_	_	_
19	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	harvested	harvest	VBN	_	_	_
3	20	20	CD	_	_	_
4	min	min	NN	_	_	_
5	after	after	IN	_	_	_
6	induction	induction	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	At	at	IN	_	_	_
9	OD450	od450	NN	_	_	_
10	=	=	JJ	_	_	_
11	0.3	0.3	CD	_	_	_
12	,	,	,	_	_	_
13	cultures	culture	NNS	_	_	_
14	induced	induce	VBN	_	_	_
15	with	with	IN	_	_	_
16	1	1	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	IPTG	iptg	NN	_	_	_
19	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	harvested	harvest	VBN	_	_	_
3	2.5	2.5	CD	_	_	_
4	min	min	NN	_	_	_
5	after	after	IN	_	_	_
6	induction	induction	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	At	at	IN	_	_	_
9	OD450	od450	NN	_	_	_
10	=	=	JJ	_	_	_
11	0.3	0.3	CD	_	_	_
12	,	,	,	_	_	_
13	cultures	culture	NNS	_	_	_
14	induced	induce	VBN	_	_	_
15	with	with	IN	_	_	_
16	1	1	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	IPTG	iptg	NN	_	_	_
19	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	harvested	harvest	VBN	_	_	_
3	30	30	CD	_	_	_
4	min	min	NN	_	_	_
5	after	after	IN	_	_	_
6	induction	induction	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	At	at	IN	_	_	_
9	OD450	od450	NN	_	_	_
10	=	=	JJ	_	_	_
11	0.3	0.3	CD	_	_	_
12	,	,	,	_	_	_
13	cultures	culture	NNS	_	_	_
14	induced	induce	VBN	_	_	_
15	with	with	IN	_	_	_
16	1	1	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	IPTG	iptg	NN	_	_	_
19	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	harvested	harvest	VBN	_	_	_
3	5	5	CD	_	_	_
4	min	min	NN	_	_	_
5	after	after	IN	_	_	_
6	induction	induction	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	At	at	IN	_	_	_
9	OD450	od450	NN	_	_	_
10	=	=	JJ	_	_	_
11	0.3	0.3	CD	_	_	_
12	,	,	,	_	_	_
13	cultures	culture	NNS	_	_	_
14	induced	induce	VBN	_	_	_
15	with	with	IN	_	_	_
16	1	1	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	IPTG	iptg	NN	_	_	_
19	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	harvested	harvest	VBN	_	_	_
3	60	60	CD	_	_	_
4	min	min	NN	_	_	_
5	after	after	IN	_	_	_
6	induction	induction	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Culture	culture	NN	_	_	_
9	samples	sample	NNS	_	_	_
10	for	for	IN	_	_	_
11	microarray	microarray	NN	_	_	_
12	analysis	analysis	NN	_	_	_
13	were	be	VBD	_	_	_
14	added	add	VBN	_	_	_
15	to	to	TO	_	_	_
16	ice-cold	ice-cold	JJ	_	_	_
17	5	5	CD	_	_	_
18	%	%	NN	_	_	_
19	water-saturated	water-saturated	JJ	_	_	_
20	phenol	phenol	NN	_	_	_
21	in	in	IN	_	_	_
22	ethanol	ethanol	NN	_	_	_
23	solution	solution	NN	_	_	_
24	,	,	,	_	_	_
25	centrifuged	centrifuge	VBN	_	_	_
26	at	at	IN	_	_	_
27	6,600	6,600	CD	_	_	_
28	g	g	NN	_	_	_
29	and	and	CC	_	_	_
30	the	the	DT	_	_	_
31	cell	cell	NN	_	_	_
32	pellets	pellet	NNS	_	_	_
33	flash	flash	VBP	_	_	_
34	frozen	freeze	VBN	_	_	_
35	in	in	IN	_	_	_
36	liquid	liquid	JJ	_	_	_
37	N2	n2	NN	_	_	_
38	before	before	IN	_	_	_
39	storing	store	VBG	_	_	_
40	at	at	IN	_	_	_
41	-80	-80	CD	_	_	_
42	degrees	degree	NNS	_	_	_
43	C	c	NN	_	_	_
44	until	until	IN	_	_	_
45	required	require	VBN	_	_	_
46	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	from	from	IN	_	_	_
6	the	the	DT	_	_	_
7	stored	store	VBN	_	_	_
8	cell	cell	NN	_	_	_
9	pellets	pellet	NNS	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	hot	hot	JJ	_	_	_
13	phenol	phenol	NN	_	_	_
14	method	method	NN	_	_	_
15	,	,	,	_	_	_
16	and	and	CC	_	_	_
17	labeled	label	VBN	_	_	_
18	Cy3	cy3	NN	_	_	_
19	and	and	CC	_	_	_
20	Cy5	cy5	NN	_	_	_
21	cDNA	cdna	NN	_	_	_
22	was	be	VBD	_	_	_
23	prepared	prepare	VBN	_	_	_
24	from	from	IN	_	_	_
25	16	16	CD	_	_	_
26	ug	ug	NN	_	_	_
27	total	total	JJ	_	_	_
28	RNA	rna	NN	_	_	_
29	with	with	IN	_	_	_
30	10	10	CD	_	_	_
31	ug	ug	NN	_	_	_
32	random	random	JJ	_	_	_
33	hexamer	hexamer	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Integrated	Integrated	NNP	_	_	_
36	DNA	DNA	NNP	_	_	_
37	Technologies	Technologies	NNPS	_	_	_
38	,	,	,	_	_	_
39	Inc.	Inc.	NNP	_	_	_
40	,	,	,	_	_	_
41	Coralville	Coralville	NNP	_	_	_
42	,	,	,	_	_	_
43	IA	IA	NNP	_	_	_
44	,	,	,	_	_	_
45	USA	USA	NNP	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	filtered	filter	VBD	_	_	_
4	for	for	IN	_	_	_
5	PCR	pcr	NN	_	_	_
6	success	success	NN	_	_	_
7	,	,	,	_	_	_
8	>	>	JJR	_	_	_
9	3x	3x	NN	_	_	_
10	local	local	JJ	_	_	_
11	background	background	NN	_	_	_
12	and	and	CC	_	_	_
13	spot	spot	NN	_	_	_
14	quality	quality	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	GenePix	GenePix	NNP	_	_	_
17	Flag	Flag	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	Normalized	normalize	VBN	_	_	_
2	using	use	VBG	_	_	_
3	Lowess	Lowess	NNP	_	_	_
4	smoothing	smooth	VBG	_	_	_
5	from	from	IN	_	_	_
6	MA	MA	NNP	_	_	_
7	plot	plot	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	EC12n090	ec12n090	NN	_	_	_
10	RpoE	rpoe	NN	_	_	_
11	2.5	2.5	CD	_	_	_
12	min	min	NN	_	_	_
13	Time	Time	NNP	_	_	_
14	course	course	NN	_	_	_
15	4	4	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	EC12n091	ec12n091	NN	_	_	_
18	RpoE	rpoe	NN	_	_	_
19	5	5	CD	_	_	_
20	min	min	NN	_	_	_
21	Time	Time	NNP	_	_	_
22	course	course	NN	_	_	_
23	4	4	CD	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	EC12n092a	ec12n092a	NN	_	_	_
26	RpoE	rpoe	NN	_	_	_
27	10	10	CD	_	_	_
28	min	min	NN	_	_	_
29	Time	Time	NNP	_	_	_
30	course	course	NN	_	_	_
31	4	4	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	EC12n093	ec12n093	NN	_	_	_
34	RpoE	rpoe	NN	_	_	_
35	20	20	CD	_	_	_
36	min	min	NN	_	_	_
37	Time	Time	NNP	_	_	_
38	course	course	NN	_	_	_
39	4	4	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	EC12n094	ec12n094	NN	_	_	_
42	RpoE	rpoe	NN	_	_	_
43	30	30	CD	_	_	_
44	min	min	NN	_	_	_
45	Time	Time	NNP	_	_	_
46	course	course	NN	_	_	_
47	4	4	CD	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	EC12n095	ec12n095	NN	_	_	_
50	RpoE	rpoe	NN	_	_	_
51	60	60	CD	_	_	_
52	min	min	NN	_	_	_
53	Time	Time	NNP	_	_	_
54	course	course	NN	_	_	_
55	4	4	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	EC12n096	ec12n096	NN	_	_	_
58	RpoE	rpoe	NN	_	_	_
59	0	0	CD	_	_	_
60	min	min	NN	_	_	_
61	Time	Time	NNP	_	_	_
62	course	course	NN	_	_	_
63	4	4	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	EC12n101	ec12n101	NN	_	_	_
66	RpoE	rpoe	NN	_	_	_
67	0	0	CD	_	_	_
68	min	min	NN	_	_	_
69	Time	Time	NNP	_	_	_
70	course	course	NN	_	_	_
71	3	3	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	EC7n018	ec7n018	NN	_	_	_
74	RpoE	rpoe	NN	_	_	_
75	5	5	CD	_	_	_
76	min	min	NN	_	_	_
77	Time	Time	NNP	_	_	_
78	course	course	NN	_	_	_
79	1	1	CD	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	EC7n019	ec7n019	NN	_	_	_
82	RpoE	rpoe	NN	_	_	_
83	15	15	CD	_	_	_
84	min	min	NN	_	_	_
85	Time	Time	NNP	_	_	_
86	course	course	NN	_	_	_
87	1	1	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	EC7n065	ec7n065	NN	_	_	_
90	RpoE	rpoe	NN	_	_	_
91	5	5	CD	_	_	_
92	min	min	NN	_	_	_
93	Time	Time	NNP	_	_	_
94	course	course	NN	_	_	_
95	2	2	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	EC7n066	ec7n066	NN	_	_	_
98	RpoE	rpoe	NN	_	_	_
99	15	15	CD	_	_	_
100	min	min	NN	_	_	_
101	Time	Time	NNP	_	_	_
102	course	course	NN	_	_	_
103	2	2	CD	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	EC7n067	ec7n067	NN	_	_	_
106	RpoE	rpoe	NN	_	_	_
107	30	30	CD	_	_	_
108	min	min	NN	_	_	_
109	Time	Time	NNP	_	_	_
110	course	course	NN	_	_	_
111	2	2	CD	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	EC7n068	ec7n068	NN	_	_	_
114	RpoE	rpoe	NN	_	_	_
115	60	60	CD	_	_	_
116	min	min	NN	_	_	_
117	Time	Time	NNP	_	_	_
118	course	course	NN	_	_	_
119	2	2	CD	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	EC7n071	ec7n071	NN	_	_	_
122	RpoE	rpoe	NN	_	_	_
123	60	60	CD	_	_	_
124	min	min	NN	_	_	_
125	Time	Time	NNP	_	_	_
126	course	course	NN	_	_	_
127	1	1	CD	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	EC8n021	ec8n021	NN	_	_	_
130	RpoE	rpoe	NN	_	_	_
131	2.5	2.5	CD	_	_	_
132	min	min	NN	_	_	_
133	Time	Time	NNP	_	_	_
134	course	course	NN	_	_	_
135	3	3	CD	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	EC8n022	ec8n022	NN	_	_	_
138	RpoE	rpoe	NN	_	_	_
139	5	5	CD	_	_	_
140	min	min	NN	_	_	_
141	Time	Time	NNP	_	_	_
142	course	course	NN	_	_	_
143	3	3	CD	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	EC8n050	ec8n050	NN	_	_	_
146	RpoE	rpoe	NN	_	_	_
147	10	10	CD	_	_	_
148	min	min	NN	_	_	_
149	Time	Time	NNP	_	_	_
150	course	course	NN	_	_	_
151	3	3	CD	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	EC8n051	ec8n051	NN	_	_	_
154	RpoE	rpoe	NN	_	_	_
155	20	20	CD	_	_	_
156	min	min	NN	_	_	_
157	Time	Time	NNP	_	_	_
158	course	course	NN	_	_	_
159	3	3	CD	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	EC8n052	ec8n052	NN	_	_	_
162	RpoE	rpoe	NN	_	_	_
163	30	30	CD	_	_	_
164	min	min	NN	_	_	_
165	Time	Time	NNP	_	_	_
166	course	course	NN	_	_	_
167	3	3	CD	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	EC8n053	ec8n053	NN	_	_	_
170	RpoE	rpoe	NN	_	_	_
171	60	60	CD	_	_	_
172	min	min	NN	_	_	_
173	Time	Time	NNP	_	_	_
174	course	course	NN	_	_	_
175	3	3	CD	_	_	_
176	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
177	Escherichia	escherichia	FW	Organism	_	_
178	coli	coli	FW	Organism	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	M9	m9	NN	_	_	_
181	minimal	minimal	JJ	_	_	_
182	complete	complete	JJ	_	_	_
183	media	media	NNS	_	_	_
184	,	,	,	_	_	_
185	cultures	culture	NNS	_	_	_
186	grown	grow	VBN	_	_	_
187	aerobically	aerobically	RB	_	_	_
188	at	at	IN	_	_	_
189	30	30	CD	_	_	_
190	degrees	degree	NNS	_	_	_
191	C	c	NN	_	_	_
192	in	in	IN	_	_	_
193	a	a	DT	_	_	_
194	gyratory	gyratory	JJ	_	_	_
195	water	water	NN	_	_	_
196	bath	bath	NN	_	_	_
197	shaking	shake	VBG	_	_	_
198	at	at	IN	_	_	_
199	240	240	CD	_	_	_
200	rpm	rpm	NN	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	MG1655	mg1655	NN	_	_	_
203	rpoHp3	rpohp3	NN	Pr	_	_
204	:	:	:	_	_	_
205	:	:	:	_	_	_
206	lacZ	lacz	NN	GEN	_	_
207	delta	delta	NN	_	_	_
208	lacX74	lacx74	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	RpoE	rpoe	NN	_	_	_
211	induced	induce	VBN	_	_	_
212	-LRB-	-lrb-	-LRB-	_	_	_
213	0	0	CD	_	_	_
214	min	min	NN	_	_	_
215	-RRB-	-rrb-	-RRB-	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	RpoE	rpoe	NN	_	_	_
218	induced	induce	VBN	_	_	_
219	-LRB-	-lrb-	-LRB-	_	_	_
220	10	10	CD	_	_	_
221	min	min	NN	_	_	_
222	-RRB-	-rrb-	-RRB-	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	RpoE	rpoe	NN	_	_	_
225	induced	induce	VBN	_	_	_
226	-LRB-	-lrb-	-LRB-	_	_	_
227	15	15	CD	_	_	_
228	min	min	NN	_	_	_
229	-RRB-	-rrb-	-RRB-	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
231	RpoE	rpoe	NN	_	_	_
232	induced	induce	VBN	_	_	_
233	-LRB-	-lrb-	-LRB-	_	_	_
234	15	15	CD	_	_	_
235	min	min	NN	_	_	_
236	-RRB-	-rrb-	-RRB-	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	RpoE	rpoe	NN	_	_	_
239	induced	induce	VBN	_	_	_
240	-LRB-	-lrb-	-LRB-	_	_	_
241	20	20	CD	_	_	_
242	min	min	NN	_	_	_
243	-RRB-	-rrb-	-RRB-	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	RpoE	rpoe	NN	_	_	_
246	induced	induce	VBN	_	_	_
247	-LRB-	-lrb-	-LRB-	_	_	_
248	2.5	2.5	CD	_	_	_
249	min	min	NN	_	_	_
250	-RRB-	-rrb-	-RRB-	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	RpoE	rpoe	NN	_	_	_
253	induced	induce	VBN	_	_	_
254	-LRB-	-lrb-	-LRB-	_	_	_
255	30	30	CD	_	_	_
256	min	min	NN	_	_	_
257	-RRB-	-rrb-	-RRB-	_	_	_
258	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
259	RpoE	rpoe	NN	_	_	_
260	induced	induce	VBN	_	_	_
261	-LRB-	-lrb-	-LRB-	_	_	_
262	5	5	CD	_	_	_
263	min	min	NN	_	_	_
264	-RRB-	-rrb-	-RRB-	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	RpoE	rpoe	NN	_	_	_
267	induced	induce	VBN	_	_	_
268	-LRB-	-lrb-	-LRB-	_	_	_
269	5	5	CD	_	_	_
270	min	min	NN	_	_	_
271	-RRB-	-rrb-	-RRB-	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	RpoE	rpoe	NN	_	_	_
274	induced	induce	VBN	_	_	_
275	-LRB-	-lrb-	-LRB-	_	_	_
276	60	60	CD	_	_	_
277	min	min	NN	_	_	_
278	-RRB-	-rrb-	-RRB-	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	Wild	Wild	NNP	_	_	_
281	type	type	NN	_	_	_
282	control	control	NN	_	_	_
283	-LRB-	-lrb-	-LRB-	_	_	_
284	0	0	CD	_	_	_
285	min	min	NN	_	_	_
286	-RRB-	-rrb-	-RRB-	_	_	_
287	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
288	Wild	Wild	NNP	_	_	_
289	type	type	NN	_	_	_
290	control	control	NN	_	_	_
291	-LRB-	-lrb-	-LRB-	_	_	_
292	10	10	CD	_	_	_
293	min	min	NN	_	_	_
294	-RRB-	-rrb-	-RRB-	_	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	Wild	Wild	NNP	_	_	_
297	type	type	NN	_	_	_
298	control	control	NN	_	_	_
299	-LRB-	-lrb-	-LRB-	_	_	_
300	15	15	CD	_	_	_
301	min	min	NN	_	_	_
302	-RRB-	-rrb-	-RRB-	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
304	Wild	Wild	NNP	_	_	_
305	type	type	NN	_	_	_
306	control	control	NN	_	_	_
307	-LRB-	-lrb-	-LRB-	_	_	_
308	20	20	CD	_	_	_
309	min	min	NN	_	_	_
310	-RRB-	-rrb-	-RRB-	_	_	_
311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
312	Wild	Wild	NNP	_	_	_
313	type	type	NN	_	_	_
314	control	control	NN	_	_	_
315	-LRB-	-lrb-	-LRB-	_	_	_
316	2.5	2.5	CD	_	_	_
317	min	min	NN	_	_	_
318	-RRB-	-rrb-	-RRB-	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
320	Wild	Wild	NNP	_	_	_
321	type	type	NN	_	_	_
322	control	control	NN	_	_	_
323	-LRB-	-lrb-	-LRB-	_	_	_
324	30	30	CD	_	_	_
325	min	min	NN	_	_	_
326	-RRB-	-rrb-	-RRB-	_	_	_
327	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
328	Wild	Wild	NNP	_	_	_
329	type	type	NN	_	_	_
330	control	control	NN	_	_	_
331	-LRB-	-lrb-	-LRB-	_	_	_
332	5	5	CD	_	_	_
333	min	min	NN	_	_	_
334	-RRB-	-rrb-	-RRB-	_	_	_
335	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
336	Wild	Wild	NNP	_	_	_
337	type	type	NN	_	_	_
338	control	control	NN	_	_	_
339	-LRB-	-lrb-	-LRB-	_	_	_
340	60	60	CD	_	_	_
341	min	min	NN	_	_	_
342	-RRB-	-rrb-	-RRB-	_	_	_
343	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
344	E.	e.	FW	_	_	_
345	coli	coli	FW	_	_	_
346	-LSB-	-lsb-	-LRB-	_	_	_
347	K-12	k-12	NN	_	_	_
348	MG1655	mg1655	NN	_	_	_
349	strain	strain	NN	_	_	_
350	-LRB-	-lrb-	-LRB-	_	_	_
351	U00096	u00096	NN	_	_	_
352	.2	.2	NN	_	_	_
353	-RRB-	-rrb-	-RRB-	_	_	_
354	-RSB-	-rsb-	-RRB-	_	_	_
355	was	be	VBD	_	_	_
356	grown	grow	VBN	_	_	_
357	overnight	overnight	RB	_	_	_
358	at	at	IN	_	_	_
359	30	30	CD	_	_	_
360	°C	°c	NN	_	_	_
361	in	in	IN	_	_	_
362	LB	lb	NN	MED	_	_
363	medium	medium	NN	MED	_	_
364	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	resulting	result	VBG	_	_	_
3	culture	culture	NN	_	_	_
4	was	be	VBD	_	_	_
5	diluted	dilute	VBN	_	_	_
6	500-fold	500-fold	JJ	_	_	_
7	in	in	IN	_	_	_
8	fresh	fresh	JJ	_	_	_
9	LB	lb	NN	MED	_	_
10	medium	medium	NN	MED	_	_
11	and	and	CC	_	_	_
12	grown	grow	VBN	_	_	_
13	at	at	IN	_	_	_
14	30	30	CD	_	_	_
15	°C	°c	NN	_	_	_
16	for	for	IN	_	_	_
17	3.5	3.5	CD	_	_	_
18	hours	hour	NNS	_	_	_
19	such	such	JJ	_	_	_
20	that	that	IN	_	_	_
21	O.D.	O.D.	NNP	_	_	_
22	at	at	IN	_	_	_
23	600	600	CD	_	_	_
24	nm	nm	NN	_	_	_
25	became	become	VBD	_	_	_
26	0.30-0.35	0.30-0.35	CD	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	E	e	NN	_	_	_
3	_	_	CD	_	_	_
4	coli	coli	NN	_	_	_
5	_	_	NN	_	_	_
6	transcriptome	transcriptome	NN	_	_	_
7	_	_	NN	_	_	_
8	1	1	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	E	e	NN	_	_	_
11	_	_	CD	_	_	_
12	coli	coli	NN	_	_	_
13	_	_	NN	_	_	_
14	transcriptome	transcriptome	NN	_	_	_
15	_	_	NN	_	_	_
16	2	2	CD	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	Escherichia	escherichia	FW	Organism	_	_
19	coli	coli	FW	Organism	_	_
20	str	str	FW	_	_	_
21	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Genome	Genome	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	-LSB-	-lsb-	-LRB-	_	_	_
9	K-12	k-12	NN	_	_	_
10	MG1655	mg1655	NN	_	_	_
11	strain	strain	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	U00096	u00096	NN	_	_	_
14	.2	.2	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	genotype	genotype	NN	_	_	_
18	:	:	:	_	_	_
19	F	f	NN	_	_	_
20	-	-	:	_	_	_
21	,	,	,	_	_	_
22	lambda	lambda	NN	_	_	_
23	-	-	:	_	_	_
24	,	,	,	_	_	_
25	rph-1	rph-1	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	reference	reference	NN	_	_	_
28	genome	genome	NN	_	_	_
29	:	:	:	_	_	_
30	U00096	u00096	NN	_	_	_
31	.2	.2	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	RNA	rna	NN	_	_	_
34	from	from	IN	_	_	_
35	Escherichia	escherichia	FW	Organism	_	_
36	coli	coli	FW	Organism	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	RNA-Seq	rna-seq	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	RNA	rna	NN	_	_	_
41	was	be	VBD	_	_	_
42	purified	purify	VBN	_	_	_
43	by	by	IN	_	_	_
44	a	a	DT	_	_	_
45	standard	standard	JJ	_	_	_
46	protocol	protocol	NN	_	_	_
47	using	use	VBG	_	_	_
48	Phenol	Phenol	NNP	_	_	_
49	Chloroform	Chloroform	NNP	_	_	_
50	.	.	.	_	_	_

1	Ribosomal	ribosomal	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Ribo-Zero	Ribo-Zero	NNP	_	_	_
7	rRNA	rrna	NN	_	_	_
8	Removal	removal	NN	_	_	_
9	Kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Gram-Negative	gram-negative	JJ	_	_	_
12	Bacteria	bacterium	NNS	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Epicentre	Epicentre	NNP	_	_	_
16	,	,	,	_	_	_
17	Illumina	Illumina	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	conventional	conventional	JJ	_	_	_
5	Illumina	Illumina	NNP	_	_	_
6	protocol	protocol	NN	_	_	_
7	for	for	IN	_	_	_
8	mRNA	mrna	NN	_	_	_
9	Sequencing	sequencing	NN	_	_	_
10	Sample	Sample	NNP	_	_	_
11	Preparation	Preparation	NNP	_	_	_
12	was	be	VBD	_	_	_
13	applied	apply	VBN	_	_	_
14	with	with	IN	_	_	_
15	a	a	DT	_	_	_
16	few	few	JJ	_	_	_
17	modifications	modification	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	see	see	VB	_	_	_
20	original	original	JJ	_	_	_
21	paper	paper	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Standard	Standard	NNP	_	_	_
3	Paired-End	Paired-End	NNP	_	_	_
4	Illumina	Illumina	NNP	_	_	_
5	Library	Library	NNP	_	_	_
6	Construction	Construction	NNP	_	_	_
7	Protocol	Protocol	NNP	_	_	_
8	was	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	with	with	IN	_	_	_
11	modified	modify	VBN	_	_	_
12	adapters	adapter	NNS	_	_	_
13	containing	contain	VBG	_	_	_
14	optimized	optimize	VBN	_	_	_
15	20	20	CD	_	_	_
16	bp	bp	NN	_	_	_
17	barcode	barcode	NN	_	_	_
18	sequences	sequence	NNS	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	see	see	VB	_	_	_
21	original	original	JJ	_	_	_
22	paper	paper	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	with	with	IN	_	_	_
3	barcoded	barcoded	JJ	_	_	_
4	adapters	adapter	NNS	_	_	_
5	were	be	VBD	_	_	_
6	sequenced	sequence	VBN	_	_	_
7	on	on	IN	_	_	_
8	an	a	DT	_	_	_
9	Illumina	Illumina	NNP	_	_	_
10	HiSeq	HiSeq	NNP	_	_	_
11	2000	2000	CD	_	_	_
12	with	with	IN	_	_	_
13	a	a	DT	_	_	_
14	2x101	2x101	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	for	for	IN	_	_	_
17	the	the	DT	_	_	_
18	first	first	JJ	_	_	_
19	sequencing	sequencing	NN	_	_	_
20	run	run	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	and	and	CC	_	_	_
23	2x51	2x51	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	for	for	IN	_	_	_
26	the	the	DT	_	_	_
27	second	second	JJ	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	base	base	NN	_	_	_
30	paired-end	paired-end	NN	_	_	_
31	reads	read	VBZ	_	_	_
32	in	in	IN	_	_	_
33	one	one	CD	_	_	_
34	lane	lane	NN	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	K-12	k-12	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Using	use	VBG	_	_	_
7	a	a	DT	_	_	_
8	combination	combination	NN	_	_	_
9	of	of	IN	_	_	_
10	python	python	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	3.2.1	3.2.1	CD	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	and	and	CC	_	_	_
15	bowtie	bowtie	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	0.12.7	0.12.7	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	from	from	IN	_	_	_
21	the	the	DT	_	_	_
22	raw	raw	JJ	_	_	_
23	sequencing	sequencing	NN	_	_	_
24	data	datum	NNS	_	_	_
25	,	,	,	_	_	_
26	we	we	PRP	_	_	_
27	isolated	isolate	VBD	_	_	_
28	reads	read	VBZ	_	_	_
29	which	which	WDT	_	_	_
30	contained	contain	VBD	_	_	_
31	barcode	barcode	NN	_	_	_
32	sequences	sequence	NNS	_	_	_
33	that	that	WDT	_	_	_
34	corresponded	correspond	VBD	_	_	_
35	to	to	TO	_	_	_
36	our	we	PRP$	_	_	_
37	original	original	JJ	_	_	_
38	list	list	NN	_	_	_
39	of	of	IN	_	_	_
40	single	single	JJ	_	_	_
41	molecule	molecule	NN	_	_	_
42	barcodes	barcode	NNS	_	_	_
43	in	in	IN	_	_	_
44	both	both	CC	_	_	_
45	forward	forward	RB	_	_	_
46	and	and	CC	_	_	_
47	reverse	reverse	VB	_	_	_
48	reads	read	VBZ	_	_	_
49	for	for	IN	_	_	_
50	each	each	DT	_	_	_
51	sequence	sequence	NN	_	_	_
52	pair	pair	NN	_	_	_
53	that	that	WDT	_	_	_
54	had	have	VBD	_	_	_
55	at	at	IN	_	_	_
56	most	most	JJS	_	_	_
57	one	one	CD	_	_	_
58	mismatch	mismatch	NN	_	_	_
59	.	.	.	_	_	_

1	We	we	PRP	_	_	_
2	then	then	RB	_	_	_
3	aligned	align	VBD	_	_	_
4	the	the	DT	_	_	_
5	first	first	JJ	_	_	_
6	28	28	CD	_	_	_
7	bases	basis	NNS	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	26	26	CD	_	_	_
10	bases	basis	NNS	_	_	_
11	for	for	IN	_	_	_
12	the	the	DT	_	_	_
13	second	second	JJ	_	_	_
14	sequencing	sequencing	NN	_	_	_
15	run	run	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	of	of	IN	_	_	_
18	the	the	DT	_	_	_
19	targeted	target	VBN	_	_	_
20	sequence	sequence	NN	_	_	_
21	of	of	IN	_	_	_
22	both	both	CC	_	_	_
23	the	the	DT	_	_	_
24	forward	forward	JJ	_	_	_
25	and	and	CC	_	_	_
26	reverse	reverse	JJ	_	_	_
27	reads	read	VBZ	_	_	_
28	of	of	IN	_	_	_
29	each	each	DT	_	_	_
30	cluster	cluster	NN	_	_	_
31	to	to	TO	_	_	_
32	the	the	DT	_	_	_
33	E.	e.	FW	_	_	_
34	coli	coli	FW	_	_	_
35	genome	genome	NN	_	_	_
36	and	and	CC	_	_	_
37	kept	keep	VBD	_	_	_
38	the	the	DT	_	_	_
39	sequences	sequence	NNS	_	_	_
40	that	that	WDT	_	_	_
41	uniquely	uniquely	RB	_	_	_
42	align	align	VB	_	_	_
43	fewer	fewer	JJR	_	_	_
44	than	than	IN	_	_	_
45	three	three	CD	_	_	_
46	mismatches	mismatch	NNS	_	_	_
47	and	and	CC	_	_	_
48	where	where	WRB	_	_	_
49	the	the	DT	_	_	_
50	two	two	CD	_	_	_
51	reads	read	VBZ	_	_	_
52	did	do	VBD	_	_	_
53	not	not	RB	_	_	_
54	map	map	VB	GEN	_	_
55	to	to	TO	_	_	_
56	the	the	DT	_	_	_
57	same	same	JJ	_	_	_
58	sense	sense	NN	_	_	_
59	or	or	CC	_	_	_
60	antisense	antisense	JJ	_	_	_
61	strand	strand	NN	_	_	_
62	of	of	IN	_	_	_
63	the	the	DT	_	_	_
64	genome	genome	NN	_	_	_
65	.	.	.	_	_	_

1	We	we	PRP	_	_	_
2	used	use	VBD	_	_	_
3	a	a	DT	_	_	_
4	detailed	detailed	JJ	_	_	_
5	filtering	filter	VBG	_	_	_
6	process	process	NN	_	_	_
7	to	to	TO	_	_	_
8	determine	determine	VB	_	_	_
9	the	the	DT	_	_	_
10	identity	identity	NN	_	_	_
11	of	of	IN	_	_	_
12	closely-mapped	closely-mapped	JJ	_	_	_
13	reads	read	VBZ	_	_	_
14	.	.	.	_	_	_

1	Mapped	map	VBN	_	_	_
2	sequence	sequence	NN	_	_	_
3	fragments	fragment	NNS	_	_	_
4	with	with	IN	_	_	_
5	a	a	DT	_	_	_
6	length	length	NN	_	_	_
7	of	of	IN	_	_	_
8	at	at	IN	_	_	_
9	least	least	JJS	_	_	_
10	1,000	1,000	CD	_	_	_
11	bases	basis	NNS	_	_	_
12	were	be	VBD	_	_	_
13	discarded	discard	VBN	_	_	_
14	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	sequences	sequence	NNS	_	_	_
3	within	within	IN	_	_	_
4	the	the	DT	_	_	_
5	same	same	JJ	_	_	_
6	transcription	transcription	NN	_	_	_
7	unit	unit	NN	_	_	_
8	that	that	WDT	_	_	_
9	had	have	VBD	_	_	_
10	the	the	DT	_	_	_
11	same	same	JJ	_	_	_
12	unique	unique	JJ	_	_	_
13	tag	tag	NN	GEN	_	_
14	were	be	VBD	_	_	_
15	analyzed	analyze	VBN	_	_	_
16	further	further	RB	_	_	_
17	.	.	.	_	_	_

1	We	we	PRP	_	_	_
2	determined	determine	VBD	_	_	_
3	that	that	IN	_	_	_
4	more	more	JJR	_	_	_
5	than	than	IN	_	_	_
6	one	one	CD	_	_	_
7	sequence	sequence	NN	_	_	_
8	with	with	IN	_	_	_
9	the	the	DT	_	_	_
10	same	same	JJ	_	_	_
11	unique	unique	JJ	_	_	_
12	tag	tag	NN	GEN	_	_
13	were	be	VBD	_	_	_
14	identical	identical	JJ	_	_	_
15	if	if	IN	_	_	_
16	the	the	DT	_	_	_
17	distance	distance	NN	_	_	_
18	between	between	IN	_	_	_
19	their	they	PRP$	_	_	_
20	center	center	NN	_	_	_
21	positions	position	NNS	_	_	_
22	was	be	VBD	_	_	_
23	less	less	JJR	_	_	_
24	than	than	IN	_	_	_
25	four	four	CD	_	_	_
26	base-pairs	base-pair	NNS	_	_	_
27	and	and	CC	_	_	_
28	if	if	IN	_	_	_
29	the	the	DT	_	_	_
30	difference	difference	NN	_	_	_
31	in	in	IN	_	_	_
32	length	length	NN	_	_	_
33	was	be	VBD	_	_	_
34	less	less	JJR	_	_	_
35	than	than	IN	_	_	_
36	9	9	CD	_	_	_
37	base-pairs	base-pair	NNS	_	_	_
38	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	for	for	IN	_	_	_
3	each	each	DT	_	_	_
4	unique	unique	JJ	_	_	_
5	sequence	sequence	NN	_	_	_
6	,	,	,	_	_	_
7	we	we	PRP	_	_	_
8	counted	count	VBD	_	_	_
9	the	the	DT	_	_	_
10	number	number	NN	_	_	_
11	of	of	IN	_	_	_
12	unique	unique	JJ	_	_	_
13	barcode	barcode	NN	_	_	_
14	tags	tag	NNS	_	_	_
15	that	that	WDT	_	_	_
16	appeared	appear	VBD	_	_	_
17	to	to	TO	_	_	_
18	determine	determine	VB	_	_	_
19	the	the	DT	_	_	_
20	copy	copy	NN	_	_	_
21	number	number	NN	_	_	_
22	of	of	IN	_	_	_
23	each	each	DT	_	_	_
24	sequence	sequence	NN	_	_	_
25	and	and	CC	_	_	_
26	mapped	map	VBD	_	_	_
27	each	each	DT	_	_	_
28	of	of	IN	_	_	_
29	them	they	PRP	_	_	_
30	to	to	TO	_	_	_
31	genes	gene	NNS	_	_	_
32	.	.	.	_	_	_

1	We	we	PRP	_	_	_
2	include	include	VBP	_	_	_
3	indexed	index	VBN	_	_	_
4	genome	genome	NN	_	_	_
5	viewer	viewer	NN	_	_	_
6	files	file	NNS	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	.	.	.	_	_	_

1	sam	sam	NN	_	_	_
2	and	and	CC	_	_	_
3	.	.	.	_	_	_

1	sai	sai	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	for	for	IN	_	_	_
4	both	both	DT	_	_	_
5	experiments	experiment	NNS	_	_	_
6	using	use	VBG	_	_	_
7	both	both	CC	_	_	_
8	the	the	DT	_	_	_
9	conventional	conventional	JJ	_	_	_
10	method	method	NN	_	_	_
11	and	and	CC	_	_	_
12	the	the	DT	_	_	_
13	digital	digital	JJ	_	_	_
14	method	method	NN	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	in	in	IN	_	_	_
4	log	log	NN	_	_	_
5	phase	phase	NN	_	_	_
6	under	under	IN	_	_	_
7	furfural	furfural	JJ	_	_	_
8	stress	stress	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Cells	cell	NNS	_	_	_
11	were	be	VBD	_	_	_
12	grown	grow	VBN	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	in	in	IN	_	_	_
17	Luria-Bertani	Luria-Bertani	NNP	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	LB	LB	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	medium	medium	NN	_	_	_
22	supplemented	supplement	VBN	_	_	_
23	with	with	IN	_	_	_
24	50	50	CD	_	_	_
25	μg	μg	NN	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	Data	Data	NNP	_	_	_
28	were	be	VBD	_	_	_
29	analyzed	analyze	VBN	_	_	_
30	using	use	VBG	_	_	_
31	GeneChip	GeneChip	NNP	_	_	_
32	Operating	Operating	NNP	_	_	_
33	Software	Software	NNP	_	_	_
34	Version	Version	NNP	_	_	_
35	1.4	1.4	CD	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	Affymetrix	Affymetrix	NNP	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
40	Escherichia	escherichia	FW	Organism	_	_
41	coli	coli	FW	Organism	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	Furfural-tolerant	furfural-tolerant	JJ	_	_	_
44	IrrE	irre	NN	_	_	_
45	mutant	mutant	JJ	_	_	_
46	F1-37	f1-37	NN	_	_	_
47	,	,	,	_	_	_
48	biological	biological	JJ	_	_	_
49	rep1	rep1	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	Furfural-tolerant	furfural-tolerant	JJ	_	_	_
52	IrrE	irre	NN	_	_	_
53	mutant	mutant	JJ	_	_	_
54	F1-37	f1-37	NN	_	_	_
55	,	,	,	_	_	_
56	biological	biological	JJ	_	_	_
57	rep2	rep2	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	Furfural-tolerant	furfural-tolerant	JJ	_	_	_
60	IrrE	irre	NN	_	_	_
61	mutant	mutant	JJ	_	_	_
62	F1-37	f1-37	NN	_	_	_
63	,	,	,	_	_	_
64	biological	biological	JJ	_	_	_
65	rep3	rep3	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	genotype	genotype	NN	_	_	_
68	:	:	:	_	_	_
69	furfural-tolerant	furfural-tolerant	JJ	_	_	_
70	mutant	mutant	JJ	_	_	_
71	F1-37	f1-37	NN	_	_	_
72	of	of	IN	_	_	_
73	IrrE	irre	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	genotype	genotype	NN	_	_	_
76	:	:	:	_	_	_
77	wild	wild	JJ	_	_	_
78	type	type	NN	_	_	_
79	IrrE	irre	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	strain	strain	NN	_	_	_
82	:	:	:	_	_	_
83	DH5a	dh5a	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
85	The	the	DT	_	_	_
86	cells	cell	NNS	_	_	_
87	were	be	VBD	_	_	_
88	centrifuged	centrifuge	VBN	_	_	_
89	when	when	WRB	_	_	_
90	they	they	PRP	_	_	_
91	reached	reach	VBD	_	_	_
92	the	the	DT	_	_	_
93	log	log	NN	_	_	_
94	phase	phase	NN	_	_	_
95	,	,	,	_	_	_
96	and	and	CC	_	_	_
97	then	then	RB	_	_	_
98	rapidly	rapidly	RB	_	_	_
99	chilled	chill	VBD	_	_	_
100	and	and	CC	_	_	_
101	stored	store	VBD	_	_	_
102	in	in	IN	_	_	_
103	liquid	liquid	JJ	_	_	_
104	nitrogen	nitrogen	NN	_	_	_
105	until	until	IN	_	_	_
106	used	use	VBN	_	_	_
107	for	for	IN	_	_	_
108	the	the	DT	_	_	_
109	DNA	dna	NN	_	_	_
110	microarray	microarray	NN	_	_	_
111	assay	assay	NN	_	_	_
112	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
113	Total	Total	NNP	_	_	_
114	RNA	rna	NN	_	_	_
115	was	be	VBD	_	_	_
116	isolated	isolate	VBN	_	_	_
117	from	from	IN	_	_	_
118	the	the	DT	_	_	_
119	cells	cell	NNS	_	_	_
120	stored	store	VBN	_	_	_
121	in	in	IN	_	_	_
122	liquid	liquid	JJ	_	_	_
123	nitrogen	nitrogen	NN	_	_	_
124	using	use	VBG	_	_	_
125	TRIzol	trizol	NN	_	_	_
126	Reagent	reagent	NN	_	_	_
127	-LRB-	-lrb-	-LRB-	_	_	_
128	Invitrogen	Invitrogen	NNP	_	_	_
129	Life	Life	NNP	_	_	_
130	Technologies	Technologies	NNPS	_	_	_
131	,	,	,	_	_	_
132	Carlsbad	Carlsbad	NNP	_	_	_
133	,	,	,	_	_	_
134	CA	CA	NNP	_	_	_
135	,	,	,	_	_	_
136	USA	USA	NNP	_	_	_
137	-RRB-	-rrb-	-RRB-	_	_	_
138	and	and	CC	_	_	_
139	RNeasy	rneasy	NN	_	_	_
140	MinElute	MinElute	NNP	_	_	_
141	Cleanup	Cleanup	NNP	_	_	_
142	Kits	kit	NNS	_	_	_
143	-LRB-	-lrb-	-LRB-	_	_	_
144	Qiagen	Qiagen	NNP	_	_	_
145	,	,	,	_	_	_
146	Valencia	Valencia	NNP	_	_	_
147	,	,	,	_	_	_
148	CA	CA	NNP	_	_	_
149	,	,	,	_	_	_
150	USA	USA	NNP	_	_	_
151	-RRB-	-rrb-	-RRB-	_	_	_
152	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
153	Wild-type	wild-type	JJ	_	_	_
154	IrrE	irre	NN	_	_	_
155	,	,	,	_	_	_
156	biological	biological	JJ	_	_	_
157	rep1	rep1	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	Wild-type	wild-type	JJ	_	_	_
160	IrrE	irre	NN	_	_	_
161	,	,	,	_	_	_
162	biological	biological	JJ	_	_	_
163	rep2	rep2	NN	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	Wild-type	wild-type	JJ	_	_	_
166	IrrE	irre	NN	_	_	_
167	,	,	,	_	_	_
168	biological	biological	JJ	_	_	_
169	rep3	rep3	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	E	e	NN	_	_	_
172	_	_	CD	_	_	_
173	coli	coli	NN	_	_	_
174	_	_	NN	_	_	_
175	negativ	negativ	NN	_	_	_
176	_	_	NN	_	_	_
177	control	control	NN	_	_	_
178	_	_	CD	_	_	_
179	left	leave	VBD	_	_	_
180	_	_	RB	_	_	_
181	chamber	chamber	NN	_	_	_
182	_	_	CD	_	_	_
183	rep1	rep1	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	E	e	NN	_	_	_
186	_	_	CD	_	_	_
187	coli	coli	NN	_	_	_
188	_	_	NN	_	_	_
189	negativ	negativ	NN	_	_	_
190	_	_	NN	_	_	_
191	control	control	NN	_	_	_
192	_	_	CD	_	_	_
193	left	leave	VBD	_	_	_
194	_	_	RB	_	_	_
195	chamber	chamber	NN	_	_	_
196	_	_	CD	_	_	_
197	rep2	rep2	NN	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	E	e	NN	_	_	_
200	_	_	CD	_	_	_
201	coli	coli	NN	_	_	_
202	_	_	NN	_	_	_
203	negativ	negativ	NN	_	_	_
204	_	_	NN	_	_	_
205	control	control	NN	_	_	_
206	_	_	CD	_	_	_
207	left	leave	VBD	_	_	_
208	_	_	RB	_	_	_
209	chamber	chamber	NN	_	_	_
210	_	_	CD	_	_	_
211	rep3	rep3	NN	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	E	e	NN	_	_	_
214	_	_	CD	_	_	_
215	coli	coli	NN	_	_	_
216	_	_	NN	_	_	_
217	negativ	negativ	NN	_	_	_
218	_	_	NN	_	_	_
219	control	control	NN	_	_	_
220	_	_	RB	_	_	_
221	right	right	JJ	_	_	_
222	_	_	NN	_	_	_
223	chamber	chamber	NN	_	_	_
224	_	_	CD	_	_	_
225	rep1	rep1	NN	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	E	e	NN	_	_	_
228	_	_	CD	_	_	_
229	coli	coli	NN	_	_	_
230	_	_	NN	_	_	_
231	negativ	negativ	NN	_	_	_
232	_	_	NN	_	_	_
233	control	control	NN	_	_	_
234	_	_	RB	_	_	_
235	right	right	JJ	_	_	_
236	_	_	NN	_	_	_
237	chamber	chamber	NN	_	_	_
238	_	_	CD	_	_	_
239	rep2	rep2	NN	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
241	E	e	NN	_	_	_
242	_	_	CD	_	_	_
243	coli	coli	NN	_	_	_
244	_	_	NN	_	_	_
245	negativ	negativ	NN	_	_	_
246	_	_	NN	_	_	_
247	control	control	NN	_	_	_
248	_	_	RB	_	_	_
249	right	right	JJ	_	_	_
250	_	_	NN	_	_	_
251	chamber	chamber	NN	_	_	_
252	_	_	CD	_	_	_
253	rep3	rep3	NN	_	_	_
254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
255	E	e	NN	_	_	_
256	_	_	CD	_	_	_
257	coli	coli	NN	_	_	_
258	_	_	NN	_	_	_
259	response	response	NN	_	_	_
260	_	_	NN	_	_	_
261	control	control	NN	_	_	_
262	_	_	CD	_	_	_
263	1mM	1mm	NN	_	_	_
264	_	_	CD	_	_	_
265	H2O2	h2o2	NN	_	_	_
266	_	_	NN	_	_	_
267	added	add	VBD	_	_	_
268	_	_	CD	_	_	_
269	rep1	rep1	NN	_	_	_
270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
271	E	e	NN	_	_	_
272	_	_	CD	_	_	_
273	coli	coli	NN	_	_	_
274	_	_	NN	_	_	_
275	response	response	NN	_	_	_
276	_	_	NN	_	_	_
277	control	control	NN	_	_	_
278	_	_	CD	_	_	_
279	1mM	1mm	NN	_	_	_
280	_	_	CD	_	_	_
281	H2O2	h2o2	NN	_	_	_
282	_	_	NN	_	_	_
283	added	add	VBD	_	_	_
284	_	_	CD	_	_	_
285	rep2	rep2	NN	_	_	_
286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
287	E	e	NN	_	_	_
288	_	_	CD	_	_	_
289	coli	coli	NN	_	_	_
290	_	_	NN	_	_	_
291	response	response	NN	_	_	_
292	_	_	NN	_	_	_
293	control	control	NN	_	_	_
294	_	_	CD	_	_	_
295	1mM	1mm	NN	_	_	_
296	_	_	CD	_	_	_
297	H2O2	h2o2	NN	_	_	_
298	_	_	NN	_	_	_
299	added	add	VBD	_	_	_
300	_	_	CD	_	_	_
301	rep3	rep3	NN	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
303	E	e	NN	_	_	_
304	_	_	CD	_	_	_
305	coli	coli	NN	_	_	_
306	_	_	NN	_	_	_
307	response	response	NN	_	_	_
308	_	_	NN	_	_	_
309	control	control	NN	_	_	_
310	_	_	CD	_	_	_
311	water	water	NN	_	_	_
312	_	_	NN	_	_	_
313	added	add	VBD	_	_	_
314	_	_	CD	_	_	_
315	rep1	rep1	NN	_	_	_
316	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
317	E	e	NN	_	_	_
318	_	_	CD	_	_	_
319	coli	coli	NN	_	_	_
320	_	_	NN	_	_	_
321	response	response	NN	_	_	_
322	_	_	NN	_	_	_
323	control	control	NN	_	_	_
324	_	_	CD	_	_	_
325	water	water	NN	_	_	_
326	_	_	NN	_	_	_
327	added	add	VBD	_	_	_
328	_	_	CD	_	_	_
329	rep2	rep2	NN	_	_	_
330	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
331	E	e	NN	_	_	_
332	_	_	CD	_	_	_
333	coli	coli	NN	_	_	_
334	_	_	NN	_	_	_
335	response	response	NN	_	_	_
336	_	_	NN	_	_	_
337	control	control	NN	_	_	_
338	_	_	CD	_	_	_
339	water	water	NN	_	_	_
340	_	_	NN	_	_	_
341	added	add	VBD	_	_	_
342	_	_	CD	_	_	_
343	rep3	rep3	NN	_	_	_
344	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
345	E	e	NN	_	_	_
346	_	_	FW	_	_	_
347	coli	coli	FW	_	_	_
348	_	_	SYM	_	_	_
349	sham	sham	FW	_	_	_
350	_	_	FW	_	_	_
351	powerline	powerline	FW	_	_	_
352	_	_	SYM	_	_	_
353	interm	interm	FW	_	_	_
354	_	_	FW	_	_	_
355	15h	15h	FW	_	_	_
356	_	_	SYM	_	_	_
357	rep1	rep1	CD	_	_	_
358	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
359	E	e	NN	_	_	_
360	_	_	FW	_	_	_
361	coli	coli	FW	_	_	_
362	_	_	SYM	_	_	_
363	sham	sham	FW	_	_	_
364	_	_	FW	_	_	_
365	powerline	powerline	FW	_	_	_
366	_	_	SYM	_	_	_
367	interm	interm	FW	_	_	_
368	_	_	FW	_	_	_
369	15h	15h	FW	_	_	_
370	_	_	SYM	_	_	_
371	rep2	rep2	CD	_	_	_
372	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
373	E	e	NN	_	_	_
374	_	_	FW	_	_	_
375	coli	coli	FW	_	_	_
376	_	_	SYM	_	_	_
377	sham	sham	FW	_	_	_
378	_	_	FW	_	_	_
379	powerline	powerline	FW	_	_	_
380	_	_	SYM	_	_	_
381	interm	interm	FW	_	_	_
382	_	_	FW	_	_	_
383	15h	15h	FW	_	_	_
384	_	_	SYM	_	_	_
385	rep3	rep3	CD	_	_	_
386	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
387	E	e	NN	_	_	_
388	_	_	FW	_	_	_
389	coli	coli	FW	_	_	_
390	_	_	SYM	_	_	_
391	sham	sham	VBP	_	_	_
392	_	_	SYM	_	_	_
393	powerline	powerline	FW	_	_	_
394	_	_	FW	_	_	_
395	interm	interm	FW	_	_	_
396	_	_	SYM	_	_	_
397	2.5	2.5	CD	_	_	_
398	h	h	NN	_	_	_
399	_	_	CD	_	_	_
400	rep1	rep1	NN	_	_	_
401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
402	E	e	NN	_	_	_
403	_	_	FW	_	_	_
404	coli	coli	FW	_	_	_
405	_	_	SYM	_	_	_
406	sham	sham	VBP	_	_	_
407	_	_	SYM	_	_	_
408	powerline	powerline	FW	_	_	_
409	_	_	FW	_	_	_
410	interm	interm	FW	_	_	_
411	_	_	SYM	_	_	_
412	2.5	2.5	CD	_	_	_
413	h	h	NN	_	_	_
414	_	_	CD	_	_	_
415	rep2	rep2	NN	_	_	_
416	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
417	E	e	NN	_	_	_
418	_	_	FW	_	_	_
419	coli	coli	FW	_	_	_
420	_	_	SYM	_	_	_
421	sham	sham	VBP	_	_	_
422	_	_	SYM	_	_	_
423	powerline	powerline	FW	_	_	_
424	_	_	FW	_	_	_
425	interm	interm	FW	_	_	_
426	_	_	SYM	_	_	_
427	2.5	2.5	CD	_	_	_
428	h	h	NN	_	_	_
429	_	_	CD	_	_	_
430	rep3	rep3	NN	_	_	_
431	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
432	E	e	NN	_	_	_
433	_	_	FW	_	_	_
434	coli	coli	FW	_	_	_
435	_	_	SYM	_	_	_
436	sham	sham	VBP	_	_	_
437	_	_	SYM	_	_	_
438	powerline	powerline	FW	_	_	_
439	_	_	FW	_	_	_
440	interm	interm	FW	_	_	_
441	_	_	SYM	_	_	_
442	8	8	CD	_	_	_
443	min	min	NN	_	_	_
444	_	_	CD	_	_	_
445	rep1	rep1	NN	_	_	_
446	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
447	E	e	NN	_	_	_
448	_	_	FW	_	_	_
449	coli	coli	FW	_	_	_
450	_	_	SYM	_	_	_
451	sham	sham	VBP	_	_	_
452	_	_	SYM	_	_	_
453	powerline	powerline	FW	_	_	_
454	_	_	FW	_	_	_
455	interm	interm	FW	_	_	_
456	_	_	SYM	_	_	_
457	8	8	CD	_	_	_
458	min	min	NN	_	_	_
459	_	_	CD	_	_	_
460	rep2	rep2	NN	_	_	_
461	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
462	E	e	NN	_	_	_
463	_	_	FW	_	_	_
464	coli	coli	FW	_	_	_
465	_	_	SYM	_	_	_
466	sham	sham	VBP	_	_	_
467	_	_	SYM	_	_	_
468	powerline	powerline	FW	_	_	_
469	_	_	FW	_	_	_
470	interm	interm	FW	_	_	_
471	_	_	SYM	_	_	_
472	8	8	CD	_	_	_
473	min	min	NN	_	_	_
474	_	_	CD	_	_	_
475	rep3	rep3	NN	_	_	_
476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
477	E	e	NN	_	_	_
478	_	_	FW	_	_	_
479	coli	coli	FW	_	_	_
480	_	_	SYM	_	_	_
481	sham	sham	VBP	_	_	_
482	_	_	SYM	_	_	_
483	sinusoidal	sinusoidal	JJ	_	_	_
484	_	_	NN	_	_	_
485	cont	cont	NN	_	_	_
486	_	_	SYM	_	_	_
487	15h	15h	CD	_	_	_
488	_	_	CD	_	_	_
489	rep1	rep1	NN	_	_	_
490	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
491	E	e	NN	_	_	_
492	_	_	FW	_	_	_
493	coli	coli	FW	_	_	_
494	_	_	SYM	_	_	_
495	sham	sham	VBP	_	_	_
496	_	_	SYM	_	_	_
497	sinusoidal	sinusoidal	JJ	_	_	_
498	_	_	NN	_	_	_
499	cont	cont	NN	_	_	_
500	_	_	SYM	_	_	_
501	15h	15h	CD	_	_	_
502	_	_	CD	_	_	_
503	rep2	rep2	NN	_	_	_
504	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
505	E	e	NN	_	_	_
506	_	_	FW	_	_	_
507	coli	coli	FW	_	_	_
508	_	_	SYM	_	_	_
509	sham	sham	VBP	_	_	_
510	_	_	SYM	_	_	_
511	sinusoidal	sinusoidal	JJ	_	_	_
512	_	_	NN	_	_	_
513	cont	cont	NN	_	_	_
514	_	_	SYM	_	_	_
515	15h	15h	CD	_	_	_
516	_	_	CD	_	_	_
517	rep3	rep3	NN	_	_	_
518	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
519	E	e	NN	_	_	_
520	_	_	FW	_	_	_
521	coli	coli	FW	_	_	_
522	_	_	SYM	_	_	_
523	sham	sham	VBP	_	_	_
524	_	_	SYM	_	_	_
525	sinusoidal	sinusoidal	JJ	_	_	_
526	_	_	NN	_	_	_
527	cont	cont	NN	_	_	_
528	_	_	SYM	_	_	_
529	2.5	2.5	CD	_	_	_
530	h	h	NN	_	_	_
531	_	_	CD	_	_	_
532	rep1	rep1	NN	_	_	_
533	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
534	E	e	NN	_	_	_
535	_	_	FW	_	_	_
536	coli	coli	FW	_	_	_
537	_	_	SYM	_	_	_
538	sham	sham	VBP	_	_	_
539	_	_	SYM	_	_	_
540	sinusoidal	sinusoidal	JJ	_	_	_
541	_	_	NN	_	_	_
542	cont	cont	NN	_	_	_
543	_	_	SYM	_	_	_
544	2.5	2.5	CD	_	_	_
545	h	h	NN	_	_	_
546	_	_	CD	_	_	_
547	rep2	rep2	NN	_	_	_
548	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
549	E	e	NN	_	_	_
550	_	_	FW	_	_	_
551	coli	coli	FW	_	_	_
552	_	_	SYM	_	_	_
553	sham	sham	VBP	_	_	_
554	_	_	SYM	_	_	_
555	sinusoidal	sinusoidal	JJ	_	_	_
556	_	_	NN	_	_	_
557	cont	cont	NN	_	_	_
558	_	_	SYM	_	_	_
559	2.5	2.5	CD	_	_	_
560	h	h	NN	_	_	_
561	_	_	CD	_	_	_
562	rep3	rep3	NN	_	_	_
563	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
564	E	e	NN	_	_	_
565	_	_	FW	_	_	_
566	coli	coli	FW	_	_	_
567	_	_	SYM	_	_	_
568	sham	sham	VBP	_	_	_
569	_	_	SYM	_	_	_
570	sinusoidal	sinusoidal	JJ	_	_	_
571	_	_	NN	_	_	_
572	cont	cont	NN	_	_	_
573	_	_	NN	_	_	_
574	8	8	CD	_	_	_
575	min	min	NN	_	_	_
576	_	_	CD	_	_	_
577	rep1	rep1	NN	_	_	_
578	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
579	E	e	NN	_	_	_
580	_	_	FW	_	_	_
581	coli	coli	FW	_	_	_
582	_	_	SYM	_	_	_
583	sham	sham	VBP	_	_	_
584	_	_	SYM	_	_	_
585	sinusoidal	sinusoidal	JJ	_	_	_
586	_	_	NN	_	_	_
587	cont	cont	NN	_	_	_
588	_	_	NN	_	_	_
589	8	8	CD	_	_	_
590	min	min	NN	_	_	_
591	_	_	CD	_	_	_
592	rep2	rep2	NN	_	_	_
593	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
594	E	e	NN	_	_	_
595	_	_	FW	_	_	_
596	coli	coli	FW	_	_	_
597	_	_	SYM	_	_	_
598	sham	sham	VBP	_	_	_
599	_	_	SYM	_	_	_
600	sinusoidal	sinusoidal	JJ	_	_	_
601	_	_	NN	_	_	_
602	cont	cont	NN	_	_	_
603	_	_	NN	_	_	_
604	8	8	CD	_	_	_
605	min	min	NN	_	_	_
606	_	_	CD	_	_	_
607	rep3	rep3	NN	_	_	_
608	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
609	E	e	NN	_	_	_
610	_	_	FW	_	_	_
611	coli	coli	FW	_	_	_
612	_	_	SYM	_	_	_
613	sham	sham	VBP	_	_	_
614	_	_	SYM	_	_	_
615	sinusoidal	sinusoidal	JJ	_	_	_
616	_	_	NN	_	_	_
617	interm	interm	NN	_	_	_
618	_	_	CD	_	_	_
619	15h	15h	JJ	_	_	_
620	_	_	NN	_	_	_
621	rep1	rep1	NN	_	_	_
622	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
623	E	e	NN	_	_	_
624	_	_	FW	_	_	_
625	coli	coli	FW	_	_	_
626	_	_	SYM	_	_	_
627	sham	sham	VBP	_	_	_
628	_	_	SYM	_	_	_
629	sinusoidal	sinusoidal	JJ	_	_	_
630	_	_	NN	_	_	_
631	interm	interm	NN	_	_	_
632	_	_	CD	_	_	_
633	15h	15h	JJ	_	_	_
634	_	_	NN	_	_	_
635	rep2	rep2	NN	_	_	_
636	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
637	E	e	NN	_	_	_
638	_	_	FW	_	_	_
639	coli	coli	FW	_	_	_
640	_	_	SYM	_	_	_
641	sham	sham	VBP	_	_	_
642	_	_	SYM	_	_	_
643	sinusoidal	sinusoidal	JJ	_	_	_
644	_	_	NN	_	_	_
645	interm	interm	NN	_	_	_
646	_	_	CD	_	_	_
647	15h	15h	JJ	_	_	_
648	_	_	NN	_	_	_
649	rep3	rep3	NN	_	_	_
650	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
651	E	e	NN	_	_	_
652	_	_	FW	_	_	_
653	coli	coli	FW	_	_	_
654	_	_	SYM	_	_	_
655	sham	sham	VBP	_	_	_
656	_	_	SYM	_	_	_
657	sinusoidal	sinusoidal	JJ	_	_	_
658	_	_	NN	_	_	_
659	interm	interm	NN	_	_	_
660	_	_	CD	_	_	_
661	2.5	2.5	CD	_	_	_
662	h	h	NN	_	_	_
663	_	_	CD	_	_	_
664	rep1	rep1	NN	_	_	_
665	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
666	E	e	NN	_	_	_
667	_	_	FW	_	_	_
668	coli	coli	FW	_	_	_
669	_	_	SYM	_	_	_
670	sham	sham	VBP	_	_	_
671	_	_	SYM	_	_	_
672	sinusoidal	sinusoidal	JJ	_	_	_
673	_	_	NN	_	_	_
674	interm	interm	NN	_	_	_
675	_	_	CD	_	_	_
676	2.5	2.5	CD	_	_	_
677	h	h	NN	_	_	_
678	_	_	CD	_	_	_
679	rep2	rep2	NN	_	_	_
680	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
681	E	e	NN	_	_	_
682	_	_	FW	_	_	_
683	coli	coli	FW	_	_	_
684	_	_	SYM	_	_	_
685	sham	sham	VBP	_	_	_
686	_	_	SYM	_	_	_
687	sinusoidal	sinusoidal	JJ	_	_	_
688	_	_	NN	_	_	_
689	interm	interm	NN	_	_	_
690	_	_	CD	_	_	_
691	2.5	2.5	CD	_	_	_
692	h	h	NN	_	_	_
693	_	_	CD	_	_	_
694	rep3	rep3	NN	_	_	_
695	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
696	E	e	NN	_	_	_
697	_	_	CD	_	_	_
698	coli	coli	NN	_	_	_
699	_	_	NN	_	_	_
700	treated	treat	VBN	_	_	_
701	_	_	SYM	_	_	_
702	powerline	powerline	FW	_	_	_
703	_	_	FW	_	_	_
704	interm	interm	FW	_	_	_
705	_	_	SYM	_	_	_
706	15h	15h	CD	_	_	_
707	_	_	CD	_	_	_
708	rep1	rep1	NN	_	_	_
709	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
710	E	e	NN	_	_	_
711	_	_	CD	_	_	_
712	coli	coli	NN	_	_	_
713	_	_	NN	_	_	_
714	treated	treat	VBN	_	_	_
715	_	_	SYM	_	_	_
716	powerline	powerline	FW	_	_	_
717	_	_	FW	_	_	_
718	interm	interm	FW	_	_	_
719	_	_	SYM	_	_	_
720	15h	15h	CD	_	_	_
721	_	_	CD	_	_	_
722	rep2	rep2	NN	_	_	_
723	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
724	E	e	NN	_	_	_
725	_	_	CD	_	_	_
726	coli	coli	NN	_	_	_
727	_	_	NN	_	_	_
728	treated	treat	VBN	_	_	_
729	_	_	SYM	_	_	_
730	powerline	powerline	FW	_	_	_
731	_	_	FW	_	_	_
732	interm	interm	FW	_	_	_
733	_	_	SYM	_	_	_
734	15h	15h	CD	_	_	_
735	_	_	CD	_	_	_
736	rep3	rep3	NN	_	_	_
737	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
738	E	e	NN	_	_	_
739	_	_	CD	_	_	_
740	coli	coli	NN	_	_	_
741	_	_	NN	_	_	_
742	treated	treat	VBN	_	_	_
743	_	_	SYM	_	_	_
744	powerline	powerline	FW	_	_	_
745	_	_	FW	_	_	_
746	interm	interm	FW	_	_	_
747	_	_	SYM	_	_	_
748	2.5	2.5	CD	_	_	_
749	h	h	NN	_	_	_
750	_	_	CD	_	_	_
751	rep1	rep1	NN	_	_	_
752	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
753	E	e	NN	_	_	_
754	_	_	CD	_	_	_
755	coli	coli	NN	_	_	_
756	_	_	NN	_	_	_
757	treated	treat	VBN	_	_	_
758	_	_	SYM	_	_	_
759	powerline	powerline	FW	_	_	_
760	_	_	FW	_	_	_
761	interm	interm	FW	_	_	_
762	_	_	SYM	_	_	_
763	2.5	2.5	CD	_	_	_
764	h	h	NN	_	_	_
765	_	_	CD	_	_	_
766	rep2	rep2	NN	_	_	_
767	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
768	E	e	NN	_	_	_
769	_	_	CD	_	_	_
770	coli	coli	NN	_	_	_
771	_	_	NN	_	_	_
772	treated	treat	VBN	_	_	_
773	_	_	SYM	_	_	_
774	powerline	powerline	FW	_	_	_
775	_	_	FW	_	_	_
776	interm	interm	FW	_	_	_
777	_	_	SYM	_	_	_
778	2.5	2.5	CD	_	_	_
779	h	h	NN	_	_	_
780	_	_	CD	_	_	_
781	rep3	rep3	NN	_	_	_
782	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
783	E	e	NN	_	_	_
784	_	_	CD	_	_	_
785	coli	coli	NN	_	_	_
786	_	_	NN	_	_	_
787	treated	treat	VBN	_	_	_
788	_	_	SYM	_	_	_
789	powerline	powerline	FW	_	_	_
790	_	_	FW	_	_	_
791	interm	interm	FW	_	_	_
792	_	_	SYM	_	_	_
793	8	8	CD	_	_	_
794	min	min	NN	_	_	_
795	_	_	CD	_	_	_
796	rep1	rep1	NN	_	_	_
797	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
798	E	e	NN	_	_	_
799	_	_	CD	_	_	_
800	coli	coli	NN	_	_	_
801	_	_	NN	_	_	_
802	treated	treat	VBN	_	_	_
803	_	_	SYM	_	_	_
804	powerline	powerline	FW	_	_	_
805	_	_	FW	_	_	_
806	interm	interm	FW	_	_	_
807	_	_	SYM	_	_	_
808	8	8	CD	_	_	_
809	min	min	NN	_	_	_
810	_	_	CD	_	_	_
811	rep2	rep2	NN	_	_	_
812	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
813	E	e	NN	_	_	_
814	_	_	CD	_	_	_
815	coli	coli	NN	_	_	_
816	_	_	NN	_	_	_
817	treated	treat	VBN	_	_	_
818	_	_	SYM	_	_	_
819	powerline	powerline	FW	_	_	_
820	_	_	FW	_	_	_
821	interm	interm	FW	_	_	_
822	_	_	SYM	_	_	_
823	8	8	CD	_	_	_
824	min	min	NN	_	_	_
825	_	_	CD	_	_	_
826	rep3	rep3	NN	_	_	_
827	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
828	E	e	NN	_	_	_
829	_	_	CD	_	_	_
830	coli	coli	NN	_	_	_
831	_	_	NN	_	_	_
832	treated	treat	VBN	_	_	_
833	_	_	SYM	_	_	_
834	sinusoidal	sinusoidal	JJ	_	_	_
835	_	_	NN	_	_	_
836	cont	cont	NN	_	_	_
837	_	_	SYM	_	_	_
838	15h	15h	CD	_	_	_
839	_	_	CD	_	_	_
840	rep1	rep1	NN	_	_	_
841	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
842	E	e	NN	_	_	_
843	_	_	CD	_	_	_
844	coli	coli	NN	_	_	_
845	_	_	NN	_	_	_
846	treated	treat	VBN	_	_	_
847	_	_	SYM	_	_	_
848	sinusoidal	sinusoidal	JJ	_	_	_
849	_	_	NN	_	_	_
850	cont	cont	NN	_	_	_
851	_	_	SYM	_	_	_
852	15h	15h	CD	_	_	_
853	_	_	CD	_	_	_
854	rep2	rep2	NN	_	_	_
855	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
856	E	e	NN	_	_	_
857	_	_	CD	_	_	_
858	coli	coli	NN	_	_	_
859	_	_	NN	_	_	_
860	treated	treat	VBN	_	_	_
861	_	_	SYM	_	_	_
862	sinusoidal	sinusoidal	JJ	_	_	_
863	_	_	NN	_	_	_
864	cont	cont	NN	_	_	_
865	_	_	SYM	_	_	_
866	15h	15h	CD	_	_	_
867	_	_	CD	_	_	_
868	rep3	rep3	NN	_	_	_
869	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
870	E	e	NN	_	_	_
871	_	_	CD	_	_	_
872	coli	coli	NN	_	_	_
873	_	_	NN	_	_	_
874	treated	treat	VBN	_	_	_
875	_	_	SYM	_	_	_
876	sinusoidal	sinusoidal	JJ	_	_	_
877	_	_	NN	_	_	_
878	cont	cont	NN	_	_	_
879	_	_	SYM	_	_	_
880	2.5	2.5	CD	_	_	_
881	h	h	NN	_	_	_
882	_	_	CD	_	_	_
883	rep1	rep1	NN	_	_	_
884	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
885	E	e	NN	_	_	_
886	_	_	CD	_	_	_
887	coli	coli	NN	_	_	_
888	_	_	NN	_	_	_
889	treated	treat	VBN	_	_	_
890	_	_	SYM	_	_	_
891	sinusoidal	sinusoidal	JJ	_	_	_
892	_	_	NN	_	_	_
893	cont	cont	NN	_	_	_
894	_	_	SYM	_	_	_
895	2.5	2.5	CD	_	_	_
896	h	h	NN	_	_	_
897	_	_	CD	_	_	_
898	rep2	rep2	NN	_	_	_
899	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
900	E	e	NN	_	_	_
901	_	_	CD	_	_	_
902	coli	coli	NN	_	_	_
903	_	_	NN	_	_	_
904	treated	treat	VBN	_	_	_
905	_	_	SYM	_	_	_
906	sinusoidal	sinusoidal	JJ	_	_	_
907	_	_	NN	_	_	_
908	cont	cont	NN	_	_	_
909	_	_	SYM	_	_	_
910	2.5	2.5	CD	_	_	_
911	h	h	NN	_	_	_
912	_	_	CD	_	_	_
913	rep3	rep3	NN	_	_	_
914	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
915	E	e	NN	_	_	_
916	_	_	CD	_	_	_
917	coli	coli	NN	_	_	_
918	_	_	NN	_	_	_
919	treated	treat	VBN	_	_	_
920	_	_	SYM	_	_	_
921	sinusoidal	sinusoidal	JJ	_	_	_
922	_	_	NN	_	_	_
923	cont	cont	NN	_	_	_
924	_	_	NN	_	_	_
925	8	8	CD	_	_	_
926	min	min	NN	_	_	_
927	_	_	CD	_	_	_
928	rep1	rep1	NN	_	_	_
929	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
930	E	e	NN	_	_	_
931	_	_	CD	_	_	_
932	coli	coli	NN	_	_	_
933	_	_	NN	_	_	_
934	treated	treat	VBN	_	_	_
935	_	_	SYM	_	_	_
936	sinusoidal	sinusoidal	JJ	_	_	_
937	_	_	NN	_	_	_
938	cont	cont	NN	_	_	_
939	_	_	NN	_	_	_
940	8	8	CD	_	_	_
941	min	min	NN	_	_	_
942	_	_	CD	_	_	_
943	rep2	rep2	NN	_	_	_
944	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
945	E	e	NN	_	_	_
946	_	_	CD	_	_	_
947	coli	coli	NN	_	_	_
948	_	_	NN	_	_	_
949	treated	treat	VBN	_	_	_
950	_	_	SYM	_	_	_
951	sinusoidal	sinusoidal	JJ	_	_	_
952	_	_	NN	_	_	_
953	cont	cont	NN	_	_	_
954	_	_	NN	_	_	_
955	8	8	CD	_	_	_
956	min	min	NN	_	_	_
957	_	_	CD	_	_	_
958	rep3	rep3	NN	_	_	_
959	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
960	E	e	NN	_	_	_
961	_	_	CD	_	_	_
962	coli	coli	NN	_	_	_
963	_	_	NN	_	_	_
964	treated	treat	VBN	_	_	_
965	_	_	SYM	_	_	_
966	sinusoidal	sinusoidal	JJ	_	_	_
967	_	_	NN	_	_	_
968	interm	interm	NN	_	_	_
969	_	_	CD	_	_	_
970	15h	15h	JJ	_	_	_
971	_	_	NN	_	_	_
972	rep1	rep1	NN	_	_	_
973	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
974	E	e	NN	_	_	_
975	_	_	CD	_	_	_
976	coli	coli	NN	_	_	_
977	_	_	NN	_	_	_
978	treated	treat	VBN	_	_	_
979	_	_	SYM	_	_	_
980	sinusoidal	sinusoidal	JJ	_	_	_
981	_	_	NN	_	_	_
982	interm	interm	NN	_	_	_
983	_	_	CD	_	_	_
984	15h	15h	JJ	_	_	_
985	_	_	NN	_	_	_
986	rep2	rep2	NN	_	_	_
987	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
988	E	e	NN	_	_	_
989	_	_	CD	_	_	_
990	coli	coli	NN	_	_	_
991	_	_	NN	_	_	_
992	treated	treat	VBN	_	_	_
993	_	_	SYM	_	_	_
994	sinusoidal	sinusoidal	JJ	_	_	_
995	_	_	NN	_	_	_
996	interm	interm	NN	_	_	_
997	_	_	CD	_	_	_
998	15h	15h	JJ	_	_	_
999	_	_	NN	_	_	_
1000	rep3	rep3	NN	_	_	_
1001	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1002	E	e	NN	_	_	_
1003	_	_	CD	_	_	_
1004	coli	coli	NN	_	_	_
1005	_	_	NN	_	_	_
1006	treated	treat	VBN	_	_	_
1007	_	_	SYM	_	_	_
1008	sinusoidal	sinusoidal	JJ	_	_	_
1009	_	_	NN	_	_	_
1010	interm	interm	NN	_	_	_
1011	_	_	CD	_	_	_
1012	2.5	2.5	CD	_	_	_
1013	h	h	NN	_	_	_
1014	_	_	CD	_	_	_
1015	rep1	rep1	NN	_	_	_
1016	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1017	E	e	NN	_	_	_
1018	_	_	CD	_	_	_
1019	coli	coli	NN	_	_	_
1020	_	_	NN	_	_	_
1021	treated	treat	VBN	_	_	_
1022	_	_	SYM	_	_	_
1023	sinusoidal	sinusoidal	JJ	_	_	_
1024	_	_	NN	_	_	_
1025	interm	interm	NN	_	_	_
1026	_	_	CD	_	_	_
1027	2.5	2.5	CD	_	_	_
1028	h	h	NN	_	_	_
1029	_	_	CD	_	_	_
1030	rep2	rep2	NN	_	_	_
1031	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1032	E	e	NN	_	_	_
1033	_	_	CD	_	_	_
1034	coli	coli	NN	_	_	_
1035	_	_	NN	_	_	_
1036	treated	treat	VBN	_	_	_
1037	_	_	SYM	_	_	_
1038	sinusoidal	sinusoidal	JJ	_	_	_
1039	_	_	NN	_	_	_
1040	interm	interm	NN	_	_	_
1041	_	_	CD	_	_	_
1042	2.5	2.5	CD	_	_	_
1043	h	h	NN	_	_	_
1044	_	_	SYM	_	_	_
1045	rep3	rep3	CD	_	_	_
1046	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1047	Escherichia	escherichia	FW	Organism	_	_
1048	coli	coli	FW	Organism	_	_
1049	K-12	k-12	NN	_	_	_
1050	strain	strain	NN	_	_	_
1051	MG1655	mg1655	NN	_	_	_
1052	was	be	VBD	_	_	_
1053	cultivated	cultivate	VBN	_	_	_
1054	aerobically	aerobically	RB	_	_	_
1055	-LRB-	-lrb-	-LRB-	_	_	_
1056	~	~	SYM	_	_	_
1057	0.5	0.5	CD	_	_	_
1058	l	l	NN	_	_	_
1059	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1060	Escherichia	escherichia	FW	Organism	_	_
1061	coli	coli	FW	Organism	_	_
1062	str	str	FW	_	_	_
1063	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	growth	growth	NN	_	_	_
4	condition	condition	NN	_	_	_
5	:	:	:	_	_	_
6	steady-state	steady-state	JJ	_	_	_
7	continuous	continuous	JJ	_	_	_
8	cultivation	cultivation	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	dilution	dilution	NN	_	_	_
11	rate	rate	NN	_	_	_
12	of	of	IN	_	_	_
13	0.4	0.4	CD	_	_	_
14	h-1	h-1	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	,	,	,	_	_	_
17	aerobic	aerobic	JJ	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	medium	medium	NN	_	_	_
20	:	:	:	_	_	_
21	defined	define	VBN	_	_	_
22	mineral	mineral	JJ	_	_	_
23	medium	medium	NN	_	_	_
24	with	with	IN	_	_	_
25	1	1	CD	_	_	_
26	g	g	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
28	Quality	quality	JJ	_	_	_
29	control	control	NN	_	_	_
30	and	and	CC	_	_	_
31	microarray	microarray	NN	_	_	_
32	data	data	NN	_	_	_
33	analysis	analysis	NN	_	_	_
34	of	of	IN	_	_	_
35	all	all	DT	_	_	_
36	60	60	CD	_	_	_
37	chips	chip	NNS	_	_	_
38	was	be	VBD	_	_	_
39	done	do	VBN	_	_	_
40	using	use	VBG	_	_	_
41	R	r	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
43	Samples	sample	NNS	_	_	_
44	of	of	IN	_	_	_
45	~	~	NN	_	_	_
46	7.2	7.2	CD	_	_	_
47	ml	ml	NN	_	_	_
48	bacterial	bacterial	JJ	_	_	_
49	culture	culture	NN	_	_	_
50	were	be	VBD	_	_	_
51	mixed	mix	VBN	_	_	_
52	with	with	IN	_	_	_
53	0.8	0.8	CD	_	_	_
54	ml	ml	NN	_	_	_
55	stop	stop	NN	_	_	_
56	solution	solution	NN	_	_	_
57	,	,	,	_	_	_
58	pelleted	pelleted	JJ	_	_	_
59	and	and	CC	_	_	_
60	total	total	JJ	_	_	_
61	RNA	rna	NN	_	_	_
62	was	be	VBD	_	_	_
63	purified	purify	VBN	_	_	_
64	using	use	VBG	_	_	_
65	RNeasy	RNeasy	NNP	_	_	_
66	Mini	Mini	NNP	_	_	_
67	Kit	kit	NN	_	_	_
68	-LRB-	-lrb-	-LRB-	_	_	_
69	Qiagen	qiagen	NN	_	_	_
70	-RRB-	-rrb-	-RRB-	_	_	_
71	.	.	.	_	_	_

1	DNase	dnase	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	was	be	VBD	_	_	_
4	done	do	VBN	_	_	_
5	twice	twice	RB	_	_	_
6	with	with	IN	_	_	_
7	RQ1	rq1	NN	_	_	_
8	DNase	dnase	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Promega	promega	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	to	to	TO	_	_	_
13	remove	remove	VB	_	_	_
14	genomic	genomic	JJ	_	_	_
15	DNA	dna	NN	_	_	_
16	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	synthesis	synthesis	NN	_	_	_
3	was	be	VBD	_	_	_
4	done	do	VBN	_	_	_
5	according	accord	VBG	_	_	_
6	to	to	TO	_	_	_
7	the	the	DT	_	_	_
8	GeneChip	GeneChip	NNP	_	_	_
9	®	®	NNP	_	_	_
10	Expression	expression	NN	_	_	_
11	Analysis	analysis	NN	_	_	_
12	Technical	Technical	NNP	_	_	_
13	Manual	Manual	NNP	_	_	_
14	of	of	IN	_	_	_
15	Affymetrix	Affymetrix	NNP	_	_	_
16	using	use	VBG	_	_	_
17	M-MLV	m-mlv	NN	_	_	_
18	reverse	reverse	JJ	_	_	_
19	transcriptase	transcriptase	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Promega	promega	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	,	,	,	_	_	_
24	without	without	IN	_	_	_
25	DTT	dtt	NN	_	_	_
26	addition	addition	NN	_	_	_
27	.	.	.	_	_	_

1	13	13	CD	_	_	_
2	µl	µl	NN	_	_	_
3	of	of	IN	_	_	_
4	EB	EB	NNP	_	_	_
5	buffer	buffer	NN	_	_	_
6	were	be	VBD	_	_	_
7	used	use	VBN	_	_	_
8	for	for	IN	_	_	_
9	elution	elution	NN	_	_	_
10	of	of	IN	_	_	_
11	cDNA	cdna	NN	_	_	_
12	after	after	IN	_	_	_
13	its	its	PRP$	_	_	_
14	clean-up	clean-up	JJ	_	_	_
15	with	with	IN	_	_	_
16	the	the	DT	_	_	_
17	MiniElute	MiniElute	NNP	_	_	_
18	CR	cr	NN	_	_	_
19	purification	purification	NN	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Qiagen	qiagen	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	fragmentation	fragmentation	NN	_	_	_
3	was	be	VBD	_	_	_
4	done	do	VBN	_	_	_
5	in	in	IN	_	_	_
6	a	a	DT	_	_	_
7	20-µl	20-µl	JJ	_	_	_
8	reaction	reaction	NN	_	_	_
9	containing	contain	VBG	_	_	_
10	3.5	3.5	CD	_	_	_
11	µg	µg	NN	_	_	_
12	cDNA	cdna	NN	_	_	_
13	,	,	,	_	_	_
14	2	2	CD	_	_	_
15	µl	µl	NN	_	_	_
16	10x	10x	CD	_	_	_
17	One	one	CD	_	_	_
18	Phor-All	phor-all	NN	_	_	_
19	buffer	buffer	NN	_	_	_
20	,	,	,	_	_	_
21	2	2	CD	_	_	_
22	µl	µl	NN	_	_	_
23	DNase	dnase	NN	_	_	_
24	I	i	CD	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	diluted	dilute	VBN	_	_	_
27	to	to	TO	_	_	_
28	0.2	0.2	CD	_	_	_
29	U	U	NNP	_	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
31	Samples	sample	NNS	_	_	_
32	of	of	IN	_	_	_
33	magnetic	magnetic	JJ	_	_	_
34	field-treated	field-treated	JJ	_	_	_
35	or	or	CC	_	_	_
36	sham-treated	sham-treated	JJ	_	_	_
37	cells	cell	NNS	_	_	_
38	were	be	VBD	_	_	_
39	withdrawn	withdraw	VBN	_	_	_
40	as	as	IN	_	_	_
41	fast	fast	JJ	_	_	_
42	as	as	IN	_	_	_
43	possible	possible	JJ	_	_	_
44	from	from	IN	_	_	_
45	the	the	DT	_	_	_
46	bioreactor	bioreactor	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	not	not	RB	_	_	_
49	later	later	RB	_	_	_
50	than	than	IN	_	_	_
51	3	3	CD	_	_	_
52	min	min	NN	_	_	_
53	-RRB-	-rrb-	-RRB-	_	_	_
54	after	after	IN	_	_	_
55	the	the	DT	_	_	_
56	specified	specify	VBN	_	_	_
57	treatement	treatement	NN	_	_	_
58	period	period	NN	_	_	_
59	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	taken	take	VBN	_	_	_
3	during	during	IN	_	_	_
4	intermittent	intermittent	JJ	_	_	_
5	exposure	exposure	NN	_	_	_
6	were	be	VBD	_	_	_
7	withdrawn	withdraw	VBN	_	_	_
8	in	in	IN	_	_	_
9	the	the	DT	_	_	_
10	4	4	CD	_	_	_
11	min	min	NN	_	_	_
12	exposure	exposure	NN	_	_	_
13	break	break	NN	_	_	_
14	.	.	.	_	_	_

1	Unexposed	unexposed	JJ	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	withdrawn	withdraw	VBN	_	_	_
5	as	as	IN	_	_	_
6	fast	fast	JJ	_	_	_
7	as	as	IN	_	_	_
8	possible	possible	JJ	_	_	_
9	during	during	IN	_	_	_
10	steady-state	steady-state	JJ	_	_	_
11	conditions	condition	NNS	_	_	_
12	in	in	IN	_	_	_
13	the	the	DT	_	_	_
14	chemostat	chemostat	NN	_	_	_
15	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	the	the	DT	_	_	_
3	response	response	NN	_	_	_
4	control	control	NN	_	_	_
5	experiment	experiment	NN	_	_	_
6	,	,	,	_	_	_
7	samples	sample	NNS	_	_	_
8	were	be	VBD	_	_	_
9	withdrawn	withdraw	VBN	_	_	_
10	10	10	CD	_	_	_
11	min	min	NN	_	_	_
12	after	after	IN	_	_	_
13	addition	addition	NN	_	_	_
14	of	of	IN	_	_	_
15	1	1	CD	_	_	_
16	mM	mm	NN	KWSUPP	_	_
17	H2O2	h2o2	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	treated	treated	JJ	_	_	_
20	culture	culture	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	or	or	CC	_	_	_
23	the	the	DT	_	_	_
24	equivalent	equivalent	JJ	_	_	_
25	water	water	NN	_	_	_
26	volume	volume	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	reference	reference	NN	_	_	_
29	culture	culture	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	duration	duration	NN	_	_	_
4	:	:	:	_	_	_
5	10	10	CD	_	_	_
6	min	min	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	treatment	treatment	NN	_	_	_
9	duration	duration	NN	_	_	_
10	:	:	:	_	_	_
11	15	15	CD	_	_	_
12	h	h	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	treatment	treatment	NN	_	_	_
15	duration	duration	NN	_	_	_
16	:	:	:	_	_	_
17	2.5	2.5	CD	_	_	_
18	h	h	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	treatment	treatment	NN	_	_	_
21	duration	duration	NN	_	_	_
22	:	:	:	_	_	_
23	8	8	CD	_	_	_
24	min	min	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	treatment	treatment	NN	_	_	_
27	duration	duration	NN	_	_	_
28	:	:	:	_	_	_
29	none	none	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	treatment	treatment	NN	_	_	_
32	:	:	:	_	_	_
33	sham-treated	sham-treated	JJ	_	_	_
34	power	power	NN	_	_	_
35	line	line	NN	_	_	_
36	intermittent	intermittent	JJ	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	2	2	CD	_	_	_
39	min	min	NN	_	_	_
40	on	on	IN	_	_	_
41	,	,	,	_	_	_
42	4	4	CD	_	_	_
43	min	min	NN	_	_	_
44	off	off	IN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	magnetic	magnetic	JJ	_	_	_
47	field	field	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	treatment	treatment	NN	_	_	_
50	:	:	:	_	_	_
51	sham-treated	sham-treated	JJ	_	_	_
52	sinusoidal	sinusoidal	JJ	_	_	_
53	continous	continous	JJ	_	_	_
54	magnetic	magnetic	JJ	_	_	_
55	field	field	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	treatment	treatment	NN	_	_	_
58	:	:	:	_	_	_
59	sham-treated	sham-treated	JJ	_	_	_
60	sinusoidal	sinusoidal	JJ	_	_	_
61	intermittent	intermittent	JJ	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	2	2	CD	_	_	_
64	min	min	NN	_	_	_
65	on	on	IN	_	_	_
66	,	,	,	_	_	_
67	4	4	CD	_	_	_
68	min	min	NN	_	_	_
69	off	off	IN	_	_	_
70	-RRB-	-rrb-	-RRB-	_	_	_
71	magnetic	magnetic	JJ	_	_	_
72	field	field	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	treatment	treatment	NN	_	_	_
75	:	:	:	_	_	_
76	treated	treat	VBN	_	_	_
77	power	power	NN	_	_	_
78	line	line	NN	_	_	_
79	intermittent	intermittent	JJ	_	_	_
80	-LRB-	-lrb-	-LRB-	_	_	_
81	2	2	CD	_	_	_
82	min	min	NN	_	_	_
83	on	on	IN	_	_	_
84	,	,	,	_	_	_
85	4	4	CD	_	_	_
86	min	min	NN	_	_	_
87	off	off	IN	_	_	_
88	-RRB-	-rrb-	-RRB-	_	_	_
89	magnetic	magnetic	JJ	_	_	_
90	field	field	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	treatment	treatment	NN	_	_	_
93	:	:	:	_	_	_
94	treated	treat	VBN	_	_	_
95	sinusoidal	sinusoidal	JJ	_	_	_
96	continous	continous	JJ	_	_	_
97	magnetic	magnetic	JJ	_	_	_
98	field	field	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	treatment	treatment	NN	_	_	_
101	:	:	:	_	_	_
102	treated	treat	VBN	_	_	_
103	sinusoidal	sinusoidal	JJ	_	_	_
104	intermittent	intermittent	JJ	_	_	_
105	-LRB-	-lrb-	-LRB-	_	_	_
106	2	2	CD	_	_	_
107	min	min	NN	_	_	_
108	on	on	IN	_	_	_
109	,	,	,	_	_	_
110	4	4	CD	_	_	_
111	min	min	NN	_	_	_
112	off	off	IN	_	_	_
113	-RRB-	-rrb-	-RRB-	_	_	_
114	magnetic	magnetic	JJ	_	_	_
115	field	field	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	treatment	treatment	NN	_	_	_
118	:	:	:	_	_	_
119	unexposed	unexposed	JJ	_	_	_
120	,	,	,	_	_	_
121	left	leave	VBD	_	_	_
122	chamber	chamber	NN	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	treatment	treatment	NN	_	_	_
125	:	:	:	_	_	_
126	unexposed	unexposed	JJ	_	_	_
127	,	,	,	_	_	_
128	right	right	JJ	_	_	_
129	chamber	chamber	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	treatment	treatment	NN	_	_	_
132	:	:	:	_	_	_
133	unexposed	unexposed	JJ	_	_	_
134	,	,	,	_	_	_
135	treated	treat	VBN	_	_	_
136	with	with	IN	_	_	_
137	1mM	1mm	NN	_	_	_
138	H2O2	h2o2	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	treatment	treatment	NN	_	_	_
141	:	:	:	_	_	_
142	unexposed	unexposed	JJ	_	_	_
143	,	,	,	_	_	_
144	treated	treat	VBN	_	_	_
145	with	with	IN	_	_	_
146	water	water	NN	_	_	_
147	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
148	After	after	IN	_	_	_
149	each	each	DT	_	_	_
150	sequenced	sequence	VBN	_	_	_
151	fragments	fragment	NNS	_	_	_
152	were	be	VBD	_	_	_
153	aligned	align	VBN	_	_	_
154	to	to	TO	_	_	_
155	the	the	DT	_	_	_
156	reference	reference	NN	_	_	_
157	genome	genome	NN	_	_	_
158	using	use	VBG	_	_	_
159	Bowtie	Bowtie	NNP	_	_	_
160	,	,	,	_	_	_
161	the	the	DT	_	_	_
162	position	position	NN	_	_	_
163	of	of	IN	_	_	_
164	each	each	DT	_	_	_
165	alignment	alignment	NN	_	_	_
166	is	be	VBZ	_	_	_
167	distributed	distribute	VBN	_	_	_
168	into	into	IN	_	_	_
169	several	several	JJ	_	_	_
170	nucleotides	nucleotide	NNS	_	_	_
171	in	in	IN	_	_	_
172	the	the	DT	_	_	_
173	center	center	NN	_	_	_
174	of	of	IN	_	_	_
175	the	the	DT	_	_	_
176	footprint	footprint	NN	_	_	_
177	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	footprint	footprint	NN	_	_	_
4	read	read	NN	_	_	_
5	,	,	,	_	_	_
6	the	the	DT	_	_	_
7	center	center	NN	_	_	_
8	residues	residue	NNS	_	_	_
9	that	that	WDT	_	_	_
10	are	be	VBP	_	_	_
11	at	at	IN	_	_	_
12	least	least	JJS	_	_	_
13	12	12	CD	_	_	_
14	nucleotides	nucleotide	NNS	_	_	_
15	away	away	RB	_	_	_
16	from	from	IN	_	_	_
17	either	either	CC	_	_	_
18	ends	end	NNS	_	_	_
19	were	be	VBD	_	_	_
20	given	give	VBN	_	_	_
21	the	the	DT	_	_	_
22	same	same	JJ	_	_	_
23	score	score	NN	_	_	_
24	,	,	,	_	_	_
25	which	which	WDT	_	_	_
26	is	be	VBZ	_	_	_
27	weighted	weight	VBN	_	_	_
28	by	by	IN	_	_	_
29	the	the	DT	_	_	_
30	length	length	NN	_	_	_
31	of	of	IN	_	_	_
32	the	the	DT	_	_	_
33	fragment	fragment	NN	_	_	_
34	-LSB-	-lsb-	-LRB-	_	_	_
35	Oh	oh	UH	_	_	_
36	et	et	FW	_	_	_
37	al	al	FW	_	_	_
38	,	,	,	_	_	_
39	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	147	147	CD	_	_	_
3	,	,	,	_	_	_
4	1295	1295	CD	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	2011	2011	CD	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	-RSB-	-rsb-	-RRB-	_	_	_
9	.	.	.	_	_	_

1	More	more	RBR	_	_	_
2	at	at	IN	_	_	_
3	G.W.	G.W.	NNP	_	_	_
4	Li	Li	NNP	_	_	_
5	,	,	,	_	_	_
6	E.	E.	NNP	_	_	_
7	Oh	oh	UH	_	_	_
8	,	,	,	_	_	_
9	and	and	CC	_	_	_
10	J.S.	J.S.	NNP	_	_	_
11	Weissman	Weissman	NNP	_	_	_
12	,	,	,	_	_	_
13	Nature	Nature	NNP	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	in	in	IN	_	_	_
16	press	press	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	E.	e.	FW	_	_	_
20	coli	coli	FW	_	_	_
21	recoded	recode	VBN	_	_	_
22	ompF	ompf	NN	GEN	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
24	E.	e.	FW	_	_	_
25	coli	coli	FW	_	_	_
26	recoded	recode	VBN	_	_	_
27	ompF	ompf	NN	GEN	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	recoded	recode	VBN	_	_	_
30	ompF	ompf	NN	GEN	_	_
31	gene	gene	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Escherichia	escherichia	FW	Organism	_	_
35	coli	coli	FW	Organism	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Genome	Genome	NNP	_	_	_
38	Build	Build	NNP	_	_	_
39	:	:	:	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	medium	medium	NN	_	_	_
42	:	:	:	_	_	_
43	MOPS	mop	NNS	MED	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	OmpFrecode	ompfrecode	NN	_	_	_
46	_	_	CD	_	_	_
47	f.wig	f.wig	NN	_	_	_
48	:	:	:	_	_	_
49	NC	nc	NN	_	_	_
50	_	_	SYM	_	_	_
51	000913.2	000913.2	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	OmpFrecode	ompfrecode	NN	_	_	_
54	_	_	CD	_	_	_
55	r.wig	r.wig	NN	_	_	_
56	:	:	:	_	_	_
57	NC	NC	NNP	_	_	_
58	_	_	NNP	_	_	_
59	000913.2	000913.2	CD	_	_	_
60	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
61	Ribosome	Ribosome	NNP	_	_	_
62	protected	protect	VBD	_	_	_
63	mRNA	mrna	NN	_	_	_
64	fragments	fragment	NNS	_	_	_
65	were	be	VBD	_	_	_
66	size	size	NN	_	_	_
67	selected	select	VBN	_	_	_
68	via	via	IN	_	_	_
69	gel	gel	NN	_	_	_
70	purification	purification	NN	_	_	_
71	,	,	,	_	_	_
72	and	and	CC	_	_	_
73	ligated	ligate	VBN	_	_	_
74	to	to	TO	_	_	_
75	5	5	CD	_	_	_
76	'	'	''	_	_	_
77	adenylated	adenylate	VBN	_	_	_
78	DNA	dna	NN	_	_	_
79	oligo	oligo	JJ	_	_	_
80	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	reverse	reverse	JJ	_	_	_
3	transcription	transcription	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	single	single	JJ	_	_	_
7	stranded	stranded	JJ	_	_	_
8	DNA	dna	NN	_	_	_
9	was	be	VBD	_	_	_
10	circularized	circularize	VBN	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	PCR	pcr	NN	_	_	_
14	amplified	amplify	VBD	_	_	_
15	-LSB-	-lsb-	-LRB-	_	_	_
16	Oh	oh	UH	_	_	_
17	et	et	FW	_	_	_
18	al	al	FW	_	_	_
19	,	,	,	_	_	_
20	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	147	147	CD	_	_	_
3	,	,	,	_	_	_
4	1295	1295	CD	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	2011	2011	CD	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	-RSB-	-rsb-	-RRB-	_	_	_
9	.	.	.	_	_	_

1	More	more	RBR	_	_	_
2	at	at	IN	_	_	_
3	G.W.	G.W.	NNP	_	_	_
4	Li	Li	NNP	_	_	_
5	,	,	,	_	_	_
6	E.	E.	NNP	_	_	_
7	Oh	oh	UH	_	_	_
8	,	,	,	_	_	_
9	and	and	CC	_	_	_
10	J.S.	J.S.	NNP	_	_	_
11	Weissman	Weissman	NNP	_	_	_
12	,	,	,	_	_	_
13	Nature	Nature	NNP	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	in	in	IN	_	_	_
16	press	press	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	RNA-Seq	rna-seq	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	strain	strain	NN	_	_	_
22	:	:	:	_	_	_
23	BJW9	bjw9	NN	_	_	_
24	w	w	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	treatment	treatment	NN	_	_	_
27	:	:	:	_	_	_
28	Ribosome-protected	ribosome-protected	JJ	_	_	_
29	mRNA	mrna	NN	_	_	_
30	,	,	,	_	_	_
31	Ribosome	ribosome	NN	_	_	_
32	footprint	footprint	NN	_	_	_
33	sample	sample	NN	_	_	_
34	digested	digest	VBN	_	_	_
35	with	with	IN	_	_	_
36	60	60	CD	_	_	_
37	units	unit	NNS	_	_	_
38	of	of	IN	_	_	_
39	micrococcal	micrococcal	JJ	_	_	_
40	nuclease	nuclease	NN	_	_	_
41	per	per	IN	_	_	_
42	A260	a260	NN	_	_	_
43	absorbance	absorbance	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	aerobic	aerobic	JJ	_	_	_
46	reference	reference	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	anaerobic	anaerobic	JJ	_	_	_
49	reference	reference	NN	_	_	_
50	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
51	Escherichia	escherichia	FW	Organism	_	_
52	coli	coli	FW	Organism	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	fnr	fnr	SYM	GEN	_	_
55	-	-	:	_	_	_
56	aerobic	aerobic	JJ	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	fnr	fnr	SYM	GEN	_	_
59	-	-	:	_	_	_
60	aerobic	aerobic	JJ	_	_	_
61	AN	a	DT	_	_	_
62	rep	rep	NN	GEN	_	_
63	1	1	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	fnr	fnr	SYM	GEN	_	_
66	-	-	:	_	_	_
67	aerobic	aerobic	JJ	_	_	_
68	AN	a	DT	_	_	_
69	rep	rep	NN	GEN	_	_
70	2	2	CD	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
72	fnr	fnr	SYM	GEN	_	_
73	-	-	:	_	_	_
74	aerobic	aerobic	JJ	_	_	_
75	AN	a	DT	_	_	_
76	rep	rep	NN	GEN	_	_
77	3	3	CD	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	fnr	fnr	SYM	GEN	_	_
80	-	-	:	_	_	_
81	aerobic	aerobic	JJ	_	_	_
82	rep	rep	NN	GEN	_	_
83	1	1	CD	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	fnr	fnr	SYM	GEN	_	_
86	-	-	:	_	_	_
87	aerobic	aerobic	JJ	_	_	_
88	rep	rep	NN	GEN	_	_
89	2	2	CD	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
91	fnr	fnr	SYM	GEN	_	_
92	-	-	:	_	_	_
93	aerobic	aerobic	JJ	_	_	_
94	rep	rep	NN	GEN	_	_
95	3	3	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	fnr	fnr	SYM	GEN	_	_
98	-	-	:	_	_	_
99	anaerobic	anaerobic	JJ	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	fnr	fnr	SYM	GEN	_	_
102	-	-	:	_	_	_
103	anaerobic	anaerobic	JJ	_	_	_
104	AN	a	DT	_	_	_
105	rep	rep	NN	GEN	_	_
106	1	1	CD	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	fnr	fnr	SYM	GEN	_	_
109	-	-	:	_	_	_
110	anaerobic	anaerobic	JJ	_	_	_
111	AN	a	DT	_	_	_
112	rep	rep	NN	GEN	_	_
113	2	2	CD	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
115	fnr	fnr	SYM	GEN	_	_
116	-	-	:	_	_	_
117	anaerobic	anaerobic	JJ	_	_	_
118	AN	a	DT	_	_	_
119	rep	rep	NN	GEN	_	_
120	3	3	CD	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	fnr	fnr	SYM	GEN	_	_
123	-	-	:	_	_	_
124	anaerobic	anaerobic	NN	_	_	_
125	plus	plus	CC	_	_	_
126	NO2	no2	NN	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
128	fnr	fnr	SYM	GEN	_	_
129	-	-	:	_	_	_
130	anaerobic	anaerobic	NN	_	_	_
131	plus	plus	CC	_	_	_
132	NO2	no2	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
134	fnr	fnr	SYM	GEN	_	_
135	-	-	:	_	_	_
136	anaerobic	anaerobic	NN	_	_	_
137	plus	plus	CC	_	_	_
138	NO2	no2	NN	_	_	_
139	AN	a	DT	_	_	_
140	rep	rep	NN	GEN	_	_
141	1	1	CD	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	fnr	fnr	SYM	GEN	_	_
144	-	-	:	_	_	_
145	anaerobic	anaerobic	NN	_	_	_
146	plus	plus	CC	_	_	_
147	NO2	no2	NN	_	_	_
148	AN	a	DT	_	_	_
149	rep	rep	NN	GEN	_	_
150	2	2	CD	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
152	fnr	fnr	SYM	GEN	_	_
153	-	-	:	_	_	_
154	anaerobic	anaerobic	NN	_	_	_
155	plus	plus	CC	_	_	_
156	NO2	no2	NN	_	_	_
157	AN	a	DT	_	_	_
158	rep	rep	NN	GEN	_	_
159	3	3	CD	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	fnr	fnr	SYM	GEN	_	_
162	-	-	:	_	_	_
163	anaerobic	anaerobic	NN	_	_	_
164	plus	plus	CC	_	_	_
165	NO2	no2	NN	_	_	_
166	rep	rep	NN	GEN	_	_
167	1	1	CD	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	fnr	fnr	SYM	GEN	_	_
170	-	-	:	_	_	_
171	anaerobic	anaerobic	NN	_	_	_
172	plus	plus	CC	_	_	_
173	NO2	no2	NN	_	_	_
174	rep	rep	NN	GEN	_	_
175	2	2	CD	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
177	fnr	fnr	SYM	GEN	_	_
178	-	-	:	_	_	_
179	anaerobic	anaerobic	NN	_	_	_
180	plus	plus	CC	_	_	_
181	NO2	no2	NN	_	_	_
182	rep	rep	NN	GEN	_	_
183	3	3	CD	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	fnr	fnr	SYM	GEN	_	_
186	-	-	:	_	_	_
187	anaerobic	anaerobic	NN	_	_	_
188	plus	plus	CC	_	_	_
189	NO3	no3	NN	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
191	fnr	fnr	SYM	GEN	_	_
192	-	-	:	_	_	_
193	anaerobic	anaerobic	NN	_	_	_
194	plus	plus	CC	_	_	_
195	NO3	no3	NN	_	_	_
196	AN	a	DT	_	_	_
197	rep	rep	NN	GEN	_	_
198	1	1	CD	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	fnr	fnr	SYM	GEN	_	_
201	-	-	:	_	_	_
202	anaerobic	anaerobic	NN	_	_	_
203	plus	plus	CC	_	_	_
204	NO3	no3	NN	_	_	_
205	AN	a	DT	_	_	_
206	rep	rep	NN	GEN	_	_
207	2	2	CD	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
209	fnr	fnr	SYM	GEN	_	_
210	-	-	:	_	_	_
211	anaerobic	anaerobic	NN	_	_	_
212	plus	plus	CC	_	_	_
213	NO3	no3	NN	_	_	_
214	AN	a	DT	_	_	_
215	rep	rep	NN	GEN	_	_
216	3	3	CD	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	fnr	fnr	SYM	GEN	_	_
219	-	-	:	_	_	_
220	anaerobic	anaerobic	NN	_	_	_
221	plus	plus	CC	_	_	_
222	NO3	no3	NN	_	_	_
223	rep	rep	NN	GEN	_	_
224	1	1	CD	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	fnr	fnr	SYM	GEN	_	_
227	-	-	:	_	_	_
228	anaerobic	anaerobic	NN	_	_	_
229	plus	plus	CC	_	_	_
230	NO3	no3	NN	_	_	_
231	rep	rep	NN	GEN	_	_
232	2	2	CD	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
234	fnr	fnr	SYM	GEN	_	_
235	-	-	:	_	_	_
236	anaerobic	anaerobic	NN	_	_	_
237	plus	plus	CC	_	_	_
238	NO3	no3	NN	_	_	_
239	rep	rep	NN	GEN	_	_
240	3	3	CD	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	fnr	fnr	SYM	GEN	_	_
243	-	-	:	_	_	_
244	anaerobic	anaerobic	JJ	_	_	_
245	rep	rep	NN	GEN	_	_
246	1	1	CD	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	fnr	fnr	SYM	GEN	_	_
249	-	-	:	_	_	_
250	anaerobic	anaerobic	JJ	_	_	_
251	rep	rep	NN	GEN	_	_
252	2	2	CD	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
254	fnr	fnr	SYM	GEN	_	_
255	-	-	:	_	_	_
256	anaerobic	anaerobic	JJ	_	_	_
257	rep	rep	NN	GEN	_	_
258	3	3	CD	_	_	_
259	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
260	Genetic	Genetic	NNP	_	_	_
261	background	background	NN	_	_	_
262	:	:	:	_	_	_
263	fnr	fnr	SYM	GEN	_	_
264	-	-	:	_	_	_
265	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
266	Genetic	Genetic	NNP	_	_	_
267	background	background	NN	_	_	_
268	:	:	:	_	_	_
269	wt	wt	JJ	_	_	_
270	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
271	Genetic	Genetic	NNP	_	_	_
272	background	background	NN	_	_	_
273	:	:	:	_	_	_
274	wt	wt	JJ	_	_	_
275	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
276	Genetic	Genetic	NNP	_	_	_
277	background	background	NN	_	_	_
278	:	:	:	_	_	_
279	wtGrowth	wtgrowth	NN	_	_	_
280	conditions	condition	NNS	_	_	_
281	:	:	:	_	_	_
282	aerobic	aerobic	JJ	_	_	_
283	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
284	Growth	growth	NN	_	_	_
285	conditions	condition	NNS	_	_	_
286	:	:	:	_	_	_
287	aaerobic	aaerobic	JJ	_	_	_
288	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
289	Growth	growth	NN	_	_	_
290	conditions	condition	NNS	_	_	_
291	:	:	:	_	_	_
292	aerobic	aerobic	JJ	_	_	_
293	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
294	Growth	growth	NN	_	_	_
295	conditions	condition	NNS	_	_	_
296	:	:	:	_	_	_
297	anaerobic	anaerobic	JJ	_	_	_
298	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
299	Growth	growth	NN	_	_	_
300	conditions	condition	NNS	_	_	_
301	:	:	:	_	_	_
302	anaerobic	anaerobic	JJ	_	_	_
303	plus	plus	CC	_	_	_
304	NO2	no2	NN	_	_	_
305	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
306	Growth	growth	NN	_	_	_
307	conditions	condition	NNS	_	_	_
308	:	:	:	_	_	_
309	anaerobic	anaerobic	JJ	_	_	_
310	plus	plus	CC	_	_	_
311	NO3	no3	NN	_	_	_
312	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
313	narXL	narxl	NN	TU	_	_
314	anaerobic	anaerobic	NN	_	_	_
315	plus	plus	CC	_	_	_
316	NO2	no2	NN	_	_	_
317	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
318	narXLP	narxlp	NN	_	_	_
319	anaerobic	anaerobic	NN	_	_	_
320	plus	plus	CC	_	_	_
321	NO2	no2	NN	_	_	_
322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
323	narXLP	narxlp	NN	_	_	_
324	rep	rep	NN	GEN	_	_
325	1	1	CD	_	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	narXLP	narxlp	NN	_	_	_
328	rep	rep	NN	GEN	_	_
329	2	2	CD	_	_	_
330	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
331	narXLP	narxlp	NN	_	_	_
332	rep	rep	NN	GEN	_	_
333	3	3	CD	_	_	_
334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
335	narXL	narxl	NN	TU	_	_
336	rep	rep	NN	GEN	_	_
337	1	1	CD	_	_	_
338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
339	narXL	narxl	NN	TU	_	_
340	rep	rep	NN	GEN	_	_
341	2	2	CD	_	_	_
342	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
343	narXL	narxl	NN	TU	_	_
344	rep	rep	NN	GEN	_	_
345	3	3	CD	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	narXL	narxl	NN	TU	_	_
348	rep	rep	NN	GEN	_	_
349	4	4	CD	_	_	_
350	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
351	Raw	raw	NN	_	_	_
352	,	,	,	_	_	_
353	not	not	RB	_	_	_
354	normalised	normalised	JJ	_	_	_
355	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
356	Strain	Strain	NNP	_	_	_
357	:	:	:	_	_	_
358	E.coli	e.coli	NNS	_	_	_
359	K-12	k-12	NN	_	_	_
360	MG1655	mg1655	NN	_	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
362	Strain	strain	NN	_	_	_
363	:	:	:	_	_	_
364	E.coli	e.coli	NNS	_	_	_
365	K-12	k-12	NN	_	_	_
366	MG1655	mg1655	NN	_	_	_
367	,	,	,	_	_	_
368	Genetic	genetic	JJ	_	_	_
369	background	background	NN	_	_	_
370	:	:	:	_	_	_
371	fnr	fnr	SYM	GEN	_	_
372	-	-	:	_	_	_
373	,	,	,	_	_	_
374	Growth	growth	NN	_	_	_
375	conditions	condition	NNS	_	_	_
376	:	:	:	_	_	_
377	aerobic	aerobic	JJ	_	_	_
378	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
379	Strain	Strain	NNP	_	_	_
380	:	:	:	_	_	_
381	E.coli	e.coli	NNS	_	_	_
382	K-12	k-12	NN	_	_	_
383	MG1655	mg1655	NN	_	_	_
384	,	,	,	_	_	_
385	Genetic	genetic	JJ	_	_	_
386	background	background	NN	_	_	_
387	:	:	:	_	_	_
388	fnr	fnr	SYM	GEN	_	_
389	-	-	:	_	_	_
390	,	,	,	_	_	_
391	Growth	growth	NN	_	_	_
392	conditions	condition	NNS	_	_	_
393	:	:	:	_	_	_
394	anaerobic	anaerobic	JJ	_	_	_
395	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
396	Strain	strain	NN	_	_	_
397	:	:	:	_	_	_
398	E.coli	e.coli	NNS	_	_	_
399	K-12	k-12	NN	_	_	_
400	MG1655	mg1655	NN	_	_	_
401	,	,	,	_	_	_
402	Genetic	genetic	JJ	_	_	_
403	background	background	NN	_	_	_
404	:	:	:	_	_	_
405	fnr	fnr	SYM	GEN	_	_
406	-	-	:	_	_	_
407	,	,	,	_	_	_
408	Growth	growth	NN	_	_	_
409	conditions	condition	NNS	_	_	_
410	:	:	:	_	_	_
411	anaerobic	anaerobic	JJ	_	_	_
412	plus	plus	CC	_	_	_
413	NO2	no2	NN	_	_	_
414	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
415	Strain	strain	NN	_	_	_
416	:	:	:	_	_	_
417	E.coli	e.coli	NNS	_	_	_
418	K-12	k-12	NN	_	_	_
419	MG1655	mg1655	NN	_	_	_
420	,	,	,	_	_	_
421	Genetic	genetic	JJ	_	_	_
422	background	background	NN	_	_	_
423	:	:	:	_	_	_
424	fnr	fnr	SYM	GEN	_	_
425	-	-	:	_	_	_
426	,	,	,	_	_	_
427	Growth	growth	NN	_	_	_
428	conditions	condition	NNS	_	_	_
429	:	:	:	_	_	_
430	anaerobic	anaerobic	JJ	_	_	_
431	plus	plus	CC	_	_	_
432	NO3	no3	NN	_	_	_
433	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
434	Strain	strain	NN	_	_	_
435	:	:	:	_	_	_
436	E.coli	e.coli	NNS	_	_	_
437	K-12	k-12	NN	_	_	_
438	MG1655	mg1655	NN	_	_	_
439	,	,	,	_	_	_
440	Genetic	genetic	JJ	_	_	_
441	background	background	NN	_	_	_
442	:	:	:	_	_	_
443	narXL	narxl	NN	TU	_	_
444	,	,	,	_	_	_
445	Growth	growth	NN	_	_	_
446	conditions	condition	NNS	_	_	_
447	:	:	:	_	_	_
448	anaerobic	anaerobic	JJ	_	_	_
449	plus	plus	CC	_	_	_
450	NO2	no2	NN	_	_	_
451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
452	Strain	strain	NN	_	_	_
453	:	:	:	_	_	_
454	E.coli	e.coli	NNS	_	_	_
455	K-12	k-12	NN	_	_	_
456	MG1655	mg1655	NN	_	_	_
457	,	,	,	_	_	_
458	Genetic	genetic	JJ	_	_	_
459	background	background	NN	_	_	_
460	:	:	:	_	_	_
461	narXLP	narxlp	NN	_	_	_
462	,	,	,	_	_	_
463	Growth	growth	NN	_	_	_
464	conditions	condition	NNS	_	_	_
465	:	:	:	_	_	_
466	anaerobic	anaerobic	JJ	_	_	_
467	plus	plus	CC	_	_	_
468	NO2	no2	NN	_	_	_
469	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
470	Strain	strain	NN	_	_	_
471	:	:	:	_	_	_
472	E.coli	e.coli	NNS	_	_	_
473	K-12	k-12	NN	_	_	_
474	MG1655	mg1655	NN	_	_	_
475	,	,	,	_	_	_
476	Genetic	genetic	JJ	_	_	_
477	background	background	NN	_	_	_
478	:	:	:	_	_	_
479	wt	wt	JJ	_	_	_
480	,	,	,	_	_	_
481	Growth	growth	NN	_	_	_
482	conditions	condition	NNS	_	_	_
483	:	:	:	_	_	_
484	aerobic	aerobic	JJ	_	_	_
485	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
486	Strain	Strain	NNP	_	_	_
487	:	:	:	_	_	_
488	E.coli	e.coli	NNS	_	_	_
489	K-12	k-12	NN	_	_	_
490	MG1655	mg1655	NN	_	_	_
491	,	,	,	_	_	_
492	Genetic	genetic	JJ	_	_	_
493	background	background	NN	_	_	_
494	:	:	:	_	_	_
495	wt	wt	JJ	_	_	_
496	,	,	,	_	_	_
497	Growth	growth	NN	_	_	_
498	conditions	condition	NNS	_	_	_
499	:	:	:	_	_	_
500	anaerobic	anaerobic	JJ	_	_	_
501	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
502	Strain	strain	NN	_	_	_
503	:	:	:	_	_	_
504	E.coli	e.coli	NNS	_	_	_
505	K-12	k-12	NN	_	_	_
506	MG1655	mg1655	NN	_	_	_
507	,	,	,	_	_	_
508	Genetic	genetic	JJ	_	_	_
509	background	background	NN	_	_	_
510	:	:	:	_	_	_
511	wt	wt	JJ	_	_	_
512	,	,	,	_	_	_
513	Growth	growth	NN	_	_	_
514	conditions	condition	NNS	_	_	_
515	:	:	:	_	_	_
516	anaerobic	anaerobic	JJ	_	_	_
517	plus	plus	CC	_	_	_
518	NO2	no2	NN	_	_	_
519	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
520	Strain	strain	NN	_	_	_
521	:	:	:	_	_	_
522	E.coli	e.coli	NNS	_	_	_
523	K-12	k-12	NN	_	_	_
524	MG1655	mg1655	NN	_	_	_
525	,	,	,	_	_	_
526	Genetic	genetic	JJ	_	_	_
527	background	background	NN	_	_	_
528	:	:	:	_	_	_
529	wt	wt	JJ	_	_	_
530	,	,	,	_	_	_
531	Growth	growth	NN	_	_	_
532	conditions	condition	NNS	_	_	_
533	:	:	:	_	_	_
534	anaerobic	anaerobic	JJ	_	_	_
535	plus	plus	CC	_	_	_
536	NO3	no3	NN	_	_	_
537	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
538	wt	wt	JJ	_	_	_
539	aerobic	aerobic	JJ	_	_	_
540	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
541	wt	wt	JJ	_	_	_
542	aerobic	aerobic	JJ	_	_	_
543	AN	a	DT	_	_	_
544	rep	rep	NN	GEN	_	_
545	1	1	CD	_	_	_
546	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
547	wt	wt	JJ	_	_	_
548	aerobic	aerobic	JJ	_	_	_
549	AN	a	DT	_	_	_
550	rep	rep	NN	GEN	_	_
551	2	2	CD	_	_	_
552	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
553	wt	wt	JJ	_	_	_
554	aerobic	aerobic	JJ	_	_	_
555	AN	a	DT	_	_	_
556	rep	rep	NN	GEN	_	_
557	3	3	CD	_	_	_
558	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
559	wt	wt	JJ	_	_	_
560	aerobic	aerobic	JJ	_	_	_
561	rep	rep	NN	GEN	_	_
562	1	1	CD	_	_	_
563	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
564	wt	wt	JJ	_	_	_
565	aerobic	aerobic	JJ	_	_	_
566	rep	rep	NN	GEN	_	_
567	2	2	CD	_	_	_
568	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
569	wt	wt	JJ	_	_	_
570	aerobic	aerobic	JJ	_	_	_
571	rep	rep	NN	GEN	_	_
572	3	3	CD	_	_	_
573	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
574	wt	wt	JJ	_	_	_
575	anaerobic	anaerobic	JJ	_	_	_
576	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
577	wt	wt	JJ	_	_	_
578	anaerobic	anaerobic	JJ	_	_	_
579	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
580	wt	wt	JJ	_	_	_
581	anaerobic	anaerobic	JJ	_	_	_
582	AN	a	DT	_	_	_
583	rep	rep	NN	GEN	_	_
584	1	1	CD	_	_	_
585	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
586	wt	wt	JJ	_	_	_
587	anaerobic	anaerobic	JJ	_	_	_
588	AN	a	DT	_	_	_
589	rep	rep	NN	GEN	_	_
590	2	2	CD	_	_	_
591	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
592	wt	wt	JJ	_	_	_
593	anaerobic	anaerobic	JJ	_	_	_
594	AN	a	DT	_	_	_
595	rep	rep	NN	GEN	_	_
596	3	3	CD	_	_	_
597	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
598	wt	wt	JJ	_	_	_
599	anaerobic	anaerobic	NN	_	_	_
600	plus	plus	CC	_	_	_
601	NO2	no2	NN	_	_	_
602	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
603	wt	wt	JJ	_	_	_
604	anaerobic	anaerobic	NN	_	_	_
605	plus	plus	CC	_	_	_
606	NO2	no2	NN	_	_	_
607	AN	a	DT	_	_	_
608	rep	rep	NN	GEN	_	_
609	1	1	CD	_	_	_
610	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
611	wt	wt	JJ	_	_	_
612	anaerobic	anaerobic	NN	_	_	_
613	plus	plus	CC	_	_	_
614	NO2	no2	NN	_	_	_
615	AN	a	DT	_	_	_
616	rep	rep	NN	GEN	_	_
617	2	2	CD	_	_	_
618	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
619	wt	wt	JJ	_	_	_
620	anaerobic	anaerobic	NN	_	_	_
621	plus	plus	CC	_	_	_
622	NO2	no2	NN	_	_	_
623	AN	a	DT	_	_	_
624	rep	rep	NN	GEN	_	_
625	3	3	CD	_	_	_
626	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
627	wt	wt	JJ	_	_	_
628	anaerobic	anaerobic	NN	_	_	_
629	plus	plus	CC	_	_	_
630	NO2	no2	NN	_	_	_
631	rep	rep	NN	GEN	_	_
632	1	1	CD	_	_	_
633	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
634	wt	wt	JJ	_	_	_
635	anaerobic	anaerobic	NN	_	_	_
636	plus	plus	CC	_	_	_
637	NO2	no2	NN	_	_	_
638	rep	rep	NN	GEN	_	_
639	2	2	CD	_	_	_
640	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
641	wt	wt	JJ	_	_	_
642	anaerobic	anaerobic	NN	_	_	_
643	plus	plus	CC	_	_	_
644	NO2	no2	NN	_	_	_
645	rep	rep	NN	GEN	_	_
646	3	3	CD	_	_	_
647	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
648	wt	wt	JJ	_	_	_
649	anaerobic	anaerobic	NN	_	_	_
650	plus	plus	CC	_	_	_
651	NO3	no3	NN	_	_	_
652	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
653	wt	wt	JJ	_	_	_
654	anaerobic	anaerobic	NN	_	_	_
655	plus	plus	CC	_	_	_
656	NO3	no3	NN	_	_	_
657	AN	a	DT	_	_	_
658	rep	rep	NN	GEN	_	_
659	1	1	CD	_	_	_
660	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
661	wt	wt	JJ	_	_	_
662	anaerobic	anaerobic	NN	_	_	_
663	plus	plus	CC	_	_	_
664	NO3	no3	NN	_	_	_
665	AN	a	DT	_	_	_
666	rep	rep	NN	GEN	_	_
667	2	2	CD	_	_	_
668	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
669	wt	wt	JJ	_	_	_
670	anaerobic	anaerobic	NN	_	_	_
671	plus	plus	CC	_	_	_
672	NO3	no3	NN	_	_	_
673	AN	a	DT	_	_	_
674	rep	rep	NN	GEN	_	_
675	3	3	CD	_	_	_
676	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
677	wt	wt	JJ	_	_	_
678	anaerobic	anaerobic	NN	_	_	_
679	plus	plus	CC	_	_	_
680	NO3	no3	NN	_	_	_
681	rep	rep	NN	GEN	_	_
682	1	1	CD	_	_	_
683	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
684	wt	wt	JJ	_	_	_
685	anaerobic	anaerobic	NN	_	_	_
686	plus	plus	CC	_	_	_
687	NO3	no3	NN	_	_	_
688	rep	rep	NN	GEN	_	_
689	2	2	CD	_	_	_
690	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
691	wt	wt	JJ	_	_	_
692	anaerobic	anaerobic	NN	_	_	_
693	plus	plus	CC	_	_	_
694	NO3	no3	NN	_	_	_
695	rep	rep	NN	GEN	_	_
696	3	3	CD	_	_	_
697	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
698	wt	wt	JJ	_	_	_
699	anaerobic	anaerobic	JJ	_	_	_
700	rep	rep	NN	GEN	_	_
701	1	1	CD	_	_	_
702	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
703	wt	wt	JJ	_	_	_
704	anaerobic	anaerobic	JJ	_	_	_
705	rep	rep	NN	GEN	_	_
706	2	2	CD	_	_	_
707	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
708	wt	wt	JJ	_	_	_
709	anaerobic	anaerobic	JJ	_	_	_
710	rep	rep	NN	GEN	_	_
711	3	3	CD	_	_	_
712	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
713	A	a	DT	_	_	_
714	5	5	CD	_	_	_
715	ml	ml	NN	_	_	_
716	overnight	overnight	JJ	_	_	_
717	culture	culture	NN	_	_	_
718	of	of	IN	_	_	_
719	E.	e.	FW	_	_	_
720	coli	coli	FW	_	_	_
721	O157	o157	NN	_	_	_
722	:	:	:	_	_	_
723	H7	h7	NN	_	_	_
724	-LRB-	-lrb-	-LRB-	_	_	_
725	Sakai	Sakai	NNP	_	_	_
726	-RRB-	-rrb-	-RRB-	_	_	_
727	was	be	VBD	_	_	_
728	grown	grow	VBN	_	_	_
729	in	in	IN	_	_	_
730	Neidhardt	Neidhardt	NNP	_	_	_
731	's	's	POS	_	_	_
732	EZ	EZ	NNP	_	_	_
733	Rich	Rich	NNP	_	_	_
734	Defined	Defined	NNP	_	_	_
735	Medium	medium	NN	_	_	_
736	for	for	IN	_	_	_
737	18	18	CD	_	_	_
738	h	h	NN	_	_	_
739	at	at	IN	_	_	_
740	37C	37c	NN	_	_	_
741	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	diluted	dilute	VBN	_	_	_
5	1:100	1:100	CD	_	_	_
6	into	into	IN	_	_	_
7	50	50	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	fresh	fresh	JJ	_	_	_
11	,	,	,	_	_	_
12	prewarmed	prewarmed	JJ	_	_	_
13	Neidhardt	Neidhardt	NNP	_	_	_
14	's	's	POS	_	_	_
15	EZ	EZ	NNP	_	_	_
16	Rich	Rich	NNP	_	_	_
17	Defined	Defined	NNP	_	_	_
18	Medium	medium	NN	_	_	_
19	in	in	IN	_	_	_
20	a	a	DT	_	_	_
21	125	125	CD	_	_	_
22	ml	ml	NN	_	_	_
23	Ehrlenmeyer	ehrlenmeyer	NN	_	_	_
24	flask	flask	NN	_	_	_
25	and	and	CC	_	_	_
26	shaken	shake	VBN	_	_	_
27	at	at	IN	_	_	_
28	37C	37c	NN	_	_	_
29	,	,	,	_	_	_
30	150	150	CD	_	_	_
31	rpm	rpm	NN	_	_	_
32	in	in	IN	_	_	_
33	a	a	DT	_	_	_
34	New	New	NNP	_	_	_
35	Brunswick	Brunswick	NNP	_	_	_
36	Shaking	shake	VBG	_	_	_
37	water	water	NN	_	_	_
38	bath	bath	NN	_	_	_
39	until	until	IN	_	_	_
40	the	the	DT	_	_	_
41	culture	culture	NN	_	_	_
42	density	density	NN	_	_	_
43	reached	reach	VBD	_	_	_
44	0.4	0.4	CD	_	_	_
45	.	.	.	_	_	_

1	Half	half	NN	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	transferred	transfer	VBN	_	_	_
7	to	to	TO	_	_	_
8	a	a	DT	_	_	_
9	second	second	JJ	_	_	_
10	identical	identical	JJ	_	_	_
11	flask	flask	NN	_	_	_
12	containing	contain	VBG	_	_	_
13	menadione	menadione	NN	_	_	_
14	bisulphite	bisulphite	NN	_	_	_
15	to	to	TO	_	_	_
16	a	a	DT	_	_	_
17	final	final	JJ	_	_	_
18	concentration	concentration	NN	_	_	_
19	of	of	IN	_	_	_
20	0.5	0.5	CD	_	_	_
21	mg	mg	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	A	a	DT	_	_	_
24	5	5	CD	_	_	_
25	ml	ml	NN	_	_	_
26	overnight	overnight	JJ	_	_	_
27	culture	culture	NN	_	_	_
28	of	of	IN	_	_	_
29	E.	e.	FW	_	_	_
30	coli	coli	FW	_	_	_
31	O157	o157	NN	_	_	_
32	:	:	:	_	_	_
33	H7	h7	NN	_	_	_
34	was	be	VBD	_	_	_
35	grown	grow	VBN	_	_	_
36	in	in	IN	_	_	_
37	Neidhardt	Neidhardt	NNP	_	_	_
38	's	's	POS	_	_	_
39	EZ	EZ	NNP	_	_	_
40	Rich	Rich	NNP	_	_	_
41	Defined	Defined	NNP	_	_	_
42	Medium	medium	NN	_	_	_
43	for	for	IN	_	_	_
44	18	18	CD	_	_	_
45	h	h	NN	_	_	_
46	at	at	IN	_	_	_
47	37C	37c	NN	_	_	_
48	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	diluted	dilute	VBN	_	_	_
5	1:100	1:100	CD	_	_	_
6	into	into	IN	_	_	_
7	50	50	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	fresh	fresh	JJ	_	_	_
11	,	,	,	_	_	_
12	prewarmed	prewarmed	JJ	_	_	_
13	Neidhardt	Neidhardt	NNP	_	_	_
14	's	's	POS	_	_	_
15	EZ	EZ	NNP	_	_	_
16	Rich	Rich	NNP	_	_	_
17	Defined	Defined	NNP	_	_	_
18	Medium	medium	NN	_	_	_
19	in	in	IN	_	_	_
20	a	a	DT	_	_	_
21	125	125	CD	_	_	_
22	ml	ml	NN	_	_	_
23	Ehrlenmeyer	ehrlenmeyer	NN	_	_	_
24	flask	flask	NN	_	_	_
25	and	and	CC	_	_	_
26	shaken	shake	VBN	_	_	_
27	at	at	IN	_	_	_
28	37C	37c	NN	_	_	_
29	,	,	,	_	_	_
30	150	150	CD	_	_	_
31	rpm	rpm	NN	_	_	_
32	in	in	IN	_	_	_
33	a	a	DT	_	_	_
34	New	New	NNP	_	_	_
35	Brunswick	Brunswick	NNP	_	_	_
36	Shaking	shake	VBG	_	_	_
37	water	water	NN	_	_	_
38	bath	bath	NN	_	_	_
39	until	until	IN	_	_	_
40	the	the	DT	_	_	_
41	culture	culture	NN	_	_	_
42	density	density	NN	_	_	_
43	reached	reach	VBD	_	_	_
44	0.4	0.4	CD	_	_	_
45	.	.	.	_	_	_

1	Half	half	NN	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	transferred	transfer	VBN	_	_	_
7	to	to	TO	_	_	_
8	a	a	DT	_	_	_
9	second	second	JJ	_	_	_
10	identical	identical	JJ	_	_	_
11	flask	flask	NN	_	_	_
12	containing	contain	VBG	_	_	_
13	menadione	menadione	NN	_	_	_
14	bisulphite	bisulphite	NN	_	_	_
15	to	to	TO	_	_	_
16	a	a	DT	_	_	_
17	final	final	JJ	_	_	_
18	concentration	concentration	NN	_	_	_
19	of	of	IN	_	_	_
20	0.5	0.5	CD	_	_	_
21	mg	mg	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	A	a	DT	_	_	_
24	5	5	CD	_	_	_
25	ml	ml	NN	_	_	_
26	overnight	overnight	JJ	_	_	_
27	culture	culture	NN	_	_	_
28	of	of	IN	_	_	_
29	MG1655	mg1655	NN	_	_	_
30	was	be	VBD	_	_	_
31	grown	grow	VBN	_	_	_
32	in	in	IN	_	_	_
33	Neidhardt	Neidhardt	NNP	_	_	_
34	's	's	POS	_	_	_
35	EZ	EZ	NNP	_	_	_
36	Rich	Rich	NNP	_	_	_
37	Defined	Defined	NNP	_	_	_
38	Medium	medium	NN	_	_	_
39	for	for	IN	_	_	_
40	18	18	CD	_	_	_
41	h	h	NN	_	_	_
42	at	at	IN	_	_	_
43	37C	37c	NN	_	_	_
44	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	diluted	dilute	VBN	_	_	_
5	1:100	1:100	CD	_	_	_
6	into	into	IN	_	_	_
7	50	50	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	fresh	fresh	JJ	_	_	_
11	,	,	,	_	_	_
12	prewarmed	prewarmed	JJ	_	_	_
13	Neidhardt	Neidhardt	NNP	_	_	_
14	's	's	POS	_	_	_
15	EZ	EZ	NNP	_	_	_
16	Rich	Rich	NNP	_	_	_
17	Defined	Defined	NNP	_	_	_
18	Medium	medium	NN	_	_	_
19	in	in	IN	_	_	_
20	a	a	DT	_	_	_
21	125	125	CD	_	_	_
22	ml	ml	NN	_	_	_
23	Ehrlenmeyer	ehrlenmeyer	NN	_	_	_
24	flask	flask	NN	_	_	_
25	and	and	CC	_	_	_
26	shaken	shake	VBN	_	_	_
27	at	at	IN	_	_	_
28	37C	37c	NN	_	_	_
29	,	,	,	_	_	_
30	150	150	CD	_	_	_
31	rpm	rpm	NN	_	_	_
32	in	in	IN	_	_	_
33	a	a	DT	_	_	_
34	New	New	NNP	_	_	_
35	Brunswick	Brunswick	NNP	_	_	_
36	Shaking	shake	VBG	_	_	_
37	water	water	NN	_	_	_
38	bath	bath	NN	_	_	_
39	until	until	IN	_	_	_
40	the	the	DT	_	_	_
41	culture	culture	NN	_	_	_
42	density	density	NN	_	_	_
43	reached	reach	VBD	_	_	_
44	0.4	0.4	CD	_	_	_
45	.	.	.	_	_	_

1	Half	half	NN	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	transferred	transfer	VBN	_	_	_
7	to	to	TO	_	_	_
8	a	a	DT	_	_	_
9	second	second	JJ	_	_	_
10	identical	identical	JJ	_	_	_
11	flask	flask	NN	_	_	_
12	containing	contain	VBG	_	_	_
13	menadione	menadione	NN	_	_	_
14	bisulphite	bisulphite	NN	_	_	_
15	to	to	TO	_	_	_
16	a	a	DT	_	_	_
17	final	final	JJ	_	_	_
18	concentration	concentration	NN	_	_	_
19	of	of	IN	_	_	_
20	0.5	0.5	CD	_	_	_
21	mg	mg	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	A	a	DT	_	_	_
24	5	5	CD	_	_	_
25	ml	ml	NN	_	_	_
26	overnight	overnight	JJ	_	_	_
27	culture	culture	NN	_	_	_
28	of	of	IN	_	_	_
29	MG1655	mg1655	NN	_	_	_
30	was	be	VBD	_	_	_
31	grown	grow	VBN	_	_	_
32	in	in	IN	_	_	_
33	Neidhardt	Neidhardt	NNP	_	_	_
34	's	's	POS	_	_	_
35	EZ	EZ	NNP	_	_	_
36	Rich	Rich	NNP	_	_	_
37	Defined	Defined	NNP	_	_	_
38	Medium	medium	NN	_	_	_
39	for	for	IN	_	_	_
40	18	18	CD	_	_	_
41	h	h	NN	_	_	_
42	at	at	IN	_	_	_
43	37C	37c	NN	_	_	_
44	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	diluted	dilute	VBN	_	_	_
5	1:100	1:100	CD	_	_	_
6	into	into	IN	_	_	_
7	50	50	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	fresh	fresh	JJ	_	_	_
11	,	,	,	_	_	_
12	prewarmed	prewarmed	JJ	_	_	_
13	Neidhardt	Neidhardt	NNP	_	_	_
14	's	's	POS	_	_	_
15	EZ	EZ	NNP	_	_	_
16	Rich	Rich	NNP	_	_	_
17	Defined	Defined	NNP	_	_	_
18	Medium	medium	NN	_	_	_
19	in	in	IN	_	_	_
20	a	a	DT	_	_	_
21	125	125	CD	_	_	_
22	ml	ml	NN	_	_	_
23	Ehrlenmeyer	ehrlenmeyer	NN	_	_	_
24	flask	flask	NN	_	_	_
25	and	and	CC	_	_	_
26	shaken	shake	VBN	_	_	_
27	at	at	IN	_	_	_
28	37C	37c	NN	_	_	_
29	,	,	,	_	_	_
30	150	150	CD	_	_	_
31	rpm	rpm	NN	_	_	_
32	in	in	IN	_	_	_
33	a	a	DT	_	_	_
34	New	New	NNP	_	_	_
35	Bruswick	Bruswick	NNP	_	_	_
36	Shaking	shake	VBG	_	_	_
37	water	water	NN	_	_	_
38	bath	bath	NN	_	_	_
39	until	until	IN	_	_	_
40	the	the	DT	_	_	_
41	culture	culture	NN	_	_	_
42	density	density	NN	_	_	_
43	reached	reach	VBD	_	_	_
44	0.4	0.4	CD	_	_	_
45	.	.	.	_	_	_

1	Half	half	NN	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	transferred	transfer	VBN	_	_	_
7	to	to	TO	_	_	_
8	a	a	DT	_	_	_
9	second	second	JJ	_	_	_
10	identical	identical	JJ	_	_	_
11	flask	flask	NN	_	_	_
12	containing	contain	VBG	_	_	_
13	menadione	menadione	NN	_	_	_
14	bisulphite	bisulphite	NN	_	_	_
15	to	to	TO	_	_	_
16	a	a	DT	_	_	_
17	final	final	JJ	_	_	_
18	concentration	concentration	NN	_	_	_
19	of	of	IN	_	_	_
20	0.5	0.5	CD	_	_	_
21	mg	mg	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	An	a	DT	_	_	_
24	RNeasy	rneasy	JJ	_	_	_
25	kit	kit	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Qiagen	Qiagen	NNP	_	_	_
28	Ltd	Ltd	NNP	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	was	be	VBD	_	_	_
31	used	use	VBN	_	_	_
32	to	to	TO	_	_	_
33	extract	extract	VB	_	_	_
34	the	the	DT	_	_	_
35	total	total	JJ	_	_	_
36	RNA	rna	NN	_	_	_
37	according	accord	VBG	_	_	_
38	to	to	TO	_	_	_
39	manufacturers	manufacturer	NNS	_	_	_
40	'	'	POS	_	_	_
41	instructions	instruction	NNS	_	_	_
42	.	.	.	_	_	_

1	Contaminating	contaminate	VBG	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	using	use	VBG	_	_	_
7	on-column	on-column	JJ	_	_	_
8	DNase	dnase	NN	_	_	_
9	I	i	CD	_	_	_
10	digestion	digestion	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	Qiagen	NNP	_	_	_
13	Ltd	Ltd	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	quality	quality	NN	_	_	_
3	and	and	CC	_	_	_
4	quantity	quantity	NN	_	_	_
5	of	of	IN	_	_	_
6	the	the	DT	_	_	_
7	RNA	rna	NN	_	_	_
8	preparations	preparation	NNS	_	_	_
9	were	be	VBD	_	_	_
10	determined	determine	VBN	_	_	_
11	with	with	IN	_	_	_
12	an	a	DT	_	_	_
13	Agilent	Agilent	NNP	_	_	_
14	2100	2100	CD	_	_	_
15	Bioanalyzer	Bioanalyzer	NNP	_	_	_
16	by	by	IN	_	_	_
17	using	use	VBG	_	_	_
18	the	the	DT	_	_	_
19	RNA	rna	NN	_	_	_
20	6000	6000	CD	_	_	_
21	nano	nano	NN	_	_	_
22	assay	assay	NN	_	_	_
23	Labchip	labchip	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Agilent	Agilent	NNP	_	_	_
26	,	,	,	_	_	_
27	Stockport	Stockport	NNP	_	_	_
28	,	,	,	_	_	_
29	United	United	NNP	_	_	_
30	Kingdom	Kingdom	NNP	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	K-12	k-12	NN	_	_	_
5	untreated	untreated	JJ	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	reference	reference	NN	_	_	_
8	sample	sample	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	_	_	SYM	_	_	_
11	rep	rep	NN	GEN	_	_
12	#	#	#	_	_	_
13	1	1	CD	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	E.	E.	NNP	_	_	_
16	coli	coli	NN	_	_	_
17	K-12	k-12	NN	_	_	_
18	untreated	untreated	JJ	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	reference	reference	NN	_	_	_
21	sample	sample	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	_	_	SYM	_	_	_
24	rep	rep	NN	GEN	_	_
25	#	#	#	_	_	_
26	2	2	CD	_	_	_
27	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
28	E.	E.	NNP	_	_	_
29	coli	coli	NN	_	_	_
30	K-12	k-12	NN	_	_	_
31	untreated	untreated	JJ	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	reference	reference	NN	_	_	_
34	sample	sample	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	_	_	SYM	_	_	_
37	rep	rep	NN	GEN	_	_
38	#	#	#	_	_	_
39	3	3	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	E.	e.	FW	_	_	_
42	coli	coli	FW	_	_	_
43	O157	o157	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	Sakai	Sakai	NNP	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	untreated	untreated	JJ	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	reference	reference	NN	_	_	_
50	sample	sample	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	_	_	SYM	_	_	_
53	rep	rep	NN	GEN	_	_
54	#	#	#	_	_	_
55	1	1	CD	_	_	_
56	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
57	E.	E.	NNP	_	_	_
58	coli	coli	NN	_	_	_
59	O157	o157	NN	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	Sakai	Sakai	NNP	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	untreated	untreated	JJ	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	reference	reference	NN	_	_	_
66	sample	sample	NN	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	_	_	SYM	_	_	_
69	rep	rep	NN	GEN	_	_
70	#	#	#	_	_	_
71	2	2	CD	_	_	_
72	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
73	E.	E.	NNP	_	_	_
74	coli	coli	NN	_	_	_
75	O157	o157	NN	_	_	_
76	-LRB-	-lrb-	-LRB-	_	_	_
77	Sakai	Sakai	NNP	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	untreated	untreated	JJ	_	_	_
80	-LRB-	-lrb-	-LRB-	_	_	_
81	reference	reference	NN	_	_	_
82	sample	sample	NN	_	_	_
83	-RRB-	-rrb-	-RRB-	_	_	_
84	_	_	SYM	_	_	_
85	rep	rep	NN	GEN	_	_
86	#	#	#	_	_	_
87	3	3	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	Escherichia	escherichia	FW	Organism	_	_
90	coli	coli	FW	Organism	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	Escherichia	escherichia	FW	Organism	_	_
93	coli	coli	FW	Organism	_	_
94	K-12	k-12	NN	_	_	_
95	treated	treat	VBN	_	_	_
96	with	with	IN	_	_	_
97	menadione	menadione	NN	_	_	_
98	_	_	CD	_	_	_
99	rep	rep	NN	GEN	_	_
100	#	#	#	_	_	_
101	1	1	CD	_	_	_
102	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
103	Escherichia	escherichia	FW	Organism	_	_
104	coli	coli	FW	Organism	_	_
105	K-12	k-12	NN	_	_	_
106	treated	treat	VBN	_	_	_
107	with	with	IN	_	_	_
108	menadione	menadione	NN	_	_	_
109	_	_	CD	_	_	_
110	rep	rep	NN	GEN	_	_
111	#	#	#	_	_	_
112	2	2	CD	_	_	_
113	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
114	Escherichia	escherichia	FW	Organism	_	_
115	coli	coli	FW	Organism	_	_
116	K-12	k-12	NN	_	_	_
117	treated	treat	VBN	_	_	_
118	with	with	IN	_	_	_
119	menadione	menadione	NN	_	_	_
120	_	_	CD	_	_	_
121	rep	rep	NN	GEN	_	_
122	#	#	#	_	_	_
123	3	3	CD	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	Escherichia	escherichia	FW	Organism	_	_
126	coli	coli	FW	Organism	_	_
127	O157	o157	NN	_	_	_
128	-LRB-	-lrb-	-LRB-	_	_	_
129	Sakai	Sakai	NNP	_	_	_
130	-RRB-	-rrb-	-RRB-	_	_	_
131	treated	treat	VBN	_	_	_
132	with	with	IN	_	_	_
133	menadione	menadione	NN	_	_	_
134	_	_	CD	_	_	_
135	rep	rep	NN	GEN	_	_
136	#	#	#	_	_	_
137	1	1	CD	_	_	_
138	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
139	Escherichia	escherichia	FW	Organism	_	_
140	coli	coli	FW	Organism	_	_
141	O157	o157	NN	_	_	_
142	-LRB-	-lrb-	-LRB-	_	_	_
143	Sakai	Sakai	NNP	_	_	_
144	-RRB-	-rrb-	-RRB-	_	_	_
145	treated	treat	VBN	_	_	_
146	with	with	IN	_	_	_
147	menadione	menadione	NN	_	_	_
148	_	_	CD	_	_	_
149	rep	rep	NN	GEN	_	_
150	#	#	#	_	_	_
151	2	2	CD	_	_	_
152	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
153	Escherichia	escherichia	FW	Organism	_	_
154	coli	coli	FW	Organism	_	_
155	O157	o157	NN	_	_	_
156	-LRB-	-lrb-	-LRB-	_	_	_
157	Sakai	Sakai	NNP	_	_	_
158	-RRB-	-rrb-	-RRB-	_	_	_
159	treated	treat	VBN	_	_	_
160	with	with	IN	_	_	_
161	menadione	menadione	NN	_	_	_
162	_	_	CD	_	_	_
163	rep	rep	NN	GEN	_	_
164	#	#	#	_	_	_
165	3	3	CD	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	GenePix	GenePix	NNP	_	_	_
168	software	software	NN	_	_	_
169	-LRB-	-lrb-	-LRB-	_	_	_
170	Axon	Axon	NNP	_	_	_
171	Instruments	Instruments	NNP	_	_	_
172	,	,	,	_	_	_
173	Union	Union	NNP	_	_	_
174	City	City	NNP	_	_	_
175	,	,	,	_	_	_
176	CA	CA	NNP	_	_	_
177	-RRB-	-rrb-	-RRB-	_	_	_
178	version	version	NN	_	_	_
179	5.1	5.1	CD	_	_	_
180	was	be	VBD	_	_	_
181	used	use	VBN	_	_	_
182	to	to	TO	_	_	_
183	process	process	VB	_	_	_
184	the	the	DT	_	_	_
185	scanned	scan	VBN	_	_	_
186	data	datum	NNS	_	_	_
187	and	and	CC	_	_	_
188	generate	generate	VB	_	_	_
189	the	the	DT	_	_	_
190	gpr	gpr	NN	GEN	_	_
191	files	file	NNS	_	_	_
192	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2	medium	medium	NN	_	_	_
3	:	:	:	_	_	_
4	Neidhardt	Neidhardt	NNP	_	_	_
5	's	's	POS	_	_	_
6	EZ	EZ	NNP	_	_	_
7	Rich	Rich	NNP	_	_	_
8	Defined	Defined	NNP	_	_	_
9	Medium	medium	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Teknova	Teknova	NNP	_	_	_
12	,	,	,	_	_	_
13	USA	USA	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	od600	od600	CD	_	_	_
17	:	:	:	_	_	_
18	0.4	0.4	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	Oxidative	oxidative	JJ	_	_	_
21	stress	stress	NN	_	_	_
22	in	in	IN	_	_	_
23	E.	e.	FW	_	_	_
24	coli	coli	FW	_	_	_
25	K-12	k-12	NN	_	_	_
26	#	#	#	_	_	_
27	1	1	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Oxidative	oxidative	JJ	_	_	_
30	stress	stress	NN	_	_	_
31	in	in	IN	_	_	_
32	E.	e.	FW	_	_	_
33	coli	coli	FW	_	_	_
34	K-12	k-12	NN	_	_	_
35	#	#	#	_	_	_
36	2	2	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
38	Oxidative	oxidative	JJ	_	_	_
39	stress	stress	NN	_	_	_
40	in	in	IN	_	_	_
41	E.	e.	FW	_	_	_
42	coli	coli	FW	_	_	_
43	K-12	k-12	NN	_	_	_
44	#	#	#	_	_	_
45	3	3	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	Oxidative	oxidative	JJ	_	_	_
48	stress	stress	NN	_	_	_
49	in	in	IN	_	_	_
50	E.	e.	FW	_	_	_
51	coli	coli	FW	_	_	_
52	O157	o157	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	Sakai	Sakai	NNP	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	#	#	#	_	_	_
57	1	1	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	Oxidative	oxidative	JJ	_	_	_
60	stress	stress	NN	_	_	_
61	in	in	IN	_	_	_
62	E.	e.	FW	_	_	_
63	coli	coli	FW	_	_	_
64	O157	o157	NN	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	Sakai	Sakai	NNP	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	#	#	#	_	_	_
69	2	2	CD	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
71	Oxidative	oxidative	JJ	_	_	_
72	stress	stress	NN	_	_	_
73	in	in	IN	_	_	_
74	E.	e.	FW	_	_	_
75	coli	coli	FW	_	_	_
76	O157	o157	NN	_	_	_
77	-LRB-	-lrb-	-LRB-	_	_	_
78	Sakai	Sakai	NNP	_	_	_
79	-RRB-	-rrb-	-RRB-	_	_	_
80	#	#	#	_	_	_
81	3	3	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	strain	strain	NN	_	_	_
84	:	:	:	_	_	_
85	k-12	k-12	NN	_	_	_
86	MG1655	mg1655	NN	_	_	_
87	wild-type	wild-type	JJ	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	strain	strain	NN	_	_	_
90	:	:	:	_	_	_
91	o157	o157	NN	_	_	_
92	:	:	:	_	_	_
93	H7	h7	NN	_	_	_
94	-LRB-	-lrb-	-LRB-	_	_	_
95	Sakai	Sakai	NNP	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	wild-type	wild-type	JJ	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	treatment	treatment	NN	_	_	_
100	:	:	:	_	_	_
101	0.5	0.5	CD	_	_	_
102	mg	mg	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	ampicilin	ampicilin	NN	_	_	_
105	treatment	treatment	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	Ampicilin	ampicilin	NN	_	_	_
108	_	_	NN	_	_	_
109	treatment	treatment	NN	_	_	_
110	_	_	NN	_	_	_
111	plasmidmappedreads	plasmidmappedread	NNS	_	_	_
112	_	_	VBP	_	_	_
113	statistical	statistical	JJ	_	_	_
114	_	_	NN	_	_	_
115	output.txt	output.txt	NN	_	_	_
116	:	:	:	_	_	_
117	NC	NC	NNP	_	_	_
118	_	_	NNP	_	_	_
119	012692.1	012692.1	CD	_	_	_
120	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
121	Amp	Amp	NNP	_	_	_
122	_	_	NNP	_	_	_
123	Treatment	treatment	NN	_	_	_
124	_	_	NN	_	_	_
125	genomemappedreads	genomemappedread	NNS	_	_	_
126	_	_	VBP	_	_	_
127	statistical	statistical	JJ	_	_	_
128	_	_	NN	_	_	_
129	output.txt	output.txt	NN	_	_	_
130	:	:	:	_	_	_
131	NC	nc	NN	_	_	_
132	_	_	SYM	_	_	_
133	000913.2	000913.2	CD	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	bacteria	bacterium	NNS	_	_	_
136	grown	grow	VBN	_	_	_
137	at	at	IN	_	_	_
138	37	37	CD	_	_	_
139	°	°	CD	_	_	_
140	C	c	NN	_	_	_
141	with	with	IN	_	_	_
142	shaking	shake	VBG	_	_	_
143	until	until	IN	_	_	_
144	log	log	NN	_	_	_
145	phase	phase	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	bacteria	bacterium	NNS	_	_	_
148	grown	grow	VBN	_	_	_
149	at	at	IN	_	_	_
150	37	37	CD	_	_	_
151	°	°	CD	_	_	_
152	C	c	NN	_	_	_
153	with	with	IN	_	_	_
154	shaking	shake	VBG	_	_	_
155	until	until	IN	_	_	_
156	log	log	NN	_	_	_
157	phase	phase	NN	_	_	_
158	with	with	IN	_	_	_
159	ampicilin	ampicilin	NN	_	_	_
160	treatment	treatment	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	bacteria	bacterium	NNS	_	_	_
163	grown	grow	VBN	_	_	_
164	at	at	IN	_	_	_
165	37	37	CD	_	_	_
166	°	°	CD	_	_	_
167	C	c	NN	_	_	_
168	with	with	IN	_	_	_
169	shaking	shake	VBG	_	_	_
170	until	until	IN	_	_	_
171	log	log	NN	_	_	_
172	phase	phase	NN	_	_	_
173	with	with	IN	_	_	_
174	florfenicol	florfenicol	NN	_	_	_
175	treatment	treatment	NN	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	bacteria	bacterium	NNS	_	_	_
178	grown	grow	VBN	_	_	_
179	at	at	IN	_	_	_
180	37	37	CD	_	_	_
181	°	°	CD	_	_	_
182	C	c	NN	_	_	_
183	with	with	IN	_	_	_
184	shaking	shake	VBG	_	_	_
185	until	until	IN	_	_	_
186	log	log	NN	_	_	_
187	phase	phase	NN	_	_	_
188	with	with	IN	_	_	_
189	streptomycin	streptomycin	NN	_	_	_
190	treatment	treatment	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	cDNA	cdna	NN	_	_	_
193	reads	read	VBZ	_	_	_
194	were	be	VBD	_	_	_
195	trimmed	trim	VBN	_	_	_
196	so	so	RB	_	_	_
197	that	that	IN	_	_	_
198	the	the	DT	_	_	_
199	quality	quality	NN	_	_	_
200	at	at	IN	_	_	_
201	each	each	DT	_	_	_
202	base	base	NN	_	_	_
203	position	position	NN	_	_	_
204	was	be	VBD	_	_	_
205	above	above	IN	_	_	_
206	30	30	CD	_	_	_
207	-LRB-	-lrb-	-LRB-	_	_	_
208	~	~	CD	_	_	_
209	15-20	15-20	CD	_	_	_
210	bp	bp	NN	_	_	_
211	-RRB-	-rrb-	-RRB-	_	_	_
212	and	and	CC	_	_	_
213	then	then	RB	_	_	_
214	mapped	map	VBD	_	_	_
215	either	either	CC	_	_	_
216	to	to	TO	_	_	_
217	the	the	DT	_	_	_
218	E.	e.	FW	_	_	_
219	coli	coli	FW	_	_	_
220	K-12	k-12	NN	_	_	_
221	MG1655	mg1655	NN	_	_	_
222	published	publish	VBN	_	_	_
223	genome	genome	NN	_	_	_
224	sequence	sequence	NN	_	_	_
225	-LRB-	-lrb-	-LRB-	_	_	_
226	Genbank	Genbank	NNP	_	_	_
227	accession	accession	NN	_	_	_
228	no	no	DT	_	_	_
229	.	.	.	_	_	_

1	NC	nc	NN	_	_	_
2	_	_	SYM	_	_	_
3	000913	000913	CD	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	or	or	CC	_	_	_
6	to	to	TO	_	_	_
7	the	the	DT	_	_	_
8	pAR060302	par060302	NN	_	_	_
9	published	publish	VBN	_	_	_
10	sequence	sequence	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Genbank	Genbank	NNP	_	_	_
13	accession	accession	NN	_	_	_
14	no	no	DT	_	_	_
15	.	.	.	_	_	_

1	NC	nc	NN	_	_	_
2	_	_	SYM	_	_	_
3	092692	092692	CD	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	using	use	VBG	_	_	_
6	BOWTIE	BOWTIE	NNP	_	_	_
7	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	E.	e.	FW	_	_	_
3	coli	coli	FW	_	_	_
4	strain	strain	NN	_	_	_
5	DH5α	dh5α	NN	_	_	_
6	has	have	VBZ	_	_	_
7	an	a	DT	_	_	_
8	incomplete	incomplete	JJ	_	_	_
9	annotation	annotation	NN	_	_	_
10	and	and	CC	_	_	_
11	for	for	IN	_	_	_
12	this	this	DT	_	_	_
13	reason	reason	NN	_	_	_
14	the	the	DT	_	_	_
15	E.	e.	FW	_	_	_
16	coli	coli	FW	_	_	_
17	K-12	k-12	NN	_	_	_
18	annotation	annotation	NN	_	_	_
19	was	be	VBD	_	_	_
20	used	use	VBN	_	_	_
21	,	,	,	_	_	_
22	representing	represent	VBG	_	_	_
23	an	a	DT	_	_	_
24	estimation	estimation	NN	_	_	_
25	of	of	IN	_	_	_
26	differentially	differentially	RB	_	_	_
27	expressed	express	VBN	_	_	_
28	genes	gene	NNS	_	_	_
29	due	due	JJ	_	_	_
30	to	to	TO	_	_	_
31	exposure	exposure	NN	_	_	_
32	of	of	IN	_	_	_
33	antimicrobials	antimicrobial	NNS	_	_	_
34	.	.	.	_	_	_

1	Mapped	map	VBN	_	_	_
2	reads	read	VBZ	_	_	_
3	for	for	IN	_	_	_
4	3	3	CD	_	_	_
5	seperate	seperate	JJ	_	_	_
6	sequencing	sequencing	NN	_	_	_
7	runs	run	NNS	_	_	_
8	were	be	VBD	_	_	_
9	combined	combine	VBN	_	_	_
10	because	because	IN	_	_	_
11	some	some	DT	_	_	_
12	sequencing	sequencing	NN	_	_	_
13	runs	run	NNS	_	_	_
14	were	be	VBD	_	_	_
15	not	not	RB	_	_	_
16	fully	fully	RB	_	_	_
17	completed	complete	VBN	_	_	_
18	due	due	JJ	_	_	_
19	to	to	TO	_	_	_
20	technical	technical	JJ	_	_	_
21	difficulties	difficulty	NNS	_	_	_
22	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	condition	condition	NN	_	_	_
4	,	,	,	_	_	_
5	graphs	graph	NNS	_	_	_
6	representing	represent	VBG	_	_	_
7	the	the	DT	_	_	_
8	number	number	NN	_	_	_
9	of	of	IN	_	_	_
10	mapped	map	VBN	_	_	_
11	reads	read	VBZ	_	_	_
12	per	per	IN	_	_	_
13	nucleotide	nucleotide	NN	_	_	_
14	were	be	VBD	_	_	_
15	generated	generate	VBN	_	_	_
16	and	and	CC	_	_	_
17	visualized	visualize	VBN	_	_	_
18	using	use	VBG	_	_	_
19	the	the	DT	_	_	_
20	Integrated	Integrated	NNP	_	_	_
21	Genome	Genome	NNP	_	_	_
22	Viewer	Viewer	NNP	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	IGV	igv	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	Images	image	NNS	_	_	_
2	were	be	VBD	_	_	_
3	created	create	VBN	_	_	_
4	using	use	VBG	_	_	_
5	XplasMap	xplasmap	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	http	http	NN	_	_	_
8	:	:	:	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
10	Cells	cell	NNS	_	_	_
11	were	be	VBD	_	_	_
12	pelleted	pelleted	JJ	_	_	_
13	and	and	CC	_	_	_
14	RNA	rna	NN	_	_	_
15	was	be	VBD	_	_	_
16	purified	purify	VBN	_	_	_
17	using	use	VBG	_	_	_
18	a	a	DT	_	_	_
19	commercially	commercially	RB	_	_	_
20	available	available	JJ	_	_	_
21	RNA	rna	NN	_	_	_
22	extraction	extraction	NN	_	_	_
23	kit	kit	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Qiagen	qiagen	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	preparations	preparation	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	subjected	subject	VBN	_	_	_
6	to	to	TO	_	_	_
7	a	a	DT	_	_	_
8	DNase	dnase	NN	_	_	_
9	treatment	treatment	NN	_	_	_
10	to	to	TO	_	_	_
11	eliminate	eliminate	VB	_	_	_
12	DNA	dna	NN	_	_	_
13	contamination	contamination	NN	_	_	_
14	from	from	IN	_	_	_
15	the	the	DT	_	_	_
16	sample	sample	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Qiagen	qiagen	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	treatment	treatment	NN	_	_	_
3	was	be	VBD	_	_	_
4	also	also	RB	_	_	_
5	included	include	VBN	_	_	_
6	to	to	TO	_	_	_
7	deplete	deplete	VB	_	_	_
8	ribosomal	ribosomal	JJ	_	_	_
9	RNA	rna	NN	_	_	_
10	using	use	VBG	_	_	_
11	a	a	DT	_	_	_
12	commercially	commercially	RB	_	_	_
13	available	available	JJ	_	_	_
14	kit	kit	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	MicrobExpress	MicrobExpress	NNP	_	_	_
17	,	,	,	_	_	_
18	Ambion	Ambion	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	two	two	CD	_	_	_
3	biological	biological	JJ	_	_	_
4	replicates	replicate	VBZ	_	_	_
5	for	for	IN	_	_	_
6	each	each	DT	_	_	_
7	growth	growth	NN	_	_	_
8	condition	condition	NN	_	_	_
9	were	be	VBD	_	_	_
10	pooled	pool	VBN	_	_	_
11	for	for	IN	_	_	_
12	sequencing	sequencing	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	strain	strain	NN	_	_	_
5	DH5α	dh5α	NN	_	_	_
6	harboring	harbor	VBG	_	_	_
7	pAR060302	par060302	NN	_	_	_
8	was	be	VBD	_	_	_
9	grown	grow	VBN	_	_	_
10	in	in	IN	_	_	_
11	10	10	CD	_	_	_
12	mL	ml	NN	_	_	_
13	DifcoTM	difcotm	NN	_	_	_
14	Luria-Bertani	luria-bertani	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	LB	lb	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	broth	broth	NN	_	_	_
19	aliquots	aliquot	NNS	_	_	_
20	at	at	IN	_	_	_
21	37º	37º	CD	_	_	_
22	C	c	NN	_	_	_
23	with	with	IN	_	_	_
24	shaking	shake	VBG	_	_	_
25	until	until	IN	_	_	_
26	an	a	DT	_	_	_
27	OD600	od600	NN	_	_	_
28	of	of	IN	_	_	_
29	0.5	0.5	CD	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	florfenicol	florfenicol	NN	_	_	_
6	treatment	treatment	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Florfenicol	florfenicol	NN	_	_	_
9	_	_	NN	_	_	_
10	treatment	treatment	NN	_	_	_
11	_	_	NN	_	_	_
12	plasmidmappedreads	plasmidmappedread	NNS	_	_	_
13	_	_	VBP	_	_	_
14	statistical	statistical	JJ	_	_	_
15	_	_	NN	_	_	_
16	output.txt	output.txt	NN	_	_	_
17	:	:	:	_	_	_
18	NC	NC	NNP	_	_	_
19	_	_	NNP	_	_	_
20	012692.1	012692.1	CD	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	Flor	Flor	NNP	_	_	_
23	_	_	JJ	_	_	_
24	treatment	treatment	NN	_	_	_
25	_	_	NN	_	_	_
26	genomemappedreads	genomemappedread	NNS	_	_	_
27	_	_	VBP	_	_	_
28	statistical	statistical	JJ	_	_	_
29	_	_	NN	_	_	_
30	output.txt	output.txt	NN	_	_	_
31	:	:	:	_	_	_
32	NC	NC	NNP	_	_	_
33	_	_	NNP	_	_	_
34	000913.2	000913.2	CD	_	_	_
35	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
36	Genome	Genome	NNP	_	_	_
37	Build	Build	NNP	_	_	_
38	:	:	:	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
40	no	no	DT	_	_	_
41	treatment	treatment	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	RNA-Seq	rna-seq	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	strain	strain	NN	_	_	_
46	:	:	:	_	_	_
47	DH5α	dh5α	NN	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	pAR060302	par060302	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	streptomycin	streptomycin	NN	_	_	_
53	treatment	treatment	NN	_	_	_
54	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
55	Streptomycin	Streptomycin	NNP	_	_	_
56	_	_	NN	_	_	_
57	treatment	treatment	NN	_	_	_
58	_	_	NN	_	_	_
59	plasmidmappedreads	plasmidmappedread	NNS	_	_	_
60	_	_	VBP	_	_	_
61	statistical	statistical	JJ	_	_	_
62	_	_	NN	_	_	_
63	output.txt	output.txt	NN	_	_	_
64	:	:	:	_	_	_
65	NC	nc	NN	_	_	_
66	_	_	SYM	_	_	_
67	012692.1	012692.1	CD	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
69	Strep	strep	JJ	_	_	_
70	_	_	NN	_	_	_
71	treatment	treatment	NN	_	_	_
72	_	_	NN	_	_	_
73	genomemappedreads	genomemappedread	NNS	_	_	_
74	_	_	VBP	_	_	_
75	statistical	statistical	JJ	_	_	_
76	_	_	NN	_	_	_
77	output.txt	output.txt	NN	_	_	_
78	:	:	:	_	_	_
79	NC	nc	NN	_	_	_
80	_	_	SYM	_	_	_
81	000913.2	000913.2	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	treatment	treatment	NN	_	_	_
84	:	:	:	_	_	_
85	ampicillin	ampicillin	NN	_	_	_
86	-LRB-	-lrb-	-LRB-	_	_	_
87	50	50	CD	_	_	_
88	µg	µg	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	treatment	treatment	NN	_	_	_
91	:	:	:	_	_	_
92	florfenicol	florfenicol	NN	_	_	_
93	-LRB-	-lrb-	-LRB-	_	_	_
94	30	30	CD	_	_	_
95	µg	µg	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	treatment	treatment	NN	_	_	_
98	:	:	:	_	_	_
99	none	none	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	treatment	treatment	NN	_	_	_
102	:	:	:	_	_	_
103	streptomycin	streptomycin	NN	_	_	_
104	-LRB-	-lrb-	-LRB-	_	_	_
105	50	50	CD	_	_	_
106	µg	µg	NN	_	_	_
107	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
108	E.	E.	NNP	_	_	_
109	coli	coli	NN	_	_	_
110	O157	o157	NN	_	_	_
111	:	:	:	_	_	_
112	H7	h7	NN	_	_	_
113	interacted	interact	VBD	_	_	_
114	with	with	IN	_	_	_
115	lettuce	lettuce	NN	_	_	_
116	rhizosphere	rhizosphere	NN	_	_	_
117	biological	biological	JJ	_	_	_
118	rep	rep	NN	GEN	_	_
119	1	1	CD	_	_	_
120	slide	slide	NN	_	_	_
121	1	1	CD	_	_	_
122	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
123	E.	E.	NNP	_	_	_
124	coli	coli	NN	_	_	_
125	O157	o157	NN	_	_	_
126	:	:	:	_	_	_
127	H7	h7	NN	_	_	_
128	interacted	interact	VBD	_	_	_
129	with	with	IN	_	_	_
130	lettuce	lettuce	NN	_	_	_
131	rhizosphere	rhizosphere	NN	_	_	_
132	biological	biological	JJ	_	_	_
133	rep	rep	NN	GEN	_	_
134	1	1	CD	_	_	_
135	slide	slide	NN	_	_	_
136	2	2	CD	_	_	_
137	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
138	E.	E.	NNP	_	_	_
139	coli	coli	NN	_	_	_
140	O157	o157	NN	_	_	_
141	:	:	:	_	_	_
142	H7	h7	NN	_	_	_
143	interacted	interact	VBD	_	_	_
144	with	with	IN	_	_	_
145	lettuce	lettuce	NN	_	_	_
146	rhizosphere	rhizosphere	NN	_	_	_
147	biological	biological	JJ	_	_	_
148	rep	rep	NN	GEN	_	_
149	2	2	CD	_	_	_
150	slide	slide	NN	_	_	_
151	3	3	CD	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	E.	e.	FW	_	_	_
154	coli	coli	FW	_	_	_
155	O157	o157	NN	_	_	_
156	:	:	:	_	_	_
157	H7	h7	NN	_	_	_
158	interacted	interact	VBD	_	_	_
159	with	with	IN	_	_	_
160	lettuce	lettuce	NN	_	_	_
161	rhizosphere	rhizosphere	NN	_	_	_
162	biological	biological	JJ	_	_	_
163	rep	rep	NN	GEN	_	_
164	2	2	CD	_	_	_
165	slide	slide	NN	_	_	_
166	4	4	CD	_	_	_
167	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
168	E.	E.	NNP	_	_	_
169	coli	coli	NN	_	_	_
170	O157	o157	NN	_	_	_
171	:	:	:	_	_	_
172	H7	h7	NN	_	_	_
173	interacted	interact	VBD	_	_	_
174	with	with	IN	_	_	_
175	lettuce	lettuce	NN	_	_	_
176	rhizosphere	rhizosphere	NN	_	_	_
177	biological	biological	JJ	_	_	_
178	rep	rep	NN	GEN	_	_
179	3	3	CD	_	_	_
180	slide	slide	NN	_	_	_
181	5	5	CD	_	_	_
182	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
183	E.	E.	NNP	_	_	_
184	coli	coli	NN	_	_	_
185	O157	o157	NN	_	_	_
186	:	:	:	_	_	_
187	H7	h7	NN	_	_	_
188	interacted	interact	VBD	_	_	_
189	with	with	IN	_	_	_
190	lettuce	lettuce	NN	_	_	_
191	rhizosphere	rhizosphere	NN	_	_	_
192	biological	biological	JJ	_	_	_
193	rep	rep	NN	GEN	_	_
194	3	3	CD	_	_	_
195	slide	slide	NN	_	_	_
196	6	6	CD	_	_	_
197	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
198	Escherichia	escherichia	FW	Organism	_	_
199	coli	coli	FW	Organism	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	Escherichia	escherichia	FW	Organism	_	_
202	coli	coli	FW	Organism	_	_
203	EDL	edl	NN	_	_	_
204	933	933	CD	_	_	_
205	cells	cell	NNS	_	_	_
206	grown	grow	VBN	_	_	_
207	in	in	IN	_	_	_
208	the	the	DT	_	_	_
209	hydroponic	hydroponic	JJ	_	_	_
210	system	system	NN	_	_	_
211	without	without	IN	_	_	_
212	interacting	interact	VBG	_	_	_
213	with	with	IN	_	_	_
214	the	the	DT	_	_	_
215	lettuce	lettuce	NN	_	_	_
216	rhizosphere	rhizosphere	NN	_	_	_
217	for	for	IN	_	_	_
218	3	3	CD	_	_	_
219	days	day	NNS	_	_	_
220	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
221	Escherichia	escherichia	FW	Organism	_	_
222	coli	coli	FW	Organism	_	_
223	EDL	edl	NN	_	_	_
224	933	933	CD	_	_	_
225	cells	cell	NNS	_	_	_
226	interacted	interact	VBD	_	_	_
227	with	with	IN	_	_	_
228	the	the	DT	_	_	_
229	lettuce	lettuce	NN	_	_	_
230	rhizosphere	rhizosphere	NN	_	_	_
231	for	for	IN	_	_	_
232	3	3	CD	_	_	_
233	days	day	NNS	_	_	_
234	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
235	Escherichia	escherichia	FW	Organism	_	_
236	coli	coli	FW	Organism	_	_
237	EDL	edl	NN	_	_	_
238	933	933	CD	_	_	_
239	were	be	VBD	_	_	_
240	grown	grow	VBN	_	_	_
241	in	in	IN	_	_	_
242	10	10	CD	_	_	_
243	ml	ml	NN	_	_	_
244	of	of	IN	_	_	_
245	LB	lb	NN	MED	_	_
246	medium	medium	NN	MED	_	_
247	until	until	IN	_	_	_
248	stationary	stationary	JJ	GrowthPhase	_	_
249	phase	phase	NN	GrowthPhase	_	_
250	,	,	,	_	_	_
251	collected	collect	VBN	_	_	_
252	by	by	IN	_	_	_
253	centrifugation	centrifugation	NN	_	_	_
254	at	at	IN	_	_	_
255	8,000	8,000	CD	_	_	_
256	×	×	CD	_	_	_
257	g	g	NN	_	_	_
258	for	for	IN	_	_	_
259	10	10	CD	_	_	_
260	min	min	NN	_	_	_
261	,	,	,	_	_	_
262	and	and	CC	_	_	_
263	washed	wash	VBN	_	_	_
264	twice	twice	RB	_	_	_
265	with	with	IN	_	_	_
266	sterilized	sterilize	VBN	_	_	_
267	,	,	,	_	_	_
268	plant	plant	NN	_	_	_
269	growth	growth	NN	_	_	_
270	medium	medium	NN	_	_	_
271	-LRB-	-lrb-	-LRB-	_	_	_
272	Caspersen	Caspersen	NNP	_	_	_
273	et	et	FW	_	_	_
274	al.	al.	FW	_	_	_
275	1999	1999	CD	_	_	_
276	-RRB-	-rrb-	-RRB-	_	_	_
277	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	resultant	resultant	JJ	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	re-suspended	re-suspended	JJ	_	_	_
6	in	in	IN	_	_	_
7	10	10	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	same	same	JJ	_	_	_
12	plant	plant	NN	_	_	_
13	growth	growth	NN	_	_	_
14	medium	medium	NN	_	_	_
15	to	to	TO	_	_	_
16	a	a	DT	_	_	_
17	final	final	JJ	_	_	_
18	concentration	concentration	NN	_	_	_
19	of	of	IN	_	_	_
20	approximately	approximately	RB	_	_	_
21	10E9	10e9	JJ	_	_	_
22	cells	cell	NNS	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
24	Following	follow	VBG	_	_	_
25	incubation	incubation	NN	_	_	_
26	,	,	,	_	_	_
27	roots	root	NNS	_	_	_
28	had	have	VBD	_	_	_
29	been	be	VBN	_	_	_
30	gently	gently	RB	_	_	_
31	rinsed	rinse	VBN	_	_	_
32	to	to	TO	_	_	_
33	remove	remove	VB	_	_	_
34	loosely	loosely	RB	_	_	_
35	attached	attach	VBN	_	_	_
36	bacteria	bacterium	NNS	_	_	_
37	and	and	CC	_	_	_
38	roots	root	NNS	_	_	_
39	were	be	VBD	_	_	_
40	cut	cut	VBN	_	_	_
41	directly	directly	RB	_	_	_
42	into	into	IN	_	_	_
43	100	100	CD	_	_	_
44	ml	ml	NN	_	_	_
45	ice	ice	NN	_	_	_
46	cold	cold	JJ	_	_	_
47	stop	stop	NN	_	_	_
48	solution	solution	NN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	5	5	CD	_	_	_
51	%	%	NN	_	_	_
52	H2O-saturated	h2o-saturated	JJ	_	_	_
53	phenol	phenol	NN	_	_	_
54	,	,	,	_	_	_
55	pH	ph	NN	_	_	_
56	4.3	4.3	CD	_	_	_
57	,	,	,	_	_	_
58	in	in	IN	_	_	_
59	95	95	CD	_	_	_
60	%	%	NN	_	_	_
61	ethanol	ethanol	NN	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	.	.	.	_	_	_

1	Root	root	NN	_	_	_
2	extracts	extract	NNS	_	_	_
3	were	be	VBD	_	_	_
4	filtered	filter	VBN	_	_	_
5	using	use	VBG	_	_	_
6	0.5	0.5	CD	_	_	_
7	µm	µm	NN	_	_	_
8	filters	filter	NNS	_	_	_
9	to	to	TO	_	_	_
10	separate	separate	JJ	_	_	_
11	bacteria	bacterium	NNS	_	_	_
12	cells	cell	NNS	_	_	_
13	from	from	IN	_	_	_
14	plant	plant	NN	_	_	_
15	cells	cell	NNS	_	_	_
16	in	in	IN	_	_	_
17	order	order	NN	_	_	_
18	to	to	TO	_	_	_
19	prevent	prevent	VB	_	_	_
20	interference	interference	NN	_	_	_
21	of	of	IN	_	_	_
22	the	the	DT	_	_	_
23	cDNA	cdna	NN	_	_	_
24	labeling	labeling	NN	_	_	_
25	.	.	.	_	_	_

1	Qiagen	Qiagen	NNP	_	_	_
2	RNA	rna	NN	_	_	_
3	protect	protect	VB	_	_	_
4	solution	solution	NN	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	to	to	TO	_	_	_
8	stabilize	stabilize	VB	_	_	_
9	RNA	rna	NN	_	_	_
10	during	during	IN	_	_	_
11	extraction	extraction	NN	_	_	_
12	.	.	.	_	_	_

1	Bacteria	bacterium	NNS	_	_	_
2	had	have	VBD	_	_	_
3	been	be	VBN	_	_	_
4	collected	collect	VBN	_	_	_
5	by	by	IN	_	_	_
6	shaking	shake	VBG	_	_	_
7	and	and	CC	_	_	_
8	washing	wash	VBG	_	_	_
9	and	and	CC	_	_	_
10	stored	store	VBN	_	_	_
11	in	in	IN	_	_	_
12	-80	-80	CD	_	_	_
13	°C	°c	NN	_	_	_
14	until	until	IN	_	_	_
15	using	use	VBG	_	_	_
16	for	for	IN	_	_	_
17	RNA	rna	NN	_	_	_
18	isolation	isolation	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	genotype	genotype	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Signal	signal	NN	_	_	_
5	intensities	intensity	NNS	_	_	_
6	were	be	VBD	_	_	_
7	normalized	normalize	VBN	_	_	_
8	for	for	IN	_	_	_
9	spot	spot	NN	_	_	_
10	and	and	CC	_	_	_
11	slide	slide	NN	_	_	_
12	abnormalities	abnormality	NNS	_	_	_
13	with	with	IN	_	_	_
14	the	the	DT	_	_	_
15	spatial	spatial	JJ	_	_	_
16	Lowess	lowess	NN	_	_	_
17	algorithm	algorithm	NN	_	_	_
18	and	and	CC	_	_	_
19	analyzed	analyze	VBN	_	_	_
20	by	by	IN	_	_	_
21	mixed-effect	mixed-effect	JJ	_	_	_
22	ANOVA	ANOVA	NNP	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	MAANOVA	MAANOVA	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Kerr	Kerr	NNP	_	_	_
28	et	et	FW	_	_	_
29	al.	al.	FW	_	_	_
30	2000	2000	CD	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	.	.	.	_	_	_

1	Both	both	DT	_	_	_
2	Lowess	lowess	NN	_	_	_
3	and	and	CC	_	_	_
4	MAANOVA	maanova	NN	_	_	_
5	are	be	VBP	_	_	_
6	part	part	NN	_	_	_
7	of	of	IN	_	_	_
8	the	the	DT	_	_	_
9	R	r	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Standard	standard	JJ	_	_	_
12	hot-phenol	hot-phenol	NN	_	_	_
13	method	method	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	strain	strain	NN	_	_	_
16	:	:	:	_	_	_
17	O157	o157	NN	_	_	_
18	:	:	:	_	_	_
19	H7	h7	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	treatment	treatment	NN	_	_	_
22	:	:	:	_	_	_
23	grown	grow	VBN	_	_	_
24	in	in	IN	_	_	_
25	lettuce	lettuce	NN	_	_	_
26	rhizosphere	rhizosphere	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	treatment	treatment	NN	_	_	_
29	:	:	:	_	_	_
30	grown	grow	VBN	_	_	_
31	without	without	IN	_	_	_
32	lettuce	lettuce	NN	_	_	_
33	rhizosphere	rhizosphere	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	control	control	NN	_	_	_
36	sample	sample	NN	_	_	_
37	at	at	IN	_	_	_
38	30	30	CD	_	_	_
39	min	min	NN	_	_	_
40	,	,	,	_	_	_
41	biological	biological	JJ	_	_	_
42	rep1	rep1	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	control	control	NN	_	_	_
45	sample	sample	NN	_	_	_
46	at	at	IN	_	_	_
47	30	30	CD	_	_	_
48	min	min	NN	_	_	_
49	,	,	,	_	_	_
50	biological	biological	JJ	_	_	_
51	rep2	rep2	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	control	control	NN	_	_	_
54	sample	sample	NN	_	_	_
55	at	at	IN	_	_	_
56	60	60	CD	_	_	_
57	min	min	NN	_	_	_
58	,	,	,	_	_	_
59	biological	biological	JJ	_	_	_
60	rep1	rep1	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	control	control	NN	_	_	_
63	sample	sample	NN	_	_	_
64	at	at	IN	_	_	_
65	60	60	CD	_	_	_
66	min	min	NN	_	_	_
67	,	,	,	_	_	_
68	biological	biological	JJ	_	_	_
69	rep2	rep2	NN	_	_	_
70	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
71	Data	Data	NNP	_	_	_
72	were	be	VBD	_	_	_
73	normalized	normalize	VBN	_	_	_
74	using	use	VBG	_	_	_
75	RMA	RMA	NNP	_	_	_
76	algorithm	algorithm	NN	_	_	_
77	from	from	IN	_	_	_
78	R	r	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
80	Escherichia	escherichia	FW	Organism	_	_
81	coli	coli	FW	Organism	_	_
82	MG1655	mg1655	NN	_	_	_
83	after	after	IN	_	_	_
84	30	30	CD	_	_	_
85	min	min	NN	_	_	_
86	incubation	incubation	NN	_	_	_
87	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
88	Escherichia	escherichia	FW	Organism	_	_
89	coli	coli	FW	Organism	_	_
90	MG1655	mg1655	NN	_	_	_
91	after	after	IN	_	_	_
92	30	30	CD	_	_	_
93	min	min	NN	_	_	_
94	incubation	incubation	NN	_	_	_
95	following	follow	VBG	_	_	_
96	colicin	colicin	NN	_	_	_
97	M	m	NN	_	_	_
98	treatment	treatment	NN	_	_	_
99	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
100	Escherichia	escherichia	FW	Organism	_	_
101	coli	coli	FW	Organism	_	_
102	MG1655	mg1655	NN	_	_	_
103	after	after	IN	_	_	_
104	60	60	CD	_	_	_
105	min	min	NN	_	_	_
106	incubation	incubation	NN	_	_	_
107	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
108	Escherichia	escherichia	FW	Organism	_	_
109	coli	coli	FW	Organism	_	_
110	MG1655	mg1655	NN	_	_	_
111	after	after	IN	_	_	_
112	60	60	CD	_	_	_
113	min	min	NN	_	_	_
114	incubation	incubation	NN	_	_	_
115	following	follow	VBG	_	_	_
116	colicin	colicin	NN	_	_	_
117	M	m	NN	_	_	_
118	treatment	treatment	NN	_	_	_
119	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
120	Escherichia	escherichia	FW	Organism	_	_
121	coli	coli	FW	Organism	_	_
122	str	str	FW	_	_	_
123	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Overnight	overnight	JJ	_	_	_
4	cultures	culture	NNS	_	_	_
5	of	of	IN	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	MG1655	mg1655	NN	_	_	_
9	grown	grow	VBN	_	_	_
10	at	at	IN	_	_	_
11	37	37	CD	_	_	_
12	°C	°c	NN	_	_	_
13	with	with	IN	_	_	_
14	shaking	shake	VBG	_	_	_
15	at	at	IN	_	_	_
16	200	200	CD	_	_	_
17	rpm	rpm	NN	_	_	_
18	were	be	VBD	_	_	_
19	diluted	dilute	VBN	_	_	_
20	1:625	1:625	CD	_	_	_
21	into	into	IN	_	_	_
22	50	50	CD	_	_	_
23	ml	ml	NN	_	_	_
24	of	of	IN	_	_	_
25	LB	lb	NN	MED	_	_
26	broth	broth	NN	MED	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Roth	Roth	NNP	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	,	,	,	_	_	_
31	and	and	CC	_	_	_
32	incubated	incubate	VBN	_	_	_
33	at	at	IN	_	_	_
34	37	37	CD	_	_	_
35	°C	°c	NN	_	_	_
36	with	with	IN	_	_	_
37	shaking	shake	VBG	_	_	_
38	at	at	IN	_	_	_
39	200	200	CD	_	_	_
40	rpm	rpm	NN	_	_	_
41	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	RNeasy	RNeasy	NNP	_	_	_
8	Mini	Mini	NNP	_	_	_
9	Kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Qiagen	qiagen	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	according	accord	VBG	_	_	_
14	to	to	TO	_	_	_
15	the	the	DT	_	_	_
16	manufacturer	manufacturer	NN	_	_	_
17	's	's	POS	_	_	_
18	protocol	protocol	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	treated	treat	VBN	_	_	_
3	sample	sample	NN	_	_	_
4	at	at	IN	_	_	_
5	30	30	CD	_	_	_
6	min	min	NN	_	_	_
7	,	,	,	_	_	_
8	biological	biological	JJ	_	_	_
9	rep1	rep1	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	treated	treat	VBN	_	_	_
12	sample	sample	NN	_	_	_
13	at	at	IN	_	_	_
14	30	30	CD	_	_	_
15	min	min	NN	_	_	_
16	,	,	,	_	_	_
17	biological	biological	JJ	_	_	_
18	rep2	rep2	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	treated	treat	VBN	_	_	_
21	sample	sample	NN	_	_	_
22	at	at	IN	_	_	_
23	60	60	CD	_	_	_
24	min	min	NN	_	_	_
25	,	,	,	_	_	_
26	biological	biological	JJ	_	_	_
27	rep1	rep1	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	treated	treat	VBN	_	_	_
30	sample	sample	NN	_	_	_
31	at	at	IN	_	_	_
32	60	60	CD	_	_	_
33	min	min	NN	_	_	_
34	,	,	,	_	_	_
35	biological	biological	JJ	_	_	_
36	rep2	rep2	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	treatment	treatment	NN	_	_	_
39	:	:	:	_	_	_
40	treated	treated	JJ	_	_	_
41	culture	culture	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	treatment	treatment	NN	_	_	_
44	:	:	:	_	_	_
45	untreated	untreated	JJ	_	_	_
46	culture	culture	NN	_	_	_
47	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
48	When	when	WRB	_	_	_
49	the	the	DT	_	_	_
50	cultures	culture	NNS	_	_	_
51	reached	reach	VBD	_	_	_
52	an	a	DT	_	_	_
53	OD600	od600	NN	_	_	_
54	0.6	0.6	CD	_	_	_
55	they	they	PRP	_	_	_
56	were	be	VBD	_	_	_
57	split	split	VBN	_	_	_
58	into	into	IN	_	_	_
59	two	two	CD	_	_	_
60	flasks	flask	NNS	_	_	_
61	,	,	,	_	_	_
62	each	each	DT	_	_	_
63	containing	contain	VBG	_	_	_
64	20	20	CD	_	_	_
65	ml	ml	NN	_	_	_
66	of	of	IN	_	_	_
67	the	the	DT	_	_	_
68	culture	culture	NN	_	_	_
69	.	.	.	_	_	_

1	One	one	CD	_	_	_
2	was	be	VBD	_	_	_
3	treated	treat	VBN	_	_	_
4	with	with	IN	_	_	_
5	a	a	DT	_	_	_
6	subinhibitory	subinhibitory	JJ	_	_	_
7	concentration	concentration	NN	_	_	_
8	of	of	IN	_	_	_
9	purified	purify	VBN	_	_	_
10	colicin	colicin	NN	_	_	_
11	M	m	NN	_	_	_
12	,	,	,	_	_	_
13	while	while	IN	_	_	_
14	the	the	DT	_	_	_
15	untreated	untreated	JJ	_	_	_
16	served	serve	VBD	_	_	_
17	as	as	IN	_	_	_
18	a	a	DT	_	_	_
19	control	control	NN	_	_	_
20	.	.	.	_	_	_

1	2-ml	2-ml	JJ	_	_	_
2	culture	culture	NN	_	_	_
3	aliquotes	aliquote	NNS	_	_	_
4	were	be	VBD	_	_	_
5	harvested	harvest	VBN	_	_	_
6	from	from	IN	_	_	_
7	each	each	DT	_	_	_
8	flask	flask	NN	_	_	_
9	after	after	IN	_	_	_
10	30	30	CD	_	_	_
11	min	min	NN	_	_	_
12	and	and	CC	_	_	_
13	60	60	CD	_	_	_
14	min	min	NN	_	_	_
15	incubation	incubation	NN	_	_	_
16	at	at	IN	_	_	_
17	37	37	CD	_	_	_
18	°C	°c	NN	_	_	_
19	and	and	CC	_	_	_
20	were	be	VBD	_	_	_
21	mixed	mix	VBN	_	_	_
22	with	with	IN	_	_	_
23	4	4	CD	_	_	_
24	ml	ml	NN	_	_	_
25	RNAProtect	rnaprotect	NN	_	_	_
26	Bacteria	bacterium	NNS	_	_	_
27	Reagent	reagent	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Qiagen	qiagen	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Bacterial	bacterial	JJ	_	_	_
3	pellets	pellet	NNS	_	_	_
4	were	be	VBD	_	_	_
5	resuspended	resuspend	VBN	_	_	_
6	in	in	IN	_	_	_
7	350µl	350µl	CD	_	_	_
8	RNAwiz	rnawiz	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Ambion	Ambion	NNP	_	_	_
11	,	,	,	_	_	_
12	Austin	Austin	NNP	_	_	_
13	,	,	,	_	_	_
14	TX	TX	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	and	and	CC	_	_	_
17	kept	keep	VBD	_	_	_
18	at	at	IN	_	_	_
19	-80	-80	CD	_	_	_
20	°C	°c	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	were	be	VBD	_	_	_
4	processed	process	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	robust	robust	JJ	_	_	_
8	multiarray	multiarray	JJ	_	_	_
9	average	average	JJ	_	_	_
10	algorithm	algorithm	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	RMA	rma	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	for	for	IN	_	_	_
15	normalization	normalization	NN	_	_	_
16	,	,	,	_	_	_
17	background	background	NN	_	_	_
18	correction	correction	NN	_	_	_
19	and	and	CC	_	_	_
20	expression	expression	NN	_	_	_
21	value	value	NN	_	_	_
22	calculation	calculation	NN	_	_	_
23	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	EB	EB	NNP	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	Wright	Wright	NNP	_	_	_
5	and	and	CC	_	_	_
6	Simon	Simon	NNP	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	test	test	NN	_	_	_
9	was	be	VBD	_	_	_
10	used	use	VBN	_	_	_
11	for	for	IN	_	_	_
12	the	the	DT	_	_	_
13	fold	fold	JJ	_	_	_
14	change	change	NN	_	_	_
15	and	and	CC	_	_	_
16	the	the	DT	_	_	_
17	pvalue	pvalue	NN	_	_	_
18	calculation	calculation	NN	_	_	_
19	,	,	,	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	E.	E.	NNP	_	_	_
22	coli	coli	NN	_	_	_
23	O157	o157	NN	_	_	_
24	:	:	:	_	_	_
25	H7	h7	NN	_	_	_
26	was	be	VBD	_	_	_
27	grown	grow	VBN	_	_	_
28	in	in	IN	_	_	_
29	15mL	15ml	NN	_	_	_
30	falcon	falcon	NN	_	_	_
31	tubes	tube	NNS	_	_	_
32	containing	contain	VBG	_	_	_
33	8mL	8ml	NN	_	_	_
34	of	of	IN	_	_	_
35	filtered	filter	VBN	_	_	_
36	rat	rat	NN	_	_	_
37	's	's	POS	_	_	_
38	caecal	caecal	JJ	_	_	_
39	content	content	NN	_	_	_
40	.	.	.	_	_	_

1	Growth	growth	NN	_	_	_
2	were	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	in	in	IN	_	_	_
5	static	static	JJ	_	_	_
6	condition	condition	NN	_	_	_
7	at	at	IN	_	_	_
8	37	37	CD	_	_	_
9	°C	°c	NN	_	_	_
10	for	for	IN	_	_	_
11	6	6	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	O157	o157	NN	_	_	_
5	:	:	:	_	_	_
6	H7	h7	NN	_	_	_
7	cultivated	cultivate	VBN	_	_	_
8	for	for	IN	_	_	_
9	6	6	CD	_	_	_
10	hours	hour	NNS	_	_	_
11	in	in	IN	_	_	_
12	the	the	DT	_	_	_
13	caecal	caecal	JJ	_	_	_
14	content	content	NN	_	_	_
15	of	of	IN	_	_	_
16	rats	rat	NNS	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	Escherichia	escherichia	FW	Organism	_	_
19	coli	coli	FW	Organism	_	_
20	O157	o157	NN	_	_	_
21	:	:	:	_	_	_
22	H7	h7	NN	_	_	_
23	str	str	NN	_	_	_
24	.	.	.	_	_	_

1	EDL933	edl933	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Germfree	germfree	JJ	_	_	_
4	rat	rat	NN	_	_	_
5	's	's	POS	_	_	_
6	caecum	caecum	NN	_	_	_
7	,	,	,	_	_	_
8	biological	biological	JJ	_	_	_
9	rep1	rep1	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Germfree	germfree	JJ	_	_	_
12	rat	rat	NN	_	_	_
13	's	's	POS	_	_	_
14	caecum	caecum	NN	_	_	_
15	,	,	,	_	_	_
16	biological	biological	JJ	_	_	_
17	rep2	rep2	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Germfree	germfree	JJ	_	_	_
20	rat	rat	NN	_	_	_
21	's	's	POS	_	_	_
22	caecum	caecum	NN	_	_	_
23	,	,	,	_	_	_
24	biological	biological	JJ	_	_	_
25	rep3	rep3	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	growth	growth	NN	_	_	_
28	protocol	protocol	NN	_	_	_
29	:	:	:	_	_	_
30	control	control	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	growth	growth	NN	_	_	_
33	protocol	protocol	NN	_	_	_
34	:	:	:	_	_	_
35	in	in	IN	_	_	_
36	the	the	DT	_	_	_
37	caecal	caecal	JJ	_	_	_
38	content	content	NN	_	_	_
39	of	of	IN	_	_	_
40	rats	rat	NNS	_	_	_
41	associated	associate	VBN	_	_	_
42	with	with	IN	_	_	_
43	the	the	DT	_	_	_
44	human	human	JJ	_	_	_
45	microbiota	microbiota	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	Human	human	JJ	_	_	_
48	intestinal	intestinal	JJ	_	_	_
49	microbiota	microbiota	NN	_	_	_
50	associated	associate	VBN	_	_	_
51	rat	rat	NN	_	_	_
52	's	's	POS	_	_	_
53	caecum	caecum	NN	_	_	_
54	,	,	,	_	_	_
55	biological	biological	JJ	_	_	_
56	rep1	rep1	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Human	human	JJ	_	_	_
59	intestinal	intestinal	JJ	_	_	_
60	microbiota	microbiota	NN	_	_	_
61	associated	associate	VBN	_	_	_
62	rat	rat	NN	_	_	_
63	's	's	POS	_	_	_
64	caecum	caecum	NN	_	_	_
65	,	,	,	_	_	_
66	biological	biological	JJ	_	_	_
67	rep2	rep2	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	Human	human	JJ	_	_	_
70	intestinal	intestinal	JJ	_	_	_
71	microbiota	microbiota	NN	_	_	_
72	associated	associate	VBN	_	_	_
73	rat	rat	NN	_	_	_
74	's	's	POS	_	_	_
75	caecum	caecum	NN	_	_	_
76	,	,	,	_	_	_
77	biological	biological	JJ	_	_	_
78	rep3	rep3	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	RNA	rna	NN	_	_	_
81	extractions	extraction	NNS	_	_	_
82	were	be	VBD	_	_	_
83	performed	perform	VBN	_	_	_
84	using	use	VBG	_	_	_
85	RiboPure	RiboPure	NNP	_	_	_
86	™	™	CD	_	_	_
87	Bacteria	bacterium	NNS	_	_	_
88	Kit	kit	NN	_	_	_
89	-LRB-	-lrb-	-LRB-	_	_	_
90	Ambion	Ambion	NNP	_	_	_
91	,	,	,	_	_	_
92	Austin	Austin	NNP	_	_	_
93	,	,	,	_	_	_
94	TX	TX	NNP	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	,	,	,	_	_	_
97	according	accord	VBG	_	_	_
98	to	to	TO	_	_	_
99	the	the	DT	_	_	_
100	manufacturer	manufacturer	NN	_	_	_
101	's	's	POS	_	_	_
102	recommendations	recommendation	NNS	_	_	_
103	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
104	Agilent	Agilent	NNP	_	_	_
105	Feature	Feature	NNP	_	_	_
106	Extraction	Extraction	NNP	_	_	_
107	Software	Software	NNP	_	_	_
108	v.	v.	CC	_	_	_
109	9.5.3.1	9.5.3.1	CD	_	_	_
110	was	be	VBD	_	_	_
111	used	use	VBN	_	_	_
112	for	for	IN	_	_	_
113	background	background	NN	_	_	_
114	subtraction	subtraction	NN	_	_	_
115	and	and	CC	_	_	_
116	LOWESS	lowess	NN	_	_	_
117	normalization	normalization	NN	_	_	_
118	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	control	control	NN	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	Escherichia	escherichia	FW	Organism	_	_
5	coli	coli	FW	Organism	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Escherichia	escherichia	FW	Organism	_	_
8	coli	coli	FW	Organism	_	_
9	control	control	NN	_	_	_
10	vs	vs	CC	_	_	_
11	H2O2	h2o2	NN	_	_	_
12	Rep1	rep1	JJ	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Escherichia	escherichia	FW	Organism	_	_
15	coli	coli	FW	Organism	_	_
16	control	control	NN	_	_	_
17	vs	vs	CC	_	_	_
18	H2O2	h2o2	NN	_	_	_
19	Rep2	rep2	JJ	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	H2O2	h2o2	NN	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	One	one	CD	_	_	_
24	conditions	condition	NNS	_	_	_
25	:	:	:	_	_	_
26	1	1	CD	_	_	_
27	%	%	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	v	v	LS	_	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
31	Overnight	overnight	JJ	_	_	_
32	culture	culture	NN	_	_	_
33	of	of	IN	_	_	_
34	E.	e.	FW	_	_	_
35	coli	coli	FW	_	_	_
36	W3110	w3110	NN	_	_	_
37	in	in	IN	_	_	_
38	LB	lb	NN	_	_	_
39	was	be	VBD	_	_	_
40	diluted	dilute	VBN	_	_	_
41	in	in	IN	_	_	_
42	M9	m9	NN	MED	_	_
43	minimal	minimal	JJ	MED	_	_
44	medium	medium	NN	MED	_	_
45	with	with	IN	_	_	_
46	supplements	supplement	NNS	_	_	_
47	to	to	TO	_	_	_
48	OD600	od600	NN	_	_	_
49	=	=	JJ	_	_	_
50	0.01	0.01	CD	_	_	_
51	and	and	CC	_	_	_
52	was	be	VBD	_	_	_
53	incubated	incubate	VBN	_	_	_
54	at	at	IN	_	_	_
55	37	37	CD	_	_	_
56	Ceilsus	ceilsus	NN	_	_	_
57	degree	degree	NN	_	_	_
58	witouth	witouth	NN	_	_	_
59	shaking	shake	VBG	_	_	_
60	until	until	IN	_	_	_
61	its	its	PRP$	_	_	_
62	OD600	od600	NN	_	_	_
63	reached	reach	VBD	_	_	_
64	0.1	0.1	CD	_	_	_
65	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	K-12	k-12	NN	_	_	_
5	W3110	w3110	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Total	total	JJ	_	_	_
8	RNA	rna	NN	_	_	_
9	was	be	VBD	_	_	_
10	extracted	extract	VBN	_	_	_
11	from	from	IN	_	_	_
12	5	5	CD	_	_	_
13	ml	ml	NN	_	_	_
14	cell	cell	NN	_	_	_
15	culture	culture	NN	_	_	_
16	at	at	IN	_	_	_
17	10	10	CD	_	_	_
18	min	min	NN	_	_	_
19	incubation	incubation	NN	_	_	_
20	with	with	IN	_	_	_
21	or	or	CC	_	_	_
22	without	without	IN	_	_	_
23	1	1	CD	_	_	_
24	%	%	NN	_	_	_
25	Hydrogen	hydrogen	NN	_	_	_
26	peroxide	peroxide	NN	_	_	_
27	using	use	VBG	_	_	_
28	RNeasy	RNeasy	NNP	_	_	_
29	Mini	Mini	NNP	_	_	_
30	kit	kit	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Qiagen	Qiagen	NNP	_	_	_
33	,	,	,	_	_	_
34	Inc.	Inc.	NNP	_	_	_
35	,	,	,	_	_	_
36	Valencia	Valencia	NNP	_	_	_
37	,	,	,	_	_	_
38	CA	CA	NNP	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	according	accord	VBG	_	_	_
41	to	to	TO	_	_	_
42	the	the	DT	_	_	_
43	manufacturer	manufacturer	NN	_	_	_
44	's	's	POS	_	_	_
45	protocol	protocol	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	treatment	treatment	NN	_	_	_
48	:	:	:	_	_	_
49	1	1	CD	_	_	_
50	%	%	NN	_	_	_
51	H202	h202	NN	_	_	_
52	,	,	,	_	_	_
53	anaerobic	anaerobic	JJ	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	treatment	treatment	NN	_	_	_
56	:	:	:	_	_	_
57	1	1	CD	_	_	_
58	%	%	NN	_	_	_
59	H2O2	h2o2	NN	_	_	_
60	,	,	,	_	_	_
61	anaerobic	anaerobic	JJ	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	treatment	treatment	NN	_	_	_
64	:	:	:	_	_	_
65	control	control	NN	_	_	_
66	,	,	,	_	_	_
67	anaerobic	anaerobic	JJ	_	_	_
68	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
69	Agilent	Agilent	NNP	_	_	_
70	Feature	Feature	NNP	_	_	_
71	Extraction	Extraction	NNP	_	_	_
72	Software	Software	NNP	_	_	_
73	v.	v.	CC	_	_	_
74	9.5.3.1	9.5.3.1	CD	_	_	_
75	was	be	VBD	_	_	_
76	used	use	VBN	_	_	_
77	for	for	IN	_	_	_
78	background	background	NN	_	_	_
79	subtraction	subtraction	NN	_	_	_
80	and	and	CC	_	_	_
81	LOWESS	lowess	NN	_	_	_
82	normalization	normalization	NN	_	_	_
83	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Escherichia	escherichia	FW	Organism	_	_
6	coli	coli	FW	Organism	_	_
7	wild	wild	JJ	_	_	_
8	type	type	NN	_	_	_
9	vs	vs	CC	_	_	_
10	luxS	luxs	NN	GEN	_	_
11	mutants	mutant	NNS	_	_	_
12	with	with	IN	_	_	_
13	10	10	CD	_	_	_
14	%	%	NN	_	_	_
15	H2O2	h2o2	NN	_	_	_
16	Rep1	rep1	JJ	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Escherichia	escherichia	FW	Organism	_	_
19	coli	coli	FW	Organism	_	_
20	wild	wild	JJ	_	_	_
21	type	type	NN	_	_	_
22	vs	vs	CC	_	_	_
23	luxS	luxs	NN	GEN	_	_
24	mutants	mutant	NNS	_	_	_
25	with	with	IN	_	_	_
26	10	10	CD	_	_	_
27	%	%	NN	_	_	_
28	H2O2	h2o2	NN	_	_	_
29	Rep2	rep2	JJ	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Escherichia	escherichia	FW	Organism	_	_
32	coli	coli	FW	Organism	_	_
33	wild	wild	JJ	_	_	_
34	type	type	NN	_	_	_
35	vs	vs	CC	_	_	_
36	luxS	luxs	NN	GEN	_	_
37	mutants	mutant	NNS	_	_	_
38	with	with	IN	_	_	_
39	30	30	CD	_	_	_
40	%	%	NN	_	_	_
41	H2O2	h2o2	NN	_	_	_
42	Rep1	rep1	JJ	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Escherichia	escherichia	FW	Organism	_	_
45	coli	coli	FW	Organism	_	_
46	wild	wild	JJ	_	_	_
47	type	type	NN	_	_	_
48	vs	vs	CC	_	_	_
49	luxS	luxs	NN	GEN	_	_
50	mutants	mutant	NNS	_	_	_
51	with	with	IN	_	_	_
52	30	30	CD	_	_	_
53	%	%	NN	_	_	_
54	H2O2	h2o2	NN	_	_	_
55	Rep2	rep2	JJ	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	Escherichia	escherichia	FW	Organism	_	_
58	coli	coli	FW	Organism	_	_
59	wild	wild	JJ	_	_	_
60	type	type	NN	_	_	_
61	vs	vs	CC	_	_	_
62	luxS	luxs	NN	GEN	_	_
63	mutants	mutant	NNS	_	_	_
64	without	without	IN	_	_	_
65	H2O2	h2o2	NN	_	_	_
66	Rep1	rep1	JJ	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	Escherichia	escherichia	FW	Organism	_	_
69	coli	coli	FW	Organism	_	_
70	wild	wild	JJ	_	_	_
71	type	type	NN	_	_	_
72	vs	vs	CC	_	_	_
73	luxS	luxs	NN	GEN	_	_
74	mutants	mutant	NNS	_	_	_
75	without	without	IN	_	_	_
76	H2O2	h2o2	NN	_	_	_
77	Rep2	rep2	JJ	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	genotype	genotype	NN	_	_	_
80	:	:	:	_	_	_
81	luxS	luxs	NN	GEN	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	genotype	genotype	NN	_	_	_
84	:	:	:	_	_	_
85	wild	wild	JJ	_	_	_
86	type	type	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	luxS	luxs	NN	GEN	_	_
89	mutants	mutant	NNS	_	_	_
90	,	,	,	_	_	_
91	10	10	CD	_	_	_
92	%	%	NN	_	_	_
93	H2O2	h2o2	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	luxS	luxs	NN	GEN	_	_
96	mutants	mutant	NNS	_	_	_
97	,	,	,	_	_	_
98	30	30	CD	_	_	_
99	%	%	NN	_	_	_
100	H2O2	h2o2	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	luxS	luxs	NN	GEN	_	_
103	mutants	mutant	NNS	_	_	_
104	,	,	,	_	_	_
105	without	without	IN	_	_	_
106	H2O2	h2o2	NN	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
108	Overnight	overnight	JJ	_	_	_
109	culture	culture	NN	_	_	_
110	of	of	IN	_	_	_
111	E.	e.	FW	_	_	_
112	coli	coli	FW	_	_	_
113	in	in	IN	_	_	_
114	LB	lb	NN	_	_	_
115	was	be	VBD	_	_	_
116	diluted	dilute	VBN	_	_	_
117	in	in	IN	_	_	_
118	LB	lb	NN	_	_	_
119	supplemented	supplement	VBN	_	_	_
120	with	with	IN	_	_	_
121	0.8	0.8	CD	_	_	_
122	%	%	NN	_	_	_
123	glucose	glucose	NN	SUPP	_	_
124	to	to	TO	_	_	_
125	OD600	od600	NN	_	_	_
126	=	=	JJ	_	_	_
127	0.02	0.02	CD	_	_	_
128	and	and	CC	_	_	_
129	was	be	VBD	_	_	_
130	continuously	continuously	RB	_	_	_
131	incubated	incubate	VBN	_	_	_
132	at	at	IN	_	_	_
133	30	30	CD	_	_	_
134	degree	degree	NN	_	_	_
135	celcius	celcius	NNS	_	_	_
136	with	with	IN	_	_	_
137	shaking	shake	VBG	_	_	_
138	until	until	IN	_	_	_
139	its	its	PRP$	_	_	_
140	OD600	od600	NN	_	_	_
141	reached	reach	VBD	_	_	_
142	1.0	1.0	CD	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	strain	strain	NN	_	_	_
145	:	:	:	_	_	_
146	K-12	k-12	NN	_	_	_
147	W3110	w3110	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	three	three	CD	_	_	_
150	different	different	JJ	_	_	_
151	concentrations	concentration	NNS	_	_	_
152	,	,	,	_	_	_
153	without	without	IN	_	_	_
154	H2O2	h2o2	NN	_	_	_
155	,	,	,	_	_	_
156	10	10	CD	_	_	_
157	%	%	NN	_	_	_
158	-LRB-	-lrb-	-LRB-	_	_	_
159	v	v	LS	_	_	_
160	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
161	Total	total	JJ	_	_	_
162	RNA	rna	NN	_	_	_
163	was	be	VBD	_	_	_
164	extracted	extract	VBN	_	_	_
165	from	from	IN	_	_	_
166	5	5	CD	_	_	_
167	ml	ml	NN	_	_	_
168	cell	cell	NN	_	_	_
169	culture	culture	NN	_	_	_
170	after	after	IN	_	_	_
171	30	30	CD	_	_	_
172	min	min	NN	_	_	_
173	incubation	incubation	NN	_	_	_
174	with	with	IN	_	_	_
175	or	or	CC	_	_	_
176	without	without	IN	_	_	_
177	H2O2	h2o2	NN	_	_	_
178	treatment	treatment	NN	_	_	_
179	using	use	VBG	_	_	_
180	RNeasy	RNeasy	NNP	_	_	_
181	Mini	Mini	NNP	_	_	_
182	kit	kit	NN	_	_	_
183	-LRB-	-lrb-	-LRB-	_	_	_
184	Qiagen	Qiagen	NNP	_	_	_
185	,	,	,	_	_	_
186	Inc.	Inc.	NNP	_	_	_
187	,	,	,	_	_	_
188	Valencia	Valencia	NNP	_	_	_
189	,	,	,	_	_	_
190	CA	CA	NNP	_	_	_
191	-RRB-	-rrb-	-RRB-	_	_	_
192	according	accord	VBG	_	_	_
193	to	to	TO	_	_	_
194	the	the	DT	_	_	_
195	manufacturer	manufacturer	NN	_	_	_
196	's	's	POS	_	_	_
197	protocol	protocol	NN	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	treatment	treatment	NN	_	_	_
200	:	:	:	_	_	_
201	10	10	CD	_	_	_
202	%	%	NN	_	_	_
203	H202	h202	NN	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	treatment	treatment	NN	_	_	_
206	:	:	:	_	_	_
207	30	30	CD	_	_	_
208	%	%	NN	_	_	_
209	H202	h202	NN	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	treatment	treatment	NN	_	_	_
212	:	:	:	_	_	_
213	none	none	NN	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	wild	wild	JJ	_	_	_
216	type	type	NN	_	_	_
217	,	,	,	_	_	_
218	10	10	CD	_	_	_
219	%	%	NN	_	_	_
220	H2O2	h2o2	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	wild	wild	JJ	_	_	_
223	type	type	NN	_	_	_
224	,	,	,	_	_	_
225	30	30	CD	_	_	_
226	%	%	NN	_	_	_
227	H2O2	h2o2	NN	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	wild	wild	JJ	_	_	_
230	type	type	NN	_	_	_
231	,	,	,	_	_	_
232	without	without	IN	_	_	_
233	H2O2	h2o2	NN	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	Escherichia	escherichia	FW	Organism	_	_
236	coli	coli	FW	Organism	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	JCB570	jcb570	NN	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	JQ004	jq004	NN	_	_	_
241	-LRB-	-lrb-	-LRB-	_	_	_
242	rraA	rraa	NN	GEN	_	_
243	-RRB-	-rrb-	-RRB-	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	rraA	rraa	NN	GEN	_	_
246	deletion	deletion	NN	_	_	_
247	,	,	,	_	_	_
248	OD600	od600	NN	_	_	_
249	=	=	JJ	_	_	_
250	0.3	0.3	CD	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	rraA	rraa	NN	GEN	_	_
253	deletion	deletion	NN	_	_	_
254	,	,	,	_	_	_
255	OD600	od600	NN	_	_	_
256	=	=	JJ	_	_	_
257	0.5	0.5	CD	_	_	_
258	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
259	rraA	rraa	NN	GEN	_	_
260	deletion	deletion	NN	_	_	_
261	,	,	,	_	_	_
262	OD600	od600	NN	_	_	_
263	=	=	JJ	_	_	_
264	1.0	1.0	CD	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	VALUE	value	NN	_	_	_
267	is	be	VBZ	_	_	_
268	Log	log	NN	_	_	_
269	-LRB-	-lrb-	-LRB-	_	_	_
270	base	base	NN	_	_	_
271	2	2	CD	_	_	_
272	-RRB-	-rrb-	-RRB-	_	_	_
273	of	of	IN	_	_	_
274	the	the	DT	_	_	_
275	ratio	ratio	NN	_	_	_
276	of	of	IN	_	_	_
277	the	the	DT	_	_	_
278	median	median	NN	_	_	_
279	of	of	IN	_	_	_
280	Channel	Channel	NNP	_	_	_
281	2	2	CD	_	_	_
282	-LRB-	-lrb-	-LRB-	_	_	_
283	usually	usually	RB	_	_	_
284	635	635	CD	_	_	_
285	nm	nm	NN	_	_	_
286	-RRB-	-rrb-	-RRB-	_	_	_
287	to	to	TO	_	_	_
288	Channel	Channel	NNP	_	_	_
289	1	1	CD	_	_	_
290	-LRB-	-lrb-	-LRB-	_	_	_
291	usually	usually	RB	_	_	_
292	532	532	CD	_	_	_
293	nm	nm	NN	_	_	_
294	-RRB-	-rrb-	-RRB-	_	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	Escherichia	escherichia	FW	Organism	_	_
297	coli	coli	FW	Organism	_	_
298	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
299	KSL2000	ksl2000	NN	_	_	_
300	,	,	,	_	_	_
301	0.1	0.1	CD	_	_	_
302	%	%	NN	_	_	_
303	arabinose	arabinose	NN	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	KSL2000	ksl2000	NN	_	_	_
306	,	,	,	_	_	_
307	no	no	DT	_	_	_
308	arabinose	arabinose	NN	_	_	_
309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
310	KSL2000	ksl2000	NN	_	_	_
311	plus	plus	CC	_	_	_
312	pTrc99A	ptrc99a	NN	_	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
314	KSL2000	ksl2000	NN	_	_	_
315	plus	plus	CC	_	_	_
316	pTrc99A-RraA	ptrc99a-rraa	NN	_	_	_
317	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
318	KSL2000-Rne	ksl2000-rne	NN	_	_	_
319	depletion	depletion	NN	_	_	_
320	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
321	KSL2000-RraA	ksl2000-rraa	NN	_	_	_
322	overexpression	overexpression	NN	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	KSL2009	ksl2009	NN	_	_	_
325	,	,	,	_	_	_
326	0.1	0.1	CD	_	_	_
327	%	%	NN	_	_	_
328	arabinose	arabinose	NN	_	_	_
329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
330	KSL2009	ksl2009	NN	_	_	_
331	,	,	,	_	_	_
332	no	no	DT	_	_	_
333	arabinose	arabinose	NN	_	_	_
334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
335	KSL2009-N-Rne	ksl2009-n-rne	NN	_	_	_
336	depletion	depletion	NN	_	_	_
337	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
338	KSL2009	ksl2009	NN	_	_	_
339	plus	plus	CC	_	_	_
340	pTrc99A	ptrc99a	NN	_	_	_
341	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
342	KSL2009	ksl2009	NN	_	_	_
343	plus	plus	CC	_	_	_
344	pTrc99A-RraA	ptrc99a-rraa	NN	_	_	_
345	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
346	KSL2009-RraA	ksl2009-rraa	NN	_	_	_
347	overexpression	overexpression	NN	_	_	_
348	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
349	VALUE	value	NN	_	_	_
350	is	be	VBZ	_	_	_
351	Log	log	NN	_	_	_
352	-LRB-	-lrb-	-LRB-	_	_	_
353	base	base	NN	_	_	_
354	2	2	CD	_	_	_
355	-RRB-	-rrb-	-RRB-	_	_	_
356	of	of	IN	_	_	_
357	the	the	DT	_	_	_
358	ratio	ratio	NN	_	_	_
359	of	of	IN	_	_	_
360	the	the	DT	_	_	_
361	median	median	NN	_	_	_
362	of	of	IN	_	_	_
363	Channel	Channel	NNP	_	_	_
364	2	2	CD	_	_	_
365	-LRB-	-lrb-	-LRB-	_	_	_
366	usually	usually	RB	_	_	_
367	635	635	CD	_	_	_
368	nm	nm	NN	_	_	_
369	-RRB-	-rrb-	-RRB-	_	_	_
370	to	to	TO	_	_	_
371	Channel	Channel	NNP	_	_	_
372	1	1	CD	_	_	_
373	-LRB-	-lrb-	-LRB-	_	_	_
374	usually	usually	RB	_	_	_
375	532	532	CD	_	_	_
376	nm	nm	NN	_	_	_
377	-RRB-	-rrb-	-RRB-	_	_	_
378	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
379	Escherichia	escherichia	FW	Organism	_	_
380	coli	coli	FW	Organism	_	_
381	O157	o157	NN	_	_	_
382	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
383	genetic	genetic	JJ	_	_	_
384	background	background	NN	_	_	_
385	:	:	:	_	_	_
386	O157	o157	NN	_	_	_
387	H19	h19	NN	_	_	_
388	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
389	genotype	genotype	NN	_	_	_
390	:	:	:	_	_	_
391	triclosan	triclosan	NN	_	_	_
392	tolerant	tolerant	JJ	_	_	_
393	mutant	mutant	JJ	_	_	_
394	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
395	genotype	genotype	NN	_	_	_
396	:	:	:	_	_	_
397	wild	wild	JJ	_	_	_
398	type	type	NN	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	Microarray	microarray	NN	_	_	_
401	analysis	analysis	NN	_	_	_
402	including	include	VBG	_	_	_
403	pre-processing	pre-processing	JJ	_	_	_
404	,	,	,	_	_	_
405	normalisation	normalisation	NN	_	_	_
406	anmd	anmd	NN	_	_	_
407	statistical	statistical	JJ	_	_	_
408	analysis	analysis	NN	_	_	_
409	were	be	VBD	_	_	_
410	performed	perform	VBN	_	_	_
411	using	use	VBG	_	_	_
412	R	r	NN	_	_	_
413	-LRB-	-lrb-	-LRB-	_	_	_
414	R	r	NN	_	_	_
415	,	,	,	_	_	_
416	2007	2007	CD	_	_	_
417	-RRB-	-rrb-	-RRB-	_	_	_
418	version	version	NN	_	_	_
419	2.6	2.6	CD	_	_	_
420	and	and	CC	_	_	_
421	Bioconductor	Bioconductor	NNP	_	_	_
422	-LRB-	-lrb-	-LRB-	_	_	_
423	Gentleman	Gentleman	NNP	_	_	_
424	et	et	FW	_	_	_
425	al.	al.	FW	_	_	_
426	2004	2004	CD	_	_	_
427	,	,	,	_	_	_
428	Genome	Genome	NNP	_	_	_
429	Biol	Biol	NNP	_	_	_
430	.	.	.	_	_	_

1	5	5	CD	_	_	_
2	:	:	:	_	_	_
3	R80	r80	NN	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	version	version	NN	_	_	_
6	2.1	2.1	CD	_	_	_
7	as	as	IN	_	_	_
8	previously	previously	RB	_	_	_
9	described	describe	VBN	_	_	_
10	by	by	IN	_	_	_
11	Morris	Morris	NNP	_	_	_
12	et	et	FW	_	_	_
13	al.	al.	FW	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	2009	2009	CD	_	_	_
16	,	,	,	_	_	_
17	Physiol	Physiol	NNP	_	_	_
18	.	.	.	_	_	_

1	Genomics	genomic	NNS	_	_	_
2	39:28-37	39:28-37	CD	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	.	.	.	_	_	_

1	Propagating	propagate	VBG	_	_	_
2	uncertainty	uncertainty	NN	_	_	_
3	in	in	IN	_	_	_
4	microarray	microarray	NN	_	_	_
5	analysis	analysis	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	puma	puma	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	method	method	NN	_	_	_
10	was	be	VBD	_	_	_
11	used	use	VBN	_	_	_
12	to	to	TO	_	_	_
13	estimate	estimate	VB	_	_	_
14	fold	fold	JJ	_	_	_
15	changes	change	NNS	_	_	_
16	and	and	CC	_	_	_
17	P-like	p-like	JJ	_	_	_
18	values	value	NNS	_	_	_
19	of	of	IN	_	_	_
20	differential	differential	JJ	_	_	_
21	gene	gene	NN	_	_	_
22	expression	expression	NN	_	_	_
23	analysis	analysis	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Pearson	Pearson	NNP	_	_	_
26	et	et	FW	_	_	_
27	al.	al.	FW	_	_	_
28	2009	2009	CD	_	_	_
29	,	,	,	_	_	_
30	BMC	BMC	NNP	_	_	_
31	Bioinformatics	Bioinformatics	NNPS	_	_	_
32	10:211	10:211	CD	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Mutant	mutant	JJ	_	_	_
3	E.	e.	FW	_	_	_
4	coli	coli	FW	_	_	_
5	O157	o157	NN	_	_	_
6	treated	treat	VBN	_	_	_
7	with	with	IN	_	_	_
8	6	6	CD	_	_	_
9	ug	ug	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Mutant	mutant	JJ	_	_	_
12	E.	e.	FW	_	_	_
13	coli	coli	FW	_	_	_
14	O157	o157	NN	_	_	_
15	untreated	untreated	JJ	_	_	_
16	,	,	,	_	_	_
17	biological	biological	JJ	_	_	_
18	rep	rep	NN	GEN	_	_
19	1	1	CD	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Mutant	mutant	JJ	_	_	_
22	E.	e.	FW	_	_	_
23	coli	coli	FW	_	_	_
24	O157	o157	NN	_	_	_
25	untreated	untreated	JJ	_	_	_
26	,	,	,	_	_	_
27	biological	biological	JJ	_	_	_
28	rep	rep	NN	GEN	_	_
29	2	2	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
31	Mutant	mutant	JJ	_	_	_
32	E.	e.	FW	_	_	_
33	coli	coli	FW	_	_	_
34	O157	o157	NN	_	_	_
35	untreated	untreated	JJ	_	_	_
36	,	,	,	_	_	_
37	biological	biological	JJ	_	_	_
38	rep	rep	NN	GEN	_	_
39	3	3	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	strain	strain	NN	_	_	_
42	:	:	:	_	_	_
43	T3	t3	NN	_	_	_
44	5H5	5h5	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	strain	strain	NN	_	_	_
47	:	:	:	_	_	_
48	T3	t3	NN	_	_	_
49	5H5	5h5	NN	_	_	_
50	M	m	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
52	The	the	DT	_	_	_
53	subculture	subculture	NN	_	_	_
54	was	be	VBD	_	_	_
55	split	split	VBN	_	_	_
56	into	into	IN	_	_	_
57	two	two	CD	_	_	_
58	10	10	CD	_	_	_
59	ml	ml	NN	_	_	_
60	portions	portion	NNS	_	_	_
61	,	,	,	_	_	_
62	one	one	CD	_	_	_
63	of	of	IN	_	_	_
64	which	which	WDT	_	_	_
65	was	be	VBD	_	_	_
66	treated	treat	VBN	_	_	_
67	with	with	IN	_	_	_
68	6ug	6ug	JJ	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
70	The	the	DT	_	_	_
71	wildtype	wildtype	JJ	_	_	_
72	and	and	CC	_	_	_
73	mutant	mutant	JJ	_	_	_
74	E.	e.	FW	_	_	_
75	coli	coli	FW	_	_	_
76	O157	o157	NN	_	_	_
77	:	:	:	_	_	_
78	H19	h19	NN	_	_	_
79	strains	strain	NNS	_	_	_
80	were	be	VBD	_	_	_
81	grown	grow	VBN	_	_	_
82	on	on	IN	_	_	_
83	LB	LB	NNP	_	_	_
84	agar	agar	NN	_	_	_
85	incubated	incubate	VBN	_	_	_
86	at	at	IN	_	_	_
87	37c	37c	CD	_	_	_
88	x	x	CC	_	_	_
89	24h	24h	CD	_	_	_
90	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	single	single	JJ	_	_	_
3	isolated	isolate	VBN	_	_	_
4	colony	colony	NN	_	_	_
5	for	for	IN	_	_	_
6	each	each	DT	_	_	_
7	strain	strain	NN	_	_	_
8	was	be	VBD	_	_	_
9	selected	select	VBN	_	_	_
10	and	and	CC	_	_	_
11	inoculated	inoculate	VBN	_	_	_
12	into	into	IN	_	_	_
13	20	20	CD	_	_	_
14	ml	ml	NN	_	_	_
15	LB	lb	NN	MED	_	_
16	broth	broth	NN	MED	_	_
17	and	and	CC	_	_	_
18	incubated	incubate	VBN	_	_	_
19	at	at	IN	_	_	_
20	37c	37c	CD	_	_	_
21	until	until	IN	_	_	_
22	growth	growth	NN	_	_	_
23	reached	reach	VBD	_	_	_
24	an	a	DT	_	_	_
25	optical	optical	JJ	_	_	_
26	density	density	NN	_	_	_
27	of	of	IN	_	_	_
28	0.6	0.6	CD	_	_	_
29	at	at	IN	_	_	_
30	600nm	600nm	CD	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	stabilised	stabilise	VBN	_	_	_
6	and	and	CC	_	_	_
7	subsequently	subsequently	RB	_	_	_
8	purified	purify	VBN	_	_	_
9	from	from	IN	_	_	_
10	a	a	DT	_	_	_
11	500	500	CD	_	_	_
12	ul	ul	NN	_	_	_
13	portion	portion	NN	_	_	_
14	of	of	IN	_	_	_
15	each	each	DT	_	_	_
16	bacterial	bacterial	JJ	_	_	_
17	culture	culture	NN	_	_	_
18	using	use	VBG	_	_	_
19	a	a	DT	_	_	_
20	RNAprotect	rnaprotect	NN	_	_	_
21	Bacterial	bacterial	JJ	_	_	_
22	Reagent	reagent	NN	_	_	_
23	Mini	Mini	NNP	_	_	_
24	Kit	kit	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	Qiagen	Qiagen	NNP	_	_	_
27	,	,	,	_	_	_
28	Crawley	Crawley	NNP	_	_	_
29	,	,	,	_	_	_
30	UK	UK	NNP	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	treatment	treatment	NN	_	_	_
34	:	:	:	_	_	_
35	triclosan	triclosan	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	treatment	treatment	NN	_	_	_
38	:	:	:	_	_	_
39	untreated	untreated	JJ	_	_	_
40	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
41	Triclosan	Triclosan	NNP	_	_	_
42	tolerant	tolerant	JJ	_	_	_
43	mutant	mutant	JJ	_	_	_
44	triclosan	triclosan	NN	_	_	_
45	treated	treat	VBN	_	_	_
46	biological	biological	JJ	_	_	_
47	rep	rep	NN	GEN	_	_
48	1	1	CD	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	Triclosan	Triclosan	NNP	_	_	_
51	tolerant	tolerant	JJ	_	_	_
52	mutant	mutant	JJ	_	_	_
53	triclosan	triclosan	NN	_	_	_
54	treated	treat	VBN	_	_	_
55	biological	biological	JJ	_	_	_
56	rep	rep	NN	GEN	_	_
57	2	2	CD	_	_	_
58	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
59	Triclosan	Triclosan	NNP	_	_	_
60	tolerant	tolerant	JJ	_	_	_
61	mutant	mutant	JJ	_	_	_
62	triclosan	triclosan	NN	_	_	_
63	treated	treat	VBN	_	_	_
64	biological	biological	JJ	_	_	_
65	rep	rep	NN	GEN	_	_
66	3	3	CD	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	Triclosan	triclosan	NN	_	_	_
69	tolerant	tolerant	JJ	_	_	_
70	mutant	mutant	JJ	_	_	_
71	untreated	untreated	JJ	_	_	_
72	biological	biological	JJ	_	_	_
73	rep	rep	NN	GEN	_	_
74	1	1	CD	_	_	_
75	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
76	Triclosan	Triclosan	NNP	_	_	_
77	tolerant	tolerant	JJ	_	_	_
78	mutant	mutant	JJ	_	_	_
79	untreated	untreated	JJ	_	_	_
80	biological	biological	JJ	_	_	_
81	rep	rep	NN	GEN	_	_
82	2	2	CD	_	_	_
83	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
84	Triclosan	Triclosan	NNP	_	_	_
85	tolerant	tolerant	JJ	_	_	_
86	mutant	mutant	JJ	_	_	_
87	untreated	untreated	JJ	_	_	_
88	biological	biological	JJ	_	_	_
89	rep	rep	NN	GEN	_	_
90	3	3	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	Wildtype	wildtype	NN	_	_	_
93	E.	e.	FW	_	_	_
94	coli	coli	FW	_	_	_
95	O157	o157	NN	_	_	_
96	treated	treat	VBN	_	_	_
97	with	with	IN	_	_	_
98	6	6	CD	_	_	_
99	ug	ug	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	Wildtype	wildtype	NN	_	_	_
102	E.	e.	FW	_	_	_
103	coli	coli	FW	_	_	_
104	O157	o157	NN	_	_	_
105	untreated	untreated	JJ	_	_	_
106	,	,	,	_	_	_
107	biological	biological	JJ	_	_	_
108	rep	rep	NN	GEN	_	_
109	1	1	CD	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	Wildtype	wildtype	NN	_	_	_
112	E.	e.	FW	_	_	_
113	coli	coli	FW	_	_	_
114	O157	o157	NN	_	_	_
115	untreated	untreated	JJ	_	_	_
116	,	,	,	_	_	_
117	biological	biological	JJ	_	_	_
118	rep	rep	NN	GEN	_	_
119	2	2	CD	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
121	Wildtype	wildtype	JJ	_	_	_
122	E.	e.	FW	_	_	_
123	coli	coli	FW	_	_	_
124	O157	o157	NN	_	_	_
125	untreated	untreated	JJ	_	_	_
126	,	,	,	_	_	_
127	biological	biological	JJ	_	_	_
128	rep	rep	NN	GEN	_	_
129	3	3	CD	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	Wildtype	wildtype	JJ	_	_	_
132	triclosan	triclosan	NN	_	_	_
133	treated	treat	VBN	_	_	_
134	biological	biological	JJ	_	_	_
135	rep	rep	NN	GEN	_	_
136	1	1	CD	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	Wildtype	wildtype	JJ	_	_	_
139	triclosan	triclosan	NN	_	_	_
140	treated	treat	VBN	_	_	_
141	biological	biological	JJ	_	_	_
142	rep	rep	NN	GEN	_	_
143	2	2	CD	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	Wildtype	wildtype	JJ	_	_	_
146	triclosan	triclosan	NN	_	_	_
147	treated	treat	VBN	_	_	_
148	biological	biological	JJ	_	_	_
149	rep	rep	NN	GEN	_	_
150	3	3	CD	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	Wildtype	wildtype	JJ	_	_	_
153	untreated	untreated	JJ	_	_	_
154	biological	biological	JJ	_	_	_
155	rep	rep	NN	GEN	_	_
156	1	1	CD	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	Wildtype	wildtype	JJ	_	_	_
159	untreated	untreated	JJ	_	_	_
160	biological	biological	JJ	_	_	_
161	rep	rep	NN	GEN	_	_
162	2	2	CD	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	Wildtype	wildtype	JJ	_	_	_
165	untreated	untreated	JJ	_	_	_
166	biological	biological	JJ	_	_	_
167	rep	rep	NN	GEN	_	_
168	3	3	CD	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	0.5	0.5	CD	_	_	_
171	MIC	mic	NN	_	_	_
172	of	of	IN	_	_	_
173	CYA	CYA	NNP	_	_	_
174	,	,	,	_	_	_
175	biological	biological	JJ	_	_	_
176	rep1	rep1	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	0.5	0.5	CD	_	_	_
179	MIC	mic	NN	_	_	_
180	of	of	IN	_	_	_
181	CYA	CYA	NNP	_	_	_
182	,	,	,	_	_	_
183	biological	biological	JJ	_	_	_
184	rep2	rep2	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	0.5	0.5	CD	_	_	_
187	MIC	mic	NN	_	_	_
188	of	of	IN	_	_	_
189	CYA	CYA	NNP	_	_	_
190	,	,	,	_	_	_
191	biological	biological	JJ	_	_	_
192	rep3	rep3	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	Cells	cell	NNS	_	_	_
195	were	be	VBD	_	_	_
196	grown	grow	VBN	_	_	_
197	in	in	IN	_	_	_
198	anaerobic	anaerobic	JJ	_	_	_
199	incubator	incubator	NN	_	_	_
200	for	for	IN	_	_	_
201	1h	1h	NN	_	_	_
202	at	at	IN	_	_	_
203	37	37	CD	_	_	_
204	℃	℃	NN	_	_	_
205	and	and	CC	_	_	_
206	drugs	drug	NNS	_	_	_
207	were	be	VBD	_	_	_
208	added	add	VBN	_	_	_
209	according	accord	VBG	_	_	_
210	to	to	TO	_	_	_
211	the	the	DT	_	_	_
212	different	different	JJ	_	_	_
213	concentrations	concentration	NNS	_	_	_
214	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	incubated	incubate	VBN	_	_	_
5	for	for	IN	_	_	_
6	30	30	CD	_	_	_
7	min	min	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Escherichia	escherichia	FW	Organism	_	_
6	coli	coli	FW	Organism	_	_
7	treated	treat	VBN	_	_	_
8	with	with	IN	_	_	_
9	0.5	0.5	CD	_	_	_
10	MIC	mic	NN	_	_	_
11	of	of	IN	_	_	_
12	cyadox	cyadox	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Escherichia	escherichia	FW	Organism	_	_
15	coli	coli	FW	Organism	_	_
16	treated	treat	VBN	_	_	_
17	with	with	IN	_	_	_
18	1	1	CD	_	_	_
19	%	%	NN	_	_	_
20	DMSO	dmso	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
22	Escherichia	escherichia	FW	Organism	_	_
23	coli	coli	FW	Organism	_	_
24	treated	treat	VBN	_	_	_
25	with	with	IN	_	_	_
26	MBC	mbc	NN	_	_	_
27	of	of	IN	_	_	_
28	cyadox	cyadox	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Escherichia	escherichia	FW	Organism	_	_
31	coli	coli	FW	Organism	_	_
32	treated	treat	VBN	_	_	_
33	with	with	IN	_	_	_
34	MBC	mbc	NN	_	_	_
35	of	of	IN	_	_	_
36	olaquindox	olaquindox	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Escherichia	escherichia	FW	Organism	_	_
39	coli	coli	FW	Organism	_	_
40	treated	treat	VBN	_	_	_
41	with	with	IN	_	_	_
42	MIC	mic	NN	_	_	_
43	of	of	IN	_	_	_
44	olaquindox	olaquindox	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	MBC	mbc	NN	_	_	_
47	of	of	IN	_	_	_
48	CYA	CYA	NNP	_	_	_
49	,	,	,	_	_	_
50	biological	biological	JJ	_	_	_
51	rep1	rep1	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	MBC	mbc	NN	_	_	_
54	of	of	IN	_	_	_
55	CYA	CYA	NNP	_	_	_
56	,	,	,	_	_	_
57	biological	biological	JJ	_	_	_
58	rep2	rep2	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	MBC	mbc	NN	_	_	_
61	of	of	IN	_	_	_
62	CYA	CYA	NNP	_	_	_
63	,	,	,	_	_	_
64	biological	biological	JJ	_	_	_
65	rep3	rep3	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	MBC	mbc	NN	_	_	_
68	of	of	IN	_	_	_
69	OLA	OLA	NNP	_	_	_
70	,	,	,	_	_	_
71	biological	biological	JJ	_	_	_
72	rep1	rep1	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	MBC	mbc	NN	_	_	_
75	of	of	IN	_	_	_
76	OLA	OLA	NNP	_	_	_
77	,	,	,	_	_	_
78	biological	biological	JJ	_	_	_
79	rep2	rep2	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	MBC	mbc	NN	_	_	_
82	of	of	IN	_	_	_
83	OLA	OLA	NNP	_	_	_
84	,	,	,	_	_	_
85	biological	biological	JJ	_	_	_
86	rep3	rep3	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	MIC	mic	NN	_	_	_
89	of	of	IN	_	_	_
90	OLA	OLA	NNP	_	_	_
91	,	,	,	_	_	_
92	biological	biological	JJ	_	_	_
93	rep1	rep1	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	MIC	mic	NN	_	_	_
96	of	of	IN	_	_	_
97	OLA	OLA	NNP	_	_	_
98	,	,	,	_	_	_
99	biological	biological	JJ	_	_	_
100	rep2	rep2	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	MIC	mic	NN	_	_	_
103	of	of	IN	_	_	_
104	OLA	OLA	NNP	_	_	_
105	,	,	,	_	_	_
106	biological	biological	JJ	_	_	_
107	rep3	rep3	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
109	Solvent	solvent	JJ	_	_	_
110	control	control	NN	_	_	_
111	,	,	,	_	_	_
112	biological	biological	JJ	_	_	_
113	rep1	rep1	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
115	Solvent	solvent	JJ	_	_	_
116	control	control	NN	_	_	_
117	,	,	,	_	_	_
118	biological	biological	JJ	_	_	_
119	rep2	rep2	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
121	Solvent	solvent	JJ	_	_	_
122	control	control	NN	_	_	_
123	,	,	,	_	_	_
124	biological	biological	JJ	_	_	_
125	rep3	rep3	NN	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	strain	strain	NN	_	_	_
128	:	:	:	_	_	_
129	CVCC2943	cvcc2943	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
131	The	the	DT	_	_	_
132	cells	cell	NNS	_	_	_
133	were	be	VBD	_	_	_
134	centrifuged	centrifuge	VBN	_	_	_
135	at	at	IN	_	_	_
136	8000	8000	CD	_	_	_
137	rpm	rpm	NN	_	_	_
138	for	for	IN	_	_	_
139	5	5	CD	_	_	_
140	min	min	NN	_	_	_
141	at	at	IN	_	_	_
142	4	4	CD	_	_	_
143	°C	°c	NN	_	_	_
144	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cell	cell	NN	_	_	_
3	pellets	pellet	NNS	_	_	_
4	were	be	VBD	_	_	_
5	snap-frozen	snap-frozen	JJ	_	_	_
6	in	in	IN	_	_	_
7	liquid	liquid	JJ	_	_	_
8	nitrogen	nitrogen	NN	_	_	_
9	and	and	CC	_	_	_
10	kept	keep	VBD	_	_	_
11	at	at	IN	_	_	_
12	-80	-80	CD	_	_	_
13	°C	°c	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
15	The	the	DT	_	_	_
16	data	datum	NNS	_	_	_
17	were	be	VBD	_	_	_
18	analyzed	analyze	VBN	_	_	_
19	with	with	IN	_	_	_
20	Partek	Partek	NNP	_	_	_
21	Genomics	Genomics	NNP	_	_	_
22	Suite	Suite	NNP	_	_	_
23	using	use	VBG	_	_	_
24	Affymetrix	Affymetrix	NNP	_	_	_
25	default	default	NN	_	_	_
26	analysis	analysis	NN	_	_	_
27	settings	setting	NNS	_	_	_
28	and	and	CC	_	_	_
29	global	global	JJ	_	_	_
30	scaling	scaling	NN	_	_	_
31	as	as	IN	_	_	_
32	normalization	normalization	NN	_	_	_
33	method	method	NN	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Trizol	trizol	NN	_	_	_
3	extraction	extraction	NN	_	_	_
4	of	of	IN	_	_	_
5	total	total	JJ	_	_	_
6	RNA	rna	NN	_	_	_
7	was	be	VBD	_	_	_
8	performed	perform	VBN	_	_	_
9	according	accord	VBG	_	_	_
10	to	to	TO	_	_	_
11	the	the	DT	_	_	_
12	manufacturer	manufacturer	NN	_	_	_
13	's	's	POS	_	_	_
14	instructions	instruction	NNS	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Eno	Eno	NNP	_	_	_
3	-	-	:	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	DF261	df261	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	in	in	IN	_	_	_
8	M9	m9	NN	_	_	_
9	0.2	0.2	CD	_	_	_
10	%	%	NN	_	_	_
11	Glycerol	glycerol	NN	_	_	_
12	0.2	0.2	CD	_	_	_
13	%	%	NN	_	_	_
14	Tryptone	tryptone	NN	_	_	_
15	40mM	40mm	NN	_	_	_
16	Suc	suc	NN	_	_	_
17	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	Eno	Eno	NNP	_	_	_
8	-	-	:	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	DF261	df261	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	in	in	IN	_	_	_
13	M9	m9	NN	_	_	_
14	+	+	CC	_	_	_
15	0.2	0.2	CD	_	_	_
16	%	%	NN	_	_	_
17	Glycerol	glycerol	NN	_	_	_
18	,	,	,	_	_	_
19	0.2	0.2	CD	_	_	_
20	%	%	NN	_	_	_
21	Tryptone	tryptone	NN	_	_	_
22	,	,	,	_	_	_
23	40mM	40mm	NN	_	_	_
24	Suc	suc	NN	_	_	_
25	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	Escherichia	escherichia	FW	Organism	_	_
8	coli	coli	FW	Organism	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	N-RNaseE	n-rnasee	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	BZ453	bz453	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	in	in	IN	_	_	_
15	M9	m9	NN	_	_	_
16	+	+	CC	_	_	_
17	0.2	0.2	CD	_	_	_
18	%	%	NN	_	_	_
19	Glycerol	glycerol	NN	_	_	_
20	,	,	,	_	_	_
21	0.2	0.2	CD	_	_	_
22	%	%	NN	_	_	_
23	Tryptone	tryptone	NN	_	_	_
24	at	at	IN	_	_	_
25	30	30	CD	_	_	_
26	C	c	NN	_	_	_
27	Mid	Mid	NNP	_	_	_
28	Log	Log	NNP	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	Pnp	Pnp	NNP	_	_	_
31	-	-	:	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	YHC012	yhc012	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	in	in	IN	_	_	_
36	M9	m9	NN	_	_	_
37	+	+	CC	_	_	_
38	0.2	0.2	CD	_	_	_
39	%	%	NN	_	_	_
40	Glycerol	glycerol	NN	_	_	_
41	,	,	,	_	_	_
42	0.2	0.2	CD	_	_	_
43	%	%	NN	_	_	_
44	Tryptone	tryptone	NN	_	_	_
45	at	at	IN	_	_	_
46	30	30	CD	_	_	_
47	C	c	NN	_	_	_
48	Mid	Mid	NNP	_	_	_
49	Log	Log	NNP	_	_	_
50	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
51	Pnp	Pnp	NNP	_	_	_
52	-	-	:	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	YHC012	yhc012	NN	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	in	in	IN	_	_	_
57	M9	m9	NN	_	_	_
58	+	+	CC	_	_	_
59	0.2	0.2	CD	_	_	_
60	%	%	NN	_	_	_
61	Glycerol	glycerol	NN	_	_	_
62	,	,	,	_	_	_
63	0.2	0.2	CD	_	_	_
64	%	%	NN	_	_	_
65	Tryptone	tryptone	NN	_	_	_
66	at	at	IN	_	_	_
67	30	30	CD	_	_	_
68	C	c	NN	_	_	_
69	Mid	Mid	NNP	_	_	_
70	Log	Log	NNP	_	_	_
71	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
72	Pnp	Pnp	NNP	_	_	_
73	-	-	:	_	_	_
74	-LRB-	-lrb-	-LRB-	_	_	_
75	YHC012	yhc012	NN	_	_	_
76	-RRB-	-rrb-	-RRB-	_	_	_
77	-RRB-	-rrb-	-RRB-	_	_	_
78	in	in	IN	_	_	_
79	M9	m9	NN	_	_	_
80	+	+	CC	_	_	_
81	0.2	0.2	CD	_	_	_
82	%	%	NN	_	_	_
83	Glycerol	glycerol	NN	_	_	_
84	,	,	,	_	_	_
85	0.2	0.2	CD	_	_	_
86	%	%	NN	_	_	_
87	Tryptone	tryptone	NN	_	_	_
88	at	at	IN	_	_	_
89	30	30	CD	_	_	_
90	C	c	NN	_	_	_
91	Mid	Mid	NNP	_	_	_
92	Log	Log	NNP	_	_	_
93	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
94	RhlB	rhlb	NN	_	_	_
95	-	-	:	_	_	_
96	-LRB-	-lrb-	-LRB-	_	_	_
97	SU02	su02	NN	_	_	_
98	-RRB-	-rrb-	-RRB-	_	_	_
99	in	in	IN	_	_	_
100	M9	m9	NN	_	_	_
101	0.2	0.2	CD	_	_	_
102	%	%	NN	_	_	_
103	Glycerol	glycerol	NN	_	_	_
104	,	,	,	_	_	_
105	0.2	0.2	CD	_	_	_
106	%	%	NN	_	_	_
107	Tryptone	tryptone	NN	_	_	_
108	at	at	IN	_	_	_
109	30	30	CD	_	_	_
110	C	c	NN	_	_	_
111	Mid	Mid	NNP	_	_	_
112	Log	Log	NNP	_	_	_
113	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
114	RhlB	rhlb	NN	_	_	_
115	-	-	:	_	_	_
116	-LRB-	-lrb-	-LRB-	_	_	_
117	SU02	su02	NN	_	_	_
118	-RRB-	-rrb-	-RRB-	_	_	_
119	in	in	IN	_	_	_
120	M9	m9	NN	_	_	_
121	+	+	CC	_	_	_
122	0.2	0.2	CD	_	_	_
123	%	%	NN	_	_	_
124	Glycerol	glycerol	NN	_	_	_
125	,	,	,	_	_	_
126	0.2	0.2	CD	_	_	_
127	%	%	NN	_	_	_
128	Tryptone	tryptone	NN	_	_	_
129	at	at	IN	_	_	_
130	30	30	CD	_	_	_
131	C	c	NN	_	_	_
132	Mid	Mid	NNP	_	_	_
133	Log	Log	NNP	_	_	_
134	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
135	RhlB	rhlb	NN	_	_	_
136	-	-	:	_	_	_
137	-LRB-	-lrb-	-LRB-	_	_	_
138	SU02	su02	NN	_	_	_
139	-RRB-	-rrb-	-RRB-	_	_	_
140	in	in	IN	_	_	_
141	M9	m9	NN	_	_	_
142	0.2	0.2	CD	_	_	_
143	%	%	NN	_	_	_
144	Glycerol	glycerol	NN	_	_	_
145	,	,	,	_	_	_
146	0.2	0.2	CD	_	_	_
147	%	%	NN	_	_	_
148	Tryptone	tryptone	NN	_	_	_
149	at	at	IN	_	_	_
150	30	30	CD	_	_	_
151	C	c	NN	_	_	_
152	Mid	Mid	NNP	_	_	_
153	Log	Log	NNP	_	_	_
154	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
155	RhlB	rhlb	NN	_	_	_
156	-	-	:	_	_	_
157	-LRB-	-lrb-	-LRB-	_	_	_
158	SU02	su02	NN	_	_	_
159	-RRB-	-rrb-	-RRB-	_	_	_
160	in	in	IN	_	_	_
161	M9	m9	NN	_	_	_
162	+	+	CC	_	_	_
163	0.2	0.2	CD	_	_	_
164	%	%	NN	_	_	_
165	Glycerol	glycerol	NN	_	_	_
166	,	,	,	_	_	_
167	0.2	0.2	CD	_	_	_
168	%	%	NN	_	_	_
169	Tryptone	tryptone	NN	_	_	_
170	at	at	IN	_	_	_
171	30	30	CD	_	_	_
172	C	c	NN	_	_	_
173	Mid	Mid	NNP	_	_	_
174	Log	Log	NNP	_	_	_
175	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
176	VALUE	VALUE	NNP	_	_	_
177	is	be	VBZ	_	_	_
178	Log	log	NN	_	_	_
179	-LRB-	-lrb-	-LRB-	_	_	_
180	base	base	NN	_	_	_
181	2	2	CD	_	_	_
182	-RRB-	-rrb-	-RRB-	_	_	_
183	of	of	IN	_	_	_
184	the	the	DT	_	_	_
185	ratio	ratio	NN	_	_	_
186	of	of	IN	_	_	_
187	the	the	DT	_	_	_
188	median	median	NN	_	_	_
189	of	of	IN	_	_	_
190	Channel	Channel	NNP	_	_	_
191	2	2	CD	_	_	_
192	-LRB-	-lrb-	-LRB-	_	_	_
193	usually	usually	RB	_	_	_
194	635	635	CD	_	_	_
195	nm	nm	NN	_	_	_
196	-RRB-	-rrb-	-RRB-	_	_	_
197	to	to	TO	_	_	_
198	Channel	Channel	NNP	_	_	_
199	1	1	CD	_	_	_
200	-LRB-	-lrb-	-LRB-	_	_	_
201	usually	usually	RB	_	_	_
202	532	532	CD	_	_	_
203	nm	nm	NN	_	_	_
204	-RRB-	-rrb-	-RRB-	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	Wild	Wild	NNP	_	_	_
207	Type	type	NN	_	_	_
208	-LRB-	-lrb-	-LRB-	_	_	_
209	K10	k10	NN	_	_	_
210	-RRB-	-rrb-	-RRB-	_	_	_
211	M9	m9	NN	_	_	_
212	+	+	CC	_	_	_
213	0.2	0.2	CD	_	_	_
214	%	%	NN	_	_	_
215	Glycerol	glycerol	NN	_	_	_
216	,	,	,	_	_	_
217	0.2	0.2	CD	_	_	_
218	%	%	NN	_	_	_
219	Tryptone	tryptone	NN	_	_	_
220	,	,	,	_	_	_
221	40	40	CD	_	_	_
222	mM	mm	NN	KWSUPP	_	_
223	Suc	suc	NN	_	_	_
224	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	Wild	Wild	NNP	_	_	_
8	Type	type	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	K10	k10	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	M9	m9	NN	_	_	_
13	+	+	CC	_	_	_
14	0.2	0.2	CD	_	_	_
15	%	%	NN	_	_	_
16	Glycerol	glycerol	NN	_	_	_
17	,	,	,	_	_	_
18	0.2	0.2	CD	_	_	_
19	%	%	NN	_	_	_
20	Tryptone	tryptone	NN	_	_	_
21	,	,	,	_	_	_
22	40	40	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	Suc	suc	NN	_	_	_
25	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	CMid	cmid	NN	_	_	_
4	Log	log	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Wild	Wild	NNP	_	_	_
7	Type	type	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	K10	k10	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	M9	m9	NN	_	_	_
12	0.2	0.2	CD	_	_	_
13	%	%	NN	_	_	_
14	Glycerol	glycerol	NN	_	_	_
15	0.2	0.2	CD	_	_	_
16	%	%	NN	_	_	_
17	Tryptone	tryptone	NN	_	_	_
18	40	40	CD	_	_	_
19	mM	mm	NN	KWSUPP	_	_
20	Suc	suc	NN	_	_	_
21	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	Wild	Wild	NNP	_	_	_
8	Type	type	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	N3433	n3433	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	in	in	IN	_	_	_
13	M9	m9	NN	_	_	_
14	0.2	0.2	CD	_	_	_
15	%	%	NN	_	_	_
16	Glycerol	glycerol	NN	_	_	_
17	,	,	,	_	_	_
18	0.2	0.2	CD	_	_	_
19	%	%	NN	_	_	_
20	Tryptone	tryptone	NN	_	_	_
21	at	at	IN	_	_	_
22	30	30	CD	_	_	_
23	C	c	NN	_	_	_
24	Mid	Mid	NNP	_	_	_
25	Log	Log	NNP	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	Wild	Wild	NNP	_	_	_
28	Type	type	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	N3433	n3433	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	M9	m9	NN	_	_	_
33	0.2	0.2	CD	_	_	_
34	%	%	NN	_	_	_
35	Glycerol	glycerol	NN	_	_	_
36	,	,	,	_	_	_
37	0.2	0.2	CD	_	_	_
38	%	%	NN	_	_	_
39	Tryptone	tryptone	NN	_	_	_
40	at	at	IN	_	_	_
41	30	30	CD	_	_	_
42	C	c	NN	_	_	_
43	Mid	Mid	NNP	_	_	_
44	Log	Log	NNP	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	Wild	Wild	NNP	_	_	_
47	Type	type	NN	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	N3433	n3433	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	M9	m9	NN	_	_	_
52	+	+	CC	_	_	_
53	0.2	0.2	CD	_	_	_
54	%	%	NN	_	_	_
55	Glycerol	glycerol	NN	_	_	_
56	,	,	,	_	_	_
57	0.2	0.2	CD	_	_	_
58	%	%	NN	_	_	_
59	Tryptone	tryptone	NN	_	_	_
60	at	at	IN	_	_	_
61	30	30	CD	_	_	_
62	C	c	NN	_	_	_
63	Mid	Mid	NNP	_	_	_
64	Log	Log	NNP	_	_	_
65	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
66	WT	WT	NNP	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	K10	k10	NN	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	vs	vs	CC	_	_	_
71	Eno	eno	NN	_	_	_
72	-	-	:	_	_	_
73	-LRB-	-lrb-	-LRB-	_	_	_
74	DF261	df261	NN	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	in	in	IN	_	_	_
77	M9	m9	NN	_	_	_
78	+	+	CC	_	_	_
79	0.2	0.2	CD	_	_	_
80	%	%	NN	_	_	_
81	Glycerol	glycerol	NN	_	_	_
82	,	,	,	_	_	_
83	0.2	0.2	CD	_	_	_
84	%	%	NN	_	_	_
85	Tryptone	tryptone	NN	_	_	_
86	,	,	,	_	_	_
87	40	40	CD	_	_	_
88	mM	mm	NN	KWSUPP	_	_
89	Suc	suc	NN	_	_	_
90	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	Trial	Trial	NNP	_	_	_
7	A	A	NNP	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	WT	WT	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	K10	k10	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	vs	vs	CC	_	_	_
14	Eno	eno	NN	_	_	_
15	-	-	:	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	DF261	df261	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	in	in	IN	_	_	_
20	M9	m9	NN	_	_	_
21	0.2	0.2	CD	_	_	_
22	%	%	NN	_	_	_
23	Glycerol	glycerol	NN	_	_	_
24	,	,	,	_	_	_
25	0.2	0.2	CD	_	_	_
26	%	%	NN	_	_	_
27	Tryptone	tryptone	NN	_	_	_
28	,	,	,	_	_	_
29	40	40	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	Suc	suc	NN	_	_	_
32	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	Trial	Trial	NNP	_	_	_
7	B	B	NNP	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	WT	WT	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	K10	k10	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	vs	vs	CC	_	_	_
14	Eno	eno	NN	_	_	_
15	-	-	:	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	DF261	df261	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	M9	m9	NN	_	_	_
20	+	+	CC	_	_	_
21	0.2	0.2	CD	_	_	_
22	%	%	NN	_	_	_
23	Glycerol	glycerol	NN	_	_	_
24	,	,	,	_	_	_
25	0.2	0.2	CD	_	_	_
26	%	%	NN	_	_	_
27	Tryptone	tryptone	NN	_	_	_
28	,	,	,	_	_	_
29	40	40	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	Suc	suc	NN	_	_	_
32	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	Trial	Trial	NNP	_	_	_
7	A1	a1	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	WT	wt	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	K10	k10	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	vs	vs	CC	_	_	_
14	Eno	eno	NN	_	_	_
15	-	-	:	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	DF261	df261	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	M9	m9	NN	_	_	_
20	+	+	CC	_	_	_
21	0.2	0.2	CD	_	_	_
22	%	%	NN	_	_	_
23	Glycerol	glycerol	NN	_	_	_
24	,	,	,	_	_	_
25	0.2	0.2	CD	_	_	_
26	%	%	NN	_	_	_
27	Tryptone	tryptone	NN	_	_	_
28	,	,	,	_	_	_
29	40	40	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	Suc	suc	NN	_	_	_
32	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	Trial	Trial	NNP	_	_	_
7	B1	b1	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	WT	wt	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	N3433	n3433	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	vs	vs	CC	_	_	_
14	Pnp	pnp	NN	_	_	_
15	-	-	:	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	YHC012	yhc012	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	in	in	IN	_	_	_
20	M9	m9	NN	_	_	_
21	+	+	CC	_	_	_
22	0.2	0.2	CD	_	_	_
23	%	%	NN	_	_	_
24	Glycerol	glycerol	NN	_	_	_
25	,	,	,	_	_	_
26	0.2	0.2	CD	_	_	_
27	%	%	NN	_	_	_
28	Tryptone	tryptone	NN	_	_	_
29	at	at	IN	_	_	_
30	30	30	CD	_	_	_
31	C	c	NN	_	_	_
32	Mid	Mid	NNP	_	_	_
33	Log	Log	NNP	_	_	_
34	Trial	Trial	NNP	_	_	_
35	A2	a2	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	WT	wt	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	N3433	n3433	NN	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	vs	vs	CC	_	_	_
42	Pnp	pnp	NN	_	_	_
43	-	-	:	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	YHC012	yhc012	NN	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	in	in	IN	_	_	_
48	M9	m9	NN	_	_	_
49	+	+	CC	_	_	_
50	0.2	0.2	CD	_	_	_
51	%	%	NN	_	_	_
52	Glycerol	glycerol	NN	_	_	_
53	,	,	,	_	_	_
54	0.2	0.2	CD	_	_	_
55	%	%	NN	_	_	_
56	Tryptone	tryptone	NN	_	_	_
57	at	at	IN	_	_	_
58	30	30	CD	_	_	_
59	C	c	NN	_	_	_
60	Mid	Mid	NNP	_	_	_
61	Log	Log	NNP	_	_	_
62	Trial	Trial	NNP	_	_	_
63	B2	b2	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	WT	wt	NN	_	_	_
66	-LRB-	-lrb-	-LRB-	_	_	_
67	N3433	n3433	NN	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	vs	vs	CC	_	_	_
70	Pnp	pnp	NN	_	_	_
71	-	-	:	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	YHC012	yhc012	NN	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	in	in	IN	_	_	_
76	M9	m9	NN	_	_	_
77	+	+	CC	_	_	_
78	0.2	0.2	CD	_	_	_
79	%	%	NN	_	_	_
80	Glycerol	glycerol	NN	_	_	_
81	,	,	,	_	_	_
82	0.2	0.2	CD	_	_	_
83	%	%	NN	_	_	_
84	Tryptone	tryptone	NN	_	_	_
85	at	at	IN	_	_	_
86	30	30	CD	_	_	_
87	C	c	NN	_	_	_
88	Mid	Mid	NNP	_	_	_
89	Log	Log	NNP	_	_	_
90	Trial	Trial	NNP	_	_	_
91	C2	c2	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	WT	wt	NN	_	_	_
94	-LRB-	-lrb-	-LRB-	_	_	_
95	N3433	n3433	NN	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	vs	vs	CC	_	_	_
98	RhlB	rhlb	NN	_	_	_
99	-	-	:	_	_	_
100	-LRB-	-lrb-	-LRB-	_	_	_
101	SU02	su02	NN	_	_	_
102	-RRB-	-rrb-	-RRB-	_	_	_
103	in	in	IN	_	_	_
104	M9	m9	NN	_	_	_
105	+	+	CC	_	_	_
106	0.2	0.2	CD	_	_	_
107	%	%	NN	_	_	_
108	Glycerol	glycerol	NN	_	_	_
109	,	,	,	_	_	_
110	0.2	0.2	CD	_	_	_
111	%	%	NN	_	_	_
112	Tryptone	tryptone	NN	_	_	_
113	at	at	IN	_	_	_
114	30	30	CD	_	_	_
115	C	c	NN	_	_	_
116	Mid	Mid	NNP	_	_	_
117	Log	Log	NNP	_	_	_
118	Trial	Trial	NNP	_	_	_
119	A	A	NNP	_	_	_
120	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
121	WT	WT	NNP	_	_	_
122	-LRB-	-lrb-	-LRB-	_	_	_
123	N3433	n3433	NN	_	_	_
124	-RRB-	-rrb-	-RRB-	_	_	_
125	vs	vs	CC	_	_	_
126	RhlB	rhlb	NN	_	_	_
127	-	-	:	_	_	_
128	-LRB-	-lrb-	-LRB-	_	_	_
129	SU02	su02	NN	_	_	_
130	-RRB-	-rrb-	-RRB-	_	_	_
131	in	in	IN	_	_	_
132	M9	m9	NN	_	_	_
133	+	+	CC	_	_	_
134	0.2	0.2	CD	_	_	_
135	%	%	NN	_	_	_
136	Glycerol	glycerol	NN	_	_	_
137	,	,	,	_	_	_
138	0.2	0.2	CD	_	_	_
139	%	%	NN	_	_	_
140	Tryptone	tryptone	NN	_	_	_
141	at	at	IN	_	_	_
142	30	30	CD	_	_	_
143	C	c	NN	_	_	_
144	Mid	Mid	NNP	_	_	_
145	Log	Log	NNP	_	_	_
146	Trial	Trial	NNP	_	_	_
147	A1	a1	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	WT	wt	NN	_	_	_
150	-LRB-	-lrb-	-LRB-	_	_	_
151	N3433	n3433	NN	_	_	_
152	-RRB-	-rrb-	-RRB-	_	_	_
153	vs	vs	CC	_	_	_
154	RhlB	rhlb	NN	_	_	_
155	-	-	:	_	_	_
156	-LRB-	-lrb-	-LRB-	_	_	_
157	SU02	su02	NN	_	_	_
158	-RRB-	-rrb-	-RRB-	_	_	_
159	in	in	IN	_	_	_
160	M9	m9	NN	_	_	_
161	0.2	0.2	CD	_	_	_
162	%	%	NN	_	_	_
163	Glycerol	glycerol	NN	_	_	_
164	,	,	,	_	_	_
165	0.2	0.2	CD	_	_	_
166	%	%	NN	_	_	_
167	Tryptone	tryptone	NN	_	_	_
168	at	at	IN	_	_	_
169	30	30	CD	_	_	_
170	C	c	NN	_	_	_
171	Mid	Mid	NNP	_	_	_
172	Log	Log	NNP	_	_	_
173	Trial	Trial	NNP	_	_	_
174	B	B	NNP	_	_	_
175	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
176	WT	WT	NNP	_	_	_
177	-LRB-	-lrb-	-LRB-	_	_	_
178	N3433	n3433	NN	_	_	_
179	-RRB-	-rrb-	-RRB-	_	_	_
180	vs	vs	CC	_	_	_
181	RhlB	rhlb	NN	_	_	_
182	-	-	:	_	_	_
183	-LRB-	-lrb-	-LRB-	_	_	_
184	SU02	su02	NN	_	_	_
185	-RRB-	-rrb-	-RRB-	_	_	_
186	in	in	IN	_	_	_
187	M9	m9	NN	_	_	_
188	+	+	CC	_	_	_
189	0.2	0.2	CD	_	_	_
190	%	%	NN	_	_	_
191	Glycerol	glycerol	NN	_	_	_
192	,	,	,	_	_	_
193	0.2	0.2	CD	_	_	_
194	%	%	NN	_	_	_
195	Tryptone	tryptone	NN	_	_	_
196	at	at	IN	_	_	_
197	30	30	CD	_	_	_
198	C	c	NN	_	_	_
199	Mid	Mid	NNP	_	_	_
200	Log	Log	NNP	_	_	_
201	Trial	Trial	NNP	_	_	_
202	B1	b1	NN	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	WT	wt	NN	_	_	_
205	-LRB-	-lrb-	-LRB-	_	_	_
206	N3433	n3433	NN	_	_	_
207	-RRB-	-rrb-	-RRB-	_	_	_
208	vs	vs	CC	_	_	_
209	RhlB	rhlb	NN	_	_	_
210	-	-	:	_	_	_
211	-LRB-	-lrb-	-LRB-	_	_	_
212	SU02	su02	NN	_	_	_
213	-RRB-	-rrb-	-RRB-	_	_	_
214	in	in	IN	_	_	_
215	M9	m9	NN	_	_	_
216	0.2	0.2	CD	_	_	_
217	%	%	NN	_	_	_
218	Glycerol	glycerol	NN	_	_	_
219	,	,	,	_	_	_
220	0.2	0.2	CD	_	_	_
221	%	%	NN	_	_	_
222	Tryptone	tryptone	NN	_	_	_
223	at	at	IN	_	_	_
224	30	30	CD	_	_	_
225	C	c	NN	_	_	_
226	Mid	Mid	NNP	_	_	_
227	Log	Log	NNP	_	_	_
228	Trial	Trial	NNP	_	_	_
229	C	C	NNP	_	_	_
230	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
231	WT	WT	NNP	_	_	_
232	-LRB-	-lrb-	-LRB-	_	_	_
233	N3433	n3433	NN	_	_	_
234	-RRB-	-rrb-	-RRB-	_	_	_
235	vs	vs	CC	_	_	_
236	RhlB	rhlb	NN	_	_	_
237	-	-	:	_	_	_
238	-LRB-	-lrb-	-LRB-	_	_	_
239	SU02	su02	NN	_	_	_
240	-RRB-	-rrb-	-RRB-	_	_	_
241	in	in	IN	_	_	_
242	M9	m9	NN	_	_	_
243	+	+	CC	_	_	_
244	0.2	0.2	CD	_	_	_
245	%	%	NN	_	_	_
246	Glycerol	glycerol	NN	_	_	_
247	,	,	,	_	_	_
248	0.2	0.2	CD	_	_	_
249	%	%	NN	_	_	_
250	Tryptone	tryptone	NN	_	_	_
251	at	at	IN	_	_	_
252	30	30	CD	_	_	_
253	C	c	NN	_	_	_
254	Mid	Mid	NNP	_	_	_
255	Log	Log	NNP	_	_	_
256	Trial	Trial	NNP	_	_	_
257	C1	c1	NN	_	_	_
258	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
259	WT	wt	NN	_	_	_
260	-LRB-	-lrb-	-LRB-	_	_	_
261	SH3208	sh3208	NN	_	_	_
262	-RRB-	-rrb-	-RRB-	_	_	_
263	M9	m9	NN	_	_	_
264	+	+	CC	_	_	_
265	0.2	0.2	CD	_	_	_
266	%	%	NN	_	_	_
267	Glycerol	glycerol	NN	_	_	_
268	,	,	,	_	_	_
269	0.2	0.2	CD	_	_	_
270	%	%	NN	_	_	_
271	Tryptone	tryptone	NN	_	_	_
272	at	at	IN	_	_	_
273	30	30	CD	_	_	_
274	C	c	NN	_	_	_
275	Mid	Mid	NNP	_	_	_
276	Log	Log	NNP	_	_	_
277	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
278	WT	WT	NNP	_	_	_
279	-LRB-	-lrb-	-LRB-	_	_	_
280	SH3208	sh3208	NN	_	_	_
281	-RRB-	-rrb-	-RRB-	_	_	_
282	vs	vs	CC	_	_	_
283	N-RNaseE	n-rnasee	NN	_	_	_
284	-LRB-	-lrb-	-LRB-	_	_	_
285	BZ453	bz453	NN	_	_	_
286	-RRB-	-rrb-	-RRB-	_	_	_
287	in	in	IN	_	_	_
288	M9	m9	NN	_	_	_
289	+	+	CC	_	_	_
290	0.2	0.2	CD	_	_	_
291	%	%	NN	_	_	_
292	Glycerol	glycerol	NN	_	_	_
293	,	,	,	_	_	_
294	0.2	0.2	CD	_	_	_
295	%	%	NN	_	_	_
296	Tryptone	tryptone	NN	_	_	_
297	at	at	IN	_	_	_
298	30	30	CD	_	_	_
299	C	c	NN	_	_	_
300	Mid	Mid	NNP	_	_	_
301	Log	Log	NNP	_	_	_
302	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
303	WT	WT	NNP	_	_	_
304	-LRB-	-lrb-	-LRB-	_	_	_
305	SH3208	sh3208	NN	_	_	_
306	-RRB-	-rrb-	-RRB-	_	_	_
307	vs	vs	CC	_	_	_
308	N-RNaseE	n-rnasee	NN	_	_	_
309	-LRB-	-lrb-	-LRB-	_	_	_
310	BZ453	bz453	NN	_	_	_
311	-RRB-	-rrb-	-RRB-	_	_	_
312	in	in	IN	_	_	_
313	M9	m9	NN	_	_	_
314	+	+	CC	_	_	_
315	0.2	0.2	CD	_	_	_
316	%	%	NN	_	_	_
317	Glycerol	glycerol	NN	_	_	_
318	,	,	,	_	_	_
319	0.2	0.2	CD	_	_	_
320	%	%	NN	_	_	_
321	Tryptone	tryptone	NN	_	_	_
322	at	at	IN	_	_	_
323	30	30	CD	_	_	_
324	C	c	NN	_	_	_
325	Mid	Mid	NNP	_	_	_
326	Log	Log	NNP	_	_	_
327	Trial	Trial	NNP	_	_	_
328	A	A	NNP	_	_	_
329	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
330	WT	WT	NNP	_	_	_
331	-LRB-	-lrb-	-LRB-	_	_	_
332	SH3208	sh3208	NN	_	_	_
333	-RRB-	-rrb-	-RRB-	_	_	_
334	vs	vs	CC	_	_	_
335	N-RNaseE	n-rnasee	NN	_	_	_
336	-LRB-	-lrb-	-LRB-	_	_	_
337	BZ453	bz453	NN	_	_	_
338	-RRB-	-rrb-	-RRB-	_	_	_
339	in	in	IN	_	_	_
340	M9	m9	NN	_	_	_
341	+	+	CC	_	_	_
342	0.2	0.2	CD	_	_	_
343	%	%	NN	_	_	_
344	Glycerol	glycerol	NN	_	_	_
345	,	,	,	_	_	_
346	0.2	0.2	CD	_	_	_
347	%	%	NN	_	_	_
348	Tryptone	tryptone	NN	_	_	_
349	at	at	IN	_	_	_
350	30	30	CD	_	_	_
351	C	c	NN	_	_	_
352	Mid	Mid	NNP	_	_	_
353	Log	Log	NNP	_	_	_
354	Trial	trial	NN	_	_	_
355	B	b	NN	_	_	_
356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
357	WT	wt	NN	_	_	_
358	-LRB-	-lrb-	-LRB-	_	_	_
359	SH3208	sh3208	NN	_	_	_
360	-RRB-	-rrb-	-RRB-	_	_	_
361	vs	vs	CC	_	_	_
362	N-RNaseE	n-rnasee	NN	_	_	_
363	-LRB-	-lrb-	-LRB-	_	_	_
364	BZ453	bz453	NN	_	_	_
365	-RRB-	-rrb-	-RRB-	_	_	_
366	in	in	IN	_	_	_
367	M9	m9	NN	_	_	_
368	+	+	CC	_	_	_
369	0.2	0.2	CD	_	_	_
370	%	%	NN	_	_	_
371	Glycerol	glycerol	NN	_	_	_
372	,	,	,	_	_	_
373	0.2	0.2	CD	_	_	_
374	%	%	NN	_	_	_
375	Tryptone	tryptone	NN	_	_	_
376	at	at	IN	_	_	_
377	30	30	CD	_	_	_
378	C	c	NN	_	_	_
379	Mid	Mid	NNP	_	_	_
380	Log	Log	NNP	_	_	_
381	Trial	Trial	NNP	_	_	_
382	C	C	NNP	_	_	_
383	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
384	1.5	1.5	CD	_	_	_
385	'	'	''	_	_	_
386	RNA	rna	NN	_	_	_
387	Decay	decay	NN	_	_	_
388	N-RNaseE	n-rnasee	NN	_	_	_
389	-LRB-	-lrb-	-LRB-	_	_	_
390	BZ453	bz453	NN	_	_	_
391	-RRB-	-rrb-	-RRB-	_	_	_
392	in	in	IN	_	_	_
393	M9	m9	NN	_	_	_
394	0.2	0.2	CD	_	_	_
395	%	%	NN	_	_	_
396	Glycerol	glycerol	NN	_	_	_
397	,	,	,	_	_	_
398	0.2	0.2	CD	_	_	_
399	%	%	NN	_	_	_
400	Tryptone	tryptone	NN	_	_	_
401	at	at	IN	_	_	_
402	30	30	CD	_	_	_
403	C	c	NN	_	_	_
404	Mid	Mid	NNP	_	_	_
405	Log	Log	NNP	_	_	_
406	Rep.	Rep.	NNP	_	_	_
407	A	A	NNP	_	_	_
408	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
409	1.5	1.5	CD	_	_	_
410	'	'	''	_	_	_
411	RNA	rna	NN	_	_	_
412	Decay	decay	NN	_	_	_
413	N-RNaseE	n-rnasee	NN	_	_	_
414	-LRB-	-lrb-	-LRB-	_	_	_
415	BZ453	bz453	NN	_	_	_
416	-RRB-	-rrb-	-RRB-	_	_	_
417	in	in	IN	_	_	_
418	M9	m9	NN	_	_	_
419	0.2	0.2	CD	_	_	_
420	%	%	NN	_	_	_
421	Glycerol	glycerol	NN	_	_	_
422	,	,	,	_	_	_
423	0.2	0.2	CD	_	_	_
424	%	%	NN	_	_	_
425	Tryptone	tryptone	NN	_	_	_
426	at	at	IN	_	_	_
427	30	30	CD	_	_	_
428	C	c	NN	_	_	_
429	Mid	Mid	NNP	_	_	_
430	Log	Log	NNP	_	_	_
431	Rep.	Rep.	NNP	_	_	_
432	A1	a1	NN	_	_	_
433	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
434	1.5	1.5	CD	_	_	_
435	'	'	''	_	_	_
436	RNA	rna	NN	_	_	_
437	Decay	decay	NN	_	_	_
438	N-RNaseE	n-rnasee	NN	_	_	_
439	-LRB-	-lrb-	-LRB-	_	_	_
440	BZ453	bz453	NN	_	_	_
441	-RRB-	-rrb-	-RRB-	_	_	_
442	in	in	IN	_	_	_
443	M9	m9	NN	_	_	_
444	+	+	CC	_	_	_
445	0.2	0.2	CD	_	_	_
446	%	%	NN	_	_	_
447	Glycerol	glycerol	NN	_	_	_
448	,	,	,	_	_	_
449	0.2	0.2	CD	_	_	_
450	%	%	NN	_	_	_
451	Tryptone	tryptone	NN	_	_	_
452	at	at	IN	_	_	_
453	30	30	CD	_	_	_
454	C	c	NN	_	_	_
455	Mid	Mid	NNP	_	_	_
456	Log	Log	NNP	_	_	_
457	Rep.	Rep.	NNP	_	_	_
458	B	B	NNP	_	_	_
459	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
460	1.5	1.5	CD	_	_	_
461	'	'	''	_	_	_
462	RNA	rna	NN	_	_	_
463	Decay	decay	NN	_	_	_
464	N-RNaseE	n-rnasee	NN	_	_	_
465	-LRB-	-lrb-	-LRB-	_	_	_
466	BZ453	bz453	NN	_	_	_
467	-RRB-	-rrb-	-RRB-	_	_	_
468	in	in	IN	_	_	_
469	M9	m9	NN	_	_	_
470	+	+	CC	_	_	_
471	0.2	0.2	CD	_	_	_
472	%	%	NN	_	_	_
473	Glycerol	glycerol	NN	_	_	_
474	,	,	,	_	_	_
475	0.2	0.2	CD	_	_	_
476	%	%	NN	_	_	_
477	Tryptone	tryptone	NN	_	_	_
478	at	at	IN	_	_	_
479	30	30	CD	_	_	_
480	C	c	NN	_	_	_
481	Mid	Mid	NNP	_	_	_
482	Log	Log	NNP	_	_	_
483	Rep.	Rep.	NNP	_	_	_
484	B1	b1	NN	_	_	_
485	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
486	1.5	1.5	CD	_	_	_
487	'	'	''	_	_	_
488	RNA	rna	NN	_	_	_
489	Decay	decay	NN	_	_	_
490	of	of	IN	_	_	_
491	Eno	Eno	NNP	_	_	_
492	-	-	:	_	_	_
493	-LRB-	-lrb-	-LRB-	_	_	_
494	DF261	df261	NN	_	_	_
495	-RRB-	-rrb-	-RRB-	_	_	_
496	in	in	IN	_	_	_
497	M9	m9	NN	_	_	_
498	0.2	0.2	CD	_	_	_
499	%	%	NN	_	_	_
500	Glycerol	glycerol	NN	_	_	_
501	0.2	0.2	CD	_	_	_
502	%	%	NN	_	_	_
503	Tryptone	tryptone	NN	_	_	_
504	,	,	,	_	_	_
505	40	40	CD	_	_	_
506	mM	mm	NN	KWSUPP	_	_
507	Suc.at	suc.at	NN	_	_	_
508	30	30	CD	_	_	_
509	C	c	NN	_	_	_
510	Mid	Mid	NNP	_	_	_
511	Log	Log	NNP	_	_	_
512	Rep	Rep	NNP	_	_	_
513	A	A	NNP	_	_	_
514	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
515	1.5	1.5	CD	_	_	_
516	'	'	''	_	_	_
517	RNA	rna	NN	_	_	_
518	Decay	decay	NN	_	_	_
519	of	of	IN	_	_	_
520	Eno	Eno	NNP	_	_	_
521	-	-	:	_	_	_
522	-LRB-	-lrb-	-LRB-	_	_	_
523	DF261	df261	NN	_	_	_
524	-RRB-	-rrb-	-RRB-	_	_	_
525	in	in	IN	_	_	_
526	M9	m9	NN	_	_	_
527	0.2	0.2	CD	_	_	_
528	%	%	NN	_	_	_
529	Glycerol	glycerol	NN	_	_	_
530	0.2	0.2	CD	_	_	_
531	%	%	NN	_	_	_
532	Tryptone	tryptone	NN	_	_	_
533	40	40	CD	_	_	_
534	mM	mm	NN	KWSUPP	_	_
535	Suc	suc	NN	_	_	_
536	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	Rep	Rep	NNP	_	_	_
7	B	B	NNP	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	1.5	1.5	CD	_	_	_
10	'	'	''	_	_	_
11	RNA	rna	NN	_	_	_
12	Decay	decay	NN	_	_	_
13	of	of	IN	_	_	_
14	Pnp	pnp	NN	_	_	_
15	-	-	:	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	YHC012	yhc012	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	in	in	IN	_	_	_
20	M9	m9	NN	_	_	_
21	+	+	CC	_	_	_
22	0.2	0.2	CD	_	_	_
23	%	%	NN	_	_	_
24	Glycerol	glycerol	NN	_	_	_
25	,	,	,	_	_	_
26	0.2	0.2	CD	_	_	_
27	%	%	NN	_	_	_
28	Tryptone	tryptone	NN	_	_	_
29	at	at	IN	_	_	_
30	30	30	CD	_	_	_
31	C	c	NN	_	_	_
32	Mid	Mid	NNP	_	_	_
33	Log	Log	NNP	_	_	_
34	Rep.	Rep.	NNP	_	_	_
35	A2	a2	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	1.5	1.5	CD	_	_	_
38	'	'	''	_	_	_
39	RNA	rna	NN	_	_	_
40	Decay	decay	NN	_	_	_
41	of	of	IN	_	_	_
42	Pnp	pnp	NN	_	_	_
43	-	-	:	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	YHC012	yhc012	NN	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	in	in	IN	_	_	_
48	M9	m9	NN	_	_	_
49	+	+	CC	_	_	_
50	0.2	0.2	CD	_	_	_
51	%	%	NN	_	_	_
52	Glycerol	glycerol	NN	_	_	_
53	,	,	,	_	_	_
54	0.2	0.2	CD	_	_	_
55	%	%	NN	_	_	_
56	Tryptone	tryptone	NN	_	_	_
57	at	at	IN	_	_	_
58	30	30	CD	_	_	_
59	C	c	NN	_	_	_
60	Mid	Mid	NNP	_	_	_
61	Log	Log	NNP	_	_	_
62	Rep.	Rep.	NNP	_	_	_
63	B2	b2	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	1.5	1.5	CD	_	_	_
66	'	'	''	_	_	_
67	RNA	rna	NN	_	_	_
68	Decay	decay	NN	_	_	_
69	of	of	IN	_	_	_
70	RhlB	rhlb	NN	_	_	_
71	-	-	:	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	SU02	su02	NN	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	in	in	IN	_	_	_
76	M9	m9	NN	_	_	_
77	+	+	CC	_	_	_
78	0.2	0.2	CD	_	_	_
79	%	%	NN	_	_	_
80	Glycerol	glycerol	NN	_	_	_
81	,	,	,	_	_	_
82	0.2	0.2	CD	_	_	_
83	%	%	NN	_	_	_
84	Tryptone	tryptone	NN	_	_	_
85	at	at	IN	_	_	_
86	30	30	CD	_	_	_
87	C	c	NN	_	_	_
88	Mid	Mid	NNP	_	_	_
89	Log	Log	NNP	_	_	_
90	Replicate	replicate	VB	_	_	_
91	A	a	DT	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	1.5	1.5	CD	_	_	_
94	'	'	''	_	_	_
95	RNA	rna	NN	_	_	_
96	Decay	decay	NN	_	_	_
97	of	of	IN	_	_	_
98	RhlB	rhlb	NN	_	_	_
99	-	-	:	_	_	_
100	-LRB-	-lrb-	-LRB-	_	_	_
101	SU02	su02	NN	_	_	_
102	-RRB-	-rrb-	-RRB-	_	_	_
103	in	in	IN	_	_	_
104	M9	m9	NN	_	_	_
105	+	+	CC	_	_	_
106	0.2	0.2	CD	_	_	_
107	%	%	NN	_	_	_
108	Glycerol	glycerol	NN	_	_	_
109	,	,	,	_	_	_
110	0.2	0.2	CD	_	_	_
111	%	%	NN	_	_	_
112	Tryptone	tryptone	NN	_	_	_
113	at	at	IN	_	_	_
114	30	30	CD	_	_	_
115	C	c	NN	_	_	_
116	Mid	Mid	NNP	_	_	_
117	Log	Log	NNP	_	_	_
118	Replicate	replicate	VB	_	_	_
119	A1	a1	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	1.5	1.5	CD	_	_	_
122	'	'	''	_	_	_
123	RNA	rna	NN	_	_	_
124	Decay	decay	NN	_	_	_
125	of	of	IN	_	_	_
126	RhlB	rhlb	NN	_	_	_
127	-	-	:	_	_	_
128	-LRB-	-lrb-	-LRB-	_	_	_
129	SU02	su02	NN	_	_	_
130	-RRB-	-rrb-	-RRB-	_	_	_
131	in	in	IN	_	_	_
132	M9	m9	NN	_	_	_
133	+	+	CC	_	_	_
134	0.2	0.2	CD	_	_	_
135	%	%	NN	_	_	_
136	Glycerol	glycerol	NN	_	_	_
137	,	,	,	_	_	_
138	0.2	0.2	CD	_	_	_
139	%	%	NN	_	_	_
140	Tryptone	tryptone	NN	_	_	_
141	at	at	IN	_	_	_
142	30	30	CD	_	_	_
143	C	c	NN	_	_	_
144	Mid	Mid	NNP	_	_	_
145	Log	Log	NNP	_	_	_
146	Replicate	replicate	VB	_	_	_
147	B	b	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	1.5	1.5	CD	_	_	_
150	'	'	''	_	_	_
151	RNA	rna	NN	_	_	_
152	Decay	decay	NN	_	_	_
153	of	of	IN	_	_	_
154	RhlB	rhlb	NN	_	_	_
155	-	-	:	_	_	_
156	-LRB-	-lrb-	-LRB-	_	_	_
157	SU02	su02	NN	_	_	_
158	-RRB-	-rrb-	-RRB-	_	_	_
159	in	in	IN	_	_	_
160	M9	m9	NN	_	_	_
161	+	+	CC	_	_	_
162	0.2	0.2	CD	_	_	_
163	%	%	NN	_	_	_
164	Glycerol	glycerol	NN	_	_	_
165	,	,	,	_	_	_
166	0.2	0.2	CD	_	_	_
167	%	%	NN	_	_	_
168	Tryptone	tryptone	NN	_	_	_
169	at	at	IN	_	_	_
170	30	30	CD	_	_	_
171	C	c	NN	_	_	_
172	Mid	Mid	NNP	_	_	_
173	Log	Log	NNP	_	_	_
174	Replicate	replicate	VB	_	_	_
175	B1	b1	NN	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	1.5	1.5	CD	_	_	_
178	'	'	''	_	_	_
179	RNA	rna	NN	_	_	_
180	Decay	decay	NN	_	_	_
181	of	of	IN	_	_	_
182	WT	WT	NNP	_	_	_
183	-LRB-	-lrb-	-LRB-	_	_	_
184	K10	k10	NN	_	_	_
185	-RRB-	-rrb-	-RRB-	_	_	_
186	in	in	IN	_	_	_
187	M9	m9	NN	_	_	_
188	0.2	0.2	CD	_	_	_
189	%	%	NN	_	_	_
190	Glycerol	glycerol	NN	_	_	_
191	0.2	0.2	CD	_	_	_
192	%	%	NN	_	_	_
193	Tryptone	tryptone	NN	_	_	_
194	,	,	,	_	_	_
195	40	40	CD	_	_	_
196	mM	mm	NN	KWSUPP	_	_
197	Suc	suc	NN	_	_	_
198	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	Rep	Rep	NNP	_	_	_
7	A	A	NNP	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	1.5	1.5	CD	_	_	_
10	'	'	''	_	_	_
11	RNA	rna	NN	_	_	_
12	Decay	decay	NN	_	_	_
13	of	of	IN	_	_	_
14	WT	WT	NNP	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	K10	k10	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	in	in	IN	_	_	_
19	M9	m9	NN	_	_	_
20	0.2	0.2	CD	_	_	_
21	%	%	NN	_	_	_
22	Glycerol	glycerol	NN	_	_	_
23	0.2	0.2	CD	_	_	_
24	%	%	NN	_	_	_
25	Tryptone	tryptone	NN	_	_	_
26	40	40	CD	_	_	_
27	mM	mm	NN	KWSUPP	_	_
28	Suc.at	suc.at	NN	_	_	_
29	30	30	CD	_	_	_
30	C	c	NN	_	_	_
31	Mid	Mid	NNP	_	_	_
32	Log	Log	NNP	_	_	_
33	Rep	Rep	NNP	_	_	_
34	B	B	NNP	_	_	_
35	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
36	1.5	1.5	CD	_	_	_
37	'	'	''	_	_	_
38	RNA	rna	NN	_	_	_
39	Decay	decay	NN	_	_	_
40	of	of	IN	_	_	_
41	WT	WT	NNP	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	N3433	n3433	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	in	in	IN	_	_	_
46	M9	m9	NN	_	_	_
47	0.2	0.2	CD	_	_	_
48	%	%	NN	_	_	_
49	Glycerol	glycerol	NN	_	_	_
50	0.2	0.2	CD	_	_	_
51	%	%	NN	_	_	_
52	Tryptone	tryptone	NN	_	_	_
53	at	at	IN	_	_	_
54	30	30	CD	_	_	_
55	C	c	NN	_	_	_
56	Mid	Mid	NNP	_	_	_
57	Log	Log	NNP	_	_	_
58	Rep.	Rep.	NNP	_	_	_
59	A2	a2	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	1.5	1.5	CD	_	_	_
62	'	'	''	_	_	_
63	RNA	rna	NN	_	_	_
64	Decay	decay	NN	_	_	_
65	of	of	IN	_	_	_
66	WT	WT	NNP	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	N3433	n3433	NN	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	in	in	IN	_	_	_
71	M9	m9	NN	_	_	_
72	0.2	0.2	CD	_	_	_
73	%	%	NN	_	_	_
74	Glycerol	glycerol	NN	_	_	_
75	0.2	0.2	CD	_	_	_
76	%	%	NN	_	_	_
77	Tryptone	tryptone	NN	_	_	_
78	at	at	IN	_	_	_
79	30	30	CD	_	_	_
80	C	c	NN	_	_	_
81	Mid	Mid	NNP	_	_	_
82	Log	Log	NNP	_	_	_
83	Rep.	Rep.	NNP	_	_	_
84	B2	b2	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	1.5	1.5	CD	_	_	_
87	'	'	''	_	_	_
88	RNA	rna	NN	_	_	_
89	Decay	decay	NN	_	_	_
90	of	of	IN	_	_	_
91	WT	WT	NNP	_	_	_
92	-LRB-	-lrb-	-LRB-	_	_	_
93	N3433	n3433	NN	_	_	_
94	-RRB-	-rrb-	-RRB-	_	_	_
95	in	in	IN	_	_	_
96	M9	m9	NN	_	_	_
97	0.2	0.2	CD	_	_	_
98	%	%	NN	_	_	_
99	Glycerol	glycerol	NN	_	_	_
100	0.2	0.2	CD	_	_	_
101	%	%	NN	_	_	_
102	Tryptone	tryptone	NN	_	_	_
103	at	at	IN	_	_	_
104	30	30	CD	_	_	_
105	C	c	NN	_	_	_
106	Mid	Mid	NNP	_	_	_
107	Log	Log	NNP	_	_	_
108	Replicate	replicate	VB	_	_	_
109	A1	a1	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	1.5	1.5	CD	_	_	_
112	'	'	''	_	_	_
113	RNA	rna	NN	_	_	_
114	Decay	decay	NN	_	_	_
115	of	of	IN	_	_	_
116	WT	WT	NNP	_	_	_
117	-LRB-	-lrb-	-LRB-	_	_	_
118	N3433	n3433	NN	_	_	_
119	-RRB-	-rrb-	-RRB-	_	_	_
120	in	in	IN	_	_	_
121	M9	m9	NN	_	_	_
122	+	+	CC	_	_	_
123	0.2	0.2	CD	_	_	_
124	%	%	NN	_	_	_
125	Glycerol	glycerol	NN	_	_	_
126	,	,	,	_	_	_
127	0.2	0.2	CD	_	_	_
128	%	%	NN	_	_	_
129	Tryptone	tryptone	NN	_	_	_
130	at	at	IN	_	_	_
131	30	30	CD	_	_	_
132	C	c	NN	_	_	_
133	Mid	Mid	NNP	_	_	_
134	Log	Log	NNP	_	_	_
135	Replicate	replicate	VB	_	_	_
136	B1	b1	NN	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	1.5	1.5	CD	_	_	_
139	'	'	''	_	_	_
140	RNA	rna	NN	_	_	_
141	Decay	decay	NN	_	_	_
142	of	of	IN	_	_	_
143	WT	WT	NNP	_	_	_
144	-LRB-	-lrb-	-LRB-	_	_	_
145	SH3208	sh3208	NN	_	_	_
146	-RRB-	-rrb-	-RRB-	_	_	_
147	in	in	IN	_	_	_
148	M9	m9	NN	_	_	_
149	0.2	0.2	CD	_	_	_
150	%	%	NN	_	_	_
151	Glycerol	glycerol	NN	_	_	_
152	0.2	0.2	CD	_	_	_
153	%	%	NN	_	_	_
154	Tryptone	tryptone	NN	_	_	_
155	at	at	IN	_	_	_
156	30	30	CD	_	_	_
157	C	c	NN	_	_	_
158	Mid	Mid	NNP	_	_	_
159	Log	Log	NNP	_	_	_
160	Rep.	Rep.	NNP	_	_	_
161	A1	a1	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	1.5	1.5	CD	_	_	_
164	'	'	''	_	_	_
165	RNA	rna	NN	_	_	_
166	Decay	decay	NN	_	_	_
167	of	of	IN	_	_	_
168	WT	WT	NNP	_	_	_
169	-LRB-	-lrb-	-LRB-	_	_	_
170	SH3208	sh3208	NN	_	_	_
171	-RRB-	-rrb-	-RRB-	_	_	_
172	in	in	IN	_	_	_
173	M9	m9	NN	_	_	_
174	0.2	0.2	CD	_	_	_
175	%	%	NN	_	_	_
176	Glycerol	glycerol	NN	_	_	_
177	0.2	0.2	CD	_	_	_
178	%	%	NN	_	_	_
179	Tryptone	tryptone	NN	_	_	_
180	at	at	IN	_	_	_
181	30	30	CD	_	_	_
182	C	c	NN	_	_	_
183	Mid	Mid	NNP	_	_	_
184	Log	Log	NNP	_	_	_
185	Rep.	Rep.	NNP	_	_	_
186	B1	b1	NN	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	3	3	CD	_	_	_
189	'	'	''	_	_	_
190	RNA	rna	NN	_	_	_
191	Decay	decay	NN	_	_	_
192	N-RNaseE	n-rnasee	NN	_	_	_
193	-LRB-	-lrb-	-LRB-	_	_	_
194	BZ453	bz453	NN	_	_	_
195	-RRB-	-rrb-	-RRB-	_	_	_
196	in	in	IN	_	_	_
197	M9	m9	NN	_	_	_
198	+	+	CC	_	_	_
199	0.2	0.2	CD	_	_	_
200	%	%	NN	_	_	_
201	Glycerol	glycerol	NN	_	_	_
202	,	,	,	_	_	_
203	0.2	0.2	CD	_	_	_
204	%	%	NN	_	_	_
205	Tryptone	tryptone	NN	_	_	_
206	at	at	IN	_	_	_
207	30	30	CD	_	_	_
208	C	c	NN	_	_	_
209	Mid	Mid	NNP	_	_	_
210	Log	Log	NNP	_	_	_
211	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
212	3	3	CD	_	_	_
213	'	'	''	_	_	_
214	RNA	rna	NN	_	_	_
215	Decay	decay	NN	_	_	_
216	N-RNaseE	n-rnasee	NN	_	_	_
217	-LRB-	-lrb-	-LRB-	_	_	_
218	BZ453	bz453	NN	_	_	_
219	-RRB-	-rrb-	-RRB-	_	_	_
220	in	in	IN	_	_	_
221	M9	m9	NN	_	_	_
222	+	+	CC	_	_	_
223	0.2	0.2	CD	_	_	_
224	%	%	NN	_	_	_
225	Glycerol	glycerol	NN	_	_	_
226	,	,	,	_	_	_
227	0.2	0.2	CD	_	_	_
228	%	%	NN	_	_	_
229	Tryptone	tryptone	NN	_	_	_
230	at	at	IN	_	_	_
231	30	30	CD	_	_	_
232	C	c	NN	_	_	_
233	Mid	Mid	NNP	_	_	_
234	Log	Log	NNP	_	_	_
235	1	1	CD	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	3	3	CD	_	_	_
238	'	'	''	_	_	_
239	RNA	rna	NN	_	_	_
240	Decay	decay	NN	_	_	_
241	of	of	IN	_	_	_
242	Eno	Eno	NNP	_	_	_
243	-	-	:	_	_	_
244	-LRB-	-lrb-	-LRB-	_	_	_
245	DF261	df261	NN	_	_	_
246	-RRB-	-rrb-	-RRB-	_	_	_
247	in	in	IN	_	_	_
248	M9	m9	NN	_	_	_
249	0.2	0.2	CD	_	_	_
250	%	%	NN	_	_	_
251	Glycerol	glycerol	NN	_	_	_
252	0.2	0.2	CD	_	_	_
253	%	%	NN	_	_	_
254	Tryptone	tryptone	NN	_	_	_
255	40	40	CD	_	_	_
256	mM	mm	NN	KWSUPP	_	_
257	Suc	suc	NN	_	_	_
258	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	Rep	Rep	NNP	_	_	_
7	A	A	NNP	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	3	3	CD	_	_	_
10	'	'	''	_	_	_
11	RNA	rna	NN	_	_	_
12	Decay	decay	NN	_	_	_
13	of	of	IN	_	_	_
14	Eno	Eno	NNP	_	_	_
15	-	-	:	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	DF261	df261	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	in	in	IN	_	_	_
20	M9	m9	NN	_	_	_
21	0.2	0.2	CD	_	_	_
22	%	%	NN	_	_	_
23	Glycerol	glycerol	NN	_	_	_
24	0.2	0.2	CD	_	_	_
25	%	%	NN	_	_	_
26	Tryptone	tryptone	NN	_	_	_
27	at	at	IN	_	_	_
28	40	40	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	Suc	suc	NN	_	_	_
31	.	.	.	_	_	_

1	30	30	CD	_	_	_
2	C	c	NN	_	_	_
3	Mid	Mid	NNP	_	_	_
4	Log	Log	NNP	_	_	_
5	Rep	Rep	NNP	_	_	_
6	B	B	NNP	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	3	3	CD	_	_	_
9	'	'	''	_	_	_
10	RNA	rna	NN	_	_	_
11	Decay	decay	NN	_	_	_
12	of	of	IN	_	_	_
13	Pnp	pnp	NN	_	_	_
14	-	-	:	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	YHC012	yhc012	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	in	in	IN	_	_	_
19	M9	m9	NN	_	_	_
20	+	+	CC	_	_	_
21	0.2	0.2	CD	_	_	_
22	%	%	NN	_	_	_
23	Glycerol	glycerol	NN	_	_	_
24	,	,	,	_	_	_
25	0.2	0.2	CD	_	_	_
26	%	%	NN	_	_	_
27	Tryptone	tryptone	NN	_	_	_
28	at	at	IN	_	_	_
29	30	30	CD	_	_	_
30	C	c	NN	_	_	_
31	Mid	Mid	NNP	_	_	_
32	Log	Log	NNP	_	_	_
33	2	2	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	3	3	CD	_	_	_
36	'	'	''	_	_	_
37	RNA	rna	NN	_	_	_
38	Decay	decay	NN	_	_	_
39	of	of	IN	_	_	_
40	RhlB	rhlb	NN	_	_	_
41	-	-	:	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	SU02	su02	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	in	in	IN	_	_	_
46	M9	m9	NN	_	_	_
47	+	+	CC	_	_	_
48	0.2	0.2	CD	_	_	_
49	%	%	NN	_	_	_
50	Glycerol	glycerol	NN	_	_	_
51	,	,	,	_	_	_
52	0.2	0.2	CD	_	_	_
53	%	%	NN	_	_	_
54	Tryptone	tryptone	NN	_	_	_
55	at	at	IN	_	_	_
56	30	30	CD	_	_	_
57	C	c	NN	_	_	_
58	Mid	Mid	NNP	_	_	_
59	Log	Log	NNP	_	_	_
60	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
61	3	3	CD	_	_	_
62	'	'	''	_	_	_
63	RNA	rna	NN	_	_	_
64	Decay	decay	NN	_	_	_
65	of	of	IN	_	_	_
66	RhlB	rhlb	NN	_	_	_
67	-	-	:	_	_	_
68	-LRB-	-lrb-	-LRB-	_	_	_
69	SU02	su02	NN	_	_	_
70	-RRB-	-rrb-	-RRB-	_	_	_
71	in	in	IN	_	_	_
72	M9	m9	NN	_	_	_
73	+	+	CC	_	_	_
74	0.2	0.2	CD	_	_	_
75	%	%	NN	_	_	_
76	Glycerol	glycerol	NN	_	_	_
77	,	,	,	_	_	_
78	0.2	0.2	CD	_	_	_
79	%	%	NN	_	_	_
80	Tryptone	tryptone	NN	_	_	_
81	at	at	IN	_	_	_
82	30	30	CD	_	_	_
83	C	c	NN	_	_	_
84	Mid	Mid	NNP	_	_	_
85	Log1	log1	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	3	3	CD	_	_	_
88	'	'	''	_	_	_
89	RNA	rna	NN	_	_	_
90	Decay	decay	NN	_	_	_
91	of	of	IN	_	_	_
92	WT	WT	NNP	_	_	_
93	-LRB-	-lrb-	-LRB-	_	_	_
94	K10	k10	NN	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	in	in	IN	_	_	_
97	M9	m9	NN	_	_	_
98	0.2	0.2	CD	_	_	_
99	%	%	NN	_	_	_
100	Glycerol	glycerol	NN	_	_	_
101	0.2	0.2	CD	_	_	_
102	%	%	NN	_	_	_
103	Tryptone	tryptone	NN	_	_	_
104	40	40	CD	_	_	_
105	mM	mm	NN	KWSUPP	_	_
106	Suc	suc	NN	_	_	_
107	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	3	3	CD	_	_	_
8	'	'	''	_	_	_
9	RNA	rna	NN	_	_	_
10	Decay	decay	NN	_	_	_
11	of	of	IN	_	_	_
12	WT	WT	NNP	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	N3433	n3433	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	in	in	IN	_	_	_
17	M9	m9	NN	_	_	_
18	+	+	CC	_	_	_
19	0.2	0.2	CD	_	_	_
20	%	%	NN	_	_	_
21	Glycerol	glycerol	NN	_	_	_
22	,	,	,	_	_	_
23	0.2	0.2	CD	_	_	_
24	%	%	NN	_	_	_
25	Tryptone	tryptone	NN	_	_	_
26	at	at	IN	_	_	_
27	30	30	CD	_	_	_
28	C	c	NN	_	_	_
29	Mid	Mid	NNP	_	_	_
30	Log1	log1	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	3	3	CD	_	_	_
33	'	'	''	_	_	_
34	RNA	rna	NN	_	_	_
35	Decay	decay	NN	_	_	_
36	of	of	IN	_	_	_
37	WT	WT	NNP	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	N3433	n3433	NN	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	in	in	IN	_	_	_
42	M9	m9	NN	_	_	_
43	+	+	CC	_	_	_
44	0.2	0.2	CD	_	_	_
45	%	%	NN	_	_	_
46	Glycerol	glycerol	NN	_	_	_
47	,	,	,	_	_	_
48	0.2	0.2	CD	_	_	_
49	%	%	NN	_	_	_
50	Tryptone	tryptone	NN	_	_	_
51	at	at	IN	_	_	_
52	30	30	CD	_	_	_
53	C	c	NN	_	_	_
54	Mid	Mid	NNP	_	_	_
55	Log	Log	NNP	_	_	_
56	2	2	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	3	3	CD	_	_	_
59	'	'	''	_	_	_
60	RNA	rna	NN	_	_	_
61	Decay	decay	NN	_	_	_
62	of	of	IN	_	_	_
63	WT	WT	NNP	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	SH3208	sh3208	NN	_	_	_
66	-RRB-	-rrb-	-RRB-	_	_	_
67	in	in	IN	_	_	_
68	M9	m9	NN	_	_	_
69	0.2	0.2	CD	_	_	_
70	%	%	NN	_	_	_
71	Glycerol	glycerol	NN	_	_	_
72	,	,	,	_	_	_
73	0.2	0.2	CD	_	_	_
74	%	%	NN	_	_	_
75	Tryptone	tryptone	NN	_	_	_
76	at	at	IN	_	_	_
77	30	30	CD	_	_	_
78	C	c	NN	_	_	_
79	Mid	Mid	NNP	_	_	_
80	Log	Log	NNP	_	_	_
81	1	1	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	4.5	4.5	CD	_	_	_
84	'	'	''	_	_	_
85	RNA	rna	NN	_	_	_
86	Decay	decay	NN	_	_	_
87	N-RNaseE	n-rnasee	NN	_	_	_
88	-LRB-	-lrb-	-LRB-	_	_	_
89	BZ453	bz453	NN	_	_	_
90	-RRB-	-rrb-	-RRB-	_	_	_
91	in	in	IN	_	_	_
92	M9	m9	NN	_	_	_
93	+	+	CC	_	_	_
94	0.2	0.2	CD	_	_	_
95	%	%	NN	_	_	_
96	Glycerol	glycerol	NN	_	_	_
97	,	,	,	_	_	_
98	0.2	0.2	CD	_	_	_
99	%	%	NN	_	_	_
100	Tryptone	tryptone	NN	_	_	_
101	at	at	IN	_	_	_
102	30	30	CD	_	_	_
103	C	c	NN	_	_	_
104	Mid	Mid	NNP	_	_	_
105	Log	Log	NNP	_	_	_
106	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
107	4.5	4.5	CD	_	_	_
108	'	'	''	_	_	_
109	RNA	rna	NN	_	_	_
110	Decay	decay	NN	_	_	_
111	N-RNaseE	n-rnasee	NN	_	_	_
112	-LRB-	-lrb-	-LRB-	_	_	_
113	BZ453	bz453	NN	_	_	_
114	-RRB-	-rrb-	-RRB-	_	_	_
115	in	in	IN	_	_	_
116	M9	m9	NN	_	_	_
117	+	+	CC	_	_	_
118	0.2	0.2	CD	_	_	_
119	%	%	NN	_	_	_
120	Glycerol	glycerol	NN	_	_	_
121	,	,	,	_	_	_
122	0.2	0.2	CD	_	_	_
123	%	%	NN	_	_	_
124	Tryptone	tryptone	NN	_	_	_
125	at	at	IN	_	_	_
126	30	30	CD	_	_	_
127	C	c	NN	_	_	_
128	Mid	Mid	NNP	_	_	_
129	Log	Log	NNP	_	_	_
130	1	1	CD	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	4.5	4.5	CD	_	_	_
133	'	'	''	_	_	_
134	RNA	rna	NN	_	_	_
135	Decay	decay	NN	_	_	_
136	of	of	IN	_	_	_
137	Eno	Eno	NNP	_	_	_
138	-	-	:	_	_	_
139	-LRB-	-lrb-	-LRB-	_	_	_
140	DF261	df261	NN	_	_	_
141	-RRB-	-rrb-	-RRB-	_	_	_
142	in	in	IN	_	_	_
143	M9	m9	NN	_	_	_
144	0.2	0.2	CD	_	_	_
145	%	%	NN	_	_	_
146	Glycerol	glycerol	NN	_	_	_
147	0.2	0.2	CD	_	_	_
148	%	%	NN	_	_	_
149	Tryptone	tryptone	NN	_	_	_
150	40	40	CD	_	_	_
151	mM	mm	NN	KWSUPP	_	_
152	Suc	suc	NN	_	_	_
153	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	4.5	4.5	CD	_	_	_
8	'	'	''	_	_	_
9	RNA	rna	NN	_	_	_
10	Decay	decay	NN	_	_	_
11	of	of	IN	_	_	_
12	Pnp	pnp	NN	_	_	_
13	-	-	:	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	YHC012	yhc012	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	in	in	IN	_	_	_
18	M9	m9	NN	_	_	_
19	+	+	CC	_	_	_
20	0.2	0.2	CD	_	_	_
21	%	%	NN	_	_	_
22	Glycerol	glycerol	NN	_	_	_
23	,	,	,	_	_	_
24	0.2	0.2	CD	_	_	_
25	%	%	NN	_	_	_
26	Tryptone	tryptone	NN	_	_	_
27	at	at	IN	_	_	_
28	30	30	CD	_	_	_
29	C	c	NN	_	_	_
30	Mid	Mid	NNP	_	_	_
31	Log	Log	NNP	_	_	_
32	2	2	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	4.5	4.5	CD	_	_	_
35	'	'	''	_	_	_
36	RNA	rna	NN	_	_	_
37	Decay	decay	NN	_	_	_
38	of	of	IN	_	_	_
39	RhlB	rhlb	NN	_	_	_
40	-	-	:	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	SU02	su02	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	in	in	IN	_	_	_
45	M9	m9	NN	_	_	_
46	+	+	CC	_	_	_
47	0.2	0.2	CD	_	_	_
48	%	%	NN	_	_	_
49	Glycerol	glycerol	NN	_	_	_
50	,	,	,	_	_	_
51	0.2	0.2	CD	_	_	_
52	%	%	NN	_	_	_
53	Tryptone	tryptone	NN	_	_	_
54	at	at	IN	_	_	_
55	30	30	CD	_	_	_
56	C	c	NN	_	_	_
57	Mid	Mid	NNP	_	_	_
58	Log	Log	NNP	_	_	_
59	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
60	4.5	4.5	CD	_	_	_
61	'	'	''	_	_	_
62	RNA	rna	NN	_	_	_
63	Decay	decay	NN	_	_	_
64	of	of	IN	_	_	_
65	RhlB	rhlb	NN	_	_	_
66	-	-	:	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	SU02	su02	NN	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	in	in	IN	_	_	_
71	M9	m9	NN	_	_	_
72	+	+	CC	_	_	_
73	0.2	0.2	CD	_	_	_
74	%	%	NN	_	_	_
75	Glycerol	glycerol	NN	_	_	_
76	,	,	,	_	_	_
77	0.2	0.2	CD	_	_	_
78	%	%	NN	_	_	_
79	Tryptone	tryptone	NN	_	_	_
80	at	at	IN	_	_	_
81	30	30	CD	_	_	_
82	C	c	NN	_	_	_
83	Mid	Mid	NNP	_	_	_
84	Log1	log1	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	4.5	4.5	CD	_	_	_
87	'	'	''	_	_	_
88	RNA	rna	NN	_	_	_
89	Decay	decay	NN	_	_	_
90	of	of	IN	_	_	_
91	WT	WT	NNP	_	_	_
92	-LRB-	-lrb-	-LRB-	_	_	_
93	K10	k10	NN	_	_	_
94	-RRB-	-rrb-	-RRB-	_	_	_
95	in	in	IN	_	_	_
96	M9	m9	NN	_	_	_
97	0.2	0.2	CD	_	_	_
98	%	%	NN	_	_	_
99	Glycerol	glycerol	NN	_	_	_
100	0.2	0.2	CD	_	_	_
101	%	%	NN	_	_	_
102	Tryptone	tryptone	NN	_	_	_
103	40	40	CD	_	_	_
104	mM	mm	NN	KWSUPP	_	_
105	Suc	suc	NN	_	_	_
106	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	4.5	4.5	CD	_	_	_
8	'	'	''	_	_	_
9	RNA	rna	NN	_	_	_
10	Decay	decay	NN	_	_	_
11	of	of	IN	_	_	_
12	WT	WT	NNP	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	N3433	n3433	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	in	in	IN	_	_	_
17	M9	m9	NN	_	_	_
18	+	+	CC	_	_	_
19	0.2	0.2	CD	_	_	_
20	%	%	NN	_	_	_
21	Glycerol	glycerol	NN	_	_	_
22	,	,	,	_	_	_
23	0.2	0.2	CD	_	_	_
24	%	%	NN	_	_	_
25	Tryptone	tryptone	NN	_	_	_
26	at	at	IN	_	_	_
27	30	30	CD	_	_	_
28	C	c	NN	_	_	_
29	Mid	Mid	NNP	_	_	_
30	Log1	log1	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	4.5	4.5	CD	_	_	_
33	'	'	''	_	_	_
34	RNA	rna	NN	_	_	_
35	Decay	decay	NN	_	_	_
36	of	of	IN	_	_	_
37	WT	WT	NNP	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	N3433	n3433	NN	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	in	in	IN	_	_	_
42	M9	m9	NN	_	_	_
43	+	+	CC	_	_	_
44	0.2	0.2	CD	_	_	_
45	%	%	NN	_	_	_
46	Glycerol	glycerol	NN	_	_	_
47	,	,	,	_	_	_
48	0.2	0.2	CD	_	_	_
49	%	%	NN	_	_	_
50	Tryptone	tryptone	NN	_	_	_
51	at	at	IN	_	_	_
52	30	30	CD	_	_	_
53	C	c	NN	_	_	_
54	Mid	Mid	NNP	_	_	_
55	Log	Log	NNP	_	_	_
56	2	2	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	4.5	4.5	CD	_	_	_
59	'	'	''	_	_	_
60	RNA	rna	NN	_	_	_
61	Decay	decay	NN	_	_	_
62	of	of	IN	_	_	_
63	WT	WT	NNP	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	SH3208	sh3208	NN	_	_	_
66	-RRB-	-rrb-	-RRB-	_	_	_
67	in	in	IN	_	_	_
68	M9	m9	NN	_	_	_
69	0.2	0.2	CD	_	_	_
70	%	%	NN	_	_	_
71	Glycerol	glycerol	NN	_	_	_
72	,	,	,	_	_	_
73	.2	.2	NN	_	_	_
74	%	%	NN	_	_	_
75	Tryptone	tryptone	NN	_	_	_
76	at	at	IN	_	_	_
77	30	30	CD	_	_	_
78	C	c	NN	_	_	_
79	Mid	Mid	NNP	_	_	_
80	Log	Log	NNP	_	_	_
81	1	1	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	6	6	CD	_	_	_
84	'	'	''	_	_	_
85	RNA	rna	NN	_	_	_
86	Decay	decay	NN	_	_	_
87	N-RNaseE	n-rnasee	NN	_	_	_
88	-LRB-	-lrb-	-LRB-	_	_	_
89	BZ453	bz453	NN	_	_	_
90	-RRB-	-rrb-	-RRB-	_	_	_
91	in	in	IN	_	_	_
92	M9	m9	NN	_	_	_
93	+	+	CC	_	_	_
94	0.2	0.2	CD	_	_	_
95	%	%	NN	_	_	_
96	Glycerol	glycerol	NN	_	_	_
97	,	,	,	_	_	_
98	0.2	0.2	CD	_	_	_
99	%	%	NN	_	_	_
100	Tryptone	tryptone	NN	_	_	_
101	at	at	IN	_	_	_
102	30	30	CD	_	_	_
103	C	c	NN	_	_	_
104	Mid	Mid	NNP	_	_	_
105	Log	Log	NNP	_	_	_
106	Rep.	Rep.	NNP	_	_	_
107	A	A	NNP	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	6	6	CD	_	_	_
110	'	'	''	_	_	_
111	RNA	rna	NN	_	_	_
112	Decay	decay	NN	_	_	_
113	N-RNaseE	n-rnasee	NN	_	_	_
114	-LRB-	-lrb-	-LRB-	_	_	_
115	BZ453	bz453	NN	_	_	_
116	-RRB-	-rrb-	-RRB-	_	_	_
117	in	in	IN	_	_	_
118	M9	m9	NN	_	_	_
119	+	+	CC	_	_	_
120	0.2	0.2	CD	_	_	_
121	%	%	NN	_	_	_
122	Glycerol	glycerol	NN	_	_	_
123	,	,	,	_	_	_
124	0.2	0.2	CD	_	_	_
125	%	%	NN	_	_	_
126	Tryptone	tryptone	NN	_	_	_
127	at	at	IN	_	_	_
128	30	30	CD	_	_	_
129	C	c	NN	_	_	_
130	Mid	Mid	NNP	_	_	_
131	Log	Log	NNP	_	_	_
132	Rep.	Rep.	NNP	_	_	_
133	A1	a1	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	6	6	CD	_	_	_
136	'	'	''	_	_	_
137	RNA	rna	NN	_	_	_
138	Decay	decay	NN	_	_	_
139	N-RNaseE	n-rnasee	NN	_	_	_
140	-LRB-	-lrb-	-LRB-	_	_	_
141	BZ453	bz453	NN	_	_	_
142	-RRB-	-rrb-	-RRB-	_	_	_
143	in	in	IN	_	_	_
144	M9	m9	NN	_	_	_
145	+	+	CC	_	_	_
146	0.2	0.2	CD	_	_	_
147	%	%	NN	_	_	_
148	Glycerol	glycerol	NN	_	_	_
149	,	,	,	_	_	_
150	0.2	0.2	CD	_	_	_
151	%	%	NN	_	_	_
152	Tryptone	tryptone	NN	_	_	_
153	at	at	IN	_	_	_
154	30	30	CD	_	_	_
155	C	c	NN	_	_	_
156	Mid	Mid	NNP	_	_	_
157	Log	Log	NNP	_	_	_
158	Rep.	Rep.	NNP	_	_	_
159	B	B	NNP	_	_	_
160	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
161	6	6	CD	_	_	_
162	'	'	''	_	_	_
163	RNA	rna	NN	_	_	_
164	Decay	decay	NN	_	_	_
165	N-RNaseE	n-rnasee	NN	_	_	_
166	-LRB-	-lrb-	-LRB-	_	_	_
167	BZ453	bz453	NN	_	_	_
168	-RRB-	-rrb-	-RRB-	_	_	_
169	in	in	IN	_	_	_
170	M9	m9	NN	_	_	_
171	+	+	CC	_	_	_
172	0.2	0.2	CD	_	_	_
173	%	%	NN	_	_	_
174	Glycerol	glycerol	NN	_	_	_
175	,	,	,	_	_	_
176	0.2	0.2	CD	_	_	_
177	%	%	NN	_	_	_
178	Tryptone	tryptone	NN	_	_	_
179	at	at	IN	_	_	_
180	30	30	CD	_	_	_
181	C	c	NN	_	_	_
182	Mid	Mid	NNP	_	_	_
183	Log	Log	NNP	_	_	_
184	Rep.	Rep.	NNP	_	_	_
185	B1	b1	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	6	6	CD	_	_	_
188	'	'	''	_	_	_
189	RNA	rna	NN	_	_	_
190	Decay	decay	NN	_	_	_
191	of	of	IN	_	_	_
192	Eno	Eno	NNP	_	_	_
193	-	-	:	_	_	_
194	-LRB-	-lrb-	-LRB-	_	_	_
195	DF261	df261	NN	_	_	_
196	-RRB-	-rrb-	-RRB-	_	_	_
197	in	in	IN	_	_	_
198	M9	m9	NN	_	_	_
199	0.2	0.2	CD	_	_	_
200	%	%	NN	_	_	_
201	Glycerol	glycerol	NN	_	_	_
202	0.2	0.2	CD	_	_	_
203	%	%	NN	_	_	_
204	Tryptone	tryptone	NN	_	_	_
205	40	40	CD	_	_	_
206	mM	mm	NN	KWSUPP	_	_
207	Suc	suc	NN	_	_	_
208	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	Rep	Rep	NNP	_	_	_
7	A	A	NNP	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	6	6	CD	_	_	_
10	'	'	''	_	_	_
11	RNA	rna	NN	_	_	_
12	Decay	decay	NN	_	_	_
13	of	of	IN	_	_	_
14	Eno	Eno	NNP	_	_	_
15	-	-	:	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	DF261	df261	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	in	in	IN	_	_	_
20	M9	m9	NN	_	_	_
21	0.2	0.2	CD	_	_	_
22	%	%	NN	_	_	_
23	Glycerol	glycerol	NN	_	_	_
24	0.2	0.2	CD	_	_	_
25	%	%	NN	_	_	_
26	Tryptone	tryptone	NN	_	_	_
27	40	40	CD	_	_	_
28	mM	mm	NN	KWSUPP	_	_
29	Suc	suc	NN	_	_	_
30	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	Rep	Rep	NNP	_	_	_
7	B	B	NNP	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	6	6	CD	_	_	_
10	'	'	''	_	_	_
11	RNA	rna	NN	_	_	_
12	Decay	decay	NN	_	_	_
13	of	of	IN	_	_	_
14	Pnp	pnp	NN	_	_	_
15	-	-	:	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	YHC012	yhc012	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	in	in	IN	_	_	_
20	M9	m9	NN	_	_	_
21	+	+	CC	_	_	_
22	0.2	0.2	CD	_	_	_
23	%	%	NN	_	_	_
24	Glycerol	glycerol	NN	_	_	_
25	,	,	,	_	_	_
26	0.2	0.2	CD	_	_	_
27	%	%	NN	_	_	_
28	Tryptone	tryptone	NN	_	_	_
29	at	at	IN	_	_	_
30	30	30	CD	_	_	_
31	C	c	NN	_	_	_
32	Mid	Mid	NNP	_	_	_
33	Log	Log	NNP	_	_	_
34	Rep.	Rep.	NNP	_	_	_
35	A2	a2	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	6	6	CD	_	_	_
38	'	'	''	_	_	_
39	RNA	rna	NN	_	_	_
40	Decay	decay	NN	_	_	_
41	of	of	IN	_	_	_
42	Pnp	pnp	NN	_	_	_
43	-	-	:	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	YHC012	yhc012	NN	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	in	in	IN	_	_	_
48	M9	m9	NN	_	_	_
49	+	+	CC	_	_	_
50	0.2	0.2	CD	_	_	_
51	%	%	NN	_	_	_
52	Glycerol	glycerol	NN	_	_	_
53	,	,	,	_	_	_
54	0.2	0.2	CD	_	_	_
55	%	%	NN	_	_	_
56	Tryptone	tryptone	NN	_	_	_
57	at	at	IN	_	_	_
58	30	30	CD	_	_	_
59	C	c	NN	_	_	_
60	Mid	Mid	NNP	_	_	_
61	Log	Log	NNP	_	_	_
62	Rep.	Rep.	NNP	_	_	_
63	B2	b2	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	6	6	CD	_	_	_
66	'	'	''	_	_	_
67	RNA	rna	NN	_	_	_
68	Decay	decay	NN	_	_	_
69	of	of	IN	_	_	_
70	RhlB	rhlb	NN	_	_	_
71	-	-	:	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	SU02	su02	NN	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	in	in	IN	_	_	_
76	M9	m9	NN	_	_	_
77	+	+	CC	_	_	_
78	0.2	0.2	CD	_	_	_
79	%	%	NN	_	_	_
80	Glycerol	glycerol	NN	_	_	_
81	,	,	,	_	_	_
82	0.2	0.2	CD	_	_	_
83	%	%	NN	_	_	_
84	Tryptone	tryptone	NN	_	_	_
85	at	at	IN	_	_	_
86	30	30	CD	_	_	_
87	C	c	NN	_	_	_
88	Mid	Mid	NNP	_	_	_
89	Log	Log	NNP	_	_	_
90	Replicate	replicate	VB	_	_	_
91	A	a	DT	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	6	6	CD	_	_	_
94	'	'	''	_	_	_
95	RNA	rna	NN	_	_	_
96	Decay	decay	NN	_	_	_
97	of	of	IN	_	_	_
98	RhlB	rhlb	NN	_	_	_
99	-	-	:	_	_	_
100	-LRB-	-lrb-	-LRB-	_	_	_
101	SU02	su02	NN	_	_	_
102	-RRB-	-rrb-	-RRB-	_	_	_
103	in	in	IN	_	_	_
104	M9	m9	NN	_	_	_
105	+	+	CC	_	_	_
106	0.2	0.2	CD	_	_	_
107	%	%	NN	_	_	_
108	Glycerol	glycerol	NN	_	_	_
109	,	,	,	_	_	_
110	0.2	0.2	CD	_	_	_
111	%	%	NN	_	_	_
112	Tryptone	tryptone	NN	_	_	_
113	at	at	IN	_	_	_
114	30	30	CD	_	_	_
115	C	c	NN	_	_	_
116	Mid	Mid	NNP	_	_	_
117	Log	Log	NNP	_	_	_
118	Replicate	replicate	VB	_	_	_
119	A1	a1	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	6	6	CD	_	_	_
122	'	'	''	_	_	_
123	RNA	rna	NN	_	_	_
124	Decay	decay	NN	_	_	_
125	of	of	IN	_	_	_
126	RhlB	rhlb	NN	_	_	_
127	-	-	:	_	_	_
128	-LRB-	-lrb-	-LRB-	_	_	_
129	SU02	su02	NN	_	_	_
130	-RRB-	-rrb-	-RRB-	_	_	_
131	in	in	IN	_	_	_
132	M9	m9	NN	_	_	_
133	+	+	CC	_	_	_
134	0.2	0.2	CD	_	_	_
135	%	%	NN	_	_	_
136	Glycerol	glycerol	NN	_	_	_
137	,	,	,	_	_	_
138	0.2	0.2	CD	_	_	_
139	%	%	NN	_	_	_
140	Tryptone	tryptone	NN	_	_	_
141	at	at	IN	_	_	_
142	30	30	CD	_	_	_
143	C	c	NN	_	_	_
144	Mid	Mid	NNP	_	_	_
145	Log	Log	NNP	_	_	_
146	Replicate	replicate	VB	_	_	_
147	B	b	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	6	6	CD	_	_	_
150	'	'	''	_	_	_
151	RNA	rna	NN	_	_	_
152	Decay	decay	NN	_	_	_
153	of	of	IN	_	_	_
154	RhlB	rhlb	NN	_	_	_
155	-	-	:	_	_	_
156	-LRB-	-lrb-	-LRB-	_	_	_
157	SU02	su02	NN	_	_	_
158	-RRB-	-rrb-	-RRB-	_	_	_
159	in	in	IN	_	_	_
160	M9	m9	NN	_	_	_
161	+	+	CC	_	_	_
162	0.2	0.2	CD	_	_	_
163	%	%	NN	_	_	_
164	Glycerol	glycerol	NN	_	_	_
165	,	,	,	_	_	_
166	0.2	0.2	CD	_	_	_
167	%	%	NN	_	_	_
168	Tryptone	tryptone	NN	_	_	_
169	at	at	IN	_	_	_
170	30	30	CD	_	_	_
171	C	c	NN	_	_	_
172	Mid	Mid	NNP	_	_	_
173	Log	Log	NNP	_	_	_
174	Replicate	replicate	VB	_	_	_
175	B1	b1	NN	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	6	6	CD	_	_	_
178	'	'	''	_	_	_
179	RNA	rna	NN	_	_	_
180	Decay	decay	NN	_	_	_
181	of	of	IN	_	_	_
182	WT	WT	NNP	_	_	_
183	-LRB-	-lrb-	-LRB-	_	_	_
184	K10	k10	NN	_	_	_
185	-RRB-	-rrb-	-RRB-	_	_	_
186	in	in	IN	_	_	_
187	M9	m9	NN	_	_	_
188	0.2	0.2	CD	_	_	_
189	%	%	NN	_	_	_
190	Glycerol	glycerol	NN	_	_	_
191	0.2	0.2	CD	_	_	_
192	%	%	NN	_	_	_
193	Tryptone	tryptone	NN	_	_	_
194	40	40	CD	_	_	_
195	mM	mm	NN	KWSUPP	_	_
196	Suc	suc	NN	_	_	_
197	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	Rep	Rep	NNP	_	_	_
7	A	A	NNP	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	6	6	CD	_	_	_
10	'	'	''	_	_	_
11	RNA	rna	NN	_	_	_
12	Decay	decay	NN	_	_	_
13	of	of	IN	_	_	_
14	WT	WT	NNP	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	K10	k10	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	in	in	IN	_	_	_
19	M9	m9	NN	_	_	_
20	0.2	0.2	CD	_	_	_
21	%	%	NN	_	_	_
22	Glycerol	glycerol	NN	_	_	_
23	0.2	0.2	CD	_	_	_
24	%	%	NN	_	_	_
25	Tryptone	tryptone	NN	_	_	_
26	40	40	CD	_	_	_
27	mM	mm	NN	KWSUPP	_	_
28	Suc	suc	NN	_	_	_
29	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	Rep	Rep	NNP	_	_	_
7	B	B	NNP	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	6	6	CD	_	_	_
10	'	'	''	_	_	_
11	RNA	rna	NN	_	_	_
12	Decay	decay	NN	_	_	_
13	of	of	IN	_	_	_
14	WT	WT	NNP	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	N3433	n3433	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	in	in	IN	_	_	_
19	M9	m9	NN	_	_	_
20	+	+	CC	_	_	_
21	0.2	0.2	CD	_	_	_
22	%	%	NN	_	_	_
23	Glycerol	glycerol	NN	_	_	_
24	,	,	,	_	_	_
25	0.2	0.2	CD	_	_	_
26	%	%	NN	_	_	_
27	Tryptone	tryptone	NN	_	_	_
28	at	at	IN	_	_	_
29	30	30	CD	_	_	_
30	C	c	NN	_	_	_
31	Mid	Mid	NNP	_	_	_
32	Log	Log	NNP	_	_	_
33	Rep	Rep	NNP	_	_	_
34	A2	a2	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	6	6	CD	_	_	_
37	'	'	''	_	_	_
38	RNA	rna	NN	_	_	_
39	Decay	decay	NN	_	_	_
40	of	of	IN	_	_	_
41	WT	WT	NNP	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	N3433	n3433	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	in	in	IN	_	_	_
46	M9	m9	NN	_	_	_
47	+	+	CC	_	_	_
48	0.2	0.2	CD	_	_	_
49	%	%	NN	_	_	_
50	Glycerol	glycerol	NN	_	_	_
51	,	,	,	_	_	_
52	0.2	0.2	CD	_	_	_
53	%	%	NN	_	_	_
54	Tryptone	tryptone	NN	_	_	_
55	at	at	IN	_	_	_
56	30	30	CD	_	_	_
57	C	c	NN	_	_	_
58	Mid	Mid	NNP	_	_	_
59	Log	Log	NNP	_	_	_
60	Replicate	replicate	VB	_	_	_
61	A1	a1	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	6	6	CD	_	_	_
64	'	'	''	_	_	_
65	RNA	rna	NN	_	_	_
66	Decay	decay	NN	_	_	_
67	of	of	IN	_	_	_
68	WT	WT	NNP	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	N3433	n3433	NN	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	in	in	IN	_	_	_
73	M9	m9	NN	_	_	_
74	+	+	CC	_	_	_
75	0.2	0.2	CD	_	_	_
76	%	%	NN	_	_	_
77	Glycerol	glycerol	NN	_	_	_
78	,	,	,	_	_	_
79	0.2	0.2	CD	_	_	_
80	%	%	NN	_	_	_
81	Tryptone	tryptone	NN	_	_	_
82	at	at	IN	_	_	_
83	30	30	CD	_	_	_
84	C	c	NN	_	_	_
85	Mid	Mid	NNP	_	_	_
86	Log	Log	NNP	_	_	_
87	Replicate	replicate	VB	_	_	_
88	B1	b1	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	6	6	CD	_	_	_
91	'	'	''	_	_	_
92	RNA	rna	NN	_	_	_
93	Decay	decay	NN	_	_	_
94	of	of	IN	_	_	_
95	WT	WT	NNP	_	_	_
96	-LRB-	-lrb-	-LRB-	_	_	_
97	N3433	n3433	NN	_	_	_
98	-RRB-	-rrb-	-RRB-	_	_	_
99	in	in	IN	_	_	_
100	M9	m9	NN	_	_	_
101	+	+	CC	_	_	_
102	0.2	0.2	CD	_	_	_
103	%	%	NN	_	_	_
104	Glycerol	glycerol	NN	_	_	_
105	,	,	,	_	_	_
106	.2	.2	NN	_	_	_
107	%	%	NN	_	_	_
108	Tryptone	tryptone	NN	_	_	_
109	at	at	IN	_	_	_
110	30	30	CD	_	_	_
111	C	c	NN	_	_	_
112	Mid	Mid	NNP	_	_	_
113	Log	Log	NNP	_	_	_
114	Rep	Rep	NNP	_	_	_
115	B2	b2	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	6	6	CD	_	_	_
118	'	'	''	_	_	_
119	RNA	rna	NN	_	_	_
120	Decay	decay	NN	_	_	_
121	of	of	IN	_	_	_
122	WT	WT	NNP	_	_	_
123	-LRB-	-lrb-	-LRB-	_	_	_
124	SH3208	sh3208	NN	_	_	_
125	-RRB-	-rrb-	-RRB-	_	_	_
126	in	in	IN	_	_	_
127	M9	m9	NN	_	_	_
128	0.2	0.2	CD	_	_	_
129	%	%	NN	_	_	_
130	Glycerol	glycerol	NN	_	_	_
131	,	,	,	_	_	_
132	0.2	0.2	CD	_	_	_
133	%	%	NN	_	_	_
134	Tryptone	tryptone	NN	_	_	_
135	at	at	IN	_	_	_
136	30	30	CD	_	_	_
137	C	c	NN	_	_	_
138	Mid	Mid	NNP	_	_	_
139	Log	Log	NNP	_	_	_
140	Rep	Rep	NNP	_	_	_
141	A1	a1	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	6	6	CD	_	_	_
144	'	'	''	_	_	_
145	RNA	rna	NN	_	_	_
146	Decay	decay	NN	_	_	_
147	of	of	IN	_	_	_
148	WT	WT	NNP	_	_	_
149	-LRB-	-lrb-	-LRB-	_	_	_
150	SH3208	sh3208	NN	_	_	_
151	-RRB-	-rrb-	-RRB-	_	_	_
152	in	in	IN	_	_	_
153	M9	m9	NN	_	_	_
154	0.2	0.2	CD	_	_	_
155	%	%	NN	_	_	_
156	Glycerol	glycerol	NN	_	_	_
157	,	,	,	_	_	_
158	0.2	0.2	CD	_	_	_
159	%	%	NN	_	_	_
160	Tryptone	tryptone	NN	_	_	_
161	at	at	IN	_	_	_
162	30	30	CD	_	_	_
163	C	c	NN	_	_	_
164	Mid	Mid	NNP	_	_	_
165	Log	Log	NNP	_	_	_
166	Rep	Rep	NNP	_	_	_
167	B1	b1	NN	_	_	_
168	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
169	Eno	Eno	NNP	_	_	_
170	-	-	:	_	_	_
171	-LRB-	-lrb-	-LRB-	_	_	_
172	DF261	df261	NN	_	_	_
173	-RRB-	-rrb-	-RRB-	_	_	_
174	in	in	IN	_	_	_
175	M9	m9	NN	_	_	_
176	0.2	0.2	CD	_	_	_
177	%	%	NN	_	_	_
178	Glycerol	glycerol	NN	_	_	_
179	0.2	0.2	CD	_	_	_
180	%	%	NN	_	_	_
181	Tryptone	tryptone	NN	_	_	_
182	40	40	CD	_	_	_
183	mM	mm	NN	KWSUPP	_	_
184	Suc	suc	NN	_	_	_
185	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	Eno	Eno	NNP	_	_	_
8	-	-	:	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	DF261	df261	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	in	in	IN	_	_	_
13	M9	m9	NN	_	_	_
14	0.2	0.2	CD	_	_	_
15	%	%	NN	_	_	_
16	Glycerol	glycerol	NN	_	_	_
17	0.2	0.2	CD	_	_	_
18	%	%	NN	_	_	_
19	Tryptone	tryptone	NN	_	_	_
20	40	40	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	Suc	suc	NN	_	_	_
23	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	Eno	Eno	NNP	_	_	_
8	-	-	:	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	DF261	df261	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	in	in	IN	_	_	_
13	M9	m9	NN	_	_	_
14	0.2	0.2	CD	_	_	_
15	%	%	NN	_	_	_
16	Glycerol	glycerol	NN	_	_	_
17	0.2	0.2	CD	_	_	_
18	%	%	NN	_	_	_
19	Tryptone	tryptone	NN	_	_	_
20	40	40	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	Suc	suc	NN	_	_	_
23	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	Eno	Eno	NNP	_	_	_
8	-	-	:	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	DF261	df261	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	in	in	IN	_	_	_
13	M9	m9	NN	_	_	_
14	0.2	0.2	CD	_	_	_
15	%	%	NN	_	_	_
16	Glycerol	glycerol	NN	_	_	_
17	0.2	0.2	CD	_	_	_
18	%	%	NN	_	_	_
19	Tryptone	tryptone	NN	_	_	_
20	40mM	40mm	NN	_	_	_
21	Suc	suc	NN	_	_	_
22	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	1.5	1.5	CD	_	_	_
7	'	'	''	_	_	_
8	post	post	JJ	_	_	_
9	rif	rif	NN	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Eno	Eno	NNP	_	_	_
12	-	-	:	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	DF261	df261	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	in	in	IN	_	_	_
17	M9	m9	NN	_	_	_
18	0.2	0.2	CD	_	_	_
19	%	%	NN	_	_	_
20	Glycerol	glycerol	NN	_	_	_
21	0.2	0.2	CD	_	_	_
22	%	%	NN	_	_	_
23	Tryptone	tryptone	NN	_	_	_
24	40mM	40mm	NN	_	_	_
25	Suc	suc	NN	_	_	_
26	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	3.0	3.0	CD	_	_	_
7	'	'	''	_	_	_
8	post	post	JJ	_	_	_
9	rif	rif	NN	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Eno	Eno	NNP	_	_	_
12	-	-	:	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	DF261	df261	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	in	in	IN	_	_	_
17	M9	m9	NN	_	_	_
18	0.2	0.2	CD	_	_	_
19	%	%	NN	_	_	_
20	Glycerol	glycerol	NN	_	_	_
21	0.2	0.2	CD	_	_	_
22	%	%	NN	_	_	_
23	Tryptone	tryptone	NN	_	_	_
24	40mM	40mm	NN	_	_	_
25	Suc	suc	NN	_	_	_
26	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	4.5	4.5	CD	_	_	_
7	'	'	''	_	_	_
8	post	post	JJ	_	_	_
9	rif	rif	NN	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Eno	Eno	NNP	_	_	_
12	-	-	:	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	DF261	df261	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	in	in	IN	_	_	_
17	M9	m9	NN	_	_	_
18	0.2	0.2	CD	_	_	_
19	%	%	NN	_	_	_
20	Glycerol	glycerol	NN	_	_	_
21	0.2	0.2	CD	_	_	_
22	%	%	NN	_	_	_
23	Tryptone	tryptone	NN	_	_	_
24	40mM	40mm	NN	_	_	_
25	Suc	suc	NN	_	_	_
26	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	6.0	6.0	CD	_	_	_
7	'	'	''	_	_	_
8	post	post	JJ	_	_	_
9	rif	rif	NN	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Escherichia	escherichia	FW	Organism	_	_
12	coli	coli	FW	Organism	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	N-RNaseE	n-rnasee	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	BZ453	bz453	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	in	in	IN	_	_	_
19	M9	m9	NN	_	_	_
20	+	+	CC	_	_	_
21	0.2	0.2	CD	_	_	_
22	%	%	NN	_	_	_
23	Glycerol	glycerol	NN	_	_	_
24	,	,	,	_	_	_
25	0.2	0.2	CD	_	_	_
26	%	%	NN	_	_	_
27	Tryptone	tryptone	NN	_	_	_
28	at	at	IN	_	_	_
29	30	30	CD	_	_	_
30	C	c	NN	_	_	_
31	Mid	Mid	NNP	_	_	_
32	Log	Log	NNP	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	N-RNaseE	n-rnasee	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	BZ453	bz453	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	in	in	IN	_	_	_
39	M9	m9	NN	_	_	_
40	+	+	CC	_	_	_
41	0.2	0.2	CD	_	_	_
42	%	%	NN	_	_	_
43	Glycerol	glycerol	NN	_	_	_
44	,	,	,	_	_	_
45	0.2	0.2	CD	_	_	_
46	%	%	NN	_	_	_
47	Tryptone	tryptone	NN	_	_	_
48	at	at	IN	_	_	_
49	30	30	CD	_	_	_
50	C	c	NN	_	_	_
51	Mid	Mid	NNP	_	_	_
52	Log	Log	NNP	_	_	_
53	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
54	N-RNaseE	n-rnasee	NN	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	BZ453	bz453	NN	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	in	in	IN	_	_	_
59	M9	m9	NN	_	_	_
60	+	+	CC	_	_	_
61	0.2	0.2	CD	_	_	_
62	%	%	NN	_	_	_
63	Glycerol	glycerol	NN	_	_	_
64	,	,	,	_	_	_
65	0.2	0.2	CD	_	_	_
66	%	%	NN	_	_	_
67	Tryptone	tryptone	NN	_	_	_
68	at	at	IN	_	_	_
69	30	30	CD	_	_	_
70	C	c	NN	_	_	_
71	Mid	Mid	NNP	_	_	_
72	Log	Log	NNP	_	_	_
73	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
74	N-RNaseE	n-rnasee	NN	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	BZ453	bz453	NN	_	_	_
77	-RRB-	-rrb-	-RRB-	_	_	_
78	in	in	IN	_	_	_
79	M9	m9	NN	_	_	_
80	+	+	CC	_	_	_
81	0.2	0.2	CD	_	_	_
82	%	%	NN	_	_	_
83	Glycerol	glycerol	NN	_	_	_
84	,	,	,	_	_	_
85	0.2	0.2	CD	_	_	_
86	%	%	NN	_	_	_
87	Tryptone	tryptone	NN	_	_	_
88	at	at	IN	_	_	_
89	30	30	CD	_	_	_
90	C	c	NN	_	_	_
91	Mid	Mid	NNP	_	_	_
92	Log	Log	NNP	_	_	_
93	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
94	N-RNaseE	n-rnasee	NN	_	_	_
95	-LRB-	-lrb-	-LRB-	_	_	_
96	BZ453	bz453	NN	_	_	_
97	-RRB-	-rrb-	-RRB-	_	_	_
98	in	in	IN	_	_	_
99	M9	m9	NN	_	_	_
100	+	+	CC	_	_	_
101	0.2	0.2	CD	_	_	_
102	%	%	NN	_	_	_
103	Glycerol	glycerol	NN	_	_	_
104	,	,	,	_	_	_
105	0.2	0.2	CD	_	_	_
106	%	%	NN	_	_	_
107	Tryptone	tryptone	NN	_	_	_
108	at	at	IN	_	_	_
109	30	30	CD	_	_	_
110	C	c	NN	_	_	_
111	Mid	Mid	NNP	_	_	_
112	Log	Log	NNP	_	_	_
113	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
114	N-RNaseE	n-rnasee	NN	_	_	_
115	-LRB-	-lrb-	-LRB-	_	_	_
116	BZ453	bz453	NN	_	_	_
117	-RRB-	-rrb-	-RRB-	_	_	_
118	in	in	IN	_	_	_
119	M9	m9	NN	_	_	_
120	+	+	CC	_	_	_
121	0.2	0.2	CD	_	_	_
122	%	%	NN	_	_	_
123	Glycerol	glycerol	NN	_	_	_
124	,	,	,	_	_	_
125	0.2	0.2	CD	_	_	_
126	%	%	NN	_	_	_
127	Tryptone	tryptone	NN	_	_	_
128	at	at	IN	_	_	_
129	30	30	CD	_	_	_
130	C	c	NN	_	_	_
131	Mid	Mid	NNP	_	_	_
132	Log	Log	NNP	_	_	_
133	1.5	1.5	CD	_	_	_
134	'	'	''	_	_	_
135	post	post	JJ	_	_	_
136	rif	rif	NN	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	N-RNaseE	n-rnasee	NN	_	_	_
139	-LRB-	-lrb-	-LRB-	_	_	_
140	BZ453	bz453	NN	_	_	_
141	-RRB-	-rrb-	-RRB-	_	_	_
142	in	in	IN	_	_	_
143	M9	m9	NN	_	_	_
144	+	+	CC	_	_	_
145	0.2	0.2	CD	_	_	_
146	%	%	NN	_	_	_
147	Glycerol	glycerol	NN	_	_	_
148	,	,	,	_	_	_
149	0.2	0.2	CD	_	_	_
150	%	%	NN	_	_	_
151	Tryptone	tryptone	NN	_	_	_
152	at	at	IN	_	_	_
153	30	30	CD	_	_	_
154	C	c	NN	_	_	_
155	Mid	Mid	NNP	_	_	_
156	Log	Log	NNP	_	_	_
157	3	3	CD	_	_	_
158	'	'	''	_	_	_
159	post	post	JJ	_	_	_
160	rif	rif	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	N-RNaseE	n-rnasee	NN	_	_	_
163	-LRB-	-lrb-	-LRB-	_	_	_
164	BZ453	bz453	NN	_	_	_
165	-RRB-	-rrb-	-RRB-	_	_	_
166	in	in	IN	_	_	_
167	M9	m9	NN	_	_	_
168	+	+	CC	_	_	_
169	0.2	0.2	CD	_	_	_
170	%	%	NN	_	_	_
171	Glycerol	glycerol	NN	_	_	_
172	,	,	,	_	_	_
173	0.2	0.2	CD	_	_	_
174	%	%	NN	_	_	_
175	Tryptone	tryptone	NN	_	_	_
176	at	at	IN	_	_	_
177	30	30	CD	_	_	_
178	C	c	NN	_	_	_
179	Mid	Mid	NNP	_	_	_
180	Log	Log	NNP	_	_	_
181	4.5	4.5	CD	_	_	_
182	'	'	''	_	_	_
183	post	post	JJ	_	_	_
184	rif	rif	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	N-RNaseE	n-rnasee	NN	_	_	_
187	-LRB-	-lrb-	-LRB-	_	_	_
188	BZ453	bz453	NN	_	_	_
189	-RRB-	-rrb-	-RRB-	_	_	_
190	in	in	IN	_	_	_
191	M9	m9	NN	_	_	_
192	+	+	CC	_	_	_
193	0.2	0.2	CD	_	_	_
194	%	%	NN	_	_	_
195	Glycerol	glycerol	NN	_	_	_
196	,	,	,	_	_	_
197	0.2	0.2	CD	_	_	_
198	%	%	NN	_	_	_
199	Tryptone	tryptone	NN	_	_	_
200	at	at	IN	_	_	_
201	30	30	CD	_	_	_
202	C	c	NN	_	_	_
203	Mid	Mid	NNP	_	_	_
204	Log	Log	NNP	_	_	_
205	4.5	4.5	CD	_	_	_
206	'	'	''	_	_	_
207	post	post	JJ	_	_	_
208	rif	rif	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	N-RNaseE	n-rnasee	NN	_	_	_
211	-LRB-	-lrb-	-LRB-	_	_	_
212	BZ453	bz453	NN	_	_	_
213	-RRB-	-rrb-	-RRB-	_	_	_
214	in	in	IN	_	_	_
215	M9	m9	NN	_	_	_
216	+	+	CC	_	_	_
217	0.2	0.2	CD	_	_	_
218	%	%	NN	_	_	_
219	Glycerol	glycerol	NN	_	_	_
220	,	,	,	_	_	_
221	0.2	0.2	CD	_	_	_
222	%	%	NN	_	_	_
223	Tryptone	tryptone	NN	_	_	_
224	at	at	IN	_	_	_
225	30	30	CD	_	_	_
226	C	c	NN	_	_	_
227	Mid	Mid	NNP	_	_	_
228	Log	Log	NNP	_	_	_
229	6	6	CD	_	_	_
230	'	'	''	_	_	_
231	post	post	JJ	_	_	_
232	rif	rif	NN	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	Pnp	pnp	NN	_	_	_
235	-	-	:	_	_	_
236	-LRB-	-lrb-	-LRB-	_	_	_
237	YHC012	yhc012	NN	_	_	_
238	-RRB-	-rrb-	-RRB-	_	_	_
239	in	in	IN	_	_	_
240	M9	m9	NN	_	_	_
241	+	+	CC	_	_	_
242	0.2	0.2	CD	_	_	_
243	%	%	NN	_	_	_
244	Glycerol	glycerol	NN	_	_	_
245	,	,	,	_	_	_
246	0.2	0.2	CD	_	_	_
247	%	%	NN	_	_	_
248	Tryptone	tryptone	NN	_	_	_
249	at	at	IN	_	_	_
250	30	30	CD	_	_	_
251	C	c	NN	_	_	_
252	Mid	Mid	NNP	_	_	_
253	Log	Log	NNP	_	_	_
254	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
255	Pnp	Pnp	NNP	_	_	_
256	-	-	:	_	_	_
257	-LRB-	-lrb-	-LRB-	_	_	_
258	YHC012	yhc012	NN	_	_	_
259	-RRB-	-rrb-	-RRB-	_	_	_
260	in	in	IN	_	_	_
261	M9	m9	NN	_	_	_
262	+	+	CC	_	_	_
263	0.2	0.2	CD	_	_	_
264	%	%	NN	_	_	_
265	Glycerol	glycerol	NN	_	_	_
266	,	,	,	_	_	_
267	0.2	0.2	CD	_	_	_
268	%	%	NN	_	_	_
269	Tryptone	tryptone	NN	_	_	_
270	at	at	IN	_	_	_
271	30	30	CD	_	_	_
272	C	c	NN	_	_	_
273	Mid	Mid	NNP	_	_	_
274	Log	Log	NNP	_	_	_
275	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
276	Pnp	Pnp	NNP	_	_	_
277	-	-	:	_	_	_
278	-LRB-	-lrb-	-LRB-	_	_	_
279	YHC012	yhc012	NN	_	_	_
280	-RRB-	-rrb-	-RRB-	_	_	_
281	in	in	IN	_	_	_
282	M9	m9	NN	_	_	_
283	+	+	CC	_	_	_
284	0.2	0.2	CD	_	_	_
285	%	%	NN	_	_	_
286	Glycerol	glycerol	NN	_	_	_
287	,	,	,	_	_	_
288	0.2	0.2	CD	_	_	_
289	%	%	NN	_	_	_
290	Tryptone	tryptone	NN	_	_	_
291	at	at	IN	_	_	_
292	30	30	CD	_	_	_
293	C	c	NN	_	_	_
294	Mid	Mid	NNP	_	_	_
295	Log	Log	NNP	_	_	_
296	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
297	Pnp	Pnp	NNP	_	_	_
298	-	-	:	_	_	_
299	-LRB-	-lrb-	-LRB-	_	_	_
300	YHC012	yhc012	NN	_	_	_
301	-RRB-	-rrb-	-RRB-	_	_	_
302	in	in	IN	_	_	_
303	M9	m9	NN	_	_	_
304	+	+	CC	_	_	_
305	0.2	0.2	CD	_	_	_
306	%	%	NN	_	_	_
307	Glycerol	glycerol	NN	_	_	_
308	,	,	,	_	_	_
309	0.2	0.2	CD	_	_	_
310	%	%	NN	_	_	_
311	Tryptone	tryptone	NN	_	_	_
312	at	at	IN	_	_	_
313	30	30	CD	_	_	_
314	C	c	NN	_	_	_
315	Mid	Mid	NNP	_	_	_
316	Log	Log	NNP	_	_	_
317	1.5	1.5	CD	_	_	_
318	'	'	''	_	_	_
319	post	post	JJ	_	_	_
320	rif	rif	NN	_	_	_
321	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
322	Pnp	pnp	NN	_	_	_
323	-	-	:	_	_	_
324	-LRB-	-lrb-	-LRB-	_	_	_
325	YHC012	yhc012	NN	_	_	_
326	-RRB-	-rrb-	-RRB-	_	_	_
327	in	in	IN	_	_	_
328	M9	m9	NN	_	_	_
329	+	+	CC	_	_	_
330	0.2	0.2	CD	_	_	_
331	%	%	NN	_	_	_
332	Glycerol	glycerol	NN	_	_	_
333	,	,	,	_	_	_
334	0.2	0.2	CD	_	_	_
335	%	%	NN	_	_	_
336	Tryptone	tryptone	NN	_	_	_
337	at	at	IN	_	_	_
338	30	30	CD	_	_	_
339	C	c	NN	_	_	_
340	Mid	Mid	NNP	_	_	_
341	Log	Log	NNP	_	_	_
342	3	3	CD	_	_	_
343	'	'	''	_	_	_
344	post	post	JJ	_	_	_
345	rif	rif	NN	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	Pnp	pnp	NN	_	_	_
348	-	-	:	_	_	_
349	-LRB-	-lrb-	-LRB-	_	_	_
350	YHC012	yhc012	NN	_	_	_
351	-RRB-	-rrb-	-RRB-	_	_	_
352	in	in	IN	_	_	_
353	M9	m9	NN	_	_	_
354	+	+	CC	_	_	_
355	0.2	0.2	CD	_	_	_
356	%	%	NN	_	_	_
357	Glycerol	glycerol	NN	_	_	_
358	,	,	,	_	_	_
359	0.2	0.2	CD	_	_	_
360	%	%	NN	_	_	_
361	Tryptone	tryptone	NN	_	_	_
362	at	at	IN	_	_	_
363	30	30	CD	_	_	_
364	C	c	NN	_	_	_
365	Mid	Mid	NNP	_	_	_
366	Log	Log	NNP	_	_	_
367	4.5	4.5	CD	_	_	_
368	'	'	''	_	_	_
369	post	post	JJ	_	_	_
370	rif	rif	NN	_	_	_
371	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
372	Pnp	pnp	NN	_	_	_
373	-	-	:	_	_	_
374	-LRB-	-lrb-	-LRB-	_	_	_
375	YHC012	yhc012	NN	_	_	_
376	-RRB-	-rrb-	-RRB-	_	_	_
377	in	in	IN	_	_	_
378	M9	m9	NN	_	_	_
379	+	+	CC	_	_	_
380	0.2	0.2	CD	_	_	_
381	%	%	NN	_	_	_
382	Glycerol	glycerol	NN	_	_	_
383	,	,	,	_	_	_
384	0.2	0.2	CD	_	_	_
385	%	%	NN	_	_	_
386	Tryptone	tryptone	NN	_	_	_
387	at	at	IN	_	_	_
388	30	30	CD	_	_	_
389	C	c	NN	_	_	_
390	Mid	Mid	NNP	_	_	_
391	Log	Log	NNP	_	_	_
392	6	6	CD	_	_	_
393	'	'	''	_	_	_
394	post	post	JJ	_	_	_
395	rif	rif	NN	_	_	_
396	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
397	RhlB	rhlb	NN	_	_	_
398	-	-	:	_	_	_
399	-LRB-	-lrb-	-LRB-	_	_	_
400	SU02	su02	NN	_	_	_
401	-RRB-	-rrb-	-RRB-	_	_	_
402	in	in	IN	_	_	_
403	M9	m9	NN	_	_	_
404	+	+	CC	_	_	_
405	0.2	0.2	CD	_	_	_
406	%	%	NN	_	_	_
407	Glycerol	glycerol	NN	_	_	_
408	,	,	,	_	_	_
409	0.2	0.2	CD	_	_	_
410	%	%	NN	_	_	_
411	Tryptone	tryptone	NN	_	_	_
412	at	at	IN	_	_	_
413	30	30	CD	_	_	_
414	C	c	NN	_	_	_
415	Mid	Mid	NNP	_	_	_
416	Log	Log	NNP	_	_	_
417	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
418	RhlB	rhlb	NN	_	_	_
419	-	-	:	_	_	_
420	-LRB-	-lrb-	-LRB-	_	_	_
421	SU02	su02	NN	_	_	_
422	-RRB-	-rrb-	-RRB-	_	_	_
423	in	in	IN	_	_	_
424	M9	m9	NN	_	_	_
425	+	+	CC	_	_	_
426	0.2	0.2	CD	_	_	_
427	%	%	NN	_	_	_
428	Glycerol	glycerol	NN	_	_	_
429	,	,	,	_	_	_
430	0.2	0.2	CD	_	_	_
431	%	%	NN	_	_	_
432	Tryptone	tryptone	NN	_	_	_
433	at	at	IN	_	_	_
434	30	30	CD	_	_	_
435	C	c	NN	_	_	_
436	Mid	Mid	NNP	_	_	_
437	Log	Log	NNP	_	_	_
438	1.5	1.5	CD	_	_	_
439	'	'	''	_	_	_
440	post	post	JJ	_	_	_
441	rif	rif	NN	_	_	_
442	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
443	RhlB	rhlb	NN	_	_	_
444	-	-	:	_	_	_
445	-LRB-	-lrb-	-LRB-	_	_	_
446	SU02	su02	NN	_	_	_
447	-RRB-	-rrb-	-RRB-	_	_	_
448	in	in	IN	_	_	_
449	M9	m9	NN	_	_	_
450	+	+	CC	_	_	_
451	0.2	0.2	CD	_	_	_
452	%	%	NN	_	_	_
453	Glycerol	glycerol	NN	_	_	_
454	,	,	,	_	_	_
455	0.2	0.2	CD	_	_	_
456	%	%	NN	_	_	_
457	Tryptone	tryptone	NN	_	_	_
458	at	at	IN	_	_	_
459	30	30	CD	_	_	_
460	C	c	NN	_	_	_
461	Mid	Mid	NNP	_	_	_
462	Log	Log	NNP	_	_	_
463	3	3	CD	_	_	_
464	'	'	''	_	_	_
465	post	post	JJ	_	_	_
466	rif	rif	NN	_	_	_
467	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
468	RhlB	rhlb	NN	_	_	_
469	-	-	:	_	_	_
470	-LRB-	-lrb-	-LRB-	_	_	_
471	SU02	su02	NN	_	_	_
472	-RRB-	-rrb-	-RRB-	_	_	_
473	in	in	IN	_	_	_
474	M9	m9	NN	_	_	_
475	+	+	CC	_	_	_
476	0.2	0.2	CD	_	_	_
477	%	%	NN	_	_	_
478	Glycerol	glycerol	NN	_	_	_
479	,	,	,	_	_	_
480	0.2	0.2	CD	_	_	_
481	%	%	NN	_	_	_
482	Tryptone	tryptone	NN	_	_	_
483	at	at	IN	_	_	_
484	30	30	CD	_	_	_
485	C	c	NN	_	_	_
486	Mid	Mid	NNP	_	_	_
487	Log	Log	NNP	_	_	_
488	3	3	CD	_	_	_
489	'	'	''	_	_	_
490	post	post	JJ	_	_	_
491	rif	rif	NN	_	_	_
492	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
493	RhlB	rhlb	NN	_	_	_
494	-	-	:	_	_	_
495	-LRB-	-lrb-	-LRB-	_	_	_
496	SU02	su02	NN	_	_	_
497	-RRB-	-rrb-	-RRB-	_	_	_
498	in	in	IN	_	_	_
499	M9	m9	NN	_	_	_
500	+	+	CC	_	_	_
501	0.2	0.2	CD	_	_	_
502	%	%	NN	_	_	_
503	Glycerol	glycerol	NN	_	_	_
504	,	,	,	_	_	_
505	0.2	0.2	CD	_	_	_
506	%	%	NN	_	_	_
507	Tryptone	tryptone	NN	_	_	_
508	at	at	IN	_	_	_
509	30	30	CD	_	_	_
510	C	c	NN	_	_	_
511	Mid	Mid	NNP	_	_	_
512	Log	Log	NNP	_	_	_
513	4.5	4.5	CD	_	_	_
514	'	'	''	_	_	_
515	post	post	JJ	_	_	_
516	rif	rif	NN	_	_	_
517	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
518	RhlB	rhlb	NN	_	_	_
519	-	-	:	_	_	_
520	-LRB-	-lrb-	-LRB-	_	_	_
521	SU02	su02	NN	_	_	_
522	-RRB-	-rrb-	-RRB-	_	_	_
523	in	in	IN	_	_	_
524	M9	m9	NN	_	_	_
525	+	+	CC	_	_	_
526	0.2	0.2	CD	_	_	_
527	%	%	NN	_	_	_
528	Glycerol	glycerol	NN	_	_	_
529	,	,	,	_	_	_
530	0.2	0.2	CD	_	_	_
531	%	%	NN	_	_	_
532	Tryptone	tryptone	NN	_	_	_
533	at	at	IN	_	_	_
534	30	30	CD	_	_	_
535	C	c	NN	_	_	_
536	Mid	Mid	NNP	_	_	_
537	Log	Log	NNP	_	_	_
538	6	6	CD	_	_	_
539	'	'	''	_	_	_
540	post	post	JJ	_	_	_
541	rif	rif	NN	_	_	_
542	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
543	RhlB	rhlb	NN	_	_	_
544	-	-	:	_	_	_
545	-LRB-	-lrb-	-LRB-	_	_	_
546	SU02	su02	NN	_	_	_
547	-RRB-	-rrb-	-RRB-	_	_	_
548	in	in	IN	_	_	_
549	M9	m9	NN	_	_	_
550	+	+	CC	_	_	_
551	0.2	0.2	CD	_	_	_
552	%	%	NN	_	_	_
553	Glycerol	glycerol	NN	_	_	_
554	,	,	,	_	_	_
555	0.2	0.2	CD	_	_	_
556	%	%	NN	_	_	_
557	Tryptone	tryptone	NN	_	_	_
558	at	at	IN	_	_	_
559	30	30	CD	_	_	_
560	Mid	Mid	NNP	_	_	_
561	Log	Log	NNP	_	_	_
562	6	6	CD	_	_	_
563	'	'	''	_	_	_
564	post	post	JJ	_	_	_
565	rif	rif	NN	_	_	_
566	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
567	VALUE	value	NN	_	_	_
568	is	be	VBZ	_	_	_
569	Log	log	NN	_	_	_
570	-LRB-	-lrb-	-LRB-	_	_	_
571	base	base	NN	_	_	_
572	2	2	CD	_	_	_
573	-RRB-	-rrb-	-RRB-	_	_	_
574	of	of	IN	_	_	_
575	the	the	DT	_	_	_
576	ratio	ratio	NN	_	_	_
577	of	of	IN	_	_	_
578	the	the	DT	_	_	_
579	median	median	NN	_	_	_
580	of	of	IN	_	_	_
581	Channel	Channel	NNP	_	_	_
582	2	2	CD	_	_	_
583	-LRB-	-lrb-	-LRB-	_	_	_
584	usually	usually	RB	_	_	_
585	635	635	CD	_	_	_
586	nm	nm	NN	_	_	_
587	-RRB-	-rrb-	-RRB-	_	_	_
588	to	to	TO	_	_	_
589	Channel	Channel	NNP	_	_	_
590	1	1	CD	_	_	_
591	-LRB-	-lrb-	-LRB-	_	_	_
592	usually	usually	RB	_	_	_
593	532	532	CD	_	_	_
594	nm	nm	NN	_	_	_
595	-RRB-	-rrb-	-RRB-	_	_	_
596	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
597	WT	wt	NN	_	_	_
598	-LRB-	-lrb-	-LRB-	_	_	_
599	K10	k10	NN	_	_	_
600	-RRB-	-rrb-	-RRB-	_	_	_
601	in	in	IN	_	_	_
602	M9	m9	NN	_	_	_
603	0.2	0.2	CD	_	_	_
604	%	%	NN	_	_	_
605	Glycerol	glycerol	NN	_	_	_
606	0.2	0.2	CD	_	_	_
607	%	%	NN	_	_	_
608	Tryptone	tryptone	NN	_	_	_
609	40	40	CD	_	_	_
610	mM	mm	NN	KWSUPP	_	_
611	Suc	suc	NN	_	_	_
612	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	0C	0c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	6.0	6.0	CD	_	_	_
7	'	'	''	_	_	_
8	post	post	JJ	_	_	_
9	rif	rif	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	WT	wt	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	K10	k10	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	in	in	IN	_	_	_
16	M9	m9	NN	_	_	_
17	0.2	0.2	CD	_	_	_
18	%	%	NN	_	_	_
19	Glycerol	glycerol	NN	_	_	_
20	0.2	0.2	CD	_	_	_
21	%	%	NN	_	_	_
22	Tryptone	tryptone	NN	_	_	_
23	40	40	CD	_	_	_
24	mM	mm	NN	KWSUPP	_	_
25	Suc	suc	NN	_	_	_
26	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	1.5	1.5	CD	_	_	_
7	'	'	''	_	_	_
8	post	post	JJ	_	_	_
9	rif	rif	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	WT	wt	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	K10	k10	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	in	in	IN	_	_	_
16	M9	m9	NN	_	_	_
17	0.2	0.2	CD	_	_	_
18	%	%	NN	_	_	_
19	Glycerol	glycerol	NN	_	_	_
20	0.2	0.2	CD	_	_	_
21	%	%	NN	_	_	_
22	Tryptone	tryptone	NN	_	_	_
23	40	40	CD	_	_	_
24	mM	mm	NN	KWSUPP	_	_
25	Suc	suc	NN	_	_	_
26	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	3	3	CD	_	_	_
7	'	'	''	_	_	_
8	post	post	JJ	_	_	_
9	rif	rif	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	WT	wt	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	K10	k10	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	in	in	IN	_	_	_
16	M9	m9	NN	_	_	_
17	0.2	0.2	CD	_	_	_
18	%	%	NN	_	_	_
19	Glycerol	glycerol	NN	_	_	_
20	0.2	0.2	CD	_	_	_
21	%	%	NN	_	_	_
22	Tryptone	tryptone	NN	_	_	_
23	40	40	CD	_	_	_
24	mM	mm	NN	KWSUPP	_	_
25	Suc	suc	NN	_	_	_
26	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	4.5	4.5	CD	_	_	_
7	'	'	''	_	_	_
8	post	post	JJ	_	_	_
9	rif	rif	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	WT	wt	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	K10	k10	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	in	in	IN	_	_	_
16	M9	m9	NN	_	_	_
17	0.2	0.2	CD	_	_	_
18	%	%	NN	_	_	_
19	Glycerol	glycerol	NN	_	_	_
20	0.2	0.2	CD	_	_	_
21	%	%	NN	_	_	_
22	Tryptone	tryptone	NN	_	_	_
23	40	40	CD	_	_	_
24	mM	mm	NN	KWSUPP	_	_
25	Suc	suc	NN	_	_	_
26	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	6.0	6.0	CD	_	_	_
7	'	'	''	_	_	_
8	post	post	JJ	_	_	_
9	rif	rif	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	WT	wt	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	K10	k10	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	M9	m9	NN	_	_	_
16	0.2	0.2	CD	_	_	_
17	%	%	NN	_	_	_
18	Glycerol	glycerol	NN	_	_	_
19	0.2	0.2	CD	_	_	_
20	%	%	NN	_	_	_
21	Tryptone	tryptone	NN	_	_	_
22	40	40	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	Suc	suc	NN	_	_	_
25	.	.	.	_	_	_

1	at	at	IN	_	_	_
2	30	30	CD	_	_	_
3	C	c	NN	_	_	_
4	Mid	Mid	NNP	_	_	_
5	Log	Log	NNP	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	WT	WT	NNP	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	K10	k10	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	M9	m9	NN	_	_	_
12	0.2	0.2	CD	_	_	_
13	%	%	NN	_	_	_
14	Glycerol	glycerol	NN	_	_	_
15	0.2	0.2	CD	_	_	_
16	%	%	NN	_	_	_
17	Tryptone	tryptone	NN	_	_	_
18	40	40	CD	_	_	_
19	mM	mm	NN	KWSUPP	_	_
20	Succinate	succinate	NN	_	_	_
21	at	at	IN	_	_	_
22	30	30	CD	_	_	_
23	C	c	NN	_	_	_
24	Mid	Mid	NNP	_	_	_
25	Log	Log	NNP	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	WT	WT	NNP	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	N3433	n3433	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	in	in	IN	_	_	_
32	M9	m9	NN	_	_	_
33	+	+	CC	_	_	_
34	0.2	0.2	CD	_	_	_
35	%	%	NN	_	_	_
36	Glycerol	glycerol	NN	_	_	_
37	,	,	,	_	_	_
38	0.2	0.2	CD	_	_	_
39	%	%	NN	_	_	_
40	Tryptone	tryptone	NN	_	_	_
41	at	at	IN	_	_	_
42	30	30	CD	_	_	_
43	C	c	NN	_	_	_
44	Mid	Mid	NNP	_	_	_
45	Log	Log	NNP	_	_	_
46	1.5	1.5	CD	_	_	_
47	'	'	''	_	_	_
48	post	post	JJ	_	_	_
49	rif	rif	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	WT	wt	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	N3433	n3433	NN	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	in	in	IN	_	_	_
56	M9	m9	NN	_	_	_
57	+	+	CC	_	_	_
58	0.2	0.2	CD	_	_	_
59	%	%	NN	_	_	_
60	Glycerol	glycerol	NN	_	_	_
61	,	,	,	_	_	_
62	0.2	0.2	CD	_	_	_
63	%	%	NN	_	_	_
64	Tryptone	tryptone	NN	_	_	_
65	at	at	IN	_	_	_
66	30	30	CD	_	_	_
67	C	c	NN	_	_	_
68	Mid	Mid	NNP	_	_	_
69	Log	Log	NNP	_	_	_
70	3.0	3.0	CD	_	_	_
71	'	'	''	_	_	_
72	post	post	JJ	_	_	_
73	rif	rif	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	WT	wt	NN	_	_	_
76	-LRB-	-lrb-	-LRB-	_	_	_
77	N3433	n3433	NN	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	in	in	IN	_	_	_
80	M9	m9	NN	_	_	_
81	+	+	CC	_	_	_
82	0.2	0.2	CD	_	_	_
83	%	%	NN	_	_	_
84	Glycerol	glycerol	NN	_	_	_
85	,	,	,	_	_	_
86	0.2	0.2	CD	_	_	_
87	%	%	NN	_	_	_
88	Tryptone	tryptone	NN	_	_	_
89	at	at	IN	_	_	_
90	30	30	CD	_	_	_
91	C	c	NN	_	_	_
92	Mid	Mid	NNP	_	_	_
93	Log	Log	NNP	_	_	_
94	3	3	CD	_	_	_
95	'	'	''	_	_	_
96	post	post	JJ	_	_	_
97	rif	rif	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	WT	wt	NN	_	_	_
100	-LRB-	-lrb-	-LRB-	_	_	_
101	N3433	n3433	NN	_	_	_
102	-RRB-	-rrb-	-RRB-	_	_	_
103	in	in	IN	_	_	_
104	M9	m9	NN	_	_	_
105	+	+	CC	_	_	_
106	0.2	0.2	CD	_	_	_
107	%	%	NN	_	_	_
108	Glycerol	glycerol	NN	_	_	_
109	,	,	,	_	_	_
110	0.2	0.2	CD	_	_	_
111	%	%	NN	_	_	_
112	Tryptone	tryptone	NN	_	_	_
113	at	at	IN	_	_	_
114	30	30	CD	_	_	_
115	C	c	NN	_	_	_
116	Mid	Mid	NNP	_	_	_
117	Log	Log	NNP	_	_	_
118	4.5	4.5	CD	_	_	_
119	'	'	''	_	_	_
120	post	post	JJ	_	_	_
121	rif	rif	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	WT	wt	NN	_	_	_
124	-LRB-	-lrb-	-LRB-	_	_	_
125	N3433	n3433	NN	_	_	_
126	-RRB-	-rrb-	-RRB-	_	_	_
127	in	in	IN	_	_	_
128	M9	m9	NN	_	_	_
129	+	+	CC	_	_	_
130	0.2	0.2	CD	_	_	_
131	%	%	NN	_	_	_
132	Glycerol	glycerol	NN	_	_	_
133	,	,	,	_	_	_
134	0.2	0.2	CD	_	_	_
135	%	%	NN	_	_	_
136	Tryptone	tryptone	NN	_	_	_
137	at	at	IN	_	_	_
138	30	30	CD	_	_	_
139	C	c	NN	_	_	_
140	Mid	Mid	NNP	_	_	_
141	Log	Log	NNP	_	_	_
142	6	6	CD	_	_	_
143	'	'	''	_	_	_
144	post	post	JJ	_	_	_
145	rif	rif	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	WT	wt	NN	_	_	_
148	-LRB-	-lrb-	-LRB-	_	_	_
149	N3433	n3433	NN	_	_	_
150	-RRB-	-rrb-	-RRB-	_	_	_
151	M9	m9	NN	_	_	_
152	+	+	CC	_	_	_
153	0.2	0.2	CD	_	_	_
154	%	%	NN	_	_	_
155	Glycerol	glycerol	NN	_	_	_
156	,	,	,	_	_	_
157	0.2	0.2	CD	_	_	_
158	%	%	NN	_	_	_
159	Tryptone	tryptone	NN	_	_	_
160	at	at	IN	_	_	_
161	30	30	CD	_	_	_
162	C	c	NN	_	_	_
163	Mid	Mid	NNP	_	_	_
164	Log	Log	NNP	_	_	_
165	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
166	WT	WT	NNP	_	_	_
167	-LRB-	-lrb-	-LRB-	_	_	_
168	N3433	n3433	NN	_	_	_
169	-RRB-	-rrb-	-RRB-	_	_	_
170	M9	m9	NN	_	_	_
171	+	+	CC	_	_	_
172	0.2	0.2	CD	_	_	_
173	%	%	NN	_	_	_
174	Glycerol	glycerol	NN	_	_	_
175	,	,	,	_	_	_
176	0.2	0.2	CD	_	_	_
177	%	%	NN	_	_	_
178	Tryptone	tryptone	NN	_	_	_
179	at	at	IN	_	_	_
180	30	30	CD	_	_	_
181	C	c	NN	_	_	_
182	Mid	Mid	NNP	_	_	_
183	Log	Log	NNP	_	_	_
184	6	6	CD	_	_	_
185	'	'	''	_	_	_
186	post	post	JJ	_	_	_
187	rif	rif	NN	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	WT	wt	NN	_	_	_
190	-LRB-	-lrb-	-LRB-	_	_	_
191	SH3208	sh3208	NN	_	_	_
192	-RRB-	-rrb-	-RRB-	_	_	_
193	in	in	IN	_	_	_
194	M9	m9	NN	_	_	_
195	+	+	CC	_	_	_
196	0.2	0.2	CD	_	_	_
197	%	%	NN	_	_	_
198	Glycerol	glycerol	NN	_	_	_
199	,	,	,	_	_	_
200	0.2	0.2	CD	_	_	_
201	%	%	NN	_	_	_
202	Tryptone	tryptone	NN	_	_	_
203	at	at	IN	_	_	_
204	30	30	CD	_	_	_
205	C	c	NN	_	_	_
206	Mid	Mid	NNP	_	_	_
207	Log	Log	NNP	_	_	_
208	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
209	WT	WT	NNP	_	_	_
210	-LRB-	-lrb-	-LRB-	_	_	_
211	SH3208	sh3208	NN	_	_	_
212	-RRB-	-rrb-	-RRB-	_	_	_
213	in	in	IN	_	_	_
214	M9	m9	NN	_	_	_
215	+	+	CC	_	_	_
216	0.2	0.2	CD	_	_	_
217	%	%	NN	_	_	_
218	Glycerol	glycerol	NN	_	_	_
219	,	,	,	_	_	_
220	0.2	0.2	CD	_	_	_
221	%	%	NN	_	_	_
222	Tryptone	tryptone	NN	_	_	_
223	at	at	IN	_	_	_
224	30	30	CD	_	_	_
225	C	c	NN	_	_	_
226	Mid	Mid	NNP	_	_	_
227	Log	Log	NNP	_	_	_
228	1.5	1.5	CD	_	_	_
229	'	'	''	_	_	_
230	post	post	JJ	_	_	_
231	rif	rif	NN	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	WT	wt	NN	_	_	_
234	-LRB-	-lrb-	-LRB-	_	_	_
235	SH3208	sh3208	NN	_	_	_
236	-RRB-	-rrb-	-RRB-	_	_	_
237	in	in	IN	_	_	_
238	M9	m9	NN	_	_	_
239	+	+	CC	_	_	_
240	0.2	0.2	CD	_	_	_
241	%	%	NN	_	_	_
242	Glycerol	glycerol	NN	_	_	_
243	,	,	,	_	_	_
244	0.2	0.2	CD	_	_	_
245	%	%	NN	_	_	_
246	Tryptone	tryptone	NN	_	_	_
247	at	at	IN	_	_	_
248	30	30	CD	_	_	_
249	C	c	NN	_	_	_
250	Mid	Mid	NNP	_	_	_
251	Log	Log	NNP	_	_	_
252	3	3	CD	_	_	_
253	'	'	''	_	_	_
254	post	post	JJ	_	_	_
255	rif	rif	NN	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
257	WT	wt	NN	_	_	_
258	-LRB-	-lrb-	-LRB-	_	_	_
259	SH3208	sh3208	NN	_	_	_
260	-RRB-	-rrb-	-RRB-	_	_	_
261	in	in	IN	_	_	_
262	M9	m9	NN	_	_	_
263	+	+	CC	_	_	_
264	0.2	0.2	CD	_	_	_
265	%	%	NN	_	_	_
266	Glycerol	glycerol	NN	_	_	_
267	,	,	,	_	_	_
268	0.2	0.2	CD	_	_	_
269	%	%	NN	_	_	_
270	Tryptone	tryptone	NN	_	_	_
271	at	at	IN	_	_	_
272	30	30	CD	_	_	_
273	C	c	NN	_	_	_
274	Mid	Mid	NNP	_	_	_
275	Log	Log	NNP	_	_	_
276	4.5	4.5	CD	_	_	_
277	'	'	''	_	_	_
278	post	post	JJ	_	_	_
279	rif	rif	NN	_	_	_
280	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
281	WT	wt	NN	_	_	_
282	-LRB-	-lrb-	-LRB-	_	_	_
283	SH3208	sh3208	NN	_	_	_
284	-RRB-	-rrb-	-RRB-	_	_	_
285	in	in	IN	_	_	_
286	M9	m9	NN	_	_	_
287	+	+	CC	_	_	_
288	0.2	0.2	CD	_	_	_
289	%	%	NN	_	_	_
290	Glycerol	glycerol	NN	_	_	_
291	,	,	,	_	_	_
292	0.2	0.2	CD	_	_	_
293	%	%	NN	_	_	_
294	Tryptone	tryptone	NN	_	_	_
295	at	at	IN	_	_	_
296	30	30	CD	_	_	_
297	C	c	NN	_	_	_
298	Mid	Mid	NNP	_	_	_
299	Log	Log	NNP	_	_	_
300	6	6	CD	_	_	_
301	'	'	''	_	_	_
302	post	post	JJ	_	_	_
303	rif	rif	NN	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	WT	wt	NN	_	_	_
306	-LRB-	-lrb-	-LRB-	_	_	_
307	SH3208	sh3208	NN	_	_	_
308	-RRB-	-rrb-	-RRB-	_	_	_
309	M9	m9	NN	_	_	_
310	+	+	CC	_	_	_
311	0.2	0.2	CD	_	_	_
312	%	%	NN	_	_	_
313	Glycerol	glycerol	NN	_	_	_
314	,	,	,	_	_	_
315	0.2	0.2	CD	_	_	_
316	%	%	NN	_	_	_
317	Tryptone	tryptone	NN	_	_	_
318	at	at	IN	_	_	_
319	30	30	CD	_	_	_
320	C	c	NN	_	_	_
321	Mid	Mid	NNP	_	_	_
322	Log	Log	NNP	_	_	_
323	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
324	1mL	1ml	NN	_	_	_
325	aliquots	aliquot	NNS	_	_	_
326	were	be	VBD	_	_	_
327	harvested	harvest	VBN	_	_	_
328	and	and	CC	_	_	_
329	mixed	mix	VBN	_	_	_
330	with	with	IN	_	_	_
331	0.5	0.5	CD	_	_	_
332	mL	ml	NN	_	_	_
333	Phenol	phenol	NN	_	_	_
334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
335	B500	b500	CD	_	_	_
336	_	_	NN	_	_	_
337	1	1	CD	_	_	_
338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
339	Bacterial	bacterial	JJ	_	_	_
340	cell	cell	NN	_	_	_
341	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
342	biological	biological	JJ	_	_	_
343	replicate	replicate	VB	_	_	_
344	:	:	:	_	_	_
345	1	1	CD	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	biological	biological	JJ	_	_	_
348	replicate	replicate	VB	_	_	_
349	:	:	:	_	_	_
350	2	2	CD	_	_	_
351	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
352	Clones	clone	NNS	_	_	_
353	were	be	VBD	_	_	_
354	grown	grow	VBN	_	_	_
355	in	in	IN	_	_	_
356	M9	m9	NN	_	_	_
357	with	with	IN	_	_	_
358	0.4	0.4	CD	_	_	_
359	%	%	NN	_	_	_
360	-LRB-	-lrb-	-LRB-	_	_	_
361	w	w	NN	_	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
363	Differentially	differentially	RB	_	_	_
364	expressed	express	VBN	_	_	_
365	-LRB-	-lrb-	-LRB-	_	_	_
366	DE	de	NN	_	_	_
367	-RRB-	-rrb-	-RRB-	_	_	_
368	genes	gene	NNS	_	_	_
369	in	in	IN	_	_	_
370	all	all	DT	_	_	_
371	stress	stress	NN	_	_	_
372	evolved	evolve	VBD	_	_	_
373	strains	strain	NNS	_	_	_
374	were	be	VBD	_	_	_
375	found	find	VBN	_	_	_
376	relative	relative	JJ	_	_	_
377	to	to	TO	_	_	_
378	the	the	DT	_	_	_
379	expression	expression	NN	_	_	_
380	levels	level	NNS	_	_	_
381	in	in	IN	_	_	_
382	the	the	DT	_	_	_
383	reference	reference	NN	_	_	_
384	G500	g500	NN	_	_	_
385	strain	strain	NN	_	_	_
386	using	use	VBG	_	_	_
387	the	the	DT	_	_	_
388	edgeR	edger	NN	_	_	_
389	R	r	NN	_	_	_
390	package	package	NN	_	_	_
391	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Differentially	differentially	RB	_	_	_
3	expressed	express	VBD	_	_	_
4	genes	gene	NNS	_	_	_
5	were	be	VBD	_	_	_
6	identified	identify	VBN	_	_	_
7	by	by	IN	_	_	_
8	processing	process	VBG	_	_	_
9	raw	raw	JJ	_	_	_
10	counts	count	NNS	_	_	_
11	of	of	IN	_	_	_
12	mapped	map	VBN	_	_	_
13	reads	read	VBZ	_	_	_
14	with	with	IN	_	_	_
15	edgeR	edger	NN	_	_	_
16	R	r	NN	_	_	_
17	library	library	NN	_	_	_
18	version	version	NN	_	_	_
19	2.6.9	2.6.9	CD	_	_	_
20	.	.	.	_	_	_

1	Normalized	normalize	VBN	_	_	_
2	counts	count	NNS	_	_	_
3	for	for	IN	_	_	_
4	each	each	DT	_	_	_
5	biological	biological	JJ	_	_	_
6	replicate	replicate	VB	_	_	_
7	were	be	VBD	_	_	_
8	averaged	average	VBN	_	_	_
9	between	between	IN	_	_	_
10	two	two	CD	_	_	_
11	technical	technical	JJ	_	_	_
12	replicates	replicate	VBZ	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	G500	g500	CD	_	_	_
6	_	_	NN	_	_	_
7	1	1	CD	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Genes	gene	NNS	_	_	_
10	from	from	IN	_	_	_
11	the	the	DT	_	_	_
12	amplified	amplify	VBN	_	_	_
13	regions	region	NNS	_	_	_
14	in	in	IN	_	_	_
15	O500	o500	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	12-fold	12-fold	JJ	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	and	and	CC	_	_	_
20	P500	p500	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	two-fold	two-fold	JJ	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	strains	strain	NNS	_	_	_
25	are	be	VBP	_	_	_
26	significantly	significantly	RB	_	_	_
27	over-expressed	over-expressed	JJ	_	_	_
28	relative	relative	JJ	_	_	_
29	to	to	TO	_	_	_
30	the	the	DT	_	_	_
31	reference	reference	NN	_	_	_
32	:	:	:	_	_	_
33	average	average	JJ	_	_	_
34	log	log	NN	_	_	_
35	Fold	Fold	NNP	_	_	_
36	Change	Change	NNP	_	_	_
37	for	for	IN	_	_	_
38	concentrations	concentration	NNS	_	_	_
39	is	be	VBZ	_	_	_
40	+3.6	+3.6	CD	_	_	_
41	and	and	CC	_	_	_
42	+0.8	+0.8	CD	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	both	both	CC	_	_	_
45	with	with	IN	_	_	_
46	p-values	p-values	NN	_	_	_
47	<	<	JJR	_	_	_
48	10-20	10-20	CD	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	,	,	,	_	_	_
51	respectively	respectively	RB	_	_	_
52	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Genes	gene	NNS	_	_	_
3	with	with	IN	_	_	_
4	BH	bh	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	Benjamini	Benjamini	NNP	_	_	_
7	and	and	CC	_	_	_
8	Hochberg	Hochberg	NNP	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	adjusted	adjust	VBN	_	_	_
11	p-values	p-value	NNS	_	_	_
12	below	below	IN	_	_	_
13	0.05	0.05	CD	_	_	_
14	threshold	threshold	NN	_	_	_
15	were	be	VBD	_	_	_
16	selected	select	VBN	_	_	_
17	as	as	IN	_	_	_
18	DE	de	NN	_	_	_
19	genes	gene	NNS	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	Escherichia	escherichia	FW	Organism	_	_
7	coli	coli	FW	Organism	_	_
8	strain	strain	NN	_	_	_
9	K12	k12	NN	_	_	_
10	sub-strain	sub-strain	JJ	_	_	_
11	MG1655	mg1655	NN	_	_	_
12	genome	genome	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	GenBank	genbank	NN	_	_	_
15	accession	accession	NN	_	_	_
16	no	no	DT	_	_	_
17	.	.	.	_	_	_

1	U00096	u00096	NN	_	_	_
2	.2	.2	NN	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	H500	h500	CD	_	_	_
6	_	_	NN	_	_	_
7	1	1	CD	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Illumina	Illumina	NNP	_	_	_
10	GAII	GAII	NNP	_	_	_
11	reads	read	VBZ	_	_	_
12	were	be	VBD	_	_	_
13	filtered	filter	VBN	_	_	_
14	by	by	IN	_	_	_
15	SGA	SGA	NNP	_	_	_
16	version	version	NN	_	_	_
17	0.9.9	0.9.9	CD	_	_	_
18	with	with	IN	_	_	_
19	the	the	DT	_	_	_
20	following	follow	VBG	_	_	_
21	options	option	NNS	_	_	_
22	:	:	:	_	_	_
23	sga	sga	NN	_	_	_
24	preprocess	preprocess	NN	_	_	_
25	-	-	:	_	_	_
26	q	q	NN	_	_	_
27	10	10	CD	_	_	_
28	-	-	:	_	_	_
29	f	f	LS	_	_	_
30	10	10	CD	_	_	_
31	-	-	:	_	_	_
32	m	m	NN	_	_	_
33	25	25	CD	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	quality	quality	NN	_	_	_
36	trim	trim	JJ	_	_	_
37	10	10	CD	_	_	_
38	,	,	,	_	_	_
39	quality	quality	NN	_	_	_
40	filter	filter	NN	_	_	_
41	10	10	CD	_	_	_
42	,	,	,	_	_	_
43	minimal	minimal	JJ	_	_	_
44	length	length	NN	_	_	_
45	25	25	CD	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	O500	o500	CD	_	_	_
49	_	_	NN	_	_	_
50	1	1	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	O500	o500	CD	_	_	_
53	_	_	NN	_	_	_
54	2	2	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	P500	p500	CD	_	_	_
57	_	_	NN	_	_	_
58	1	1	CD	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	preprocessed	preprocessed	JJ	_	_	_
61	RNA-Seq	rna-seq	NN	_	_	_
62	reads	read	VBZ	_	_	_
63	were	be	VBD	_	_	_
64	mapped	map	VBN	_	_	_
65	to	to	TO	_	_	_
66	the	the	DT	_	_	_
67	reference	reference	NN	_	_	_
68	Escherichia	escherichia	FW	Organism	_	_
69	coli	coli	FW	Organism	_	_
70	strain	strain	NN	_	_	_
71	K12	k12	NN	_	_	_
72	sub-strain	sub-strain	JJ	_	_	_
73	MG1655	mg1655	NN	_	_	_
74	genome	genome	NN	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	GenBank	genbank	NN	_	_	_
77	accession	accession	NN	_	_	_
78	no	no	DT	_	_	_
79	.	.	.	_	_	_

1	U00096	u00096	NN	_	_	_
2	.2	.2	NN	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	by	by	IN	_	_	_
5	BWA	BWA	NNP	_	_	_
6	toolkit	toolkit	NN	_	_	_
7	version	version	NN	_	_	_
8	0.5.9-r16	0.5.9-r16	NN	_	_	_
9	with	with	IN	_	_	_
10	the	the	DT	_	_	_
11	following	follow	VBG	_	_	_
12	options	option	NNS	_	_	_
13	:	:	:	_	_	_
14	bwa	bwa	NN	_	_	_
15	aln	aln	NN	_	_	_
16	-	-	:	_	_	_
17	q	q	NN	_	_	_
18	20	20	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	RNA-Seq	rna-seq	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	RNA	rna	NN	_	_	_
23	was	be	VBD	_	_	_
24	extracted	extract	VBN	_	_	_
25	using	use	VBG	_	_	_
26	an	a	DT	_	_	_
27	RNeasy	rneasy	JJ	_	_	_
28	kit	kit	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Qiagen	qiagen	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	and	and	CC	_	_	_
33	after	after	IN	_	_	_
34	1st	1st	JJ	_	_	_
35	and	and	CC	_	_	_
36	2nd	2nd	JJ	_	_	_
37	strand	strand	NN	_	_	_
38	cDNA	cdna	NN	_	_	_
39	synthesis	synthesis	NN	_	_	_
40	,	,	,	_	_	_
41	linker	linker	NN	_	_	_
42	ligation	ligation	NN	_	_	_
43	and	and	CC	_	_	_
44	size	size	NN	_	_	_
45	selection	selection	NN	_	_	_
46	subjected	subject	VBN	_	_	_
47	to	to	TO	_	_	_
48	shotgun	shotgun	NN	_	_	_
49	sequencing	sequencing	NN	_	_	_
50	using	use	VBG	_	_	_
51	single	single	JJ	_	_	_
52	read	read	NN	_	_	_
53	40bp	40bp	JJ	_	_	_
54	read	read	NN	_	_	_
55	length	length	NN	_	_	_
56	runs	run	VBZ	_	_	_
57	on	on	IN	_	_	_
58	an	a	DT	_	_	_
59	Illumina	Illumina	NNP	_	_	_
60	Genome	Genome	NNP	_	_	_
61	Analyzer	Analyzer	NNP	_	_	_
62	GAII	GAII	NNP	_	_	_
63	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MG	mg	NN	_	_	_
5	1655	1655	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	stress	stress	NN	_	_	_
8	:	:	:	_	_	_
9	acidic	acidic	JJ	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
11	stress	stress	NN	_	_	_
12	:	:	:	_	_	_
13	Minimal	minimal	JJ	_	_	_
14	medium	medium	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	stress	stress	NN	_	_	_
17	:	:	:	_	_	_
18	n-butanol	n-butanol	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	stress	stress	NN	_	_	_
21	:	:	:	_	_	_
22	osmotic	osmotic	JJ	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	stress	stress	NN	_	_	_
25	:	:	:	_	_	_
26	oxidative	oxidative	JJ	_	_	_
27	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
28	Supplementary	Supplementary	NNP	_	_	_
29	_	_	VBD	_	_	_
30	files	file	NNS	_	_	_
31	_	_	IN	_	_	_
32	format	format	NN	_	_	_
33	_	_	NN	_	_	_
34	and	and	CC	_	_	_
35	_	_	NN	_	_	_
36	content	content	NN	_	_	_
37	:	:	:	_	_	_
38	Tab	tab	NN	_	_	_
39	delimited	delimit	VBN	_	_	_
40	text	text	NN	_	_	_
41	file	file	NN	_	_	_
42	;	;	:	_	_	_
43	includes	include	VBZ	_	_	_
44	:	:	:	_	_	_
45	gene	gene	NN	_	_	_
46	differential	differential	JJ	_	_	_
47	expression	expression	NN	_	_	_
48	levels	level	NNS	_	_	_
49	relative	relative	JJ	_	_	_
50	to	to	TO	_	_	_
51	the	the	DT	_	_	_
52	G500	g500	NN	_	_	_
53	strain	strain	NN	_	_	_
54	with	with	IN	_	_	_
55	corresponding	corresponding	JJ	_	_	_
56	p-values	p-value	NNS	_	_	_
57	and	and	CC	_	_	_
58	processed	process	VBN	_	_	_
59	counts	count	NNS	_	_	_
60	for	for	IN	_	_	_
61	each	each	DT	_	_	_
62	biological	biological	JJ	_	_	_
63	replicate	replicate	VB	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	each	each	DT	_	_	_
66	normolized	normolized	NN	_	_	_
67	and	and	CC	_	_	_
68	averaged	average	VBD	_	_	_
69	between	between	IN	_	_	_
70	2	2	CD	_	_	_
71	technical	technical	JJ	_	_	_
72	replicates	replicate	VBZ	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	.	.	.	_	_	_

1	Linked	link	VBN	_	_	_
2	as	as	IN	_	_	_
3	supplementary	supplementary	JJ	_	_	_
4	file	file	NN	_	_	_
5	on	on	IN	_	_	_
6	Series	Series	NNP	_	_	_
7	record	record	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	technical	technical	JJ	_	_	_
3	replicates	replicate	VBZ	_	_	_
4	:	:	:	_	_	_
5	2	2	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	After	after	IN	_	_	_
8	reaching	reach	VBG	_	_	_
9	an	a	DT	_	_	_
10	OD600nm	od600nm	NN	_	_	_
11	of	of	IN	_	_	_
12	0.9	0.9	CD	_	_	_
13	,	,	,	_	_	_
14	cell	cell	NN	_	_	_
15	cultures	culture	NNS	_	_	_
16	were	be	VBD	_	_	_
17	placed	place	VBN	_	_	_
18	immediately	immediately	RB	_	_	_
19	in	in	IN	_	_	_
20	a	a	DT	_	_	_
21	shaking	shake	VBG	_	_	_
22	water	water	NN	_	_	_
23	bath	bath	NN	_	_	_
24	along	along	IN	_	_	_
25	with	with	IN	_	_	_
26	another	another	DT	_	_	_
27	BHI	BHI	NNP	_	_	_
28	flask	flask	NN	_	_	_
29	carrying	carry	VBG	_	_	_
30	a	a	DT	_	_	_
31	type	type	NN	_	_	_
32	T	t	NN	_	_	_
33	thermocouple	thermocouple	NN	_	_	_
34	connected	connect	VBN	_	_	_
35	to	to	TO	_	_	_
36	a	a	DT	_	_	_
37	MultiPaq	MultiPaq	NNP	_	_	_
38	21	21	CD	_	_	_
39	datalogger	datalogger	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	Datapaq	Datapaq	NNP	_	_	_
42	Inc.	Inc.	NNP	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	for	for	IN	_	_	_
45	temperature	temperature	NN	_	_	_
46	profile	profile	NN	_	_	_
47	and	and	CC	_	_	_
48	the	the	DT	_	_	_
49	process	process	NN	_	_	_
50	lethality	lethality	NN	_	_	_
51	values	value	NNS	_	_	_
52	monitoring	monitor	VBG	_	_	_
53	in	in	IN	_	_	_
54	real	real	JJ	_	_	_
55	time	time	NN	_	_	_
56	.	.	.	_	_	_

1	Bacteria	bacterium	NNS	_	_	_
2	suspension	suspension	NN	_	_	_
3	were	be	VBD	_	_	_
4	heated	heat	VBN	_	_	_
5	at	at	IN	_	_	_
6	58	58	CD	_	_	_
7	°C	°c	NN	_	_	_
8	to	to	TO	_	_	_
9	process	process	NN	_	_	_
10	lethality	lethality	NN	_	_	_
11	values	value	NNS	_	_	_
12	of	of	IN	_	_	_
13	2	2	CD	_	_	_
14	and	and	CC	_	_	_
15	3	3	CD	_	_	_
16	,	,	,	_	_	_
17	at	at	IN	_	_	_
18	60	60	CD	_	_	_
19	°C	°c	NN	_	_	_
20	to	to	TO	_	_	_
21	a	a	DT	_	_	_
22	process	process	NN	_	_	_
23	lethality	lethality	NN	_	_	_
24	value	value	NN	_	_	_
25	of	of	IN	_	_	_
26	3	3	CD	_	_	_
27	,	,	,	_	_	_
28	or	or	CC	_	_	_
29	until	until	IN	_	_	_
30	a	a	DT	_	_	_
31	temperature	temperature	NN	_	_	_
32	of	of	IN	_	_	_
33	71	71	CD	_	_	_
34	°C	°c	NN	_	_	_
35	was	be	VBD	_	_	_
36	reached	reach	VBN	_	_	_
37	.	.	.	_	_	_

1	Just	just	RB	_	_	_
2	after	after	IN	_	_	_
3	heating	heating	NN	_	_	_
4	,	,	,	_	_	_
5	cell	cell	NN	_	_	_
6	suspension	suspension	NN	_	_	_
7	was	be	VBD	_	_	_
8	cooled	cool	VBN	_	_	_
9	in	in	IN	_	_	_
10	an	a	DT	_	_	_
11	iced	iced	JJ	_	_	_
12	water	water	NN	_	_	_
13	bath	bath	NN	_	_	_
14	under	under	IN	_	_	_
15	constant	constant	JJ	_	_	_
16	agitation	agitation	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	150	150	CD	_	_	_
19	rpm	rpm	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	until	until	IN	_	_	_
22	the	the	DT	_	_	_
23	temperature	temperature	NN	_	_	_
24	dropped	drop	VBD	_	_	_
25	back	back	RB	_	_	_
26	to	to	TO	_	_	_
27	no	no	DT	_	_	_
28	less	less	JJR	_	_	_
29	than	than	IN	_	_	_
30	37	37	CD	_	_	_
31	°C	°c	NN	_	_	_
32	in	in	IN	_	_	_
33	order	order	NN	_	_	_
34	to	to	TO	_	_	_
35	avoid	avoid	VB	_	_	_
36	cold	cold	JJ	_	_	_
37	stress	stress	NN	_	_	_
38	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	suspensions	suspension	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	centrifuged	centrifuge	VBN	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	remaining	remain	VBG	_	_	_
9	cell	cell	NN	_	_	_
10	pellets	pellet	NNS	_	_	_
11	were	be	VBD	_	_	_
12	treated	treat	VBN	_	_	_
13	with	with	IN	_	_	_
14	RNA	rna	NN	_	_	_
15	protect	protect	VBP	_	_	_
16	bacteria	bacterium	NNS	_	_	_
17	reagent	reagent	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	Inc.	Inc.	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	prior	prior	RB	_	_	_
23	to	to	TO	_	_	_
24	freezing	freezing	NN	_	_	_
25	at	at	IN	_	_	_
26	-80	-80	CD	_	_	_
27	°C	°c	NN	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Bacteria	bacterium	NNS	_	_	_
3	at	at	IN	_	_	_
4	58	58	CD	_	_	_
5	°C	°c	NN	_	_	_
6	F	f	NN	_	_	_
7	=	=	JJ	_	_	_
8	2	2	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Bacteria	bacterium	NNS	_	_	_
11	at	at	IN	_	_	_
12	58	58	CD	_	_	_
13	°C	°c	NN	_	_	_
14	F	f	NN	_	_	_
15	=	=	JJ	_	_	_
16	3	3	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Bacteria	bacterium	NNS	_	_	_
19	at	at	IN	_	_	_
20	60	60	CD	_	_	_
21	°C	°c	NN	_	_	_
22	F	f	NN	_	_	_
23	=	=	JJ	_	_	_
24	3	3	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Bacteria	bacterium	NNS	_	_	_
27	at	at	IN	_	_	_
28	71	71	CD	_	_	_
29	°C	°c	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Bacteria	bacterium	NNS	_	_	_
32	suspension	suspension	NN	_	_	_
33	heated	heat	VBN	_	_	_
34	at	at	IN	_	_	_
35	58	58	CD	_	_	_
36	°C	°c	NN	_	_	_
37	to	to	TO	_	_	_
38	a	a	DT	_	_	_
39	process	process	NN	_	_	_
40	lethality	lethality	NN	_	_	_
41	value	value	NN	_	_	_
42	of	of	IN	_	_	_
43	2	2	CD	_	_	_
44	-	-	:	_	_	_
45	Replicate	replicate	VB	_	_	_
46	1	1	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	Bacteria	bacterium	NNS	_	_	_
49	suspension	suspension	NN	_	_	_
50	heated	heat	VBN	_	_	_
51	at	at	IN	_	_	_
52	58	58	CD	_	_	_
53	°C	°c	NN	_	_	_
54	to	to	TO	_	_	_
55	a	a	DT	_	_	_
56	process	process	NN	_	_	_
57	lethality	lethality	NN	_	_	_
58	value	value	NN	_	_	_
59	of	of	IN	_	_	_
60	2	2	CD	_	_	_
61	-	-	:	_	_	_
62	Replicate	replicate	VB	_	_	_
63	2	2	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
65	Bacteria	bacterium	NNS	_	_	_
66	suspension	suspension	NN	_	_	_
67	heated	heat	VBN	_	_	_
68	at	at	IN	_	_	_
69	58	58	CD	_	_	_
70	°C	°c	NN	_	_	_
71	to	to	TO	_	_	_
72	a	a	DT	_	_	_
73	process	process	NN	_	_	_
74	lethality	lethality	NN	_	_	_
75	value	value	NN	_	_	_
76	of	of	IN	_	_	_
77	2	2	CD	_	_	_
78	-	-	:	_	_	_
79	Replicate	replicate	VB	_	_	_
80	3	3	CD	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	Bacteria	bacterium	NNS	_	_	_
83	suspension	suspension	NN	_	_	_
84	heated	heat	VBN	_	_	_
85	at	at	IN	_	_	_
86	58	58	CD	_	_	_
87	°C	°c	NN	_	_	_
88	to	to	TO	_	_	_
89	a	a	DT	_	_	_
90	process	process	NN	_	_	_
91	lethality	lethality	NN	_	_	_
92	value	value	NN	_	_	_
93	of	of	IN	_	_	_
94	2	2	CD	_	_	_
95	-	-	:	_	_	_
96	Replicate	replicate	VB	_	_	_
97	4	4	CD	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
99	Bacteria	bacterium	NNS	_	_	_
100	suspension	suspension	NN	_	_	_
101	heated	heat	VBN	_	_	_
102	at	at	IN	_	_	_
103	58	58	CD	_	_	_
104	°C	°c	NN	_	_	_
105	to	to	TO	_	_	_
106	a	a	DT	_	_	_
107	process	process	NN	_	_	_
108	lethality	lethality	NN	_	_	_
109	value	value	NN	_	_	_
110	of	of	IN	_	_	_
111	2	2	CD	_	_	_
112	-	-	:	_	_	_
113	Replicate	replicate	VB	_	_	_
114	5	5	CD	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
116	Bacteria	bacterium	NNS	_	_	_
117	suspension	suspension	NN	_	_	_
118	heated	heat	VBN	_	_	_
119	at	at	IN	_	_	_
120	58	58	CD	_	_	_
121	°C	°c	NN	_	_	_
122	to	to	TO	_	_	_
123	a	a	DT	_	_	_
124	process	process	NN	_	_	_
125	lethality	lethality	NN	_	_	_
126	value	value	NN	_	_	_
127	of	of	IN	_	_	_
128	3	3	CD	_	_	_
129	-	-	:	_	_	_
130	Replicate	replicate	VB	_	_	_
131	1	1	CD	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	Bacteria	bacterium	NNS	_	_	_
134	suspension	suspension	NN	_	_	_
135	heated	heat	VBN	_	_	_
136	at	at	IN	_	_	_
137	58	58	CD	_	_	_
138	°C	°c	NN	_	_	_
139	to	to	TO	_	_	_
140	a	a	DT	_	_	_
141	process	process	NN	_	_	_
142	lethality	lethality	NN	_	_	_
143	value	value	NN	_	_	_
144	of	of	IN	_	_	_
145	3	3	CD	_	_	_
146	-	-	:	_	_	_
147	Replicate	replicate	VB	_	_	_
148	2	2	CD	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
150	Bacteria	bacterium	NNS	_	_	_
151	suspension	suspension	NN	_	_	_
152	heated	heat	VBN	_	_	_
153	at	at	IN	_	_	_
154	58	58	CD	_	_	_
155	°C	°c	NN	_	_	_
156	to	to	TO	_	_	_
157	a	a	DT	_	_	_
158	process	process	NN	_	_	_
159	lethality	lethality	NN	_	_	_
160	value	value	NN	_	_	_
161	of	of	IN	_	_	_
162	3	3	CD	_	_	_
163	-	-	:	_	_	_
164	Replicate	replicate	VB	_	_	_
165	3	3	CD	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	Bacteria	bacterium	NNS	_	_	_
168	suspension	suspension	NN	_	_	_
169	heated	heat	VBN	_	_	_
170	at	at	IN	_	_	_
171	58	58	CD	_	_	_
172	°C	°c	NN	_	_	_
173	to	to	TO	_	_	_
174	a	a	DT	_	_	_
175	process	process	NN	_	_	_
176	lethality	lethality	NN	_	_	_
177	value	value	NN	_	_	_
178	of	of	IN	_	_	_
179	3	3	CD	_	_	_
180	-	-	:	_	_	_
181	Replicate	replicate	VB	_	_	_
182	4	4	CD	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
184	Bacteria	bacterium	NNS	_	_	_
185	suspension	suspension	NN	_	_	_
186	heated	heat	VBN	_	_	_
187	at	at	IN	_	_	_
188	60	60	CD	_	_	_
189	°C	°c	NN	_	_	_
190	to	to	TO	_	_	_
191	a	a	DT	_	_	_
192	process	process	NN	_	_	_
193	lethality	lethality	NN	_	_	_
194	value	value	NN	_	_	_
195	of	of	IN	_	_	_
196	3	3	CD	_	_	_
197	-	-	:	_	_	_
198	Replicate	replicate	VB	_	_	_
199	1	1	CD	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	Bacteria	bacterium	NNS	_	_	_
202	suspension	suspension	NN	_	_	_
203	heated	heat	VBN	_	_	_
204	at	at	IN	_	_	_
205	60	60	CD	_	_	_
206	°C	°c	NN	_	_	_
207	to	to	TO	_	_	_
208	a	a	DT	_	_	_
209	process	process	NN	_	_	_
210	lethality	lethality	NN	_	_	_
211	value	value	NN	_	_	_
212	of	of	IN	_	_	_
213	3	3	CD	_	_	_
214	-	-	:	_	_	_
215	Replicate	replicate	VB	_	_	_
216	2	2	CD	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
218	Bacteria	bacterium	NNS	_	_	_
219	suspension	suspension	NN	_	_	_
220	heated	heat	VBN	_	_	_
221	at	at	IN	_	_	_
222	60	60	CD	_	_	_
223	°C	°c	NN	_	_	_
224	to	to	TO	_	_	_
225	a	a	DT	_	_	_
226	process	process	NN	_	_	_
227	lethality	lethality	NN	_	_	_
228	value	value	NN	_	_	_
229	of	of	IN	_	_	_
230	3	3	CD	_	_	_
231	-	-	:	_	_	_
232	Replicate	replicate	VB	_	_	_
233	3	3	CD	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	Bacteria	bacterium	NNS	_	_	_
236	suspension	suspension	NN	_	_	_
237	heated	heat	VBN	_	_	_
238	at	at	IN	_	_	_
239	60	60	CD	_	_	_
240	°C	°c	NN	_	_	_
241	to	to	TO	_	_	_
242	a	a	DT	_	_	_
243	process	process	NN	_	_	_
244	lethality	lethality	NN	_	_	_
245	value	value	NN	_	_	_
246	of	of	IN	_	_	_
247	3	3	CD	_	_	_
248	-	-	:	_	_	_
249	Replicate	replicate	VB	_	_	_
250	4	4	CD	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
252	Bacteria	bacterium	NNS	_	_	_
253	suspension	suspension	NN	_	_	_
254	heated	heat	VBN	_	_	_
255	to	to	TO	_	_	_
256	a	a	DT	_	_	_
257	core	core	NN	_	_	_
258	temperature	temperature	NN	_	_	_
259	of	of	IN	_	_	_
260	71	71	CD	_	_	_
261	°C	°c	NN	_	_	_
262	-	-	:	_	_	_
263	Replicate	replicate	VB	_	_	_
264	1	1	CD	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	Bacteria	bacterium	NNS	_	_	_
267	suspension	suspension	NN	_	_	_
268	heated	heat	VBN	_	_	_
269	to	to	TO	_	_	_
270	a	a	DT	_	_	_
271	core	core	NN	_	_	_
272	temperature	temperature	NN	_	_	_
273	of	of	IN	_	_	_
274	71	71	CD	_	_	_
275	°C	°c	NN	_	_	_
276	-	-	:	_	_	_
277	Replicate	replicate	VB	_	_	_
278	2	2	CD	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
280	Bacteria	bacterium	NNS	_	_	_
281	suspension	suspension	NN	_	_	_
282	heated	heat	VBN	_	_	_
283	to	to	TO	_	_	_
284	a	a	DT	_	_	_
285	core	core	NN	_	_	_
286	temperature	temperature	NN	_	_	_
287	of	of	IN	_	_	_
288	71	71	CD	_	_	_
289	°C	°c	NN	_	_	_
290	-	-	:	_	_	_
291	Replicate	replicate	VB	_	_	_
292	3	3	CD	_	_	_
293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
294	Bacteria	bacterium	NNS	_	_	_
295	suspension	suspension	NN	_	_	_
296	heated	heat	VBN	_	_	_
297	to	to	TO	_	_	_
298	a	a	DT	_	_	_
299	core	core	NN	_	_	_
300	temperature	temperature	NN	_	_	_
301	of	of	IN	_	_	_
302	71	71	CD	_	_	_
303	°C	°c	NN	_	_	_
304	-	-	:	_	_	_
305	Replicate	replicate	VB	_	_	_
306	4	4	CD	_	_	_
307	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
308	Bacteria	bacterium	NNS	_	_	_
309	suspension	suspension	NN	_	_	_
310	heated	heat	VBN	_	_	_
311	to	to	TO	_	_	_
312	a	a	DT	_	_	_
313	core	core	NN	_	_	_
314	temperature	temperature	NN	_	_	_
315	of	of	IN	_	_	_
316	71	71	CD	_	_	_
317	°C	°c	NN	_	_	_
318	-	-	:	_	_	_
319	Replicate	replicate	VB	_	_	_
320	5	5	CD	_	_	_
321	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
322	Control	Control	NNP	_	_	_
323	bacteria	bacterium	NNS	_	_	_
324	at	at	IN	_	_	_
325	37	37	CD	_	_	_
326	°C	°c	NN	_	_	_
327	-LRB-	-lrb-	-LRB-	_	_	_
328	common	common	JJ	_	_	_
329	reference	reference	NN	_	_	_
330	-RRB-	-rrb-	-RRB-	_	_	_
331	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	isolated	isolate	VBN	_	_	_
4	from	from	IN	_	_	_
5	5	5	CD	_	_	_
6	indepedent	indepedent	NN	_	_	_
7	cultures	culture	NNS	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	pooled	pool	VBN	_	_	_
10	after	after	IN	_	_	_
11	cDNA	cdna	NN	_	_	_
12	labeling	labeling	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	For	for	IN	_	_	_
4	each	each	DT	_	_	_
5	biological	biological	JJ	_	_	_
6	replicate	replicate	VB	_	_	_
7	,	,	,	_	_	_
8	frozen	frozen	JJ	_	_	_
9	aliquots	aliquot	NNS	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	500μl	500μl	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	of	of	IN	_	_	_
14	E.	e.	FW	_	_	_
15	coli	coli	FW	_	_	_
16	K12	k12	NN	_	_	_
17	stock	stock	NN	_	_	_
18	cultures	culture	NNS	_	_	_
19	were	be	VBD	_	_	_
20	subcultured	subculture	VBN	_	_	_
21	in	in	IN	_	_	_
22	10	10	CD	_	_	_
23	ml	ml	NN	_	_	_
24	of	of	IN	_	_	_
25	Brain	brain	NN	_	_	_
26	Heart	Heart	NNP	_	_	_
27	Infusion	Infusion	NNP	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	BHI	BHI	NNP	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	and	and	CC	_	_	_
32	incubated	incubate	VBN	_	_	_
33	overnight	overnight	JJ	_	_	_
34	at	at	IN	_	_	_
35	37	37	CD	_	_	_
36	°C	°c	NN	_	_	_
37	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	sub-cultured	sub-cultured	JJ	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	1	1	CD	_	_	_
7	%	%	NN	_	_	_
8	v	v	LS	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
10	Frozen	frozen	JJ	_	_	_
11	cell	cell	NN	_	_	_
12	pellets	pellet	NNS	_	_	_
13	were	be	VBD	_	_	_
14	lyzed	lyze	VBN	_	_	_
15	with	with	IN	_	_	_
16	lysozyme	lysozyme	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Sigma	Sigma	NNP	_	_	_
19	Aldrich	Aldrich	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	and	and	CC	_	_	_
22	proteinase	proteinase	NN	_	_	_
23	K	k	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Qiagen	Qiagen	NNP	_	_	_
26	Inc.	Inc.	NNP	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	at	at	IN	_	_	_
29	room	room	NN	_	_	_
30	temperature	temperature	NN	_	_	_
31	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	from	from	IN	_	_	_
6	cell	cell	NN	_	_	_
7	lysates	lysate	NNS	_	_	_
8	using	use	VBG	_	_	_
9	RNeasy	RNeasy	NNP	_	_	_
10	Midi	Midi	NNP	_	_	_
11	Kit	kit	NN	_	_	_
12	according	accord	VBG	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	manufacturer	manufacturer	NN	_	_	_
16	's	's	POS	_	_	_
17	instructions	instruction	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	Inc.	Inc.	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	RNA	rna	NN	_	_	_
3	samples	sample	NNS	_	_	_
4	were	be	VBD	_	_	_
5	then	then	RB	_	_	_
6	treated	treat	VBN	_	_	_
7	with	with	IN	_	_	_
8	DNase	dnase	NN	_	_	_
9	I	i	CD	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Ambion	Ambion	NNP	_	_	_
12	,	,	,	_	_	_
13	Life	Life	NNP	_	_	_
14	technologies	technology	NNS	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	before	before	IN	_	_	_
17	a	a	DT	_	_	_
18	phenol	phenol	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	growth	growth	NN	_	_	_
21	phase	phase	NN	_	_	_
22	:	:	:	_	_	_
23	stationary	stationary	JJ	GrowthPhase	_	_
24	phase	phase	NN	GrowthPhase	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	grown	grow	VBN	_	_	_
27	to	to	TO	_	_	_
28	an	a	DT	_	_	_
29	OD600nm	od600nm	NN	_	_	_
30	of	of	IN	_	_	_
31	0.9	0.9	CD	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	growth	growth	NN	_	_	_
35	protocol	protocol	NN	_	_	_
36	:	:	:	_	_	_
37	Controls	Controls	NNP	_	_	_
38	grown	grow	VBN	_	_	_
39	to	to	TO	_	_	_
40	an	a	DT	_	_	_
41	optimal	optimal	JJ	_	_	_
42	temperature	temperature	NN	_	_	_
43	of	of	IN	_	_	_
44	37	37	CD	_	_	_
45	°C	°c	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	growth	growth	NN	_	_	_
48	protocol	protocol	NN	_	_	_
49	:	:	:	_	_	_
50	Treatment	treatment	NN	_	_	_
51	1	1	CD	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	58	58	CD	_	_	_
54	°C	°c	NN	_	_	_
55	F	f	NN	_	_	_
56	=	=	JJ	_	_	_
57	2	2	CD	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	growth	growth	NN	_	_	_
61	protocol	protocol	NN	_	_	_
62	:	:	:	_	_	_
63	Treatment	treatment	NN	_	_	_
64	2	2	CD	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	58	58	CD	_	_	_
67	°C	°c	NN	_	_	_
68	F	f	NN	_	_	_
69	=	=	JJ	_	_	_
70	3	3	CD	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	growth	growth	NN	_	_	_
74	protocol	protocol	NN	_	_	_
75	:	:	:	_	_	_
76	Treatment	treatment	NN	_	_	_
77	3	3	CD	_	_	_
78	-LRB-	-lrb-	-LRB-	_	_	_
79	60	60	CD	_	_	_
80	°C	°c	NN	_	_	_
81	F	f	NN	_	_	_
82	=	=	JJ	_	_	_
83	3	3	CD	_	_	_
84	-RRB-	-rrb-	-RRB-	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	growth	growth	NN	_	_	_
87	protocol	protocol	NN	_	_	_
88	:	:	:	_	_	_
89	Treatment	treatment	NN	_	_	_
90	4	4	CD	_	_	_
91	-LRB-	-lrb-	-LRB-	_	_	_
92	core	core	NN	_	_	_
93	temperature	temperature	NN	_	_	_
94	of	of	IN	_	_	_
95	71	71	CD	_	_	_
96	°C	°c	NN	_	_	_
97	-RRB-	-rrb-	-RRB-	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	LOWESS	lowess	NN	_	_	_
100	normalized	normalize	VBD	_	_	_
101	data	datum	NNS	_	_	_
102	obtained	obtain	VBN	_	_	_
103	from	from	IN	_	_	_
104	log2	log2	NN	_	_	_
105	of	of	IN	_	_	_
106	processed	process	VBN	_	_	_
107	Red	red	JJ	_	_	_
108	signal	signal	NN	_	_	_
109	-LRB-	-lrb-	-LRB-	_	_	_
110	treated	treat	VBN	_	_	_
111	-RRB-	-rrb-	-RRB-	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	strain	strain	NN	_	_	_
114	:	:	:	_	_	_
115	strain	strain	NN	_	_	_
116	K12	k12	NN	_	_	_
117	substrain	substrain	NN	_	_	_
118	MG1655	mg1655	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	Agilent	Agilent	NNP	_	_	_
121	Feature	Feature	NNP	_	_	_
122	Extraction	Extraction	NNP	_	_	_
123	Software	Software	NNP	_	_	_
124	-LRB-	-lrb-	-LRB-	_	_	_
125	v	v	LS	_	_	_
126	10.10.1.1	10.10.1.1	CD	_	_	_
127	-RRB-	-rrb-	-RRB-	_	_	_
128	was	be	VBD	_	_	_
129	used	use	VBN	_	_	_
130	for	for	IN	_	_	_
131	background	background	NN	_	_	_
132	subtraction	subtraction	NN	_	_	_
133	and	and	CC	_	_	_
134	LOWESS	lowess	NN	_	_	_
135	normalization	normalization	NN	_	_	_
136	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Continuous	continuous	JJ	_	_	_
3	aerobically	aerobically	RB	_	_	_
4	grown	grow	VBN	_	_	_
5	cultures	culture	NNS	_	_	_
6	in	in	IN	_	_	_
7	Evans	Evans	NNP	_	_	_
8	medium	medium	NN	_	_	_
9	,	,	,	_	_	_
10	exposed	expose	VBN	_	_	_
11	to	to	TO	_	_	_
12	40uM	40um	NN	_	_	_
13	CORM-3	corm-3	NN	_	_	_
14	for	for	IN	_	_	_
15	10	10	CD	_	_	_
16	min	min	NN	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	Continuous	continuous	JJ	_	_	_
19	aerobically	aerobically	RB	_	_	_
20	grown	grow	VBN	_	_	_
21	cultures	culture	NNS	_	_	_
22	in	in	IN	_	_	_
23	Evans	Evans	NNP	_	_	_
24	medium	medium	NN	_	_	_
25	,	,	,	_	_	_
26	exposed	expose	VBN	_	_	_
27	to	to	TO	_	_	_
28	40uM	40um	NN	_	_	_
29	CORM-3	corm-3	NN	_	_	_
30	for	for	IN	_	_	_
31	20	20	CD	_	_	_
32	min	min	NN	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	Continuous	continuous	JJ	_	_	_
35	aerobically	aerobically	RB	_	_	_
36	grown	grow	VBN	_	_	_
37	cultures	culture	NNS	_	_	_
38	in	in	IN	_	_	_
39	Evans	Evans	NNP	_	_	_
40	medium	medium	NN	_	_	_
41	,	,	,	_	_	_
42	exposed	expose	VBN	_	_	_
43	to	to	TO	_	_	_
44	40uM	40um	NN	_	_	_
45	CORM-3	corm-3	NN	_	_	_
46	for	for	IN	_	_	_
47	2.5	2.5	CD	_	_	_
48	min	min	NN	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	Continuous	continuous	JJ	_	_	_
51	aerobically	aerobically	RB	_	_	_
52	grown	grow	VBN	_	_	_
53	cultures	culture	NNS	_	_	_
54	in	in	IN	_	_	_
55	Evans	Evans	NNP	_	_	_
56	medium	medium	NN	_	_	_
57	,	,	,	_	_	_
58	exposed	expose	VBN	_	_	_
59	to	to	TO	_	_	_
60	40uM	40um	NN	_	_	_
61	CORM-3	corm-3	NN	_	_	_
62	for	for	IN	_	_	_
63	40	40	CD	_	_	_
64	min	min	NN	_	_	_
65	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
66	Continuous	continuous	JJ	_	_	_
67	aerobically	aerobically	RB	_	_	_
68	grown	grow	VBN	_	_	_
69	cultures	culture	NNS	_	_	_
70	in	in	IN	_	_	_
71	Evans	Evans	NNP	_	_	_
72	medium	medium	NN	_	_	_
73	,	,	,	_	_	_
74	exposed	expose	VBN	_	_	_
75	to	to	TO	_	_	_
76	40uM	40um	NN	_	_	_
77	CORM-3	corm-3	NN	_	_	_
78	for	for	IN	_	_	_
79	5	5	CD	_	_	_
80	min	min	NN	_	_	_
81	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
82	Continuous	continuous	JJ	_	_	_
83	aerobically	aerobically	RB	_	_	_
84	grown	grow	VBN	_	_	_
85	cultures	culture	NNS	_	_	_
86	in	in	IN	_	_	_
87	Evans	Evans	NNP	_	_	_
88	medium	medium	NN	_	_	_
89	,	,	,	_	_	_
90	exposed	expose	VBN	_	_	_
91	to	to	TO	_	_	_
92	40uM	40um	NN	_	_	_
93	CORM-3	corm-3	NN	_	_	_
94	for	for	IN	_	_	_
95	80	80	CD	_	_	_
96	min	min	NN	_	_	_
97	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
98	Continuous	continuous	JJ	_	_	_
99	aerobically	aerobically	RB	_	_	_
100	grown	grow	VBN	_	_	_
101	cultures	culture	NNS	_	_	_
102	in	in	IN	_	_	_
103	Evans	Evans	NNP	_	_	_
104	medium	medium	NN	_	_	_
105	,	,	,	_	_	_
106	exposed	expose	VBN	_	_	_
107	to	to	TO	_	_	_
108	40uM	40um	NN	_	_	_
109	iCORM-3	icorm-3	NN	_	_	_
110	for	for	IN	_	_	_
111	10	10	CD	_	_	_
112	min	min	NN	_	_	_
113	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
114	Continuous	continuous	JJ	_	_	_
115	aerobically	aerobically	RB	_	_	_
116	grown	grow	VBN	_	_	_
117	cultures	culture	NNS	_	_	_
118	in	in	IN	_	_	_
119	Evans	Evans	NNP	_	_	_
120	medium	medium	NN	_	_	_
121	,	,	,	_	_	_
122	exposed	expose	VBN	_	_	_
123	to	to	TO	_	_	_
124	40uM	40um	NN	_	_	_
125	iCORM-3	icorm-3	NN	_	_	_
126	for	for	IN	_	_	_
127	20	20	CD	_	_	_
128	min	min	NN	_	_	_
129	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
130	Continuous	continuous	JJ	_	_	_
131	aerobically	aerobically	RB	_	_	_
132	grown	grow	VBN	_	_	_
133	cultures	culture	NNS	_	_	_
134	in	in	IN	_	_	_
135	Evans	Evans	NNP	_	_	_
136	medium	medium	NN	_	_	_
137	,	,	,	_	_	_
138	exposed	expose	VBN	_	_	_
139	to	to	TO	_	_	_
140	40uM	40um	NN	_	_	_
141	iCORM-3	icorm-3	NN	_	_	_
142	for	for	IN	_	_	_
143	2.5	2.5	CD	_	_	_
144	min	min	NN	_	_	_
145	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
146	Continuous	continuous	JJ	_	_	_
147	aerobically	aerobically	RB	_	_	_
148	grown	grow	VBN	_	_	_
149	cultures	culture	NNS	_	_	_
150	in	in	IN	_	_	_
151	Evans	Evans	NNP	_	_	_
152	medium	medium	NN	_	_	_
153	,	,	,	_	_	_
154	exposed	expose	VBN	_	_	_
155	to	to	TO	_	_	_
156	40uM	40um	NN	_	_	_
157	iCORM-3	icorm-3	NN	_	_	_
158	for	for	IN	_	_	_
159	40	40	CD	_	_	_
160	min	min	NN	_	_	_
161	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
162	Continuous	continuous	JJ	_	_	_
163	aerobically	aerobically	RB	_	_	_
164	grown	grow	VBN	_	_	_
165	cultures	culture	NNS	_	_	_
166	in	in	IN	_	_	_
167	Evans	Evans	NNP	_	_	_
168	medium	medium	NN	_	_	_
169	,	,	,	_	_	_
170	exposed	expose	VBN	_	_	_
171	to	to	TO	_	_	_
172	40uM	40um	NN	_	_	_
173	iCORM-3	icorm-3	NN	_	_	_
174	for	for	IN	_	_	_
175	5	5	CD	_	_	_
176	min	min	NN	_	_	_
177	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
178	Continuous	continuous	JJ	_	_	_
179	aerobically	aerobically	RB	_	_	_
180	grown	grow	VBN	_	_	_
181	cultures	culture	NNS	_	_	_
182	in	in	IN	_	_	_
183	Evans	Evans	NNP	_	_	_
184	medium	medium	NN	_	_	_
185	,	,	,	_	_	_
186	exposed	expose	VBN	_	_	_
187	to	to	TO	_	_	_
188	40uM	40um	NN	_	_	_
189	iCORM-3	icorm-3	NN	_	_	_
190	for	for	IN	_	_	_
191	80	80	CD	_	_	_
192	min	min	NN	_	_	_
193	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
194	Continuous	continuous	JJ	_	_	_
195	aerobically	aerobically	RB	_	_	_
196	grown	grow	VBN	_	_	_
197	cultures	culture	NNS	_	_	_
198	in	in	IN	_	_	_
199	Evans	Evans	NNP	_	_	_
200	medium	medium	NN	_	_	_
201	,	,	,	_	_	_
202	prior	prior	RB	_	_	_
203	to	to	TO	_	_	_
204	CORM-3	corm-3	NN	_	_	_
205	addition	addition	NN	_	_	_
206	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
207	Continuous	continuous	JJ	_	_	_
208	anaerobically	anaerobically	RB	_	_	_
209	grown	grow	VBN	_	_	_
210	cultures	culture	NNS	_	_	_
211	in	in	IN	_	_	_
212	Evans	Evans	NNP	_	_	_
213	medium	medium	NN	_	_	_
214	,	,	,	_	_	_
215	exposed	expose	VBN	_	_	_
216	to	to	TO	_	_	_
217	40uM	40um	NN	_	_	_
218	CORM-3	corm-3	NN	_	_	_
219	for	for	IN	_	_	_
220	10	10	CD	_	_	_
221	min	min	NN	_	_	_
222	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
223	Continuous	continuous	JJ	_	_	_
224	anaerobically	anaerobically	RB	_	_	_
225	grown	grow	VBN	_	_	_
226	cultures	culture	NNS	_	_	_
227	in	in	IN	_	_	_
228	Evans	Evans	NNP	_	_	_
229	medium	medium	NN	_	_	_
230	,	,	,	_	_	_
231	exposed	expose	VBN	_	_	_
232	to	to	TO	_	_	_
233	40uM	40um	NN	_	_	_
234	CORM-3	corm-3	NN	_	_	_
235	for	for	IN	_	_	_
236	20	20	CD	_	_	_
237	min	min	NN	_	_	_
238	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
239	Continuous	continuous	JJ	_	_	_
240	anaerobically	anaerobically	RB	_	_	_
241	grown	grow	VBN	_	_	_
242	cultures	culture	NNS	_	_	_
243	in	in	IN	_	_	_
244	Evans	Evans	NNP	_	_	_
245	medium	medium	NN	_	_	_
246	,	,	,	_	_	_
247	exposed	expose	VBN	_	_	_
248	to	to	TO	_	_	_
249	40uM	40um	NN	_	_	_
250	CORM-3	corm-3	NN	_	_	_
251	for	for	IN	_	_	_
252	2.5	2.5	CD	_	_	_
253	min	min	NN	_	_	_
254	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
255	Continuous	continuous	JJ	_	_	_
256	anaerobically	anaerobically	RB	_	_	_
257	grown	grow	VBN	_	_	_
258	cultures	culture	NNS	_	_	_
259	in	in	IN	_	_	_
260	Evans	Evans	NNP	_	_	_
261	medium	medium	NN	_	_	_
262	,	,	,	_	_	_
263	exposed	expose	VBN	_	_	_
264	to	to	TO	_	_	_
265	40uM	40um	NN	_	_	_
266	CORM-3	corm-3	NN	_	_	_
267	for	for	IN	_	_	_
268	40	40	CD	_	_	_
269	min	min	NN	_	_	_
270	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
271	Continuous	continuous	JJ	_	_	_
272	anaerobically	anaerobically	RB	_	_	_
273	grown	grow	VBN	_	_	_
274	cultures	culture	NNS	_	_	_
275	in	in	IN	_	_	_
276	Evans	Evans	NNP	_	_	_
277	medium	medium	NN	_	_	_
278	,	,	,	_	_	_
279	exposed	expose	VBN	_	_	_
280	to	to	TO	_	_	_
281	40uM	40um	NN	_	_	_
282	CORM-3	corm-3	NN	_	_	_
283	for	for	IN	_	_	_
284	5	5	CD	_	_	_
285	min	min	NN	_	_	_
286	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
287	Continuous	continuous	JJ	_	_	_
288	anaerobically	anaerobically	RB	_	_	_
289	grown	grow	VBN	_	_	_
290	cultures	culture	NNS	_	_	_
291	in	in	IN	_	_	_
292	Evans	Evans	NNP	_	_	_
293	medium	medium	NN	_	_	_
294	,	,	,	_	_	_
295	exposed	expose	VBN	_	_	_
296	to	to	TO	_	_	_
297	40uM	40um	NN	_	_	_
298	CORM-3	corm-3	NN	_	_	_
299	for	for	IN	_	_	_
300	80	80	CD	_	_	_
301	min	min	NN	_	_	_
302	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
303	Continuous	continuous	JJ	_	_	_
304	anaerobically	anaerobically	RB	_	_	_
305	grown	grow	VBN	_	_	_
306	cultures	culture	NNS	_	_	_
307	in	in	IN	_	_	_
308	Evans	Evans	NNP	_	_	_
309	medium	medium	NN	_	_	_
310	,	,	,	_	_	_
311	exposed	expose	VBN	_	_	_
312	to	to	TO	_	_	_
313	40uM	40um	NN	_	_	_
314	iCORM-3	icorm-3	NN	_	_	_
315	for	for	IN	_	_	_
316	10	10	CD	_	_	_
317	min	min	NN	_	_	_
318	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
319	Continuous	continuous	JJ	_	_	_
320	anaerobically	anaerobically	RB	_	_	_
321	grown	grow	VBN	_	_	_
322	cultures	culture	NNS	_	_	_
323	in	in	IN	_	_	_
324	Evans	Evans	NNP	_	_	_
325	medium	medium	NN	_	_	_
326	,	,	,	_	_	_
327	exposed	expose	VBN	_	_	_
328	to	to	TO	_	_	_
329	40uM	40um	NN	_	_	_
330	iCORM-3	icorm-3	NN	_	_	_
331	for	for	IN	_	_	_
332	20	20	CD	_	_	_
333	min	min	NN	_	_	_
334	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
335	Continuous	continuous	JJ	_	_	_
336	anaerobically	anaerobically	RB	_	_	_
337	grown	grow	VBN	_	_	_
338	cultures	culture	NNS	_	_	_
339	in	in	IN	_	_	_
340	Evans	Evans	NNP	_	_	_
341	medium	medium	NN	_	_	_
342	,	,	,	_	_	_
343	exposed	expose	VBN	_	_	_
344	to	to	TO	_	_	_
345	40uM	40um	NN	_	_	_
346	iCORM-3	icorm-3	NN	_	_	_
347	for	for	IN	_	_	_
348	2.5	2.5	CD	_	_	_
349	min	min	NN	_	_	_
350	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
351	Continuous	continuous	JJ	_	_	_
352	anaerobically	anaerobically	RB	_	_	_
353	grown	grow	VBN	_	_	_
354	cultures	culture	NNS	_	_	_
355	in	in	IN	_	_	_
356	Evans	Evans	NNP	_	_	_
357	medium	medium	NN	_	_	_
358	,	,	,	_	_	_
359	exposed	expose	VBN	_	_	_
360	to	to	TO	_	_	_
361	40uM	40um	NN	_	_	_
362	iCORM-3	icorm-3	NN	_	_	_
363	for	for	IN	_	_	_
364	40	40	CD	_	_	_
365	min	min	NN	_	_	_
366	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
367	Continuous	continuous	JJ	_	_	_
368	anaerobically	anaerobically	RB	_	_	_
369	grown	grow	VBN	_	_	_
370	cultures	culture	NNS	_	_	_
371	in	in	IN	_	_	_
372	Evans	Evans	NNP	_	_	_
373	medium	medium	NN	_	_	_
374	,	,	,	_	_	_
375	exposed	expose	VBN	_	_	_
376	to	to	TO	_	_	_
377	40uM	40um	NN	_	_	_
378	iCORM-3	icorm-3	NN	_	_	_
379	for	for	IN	_	_	_
380	5	5	CD	_	_	_
381	min	min	NN	_	_	_
382	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
383	Continuous	continuous	JJ	_	_	_
384	anaerobically	anaerobically	RB	_	_	_
385	grown	grow	VBN	_	_	_
386	cultures	culture	NNS	_	_	_
387	in	in	IN	_	_	_
388	Evans	Evans	NNP	_	_	_
389	medium	medium	NN	_	_	_
390	,	,	,	_	_	_
391	exposed	expose	VBN	_	_	_
392	to	to	TO	_	_	_
393	40uM	40um	NN	_	_	_
394	iCORM-3	icorm-3	NN	_	_	_
395	for	for	IN	_	_	_
396	80	80	CD	_	_	_
397	min	min	NN	_	_	_
398	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
399	Continuous	continuous	JJ	_	_	_
400	anaerobically	anaerobically	RB	_	_	_
401	grown	grow	VBN	_	_	_
402	cultures	culture	NNS	_	_	_
403	in	in	IN	_	_	_
404	Evans	Evans	NNP	_	_	_
405	medium	medium	NN	_	_	_
406	,	,	,	_	_	_
407	prior	prior	RB	_	_	_
408	to	to	TO	_	_	_
409	CORM-3	corm-3	NN	_	_	_
410	addition	addition	NN	_	_	_
411	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
412	Escherichia	escherichia	FW	Organism	_	_
413	coli	coli	FW	Organism	_	_
414	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
415	Slide	slide	NN	_	_	_
416	10	10	CD	_	_	_
417	_	_	SYM	_	_	_
418	Anaerobic	anaerobic	JJ	_	_	_
419	culture	culture	NN	_	_	_
420	_	_	SYM	_	_	_
421	CORM-3	corm-3	NN	_	_	_
422	_	_	NN	_	_	_
423	biol	biol	NN	_	_	_
424	rep	rep	NN	GEN	_	_
425	1	1	CD	_	_	_
426	_	_	NN	_	_	_
427	Cy3	cy3	NN	_	_	_
428	0	0	CD	_	_	_
429	Cy5	cy5	NN	_	_	_
430	10	10	CD	_	_	_
431	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
432	Slide	Slide	NNP	_	_	_
433	10	10	CD	_	_	_
434	_	_	SYM	_	_	_
435	Anaerobic	anaerobic	JJ	_	_	_
436	culture	culture	NN	_	_	_
437	_	_	SYM	_	_	_
438	CORM-3	corm-3	NN	_	_	_
439	_	_	NN	_	_	_
440	biol	biol	NN	_	_	_
441	rep	rep	NN	GEN	_	_
442	1	1	CD	_	_	_
443	_	_	NN	_	_	_
444	Cy3	cy3	NN	_	_	_
445	0	0	CD	_	_	_
446	Cy5	cy5	NN	_	_	_
447	5	5	CD	_	_	_
448	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
449	Slide	Slide	NNP	_	_	_
450	10	10	CD	_	_	_
451	_	_	SYM	_	_	_
452	Anaerobic	anaerobic	JJ	_	_	_
453	culture	culture	NN	_	_	_
454	_	_	SYM	_	_	_
455	CORM-3	corm-3	NN	_	_	_
456	_	_	NN	_	_	_
457	biol	biol	NN	_	_	_
458	rep	rep	NN	GEN	_	_
459	2	2	CD	_	_	_
460	_	_	CD	_	_	_
461	Cy3	cy3	NN	_	_	_
462	0	0	CD	_	_	_
463	Cy5	cy5	NN	_	_	_
464	10	10	CD	_	_	_
465	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
466	Slide	Slide	NNP	_	_	_
467	10	10	CD	_	_	_
468	_	_	SYM	_	_	_
469	Anaerobic	anaerobic	JJ	_	_	_
470	culture	culture	NN	_	_	_
471	_	_	SYM	_	_	_
472	CORM-3	corm-3	NN	_	_	_
473	_	_	NN	_	_	_
474	biol	biol	NN	_	_	_
475	rep	rep	NN	GEN	_	_
476	2	2	CD	_	_	_
477	_	_	CD	_	_	_
478	Cy3	cy3	NN	_	_	_
479	0	0	CD	_	_	_
480	Cy5	cy5	NN	_	_	_
481	20	20	CD	_	_	_
482	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
483	Slide	Slide	NNP	_	_	_
484	10	10	CD	_	_	_
485	_	_	SYM	_	_	_
486	Anaerobic	anaerobic	JJ	_	_	_
487	culture	culture	NN	_	_	_
488	_	_	SYM	_	_	_
489	CORM-3	corm-3	NN	_	_	_
490	_	_	NN	_	_	_
491	biol	biol	NN	_	_	_
492	rep	rep	NN	GEN	_	_
493	2	2	CD	_	_	_
494	_	_	CD	_	_	_
495	Cy3	cy3	NN	_	_	_
496	0	0	CD	_	_	_
497	Cy5	cy5	NN	_	_	_
498	2.5	2.5	CD	_	_	_
499	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
500	Slide	Slide	NNP	_	_	_
501	10	10	CD	_	_	_
502	_	_	SYM	_	_	_
503	Anaerobic	anaerobic	JJ	_	_	_
504	culture	culture	NN	_	_	_
505	_	_	SYM	_	_	_
506	CORM-3	corm-3	NN	_	_	_
507	_	_	NN	_	_	_
508	biol	biol	NN	_	_	_
509	rep	rep	NN	GEN	_	_
510	2	2	CD	_	_	_
511	_	_	CD	_	_	_
512	Cy3	cy3	NN	_	_	_
513	0	0	CD	_	_	_
514	Cy5	cy5	NN	_	_	_
515	40	40	CD	_	_	_
516	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
517	Slide	slide	NN	_	_	_
518	10	10	CD	_	_	_
519	_	_	SYM	_	_	_
520	Anaerobic	anaerobic	JJ	_	_	_
521	culture	culture	NN	_	_	_
522	_	_	SYM	_	_	_
523	CORM-3	corm-3	NN	_	_	_
524	_	_	NN	_	_	_
525	biol	biol	NN	_	_	_
526	rep	rep	NN	GEN	_	_
527	2	2	CD	_	_	_
528	_	_	CD	_	_	_
529	Cy3	cy3	NN	_	_	_
530	0	0	CD	_	_	_
531	Cy5	cy5	NN	_	_	_
532	5	5	CD	_	_	_
533	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
534	Slide	Slide	NNP	_	_	_
535	10	10	CD	_	_	_
536	_	_	SYM	_	_	_
537	Anaerobic	anaerobic	JJ	_	_	_
538	culture	culture	NN	_	_	_
539	_	_	SYM	_	_	_
540	CORM-3	corm-3	NN	_	_	_
541	_	_	NN	_	_	_
542	biol	biol	NN	_	_	_
543	rep	rep	NN	GEN	_	_
544	2	2	CD	_	_	_
545	_	_	CD	_	_	_
546	Cy3	cy3	NN	_	_	_
547	0	0	CD	_	_	_
548	Cy5	cy5	NN	_	_	_
549	80	80	CD	_	_	_
550	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
551	Slide	Slide	NNP	_	_	_
552	11	11	CD	_	_	_
553	_	_	SYM	_	_	_
554	Anaerobic	anaerobic	JJ	_	_	_
555	culture	culture	NN	_	_	_
556	_	_	SYM	_	_	_
557	CORM-3	corm-3	NN	_	_	_
558	_	_	NN	_	_	_
559	biol	biol	NN	_	_	_
560	rep	rep	NN	GEN	_	_
561	1	1	CD	_	_	_
562	_	_	CD	_	_	_
563	Cy3	cy3	NN	_	_	_
564	20	20	CD	_	_	_
565	Cy5	cy5	NN	_	_	_
566	0	0	CD	_	_	_
567	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
568	Slide	Slide	NNP	_	_	_
569	11	11	CD	_	_	_
570	_	_	SYM	_	_	_
571	Anaerobic	anaerobic	JJ	_	_	_
572	culture	culture	NN	_	_	_
573	_	_	SYM	_	_	_
574	CORM-3	corm-3	NN	_	_	_
575	_	_	NN	_	_	_
576	biol	biol	NN	_	_	_
577	rep	rep	NN	GEN	_	_
578	1	1	CD	_	_	_
579	_	_	CD	_	_	_
580	Cy3	cy3	NN	_	_	_
581	5	5	CD	_	_	_
582	Cy5	cy5	NN	_	_	_
583	0	0	CD	_	_	_
584	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
585	Slide	Slide	NNP	_	_	_
586	11	11	CD	_	_	_
587	_	_	SYM	_	_	_
588	Anaerobic	anaerobic	JJ	_	_	_
589	culture	culture	NN	_	_	_
590	_	_	SYM	_	_	_
591	CORM-3	corm-3	NN	_	_	_
592	_	_	NN	_	_	_
593	biol	biol	NN	_	_	_
594	rep	rep	NN	GEN	_	_
595	2	2	CD	_	_	_
596	_	_	CD	_	_	_
597	Cy3	cy3	NN	_	_	_
598	10	10	CD	_	_	_
599	Cy5	cy5	NN	_	_	_
600	0	0	CD	_	_	_
601	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
602	Slide	Slide	NNP	_	_	_
603	11	11	CD	_	_	_
604	_	_	SYM	_	_	_
605	Anaerobic	anaerobic	JJ	_	_	_
606	culture	culture	NN	_	_	_
607	_	_	SYM	_	_	_
608	CORM-3	corm-3	NN	_	_	_
609	_	_	NN	_	_	_
610	biol	biol	NN	_	_	_
611	rep	rep	NN	GEN	_	_
612	2	2	CD	_	_	_
613	_	_	CD	_	_	_
614	Cy3	cy3	NN	_	_	_
615	20	20	CD	_	_	_
616	Cy5	cy5	NN	_	_	_
617	0	0	CD	_	_	_
618	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
619	Slide	Slide	NNP	_	_	_
620	11	11	CD	_	_	_
621	_	_	SYM	_	_	_
622	Anaerobic	anaerobic	JJ	_	_	_
623	culture	culture	NN	_	_	_
624	_	_	SYM	_	_	_
625	CORM-3	corm-3	NN	_	_	_
626	_	_	NN	_	_	_
627	biol	biol	NN	_	_	_
628	rep	rep	NN	GEN	_	_
629	2	2	CD	_	_	_
630	_	_	CD	_	_	_
631	Cy3	cy3	NN	_	_	_
632	2.5	2.5	CD	_	_	_
633	Cy5	cy5	NN	_	_	_
634	0	0	CD	_	_	_
635	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
636	Slide	Slide	NNP	_	_	_
637	11	11	CD	_	_	_
638	_	_	SYM	_	_	_
639	Anaerobic	anaerobic	JJ	_	_	_
640	culture	culture	NN	_	_	_
641	_	_	SYM	_	_	_
642	CORM-3	corm-3	NN	_	_	_
643	_	_	NN	_	_	_
644	biol	biol	NN	_	_	_
645	rep	rep	NN	GEN	_	_
646	2	2	CD	_	_	_
647	_	_	CD	_	_	_
648	Cy3	cy3	NN	_	_	_
649	40	40	CD	_	_	_
650	Cy5	cy5	NN	_	_	_
651	0	0	CD	_	_	_
652	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
653	Slide	Slide	NNP	_	_	_
654	11	11	CD	_	_	_
655	_	_	SYM	_	_	_
656	Anaerobic	anaerobic	JJ	_	_	_
657	culture	culture	NN	_	_	_
658	_	_	SYM	_	_	_
659	CORM-3	corm-3	NN	_	_	_
660	_	_	NN	_	_	_
661	biol	biol	NN	_	_	_
662	rep	rep	NN	GEN	_	_
663	2	2	CD	_	_	_
664	_	_	CD	_	_	_
665	Cy3	cy3	NN	_	_	_
666	5	5	CD	_	_	_
667	Cy5	cy5	NN	_	_	_
668	0	0	CD	_	_	_
669	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
670	Slide	Slide	NNP	_	_	_
671	11	11	CD	_	_	_
672	_	_	SYM	_	_	_
673	Anaerobic	anaerobic	JJ	_	_	_
674	culture	culture	NN	_	_	_
675	_	_	SYM	_	_	_
676	CORM-3	corm-3	NN	_	_	_
677	_	_	NN	_	_	_
678	biol	biol	NN	_	_	_
679	rep	rep	NN	GEN	_	_
680	2	2	CD	_	_	_
681	_	_	CD	_	_	_
682	Cy3	cy3	NN	_	_	_
683	80	80	CD	_	_	_
684	Cy5	cy5	NN	_	_	_
685	0	0	CD	_	_	_
686	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
687	Slide	Slide	NNP	_	_	_
688	12	12	CD	_	_	_
689	_	_	SYM	_	_	_
690	Anaerobic	anaerobic	JJ	_	_	_
691	culture	culture	NN	_	_	_
692	_	_	SYM	_	_	_
693	CORM-3	corm-3	NN	_	_	_
694	_	_	NN	_	_	_
695	biol	biol	NN	_	_	_
696	rep	rep	NN	GEN	_	_
697	1	1	CD	_	_	_
698	_	_	NN	_	_	_
699	Cy3	cy3	NN	_	_	_
700	0	0	CD	_	_	_
701	Cy5	cy5	NN	_	_	_
702	20	20	CD	_	_	_
703	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
704	Slide	Slide	NNP	_	_	_
705	12	12	CD	_	_	_
706	_	_	SYM	_	_	_
707	Anaerobic	anaerobic	JJ	_	_	_
708	culture	culture	NN	_	_	_
709	_	_	SYM	_	_	_
710	CORM-3	corm-3	NN	_	_	_
711	_	_	NN	_	_	_
712	biol	biol	NN	_	_	_
713	rep	rep	NN	GEN	_	_
714	1	1	CD	_	_	_
715	_	_	NN	_	_	_
716	Cy3	cy3	NN	_	_	_
717	0	0	CD	_	_	_
718	Cy5	cy5	NN	_	_	_
719	2.5	2.5	CD	_	_	_
720	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
721	Slide	Slide	NNP	_	_	_
722	12	12	CD	_	_	_
723	_	_	SYM	_	_	_
724	Anaerobic	anaerobic	JJ	_	_	_
725	culture	culture	NN	_	_	_
726	_	_	SYM	_	_	_
727	CORM-3	corm-3	NN	_	_	_
728	_	_	NN	_	_	_
729	biol	biol	NN	_	_	_
730	rep	rep	NN	GEN	_	_
731	1	1	CD	_	_	_
732	_	_	NN	_	_	_
733	Cy3	cy3	NN	_	_	_
734	0	0	CD	_	_	_
735	Cy5	cy5	NN	_	_	_
736	40	40	CD	_	_	_
737	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
738	Slide	slide	NN	_	_	_
739	12	12	CD	_	_	_
740	_	_	SYM	_	_	_
741	Anaerobic	anaerobic	JJ	_	_	_
742	culture	culture	NN	_	_	_
743	_	_	SYM	_	_	_
744	CORM-3	corm-3	NN	_	_	_
745	_	_	NN	_	_	_
746	biol	biol	NN	_	_	_
747	rep	rep	NN	GEN	_	_
748	1	1	CD	_	_	_
749	_	_	NN	_	_	_
750	Cy3	cy3	NN	_	_	_
751	0	0	CD	_	_	_
752	Cy5	cy5	NN	_	_	_
753	80	80	CD	_	_	_
754	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
755	Slide	Slide	NNP	_	_	_
756	12	12	CD	_	_	_
757	_	_	SYM	_	_	_
758	Anaerobic	anaerobic	JJ	_	_	_
759	culture	culture	NN	_	_	_
760	_	_	SYM	_	_	_
761	CORM-3	corm-3	NN	_	_	_
762	_	_	NN	_	_	_
763	biol	biol	NN	_	_	_
764	rep	rep	NN	GEN	_	_
765	1	1	CD	_	_	_
766	_	_	CD	_	_	_
767	Cy3	cy3	NN	_	_	_
768	10	10	CD	_	_	_
769	Cy5	cy5	NN	_	_	_
770	0	0	CD	_	_	_
771	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
772	Slide	Slide	NNP	_	_	_
773	12	12	CD	_	_	_
774	_	_	SYM	_	_	_
775	Anaerobic	anaerobic	JJ	_	_	_
776	culture	culture	NN	_	_	_
777	_	_	SYM	_	_	_
778	CORM-3	corm-3	NN	_	_	_
779	_	_	NN	_	_	_
780	biol	biol	NN	_	_	_
781	rep	rep	NN	GEN	_	_
782	1	1	CD	_	_	_
783	_	_	CD	_	_	_
784	Cy3	cy3	NN	_	_	_
785	2.5	2.5	CD	_	_	_
786	Cy5	cy5	NN	_	_	_
787	0	0	CD	_	_	_
788	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
789	Slide	Slide	NNP	_	_	_
790	12	12	CD	_	_	_
791	_	_	SYM	_	_	_
792	Anaerobic	anaerobic	JJ	_	_	_
793	culture	culture	NN	_	_	_
794	_	_	SYM	_	_	_
795	CORM-3	corm-3	NN	_	_	_
796	_	_	NN	_	_	_
797	biol	biol	NN	_	_	_
798	rep	rep	NN	GEN	_	_
799	1	1	CD	_	_	_
800	_	_	CD	_	_	_
801	Cy3	cy3	NN	_	_	_
802	40	40	CD	_	_	_
803	Cy5	cy5	NN	_	_	_
804	0	0	CD	_	_	_
805	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
806	Slide	Slide	NNP	_	_	_
807	12	12	CD	_	_	_
808	_	_	SYM	_	_	_
809	Anaerobic	anaerobic	JJ	_	_	_
810	culture	culture	NN	_	_	_
811	_	_	SYM	_	_	_
812	CORM-3	corm-3	NN	_	_	_
813	_	_	NN	_	_	_
814	biol	biol	NN	_	_	_
815	rep	rep	NN	GEN	_	_
816	1	1	CD	_	_	_
817	_	_	CD	_	_	_
818	Cy3	cy3	NN	_	_	_
819	80	80	CD	_	_	_
820	Cy5	cy5	NN	_	_	_
821	0	0	CD	_	_	_
822	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
823	Slide	Slide	NNP	_	_	_
824	18	18	CD	_	_	_
825	_	_	SYM	_	_	_
826	Aerobic	aerobic	JJ	_	_	_
827	culture	culture	NN	_	_	_
828	_	_	SYM	_	_	_
829	CORM-3	corm-3	NN	_	_	_
830	_	_	NN	_	_	_
831	biol	biol	NN	_	_	_
832	rep	rep	NN	GEN	_	_
833	1	1	CD	_	_	_
834	_	_	NN	_	_	_
835	Cy3	cy3	NN	_	_	_
836	0	0	CD	_	_	_
837	Cy5	cy5	NN	_	_	_
838	10	10	CD	_	_	_
839	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
840	Slide	slide	NN	_	_	_
841	18	18	CD	_	_	_
842	_	_	SYM	_	_	_
843	Aerobic	aerobic	JJ	_	_	_
844	culture	culture	NN	_	_	_
845	_	_	SYM	_	_	_
846	CORM-3	corm-3	NN	_	_	_
847	_	_	NN	_	_	_
848	biol	biol	NN	_	_	_
849	rep	rep	NN	GEN	_	_
850	1	1	CD	_	_	_
851	_	_	NN	_	_	_
852	Cy3	cy3	NN	_	_	_
853	0	0	CD	_	_	_
854	Cy5	cy5	NN	_	_	_
855	20	20	CD	_	_	_
856	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
857	Slide	slide	NN	_	_	_
858	18	18	CD	_	_	_
859	_	_	SYM	_	_	_
860	Aerobic	aerobic	JJ	_	_	_
861	culture	culture	NN	_	_	_
862	_	_	SYM	_	_	_
863	CORM-3	corm-3	NN	_	_	_
864	_	_	NN	_	_	_
865	biol	biol	NN	_	_	_
866	rep	rep	NN	GEN	_	_
867	1	1	CD	_	_	_
868	_	_	NN	_	_	_
869	Cy3	cy3	NN	_	_	_
870	0	0	CD	_	_	_
871	Cy5	cy5	NN	_	_	_
872	2.5	2.5	CD	_	_	_
873	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
874	Slide	Slide	NNP	_	_	_
875	18	18	CD	_	_	_
876	_	_	SYM	_	_	_
877	Aerobic	aerobic	JJ	_	_	_
878	culture	culture	NN	_	_	_
879	_	_	SYM	_	_	_
880	CORM-3	corm-3	NN	_	_	_
881	_	_	NN	_	_	_
882	biol	biol	NN	_	_	_
883	rep	rep	NN	GEN	_	_
884	1	1	CD	_	_	_
885	_	_	NN	_	_	_
886	Cy3	cy3	NN	_	_	_
887	0	0	CD	_	_	_
888	Cy5	cy5	NN	_	_	_
889	40	40	CD	_	_	_
890	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
891	Slide	slide	NN	_	_	_
892	18	18	CD	_	_	_
893	_	_	SYM	_	_	_
894	Aerobic	aerobic	JJ	_	_	_
895	culture	culture	NN	_	_	_
896	_	_	SYM	_	_	_
897	CORM-3	corm-3	NN	_	_	_
898	_	_	NN	_	_	_
899	biol	biol	NN	_	_	_
900	rep	rep	NN	GEN	_	_
901	1	1	CD	_	_	_
902	_	_	NN	_	_	_
903	Cy3	cy3	NN	_	_	_
904	0	0	CD	_	_	_
905	Cy5	cy5	NN	_	_	_
906	5	5	CD	_	_	_
907	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
908	Slide	Slide	NNP	_	_	_
909	18	18	CD	_	_	_
910	_	_	SYM	_	_	_
911	Aerobic	aerobic	JJ	_	_	_
912	culture	culture	NN	_	_	_
913	_	_	SYM	_	_	_
914	CORM-3	corm-3	NN	_	_	_
915	_	_	NN	_	_	_
916	biol	biol	NN	_	_	_
917	rep	rep	NN	GEN	_	_
918	1	1	CD	_	_	_
919	_	_	NN	_	_	_
920	Cy3	cy3	NN	_	_	_
921	0	0	CD	_	_	_
922	Cy5	cy5	NN	_	_	_
923	80	80	CD	_	_	_
924	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
925	Slide	Slide	NNP	_	_	_
926	18	18	CD	_	_	_
927	_	_	SYM	_	_	_
928	Aerobic	aerobic	JJ	_	_	_
929	culture	culture	NN	_	_	_
930	_	_	SYM	_	_	_
931	CORM-3	corm-3	NN	_	_	_
932	_	_	NN	_	_	_
933	biol	biol	NN	_	_	_
934	rep	rep	NN	GEN	_	_
935	1	1	CD	_	_	_
936	_	_	CD	_	_	_
937	Cy3	cy3	NN	_	_	_
938	2.5	2.5	CD	_	_	_
939	Cy5	cy5	NN	_	_	_
940	0	0	CD	_	_	_
941	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
942	Slide	Slide	NNP	_	_	_
943	18	18	CD	_	_	_
944	_	_	SYM	_	_	_
945	Aerobic	aerobic	JJ	_	_	_
946	culture	culture	NN	_	_	_
947	_	_	SYM	_	_	_
948	CORM-3	corm-3	NN	_	_	_
949	_	_	NN	_	_	_
950	biol	biol	NN	_	_	_
951	rep	rep	NN	GEN	_	_
952	1	1	CD	_	_	_
953	_	_	CD	_	_	_
954	Cy3	cy3	NN	_	_	_
955	5	5	CD	_	_	_
956	Cy5	cy5	NN	_	_	_
957	0	0	CD	_	_	_
958	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
959	Slide	Slide	NNP	_	_	_
960	19	19	CD	_	_	_
961	_	_	SYM	_	_	_
962	Aerobic	aerobic	JJ	_	_	_
963	culture	culture	NN	_	_	_
964	_	_	SYM	_	_	_
965	CORM-3	corm-3	NN	_	_	_
966	_	_	NN	_	_	_
967	biol	biol	NN	_	_	_
968	rep	rep	NN	GEN	_	_
969	1	1	CD	_	_	_
970	_	_	CD	_	_	_
971	Cy3	cy3	NN	_	_	_
972	10	10	CD	_	_	_
973	Cy5	cy5	NN	_	_	_
974	0	0	CD	_	_	_
975	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
976	Slide	Slide	NNP	_	_	_
977	19	19	CD	_	_	_
978	_	_	SYM	_	_	_
979	Aerobic	aerobic	JJ	_	_	_
980	culture	culture	NN	_	_	_
981	_	_	SYM	_	_	_
982	CORM-3	corm-3	NN	_	_	_
983	_	_	NN	_	_	_
984	biol	biol	NN	_	_	_
985	rep	rep	NN	GEN	_	_
986	1	1	CD	_	_	_
987	_	_	CD	_	_	_
988	Cy3	cy3	NN	_	_	_
989	20	20	CD	_	_	_
990	Cy5	cy5	NN	_	_	_
991	0	0	CD	_	_	_
992	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
993	Slide	Slide	NNP	_	_	_
994	19	19	CD	_	_	_
995	_	_	SYM	_	_	_
996	Aerobic	aerobic	JJ	_	_	_
997	culture	culture	NN	_	_	_
998	_	_	SYM	_	_	_
999	CORM-3	corm-3	NN	_	_	_
1000	_	_	NN	_	_	_
1001	biol	biol	NN	_	_	_
1002	rep	rep	NN	GEN	_	_
1003	1	1	CD	_	_	_
1004	_	_	CD	_	_	_
1005	Cy3	cy3	NN	_	_	_
1006	40	40	CD	_	_	_
1007	Cy5	cy5	NN	_	_	_
1008	0	0	CD	_	_	_
1009	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1010	Slide	Slide	NNP	_	_	_
1011	19	19	CD	_	_	_
1012	_	_	SYM	_	_	_
1013	Aerobic	aerobic	JJ	_	_	_
1014	culture	culture	NN	_	_	_
1015	_	_	SYM	_	_	_
1016	CORM-3	corm-3	NN	_	_	_
1017	_	_	NN	_	_	_
1018	biol	biol	NN	_	_	_
1019	rep	rep	NN	GEN	_	_
1020	1	1	CD	_	_	_
1021	_	_	CD	_	_	_
1022	Cy3	cy3	NN	_	_	_
1023	80	80	CD	_	_	_
1024	Cy5	cy5	NN	_	_	_
1025	0	0	CD	_	_	_
1026	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1027	Slide	Slide	NNP	_	_	_
1028	19	19	CD	_	_	_
1029	_	_	SYM	_	_	_
1030	Aerobic	aerobic	JJ	_	_	_
1031	culture	culture	NN	_	_	_
1032	_	_	SYM	_	_	_
1033	CORM-3	corm-3	NN	_	_	_
1034	_	_	NN	_	_	_
1035	biol	biol	NN	_	_	_
1036	rep	rep	NN	GEN	_	_
1037	2	2	CD	_	_	_
1038	_	_	CD	_	_	_
1039	Cy3	cy3	NN	_	_	_
1040	0	0	CD	_	_	_
1041	Cy5	cy5	NN	_	_	_
1042	10	10	CD	_	_	_
1043	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1044	Slide	slide	NN	_	_	_
1045	19	19	CD	_	_	_
1046	_	_	SYM	_	_	_
1047	Aerobic	aerobic	JJ	_	_	_
1048	culture	culture	NN	_	_	_
1049	_	_	SYM	_	_	_
1050	CORM-3	corm-3	NN	_	_	_
1051	_	_	NN	_	_	_
1052	biol	biol	NN	_	_	_
1053	rep	rep	NN	GEN	_	_
1054	2	2	CD	_	_	_
1055	_	_	CD	_	_	_
1056	Cy3	cy3	NN	_	_	_
1057	0	0	CD	_	_	_
1058	Cy5	cy5	NN	_	_	_
1059	20	20	CD	_	_	_
1060	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1061	Slide	slide	NN	_	_	_
1062	19	19	CD	_	_	_
1063	_	_	SYM	_	_	_
1064	Aerobic	aerobic	JJ	_	_	_
1065	culture	culture	NN	_	_	_
1066	_	_	SYM	_	_	_
1067	CORM-3	corm-3	NN	_	_	_
1068	_	_	NN	_	_	_
1069	biol	biol	NN	_	_	_
1070	rep	rep	NN	GEN	_	_
1071	2	2	CD	_	_	_
1072	_	_	CD	_	_	_
1073	Cy3	cy3	NN	_	_	_
1074	0	0	CD	_	_	_
1075	Cy5	cy5	NN	_	_	_
1076	2.5	2.5	CD	_	_	_
1077	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1078	Slide	Slide	NNP	_	_	_
1079	19	19	CD	_	_	_
1080	_	_	SYM	_	_	_
1081	Aerobic	aerobic	JJ	_	_	_
1082	culture	culture	NN	_	_	_
1083	_	_	SYM	_	_	_
1084	CORM-3	corm-3	NN	_	_	_
1085	_	_	NN	_	_	_
1086	biol	biol	NN	_	_	_
1087	rep	rep	NN	GEN	_	_
1088	2	2	CD	_	_	_
1089	_	_	CD	_	_	_
1090	Cy3	cy3	NN	_	_	_
1091	0	0	CD	_	_	_
1092	Cy5	cy5	NN	_	_	_
1093	5	5	CD	_	_	_
1094	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1095	Slide	Slide	NNP	_	_	_
1096	20	20	CD	_	_	_
1097	_	_	SYM	_	_	_
1098	Aerobic	aerobic	JJ	_	_	_
1099	culture	culture	NN	_	_	_
1100	_	_	SYM	_	_	_
1101	CORM-3	corm-3	NN	_	_	_
1102	_	_	NN	_	_	_
1103	biol	biol	NN	_	_	_
1104	rep	rep	NN	GEN	_	_
1105	2	2	CD	_	_	_
1106	_	_	CD	_	_	_
1107	Cy3	cy3	NN	_	_	_
1108	0	0	CD	_	_	_
1109	Cy5	cy5	NN	_	_	_
1110	40	40	CD	_	_	_
1111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1112	Slide	slide	NN	_	_	_
1113	20	20	CD	_	_	_
1114	_	_	SYM	_	_	_
1115	Aerobic	aerobic	JJ	_	_	_
1116	culture	culture	NN	_	_	_
1117	_	_	SYM	_	_	_
1118	CORM-3	corm-3	NN	_	_	_
1119	_	_	NN	_	_	_
1120	biol	biol	NN	_	_	_
1121	rep	rep	NN	GEN	_	_
1122	2	2	CD	_	_	_
1123	_	_	CD	_	_	_
1124	Cy3	cy3	NN	_	_	_
1125	0	0	CD	_	_	_
1126	Cy5	cy5	NN	_	_	_
1127	80	80	CD	_	_	_
1128	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1129	Slide	Slide	NNP	_	_	_
1130	20	20	CD	_	_	_
1131	_	_	SYM	_	_	_
1132	Aerobic	aerobic	JJ	_	_	_
1133	culture	culture	NN	_	_	_
1134	_	_	SYM	_	_	_
1135	CORM-3	corm-3	NN	_	_	_
1136	_	_	NN	_	_	_
1137	biol	biol	NN	_	_	_
1138	rep	rep	NN	GEN	_	_
1139	2	2	CD	_	_	_
1140	_	_	CD	_	_	_
1141	Cy3	cy3	NN	_	_	_
1142	10	10	CD	_	_	_
1143	Cy5	cy5	NN	_	_	_
1144	0	0	CD	_	_	_
1145	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1146	Slide	Slide	NNP	_	_	_
1147	20	20	CD	_	_	_
1148	_	_	SYM	_	_	_
1149	Aerobic	aerobic	JJ	_	_	_
1150	culture	culture	NN	_	_	_
1151	_	_	SYM	_	_	_
1152	CORM-3	corm-3	NN	_	_	_
1153	_	_	NN	_	_	_
1154	biol	biol	NN	_	_	_
1155	rep	rep	NN	GEN	_	_
1156	2	2	CD	_	_	_
1157	_	_	CD	_	_	_
1158	Cy3	cy3	NN	_	_	_
1159	20	20	CD	_	_	_
1160	Cy5	cy5	NN	_	_	_
1161	0	0	CD	_	_	_
1162	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1163	Slide	Slide	NNP	_	_	_
1164	20	20	CD	_	_	_
1165	_	_	SYM	_	_	_
1166	Aerobic	aerobic	JJ	_	_	_
1167	culture	culture	NN	_	_	_
1168	_	_	SYM	_	_	_
1169	CORM-3	corm-3	NN	_	_	_
1170	_	_	NN	_	_	_
1171	biol	biol	NN	_	_	_
1172	rep	rep	NN	GEN	_	_
1173	2	2	CD	_	_	_
1174	_	_	CD	_	_	_
1175	Cy3	cy3	NN	_	_	_
1176	2.5	2.5	CD	_	_	_
1177	Cy5	cy5	NN	_	_	_
1178	0	0	CD	_	_	_
1179	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1180	Slide	Slide	NNP	_	_	_
1181	20	20	CD	_	_	_
1182	_	_	SYM	_	_	_
1183	Aerobic	aerobic	JJ	_	_	_
1184	culture	culture	NN	_	_	_
1185	_	_	SYM	_	_	_
1186	CORM-3	corm-3	NN	_	_	_
1187	_	_	NN	_	_	_
1188	biol	biol	NN	_	_	_
1189	rep	rep	NN	GEN	_	_
1190	2	2	CD	_	_	_
1191	_	_	CD	_	_	_
1192	Cy3	cy3	NN	_	_	_
1193	40	40	CD	_	_	_
1194	Cy5	cy5	NN	_	_	_
1195	0	0	CD	_	_	_
1196	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1197	Slide	Slide	NNP	_	_	_
1198	20	20	CD	_	_	_
1199	_	_	SYM	_	_	_
1200	Aerobic	aerobic	JJ	_	_	_
1201	culture	culture	NN	_	_	_
1202	_	_	SYM	_	_	_
1203	CORM-3	corm-3	NN	_	_	_
1204	_	_	NN	_	_	_
1205	biol	biol	NN	_	_	_
1206	rep	rep	NN	GEN	_	_
1207	2	2	CD	_	_	_
1208	_	_	CD	_	_	_
1209	Cy3	cy3	NN	_	_	_
1210	5	5	CD	_	_	_
1211	Cy5	cy5	NN	_	_	_
1212	0	0	CD	_	_	_
1213	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1214	Slide	Slide	NNP	_	_	_
1215	20	20	CD	_	_	_
1216	_	_	SYM	_	_	_
1217	Aerobic	aerobic	JJ	_	_	_
1218	culture	culture	NN	_	_	_
1219	_	_	SYM	_	_	_
1220	CORM-3	corm-3	NN	_	_	_
1221	_	_	NN	_	_	_
1222	biol	biol	NN	_	_	_
1223	rep	rep	NN	GEN	_	_
1224	2	2	CD	_	_	_
1225	_	_	CD	_	_	_
1226	Cy3	cy3	NN	_	_	_
1227	80	80	CD	_	_	_
1228	Cy5	cy5	NN	_	_	_
1229	0	0	CD	_	_	_
1230	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1231	Slide	Slide	NNP	_	_	_
1232	25	25	CD	_	_	_
1233	_	_	SYM	_	_	_
1234	Aerobic	aerobic	JJ	_	_	_
1235	culture	culture	NN	_	_	_
1236	_	_	SYM	_	_	_
1237	iCORM-3	icorm-3	NN	_	_	_
1238	_	_	NN	_	_	_
1239	biol	biol	NN	_	_	_
1240	rep	rep	NN	GEN	_	_
1241	1	1	CD	_	_	_
1242	_	_	NN	_	_	_
1243	Cy3	cy3	NN	_	_	_
1244	0	0	CD	_	_	_
1245	Cy5	cy5	NN	_	_	_
1246	10	10	CD	_	_	_
1247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1248	Slide	slide	NN	_	_	_
1249	25	25	CD	_	_	_
1250	_	_	SYM	_	_	_
1251	Aerobic	aerobic	JJ	_	_	_
1252	culture	culture	NN	_	_	_
1253	_	_	SYM	_	_	_
1254	iCORM-3	icorm-3	NN	_	_	_
1255	_	_	NN	_	_	_
1256	biol	biol	NN	_	_	_
1257	rep	rep	NN	GEN	_	_
1258	1	1	CD	_	_	_
1259	_	_	NN	_	_	_
1260	Cy3	cy3	NN	_	_	_
1261	0	0	CD	_	_	_
1262	Cy5	cy5	NN	_	_	_
1263	20	20	CD	_	_	_
1264	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1265	Slide	slide	NN	_	_	_
1266	25	25	CD	_	_	_
1267	_	_	SYM	_	_	_
1268	Aerobic	aerobic	JJ	_	_	_
1269	culture	culture	NN	_	_	_
1270	_	_	SYM	_	_	_
1271	iCORM-3	icorm-3	NN	_	_	_
1272	_	_	NN	_	_	_
1273	biol	biol	NN	_	_	_
1274	rep	rep	NN	GEN	_	_
1275	1	1	CD	_	_	_
1276	_	_	NN	_	_	_
1277	Cy3	cy3	NN	_	_	_
1278	0	0	CD	_	_	_
1279	Cy5	cy5	NN	_	_	_
1280	2.5	2.5	CD	_	_	_
1281	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1282	Slide	Slide	NNP	_	_	_
1283	25	25	CD	_	_	_
1284	_	_	SYM	_	_	_
1285	Aerobic	aerobic	JJ	_	_	_
1286	culture	culture	NN	_	_	_
1287	_	_	SYM	_	_	_
1288	iCORM-3	icorm-3	NN	_	_	_
1289	_	_	NN	_	_	_
1290	biol	biol	NN	_	_	_
1291	rep	rep	NN	GEN	_	_
1292	1	1	CD	_	_	_
1293	_	_	NN	_	_	_
1294	Cy3	cy3	NN	_	_	_
1295	0	0	CD	_	_	_
1296	Cy5	cy5	NN	_	_	_
1297	40	40	CD	_	_	_
1298	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1299	Slide	slide	NN	_	_	_
1300	25	25	CD	_	_	_
1301	_	_	SYM	_	_	_
1302	Aerobic	aerobic	JJ	_	_	_
1303	culture	culture	NN	_	_	_
1304	_	_	SYM	_	_	_
1305	iCORM-3	icorm-3	NN	_	_	_
1306	_	_	NN	_	_	_
1307	biol	biol	NN	_	_	_
1308	rep	rep	NN	GEN	_	_
1309	1	1	CD	_	_	_
1310	_	_	NN	_	_	_
1311	Cy3	cy3	NN	_	_	_
1312	0	0	CD	_	_	_
1313	Cy5	cy5	NN	_	_	_
1314	5	5	CD	_	_	_
1315	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1316	Slide	Slide	NNP	_	_	_
1317	25	25	CD	_	_	_
1318	_	_	SYM	_	_	_
1319	Aerobic	aerobic	JJ	_	_	_
1320	culture	culture	NN	_	_	_
1321	_	_	SYM	_	_	_
1322	iCORM-3	icorm-3	NN	_	_	_
1323	_	_	NN	_	_	_
1324	biol	biol	NN	_	_	_
1325	rep	rep	NN	GEN	_	_
1326	1	1	CD	_	_	_
1327	_	_	NN	_	_	_
1328	Cy3	cy3	NN	_	_	_
1329	0	0	CD	_	_	_
1330	Cy5	cy5	NN	_	_	_
1331	80	80	CD	_	_	_
1332	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1333	Slide	Slide	NNP	_	_	_
1334	25	25	CD	_	_	_
1335	_	_	SYM	_	_	_
1336	Aerobic	aerobic	JJ	_	_	_
1337	culture	culture	NN	_	_	_
1338	_	_	SYM	_	_	_
1339	iCORM-3	icorm-3	NN	_	_	_
1340	_	_	NN	_	_	_
1341	biol	biol	NN	_	_	_
1342	rep	rep	NN	GEN	_	_
1343	1	1	CD	_	_	_
1344	_	_	CD	_	_	_
1345	Cy3	cy3	NN	_	_	_
1346	2.5	2.5	CD	_	_	_
1347	Cy5	cy5	NN	_	_	_
1348	0	0	CD	_	_	_
1349	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1350	Slide	Slide	NNP	_	_	_
1351	25	25	CD	_	_	_
1352	_	_	SYM	_	_	_
1353	Aerobic	aerobic	JJ	_	_	_
1354	culture	culture	NN	_	_	_
1355	_	_	SYM	_	_	_
1356	iCORM-3	icorm-3	NN	_	_	_
1357	_	_	NN	_	_	_
1358	biol	biol	NN	_	_	_
1359	rep	rep	NN	GEN	_	_
1360	1	1	CD	_	_	_
1361	_	_	CD	_	_	_
1362	Cy3	cy3	NN	_	_	_
1363	5	5	CD	_	_	_
1364	Cy5	cy5	NN	_	_	_
1365	0	0	CD	_	_	_
1366	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1367	Slide	Slide	NNP	_	_	_
1368	26	26	CD	_	_	_
1369	_	_	SYM	_	_	_
1370	Aerobic	aerobic	JJ	_	_	_
1371	culture	culture	NN	_	_	_
1372	_	_	SYM	_	_	_
1373	iCORM-3	icorm-3	NN	_	_	_
1374	_	_	NN	_	_	_
1375	biol	biol	NN	_	_	_
1376	rep	rep	NN	GEN	_	_
1377	1	1	CD	_	_	_
1378	_	_	CD	_	_	_
1379	Cy3	cy3	NN	_	_	_
1380	10	10	CD	_	_	_
1381	Cy5	cy5	NN	_	_	_
1382	0	0	CD	_	_	_
1383	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1384	Slide	Slide	NNP	_	_	_
1385	26	26	CD	_	_	_
1386	_	_	SYM	_	_	_
1387	Aerobic	aerobic	JJ	_	_	_
1388	culture	culture	NN	_	_	_
1389	_	_	SYM	_	_	_
1390	iCORM-3	icorm-3	NN	_	_	_
1391	_	_	NN	_	_	_
1392	biol	biol	NN	_	_	_
1393	rep	rep	NN	GEN	_	_
1394	1	1	CD	_	_	_
1395	_	_	CD	_	_	_
1396	Cy3	cy3	NN	_	_	_
1397	20	20	CD	_	_	_
1398	Cy5	cy5	NN	_	_	_
1399	0	0	CD	_	_	_
1400	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1401	Slide	Slide	NNP	_	_	_
1402	26	26	CD	_	_	_
1403	_	_	SYM	_	_	_
1404	Aerobic	aerobic	JJ	_	_	_
1405	culture	culture	NN	_	_	_
1406	_	_	SYM	_	_	_
1407	iCORM-3	icorm-3	NN	_	_	_
1408	_	_	NN	_	_	_
1409	biol	biol	NN	_	_	_
1410	rep	rep	NN	GEN	_	_
1411	1	1	CD	_	_	_
1412	_	_	CD	_	_	_
1413	Cy3	cy3	NN	_	_	_
1414	40	40	CD	_	_	_
1415	Cy5	cy5	NN	_	_	_
1416	0	0	CD	_	_	_
1417	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1418	Slide	Slide	NNP	_	_	_
1419	26	26	CD	_	_	_
1420	_	_	SYM	_	_	_
1421	Aerobic	aerobic	JJ	_	_	_
1422	culture	culture	NN	_	_	_
1423	_	_	SYM	_	_	_
1424	iCORM-3	icorm-3	NN	_	_	_
1425	_	_	NN	_	_	_
1426	biol	biol	NN	_	_	_
1427	rep	rep	NN	GEN	_	_
1428	1	1	CD	_	_	_
1429	_	_	CD	_	_	_
1430	Cy3	cy3	NN	_	_	_
1431	80	80	CD	_	_	_
1432	Cy5	cy5	NN	_	_	_
1433	0	0	CD	_	_	_
1434	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1435	Slide	Slide	NNP	_	_	_
1436	26	26	CD	_	_	_
1437	_	_	SYM	_	_	_
1438	Aerobic	aerobic	JJ	_	_	_
1439	culture	culture	NN	_	_	_
1440	_	_	SYM	_	_	_
1441	iCORM-3	icorm-3	NN	_	_	_
1442	_	_	NN	_	_	_
1443	biol	biol	NN	_	_	_
1444	rep	rep	NN	GEN	_	_
1445	2	2	CD	_	_	_
1446	_	_	CD	_	_	_
1447	Cy3	cy3	NN	_	_	_
1448	0	0	CD	_	_	_
1449	Cy5	cy5	NN	_	_	_
1450	10	10	CD	_	_	_
1451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1452	Slide	slide	NN	_	_	_
1453	26	26	CD	_	_	_
1454	_	_	SYM	_	_	_
1455	Aerobic	aerobic	JJ	_	_	_
1456	culture	culture	NN	_	_	_
1457	_	_	SYM	_	_	_
1458	iCORM-3	icorm-3	NN	_	_	_
1459	_	_	NN	_	_	_
1460	biol	biol	NN	_	_	_
1461	rep	rep	NN	GEN	_	_
1462	2	2	CD	_	_	_
1463	_	_	CD	_	_	_
1464	Cy3	cy3	NN	_	_	_
1465	0	0	CD	_	_	_
1466	Cy5	cy5	NN	_	_	_
1467	20	20	CD	_	_	_
1468	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1469	Slide	slide	NN	_	_	_
1470	26	26	CD	_	_	_
1471	_	_	SYM	_	_	_
1472	Aerobic	aerobic	JJ	_	_	_
1473	culture	culture	NN	_	_	_
1474	_	_	SYM	_	_	_
1475	iCORM-3	icorm-3	NN	_	_	_
1476	_	_	NN	_	_	_
1477	biol	biol	NN	_	_	_
1478	rep	rep	NN	GEN	_	_
1479	2	2	CD	_	_	_
1480	_	_	CD	_	_	_
1481	Cy3	cy3	NN	_	_	_
1482	0	0	CD	_	_	_
1483	Cy5	cy5	NN	_	_	_
1484	2.5	2.5	CD	_	_	_
1485	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1486	Slide	Slide	NNP	_	_	_
1487	26	26	CD	_	_	_
1488	_	_	SYM	_	_	_
1489	Aerobic	aerobic	JJ	_	_	_
1490	culture	culture	NN	_	_	_
1491	_	_	SYM	_	_	_
1492	iCORM-3	icorm-3	NN	_	_	_
1493	_	_	NN	_	_	_
1494	biol	biol	NN	_	_	_
1495	rep	rep	NN	GEN	_	_
1496	2	2	CD	_	_	_
1497	_	_	CD	_	_	_
1498	Cy3	cy3	NN	_	_	_
1499	0	0	CD	_	_	_
1500	Cy5	cy5	NN	_	_	_
1501	5	5	CD	_	_	_
1502	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1503	Slide	Slide	NNP	_	_	_
1504	27	27	CD	_	_	_
1505	_	_	SYM	_	_	_
1506	Aerobic	aerobic	JJ	_	_	_
1507	culture	culture	NN	_	_	_
1508	_	_	SYM	_	_	_
1509	iCORM-3	icorm-3	NN	_	_	_
1510	_	_	NN	_	_	_
1511	biol	biol	NN	_	_	_
1512	rep	rep	NN	GEN	_	_
1513	2	2	CD	_	_	_
1514	_	_	CD	_	_	_
1515	Cy3	cy3	NN	_	_	_
1516	0	0	CD	_	_	_
1517	Cy5	cy5	NN	_	_	_
1518	40	40	CD	_	_	_
1519	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1520	Slide	slide	NN	_	_	_
1521	27	27	CD	_	_	_
1522	_	_	SYM	_	_	_
1523	Aerobic	aerobic	JJ	_	_	_
1524	culture	culture	NN	_	_	_
1525	_	_	SYM	_	_	_
1526	iCORM-3	icorm-3	NN	_	_	_
1527	_	_	NN	_	_	_
1528	biol	biol	NN	_	_	_
1529	rep	rep	NN	GEN	_	_
1530	2	2	CD	_	_	_
1531	_	_	CD	_	_	_
1532	Cy3	cy3	NN	_	_	_
1533	0	0	CD	_	_	_
1534	Cy5	cy5	NN	_	_	_
1535	80	80	CD	_	_	_
1536	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1537	Slide	Slide	NNP	_	_	_
1538	27	27	CD	_	_	_
1539	_	_	SYM	_	_	_
1540	Aerobic	aerobic	JJ	_	_	_
1541	culture	culture	NN	_	_	_
1542	_	_	SYM	_	_	_
1543	iCORM-3	icorm-3	NN	_	_	_
1544	_	_	NN	_	_	_
1545	biol	biol	NN	_	_	_
1546	rep	rep	NN	GEN	_	_
1547	2	2	CD	_	_	_
1548	_	_	CD	_	_	_
1549	Cy3	cy3	NN	_	_	_
1550	10	10	CD	_	_	_
1551	Cy5	cy5	NN	_	_	_
1552	0	0	CD	_	_	_
1553	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1554	Slide	Slide	NNP	_	_	_
1555	27	27	CD	_	_	_
1556	_	_	SYM	_	_	_
1557	Aerobic	aerobic	JJ	_	_	_
1558	culture	culture	NN	_	_	_
1559	_	_	SYM	_	_	_
1560	iCORM-3	icorm-3	NN	_	_	_
1561	_	_	NN	_	_	_
1562	biol	biol	NN	_	_	_
1563	rep	rep	NN	GEN	_	_
1564	2	2	CD	_	_	_
1565	_	_	CD	_	_	_
1566	Cy3	cy3	NN	_	_	_
1567	20	20	CD	_	_	_
1568	Cy5	cy5	NN	_	_	_
1569	0	0	CD	_	_	_
1570	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1571	Slide	Slide	NNP	_	_	_
1572	27	27	CD	_	_	_
1573	_	_	SYM	_	_	_
1574	Aerobic	aerobic	JJ	_	_	_
1575	culture	culture	NN	_	_	_
1576	_	_	SYM	_	_	_
1577	iCORM-3	icorm-3	NN	_	_	_
1578	_	_	NN	_	_	_
1579	biol	biol	NN	_	_	_
1580	rep	rep	NN	GEN	_	_
1581	2	2	CD	_	_	_
1582	_	_	CD	_	_	_
1583	Cy3	cy3	NN	_	_	_
1584	2.5	2.5	CD	_	_	_
1585	Cy5	cy5	NN	_	_	_
1586	0	0	CD	_	_	_
1587	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1588	Slide	Slide	NNP	_	_	_
1589	27	27	CD	_	_	_
1590	_	_	SYM	_	_	_
1591	Aerobic	aerobic	JJ	_	_	_
1592	culture	culture	NN	_	_	_
1593	_	_	SYM	_	_	_
1594	iCORM-3	icorm-3	NN	_	_	_
1595	_	_	NN	_	_	_
1596	biol	biol	NN	_	_	_
1597	rep	rep	NN	GEN	_	_
1598	2	2	CD	_	_	_
1599	_	_	CD	_	_	_
1600	Cy3	cy3	NN	_	_	_
1601	40	40	CD	_	_	_
1602	Cy5	cy5	NN	_	_	_
1603	0	0	CD	_	_	_
1604	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1605	Slide	Slide	NNP	_	_	_
1606	27	27	CD	_	_	_
1607	_	_	SYM	_	_	_
1608	Aerobic	aerobic	JJ	_	_	_
1609	culture	culture	NN	_	_	_
1610	_	_	SYM	_	_	_
1611	iCORM-3	icorm-3	NN	_	_	_
1612	_	_	NN	_	_	_
1613	biol	biol	NN	_	_	_
1614	rep	rep	NN	GEN	_	_
1615	2	2	CD	_	_	_
1616	_	_	CD	_	_	_
1617	Cy3	cy3	NN	_	_	_
1618	5	5	CD	_	_	_
1619	Cy5	cy5	NN	_	_	_
1620	0	0	CD	_	_	_
1621	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1622	Slide	Slide	NNP	_	_	_
1623	27	27	CD	_	_	_
1624	_	_	SYM	_	_	_
1625	Aerobic	aerobic	JJ	_	_	_
1626	culture	culture	NN	_	_	_
1627	_	_	SYM	_	_	_
1628	iCORM-3	icorm-3	NN	_	_	_
1629	_	_	NN	_	_	_
1630	biol	biol	NN	_	_	_
1631	rep	rep	NN	GEN	_	_
1632	2	2	CD	_	_	_
1633	_	_	CD	_	_	_
1634	Cy3	cy3	NN	_	_	_
1635	80	80	CD	_	_	_
1636	Cy5	cy5	NN	_	_	_
1637	0	0	CD	_	_	_
1638	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1639	Slide	Slide	NNP	_	_	_
1640	28	28	CD	_	_	_
1641	_	_	SYM	_	_	_
1642	Anaerobic	anaerobic	JJ	_	_	_
1643	culture	culture	NN	_	_	_
1644	_	_	SYM	_	_	_
1645	iCORM-3	icorm-3	NN	_	_	_
1646	_	_	NN	_	_	_
1647	biol	biol	NN	_	_	_
1648	rep	rep	NN	GEN	_	_
1649	1	1	CD	_	_	_
1650	_	_	NN	_	_	_
1651	Cy3	cy3	NN	_	_	_
1652	0	0	CD	_	_	_
1653	Cy5	cy5	NN	_	_	_
1654	2.5	2.5	CD	_	_	_
1655	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1656	Slide	Slide	NNP	_	_	_
1657	28	28	CD	_	_	_
1658	_	_	SYM	_	_	_
1659	Anaerobic	anaerobic	JJ	_	_	_
1660	culture	culture	NN	_	_	_
1661	_	_	SYM	_	_	_
1662	iCORM-3	icorm-3	NN	_	_	_
1663	_	_	NN	_	_	_
1664	biol	biol	NN	_	_	_
1665	rep	rep	NN	GEN	_	_
1666	1	1	CD	_	_	_
1667	_	_	NN	_	_	_
1668	Cy3	cy3	NN	_	_	_
1669	0	0	CD	_	_	_
1670	Cy5	cy5	NN	_	_	_
1671	5	5	CD	_	_	_
1672	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1673	Slide	Slide	NNP	_	_	_
1674	28	28	CD	_	_	_
1675	_	_	SYM	_	_	_
1676	Anaerobic	anaerobic	JJ	_	_	_
1677	culture	culture	NN	_	_	_
1678	_	_	SYM	_	_	_
1679	iCORM-3	icorm-3	NN	_	_	_
1680	_	_	NN	_	_	_
1681	biol	biol	NN	_	_	_
1682	rep	rep	NN	GEN	_	_
1683	1	1	CD	_	_	_
1684	_	_	CD	_	_	_
1685	Cy3	cy3	NN	_	_	_
1686	10	10	CD	_	_	_
1687	Cy5	cy5	NN	_	_	_
1688	0	0	CD	_	_	_
1689	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1690	Slide	Slide	NNP	_	_	_
1691	28	28	CD	_	_	_
1692	_	_	SYM	_	_	_
1693	Anaerobic	anaerobic	JJ	_	_	_
1694	culture	culture	NN	_	_	_
1695	_	_	SYM	_	_	_
1696	iCORM-3	icorm-3	NN	_	_	_
1697	_	_	NN	_	_	_
1698	biol	biol	NN	_	_	_
1699	rep	rep	NN	GEN	_	_
1700	1	1	CD	_	_	_
1701	_	_	CD	_	_	_
1702	Cy3	cy3	NN	_	_	_
1703	20	20	CD	_	_	_
1704	Cy5	cy5	NN	_	_	_
1705	0	0	CD	_	_	_
1706	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1707	Slide	Slide	NNP	_	_	_
1708	28	28	CD	_	_	_
1709	_	_	SYM	_	_	_
1710	Anaerobic	anaerobic	JJ	_	_	_
1711	culture	culture	NN	_	_	_
1712	_	_	SYM	_	_	_
1713	iCORM-3	icorm-3	NN	_	_	_
1714	_	_	NN	_	_	_
1715	biol	biol	NN	_	_	_
1716	rep	rep	NN	GEN	_	_
1717	1	1	CD	_	_	_
1718	_	_	CD	_	_	_
1719	Cy3	cy3	NN	_	_	_
1720	2.5	2.5	CD	_	_	_
1721	Cy5	cy5	NN	_	_	_
1722	0	0	CD	_	_	_
1723	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1724	Slide	Slide	NNP	_	_	_
1725	28	28	CD	_	_	_
1726	_	_	SYM	_	_	_
1727	Anaerobic	anaerobic	JJ	_	_	_
1728	culture	culture	NN	_	_	_
1729	_	_	SYM	_	_	_
1730	iCORM-3	icorm-3	NN	_	_	_
1731	_	_	NN	_	_	_
1732	biol	biol	NN	_	_	_
1733	rep	rep	NN	GEN	_	_
1734	1	1	CD	_	_	_
1735	_	_	CD	_	_	_
1736	Cy3	cy3	NN	_	_	_
1737	40	40	CD	_	_	_
1738	Cy5	cy5	NN	_	_	_
1739	0	0	CD	_	_	_
1740	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1741	Slide	Slide	NNP	_	_	_
1742	28	28	CD	_	_	_
1743	_	_	SYM	_	_	_
1744	Anaerobic	anaerobic	JJ	_	_	_
1745	culture	culture	NN	_	_	_
1746	_	_	SYM	_	_	_
1747	iCORM-3	icorm-3	NN	_	_	_
1748	_	_	NN	_	_	_
1749	biol	biol	NN	_	_	_
1750	rep	rep	NN	GEN	_	_
1751	1	1	CD	_	_	_
1752	_	_	CD	_	_	_
1753	Cy3	cy3	NN	_	_	_
1754	5	5	CD	_	_	_
1755	Cy5	cy5	NN	_	_	_
1756	0	0	CD	_	_	_
1757	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1758	Slide	Slide	NNP	_	_	_
1759	28	28	CD	_	_	_
1760	_	_	SYM	_	_	_
1761	Anaerobic	anaerobic	JJ	_	_	_
1762	culture	culture	NN	_	_	_
1763	_	_	SYM	_	_	_
1764	iCORM-3	icorm-3	NN	_	_	_
1765	_	_	NN	_	_	_
1766	biol	biol	NN	_	_	_
1767	rep	rep	NN	GEN	_	_
1768	1	1	CD	_	_	_
1769	_	_	CD	_	_	_
1770	Cy3	cy3	NN	_	_	_
1771	80	80	CD	_	_	_
1772	Cy5	cy5	NN	_	_	_
1773	0	0	CD	_	_	_
1774	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1775	Slide	Slide	NNP	_	_	_
1776	29	29	CD	_	_	_
1777	_	_	SYM	_	_	_
1778	Anaerobic	anaerobic	JJ	_	_	_
1779	culture	culture	NN	_	_	_
1780	_	_	SYM	_	_	_
1781	iCORM-3	icorm-3	NN	_	_	_
1782	_	_	NN	_	_	_
1783	biol	biol	NN	_	_	_
1784	rep	rep	NN	GEN	_	_
1785	1	1	CD	_	_	_
1786	_	_	CD	_	_	_
1787	Cy3	cy3	NN	_	_	_
1788	10	10	CD	_	_	_
1789	Cy5	cy5	NN	_	_	_
1790	0	0	CD	_	_	_
1791	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1792	Slide	Slide	NNP	_	_	_
1793	29	29	CD	_	_	_
1794	_	_	SYM	_	_	_
1795	Anaerobic	anaerobic	JJ	_	_	_
1796	culture	culture	NN	_	_	_
1797	_	_	SYM	_	_	_
1798	iCORM-3	icorm-3	NN	_	_	_
1799	_	_	NN	_	_	_
1800	biol	biol	NN	_	_	_
1801	rep	rep	NN	GEN	_	_
1802	1	1	CD	_	_	_
1803	_	_	CD	_	_	_
1804	Cy3	cy3	NN	_	_	_
1805	20	20	CD	_	_	_
1806	Cy5	cy5	NN	_	_	_
1807	0	0	CD	_	_	_
1808	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1809	Slide	Slide	NNP	_	_	_
1810	29	29	CD	_	_	_
1811	_	_	SYM	_	_	_
1812	Anaerobic	anaerobic	JJ	_	_	_
1813	culture	culture	NN	_	_	_
1814	_	_	SYM	_	_	_
1815	iCORM-3	icorm-3	NN	_	_	_
1816	_	_	NN	_	_	_
1817	biol	biol	NN	_	_	_
1818	rep	rep	NN	GEN	_	_
1819	1	1	CD	_	_	_
1820	_	_	CD	_	_	_
1821	Cy3	cy3	NN	_	_	_
1822	40	40	CD	_	_	_
1823	Cy5	cy5	NN	_	_	_
1824	0	0	CD	_	_	_
1825	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1826	Slide	Slide	NNP	_	_	_
1827	29	29	CD	_	_	_
1828	_	_	SYM	_	_	_
1829	Anaerobic	anaerobic	JJ	_	_	_
1830	culture	culture	NN	_	_	_
1831	_	_	SYM	_	_	_
1832	iCORM-3	icorm-3	NN	_	_	_
1833	_	_	NN	_	_	_
1834	biol	biol	NN	_	_	_
1835	rep	rep	NN	GEN	_	_
1836	1	1	CD	_	_	_
1837	_	_	CD	_	_	_
1838	Cy3	cy3	NN	_	_	_
1839	80	80	CD	_	_	_
1840	Cy5	cy5	NN	_	_	_
1841	0	0	CD	_	_	_
1842	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1843	Slide	Slide	NNP	_	_	_
1844	29	29	CD	_	_	_
1845	_	_	SYM	_	_	_
1846	Anaerobic	anaerobic	JJ	_	_	_
1847	culture	culture	NN	_	_	_
1848	_	_	SYM	_	_	_
1849	iCORM-3	icorm-3	NN	_	_	_
1850	_	_	NN	_	_	_
1851	biol	biol	NN	_	_	_
1852	rep	rep	NN	GEN	_	_
1853	2	2	CD	_	_	_
1854	_	_	CD	_	_	_
1855	Cy3	cy3	NN	_	_	_
1856	0	0	CD	_	_	_
1857	Cy5	cy5	NN	_	_	_
1858	10	10	CD	_	_	_
1859	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1860	Slide	Slide	NNP	_	_	_
1861	29	29	CD	_	_	_
1862	_	_	SYM	_	_	_
1863	Anaerobic	anaerobic	JJ	_	_	_
1864	culture	culture	NN	_	_	_
1865	_	_	SYM	_	_	_
1866	iCORM-3	icorm-3	NN	_	_	_
1867	_	_	NN	_	_	_
1868	biol	biol	NN	_	_	_
1869	rep	rep	NN	GEN	_	_
1870	2	2	CD	_	_	_
1871	_	_	CD	_	_	_
1872	Cy3	cy3	NN	_	_	_
1873	0	0	CD	_	_	_
1874	Cy5	cy5	NN	_	_	_
1875	20	20	CD	_	_	_
1876	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1877	Slide	slide	NN	_	_	_
1878	29	29	CD	_	_	_
1879	_	_	SYM	_	_	_
1880	Anaerobic	anaerobic	JJ	_	_	_
1881	culture	culture	NN	_	_	_
1882	_	_	SYM	_	_	_
1883	iCORM-3	icorm-3	NN	_	_	_
1884	_	_	NN	_	_	_
1885	biol	biol	NN	_	_	_
1886	rep	rep	NN	GEN	_	_
1887	2	2	CD	_	_	_
1888	_	_	CD	_	_	_
1889	Cy3	cy3	NN	_	_	_
1890	0	0	CD	_	_	_
1891	Cy5	cy5	NN	_	_	_
1892	2.5	2.5	CD	_	_	_
1893	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1894	Slide	Slide	NNP	_	_	_
1895	29	29	CD	_	_	_
1896	_	_	SYM	_	_	_
1897	Anaerobic	anaerobic	JJ	_	_	_
1898	culture	culture	NN	_	_	_
1899	_	_	SYM	_	_	_
1900	iCORM-3	icorm-3	NN	_	_	_
1901	_	_	NN	_	_	_
1902	biol	biol	NN	_	_	_
1903	rep	rep	NN	GEN	_	_
1904	2	2	CD	_	_	_
1905	_	_	CD	_	_	_
1906	Cy3	cy3	NN	_	_	_
1907	0	0	CD	_	_	_
1908	Cy5	cy5	NN	_	_	_
1909	5	5	CD	_	_	_
1910	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1911	Slide	Slide	NNP	_	_	_
1912	30	30	CD	_	_	_
1913	_	_	SYM	_	_	_
1914	Anaerobic	anaerobic	JJ	_	_	_
1915	culture	culture	NN	_	_	_
1916	_	_	SYM	_	_	_
1917	iCORM-3	icorm-3	NN	_	_	_
1918	_	_	NN	_	_	_
1919	biol	biol	NN	_	_	_
1920	rep	rep	NN	GEN	_	_
1921	2	2	CD	_	_	_
1922	_	_	CD	_	_	_
1923	Cy3	cy3	NN	_	_	_
1924	0	0	CD	_	_	_
1925	Cy5	cy5	NN	_	_	_
1926	40	40	CD	_	_	_
1927	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1928	Slide	slide	NN	_	_	_
1929	30	30	CD	_	_	_
1930	_	_	SYM	_	_	_
1931	Anaerobic	anaerobic	JJ	_	_	_
1932	culture	culture	NN	_	_	_
1933	_	_	SYM	_	_	_
1934	iCORM-3	icorm-3	NN	_	_	_
1935	_	_	NN	_	_	_
1936	biol	biol	NN	_	_	_
1937	rep	rep	NN	GEN	_	_
1938	2	2	CD	_	_	_
1939	_	_	CD	_	_	_
1940	Cy3	cy3	NN	_	_	_
1941	0	0	CD	_	_	_
1942	Cy5	cy5	NN	_	_	_
1943	80	80	CD	_	_	_
1944	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1945	Slide	Slide	NNP	_	_	_
1946	30	30	CD	_	_	_
1947	_	_	SYM	_	_	_
1948	Anaerobic	anaerobic	JJ	_	_	_
1949	culture	culture	NN	_	_	_
1950	_	_	SYM	_	_	_
1951	iCORM-3	icorm-3	NN	_	_	_
1952	_	_	NN	_	_	_
1953	biol	biol	NN	_	_	_
1954	rep	rep	NN	GEN	_	_
1955	2	2	CD	_	_	_
1956	_	_	CD	_	_	_
1957	Cy3	cy3	NN	_	_	_
1958	10	10	CD	_	_	_
1959	Cy5	cy5	NN	_	_	_
1960	0	0	CD	_	_	_
1961	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1962	Slide	Slide	NNP	_	_	_
1963	30	30	CD	_	_	_
1964	_	_	SYM	_	_	_
1965	Anaerobic	anaerobic	JJ	_	_	_
1966	culture	culture	NN	_	_	_
1967	_	_	SYM	_	_	_
1968	iCORM-3	icorm-3	NN	_	_	_
1969	_	_	NN	_	_	_
1970	biol	biol	NN	_	_	_
1971	rep	rep	NN	GEN	_	_
1972	2	2	CD	_	_	_
1973	_	_	CD	_	_	_
1974	Cy3	cy3	NN	_	_	_
1975	20	20	CD	_	_	_
1976	Cy5	cy5	NN	_	_	_
1977	0	0	CD	_	_	_
1978	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1979	Slide	Slide	NNP	_	_	_
1980	30	30	CD	_	_	_
1981	_	_	SYM	_	_	_
1982	Anaerobic	anaerobic	JJ	_	_	_
1983	culture	culture	NN	_	_	_
1984	_	_	SYM	_	_	_
1985	iCORM-3	icorm-3	NN	_	_	_
1986	_	_	NN	_	_	_
1987	biol	biol	NN	_	_	_
1988	rep	rep	NN	GEN	_	_
1989	2	2	CD	_	_	_
1990	_	_	CD	_	_	_
1991	Cy3	cy3	NN	_	_	_
1992	2.5	2.5	CD	_	_	_
1993	Cy5	cy5	NN	_	_	_
1994	0	0	CD	_	_	_
1995	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1996	Slide	Slide	NNP	_	_	_
1997	30	30	CD	_	_	_
1998	_	_	SYM	_	_	_
1999	Anaerobic	anaerobic	JJ	_	_	_
2000	culture	culture	NN	_	_	_
2001	_	_	SYM	_	_	_
2002	iCORM-3	icorm-3	NN	_	_	_
2003	_	_	NN	_	_	_
2004	biol	biol	NN	_	_	_
2005	rep	rep	NN	GEN	_	_
2006	2	2	CD	_	_	_
2007	_	_	CD	_	_	_
2008	Cy3	cy3	NN	_	_	_
2009	40	40	CD	_	_	_
2010	Cy5	cy5	NN	_	_	_
2011	0	0	CD	_	_	_
2012	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2013	Slide	Slide	NNP	_	_	_
2014	30	30	CD	_	_	_
2015	_	_	SYM	_	_	_
2016	Anaerobic	anaerobic	JJ	_	_	_
2017	culture	culture	NN	_	_	_
2018	_	_	SYM	_	_	_
2019	iCORM-3	icorm-3	NN	_	_	_
2020	_	_	NN	_	_	_
2021	biol	biol	NN	_	_	_
2022	rep	rep	NN	GEN	_	_
2023	2	2	CD	_	_	_
2024	_	_	CD	_	_	_
2025	Cy3	cy3	NN	_	_	_
2026	5	5	CD	_	_	_
2027	Cy5	cy5	NN	_	_	_
2028	0	0	CD	_	_	_
2029	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2030	Slide	Slide	NNP	_	_	_
2031	30	30	CD	_	_	_
2032	_	_	SYM	_	_	_
2033	Anaerobic	anaerobic	JJ	_	_	_
2034	culture	culture	NN	_	_	_
2035	_	_	SYM	_	_	_
2036	iCORM-3	icorm-3	NN	_	_	_
2037	_	_	NN	_	_	_
2038	biol	biol	NN	_	_	_
2039	rep	rep	NN	GEN	_	_
2040	2	2	CD	_	_	_
2041	_	_	CD	_	_	_
2042	Cy3	cy3	NN	_	_	_
2043	80	80	CD	_	_	_
2044	Cy5	cy5	NN	_	_	_
2045	0	0	CD	_	_	_
2046	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2047	strain	strain	NN	_	_	_
2048	:	:	:	_	_	_
2049	Wild	Wild	NNP	_	_	_
2050	type	type	NN	_	_	_
2051	strain	strain	NN	_	_	_
2052	MG1655	mg1655	NN	_	_	_
2053	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2054	Total	total	JJ	_	_	_
2055	RNA	rna	NN	_	_	_
2056	extracted	extract	VBN	_	_	_
2057	using	use	VBG	_	_	_
2058	Trizol	Trizol	NNP	_	_	_
2059	following	follow	VBG	_	_	_
2060	manufacturer	manufacturer	NN	_	_	_
2061	's	's	POS	_	_	_
2062	instructions	instruction	NNS	_	_	_
2063	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2064	dpiA	dpia	NN	GEN	_	_
2065	2x	2x	NN	_	_	_
2066	Overexpression	overexpression	NN	_	_	_
2067	pHI1429	phi1429	NN	_	_	_
2068	in	in	IN	_	_	_
2069	LB	lb	NN	_	_	_
2070	at	at	IN	_	_	_
2071	37	37	CD	_	_	_
2072	Mid	Mid	NNP	_	_	_
2073	Log	Log	NNP	_	_	_
2074	Phase	phase	NN	_	_	_
2075	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2076	dpiAoverexpressor	dpiaoverexpressor	NN	_	_	_
2077	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2078	ecd3-c-0081429	ecd3-c-0081429	NN	_	_	_
2079	wt	wt	JJ	_	_	_
2080	vs	vs	CC	_	_	_
2081	dpiAoverexpressor	dpiaoverexpressor	JJ	_	_	_
2082	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2083	ecd3-c-0101429	ecd3-c-0101429	NN	_	_	_
2084	wt	wt	JJ	_	_	_
2085	vs	vs	CC	_	_	_
2086	dpiAoverexpressor	dpiaoverexpressor	JJ	_	_	_
2087	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2088	Escherichia	escherichia	FW	Organism	_	_
2089	coli	coli	FW	Organism	_	_
2090	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2091	VALUE	value	NN	_	_	_
2092	is	be	VBZ	_	_	_
2093	Log	log	NN	_	_	_
2094	-LRB-	-lrb-	-LRB-	_	_	_
2095	base	base	NN	_	_	_
2096	2	2	CD	_	_	_
2097	-RRB-	-rrb-	-RRB-	_	_	_
2098	of	of	IN	_	_	_
2099	the	the	DT	_	_	_
2100	ratio	ratio	NN	_	_	_
2101	of	of	IN	_	_	_
2102	the	the	DT	_	_	_
2103	median	median	NN	_	_	_
2104	of	of	IN	_	_	_
2105	Channel	Channel	NNP	_	_	_
2106	2	2	CD	_	_	_
2107	-LRB-	-lrb-	-LRB-	_	_	_
2108	usually	usually	RB	_	_	_
2109	635	635	CD	_	_	_
2110	nm	nm	NN	_	_	_
2111	-RRB-	-rrb-	-RRB-	_	_	_
2112	to	to	TO	_	_	_
2113	Channel	Channel	NNP	_	_	_
2114	1	1	CD	_	_	_
2115	-LRB-	-lrb-	-LRB-	_	_	_
2116	usually	usually	RB	_	_	_
2117	532	532	CD	_	_	_
2118	nm	nm	NN	_	_	_
2119	-RRB-	-rrb-	-RRB-	_	_	_
2120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2121	WT1088	wt1088	NN	_	_	_
2122	in	in	IN	_	_	_
2123	LB	lb	NN	_	_	_
2124	at	at	IN	_	_	_
2125	37	37	CD	_	_	_
2126	Mid	Mid	NNP	_	_	_
2127	Log	Log	NNP	_	_	_
2128	Phase	phase	NN	_	_	_
2129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2130	WT1088	wt1088	NN	_	_	_
2131	vs.	vs.	CC	_	_	_
2132	dpiA	dpia	NN	GEN	_	_
2133	2x	2x	NN	_	_	_
2134	Overexpression	overexpression	NN	_	_	_
2135	pHI1429	phi1429	NN	_	_	_
2136	in	in	IN	_	_	_
2137	LB	lb	NN	_	_	_
2138	at	at	IN	_	_	_
2139	37	37	CD	_	_	_
2140	Mid	Mid	NNP	_	_	_
2141	Log	Log	NNP	_	_	_
2142	Phase	phase	NN	_	_	_
2143	Trial	trial	NN	_	_	_
2144	A	a	NN	_	_	_
2145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2146	WT1088	wt1088	NN	_	_	_
2147	vs.	vs.	CC	_	_	_
2148	dpiA	dpia	NN	GEN	_	_
2149	2x	2x	NN	_	_	_
2150	Overexpression	overexpression	NN	_	_	_
2151	pHI1429	phi1429	NN	_	_	_
2152	in	in	IN	_	_	_
2153	LB	lb	NN	_	_	_
2154	at	at	IN	_	_	_
2155	37	37	CD	_	_	_
2156	Mid	Mid	NNP	_	_	_
2157	Log	Log	NNP	_	_	_
2158	Phase	phase	NN	_	_	_
2159	Trial	trial	NN	_	_	_
2160	B	b	NN	_	_	_
2161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2162	antibody	antibody	NN	_	_	_
2163	:	:	:	_	_	_
2164	Affinity	affinity	NN	_	_	_
2165	Purified	purify	VBN	_	_	_
2166	FNR	fnr	NN	TF	_	_
2167	antibody	antibody	NN	_	_	_
2168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2169	antibody	antibody	NN	_	_	_
2170	:	:	:	_	_	_
2171	Pre-cleared	pre-cleared	JJ	_	_	_
2172	FNR	fnr	NN	TF	_	_
2173	antibody	antibody	NN	_	_	_
2174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2175	antibody	antibody	NN	_	_	_
2176	:	:	:	_	_	_
2177	Pre-cleared	pre-cleared	JJ	_	_	_
2178	H-NS	h-ns	NN	_	_	_
2179	polyclonal	polyclonal	JJ	_	_	_
2180	antibody	antibody	NN	_	_	_
2181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2182	antibody	antibody	NN	_	_	_
2183	:	:	:	_	_	_
2184	Pre-cleared	pre-cleared	JJ	_	_	_
2185	IHF	ihf	NN	TF	_	_
2186	polyclonal	polyclonal	JJ	_	_	_
2187	antibody	antibody	NN	_	_	_
2188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2189	antibody	antibody	NN	_	_	_
2190	:	:	:	_	_	_
2191	RNA	rna	NN	_	_	_
2192	Polymerase	polymerase	NN	_	_	_
2193	ß	ß	NN	_	_	_
2194	monoclonal	monoclonal	JJ	_	_	_
2195	antibody	antibody	NN	_	_	_
2196	from	from	IN	_	_	_
2197	NeoClone	NeoClone	NNP	_	_	_
2198	-LRB-	-lrb-	-LRB-	_	_	_
2199	W0002	w0002	NN	_	_	_
2200	-RRB-	-rrb-	-RRB-	_	_	_
2201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2202	Arrays	array	NNS	_	_	_
2203	were	be	VBD	_	_	_
2204	processed	process	VBN	_	_	_
2205	using	use	VBG	_	_	_
2206	Nimblegen	Nimblegen	NNP	_	_	_
2207	's	's	POS	_	_	_
2208	standard	standard	JJ	_	_	_
2209	protocol	protocol	NN	_	_	_
2210	for	for	IN	_	_	_
2211	Nimblescan	nimblescan	JJ	_	_	_
2212	2.4	2.4	CD	_	_	_
2213	ChIP	chip	NN	_	_	_
2214	data	datum	NNS	_	_	_
2215	extraction	extraction	NN	_	_	_
2216	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cell	cell	NN	_	_	_
3	pellets	pellet	NNS	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	from	from	IN	_	_	_
6	initial	initial	JJ	_	_	_
7	50	50	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	culture	culture	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	were	be	VBD	_	_	_
13	thawed	thaw	VBN	_	_	_
14	and	and	CC	_	_	_
15	resuspended	resuspend	VBN	_	_	_
16	in	in	IN	_	_	_
17	250ul	250ul	NN	_	_	_
18	of	of	IN	_	_	_
19	IP	IP	NNP	_	_	_
20	buffer	buffer	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	100	100	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	Tris	Tris	NNP	_	_	_
25	pH	ph	NN	_	_	_
26	8	8	CD	_	_	_
27	,	,	,	_	_	_
28	300	300	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	NaCl	nacl	NN	_	_	_
31	,	,	,	_	_	_
32	2	2	CD	_	_	_
33	%	%	NN	_	_	_
34	TritonX-100	tritonx-100	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	and	and	CC	_	_	_
37	sonicated	sonicate	VBN	_	_	_
38	using	use	VBG	_	_	_
39	a	a	DT	_	_	_
40	microtip	microtip	NN	_	_	_
41	sonicator	sonicator	NN	_	_	_
42	set	set	VBN	_	_	_
43	at	at	IN	_	_	_
44	10	10	CD	_	_	_
45	%	%	NN	_	_	_
46	output	output	NN	_	_	_
47	for	for	IN	_	_	_
48	20	20	CD	_	_	_
49	second	second	JJ	_	_	_
50	intervals	interval	NNS	_	_	_
51	with	with	IN	_	_	_
52	periods	period	NNS	_	_	_
53	of	of	IN	_	_	_
54	cooling	cool	VBG	_	_	_
55	in	in	IN	_	_	_
56	between	between	IN	_	_	_
57	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	treated	treat	VBN	_	_	_
5	for	for	IN	_	_	_
6	one	one	CD	_	_	_
7	hour	hour	NN	_	_	_
8	at	at	IN	_	_	_
9	4	4	CD	_	_	_
10	°C	°c	NN	_	_	_
11	with	with	IN	_	_	_
12	RNase	rnase	NN	_	_	_
13	A	a	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	2	2	CD	_	_	_
16	ng	ng	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Cells	cell	NNS	_	_	_
19	were	be	VBD	_	_	_
20	grown	grow	VBN	_	_	_
21	aerobically	aerobically	RB	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	25	25	CD	_	_	_
24	%	%	NN	_	_	_
25	O2	o2	CD	_	_	_
26	,	,	,	_	_	_
27	70	70	CD	_	_	_
28	%	%	NN	_	_	_
29	N2	n2	NN	_	_	_
30	and	and	CC	_	_	_
31	5	5	CD	_	_	_
32	%	%	NN	_	_	_
33	CO2	co2	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	until	until	IN	_	_	_
36	mid-log	mid-log	JJ	_	_	_
37	phase	phase	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	OD600	od600	NN	_	_	_
40	of	of	IN	_	_	_
41	0.35	0.35	CD	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	and	and	CC	_	_	_
44	treated	treat	VBN	_	_	_
45	with	with	IN	_	_	_
46	1	1	CD	_	_	_
47	%	%	NN	_	_	_
48	final	final	JJ	_	_	_
49	volumen	voluman	NNS	_	_	_
50	formaldehyde	formaldehyde	NN	_	_	_
51	for	for	IN	_	_	_
52	ten	ten	CD	_	_	_
53	minutes	minute	NNS	_	_	_
54	.	.	.	_	_	_

1	Sodium	sodium	NN	_	_	_
2	phosphate	phosphate	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Cells	cell	NNS	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	anaerobically	anaerobically	RB	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	95	95	CD	_	_	_
12	%	%	NN	_	_	_
13	N2	n2	NN	_	_	_
14	and	and	CC	_	_	_
15	5	5	CD	_	_	_
16	%	%	NN	_	_	_
17	CO2	co2	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	until	until	IN	_	_	_
20	mid-log	mid-log	JJ	_	_	_
21	phase	phase	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	OD600	od600	NN	_	_	_
24	of	of	IN	_	_	_
25	0.3	0.3	CD	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	and	and	CC	_	_	_
28	treated	treat	VBN	_	_	_
29	with	with	IN	_	_	_
30	1	1	CD	_	_	_
31	%	%	NN	_	_	_
32	final	final	JJ	_	_	_
33	volumen	voluman	NNS	_	_	_
34	formaldehyde	formaldehyde	NN	_	_	_
35	for	for	IN	_	_	_
36	ten	ten	CD	_	_	_
37	minutes	minute	NNS	_	_	_
38	.	.	.	_	_	_

1	Sodium	sodium	NN	_	_	_
2	phosphate	phosphate	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Cells	cell	NNS	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	with	with	IN	_	_	_
10	16	16	CD	_	_	_
11	µM	µm	NN	_	_	_
12	IPTG	iptg	NN	_	_	_
13	and	and	CC	_	_	_
14	300	300	CD	_	_	_
15	µL	µl	NN	_	_	_
16	Cm20	cm20	NN	_	_	_
17	anaerobically	anaerobically	RB	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	95	95	CD	_	_	_
20	%	%	NN	_	_	_
21	N2	n2	NN	_	_	_
22	and	and	CC	_	_	_
23	5	5	CD	_	_	_
24	%	%	NN	_	_	_
25	CO2	co2	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	until	until	IN	_	_	_
28	mid-log	mid-log	JJ	_	_	_
29	phase	phase	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	OD600	od600	NN	_	_	_
32	of	of	IN	_	_	_
33	0.3	0.3	CD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	and	and	CC	_	_	_
36	treated	treat	VBN	_	_	_
37	with	with	IN	_	_	_
38	1	1	CD	_	_	_
39	%	%	NN	_	_	_
40	final	final	JJ	_	_	_
41	volumen	voluman	NNS	_	_	_
42	formaldehyde	formaldehyde	NN	_	_	_
43	for	for	IN	_	_	_
44	ten	ten	CD	_	_	_
45	minutes	minute	NNS	_	_	_
46	.	.	.	_	_	_

1	Sodium	sodium	NN	_	_	_
2	phosphate	phosphate	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Cells	cell	NNS	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	with	with	IN	_	_	_
10	4	4	CD	_	_	_
11	µM	µm	NN	_	_	_
12	IPTG	iptg	NN	_	_	_
13	and	and	CC	_	_	_
14	300	300	CD	_	_	_
15	µL	µl	NN	_	_	_
16	Cm20	cm20	NN	_	_	_
17	anaerobically	anaerobically	RB	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	95	95	CD	_	_	_
20	%	%	NN	_	_	_
21	N2	n2	NN	_	_	_
22	and	and	CC	_	_	_
23	5	5	CD	_	_	_
24	%	%	NN	_	_	_
25	CO2	co2	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	until	until	IN	_	_	_
28	mid-log	mid-log	JJ	_	_	_
29	phase	phase	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	OD600	od600	NN	_	_	_
32	of	of	IN	_	_	_
33	0.3	0.3	CD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	and	and	CC	_	_	_
36	treated	treat	VBN	_	_	_
37	with	with	IN	_	_	_
38	1	1	CD	_	_	_
39	%	%	NN	_	_	_
40	final	final	JJ	_	_	_
41	volumen	voluman	NNS	_	_	_
42	formaldehyde	formaldehyde	NN	_	_	_
43	for	for	IN	_	_	_
44	ten	ten	CD	_	_	_
45	minutes	minute	NNS	_	_	_
46	.	.	.	_	_	_

1	Sodium	sodium	NN	_	_	_
2	phosphate	phosphate	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Cells	cell	NNS	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	with	with	IN	_	_	_
10	8	8	CD	_	_	_
11	µM	µm	NN	_	_	_
12	IPTG	iptg	NN	_	_	_
13	and	and	CC	_	_	_
14	300	300	CD	_	_	_
15	µL	µl	NN	_	_	_
16	Cm20	cm20	NN	_	_	_
17	anaerobically	anaerobically	RB	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	95	95	CD	_	_	_
20	%	%	NN	_	_	_
21	N2	n2	NN	_	_	_
22	and	and	CC	_	_	_
23	5	5	CD	_	_	_
24	%	%	NN	_	_	_
25	CO2	co2	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	until	until	IN	_	_	_
28	mid-log	mid-log	JJ	_	_	_
29	phase	phase	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	OD600	od600	NN	_	_	_
32	of	of	IN	_	_	_
33	0.3	0.3	CD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	and	and	CC	_	_	_
36	treated	treat	VBN	_	_	_
37	with	with	IN	_	_	_
38	1	1	CD	_	_	_
39	%	%	NN	_	_	_
40	final	final	JJ	_	_	_
41	volumen	voluman	NNS	_	_	_
42	formaldehyde	formaldehyde	NN	_	_	_
43	for	for	IN	_	_	_
44	ten	ten	CD	_	_	_
45	minutes	minute	NNS	_	_	_
46	.	.	.	_	_	_

1	Sodium	sodium	NN	_	_	_
2	phosphate	phosphate	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Escherichia	escherichia	FW	Organism	_	_
7	coli	coli	FW	Organism	_	_
8	str	str	FW	_	_	_
9	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Escherichia	escherichia	FW	Organism	_	_
4	coli	coli	FW	Organism	_	_
5	str	str	FW	_	_	_
6	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655star	mg1655star	JJ	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	FNR	fnr	SYM	TF	_	_
4	-	-	:	_	_	_
5	Anaerobic	anaerobic	JJ	_	_	_
6	-	-	:	_	_	_
7	A	a	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	FNR	fnr	SYM	TF	_	_
10	-	-	:	_	_	_
11	Anaerobic	anaerobic	JJ	_	_	_
12	-	-	:	_	_	_
13	Affinity	affinity	NN	_	_	_
14	Purified	purify	VBN	_	_	_
15	-	-	:	_	_	_
16	A	a	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	FNR	fnr	SYM	TF	_	_
19	-	-	:	_	_	_
20	Anaerobic	anaerobic	JJ	_	_	_
21	-	-	:	_	_	_
22	Affinity	affinity	NN	_	_	_
23	Purified	purify	VBN	_	_	_
24	-	-	:	_	_	_
25	B	b	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	FNR	fnr	SYM	TF	_	_
28	-	-	:	_	_	_
29	Anaerobic	anaerobic	JJ	_	_	_
30	-	-	:	_	_	_
31	B	b	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	FNR	fnr	SYM	TF	_	_
34	-	-	:	_	_	_
35	Anaerobic	anaerobic	JJ	_	_	_
36	-	-	:	_	_	_
37	C	c	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	∆	∆	CD	_	_	_
40	fnr	fnr	SYM	GEN	_	_
41	-	-	:	_	_	_
42	Anaeroibc	Anaeroibc	NNP	_	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	FNR	FNR	NNP	TF	_	_
45	ChIP	chip	NN	_	_	_
46	DNA	dna	NN	_	_	_
47	from	from	IN	_	_	_
48	∆	∆	CD	_	_	_
49	hns	hn	NNS	GEN	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	∆	∆	CD	_	_	_
52	fnr	fnr	NN	GEN	_	_
53	ChIP	chip	NN	_	_	_
54	DNA	dna	NN	_	_	_
55	from	from	IN	_	_	_
56	PK4854	pk4854	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	FNR	fnr	NN	TF	_	_
59	ChIP	chip	NN	_	_	_
60	DNA	dna	NN	_	_	_
61	from	from	IN	_	_	_
62	WT	WT	NNP	_	_	_
63	Escherchia	Escherchia	NNP	_	_	_
64	coli	coli	NN	_	_	_
65	MG1655	mg1655	NN	_	_	_
66	K-12	k-12	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	FNR	fnr	SYM	TF	_	_
69	-	-	:	_	_	_
70	∆	∆	SYM	_	_	_
71	hns	hn	VBZ	GEN	_	_
72	∆	∆	SYM	_	_	_
73	stpA	stpa	NN	GEN	_	_
74	A	a	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	FNR	fnr	SYM	TF	_	_
77	-	-	:	_	_	_
78	∆	∆	SYM	_	_	_
79	hns	hn	VBZ	GEN	_	_
80	∆	∆	SYM	_	_	_
81	stpA	stpa	NN	GEN	_	_
82	B	b	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	FNR	fnr	NN	TF	_	_
85	INPUT	input	NN	_	_	_
86	from	from	IN	_	_	_
87	PK8263	pk8263	NN	_	_	_
88	with	with	IN	_	_	_
89	16	16	CD	_	_	_
90	µM	µm	NN	_	_	_
91	INPUTTG	inputtg	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	FNR	fnr	NN	TF	_	_
94	INPUT	input	NN	_	_	_
95	from	from	IN	_	_	_
96	PK8263	pk8263	NN	_	_	_
97	with	with	IN	_	_	_
98	4	4	CD	_	_	_
99	µM	µm	NN	_	_	_
100	INPUTTG	inputtg	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	FNR	fnr	NN	TF	_	_
103	INPUT	input	NN	_	_	_
104	from	from	IN	_	_	_
105	PK8263	pk8263	NN	_	_	_
106	with	with	IN	_	_	_
107	8	8	CD	_	_	_
108	µM	µm	NN	_	_	_
109	INPUTTG	inputtg	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	FNR	fnr	NN	TF	_	_
112	INPUT	input	NN	_	_	_
113	from	from	IN	_	_	_
114	WT	WT	NNP	_	_	_
115	Escherichia	escherichia	FW	Organism	_	_
116	coli	coli	FW	Organism	_	_
117	MG1655	mg1655	NN	_	_	_
118	K-12	k-12	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	FNR	fnr	NN	TF	_	_
121	IP	IP	NNP	_	_	_
122	from	from	IN	_	_	_
123	PK8263	pk8263	NN	_	_	_
124	with	with	IN	_	_	_
125	16	16	CD	_	_	_
126	µM	µm	NN	_	_	_
127	IPTG	iptg	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	FNR	fnr	NN	TF	_	_
130	IP	IP	NNP	_	_	_
131	from	from	IN	_	_	_
132	PK8263	pk8263	NN	_	_	_
133	with	with	IN	_	_	_
134	4	4	CD	_	_	_
135	µM	µm	NN	_	_	_
136	IPTG	iptg	NN	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	FNR	fnr	NN	TF	_	_
139	IP	IP	NNP	_	_	_
140	from	from	IN	_	_	_
141	PK8263	pk8263	NN	_	_	_
142	with	with	IN	_	_	_
143	8	8	CD	_	_	_
144	µM	µm	NN	_	_	_
145	IPTG	iptg	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	FNR	fnr	NN	TF	_	_
148	IP	IP	NNP	_	_	_
149	from	from	IN	_	_	_
150	WT	WT	NNP	_	_	_
151	Escherichia	escherichia	FW	Organism	_	_
152	coli	coli	FW	Organism	_	_
153	MG1655	mg1655	NN	_	_	_
154	K-12	k-12	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	growth	growth	NN	_	_	_
157	condition	condition	NN	_	_	_
158	:	:	:	_	_	_
159	16	16	CD	_	_	_
160	µM	µm	NN	_	_	_
161	IPTG	iptg	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	growth	growth	NN	_	_	_
164	condition	condition	NN	_	_	_
165	:	:	:	_	_	_
166	4	4	CD	_	_	_
167	µM	µm	NN	_	_	_
168	IPTG	iptg	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	growth	growth	NN	_	_	_
171	condition	condition	NN	_	_	_
172	:	:	:	_	_	_
173	8	8	CD	_	_	_
174	µM	µm	NN	_	_	_
175	IPTG	iptg	NN	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	growth	growth	NN	_	_	_
178	condition	condition	NN	_	_	_
179	:	:	:	_	_	_
180	Aerobic	aerobic	JJ	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	growth	growth	NN	_	_	_
183	condition	condition	NN	_	_	_
184	:	:	:	_	_	_
185	anaerobic	anaerobic	JJ	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	growth	growth	NN	_	_	_
188	condition	condition	NN	_	_	_
189	:	:	:	_	_	_
190	Anaerobic	anaerobic	JJ	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	HNS	hns	SYM	_	_	_
193	-	-	:	_	_	_
194	Aerobic	aerobic	JJ	_	_	_
195	A	a	NN	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	HNS	hns	SYM	_	_	_
198	-	-	:	_	_	_
199	Aerobic	aerobic	JJ	_	_	_
200	B	b	NN	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
202	HNS	hns	SYM	_	_	_
203	-	-	:	_	_	_
204	Anaerobic	anaerobic	JJ	_	_	_
205	A	a	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	HNS	hns	SYM	_	_	_
208	-	-	:	_	_	_
209	Anaerobic	anaerobic	JJ	_	_	_
210	B	b	NN	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	HNS	hn	VBZ	_	_	_
213	ChIP	chip	NN	_	_	_
214	DNA	dna	NN	_	_	_
215	from	from	IN	_	_	_
216	WT	WT	NNP	_	_	_
217	Escherichia	escherichia	FW	Organism	_	_
218	coli	coli	FW	Organism	_	_
219	MG1655	mg1655	NN	_	_	_
220	K-12	k-12	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	HNS	hn	VBZ	_	_	_
223	ChIP	chip	NN	_	_	_
224	DNA	dna	NN	_	_	_
225	from	from	IN	_	_	_
226	WT	WT	NNP	_	_	_
227	Escherichia	escherichia	FW	Organism	_	_
228	coli	coli	FW	Organism	_	_
229	MG1655	mg1655	NN	_	_	_
230	K-12	k-12	NN	_	_	_
231	Replicate	replicate	VB	_	_	_
232	B	b	NN	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
234	IHF	ihf	SYM	TF	_	_
235	-	-	:	_	_	_
236	Anaerobic	anaerobic	JJ	_	_	_
237	A	a	NN	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	IHF	ihf	SYM	TF	_	_
240	-	-	:	_	_	_
241	Anaerobic	anaerobic	JJ	_	_	_
242	B	b	NN	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	IHF	ihf	NN	TF	_	_
245	ChIP	chip	NN	_	_	_
246	DNA	dna	NN	_	_	_
247	from	from	IN	_	_	_
248	WT	WT	NNP	_	_	_
249	Escherichia	escherichia	FW	Organism	_	_
250	coli	coli	FW	Organism	_	_
251	MG1655	mg1655	NN	_	_	_
252	K-12	k-12	NN	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
254	IHF	ihf	VBP	TF	_	_
255	ChIP	chip	NN	_	_	_
256	DNA	dna	NN	_	_	_
257	from	from	IN	_	_	_
258	WT	WT	NNP	_	_	_
259	Escherichia	escherichia	FW	Organism	_	_
260	coli	coli	FW	Organism	_	_
261	MG1655	mg1655	NN	_	_	_
262	K-12	k-12	NN	_	_	_
263	Replicate	replicate	VB	_	_	_
264	B	b	NN	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
266	INPUT	input	VBP	_	_	_
267	ChIP	chip	NN	_	_	_
268	DNA	dna	NN	_	_	_
269	from	from	IN	_	_	_
270	∆	∆	CD	_	_	_
271	hns	hn	NNS	GEN	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	INPUT	input	NN	_	_	_
274	ChIP	chip	NN	_	_	_
275	DNA	dna	NN	_	_	_
276	from	from	IN	_	_	_
277	WT	WT	NNP	_	_	_
278	Escherchia	Escherchia	NNP	_	_	_
279	coli	coli	NN	_	_	_
280	MG1655	mg1655	NN	_	_	_
281	K-12	k-12	NN	_	_	_
282	,	,	,	_	_	_
283	no	no	DT	_	_	_
284	antibody	antibody	NN	_	_	_
285	control	control	NN	_	_	_
286	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
287	INPUT	INPUT	NNP	_	_	_
288	ChIP	chip	NN	_	_	_
289	DNA	dna	NN	_	_	_
290	from	from	IN	_	_	_
291	WT	WT	NNP	_	_	_
292	Escherchia	Escherchia	NNP	_	_	_
293	coli	coli	NN	_	_	_
294	MG1655	mg1655	NN	_	_	_
295	K-12	k-12	NN	_	_	_
296	,	,	,	_	_	_
297	no	no	DT	_	_	_
298	antibody	antibody	NN	_	_	_
299	control	control	NN	_	_	_
300	,	,	,	_	_	_
301	Replicate	replicate	VB	_	_	_
302	B	b	NN	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
304	INPUT	input	VBP	_	_	_
305	ChIP	chip	NN	_	_	_
306	DNA	dna	NN	_	_	_
307	from	from	IN	_	_	_
308	WTPK4854	wtpk4854	NN	_	_	_
309	,	,	,	_	_	_
310	no	no	DT	_	_	_
311	antibody	antibody	NN	_	_	_
312	control	control	NN	_	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
314	Ptac	ptac	NN	_	_	_
315	:	:	:	_	_	_
316	:	:	:	_	_	_
317	fnr	fnr	SYM	GEN	_	_
318	-	-	:	_	_	_
319	A	a	NN	_	_	_
320	-	-	:	_	_	_
321	16	16	CD	_	_	_
322	µM	µm	NN	_	_	_
323	IPTG	iptg	NN	_	_	_
324	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
325	Ptac	ptac	NN	_	_	_
326	:	:	:	_	_	_
327	:	:	:	_	_	_
328	fnr	fnr	SYM	GEN	_	_
329	-	-	:	_	_	_
330	A	a	NN	_	_	_
331	-	-	:	_	_	_
332	4	4	CD	_	_	_
333	µM	µm	NN	_	_	_
334	IPTG	iptg	NN	_	_	_
335	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
336	Ptac	ptac	NN	_	_	_
337	:	:	:	_	_	_
338	:	:	:	_	_	_
339	fnr	fnr	SYM	GEN	_	_
340	-	-	:	_	_	_
341	A	a	NN	_	_	_
342	-	-	:	_	_	_
343	8	8	CD	_	_	_
344	µM	µm	NN	_	_	_
345	IPTG	iptg	NN	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	Ptac	ptac	NN	_	_	_
348	:	:	:	_	_	_
349	:	:	:	_	_	_
350	fnr	fnr	SYM	GEN	_	_
351	-	-	:	_	_	_
352	B	b	NN	_	_	_
353	-	-	:	_	_	_
354	16	16	CD	_	_	_
355	µM	µm	NN	_	_	_
356	IPTG	iptg	NN	_	_	_
357	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
358	Ptac	ptac	NN	_	_	_
359	:	:	:	_	_	_
360	:	:	:	_	_	_
361	fnr	fnr	SYM	GEN	_	_
362	-	-	:	_	_	_
363	B	b	NN	_	_	_
364	-	-	:	_	_	_
365	4	4	CD	_	_	_
366	µM	µm	NN	_	_	_
367	IPTG	iptg	NN	_	_	_
368	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
369	Ptac	ptac	NN	_	_	_
370	:	:	:	_	_	_
371	:	:	:	_	_	_
372	fnr	fnr	SYM	GEN	_	_
373	-	-	:	_	_	_
374	B	b	NN	_	_	_
375	-	-	:	_	_	_
376	8	8	CD	_	_	_
377	µM	µm	NN	_	_	_
378	IPTG	iptg	NN	_	_	_
379	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
380	Ptac	ptac	NN	_	_	_
381	:	:	:	_	_	_
382	:	:	:	_	_	_
383	fnr	fnr	SYM	GEN	_	_
384	-	-	:	_	_	_
385	C	c	NN	_	_	_
386	-	-	:	_	_	_
387	16	16	CD	_	_	_
388	µM	µm	NN	_	_	_
389	IPTG	iptg	NN	_	_	_
390	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
391	ß	ß	SYM	_	_	_
392	-	-	:	_	_	_
393	Aerobic	aerobic	JJ	_	_	_
394	-	-	:	_	_	_
395	A	a	NN	_	_	_
396	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
397	ß	ß	SYM	_	_	_
398	-	-	:	_	_	_
399	Aerobic	aerobic	JJ	_	_	_
400	-	-	:	_	_	_
401	B	b	NN	_	_	_
402	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
403	ß	ß	SYM	_	_	_
404	-	-	:	_	_	_
405	Anaerobic	anaerobic	JJ	_	_	_
406	-	-	:	_	_	_
407	A	a	NN	_	_	_
408	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
409	ß	ß	SYM	_	_	_
410	-	-	:	_	_	_
411	Anaerobic	anaerobic	JJ	_	_	_
412	-	-	:	_	_	_
413	B	b	NN	_	_	_
414	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
415	ß	ß	NN	_	_	_
416	ChIP	chip	NN	_	_	_
417	DNA	dna	NN	_	_	_
418	from	from	IN	_	_	_
419	WT	WT	NNP	_	_	_
420	Escherichia	escherichia	FW	Organism	_	_
421	coli	coli	FW	Organism	_	_
422	MG1655	mg1655	NN	_	_	_
423	K-12	k-12	NN	_	_	_
424	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
425	strain	strain	NN	_	_	_
426	:	:	:	_	_	_
427	∆	∆	CD	_	_	_
428	hns	hn	NNS	GEN	_	_
429	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
430	strain	strain	NN	_	_	_
431	:	:	:	_	_	_
432	MG1655	mg1655	NN	_	_	_
433	K-12	k-12	NN	_	_	_
434	WT	wt	JJ	_	_	_
435	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
436	strain	strain	NN	_	_	_
437	:	:	:	_	_	_
438	PK4854	pk4854	NN	_	_	_
439	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
440	strain	strain	NN	_	_	_
441	:	:	:	_	_	_
442	PK8263	pk8263	NN	_	_	_
443	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
444	tag	tag	NN	GEN	_	_
445	:	:	:	_	_	_
446	MG1655	mg1655	NN	_	_	_
447	K-12	k-12	NN	_	_	_
448	WT	wt	JJ	_	_	_
449	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
450	10	10	CD	_	_	_
451	ng	ng	NN	_	_	_
452	of	of	IN	_	_	_
453	DNA	dna	NN	_	_	_
454	were	be	VBD	_	_	_
455	submitted	submit	VBN	_	_	_
456	to	to	TO	_	_	_
457	the	the	DT	_	_	_
458	University	University	NNP	_	_	_
459	of	of	IN	_	_	_
460	Wisconsin-Madison	Wisconsin-Madison	NNP	_	_	_
461	DNA	DNA	NNP	_	_	_
462	Sequencing	sequencing	NN	_	_	_
463	Facility	facility	NN	_	_	_
464	for	for	IN	_	_	_
465	ChIP-seq	ChIP-seq	NNP	_	_	_
466	library	library	NN	_	_	_
467	preparation	preparation	NN	_	_	_
468	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	sheared	shear	VBN	_	_	_
4	to	to	TO	_	_	_
5	200-500	200-500	CD	_	_	_
6	nt	nt	NNS	_	_	_
7	during	during	IN	_	_	_
8	the	the	DT	_	_	_
9	IP	IP	NNP	_	_	_
10	process	process	NN	_	_	_
11	to	to	TO	_	_	_
12	facilitate	facilitate	VB	_	_	_
13	library	library	NN	_	_	_
14	preparation	preparation	NN	_	_	_
15	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	libraries	library	NNS	_	_	_
3	were	be	VBD	_	_	_
4	generated	generate	VBN	_	_	_
5	using	use	VBG	_	_	_
6	reagents	reagent	NNS	_	_	_
7	from	from	IN	_	_	_
8	the	the	DT	_	_	_
9	Illumina	Illumina	NNP	_	_	_
10	Paired	Paired	NNP	_	_	_
11	End	End	NNP	_	_	_
12	Sample	Sample	NNP	_	_	_
13	Preparation	Preparation	NNP	_	_	_
14	Kit	kit	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Illumina	Illumina	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	the	the	DT	_	_	_
20	Illumina	Illumina	NNP	_	_	_
21	protocol	protocol	NN	_	_	_
22	``	``	``	_	_	_
23	Preparing	prepare	VBG	_	_	_
24	Samples	sample	NNS	_	_	_
25	for	for	IN	_	_	_
26	ChIP	chip	NN	_	_	_
27	Sequencing	sequencing	NN	_	_	_
28	of	of	IN	_	_	_
29	DNA	dna	NN	_	_	_
30	''	''	''	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Illumina	Illumina	NNP	_	_	_
33	part	part	NN	_	_	_
34	#	#	#	_	_	_
35	11257047	11257047	CD	_	_	_
36	RevA	reva	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	as	as	IN	_	_	_
39	per	per	IN	_	_	_
40	the	the	DT	_	_	_
41	manufacturer	manufacturer	NN	_	_	_
42	's	's	POS	_	_	_
43	instructions	instruction	NNS	_	_	_
44	,	,	,	_	_	_
45	except	except	IN	_	_	_
46	products	product	NNS	_	_	_
47	of	of	IN	_	_	_
48	the	the	DT	_	_	_
49	ligation	ligation	NN	_	_	_
50	reaction	reaction	NN	_	_	_
51	were	be	VBD	_	_	_
52	purified	purify	VBN	_	_	_
53	by	by	IN	_	_	_
54	gel	gel	NN	_	_	_
55	electrophoresis	electrophoresis	NN	_	_	_
56	using	use	VBG	_	_	_
57	2	2	CD	_	_	_
58	%	%	NN	_	_	_
59	SizeSelect	sizeselect	NN	_	_	_
60	agarose	agarose	NN	_	_	_
61	gels	gel	NNS	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	Invitrogen	Invitrogen	NNP	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	targeting	target	VBG	_	_	_
66	either	either	CC	_	_	_
67	275	275	CD	_	_	_
68	bp	bp	NN	_	_	_
69	fragments	fragment	NNS	_	_	_
70	-LRB-	-lrb-	-LRB-	_	_	_
71	s70	s70	NN	_	_	_
72	libraries	library	NNS	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	or	or	CC	_	_	_
75	400	400	CD	_	_	_
76	bp	bp	NN	_	_	_
77	fragments	fragment	NNS	_	_	_
78	-LRB-	-lrb-	-LRB-	_	_	_
79	FNR	fnr	NN	TF	_	_
80	libraries	library	NNS	_	_	_
81	-RRB-	-rrb-	-RRB-	_	_	_
82	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	library	library	NN	_	_	_
3	construction	construction	NN	_	_	_
4	and	and	CC	_	_	_
5	amplification	amplification	NN	_	_	_
6	,	,	,	_	_	_
7	quality	quality	NN	_	_	_
8	and	and	CC	_	_	_
9	quantity	quantity	NN	_	_	_
10	were	be	VBD	_	_	_
11	assessed	assess	VBN	_	_	_
12	using	use	VBG	_	_	_
13	an	a	DT	_	_	_
14	Agilent	agilent	JJ	_	_	_
15	DNA	dna	NN	_	_	_
16	1000	1000	CD	_	_	_
17	series	series	NN	_	_	_
18	chip	chip	NN	_	_	_
19	assay	assay	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Agilent	agilent	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	and	and	CC	_	_	_
24	QuantIT	quantit	NN	_	_	_
25	PicoGreen	picogreen	NN	_	_	_
26	dsDNA	dsdna	NN	_	_	_
27	Kit	kit	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Invitrogen	invitrogen	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	,	,	,	_	_	_
32	respectively	respectively	RB	_	_	_
33	,	,	,	_	_	_
34	and	and	CC	_	_	_
35	libraries	library	NNS	_	_	_
36	were	be	VBD	_	_	_
37	standardized	standardized	JJ	_	_	_
38	to	to	TO	_	_	_
39	10μM	10μm	NN	_	_	_
40	.	.	.	_	_	_

1	Cluster	cluster	NN	_	_	_
2	generation	generation	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	using	use	VBG	_	_	_
6	a	a	DT	_	_	_
7	cBot	cBot	NNP	_	_	_
8	Single	single	JJ	_	_	_
9	Read	Read	NNP	_	_	_
10	Cluster	Cluster	NNP	_	_	_
11	Generation	Generation	NNP	_	_	_
12	Kit	kit	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	v4	v4	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	and	and	CC	_	_	_
17	placed	place	VBN	_	_	_
18	on	on	IN	_	_	_
19	the	the	DT	_	_	_
20	Illumina	Illumina	NNP	_	_	_
21	cBot	cBot	NNP	_	_	_
22	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	single	single	JJ	_	_	_
3	read	read	NN	_	_	_
4	,	,	,	_	_	_
5	36	36	CD	_	_	_
6	bp	bp	NN	_	_	_
7	run	run	NN	_	_	_
8	was	be	VBD	_	_	_
9	performed	perform	VBN	_	_	_
10	,	,	,	_	_	_
11	using	use	VBG	_	_	_
12	standard	standard	JJ	_	_	_
13	SBS	SBS	NNP	_	_	_
14	kits	kit	NNS	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	v4	v4	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	SCS	scs	NN	_	_	_
20	2.6	2.6	CD	_	_	_
21	on	on	IN	_	_	_
22	an	a	DT	_	_	_
23	Illumina	Illumina	NNP	_	_	_
24	Genome	Genome	NNP	_	_	_
25	Analyzer	Analyzer	NNP	_	_	_
26	IIx	IIx	NNP	_	_	_
27	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	paired	paired	JJ	_	_	_
3	read	read	NN	_	_	_
4	,	,	,	_	_	_
5	100	100	CD	_	_	_
6	bp	bp	NN	_	_	_
7	runs	run	NNS	_	_	_
8	were	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	for	for	IN	_	_	_
11	one	one	CD	_	_	_
12	replicate	replicate	VB	_	_	_
13	of	of	IN	_	_	_
14	each	each	DT	_	_	_
15	s70	s70	NN	_	_	_
16	aerobic	aerobic	JJ	_	_	_
17	and	and	CC	_	_	_
18	anaerobic	anaerobic	JJ	_	_	_
19	growth	growth	NN	_	_	_
20	conditions	condition	NNS	_	_	_
21	,	,	,	_	_	_
22	using	use	VBG	_	_	_
23	standard	standard	JJ	_	_	_
24	SBS	SBS	NNP	_	_	_
25	kits	kit	NNS	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	v4	v4	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	and	and	CC	_	_	_
30	SCS	scs	NN	_	_	_
31	2.6	2.6	CD	_	_	_
32	on	on	IN	_	_	_
33	an	a	DT	_	_	_
34	Illumina	Illumina	NNP	_	_	_
35	HiSeq	HiSeq	NNP	_	_	_
36	.	.	.	_	_	_

1	Basecalling	basecall	VBG	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	using	use	VBG	_	_	_
5	the	the	DT	_	_	_
6	standard	standard	JJ	_	_	_
7	Illumina	Illumina	NNP	_	_	_
8	Pipeline	Pipeline	NNP	_	_	_
9	version	version	NN	_	_	_
10	1.6	1.6	CD	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Aerobic	Aerobic	NNP	_	_	_
3	Cultures	Cultures	NNP	_	_	_
4	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
5	aerobic	aerobic	JJ	_	_	_
6	INPUT	input	NN	_	_	_
7	DNA	dna	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Anaerobic	anaerobic	JJ	_	_	_
10	Cultures	culture	NNS	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	anaerobic	anaerobic	JJ	_	_	_
13	INPUT	input	NN	_	_	_
14	DNA	dna	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Antibodies	antibody	NNS	_	_	_
17	for	for	IN	_	_	_
18	beta	beta	NN	_	_	_
19	of	of	IN	_	_	_
20	RNAP	rnap	NN	_	_	_
21	-	-	:	_	_	_
22	NeoClone	NeoClone	NNP	_	_	_
23	,	,	,	_	_	_
24	Cat	Cat	NNP	_	_	_
25	Number	number	NN	_	_	_
26	:	:	:	_	_	_
27	W0002	w0002	NN	_	_	_
28	,	,	,	_	_	_
29	Lot	lot	NN	_	_	_
30	Number	number	NN	_	_	_
31	:	:	:	_	_	_
32	2008L10-001	2008l10-001	NN	_	_	_
33	Antibodies	antibody	NNS	_	_	_
34	for	for	IN	_	_	_
35	sigma70	sigma70	NN	_	_	_
36	of	of	IN	_	_	_
37	RNAP	rnap	NN	_	_	_
38	-	-	:	_	_	_
39	NeoClone	NeoClone	NNP	_	_	_
40	,	,	,	_	_	_
41	Cat	Cat	NNP	_	_	_
42	Number	number	NN	_	_	_
43	:	:	:	_	_	_
44	W0004	w0004	NN	_	_	_
45	,	,	,	_	_	_
46	Lot	lot	NN	_	_	_
47	Number	number	NN	_	_	_
48	:	:	:	_	_	_
49	2008K12-001	2008k12-001	NN	_	_	_
50	All	all	DT	_	_	_
51	other	other	JJ	_	_	_
52	antibodies	antibody	NNS	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	FNR	fnr	NN	TF	_	_
55	,	,	,	_	_	_
56	H-NS	h-ns	NN	_	_	_
57	,	,	,	_	_	_
58	IHF	ihf	NN	TF	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	were	be	VBD	_	_	_
61	produced	produce	VBN	_	_	_
62	in	in	IN	_	_	_
63	this	this	DT	_	_	_
64	study	study	NN	_	_	_
65	and	and	CC	_	_	_
66	are	be	VBP	_	_	_
67	not	not	RB	_	_	_
68	commercially	commercially	RB	_	_	_
69	available	available	JJ	_	_	_
70	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2	antibody	antibody	NN	_	_	_
3	:	:	:	_	_	_
4	Affinity	affinity	NN	_	_	_
5	purified	purify	VBN	_	_	_
6	FNR	fnr	NN	TF	_	_
7	polyclonal	polyclonal	JJ	_	_	_
8	antibody	antibody	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	antibody	antibody	NN	_	_	_
11	:	:	:	_	_	_
12	INPUT	INPUT	NNP	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
14	antibody	antibody	NN	_	_	_
15	:	:	:	_	_	_
16	RNA	rna	NN	_	_	_
17	Polymerase	polymerase	NN	_	_	_
18	σ70	σ70	NN	_	_	_
19	monoclonal	monoclonal	JJ	_	_	_
20	antibody	antibody	NN	_	_	_
21	from	from	IN	_	_	_
22	NeoClone	NeoClone	NNP	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	W0004	w0004	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	Cell	cell	NN	_	_	_
28	pellets	pellet	NNS	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	from	from	IN	_	_	_
31	initial	initial	JJ	_	_	_
32	50	50	CD	_	_	_
33	ml	ml	NN	_	_	_
34	of	of	IN	_	_	_
35	culture	culture	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	were	be	VBD	_	_	_
38	thawed	thaw	VBN	_	_	_
39	and	and	CC	_	_	_
40	resuspended	resuspend	VBN	_	_	_
41	in	in	IN	_	_	_
42	250ul	250ul	NN	_	_	_
43	of	of	IN	_	_	_
44	IP	IP	NNP	_	_	_
45	buffer	buffer	NN	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	100	100	CD	_	_	_
48	mM	mm	NN	KWSUPP	_	_
49	Tris	Tris	NNP	_	_	_
50	pH	ph	NN	_	_	_
51	8	8	CD	_	_	_
52	,	,	,	_	_	_
53	300	300	CD	_	_	_
54	mM	mm	NN	KWSUPP	_	_
55	NaCl	nacl	NN	_	_	_
56	,	,	,	_	_	_
57	2	2	CD	_	_	_
58	%	%	NN	_	_	_
59	TritonX-100	tritonx-100	NN	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	and	and	CC	_	_	_
62	sonicated	sonicate	VBN	_	_	_
63	using	use	VBG	_	_	_
64	a	a	DT	_	_	_
65	microtip	microtip	NN	_	_	_
66	sonicator	sonicator	NN	_	_	_
67	set	set	VBN	_	_	_
68	at	at	IN	_	_	_
69	10	10	CD	_	_	_
70	%	%	NN	_	_	_
71	output	output	NN	_	_	_
72	for	for	IN	_	_	_
73	20	20	CD	_	_	_
74	second	second	JJ	_	_	_
75	intervals	interval	NNS	_	_	_
76	with	with	IN	_	_	_
77	periods	period	NNS	_	_	_
78	of	of	IN	_	_	_
79	cooling	cool	VBG	_	_	_
80	in	in	IN	_	_	_
81	between	between	IN	_	_	_
82	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	treated	treat	VBN	_	_	_
5	for	for	IN	_	_	_
6	one	one	CD	_	_	_
7	hour	hour	NN	_	_	_
8	at	at	IN	_	_	_
9	4	4	CD	_	_	_
10	°C	°c	NN	_	_	_
11	with	with	IN	_	_	_
12	RNase	rnase	NN	_	_	_
13	A	a	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	2	2	CD	_	_	_
16	ng	ng	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Cells	cell	NNS	_	_	_
19	were	be	VBD	_	_	_
20	grown	grow	VBN	_	_	_
21	anaerobically	anaerobically	RB	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	95	95	CD	_	_	_
24	%	%	NN	_	_	_
25	N2	n2	NN	_	_	_
26	and	and	CC	_	_	_
27	5	5	CD	_	_	_
28	%	%	NN	_	_	_
29	CO2	co2	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	until	until	IN	_	_	_
32	mid-log	mid-log	JJ	_	_	_
33	phase	phase	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	OD600	od600	NN	_	_	_
36	of	of	IN	_	_	_
37	0.3	0.3	CD	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	and	and	CC	_	_	_
40	treated	treat	VBN	_	_	_
41	with	with	IN	_	_	_
42	1	1	CD	_	_	_
43	%	%	NN	_	_	_
44	final	final	JJ	_	_	_
45	volumen	voluman	NNS	_	_	_
46	formaldehyde	formaldehyde	NN	_	_	_
47	for	for	IN	_	_	_
48	ten	ten	CD	_	_	_
49	minutes	minute	NNS	_	_	_
50	.	.	.	_	_	_

1	Sodium	sodium	NN	_	_	_
2	phosphate	phosphate	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	ChIP-Seq	chip-seq	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	DNA	dna	NN	_	_	_
9	were	be	VBD	_	_	_
10	submitted	submit	VBN	_	_	_
11	to	to	TO	_	_	_
12	the	the	DT	_	_	_
13	Joint	Joint	NNP	_	_	_
14	Genome	Genome	NNP	_	_	_
15	Institute	Institute	NNP	_	_	_
16	for	for	IN	_	_	_
17	ChIP-seq	ChIP-seq	NNP	_	_	_
18	library	library	NN	_	_	_
19	preparation	preparation	NN	_	_	_
20	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	sheared	shear	VBN	_	_	_
4	to	to	TO	_	_	_
5	200-500	200-500	CD	_	_	_
6	nt	nt	NNS	_	_	_
7	during	during	IN	_	_	_
8	the	the	DT	_	_	_
9	IP	IP	NNP	_	_	_
10	process	process	NN	_	_	_
11	to	to	TO	_	_	_
12	facilitate	facilitate	VB	_	_	_
13	library	library	NN	_	_	_
14	preparation	preparation	NN	_	_	_
15	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	libraries	library	NNS	_	_	_
3	were	be	VBD	_	_	_
4	generated	generate	VBN	_	_	_
5	using	use	VBG	_	_	_
6	reagents	reagent	NNS	_	_	_
7	from	from	IN	_	_	_
8	the	the	DT	_	_	_
9	Illumina	Illumina	NNP	_	_	_
10	Paired	Paired	NNP	_	_	_
11	End	End	NNP	_	_	_
12	Sample	Sample	NNP	_	_	_
13	Preparation	Preparation	NNP	_	_	_
14	Kit	kit	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Illumina	Illumina	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	the	the	DT	_	_	_
20	Illumina	Illumina	NNP	_	_	_
21	protocol	protocol	NN	_	_	_
22	``	``	``	_	_	_
23	Preparing	prepare	VBG	_	_	_
24	Samples	sample	NNS	_	_	_
25	for	for	IN	_	_	_
26	ChIP	chip	NN	_	_	_
27	Sequencing	sequencing	NN	_	_	_
28	of	of	IN	_	_	_
29	DNA	dna	NN	_	_	_
30	''	''	''	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Illumina	Illumina	NNP	_	_	_
33	part	part	NN	_	_	_
34	#	#	#	_	_	_
35	11257047	11257047	CD	_	_	_
36	RevA	reva	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	as	as	IN	_	_	_
39	per	per	IN	_	_	_
40	the	the	DT	_	_	_
41	manufacturer	manufacturer	NN	_	_	_
42	's	's	POS	_	_	_
43	instructions	instruction	NNS	_	_	_
44	,	,	,	_	_	_
45	except	except	IN	_	_	_
46	products	product	NNS	_	_	_
47	of	of	IN	_	_	_
48	the	the	DT	_	_	_
49	ligation	ligation	NN	_	_	_
50	reaction	reaction	NN	_	_	_
51	were	be	VBD	_	_	_
52	purified	purify	VBN	_	_	_
53	by	by	IN	_	_	_
54	gel	gel	NN	_	_	_
55	electrophoresis	electrophoresis	NN	_	_	_
56	using	use	VBG	_	_	_
57	2	2	CD	_	_	_
58	%	%	NN	_	_	_
59	SizeSelect	sizeselect	NN	_	_	_
60	agarose	agarose	NN	_	_	_
61	gels	gel	NNS	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	Invitrogen	Invitrogen	NNP	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	targeting	target	VBG	_	_	_
66	either	either	CC	_	_	_
67	275	275	CD	_	_	_
68	bp	bp	NN	_	_	_
69	fragments	fragment	NNS	_	_	_
70	-LRB-	-lrb-	-LRB-	_	_	_
71	s70	s70	NN	_	_	_
72	libraries	library	NNS	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	library	library	NN	_	_	_
3	construction	construction	NN	_	_	_
4	and	and	CC	_	_	_
5	amplification	amplification	NN	_	_	_
6	,	,	,	_	_	_
7	quality	quality	NN	_	_	_
8	and	and	CC	_	_	_
9	quantity	quantity	NN	_	_	_
10	were	be	VBD	_	_	_
11	assessed	assess	VBN	_	_	_
12	using	use	VBG	_	_	_
13	an	a	DT	_	_	_
14	Agilent	agilent	JJ	_	_	_
15	DNA	dna	NN	_	_	_
16	1000	1000	CD	_	_	_
17	series	series	NN	_	_	_
18	chip	chip	NN	_	_	_
19	assay	assay	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Agilent	agilent	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	and	and	CC	_	_	_
24	QuantIT	quantit	NN	_	_	_
25	PicoGreen	picogreen	NN	_	_	_
26	dsDNA	dsdna	NN	_	_	_
27	Kit	kit	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Invitrogen	invitrogen	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	,	,	,	_	_	_
32	respectively	respectively	RB	_	_	_
33	,	,	,	_	_	_
34	and	and	CC	_	_	_
35	libraries	library	NNS	_	_	_
36	were	be	VBD	_	_	_
37	standardized	standardized	JJ	_	_	_
38	to	to	TO	_	_	_
39	10μM	10μm	NN	_	_	_
40	.	.	.	_	_	_

1	Cluster	cluster	NN	_	_	_
2	generation	generation	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	using	use	VBG	_	_	_
6	a	a	DT	_	_	_
7	cBot	cBot	NNP	_	_	_
8	Single	single	JJ	_	_	_
9	Read	Read	NNP	_	_	_
10	Cluster	Cluster	NNP	_	_	_
11	Generation	Generation	NNP	_	_	_
12	Kit	kit	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	v4	v4	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	and	and	CC	_	_	_
17	placed	place	VBN	_	_	_
18	on	on	IN	_	_	_
19	the	the	DT	_	_	_
20	Illumina	Illumina	NNP	_	_	_
21	cBot	cBot	NNP	_	_	_
22	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	single	single	JJ	_	_	_
3	read	read	NN	_	_	_
4	,	,	,	_	_	_
5	36	36	CD	_	_	_
6	bp	bp	NN	_	_	_
7	run	run	NN	_	_	_
8	was	be	VBD	_	_	_
9	performed	perform	VBN	_	_	_
10	,	,	,	_	_	_
11	using	use	VBG	_	_	_
12	standard	standard	JJ	_	_	_
13	SBS	SBS	NNP	_	_	_
14	kits	kit	NNS	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	v4	v4	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	SCS	scs	NN	_	_	_
20	2.6	2.6	CD	_	_	_
21	on	on	IN	_	_	_
22	an	a	DT	_	_	_
23	Illumina	Illumina	NNP	_	_	_
24	Genome	Genome	NNP	_	_	_
25	Analyzer	Analyzer	NNP	_	_	_
26	IIx	IIx	NNP	_	_	_
27	.	.	.	_	_	_

1	Basecalling	basecall	VBG	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	using	use	VBG	_	_	_
5	the	the	DT	_	_	_
6	standard	standard	JJ	_	_	_
7	Illumina	Illumina	NNP	_	_	_
8	Pipeline	Pipeline	NNP	_	_	_
9	version	version	NN	_	_	_
10	1.6	1.6	CD	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655star	mg1655star	JJ	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	FNR	fnr	NN	TF	_	_
4	IP	IP	NNP	_	_	_
5	ChIP-seq	ChIP-seq	NNP	_	_	_
6	Anaerobic	Anaerobic	NNP	_	_	_
7	A	A	NNP	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	FNR	FNR	NNP	TF	_	_
10	_	_	SYM	_	_	_
11	IP	IP	NNP	_	_	_
12	_	_	SYM	_	_	_
13	ChIP-seq	ChIP-seq	NNP	_	_	_
14	_	_	SYM	_	_	_
15	Anaerobic	anaerobic	JJ	_	_	_
16	_	_	NN	_	_	_
17	A	a	DT	_	_	_
18	_	_	NN	_	_	_
19	WIG.wig	wig.wig	NN	_	_	_
20	:	:	:	_	_	_
21	U00096	u00096	NN	_	_	_
22	.2	.2	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	FNR	fnr	NN	TF	_	_
25	IP	IP	NNP	_	_	_
26	ChIP-seq	ChIP-seq	NNP	_	_	_
27	Anaerobic	anaerobic	JJ	_	_	_
28	B	b	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	FNR	fnr	NN	TF	_	_
31	_	_	CD	_	_	_
32	IP	IP	NNP	_	_	_
33	_	_	SYM	_	_	_
34	ChIP-seq	ChIP-seq	NNP	_	_	_
35	_	_	SYM	_	_	_
36	Anaerobic	anaerobic	JJ	_	_	_
37	_	_	NN	_	_	_
38	B	b	NN	_	_	_
39	_	_	CD	_	_	_
40	WIG.wig	wig.wig	NN	_	_	_
41	:	:	:	_	_	_
42	U00096	u00096	NN	_	_	_
43	.2	.2	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	Genome	Genome	NNP	_	_	_
46	Build	Build	NNP	_	_	_
47	:	:	:	_	_	_
48	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
49	Genome	Genome	NNP	_	_	_
50	_	_	NNP	_	_	_
51	build	build	VB	_	_	_
52	:	:	:	_	_	_
53	U00096	u00096	NN	_	_	_
54	.2	.2	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	growth	growth	NN	_	_	_
57	condition	condition	NN	_	_	_
58	:	:	:	_	_	_
59	Aerobic	Aerobic	NNP	_	_	_
60	Cultures	Cultures	NNP	_	_	_
61	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
62	growth	growth	NN	_	_	_
63	condition	condition	NN	_	_	_
64	:	:	:	_	_	_
65	Anaerobic	anaerobic	JJ	_	_	_
66	Cultures	culture	NNS	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
68	INPUT	input	VBP	_	_	_
69	_	_	SYM	_	_	_
70	ChIP-seq	ChIP-seq	NNP	_	_	_
71	_	_	NNP	_	_	_
72	Aerobic	Aerobic	NNP	_	_	_
73	_	_	SYM	_	_	_
74	WIG.wig	WIG.wig	NNP	_	_	_
75	:	:	:	_	_	_
76	U00096	u00096	NN	_	_	_
77	.2	.2	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
79	INPUT	input	VBP	_	_	_
80	_	_	SYM	_	_	_
81	ChIP-seq	ChIP-seq	NNP	_	_	_
82	_	_	SYM	_	_	_
83	Anaerobic	anaerobic	JJ	_	_	_
84	_	_	NN	_	_	_
85	WIG.wig	wig.wig	NN	_	_	_
86	:	:	:	_	_	_
87	U00096	u00096	NN	_	_	_
88	.2	.2	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	INPUT	input	NN	_	_	_
91	DNA	dna	NN	_	_	_
92	B	b	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	Sequence	sequence	NN	_	_	_
95	reads	read	VBZ	_	_	_
96	were	be	VBD	_	_	_
97	aligned	align	VBN	_	_	_
98	to	to	TO	_	_	_
99	the	the	DT	_	_	_
100	published	publish	VBN	_	_	_
101	E.	e.	FW	_	_	_
102	coli	coli	FW	_	_	_
103	K-12	k-12	NN	_	_	_
104	MG1655	mg1655	NN	_	_	_
105	genome	genome	NN	_	_	_
106	-LRB-	-lrb-	-LRB-	_	_	_
107	U00096	u00096	NN	_	_	_
108	.2	.2	NN	_	_	_
109	-RRB-	-rrb-	-RRB-	_	_	_
110	using	use	VBG	_	_	_
111	the	the	DT	_	_	_
112	software	software	NN	_	_	_
113	packages	package	NNS	_	_	_
114	SOAP	soap	NN	_	_	_
115	-LRB-	-lrb-	-LRB-	_	_	_
116	Li	Li	NNP	_	_	_
117	et	et	FW	_	_	_
118	al	al	FW	_	_	_
119	,	,	,	_	_	_
120	2009	2009	CD	_	_	_
121	-RRB-	-rrb-	-RRB-	_	_	_
122	and	and	CC	_	_	_
123	ELAND	ELAND	NNP	_	_	_
124	-LRB-	-lrb-	-LRB-	_	_	_
125	within	within	IN	_	_	_
126	the	the	DT	_	_	_
127	Illumina	Illumina	NNP	_	_	_
128	Genome	Genome	NNP	_	_	_
129	Analyzer	Analyzer	NNP	_	_	_
130	Pipeline	Pipeline	NNP	_	_	_
131	Software	Software	NNP	_	_	_
132	-RRB-	-rrb-	-RRB-	_	_	_
133	,	,	,	_	_	_
134	allowing	allow	VBG	_	_	_
135	at	at	IN	_	_	_
136	most	most	JJS	_	_	_
137	two	two	CD	_	_	_
138	mismatches	mismatch	NNS	_	_	_
139	.	.	.	_	_	_

1	Sequence	sequence	NN	_	_	_
2	reads	read	VBZ	_	_	_
3	with	with	IN	_	_	_
4	sequences	sequence	NNS	_	_	_
5	that	that	WDT	_	_	_
6	did	do	VBD	_	_	_
7	not	not	RB	_	_	_
8	align	align	VB	_	_	_
9	to	to	TO	_	_	_
10	the	the	DT	_	_	_
11	genome	genome	NN	_	_	_
12	,	,	,	_	_	_
13	aligned	align	VBN	_	_	_
14	to	to	TO	_	_	_
15	multiple	multiple	JJ	_	_	_
16	locations	location	NNS	_	_	_
17	on	on	IN	_	_	_
18	the	the	DT	_	_	_
19	genome	genome	NN	_	_	_
20	,	,	,	_	_	_
21	or	or	CC	_	_	_
22	contained	contain	VBD	_	_	_
23	more	more	JJR	_	_	_
24	than	than	IN	_	_	_
25	two	two	CD	_	_	_
26	mismatches	mismatch	NNS	_	_	_
27	were	be	VBD	_	_	_
28	discarded	discard	VBN	_	_	_
29	from	from	IN	_	_	_
30	further	further	JJ	_	_	_
31	analysis	analysis	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	<	<	JJR	_	_	_
34	10	10	CD	_	_	_
35	%	%	NN	_	_	_
36	of	of	IN	_	_	_
37	reads	read	VBZ	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	Supplemental	Supplemental	NNP	_	_	_
41	Files	Files	NNP	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	visualization	visualization	NN	_	_	_
3	the	the	DT	_	_	_
4	raw	raw	JJ	_	_	_
5	tag	tag	NN	GEN	_	_
6	density	density	NN	_	_	_
7	at	at	IN	_	_	_
8	each	each	DT	_	_	_
9	position	position	NN	_	_	_
10	was	be	VBD	_	_	_
11	calculated	calculate	VBN	_	_	_
12	using	use	VBG	_	_	_
13	QuEST	quest	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Valouev	Valouev	NNP	_	_	_
16	et	et	FW	_	_	_
17	al	al	FW	_	_	_
18	,	,	,	_	_	_
19	2008	2008	CD	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	and	and	CC	_	_	_
22	normalized	normalize	VBD	_	_	_
23	as	as	IN	_	_	_
24	tag	tag	NN	GEN	_	_
25	density	density	NN	_	_	_
26	per	per	IN	_	_	_
27	million	million	CD	_	_	_
28	uniquely	uniquely	RB	_	_	_
29	mapped	map	VBN	_	_	_
30	reads	read	VBZ	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Sigma70	sigma70	NN	_	_	_
3	_	_	CD	_	_	_
4	IP	IP	NNP	_	_	_
5	_	_	SYM	_	_	_
6	ChIP-seq	ChIP-seq	NNP	_	_	_
7	_	_	NNP	_	_	_
8	Aerobic	Aerobic	NNP	_	_	_
9	_	_	SYM	_	_	_
10	A	a	DT	_	_	_
11	_	_	JJ	_	_	_
12	SET	SET	NNP	_	_	_
13	_	_	SYM	_	_	_
14	WIG.wig	WIG.wig	NNP	_	_	_
15	:	:	:	_	_	_
16	U00096	u00096	NN	_	_	_
17	.2	.2	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Sigma70	sigma70	NN	_	_	_
20	_	_	CD	_	_	_
21	IP	IP	NNP	_	_	_
22	_	_	SYM	_	_	_
23	ChIP-seq	ChIP-seq	NNP	_	_	_
24	_	_	SYM	_	_	_
25	Anaerobic	anaerobic	JJ	_	_	_
26	_	_	NN	_	_	_
27	A	a	DT	_	_	_
28	_	_	JJ	_	_	_
29	SET	SET	NNP	_	_	_
30	_	_	SYM	_	_	_
31	WIG.wig	WIG.wig	NNP	_	_	_
32	:	:	:	_	_	_
33	U00096	u00096	NN	_	_	_
34	.2	.2	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	strain	strain	NN	_	_	_
37	:	:	:	_	_	_
38	Wild	Wild	NNP	_	_	_
39	Type	type	NN	_	_	_
40	K-12	k-12	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	σ70	σ70	NN	_	_	_
43	IP	IP	NNP	_	_	_
44	ChIP-seq	ChIP-seq	NNP	_	_	_
45	Aerobic	Aerobic	NNP	_	_	_
46	A	A	NNP	_	_	_
47	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
48	σ70	σ70	NN	_	_	_
49	IP	IP	NNP	_	_	_
50	ChIP-seq	ChIP-seq	NNP	_	_	_
51	Aerobic	Aerobic	NNP	_	_	_
52	B	B	NNP	_	_	_
53	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
54	σ70	σ70	NN	_	_	_
55	IP	IP	NNP	_	_	_
56	ChIP-seq	ChIP-seq	NNP	_	_	_
57	Anaerobic	Anaerobic	NNP	_	_	_
58	A	A	NNP	_	_	_
59	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
60	σ70	σ70	NN	_	_	_
61	IP	IP	NNP	_	_	_
62	ChIP-seq	ChIP-seq	NNP	_	_	_
63	Anaerobic	anaerobic	JJ	_	_	_
64	B	b	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	Cells	cell	NNS	_	_	_
67	were	be	VBD	_	_	_
68	treated	treat	VBN	_	_	_
69	with	with	IN	_	_	_
70	a	a	DT	_	_	_
71	stop	stop	NN	_	_	_
72	solution	solution	NN	_	_	_
73	of	of	IN	_	_	_
74	Phenol	phenol	NN	_	_	_
75	and	and	CC	_	_	_
76	Ethanol	ethanol	NN	_	_	_
77	,	,	,	_	_	_
78	spun	spin	VBD	_	_	_
79	down	down	RB	_	_	_
80	and	and	CC	_	_	_
81	flash	flash	VB	_	_	_
82	frozen	frozen	JJ	_	_	_
83	and	and	CC	_	_	_
84	stored	store	VBN	_	_	_
85	at	at	IN	_	_	_
86	-80	-80	CD	_	_	_
87	°C	°c	NN	_	_	_
88	-LRB-	-lrb-	-LRB-	_	_	_
89	ref	ref	NN	_	_	_
90	-RRB-	-rrb-	-RRB-	_	_	_
91	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	using	use	VBG	_	_	_
6	a	a	DT	_	_	_
7	hot	hot	JJ	_	_	_
8	phenol	phenol	NN	_	_	_
9	method	method	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	ref	ref	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	quality	quality	NN	_	_	_
3	was	be	VBD	_	_	_
4	determined	determine	VBN	_	_	_
5	by	by	IN	_	_	_
6	analysis	analysis	NN	_	_	_
7	with	with	IN	_	_	_
8	an	a	DT	_	_	_
9	Agilent	Agilent	NNP	_	_	_
10	2100	2100	CD	_	_	_
11	bioanalyzer	bioanalyzer	NN	_	_	_
12	and	and	CC	_	_	_
13	quantity	quantity	NN	_	_	_
14	was	be	VBD	_	_	_
15	determined	determine	VBN	_	_	_
16	using	use	VBG	_	_	_
17	a	a	DT	_	_	_
18	NanoDrop	NanoDrop	NNP	_	_	_
19	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	enrich	enrich	VB	_	_	_
3	for	for	IN	_	_	_
4	mRNA	mrna	NN	_	_	_
5	,	,	,	_	_	_
6	the	the	DT	_	_	_
7	23S	23s	NN	_	_	_
8	and	and	CC	_	_	_
9	16S	16s	NN	_	_	_
10	rRNA	rrna	NN	_	_	_
11	were	be	VBD	_	_	_
12	removed	remove	VBN	_	_	_
13	using	use	VBG	_	_	_
14	the	the	DT	_	_	_
15	Ambion	Ambion	NNP	_	_	_
16	MICROBExpress	MICROBExpress	NNP	_	_	_
17	kit	kit	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Ambion	ambion	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	following	follow	VBG	_	_	_
22	manufacturer	manufacturer	NN	_	_	_
23	's	's	POS	_	_	_
24	guidelines	guideline	NNS	_	_	_
25	,	,	,	_	_	_
26	except	except	IN	_	_	_
27	the	the	DT	_	_	_
28	total	total	JJ	_	_	_
29	RNA	rna	NN	_	_	_
30	was	be	VBD	_	_	_
31	incubated	incubate	VBN	_	_	_
32	with	with	IN	_	_	_
33	the	the	DT	_	_	_
34	rRNA	rrna	NN	_	_	_
35	oligonucleotides	oligonucleotide	NNS	_	_	_
36	for	for	IN	_	_	_
37	one	one	CD	_	_	_
38	hour	hour	NN	_	_	_
39	instead	instead	RB	_	_	_
40	of	of	IN	_	_	_
41	15	15	CD	_	_	_
42	minutes	minute	NNS	_	_	_
43	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Ecoli	Ecoli	NNP	_	_	_
3	_	_	SYM	_	_	_
4	dFNR	dfnr	NN	_	_	_
5	_	_	CD	_	_	_
6	rep1	rep1	NN	_	_	_
7	_	_	NN	_	_	_
8	anaerobic	anaerobic	JJ	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Ecoli	ecolus	NNS	_	_	_
11	_	_	VBP	_	_	_
12	dFNR	dfnr	NN	_	_	_
13	_	_	CD	_	_	_
14	rep2	rep2	NN	_	_	_
15	_	_	NN	_	_	_
16	anaerobic	anaerobic	JJ	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Ecoli	ecolus	NNS	_	_	_
19	_	_	VBP	_	_	_
20	wild-type	wild-type	JJ	_	_	_
21	_	_	NN	_	_	_
22	rep1	rep1	NN	_	_	_
23	_	_	NN	_	_	_
24	anaerobic	anaerobic	JJ	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Ecoli	ecolus	NNS	_	_	_
27	_	_	VBP	_	_	_
28	wild-type	wild-type	JJ	_	_	_
29	_	_	NN	_	_	_
30	rep2	rep2	NN	_	_	_
31	_	_	CD	_	_	_
32	anaerobic	anaerobic	JJ	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	Escherichia	escherichia	FW	Organism	_	_
35	coli	coli	FW	Organism	_	_
36	MG1655	mg1655	NN	_	_	_
37	K-12	k-12	NN	_	_	_
38	dFNR	dfnr	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	PK4854	pk4854	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	Escherichia	escherichia	FW	Organism	_	_
44	coli	coli	FW	Organism	_	_
45	MG1655	mg1655	NN	_	_	_
46	K-12	k-12	NN	_	_	_
47	WT	WT	NNP	_	_	_
48	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
49	Escherichia	escherichia	FW	Organism	_	_
50	coli	coli	FW	Organism	_	_
51	MG1655	mg1655	NN	_	_	_
52	K-12	k-12	NN	_	_	_
53	WT	wt	NN	_	_	_
54	and	and	CC	_	_	_
55	∆	∆	NN	_	_	_
56	fnr	fnr	NN	GEN	_	_
57	were	be	VBD	_	_	_
58	grown	grow	VBN	_	_	_
59	to	to	TO	_	_	_
60	mid-log	mid-log	JJ	_	_	_
61	phase	phase	NN	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	O.D.	o.d.	NN	_	_	_
64	600nm	600nm	CD	_	_	_
65	0.3	0.3	CD	_	_	_
66	-RRB-	-rrb-	-RRB-	_	_	_
67	anerobically	anerobically	RB	_	_	_
68	-LRB-	-lrb-	-LRB-	_	_	_
69	95	95	CD	_	_	_
70	%	%	NN	_	_	_
71	N2	n2	NN	_	_	_
72	,	,	,	_	_	_
73	5	5	CD	_	_	_
74	%	%	NN	_	_	_
75	CO2	co2	NN	_	_	_
76	-RRB-	-rrb-	-RRB-	_	_	_
77	at	at	IN	_	_	_
78	37	37	CD	_	_	_
79	°C	°c	NN	_	_	_
80	in	in	IN	_	_	_
81	MOPS	MOPS	NNP	MED	_	_
82	+0.2	+0.2	CD	_	_	_
83	%	%	NN	_	_	_
84	glucose	glucose	NN	SUPP	_	_
85	media	media	NNS	_	_	_
86	-LRB-	-lrb-	-LRB-	_	_	_
87	Ref	ref	NN	_	_	_
88	-RRB-	-rrb-	-RRB-	_	_	_
89	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655star	mg1655star	JJ	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	FNR	fnr	SYM	TF	_	_
4	-	-	:	_	_	_
5	_	_	SYM	_	_	_
6	Anaerobic	anaerobic	JJ	_	_	_
7	_	_	NN	_	_	_
8	RNAseq	rnaseq	NN	_	_	_
9	_	_	CD	_	_	_
10	A	a	DT	_	_	_
11	_	_	NN	_	_	_
12	Tag	tag	NN	_	_	_
13	_	_	CD	_	_	_
14	Count.txt	count.txt	NN	_	_	_
15	:	:	:	_	_	_
16	U00096	u00096	NN	_	_	_
17	.2	.2	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	FNR	fnr	SYM	TF	_	_
20	-	-	:	_	_	_
21	_	_	SYM	_	_	_
22	Anaerobic	anaerobic	JJ	_	_	_
23	_	_	NN	_	_	_
24	RNAseq	rnaseq	NN	_	_	_
25	_	_	CD	_	_	_
26	A	a	DT	_	_	_
27	_	_	NN	_	_	_
28	WIG.wig	wig.wig	NN	_	_	_
29	:	:	:	_	_	_
30	U00096	u00096	NN	_	_	_
31	.2	.2	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	FNR	fnr	SYM	TF	_	_
34	-	-	:	_	_	_
35	_	_	SYM	_	_	_
36	Anaerobic	anaerobic	JJ	_	_	_
37	_	_	NN	_	_	_
38	RNAseq	rnaseq	NN	_	_	_
39	_	_	NN	_	_	_
40	B	b	NN	_	_	_
41	_	_	CD	_	_	_
42	Tag	tag	NN	_	_	_
43	_	_	CD	_	_	_
44	Count.txt	count.txt	NN	_	_	_
45	:	:	:	_	_	_
46	U00096	u00096	NN	_	_	_
47	.2	.2	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	FNR	fnr	SYM	TF	_	_
50	-	-	:	_	_	_
51	_	_	SYM	_	_	_
52	Anaerobic	anaerobic	JJ	_	_	_
53	_	_	NN	_	_	_
54	RNAseq	rnaseq	NN	_	_	_
55	_	_	NN	_	_	_
56	B	b	NN	_	_	_
57	_	_	CD	_	_	_
58	WIG.wig	wig.wig	NN	_	_	_
59	:	:	:	_	_	_
60	U00096	u00096	NN	_	_	_
61	.2	.2	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	Genome	Genome	NNP	_	_	_
64	Build	Build	NNP	_	_	_
65	:	:	:	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	genoype	genoype	NN	_	_	_
68	:	:	:	_	_	_
69	dFNR	dfnr	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	genoype	genoype	NN	_	_	_
72	:	:	:	_	_	_
73	Wild-Type	wild-type	JJ	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	growth	growth	NN	_	_	_
76	condition	condition	NN	_	_	_
77	:	:	:	_	_	_
78	anaerobic	anaerobic	JJ	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	phenotype	phenotype	NN	_	_	_
81	:	:	:	_	_	_
82	lacking	lack	VBG	_	_	_
83	FNR	fnr	NN	TF	_	_
84	protein	protein	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	phenotype	phenotype	NN	_	_	_
87	:	:	:	_	_	_
88	normal	normal	JJ	_	_	_
89	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
90	Resulting	result	VBG	_	_	_
91	reads	read	VBZ	_	_	_
92	were	be	VBD	_	_	_
93	aligned	align	VBN	_	_	_
94	to	to	TO	_	_	_
95	the	the	DT	_	_	_
96	published	publish	VBN	_	_	_
97	E.	e.	FW	_	_	_
98	coli	coli	FW	_	_	_
99	K-12	k-12	NN	_	_	_
100	MG1655	mg1655	NN	_	_	_
101	genome	genome	NN	_	_	_
102	-LRB-	-lrb-	-LRB-	_	_	_
103	U00096	u00096	NN	_	_	_
104	.2	.2	NN	_	_	_
105	-RRB-	-rrb-	-RRB-	_	_	_
106	using	use	VBG	_	_	_
107	the	the	DT	_	_	_
108	software	software	NN	_	_	_
109	package	package	NN	_	_	_
110	SOAP	soap	NN	_	_	_
111	-LRB-	-lrb-	-LRB-	_	_	_
112	Li	Li	NNP	_	_	_
113	et	et	FW	_	_	_
114	al	al	FW	_	_	_
115	,	,	,	_	_	_
116	2009	2009	CD	_	_	_
117	-RRB-	-rrb-	-RRB-	_	_	_
118	,	,	,	_	_	_
119	allowing	allow	VBG	_	_	_
120	no	no	RB	_	_	_
121	more	more	JJR	_	_	_
122	than	than	IN	_	_	_
123	two	two	CD	_	_	_
124	mismatches	mismatch	NNS	_	_	_
125	-LRB-	-lrb-	-LRB-	_	_	_
126	Supplemental	Supplemental	NNP	_	_	_
127	File	File	NNP	_	_	_
128	-RRB-	-rrb-	-RRB-	_	_	_
129	.	.	.	_	_	_

1	Reads	read	VBZ	_	_	_
2	aligning	align	VBG	_	_	_
3	to	to	TO	_	_	_
4	repeated	repeated	JJ	_	_	_
5	elements	element	NNS	_	_	_
6	in	in	IN	_	_	_
7	the	the	DT	_	_	_
8	genome	genome	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	e.g.	e.g.	FW	_	_	_
11	rRNA	rrna	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	were	be	VBD	_	_	_
14	removed	remove	VBN	_	_	_
15	from	from	IN	_	_	_
16	analysis	analysis	NN	_	_	_
17	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	reads	read	VBZ	_	_	_
3	that	that	IN	_	_	_
4	had	have	VBD	_	_	_
5	no	no	DT	_	_	_
6	mapping	mapping	NN	_	_	_
7	locations	location	NNS	_	_	_
8	for	for	IN	_	_	_
9	the	the	DT	_	_	_
10	first	first	JJ	_	_	_
11	36	36	CD	_	_	_
12	bp	bp	NN	_	_	_
13	,	,	,	_	_	_
14	the	the	DT	_	_	_
15	3-30	3-30	CD	_	_	_
16	bp	bp	NN	_	_	_
17	subsequences	subsequence	NNS	_	_	_
18	were	be	VBD	_	_	_
19	used	use	VBN	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	subsequent	subsequent	JJ	_	_	_
23	mapping	mapping	NN	_	_	_
24	to	to	TO	_	_	_
25	the	the	DT	_	_	_
26	reference	reference	NN	_	_	_
27	genome	genome	NN	_	_	_
28	.	.	.	_	_	_

1	Reads	read	NNS	_	_	_
2	that	that	WDT	_	_	_
3	had	have	VBD	_	_	_
4	unique	unique	JJ	_	_	_
5	mapping	mapping	NN	_	_	_
6	locations	location	NNS	_	_	_
7	and	and	CC	_	_	_
8	did	do	VBD	_	_	_
9	not	not	RB	_	_	_
10	match	match	VB	_	_	_
11	annotated	annotated	JJ	_	_	_
12	rRNA	rrna	NN	_	_	_
13	genes	gene	NNS	_	_	_
14	were	be	VBD	_	_	_
15	used	use	VBN	_	_	_
16	for	for	IN	_	_	_
17	further	further	JJ	_	_	_
18	analysis	analysis	NN	_	_	_
19	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	gene	gene	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	tag	tag	NN	GEN	_	_
7	density	density	NN	_	_	_
8	was	be	VBD	_	_	_
9	estimated	estimate	VBN	_	_	_
10	as	as	IN	_	_	_
11	the	the	DT	_	_	_
12	number	number	NN	_	_	_
13	of	of	IN	_	_	_
14	aligned	align	VBN	_	_	_
15	sequencing	sequencing	NN	_	_	_
16	tags	tag	NNS	_	_	_
17	divided	divide	VBN	_	_	_
18	by	by	IN	_	_	_
19	gene	gene	NN	_	_	_
20	size	size	NN	_	_	_
21	in	in	IN	_	_	_
22	kb	kb	NN	_	_	_
23	.	.	.	_	_	_

1	Per-gene	per-gene	JJ	_	_	_
2	tag	tag	NN	GEN	_	_
3	density	density	NN	_	_	_
4	was	be	VBD	_	_	_
5	normalized	normalize	VBN	_	_	_
6	using	use	VBG	_	_	_
7	quantile	quantile	JJ	_	_	_
8	normalization	normalization	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Supplemental	Supplemental	NNP	_	_	_
11	Files	Files	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	tag	tag	NN	GEN	_	_
3	density	density	NN	_	_	_
4	data	datum	NNS	_	_	_
5	were	be	VBD	_	_	_
6	analyzed	analyze	VBN	_	_	_
7	for	for	IN	_	_	_
8	statistically	statistically	RB	_	_	_
9	significant	significant	JJ	_	_	_
10	differential	differential	JJ	_	_	_
11	expression	expression	NN	_	_	_
12	using	use	VBG	_	_	_
13	BaySeq	BaySeq	NNP	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Hardcastle	Hardcastle	NNP	_	_	_
16	&	&	CC	_	_	_
17	Kelly	Kelly	NNP	_	_	_
18	,	,	,	_	_	_
19	2010	2010	CD	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	with	with	IN	_	_	_
22	a	a	DT	_	_	_
23	FDR	FDR	NNP	_	_	_
24	of	of	IN	_	_	_
25	0.01	0.01	CD	_	_	_
26	,	,	,	_	_	_
27	and	and	CC	_	_	_
28	genes	gene	NNS	_	_	_
29	were	be	VBD	_	_	_
30	organized	organize	VBN	_	_	_
31	into	into	IN	_	_	_
32	operons	operon	NNS	_	_	_
33	using	use	VBG	_	_	_
34	data	datum	NNS	_	_	_
35	from	from	IN	_	_	_
36	EcoCyc	EcoCyc	NNP	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Keseler	Keseler	NNP	_	_	_
39	et	et	FW	_	_	_
40	al	al	FW	_	_	_
41	,	,	,	_	_	_
42	2011	2011	CD	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	strain	strain	NN	_	_	_
5	:	:	:	_	_	_
6	K-12	k-12	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	The	the	DT	_	_	_
9	RNAs	rna	NNS	_	_	_
10	were	be	VBD	_	_	_
11	chemically	chemically	RB	_	_	_
12	fragmented	fragment	VBN	_	_	_
13	using	use	VBG	_	_	_
14	RNA	rna	NN	_	_	_
15	Fragmentation	fragmentation	NN	_	_	_
16	Reagents	reagent	NNS	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Ambion	Ambion	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	to	to	TO	_	_	_
21	the	the	DT	_	_	_
22	size	size	NN	_	_	_
23	range	range	NN	_	_	_
24	of	of	IN	_	_	_
25	200-250	200-250	CD	_	_	_
26	bp	bp	NN	_	_	_
27	using	use	VBG	_	_	_
28	1x	1x	NN	_	_	_
29	fragmentation	fragmentation	NN	_	_	_
30	solution	solution	NN	_	_	_
31	for	for	IN	_	_	_
32	5	5	CD	_	_	_
33	minutes	minute	NNS	_	_	_
34	at	at	IN	_	_	_
35	70	70	CD	_	_	_
36	°C	°c	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Ambion	ambion	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	.	.	.	_	_	_

1	Double	double	JJ	_	_	_
2	stranded	strand	VBN	_	_	_
3	cDNA	cdna	NN	_	_	_
4	was	be	VBD	_	_	_
5	generated	generate	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	SuperScript	SuperScript	NNP	_	_	_
9	Double-Stranded	Double-Stranded	NNP	_	_	_
10	cDNA	cdna	NN	_	_	_
11	Synthesis	synthesis	NN	_	_	_
12	Kit	kit	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Invitrogen	invitrogen	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	following	follow	VBG	_	_	_
17	the	the	DT	_	_	_
18	manufacturer	manufacturer	NN	_	_	_
19	's	's	POS	_	_	_
20	protocol	protocol	NN	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	Illumina	Illumina	NNP	_	_	_
3	Paired	Paired	NNP	_	_	_
4	End	End	NNP	_	_	_
5	Sample	Sample	NNP	_	_	_
6	Prep	Prep	NNP	_	_	_
7	kit	kit	NN	_	_	_
8	was	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	for	for	IN	_	_	_
11	Illumina	Illumina	NNP	_	_	_
12	RNA-seq	RNA-seq	NNP	_	_	_
13	library	library	NN	_	_	_
14	creation	creation	NN	_	_	_
15	using	use	VBG	_	_	_
16	the	the	DT	_	_	_
17	manufacturer	manufacturer	NN	_	_	_
18	's	's	POS	_	_	_
19	instructions	instruction	NNS	_	_	_
20	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	fragmented	fragmented	JJ	_	_	_
5	cDNA	cdna	NN	_	_	_
6	was	be	VBD	_	_	_
7	end	end	NN	_	_	_
8	repaired	repair	VBN	_	_	_
9	,	,	,	_	_	_
10	ligated	ligate	VBN	_	_	_
11	to	to	TO	_	_	_
12	Illumina	Illumina	NNP	_	_	_
13	specific	specific	JJ	_	_	_
14	adapters	adapter	NNS	_	_	_
15	and	and	CC	_	_	_
16	amplified	amplify	VBN	_	_	_
17	with	with	IN	_	_	_
18	10	10	CD	_	_	_
19	cycles	cycle	NNS	_	_	_
20	of	of	IN	_	_	_
21	PCR	pcr	NN	_	_	_
22	using	use	VBG	_	_	_
23	the	the	DT	_	_	_
24	TruSeq	TruSeq	NNP	_	_	_
25	SR	sr	JJ	_	_	_
26	Cluster	Cluster	NNP	_	_	_
27	Kit	kit	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	v2	v2	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	Single-end	single-end	JJ	_	_	_
2	36	36	CD	_	_	_
3	bp	bp	NN	_	_	_
4	reads	read	VBZ	_	_	_
5	were	be	VBD	_	_	_
6	generated	generate	VBN	_	_	_
7	by	by	IN	_	_	_
8	sequencing	sequencing	NN	_	_	_
9	on	on	IN	_	_	_
10	the	the	DT	_	_	_
11	Illumina	Illumina	NNP	_	_	_
12	Genome	Genome	NNP	_	_	_
13	Analyzer	Analyzer	NNP	_	_	_
14	IIx	IIx	NNP	_	_	_
15	,	,	,	_	_	_
16	using	use	VBG	_	_	_
17	the	the	DT	_	_	_
18	TruSeq	TruSeq	NNP	_	_	_
19	SBS	SBS	NNP	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	v5	v5	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	following	follow	VBG	_	_	_
25	the	the	DT	_	_	_
26	manufacturer	manufacturer	NN	_	_	_
27	's	's	POS	_	_	_
28	protocol	protocol	NN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	WT	wt	SYM	_	_	_
3	_	_	SYM	_	_	_
4	Anaerobic	anaerobic	JJ	_	_	_
5	_	_	NN	_	_	_
6	RNAseq	rnaseq	NN	_	_	_
7	_	_	CD	_	_	_
8	A	a	DT	_	_	_
9	_	_	NN	_	_	_
10	Tag	tag	NN	_	_	_
11	_	_	CD	_	_	_
12	Count.txt	count.txt	NN	_	_	_
13	:	:	:	_	_	_
14	U00096	u00096	NN	_	_	_
15	.2	.2	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	WT	wt	VBD	_	_	_
18	_	_	CD	_	_	_
19	Anaerobic	anaerobic	JJ	_	_	_
20	_	_	NN	_	_	_
21	RNAseq	rnaseq	NN	_	_	_
22	_	_	CD	_	_	_
23	A	a	DT	_	_	_
24	_	_	NN	_	_	_
25	WIG.wig	wig.wig	NN	_	_	_
26	:	:	:	_	_	_
27	U00096	u00096	NN	_	_	_
28	.2	.2	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	WT	wt	VBD	_	_	_
31	_	_	CD	_	_	_
32	Anaerobic	anaerobic	JJ	_	_	_
33	_	_	NN	_	_	_
34	RNAseq	rnaseq	NN	_	_	_
35	_	_	NN	_	_	_
36	B	b	NN	_	_	_
37	_	_	CD	_	_	_
38	Tag	tag	NN	_	_	_
39	_	_	CD	_	_	_
40	Count.txt	count.txt	NN	_	_	_
41	:	:	:	_	_	_
42	U00096	u00096	NN	_	_	_
43	.2	.2	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	WT	wt	VBD	_	_	_
46	_	_	CD	_	_	_
47	Anaerobic	anaerobic	JJ	_	_	_
48	_	_	NN	_	_	_
49	RNAseq	rnaseq	NN	_	_	_
50	_	_	NN	_	_	_
51	B	b	NN	_	_	_
52	_	_	CD	_	_	_
53	WIG.wig	wig.wig	NN	_	_	_
54	:	:	:	_	_	_
55	U00096	u00096	NN	_	_	_
56	.2	.2	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Cell	cell	NN	_	_	_
59	pellets	pellet	NNS	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	from	from	IN	_	_	_
62	initial	initial	JJ	_	_	_
63	50	50	CD	_	_	_
64	ml	ml	NN	_	_	_
65	of	of	IN	_	_	_
66	culture	culture	NN	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	were	be	VBD	_	_	_
69	thawed	thaw	VBN	_	_	_
70	and	and	CC	_	_	_
71	resuspended	resuspend	VBN	_	_	_
72	in	in	IN	_	_	_
73	250ul	250ul	NN	_	_	_
74	of	of	IN	_	_	_
75	IP	IP	NNP	_	_	_
76	buffer	buffer	NN	_	_	_
77	-LRB-	-lrb-	-LRB-	_	_	_
78	100	100	CD	_	_	_
79	mM	mm	NN	KWSUPP	_	_
80	Tris	Tris	NNP	_	_	_
81	pH	ph	NN	_	_	_
82	8	8	CD	_	_	_
83	,	,	,	_	_	_
84	300	300	CD	_	_	_
85	mM	mm	NN	KWSUPP	_	_
86	NaCl	nacl	NN	_	_	_
87	,	,	,	_	_	_
88	2	2	CD	_	_	_
89	%	%	NN	_	_	_
90	TritonX-100	tritonx-100	NN	_	_	_
91	-RRB-	-rrb-	-RRB-	_	_	_
92	and	and	CC	_	_	_
93	sonicated	sonicate	VBN	_	_	_
94	using	use	VBG	_	_	_
95	a	a	DT	_	_	_
96	microtip	microtip	NN	_	_	_
97	sonicator	sonicator	NN	_	_	_
98	set	set	VBN	_	_	_
99	at	at	IN	_	_	_
100	10	10	CD	_	_	_
101	%	%	NN	_	_	_
102	output	output	NN	_	_	_
103	for	for	IN	_	_	_
104	20	20	CD	_	_	_
105	second	second	JJ	_	_	_
106	intervals	interval	NNS	_	_	_
107	with	with	IN	_	_	_
108	periods	period	NNS	_	_	_
109	of	of	IN	_	_	_
110	cooling	cool	VBG	_	_	_
111	in	in	IN	_	_	_
112	between	between	IN	_	_	_
113	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	treated	treat	VBN	_	_	_
5	for	for	IN	_	_	_
6	one	one	CD	_	_	_
7	hour	hour	NN	_	_	_
8	at	at	IN	_	_	_
9	4	4	CD	_	_	_
10	°C	°c	NN	_	_	_
11	with	with	IN	_	_	_
12	RNase	rnase	NN	_	_	_
13	A	a	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	2	2	CD	_	_	_
16	ng	ng	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Cells	cell	NNS	_	_	_
19	were	be	VBD	_	_	_
20	cross-linked	cross-link	VBN	_	_	_
21	by	by	IN	_	_	_
22	the	the	DT	_	_	_
23	addition	addition	NN	_	_	_
24	of	of	IN	_	_	_
25	formaldehyde	formaldehyde	NN	_	_	_
26	at	at	IN	_	_	_
27	1	1	CD	_	_	_
28	%	%	NN	_	_	_
29	final	final	JJ	_	_	_
30	concentration	concentration	NN	_	_	_
31	with	with	IN	_	_	_
32	continued	continued	JJ	_	_	_
33	shaking	shake	VBG	_	_	_
34	at	at	IN	_	_	_
35	37	37	CD	_	_	_
36	°C	°c	NN	_	_	_
37	for	for	IN	_	_	_
38	5	5	CD	_	_	_
39	min	min	NN	_	_	_
40	before	before	IN	_	_	_
41	quenching	quench	VBG	_	_	_
42	with	with	IN	_	_	_
43	glycine	glycine	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	100	100	CD	_	_	_
46	mM	mm	NN	KWSUPP	_	_
47	final	final	JJ	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	MOPS	mop	NNS	MED	_	_
7	minimal	minimal	JJ	_	_	_
8	medium	medium	NN	_	_	_
9	with	with	IN	_	_	_
10	0.2	0.2	CD	_	_	_
11	%	%	NN	_	_	_
12	glucose	glucose	NN	SUPP	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	oC	oc	NN	_	_	_
16	in	in	IN	_	_	_
17	gas-sparged	gas-sparged	JJ	_	_	_
18	Roux	Roux	NNP	_	_	_
19	bottles	bottle	NNS	_	_	_
20	or	or	CC	_	_	_
21	shaking	shake	VBG	_	_	_
22	flasks	flask	NNS	_	_	_
23	to	to	TO	_	_	_
24	mid-log	mid-log	JJ	_	_	_
25	phase	phase	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	OD600	od600	NN	_	_	_
28	~	~	NN	_	_	_
29	0.3-0.4	0.3-0.4	CD	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	cell	cell	NN	_	_	_
3	type	type	NN	_	_	_
4	:	:	:	_	_	_
5	bacterial	bacterial	JJ	_	_	_
6	cells	cell	NNS	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	chip	chip	NN	_	_	_
9	antibody	antibody	NN	_	_	_
10	:	:	:	_	_	_
11	anti-b	anti-b	JJ	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	RNAP	rnap	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	NT63	nt63	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
17	chip	chip	NN	_	_	_
18	antibody	antibody	NN	_	_	_
19	:	:	:	_	_	_
20	anti-H-NS	anti-h-ns	JJ	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
22	chip	chip	NN	_	_	_
23	antibody	antibody	NN	_	_	_
24	cat	cat	NN	_	_	_
25	.	.	.	_	_	_

1	#	#	#	_	_	_
2	:	:	:	_	_	_
3	W0002	w0002	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
5	chip	chip	NN	_	_	_
6	antibody	antibody	NN	_	_	_
7	vendor	vendor	NN	_	_	_
8	:	:	:	_	_	_
9	Neoclone	Neoclone	NNP	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Datasets	Datasets	NNPS	_	_	_
12	were	be	VBD	_	_	_
13	normalized	normalize	VBN	_	_	_
14	using	use	VBG	_	_	_
15	locally	locally	RB	_	_	_
16	weighted	weighted	JJ	_	_	_
17	linear	linear	JJ	_	_	_
18	regression	regression	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	LOWESS	lowess	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	normalization	normalization	NN	_	_	_
23	on	on	IN	_	_	_
24	raw	raw	JJ	_	_	_
25	Cy3	cy3	NN	_	_	_
26	and	and	CC	_	_	_
27	Cy5	cy5	NN	_	_	_
28	signals	signal	NNS	_	_	_
29	to	to	TO	_	_	_
30	correct	correct	VB	_	_	_
31	for	for	IN	_	_	_
32	intensity-dependent	intensity-dependent	JJ	_	_	_
33	dye	dye	VB	_	_	_
34	effects	effect	NNS	_	_	_
35	within	within	IN	_	_	_
36	each	each	DT	_	_	_
37	array	array	NN	_	_	_
38	using	use	VBG	_	_	_
39	the	the	DT	_	_	_
40	``	``	``	_	_	_
41	normalizeWithinArrays	normalizewithinarrays	NN	_	_	_
42	''	''	''	_	_	_
43	function	function	NN	_	_	_
44	in	in	IN	_	_	_
45	the	the	DT	_	_	_
46	limma	limma	NN	_	_	_
47	package	package	NN	_	_	_
48	for	for	IN	_	_	_
49	the	the	DT	_	_	_
50	statistical	statistical	JJ	_	_	_
51	program	program	NN	_	_	_
52	R	r	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	v.	v.	CC	_	_	_
55	2.14.2	2.14.2	CD	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	K-12	k-12	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	genotype	genotype	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	H-NS	h-ns	NN	_	_	_
9	ChIP	chip	NN	_	_	_
10	DNA	dna	NN	_	_	_
11	from	from	IN	_	_	_
12	MG1655	mg1655	NN	_	_	_
13	cells	cell	NNS	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	Input	Input	NNP	_	_	_
16	DNA	dna	NN	_	_	_
17	from	from	IN	_	_	_
18	MDS42	mds42	NN	_	_	_
19	cells	cell	NNS	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	Input	Input	NNP	_	_	_
22	DNA	dna	NN	_	_	_
23	from	from	IN	_	_	_
24	MDS42	mds42	NN	_	_	_
25	ΔnusA	δnusa	NN	_	_	_
26	*	*	SYM	_	_	_
27	cells	cell	NNS	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	Input	Input	NNP	_	_	_
30	DNA	dna	NN	_	_	_
31	from	from	IN	_	_	_
32	MDS42	mds42	NN	_	_	_
33	ΔnusG	δnusg	NN	_	_	_
34	cells	cell	NNS	_	_	_
35	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
36	Input	Input	NNP	_	_	_
37	DNA	dna	NN	_	_	_
38	from	from	IN	_	_	_
39	MG1655	mg1655	NN	_	_	_
40	cells	cell	NNS	_	_	_
41	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
42	Input	Input	NNP	_	_	_
43	DNA	dna	NN	_	_	_
44	from	from	IN	_	_	_
45	MG1655	mg1655	NN	_	_	_
46	Δhns	δhns	NN	_	_	_
47	cells	cell	NNS	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
49	MDS42	mds42	NN	_	_	_
50	RNAP	rnap	NN	_	_	_
51	1	1	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	MDS42	mds42	NN	_	_	_
54	RNAP	rnap	NN	_	_	_
55	2	2	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	MDS42	mds42	NN	_	_	_
58	ΔnusA	δnusa	NN	_	_	_
59	*	*	SYM	_	_	_
60	RNAP	rnap	NN	_	_	_
61	1	1	CD	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	MDS42	mds42	NN	_	_	_
64	ΔnusA	δnusa	NN	_	_	_
65	*	*	SYM	_	_	_
66	RNAP	rnap	NN	_	_	_
67	2	2	CD	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	MDS42	mds42	NN	_	_	_
70	ΔnusG	δnusg	NN	_	_	_
71	RNAP	rnap	NN	_	_	_
72	1	1	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	MDS42	mds42	NN	_	_	_
75	ΔnusG	δnusg	NN	_	_	_
76	RNAP	rnap	NN	_	_	_
77	2	2	CD	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	MG1655	mg1655	NN	_	_	_
80	H-NS	h-ns	NN	_	_	_
81	1	1	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	MG1655	mg1655	NN	_	_	_
84	H-NS	h-ns	NN	_	_	_
85	2	2	CD	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	MG1655	mg1655	NN	_	_	_
88	RNAP	rnap	NN	_	_	_
89	1	1	CD	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	MG1655	mg1655	NN	_	_	_
92	RNAP	rnap	NN	_	_	_
93	2	2	CD	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	MG1655	mg1655	NN	_	_	_
96	Δhns	δhns	NNS	_	_	_
97	RNAP	rnap	NN	_	_	_
98	1	1	CD	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	MG1655	mg1655	NN	_	_	_
101	Δhns	δhns	NNS	_	_	_
102	RNAP	rnap	NN	_	_	_
103	2	2	CD	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	RNAP	rnap	NN	_	_	_
106	ChIP	chip	NN	_	_	_
107	DNA	dna	NN	_	_	_
108	from	from	IN	_	_	_
109	MDS42	mds42	NN	_	_	_
110	cells	cell	NNS	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
112	RNAP	rnap	NN	_	_	_
113	ChIP	chip	NN	_	_	_
114	DNA	dna	NN	_	_	_
115	from	from	IN	_	_	_
116	MDS42	mds42	NN	_	_	_
117	ΔnusA	δnusa	NN	_	_	_
118	*	*	NN	_	_	_
119	cells	cell	NNS	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
121	RNAP	rnap	NN	_	_	_
122	ChIP	chip	NN	_	_	_
123	DNA	dna	NN	_	_	_
124	from	from	IN	_	_	_
125	MDS42	mds42	NN	_	_	_
126	ΔnusG	δnusg	NN	_	_	_
127	cells	cell	NNS	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
129	RNAP	rnap	NN	_	_	_
130	ChIP	chip	NN	_	_	_
131	DNA	dna	NN	_	_	_
132	from	from	IN	_	_	_
133	MG1655	mg1655	NN	_	_	_
134	cells	cell	NNS	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
136	RNAP	rnap	NN	_	_	_
137	ChIP	chip	NN	_	_	_
138	DNA	dna	NN	_	_	_
139	from	from	IN	_	_	_
140	MG1655	mg1655	NN	_	_	_
141	Δhns	δhns	NN	_	_	_
142	cells	cell	NNS	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	sample	sample	NN	_	_	_
145	type	type	NN	_	_	_
146	:	:	:	_	_	_
147	input	input	NN	_	_	_
148	DNA	dna	NN	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	strain	strain	NN	_	_	_
151	:	:	:	_	_	_
152	MDS42	mds42	NN	_	_	_
153	-LRB-	-lrb-	-LRB-	_	_	_
154	RL1961	rl1961	NN	_	_	_
155	-RRB-	-rrb-	-RRB-	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
157	strain	strain	NN	_	_	_
158	:	:	:	_	_	_
159	MG1655	mg1655	NN	_	_	_
160	-LRB-	-lrb-	-LRB-	_	_	_
161	RL1655	rl1655	NN	_	_	_
162	-RRB-	-rrb-	-RRB-	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	strain	strain	NN	_	_	_
165	:	:	:	_	_	_
166	RL2673	rl2673	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	strain	strain	NN	_	_	_
169	:	:	:	_	_	_
170	RSW421	rsw421	NN	_	_	_
171	-LRB-	-lrb-	-LRB-	_	_	_
172	RL1962	rl1962	NN	_	_	_
173	-RRB-	-rrb-	-RRB-	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	strain	strain	NN	_	_	_
176	:	:	:	_	_	_
177	RSW422	rsw422	NN	_	_	_
178	-LRB-	-lrb-	-LRB-	_	_	_
179	RL1963	rl1963	NN	_	_	_
180	-RRB-	-rrb-	-RRB-	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	Cells	cell	NNS	_	_	_
183	were	be	VBD	_	_	_
184	grown	grow	VBN	_	_	_
185	in	in	IN	_	_	_
186	MOPS	mop	NNS	MED	_	_
187	minimal	minimal	JJ	_	_	_
188	medium	medium	NN	_	_	_
189	with	with	IN	_	_	_
190	0.2	0.2	CD	_	_	_
191	%	%	NN	_	_	_
192	glucose	glucose	NN	SUPP	_	_
193	at	at	IN	_	_	_
194	37	37	CD	_	_	_
195	oC	oc	NN	_	_	_
196	in	in	IN	_	_	_
197	gas-sparged	gas-sparged	JJ	_	_	_
198	Roux	Roux	NNP	_	_	_
199	bottles	bottle	NNS	_	_	_
200	or	or	CC	_	_	_
201	shaking	shake	VBG	_	_	_
202	flasks	flask	NNS	_	_	_
203	to	to	TO	_	_	_
204	mid-log	mid-log	JJ	_	_	_
205	phase	phase	NN	_	_	_
206	-LRB-	-lrb-	-LRB-	_	_	_
207	OD600	od600	NN	_	_	_
208	~	~	NN	_	_	_
209	0.3-0.4	0.3-0.4	CD	_	_	_
210	-RRB-	-rrb-	-RRB-	_	_	_
211	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	transferred	transfer	VBN	_	_	_
5	directly	directly	RB	_	_	_
6	into	into	IN	_	_	_
7	an	a	DT	_	_	_
8	ice-cold	ice-cold	JJ	_	_	_
9	ethanol	ethanol	NN	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Escherichia	escherichia	FW	Organism	_	_
12	coli	coli	FW	Organism	_	_
13	K-12	k-12	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	genotype	genotype	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	MDS42	mds42	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	MDS42	mds42	NN	_	_	_
20	1	1	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	MDS42	mds42	NN	_	_	_
23	2	2	CD	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	MDS42	mds42	NN	_	_	_
26	+	+	CC	_	_	_
27	20	20	CD	_	_	_
28	ug	ug	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	MDS42	mds42	NN	_	_	_
31	ΔnusA	δnusa	NN	_	_	_
32	*	*	SYM	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	MDS42	mds42	NN	_	_	_
35	ΔnusA	δnusa	NN	_	_	_
36	*	*	SYM	_	_	_
37	1	1	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	MDS42	mds42	NN	_	_	_
40	ΔnusA	δnusa	NN	_	_	_
41	*	*	SYM	_	_	_
42	2	2	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	MDS42	mds42	NN	_	_	_
45	ΔnusG	δnusg	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	MDS42	mds42	NN	_	_	_
48	ΔnusG	δnusg	NN	_	_	_
49	1	1	CD	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	MDS42	mds42	NN	_	_	_
52	ΔnusG	δnusg	NN	_	_	_
53	2	2	CD	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
55	Raw	raw	NN	_	_	_
56	probe	probe	NN	_	_	_
57	intensities	intensity	NNS	_	_	_
58	were	be	VBD	_	_	_
59	normalized	normalize	VBN	_	_	_
60	across	across	IN	_	_	_
61	samples	sample	NNS	_	_	_
62	using	use	VBG	_	_	_
63	RMA	rma	NN	_	_	_
64	analysis	analysis	NN	_	_	_
65	implemented	implement	VBD	_	_	_
66	in	in	IN	_	_	_
67	the	the	DT	_	_	_
68	NimbleScan	NimbleScan	NNP	_	_	_
69	software	software	NN	_	_	_
70	package	package	NN	_	_	_
71	-LRB-	-lrb-	-LRB-	_	_	_
72	v.	v.	CC	_	_	_
73	2.4	2.4	CD	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MDS42	mds42	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	RL1961	rl1961	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	strain	strain	NN	_	_	_
10	:	:	:	_	_	_
11	RSW421	rsw421	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	RL1962	rl1962	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	strain	strain	NN	_	_	_
17	:	:	:	_	_	_
18	RSW421	rsw421	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	RL1967	rl1967	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	strain	strain	NN	_	_	_
24	:	:	:	_	_	_
25	RSW422	rsw422	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	RL1963	rl1963	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	strain	strain	NN	_	_	_
31	:	:	:	_	_	_
32	RSW472	rsw472	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	RL1966	rl1966	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Total	total	JJ	_	_	_
38	RNA	rna	NN	_	_	_
39	was	be	VBD	_	_	_
40	extracted	extract	VBN	_	_	_
41	from	from	IN	_	_	_
42	cell	cell	NN	_	_	_
43	pellets	pellet	NNS	_	_	_
44	by	by	IN	_	_	_
45	hot	hot	JJ	_	_	_
46	phenol	phenol	NN	_	_	_
47	extraction	extraction	NN	_	_	_
48	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	integrity	integrity	NN	_	_	_
3	of	of	IN	_	_	_
4	total	total	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	was	be	VBD	_	_	_
7	determined	determine	VBN	_	_	_
8	from	from	IN	_	_	_
9	agarose	agarose	NN	_	_	_
10	gel	gel	NN	_	_	_
11	or	or	CC	_	_	_
12	microchannel	microchannel	NN	_	_	_
13	electrophoretograms	electrophoretogram	NNS	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	treated	treat	VBN	_	_	_
3	with	with	IN	_	_	_
4	:	:	:	_	_	_
5	20	20	CD	_	_	_
6	ug	ug	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Δrac	δrac	JJ	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Δrac	δrac	NN	_	_	_
11	1	1	CD	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	Δrac	δrac	NN	_	_	_
14	2	2	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Δrac	δrac	NN	_	_	_
17	+	+	CC	_	_	_
18	20	20	CD	_	_	_
19	ug	ug	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Δrac	δrac	NN	_	_	_
22	ΔnusG	δnusg	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	Δrac	δrac	NN	_	_	_
25	ΔnusG	δnusg	NN	_	_	_
26	1	1	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Δrac	δrac	NN	_	_	_
29	ΔnusG	δnusg	NN	_	_	_
30	2	2	CD	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	Base	Base	NNP	_	_	_
33	calling	call	VBG	_	_	_
34	was	be	VBD	_	_	_
35	performed	perform	VBN	_	_	_
36	by	by	IN	_	_	_
37	the	the	DT	_	_	_
38	DOE	DOE	NNP	_	_	_
39	Joint	Joint	NNP	_	_	_
40	Genome	Genome	NNP	_	_	_
41	Institute	Institute	NNP	_	_	_
42	using	use	VBG	_	_	_
43	Illumina	Illumina	NNP	_	_	_
44	software	software	NN	_	_	_
45	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	MOPS	mop	NNS	MED	_	_
7	minimal	minimal	JJ	_	_	_
8	medium	medium	NN	_	_	_
9	with	with	IN	_	_	_
10	0.2	0.2	CD	_	_	_
11	%	%	NN	_	_	_
12	glucose	glucose	NN	SUPP	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	oC	oc	NN	_	_	_
16	in	in	IN	_	_	_
17	gas-sparged	gas-sparged	JJ	_	_	_
18	Roux	Roux	NNP	_	_	_
19	bottles	bottle	NNS	_	_	_
20	or	or	CC	_	_	_
21	shaking	shake	VBG	_	_	_
22	flasks	flask	NNS	_	_	_
23	to	to	TO	_	_	_
24	mid-log	mid-log	JJ	_	_	_
25	phase	phase	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	OD600	od600	NN	_	_	_
28	~	~	NN	_	_	_
29	0.3-0.4	0.3-0.4	CD	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Counts	count	VBZ	_	_	_
3	per	per	IN	_	_	_
4	million	million	CD	_	_	_
5	unique	unique	JJ	_	_	_
6	reads	read	VBZ	_	_	_
7	were	be	VBD	_	_	_
8	calculated	calculate	VBN	_	_	_
9	for	for	IN	_	_	_
10	each	each	DT	_	_	_
11	gene	gene	NN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	transferred	transfer	VBN	_	_	_
5	directly	directly	RB	_	_	_
6	into	into	IN	_	_	_
7	an	a	DT	_	_	_
8	ice-cold	ice-cold	JJ	_	_	_
9	ethanol	ethanol	NN	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Escherichia	escherichia	FW	Organism	_	_
12	coli	coli	FW	Organism	_	_
13	K-12	k-12	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Genome	Genome	NNP	_	_	_
16	_	_	NNP	_	_	_
17	build	build	VB	_	_	_
18	:	:	:	_	_	_
19	U00096	u00096	NN	_	_	_
20	.2	.2	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	genotype	genotype	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	MG1655	mg1655	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	MG1655	mg1655	NN	_	_	_
27	1	1	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	MG1655	mg1655	NN	_	_	_
30	2	2	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	MG1655	mg1655	NN	_	_	_
33	+	+	CC	_	_	_
34	20	20	CD	_	_	_
35	ug	ug	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	molecule	molecule	NN	_	_	_
38	subtype	subtype	NN	_	_	_
39	:	:	:	_	_	_
40	ribosome-depeleted	ribosome-depeleted	JJ	_	_	_
41	RNA	rna	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	RNA-Seq	rna-seq	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	RNA-Seq	rna-seq	NN	_	_	_
46	was	be	VBD	_	_	_
47	performed	perform	VBN	_	_	_
48	by	by	IN	_	_	_
49	the	the	DT	_	_	_
50	DOE	DOE	NNP	_	_	_
51	Joint	Joint	NNP	_	_	_
52	Genome	Genome	NNP	_	_	_
53	Institute	Institute	NNP	_	_	_
54	using	use	VBG	_	_	_
55	the	the	DT	_	_	_
56	dUTP	dutp	NN	_	_	_
57	method	method	NN	_	_	_
58	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	ribosome-depleted	ribosome-depleted	JJ	_	_	_
4	RNA	rna	NN	_	_	_
5	was	be	VBD	_	_	_
6	fragmented	fragmented	JJ	_	_	_
7	in	in	IN	_	_	_
8	a	a	DT	_	_	_
9	buffered	buffer	VBN	_	_	_
10	zinc	zinc	NN	_	_	_
11	solution	solution	NN	_	_	_
12	,	,	,	_	_	_
13	then	then	RB	_	_	_
14	purified	purify	VBN	_	_	_
15	using	use	VBG	_	_	_
16	AMPure	ampure	NN	_	_	_
17	SPRI	spri	NN	_	_	_
18	beads	bead	NNS	_	_	_
19	.	.	.	_	_	_

1	First-strand	first-strand	JJ	_	_	_
2	cDNAs	cdna	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	synthesized	synthesize	VBN	_	_	_
6	from	from	IN	_	_	_
7	the	the	DT	_	_	_
8	fragmented	fragmented	JJ	_	_	_
9	RNA	rna	NN	_	_	_
10	using	use	VBG	_	_	_
11	Superscript	Superscript	NNP	_	_	_
12	II	II	NNP	_	_	_
13	reverse	reverse	JJ	_	_	_
14	transcriptase	transcriptase	NN	_	_	_
15	,	,	,	_	_	_
16	followed	follow	VBN	_	_	_
17	by	by	IN	_	_	_
18	a	a	DT	_	_	_
19	second	second	JJ	_	_	_
20	bead	bead	NN	_	_	_
21	purification	purification	NN	_	_	_
22	.	.	.	_	_	_

1	dUTP	dutp	NN	_	_	_
2	was	be	VBD	_	_	_
3	included	include	VBN	_	_	_
4	in	in	IN	_	_	_
5	the	the	DT	_	_	_
6	second	second	JJ	_	_	_
7	strand	strand	NN	_	_	_
8	synthesis	synthesis	NN	_	_	_
9	reaction	reaction	NN	_	_	_
10	in	in	IN	_	_	_
11	addition	addition	NN	_	_	_
12	to	to	TO	_	_	_
13	dTTP	dttp	NN	_	_	_
14	to	to	TO	_	_	_
15	chemically	chemically	RB	_	_	_
16	mark	mark	VB	_	_	_
17	the	the	DT	_	_	_
18	second	second	JJ	_	_	_
19	strand	strand	NN	_	_	_
20	.	.	.	_	_	_

1	Two	two	CD	_	_	_
2	further	further	JJ	_	_	_
3	bead	bead	NN	_	_	_
4	purification	purification	NN	_	_	_
5	steps	step	NNS	_	_	_
6	using	use	VBG	_	_	_
7	different	different	JJ	_	_	_
8	ratios	ratio	NNS	_	_	_
9	of	of	IN	_	_	_
10	beads	bead	NNS	_	_	_
11	to	to	TO	_	_	_
12	cDNA	cdna	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	85	85	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Sequenced	sequence	VBN	_	_	_
17	reads	read	VBZ	_	_	_
18	were	be	VBD	_	_	_
19	trimmed	trim	VBN	_	_	_
20	,	,	,	_	_	_
21	the	the	DT	_	_	_
22	mapped	map	VBN	_	_	_
23	to	to	TO	_	_	_
24	the	the	DT	_	_	_
25	Escherichia	escherichia	FW	Organism	_	_
26	coli	coli	FW	Organism	_	_
27	K-12	k-12	NN	_	_	_
28	MG1655	mg1655	NN	_	_	_
29	genome	genome	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	U00096	u00096	NN	_	_	_
32	.2	.2	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	using	use	VBG	_	_	_
35	SOAP	soap	NN	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Supplementary	supplementary	JJ	_	_	_
7	_	_	NN	_	_	_
8	files	file	NNS	_	_	_
9	_	_	IN	_	_	_
10	format	format	NN	_	_	_
11	_	_	NN	_	_	_
12	and	and	CC	_	_	_
13	_	_	NN	_	_	_
14	content	content	NN	_	_	_
15	:	:	:	_	_	_
16	tab-delimited	tab-delimited	JJ	_	_	_
17	text	text	NN	_	_	_
18	files	file	NNS	_	_	_
19	include	include	VBP	_	_	_
20	CPM	CPM	NNP	_	_	_
21	values	value	NNS	_	_	_
22	for	for	IN	_	_	_
23	each	each	DT	_	_	_
24	Sample	Sample	NNP	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	Total	Total	NNP	_	_	_
27	RNA	rna	NN	_	_	_
28	was	be	VBD	_	_	_
29	extracted	extract	VBN	_	_	_
30	from	from	IN	_	_	_
31	cell	cell	NN	_	_	_
32	pellets	pellet	NNS	_	_	_
33	by	by	IN	_	_	_
34	hot	hot	JJ	_	_	_
35	phenol	phenol	NN	_	_	_
36	extraction	extraction	NN	_	_	_
37	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	integrity	integrity	NN	_	_	_
3	of	of	IN	_	_	_
4	total	total	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	was	be	VBD	_	_	_
7	determined	determine	VBN	_	_	_
8	from	from	IN	_	_	_
9	agarose	agarose	NN	_	_	_
10	gel	gel	NN	_	_	_
11	or	or	CC	_	_	_
12	microchannel	microchannel	NN	_	_	_
13	electrophoretograms	electrophoretogram	NNS	_	_	_
14	.	.	.	_	_	_

1	16S	16s	NN	_	_	_
2	and	and	CC	_	_	_
3	23S	23s	NN	_	_	_
4	Ribosomal	ribosomal	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	was	be	VBD	_	_	_
7	depleted	deplete	VBN	_	_	_
8	prior	prior	RB	_	_	_
9	to	to	TO	_	_	_
10	construction	construction	NN	_	_	_
11	of	of	IN	_	_	_
12	RNAseq	rnaseq	NN	_	_	_
13	libraries	library	NNS	_	_	_
14	using	use	VBG	_	_	_
15	MICROBExpress	microbexpress	NN	_	_	_
16	reagents	reagent	NNS	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	1	1	CD	_	_	_
3	ml	ml	NN	_	_	_
4	of	of	IN	_	_	_
5	VWPE	VWPE	NNP	_	_	_
6	extract	extract	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	1	1	CD	_	_	_
9	mg	mg	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	agent	agent	NN	_	_	_
12	:	:	:	_	_	_
13	control	control	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	1	1	CD	_	_	_
16	ml	ml	NN	_	_	_
17	of	of	IN	_	_	_
18	LB	lb	NN	MED	_	_
19	broth	broth	NN	MED	_	_
20	added	add	VBD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	agent	agent	NN	_	_	_
24	:	:	:	_	_	_
25	ethanol	ethanol	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	1	1	CD	_	_	_
28	ml	ml	NN	_	_	_
29	of	of	IN	_	_	_
30	ethanol	ethanol	NN	_	_	_
31	20	20	CD	_	_	_
32	%	%	NN	_	_	_
33	added	add	VBD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	agent	agent	NN	_	_	_
37	:	:	:	_	_	_
38	polyphenols	polyphenol	NNS	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	1	1	CD	_	_	_
41	ml	ml	NN	_	_	_
42	of	of	IN	_	_	_
43	OVWPE	ovwpe	NN	_	_	_
44	diluted	dilute	VBN	_	_	_
45	in	in	IN	_	_	_
46	ethanol	ethanol	NN	_	_	_
47	20	20	CD	_	_	_
48	%	%	NN	_	_	_
49	added	add	VBD	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
52	Data	Data	NNP	_	_	_
53	processed	process	VBN	_	_	_
54	with	with	IN	_	_	_
55	FeatureExtraction	FeatureExtraction	NNP	_	_	_
56	v9	v9	NN	_	_	_
57	.5.1	.5.1	NN	_	_	_
58	and	and	CC	_	_	_
59	quantile	quantile	NN	_	_	_
60	normalized	normalize	VBD	_	_	_
61	using	use	VBG	_	_	_
62	R2	r2	NN	_	_	_
63	.6.1	.6.1	CD	_	_	_
64	statistical	statistical	JJ	_	_	_
65	software	software	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	E.coli	e.coli	NNS	_	_	_
68	,	,	,	_	_	_
69	control	control	JJ	_	_	_
70	culture	culture	NN	_	_	_
71	,	,	,	_	_	_
72	20	20	CD	_	_	_
73	minutes	minute	NNS	_	_	_
74	-LRB-	-lrb-	-LRB-	_	_	_
75	t2	t2	NN	_	_	_
76	-RRB-	-rrb-	-RRB-	_	_	_
77	after	after	IN	_	_	_
78	treatment	treatment	NN	_	_	_
79	,	,	,	_	_	_
80	replicate	replicate	VB	_	_	_
81	A	a	DT	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	E.coli	e.coli	NNS	_	_	_
84	,	,	,	_	_	_
85	control	control	JJ	_	_	_
86	culture	culture	NN	_	_	_
87	,	,	,	_	_	_
88	20	20	CD	_	_	_
89	minutes	minute	NNS	_	_	_
90	-LRB-	-lrb-	-LRB-	_	_	_
91	t2	t2	NN	_	_	_
92	-RRB-	-rrb-	-RRB-	_	_	_
93	after	after	IN	_	_	_
94	treatment	treatment	NN	_	_	_
95	,	,	,	_	_	_
96	replicate	replicate	VB	_	_	_
97	B	b	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	E.coli	e.coli	NNS	_	_	_
100	,	,	,	_	_	_
101	control	control	JJ	_	_	_
102	culture	culture	NN	_	_	_
103	,	,	,	_	_	_
104	20	20	CD	_	_	_
105	minutes	minute	NNS	_	_	_
106	-LRB-	-lrb-	-LRB-	_	_	_
107	t2	t2	NN	_	_	_
108	-RRB-	-rrb-	-RRB-	_	_	_
109	after	after	IN	_	_	_
110	treatment	treatment	NN	_	_	_
111	,	,	,	_	_	_
112	replicate	replicate	VB	_	_	_
113	C	c	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	E.coli	e.coli	NNS	_	_	_
116	,	,	,	_	_	_
117	control	control	JJ	_	_	_
118	culture	culture	NN	_	_	_
119	,	,	,	_	_	_
120	40	40	CD	_	_	_
121	minutes	minute	NNS	_	_	_
122	-LRB-	-lrb-	-LRB-	_	_	_
123	t3	t3	NN	_	_	_
124	-RRB-	-rrb-	-RRB-	_	_	_
125	after	after	IN	_	_	_
126	treatment	treatment	NN	_	_	_
127	,	,	,	_	_	_
128	replicate	replicate	VB	_	_	_
129	A	a	DT	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	E.coli	e.coli	NNS	_	_	_
132	,	,	,	_	_	_
133	control	control	JJ	_	_	_
134	culture	culture	NN	_	_	_
135	,	,	,	_	_	_
136	40	40	CD	_	_	_
137	minutes	minute	NNS	_	_	_
138	-LRB-	-lrb-	-LRB-	_	_	_
139	t3	t3	NN	_	_	_
140	-RRB-	-rrb-	-RRB-	_	_	_
141	after	after	IN	_	_	_
142	treatment	treatment	NN	_	_	_
143	,	,	,	_	_	_
144	replicate	replicate	VB	_	_	_
145	B	b	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	E.coli	e.coli	NNS	_	_	_
148	,	,	,	_	_	_
149	control	control	JJ	_	_	_
150	culture	culture	NN	_	_	_
151	,	,	,	_	_	_
152	40	40	CD	_	_	_
153	minutes	minute	NNS	_	_	_
154	-LRB-	-lrb-	-LRB-	_	_	_
155	t3	t3	NN	_	_	_
156	-RRB-	-rrb-	-RRB-	_	_	_
157	after	after	IN	_	_	_
158	treatment	treatment	NN	_	_	_
159	,	,	,	_	_	_
160	replicate	replicate	VB	_	_	_
161	C	c	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	E.coli	e.coli	NNS	_	_	_
164	,	,	,	_	_	_
165	control	control	JJ	_	_	_
166	culture	culture	NN	_	_	_
167	,	,	,	_	_	_
168	at	at	IN	_	_	_
169	the	the	DT	_	_	_
170	time	time	NN	_	_	_
171	of	of	IN	_	_	_
172	treatment	treatment	NN	_	_	_
173	-LRB-	-lrb-	-LRB-	_	_	_
174	t1	t1	NN	_	_	_
175	-RRB-	-rrb-	-RRB-	_	_	_
176	,	,	,	_	_	_
177	replicate	replicate	VB	_	_	_
178	A	a	DT	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	E.coli	e.coli	NNS	_	_	_
181	,	,	,	_	_	_
182	control	control	JJ	_	_	_
183	culture	culture	NN	_	_	_
184	,	,	,	_	_	_
185	at	at	IN	_	_	_
186	the	the	DT	_	_	_
187	time	time	NN	_	_	_
188	of	of	IN	_	_	_
189	treatment	treatment	NN	_	_	_
190	-LRB-	-lrb-	-LRB-	_	_	_
191	t1	t1	NN	_	_	_
192	-RRB-	-rrb-	-RRB-	_	_	_
193	,	,	,	_	_	_
194	replicate	replicate	VB	_	_	_
195	B	b	NN	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	E.coli	e.coli	NNS	_	_	_
198	,	,	,	_	_	_
199	control	control	JJ	_	_	_
200	culture	culture	NN	_	_	_
201	,	,	,	_	_	_
202	at	at	IN	_	_	_
203	the	the	DT	_	_	_
204	time	time	NN	_	_	_
205	of	of	IN	_	_	_
206	treatment	treatment	NN	_	_	_
207	-LRB-	-lrb-	-LRB-	_	_	_
208	t1	t1	NN	_	_	_
209	-RRB-	-rrb-	-RRB-	_	_	_
210	,	,	,	_	_	_
211	replicate	replicate	VB	_	_	_
212	C	c	NN	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
214	E.coli	e.coli	JJ	_	_	_
215	_	_	NN	_	_	_
216	control	control	NN	_	_	_
217	_	_	CD	_	_	_
218	repA	repa	NN	_	_	_
219	_	_	CD	_	_	_
220	t1	t1	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	E.coli	e.coli	NNS	_	_	_
223	_	_	VBP	_	_	_
224	control	control	NN	_	_	_
225	_	_	CD	_	_	_
226	repA	repa	NN	_	_	_
227	_	_	CD	_	_	_
228	t2	t2	NN	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
230	E.coli	e.coli	NNS	_	_	_
231	_	_	VBP	_	_	_
232	control	control	NN	_	_	_
233	_	_	CD	_	_	_
234	repA	repa	NN	_	_	_
235	_	_	CD	_	_	_
236	t3	t3	NN	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	E.coli	e.coli	NNS	_	_	_
239	_	_	VBP	_	_	_
240	control	control	NN	_	_	_
241	_	_	CD	_	_	_
242	repB	repb	NN	_	_	_
243	_	_	CD	_	_	_
244	t1	t1	NN	_	_	_
245	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
246	E.coli	e.coli	NNS	_	_	_
247	_	_	VBP	_	_	_
248	control	control	NN	_	_	_
249	_	_	CD	_	_	_
250	repB	repb	NN	_	_	_
251	_	_	CD	_	_	_
252	t2	t2	NN	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
254	E.coli	e.coli	NNS	_	_	_
255	_	_	VBP	_	_	_
256	control	control	NN	_	_	_
257	_	_	CD	_	_	_
258	repB	repb	NN	_	_	_
259	_	_	CD	_	_	_
260	t3	t3	NN	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
262	E.coli	e.coli	NNS	_	_	_
263	_	_	VBP	_	_	_
264	control	control	NN	_	_	_
265	_	_	CD	_	_	_
266	repC	repc	NN	_	_	_
267	_	_	CD	_	_	_
268	t1	t1	NN	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	E.coli	e.coli	NNS	_	_	_
271	_	_	VBP	_	_	_
272	control	control	NN	_	_	_
273	_	_	CD	_	_	_
274	repC	repc	NN	_	_	_
275	_	_	CD	_	_	_
276	t2	t2	NN	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	E.coli	e.coli	NNS	_	_	_
279	_	_	VBP	_	_	_
280	control	control	NN	_	_	_
281	_	_	CD	_	_	_
282	repC	repc	NN	_	_	_
283	_	_	CD	_	_	_
284	t3	t3	NN	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
286	E.coli	e.coli	NNS	_	_	_
287	,	,	,	_	_	_
288	culture	culture	NN	_	_	_
289	with	with	IN	_	_	_
290	ethanol	ethanol	NN	_	_	_
291	20	20	CD	_	_	_
292	%	%	NN	_	_	_
293	,	,	,	_	_	_
294	20	20	CD	_	_	_
295	minutes	minute	NNS	_	_	_
296	-LRB-	-lrb-	-LRB-	_	_	_
297	t2	t2	NN	_	_	_
298	-RRB-	-rrb-	-RRB-	_	_	_
299	after	after	IN	_	_	_
300	treatment	treatment	NN	_	_	_
301	,	,	,	_	_	_
302	replicate	replicate	VB	_	_	_
303	A	a	DT	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	E.coli	e.coli	NNS	_	_	_
306	,	,	,	_	_	_
307	culture	culture	NN	_	_	_
308	with	with	IN	_	_	_
309	ethanol	ethanol	NN	_	_	_
310	20	20	CD	_	_	_
311	%	%	NN	_	_	_
312	,	,	,	_	_	_
313	20	20	CD	_	_	_
314	minutes	minute	NNS	_	_	_
315	-LRB-	-lrb-	-LRB-	_	_	_
316	t2	t2	NN	_	_	_
317	-RRB-	-rrb-	-RRB-	_	_	_
318	after	after	IN	_	_	_
319	treatment	treatment	NN	_	_	_
320	,	,	,	_	_	_
321	replicate	replicate	VB	_	_	_
322	B	b	NN	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	E.coli	e.coli	NNS	_	_	_
325	,	,	,	_	_	_
326	culture	culture	NN	_	_	_
327	with	with	IN	_	_	_
328	ethanol	ethanol	NN	_	_	_
329	20	20	CD	_	_	_
330	%	%	NN	_	_	_
331	,	,	,	_	_	_
332	20	20	CD	_	_	_
333	minutes	minute	NNS	_	_	_
334	-LRB-	-lrb-	-LRB-	_	_	_
335	t2	t2	NN	_	_	_
336	-RRB-	-rrb-	-RRB-	_	_	_
337	after	after	IN	_	_	_
338	treatment	treatment	NN	_	_	_
339	,	,	,	_	_	_
340	replicate	replicate	VB	_	_	_
341	C	c	NN	_	_	_
342	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
343	E.coli	e.coli	NNS	_	_	_
344	,	,	,	_	_	_
345	culture	culture	NN	_	_	_
346	with	with	IN	_	_	_
347	ethanol	ethanol	NN	_	_	_
348	20	20	CD	_	_	_
349	%	%	NN	_	_	_
350	,	,	,	_	_	_
351	40	40	CD	_	_	_
352	minutes	minute	NNS	_	_	_
353	-LRB-	-lrb-	-LRB-	_	_	_
354	t3	t3	NN	_	_	_
355	-RRB-	-rrb-	-RRB-	_	_	_
356	after	after	IN	_	_	_
357	treatment	treatment	NN	_	_	_
358	,	,	,	_	_	_
359	replicate	replicate	VB	_	_	_
360	A	a	DT	_	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
362	E.coli	e.coli	NNS	_	_	_
363	,	,	,	_	_	_
364	culture	culture	NN	_	_	_
365	with	with	IN	_	_	_
366	ethanol	ethanol	NN	_	_	_
367	20	20	CD	_	_	_
368	%	%	NN	_	_	_
369	,	,	,	_	_	_
370	40	40	CD	_	_	_
371	minutes	minute	NNS	_	_	_
372	-LRB-	-lrb-	-LRB-	_	_	_
373	t3	t3	NN	_	_	_
374	-RRB-	-rrb-	-RRB-	_	_	_
375	after	after	IN	_	_	_
376	treatment	treatment	NN	_	_	_
377	,	,	,	_	_	_
378	replicate	replicate	VB	_	_	_
379	B	b	NN	_	_	_
380	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
381	E.coli	e.coli	NNS	_	_	_
382	,	,	,	_	_	_
383	culture	culture	NN	_	_	_
384	with	with	IN	_	_	_
385	ethanol	ethanol	NN	_	_	_
386	20	20	CD	_	_	_
387	%	%	NN	_	_	_
388	,	,	,	_	_	_
389	40	40	CD	_	_	_
390	minutes	minute	NNS	_	_	_
391	-LRB-	-lrb-	-LRB-	_	_	_
392	t3	t3	NN	_	_	_
393	-RRB-	-rrb-	-RRB-	_	_	_
394	after	after	IN	_	_	_
395	treatment	treatment	NN	_	_	_
396	,	,	,	_	_	_
397	replicate	replicate	VB	_	_	_
398	C	c	NN	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	E.coli	e.coli	NNS	_	_	_
401	,	,	,	_	_	_
402	culture	culture	NN	_	_	_
403	with	with	IN	_	_	_
404	ethanol	ethanol	NN	_	_	_
405	20	20	CD	_	_	_
406	%	%	NN	_	_	_
407	,	,	,	_	_	_
408	at	at	IN	_	_	_
409	the	the	DT	_	_	_
410	time	time	NN	_	_	_
411	of	of	IN	_	_	_
412	treatment	treatment	NN	_	_	_
413	-LRB-	-lrb-	-LRB-	_	_	_
414	t1	t1	NN	_	_	_
415	-RRB-	-rrb-	-RRB-	_	_	_
416	,	,	,	_	_	_
417	replicate	replicate	VB	_	_	_
418	A	a	DT	_	_	_
419	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
420	E.coli	e.coli	NNS	_	_	_
421	,	,	,	_	_	_
422	culture	culture	NN	_	_	_
423	with	with	IN	_	_	_
424	ethanol	ethanol	NN	_	_	_
425	20	20	CD	_	_	_
426	%	%	NN	_	_	_
427	,	,	,	_	_	_
428	at	at	IN	_	_	_
429	the	the	DT	_	_	_
430	time	time	NN	_	_	_
431	of	of	IN	_	_	_
432	treatment	treatment	NN	_	_	_
433	-LRB-	-lrb-	-LRB-	_	_	_
434	t1	t1	NN	_	_	_
435	-RRB-	-rrb-	-RRB-	_	_	_
436	,	,	,	_	_	_
437	replicate	replicate	VB	_	_	_
438	B	b	NN	_	_	_
439	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
440	E.coli	e.coli	NNS	_	_	_
441	,	,	,	_	_	_
442	culture	culture	NN	_	_	_
443	with	with	IN	_	_	_
444	ethanol	ethanol	NN	_	_	_
445	20	20	CD	_	_	_
446	%	%	NN	_	_	_
447	,	,	,	_	_	_
448	at	at	IN	_	_	_
449	the	the	DT	_	_	_
450	time	time	NN	_	_	_
451	of	of	IN	_	_	_
452	treatment	treatment	NN	_	_	_
453	-LRB-	-lrb-	-LRB-	_	_	_
454	t1	t1	NN	_	_	_
455	-RRB-	-rrb-	-RRB-	_	_	_
456	,	,	,	_	_	_
457	replicate	replicate	VB	_	_	_
458	C	c	NN	_	_	_
459	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
460	E.coli	e.coli	NNS	_	_	_
461	,	,	,	_	_	_
462	culture	culture	NN	_	_	_
463	with	with	IN	_	_	_
464	VWPE	vwpe	NN	_	_	_
465	extract	extract	NN	_	_	_
466	diluted	dilute	VBN	_	_	_
467	in	in	IN	_	_	_
468	ethanol	ethanol	NN	_	_	_
469	20	20	CD	_	_	_
470	%	%	NN	_	_	_
471	,	,	,	_	_	_
472	20	20	CD	_	_	_
473	minutes	minute	NNS	_	_	_
474	-LRB-	-lrb-	-LRB-	_	_	_
475	t2	t2	NN	_	_	_
476	-RRB-	-rrb-	-RRB-	_	_	_
477	after	after	IN	_	_	_
478	treatment	treatment	NN	_	_	_
479	,	,	,	_	_	_
480	replicate	replicate	VB	_	_	_
481	A	a	DT	_	_	_
482	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
483	E.coli	e.coli	NNS	_	_	_
484	,	,	,	_	_	_
485	culture	culture	NN	_	_	_
486	with	with	IN	_	_	_
487	VWPE	vwpe	NN	_	_	_
488	extract	extract	NN	_	_	_
489	diluted	dilute	VBN	_	_	_
490	in	in	IN	_	_	_
491	ethanol	ethanol	NN	_	_	_
492	20	20	CD	_	_	_
493	%	%	NN	_	_	_
494	,	,	,	_	_	_
495	20	20	CD	_	_	_
496	minutes	minute	NNS	_	_	_
497	-LRB-	-lrb-	-LRB-	_	_	_
498	t2	t2	NN	_	_	_
499	-RRB-	-rrb-	-RRB-	_	_	_
500	after	after	IN	_	_	_
501	treatment	treatment	NN	_	_	_
502	,	,	,	_	_	_
503	replicate	replicate	VB	_	_	_
504	B	b	NN	_	_	_
505	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
506	E.coli	e.coli	NNS	_	_	_
507	,	,	,	_	_	_
508	culture	culture	NN	_	_	_
509	with	with	IN	_	_	_
510	VWPE	vwpe	NN	_	_	_
511	extract	extract	NN	_	_	_
512	diluted	dilute	VBN	_	_	_
513	in	in	IN	_	_	_
514	ethanol	ethanol	NN	_	_	_
515	20	20	CD	_	_	_
516	%	%	NN	_	_	_
517	,	,	,	_	_	_
518	20	20	CD	_	_	_
519	minutes	minute	NNS	_	_	_
520	-LRB-	-lrb-	-LRB-	_	_	_
521	t2	t2	NN	_	_	_
522	-RRB-	-rrb-	-RRB-	_	_	_
523	after	after	IN	_	_	_
524	treatment	treatment	NN	_	_	_
525	,	,	,	_	_	_
526	replicate	replicate	VB	_	_	_
527	C	c	NN	_	_	_
528	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
529	E.coli	e.coli	NNS	_	_	_
530	,	,	,	_	_	_
531	culture	culture	NN	_	_	_
532	with	with	IN	_	_	_
533	VWPE	vwpe	NN	_	_	_
534	extract	extract	NN	_	_	_
535	diluted	dilute	VBN	_	_	_
536	in	in	IN	_	_	_
537	ethanol	ethanol	NN	_	_	_
538	20	20	CD	_	_	_
539	%	%	NN	_	_	_
540	,	,	,	_	_	_
541	40	40	CD	_	_	_
542	minutes	minute	NNS	_	_	_
543	-LRB-	-lrb-	-LRB-	_	_	_
544	t3	t3	NN	_	_	_
545	-RRB-	-rrb-	-RRB-	_	_	_
546	after	after	IN	_	_	_
547	treatment	treatment	NN	_	_	_
548	,	,	,	_	_	_
549	replicate	replicate	VB	_	_	_
550	A	a	DT	_	_	_
551	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
552	E.coli	e.coli	NNS	_	_	_
553	,	,	,	_	_	_
554	culture	culture	NN	_	_	_
555	with	with	IN	_	_	_
556	VWPE	vwpe	NN	_	_	_
557	extract	extract	NN	_	_	_
558	diluted	dilute	VBN	_	_	_
559	in	in	IN	_	_	_
560	ethanol	ethanol	NN	_	_	_
561	20	20	CD	_	_	_
562	%	%	NN	_	_	_
563	,	,	,	_	_	_
564	40	40	CD	_	_	_
565	minutes	minute	NNS	_	_	_
566	-LRB-	-lrb-	-LRB-	_	_	_
567	t3	t3	NN	_	_	_
568	-RRB-	-rrb-	-RRB-	_	_	_
569	after	after	IN	_	_	_
570	treatment	treatment	NN	_	_	_
571	,	,	,	_	_	_
572	replicate	replicate	VB	_	_	_
573	B	b	NN	_	_	_
574	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
575	E.coli	e.coli	NNS	_	_	_
576	,	,	,	_	_	_
577	culture	culture	NN	_	_	_
578	with	with	IN	_	_	_
579	VWPE	vwpe	NN	_	_	_
580	extract	extract	NN	_	_	_
581	diluted	dilute	VBN	_	_	_
582	in	in	IN	_	_	_
583	ethanol	ethanol	NN	_	_	_
584	20	20	CD	_	_	_
585	%	%	NN	_	_	_
586	,	,	,	_	_	_
587	40	40	CD	_	_	_
588	minutes	minute	NNS	_	_	_
589	-LRB-	-lrb-	-LRB-	_	_	_
590	t3	t3	NN	_	_	_
591	-RRB-	-rrb-	-RRB-	_	_	_
592	after	after	IN	_	_	_
593	treatment	treatment	NN	_	_	_
594	,	,	,	_	_	_
595	replicate	replicate	VB	_	_	_
596	C	c	NN	_	_	_
597	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
598	E.coli	e.coli	NNS	_	_	_
599	,	,	,	_	_	_
600	culture	culture	NN	_	_	_
601	with	with	IN	_	_	_
602	VWPE	vwpe	NN	_	_	_
603	extract	extract	NN	_	_	_
604	diluted	dilute	VBN	_	_	_
605	in	in	IN	_	_	_
606	ethanol	ethanol	NN	_	_	_
607	20	20	CD	_	_	_
608	%	%	NN	_	_	_
609	,	,	,	_	_	_
610	at	at	IN	_	_	_
611	the	the	DT	_	_	_
612	time	time	NN	_	_	_
613	of	of	IN	_	_	_
614	treatment	treatment	NN	_	_	_
615	-LRB-	-lrb-	-LRB-	_	_	_
616	t1	t1	NN	_	_	_
617	-RRB-	-rrb-	-RRB-	_	_	_
618	,	,	,	_	_	_
619	replicate	replicate	VB	_	_	_
620	A	a	DT	_	_	_
621	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
622	E.coli	e.coli	NNS	_	_	_
623	,	,	,	_	_	_
624	culture	culture	NN	_	_	_
625	with	with	IN	_	_	_
626	VWPE	vwpe	NN	_	_	_
627	extract	extract	NN	_	_	_
628	diluted	dilute	VBN	_	_	_
629	in	in	IN	_	_	_
630	ethanol	ethanol	NN	_	_	_
631	20	20	CD	_	_	_
632	%	%	NN	_	_	_
633	,	,	,	_	_	_
634	at	at	IN	_	_	_
635	the	the	DT	_	_	_
636	time	time	NN	_	_	_
637	of	of	IN	_	_	_
638	treatment	treatment	NN	_	_	_
639	-LRB-	-lrb-	-LRB-	_	_	_
640	t1	t1	NN	_	_	_
641	-RRB-	-rrb-	-RRB-	_	_	_
642	,	,	,	_	_	_
643	replicate	replicate	VB	_	_	_
644	B	b	NN	_	_	_
645	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
646	E.coli	e.coli	NNS	_	_	_
647	,	,	,	_	_	_
648	culture	culture	NN	_	_	_
649	with	with	IN	_	_	_
650	VWPE	vwpe	NN	_	_	_
651	extract	extract	NN	_	_	_
652	diluted	dilute	VBN	_	_	_
653	in	in	IN	_	_	_
654	ethanol	ethanol	NN	_	_	_
655	20	20	CD	_	_	_
656	%	%	NN	_	_	_
657	,	,	,	_	_	_
658	at	at	IN	_	_	_
659	the	the	DT	_	_	_
660	time	time	NN	_	_	_
661	of	of	IN	_	_	_
662	treatment	treatment	NN	_	_	_
663	-LRB-	-lrb-	-LRB-	_	_	_
664	t1	t1	NN	_	_	_
665	-RRB-	-rrb-	-RRB-	_	_	_
666	,	,	,	_	_	_
667	replicate	replicate	VB	_	_	_
668	C	c	NN	_	_	_
669	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
670	E.coli	e.coli	NNS	_	_	_
671	_	_	VBP	_	_	_
672	ethanol	ethanol	NN	_	_	_
673	_	_	NN	_	_	_
674	repA	repa	NN	_	_	_
675	_	_	CD	_	_	_
676	t1	t1	NN	_	_	_
677	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
678	E.coli	e.coli	NNS	_	_	_
679	_	_	VBP	_	_	_
680	ethanol	ethanol	NN	_	_	_
681	_	_	NN	_	_	_
682	repA	repa	NN	_	_	_
683	_	_	CD	_	_	_
684	t2	t2	NN	_	_	_
685	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
686	E.coli	e.coli	NNS	_	_	_
687	_	_	VBP	_	_	_
688	ethanol	ethanol	NN	_	_	_
689	_	_	NN	_	_	_
690	repA	repa	NN	_	_	_
691	_	_	CD	_	_	_
692	t3	t3	NN	_	_	_
693	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
694	E.coli	e.coli	NNS	_	_	_
695	_	_	VBP	_	_	_
696	ethanol	ethanol	NN	_	_	_
697	_	_	NN	_	_	_
698	repB	repb	NN	_	_	_
699	_	_	CD	_	_	_
700	t1	t1	NN	_	_	_
701	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
702	E.coli	e.coli	NNS	_	_	_
703	_	_	VBP	_	_	_
704	ethanol	ethanol	NN	_	_	_
705	_	_	NN	_	_	_
706	repB	repb	NN	_	_	_
707	_	_	CD	_	_	_
708	t2	t2	NN	_	_	_
709	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
710	E.coli	e.coli	NNS	_	_	_
711	_	_	VBP	_	_	_
712	ethanol	ethanol	NN	_	_	_
713	_	_	NN	_	_	_
714	repB	repb	NN	_	_	_
715	_	_	CD	_	_	_
716	t3	t3	NN	_	_	_
717	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
718	E.coli	e.coli	NNS	_	_	_
719	_	_	VBP	_	_	_
720	ethanol	ethanol	NN	_	_	_
721	_	_	NN	_	_	_
722	repC	repc	NN	_	_	_
723	_	_	CD	_	_	_
724	t1	t1	NN	_	_	_
725	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
726	E.coli	e.coli	NNS	_	_	_
727	_	_	VBP	_	_	_
728	ethanol	ethanol	NN	_	_	_
729	_	_	NN	_	_	_
730	repC	repc	NN	_	_	_
731	_	_	CD	_	_	_
732	t2	t2	NN	_	_	_
733	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
734	E.coli	e.coli	NNS	_	_	_
735	_	_	VBP	_	_	_
736	ethanol	ethanol	NN	_	_	_
737	_	_	NN	_	_	_
738	repC	repc	NN	_	_	_
739	_	_	CD	_	_	_
740	t3	t3	NN	_	_	_
741	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
742	E.coli	e.coli	NN	_	_	_
743	K12	k12	NN	_	_	_
744	was	be	VBD	_	_	_
745	cultured	culture	VBN	_	_	_
746	in	in	IN	_	_	_
747	LB	lb	NN	_	_	_
748	and	and	CC	_	_	_
749	grown	grow	VBN	_	_	_
750	at	at	IN	_	_	_
751	37	37	CD	_	_	_
752	°C	°c	NN	_	_	_
753	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
754	E.coli	e.coli	NNS	_	_	_
755	_	_	VBP	_	_	_
756	polyphenols	polyphenol	NNS	_	_	_
757	_	_	VBP	_	_	_
758	repA	repa	NN	_	_	_
759	_	_	CD	_	_	_
760	t1	t1	NN	_	_	_
761	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
762	E.coli	e.coli	NNS	_	_	_
763	_	_	VBP	_	_	_
764	polyphenols	polyphenol	NNS	_	_	_
765	_	_	SYM	_	_	_
766	repA	repA	NNP	_	_	_
767	_	_	SYM	_	_	_
768	t2	t2	FW	_	_	_
769	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
770	E.coli	e.coli	FW	_	_	_
771	_	_	SYM	_	_	_
772	polyphenols	polyphenol	NNS	_	_	_
773	_	_	VBP	_	_	_
774	repA	repa	NN	_	_	_
775	_	_	CD	_	_	_
776	t3	t3	NN	_	_	_
777	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
778	E.coli	e.coli	NNS	_	_	_
779	_	_	VBP	_	_	_
780	polyphenols	polyphenol	NNS	_	_	_
781	_	_	VBP	_	_	_
782	repB	repb	NN	_	_	_
783	_	_	CD	_	_	_
784	t1	t1	NN	_	_	_
785	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
786	E.coli	e.coli	NNS	_	_	_
787	_	_	VBP	_	_	_
788	polyphenols	polyphenol	NNS	_	_	_
789	_	_	VBP	_	_	_
790	repB	repb	NN	_	_	_
791	_	_	CD	_	_	_
792	t2	t2	NN	_	_	_
793	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
794	E.coli	e.coli	NNS	_	_	_
795	_	_	VBP	_	_	_
796	polyphenols	polyphenol	NNS	_	_	_
797	_	_	VBP	_	_	_
798	repB	repb	NN	_	_	_
799	_	_	CD	_	_	_
800	t3	t3	NN	_	_	_
801	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
802	E.coli	e.coli	NNS	_	_	_
803	_	_	VBP	_	_	_
804	polyphenols	polyphenol	NNS	_	_	_
805	_	_	VBP	_	_	_
806	repC	repc	NN	_	_	_
807	_	_	CD	_	_	_
808	t1	t1	NN	_	_	_
809	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
810	E.coli	e.coli	NNS	_	_	_
811	_	_	VBP	_	_	_
812	polyphenols	polyphenol	NNS	_	_	_
813	_	_	VBP	_	_	_
814	repC	repc	NN	_	_	_
815	_	_	CD	_	_	_
816	t2	t2	NN	_	_	_
817	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
818	E.coli	e.coli	NNS	_	_	_
819	_	_	VBP	_	_	_
820	polyphenols	polyphenol	NNS	_	_	_
821	_	_	VBP	_	_	_
822	repC	repc	NN	_	_	_
823	_	_	CD	_	_	_
824	t3	t3	NN	_	_	_
825	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
826	Escherichia	escherichia	FW	Organism	_	_
827	coli	coli	FW	Organism	_	_
828	K-12	k-12	NN	_	_	_
829	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
830	RNA	rna	NN	_	_	_
831	extracted	extract	VBN	_	_	_
832	according	accord	VBG	_	_	_
833	to	to	TO	_	_	_
834	QiAgen	QiAgen	NNP	_	_	_
835	RNeasy	RNeasy	NNP	_	_	_
836	MiniKit	MiniKit	NNP	_	_	_
837	protocol	protocol	NN	_	_	_
838	for	for	IN	_	_	_
839	bacterial	bacterial	JJ	_	_	_
840	samples	sample	NNS	_	_	_
841	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
842	time	time	NN	_	_	_
843	:	:	:	_	_	_
844	20	20	CD	_	_	_
845	minutes	minute	NNS	_	_	_
846	-LRB-	-lrb-	-LRB-	_	_	_
847	t2	t2	NN	_	_	_
848	-RRB-	-rrb-	-RRB-	_	_	_
849	after	after	IN	_	_	_
850	treatment	treatment	NN	_	_	_
851	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
852	time	time	NN	_	_	_
853	:	:	:	_	_	_
854	40	40	CD	_	_	_
855	minutes	minute	NNS	_	_	_
856	-LRB-	-lrb-	-LRB-	_	_	_
857	t3	t3	NN	_	_	_
858	-RRB-	-rrb-	-RRB-	_	_	_
859	after	after	IN	_	_	_
860	treatment	treatment	NN	_	_	_
861	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
862	time	time	NN	_	_	_
863	:	:	:	_	_	_
864	at	at	IN	_	_	_
865	time	time	NN	_	_	_
866	of	of	IN	_	_	_
867	treatment	treatment	NN	_	_	_
868	-LRB-	-lrb-	-LRB-	_	_	_
869	t1	t1	NN	_	_	_
870	-RRB-	-rrb-	-RRB-	_	_	_
871	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
872	Escherichia	escherichia	FW	Organism	_	_
873	coli	coli	FW	Organism	_	_
874	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
875	genotype	genotype	NN	_	_	_
876	:	:	:	_	_	_
877	wild	wild	JJ	_	_	_
878	type	type	NN	_	_	_
879	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
880	genotype	genotype	NN	_	_	_
881	:	:	:	_	_	_
882	yajL	yajl	NN	GEN	_	_
883	mutant	mutant	JJ	_	_	_
884	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
885	growth	growth	NN	_	_	_
886	phase	phase	NN	_	_	_
887	:	:	:	_	_	_
888	exponential	exponential	JJ	_	_	_
889	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
890	Intensity	intensity	NN	_	_	_
891	measures	measure	NNS	_	_	_
892	in	in	IN	_	_	_
893	wild	wild	JJ	_	_	_
894	type	type	NN	_	_	_
895	strain	strain	NN	_	_	_
896	,	,	,	_	_	_
897	replicate	replicate	VBP	_	_	_
898	1	1	CD	_	_	_
899	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
900	Intensity	intensity	NN	_	_	_
901	measures	measure	NNS	_	_	_
902	in	in	IN	_	_	_
903	wild	wild	JJ	_	_	_
904	type	type	NN	_	_	_
905	strain	strain	NN	_	_	_
906	,	,	,	_	_	_
907	replicate	replicate	VB	_	_	_
908	2	2	CD	_	_	_
909	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
910	Intensity	intensity	NN	_	_	_
911	measures	measure	NNS	_	_	_
912	in	in	IN	_	_	_
913	yajL	yajl	NN	GEN	_	_
914	mutant	mutant	JJ	_	_	_
915	strain	strain	NN	_	_	_
916	,	,	,	_	_	_
917	replicate	replicate	VBP	_	_	_
918	1	1	CD	_	_	_
919	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
920	Intensity	intensity	NN	_	_	_
921	measures	measure	NNS	_	_	_
922	in	in	IN	_	_	_
923	yajL	yajl	NN	GEN	_	_
924	mutant	mutant	JJ	_	_	_
925	strain	strain	NN	_	_	_
926	,	,	,	_	_	_
927	replicate	replicate	VB	_	_	_
928	2	2	CD	_	_	_
929	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
930	Luria	Luria	NNP	MED	_	_
931	broth	broth	NN	MED	_	_
932	-LRB-	-lrb-	-LRB-	_	_	_
933	LB	lb	NN	_	_	_
934	-RRB-	-rrb-	-RRB-	_	_	_
935	medium	medium	NN	_	_	_
936	under	under	IN	_	_	_
937	aeration	aeration	NN	_	_	_
938	,	,	,	_	_	_
939	exponential	exponential	JJ	GrowthPhase	_	_
940	phase	phase	NN	GrowthPhase	_	_
941	OD600	od600	NN	_	_	_
942	=	=	JJ	_	_	_
943	0.3	0.3	CD	_	_	_
944	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	extraction	extraction	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	using	use	VBG	_	_	_
7	phenol	phenol	NN	_	_	_
8	treatment	treatment	NN	_	_	_
9	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
4	The	the	DT	_	_	_
5	CEL	cel	NN	_	_	_
6	files	file	VBZ	_	_	_
7	generated	generate	VBN	_	_	_
8	for	for	IN	_	_	_
9	each	each	DT	_	_	_
10	array	array	NN	_	_	_
11	were	be	VBD	_	_	_
12	analyzed	analyze	VBN	_	_	_
13	using	use	VBG	_	_	_
14	Affymetrix	Affymetrix	NNP	_	_	_
15	Expression	expression	NN	_	_	_
16	Console	console	NN	_	_	_
17	software	software	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	none	none	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Untreated	untreated	JJ	_	_	_
7	wild	wild	JJ	_	_	_
8	type	type	NN	_	_	_
9	versus	versus	CC	_	_	_
10	untreated	untreated	JJ	_	_	_
11	yajL	yajl	NN	GEN	_	_
12	mutant	mutant	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	wild	wild	JJ	_	_	_
3	type	type	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	yajL	yajl	NN	GEN	_	_
7	mutant	mutant	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	genetic	genetic	JJ	_	_	_
10	background	background	NN	_	_	_
11	MG1655	mg1655	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	At	at	IN	_	_	_
15	OD600	od600	NN	_	_	_
16	of	of	IN	_	_	_
17	0.5	0.5	CD	_	_	_
18	,	,	,	_	_	_
19	cell	cell	NN	_	_	_
20	cultures	culture	NNS	_	_	_
21	were	be	VBD	_	_	_
22	separated	separate	VBN	_	_	_
23	into	into	IN	_	_	_
24	two	two	CD	_	_	_
25	flasks	flask	NNS	_	_	_
26	.	.	.	_	_	_

1	D-galactose	d-galactose	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	final	final	JJ	_	_	_
4	0.3	0.3	CD	_	_	_
5	%	%	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	was	be	VBD	_	_	_
8	added	add	VBN	_	_	_
9	to	to	TO	_	_	_
10	one	one	CD	_	_	_
11	and	and	CC	_	_	_
12	cells	cell	NNS	_	_	_
13	were	be	VBD	_	_	_
14	grown	grow	VBN	_	_	_
15	for	for	IN	_	_	_
16	1.5	1.5	CD	_	_	_
17	h	h	NN	_	_	_
18	further	further	RB	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	placed	place	VBN	_	_	_
6	on	on	IN	_	_	_
7	ice	ice	NN	_	_	_
8	and	and	CC	_	_	_
9	RNAprotect	rnaprotect	NN	_	_	_
10	™	™	NN	_	_	_
11	bacteria	bacterium	NNS	_	_	_
12	reagent	reagent	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Qiagen	qiagen	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	was	be	VBD	_	_	_
17	added	add	VBN	_	_	_
18	to	to	TO	_	_	_
19	stabilize	stabilize	VB	_	_	_
20	the	the	DT	_	_	_
21	RNA	rna	NN	_	_	_
22	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNAs	rna	NNS	_	_	_
3	of	of	IN	_	_	_
4	cells	cell	NNS	_	_	_
5	were	be	VBD	_	_	_
6	purified	purify	VBN	_	_	_
7	by	by	IN	_	_	_
8	RNeasy	rneasy	NN	_	_	_
9	mini	minus	NNS	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	qiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	Isolated	isolate	VBN	_	_	_
2	RNA	rna	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	10	10	CD	_	_	_
5	ug	ug	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	was	be	VBD	_	_	_
8	used	use	VBN	_	_	_
9	for	for	IN	_	_	_
10	random	random	JJ	_	_	_
11	primer	primer	NN	_	_	_
12	cDNA	cdna	NN	_	_	_
13	synthesis	synthesis	NN	_	_	_
14	using	use	VBG	_	_	_
15	SuperScript	SuperScript	NNP	_	_	_
16	II	II	NNP	_	_	_
17	reverse	reverse	JJ	_	_	_
18	transcriptase	transcriptase	NN	_	_	_
19	,	,	,	_	_	_
20	18064	18064	CD	_	_	_
21	--	--	:	_	_	_
22	071	071	CD	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Invitrogen	invitrogen	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	reaction	reaction	NN	_	_	_
3	mixture	mixture	NN	_	_	_
4	was	be	VBD	_	_	_
5	then	then	RB	_	_	_
6	subsequently	subsequently	RB	_	_	_
7	treated	treat	VBN	_	_	_
8	with	with	IN	_	_	_
9	1	1	CD	_	_	_
10	N	n	NN	_	_	_
11	NaOH	naoh	NN	_	_	_
12	to	to	TO	_	_	_
13	degrade	degrade	VB	_	_	_
14	any	any	DT	_	_	_
15	remaining	remain	VBG	_	_	_
16	RNA	rna	NN	_	_	_
17	and	and	CC	_	_	_
18	treated	treat	VBN	_	_	_
19	with	with	IN	_	_	_
20	1	1	CD	_	_	_
21	N	n	NN	_	_	_
22	HCl	hcl	NN	_	_	_
23	to	to	TO	_	_	_
24	neutralize	neutralize	VB	_	_	_
25	the	the	DT	_	_	_
26	NaOH	naoh	NN	_	_	_
27	.	.	.	_	_	_

1	Synthesized	synthesize	VBN	_	_	_
2	cDNA	cdna	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	purified	purify	VBN	_	_	_
6	using	use	VBG	_	_	_
7	MiniElute	MiniElute	NNP	_	_	_
8	PCR	pcr	NN	_	_	_
9	purification	purification	NN	_	_	_
10	columns	column	NNS	_	_	_
11	,	,	,	_	_	_
12	28004	28004	CD	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Qiagen	qiagen	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	Purified	purify	VBN	_	_	_
2	cDNA	cdna	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	3	3	CD	_	_	_
5	ug	ug	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	was	be	VBD	_	_	_
8	fragmented	fragmented	JJ	_	_	_
9	to	to	TO	_	_	_
10	between	between	IN	_	_	_
11	50	50	CD	_	_	_
12	and	and	CC	_	_	_
13	200	200	CD	_	_	_
14	bps	bp	NNS	_	_	_
15	by	by	IN	_	_	_
16	0.6	0.6	CD	_	_	_
17	U	U	NNP	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Computation	Computation	NNP	_	_	_
20	of	of	IN	_	_	_
21	genomic	genomic	JJ	_	_	_
22	intervals	interval	NNS	_	_	_
23	based	base	VBN	_	_	_
24	on	on	IN	_	_	_
25	computed	computed	JJ	_	_	_
26	signal	signal	NN	_	_	_
27	and	and	CC	_	_	_
28	p-values	p-values	JJ	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Computation	computation	NN	_	_	_
31	of	of	IN	_	_	_
32	summary	summary	NN	_	_	_
33	statistics	statistics	NNS	_	_	_
34	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
35	E.	e.	FW	_	_	_
36	coli	coli	FW	_	_	_
37	galT	galt	NN	GEN	_	_
38	mutant	mutant	JJ	_	_	_
39	cells	cell	NNS	_	_	_
40	were	be	VBD	_	_	_
41	cultivated	cultivate	VBN	_	_	_
42	in	in	IN	_	_	_
43	125-mL	125-ml	NN	_	_	_
44	corning	corning	NN	_	_	_
45	flasks	flask	NNS	_	_	_
46	containing	contain	VBG	_	_	_
47	30	30	CD	_	_	_
48	mL	ml	NN	_	_	_
49	of	of	IN	_	_	_
50	M63	m63	NN	_	_	_
51	minimal	minimal	JJ	_	_	_
52	medium	medium	NN	_	_	_
53	plus	plus	CC	_	_	_
54	glycerol	glycerol	NN	SUPP	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	final	final	JJ	_	_	_
57	0.3	0.3	CD	_	_	_
58	%	%	NN	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	at	at	IN	_	_	_
61	37	37	CD	_	_	_
62	°C	°c	NN	_	_	_
63	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	galT	galt	NN	GEN	_	_
5	mutant	mutant	NN	_	_	_
6	with	with	IN	_	_	_
7	galactose	galactose	NN	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	E.	E.	NNP	_	_	_
10	coli	coli	NN	_	_	_
11	galT	galt	NN	GEN	_	_
12	mutant	mutant	NN	_	_	_
13	without	without	IN	_	_	_
14	galactose	galactose	NN	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	Escherichia	escherichia	FW	Organism	_	_
17	coli	coli	FW	Organism	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	genotype	genotype	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Signal	signal	NN	_	_	_
22	and	and	CC	_	_	_
23	p-values	p-value	NNS	_	_	_
24	for	for	IN	_	_	_
25	each	each	DT	_	_	_
26	genomic	genomic	JJ	_	_	_
27	position	position	NN	_	_	_
28	interrogated	interrogate	VBN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	program	program	NN	_	_	_
4	used	use	VBN	_	_	_
5	to	to	TO	_	_	_
6	generate	generate	VB	_	_	_
7	the	the	DT	_	_	_
8	bed	bed	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	The	the	DT	_	_	_
11	TAS	tas	NN	_	_	_
12	software	software	NN	_	_	_
13	provides	provide	VBZ	_	_	_
14	analysis	analysis	NN	_	_	_
15	capabilities	capability	NNS	_	_	_
16	specifically	specifically	RB	_	_	_
17	for	for	IN	_	_	_
18	the	the	DT	_	_	_
19	GeneChip	GeneChip	NNP	_	_	_
20	®	®	NNP	_	_	_
21	Tiling	Tiling	NNP	_	_	_
22	Arrays	Arrays	NNPS	_	_	_
23	.	.	.	_	_	_

1	TAS	tas	NN	_	_	_
2	analyzes	analyze	VBZ	_	_	_
3	feature	feature	NN	_	_	_
4	intensity	intensity	NN	_	_	_
5	data	datum	NNS	_	_	_
6	stored	store	VBN	_	_	_
7	in	in	IN	_	_	_
8	GCOS	gcos	NN	_	_	_
9	output	output	NN	_	_	_
10	.	.	.	_	_	_

1	CEL	CEL	NNP	_	_	_
2	files	file	NNS	_	_	_
3	and	and	CC	_	_	_
4	produces	produce	VBZ	_	_	_
5	:	:	:	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	Visualizations	visualization	NNS	_	_	_
8	for	for	IN	_	_	_
9	assessing	assess	VBG	_	_	_
10	the	the	DT	_	_	_
11	quality	quality	NN	_	_	_
12	of	of	IN	_	_	_
13	the	the	DT	_	_	_
14	array	array	NN	_	_	_
15	data	datum	NNS	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	with	with	IN	_	_	_
18	D-galactose	d-galactose	JJ	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	without	without	IN	_	_	_
21	D-galactose	d-galactose	JJ	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	At	at	IN	_	_	_
24	OD450	od450	NN	_	_	_
25	=	=	JJ	_	_	_
26	0.3	0.3	CD	_	_	_
27	,	,	,	_	_	_
28	cultures	culture	NNS	_	_	_
29	induced	induce	VBN	_	_	_
30	with	with	IN	_	_	_
31	1	1	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	IPTG	iptg	NN	_	_	_
34	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	harvested	harvest	VBD	_	_	_
3	0	0	CD	_	_	_
4	min	min	NN	_	_	_
5	after	after	IN	_	_	_
6	induction	induction	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	At	at	IN	_	_	_
9	OD450	od450	NN	_	_	_
10	=	=	JJ	_	_	_
11	0.3	0.3	CD	_	_	_
12	,	,	,	_	_	_
13	cultures	culture	NNS	_	_	_
14	induced	induce	VBN	_	_	_
15	with	with	IN	_	_	_
16	1	1	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	IPTG	iptg	NN	_	_	_
19	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	harvested	harvest	VBD	_	_	_
3	10	10	CD	_	_	_
4	min	min	NN	_	_	_
5	after	after	IN	_	_	_
6	induction	induction	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	At	at	IN	_	_	_
9	OD450	od450	NN	_	_	_
10	=	=	JJ	_	_	_
11	0.3	0.3	CD	_	_	_
12	,	,	,	_	_	_
13	cultures	culture	NNS	_	_	_
14	induced	induce	VBN	_	_	_
15	with	with	IN	_	_	_
16	1	1	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	IPTG	iptg	NN	_	_	_
19	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	harvested	harvest	VBN	_	_	_
3	20	20	CD	_	_	_
4	min	min	NN	_	_	_
5	after	after	IN	_	_	_
6	induction	induction	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	At	at	IN	_	_	_
9	OD450	od450	NN	_	_	_
10	=	=	JJ	_	_	_
11	0.3	0.3	CD	_	_	_
12	,	,	,	_	_	_
13	cultures	culture	NNS	_	_	_
14	induced	induce	VBN	_	_	_
15	with	with	IN	_	_	_
16	1	1	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	IPTG	iptg	NN	_	_	_
19	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	harvested	harvest	VBN	_	_	_
3	2.5	2.5	CD	_	_	_
4	min	min	NN	_	_	_
5	after	after	IN	_	_	_
6	induction	induction	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	At	at	IN	_	_	_
9	OD450	od450	NN	_	_	_
10	=	=	JJ	_	_	_
11	0.3	0.3	CD	_	_	_
12	,	,	,	_	_	_
13	cultures	culture	NNS	_	_	_
14	induced	induce	VBN	_	_	_
15	with	with	IN	_	_	_
16	1	1	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	IPTG	iptg	NN	_	_	_
19	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	harvested	harvest	VBN	_	_	_
3	5	5	CD	_	_	_
4	min	min	NN	_	_	_
5	after	after	IN	_	_	_
6	induction	induction	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Culture	culture	NN	_	_	_
9	samples	sample	NNS	_	_	_
10	for	for	IN	_	_	_
11	microarray	microarray	NN	_	_	_
12	analysis	analysis	NN	_	_	_
13	were	be	VBD	_	_	_
14	added	add	VBN	_	_	_
15	to	to	TO	_	_	_
16	ice-cold	ice-cold	JJ	_	_	_
17	5	5	CD	_	_	_
18	%	%	NN	_	_	_
19	water-saturated	water-saturated	JJ	_	_	_
20	phenol	phenol	NN	_	_	_
21	in	in	IN	_	_	_
22	ethanol	ethanol	NN	_	_	_
23	solution	solution	NN	_	_	_
24	,	,	,	_	_	_
25	centrifuged	centrifuge	VBN	_	_	_
26	at	at	IN	_	_	_
27	6,600	6,600	CD	_	_	_
28	g	g	NN	_	_	_
29	and	and	CC	_	_	_
30	the	the	DT	_	_	_
31	cell	cell	NN	_	_	_
32	pellets	pellet	NNS	_	_	_
33	flash	flash	VBP	_	_	_
34	frozen	freeze	VBN	_	_	_
35	in	in	IN	_	_	_
36	liquid	liquid	JJ	_	_	_
37	N2	n2	NN	_	_	_
38	before	before	IN	_	_	_
39	storing	store	VBG	_	_	_
40	at	at	IN	_	_	_
41	-80	-80	CD	_	_	_
42	degrees	degree	NNS	_	_	_
43	C	c	NN	_	_	_
44	until	until	IN	_	_	_
45	required	require	VBN	_	_	_
46	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	from	from	IN	_	_	_
6	the	the	DT	_	_	_
7	stored	store	VBN	_	_	_
8	cell	cell	NN	_	_	_
9	pellets	pellet	NNS	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	hot	hot	JJ	_	_	_
13	phenol	phenol	NN	_	_	_
14	method	method	NN	_	_	_
15	,	,	,	_	_	_
16	and	and	CC	_	_	_
17	labeled	label	VBN	_	_	_
18	Cy3	cy3	NN	_	_	_
19	and	and	CC	_	_	_
20	Cy5	cy5	NN	_	_	_
21	cDNA	cdna	NN	_	_	_
22	was	be	VBD	_	_	_
23	prepared	prepare	VBN	_	_	_
24	from	from	IN	_	_	_
25	16	16	CD	_	_	_
26	ug	ug	NN	_	_	_
27	total	total	JJ	_	_	_
28	RNA	rna	NN	_	_	_
29	with	with	IN	_	_	_
30	10	10	CD	_	_	_
31	ug	ug	NN	_	_	_
32	random	random	JJ	_	_	_
33	hexamer	hexamer	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Integrated	Integrated	NNP	_	_	_
36	DNA	DNA	NNP	_	_	_
37	Technologies	Technologies	NNPS	_	_	_
38	,	,	,	_	_	_
39	Inc.	Inc.	NNP	_	_	_
40	,	,	,	_	_	_
41	Coralville	Coralville	NNP	_	_	_
42	,	,	,	_	_	_
43	IA	IA	NNP	_	_	_
44	,	,	,	_	_	_
45	USA	USA	NNP	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	filtered	filter	VBD	_	_	_
4	for	for	IN	_	_	_
5	PCR	pcr	NN	_	_	_
6	success	success	NN	_	_	_
7	,	,	,	_	_	_
8	>	>	JJR	_	_	_
9	3x	3x	NN	_	_	_
10	local	local	JJ	_	_	_
11	background	background	NN	_	_	_
12	and	and	CC	_	_	_
13	spot	spot	NN	_	_	_
14	quality	quality	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	GenePix	GenePix	NNP	_	_	_
17	Flag	Flag	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	Normalized	normalize	VBN	_	_	_
2	using	use	VBG	_	_	_
3	Lowess	Lowess	NNP	_	_	_
4	smoothing	smooth	VBG	_	_	_
5	from	from	IN	_	_	_
6	MA	MA	NNP	_	_	_
7	plot	plot	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	EC18n122	ec18n122	NN	_	_	_
10	RpoH	rpoh	NN	_	_	_
11	10	10	CD	_	_	_
12	min	min	NN	_	_	_
13	Time	Time	NNP	_	_	_
14	course	course	NN	_	_	_
15	4	4	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	EC18n167	ec18n167	NN	_	_	_
18	RpoH	rpoh	NN	_	_	_
19	0	0	CD	_	_	_
20	min	min	NN	_	_	_
21	Time	Time	NNP	_	_	_
22	course	course	NN	_	_	_
23	2	2	CD	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	EC18n168	ec18n168	NN	_	_	_
26	RpoH	rpoh	NN	_	_	_
27	2.5	2.5	CD	_	_	_
28	min	min	NN	_	_	_
29	Time	Time	NNP	_	_	_
30	course	course	NN	_	_	_
31	2	2	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	EC18n169	ec18n169	NN	_	_	_
34	RpoH	rpoh	NN	_	_	_
35	5	5	CD	_	_	_
36	min	min	NN	_	_	_
37	Time	Time	NNP	_	_	_
38	course	course	NN	_	_	_
39	2	2	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	EC18n170	ec18n170	NN	_	_	_
42	RpoH	rpoh	NN	_	_	_
43	10	10	CD	_	_	_
44	min	min	NN	_	_	_
45	Time	Time	NNP	_	_	_
46	course	course	NN	_	_	_
47	2	2	CD	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	EC18n171	ec18n171	NN	_	_	_
50	RpoH	rpoh	NN	_	_	_
51	20	20	CD	_	_	_
52	min	min	NN	_	_	_
53	Time	Time	NNP	_	_	_
54	course	course	NN	_	_	_
55	2	2	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	EC18n177	ec18n177	NN	_	_	_
58	RpoH	rpoh	NN	_	_	_
59	0	0	CD	_	_	_
60	min	min	NN	_	_	_
61	Time	Time	NNP	_	_	_
62	course	course	NN	_	_	_
63	1	1	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	EC18n178	ec18n178	NN	_	_	_
66	RpoH	rpoh	NN	_	_	_
67	2.5	2.5	CD	_	_	_
68	min	min	NN	_	_	_
69	Time	Time	NNP	_	_	_
70	course	course	NN	_	_	_
71	1	1	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	EC18n179	ec18n179	NN	_	_	_
74	RpoH	rpoh	NN	_	_	_
75	5	5	CD	_	_	_
76	min	min	NN	_	_	_
77	Time	Time	NNP	_	_	_
78	course	course	NN	_	_	_
79	1	1	CD	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	EC18n180	ec18n180	NN	_	_	_
82	RpoH	rpoh	NN	_	_	_
83	10	10	CD	_	_	_
84	min	min	NN	_	_	_
85	Time	Time	NNP	_	_	_
86	course	course	NN	_	_	_
87	1	1	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	EC18n181	ec18n181	NN	_	_	_
90	RpoH	rpoh	NN	_	_	_
91	20	20	CD	_	_	_
92	min	min	NN	_	_	_
93	Time	Time	NNP	_	_	_
94	course	course	NN	_	_	_
95	1	1	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	EC18n182	ec18n182	NN	_	_	_
98	RpoH	rpoh	NN	_	_	_
99	0	0	CD	_	_	_
100	min	min	NN	_	_	_
101	Time	Time	NNP	_	_	_
102	course	course	NN	_	_	_
103	3	3	CD	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	EC18n183	ec18n183	NN	_	_	_
106	RpoH	rpoh	NN	_	_	_
107	2.5	2.5	CD	_	_	_
108	min	min	NN	_	_	_
109	Time	Time	NNP	_	_	_
110	course	course	NN	_	_	_
111	3	3	CD	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	EC18n184	ec18n184	NN	_	_	_
114	RpoH	rpoh	NN	_	_	_
115	5	5	CD	_	_	_
116	min	min	NN	_	_	_
117	Time	Time	NNP	_	_	_
118	course	course	NN	_	_	_
119	3	3	CD	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	EC18n185	ec18n185	NN	_	_	_
122	RpoH	rpoh	NN	_	_	_
123	10	10	CD	_	_	_
124	min	min	NN	_	_	_
125	Time	Time	NNP	_	_	_
126	course	course	NN	_	_	_
127	3	3	CD	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	EC18n186	ec18n186	NN	_	_	_
130	RpoH	rpoh	NN	_	_	_
131	20	20	CD	_	_	_
132	min	min	NN	_	_	_
133	Time	Time	NNP	_	_	_
134	course	course	NN	_	_	_
135	3	3	CD	_	_	_
136	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
137	Escherichia	escherichia	FW	Organism	_	_
138	coli	coli	FW	Organism	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	M9	m9	NN	_	_	_
141	minimal	minimal	JJ	_	_	_
142	complete	complete	JJ	_	_	_
143	media	media	NNS	_	_	_
144	,	,	,	_	_	_
145	cultures	culture	NNS	_	_	_
146	grown	grow	VBN	_	_	_
147	aerobically	aerobically	RB	_	_	_
148	at	at	IN	_	_	_
149	30	30	CD	_	_	_
150	degrees	degree	NNS	_	_	_
151	C	c	NN	_	_	_
152	in	in	IN	_	_	_
153	a	a	DT	_	_	_
154	gyratory	gyratory	JJ	_	_	_
155	water	water	NN	_	_	_
156	bath	bath	NN	_	_	_
157	shaking	shake	VBG	_	_	_
158	at	at	IN	_	_	_
159	240	240	CD	_	_	_
160	rpm	rpm	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	MG1655	mg1655	NN	_	_	_
163	PhtpG	phtpg	NN	_	_	_
164	:	:	:	_	_	_
165	:	:	:	_	_	_
166	lacZ	lacz	NN	GEN	_	_
167	delta	delta	NN	_	_	_
168	lacX74	lacx74	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	RpoH	rpoh	NN	_	_	_
171	induced	induce	VBN	_	_	_
172	-LRB-	-lrb-	-LRB-	_	_	_
173	0	0	CD	_	_	_
174	min	min	NN	_	_	_
175	-RRB-	-rrb-	-RRB-	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	RpoH	rpoh	NN	_	_	_
178	induced	induce	VBN	_	_	_
179	-LRB-	-lrb-	-LRB-	_	_	_
180	10	10	CD	_	_	_
181	min	min	NN	_	_	_
182	-RRB-	-rrb-	-RRB-	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	RpoH	rpoh	NN	_	_	_
185	induced	induce	VBN	_	_	_
186	-LRB-	-lrb-	-LRB-	_	_	_
187	20	20	CD	_	_	_
188	min	min	NN	_	_	_
189	-RRB-	-rrb-	-RRB-	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	RpoH	rpoh	NN	_	_	_
192	induced	induce	VBN	_	_	_
193	-LRB-	-lrb-	-LRB-	_	_	_
194	2.5	2.5	CD	_	_	_
195	min	min	NN	_	_	_
196	-RRB-	-rrb-	-RRB-	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	RpoH	rpoh	NN	_	_	_
199	induced	induce	VBN	_	_	_
200	-LRB-	-lrb-	-LRB-	_	_	_
201	5	5	CD	_	_	_
202	min	min	NN	_	_	_
203	-RRB-	-rrb-	-RRB-	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	Wild	Wild	NNP	_	_	_
206	type	type	NN	_	_	_
207	control	control	NN	_	_	_
208	-LRB-	-lrb-	-LRB-	_	_	_
209	0	0	CD	_	_	_
210	min	min	NN	_	_	_
211	-RRB-	-rrb-	-RRB-	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	Wild	Wild	NNP	_	_	_
214	type	type	NN	_	_	_
215	control	control	NN	_	_	_
216	-LRB-	-lrb-	-LRB-	_	_	_
217	10	10	CD	_	_	_
218	min	min	NN	_	_	_
219	-RRB-	-rrb-	-RRB-	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	Wild	Wild	NNP	_	_	_
222	type	type	NN	_	_	_
223	control	control	NN	_	_	_
224	-LRB-	-lrb-	-LRB-	_	_	_
225	20	20	CD	_	_	_
226	min	min	NN	_	_	_
227	-RRB-	-rrb-	-RRB-	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	Wild	Wild	NNP	_	_	_
230	type	type	NN	_	_	_
231	control	control	NN	_	_	_
232	-LRB-	-lrb-	-LRB-	_	_	_
233	2.5	2.5	CD	_	_	_
234	min	min	NN	_	_	_
235	-RRB-	-rrb-	-RRB-	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	Wild	Wild	NNP	_	_	_
238	type	type	NN	_	_	_
239	control	control	NN	_	_	_
240	-LRB-	-lrb-	-LRB-	_	_	_
241	5	5	CD	_	_	_
242	min	min	NN	_	_	_
243	-RRB-	-rrb-	-RRB-	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	Ecoli	ecolus	NNS	_	_	_
246	_	_	VBP	_	_	_
247	Ampicillin	ampicillin	NN	_	_	_
248	treatment	treatment	NN	_	_	_
249	T1	t1	NN	_	_	_
250	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
251	Ecoli	Ecoli	NNP	_	_	_
252	_	_	NNP	_	_	_
253	Ampicillin	Ampicillin	NNP	_	_	_
254	treatment	treatment	NN	_	_	_
255	T2	t2	NN	_	_	_
256	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
257	Ecoli	Ecoli	NNP	_	_	_
258	_	_	NNP	_	_	_
259	Ampicillin	Ampicillin	NNP	_	_	_
260	treatment	treatment	NN	_	_	_
261	T3	t3	NN	_	_	_
262	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
263	Ecoli	Ecoli	NNP	_	_	_
264	_	_	NNP	_	_	_
265	Ampicillin	Ampicillin	NNP	_	_	_
266	treatment	treatment	NN	_	_	_
267	T4	t4	NN	_	_	_
268	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
269	Ecoli	Ecoli	NNP	_	_	_
270	_	_	NNP	_	_	_
271	Ampicillin	Ampicillin	NNP	_	_	_
272	treatment	treatment	NN	_	_	_
273	T5	t5	NN	_	_	_
274	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
275	Ecoli	Ecoli	NNP	_	_	_
276	_	_	NNP	_	_	_
277	Ampicillin	Ampicillin	NNP	_	_	_
278	treatment	treatment	NN	_	_	_
279	T6	t6	NN	_	_	_
280	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
281	Escherichia	escherichia	FW	Organism	_	_
282	coli	coli	FW	Organism	_	_
283	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
284	Escherichia	escherichia	FW	Organism	_	_
285	coli	coli	FW	Organism	_	_
286	MG1655	mg1655	NN	_	_	_
287	,	,	,	_	_	_
288	0	0	CD	_	_	_
289	min	min	NN	_	_	_
290	after	after	IN	_	_	_
291	Ampicillin	Ampicillin	NNP	_	_	_
292	-LRB-	-lrb-	-LRB-	_	_	_
293	100	100	CD	_	_	_
294	ug	ug	NN	_	_	_
295	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
296	Escherichia	escherichia	FW	Organism	_	_
297	coli	coli	FW	Organism	_	_
298	MG1655	mg1655	NN	_	_	_
299	,	,	,	_	_	_
300	10	10	CD	_	_	_
301	min	min	NN	_	_	_
302	after	after	IN	_	_	_
303	Ampicillin	Ampicillin	NNP	_	_	_
304	-LRB-	-lrb-	-LRB-	_	_	_
305	100	100	CD	_	_	_
306	ug	ug	NN	_	_	_
307	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
308	Escherichia	escherichia	FW	Organism	_	_
309	coli	coli	FW	Organism	_	_
310	MG1655	mg1655	NN	_	_	_
311	,	,	,	_	_	_
312	15	15	CD	_	_	_
313	min	min	NN	_	_	_
314	after	after	IN	_	_	_
315	Ampicillin	Ampicillin	NNP	_	_	_
316	-LRB-	-lrb-	-LRB-	_	_	_
317	100	100	CD	_	_	_
318	ug	ug	NN	_	_	_
319	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
320	Escherichia	escherichia	FW	Organism	_	_
321	coli	coli	FW	Organism	_	_
322	MG1655	mg1655	NN	_	_	_
323	,	,	,	_	_	_
324	20	20	CD	_	_	_
325	min	min	NN	_	_	_
326	after	after	IN	_	_	_
327	Ampicillin	Ampicillin	NNP	_	_	_
328	-LRB-	-lrb-	-LRB-	_	_	_
329	100	100	CD	_	_	_
330	ug	ug	NN	_	_	_
331	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
332	Escherichia	escherichia	FW	Organism	_	_
333	coli	coli	FW	Organism	_	_
334	MG1655	mg1655	NN	_	_	_
335	,	,	,	_	_	_
336	30	30	CD	_	_	_
337	min	min	NN	_	_	_
338	after	after	IN	_	_	_
339	Ampicillin	Ampicillin	NNP	_	_	_
340	-LRB-	-lrb-	-LRB-	_	_	_
341	100	100	CD	_	_	_
342	ug	ug	NN	_	_	_
343	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
344	Escherichia	escherichia	FW	Organism	_	_
345	coli	coli	FW	Organism	_	_
346	MG1655	mg1655	NN	_	_	_
347	,	,	,	_	_	_
348	40	40	CD	_	_	_
349	min	min	NN	_	_	_
350	after	after	IN	_	_	_
351	Ampicillin	Ampicillin	NNP	_	_	_
352	-LRB-	-lrb-	-LRB-	_	_	_
353	100	100	CD	_	_	_
354	ug	ug	NN	_	_	_
355	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
356	Escherichia	escherichia	FW	Organism	_	_
357	coli	coli	FW	Organism	_	_
358	MG1655	mg1655	NN	_	_	_
359	,	,	,	_	_	_
360	45	45	CD	_	_	_
361	min	min	NN	_	_	_
362	after	after	IN	_	_	_
363	Ampicillin	Ampicillin	NNP	_	_	_
364	-LRB-	-lrb-	-LRB-	_	_	_
365	100	100	CD	_	_	_
366	ug	ug	NN	_	_	_
367	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
368	Escherichia	escherichia	FW	Organism	_	_
369	coli	coli	FW	Organism	_	_
370	MG1655	mg1655	NN	_	_	_
371	,	,	,	_	_	_
372	50	50	CD	_	_	_
373	min	min	NN	_	_	_
374	after	after	IN	_	_	_
375	Ampicillin	Ampicillin	NNP	_	_	_
376	-LRB-	-lrb-	-LRB-	_	_	_
377	100	100	CD	_	_	_
378	ug	ug	NN	_	_	_
379	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
380	Escherichia	escherichia	FW	Organism	_	_
381	coli	coli	FW	Organism	_	_
382	MG1655	mg1655	NN	_	_	_
383	,	,	,	_	_	_
384	5	5	CD	_	_	_
385	min	min	NN	_	_	_
386	after	after	IN	_	_	_
387	Ampicillin	Ampicillin	NNP	_	_	_
388	-LRB-	-lrb-	-LRB-	_	_	_
389	100	100	CD	_	_	_
390	ug	ug	NN	_	_	_
391	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
392	Escherichia	escherichia	FW	Organism	_	_
393	coli	coli	FW	Organism	_	_
394	MG1655	mg1655	NN	_	_	_
395	,	,	,	_	_	_
396	60	60	CD	_	_	_
397	min	min	NN	_	_	_
398	after	after	IN	_	_	_
399	Ampicillin	Ampicillin	NNP	_	_	_
400	-LRB-	-lrb-	-LRB-	_	_	_
401	100	100	CD	_	_	_
402	ug	ug	NN	_	_	_
403	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
404	Escherichia	escherichia	FW	Organism	_	_
405	coli	coli	FW	Organism	_	_
406	MG1655	mg1655	NN	_	_	_
407	,	,	,	_	_	_
408	75	75	CD	_	_	_
409	min	min	NN	_	_	_
410	after	after	IN	_	_	_
411	Ampicillin	Ampicillin	NNP	_	_	_
412	-LRB-	-lrb-	-LRB-	_	_	_
413	100	100	CD	_	_	_
414	ug	ug	NN	_	_	_
415	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
416	Escherichia	escherichia	FW	Organism	_	_
417	coli	coli	FW	Organism	_	_
418	MG1655	mg1655	NN	_	_	_
419	,	,	,	_	_	_
420	M9	m9	NN	_	_	_
421	+	+	CC	_	_	_
422	glucose	glucose	NN	SUPP	_	_
423	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
424	Escherichia	escherichia	FW	Organism	_	_
425	coli	coli	FW	Organism	_	_
426	MG1655	mg1655	NN	_	_	_
427	,	,	,	_	_	_
428	M9	m9	NN	_	_	_
429	+	+	CC	_	_	_
430	glucose	glucose	NN	SUPP	_	_
431	,	,	,	_	_	_
432	0	0	CD	_	_	_
433	min	min	NN	_	_	_
434	before	before	IN	_	_	_
435	treatment	treatment	NN	_	_	_
436	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
437	Normalized	normalize	VBN	_	_	_
438	log	log	NN	_	_	_
439	-LRB-	-lrb-	-LRB-	_	_	_
440	2	2	CD	_	_	_
441	-RRB-	-rrb-	-RRB-	_	_	_
442	ratio	ratio	NN	_	_	_
443	of	of	IN	_	_	_
444	Cy5	cy5	NN	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	Ecoli	ecolus	NNS	_	_	_
447	_	_	VBP	_	_	_
448	CaCl2	cacl2	NN	_	_	_
449	wash	wash	NN	_	_	_
450	T1	t1	NN	_	_	_
451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
452	Ecoli	ecolus	NNS	_	_	_
453	_	_	VBP	_	_	_
454	CaCl2	cacl2	NN	_	_	_
455	wash	wash	NN	_	_	_
456	T2	t2	NN	_	_	_
457	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
458	Ecoli	ecolus	NNS	_	_	_
459	_	_	VBP	_	_	_
460	CaCl2	cacl2	NN	_	_	_
461	wash	wash	NN	_	_	_
462	T3	t3	NN	_	_	_
463	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
464	Ecoli	ecolus	NNS	_	_	_
465	_	_	VBP	_	_	_
466	CaCl2	cacl2	NN	_	_	_
467	wash	wash	NN	_	_	_
468	T4	t4	NN	_	_	_
469	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
470	Ecoli	ecolus	NNS	_	_	_
471	_	_	VBP	_	_	_
472	CaCl2	cacl2	NN	_	_	_
473	wash	wash	NN	_	_	_
474	T5	t5	NN	_	_	_
475	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
476	Ecoli	ecolus	NNS	_	_	_
477	_	_	VBP	_	_	_
478	CaCl2	cacl2	NN	_	_	_
479	wash	wash	NN	_	_	_
480	T6	t6	NN	_	_	_
481	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
482	Escherichia	escherichia	FW	Organism	_	_
483	coli	coli	FW	Organism	_	_
484	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
485	Escherichia	escherichia	FW	Organism	_	_
486	coli	coli	FW	Organism	_	_
487	MG1655	mg1655	NN	_	_	_
488	,	,	,	_	_	_
489	OD	od	NN	_	_	_
490	0.43	0.43	CD	_	_	_
491	LB	lb	NN	_	_	_
492	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
493	Escherichia	escherichia	FW	Organism	_	_
494	coli	coli	FW	Organism	_	_
495	MG1655	mg1655	NN	_	_	_
496	,	,	,	_	_	_
497	Sample	sample	NN	_	_	_
498	washed	wash	VBN	_	_	_
499	in	in	IN	_	_	_
500	0.1	0.1	CD	_	_	_
501	M	m	NN	_	_	_
502	CaCl2	cacl2	NN	_	_	_
503	+	+	CC	_	_	_
504	15	15	CD	_	_	_
505	%	%	NN	_	_	_
506	glycerol	glycerol	NN	SUPP	_	_
507	vs	vs	CC	_	_	_
508	before	before	IN	_	_	_
509	washing	wash	VBG	_	_	_
510	OD	od	NN	_	_	_
511	0.43	0.43	CD	_	_	_
512	in	in	IN	_	_	_
513	LB	LB	NNP	_	_	_
514	,	,	,	_	_	_
515	10	10	CD	_	_	_
516	min	min	NN	_	_	_
517	timepoint	timepoint	NN	_	_	_
518	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
519	Escherichia	escherichia	FW	Organism	_	_
520	coli	coli	FW	Organism	_	_
521	MG1655	mg1655	NN	_	_	_
522	,	,	,	_	_	_
523	Sample	sample	NN	_	_	_
524	washed	wash	VBN	_	_	_
525	in	in	IN	_	_	_
526	0.1	0.1	CD	_	_	_
527	M	m	NN	_	_	_
528	CaCl2	cacl2	NN	_	_	_
529	+	+	CC	_	_	_
530	15	15	CD	_	_	_
531	%	%	NN	_	_	_
532	glycerol	glycerol	NN	SUPP	_	_
533	vs	vs	CC	_	_	_
534	before	before	IN	_	_	_
535	washing	wash	VBG	_	_	_
536	OD	od	NN	_	_	_
537	0.43	0.43	CD	_	_	_
538	in	in	IN	_	_	_
539	LB	LB	NNP	_	_	_
540	,	,	,	_	_	_
541	20	20	CD	_	_	_
542	min	min	NN	_	_	_
543	timepoint	timepoint	NN	_	_	_
544	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
545	Escherichia	escherichia	FW	Organism	_	_
546	coli	coli	FW	Organism	_	_
547	MG1655	mg1655	NN	_	_	_
548	,	,	,	_	_	_
549	Sample	sample	NN	_	_	_
550	washed	wash	VBN	_	_	_
551	in	in	IN	_	_	_
552	0.1	0.1	CD	_	_	_
553	M	m	NN	_	_	_
554	CaCl2	cacl2	NN	_	_	_
555	+	+	CC	_	_	_
556	15	15	CD	_	_	_
557	%	%	NN	_	_	_
558	glycerol	glycerol	NN	SUPP	_	_
559	vs	vs	CC	_	_	_
560	before	before	IN	_	_	_
561	washing	wash	VBG	_	_	_
562	OD	od	NN	_	_	_
563	0.43	0.43	CD	_	_	_
564	in	in	IN	_	_	_
565	LB	LB	NNP	_	_	_
566	,	,	,	_	_	_
567	2	2	CD	_	_	_
568	min	min	NN	_	_	_
569	timepoint	timepoint	NN	_	_	_
570	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
571	Escherichia	escherichia	FW	Organism	_	_
572	coli	coli	FW	Organism	_	_
573	MG1655	mg1655	NN	_	_	_
574	,	,	,	_	_	_
575	Sample	sample	NN	_	_	_
576	washed	wash	VBN	_	_	_
577	in	in	IN	_	_	_
578	0.1	0.1	CD	_	_	_
579	M	m	NN	_	_	_
580	CaCl2	cacl2	NN	_	_	_
581	+	+	CC	_	_	_
582	15	15	CD	_	_	_
583	%	%	NN	_	_	_
584	glycerol	glycerol	NN	SUPP	_	_
585	vs	vs	CC	_	_	_
586	before	before	IN	_	_	_
587	washing	wash	VBG	_	_	_
588	OD	od	NN	_	_	_
589	0.43	0.43	CD	_	_	_
590	in	in	IN	_	_	_
591	LB	LB	NNP	_	_	_
592	,	,	,	_	_	_
593	40	40	CD	_	_	_
594	min	min	NN	_	_	_
595	timepoint	timepoint	NN	_	_	_
596	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
597	Escherichia	escherichia	FW	Organism	_	_
598	coli	coli	FW	Organism	_	_
599	MG1655	mg1655	NN	_	_	_
600	,	,	,	_	_	_
601	Sample	sample	NN	_	_	_
602	washed	wash	VBN	_	_	_
603	in	in	IN	_	_	_
604	0.1	0.1	CD	_	_	_
605	M	m	NN	_	_	_
606	CaCl2	cacl2	NN	_	_	_
607	+	+	CC	_	_	_
608	15	15	CD	_	_	_
609	%	%	NN	_	_	_
610	glycerol	glycerol	NN	SUPP	_	_
611	vs	vs	CC	_	_	_
612	before	before	IN	_	_	_
613	washing	wash	VBG	_	_	_
614	OD	od	NN	_	_	_
615	0.43	0.43	CD	_	_	_
616	in	in	IN	_	_	_
617	LB	LB	NNP	_	_	_
618	,	,	,	_	_	_
619	5	5	CD	_	_	_
620	min	min	NN	_	_	_
621	timepoint	timepoint	NN	_	_	_
622	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
623	Escherichia	escherichia	FW	Organism	_	_
624	coli	coli	FW	Organism	_	_
625	MG1655	mg1655	NN	_	_	_
626	,	,	,	_	_	_
627	Sample	sample	NN	_	_	_
628	washed	wash	VBN	_	_	_
629	in	in	IN	_	_	_
630	0.1	0.1	CD	_	_	_
631	M	m	NN	_	_	_
632	CaCl2	cacl2	NN	_	_	_
633	+	+	CC	_	_	_
634	15	15	CD	_	_	_
635	%	%	NN	_	_	_
636	glycerol	glycerol	NN	SUPP	_	_
637	vs	vs	CC	_	_	_
638	before	before	IN	_	_	_
639	washing	wash	VBG	_	_	_
640	OD	od	NN	_	_	_
641	0.43	0.43	CD	_	_	_
642	in	in	IN	_	_	_
643	LB	LB	NNP	_	_	_
644	,	,	,	_	_	_
645	60	60	CD	_	_	_
646	min	min	NN	_	_	_
647	timepoint	timepoint	NN	_	_	_
648	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
649	Normalized	normalize	VBN	_	_	_
650	log	log	NN	_	_	_
651	-LRB-	-lrb-	-LRB-	_	_	_
652	2	2	CD	_	_	_
653	-RRB-	-rrb-	-RRB-	_	_	_
654	ratio	ratio	NN	_	_	_
655	of	of	IN	_	_	_
656	Cy5	cy5	NN	_	_	_
657	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
658	Ecoli	Ecoli	NNP	_	_	_
659	_	_	NNP	_	_	_
660	Early	Early	NNP	_	_	_
661	Recovery	Recovery	NNP	_	_	_
662	in	in	IN	_	_	_
663	LB	LB	NNP	_	_	_
664	T1	t1	NN	_	_	_
665	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
666	Ecoli	Ecoli	NNP	_	_	_
667	_	_	NNP	_	_	_
668	Early	Early	NNP	_	_	_
669	Recovery	Recovery	NNP	_	_	_
670	in	in	IN	_	_	_
671	LB	LB	NNP	_	_	_
672	T2	t2	NN	_	_	_
673	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
674	Ecoli	Ecoli	NNP	_	_	_
675	_	_	NNP	_	_	_
676	Early	Early	NNP	_	_	_
677	Recovery	Recovery	NNP	_	_	_
678	in	in	IN	_	_	_
679	LB	LB	NNP	_	_	_
680	T3	t3	NN	_	_	_
681	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
682	Ecoli	Ecoli	NNP	_	_	_
683	_	_	NNP	_	_	_
684	Early	Early	NNP	_	_	_
685	Recovery	Recovery	NNP	_	_	_
686	in	in	IN	_	_	_
687	LB	LB	NNP	_	_	_
688	T4	t4	NN	_	_	_
689	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
690	Ecoli	Ecoli	NNP	_	_	_
691	_	_	NNP	_	_	_
692	Early	Early	NNP	_	_	_
693	Recovery	Recovery	NNP	_	_	_
694	in	in	IN	_	_	_
695	LB	LB	NNP	_	_	_
696	T5	T5	NNP	_	_	_
697	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
698	Ecoli	Ecoli	NNP	_	_	_
699	_	_	NNP	_	_	_
700	Early	Early	NNP	_	_	_
701	Recovery	Recovery	NNP	_	_	_
702	in	in	IN	_	_	_
703	LB	LB	NNP	_	_	_
704	T6	T6	NNP	_	_	_
705	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
706	Ecoli	Ecoli	NNP	_	_	_
707	_	_	NNP	_	_	_
708	Early	Early	NNP	_	_	_
709	Recovery	Recovery	NNP	_	_	_
710	in	in	IN	_	_	_
711	LB	LB	NNP	_	_	_
712	T7	T7	NNP	_	_	_
713	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
714	Escherichia	escherichia	FW	Organism	_	_
715	coli	coli	FW	Organism	_	_
716	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
717	Escherichia	escherichia	FW	Organism	_	_
718	coli	coli	FW	Organism	_	_
719	MG1655	mg1655	NN	_	_	_
720	,	,	,	_	_	_
721	0	0	CD	_	_	_
722	min	min	NN	_	_	_
723	recovery	recovery	NN	_	_	_
724	in	in	IN	_	_	_
725	LB	lb	NN	_	_	_
726	+	+	CC	_	_	_
727	glucose	glucose	NN	SUPP	_	_
728	at	at	IN	_	_	_
729	OD	od	NN	_	_	_
730	0.4	0.4	CD	_	_	_
731	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
732	Escherichia	escherichia	FW	Organism	_	_
733	coli	coli	FW	Organism	_	_
734	MG1655	mg1655	NN	_	_	_
735	,	,	,	_	_	_
736	15	15	CD	_	_	_
737	min	min	NN	_	_	_
738	recovery	recovery	NN	_	_	_
739	in	in	IN	_	_	_
740	LB	lb	NN	_	_	_
741	+	+	CC	_	_	_
742	glucose	glucose	NN	SUPP	_	_
743	at	at	IN	_	_	_
744	OD	od	NN	_	_	_
745	0.4	0.4	CD	_	_	_
746	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
747	Escherichia	escherichia	FW	Organism	_	_
748	coli	coli	FW	Organism	_	_
749	MG1655	mg1655	NN	_	_	_
750	,	,	,	_	_	_
751	30	30	CD	_	_	_
752	min	min	NN	_	_	_
753	recovery	recovery	NN	_	_	_
754	in	in	IN	_	_	_
755	LB	lb	NN	_	_	_
756	+	+	CC	_	_	_
757	glucose	glucose	NN	SUPP	_	_
758	at	at	IN	_	_	_
759	OD	od	NN	_	_	_
760	0.4	0.4	CD	_	_	_
761	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
762	Escherichia	escherichia	FW	Organism	_	_
763	coli	coli	FW	Organism	_	_
764	MG1655	mg1655	NN	_	_	_
765	,	,	,	_	_	_
766	45	45	CD	_	_	_
767	min	min	NN	_	_	_
768	recovery	recovery	NN	_	_	_
769	in	in	IN	_	_	_
770	LB	lb	NN	_	_	_
771	+	+	CC	_	_	_
772	glucose	glucose	NN	SUPP	_	_
773	at	at	IN	_	_	_
774	OD	od	NN	_	_	_
775	0.4	0.4	CD	_	_	_
776	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
777	Escherichia	escherichia	FW	Organism	_	_
778	coli	coli	FW	Organism	_	_
779	MG1655	mg1655	NN	_	_	_
780	,	,	,	_	_	_
781	60	60	CD	_	_	_
782	min	min	NN	_	_	_
783	recovery	recovery	NN	_	_	_
784	in	in	IN	_	_	_
785	LB	lb	NN	_	_	_
786	+	+	CC	_	_	_
787	glucose	glucose	NN	SUPP	_	_
788	at	at	IN	_	_	_
789	OD	od	NN	_	_	_
790	0.4	0.4	CD	_	_	_
791	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
792	Escherichia	escherichia	FW	Organism	_	_
793	coli	coli	FW	Organism	_	_
794	MG1655	mg1655	NN	_	_	_
795	,	,	,	_	_	_
796	75	75	CD	_	_	_
797	min	min	NN	_	_	_
798	recovery	recovery	NN	_	_	_
799	in	in	IN	_	_	_
800	LB	lb	NN	_	_	_
801	+	+	CC	_	_	_
802	glucose	glucose	NN	SUPP	_	_
803	at	at	IN	_	_	_
804	OD	od	NN	_	_	_
805	0.4	0.4	CD	_	_	_
806	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
807	Escherichia	escherichia	FW	Organism	_	_
808	coli	coli	FW	Organism	_	_
809	MG1655	mg1655	NN	_	_	_
810	,	,	,	_	_	_
811	90	90	CD	_	_	_
812	min	min	NN	_	_	_
813	recovery	recovery	NN	_	_	_
814	in	in	IN	_	_	_
815	LB	lb	NN	_	_	_
816	+	+	CC	_	_	_
817	glucose	glucose	NN	SUPP	_	_
818	at	at	IN	_	_	_
819	OD	od	NN	_	_	_
820	0.4	0.4	CD	_	_	_
821	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
822	Escherichia	escherichia	FW	Organism	_	_
823	coli	coli	FW	Organism	_	_
824	MG1655	mg1655	NN	_	_	_
825	,	,	,	_	_	_
826	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
827	OD	OD	NNP	_	_	_
828	~	~	SYM	_	_	_
829	0.5	0.5	CD	_	_	_
830	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
831	Normalized	normalize	VBN	_	_	_
832	log	log	NN	_	_	_
833	-LRB-	-lrb-	-LRB-	_	_	_
834	2	2	CD	_	_	_
835	-RRB-	-rrb-	-RRB-	_	_	_
836	ratio	ratio	NN	_	_	_
837	of	of	IN	_	_	_
838	Cy5	cy5	NN	_	_	_
839	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
840	Ecoli	ecolus	NNS	_	_	_
841	_	_	VBP	_	_	_
842	Indol-acrylate	indol-acrylate	JJ	_	_	_
843	-LRB-	-lrb-	-LRB-	_	_	_
844	10	10	CD	_	_	_
845	ug	ug	NN	_	_	_
846	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
847	Escherichia	escherichia	FW	Organism	_	_
848	coli	coli	FW	Organism	_	_
849	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
850	Escherichia	escherichia	FW	Organism	_	_
851	coli	coli	FW	Organism	_	_
852	MG1655	mg1655	NN	_	_	_
853	,	,	,	_	_	_
854	15	15	CD	_	_	_
855	min	min	NN	_	_	_
856	after	after	IN	_	_	_
857	Indol-acrylate	indol-acrylate	JJ	_	_	_
858	-LRB-	-lrb-	-LRB-	_	_	_
859	10	10	CD	_	_	_
860	ug	ug	NN	_	_	_
861	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
862	Escherichia	escherichia	FW	Organism	_	_
863	coli	coli	FW	Organism	_	_
864	MG1655	mg1655	NN	_	_	_
865	,	,	,	_	_	_
866	30	30	CD	_	_	_
867	min	min	NN	_	_	_
868	after	after	IN	_	_	_
869	Indol-acrylate	indol-acrylate	JJ	_	_	_
870	-LRB-	-lrb-	-LRB-	_	_	_
871	10	10	CD	_	_	_
872	ug	ug	NN	_	_	_
873	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
874	Escherichia	escherichia	FW	Organism	_	_
875	coli	coli	FW	Organism	_	_
876	MG1655	mg1655	NN	_	_	_
877	,	,	,	_	_	_
878	5	5	CD	_	_	_
879	min	min	NN	_	_	_
880	after	after	IN	_	_	_
881	Indol-acrylate	indol-acrylate	JJ	_	_	_
882	-LRB-	-lrb-	-LRB-	_	_	_
883	10	10	CD	_	_	_
884	ug	ug	NN	_	_	_
885	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
886	Escherichia	escherichia	FW	Organism	_	_
887	coli	coli	FW	Organism	_	_
888	MG1655	mg1655	NN	_	_	_
889	,	,	,	_	_	_
890	60	60	CD	_	_	_
891	min	min	NN	_	_	_
892	after	after	IN	_	_	_
893	Indol-acrylate	indol-acrylate	JJ	_	_	_
894	-LRB-	-lrb-	-LRB-	_	_	_
895	10	10	CD	_	_	_
896	ug	ug	NN	_	_	_
897	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
898	Escherichia	escherichia	FW	Organism	_	_
899	coli	coli	FW	Organism	_	_
900	MG1655	mg1655	NN	_	_	_
901	,	,	,	_	_	_
902	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
903	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
904	Escherichia	escherichia	FW	Organism	_	_
905	coli	coli	FW	Organism	_	_
906	MG1655	mg1655	NN	_	_	_
907	,	,	,	_	_	_
908	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
909	,	,	,	_	_	_
910	0	0	CD	_	_	_
911	min	min	NN	_	_	_
912	before	before	IN	_	_	_
913	treatment	treatment	NN	_	_	_
914	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
915	Normalized	normalize	VBN	_	_	_
916	log	log	NN	_	_	_
917	-LRB-	-lrb-	-LRB-	_	_	_
918	2	2	CD	_	_	_
919	-RRB-	-rrb-	-RRB-	_	_	_
920	ratio	ratio	NN	_	_	_
921	of	of	IN	_	_	_
922	Cy5	cy5	NN	_	_	_
923	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
924	Ecoli	ecolus	NNS	_	_	_
925	_	_	VBP	_	_	_
926	Indol-acrylate	indol-acrylate	JJ	_	_	_
927	-LRB-	-lrb-	-LRB-	_	_	_
928	15	15	CD	_	_	_
929	ug	ug	NN	_	_	_
930	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
931	Escherichia	escherichia	FW	Organism	_	_
932	coli	coli	FW	Organism	_	_
933	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
934	Escherichia	escherichia	FW	Organism	_	_
935	coli	coli	FW	Organism	_	_
936	MG1655	mg1655	NN	_	_	_
937	,	,	,	_	_	_
938	15	15	CD	_	_	_
939	min	min	NN	_	_	_
940	after	after	IN	_	_	_
941	Indol-acrylate	indol-acrylate	JJ	_	_	_
942	-LRB-	-lrb-	-LRB-	_	_	_
943	15	15	CD	_	_	_
944	ug	ug	NN	_	_	_
945	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
946	Escherichia	escherichia	FW	Organism	_	_
947	coli	coli	FW	Organism	_	_
948	MG1655	mg1655	NN	_	_	_
949	,	,	,	_	_	_
950	30	30	CD	_	_	_
951	min	min	NN	_	_	_
952	after	after	IN	_	_	_
953	Indol-acrylate	indol-acrylate	JJ	_	_	_
954	-LRB-	-lrb-	-LRB-	_	_	_
955	15	15	CD	_	_	_
956	ug	ug	NN	_	_	_
957	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
958	Escherichia	escherichia	FW	Organism	_	_
959	coli	coli	FW	Organism	_	_
960	MG1655	mg1655	NN	_	_	_
961	,	,	,	_	_	_
962	5	5	CD	_	_	_
963	min	min	NN	_	_	_
964	after	after	IN	_	_	_
965	Indol-acrylate	indol-acrylate	JJ	_	_	_
966	-LRB-	-lrb-	-LRB-	_	_	_
967	15	15	CD	_	_	_
968	ug	ug	NN	_	_	_
969	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
970	Escherichia	escherichia	FW	Organism	_	_
971	coli	coli	FW	Organism	_	_
972	MG1655	mg1655	NN	_	_	_
973	,	,	,	_	_	_
974	60	60	CD	_	_	_
975	min	min	NN	_	_	_
976	after	after	IN	_	_	_
977	Indol-acrylate	indol-acrylate	JJ	_	_	_
978	-LRB-	-lrb-	-LRB-	_	_	_
979	15	15	CD	_	_	_
980	ug	ug	NN	_	_	_
981	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
982	Escherichia	escherichia	FW	Organism	_	_
983	coli	coli	FW	Organism	_	_
984	MG1655	mg1655	NN	_	_	_
985	,	,	,	_	_	_
986	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
987	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
988	Escherichia	escherichia	FW	Organism	_	_
989	coli	coli	FW	Organism	_	_
990	MG1655	mg1655	NN	_	_	_
991	,	,	,	_	_	_
992	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
993	,	,	,	_	_	_
994	0	0	CD	_	_	_
995	min	min	NN	_	_	_
996	before	before	IN	_	_	_
997	treatment	treatment	NN	_	_	_
998	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
999	Normalized	normalize	VBN	_	_	_
1000	log	log	NN	_	_	_
1001	-LRB-	-lrb-	-LRB-	_	_	_
1002	2	2	CD	_	_	_
1003	-RRB-	-rrb-	-RRB-	_	_	_
1004	ratio	ratio	NN	_	_	_
1005	of	of	IN	_	_	_
1006	Cy5	cy5	NN	_	_	_
1007	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1008	Ecoli	ecolus	NNS	_	_	_
1009	_	_	VBP	_	_	_
1010	Kanamycin	kanamycin	NN	_	_	_
1011	treatment	treatment	NN	_	_	_
1012	T1	t1	NN	_	_	_
1013	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1014	Ecoli	ecolus	NNS	_	_	_
1015	_	_	VBP	_	_	_
1016	Kanamycin	kanamycin	NN	_	_	_
1017	treatment	treatment	NN	_	_	_
1018	T2	t2	NN	_	_	_
1019	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1020	Ecoli	ecolus	NNS	_	_	_
1021	_	_	VBP	_	_	_
1022	Kanamycin	kanamycin	NN	_	_	_
1023	treatment	treatment	NN	_	_	_
1024	T3	t3	NN	_	_	_
1025	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1026	Ecoli	ecolus	NNS	_	_	_
1027	_	_	VBP	_	_	_
1028	Kanamycin	kanamycin	NN	_	_	_
1029	treatment	treatment	NN	_	_	_
1030	T4	t4	NN	_	_	_
1031	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1032	Ecoli	ecolus	NNS	_	_	_
1033	_	_	VBP	_	_	_
1034	Kanamycin	kanamycin	NN	_	_	_
1035	treatment	treatment	NN	_	_	_
1036	T5	t5	NN	_	_	_
1037	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1038	Ecoli	ecolus	NNS	_	_	_
1039	_	_	VBP	_	_	_
1040	Kanamycin	kanamycin	NN	_	_	_
1041	treatment	treatment	NN	_	_	_
1042	T6	t6	NN	_	_	_
1043	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1044	Escherichia	escherichia	FW	Organism	_	_
1045	coli	coli	FW	Organism	_	_
1046	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1047	Escherichia	escherichia	FW	Organism	_	_
1048	coli	coli	FW	Organism	_	_
1049	MG1655	mg1655	NN	_	_	_
1050	,	,	,	_	_	_
1051	0	0	CD	_	_	_
1052	min	min	NN	_	_	_
1053	after	after	IN	_	_	_
1054	Kanamycin	Kanamycin	NNP	_	_	_
1055	-LRB-	-lrb-	-LRB-	_	_	_
1056	100	100	CD	_	_	_
1057	ug	ug	NN	_	_	_
1058	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1059	Escherichia	escherichia	FW	Organism	_	_
1060	coli	coli	FW	Organism	_	_
1061	MG1655	mg1655	NN	_	_	_
1062	,	,	,	_	_	_
1063	10	10	CD	_	_	_
1064	min	min	NN	_	_	_
1065	after	after	IN	_	_	_
1066	Kanamycin	Kanamycin	NNP	_	_	_
1067	-LRB-	-lrb-	-LRB-	_	_	_
1068	100	100	CD	_	_	_
1069	ug	ug	NN	_	_	_
1070	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1071	Escherichia	escherichia	FW	Organism	_	_
1072	coli	coli	FW	Organism	_	_
1073	MG1655	mg1655	NN	_	_	_
1074	,	,	,	_	_	_
1075	15	15	CD	_	_	_
1076	min	min	NN	_	_	_
1077	after	after	IN	_	_	_
1078	Kanamycin	Kanamycin	NNP	_	_	_
1079	-LRB-	-lrb-	-LRB-	_	_	_
1080	100	100	CD	_	_	_
1081	ug	ug	NN	_	_	_
1082	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1083	Escherichia	escherichia	FW	Organism	_	_
1084	coli	coli	FW	Organism	_	_
1085	MG1655	mg1655	NN	_	_	_
1086	,	,	,	_	_	_
1087	20	20	CD	_	_	_
1088	min	min	NN	_	_	_
1089	after	after	IN	_	_	_
1090	Kanamycin	Kanamycin	NNP	_	_	_
1091	-LRB-	-lrb-	-LRB-	_	_	_
1092	100	100	CD	_	_	_
1093	ug	ug	NN	_	_	_
1094	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1095	Escherichia	escherichia	FW	Organism	_	_
1096	coli	coli	FW	Organism	_	_
1097	MG1655	mg1655	NN	_	_	_
1098	,	,	,	_	_	_
1099	30	30	CD	_	_	_
1100	min	min	NN	_	_	_
1101	after	after	IN	_	_	_
1102	Kanamycin	Kanamycin	NNP	_	_	_
1103	-LRB-	-lrb-	-LRB-	_	_	_
1104	100	100	CD	_	_	_
1105	ug	ug	NN	_	_	_
1106	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1107	Escherichia	escherichia	FW	Organism	_	_
1108	coli	coli	FW	Organism	_	_
1109	MG1655	mg1655	NN	_	_	_
1110	,	,	,	_	_	_
1111	40	40	CD	_	_	_
1112	min	min	NN	_	_	_
1113	after	after	IN	_	_	_
1114	Kanamycin	Kanamycin	NNP	_	_	_
1115	-LRB-	-lrb-	-LRB-	_	_	_
1116	100	100	CD	_	_	_
1117	ug	ug	NN	_	_	_
1118	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1119	Escherichia	escherichia	FW	Organism	_	_
1120	coli	coli	FW	Organism	_	_
1121	MG1655	mg1655	NN	_	_	_
1122	,	,	,	_	_	_
1123	45	45	CD	_	_	_
1124	min	min	NN	_	_	_
1125	after	after	IN	_	_	_
1126	Kanamycin	Kanamycin	NNP	_	_	_
1127	-LRB-	-lrb-	-LRB-	_	_	_
1128	100	100	CD	_	_	_
1129	ug	ug	NN	_	_	_
1130	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1131	Escherichia	escherichia	FW	Organism	_	_
1132	coli	coli	FW	Organism	_	_
1133	MG1655	mg1655	NN	_	_	_
1134	,	,	,	_	_	_
1135	50	50	CD	_	_	_
1136	min	min	NN	_	_	_
1137	after	after	IN	_	_	_
1138	Kanamycin	Kanamycin	NNP	_	_	_
1139	-LRB-	-lrb-	-LRB-	_	_	_
1140	100	100	CD	_	_	_
1141	ug	ug	NN	_	_	_
1142	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1143	Escherichia	escherichia	FW	Organism	_	_
1144	coli	coli	FW	Organism	_	_
1145	MG1655	mg1655	NN	_	_	_
1146	,	,	,	_	_	_
1147	5	5	CD	_	_	_
1148	min	min	NN	_	_	_
1149	after	after	IN	_	_	_
1150	Kanamycin	Kanamycin	NNP	_	_	_
1151	-LRB-	-lrb-	-LRB-	_	_	_
1152	100	100	CD	_	_	_
1153	ug	ug	NN	_	_	_
1154	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1155	Escherichia	escherichia	FW	Organism	_	_
1156	coli	coli	FW	Organism	_	_
1157	MG1655	mg1655	NN	_	_	_
1158	,	,	,	_	_	_
1159	60	60	CD	_	_	_
1160	min	min	NN	_	_	_
1161	after	after	IN	_	_	_
1162	Kanamycin	Kanamycin	NNP	_	_	_
1163	-LRB-	-lrb-	-LRB-	_	_	_
1164	100	100	CD	_	_	_
1165	ug	ug	NN	_	_	_
1166	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1167	Escherichia	escherichia	FW	Organism	_	_
1168	coli	coli	FW	Organism	_	_
1169	MG1655	mg1655	NN	_	_	_
1170	,	,	,	_	_	_
1171	75	75	CD	_	_	_
1172	min	min	NN	_	_	_
1173	after	after	IN	_	_	_
1174	Kanamycin	Kanamycin	NNP	_	_	_
1175	-LRB-	-lrb-	-LRB-	_	_	_
1176	100	100	CD	_	_	_
1177	ug	ug	NN	_	_	_
1178	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1179	Escherichia	escherichia	FW	Organism	_	_
1180	coli	coli	FW	Organism	_	_
1181	MG1655	mg1655	NN	_	_	_
1182	,	,	,	_	_	_
1183	M9	m9	NN	_	_	_
1184	+	+	CC	_	_	_
1185	glucose	glucose	NN	SUPP	_	_
1186	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1187	Escherichia	escherichia	FW	Organism	_	_
1188	coli	coli	FW	Organism	_	_
1189	MG1655	mg1655	NN	_	_	_
1190	,	,	,	_	_	_
1191	M9	m9	NN	_	_	_
1192	+	+	CC	_	_	_
1193	glucose	glucose	NN	SUPP	_	_
1194	,	,	,	_	_	_
1195	0	0	CD	_	_	_
1196	min	min	NN	_	_	_
1197	before	before	IN	_	_	_
1198	treatment	treatment	NN	_	_	_
1199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1200	Normalized	normalize	VBN	_	_	_
1201	log	log	NN	_	_	_
1202	-LRB-	-lrb-	-LRB-	_	_	_
1203	2	2	CD	_	_	_
1204	-RRB-	-rrb-	-RRB-	_	_	_
1205	ratio	ratio	NN	_	_	_
1206	of	of	IN	_	_	_
1207	Cy5	cy5	NN	_	_	_
1208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1209	Ecoli	ecolus	NNS	_	_	_
1210	_	_	VBP	_	_	_
1211	LB	lb	NN	_	_	_
1212	growth	growth	NN	_	_	_
1213	T1	t1	NN	_	_	_
1214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1215	Ecoli	ecolus	NNS	_	_	_
1216	_	_	VBP	_	_	_
1217	LB	lb	NN	_	_	_
1218	growth	growth	NN	_	_	_
1219	T10	t10	NN	_	_	_
1220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1221	Ecoli	ecolus	NNS	_	_	_
1222	_	_	VBP	_	_	_
1223	LB	lb	NN	_	_	_
1224	growth	growth	NN	_	_	_
1225	T11	t11	NN	_	_	_
1226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1227	Ecoli	ecolus	NNS	_	_	_
1228	_	_	VBP	_	_	_
1229	LB	lb	NN	_	_	_
1230	growth	growth	NN	_	_	_
1231	T2	t2	NN	_	_	_
1232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1233	Ecoli	ecolus	NNS	_	_	_
1234	_	_	VBP	_	_	_
1235	LB	lb	NN	_	_	_
1236	growth	growth	NN	_	_	_
1237	T3	t3	NN	_	_	_
1238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1239	Ecoli	ecolus	NNS	_	_	_
1240	_	_	VBP	_	_	_
1241	LB	lb	NN	_	_	_
1242	growth	growth	NN	_	_	_
1243	T4	t4	NN	_	_	_
1244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1245	Ecoli	ecolus	NNS	_	_	_
1246	_	_	VBP	_	_	_
1247	LB	lb	NN	_	_	_
1248	growth	growth	NN	_	_	_
1249	T5	t5	NN	_	_	_
1250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1251	Ecoli	ecolus	NNS	_	_	_
1252	_	_	VBP	_	_	_
1253	LB	lb	NN	_	_	_
1254	growth	growth	NN	_	_	_
1255	T6	t6	NN	_	_	_
1256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1257	Ecoli	ecolus	NNS	_	_	_
1258	_	_	VBP	_	_	_
1259	LB	lb	NN	_	_	_
1260	growth	growth	NN	_	_	_
1261	T7	t7	NN	_	_	_
1262	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1263	Ecoli	ecolus	NNS	_	_	_
1264	_	_	VBP	_	_	_
1265	LB	lb	NN	_	_	_
1266	growth	growth	NN	_	_	_
1267	T8	t8	NN	_	_	_
1268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1269	Ecoli	ecolus	NNS	_	_	_
1270	_	_	VBP	_	_	_
1271	LB	lb	NN	_	_	_
1272	growth	growth	NN	_	_	_
1273	T9	t9	NN	_	_	_
1274	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1275	Escherichia	escherichia	FW	Organism	_	_
1276	coli	coli	FW	Organism	_	_
1277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1278	Escherichia	escherichia	FW	Organism	_	_
1279	coli	coli	FW	Organism	_	_
1280	MG1655	mg1655	NN	_	_	_
1281	,	,	,	_	_	_
1282	0	0	CD	_	_	_
1283	min	min	NN	_	_	_
1284	recovery	recovery	NN	_	_	_
1285	in	in	IN	_	_	_
1286	LB	lb	NN	_	_	_
1287	+0.2	+0.2	CD	_	_	_
1288	%	%	NN	_	_	_
1289	glc	glc	NN	_	_	_
1290	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1291	Escherichia	escherichia	FW	Organism	_	_
1292	coli	coli	FW	Organism	_	_
1293	MG1655	mg1655	NN	_	_	_
1294	,	,	,	_	_	_
1295	105	105	CD	_	_	_
1296	min	min	NN	_	_	_
1297	recovery	recovery	NN	_	_	_
1298	in	in	IN	_	_	_
1299	LB	lb	NN	_	_	_
1300	+0.2	+0.2	CD	_	_	_
1301	%	%	NN	_	_	_
1302	glc	glc	NN	_	_	_
1303	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1304	Escherichia	escherichia	FW	Organism	_	_
1305	coli	coli	FW	Organism	_	_
1306	MG1655	mg1655	NN	_	_	_
1307	,	,	,	_	_	_
1308	133	133	CD	_	_	_
1309	min	min	NN	_	_	_
1310	recovery	recovery	NN	_	_	_
1311	in	in	IN	_	_	_
1312	LB	lb	NN	_	_	_
1313	+0.2	+0.2	CD	_	_	_
1314	%	%	NN	_	_	_
1315	glc	glc	NN	_	_	_
1316	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1317	Escherichia	escherichia	FW	Organism	_	_
1318	coli	coli	FW	Organism	_	_
1319	MG1655	mg1655	NN	_	_	_
1320	,	,	,	_	_	_
1321	1440	1440	CD	_	_	_
1322	min	min	NN	_	_	_
1323	recovery	recovery	NN	_	_	_
1324	in	in	IN	_	_	_
1325	LB	lb	NN	_	_	_
1326	+0.2	+0.2	CD	_	_	_
1327	%	%	NN	_	_	_
1328	glc	glc	NN	_	_	_
1329	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1330	Escherichia	escherichia	FW	Organism	_	_
1331	coli	coli	FW	Organism	_	_
1332	MG1655	mg1655	NN	_	_	_
1333	,	,	,	_	_	_
1334	163	163	CD	_	_	_
1335	min	min	NN	_	_	_
1336	recovery	recovery	NN	_	_	_
1337	in	in	IN	_	_	_
1338	LB	lb	NN	_	_	_
1339	+0.2	+0.2	CD	_	_	_
1340	%	%	NN	_	_	_
1341	glc	glc	NN	_	_	_
1342	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1343	Escherichia	escherichia	FW	Organism	_	_
1344	coli	coli	FW	Organism	_	_
1345	MG1655	mg1655	NN	_	_	_
1346	,	,	,	_	_	_
1347	191	191	CD	_	_	_
1348	min	min	NN	_	_	_
1349	recovery	recovery	NN	_	_	_
1350	in	in	IN	_	_	_
1351	LB	lb	NN	_	_	_
1352	+0.2	+0.2	CD	_	_	_
1353	%	%	NN	_	_	_
1354	glc	glc	NN	_	_	_
1355	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1356	Escherichia	escherichia	FW	Organism	_	_
1357	coli	coli	FW	Organism	_	_
1358	MG1655	mg1655	NN	_	_	_
1359	,	,	,	_	_	_
1360	218	218	CD	_	_	_
1361	min	min	NN	_	_	_
1362	recovery	recovery	NN	_	_	_
1363	in	in	IN	_	_	_
1364	LB	lb	NN	_	_	_
1365	+0.2	+0.2	CD	_	_	_
1366	%	%	NN	_	_	_
1367	glc	glc	NN	_	_	_
1368	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1369	Escherichia	escherichia	FW	Organism	_	_
1370	coli	coli	FW	Organism	_	_
1371	MG1655	mg1655	NN	_	_	_
1372	,	,	,	_	_	_
1373	261	261	CD	_	_	_
1374	min	min	NN	_	_	_
1375	recovery	recovery	NN	_	_	_
1376	in	in	IN	_	_	_
1377	LB	lb	NN	_	_	_
1378	+0.2	+0.2	CD	_	_	_
1379	%	%	NN	_	_	_
1380	glc	glc	NN	_	_	_
1381	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1382	Escherichia	escherichia	FW	Organism	_	_
1383	coli	coli	FW	Organism	_	_
1384	MG1655	mg1655	NN	_	_	_
1385	,	,	,	_	_	_
1386	313	313	CD	_	_	_
1387	min	min	NN	_	_	_
1388	recovery	recovery	NN	_	_	_
1389	in	in	IN	_	_	_
1390	LB	lb	NN	_	_	_
1391	+0.2	+0.2	CD	_	_	_
1392	%	%	NN	_	_	_
1393	glc	glc	NN	_	_	_
1394	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1395	Escherichia	escherichia	FW	Organism	_	_
1396	coli	coli	FW	Organism	_	_
1397	MG1655	mg1655	NN	_	_	_
1398	,	,	,	_	_	_
1399	443	443	CD	_	_	_
1400	min	min	NN	_	_	_
1401	recovery	recovery	NN	_	_	_
1402	in	in	IN	_	_	_
1403	LB	lb	NN	_	_	_
1404	+0.2	+0.2	CD	_	_	_
1405	%	%	NN	_	_	_
1406	glc	glc	NN	_	_	_
1407	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1408	Escherichia	escherichia	FW	Organism	_	_
1409	coli	coli	FW	Organism	_	_
1410	MG1655	mg1655	NN	_	_	_
1411	,	,	,	_	_	_
1412	78	78	CD	_	_	_
1413	min	min	NN	_	_	_
1414	recovery	recovery	NN	_	_	_
1415	in	in	IN	_	_	_
1416	LB	lb	NN	_	_	_
1417	+0.2	+0.2	CD	_	_	_
1418	%	%	NN	_	_	_
1419	glc	glc	NN	_	_	_
1420	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1421	Escherichia	escherichia	FW	Organism	_	_
1422	coli	coli	FW	Organism	_	_
1423	MG1655	mg1655	NN	_	_	_
1424	,	,	,	_	_	_
1425	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
1426	OD	OD	NNP	_	_	_
1427	~	~	SYM	_	_	_
1428	0.5	0.5	CD	_	_	_
1429	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1430	Normalized	normalize	VBN	_	_	_
1431	log	log	NN	_	_	_
1432	-LRB-	-lrb-	-LRB-	_	_	_
1433	2	2	CD	_	_	_
1434	-RRB-	-rrb-	-RRB-	_	_	_
1435	ratio	ratio	NN	_	_	_
1436	of	of	IN	_	_	_
1437	Cy5	cy5	NN	_	_	_
1438	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1439	Ecoli	Ecoli	NNP	_	_	_
1440	_	_	NNP	_	_	_
1441	Late	Late	NNP	_	_	_
1442	Recovery	Recovery	NNP	_	_	_
1443	in	in	IN	_	_	_
1444	LB	LB	NNP	_	_	_
1445	T1	t1	NN	_	_	_
1446	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1447	Ecoli	Ecoli	NNP	_	_	_
1448	_	_	NNP	_	_	_
1449	Late	Late	NNP	_	_	_
1450	Recovery	Recovery	NNP	_	_	_
1451	in	in	IN	_	_	_
1452	LB	LB	NNP	_	_	_
1453	T2	t2	NN	_	_	_
1454	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1455	Ecoli	Ecoli	NNP	_	_	_
1456	_	_	NNP	_	_	_
1457	Late	Late	NNP	_	_	_
1458	Recovery	Recovery	NNP	_	_	_
1459	in	in	IN	_	_	_
1460	LB	LB	NNP	_	_	_
1461	T3	t3	NN	_	_	_
1462	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1463	Ecoli	Ecoli	NNP	_	_	_
1464	_	_	NNP	_	_	_
1465	Late	Late	NNP	_	_	_
1466	Recovery	Recovery	NNP	_	_	_
1467	in	in	IN	_	_	_
1468	LB	LB	NNP	_	_	_
1469	T4	t4	NN	_	_	_
1470	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1471	Ecoli	Ecoli	NNP	_	_	_
1472	_	_	NNP	_	_	_
1473	Late	Late	NNP	_	_	_
1474	Recovery	Recovery	NNP	_	_	_
1475	in	in	IN	_	_	_
1476	LB	LB	NNP	_	_	_
1477	T5	T5	NNP	_	_	_
1478	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1479	Ecoli	Ecoli	NNP	_	_	_
1480	_	_	NNP	_	_	_
1481	Late	Late	NNP	_	_	_
1482	Recovery	Recovery	NNP	_	_	_
1483	in	in	IN	_	_	_
1484	LB	LB	NNP	_	_	_
1485	T6	T6	NNP	_	_	_
1486	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1487	Ecoli	Ecoli	NNP	_	_	_
1488	_	_	NNP	_	_	_
1489	Late	Late	NNP	_	_	_
1490	Recovery	Recovery	NNP	_	_	_
1491	in	in	IN	_	_	_
1492	LB	LB	NNP	_	_	_
1493	T7	T7	NNP	_	_	_
1494	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1495	Escherichia	escherichia	FW	Organism	_	_
1496	coli	coli	FW	Organism	_	_
1497	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1498	Escherichia	escherichia	FW	Organism	_	_
1499	coli	coli	FW	Organism	_	_
1500	MG1655	mg1655	NN	_	_	_
1501	,	,	,	_	_	_
1502	0	0	CD	_	_	_
1503	min	min	NN	_	_	_
1504	recovery	recovery	NN	_	_	_
1505	in	in	IN	_	_	_
1506	LB	lb	NN	_	_	_
1507	+	+	CC	_	_	_
1508	glucose	glucose	NN	SUPP	_	_
1509	at	at	IN	_	_	_
1510	OD	od	NN	_	_	_
1511	1.0	1.0	CD	_	_	_
1512	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1513	Escherichia	escherichia	FW	Organism	_	_
1514	coli	coli	FW	Organism	_	_
1515	MG1655	mg1655	NN	_	_	_
1516	,	,	,	_	_	_
1517	15	15	CD	_	_	_
1518	min	min	NN	_	_	_
1519	recovery	recovery	NN	_	_	_
1520	in	in	IN	_	_	_
1521	LB	lb	NN	_	_	_
1522	+	+	CC	_	_	_
1523	glucose	glucose	NN	SUPP	_	_
1524	at	at	IN	_	_	_
1525	OD	od	NN	_	_	_
1526	1.0	1.0	CD	_	_	_
1527	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1528	Escherichia	escherichia	FW	Organism	_	_
1529	coli	coli	FW	Organism	_	_
1530	MG1655	mg1655	NN	_	_	_
1531	,	,	,	_	_	_
1532	30	30	CD	_	_	_
1533	min	min	NN	_	_	_
1534	recovery	recovery	NN	_	_	_
1535	in	in	IN	_	_	_
1536	LB	lb	NN	_	_	_
1537	+	+	CC	_	_	_
1538	glucose	glucose	NN	SUPP	_	_
1539	at	at	IN	_	_	_
1540	OD	od	NN	_	_	_
1541	1.0	1.0	CD	_	_	_
1542	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1543	Escherichia	escherichia	FW	Organism	_	_
1544	coli	coli	FW	Organism	_	_
1545	MG1655	mg1655	NN	_	_	_
1546	,	,	,	_	_	_
1547	45	45	CD	_	_	_
1548	min	min	NN	_	_	_
1549	recovery	recovery	NN	_	_	_
1550	in	in	IN	_	_	_
1551	LB	lb	NN	_	_	_
1552	+	+	CC	_	_	_
1553	glucose	glucose	NN	SUPP	_	_
1554	at	at	IN	_	_	_
1555	OD	od	NN	_	_	_
1556	1.0	1.0	CD	_	_	_
1557	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1558	Escherichia	escherichia	FW	Organism	_	_
1559	coli	coli	FW	Organism	_	_
1560	MG1655	mg1655	NN	_	_	_
1561	,	,	,	_	_	_
1562	60	60	CD	_	_	_
1563	min	min	NN	_	_	_
1564	recovery	recovery	NN	_	_	_
1565	in	in	IN	_	_	_
1566	LB	lb	NN	_	_	_
1567	+	+	CC	_	_	_
1568	glucose	glucose	NN	SUPP	_	_
1569	at	at	IN	_	_	_
1570	OD	od	NN	_	_	_
1571	1.0	1.0	CD	_	_	_
1572	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1573	Escherichia	escherichia	FW	Organism	_	_
1574	coli	coli	FW	Organism	_	_
1575	MG1655	mg1655	NN	_	_	_
1576	,	,	,	_	_	_
1577	75	75	CD	_	_	_
1578	min	min	NN	_	_	_
1579	recovery	recovery	NN	_	_	_
1580	in	in	IN	_	_	_
1581	LB	lb	NN	_	_	_
1582	+	+	CC	_	_	_
1583	glucose	glucose	NN	SUPP	_	_
1584	at	at	IN	_	_	_
1585	OD	od	NN	_	_	_
1586	1.0	1.0	CD	_	_	_
1587	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1588	Escherichia	escherichia	FW	Organism	_	_
1589	coli	coli	FW	Organism	_	_
1590	MG1655	mg1655	NN	_	_	_
1591	,	,	,	_	_	_
1592	90	90	CD	_	_	_
1593	min	min	NN	_	_	_
1594	recovery	recovery	NN	_	_	_
1595	in	in	IN	_	_	_
1596	LB	lb	NN	_	_	_
1597	+	+	CC	_	_	_
1598	glucose	glucose	NN	SUPP	_	_
1599	at	at	IN	_	_	_
1600	OD	od	NN	_	_	_
1601	1.0	1.0	CD	_	_	_
1602	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1603	Escherichia	escherichia	FW	Organism	_	_
1604	coli	coli	FW	Organism	_	_
1605	MG1655	mg1655	NN	_	_	_
1606	,	,	,	_	_	_
1607	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
1608	OD	OD	NNP	_	_	_
1609	~	~	SYM	_	_	_
1610	0.5	0.5	CD	_	_	_
1611	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1612	Normalized	normalize	VBN	_	_	_
1613	log	log	NN	_	_	_
1614	-LRB-	-lrb-	-LRB-	_	_	_
1615	2	2	CD	_	_	_
1616	-RRB-	-rrb-	-RRB-	_	_	_
1617	ratio	ratio	NN	_	_	_
1618	of	of	IN	_	_	_
1619	Cy5	cy5	NN	_	_	_
1620	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1621	Ecoli	ecolus	NNS	_	_	_
1622	_	_	VBP	_	_	_
1623	NOX	nox	NN	_	_	_
1624	+	+	CC	_	_	_
1625	_	_	NN	_	_	_
1626	balanced	balanced	JJ	_	_	_
1627	growth	growth	NN	_	_	_
1628	at	at	IN	_	_	_
1629	OD	OD	NNP	_	_	_
1630	0.13	0.13	CD	_	_	_
1631	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1632	Ecoli	Ecoli	NNP	_	_	_
1633	_	_	SYM	_	_	_
1634	NOX	nox	NN	_	_	_
1635	+	+	CC	_	_	_
1636	_	_	NN	_	_	_
1637	balanced	balanced	JJ	_	_	_
1638	growth	growth	NN	_	_	_
1639	at	at	IN	_	_	_
1640	OD	OD	NNP	_	_	_
1641	0.21	0.21	CD	_	_	_
1642	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1643	Ecoli	Ecoli	NNP	_	_	_
1644	_	_	SYM	_	_	_
1645	NOX	nox	NN	_	_	_
1646	+	+	CC	_	_	_
1647	_	_	NN	_	_	_
1648	balanced	balanced	JJ	_	_	_
1649	growth	growth	NN	_	_	_
1650	at	at	IN	_	_	_
1651	OD	OD	NNP	_	_	_
1652	0.28	0.28	CD	_	_	_
1653	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1654	Ecoli	Ecoli	NNP	_	_	_
1655	_	_	SYM	_	_	_
1656	NOX	nox	NN	_	_	_
1657	+	+	CC	_	_	_
1658	_	_	NN	_	_	_
1659	balanced	balanced	JJ	_	_	_
1660	growth	growth	NN	_	_	_
1661	at	at	IN	_	_	_
1662	OD	OD	NNP	_	_	_
1663	0.34	0.34	CD	_	_	_
1664	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1665	Ecoli	Ecoli	NNP	_	_	_
1666	_	_	SYM	_	_	_
1667	NOX	nox	NN	_	_	_
1668	+	+	CC	_	_	_
1669	_	_	NN	_	_	_
1670	balanced	balanced	JJ	_	_	_
1671	growth	growth	NN	_	_	_
1672	at	at	IN	_	_	_
1673	OD	od	NN	_	_	_
1674	0.4	0.4	CD	_	_	_
1675	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1676	Escherichia	escherichia	FW	Organism	_	_
1677	coli	coli	FW	Organism	_	_
1678	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1679	Escherichia	escherichia	FW	Organism	_	_
1680	coli	coli	FW	Organism	_	_
1681	MG1655	mg1655	NN	_	_	_
1682	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1683	Normalized	normalize	VBN	_	_	_
1684	log	log	NN	_	_	_
1685	-LRB-	-lrb-	-LRB-	_	_	_
1686	2	2	CD	_	_	_
1687	-RRB-	-rrb-	-RRB-	_	_	_
1688	ratio	ratio	NN	_	_	_
1689	of	of	IN	_	_	_
1690	Cy5	cy5	NN	_	_	_
1691	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1692	Ecoli	ecoli	JJ	_	_	_
1693	_	_	SYM	_	_	_
1694	NOX	nox	SYM	_	_	_
1695	-	-	:	_	_	_
1696	_	_	NN	_	_	_
1697	balanced	balanced	JJ	_	_	_
1698	groNOX-h	gronox-h	NN	_	_	_
1699	at	at	IN	_	_	_
1700	OD	OD	NNP	_	_	_
1701	0.19	0.19	CD	_	_	_
1702	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1703	Ecoli	Ecoli	NNP	_	_	_
1704	_	_	NNP	_	_	_
1705	NOX	NOX	NNP	_	_	_
1706	-	-	:	_	_	_
1707	_	_	NN	_	_	_
1708	balanced	balanced	JJ	_	_	_
1709	groNOX-h	gronox-h	NN	_	_	_
1710	at	at	IN	_	_	_
1711	OD	od	NN	_	_	_
1712	0.3	0.3	CD	_	_	_
1713	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1714	Ecoli	Ecoli	NNP	_	_	_
1715	_	_	NNP	_	_	_
1716	NOX	NOX	NNP	_	_	_
1717	-	-	:	_	_	_
1718	_	_	NN	_	_	_
1719	balanced	balanced	JJ	_	_	_
1720	groNOX-h	gronox-h	NN	_	_	_
1721	at	at	IN	_	_	_
1722	OD	OD	NNP	_	_	_
1723	0.41	0.41	CD	_	_	_
1724	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1725	Ecoli	Ecoli	NNP	_	_	_
1726	_	_	NNP	_	_	_
1727	NOX	NOX	NNP	_	_	_
1728	-	-	:	_	_	_
1729	_	_	NN	_	_	_
1730	balanced	balanced	JJ	_	_	_
1731	groNOX-h	gronox-h	NN	_	_	_
1732	at	at	IN	_	_	_
1733	OD	OD	NNP	_	_	_
1734	0.49	0.49	CD	_	_	_
1735	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1736	Ecoli	Ecoli	NNP	_	_	_
1737	_	_	NNP	_	_	_
1738	NOX	NOX	NNP	_	_	_
1739	-	-	:	_	_	_
1740	_	_	NN	_	_	_
1741	balanced	balanced	JJ	_	_	_
1742	groNOX-h	gronox-h	NN	_	_	_
1743	at	at	IN	_	_	_
1744	OD	od	NN	_	_	_
1745	0.6	0.6	CD	_	_	_
1746	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1747	Escherichia	escherichia	FW	Organism	_	_
1748	coli	coli	FW	Organism	_	_
1749	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1750	Escherichia	escherichia	FW	Organism	_	_
1751	coli	coli	FW	Organism	_	_
1752	MG1655	mg1655	NN	_	_	_
1753	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1754	Normalized	normalize	VBN	_	_	_
1755	log	log	NN	_	_	_
1756	-LRB-	-lrb-	-LRB-	_	_	_
1757	2	2	CD	_	_	_
1758	-RRB-	-rrb-	-RRB-	_	_	_
1759	ratio	ratio	NN	_	_	_
1760	of	of	IN	_	_	_
1761	Cy5	cy5	NN	_	_	_
1762	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1763	Ecoli	ecolus	NNS	_	_	_
1764	_	_	VBP	_	_	_
1765	Norfloxacin	norfloxacin	NN	_	_	_
1766	-LRB-	-lrb-	-LRB-	_	_	_
1767	50	50	CD	_	_	_
1768	ug	ug	NN	_	_	_
1769	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1770	Escherichia	escherichia	FW	Organism	_	_
1771	coli	coli	FW	Organism	_	_
1772	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1773	Escherichia	escherichia	FW	Organism	_	_
1774	coli	coli	FW	Organism	_	_
1775	C600	c600	NN	_	_	_
1776	,	,	,	_	_	_
1777	10	10	CD	_	_	_
1778	min	min	NN	_	_	_
1779	after	after	IN	_	_	_
1780	Norfloxacin	Norfloxacin	NNP	_	_	_
1781	-LRB-	-lrb-	-LRB-	_	_	_
1782	50	50	CD	_	_	_
1783	ug	ug	NN	_	_	_
1784	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1785	Escherichia	escherichia	FW	Organism	_	_
1786	coli	coli	FW	Organism	_	_
1787	C600	c600	NN	_	_	_
1788	,	,	,	_	_	_
1789	20	20	CD	_	_	_
1790	min	min	NN	_	_	_
1791	after	after	IN	_	_	_
1792	Norfloxacin	Norfloxacin	NNP	_	_	_
1793	-LRB-	-lrb-	-LRB-	_	_	_
1794	50	50	CD	_	_	_
1795	ug	ug	NN	_	_	_
1796	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1797	Escherichia	escherichia	FW	Organism	_	_
1798	coli	coli	FW	Organism	_	_
1799	C600	c600	NN	_	_	_
1800	,	,	,	_	_	_
1801	2	2	CD	_	_	_
1802	min	min	NN	_	_	_
1803	after	after	IN	_	_	_
1804	Norfloxacin	Norfloxacin	NNP	_	_	_
1805	-LRB-	-lrb-	-LRB-	_	_	_
1806	50	50	CD	_	_	_
1807	ug	ug	NN	_	_	_
1808	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1809	Escherichia	escherichia	FW	Organism	_	_
1810	coli	coli	FW	Organism	_	_
1811	C600	c600	NN	_	_	_
1812	,	,	,	_	_	_
1813	30	30	CD	_	_	_
1814	min	min	NN	_	_	_
1815	after	after	IN	_	_	_
1816	Norfloxacin	Norfloxacin	NNP	_	_	_
1817	-LRB-	-lrb-	-LRB-	_	_	_
1818	50	50	CD	_	_	_
1819	ug	ug	NN	_	_	_
1820	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1821	Escherichia	escherichia	FW	Organism	_	_
1822	coli	coli	FW	Organism	_	_
1823	C600	c600	NN	_	_	_
1824	,	,	,	_	_	_
1825	5	5	CD	_	_	_
1826	min	min	NN	_	_	_
1827	after	after	IN	_	_	_
1828	Norfloxacin	Norfloxacin	NNP	_	_	_
1829	-LRB-	-lrb-	-LRB-	_	_	_
1830	50	50	CD	_	_	_
1831	ug	ug	NN	_	_	_
1832	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1833	Escherichia	escherichia	FW	Organism	_	_
1834	coli	coli	FW	Organism	_	_
1835	C600	c600	NN	_	_	_
1836	,	,	,	_	_	_
1837	LB	lb	NN	_	_	_
1838	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1839	Escherichia	escherichia	FW	Organism	_	_
1840	coli	coli	FW	Organism	_	_
1841	C600	c600	NN	_	_	_
1842	,	,	,	_	_	_
1843	LB	lb	NN	_	_	_
1844	,	,	,	_	_	_
1845	0	0	CD	_	_	_
1846	min	min	NN	_	_	_
1847	before	before	IN	_	_	_
1848	treatment	treatment	NN	_	_	_
1849	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1850	Normalized	normalize	VBN	_	_	_
1851	log	log	NN	_	_	_
1852	-LRB-	-lrb-	-LRB-	_	_	_
1853	2	2	CD	_	_	_
1854	-RRB-	-rrb-	-RRB-	_	_	_
1855	ratio	ratio	NN	_	_	_
1856	of	of	IN	_	_	_
1857	Cy5	cy5	NN	_	_	_
1858	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1859	Ecoli	ecolus	NNS	_	_	_
1860	_	_	VBP	_	_	_
1861	gyrArparCr	gyrarparcr	NN	_	_	_
1862	_	_	CD	_	_	_
1863	Norfloxacin	norfloxacin	NN	_	_	_
1864	-LRB-	-lrb-	-LRB-	_	_	_
1865	15	15	CD	_	_	_
1866	ug	ug	NN	_	_	_
1867	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1868	Escherichia	escherichia	FW	Organism	_	_
1869	coli	coli	FW	Organism	_	_
1870	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1871	Escherichia	escherichia	FW	Organism	_	_
1872	coli	coli	FW	Organism	_	_
1873	C600	c600	NN	_	_	_
1874	-LRB-	-lrb-	-LRB-	_	_	_
1875	gyrArparCr	gyrarparcr	NN	_	_	_
1876	-RRB-	-rrb-	-RRB-	_	_	_
1877	,	,	,	_	_	_
1878	10	10	CD	_	_	_
1879	min	min	NN	_	_	_
1880	after	after	IN	_	_	_
1881	Norfloxacin	Norfloxacin	NNP	_	_	_
1882	-LRB-	-lrb-	-LRB-	_	_	_
1883	15	15	CD	_	_	_
1884	ug	ug	NN	_	_	_
1885	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1886	Escherichia	escherichia	FW	Organism	_	_
1887	coli	coli	FW	Organism	_	_
1888	C600	c600	NN	_	_	_
1889	-LRB-	-lrb-	-LRB-	_	_	_
1890	gyrArparCr	gyrarparcr	NN	_	_	_
1891	-RRB-	-rrb-	-RRB-	_	_	_
1892	,	,	,	_	_	_
1893	20	20	CD	_	_	_
1894	min	min	NN	_	_	_
1895	after	after	IN	_	_	_
1896	Norfloxacin	Norfloxacin	NNP	_	_	_
1897	-LRB-	-lrb-	-LRB-	_	_	_
1898	15	15	CD	_	_	_
1899	ug	ug	NN	_	_	_
1900	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1901	Escherichia	escherichia	FW	Organism	_	_
1902	coli	coli	FW	Organism	_	_
1903	C600	c600	NN	_	_	_
1904	-LRB-	-lrb-	-LRB-	_	_	_
1905	gyrArparCr	gyrarparcr	NN	_	_	_
1906	-RRB-	-rrb-	-RRB-	_	_	_
1907	,	,	,	_	_	_
1908	2	2	CD	_	_	_
1909	min	min	NN	_	_	_
1910	after	after	IN	_	_	_
1911	Norfloxacin	Norfloxacin	NNP	_	_	_
1912	-LRB-	-lrb-	-LRB-	_	_	_
1913	15	15	CD	_	_	_
1914	ug	ug	NN	_	_	_
1915	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1916	Escherichia	escherichia	FW	Organism	_	_
1917	coli	coli	FW	Organism	_	_
1918	C600	c600	NN	_	_	_
1919	-LRB-	-lrb-	-LRB-	_	_	_
1920	gyrArparCr	gyrarparcr	NN	_	_	_
1921	-RRB-	-rrb-	-RRB-	_	_	_
1922	,	,	,	_	_	_
1923	30	30	CD	_	_	_
1924	min	min	NN	_	_	_
1925	after	after	IN	_	_	_
1926	Norfloxacin	Norfloxacin	NNP	_	_	_
1927	-LRB-	-lrb-	-LRB-	_	_	_
1928	15	15	CD	_	_	_
1929	ug	ug	NN	_	_	_
1930	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1931	Escherichia	escherichia	FW	Organism	_	_
1932	coli	coli	FW	Organism	_	_
1933	C600	c600	NN	_	_	_
1934	-LRB-	-lrb-	-LRB-	_	_	_
1935	gyrArparCr	gyrarparcr	NN	_	_	_
1936	-RRB-	-rrb-	-RRB-	_	_	_
1937	,	,	,	_	_	_
1938	5	5	CD	_	_	_
1939	min	min	NN	_	_	_
1940	after	after	IN	_	_	_
1941	Norfloxacin	Norfloxacin	NNP	_	_	_
1942	-LRB-	-lrb-	-LRB-	_	_	_
1943	15	15	CD	_	_	_
1944	ug	ug	NN	_	_	_
1945	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1946	Escherichia	escherichia	FW	Organism	_	_
1947	coli	coli	FW	Organism	_	_
1948	C600	c600	NN	_	_	_
1949	-LRB-	-lrb-	-LRB-	_	_	_
1950	gyrArparCr	gyrarparcr	NN	_	_	_
1951	-RRB-	-rrb-	-RRB-	_	_	_
1952	,	,	,	_	_	_
1953	LB	lb	NN	_	_	_
1954	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1955	Escherichia	escherichia	FW	Organism	_	_
1956	coli	coli	FW	Organism	_	_
1957	C600	c600	NN	_	_	_
1958	-LRB-	-lrb-	-LRB-	_	_	_
1959	gyrArparCr	gyrarparcr	NN	_	_	_
1960	-RRB-	-rrb-	-RRB-	_	_	_
1961	,	,	,	_	_	_
1962	LB	lb	NN	_	_	_
1963	,	,	,	_	_	_
1964	0	0	CD	_	_	_
1965	min	min	NN	_	_	_
1966	before	before	IN	_	_	_
1967	treatment	treatment	NN	_	_	_
1968	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1969	Normalized	normalize	VBN	_	_	_
1970	log	log	NN	_	_	_
1971	-LRB-	-lrb-	-LRB-	_	_	_
1972	2	2	CD	_	_	_
1973	-RRB-	-rrb-	-RRB-	_	_	_
1974	ratio	ratio	NN	_	_	_
1975	of	of	IN	_	_	_
1976	Cy5	cy5	NN	_	_	_
1977	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1978	Ecoli	ecolus	NNS	_	_	_
1979	_	_	VBP	_	_	_
1980	gyrArparCr	gyrarparcr	NN	_	_	_
1981	_	_	CD	_	_	_
1982	Norfloxacin	norfloxacin	NN	_	_	_
1983	-LRB-	-lrb-	-LRB-	_	_	_
1984	50	50	CD	_	_	_
1985	ug	ug	NN	_	_	_
1986	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1987	Escherichia	escherichia	FW	Organism	_	_
1988	coli	coli	FW	Organism	_	_
1989	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1990	Escherichia	escherichia	FW	Organism	_	_
1991	coli	coli	FW	Organism	_	_
1992	C600	c600	NN	_	_	_
1993	-LRB-	-lrb-	-LRB-	_	_	_
1994	gyrArparCr	gyrarparcr	NN	_	_	_
1995	-RRB-	-rrb-	-RRB-	_	_	_
1996	,	,	,	_	_	_
1997	10	10	CD	_	_	_
1998	min	min	NN	_	_	_
1999	after	after	IN	_	_	_
2000	Norfloxacin	Norfloxacin	NNP	_	_	_
2001	-LRB-	-lrb-	-LRB-	_	_	_
2002	50	50	CD	_	_	_
2003	ug	ug	NN	_	_	_
2004	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2005	Escherichia	escherichia	FW	Organism	_	_
2006	coli	coli	FW	Organism	_	_
2007	C600	c600	NN	_	_	_
2008	-LRB-	-lrb-	-LRB-	_	_	_
2009	gyrArparCr	gyrarparcr	NN	_	_	_
2010	-RRB-	-rrb-	-RRB-	_	_	_
2011	,	,	,	_	_	_
2012	20	20	CD	_	_	_
2013	min	min	NN	_	_	_
2014	after	after	IN	_	_	_
2015	Norfloxacin	Norfloxacin	NNP	_	_	_
2016	-LRB-	-lrb-	-LRB-	_	_	_
2017	50	50	CD	_	_	_
2018	ug	ug	NN	_	_	_
2019	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2020	Escherichia	escherichia	FW	Organism	_	_
2021	coli	coli	FW	Organism	_	_
2022	C600	c600	NN	_	_	_
2023	-LRB-	-lrb-	-LRB-	_	_	_
2024	gyrArparCr	gyrarparcr	NN	_	_	_
2025	-RRB-	-rrb-	-RRB-	_	_	_
2026	,	,	,	_	_	_
2027	2	2	CD	_	_	_
2028	min	min	NN	_	_	_
2029	after	after	IN	_	_	_
2030	Norfloxacin	Norfloxacin	NNP	_	_	_
2031	-LRB-	-lrb-	-LRB-	_	_	_
2032	50	50	CD	_	_	_
2033	ug	ug	NN	_	_	_
2034	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2035	Escherichia	escherichia	FW	Organism	_	_
2036	coli	coli	FW	Organism	_	_
2037	C600	c600	NN	_	_	_
2038	-LRB-	-lrb-	-LRB-	_	_	_
2039	gyrArparCr	gyrarparcr	NN	_	_	_
2040	-RRB-	-rrb-	-RRB-	_	_	_
2041	,	,	,	_	_	_
2042	30	30	CD	_	_	_
2043	min	min	NN	_	_	_
2044	after	after	IN	_	_	_
2045	Norfloxacin	Norfloxacin	NNP	_	_	_
2046	-LRB-	-lrb-	-LRB-	_	_	_
2047	50	50	CD	_	_	_
2048	ug	ug	NN	_	_	_
2049	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2050	Escherichia	escherichia	FW	Organism	_	_
2051	coli	coli	FW	Organism	_	_
2052	C600	c600	NN	_	_	_
2053	-LRB-	-lrb-	-LRB-	_	_	_
2054	gyrArparCr	gyrarparcr	NN	_	_	_
2055	-RRB-	-rrb-	-RRB-	_	_	_
2056	,	,	,	_	_	_
2057	5	5	CD	_	_	_
2058	min	min	NN	_	_	_
2059	after	after	IN	_	_	_
2060	Norfloxacin	Norfloxacin	NNP	_	_	_
2061	-LRB-	-lrb-	-LRB-	_	_	_
2062	50	50	CD	_	_	_
2063	ug	ug	NN	_	_	_
2064	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2065	Escherichia	escherichia	FW	Organism	_	_
2066	coli	coli	FW	Organism	_	_
2067	C600	c600	NN	_	_	_
2068	-LRB-	-lrb-	-LRB-	_	_	_
2069	gyrArparCr	gyrarparcr	NN	_	_	_
2070	-RRB-	-rrb-	-RRB-	_	_	_
2071	,	,	,	_	_	_
2072	LB	lb	NN	_	_	_
2073	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2074	Escherichia	escherichia	FW	Organism	_	_
2075	coli	coli	FW	Organism	_	_
2076	C600	c600	NN	_	_	_
2077	-LRB-	-lrb-	-LRB-	_	_	_
2078	gyrArparCr	gyrarparcr	NN	_	_	_
2079	-RRB-	-rrb-	-RRB-	_	_	_
2080	,	,	,	_	_	_
2081	LB	lb	NN	_	_	_
2082	,	,	,	_	_	_
2083	0	0	CD	_	_	_
2084	min	min	NN	_	_	_
2085	before	before	IN	_	_	_
2086	treatment	treatment	NN	_	_	_
2087	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2088	Normalized	normalize	VBN	_	_	_
2089	log	log	NN	_	_	_
2090	-LRB-	-lrb-	-LRB-	_	_	_
2091	2	2	CD	_	_	_
2092	-RRB-	-rrb-	-RRB-	_	_	_
2093	ratio	ratio	NN	_	_	_
2094	of	of	IN	_	_	_
2095	Cy5	cy5	NN	_	_	_
2096	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2097	Ecoli	ecolus	NNS	_	_	_
2098	_	_	VBP	_	_	_
2099	Recovery	recovery	NN	_	_	_
2100	in	in	IN	_	_	_
2101	10mM	10mm	NN	_	_	_
2102	Na-P	na-p	NN	_	_	_
2103	T1	t1	NN	_	_	_
2104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2105	Ecoli	ecolus	NNS	_	_	_
2106	_	_	VBP	_	_	_
2107	Recovery	recovery	NN	_	_	_
2108	in	in	IN	_	_	_
2109	10mM	10mm	NN	_	_	_
2110	Na-P	na-p	NN	_	_	_
2111	T2	t2	NN	_	_	_
2112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2113	Ecoli	ecolus	NNS	_	_	_
2114	_	_	VBP	_	_	_
2115	Recovery	recovery	NN	_	_	_
2116	in	in	IN	_	_	_
2117	10mM	10mm	NN	_	_	_
2118	Na-P	na-p	NN	_	_	_
2119	T3	t3	NN	_	_	_
2120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2121	Ecoli	ecolus	NNS	_	_	_
2122	_	_	VBP	_	_	_
2123	Recovery	recovery	NN	_	_	_
2124	in	in	IN	_	_	_
2125	10mM	10mm	NN	_	_	_
2126	Na-P	na-p	NN	_	_	_
2127	T4	t4	NN	_	_	_
2128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2129	Ecoli	ecolus	NNS	_	_	_
2130	_	_	VBP	_	_	_
2131	Recovery	recovery	NN	_	_	_
2132	in	in	IN	_	_	_
2133	10mM	10mm	NN	_	_	_
2134	Na-P	na-p	NN	_	_	_
2135	T5	t5	NN	_	_	_
2136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2137	Ecoli	ecolus	NNS	_	_	_
2138	_	_	VBP	_	_	_
2139	Recovery	recovery	NN	_	_	_
2140	in	in	IN	_	_	_
2141	10mM	10mm	NN	_	_	_
2142	Na-P	na-p	NN	_	_	_
2143	T6	t6	NN	_	_	_
2144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2145	Ecoli	ecolus	NNS	_	_	_
2146	_	_	VBP	_	_	_
2147	Recovery	recovery	NN	_	_	_
2148	in	in	IN	_	_	_
2149	10mM	10mm	NN	_	_	_
2150	Na-P	na-p	NN	_	_	_
2151	T7	t7	NN	_	_	_
2152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2153	Escherichia	escherichia	FW	Organism	_	_
2154	coli	coli	FW	Organism	_	_
2155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2156	Escherichia	escherichia	FW	Organism	_	_
2157	coli	coli	FW	Organism	_	_
2158	MG1655	mg1655	NN	_	_	_
2159	,	,	,	_	_	_
2160	0	0	CD	_	_	_
2161	min	min	NN	_	_	_
2162	recovery	recovery	NN	_	_	_
2163	in	in	IN	_	_	_
2164	10mM	10mm	NN	_	_	_
2165	Na-P	na-p	NN	_	_	_
2166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2167	Escherichia	escherichia	FW	Organism	_	_
2168	coli	coli	FW	Organism	_	_
2169	MG1655	mg1655	NN	_	_	_
2170	,	,	,	_	_	_
2171	0	0	CD	_	_	_
2172	min	min	NN	_	_	_
2173	recovery	recovery	NN	_	_	_
2174	in	in	IN	_	_	_
2175	10	10	CD	_	_	_
2176	mM	mm	NN	KWSUPP	_	_
2177	Na-P	na-p	NN	_	_	_
2178	-LRB-	-lrb-	-LRB-	_	_	_
2179	pH	ph	NN	_	_	_
2180	7.5	7.5	CD	_	_	_
2181	-RRB-	-rrb-	-RRB-	_	_	_
2182	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2183	Escherichia	escherichia	FW	Organism	_	_
2184	coli	coli	FW	Organism	_	_
2185	MG1655	mg1655	NN	_	_	_
2186	,	,	,	_	_	_
2187	15	15	CD	_	_	_
2188	min	min	NN	_	_	_
2189	recovery	recovery	NN	_	_	_
2190	in	in	IN	_	_	_
2191	10mM	10mm	NN	_	_	_
2192	Na-P	na-p	NN	_	_	_
2193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2194	Escherichia	escherichia	FW	Organism	_	_
2195	coli	coli	FW	Organism	_	_
2196	MG1655	mg1655	NN	_	_	_
2197	,	,	,	_	_	_
2198	15	15	CD	_	_	_
2199	min	min	NN	_	_	_
2200	recovery	recovery	NN	_	_	_
2201	in	in	IN	_	_	_
2202	10	10	CD	_	_	_
2203	mM	mm	NN	KWSUPP	_	_
2204	Na-P	na-p	NN	_	_	_
2205	-LRB-	-lrb-	-LRB-	_	_	_
2206	pH	ph	NN	_	_	_
2207	7.5	7.5	CD	_	_	_
2208	-RRB-	-rrb-	-RRB-	_	_	_
2209	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2210	Escherichia	escherichia	FW	Organism	_	_
2211	coli	coli	FW	Organism	_	_
2212	MG1655	mg1655	NN	_	_	_
2213	,	,	,	_	_	_
2214	30	30	CD	_	_	_
2215	min	min	NN	_	_	_
2216	recovery	recovery	NN	_	_	_
2217	in	in	IN	_	_	_
2218	10mM	10mm	NN	_	_	_
2219	Na-P	na-p	NN	_	_	_
2220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2221	Escherichia	escherichia	FW	Organism	_	_
2222	coli	coli	FW	Organism	_	_
2223	MG1655	mg1655	NN	_	_	_
2224	,	,	,	_	_	_
2225	30	30	CD	_	_	_
2226	min	min	NN	_	_	_
2227	recovery	recovery	NN	_	_	_
2228	in	in	IN	_	_	_
2229	10	10	CD	_	_	_
2230	mM	mm	NN	KWSUPP	_	_
2231	Na-P	na-p	NN	_	_	_
2232	-LRB-	-lrb-	-LRB-	_	_	_
2233	pH	ph	NN	_	_	_
2234	7.5	7.5	CD	_	_	_
2235	-RRB-	-rrb-	-RRB-	_	_	_
2236	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2237	Escherichia	escherichia	FW	Organism	_	_
2238	coli	coli	FW	Organism	_	_
2239	MG1655	mg1655	NN	_	_	_
2240	,	,	,	_	_	_
2241	45	45	CD	_	_	_
2242	min	min	NN	_	_	_
2243	recovery	recovery	NN	_	_	_
2244	in	in	IN	_	_	_
2245	10mM	10mm	NN	_	_	_
2246	Na-P	na-p	NN	_	_	_
2247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2248	Escherichia	escherichia	FW	Organism	_	_
2249	coli	coli	FW	Organism	_	_
2250	MG1655	mg1655	NN	_	_	_
2251	,	,	,	_	_	_
2252	45	45	CD	_	_	_
2253	min	min	NN	_	_	_
2254	recovery	recovery	NN	_	_	_
2255	in	in	IN	_	_	_
2256	10	10	CD	_	_	_
2257	mM	mm	NN	KWSUPP	_	_
2258	Na-P	na-p	NN	_	_	_
2259	-LRB-	-lrb-	-LRB-	_	_	_
2260	pH	ph	NN	_	_	_
2261	7.5	7.5	CD	_	_	_
2262	-RRB-	-rrb-	-RRB-	_	_	_
2263	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2264	Escherichia	escherichia	FW	Organism	_	_
2265	coli	coli	FW	Organism	_	_
2266	MG1655	mg1655	NN	_	_	_
2267	,	,	,	_	_	_
2268	60	60	CD	_	_	_
2269	min	min	NN	_	_	_
2270	recovery	recovery	NN	_	_	_
2271	in	in	IN	_	_	_
2272	10mM	10mm	NN	_	_	_
2273	Na-P	na-p	NN	_	_	_
2274	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2275	Escherichia	escherichia	FW	Organism	_	_
2276	coli	coli	FW	Organism	_	_
2277	MG1655	mg1655	NN	_	_	_
2278	,	,	,	_	_	_
2279	60	60	CD	_	_	_
2280	min	min	NN	_	_	_
2281	recovery	recovery	NN	_	_	_
2282	in	in	IN	_	_	_
2283	10	10	CD	_	_	_
2284	mM	mm	NN	KWSUPP	_	_
2285	Na-P	na-p	NN	_	_	_
2286	-LRB-	-lrb-	-LRB-	_	_	_
2287	pH	ph	NN	_	_	_
2288	7.5	7.5	CD	_	_	_
2289	-RRB-	-rrb-	-RRB-	_	_	_
2290	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2291	Escherichia	escherichia	FW	Organism	_	_
2292	coli	coli	FW	Organism	_	_
2293	MG1655	mg1655	NN	_	_	_
2294	,	,	,	_	_	_
2295	75	75	CD	_	_	_
2296	min	min	NN	_	_	_
2297	recovery	recovery	NN	_	_	_
2298	in	in	IN	_	_	_
2299	10mM	10mm	NN	_	_	_
2300	Na-P	na-p	NN	_	_	_
2301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2302	Escherichia	escherichia	FW	Organism	_	_
2303	coli	coli	FW	Organism	_	_
2304	MG1655	mg1655	NN	_	_	_
2305	,	,	,	_	_	_
2306	75	75	CD	_	_	_
2307	min	min	NN	_	_	_
2308	recovery	recovery	NN	_	_	_
2309	in	in	IN	_	_	_
2310	10	10	CD	_	_	_
2311	mM	mm	NN	KWSUPP	_	_
2312	Na-P	na-p	NN	_	_	_
2313	-LRB-	-lrb-	-LRB-	_	_	_
2314	pH	ph	NN	_	_	_
2315	7.5	7.5	CD	_	_	_
2316	-RRB-	-rrb-	-RRB-	_	_	_
2317	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2318	Escherichia	escherichia	FW	Organism	_	_
2319	coli	coli	FW	Organism	_	_
2320	MG1655	mg1655	NN	_	_	_
2321	,	,	,	_	_	_
2322	90	90	CD	_	_	_
2323	min	min	NN	_	_	_
2324	recovery	recovery	NN	_	_	_
2325	in	in	IN	_	_	_
2326	10mM	10mm	NN	_	_	_
2327	Na-P	na-p	NN	_	_	_
2328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2329	Escherichia	escherichia	FW	Organism	_	_
2330	coli	coli	FW	Organism	_	_
2331	MG1655	mg1655	NN	_	_	_
2332	,	,	,	_	_	_
2333	90	90	CD	_	_	_
2334	min	min	NN	_	_	_
2335	recovery	recovery	NN	_	_	_
2336	in	in	IN	_	_	_
2337	10	10	CD	_	_	_
2338	mM	mm	NN	KWSUPP	_	_
2339	Na-P	na-p	NN	_	_	_
2340	-LRB-	-lrb-	-LRB-	_	_	_
2341	pH	ph	NN	_	_	_
2342	7.5	7.5	CD	_	_	_
2343	-RRB-	-rrb-	-RRB-	_	_	_
2344	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2345	Escherichia	escherichia	FW	Organism	_	_
2346	coli	coli	FW	Organism	_	_
2347	MG1655	mg1655	NN	_	_	_
2348	,	,	,	_	_	_
2349	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
2350	OD	OD	NNP	_	_	_
2351	~	~	SYM	_	_	_
2352	0.5	0.5	CD	_	_	_
2353	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2354	Normalized	normalize	VBN	_	_	_
2355	log	log	NN	_	_	_
2356	-LRB-	-lrb-	-LRB-	_	_	_
2357	2	2	CD	_	_	_
2358	-RRB-	-rrb-	-RRB-	_	_	_
2359	ratio	ratio	NN	_	_	_
2360	of	of	IN	_	_	_
2361	Cy5	cy5	NN	_	_	_
2362	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2363	Ecoli	ecolus	NNS	_	_	_
2364	_	_	VBP	_	_	_
2365	Recovery	recovery	NN	_	_	_
2366	in	in	IN	_	_	_
2367	10mM	10mm	NN	_	_	_
2368	Na-P	na-p	NN	_	_	_
2369	+	+	CC	_	_	_
2370	0.2	0.2	CD	_	_	_
2371	%	%	NN	_	_	_
2372	glucose	glucose	NN	SUPP	_	_
2373	T1	t1	NN	_	_	_
2374	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2375	Ecoli	ecolus	NNS	_	_	_
2376	_	_	VBP	_	_	_
2377	Recovery	recovery	NN	_	_	_
2378	in	in	IN	_	_	_
2379	10mM	10mm	NN	_	_	_
2380	Na-P	na-p	NN	_	_	_
2381	+	+	CC	_	_	_
2382	0.2	0.2	CD	_	_	_
2383	%	%	NN	_	_	_
2384	glucose	glucose	NN	SUPP	_	_
2385	T2	t2	NN	_	_	_
2386	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2387	Ecoli	ecolus	NNS	_	_	_
2388	_	_	VBP	_	_	_
2389	Recovery	recovery	NN	_	_	_
2390	in	in	IN	_	_	_
2391	10mM	10mm	NN	_	_	_
2392	Na-P	na-p	NN	_	_	_
2393	+	+	CC	_	_	_
2394	0.2	0.2	CD	_	_	_
2395	%	%	NN	_	_	_
2396	glucose	glucose	NN	SUPP	_	_
2397	T3	t3	NN	_	_	_
2398	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2399	Ecoli	ecolus	NNS	_	_	_
2400	_	_	VBP	_	_	_
2401	Recovery	recovery	NN	_	_	_
2402	in	in	IN	_	_	_
2403	10mM	10mm	NN	_	_	_
2404	Na-P	na-p	NN	_	_	_
2405	+	+	CC	_	_	_
2406	0.2	0.2	CD	_	_	_
2407	%	%	NN	_	_	_
2408	glucose	glucose	NN	SUPP	_	_
2409	T4	t4	NN	_	_	_
2410	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2411	Ecoli	ecolus	NNS	_	_	_
2412	_	_	VBP	_	_	_
2413	Recovery	recovery	NN	_	_	_
2414	in	in	IN	_	_	_
2415	10mM	10mm	NN	_	_	_
2416	Na-P	na-p	NN	_	_	_
2417	+	+	CC	_	_	_
2418	0.2	0.2	CD	_	_	_
2419	%	%	NN	_	_	_
2420	glucose	glucose	NN	SUPP	_	_
2421	T5	t5	NN	_	_	_
2422	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2423	Ecoli	ecolus	NNS	_	_	_
2424	_	_	VBP	_	_	_
2425	Recovery	recovery	NN	_	_	_
2426	in	in	IN	_	_	_
2427	10mM	10mm	NN	_	_	_
2428	Na-P	na-p	NN	_	_	_
2429	+	+	CC	_	_	_
2430	0.2	0.2	CD	_	_	_
2431	%	%	NN	_	_	_
2432	glucose	glucose	NN	SUPP	_	_
2433	T6	t6	NN	_	_	_
2434	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2435	Ecoli	ecolus	NNS	_	_	_
2436	_	_	VBP	_	_	_
2437	Recovery	recovery	NN	_	_	_
2438	in	in	IN	_	_	_
2439	10mM	10mm	NN	_	_	_
2440	Na-P	na-p	NN	_	_	_
2441	+	+	CC	_	_	_
2442	0.2	0.2	CD	_	_	_
2443	%	%	NN	_	_	_
2444	glucose	glucose	NN	SUPP	_	_
2445	T7	t7	NN	_	_	_
2446	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2447	Escherichia	escherichia	FW	Organism	_	_
2448	coli	coli	FW	Organism	_	_
2449	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2450	Escherichia	escherichia	FW	Organism	_	_
2451	coli	coli	FW	Organism	_	_
2452	MG1655	mg1655	NN	_	_	_
2453	,	,	,	_	_	_
2454	0	0	CD	_	_	_
2455	min	min	NN	_	_	_
2456	recovery	recovery	NN	_	_	_
2457	in	in	IN	_	_	_
2458	10mM	10mm	NN	_	_	_
2459	Na-P	na-p	NN	_	_	_
2460	+	+	CC	_	_	_
2461	0.2	0.2	CD	_	_	_
2462	%	%	NN	_	_	_
2463	glucose	glucose	NN	SUPP	_	_
2464	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2465	Escherichia	escherichia	FW	Organism	_	_
2466	coli	coli	FW	Organism	_	_
2467	MG1655	mg1655	NN	_	_	_
2468	,	,	,	_	_	_
2469	0	0	CD	_	_	_
2470	min	min	NN	_	_	_
2471	recovery	recovery	NN	_	_	_
2472	in	in	IN	_	_	_
2473	10	10	CD	_	_	_
2474	mM	mm	NN	KWSUPP	_	_
2475	Na-P	na-p	NN	_	_	_
2476	+	+	CC	_	_	_
2477	0.2	0.2	CD	_	_	_
2478	%	%	NN	_	_	_
2479	glucose	glucose	NN	SUPP	_	_
2480	-LRB-	-lrb-	-LRB-	_	_	_
2481	pH	ph	NN	_	_	_
2482	7.5	7.5	CD	_	_	_
2483	-RRB-	-rrb-	-RRB-	_	_	_
2484	at	at	IN	_	_	_
2485	OD	od	NN	_	_	_
2486	0.4	0.4	CD	_	_	_
2487	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2488	Escherichia	escherichia	FW	Organism	_	_
2489	coli	coli	FW	Organism	_	_
2490	MG1655	mg1655	NN	_	_	_
2491	,	,	,	_	_	_
2492	15	15	CD	_	_	_
2493	min	min	NN	_	_	_
2494	recovery	recovery	NN	_	_	_
2495	in	in	IN	_	_	_
2496	10mM	10mm	NN	_	_	_
2497	Na-P	na-p	NN	_	_	_
2498	+	+	CC	_	_	_
2499	0.2	0.2	CD	_	_	_
2500	%	%	NN	_	_	_
2501	glucose	glucose	NN	SUPP	_	_
2502	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2503	Escherichia	escherichia	FW	Organism	_	_
2504	coli	coli	FW	Organism	_	_
2505	MG1655	mg1655	NN	_	_	_
2506	,	,	,	_	_	_
2507	15	15	CD	_	_	_
2508	min	min	NN	_	_	_
2509	recovery	recovery	NN	_	_	_
2510	in	in	IN	_	_	_
2511	10	10	CD	_	_	_
2512	mM	mm	NN	KWSUPP	_	_
2513	Na-P	na-p	NN	_	_	_
2514	+	+	CC	_	_	_
2515	0.2	0.2	CD	_	_	_
2516	%	%	NN	_	_	_
2517	glucose	glucose	NN	SUPP	_	_
2518	-LRB-	-lrb-	-LRB-	_	_	_
2519	pH	ph	NN	_	_	_
2520	7.5	7.5	CD	_	_	_
2521	-RRB-	-rrb-	-RRB-	_	_	_
2522	at	at	IN	_	_	_
2523	OD	od	NN	_	_	_
2524	0.4	0.4	CD	_	_	_
2525	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2526	Escherichia	escherichia	FW	Organism	_	_
2527	coli	coli	FW	Organism	_	_
2528	MG1655	mg1655	NN	_	_	_
2529	,	,	,	_	_	_
2530	30	30	CD	_	_	_
2531	min	min	NN	_	_	_
2532	recovery	recovery	NN	_	_	_
2533	in	in	IN	_	_	_
2534	10mM	10mm	NN	_	_	_
2535	Na-P	na-p	NN	_	_	_
2536	+	+	CC	_	_	_
2537	0.2	0.2	CD	_	_	_
2538	%	%	NN	_	_	_
2539	glucose	glucose	NN	SUPP	_	_
2540	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2541	Escherichia	escherichia	FW	Organism	_	_
2542	coli	coli	FW	Organism	_	_
2543	MG1655	mg1655	NN	_	_	_
2544	,	,	,	_	_	_
2545	30	30	CD	_	_	_
2546	min	min	NN	_	_	_
2547	recovery	recovery	NN	_	_	_
2548	in	in	IN	_	_	_
2549	10	10	CD	_	_	_
2550	mM	mm	NN	KWSUPP	_	_
2551	Na-P	na-p	NN	_	_	_
2552	+	+	CC	_	_	_
2553	0.2	0.2	CD	_	_	_
2554	%	%	NN	_	_	_
2555	glucose	glucose	NN	SUPP	_	_
2556	-LRB-	-lrb-	-LRB-	_	_	_
2557	pH	ph	NN	_	_	_
2558	7.5	7.5	CD	_	_	_
2559	-RRB-	-rrb-	-RRB-	_	_	_
2560	at	at	IN	_	_	_
2561	OD	od	NN	_	_	_
2562	0.4	0.4	CD	_	_	_
2563	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2564	Escherichia	escherichia	FW	Organism	_	_
2565	coli	coli	FW	Organism	_	_
2566	MG1655	mg1655	NN	_	_	_
2567	,	,	,	_	_	_
2568	45	45	CD	_	_	_
2569	min	min	NN	_	_	_
2570	recovery	recovery	NN	_	_	_
2571	in	in	IN	_	_	_
2572	10mM	10mm	NN	_	_	_
2573	Na-P	na-p	NN	_	_	_
2574	+	+	CC	_	_	_
2575	0.2	0.2	CD	_	_	_
2576	%	%	NN	_	_	_
2577	glucose	glucose	NN	SUPP	_	_
2578	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2579	Escherichia	escherichia	FW	Organism	_	_
2580	coli	coli	FW	Organism	_	_
2581	MG1655	mg1655	NN	_	_	_
2582	,	,	,	_	_	_
2583	45	45	CD	_	_	_
2584	min	min	NN	_	_	_
2585	recovery	recovery	NN	_	_	_
2586	in	in	IN	_	_	_
2587	10	10	CD	_	_	_
2588	mM	mm	NN	KWSUPP	_	_
2589	Na-P	na-p	NN	_	_	_
2590	+	+	CC	_	_	_
2591	0.2	0.2	CD	_	_	_
2592	%	%	NN	_	_	_
2593	glucose	glucose	NN	SUPP	_	_
2594	-LRB-	-lrb-	-LRB-	_	_	_
2595	pH	ph	NN	_	_	_
2596	7.5	7.5	CD	_	_	_
2597	-RRB-	-rrb-	-RRB-	_	_	_
2598	at	at	IN	_	_	_
2599	OD	od	NN	_	_	_
2600	0.4	0.4	CD	_	_	_
2601	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2602	Escherichia	escherichia	FW	Organism	_	_
2603	coli	coli	FW	Organism	_	_
2604	MG1655	mg1655	NN	_	_	_
2605	,	,	,	_	_	_
2606	60	60	CD	_	_	_
2607	min	min	NN	_	_	_
2608	recovery	recovery	NN	_	_	_
2609	in	in	IN	_	_	_
2610	10mM	10mm	NN	_	_	_
2611	Na-P	na-p	NN	_	_	_
2612	+	+	CC	_	_	_
2613	0.2	0.2	CD	_	_	_
2614	%	%	NN	_	_	_
2615	glucose	glucose	NN	SUPP	_	_
2616	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2617	Escherichia	escherichia	FW	Organism	_	_
2618	coli	coli	FW	Organism	_	_
2619	MG1655	mg1655	NN	_	_	_
2620	,	,	,	_	_	_
2621	60	60	CD	_	_	_
2622	min	min	NN	_	_	_
2623	recovery	recovery	NN	_	_	_
2624	in	in	IN	_	_	_
2625	10	10	CD	_	_	_
2626	mM	mm	NN	KWSUPP	_	_
2627	Na-P	na-p	NN	_	_	_
2628	+	+	CC	_	_	_
2629	0.2	0.2	CD	_	_	_
2630	%	%	NN	_	_	_
2631	glucose	glucose	NN	SUPP	_	_
2632	-LRB-	-lrb-	-LRB-	_	_	_
2633	pH	ph	NN	_	_	_
2634	7.5	7.5	CD	_	_	_
2635	-RRB-	-rrb-	-RRB-	_	_	_
2636	at	at	IN	_	_	_
2637	OD	od	NN	_	_	_
2638	0.4	0.4	CD	_	_	_
2639	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2640	Escherichia	escherichia	FW	Organism	_	_
2641	coli	coli	FW	Organism	_	_
2642	MG1655	mg1655	NN	_	_	_
2643	,	,	,	_	_	_
2644	75	75	CD	_	_	_
2645	min	min	NN	_	_	_
2646	recovery	recovery	NN	_	_	_
2647	in	in	IN	_	_	_
2648	10mM	10mm	NN	_	_	_
2649	Na-P	na-p	NN	_	_	_
2650	+	+	CC	_	_	_
2651	0.2	0.2	CD	_	_	_
2652	%	%	NN	_	_	_
2653	glucose	glucose	NN	SUPP	_	_
2654	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2655	Escherichia	escherichia	FW	Organism	_	_
2656	coli	coli	FW	Organism	_	_
2657	MG1655	mg1655	NN	_	_	_
2658	,	,	,	_	_	_
2659	75	75	CD	_	_	_
2660	min	min	NN	_	_	_
2661	recovery	recovery	NN	_	_	_
2662	in	in	IN	_	_	_
2663	10	10	CD	_	_	_
2664	mM	mm	NN	KWSUPP	_	_
2665	Na-P	na-p	NN	_	_	_
2666	+	+	CC	_	_	_
2667	0.2	0.2	CD	_	_	_
2668	%	%	NN	_	_	_
2669	glucose	glucose	NN	SUPP	_	_
2670	-LRB-	-lrb-	-LRB-	_	_	_
2671	pH	ph	NN	_	_	_
2672	7.5	7.5	CD	_	_	_
2673	-RRB-	-rrb-	-RRB-	_	_	_
2674	at	at	IN	_	_	_
2675	OD	od	NN	_	_	_
2676	0.4	0.4	CD	_	_	_
2677	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2678	Escherichia	escherichia	FW	Organism	_	_
2679	coli	coli	FW	Organism	_	_
2680	MG1655	mg1655	NN	_	_	_
2681	,	,	,	_	_	_
2682	90	90	CD	_	_	_
2683	min	min	NN	_	_	_
2684	recovery	recovery	NN	_	_	_
2685	in	in	IN	_	_	_
2686	10mM	10mm	NN	_	_	_
2687	Na-P	na-p	NN	_	_	_
2688	+	+	CC	_	_	_
2689	0.2	0.2	CD	_	_	_
2690	%	%	NN	_	_	_
2691	glucose	glucose	NN	SUPP	_	_
2692	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2693	Escherichia	escherichia	FW	Organism	_	_
2694	coli	coli	FW	Organism	_	_
2695	MG1655	mg1655	NN	_	_	_
2696	,	,	,	_	_	_
2697	90	90	CD	_	_	_
2698	min	min	NN	_	_	_
2699	recovery	recovery	NN	_	_	_
2700	in	in	IN	_	_	_
2701	10	10	CD	_	_	_
2702	mM	mm	NN	KWSUPP	_	_
2703	Na-P	na-p	NN	_	_	_
2704	+	+	CC	_	_	_
2705	0.2	0.2	CD	_	_	_
2706	%	%	NN	_	_	_
2707	glucose	glucose	NN	SUPP	_	_
2708	-LRB-	-lrb-	-LRB-	_	_	_
2709	pH	ph	NN	_	_	_
2710	7.5	7.5	CD	_	_	_
2711	-RRB-	-rrb-	-RRB-	_	_	_
2712	at	at	IN	_	_	_
2713	OD	od	NN	_	_	_
2714	0.4	0.4	CD	_	_	_
2715	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2716	Escherichia	escherichia	FW	Organism	_	_
2717	coli	coli	FW	Organism	_	_
2718	MG1655	mg1655	NN	_	_	_
2719	,	,	,	_	_	_
2720	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
2721	OD	OD	NNP	_	_	_
2722	~	~	SYM	_	_	_
2723	0.5	0.5	CD	_	_	_
2724	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2725	Normalized	normalize	VBN	_	_	_
2726	log	log	NN	_	_	_
2727	-LRB-	-lrb-	-LRB-	_	_	_
2728	2	2	CD	_	_	_
2729	-RRB-	-rrb-	-RRB-	_	_	_
2730	ratio	ratio	NN	_	_	_
2731	of	of	IN	_	_	_
2732	Cy5	cy5	NN	_	_	_
2733	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2734	Ecoli	ecolus	NNS	_	_	_
2735	_	_	VBP	_	_	_
2736	Sodium	sodium	NN	_	_	_
2737	Azide	azide	NN	_	_	_
2738	treatment	treatment	NN	_	_	_
2739	T1	t1	NN	_	_	_
2740	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2741	Ecoli	ecolus	NNS	_	_	_
2742	_	_	VBP	_	_	_
2743	Sodium	sodium	NN	_	_	_
2744	Azide	azide	NN	_	_	_
2745	treatment	treatment	NN	_	_	_
2746	T2	t2	NN	_	_	_
2747	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2748	Ecoli	ecolus	NNS	_	_	_
2749	_	_	VBP	_	_	_
2750	Sodium	sodium	NN	_	_	_
2751	Azide	azide	NN	_	_	_
2752	treatment	treatment	NN	_	_	_
2753	T3	t3	NN	_	_	_
2754	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2755	Ecoli	ecolus	NNS	_	_	_
2756	_	_	VBP	_	_	_
2757	Sodium	sodium	NN	_	_	_
2758	Azide	azide	NN	_	_	_
2759	treatment	treatment	NN	_	_	_
2760	T4	t4	NN	_	_	_
2761	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2762	Escherichia	escherichia	FW	Organism	_	_
2763	coli	coli	FW	Organism	_	_
2764	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2765	Escherichia	escherichia	FW	Organism	_	_
2766	coli	coli	FW	Organism	_	_
2767	W3110	w3110	NN	_	_	_
2768	,	,	,	_	_	_
2769	0	0	CD	_	_	_
2770	min	min	NN	_	_	_
2771	before	before	IN	_	_	_
2772	treatment	treatment	NN	_	_	_
2773	,	,	,	_	_	_
2774	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
2775	+	+	CC	_	_	_
2776	50	50	CD	_	_	_
2777	ug	ug	NN	_	_	_
2778	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2779	Escherichia	escherichia	FW	Organism	_	_
2780	coli	coli	FW	Organism	_	_
2781	W3110	w3110	NN	_	_	_
2782	,	,	,	_	_	_
2783	0	0	CD	_	_	_
2784	min	min	NN	_	_	_
2785	before	before	IN	_	_	_
2786	treatment	treatment	NN	_	_	_
2787	in	in	IN	_	_	_
2788	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
2789	+	+	CC	_	_	_
2790	50	50	CD	_	_	_
2791	ug	ug	NN	_	_	_
2792	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2793	Escherichia	escherichia	FW	Organism	_	_
2794	coli	coli	FW	Organism	_	_
2795	W3110	w3110	NN	_	_	_
2796	,5	,5	CD	_	_	_
2797	min	min	NN	_	_	_
2798	0.01	0.01	CD	_	_	_
2799	M	m	NN	_	_	_
2800	Sodium	sodium	NN	_	_	_
2801	Azide	azide	NN	_	_	_
2802	treatment	treatment	NN	_	_	_
2803	vs	vs	CC	_	_	_
2804	0	0	CD	_	_	_
2805	min	min	NN	_	_	_
2806	before	before	IN	_	_	_
2807	treatment	treatment	NN	_	_	_
2808	in	in	IN	_	_	_
2809	Bonner-Vogel	Bonner-Vogel	NNP	_	_	_
2810	+	+	CC	_	_	_
2811	50	50	CD	_	_	_
2812	ug	ug	NN	_	_	_
2813	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2814	Normalized	normalize	VBN	_	_	_
2815	log	log	NN	_	_	_
2816	-LRB-	-lrb-	-LRB-	_	_	_
2817	2	2	CD	_	_	_
2818	-RRB-	-rrb-	-RRB-	_	_	_
2819	ratio	ratio	NN	_	_	_
2820	of	of	IN	_	_	_
2821	Cy5	cy5	NN	_	_	_
2822	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2823	Ecoli	ecolus	NNS	_	_	_
2824	_	_	VBP	_	_	_
2825	Anaerobic	anaerobic	JJ	_	_	_
2826	growth	growth	NN	_	_	_
2827	in	in	IN	_	_	_
2828	M9	m9	NN	_	_	_
2829	+	+	CC	_	_	_
2830	glucose	glucose	NN	SUPP	_	_
2831	,	,	,	_	_	_
2832	reference	reference	NN	_	_	_
2833	Genomic	genomic	JJ	_	_	_
2834	DNA	dna	NN	_	_	_
2835	T1	t1	NN	_	_	_
2836	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2837	Ecoli	ecolus	NNS	_	_	_
2838	_	_	VBP	_	_	_
2839	Anaerobic	anaerobic	JJ	_	_	_
2840	growth	growth	NN	_	_	_
2841	in	in	IN	_	_	_
2842	M9	m9	NN	_	_	_
2843	+	+	CC	_	_	_
2844	glucose	glucose	NN	SUPP	_	_
2845	,	,	,	_	_	_
2846	reference	reference	NN	_	_	_
2847	Genomic	genomic	JJ	_	_	_
2848	DNA	dna	NN	_	_	_
2849	T2	t2	NN	_	_	_
2850	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2851	Ecoli	ecolus	NNS	_	_	_
2852	_	_	VBP	_	_	_
2853	Anaerobic	anaerobic	JJ	_	_	_
2854	growth	growth	NN	_	_	_
2855	in	in	IN	_	_	_
2856	M9	m9	NN	_	_	_
2857	+	+	CC	_	_	_
2858	glucose	glucose	NN	SUPP	_	_
2859	,	,	,	_	_	_
2860	reference	reference	NN	_	_	_
2861	Genomic	genomic	JJ	_	_	_
2862	DNA	dna	NN	_	_	_
2863	T3	t3	NN	_	_	_
2864	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2865	Ecoli	ecolus	NNS	_	_	_
2866	_	_	VBP	_	_	_
2867	Anaerobic	anaerobic	JJ	_	_	_
2868	growth	growth	NN	_	_	_
2869	in	in	IN	_	_	_
2870	M9	m9	NN	_	_	_
2871	+	+	CC	_	_	_
2872	glucose	glucose	NN	SUPP	_	_
2873	,	,	,	_	_	_
2874	reference	reference	NN	_	_	_
2875	Genomic	genomic	JJ	_	_	_
2876	DNA	dna	NN	_	_	_
2877	T4	t4	NN	_	_	_
2878	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2879	Ecoli	ecolus	NNS	_	_	_
2880	_	_	VBP	_	_	_
2881	Anaerobic	anaerobic	JJ	_	_	_
2882	growth	growth	NN	_	_	_
2883	in	in	IN	_	_	_
2884	M9	m9	NN	_	_	_
2885	+	+	CC	_	_	_
2886	glucose	glucose	NN	SUPP	_	_
2887	,	,	,	_	_	_
2888	reference	reference	NN	_	_	_
2889	Genomic	genomic	JJ	_	_	_
2890	DNA	dna	NN	_	_	_
2891	T5	t5	NN	_	_	_
2892	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2893	Ecoli	ecolus	NNS	_	_	_
2894	_	_	VBP	_	_	_
2895	Anaerobic	anaerobic	JJ	_	_	_
2896	growth	growth	NN	_	_	_
2897	in	in	IN	_	_	_
2898	M9	m9	NN	_	_	_
2899	+	+	CC	_	_	_
2900	glucose	glucose	NN	SUPP	_	_
2901	,	,	,	_	_	_
2902	reference	reference	NN	_	_	_
2903	Genomic	genomic	JJ	_	_	_
2904	DNA	dna	NN	_	_	_
2905	T6	t6	NN	_	_	_
2906	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2907	Escherichia	escherichia	FW	Organism	_	_
2908	coli	coli	FW	Organism	_	_
2909	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2910	Escherichia	escherichia	FW	Organism	_	_
2911	coli	coli	FW	Organism	_	_
2912	MG1655	mg1655	NN	_	_	_
2913	genomic	genomic	JJ	_	_	_
2914	DNA	dna	NN	_	_	_
2915	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2916	Escherichia	escherichia	FW	Organism	_	_
2917	coli	coli	FW	Organism	_	_
2918	MG1655	mg1655	NN	_	_	_
2919	,	,	,	_	_	_
2920	OD	od	NN	_	_	_
2921	0.03	0.03	CD	_	_	_
2922	,	,	,	_	_	_
2923	anaerobic	anaerobic	JJ	_	_	_
2924	growth	growth	NN	_	_	_
2925	in	in	IN	_	_	_
2926	M9	m9	NN	_	_	_
2927	+	+	CC	_	_	_
2928	glucose	glucose	NN	SUPP	_	_
2929	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2930	Escherichia	escherichia	FW	Organism	_	_
2931	coli	coli	FW	Organism	_	_
2932	MG1655	mg1655	NN	_	_	_
2933	,	,	,	_	_	_
2934	OD	od	NN	_	_	_
2935	0.2	0.2	CD	_	_	_
2936	,	,	,	_	_	_
2937	anaerobic	anaerobic	JJ	_	_	_
2938	growth	growth	NN	_	_	_
2939	in	in	IN	_	_	_
2940	M9	m9	NN	_	_	_
2941	+	+	CC	_	_	_
2942	glucose	glucose	NN	SUPP	_	_
2943	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2944	Escherichia	escherichia	FW	Organism	_	_
2945	coli	coli	FW	Organism	_	_
2946	MG1655	mg1655	NN	_	_	_
2947	,	,	,	_	_	_
2948	OD	od	NN	_	_	_
2949	0.35	0.35	CD	_	_	_
2950	,	,	,	_	_	_
2951	anaerobic	anaerobic	JJ	_	_	_
2952	growth	growth	NN	_	_	_
2953	in	in	IN	_	_	_
2954	M9	m9	NN	_	_	_
2955	+	+	CC	_	_	_
2956	glucose	glucose	NN	SUPP	_	_
2957	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2958	Escherichia	escherichia	FW	Organism	_	_
2959	coli	coli	FW	Organism	_	_
2960	MG1655	mg1655	NN	_	_	_
2961	,	,	,	_	_	_
2962	OD	od	NN	_	_	_
2963	0.6	0.6	CD	_	_	_
2964	,	,	,	_	_	_
2965	anaerobic	anaerobic	JJ	_	_	_
2966	growth	growth	NN	_	_	_
2967	in	in	IN	_	_	_
2968	M9	m9	NN	_	_	_
2969	+	+	CC	_	_	_
2970	glucose	glucose	NN	SUPP	_	_
2971	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2972	Escherichia	escherichia	FW	Organism	_	_
2973	coli	coli	FW	Organism	_	_
2974	MG1655	mg1655	NN	_	_	_
2975	,	,	,	_	_	_
2976	OD	od	NN	_	_	_
2977	0.9	0.9	CD	_	_	_
2978	,	,	,	_	_	_
2979	anaerobic	anaerobic	JJ	_	_	_
2980	growth	growth	NN	_	_	_
2981	in	in	IN	_	_	_
2982	M9	m9	NN	_	_	_
2983	+	+	CC	_	_	_
2984	glucose	glucose	NN	SUPP	_	_
2985	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2986	Escherichia	escherichia	FW	Organism	_	_
2987	coli	coli	FW	Organism	_	_
2988	MG1655	mg1655	NN	_	_	_
2989	,	,	,	_	_	_
2990	stationary	stationary	JJ	GrowthPhase	_	_
2991	phase	phase	NN	GrowthPhase	_	_
2992	anaerobic	anaerobic	JJ	_	_	_
2993	growth	growth	NN	_	_	_
2994	in	in	IN	_	_	_
2995	M9	m9	NN	_	_	_
2996	+	+	CC	_	_	_
2997	glucose	glucose	NN	SUPP	_	_
2998	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2999	Normalized	normalize	VBN	_	_	_
3000	log	log	NN	_	_	_
3001	-LRB-	-lrb-	-LRB-	_	_	_
3002	2	2	CD	_	_	_
3003	-RRB-	-rrb-	-RRB-	_	_	_
3004	ratio	ratio	NN	_	_	_
3005	of	of	IN	_	_	_
3006	Cy5	cy5	NN	_	_	_
3007	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3008	Ecoli	ecolus	NNS	_	_	_
3009	_	_	VBP	_	_	_
3010	Anaerobic	anaerobic	JJ	_	_	_
3011	growth	growth	NN	_	_	_
3012	in	in	IN	_	_	_
3013	M9	m9	NN	_	_	_
3014	+	+	CC	_	_	_
3015	glucose	glucose	NN	SUPP	_	_
3016	+	+	CC	_	_	_
3017	fumarate	fumarate	NN	SUPP	_	_
3018	,	,	,	_	_	_
3019	reference	reference	NN	_	_	_
3020	Genomic	genomic	JJ	_	_	_
3021	DNA	dna	NN	_	_	_
3022	T1	t1	NN	_	_	_
3023	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3024	Ecoli	ecolus	NNS	_	_	_
3025	_	_	VBP	_	_	_
3026	Anaerobic	anaerobic	JJ	_	_	_
3027	growth	growth	NN	_	_	_
3028	in	in	IN	_	_	_
3029	M9	m9	NN	_	_	_
3030	+	+	CC	_	_	_
3031	glucose	glucose	NN	SUPP	_	_
3032	+	+	CC	_	_	_
3033	fumarate	fumarate	NN	SUPP	_	_
3034	,	,	,	_	_	_
3035	reference	reference	NN	_	_	_
3036	Genomic	genomic	JJ	_	_	_
3037	DNA	dna	NN	_	_	_
3038	T2	t2	NN	_	_	_
3039	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3040	Ecoli	ecolus	NNS	_	_	_
3041	_	_	VBP	_	_	_
3042	Anaerobic	anaerobic	JJ	_	_	_
3043	growth	growth	NN	_	_	_
3044	in	in	IN	_	_	_
3045	M9	m9	NN	_	_	_
3046	+	+	CC	_	_	_
3047	glucose	glucose	NN	SUPP	_	_
3048	+	+	CC	_	_	_
3049	fumarate	fumarate	NN	SUPP	_	_
3050	,	,	,	_	_	_
3051	reference	reference	NN	_	_	_
3052	Genomic	genomic	JJ	_	_	_
3053	DNA	dna	NN	_	_	_
3054	T3	t3	NN	_	_	_
3055	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3056	Ecoli	ecolus	NNS	_	_	_
3057	_	_	VBP	_	_	_
3058	Anaerobic	anaerobic	JJ	_	_	_
3059	growth	growth	NN	_	_	_
3060	in	in	IN	_	_	_
3061	M9	m9	NN	_	_	_
3062	+	+	CC	_	_	_
3063	glucose	glucose	NN	SUPP	_	_
3064	+	+	CC	_	_	_
3065	fumarate	fumarate	NN	SUPP	_	_
3066	,	,	,	_	_	_
3067	reference	reference	NN	_	_	_
3068	Genomic	genomic	JJ	_	_	_
3069	DNA	dna	NN	_	_	_
3070	T4	t4	NN	_	_	_
3071	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3072	Ecoli	ecolus	NNS	_	_	_
3073	_	_	VBP	_	_	_
3074	Anaerobic	anaerobic	JJ	_	_	_
3075	growth	growth	NN	_	_	_
3076	in	in	IN	_	_	_
3077	M9	m9	NN	_	_	_
3078	+	+	CC	_	_	_
3079	glucose	glucose	NN	SUPP	_	_
3080	+	+	CC	_	_	_
3081	fumarate	fumarate	NN	SUPP	_	_
3082	,	,	,	_	_	_
3083	reference	reference	NN	_	_	_
3084	Genomic	genomic	JJ	_	_	_
3085	DNA	dna	NN	_	_	_
3086	T5	t5	NN	_	_	_
3087	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3088	Ecoli	ecolus	NNS	_	_	_
3089	_	_	VBP	_	_	_
3090	Anaerobic	anaerobic	JJ	_	_	_
3091	growth	growth	NN	_	_	_
3092	in	in	IN	_	_	_
3093	M9	m9	NN	_	_	_
3094	+	+	CC	_	_	_
3095	glucose	glucose	NN	SUPP	_	_
3096	+	+	CC	_	_	_
3097	fumarate	fumarate	NN	SUPP	_	_
3098	,	,	,	_	_	_
3099	reference	reference	NN	_	_	_
3100	Genomic	genomic	JJ	_	_	_
3101	DNA	dna	NN	_	_	_
3102	T6	t6	NN	_	_	_
3103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3104	Escherichia	escherichia	FW	Organism	_	_
3105	coli	coli	FW	Organism	_	_
3106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3107	Escherichia	escherichia	FW	Organism	_	_
3108	coli	coli	FW	Organism	_	_
3109	MG1655	mg1655	NN	_	_	_
3110	genomic	genomic	JJ	_	_	_
3111	DNA	dna	NN	_	_	_
3112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3113	Escherichia	escherichia	FW	Organism	_	_
3114	coli	coli	FW	Organism	_	_
3115	MG1655	mg1655	NN	_	_	_
3116	,	,	,	_	_	_
3117	OD	od	NN	_	_	_
3118	0.05	0.05	CD	_	_	_
3119	,	,	,	_	_	_
3120	anaerobic	anaerobic	JJ	_	_	_
3121	growth	growth	NN	_	_	_
3122	in	in	IN	_	_	_
3123	M9	m9	NN	_	_	_
3124	+	+	CC	_	_	_
3125	glucose	glucose	NN	SUPP	_	_
3126	+	+	CC	_	_	_
3127	fumarate	fumarate	NN	SUPP	_	_
3128	,	,	,	_	_	_
3129	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3130	Escherichia	escherichia	FW	Organism	_	_
3131	coli	coli	FW	Organism	_	_
3132	MG1655	mg1655	NN	_	_	_
3133	,	,	,	_	_	_
3134	OD	od	NN	_	_	_
3135	0.21	0.21	CD	_	_	_
3136	,	,	,	_	_	_
3137	anaerobic	anaerobic	JJ	_	_	_
3138	growth	growth	NN	_	_	_
3139	in	in	IN	_	_	_
3140	M9	m9	NN	_	_	_
3141	+	+	CC	_	_	_
3142	glucose	glucose	NN	SUPP	_	_
3143	+	+	CC	_	_	_
3144	fumarate	fumarate	NN	SUPP	_	_
3145	,	,	,	_	_	_
3146	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3147	Escherichia	escherichia	FW	Organism	_	_
3148	coli	coli	FW	Organism	_	_
3149	MG1655	mg1655	NN	_	_	_
3150	,	,	,	_	_	_
3151	OD	od	NN	_	_	_
3152	0.43	0.43	CD	_	_	_
3153	,	,	,	_	_	_
3154	anaerobic	anaerobic	JJ	_	_	_
3155	growth	growth	NN	_	_	_
3156	in	in	IN	_	_	_
3157	M9	m9	NN	_	_	_
3158	+	+	CC	_	_	_
3159	glucose	glucose	NN	SUPP	_	_
3160	+	+	CC	_	_	_
3161	fumarate	fumarate	NN	SUPP	_	_
3162	,	,	,	_	_	_
3163	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3164	Escherichia	escherichia	FW	Organism	_	_
3165	coli	coli	FW	Organism	_	_
3166	MG1655	mg1655	NN	_	_	_
3167	,	,	,	_	_	_
3168	OD	od	NN	_	_	_
3169	0.7	0.7	CD	_	_	_
3170	,	,	,	_	_	_
3171	anaerobic	anaerobic	JJ	_	_	_
3172	growth	growth	NN	_	_	_
3173	in	in	IN	_	_	_
3174	M9	m9	NN	_	_	_
3175	+	+	CC	_	_	_
3176	glucose	glucose	NN	SUPP	_	_
3177	+	+	CC	_	_	_
3178	fumarate	fumarate	NN	SUPP	_	_
3179	,	,	,	_	_	_
3180	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3181	Escherichia	escherichia	FW	Organism	_	_
3182	coli	coli	FW	Organism	_	_
3183	MG1655	mg1655	NN	_	_	_
3184	,	,	,	_	_	_
3185	OD	od	NN	_	_	_
3186	1.2	1.2	CD	_	_	_
3187	,	,	,	_	_	_
3188	anaerobic	anaerobic	JJ	_	_	_
3189	growth	growth	NN	_	_	_
3190	in	in	IN	_	_	_
3191	M9	m9	NN	_	_	_
3192	+	+	CC	_	_	_
3193	glucose	glucose	NN	SUPP	_	_
3194	+	+	CC	_	_	_
3195	fumarate	fumarate	NN	SUPP	_	_
3196	,	,	,	_	_	_
3197	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3198	Escherichia	escherichia	FW	Organism	_	_
3199	coli	coli	FW	Organism	_	_
3200	MG1655	mg1655	NN	_	_	_
3201	,	,	,	_	_	_
3202	stationary	stationary	JJ	GrowthPhase	_	_
3203	phase	phase	NN	GrowthPhase	_	_
3204	anaerobic	anaerobic	JJ	_	_	_
3205	growth	growth	NN	_	_	_
3206	in	in	IN	_	_	_
3207	M9	m9	NN	_	_	_
3208	+	+	CC	_	_	_
3209	glucose	glucose	NN	SUPP	_	_
3210	+	+	CC	_	_	_
3211	fumarate	fumarate	NN	SUPP	_	_
3212	,	,	,	_	_	_
3213	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3214	Normalized	normalize	VBD	_	_	_
3215	log	log	NN	_	_	_
3216	-LRB-	-lrb-	-LRB-	_	_	_
3217	2	2	CD	_	_	_
3218	-RRB-	-rrb-	-RRB-	_	_	_
3219	ratio	ratio	NN	_	_	_
3220	of	of	IN	_	_	_
3221	Cy5	cy5	NN	_	_	_
3222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3223	Ecoli	ecolus	NNS	_	_	_
3224	_	_	VBP	_	_	_
3225	Anaerobic	anaerobic	JJ	_	_	_
3226	growth	growth	NN	_	_	_
3227	in	in	IN	_	_	_
3228	M9	m9	NN	_	_	_
3229	+	+	CC	_	_	_
3230	glucose	glucose	NN	SUPP	_	_
3231	vs	vs	CC	_	_	_
3232	Aerobic	aerobic	JJ	_	_	_
3233	OD	od	NN	_	_	_
3234	0.4	0.4	CD	_	_	_
3235	T1	t1	NN	_	_	_
3236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3237	Ecoli	ecolus	NNS	_	_	_
3238	_	_	VBP	_	_	_
3239	Anaerobic	anaerobic	JJ	_	_	_
3240	growth	growth	NN	_	_	_
3241	in	in	IN	_	_	_
3242	M9	m9	NN	_	_	_
3243	+	+	CC	_	_	_
3244	glucose	glucose	NN	SUPP	_	_
3245	vs	vs	CC	_	_	_
3246	Aerobic	aerobic	JJ	_	_	_
3247	OD	od	NN	_	_	_
3248	0.4	0.4	CD	_	_	_
3249	T2	t2	NN	_	_	_
3250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3251	Ecoli	ecolus	NNS	_	_	_
3252	_	_	VBP	_	_	_
3253	Anaerobic	anaerobic	JJ	_	_	_
3254	growth	growth	NN	_	_	_
3255	in	in	IN	_	_	_
3256	M9	m9	NN	_	_	_
3257	+	+	CC	_	_	_
3258	glucose	glucose	NN	SUPP	_	_
3259	vs	vs	CC	_	_	_
3260	Aerobic	aerobic	JJ	_	_	_
3261	OD	od	NN	_	_	_
3262	0.4	0.4	CD	_	_	_
3263	T3	t3	NN	_	_	_
3264	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3265	Ecoli	ecolus	NNS	_	_	_
3266	_	_	VBP	_	_	_
3267	Anaerobic	anaerobic	JJ	_	_	_
3268	growth	growth	NN	_	_	_
3269	in	in	IN	_	_	_
3270	M9	m9	NN	_	_	_
3271	+	+	CC	_	_	_
3272	glucose	glucose	NN	SUPP	_	_
3273	vs	vs	CC	_	_	_
3274	Aerobic	aerobic	JJ	_	_	_
3275	OD	od	NN	_	_	_
3276	0.4	0.4	CD	_	_	_
3277	T4	t4	NN	_	_	_
3278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3279	Ecoli	ecolus	NNS	_	_	_
3280	_	_	VBP	_	_	_
3281	Anaerobic	anaerobic	JJ	_	_	_
3282	growth	growth	NN	_	_	_
3283	in	in	IN	_	_	_
3284	M9	m9	NN	_	_	_
3285	+	+	CC	_	_	_
3286	glucose	glucose	NN	SUPP	_	_
3287	vs	vs	CC	_	_	_
3288	Aerobic	aerobic	JJ	_	_	_
3289	OD	od	NN	_	_	_
3290	0.4	0.4	CD	_	_	_
3291	T5	t5	NN	_	_	_
3292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3293	Ecoli	ecolus	NNS	_	_	_
3294	_	_	VBP	_	_	_
3295	Anaerobic	anaerobic	JJ	_	_	_
3296	growth	growth	NN	_	_	_
3297	in	in	IN	_	_	_
3298	M9	m9	NN	_	_	_
3299	+	+	CC	_	_	_
3300	glucose	glucose	NN	SUPP	_	_
3301	vs	vs	CC	_	_	_
3302	Aerobic	aerobic	JJ	_	_	_
3303	OD	od	NN	_	_	_
3304	0.4	0.4	CD	_	_	_
3305	T6	t6	NN	_	_	_
3306	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3307	Escherichia	escherichia	FW	Organism	_	_
3308	coli	coli	FW	Organism	_	_
3309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3310	Escherichia	escherichia	FW	Organism	_	_
3311	coli	coli	FW	Organism	_	_
3312	MG1655	mg1655	NN	_	_	_
3313	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3314	Escherichia	escherichia	FW	Organism	_	_
3315	coli	coli	FW	Organism	_	_
3316	MG1655	mg1655	NN	_	_	_
3317	Aerobic	aerobic	JJ	_	_	_
3318	growth	growth	NN	_	_	_
3319	OD	od	NN	_	_	_
3320	0.4	0.4	CD	_	_	_
3321	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3322	Escherichia	escherichia	FW	Organism	_	_
3323	coli	coli	FW	Organism	_	_
3324	MG1655	mg1655	NN	_	_	_
3325	Aerobic	aerobic	JJ	_	_	_
3326	growth	growth	NN	_	_	_
3327	on	on	IN	_	_	_
3328	M9	m9	NN	_	_	_
3329	+	+	CC	_	_	_
3330	glucose	glucose	NN	SUPP	_	_
3331	,	,	,	_	_	_
3332	OD	od	NN	_	_	_
3333	0.4	0.4	CD	_	_	_
3334	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3335	Escherichia	escherichia	FW	Organism	_	_
3336	coli	coli	FW	Organism	_	_
3337	MG1655	mg1655	NN	_	_	_
3338	,	,	,	_	_	_
3339	OD	od	NN	_	_	_
3340	0.08	0.08	CD	_	_	_
3341	,	,	,	_	_	_
3342	anaerobic	anaerobic	JJ	_	_	_
3343	growth	growth	NN	_	_	_
3344	in	in	IN	_	_	_
3345	M9	m9	NN	_	_	_
3346	+	+	CC	_	_	_
3347	glucose	glucose	NN	SUPP	_	_
3348	,	,	,	_	_	_
3349	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3350	Escherichia	escherichia	FW	Organism	_	_
3351	coli	coli	FW	Organism	_	_
3352	MG1655	mg1655	NN	_	_	_
3353	,	,	,	_	_	_
3354	OD	od	NN	_	_	_
3355	0.15	0.15	CD	_	_	_
3356	,	,	,	_	_	_
3357	anaerobic	anaerobic	JJ	_	_	_
3358	growth	growth	NN	_	_	_
3359	in	in	IN	_	_	_
3360	M9	m9	NN	_	_	_
3361	+	+	CC	_	_	_
3362	glucose	glucose	NN	SUPP	_	_
3363	,	,	,	_	_	_
3364	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3365	Escherichia	escherichia	FW	Organism	_	_
3366	coli	coli	FW	Organism	_	_
3367	MG1655	mg1655	NN	_	_	_
3368	,	,	,	_	_	_
3369	OD	od	NN	_	_	_
3370	0.34	0.34	CD	_	_	_
3371	,	,	,	_	_	_
3372	anaerobic	anaerobic	JJ	_	_	_
3373	growth	growth	NN	_	_	_
3374	in	in	IN	_	_	_
3375	M9	m9	NN	_	_	_
3376	+	+	CC	_	_	_
3377	glucose	glucose	NN	SUPP	_	_
3378	,	,	,	_	_	_
3379	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3380	Escherichia	escherichia	FW	Organism	_	_
3381	coli	coli	FW	Organism	_	_
3382	MG1655	mg1655	NN	_	_	_
3383	,	,	,	_	_	_
3384	OD	od	NN	_	_	_
3385	0.73	0.73	CD	_	_	_
3386	,	,	,	_	_	_
3387	anaerobic	anaerobic	JJ	_	_	_
3388	growth	growth	NN	_	_	_
3389	in	in	IN	_	_	_
3390	M9	m9	NN	_	_	_
3391	+	+	CC	_	_	_
3392	glucose	glucose	NN	SUPP	_	_
3393	,	,	,	_	_	_
3394	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3395	Escherichia	escherichia	FW	Organism	_	_
3396	coli	coli	FW	Organism	_	_
3397	MG1655	mg1655	NN	_	_	_
3398	,	,	,	_	_	_
3399	OD	od	NN	_	_	_
3400	1.02	1.02	CD	_	_	_
3401	,	,	,	_	_	_
3402	anaerobic	anaerobic	JJ	_	_	_
3403	growth	growth	NN	_	_	_
3404	in	in	IN	_	_	_
3405	M9	m9	NN	_	_	_
3406	+	+	CC	_	_	_
3407	glucose	glucose	NN	SUPP	_	_
3408	,	,	,	_	_	_
3409	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3410	Escherichia	escherichia	FW	Organism	_	_
3411	coli	coli	FW	Organism	_	_
3412	MG1655	mg1655	NN	_	_	_
3413	,	,	,	_	_	_
3414	OD	od	NN	_	_	_
3415	1.27	1.27	CD	_	_	_
3416	anaerobic	anaerobic	JJ	_	_	_
3417	growth	growth	NN	_	_	_
3418	in	in	IN	_	_	_
3419	M9	m9	NN	_	_	_
3420	+	+	CC	_	_	_
3421	glucose	glucose	NN	SUPP	_	_
3422	,	,	,	_	_	_
3423	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3424	Normalized	normalize	VBD	_	_	_
3425	log	log	NN	_	_	_
3426	-LRB-	-lrb-	-LRB-	_	_	_
3427	2	2	CD	_	_	_
3428	-RRB-	-rrb-	-RRB-	_	_	_
3429	ratio	ratio	NN	_	_	_
3430	of	of	IN	_	_	_
3431	Cy5	cy5	NN	_	_	_
3432	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3433	Ecoli	ecolus	NNS	_	_	_
3434	_	_	VBP	_	_	_
3435	Anaerobic	anaerobic	JJ	_	_	_
3436	growth	growth	NN	_	_	_
3437	in	in	IN	_	_	_
3438	M9	m9	NN	_	_	_
3439	+	+	CC	_	_	_
3440	glucose	glucose	NN	SUPP	_	_
3441	+	+	CC	_	_	_
3442	fumarate	fumarate	NN	SUPP	_	_
3443	vs	vs	CC	_	_	_
3444	Aerobic	aerobic	JJ	_	_	_
3445	OD	od	NN	_	_	_
3446	0.4	0.4	CD	_	_	_
3447	T1	t1	NN	_	_	_
3448	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3449	Ecoli	ecolus	NNS	_	_	_
3450	_	_	VBP	_	_	_
3451	Anaerobic	anaerobic	JJ	_	_	_
3452	growth	growth	NN	_	_	_
3453	in	in	IN	_	_	_
3454	M9	m9	NN	_	_	_
3455	+	+	CC	_	_	_
3456	glucose	glucose	NN	SUPP	_	_
3457	+	+	CC	_	_	_
3458	fumarate	fumarate	NN	SUPP	_	_
3459	vs	vs	CC	_	_	_
3460	Aerobic	aerobic	JJ	_	_	_
3461	OD	od	NN	_	_	_
3462	0.4	0.4	CD	_	_	_
3463	T2	t2	NN	_	_	_
3464	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3465	Ecoli	ecolus	NNS	_	_	_
3466	_	_	VBP	_	_	_
3467	Anaerobic	anaerobic	JJ	_	_	_
3468	growth	growth	NN	_	_	_
3469	in	in	IN	_	_	_
3470	M9	m9	NN	_	_	_
3471	+	+	CC	_	_	_
3472	glucose	glucose	NN	SUPP	_	_
3473	+	+	CC	_	_	_
3474	fumarate	fumarate	NN	SUPP	_	_
3475	vs	vs	CC	_	_	_
3476	Aerobic	aerobic	JJ	_	_	_
3477	OD	od	NN	_	_	_
3478	0.4	0.4	CD	_	_	_
3479	T3	t3	NN	_	_	_
3480	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3481	Ecoli	ecolus	NNS	_	_	_
3482	_	_	VBP	_	_	_
3483	Anaerobic	anaerobic	JJ	_	_	_
3484	growth	growth	NN	_	_	_
3485	in	in	IN	_	_	_
3486	M9	m9	NN	_	_	_
3487	+	+	CC	_	_	_
3488	glucose	glucose	NN	SUPP	_	_
3489	+	+	CC	_	_	_
3490	fumarate	fumarate	NN	SUPP	_	_
3491	vs	vs	CC	_	_	_
3492	Aerobic	aerobic	JJ	_	_	_
3493	OD	od	NN	_	_	_
3494	0.4	0.4	CD	_	_	_
3495	T4	t4	NN	_	_	_
3496	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3497	Ecoli	ecolus	NNS	_	_	_
3498	_	_	VBP	_	_	_
3499	Anaerobic	anaerobic	JJ	_	_	_
3500	growth	growth	NN	_	_	_
3501	in	in	IN	_	_	_
3502	M9	m9	NN	_	_	_
3503	+	+	CC	_	_	_
3504	glucose	glucose	NN	SUPP	_	_
3505	+	+	CC	_	_	_
3506	fumarate	fumarate	NN	SUPP	_	_
3507	vs	vs	CC	_	_	_
3508	Aerobic	aerobic	JJ	_	_	_
3509	OD	od	NN	_	_	_
3510	0.4	0.4	CD	_	_	_
3511	T5	t5	NN	_	_	_
3512	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3513	Ecoli	ecolus	NNS	_	_	_
3514	_	_	VBP	_	_	_
3515	Anaerobic	anaerobic	JJ	_	_	_
3516	growth	growth	NN	_	_	_
3517	in	in	IN	_	_	_
3518	M9	m9	NN	_	_	_
3519	+	+	CC	_	_	_
3520	glucose	glucose	NN	SUPP	_	_
3521	+	+	CC	_	_	_
3522	fumarate	fumarate	NN	SUPP	_	_
3523	vs	vs	CC	_	_	_
3524	Aerobic	aerobic	JJ	_	_	_
3525	OD	od	NN	_	_	_
3526	0.4	0.4	CD	_	_	_
3527	T6	t6	NN	_	_	_
3528	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3529	Escherichia	escherichia	FW	Organism	_	_
3530	coli	coli	FW	Organism	_	_
3531	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3532	Escherichia	escherichia	FW	Organism	_	_
3533	coli	coli	FW	Organism	_	_
3534	MG1655	mg1655	NN	_	_	_
3535	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3536	Escherichia	escherichia	FW	Organism	_	_
3537	coli	coli	FW	Organism	_	_
3538	MG1655	mg1655	NN	_	_	_
3539	Aerobic	aerobic	JJ	_	_	_
3540	growth	growth	NN	_	_	_
3541	on	on	IN	_	_	_
3542	M9	m9	NN	_	_	_
3543	+	+	CC	_	_	_
3544	glucose	glucose	NN	SUPP	_	_
3545	+	+	CC	_	_	_
3546	fumarate	fumarate	NN	SUPP	_	_
3547	,	,	,	_	_	_
3548	OD	od	NN	_	_	_
3549	0.4	0.4	CD	_	_	_
3550	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3551	Escherichia	escherichia	FW	Organism	_	_
3552	coli	coli	FW	Organism	_	_
3553	MG1655	mg1655	NN	_	_	_
3554	,	,	,	_	_	_
3555	OD	od	NN	_	_	_
3556	0.15	0.15	CD	_	_	_
3557	,	,	,	_	_	_
3558	anaerobic	anaerobic	JJ	_	_	_
3559	growth	growth	NN	_	_	_
3560	in	in	IN	_	_	_
3561	M9	m9	NN	_	_	_
3562	+	+	CC	_	_	_
3563	glucose	glucose	NN	SUPP	_	_
3564	+	+	CC	_	_	_
3565	fumarate	fumarate	NN	SUPP	_	_
3566	,	,	,	_	_	_
3567	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3568	Escherichia	escherichia	FW	Organism	_	_
3569	coli	coli	FW	Organism	_	_
3570	MG1655	mg1655	NN	_	_	_
3571	,	,	,	_	_	_
3572	OD	od	NN	_	_	_
3573	0.30	0.30	CD	_	_	_
3574	,	,	,	_	_	_
3575	anaerobic	anaerobic	JJ	_	_	_
3576	growth	growth	NN	_	_	_
3577	in	in	IN	_	_	_
3578	M9	m9	NN	_	_	_
3579	+	+	CC	_	_	_
3580	glucose	glucose	NN	SUPP	_	_
3581	+	+	CC	_	_	_
3582	fumarate	fumarate	NN	SUPP	_	_
3583	,	,	,	_	_	_
3584	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3585	Escherichia	escherichia	FW	Organism	_	_
3586	coli	coli	FW	Organism	_	_
3587	MG1655	mg1655	NN	_	_	_
3588	,	,	,	_	_	_
3589	OD	od	NN	_	_	_
3590	0.63	0.63	CD	_	_	_
3591	,	,	,	_	_	_
3592	anaerobic	anaerobic	JJ	_	_	_
3593	growth	growth	NN	_	_	_
3594	in	in	IN	_	_	_
3595	M9	m9	NN	_	_	_
3596	+	+	CC	_	_	_
3597	glucose	glucose	NN	SUPP	_	_
3598	+	+	CC	_	_	_
3599	fumarate	fumarate	NN	SUPP	_	_
3600	,	,	,	_	_	_
3601	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3602	Escherichia	escherichia	FW	Organism	_	_
3603	coli	coli	FW	Organism	_	_
3604	MG1655	mg1655	NN	_	_	_
3605	,	,	,	_	_	_
3606	OD	od	NN	_	_	_
3607	0.85	0.85	CD	_	_	_
3608	,	,	,	_	_	_
3609	anaerobic	anaerobic	JJ	_	_	_
3610	growth	growth	NN	_	_	_
3611	in	in	IN	_	_	_
3612	M9	m9	NN	_	_	_
3613	+	+	CC	_	_	_
3614	glucose	glucose	NN	SUPP	_	_
3615	+	+	CC	_	_	_
3616	fumarate	fumarate	NN	SUPP	_	_
3617	,	,	,	_	_	_
3618	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3619	Escherichia	escherichia	FW	Organism	_	_
3620	coli	coli	FW	Organism	_	_
3621	MG1655	mg1655	NN	_	_	_
3622	,	,	,	_	_	_
3623	OD	od	NN	_	_	_
3624	1.07	1.07	CD	_	_	_
3625	,	,	,	_	_	_
3626	anaerobic	anaerobic	JJ	_	_	_
3627	growth	growth	NN	_	_	_
3628	in	in	IN	_	_	_
3629	M9	m9	NN	_	_	_
3630	+	+	CC	_	_	_
3631	glucose	glucose	NN	SUPP	_	_
3632	+	+	CC	_	_	_
3633	fumarate	fumarate	NN	SUPP	_	_
3634	,	,	,	_	_	_
3635	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3636	Escherichia	escherichia	FW	Organism	_	_
3637	coli	coli	FW	Organism	_	_
3638	MG1655	mg1655	NN	_	_	_
3639	,	,	,	_	_	_
3640	OD	od	NN	_	_	_
3641	1.29	1.29	CD	_	_	_
3642	anaerobic	anaerobic	JJ	_	_	_
3643	growth	growth	NN	_	_	_
3644	in	in	IN	_	_	_
3645	M9	m9	NN	_	_	_
3646	+	+	CC	_	_	_
3647	glucose	glucose	NN	SUPP	_	_
3648	+	+	CC	_	_	_
3649	fumarate	fumarate	NN	SUPP	_	_
3650	,	,	,	_	_	_
3651	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3652	Normalized	normalize	VBD	_	_	_
3653	log	log	NN	_	_	_
3654	-LRB-	-lrb-	-LRB-	_	_	_
3655	2	2	CD	_	_	_
3656	-RRB-	-rrb-	-RRB-	_	_	_
3657	ratio	ratio	NN	_	_	_
3658	of	of	IN	_	_	_
3659	Cy5	cy5	NN	_	_	_
3660	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3661	Ecoli	ecolus	NNS	_	_	_
3662	_	_	VBP	_	_	_
3663	Gamma	gamma	NN	_	_	_
3664	treatment	treatment	NN	_	_	_
3665	T1	t1	NN	_	_	_
3666	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3667	Ecoli	ecolus	NNS	_	_	_
3668	_	_	VBP	_	_	_
3669	Gamma	gamma	NN	_	_	_
3670	treatment	treatment	NN	_	_	_
3671	T2	t2	NN	_	_	_
3672	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3673	Ecoli	ecolus	NNS	_	_	_
3674	_	_	VBP	_	_	_
3675	Gamma	gamma	NN	_	_	_
3676	treatment	treatment	NN	_	_	_
3677	T3	t3	NN	_	_	_
3678	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3679	Ecoli	ecolus	NNS	_	_	_
3680	_	_	VBP	_	_	_
3681	Gamma	gamma	NN	_	_	_
3682	treatment	treatment	NN	_	_	_
3683	T4	t4	NN	_	_	_
3684	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3685	Ecoli	ecolus	NNS	_	_	_
3686	_	_	VBP	_	_	_
3687	Gamma	gamma	NN	_	_	_
3688	treatment	treatment	NN	_	_	_
3689	T5	t5	NN	_	_	_
3690	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3691	Escherichia	escherichia	FW	Organism	_	_
3692	coli	coli	FW	Organism	_	_
3693	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3694	Escherichia	escherichia	FW	Organism	_	_
3695	coli	coli	FW	Organism	_	_
3696	MG1655	mg1655	NN	_	_	_
3697	,	,	,	_	_	_
3698	0	0	CD	_	_	_
3699	min	min	NN	_	_	_
3700	before	before	IN	_	_	_
3701	treatment	treatment	NN	_	_	_
3702	,	,	,	_	_	_
3703	Davis	Davis	NNP	_	_	_
3704	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3705	Escherichia	escherichia	FW	Organism	_	_
3706	coli	coli	FW	Organism	_	_
3707	MG1655	mg1655	NN	_	_	_
3708	,	,	,	_	_	_
3709	10	10	CD	_	_	_
3710	min	min	NN	_	_	_
3711	after	after	IN	_	_	_
3712	Gamma	gamma	NN	_	_	_
3713	treatment	treatment	NN	_	_	_
3714	in	in	IN	_	_	_
3715	Davis	Davis	NNP	_	_	_
3716	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3717	Escherichia	escherichia	FW	Organism	_	_
3718	coli	coli	FW	Organism	_	_
3719	MG1655	mg1655	NN	_	_	_
3720	,	,	,	_	_	_
3721	20	20	CD	_	_	_
3722	min	min	NN	_	_	_
3723	after	after	IN	_	_	_
3724	Gamma	gamma	NN	_	_	_
3725	treatment	treatment	NN	_	_	_
3726	in	in	IN	_	_	_
3727	Davis	Davis	NNP	_	_	_
3728	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3729	Escherichia	escherichia	FW	Organism	_	_
3730	coli	coli	FW	Organism	_	_
3731	MG1655	mg1655	NN	_	_	_
3732	,	,	,	_	_	_
3733	40	40	CD	_	_	_
3734	min	min	NN	_	_	_
3735	after	after	IN	_	_	_
3736	Gamma	gamma	NN	_	_	_
3737	treatment	treatment	NN	_	_	_
3738	in	in	IN	_	_	_
3739	Davis	Davis	NNP	_	_	_
3740	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3741	Escherichia	escherichia	FW	Organism	_	_
3742	coli	coli	FW	Organism	_	_
3743	MG1655	mg1655	NN	_	_	_
3744	,	,	,	_	_	_
3745	5	5	CD	_	_	_
3746	min	min	NN	_	_	_
3747	after	after	IN	_	_	_
3748	Gamma	gamma	NN	_	_	_
3749	treatment	treatment	NN	_	_	_
3750	in	in	IN	_	_	_
3751	Davis	Davis	NNP	_	_	_
3752	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3753	Escherichia	escherichia	FW	Organism	_	_
3754	coli	coli	FW	Organism	_	_
3755	MG1655	mg1655	NN	_	_	_
3756	,	,	,	_	_	_
3757	60	60	CD	_	_	_
3758	min	min	NN	_	_	_
3759	after	after	IN	_	_	_
3760	Gamma	gamma	NN	_	_	_
3761	treatment	treatment	NN	_	_	_
3762	in	in	IN	_	_	_
3763	Davis	Davis	NNP	_	_	_
3764	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3765	Escherichia	escherichia	FW	Organism	_	_
3766	coli	coli	FW	Organism	_	_
3767	MG1655	mg1655	NN	_	_	_
3768	,	,	,	_	_	_
3769	Davis	Davis	NNP	_	_	_
3770	,	,	,	_	_	_
3771	0	0	CD	_	_	_
3772	min	min	NN	_	_	_
3773	before	before	IN	_	_	_
3774	treatment	treatment	NN	_	_	_
3775	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3776	Normalized	normalize	VBN	_	_	_
3777	log	log	NN	_	_	_
3778	-LRB-	-lrb-	-LRB-	_	_	_
3779	2	2	CD	_	_	_
3780	-RRB-	-rrb-	-RRB-	_	_	_
3781	ratio	ratio	NN	_	_	_
3782	of	of	IN	_	_	_
3783	Cy5	cy5	NN	_	_	_
3784	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3785	Ecoli	ecolus	NNS	_	_	_
3786	_	_	VBP	_	_	_
3787	Novobiocin	novobiocin	NN	_	_	_
3788	treatment	treatment	NN	_	_	_
3789	-LRB-	-lrb-	-LRB-	_	_	_
3790	200	200	CD	_	_	_
3791	ug	ug	NN	_	_	_
3792	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3793	Ecoli	Ecoli	NNP	_	_	_
3794	_	_	NNP	_	_	_
3795	Novobiocin	Novobiocin	NNP	_	_	_
3796	treatment	treatment	NN	_	_	_
3797	-LRB-	-lrb-	-LRB-	_	_	_
3798	20	20	CD	_	_	_
3799	ug	ug	NN	_	_	_
3800	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3801	Ecoli	Ecoli	NNP	_	_	_
3802	_	_	NNP	_	_	_
3803	Novobiocin	Novobiocin	NNP	_	_	_
3804	treatment	treatment	NN	_	_	_
3805	-LRB-	-lrb-	-LRB-	_	_	_
3806	50	50	CD	_	_	_
3807	ug	ug	NN	_	_	_
3808	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3809	Ecoli	Ecoli	NNP	_	_	_
3810	_	_	NNP	_	_	_
3811	Novobiocin	Novobiocin	NNP	_	_	_
3812	treatment	treatment	NN	_	_	_
3813	-LRB-	-lrb-	-LRB-	_	_	_
3814	5	5	CD	_	_	_
3815	ug	ug	NN	_	_	_
3816	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3817	Escherichia	escherichia	FW	Organism	_	_
3818	coli	coli	FW	Organism	_	_
3819	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3820	Escherichia	escherichia	FW	Organism	_	_
3821	coli	coli	FW	Organism	_	_
3822	LE234	le234	NN	_	_	_
3823	acrD	acrd	NN	GEN	_	_
3824	-	-	:	_	_	_
3825	,	,	,	_	_	_
3826	0	0	CD	_	_	_
3827	min	min	NN	_	_	_
3828	before	before	IN	_	_	_
3829	treatment	treatment	NN	_	_	_
3830	in	in	IN	_	_	_
3831	LB	LB	NNP	_	_	_
3832	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3833	Escherichia	escherichia	FW	Organism	_	_
3834	coli	coli	FW	Organism	_	_
3835	LE234	le234	NN	_	_	_
3836	acrD	acrd	NN	GEN	_	_
3837	-	-	:	_	_	_
3838	,	,	,	_	_	_
3839	5	5	CD	_	_	_
3840	min	min	NN	_	_	_
3841	after	after	IN	_	_	_
3842	Novobiocin	Novobiocin	NNP	_	_	_
3843	-LRB-	-lrb-	-LRB-	_	_	_
3844	200	200	CD	_	_	_
3845	ug	ug	NN	_	_	_
3846	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3847	Escherichia	escherichia	FW	Organism	_	_
3848	coli	coli	FW	Organism	_	_
3849	LE234	le234	NN	_	_	_
3850	acrD	acrd	NN	GEN	_	_
3851	-	-	:	_	_	_
3852	,	,	,	_	_	_
3853	5	5	CD	_	_	_
3854	min	min	NN	_	_	_
3855	after	after	IN	_	_	_
3856	Novobiocin	Novobiocin	NNP	_	_	_
3857	-LRB-	-lrb-	-LRB-	_	_	_
3858	20	20	CD	_	_	_
3859	ug	ug	NN	_	_	_
3860	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3861	Escherichia	escherichia	FW	Organism	_	_
3862	coli	coli	FW	Organism	_	_
3863	LE234	le234	NN	_	_	_
3864	acrD	acrd	NN	GEN	_	_
3865	-	-	:	_	_	_
3866	,	,	,	_	_	_
3867	5	5	CD	_	_	_
3868	min	min	NN	_	_	_
3869	after	after	IN	_	_	_
3870	Novobiocin	Novobiocin	NNP	_	_	_
3871	-LRB-	-lrb-	-LRB-	_	_	_
3872	50	50	CD	_	_	_
3873	ug	ug	NN	_	_	_
3874	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3875	Escherichia	escherichia	FW	Organism	_	_
3876	coli	coli	FW	Organism	_	_
3877	LE234	le234	NN	_	_	_
3878	acrD	acrd	NN	GEN	_	_
3879	-	-	:	_	_	_
3880	,	,	,	_	_	_
3881	5	5	CD	_	_	_
3882	min	min	NN	_	_	_
3883	after	after	IN	_	_	_
3884	Novobiocin	Novobiocin	NNP	_	_	_
3885	-LRB-	-lrb-	-LRB-	_	_	_
3886	5	5	CD	_	_	_
3887	ug	ug	NN	_	_	_
3888	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3889	Escherichia	escherichia	FW	Organism	_	_
3890	coli	coli	FW	Organism	_	_
3891	LE234	le234	NN	_	_	_
3892	acrD	acrd	NN	GEN	_	_
3893	-	-	:	_	_	_
3894	,	,	,	_	_	_
3895	LB	LB	NNP	_	_	_
3896	,	,	,	_	_	_
3897	0	0	CD	_	_	_
3898	min	min	NN	_	_	_
3899	before	before	IN	_	_	_
3900	treatment	treatment	NN	_	_	_
3901	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3902	Normalized	normalize	VBN	_	_	_
3903	log	log	NN	_	_	_
3904	-LRB-	-lrb-	-LRB-	_	_	_
3905	2	2	CD	_	_	_
3906	-RRB-	-rrb-	-RRB-	_	_	_
3907	ratio	ratio	NN	_	_	_
3908	of	of	IN	_	_	_
3909	Cy5	cy5	NN	_	_	_
3910	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3911	Ecoli	ecolus	NNS	_	_	_
3912	_	_	VBP	_	_	_
3913	pUC	puc	NN	_	_	_
3914	expression	expression	NN	_	_	_
3915	OD	od	NN	_	_	_
3916	0.2	0.2	CD	_	_	_
3917	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3918	Ecoli	Ecoli	NNP	_	_	_
3919	_	_	NNP	_	_	_
3920	pUC	puc	NN	_	_	_
3921	expression	expression	NN	_	_	_
3922	OD	od	NN	_	_	_
3923	0.5	0.5	CD	_	_	_
3924	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3925	Ecoli	Ecoli	NNP	_	_	_
3926	_	_	NNP	_	_	_
3927	pUC	puc	NN	_	_	_
3928	expression	expression	NN	_	_	_
3929	OD	od	NN	_	_	_
3930	0.9	0.9	CD	_	_	_
3931	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3932	Escherichia	escherichia	FW	Organism	_	_
3933	coli	coli	FW	Organism	_	_
3934	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3935	Escherichia	escherichia	FW	Organism	_	_
3936	coli	coli	FW	Organism	_	_
3937	DH5alpha	dh5alpha	NN	_	_	_
3938	-LRB-	-lrb-	-LRB-	_	_	_
3939	NEB	neb	NN	_	_	_
3940	-RRB-	-rrb-	-RRB-	_	_	_
3941	,	,	,	_	_	_
3942	OD	od	NN	_	_	_
3943	0.2	0.2	CD	_	_	_
3944	in	in	IN	_	_	_
3945	LB	lb	NN	_	_	_
3946	+	+	CC	_	_	_
3947	Amp	amp	NN	_	_	_
3948	,	,	,	_	_	_
3949	pUC	puc	NN	_	_	_
3950	expression	expression	NN	_	_	_
3951	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3952	Escherichia	escherichia	FW	Organism	_	_
3953	coli	coli	FW	Organism	_	_
3954	DH5alpha	dh5alpha	NN	_	_	_
3955	-LRB-	-lrb-	-LRB-	_	_	_
3956	NEB	neb	NN	_	_	_
3957	-RRB-	-rrb-	-RRB-	_	_	_
3958	,	,	,	_	_	_
3959	OD	od	NN	_	_	_
3960	0.2	0.2	CD	_	_	_
3961	in	in	IN	_	_	_
3962	LB	LB	NNP	_	_	_
3963	,	,	,	_	_	_
3964	no	no	DT	_	_	_
3965	pUC	puc	NN	_	_	_
3966	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3967	Escherichia	escherichia	FW	Organism	_	_
3968	coli	coli	FW	Organism	_	_
3969	DH5alpha	dh5alpha	NN	_	_	_
3970	-LRB-	-lrb-	-LRB-	_	_	_
3971	NEB	neb	NN	_	_	_
3972	-RRB-	-rrb-	-RRB-	_	_	_
3973	,	,	,	_	_	_
3974	OD	od	NN	_	_	_
3975	0.5	0.5	CD	_	_	_
3976	in	in	IN	_	_	_
3977	LB	lb	NN	_	_	_
3978	+	+	CC	_	_	_
3979	Amp	amp	NN	_	_	_
3980	,	,	,	_	_	_
3981	pUC	puc	NN	_	_	_
3982	expression	expression	NN	_	_	_
3983	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3984	Escherichia	escherichia	FW	Organism	_	_
3985	coli	coli	FW	Organism	_	_
3986	DH5alpha	dh5alpha	NN	_	_	_
3987	-LRB-	-lrb-	-LRB-	_	_	_
3988	NEB	neb	NN	_	_	_
3989	-RRB-	-rrb-	-RRB-	_	_	_
3990	,	,	,	_	_	_
3991	OD	od	NN	_	_	_
3992	0.5	0.5	CD	_	_	_
3993	in	in	IN	_	_	_
3994	LB	LB	NNP	_	_	_
3995	,	,	,	_	_	_
3996	no	no	DT	_	_	_
3997	pUC	puc	NN	_	_	_
3998	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3999	Escherichia	escherichia	FW	Organism	_	_
4000	coli	coli	FW	Organism	_	_
4001	DH5alpha	dh5alpha	NN	_	_	_
4002	-LRB-	-lrb-	-LRB-	_	_	_
4003	NEB	neb	NN	_	_	_
4004	-RRB-	-rrb-	-RRB-	_	_	_
4005	,	,	,	_	_	_
4006	OD	od	NN	_	_	_
4007	0.9	0.9	CD	_	_	_
4008	in	in	IN	_	_	_
4009	LB	lb	NN	_	_	_
4010	+	+	CC	_	_	_
4011	Amp	amp	NN	_	_	_
4012	,	,	,	_	_	_
4013	pUC	puc	NN	_	_	_
4014	expression	expression	NN	_	_	_
4015	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4016	Escherichia	escherichia	FW	Organism	_	_
4017	coli	coli	FW	Organism	_	_
4018	DH5alpha	dh5alpha	NN	_	_	_
4019	-LRB-	-lrb-	-LRB-	_	_	_
4020	NEB	neb	NN	_	_	_
4021	-RRB-	-rrb-	-RRB-	_	_	_
4022	,	,	,	_	_	_
4023	OD	od	NN	_	_	_
4024	0.9	0.9	CD	_	_	_
4025	in	in	IN	_	_	_
4026	LB	LB	NNP	_	_	_
4027	,	,	,	_	_	_
4028	no	no	DT	_	_	_
4029	pUC	puc	NN	_	_	_
4030	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4031	Normalized	normalize	VBN	_	_	_
4032	log	log	NN	_	_	_
4033	-LRB-	-lrb-	-LRB-	_	_	_
4034	2	2	CD	_	_	_
4035	-RRB-	-rrb-	-RRB-	_	_	_
4036	ratio	ratio	NN	_	_	_
4037	of	of	IN	_	_	_
4038	Cy5	cy5	NN	_	_	_
4039	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4040	Ecoli	ecolus	NNS	_	_	_
4041	_	_	VBP	_	_	_
4042	Stationary	stationary	JJ	_	_	_
4043	phase	phase	NN	_	_	_
4044	in	in	IN	_	_	_
4045	LB	lb	NN	_	_	_
4046	T1	t1	NN	_	_	_
4047	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4048	Ecoli	ecolus	NNS	_	_	_
4049	_	_	VBP	_	_	_
4050	Stationary	stationary	JJ	_	_	_
4051	phase	phase	NN	_	_	_
4052	in	in	IN	_	_	_
4053	LB	lb	NN	_	_	_
4054	T2	t2	NN	_	_	_
4055	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4056	Ecoli	ecolus	NNS	_	_	_
4057	_	_	VBP	_	_	_
4058	Stationary	stationary	JJ	_	_	_
4059	phase	phase	NN	_	_	_
4060	in	in	IN	_	_	_
4061	LB	lb	NN	_	_	_
4062	T3	t3	NN	_	_	_
4063	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4064	Ecoli	ecolus	NNS	_	_	_
4065	_	_	VBP	_	_	_
4066	Stationary	stationary	JJ	_	_	_
4067	phase	phase	NN	_	_	_
4068	in	in	IN	_	_	_
4069	LB	lb	NN	_	_	_
4070	T4	t4	NN	_	_	_
4071	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4072	Ecoli	ecolus	NNS	_	_	_
4073	_	_	VBP	_	_	_
4074	Stationary	stationary	JJ	_	_	_
4075	phase	phase	NN	_	_	_
4076	in	in	IN	_	_	_
4077	LB	LB	NNP	_	_	_
4078	T5	T5	NNP	_	_	_
4079	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4080	Ecoli	Ecoli	NNP	_	_	_
4081	_	_	NNP	_	_	_
4082	Stationary	Stationary	NNP	_	_	_
4083	phase	phase	NN	_	_	_
4084	in	in	IN	_	_	_
4085	LB	LB	NNP	_	_	_
4086	T6	T6	NNP	_	_	_
4087	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4088	Escherichia	escherichia	FW	Organism	_	_
4089	coli	coli	FW	Organism	_	_
4090	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4091	Escherichia	escherichia	FW	Organism	_	_
4092	coli	coli	FW	Organism	_	_
4093	MG1655	mg1655	NN	_	_	_
4094	genomic	genomic	JJ	_	_	_
4095	DNA	dna	NN	_	_	_
4096	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4097	Escherichia	escherichia	FW	Organism	_	_
4098	coli	coli	FW	Organism	_	_
4099	MG1655	mg1655	NN	_	_	_
4100	,	,	,	_	_	_
4101	Stationary	stationary	JJ	_	_	_
4102	phase	phase	NN	_	_	_
4103	in	in	IN	_	_	_
4104	LB	lb	NN	_	_	_
4105	OD	od	NN	_	_	_
4106	2.4	2.4	CD	_	_	_
4107	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4108	Escherichia	escherichia	FW	Organism	_	_
4109	coli	coli	FW	Organism	_	_
4110	MG1655	mg1655	NN	_	_	_
4111	,	,	,	_	_	_
4112	Stationary	stationary	JJ	_	_	_
4113	phase	phase	NN	_	_	_
4114	in	in	IN	_	_	_
4115	LB	lb	NN	_	_	_
4116	OD	od	NN	_	_	_
4117	2.8	2.8	CD	_	_	_
4118	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4119	Escherichia	escherichia	FW	Organism	_	_
4120	coli	coli	FW	Organism	_	_
4121	MG1655	mg1655	NN	_	_	_
4122	,	,	,	_	_	_
4123	Stationary	stationary	JJ	_	_	_
4124	phase	phase	NN	_	_	_
4125	in	in	IN	_	_	_
4126	LB	lb	NN	_	_	_
4127	OD	od	NN	_	_	_
4128	3.1	3.1	CD	_	_	_
4129	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4130	Escherichia	escherichia	FW	Organism	_	_
4131	coli	coli	FW	Organism	_	_
4132	MG1655	mg1655	NN	_	_	_
4133	,	,	,	_	_	_
4134	Stationary	stationary	JJ	_	_	_
4135	phase	phase	NN	_	_	_
4136	in	in	IN	_	_	_
4137	LB	lb	NN	_	_	_
4138	OD	od	NN	_	_	_
4139	3.1	3.1	CD	_	_	_
4140	for	for	IN	_	_	_
4141	20	20	CD	_	_	_
4142	min	min	NN	_	_	_
4143	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4144	Escherichia	escherichia	FW	Organism	_	_
4145	coli	coli	FW	Organism	_	_
4146	MG1655	mg1655	NN	_	_	_
4147	,	,	,	_	_	_
4148	Stationary	stationary	JJ	_	_	_
4149	phase	phase	NN	_	_	_
4150	in	in	IN	_	_	_
4151	LB	lb	NN	_	_	_
4152	OD	od	NN	_	_	_
4153	3.1	3.1	CD	_	_	_
4154	for	for	IN	_	_	_
4155	40	40	CD	_	_	_
4156	min	min	NN	_	_	_
4157	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4158	Escherichia	escherichia	FW	Organism	_	_
4159	coli	coli	FW	Organism	_	_
4160	MG1655	mg1655	NN	_	_	_
4161	,	,	,	_	_	_
4162	stationary	stationary	JJ	GrowthPhase	_	_
4163	phase	phase	NN	GrowthPhase	_	_
4164	in	in	IN	_	_	_
4165	LB	lb	NN	_	_	_
4166	,	,	,	_	_	_
4167	OD	od	NN	_	_	_
4168	3.1	3.1	CD	_	_	_
4169	for	for	IN	_	_	_
4170	60	60	CD	_	_	_
4171	min	min	NN	_	_	_
4172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4173	Normalized	normalize	VBN	_	_	_
4174	log	log	NN	_	_	_
4175	-LRB-	-lrb-	-LRB-	_	_	_
4176	2	2	CD	_	_	_
4177	-RRB-	-rrb-	-RRB-	_	_	_
4178	ratio	ratio	NN	_	_	_
4179	of	of	IN	_	_	_
4180	Cy5	cy5	NN	_	_	_
4181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4182	Ecoli	ecolus	NNS	_	_	_
4183	_	_	VBP	_	_	_
4184	Temperature	temperature	NN	_	_	_
4185	upshift	upshift	NN	_	_	_
4186	in	in	IN	_	_	_
4187	gyrBT	gyrBT	NNP	_	_	_
4188	mutant	mutant	JJ	_	_	_
4189	T1	t1	NN	_	_	_
4190	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4191	Ecoli	Ecoli	NNP	_	_	_
4192	_	_	NNP	_	_	_
4193	Temperature	Temperature	NNP	_	_	_
4194	upshift	upshift	NN	_	_	_
4195	in	in	IN	_	_	_
4196	gyrBT	gyrBT	NNP	_	_	_
4197	mutant	mutant	JJ	_	_	_
4198	T2	t2	NN	_	_	_
4199	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4200	Ecoli	Ecoli	NNP	_	_	_
4201	_	_	NNP	_	_	_
4202	Temperature	Temperature	NNP	_	_	_
4203	upshift	upshift	NN	_	_	_
4204	in	in	IN	_	_	_
4205	gyrBT	gyrBT	NNP	_	_	_
4206	mutant	mutant	JJ	_	_	_
4207	T3	t3	NN	_	_	_
4208	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4209	Ecoli	Ecoli	NNP	_	_	_
4210	_	_	NNP	_	_	_
4211	Temperature	Temperature	NNP	_	_	_
4212	upshift	upshift	NN	_	_	_
4213	in	in	IN	_	_	_
4214	gyrBT	gyrBT	NNP	_	_	_
4215	mutant	mutant	JJ	_	_	_
4216	T4	t4	NN	_	_	_
4217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4218	Escherichia	escherichia	FW	Organism	_	_
4219	coli	coli	FW	Organism	_	_
4220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4221	Escherichia	escherichia	FW	Organism	_	_
4222	coli	coli	FW	Organism	_	_
4223	W3110gyrb234	w3110gyrb234	NN	_	_	_
4224	,	,	,	_	_	_
4225	LB	lb	NN	_	_	_
4226	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4227	Escherichia	escherichia	FW	Organism	_	_
4228	coli	coli	FW	Organism	_	_
4229	W3110gyrb234	w3110gyrb234	NN	_	_	_
4230	,	,	,	_	_	_
4231	LB	lb	NN	_	_	_
4232	,	,	,	_	_	_
4233	10	10	CD	_	_	_
4234	min	min	NN	_	_	_
4235	after	after	IN	_	_	_
4236	upshift	upshift	NN	_	_	_
4237	to	to	TO	_	_	_
4238	42	42	CD	_	_	_
4239	C	c	NN	_	_	_
4240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4241	Escherichia	escherichia	FW	Organism	_	_
4242	coli	coli	FW	Organism	_	_
4243	W3110gyrb234	w3110gyrb234	NN	_	_	_
4244	,	,	,	_	_	_
4245	LB	lb	NN	_	_	_
4246	,	,	,	_	_	_
4247	20	20	CD	_	_	_
4248	min	min	NN	_	_	_
4249	after	after	IN	_	_	_
4250	upshift	upshift	NN	_	_	_
4251	to	to	TO	_	_	_
4252	42	42	CD	_	_	_
4253	C	c	NN	_	_	_
4254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4255	Escherichia	escherichia	FW	Organism	_	_
4256	coli	coli	FW	Organism	_	_
4257	W3110gyrb234	w3110gyrb234	NN	_	_	_
4258	,	,	,	_	_	_
4259	LB	lb	NN	_	_	_
4260	,	,	,	_	_	_
4261	2	2	CD	_	_	_
4262	min	min	NN	_	_	_
4263	after	after	IN	_	_	_
4264	upshift	upshift	NN	_	_	_
4265	to	to	TO	_	_	_
4266	42	42	CD	_	_	_
4267	C	c	NN	_	_	_
4268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4269	Escherichia	escherichia	FW	Organism	_	_
4270	coli	coli	FW	Organism	_	_
4271	W3110gyrb234	w3110gyrb234	NN	_	_	_
4272	,	,	,	_	_	_
4273	LB	lb	NN	_	_	_
4274	,	,	,	_	_	_
4275	5	5	CD	_	_	_
4276	min	min	NN	_	_	_
4277	after	after	IN	_	_	_
4278	upshift	upshift	NN	_	_	_
4279	to	to	TO	_	_	_
4280	42	42	CD	_	_	_
4281	C	c	NN	_	_	_
4282	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4283	Normalized	normalize	VBN	_	_	_
4284	log	log	NN	_	_	_
4285	-LRB-	-lrb-	-LRB-	_	_	_
4286	2	2	CD	_	_	_
4287	-RRB-	-rrb-	-RRB-	_	_	_
4288	ratio	ratio	NN	_	_	_
4289	of	of	IN	_	_	_
4290	Cy5	cy5	NN	_	_	_
4291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4292	CCCP-1	cccp-1	NN	_	_	_
4293	,	,	,	_	_	_
4294	biological	biological	JJ	_	_	_
4295	rep1	rep1	NN	_	_	_
4296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4297	CCCP-2	cccp-2	NN	_	_	_
4298	,	,	,	_	_	_
4299	biological	biological	JJ	_	_	_
4300	rep2	rep2	NN	_	_	_
4301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4302	CCCP-3	cccp-3	NN	_	_	_
4303	,	,	,	_	_	_
4304	biological	biological	JJ	_	_	_
4305	rep3	rep3	NN	_	_	_
4306	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4307	Control-1	control-1	NN	_	_	_
4308	,	,	,	_	_	_
4309	biological	biological	JJ	_	_	_
4310	rep1	rep1	NN	_	_	_
4311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4312	Control-2	control-2	NN	_	_	_
4313	,	,	,	_	_	_
4314	biological	biological	JJ	_	_	_
4315	rep2	rep2	NN	_	_	_
4316	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4317	Control-3	control-3	NN	_	_	_
4318	,	,	,	_	_	_
4319	biological	biological	JJ	_	_	_
4320	rep3	rep3	NN	_	_	_
4321	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4322	E.	e.	FW	_	_	_
4323	coli	coli	FW	_	_	_
4324	_	_	SYM	_	_	_
4325	CCCP	CCCP	NNP	_	_	_
4326	_	_	SYM	_	_	_
4327	15	15	CD	_	_	_
4328	min	min	NN	_	_	_
4329	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4330	E.	E.	NNP	_	_	_
4331	coli	coli	NN	_	_	_
4332	_	_	NN	_	_	_
4333	control	control	NN	_	_	_
4334	_	_	CD	_	_	_
4335	30	30	CD	_	_	_
4336	min	min	NN	_	_	_
4337	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4338	E.	E.	NNP	_	_	_
4339	coli	coli	NN	_	_	_
4340	_	_	NN	_	_	_
4341	gentamicin	gentamicin	NN	_	_	_
4342	_	_	CD	_	_	_
4343	30	30	CD	_	_	_
4344	min	min	NN	_	_	_
4345	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4346	E.	E.	NNP	_	_	_
4347	coli	coli	NN	_	_	_
4348	-LRB-	-lrb-	-LRB-	_	_	_
4349	OD660	od660	NN	_	_	_
4350	nm	nm	NN	_	_	_
4351	=	=	JJ	_	_	_
4352	0.3	0.3	CD	_	_	_
4353	-RRB-	-rrb-	-RRB-	_	_	_
4354	was	be	VBD	_	_	_
4355	incubated	incubate	VBN	_	_	_
4356	with	with	IN	_	_	_
4357	control	control	NN	_	_	_
4358	protein	protein	NN	_	_	_
4359	or	or	CC	_	_	_
4360	antibacterial	antibacterial	JJ	_	_	_
4361	preparations	preparation	NNS	_	_	_
4362	in	in	IN	_	_	_
4363	5	5	CD	_	_	_
4364	mM	mm	NN	KWSUPP	_	_
4365	TRIS	tris	NN	_	_	_
4366	-LRB-	-lrb-	-LRB-	_	_	_
4367	pH	ph	NN	_	_	_
4368	7.6	7.6	CD	_	_	_
4369	-RRB-	-rrb-	-RRB-	_	_	_
4370	with	with	IN	_	_	_
4371	150	150	CD	_	_	_
4372	mM	mm	NN	KWSUPP	_	_
4373	NaCl	nacl	NN	_	_	_
4374	,	,	,	_	_	_
4375	10	10	CD	_	_	_
4376	µM	µm	NN	_	_	_
4377	ZnSO4	znso4	NN	_	_	_
4378	,	,	,	_	_	_
4379	and	and	CC	_	_	_
4380	2	2	CD	_	_	_
4381	%	%	NN	_	_	_
4382	LB	lb	NN	_	_	_
4383	,	,	,	_	_	_
4384	at	at	IN	_	_	_
4385	37oC	37oc	NN	_	_	_
4386	aerobically	aerobically	RB	_	_	_
4387	with	with	IN	_	_	_
4388	shaking	shake	VBG	_	_	_
4389	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	_	_	SYM	_	_	_
5	PGRP	pgrp	SYM	_	_	_
6	_	_	SYM	_	_	_
7	30	30	CD	_	_	_
8	min	min	NN	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	E.	E.	NNP	_	_	_
11	coli	coli	NN	_	_	_
12	was	be	VBD	_	_	_
13	treated	treat	VBN	_	_	_
14	at	at	IN	_	_	_
15	37C	37c	NN	_	_	_
16	aerobically	aerobically	RB	_	_	_
17	with	with	IN	_	_	_
18	shaking	shake	VBG	_	_	_
19	with	with	IN	_	_	_
20	BSA	bsa	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	control	control	NN	_	_	_
23	,	,	,	_	_	_
24	100	100	CD	_	_	_
25	µg	µg	NN	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	Escherichia	escherichia	FW	Organism	_	_
28	coli	coli	FW	Organism	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Gentamicin-1	gentamicin-1	NN	_	_	_
31	,	,	,	_	_	_
32	biological	biological	JJ	_	_	_
33	rep1	rep1	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	Gentamicin-2	gentamicin-2	NN	_	_	_
36	,	,	,	_	_	_
37	biological	biological	JJ	_	_	_
38	rep2	rep2	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Gentamicin-3	gentamicin-3	NN	_	_	_
41	,	,	,	_	_	_
42	biological	biological	JJ	_	_	_
43	rep3	rep3	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	growth	growth	NN	_	_	_
46	phase	phase	NN	_	_	_
47	:	:	:	_	_	_
48	logarithmic	logarithmic	JJ	_	_	_
49	growth	growth	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	PGRP-1	pgrp-1	NN	_	_	_
52	,	,	,	_	_	_
53	biological	biological	JJ	_	_	_
54	rep1	rep1	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	PGRP-2	pgrp-2	NN	_	_	_
57	,	,	,	_	_	_
58	biological	biological	JJ	_	_	_
59	rep2	rep2	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	PGRP-3	pgrp-3	NN	_	_	_
62	,	,	,	_	_	_
63	biological	biological	JJ	_	_	_
64	rep3	rep3	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	RNA	rna	NN	_	_	_
67	was	be	VBD	_	_	_
68	obtained	obtain	VBN	_	_	_
69	from	from	IN	_	_	_
70	each	each	DT	_	_	_
71	culture	culture	NN	_	_	_
72	using	use	VBG	_	_	_
73	Ambion	Ambion	NNP	_	_	_
74	RiboPureTM-bacteria	RiboPureTM-bacteria	NNP	_	_	_
75	RNA	rna	NN	_	_	_
76	extraction	extraction	NN	_	_	_
77	kit	kit	NN	_	_	_
78	according	accord	VBG	_	_	_
79	to	to	TO	_	_	_
80	the	the	DT	_	_	_
81	manufacturer	manufacturer	NN	_	_	_
82	's	's	POS	_	_	_
83	instructions	instruction	NNS	_	_	_
84	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Signal	signal	NN	_	_	_
3	intensities	intensity	NNS	_	_	_
4	with	with	IN	_	_	_
5	all	all	DT	_	_	_
6	probes	probe	NNS	_	_	_
7	are	be	VBP	_	_	_
8	shown	show	VBN	_	_	_
9	in	in	IN	_	_	_
10	Sample	Sample	NNP	_	_	_
11	data	datum	NNS	_	_	_
12	table	table	NN	_	_	_
13	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	`	`	``	_	_	_
3	expressed_present_probes.txt	expressed_present_probes.txt	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	available	available	JJ	_	_	_
6	on	on	IN	_	_	_
7	Series	Series	NNP	_	_	_
8	records	record	NNS	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	contains	contain	VBZ	_	_	_
11	Signal	signal	NN	_	_	_
12	intensities	intensity	NNS	_	_	_
13	with	with	IN	_	_	_
14	present	present	JJ	_	_	_
15	probes	probe	NNS	_	_	_
16	.	.	.	_	_	_

1	Average	average	JJ	_	_	_
2	signal	signal	NN	_	_	_
3	intensities	intensity	NNS	_	_	_
4	from	from	IN	_	_	_
5	3	3	CD	_	_	_
6	experiments	experiment	NNS	_	_	_
7	were	be	VBD	_	_	_
8	used	use	VBN	_	_	_
9	to	to	TO	_	_	_
10	calculate	calculate	VB	_	_	_
11	fold	fold	JJ	_	_	_
12	increases	increase	NNS	_	_	_
13	in	in	IN	_	_	_
14	gene	gene	NN	_	_	_
15	expression	expression	NN	_	_	_
16	between	between	IN	_	_	_
17	treated	treated	JJ	_	_	_
18	and	and	CC	_	_	_
19	control	control	JJ	_	_	_
20	groups	group	NNS	_	_	_
21	,	,	,	_	_	_
22	with	with	IN	_	_	_
23	signal	signal	NN	_	_	_
24	intensity	intensity	NN	_	_	_
25	of	of	IN	_	_	_
26	39	39	CD	_	_	_
27	used	use	VBN	_	_	_
28	as	as	IN	_	_	_
29	a	a	DT	_	_	_
30	minimum	minimum	JJ	_	_	_
31	intensity	intensity	NN	_	_	_
32	,	,	,	_	_	_
33	using	use	VBG	_	_	_
34	the	the	DT	_	_	_
35	formula	formula	NN	_	_	_
36	:	:	:	_	_	_
37	average	average	JJ	_	_	_
38	intensity	intensity	NN	_	_	_
39	in	in	IN	_	_	_
40	treated	treated	JJ	_	_	_
41	group	group	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	strain	strain	NN	_	_	_
44	:	:	:	_	_	_
45	K-12	k-12	NN	_	_	_
46	substrain	substrain	NN	_	_	_
47	MG1655	mg1655	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
49	The	the	DT	_	_	_
50	hybridization	hybridization	NN	_	_	_
51	intensity	intensity	NN	_	_	_
52	data	datum	NNS	_	_	_
53	signals	signal	NNS	_	_	_
54	were	be	VBD	_	_	_
55	analyzed	analyze	VBN	_	_	_
56	,	,	,	_	_	_
57	normalized	normalize	VBD	_	_	_
58	,	,	,	_	_	_
59	and	and	CC	_	_	_
60	corrected	correct	VBN	_	_	_
61	for	for	IN	_	_	_
62	batch	batch	NN	_	_	_
63	effect	effect	NN	_	_	_
64	using	use	VBG	_	_	_
65	Affymetrix	Affymetrix	NNP	_	_	_
66	GeneChip	GeneChip	NNP	_	_	_
67	®	®	NNP	_	_	_
68	Command	command	NN	_	_	_
69	Console	Console	NNP	_	_	_
70	®	®	NNP	_	_	_
71	Software	Software	NNP	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	AGCC	AGCC	NNP	_	_	_
74	v.	v.	CC	_	_	_
75	3.0	3.0	CD	_	_	_
76	-RRB-	-rrb-	-RRB-	_	_	_
77	.	.	.	_	_	_

1	Signal	signal	NN	_	_	_
2	average	average	NN	_	_	_
3	,	,	,	_	_	_
4	noise	noise	NN	_	_	_
5	average	average	NN	_	_	_
6	,	,	,	_	_	_
7	scaling	scaling	NN	_	_	_
8	factor	factor	NN	_	_	_
9	,	,	,	_	_	_
10	%	%	NN	_	_	_
11	present	present	JJ	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	%	%	NN	_	_	_
15	absent	absent	JJ	_	_	_
16	were	be	VBD	_	_	_
17	calculated	calculate	VBN	_	_	_
18	for	for	IN	_	_	_
19	each	each	DT	_	_	_
20	probe	probe	NN	_	_	_
21	,	,	,	_	_	_
22	from	from	IN	_	_	_
23	which	which	WDT	_	_	_
24	the	the	DT	_	_	_
25	signal	signal	NN	_	_	_
26	intensity	intensity	NN	_	_	_
27	of	of	IN	_	_	_
28	>	>	JJR	_	_	_
29	39	39	CD	_	_	_
30	was	be	VBD	_	_	_
31	calculated	calculate	VBN	_	_	_
32	as	as	IN	_	_	_
33	reliable	reliable	JJ	_	_	_
34	expression	expression	NN	_	_	_
35	.	.	.	_	_	_

1	Using	use	VBG	_	_	_
2	this	this	DT	_	_	_
3	cutoff	cutoff	NN	_	_	_
4	,	,	,	_	_	_
5	5531	5531	CD	_	_	_
6	probes	probe	NNS	_	_	_
7	were	be	VBD	_	_	_
8	classified	classify	VBN	_	_	_
9	as	as	IN	_	_	_
10	present	present	JJ	_	_	_
11	out	out	IN	_	_	_
12	of	of	IN	_	_	_
13	total	total	JJ	_	_	_
14	10208	10208	CD	_	_	_
15	probes	probe	NNS	_	_	_
16	on	on	IN	_	_	_
17	the	the	DT	_	_	_
18	array	array	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	full_expressed_data.txt	full_expressed_data.txt	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	tissue	tissue	NN	_	_	_
3	:	:	:	_	_	_
4	entire	entire	JJ	_	_	_
5	bacterial	bacterial	JJ	_	_	_
6	cell	cell	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	treated	treat	VBN	_	_	_
9	with	with	IN	_	_	_
10	:	:	:	_	_	_
11	100	100	CD	_	_	_
12	µg	µg	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	treated	treat	VBN	_	_	_
15	with	with	IN	_	_	_
16	:	:	:	_	_	_
17	5	5	CD	_	_	_
18	µg	µg	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	treated	treat	VBN	_	_	_
21	with	with	IN	_	_	_
22	:	:	:	_	_	_
23	800	800	CD	_	_	_
24	µM	µm	NN	_	_	_
25	CCCP	cccp	NN	_	_	_
26	for	for	IN	_	_	_
27	15	15	CD	_	_	_
28	min	min	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	BWG	bwg	NN	_	_	_
31	_	_	CD	_	_	_
32	butanol	butanol	NN	_	_	_
33	_	_	CD	_	_	_
34	3passages	3passage	NNS	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	BWG	bwg	NN	_	_	_
37	_	_	NN	_	_	_
38	replicated	replicate	VBN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	BWY	bwy	NN	_	_	_
41	_	_	NN	_	_	_
42	butanol	butanol	NN	_	_	_
43	_	_	CD	_	_	_
44	3passages	3passage	NNS	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	BWY	bwy	NN	_	_	_
47	_	_	NN	_	_	_
48	replicated	replicate	VBD	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	Data	Data	NNP	_	_	_
51	were	be	VBD	_	_	_
52	extracted	extract	VBN	_	_	_
53	in	in	IN	_	_	_
54	GenePix	GenePix	NNP	_	_	_
55	4100A	4100a	CD	_	_	_
56	scanning	scanning	NN	_	_	_
57	software	software	NN	_	_	_
58	and	and	CC	_	_	_
59	normalized	normalize	VBD	_	_	_
60	using	use	VBG	_	_	_
61	the	the	DT	_	_	_
62	lowess	lowess	NN	_	_	_
63	method	method	NN	_	_	_
64	implemented	implement	VBN	_	_	_
65	in	in	IN	_	_	_
66	TM4	tm4	NN	_	_	_
67	MIDAS	MIDAS	NNP	_	_	_
68	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
69	Donor	Donor	NNP	_	_	_
70	was	be	VBD	_	_	_
71	transformed	transform	VBN	_	_	_
72	with	with	IN	_	_	_
73	a	a	DT	_	_	_
74	random	random	JJ	_	_	_
75	genomic	genomic	JJ	_	_	_
76	library	library	NN	_	_	_
77	made	make	VBN	_	_	_
78	from	from	IN	_	_	_
79	E.	e.	FW	_	_	_
80	coli	coli	FW	_	_	_
81	and	and	CC	_	_	_
82	stored	store	VBN	_	_	_
83	as	as	IN	_	_	_
84	glycerol	glycerol	NN	SUPP	_	_
85	stocks	stock	NNS	_	_	_
86	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	library	library	NN	_	_	_
3	was	be	VBD	_	_	_
4	revived	revive	VBN	_	_	_
5	and	and	CC	_	_	_
6	transferred	transfer	VBN	_	_	_
7	to	to	TO	_	_	_
8	four	four	CD	_	_	_
9	recipient	recipient	JJ	_	_	_
10	strains	strain	NNS	_	_	_
11	using	use	VBG	_	_	_
12	conjugation	conjugation	NN	_	_	_
13	;	;	:	_	_	_
14	the	the	DT	_	_	_
15	donor	donor	NN	_	_	_
16	was	be	VBD	_	_	_
17	miniprepped	miniprepp	VBN	_	_	_
18	at	at	IN	_	_	_
19	this	this	DT	_	_	_
20	time	time	NN	_	_	_
21	,	,	,	_	_	_
22	and	and	CC	_	_	_
23	the	the	DT	_	_	_
24	recipients	recipient	NNS	_	_	_
25	were	be	VBD	_	_	_
26	miniprepped	miniprepp	VBN	_	_	_
27	after	after	IN	_	_	_
28	outgrowth	outgrowth	NN	_	_	_
29	under	under	IN	_	_	_
30	dual	dual	JJ	_	_	_
31	selection	selection	NN	_	_	_
32	.	.	.	_	_	_

1	Two	two	CD	_	_	_
2	recipient	recipient	JJ	_	_	_
3	libraries	library	NNS	_	_	_
4	in	in	IN	_	_	_
5	BWG	bwg	NN	_	_	_
6	and	and	CC	_	_	_
7	BWY	bwy	NN	_	_	_
8	were	be	VBD	_	_	_
9	propagated	propagate	VBN	_	_	_
10	under	under	IN	_	_	_
11	n-butanol	n-butanol	JJ	_	_	_
12	stress	stress	NN	_	_	_
13	for	for	IN	_	_	_
14	three	three	CD	_	_	_
15	days	day	NNS	_	_	_
16	,	,	,	_	_	_
17	and	and	CC	_	_	_
18	then	then	RB	_	_	_
19	miniprepped	miniprepp	VBD	_	_	_
20	as	as	RB	_	_	_
21	well	well	RB	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Escherichia	escherichia	FW	Organism	_	_
6	coli	coli	FW	Organism	_	_
7	BW25113	bw25113	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Library	Library	NNP	_	_	_
10	minipreps	miniprep	NNS	_	_	_
11	were	be	VBD	_	_	_
12	performed	perform	VBN	_	_	_
13	with	with	IN	_	_	_
14	the	the	DT	_	_	_
15	Zyppy	Zyppy	NNP	_	_	_
16	Miniprep	Miniprep	NNP	_	_	_
17	kit	kit	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Zymo	Zymo	NNP	_	_	_
20	Technologies	Technologies	NNPS	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	and	and	CC	_	_	_
23	quantified	quantify	VBN	_	_	_
24	using	use	VBG	_	_	_
25	the	the	DT	_	_	_
26	Qubit	Qubit	NNP	_	_	_
27	dsDNA	dsDNA	NNP	_	_	_
28	BR	BR	NNP	_	_	_
29	kit	kit	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Invitrogen	invitrogen	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	and	and	CC	_	_	_
34	the	the	DT	_	_	_
35	Nanodrop	Nanodrop	NNP	_	_	_
36	spectrophotometer	spectrophotometer	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Thermo	Thermo	NNP	_	_	_
39	Scientific	Scientific	NNP	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	MG6	mg6	NN	_	_	_
43	_	_	NN	_	_	_
44	replicated	replicate	VBN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	MY4	my4	NN	_	_	_
47	_	_	NN	_	_	_
48	replicated	replicate	VBN	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	Plasmid	plasmid	NN	_	_	_
51	DNA	dna	NN	_	_	_
52	,	,	,	_	_	_
53	after	after	IN	_	_	_
54	n-butanol	n-butanol	NN	_	_	_
55	selection	selection	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	Plasmid	plasmid	NN	_	_	_
58	DNA	dna	NN	_	_	_
59	,	,	,	_	_	_
60	BWG	BWG	NNP	_	_	_
61	post	post	NN	_	_	_
62	conjugation	conjugation	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	Plasmid	plasmid	NN	_	_	_
65	DNA	dna	NN	_	_	_
66	,	,	,	_	_	_
67	BWY	BWY	NNP	_	_	_
68	post	post	NN	_	_	_
69	conjugation	conjugation	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	Plasmid	plasmid	NN	_	_	_
72	DNA	dna	NN	_	_	_
73	,	,	,	_	_	_
74	donor	donor	NN	_	_	_
75	,	,	,	_	_	_
76	XL1-Blue	xl1-blue	JJ	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
78	Plasmid	plasmid	NN	_	_	_
79	DNA	dna	NN	_	_	_
80	,	,	,	_	_	_
81	post	post	NN	_	_	_
82	conjugation	conjugation	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	plasmid	plasmid	NN	_	_	_
85	:	:	:	_	_	_
86	Donor	Donor	NNP	_	_	_
87	Library	Library	NNP	_	_	_
88	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
89	plasmid	plasmid	NN	_	_	_
90	:	:	:	_	_	_
91	Initial	initial	JJ	_	_	_
92	Recipient	Recipient	NNP	_	_	_
93	Library	Library	NNP	_	_	_
94	-LRB-	-lrb-	-LRB-	_	_	_
95	BWG	BWG	NNP	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	plasmid	plasmid	NN	_	_	_
99	:	:	:	_	_	_
100	Initial	initial	JJ	_	_	_
101	Recipient	Recipient	NNP	_	_	_
102	Library	Library	NNP	_	_	_
103	-LRB-	-lrb-	-LRB-	_	_	_
104	BWY	BWY	NNP	_	_	_
105	-RRB-	-rrb-	-RRB-	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	plasmid	plasmid	NN	_	_	_
108	source	source	NN	_	_	_
109	:	:	:	_	_	_
110	Initial	initial	JJ	_	_	_
111	Recipient	Recipient	NNP	_	_	_
112	Library	Library	NNP	_	_	_
113	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
114	plasmid	plasmid	NN	_	_	_
115	source	source	NN	_	_	_
116	:	:	:	_	_	_
117	Post	Post	NNP	_	_	_
118	Selection	selection	NN	_	_	_
119	Library	Library	NNP	_	_	_
120	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
121	cell	cell	NN	_	_	_
122	type	type	NN	_	_	_
123	:	:	:	_	_	_
124	Persister	persister	NN	_	_	_
125	cells	cell	NNS	_	_	_
126	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
127	Escherichia	escherichia	FW	Organism	_	_
128	coli	coli	FW	Organism	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	furanone-free	furanone-free	JJ	_	_	_
131	control	control	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
133	GeneChip	GeneChip	NNP	_	_	_
134	Operating	Operating	NNP	_	_	_
135	Software	Software	NNP	_	_	_
136	-LRB-	-lrb-	-LRB-	_	_	_
137	MAS	MAS	NNP	_	_	_
138	5.0	5.0	CD	_	_	_
139	-RRB-	-rrb-	-RRB-	_	_	_
140	using	use	VBG	_	_	_
141	Affymetrix	Affymetrix	NNP	_	_	_
142	default	default	NN	_	_	_
143	analysis	analysis	NN	_	_	_
144	settings	setting	NNS	_	_	_
145	and	and	CC	_	_	_
146	global	global	JJ	_	_	_
147	scaling	scaling	NN	_	_	_
148	as	as	IN	_	_	_
149	normalization	normalization	NN	_	_	_
150	method	method	NN	_	_	_
151	,	,	,	_	_	_
152	genes	gene	NNS	_	_	_
153	with	with	IN	_	_	_
154	a	a	DT	_	_	_
155	p-value	p-value	NN	_	_	_
156	of	of	IN	_	_	_
157	less	less	JJR	_	_	_
158	than	than	IN	_	_	_
159	0.0025	0.0025	CD	_	_	_
160	or	or	CC	_	_	_
161	greater	greater	JJR	_	_	_
162	than	than	IN	_	_	_
163	0.9975	0.9975	CD	_	_	_
164	were	be	VBD	_	_	_
165	considered	consider	VBN	_	_	_
166	statistically	statistically	RB	_	_	_
167	significant	significant	JJ	_	_	_
168	based	base	VBN	_	_	_
169	on	on	IN	_	_	_
170	Wilcoxon	Wilcoxon	NNP	_	_	_
171	signed	sign	VBD	_	_	_
172	rank	rank	JJ	_	_	_
173	test	test	NN	_	_	_
174	and	and	CC	_	_	_
175	Tukey	tukey	NN	_	_	_
176	Byweight	byweight	NN	_	_	_
177	,	,	,	_	_	_
178	labeled	label	VBN	_	_	_
179	as	as	IN	_	_	_
180	I	I	PRP	_	_	_
181	and	and	CC	_	_	_
182	D	d	NN	_	_	_
183	in	in	IN	_	_	_
184	the	the	DT	_	_	_
185	attached	attach	VBN	_	_	_
186	txt	txt	NN	_	_	_
187	file	file	NN	_	_	_
188	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	ensure	ensure	VB	_	_	_
3	the	the	DT	_	_	_
4	significance	significance	NN	_	_	_
5	of	of	IN	_	_	_
6	microarray	microarray	NN	_	_	_
7	data	datum	NNS	_	_	_
8	,	,	,	_	_	_
9	an	a	DT	_	_	_
10	additional	additional	JJ	_	_	_
11	criterion	criterion	NN	_	_	_
12	was	be	VBD	_	_	_
13	applied	apply	VBN	_	_	_
14	to	to	TO	_	_	_
15	only	only	RB	_	_	_
16	select	select	VB	_	_	_
17	the	the	DT	_	_	_
18	genes	gene	NNS	_	_	_
19	with	with	IN	_	_	_
20	an	a	DT	_	_	_
21	expression	expression	NN	_	_	_
22	ratio	ratio	NN	_	_	_
23	of	of	IN	_	_	_
24	2	2	CD	_	_	_
25	or	or	CC	_	_	_
26	high	high	JJ	_	_	_
27	from	from	IN	_	_	_
28	this	this	DT	_	_	_
29	group	group	NN	_	_	_
30	as	as	IN	_	_	_
31	induced	induce	VBN	_	_	_
32	and	and	CC	_	_	_
33	repressed	repress	VBN	_	_	_
34	genes	gene	NNS	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNeasy	rneasy	NN	_	_	_
3	Mini	Mini	NNP	_	_	_
4	Kit	kit	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	Qiagen	Qiagen	NNP	_	_	_
7	,	,	,	_	_	_
8	Austin	Austin	NNP	_	_	_
9	,	,	,	_	_	_
10	TX	TX	NNP	_	_	_
11	,	,	,	_	_	_
12	USA	USA	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	with	with	IN	_	_	_
15	on-column	on-column	JJ	_	_	_
16	DNase	dnase	NN	_	_	_
17	treatment	treatment	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	RNase-Free	rnase-free	JJ	_	_	_
20	DNase	dnase	NN	_	_	_
21	Set	set	VB	_	_	_
22	,	,	,	_	_	_
23	Qiagen	Qiagen	NNP	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RP437	rp437	NN	_	_	_
3	persisters	persister	NNS	_	_	_
4	treated	treat	VBN	_	_	_
5	with	with	IN	_	_	_
6	BF8	bf8	NN	_	_	_
7	at	at	IN	_	_	_
8	5	5	CD	_	_	_
9	µg	µg	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	RP437	rp437	NN	_	_	_
12	was	be	VBD	_	_	_
13	inoculated	inoculate	VBN	_	_	_
14	in	in	IN	_	_	_
15	100	100	CD	_	_	_
16	mL	ml	NN	_	_	_
17	LB	lb	NN	_	_	_
18	and	and	CC	_	_	_
19	grown	grow	VBN	_	_	_
20	for	for	IN	_	_	_
21	18	18	CD	_	_	_
22	h	h	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	200	200	CD	_	_	_
25	rpm	rpm	NN	_	_	_
26	,	,	,	_	_	_
27	37oC	37oc	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	Persister	persister	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	by	by	IN	_	_	_
6	lysing	lyse	VBG	_	_	_
7	the	the	DT	_	_	_
8	normal	normal	JJ	_	_	_
9	cells	cell	NNS	_	_	_
10	with	with	IN	_	_	_
11	5	5	CD	_	_	_
12	µg	µg	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	strain	strain	NN	_	_	_
15	:	:	:	_	_	_
16	E.	e.	FW	_	_	_
17	coli	coli	FW	_	_	_
18	RP437	rp437	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	The	the	DT	_	_	_
21	isolated	isolate	VBN	_	_	_
22	persisters	persister	NNS	_	_	_
23	were	be	VBD	_	_	_
24	incubated	incubate	VBN	_	_	_
25	in	in	IN	_	_	_
26	0.85	0.85	CD	_	_	_
27	%	%	NN	_	_	_
28	NaCl	nacl	NN	_	_	_
29	solution	solution	NN	_	_	_
30	for	for	IN	_	_	_
31	1	1	CD	_	_	_
32	h	h	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	200	200	CD	_	_	_
35	rpm	rpm	NN	_	_	_
36	,	,	,	_	_	_
37	37oC	37oc	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	with	with	IN	_	_	_
40	or	or	CC	_	_	_
41	without	without	IN	_	_	_
42	5	5	CD	_	_	_
43	µg	µg	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	Cells	cell	NNS	_	_	_
46	of	of	IN	_	_	_
47	each	each	DT	_	_	_
48	evolved	evolve	VBD	_	_	_
49	colony	colony	NN	_	_	_
50	type	type	NN	_	_	_
51	were	be	VBD	_	_	_
52	collected	collect	VBN	_	_	_
53	by	by	IN	_	_	_
54	centrifugation	centrifugation	NN	_	_	_
55	at	at	IN	_	_	_
56	13,000	13,000	CD	_	_	_
57	×	×	CD	_	_	_
58	g	g	NN	_	_	_
59	for	for	IN	_	_	_
60	1	1	CD	_	_	_
61	min	min	NN	_	_	_
62	at	at	IN	_	_	_
63	4	4	CD	_	_	_
64	°C	°c	NN	_	_	_
65	and	and	CC	_	_	_
66	were	be	VBD	_	_	_
67	immediately	immediately	RB	_	_	_
68	used	use	VBN	_	_	_
69	for	for	IN	_	_	_
70	total	total	JJ	_	_	_
71	RNA	rna	NN	_	_	_
72	isolation	isolation	NN	_	_	_
73	with	with	IN	_	_	_
74	NucleoSpin	nucleospin	NN	_	_	_
75	RNA	rna	NN	_	_	_
76	II	ii	CD	_	_	_
77	isolation	isolation	NN	_	_	_
78	kit	kit	NN	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	Macherey	macherey	NN	_	_	_
81	--	--	:	_	_	_
82	Nagel	Nagel	NNP	_	_	_
83	,	,	,	_	_	_
84	Biokè	Biokè	NNP	_	_	_
85	,	,	,	_	_	_
86	Leiden	Leiden	NNP	_	_	_
87	,	,	,	_	_	_
88	the	the	DT	_	_	_
89	Netherlands	Netherlands	NNP	_	_	_
90	-RRB-	-rrb-	-RRB-	_	_	_
91	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2	culture	culture	NN	_	_	_
3	type	type	NN	_	_	_
4	:	:	:	_	_	_
5	Ancestor	Ancestor	NNP	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	culture	culture	NN	_	_	_
8	type	type	NN	_	_	_
9	:	:	:	_	_	_
10	evolved	evolve	VBD	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	Escherichia	escherichia	FW	Organism	_	_
13	coli	coli	FW	Organism	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Growth	growth	NN	_	_	_
16	curves	curve	NNS	_	_	_
17	of	of	IN	_	_	_
18	all	all	DT	_	_	_
19	selected	select	VBN	_	_	_
20	evolved	evolve	VBD	_	_	_
21	colony	colony	NN	_	_	_
22	types	type	NNS	_	_	_
23	and	and	CC	_	_	_
24	the	the	DT	_	_	_
25	ancestor	ancestor	NN	_	_	_
26	were	be	VBD	_	_	_
27	obtained	obtain	VBN	_	_	_
28	by	by	IN	_	_	_
29	growing	grow	VBG	_	_	_
30	them	they	PRP	_	_	_
31	under	under	IN	_	_	_
32	their	they	PRP$	_	_	_
33	evolved	evolve	VBN	_	_	_
34	environmental	environmental	JJ	_	_	_
35	conditions	condition	NNS	_	_	_
36	in	in	IN	_	_	_
37	LB	lb	NN	MED	_	_
38	medium	medium	NN	MED	_	_
39	until	until	IN	_	_	_
40	Log-phase	log-phase	NN	_	_	_
41	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	this	this	DT	_	_	_
3	,	,	,	_	_	_
4	optical	optical	JJ	_	_	_
5	density	density	NN	_	_	_
6	was	be	VBD	_	_	_
7	recorded	record	VBN	_	_	_
8	at	at	IN	_	_	_
9	600nm	600nm	CD	_	_	_
10	at	at	IN	_	_	_
11	a	a	DT	_	_	_
12	value	value	NN	_	_	_
13	of	of	IN	_	_	_
14	0.6	0.6	CD	_	_	_
15	to	to	TO	_	_	_
16	0.7	0.7	CD	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	morphology	morphology	NN	_	_	_
3	:	:	:	_	_	_
4	a	a	DT	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	morphology	morphology	NN	_	_	_
7	:	:	:	_	_	_
8	b	b	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	morphology	morphology	NN	_	_	_
11	:	:	:	_	_	_
12	c	c	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	oxygen	oxygen	NN	_	_	_
15	regime	regime	NN	_	_	_
16	:	:	:	_	_	_
17	daily	daily	JJ	_	_	_
18	shift	shift	NN	_	_	_
19	between	between	IN	_	_	_
20	shaking	shake	VBG	_	_	_
21	and	and	CC	_	_	_
22	static	static	JJ	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	no	no	DT	_	_	_
25	shaking	shake	VBG	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	conditions	condition	NNS	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
29	oxygen	oxygen	NN	_	_	_
30	regime	regime	NN	_	_	_
31	:	:	:	_	_	_
32	transfers	transfer	NNS	_	_	_
33	in	in	IN	_	_	_
34	constant	constant	JJ	_	_	_
35	static	static	JJ	_	_	_
36	conditions	condition	NNS	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
38	oxygen	oxygen	NN	_	_	_
39	regime	regime	NN	_	_	_
40	:	:	:	_	_	_
41	transfers	transfer	NNS	_	_	_
42	under	under	IN	_	_	_
43	constant	constant	JJ	_	_	_
44	shaking	shake	VBG	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	200rpm	200rpm	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	population	population	NN	_	_	_
50	:	:	:	_	_	_
51	1	1	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	population	population	NN	_	_	_
54	:	:	:	_	_	_
55	2	2	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
57	population	population	NN	_	_	_
58	:	:	:	_	_	_
59	3	3	CD	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	population	population	NN	_	_	_
62	:	:	:	_	_	_
63	4	4	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
65	population	population	NN	_	_	_
66	:	:	:	_	_	_
67	5	5	CD	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
69	population	population	NN	_	_	_
70	:	:	:	_	_	_
71	6	6	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
73	population	population	NN	_	_	_
74	:	:	:	_	_	_
75	7	7	CD	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
77	Pure	pure	JJ	_	_	_
78	culture	culture	NN	_	_	_
79	in	in	IN	_	_	_
80	LB	LB	NNP	_	_	_
81	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
82	Statistical	statistical	JJ	_	_	_
83	analysis	analysis	NN	_	_	_
84	was	be	VBD	_	_	_
85	performed	perform	VBN	_	_	_
86	using	use	VBG	_	_	_
87	R	r	NN	_	_	_
88	Limma	limma	NN	_	_	_
89	package	package	NN	_	_	_
90	-LRB-	-lrb-	-LRB-	_	_	_
91	Linear	linear	JJ	_	_	_
92	Models	model	NNS	_	_	_
93	for	for	IN	_	_	_
94	Microarrays	Microarrays	NNP	_	_	_
95	Data	Data	NNP	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	-LRB-	-lrb-	-LRB-	_	_	_
98	Smyth	Smyth	NNP	_	_	_
99	2004	2004	CD	_	_	_
100	-RRB-	-rrb-	-RRB-	_	_	_
101	,	,	,	_	_	_
102	where	where	WRB	_	_	_
103	the	the	DT	_	_	_
104	two	two	CD	_	_	_
105	microarrays	microarray	NNS	_	_	_
106	per	per	IN	_	_	_
107	sample	sample	NN	_	_	_
108	were	be	VBD	_	_	_
109	normalized	normalize	VBN	_	_	_
110	using	use	VBG	_	_	_
111	lowess	lowess	JJ	_	_	_
112	normalization	normalization	NN	_	_	_
113	method	method	NN	_	_	_
114	.	.	.	_	_	_

1	Multiple-gene	multiple-gene	JJ	_	_	_
2	probes	probe	NNS	_	_	_
3	results	result	NNS	_	_	_
4	were	be	VBD	_	_	_
5	merged	merge	VBN	_	_	_
6	and	and	CC	_	_	_
7	normalized	normalize	VBN	_	_	_
8	using	use	VBG	_	_	_
9	the	the	DT	_	_	_
10	MA	MA	NNP	_	_	_
11	table	table	NN	_	_	_
12	conversion	conversion	NN	_	_	_
13	tool	tool	NN	_	_	_
14	available	available	JJ	_	_	_
15	on	on	IN	_	_	_
16	the	the	DT	_	_	_
17	MOLGEN	MOLGEN	NNP	_	_	_
18	Bioinformatics	Bioinformatics	NNPS	_	_	_
19	Server	server	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	http	http	NN	_	_	_
22	:	:	:	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	strain	strain	NN	_	_	_
25	:	:	:	_	_	_
26	MC1000	mc1000	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Treatment	treatment	NN	_	_	_
29	A	a	NN	_	_	_
30	Population	Population	NNP	_	_	_
31	1	1	CD	_	_	_
32	Colony	Colony	NNP	_	_	_
33	a	a	DT	_	_	_
34	replica	replica	NN	_	_	_
35	1	1	CD	_	_	_
36	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
37	Treatment	treatment	NN	_	_	_
38	A	a	DT	_	_	_
39	Population	Population	NNP	_	_	_
40	1	1	CD	_	_	_
41	Colony	Colony	NNP	_	_	_
42	a	a	DT	_	_	_
43	replica	replica	NN	_	_	_
44	2	2	CD	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	Treatment	treatment	NN	_	_	_
47	A	a	DT	_	_	_
48	Population	Population	NNP	_	_	_
49	1	1	CD	_	_	_
50	Colony	Colony	NNP	_	_	_
51	b	b	NN	_	_	_
52	replica	replica	NN	_	_	_
53	1	1	CD	_	_	_
54	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
55	Treatment	treatment	NN	_	_	_
56	A	a	DT	_	_	_
57	Population	Population	NNP	_	_	_
58	1	1	CD	_	_	_
59	Colony	Colony	NNP	_	_	_
60	b	b	NN	_	_	_
61	replica	replica	NN	_	_	_
62	2	2	CD	_	_	_
63	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
64	Treatment	treatment	NN	_	_	_
65	A	a	DT	_	_	_
66	Population	Population	NNP	_	_	_
67	1	1	CD	_	_	_
68	Colony	Colony	NNP	_	_	_
69	c	c	NN	_	_	_
70	replica	replica	NN	_	_	_
71	1	1	CD	_	_	_
72	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
73	Treatment	treatment	NN	_	_	_
74	A	a	DT	_	_	_
75	Population	Population	NNP	_	_	_
76	1	1	CD	_	_	_
77	Colony	Colony	NNP	_	_	_
78	c	c	NN	_	_	_
79	replica	replica	NN	_	_	_
80	2	2	CD	_	_	_
81	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
82	Treatment	treatment	NN	_	_	_
83	A	a	DT	_	_	_
84	Population	Population	NNP	_	_	_
85	2	2	CD	_	_	_
86	Colony	Colony	NNP	_	_	_
87	a	a	DT	_	_	_
88	replica	replica	NN	_	_	_
89	1	1	CD	_	_	_
90	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
91	Treatment	treatment	NN	_	_	_
92	A	a	DT	_	_	_
93	Population	Population	NNP	_	_	_
94	2	2	CD	_	_	_
95	Colony	Colony	NNP	_	_	_
96	a	a	DT	_	_	_
97	replica	replica	NN	_	_	_
98	2	2	CD	_	_	_
99	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
100	Treatment	treatment	NN	_	_	_
101	A	a	DT	_	_	_
102	Population	Population	NNP	_	_	_
103	2	2	CD	_	_	_
104	Colony	Colony	NNP	_	_	_
105	b	b	NN	_	_	_
106	replica	replica	NN	_	_	_
107	1	1	CD	_	_	_
108	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
109	Treatment	treatment	NN	_	_	_
110	A	a	DT	_	_	_
111	Population	Population	NNP	_	_	_
112	2	2	CD	_	_	_
113	Colony	Colony	NNP	_	_	_
114	b	b	NN	_	_	_
115	replica	replica	NN	_	_	_
116	2	2	CD	_	_	_
117	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
118	Treatment	treatment	NN	_	_	_
119	A	a	DT	_	_	_
120	Population	Population	NNP	_	_	_
121	2	2	CD	_	_	_
122	Colony	Colony	NNP	_	_	_
123	c	c	NN	_	_	_
124	replica	replica	NN	_	_	_
125	1	1	CD	_	_	_
126	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
127	Treatment	treatment	NN	_	_	_
128	A	a	DT	_	_	_
129	Population	Population	NNP	_	_	_
130	2	2	CD	_	_	_
131	Colony	Colony	NNP	_	_	_
132	c	c	NN	_	_	_
133	replica	replica	NN	_	_	_
134	2	2	CD	_	_	_
135	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
136	Treatment	treatment	NN	_	_	_
137	B	b	NN	_	_	_
138	Population	Population	NNP	_	_	_
139	3	3	CD	_	_	_
140	Colony	Colony	NNP	_	_	_
141	a	a	DT	_	_	_
142	replica	replica	NN	_	_	_
143	1	1	CD	_	_	_
144	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
145	Treatment	treatment	NN	_	_	_
146	B	b	NN	_	_	_
147	Population	Population	NNP	_	_	_
148	3	3	CD	_	_	_
149	Colony	Colony	NNP	_	_	_
150	a	a	DT	_	_	_
151	replica	replica	NN	_	_	_
152	2	2	CD	_	_	_
153	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
154	Treatment	treatment	NN	_	_	_
155	B	b	NN	_	_	_
156	Population	Population	NNP	_	_	_
157	3	3	CD	_	_	_
158	Colony	Colony	NNP	_	_	_
159	b	b	NN	_	_	_
160	replica	replica	NN	_	_	_
161	1	1	CD	_	_	_
162	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
163	Treatment	treatment	NN	_	_	_
164	B	b	NN	_	_	_
165	Population	Population	NNP	_	_	_
166	3	3	CD	_	_	_
167	Colony	Colony	NNP	_	_	_
168	b	b	NN	_	_	_
169	replica	replica	NN	_	_	_
170	2	2	CD	_	_	_
171	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
172	Treatment	treatment	NN	_	_	_
173	B	b	NN	_	_	_
174	Population	Population	NNP	_	_	_
175	3	3	CD	_	_	_
176	Colony	Colony	NNP	_	_	_
177	c	c	NN	_	_	_
178	replica	replica	NN	_	_	_
179	1	1	CD	_	_	_
180	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
181	Treatment	treatment	NN	_	_	_
182	B	b	NN	_	_	_
183	Population	Population	NNP	_	_	_
184	3	3	CD	_	_	_
185	Colony	Colony	NNP	_	_	_
186	c	c	NN	_	_	_
187	replica	replica	NN	_	_	_
188	2	2	CD	_	_	_
189	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
190	Treatment	treatment	NN	_	_	_
191	B	b	NN	_	_	_
192	Population	Population	NNP	_	_	_
193	4	4	CD	_	_	_
194	Colony	Colony	NNP	_	_	_
195	a	a	DT	_	_	_
196	replica	replica	NN	_	_	_
197	1	1	CD	_	_	_
198	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
199	Treatment	treatment	NN	_	_	_
200	B	b	NN	_	_	_
201	Population	Population	NNP	_	_	_
202	4	4	CD	_	_	_
203	Colony	Colony	NNP	_	_	_
204	a	a	DT	_	_	_
205	replica	replica	NN	_	_	_
206	2	2	CD	_	_	_
207	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
208	Treatment	treatment	NN	_	_	_
209	B	b	NN	_	_	_
210	Population	Population	NNP	_	_	_
211	4	4	CD	_	_	_
212	Colony	Colony	NNP	_	_	_
213	b	b	NN	_	_	_
214	replica	replica	NN	_	_	_
215	1	1	CD	_	_	_
216	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
217	Treatment	treatment	NN	_	_	_
218	B	b	NN	_	_	_
219	Population	Population	NNP	_	_	_
220	4	4	CD	_	_	_
221	Colony	Colony	NNP	_	_	_
222	b	b	NN	_	_	_
223	replica	replica	NN	_	_	_
224	2	2	CD	_	_	_
225	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
226	Treatment	treatment	NN	_	_	_
227	B	b	NN	_	_	_
228	Population	Population	NNP	_	_	_
229	4	4	CD	_	_	_
230	Colony	Colony	NNP	_	_	_
231	c	c	NN	_	_	_
232	replica	replica	NN	_	_	_
233	1	1	CD	_	_	_
234	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
235	Treatment	treatment	NN	_	_	_
236	B	b	NN	_	_	_
237	Population	Population	NNP	_	_	_
238	4	4	CD	_	_	_
239	Colony	Colony	NNP	_	_	_
240	c	c	NN	_	_	_
241	replica	replica	NN	_	_	_
242	2	2	CD	_	_	_
243	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
244	Treatment	treatment	NN	_	_	_
245	B	b	NN	_	_	_
246	Population	Population	NNP	_	_	_
247	5	5	CD	_	_	_
248	Colony	Colony	NNP	_	_	_
249	a	a	DT	_	_	_
250	replica	replica	NN	_	_	_
251	1	1	CD	_	_	_
252	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
253	Treatment	treatment	NN	_	_	_
254	B	b	NN	_	_	_
255	Population	Population	NNP	_	_	_
256	5	5	CD	_	_	_
257	Colony	Colony	NNP	_	_	_
258	a	a	DT	_	_	_
259	replica	replica	NN	_	_	_
260	2	2	CD	_	_	_
261	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
262	Treatment	treatment	NN	_	_	_
263	B	b	NN	_	_	_
264	Population	Population	NNP	_	_	_
265	5	5	CD	_	_	_
266	Colony	Colony	NNP	_	_	_
267	b	b	NN	_	_	_
268	replica	replica	NN	_	_	_
269	1	1	CD	_	_	_
270	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
271	Treatment	treatment	NN	_	_	_
272	B	b	NN	_	_	_
273	Population	Population	NNP	_	_	_
274	5	5	CD	_	_	_
275	Colony	Colony	NNP	_	_	_
276	b	b	NN	_	_	_
277	replica	replica	NN	_	_	_
278	2	2	CD	_	_	_
279	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
280	Treatment	treatment	NN	_	_	_
281	B	b	NN	_	_	_
282	Population	Population	NNP	_	_	_
283	5	5	CD	_	_	_
284	Colony	Colony	NNP	_	_	_
285	c	c	NN	_	_	_
286	replica	replica	NN	_	_	_
287	1	1	CD	_	_	_
288	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
289	Treatment	treatment	NN	_	_	_
290	B	b	NN	_	_	_
291	Population	Population	NNP	_	_	_
292	5	5	CD	_	_	_
293	Colony	Colony	NNP	_	_	_
294	c	c	NN	_	_	_
295	replica	replica	NN	_	_	_
296	2	2	CD	_	_	_
297	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
298	Treatment	treatment	NN	_	_	_
299	C	c	NN	_	_	_
300	Population	Population	NNP	_	_	_
301	6	6	CD	_	_	_
302	Colony	Colony	NNP	_	_	_
303	b	b	NN	_	_	_
304	replica	replica	NN	_	_	_
305	1	1	CD	_	_	_
306	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
307	Treatment	treatment	NN	_	_	_
308	C	c	NN	_	_	_
309	Population	Population	NNP	_	_	_
310	6	6	CD	_	_	_
311	Colony	Colony	NNP	_	_	_
312	b	b	NN	_	_	_
313	replica	replica	NN	_	_	_
314	2	2	CD	_	_	_
315	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
316	Treatment	treatment	NN	_	_	_
317	C	c	NN	_	_	_
318	Population	Population	NNP	_	_	_
319	6	6	CD	_	_	_
320	Colony	Colony	NNP	_	_	_
321	c	c	NN	_	_	_
322	replica	replica	NN	_	_	_
323	1	1	CD	_	_	_
324	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
325	Treatment	treatment	NN	_	_	_
326	C	c	NN	_	_	_
327	Population	Population	NNP	_	_	_
328	6	6	CD	_	_	_
329	Colony	Colony	NNP	_	_	_
330	c	c	NN	_	_	_
331	replica	replica	NN	_	_	_
332	2	2	CD	_	_	_
333	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
334	Treatment	treatment	NN	_	_	_
335	C	c	NN	_	_	_
336	Population	Population	NNP	_	_	_
337	7	7	CD	_	_	_
338	Colony	Colony	NNP	_	_	_
339	b	b	NN	_	_	_
340	replica	replica	NN	_	_	_
341	1	1	CD	_	_	_
342	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
343	Treatment	treatment	NN	_	_	_
344	C	c	NN	_	_	_
345	Population	Population	NNP	_	_	_
346	7	7	CD	_	_	_
347	Colony	Colony	NNP	_	_	_
348	b	b	NN	_	_	_
349	replica	replica	NN	_	_	_
350	2	2	CD	_	_	_
351	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
352	Treatment	treatment	NN	_	_	_
353	C	c	NN	_	_	_
354	Population	Population	NNP	_	_	_
355	7	7	CD	_	_	_
356	Colony	Colony	NNP	_	_	_
357	c	c	NN	_	_	_
358	replica	replica	NN	_	_	_
359	1	1	CD	_	_	_
360	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
361	Treatment	treatment	NN	_	_	_
362	C	c	NN	_	_	_
363	Population	Population	NNP	_	_	_
364	7	7	CD	_	_	_
365	Colony	Colony	NNP	_	_	_
366	c	c	NN	_	_	_
367	replica	replica	NN	_	_	_
368	2	2	CD	_	_	_
369	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
370	100ng	100ng	CD	_	_	_
371	16S	16s	NN	_	_	_
372	rRNA	rrna	NN	_	_	_
373	gene	gene	NN	_	_	_
374	amplicon	amplicon	NN	_	_	_
375	of	of	IN	_	_	_
376	a	a	DT	_	_	_
377	mock	mock	JJ	_	_	_
378	community	community	NN	_	_	_
379	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
380	Bacteroides	Bacteroides	NNPS	_	_	_
381	fragilis	fragili	VBZ	_	_	_
382	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
383	Blautia	Blautia	NNP	_	_	_
384	coccoides	coccoide	VBZ	_	_	_
385	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
386	-LSB-	-lsb-	-LRB-	_	_	_
387	Clostridium	clostridium	NN	_	_	_
388	-RSB-	-rsb-	-RRB-	_	_	_
389	leptum	leptum	NN	_	_	_
390	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
391	Escherichia	escherichia	FW	Organism	_	_
392	coli	coli	FW	Organism	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
394	Faecal	faecal	JJ	_	_	_
395	samples	sample	NNS	_	_	_
396	were	be	VBD	_	_	_
397	collected	collect	VBN	_	_	_
398	by	by	IN	_	_	_
399	the	the	DT	_	_	_
400	Department	Department	NNP	_	_	_
401	of	of	IN	_	_	_
402	Microbiology	Microbiology	NNP	_	_	_
403	and	and	CC	_	_	_
404	Alimentary	Alimentary	NNP	_	_	_
405	Pharmabiotic	Pharmabiotic	NNP	_	_	_
406	Centre	Centre	NNP	_	_	_
407	-LRB-	-lrb-	-LRB-	_	_	_
408	Cork	Cork	NNP	_	_	_
409	,	,	,	_	_	_
410	Ireland	Ireland	NNP	_	_	_
411	-RRB-	-rrb-	-RRB-	_	_	_
412	from	from	IN	_	_	_
413	three	three	CD	_	_	_
414	elderly	elderly	JJ	_	_	_
415	patients	patient	NNS	_	_	_
416	-LRB-	-lrb-	-LRB-	_	_	_
417	176	176	CD	_	_	_
418	,	,	,	_	_	_
419	204	204	CD	_	_	_
420	and	and	CC	_	_	_
421	205	205	CD	_	_	_
422	-RRB-	-rrb-	-RRB-	_	_	_
423	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	mock	mock	JJ	_	_	_
3	community	community	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	after	after	IN	_	_	_
7	culture	culture	NN	_	_	_
8	of	of	IN	_	_	_
9	each	each	DT	_	_	_
10	individual	individual	JJ	_	_	_
11	bacterial	bacterial	JJ	_	_	_
12	strain	strain	NN	_	_	_
13	in	in	IN	_	_	_
14	their	they	PRP$	_	_	_
15	reference	reference	NN	_	_	_
16	medium	medium	NN	_	_	_
17	at	at	IN	_	_	_
18	their	they	PRP$	_	_	_
19	optimal	optimal	JJ	_	_	_
20	temperature	temperature	NN	_	_	_
21	for	for	IN	_	_	_
22	several	several	JJ	_	_	_
23	days	day	NNS	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Lactobacillus	lactobacillus	NN	_	_	_
3	acidophilus	acidophilus	NN	_	_	_
4	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
5	Mock	Mock	NNP	_	_	_
6	community	community	NN	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	No	No	NNP	_	_	_
9	treatment	treatment	NN	_	_	_
10	were	be	VBD	_	_	_
11	studied	study	VBN	_	_	_
12	in	in	IN	_	_	_
13	this	this	DT	_	_	_
14	experience	experience	NN	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	Pixel	Pixel	NNP	_	_	_
17	intensities	intensity	NNS	_	_	_
18	were	be	VBD	_	_	_
19	extracted	extract	VBN	_	_	_
20	using	use	VBG	_	_	_
21	the	the	DT	_	_	_
22	``	``	``	_	_	_
23	Feature	Feature	NNP	_	_	_
24	Extraction	Extraction	NNP	_	_	_
25	''	''	''	_	_	_
26	software	software	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Agilent	Agilent	NNP	_	_	_
29	Technologies	Technologies	NNPS	_	_	_
30	,	,	,	_	_	_
31	Palo	Palo	NNP	_	_	_
32	Alto	Alto	NNP	_	_	_
33	,	,	,	_	_	_
34	CA	CA	NNP	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	.	.	.	_	_	_

1	No	no	DT	_	_	_
2	normalization	normalization	NN	_	_	_
3	step	step	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	retained	retain	VBN	_	_	_
9	intensity	intensity	NN	_	_	_
10	value	value	NN	_	_	_
11	for	for	IN	_	_	_
12	each	each	DT	_	_	_
13	probe	probe	NN	_	_	_
14	was	be	VBD	_	_	_
15	the	the	DT	_	_	_
16	ratio	ratio	NN	_	_	_
17	between	between	IN	_	_	_
18	the	the	DT	_	_	_
19	spot	spot	NN	_	_	_
20	's	's	POS	_	_	_
21	median	median	JJ	_	_	_
22	intensity	intensity	NN	_	_	_
23	signals	signal	NNS	_	_	_
24	and	and	CC	_	_	_
25	the	the	DT	_	_	_
26	median	median	NN	_	_	_
27	of	of	IN	_	_	_
28	background	background	NN	_	_	_
29	signals	signal	NNS	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	sample	sample	NN	_	_	_
3	type	type	NN	_	_	_
4	:	:	:	_	_	_
5	mock	mock	JJ	_	_	_
6	community	community	NN	_	_	_
7	-LSB-	-lsb-	-LRB-	_	_	_
8	artificial	artificial	JJ	_	_	_
9	bacterial	bacterial	JJ	_	_	_
10	DNA	dna	NN	_	_	_
11	mix	mix	NN	_	_	_
12	-RSB-	-rsb-	-RRB-	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Total	total	JJ	_	_	_
15	DNA	dna	NN	_	_	_
16	was	be	VBD	_	_	_
17	extracted	extract	VBN	_	_	_
18	from	from	IN	_	_	_
19	three	three	CD	_	_	_
20	human	human	JJ	_	_	_
21	faecal	faecal	JJ	_	_	_
22	samples	sample	NNS	_	_	_
23	using	use	VBG	_	_	_
24	Qiagen	Qiagen	NNP	_	_	_
25	's	's	POS	_	_	_
26	DNA	dna	NN	_	_	_
27	Stool	Stool	NNP	_	_	_
28	Kit	kit	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Qiagen	Qiagen	NNP	_	_	_
31	,	,	,	_	_	_
32	West	West	NNP	_	_	_
33	Sussex	Sussex	NNP	_	_	_
34	,	,	,	_	_	_
35	UK	UK	NNP	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	genomic	genomic	JJ	_	_	_
3	DNA	dna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	from	from	IN	_	_	_
7	pure	pure	JJ	_	_	_
8	bacterial	bacterial	JJ	_	_	_
9	cultures	culture	NNS	_	_	_
10	using	use	VBG	_	_	_
11	DNeasy	dneasy	JJ	_	_	_
12	Blood	blood	NN	_	_	_
13	and	and	CC	_	_	_
14	Tissue	tissue	NN	_	_	_
15	Kit	kit	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	,	,	,	_	_	_
19	West	West	NNP	_	_	_
20	Sussex	Sussex	NNP	_	_	_
21	,	,	,	_	_	_
22	UK	UK	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	10ng	10ng	NN	_	_	_
2	of	of	IN	_	_	_
3	sample	sample	NN	_	_	_
4	was	be	VBD	_	_	_
5	then	then	RB	_	_	_
6	used	use	VBN	_	_	_
7	for	for	IN	_	_	_
8	PCR	pcr	NN	_	_	_
9	amplification	amplification	NN	_	_	_
10	.	.	.	_	_	_

1	16S	16s	CD	_	_	_
2	rRNA	rrna	NN	_	_	_
3	genes	gene	NNS	_	_	_
4	were	be	VBD	_	_	_
5	amplified	amplify	VBN	_	_	_
6	using	use	VBG	_	_	_
7	universal	universal	JJ	_	_	_
8	primers	primer	NNS	_	_	_
9	27F	27f	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	AGAGTTTGATCMTGGCTCAG	agagtttgatcmtggctcag	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	1492R	1492r	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	TACGGYTACCTTGTTACGACT	tacggytaccttgttacgact	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

1	PCR	pcr	NN	_	_	_
2	reactions	reaction	NNS	_	_	_
3	were	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	in	in	IN	_	_	_
6	a	a	DT	_	_	_
7	50µl	50µl	JJ	_	_	_
8	volume	volume	NN	_	_	_
9	,	,	,	_	_	_
10	using	use	VBG	_	_	_
11	DreamTaq	DreamTaq	NNP	_	_	_
12	DNA	DNA	NNP	_	_	_
13	polymerase	polymerase	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Fermentas	Fermentas	NNP	_	_	_
16	,	,	,	_	_	_
17	St.	St.	NNP	_	_	_
18	Leon-Rot	Leon-Rot	NNP	_	_	_
19	,	,	,	_	_	_
20	Germany	Germany	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	PCR	pcr	NN	_	_	_
3	reaction	reaction	NN	_	_	_
4	consisted	consist	VBD	_	_	_
5	of	of	IN	_	_	_
6	an	a	DT	_	_	_
7	initial	initial	JJ	_	_	_
8	denaturation	denaturation	NN	_	_	_
9	step	step	NN	_	_	_
10	at	at	IN	_	_	_
11	95	95	CD	_	_	_
12	°C	°c	NN	_	_	_
13	for	for	IN	_	_	_
14	5	5	CD	_	_	_
15	min	min	NN	_	_	_
16	followed	follow	VBN	_	_	_
17	by	by	IN	_	_	_
18	35	35	CD	_	_	_
19	cycles	cycle	NNS	_	_	_
20	of	of	IN	_	_	_
21	denaturation	denaturation	NN	_	_	_
22	at	at	IN	_	_	_
23	95	95	CD	_	_	_
24	°C	°c	NN	_	_	_
25	for	for	IN	_	_	_
26	30	30	CD	_	_	_
27	s	s	NNS	_	_	_
28	,	,	,	_	_	_
29	annealing	annealing	NN	_	_	_
30	at	at	IN	_	_	_
31	58	58	CD	_	_	_
32	°C	°c	NN	_	_	_
33	for	for	IN	_	_	_
34	40	40	CD	_	_	_
35	s	s	NNS	_	_	_
36	and	and	CC	_	_	_
37	elongation	elongation	NN	_	_	_
38	at	at	IN	_	_	_
39	72	72	CD	_	_	_
40	°C	°c	NN	_	_	_
41	for	for	IN	_	_	_
42	2	2	CD	_	_	_
43	min	min	NN	_	_	_
44	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	final	final	JJ	_	_	_
3	extension	extension	NN	_	_	_
4	step	step	NN	_	_	_
5	was	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	at	at	IN	_	_	_
8	72	72	CD	_	_	_
9	°C	°c	NN	_	_	_
10	for	for	IN	_	_	_
11	5	5	CD	_	_	_
12	min	min	NN	_	_	_
13	.	.	.	_	_	_

1	PCR	pcr	NN	_	_	_
2	product	product	NN	_	_	_
3	size	size	NN	_	_	_
4	was	be	VBD	_	_	_
5	verified	verify	VBN	_	_	_
6	by	by	IN	_	_	_
7	electrophoresis	electrophoresis	NN	_	_	_
8	with	with	IN	_	_	_
9	1	1	CD	_	_	_
10	%	%	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	w	w	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	All	all	DT	_	_	_
15	RNA	rna	NN	_	_	_
16	data	datum	NNS	_	_	_
17	were	be	VBD	_	_	_
18	mapped	map	VBN	_	_	_
19	to	to	TO	_	_	_
20	the	the	DT	_	_	_
21	reference	reference	NN	_	_	_
22	genome	genome	NN	_	_	_
23	Xuzhou21	xuzhou21	NN	_	_	_
24	using	use	VBG	_	_	_
25	SOAP2	soap2	NN	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	O157	o157	NN	_	_	_
5	:	:	:	_	_	_
6	H7	h7	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	For	for	IN	_	_	_
9	total	total	JJ	_	_	_
10	RNA	rna	NN	_	_	_
11	isolation	isolation	NN	_	_	_
12	,	,	,	_	_	_
13	the	the	DT	_	_	_
14	bacteria	bacterium	NNS	_	_	_
15	were	be	VBD	_	_	_
16	inoculated	inoculate	VBN	_	_	_
17	in	in	IN	_	_	_
18	5	5	CD	_	_	_
19	ml	ml	NN	_	_	_
20	LB	lb	NN	MED	_	_
21	broth	broth	NN	MED	_	_
22	at	at	IN	_	_	_
23	37	37	CD	_	_	_
24	℃	℃	NN	_	_	_
25	with	with	IN	_	_	_
26	shaking	shake	VBG	_	_	_
27	for	for	IN	_	_	_
28	16	16	CD	_	_	_
29	h.	h.	NN	_	_	_
30	50	50	CD	_	_	_
31	µl	µl	NN	_	_	_
32	of	of	IN	_	_	_
33	the	the	DT	_	_	_
34	above	above	JJ	_	_	_
35	culture	culture	NN	_	_	_
36	was	be	VBD	_	_	_
37	inoculated	inoculate	VBN	_	_	_
38	in	in	IN	_	_	_
39	5	5	CD	_	_	_
40	ml	ml	NN	_	_	_
41	fresh	fresh	JJ	_	_	_
42	LB	lb	NN	MED	_	_
43	broth	broth	NN	MED	_	_
44	and	and	CC	_	_	_
45	the	the	DT	_	_	_
46	culture	culture	NN	_	_	_
47	was	be	VBD	_	_	_
48	shaken	shake	VBN	_	_	_
49	at	at	IN	_	_	_
50	37	37	CD	_	_	_
51	°C	°c	NN	_	_	_
52	for	for	IN	_	_	_
53	about	about	IN	_	_	_
54	2.5	2.5	CD	_	_	_
55	h	h	NN	_	_	_
56	until	until	IN	_	_	_
57	the	the	DT	_	_	_
58	OD600	od600	NN	_	_	_
59	reached	reach	VBD	_	_	_
60	0.6	0.6	CD	_	_	_
61	.	.	.	_	_	_

1	500	500	CD	_	_	_
2	µl	µl	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	culture	culture	NN	_	_	_
6	were	be	VBD	_	_	_
7	mixed	mix	VBN	_	_	_
8	with	with	IN	_	_	_
9	1	1	CD	_	_	_
10	ml	ml	NN	_	_	_
11	RNA	rna	NN	_	_	_
12	protect	protect	VBP	_	_	_
13	bacterial	bacterial	JJ	_	_	_
14	reagent	reagent	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Qiagen	Qiagen	NNP	_	_	_
17	,	,	,	_	_	_
18	Hilden	Hilden	NNP	_	_	_
19	,	,	,	_	_	_
20	Germany	Germany	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	to	to	TO	_	_	_
23	stabilize	stabilize	VB	_	_	_
24	RNA	rna	NN	_	_	_
25	according	accord	VBG	_	_	_
26	to	to	TO	_	_	_
27	the	the	DT	_	_	_
28	manufacturer	manufacturer	NN	_	_	_
29	's	's	POS	_	_	_
30	instructions	instruction	NNS	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	genotype	genotype	NN	_	_	_
3	:	:	:	_	_	_
4	plasmid	plasmid	NN	_	_	_
5	cured	cure	VBD	_	_	_
6	strain	strain	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	genotype	genotype	NN	_	_	_
9	:	:	:	_	_	_
10	wild	wild	JJ	_	_	_
11	type	type	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	Isolated	isolate	VBN	_	_	_
14	from	from	IN	_	_	_
15	feces	fece	NNS	_	_	_
16	of	of	IN	_	_	_
17	a	a	DT	_	_	_
18	HUS	hus	NN	_	_	_
19	patient	patient	NN	_	_	_
20	from	from	IN	_	_	_
21	an	a	DT	_	_	_
22	outbreak	outbreak	NN	_	_	_
23	in	in	IN	_	_	_
24	China	China	NNP	_	_	_
25	in	in	IN	_	_	_
26	1999	1999	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
28	plasmid	plasmid	NN	_	_	_
29	cured	cure	VBD	_	_	_
30	rep1	rep1	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	plasmid	plasmid	NN	_	_	_
33	cured	cure	VBD	_	_	_
34	rep2	rep2	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	RNA-Seq	rna-seq	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	strain	strain	NN	_	_	_
39	:	:	:	_	_	_
40	Xuzhou21	xuzhou21	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	strain	strain	NN	_	_	_
43	:	:	:	_	_	_
44	Xuzhou21m	xuzhou21m	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	Supplementary	supplementary	JJ	_	_	_
47	_	_	NN	_	_	_
48	files	file	NNS	_	_	_
49	_	_	IN	_	_	_
50	format	format	NN	_	_	_
51	_	_	NN	_	_	_
52	and	and	CC	_	_	_
53	_	_	NN	_	_	_
54	content	content	NN	_	_	_
55	:	:	:	_	_	_
56	tab-delimited	tab-delimited	JJ	_	_	_
57	text	text	NN	_	_	_
58	files	file	NNS	_	_	_
59	include	include	VBP	_	_	_
60	RPKM	rpkm	NN	_	_	_
61	values	value	NNS	_	_	_
62	for	for	IN	_	_	_
63	each	each	DT	_	_	_
64	Sample	Sample	NNP	_	_	_
65	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
66	The	The	NNP	_	_	_
67	bacteria	bacterium	NNS	_	_	_
68	were	be	VBD	_	_	_
69	routinely	routinely	RB	_	_	_
70	grown	grow	VBN	_	_	_
71	in	in	IN	_	_	_
72	Luria-Bertani	Luria-Bertani	NNP	_	_	_
73	-LRB-	-lrb-	-LRB-	_	_	_
74	LB	LB	NNP	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	broth	broth	NN	_	_	_
77	or	or	CC	_	_	_
78	on	on	IN	_	_	_
79	LB	LB	NNP	_	_	_
80	agar	agar	NN	_	_	_
81	plates	plate	NNS	_	_	_
82	-LRB-	-lrb-	-LRB-	_	_	_
83	pH	ph	NN	_	_	_
84	7.2	7.2	CD	_	_	_
85	-RRB-	-rrb-	-RRB-	_	_	_
86	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	distribution	distribution	NN	_	_	_
4	of	of	IN	_	_	_
5	reads	read	VBZ	_	_	_
6	was	be	VBD	_	_	_
7	plotted	plot	VBN	_	_	_
8	by	by	IN	_	_	_
9	its	its	PRP$	_	_	_
10	location	location	NN	_	_	_
11	in	in	IN	_	_	_
12	the	the	DT	_	_	_
13	reference	reference	NN	_	_	_
14	genome	genome	NN	_	_	_
15	,	,	,	_	_	_
16	and	and	CC	_	_	_
17	then	then	RB	_	_	_
18	divided	divide	VBN	_	_	_
19	into	into	IN	_	_	_
20	gene	gene	NN	_	_	_
21	region	region	NN	_	_	_
22	and	and	CC	_	_	_
23	intergenic	intergenic	JJ	_	_	_
24	region	region	NN	_	_	_
25	.	.	.	_	_	_

1	Genome	Genome	NNP	_	_	_
2	and	and	CC	_	_	_
3	gene	gene	NN	_	_	_
4	coverage	coverage	NN	_	_	_
5	was	be	VBD	_	_	_
6	calculated	calculate	VBN	_	_	_
7	by	by	IN	_	_	_
8	counting	count	VBG	_	_	_
9	the	the	DT	_	_	_
10	number	number	NN	_	_	_
11	of	of	IN	_	_	_
12	reads	read	VBZ	_	_	_
13	mapped	map	VBN	_	_	_
14	to	to	TO	_	_	_
15	the	the	DT	_	_	_
16	genome	genome	NN	_	_	_
17	and	and	CC	_	_	_
18	individual	individual	JJ	_	_	_
19	genes	gene	NNS	_	_	_
20	respectively	respectively	RB	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	gene	gene	NN	_	_	_
4	expression	expression	NN	_	_	_
5	was	be	VBD	_	_	_
6	calculated	calculate	VBN	_	_	_
7	using	use	VBG	_	_	_
8	the	the	DT	_	_	_
9	RPKM	rpkm	NN	_	_	_
10	method	method	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	The	the	DT	_	_	_
13	total	total	JJ	_	_	_
14	RNA	rna	NN	_	_	_
15	extracted	extract	VBN	_	_	_
16	from	from	IN	_	_	_
17	Xuzhou21	xuzhou21	NN	_	_	_
18	and	and	CC	_	_	_
19	Xuzhou21m	xuzhou21m	NN	_	_	_
20	were	be	VBD	_	_	_
21	first	first	JJ	_	_	_
22	treated	treat	VBN	_	_	_
23	with	with	IN	_	_	_
24	Ribo-Zero	ribo-zero	NN	_	_	_
25	™	™	CD	_	_	_
26	rRNA	rrna	NN	_	_	_
27	Removal	removal	NN	_	_	_
28	kit	kit	NN	_	_	_
29	to	to	TO	_	_	_
30	remove	remove	VB	_	_	_
31	rRNA	rrna	NN	_	_	_
32	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	mRNA	mrna	NN	_	_	_
3	was	be	VBD	_	_	_
4	fragmented	fragmented	JJ	_	_	_
5	and	and	CC	_	_	_
6	produced	produce	VBD	_	_	_
7	cDNA	cdna	NN	_	_	_
8	libraries	library	NNS	_	_	_
9	primed	prime	VBN	_	_	_
10	with	with	IN	_	_	_
11	random	random	JJ	_	_	_
12	hexamers	hexamer	NNS	_	_	_
13	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	was	be	VBD	_	_	_
3	selected	select	VBN	_	_	_
4	by	by	IN	_	_	_
5	size	size	NN	_	_	_
6	,	,	,	_	_	_
7	amplificated	amplificate	VBN	_	_	_
8	using	use	VBG	_	_	_
9	PCR	pcr	NN	_	_	_
10	and	and	CC	_	_	_
11	and	and	CC	_	_	_
12	then	then	RB	_	_	_
13	sent	send	VBD	_	_	_
14	to	to	TO	_	_	_
15	sequencing	sequencing	NN	_	_	_
16	using	use	VBG	_	_	_
17	Illumina	Illumina	NNP	_	_	_
18	HiseqTM	HiseqTM	NNP	_	_	_
19	2000	2000	CD	_	_	_
20	commercially	commercially	RB	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	were	be	VBD	_	_	_
5	then	then	RB	_	_	_
6	isolated	isolate	VBN	_	_	_
7	according	accord	VBG	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	standard	standard	JJ	_	_	_
11	protocol	protocol	NN	_	_	_
12	using	use	VBG	_	_	_
13	an	a	DT	_	_	_
14	RNeasy	rneasy	NN	_	_	_
15	mini	minus	NNS	_	_	_
16	kit	kit	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Qiagen	qiagen	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	Genomic	genomic	JJ	_	_	_
2	DNA	dna	NN	_	_	_
3	were	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	from	from	IN	_	_	_
6	both	both	DT	_	_	_
7	Xuzhou21	xuzhou21	NN	_	_	_
8	and	and	CC	_	_	_
9	Xuzhou21m	xuzhou21m	NN	_	_	_
10	using	use	VBG	_	_	_
11	Wizard	Wizard	NNP	_	_	_
12	Genomic	genomic	JJ	_	_	_
13	DNA	dna	NN	_	_	_
14	purification	purification	NN	_	_	_
15	kit	kit	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Promega	Promega	NNP	_	_	_
18	,	,	,	_	_	_
19	Madison	Madison	NNP	_	_	_
20	,	,	,	_	_	_
21	WI	WI	NNP	_	_	_
22	,	,	,	_	_	_
23	USA	USA	NNP	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	according	accord	VBG	_	_	_
26	to	to	TO	_	_	_
27	the	the	DT	_	_	_
28	manufacturer	manufacturer	NN	_	_	_
29	's	's	POS	_	_	_
30	protocols	protocol	NNS	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	WT	WT	NNP	_	_	_
3	rep1	rep1	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	WT	wt	JJ	_	_	_
6	rep2	rep2	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Xuzhou21	xuzhou21	NN	_	_	_
9	cured	cure	VBD	_	_	_
10	of	of	IN	_	_	_
11	the	the	DT	_	_	_
12	pO157	po157	NN	_	_	_
13	_	_	CD	_	_	_
14	Sal	Sal	NNP	_	_	_
15	plasmid	plasmid	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	bacterial	bacterial	JJ	_	_	_
18	cells	cell	NNS	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
20	BL21	bl21	NN	_	_	_
21	_	_	NN	_	_	_
22	1	1	CD	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	BL21	bl21	NN	_	_	_
25	_	_	NN	_	_	_
26	2	2	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Cells	cell	NNS	_	_	_
29	were	be	VBD	_	_	_
30	grown	grow	VBN	_	_	_
31	in	in	IN	_	_	_
32	a	a	DT	_	_	_
33	250	250	CD	_	_	_
34	ml	ml	NN	_	_	_
35	fermenter	fermenter	NN	_	_	_
36	containing	contain	VBG	_	_	_
37	100	100	CD	_	_	_
38	ml	ml	NN	_	_	_
39	LB	lb	NN	MED	_	_
40	medium	medium	NN	MED	_	_
41	supplemented	supplement	VBN	_	_	_
42	with	with	IN	_	_	_
43	3	3	CD	_	_	_
44	g	g	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	condition	condition	NN	_	_	_
47	:	:	:	_	_	_
48	LB	lb	NN	_	_	_
49	+3	+3	CD	_	_	_
50	g	g	NN	_	_	_
51	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
52	Escherichia	escherichia	FW	Organism	_	_
53	coli	coli	FW	Organism	_	_
54	BL21	bl21	NN	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	DE3	de3	NN	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
59	First	First	NNP	_	_	_
60	and	and	CC	_	_	_
61	second	second	JJ	_	_	_
62	strand	strand	NN	_	_	_
63	cDNA	cdna	NN	_	_	_
64	synthesis	synthesis	NN	_	_	_
65	was	be	VBD	_	_	_
66	carried	carry	VBN	_	_	_
67	out	out	RP	_	_	_
68	using	use	VBG	_	_	_
69	the	the	DT	_	_	_
70	Ovation	Ovation	NNP	_	_	_
71	®	®	NNP	_	_	_
72	Prokaryotic	Prokaryotic	NNP	_	_	_
73	RNA-Seq	RNA-Seq	NNP	_	_	_
74	System	System	NNP	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	NuGEN	NuGEN	NNP	_	_	_
77	Technologies	Technologies	NNPS	_	_	_
78	Inc.	Inc.	NNP	_	_	_
79	,	,	,	_	_	_
80	San	San	NNP	_	_	_
81	Carlos	Carlos	NNP	_	_	_
82	,	,	,	_	_	_
83	CA	CA	NNP	_	_	_
84	,	,	,	_	_	_
85	USA	USA	NNP	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	,	,	,	_	_	_
88	and	and	CC	_	_	_
89	NuGEN	nugen	NN	_	_	_
90	's	's	POS	_	_	_
91	Encore	encore	NN	_	_	_
92	NGS	ngs	NN	_	_	_
93	Library	Library	NNP	_	_	_
94	System	System	NNP	_	_	_
95	was	be	VBD	_	_	_
96	applied	apply	VBN	_	_	_
97	to	to	TO	_	_	_
98	construct	construct	VB	_	_	_
99	the	the	DT	_	_	_
100	cDNA	cdna	NN	_	_	_
101	library	library	NN	_	_	_
102	for	for	IN	_	_	_
103	the	the	DT	_	_	_
104	IlluminaHiSeq	IlluminaHiSeq	NNP	_	_	_
105	platform	platform	NN	_	_	_
106	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	gi	gi	NN	_	_	_
7	|	|	SYM	_	_	_
8	387825439	387825439	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	genotype	genotype	NN	_	_	_
11	:	:	:	_	_	_
12	Pck	pck	NN	_	_	_
13	over-expressed	over-expressed	JJ	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	genotype	genotype	NN	_	_	_
16	:	:	:	_	_	_
17	wild-type	wild-type	JJ	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	PCK	pck	NN	_	_	_
20	over	over	IN	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	Raw	raw	NN	_	_	_
23	sequencing	sequencing	NN	_	_	_
24	reads	read	VBZ	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	FASTQ	fastq	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	were	be	VBD	_	_	_
29	processed	process	VBN	_	_	_
30	by	by	IN	_	_	_
31	Xpression	xpression	NN	_	_	_
32	and	and	CC	_	_	_
33	only	only	RB	_	_	_
34	the	the	DT	_	_	_
35	uniquely	uniquely	RB	_	_	_
36	mapped	map	VBN	_	_	_
37	reads	read	VBZ	_	_	_
38	were	be	VBD	_	_	_
39	subjected	subject	VBN	_	_	_
40	to	to	TO	_	_	_
41	further	further	JJ	_	_	_
42	analysis	analysis	NN	_	_	_
43	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Reference	Reference	NNP	_	_	_
3	files	file	VBZ	_	_	_
4	for	for	IN	_	_	_
5	the	the	DT	_	_	_
6	genome	genome	NN	_	_	_
7	sequence	sequence	NN	_	_	_
8	being	be	VBG	_	_	_
9	queried	query	VBN	_	_	_
10	,	,	,	_	_	_
11	Escherichia	escherichia	FW	Organism	_	_
12	coli	coli	FW	Organism	_	_
13	BL21	bl21	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	DE3	de3	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	genome	genome	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	NC	nc	NN	_	_	_
20	_	_	CD	_	_	_
21	012971	012971	CD	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	were	be	VBD	_	_	_
24	uploaded	upload	VBN	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	strain	strain	NN	_	_	_
5	:	:	:	_	_	_
6	BL21	bl21	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	DE3	de3	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	The	the	DT	_	_	_
12	number	number	NN	_	_	_
13	of	of	IN	_	_	_
14	reads	read	VBZ	_	_	_
15	overlapping	overlap	VBG	_	_	_
16	each	each	DT	_	_	_
17	gene	gene	NN	_	_	_
18	was	be	VBD	_	_	_
19	recorded	record	VBN	_	_	_
20	and	and	CC	_	_	_
21	normalized	normalize	VBN	_	_	_
22	based	base	VBN	_	_	_
23	on	on	IN	_	_	_
24	reads	read	VBZ	_	_	_
25	per	per	IN	_	_	_
26	kilobase	kilobase	NN	_	_	_
27	per	per	IN	_	_	_
28	million	million	CD	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	RPKM	rpkm	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	uniquely	uniquely	RB	_	_	_
33	mapped	map	VBD	_	_	_
34	reads	read	VBZ	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	harvested	harvest	VBN	_	_	_
6	from	from	IN	_	_	_
7	C.	C.	NNP	_	_	_
8	glutamicum	glutamicum	NN	_	_	_
9	cells	cell	NNS	_	_	_
10	using	use	VBG	_	_	_
11	TRIzol	trizol	NN	_	_	_
12	®	®	NN	_	_	_
13	reagent	reagent	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Invitrogen	Invitrogen	NNP	_	_	_
16	,	,	,	_	_	_
17	Carlsbad	Carlsbad	NNP	_	_	_
18	,	,	,	_	_	_
19	CA	CA	NNP	_	_	_
20	,	,	,	_	_	_
21	USA	USA	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	and	and	CC	_	_	_
24	NucleoSpin	NucleoSpin	NNP	_	_	_
25	®	®	NNP	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Macherey-Nagel	Macherey-Nagel	NNP	_	_	_
28	,	,	,	_	_	_
29	Düren	Düren	NNP	_	_	_
30	,	,	,	_	_	_
31	Germany	Germany	NNP	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	according	accord	VBG	_	_	_
34	to	to	TO	_	_	_
35	the	the	DT	_	_	_
36	manufacturer	manufacturer	NN	_	_	_
37	's	's	POS	_	_	_
38	instructions	instruction	NNS	_	_	_
39	with	with	IN	_	_	_
40	the	the	DT	_	_	_
41	following	follow	VBG	_	_	_
42	modifications	modification	NNS	_	_	_
43	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	harvested	harvest	VBN	_	_	_
4	by	by	IN	_	_	_
5	centrifugation	centrifugation	NN	_	_	_
6	,	,	,	_	_	_
7	resuspended	resuspend	VBN	_	_	_
8	in	in	IN	_	_	_
9	TRIzol	trizol	NN	_	_	_
10	®	®	NN	_	_	_
11	reagent	reagent	NN	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	transferred	transfer	VBN	_	_	_
15	to	to	TO	_	_	_
16	a	a	DT	_	_	_
17	vial	vial	NN	_	_	_
18	containing	contain	VBG	_	_	_
19	Lysing	lyse	VBG	_	_	_
20	Matrix	Matrix	NNP	_	_	_
21	B	B	NNP	_	_	_
22	®	®	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	MP	mp	NN	_	_	_
25	Biomedicals	biomedical	NNS	_	_	_
26	,	,	,	_	_	_
27	Solon	Solon	NNP	_	_	_
28	,	,	,	_	_	_
29	OH	oh	NN	_	_	_
30	,	,	,	_	_	_
31	USA	USA	NNP	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	for	for	IN	_	_	_
34	lysis	lysis	NN	_	_	_
35	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	suspension	suspension	NN	_	_	_
3	was	be	VBD	_	_	_
4	centrifuged	centrifuge	VBN	_	_	_
5	,	,	,	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	supernatant	supernatant	NN	_	_	_
9	was	be	VBD	_	_	_
10	applied	apply	VBN	_	_	_
11	to	to	TO	_	_	_
12	a	a	DT	_	_	_
13	NucleoSpin	NucleoSpin	NNP	_	_	_
14	®	®	NN	_	_	_
15	RNA	rna	NN	_	_	_
16	II	ii	CD	_	_	_
17	kit	kit	NN	_	_	_
18	for	for	IN	_	_	_
19	purification	purification	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Xpression	xpression	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	https	http	NNS	_	_	_
5	:	:	:	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Xpression	xpression	NN	_	_	_
8	was	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	for	for	IN	_	_	_
11	filtering	filter	VBG	_	_	_
12	and	and	CC	_	_	_
13	trimming	trim	VBG	_	_	_
14	reads	read	VBZ	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	control	control	VBP	_	_	_
3	12h	12h	JJ	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
5	control	control	VBP	_	_	_
6	24h	24h	JJ	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	control	control	VBP	_	_	_
9	6h	6h	JJ	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Cy3	cy3	NN	_	_	_
12	and	and	CC	_	_	_
13	Cy5	cy5	NN	_	_	_
14	intensities	intensity	NNS	_	_	_
15	were	be	VBD	_	_	_
16	normalized	normalize	VBN	_	_	_
17	by	by	IN	_	_	_
18	scaling	scale	VBG	_	_	_
19	so	so	RB	_	_	_
20	that	that	IN	_	_	_
21	the	the	DT	_	_	_
22	75th	75th	JJ	_	_	_
23	percentile	percentile	NN	_	_	_
24	in	in	IN	_	_	_
25	the	the	DT	_	_	_
26	Cy3	cy3	NN	_	_	_
27	and	and	CC	_	_	_
28	Cy5	cy5	NN	_	_	_
29	channels	channel	NNS	_	_	_
30	were	be	VBD	_	_	_
31	equal	equal	JJ	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	expose	expose	VBP	_	_	_
4	Bacillus	bacillus	NN	_	_	_
5	VOC	voc	NN	_	_	_
6	12h	12h	VBP	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	Expose	expose	VB	_	_	_
9	Bacillus	bacillus	NN	_	_	_
10	VOC-12h	voc-12h	JJ	_	_	_
11	rep1	rep1	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
13	Expose	expose	VB	_	_	_
14	Bacillus	bacillus	NN	_	_	_
15	VOC-12h	voc-12h	JJ	_	_	_
16	rep2	rep2	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
18	Expose	expose	VB	_	_	_
19	Bacillus	bacillus	NN	_	_	_
20	VOC-12h	voc-12h	JJ	_	_	_
21	rep3	rep3	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	Expose	expose	VB	_	_	_
24	Bacillus	bacillus	NN	_	_	_
25	VOC-12h	voc-12h	JJ	_	_	_
26	rep4	rep4	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
28	expose	expose	VBP	_	_	_
29	Bacillus	bacillus	NN	_	_	_
30	VOC24h	voc24h	JJ	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
32	Expose	expose	VB	_	_	_
33	Bacillus	bacillus	NN	_	_	_
34	VOC-24h	voc-24h	JJ	_	_	_
35	rep1	rep1	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
37	Expose	expose	VB	_	_	_
38	Bacillus	bacillus	NN	_	_	_
39	VOC-24h	voc-24h	JJ	_	_	_
40	rep2	rep2	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
42	Expose	expose	VB	_	_	_
43	Bacillus	bacillus	NN	_	_	_
44	VOC-24h	voc-24h	JJ	_	_	_
45	rep3	rep3	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
47	Expose	expose	VB	_	_	_
48	Bacillus	bacillus	NN	_	_	_
49	VOC-24h	voc-24h	JJ	_	_	_
50	rep4	rep4	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
52	expose	expose	VBP	_	_	_
53	Bacillus	bacillus	NN	_	_	_
54	VOC	voc	NN	_	_	_
55	6h	6h	VBP	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
57	Expose	expose	VB	_	_	_
58	Bacillus	bacillus	NN	_	_	_
59	VOC-6h	voc-6h	JJ	_	_	_
60	rep1	rep1	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
62	Expose	expose	VB	_	_	_
63	Bacillus	bacillus	NN	_	_	_
64	VOC-6h	voc-6h	JJ	_	_	_
65	rep2	rep2	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
67	Expose	expose	VB	_	_	_
68	Bacillus	bacillus	NN	_	_	_
69	VOC-6h	voc-6h	JJ	_	_	_
70	rep3	rep3	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
72	Expose	expose	VB	_	_	_
73	Bacillus	bacillus	NN	_	_	_
74	VOC-6h	voc-6h	JJ	_	_	_
75	rep4	rep4	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	strain	strain	NN	_	_	_
78	:	:	:	_	_	_
79	MG1655	mg1655	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	time	time	NN	_	_	_
82	:	:	:	_	_	_
83	12	12	CD	_	_	_
84	h	h	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	time	time	NN	_	_	_
87	:	:	:	_	_	_
88	24	24	CD	_	_	_
89	h	h	NN	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	time	time	NN	_	_	_
92	:	:	:	_	_	_
93	6	6	CD	_	_	_
94	h	h	NN	_	_	_
95	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
96	Total	Total	NNP	_	_	_
97	RNAs	rna	NNS	_	_	_
98	were	be	VBD	_	_	_
99	extracted	extract	VBN	_	_	_
100	using	use	VBG	_	_	_
101	RNeasy	RNeasy	NNP	_	_	_
102	mini	minus	NNS	_	_	_
103	kit	kit	NN	_	_	_
104	-LRB-	-lrb-	-LRB-	_	_	_
105	Qiagen	Qiagen	NNP	_	_	_
106	,	,	,	_	_	_
107	#	#	#	_	_	_
108	74104	74104	CD	_	_	_
109	-RRB-	-rrb-	-RRB-	_	_	_
110	following	follow	VBG	_	_	_
111	manufacture	manufacture	NN	_	_	_
112	's	's	POS	_	_	_
113	instruction	instruction	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	treatment	treatment	NN	_	_	_
116	:	:	:	_	_	_
117	Bacillus	bacillus	NN	_	_	_
118	volatile	volatile	JJ	_	_	_
119	organic	organic	JJ	_	_	_
120	compounds	compound	NNS	_	_	_
121	-LRB-	-lrb-	-LRB-	_	_	_
122	VOCs	voc	NNS	_	_	_
123	-RRB-	-rrb-	-RRB-	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	treatment	treatment	NN	_	_	_
126	:	:	:	_	_	_
127	control	control	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
129	Aerobic	aerobic	JJ	_	_	_
130	growth	growth	NN	_	_	_
131	at	at	IN	_	_	_
132	37	37	CD	_	_	_
133	°C	°c	NN	_	_	_
134	in	in	IN	_	_	_
135	specified	specify	VBN	_	_	_
136	media	media	NNS	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	Cells	cell	NNS	_	_	_
139	treated	treat	VBN	_	_	_
140	during	during	IN	_	_	_
141	mid-exponential	mid-exponential	JJ	_	_	_
142	growth	growth	NN	_	_	_
143	phase	phase	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	CV108	cv108	NN	_	_	_
146	_	_	CD	_	_	_
147	minus	minus	CC	_	_	_
148	_	_	SYM	_	_	_
149	aMG	aMG	NNP	_	_	_
150	_	_	SYM	_	_	_
151	1	1	CD	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	CV108	cv108	NN	_	_	_
154	_	_	CD	_	_	_
155	minus	minus	CC	_	_	_
156	_	_	SYM	_	_	_
157	aMG	aMG	NNP	_	_	_
158	_	_	SYM	_	_	_
159	2	2	CD	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	CV108	cv108	NN	_	_	_
162	_	_	CD	_	_	_
163	minus	minus	CC	_	_	_
164	_	_	SYM	_	_	_
165	aMG	aMG	NNP	_	_	_
166	_	_	SYM	_	_	_
167	3	3	CD	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	CV108	cv108	NN	_	_	_
170	_	_	NN	_	_	_
171	plus	plus	CC	_	_	_
172	_	_	SYM	_	_	_
173	aMG	aMG	NNP	_	_	_
174	_	_	SYM	_	_	_
175	1	1	CD	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	CV108	cv108	NN	_	_	_
178	_	_	NN	_	_	_
179	plus	plus	CC	_	_	_
180	_	_	SYM	_	_	_
181	aMG	aMG	NNP	_	_	_
182	_	_	SYM	_	_	_
183	2	2	CD	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	CV108	cv108	NN	_	_	_
186	_	_	NN	_	_	_
187	plus	plus	CC	_	_	_
188	_	_	SYM	_	_	_
189	aMG	aMG	NNP	_	_	_
190	_	_	SYM	_	_	_
191	3	3	CD	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	Escherichia	escherichia	FW	Organism	_	_
194	coli	coli	FW	Organism	_	_
195	str	str	FW	_	_	_
196	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Galaxy1	galaxy1	NN	_	_	_
4	-	-	:	_	_	_
5	-LSB-	-lsb-	-LRB-	_	_	_
6	CV104	cv104	NN	_	_	_
7	_	_	CD	_	_	_
8	pHDB3	phdb3	NN	_	_	_
9	_	_	CD	_	_	_
10	5	5	CD	_	_	_
11	.	.	.	_	_	_

1	txt	txt	NN	_	_	_
2	-RSB-	-rsb-	-RRB-	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Galaxy2	galaxy2	NN	_	_	_
5	-	-	:	_	_	_
6	-LSB-	-lsb-	-LRB-	_	_	_
7	CV104	cv104	NN	_	_	_
8	_	_	CD	_	_	_
9	pLCV1	plcv1	NN	_	_	_
10	_	_	CD	_	_	_
11	5	5	CD	_	_	_
12	.	.	.	_	_	_

1	txt	txt	NN	_	_	_
2	-RSB-	-rsb-	-RRB-	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Galaxy3	galaxy3	NN	_	_	_
5	-	-	:	_	_	_
6	-LSB-	-lsb-	-LRB-	_	_	_
7	CV104	cv104	NN	_	_	_
8	_	_	CD	_	_	_
9	pLCV1	plcv1	NN	_	_	_
10	_	_	NN	_	_	_
11	10	10	CD	_	_	_
12	.	.	.	_	_	_

1	txt	txt	NN	_	_	_
2	-RSB-	-rsb-	-RRB-	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Galaxy4	galaxy4	NN	_	_	_
5	-	-	:	_	_	_
6	-LSB-	-lsb-	-LRB-	_	_	_
7	CV104	cv104	NN	_	_	_
8	_	_	CD	_	_	_
9	pHDB3	phdb3	NN	_	_	_
10	_	_	CD	_	_	_
11	20	20	CD	_	_	_
12	.	.	.	_	_	_

1	txt	txt	NN	_	_	_
2	-RSB-	-rsb-	-RRB-	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Galaxy5	galaxy5	NN	_	_	_
5	-	-	:	_	_	_
6	-LSB-	-lsb-	-LRB-	_	_	_
7	CV104	cv104	NN	_	_	_
8	_	_	CD	_	_	_
9	pLCV1	plcv1	NN	_	_	_
10	_	_	CD	_	_	_
11	20	20	CD	_	_	_
12	.	.	.	_	_	_

1	txt	txt	NN	_	_	_
2	-RSB-	-rsb-	-RRB-	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Galaxy6	galaxy6	NN	_	_	_
5	-	-	:	_	_	_
6	-LSB-	-lsb-	-LRB-	_	_	_
7	CV104	cv104	NN	_	_	_
8	_	_	CD	_	_	_
9	pHDB3	phdb3	NN	_	_	_
10	_	_	NN	_	_	_
11	10	10	CD	_	_	_
12	.	.	.	_	_	_

1	txt	txt	NN	_	_	_
2	-RSB-	-rsb-	-RRB-	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Genome	Genome	NNP	_	_	_
5	_	_	NNP	_	_	_
6	build	build	VB	_	_	_
7	:	:	:	_	_	_
8	K-12	k-12	NN	_	_	_
9	substr	substr	NN	_	_	_
10	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	genome	genome	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	NC	nc	NN	_	_	_
5	_	_	CD	_	_	_
6	000913.3	000913.3	CD	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	genotype	genotype	NN	_	_	_
10	:	:	:	_	_	_
11	CV108	cv108	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	genotype	genotype	NN	_	_	_
14	:	:	:	_	_	_
15	Galaxy1	galaxy1	NN	_	_	_
16	-	-	:	_	_	_
17	-LSB-	-lsb-	-LRB-	_	_	_
18	CV104	cv104	NN	_	_	_
19	_	_	CD	_	_	_
20	pHDB3	phdb3	NN	_	_	_
21	_	_	CD	_	_	_
22	5	5	CD	_	_	_
23	-RSB-	-rsb-	-RRB-	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	genotype	genotype	NN	_	_	_
26	:	:	:	_	_	_
27	Galaxy2	galaxy2	NN	_	_	_
28	-	-	:	_	_	_
29	-LSB-	-lsb-	-LRB-	_	_	_
30	CV104	cv104	NN	_	_	_
31	_	_	CD	_	_	_
32	pLCV1	plcv1	NN	_	_	_
33	_	_	CD	_	_	_
34	5	5	CD	_	_	_
35	-RSB-	-rsb-	-RRB-	_	_	_
36	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
37	genotype	genotype	NN	_	_	_
38	:	:	:	_	_	_
39	Galaxy3	galaxy3	NN	_	_	_
40	-	-	:	_	_	_
41	-LSB-	-lsb-	-LRB-	_	_	_
42	CV104	cv104	NN	_	_	_
43	_	_	CD	_	_	_
44	pLCV1	plcv1	NN	_	_	_
45	_	_	NN	_	_	_
46	10	10	CD	_	_	_
47	-RSB-	-rsb-	-RRB-	_	_	_
48	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
49	genotype	genotype	NN	_	_	_
50	:	:	:	_	_	_
51	Galaxy4	galaxy4	NN	_	_	_
52	-	-	:	_	_	_
53	-LSB-	-lsb-	-LRB-	_	_	_
54	CV104	cv104	NN	_	_	_
55	_	_	CD	_	_	_
56	pHDB3	phdb3	NN	_	_	_
57	_	_	CD	_	_	_
58	20	20	CD	_	_	_
59	-RSB-	-rsb-	-RRB-	_	_	_
60	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
61	genotype	genotype	NN	_	_	_
62	:	:	:	_	_	_
63	Galaxy5	galaxy5	NN	_	_	_
64	-	-	:	_	_	_
65	-LSB-	-lsb-	-LRB-	_	_	_
66	CV104	cv104	NN	_	_	_
67	_	_	CD	_	_	_
68	pLCV1	plcv1	NN	_	_	_
69	_	_	CD	_	_	_
70	20	20	CD	_	_	_
71	-RSB-	-rsb-	-RRB-	_	_	_
72	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
73	genotype	genotype	NN	_	_	_
74	:	:	:	_	_	_
75	Galaxy6	galaxy6	NN	_	_	_
76	-	-	:	_	_	_
77	-LSB-	-lsb-	-LRB-	_	_	_
78	CV104	cv104	NN	_	_	_
79	_	_	CD	_	_	_
80	pHDB3	phdb3	NN	_	_	_
81	_	_	NN	_	_	_
82	10	10	CD	_	_	_
83	-RSB-	-rsb-	-RRB-	_	_	_
84	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
85	genotype	genotype	NN	_	_	_
86	:	:	:	_	_	_
87	MG1655	mg1655	NN	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	genotype	genotype	NN	_	_	_
90	:	:	:	_	_	_
91	pHDB3	phdb3	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	genotype	genotype	NN	_	_	_
94	:	:	:	_	_	_
95	pLCV1	plcv1	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	genotype	genotype	NN	_	_	_
98	:	:	:	_	_	_
99	SgrR	sgrr	NN	TF	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	genotype	genotype	NN	_	_	_
102	:	:	:	_	_	_
103	sgrS	sgrs	NN	GEN	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	genotype	genotype	NN	_	_	_
106	:	:	:	_	_	_
107	WT	WT	NNP	_	_	_
108	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
109	Hot	Hot	NNP	_	_	_
110	phenol	phenol	NN	_	_	_
111	RNA	rna	NN	_	_	_
112	extraction	extraction	NN	_	_	_
113	as	as	IN	_	_	_
114	described	describe	VBN	_	_	_
115	in	in	IN	_	_	_
116	Aiba	Aiba	NNP	_	_	_
117	.	.	.	_	_	_

1	Adhya	Adhya	NNP	_	_	_
2	and	and	CC	_	_	_
3	Crombrugghe	Crombrugghe	NNP	_	_	_
4	.	.	.	_	_	_

1	J.	J.	NNP	_	_	_
2	Bio	Bio	NNP	_	_	_
3	Chem	Chem	NNP	_	_	_
4	.	.	.	_	_	_

1	1981	1981	CD	_	_	_
2	,	,	,	_	_	_
3	256	256	CD	_	_	_
4	:	:	:	_	_	_
5	p.	p.	NN	_	_	_
6	11905-11910	11905-11910	CD	_	_	_
7	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	media	media	NNS	_	_	_
3	:	:	:	_	_	_
4	Defined	define	VBN	_	_	_
5	MOPS	mop	NNS	MED	_	_
6	Minimal	minimal	JJ	_	_	_
7	+	+	CC	_	_	_
8	0.4	0.4	CD	_	_	_
9	%	%	NN	_	_	_
10	Glycerol	glycerol	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	media	media	NNS	_	_	_
13	:	:	:	_	_	_
14	Defined	define	VBN	_	_	_
15	MOPS	mop	NNS	MED	_	_
16	Minimal	minimal	JJ	_	_	_
17	+	+	CC	_	_	_
18	0.4	0.4	CD	_	_	_
19	%	%	NN	_	_	_
20	Glycerol	glycerol	NN	_	_	_
21	+0.5	+0.5	CD	_	_	_
22	%	%	NN	_	_	_
23	2-DG	2-dg	JJ	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
25	media	media	NNS	_	_	_
26	:	:	:	_	_	_
27	Defined	define	VBN	_	_	_
28	MOPS	mop	NNS	MED	_	_
29	Minimal	minimal	JJ	_	_	_
30	+	+	CC	_	_	_
31	0.4	0.4	CD	_	_	_
32	%	%	NN	_	_	_
33	Glycerol	glycerol	NN	_	_	_
34	+0.5	+0.5	CD	_	_	_
35	%	%	NN	_	_	_
36	aMG	amg	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	media	media	NNS	_	_	_
39	:	:	:	_	_	_
40	Defined	define	VBN	_	_	_
41	MOPS	mop	NNS	MED	_	_
42	Rich	rich	JJ	_	_	_
43	+	+	CC	_	_	_
44	0.2	0.2	CD	_	_	_
45	%	%	NN	_	_	_
46	Glucose	glucose	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	media	media	NNS	_	_	_
49	:	:	:	_	_	_
50	Defined	define	VBN	_	_	_
51	MOPS	mop	NNS	MED	_	_
52	Rich	rich	JJ	_	_	_
53	+	+	CC	_	_	_
54	0.4	0.4	CD	_	_	_
55	%	%	NN	_	_	_
56	Glycerol	glycerol	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	media	media	NNS	_	_	_
59	:	:	:	_	_	_
60	Defined	define	VBN	_	_	_
61	MOPS	mop	NNS	MED	_	_
62	Rich	rich	JJ	_	_	_
63	+	+	CC	_	_	_
64	0.4	0.4	CD	_	_	_
65	%	%	NN	_	_	_
66	Glycerol	glycerol	NN	_	_	_
67	+0.5	+0.5	CD	_	_	_
68	%	%	NN	_	_	_
69	aMG	amg	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	media	media	NNS	_	_	_
72	:	:	:	_	_	_
73	LB	lb	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	media	media	NNS	_	_	_
76	:	:	:	_	_	_
77	LB	lb	NN	_	_	_
78	+	+	CC	_	_	_
79	0.5	0.5	CD	_	_	_
80	%	%	NN	_	_	_
81	aMG	amg	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	MG1655-aMG	mg1655-amg	NN	_	_	_
84	_	_	NN	_	_	_
85	1	1	CD	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	MG1655	mg1655	NN	_	_	_
88	+	+	CC	_	_	_
89	aMG	amg	NN	_	_	_
90	_	_	NN	_	_	_
91	1	1	CD	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	MG1655-aMG	mg1655-amg	NN	_	_	_
94	_	_	NN	_	_	_
95	2	2	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	MG1655	mg1655	NN	_	_	_
98	+	+	CC	_	_	_
99	aMG	amg	NN	_	_	_
100	_	_	NN	_	_	_
101	2	2	CD	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	MG1655-aMG	mg1655-amg	NN	_	_	_
104	_	_	CD	_	_	_
105	3	3	CD	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	MG1655	mg1655	NN	_	_	_
108	+	+	CC	_	_	_
109	aMG	amg	NN	_	_	_
110	_	_	CD	_	_	_
111	3	3	CD	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	MG1655	mg1655	NN	_	_	_
114	_	_	CD	_	_	_
115	minus	minus	CC	_	_	_
116	_	_	SYM	_	_	_
117	aMG	aMG	NNP	_	_	_
118	_	_	SYM	_	_	_
119	1	1	CD	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	MG1655	mg1655	NN	_	_	_
122	_	_	CD	_	_	_
123	minus	minus	CC	_	_	_
124	_	_	SYM	_	_	_
125	aMG	aMG	NNP	_	_	_
126	_	_	SYM	_	_	_
127	2	2	CD	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	MG1655	mg1655	NN	_	_	_
130	_	_	CD	_	_	_
131	minus	minus	CC	_	_	_
132	_	_	SYM	_	_	_
133	aMG	aMG	NNP	_	_	_
134	_	_	SYM	_	_	_
135	3	3	CD	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	MG1655	mg1655	NN	_	_	_
138	_	_	NN	_	_	_
139	plus	plus	CC	_	_	_
140	_	_	SYM	_	_	_
141	aMG	aMG	NNP	_	_	_
142	_	_	SYM	_	_	_
143	1	1	CD	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	MG1655	mg1655	NN	_	_	_
146	_	_	NN	_	_	_
147	plus	plus	CC	_	_	_
148	_	_	SYM	_	_	_
149	aMG	aMG	NNP	_	_	_
150	_	_	SYM	_	_	_
151	2	2	CD	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	MG1655	mg1655	NN	_	_	_
154	_	_	NN	_	_	_
155	plus	plus	CC	_	_	_
156	_	_	SYM	_	_	_
157	aMG	aMG	NNP	_	_	_
158	_	_	SYM	_	_	_
159	3	3	CD	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	pHDB3	phdb3	NN	_	_	_
162	_	_	NN	_	_	_
163	1	1	CD	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	pHDB3	phdb3	NN	_	_	_
166	_	_	NN	_	_	_
167	2	2	CD	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	pHDB3	phdb3	NN	_	_	_
170	_	_	CD	_	_	_
171	3	3	CD	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	pLCV1	plcv1	NN	_	_	_
174	_	_	NN	_	_	_
175	1	1	CD	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	pLCV1	plcv1	NN	_	_	_
178	_	_	NN	_	_	_
179	2	2	CD	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	pLCV1	plcv1	NN	_	_	_
182	_	_	CD	_	_	_
183	3	3	CD	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	Ribosomal	ribosomal	JJ	_	_	_
186	RNA	rna	NN	_	_	_
187	was	be	VBD	_	_	_
188	first	first	JJ	_	_	_
189	removed	remove	VBN	_	_	_
190	using	use	VBG	_	_	_
191	the	the	DT	_	_	_
192	Ribozero	Ribozero	NNP	_	_	_
193	rRNA	rrna	NN	_	_	_
194	Removal	removal	NN	_	_	_
195	Meta-Bacteria	Meta-Bacteria	NNP	_	_	_
196	kit	kit	NN	_	_	_
197	.	.	.	_	_	_

1	Enriched	enriched	JJ	_	_	_
2	mRNAs	mrna	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	converted	convert	VBN	_	_	_
6	into	into	IN	_	_	_
7	indexed	index	VBN	_	_	_
8	libraries	library	NNS	_	_	_
9	using	use	VBG	_	_	_
10	the	the	DT	_	_	_
11	into	into	IN	_	_	_
12	ScriptSeqTM	scriptseqtm	NN	_	_	_
13	v2	v2	NN	_	_	_
14	RNA-Seq	rna-seq	NN	_	_	_
15	Library	Library	NNP	_	_	_
16	Preparation	Preparation	NNP	_	_	_
17	Kit	kit	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	RNA-Seq	rna-seq	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Rockhopper	rockhopper	NN	_	_	_
22	version	version	NN	_	_	_
23	1.20	1.20	CD	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	manuscript	manuscript	NN	_	_	_
26	submitted	submit	VBN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	was	be	VBD	_	_	_
29	used	use	VBN	_	_	_
30	for	for	IN	_	_	_
31	alignment	alignment	NN	_	_	_
32	,	,	,	_	_	_
33	normalization	normalization	NN	_	_	_
34	,	,	,	_	_	_
35	and	and	CC	_	_	_
36	quantification	quantification	NN	_	_	_
37	.	.	.	_	_	_

1	Rockhopper	Rockhopper	NNP	_	_	_
2	is	be	VBZ	_	_	_
3	available	available	JJ	_	_	_
4	for	for	IN	_	_	_
5	download	download	NN	_	_	_
6	from	from	IN	_	_	_
7	http	http	NN	_	_	_
8	:	:	:	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	SgrR	sgrr	NN	TF	_	_
11	_	_	NN	_	_	_
12	1	1	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	SgrR	sgrr	NN	TF	_	_
15	_	_	NN	_	_	_
16	2	2	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	SgrR	sgrr	NN	TF	_	_
19	_	_	CD	_	_	_
20	3	3	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	sgrS	sgrs	NN	GEN	_	_
23	_	_	CD	_	_	_
24	T	t	NN	_	_	_
25	_	_	NN	_	_	_
26	1	1	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	sgrS	sgrs	NN	GEN	_	_
29	_	_	CD	_	_	_
30	T	t	NN	_	_	_
31	_	_	NN	_	_	_
32	2	2	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	sgrS	sgrs	NN	GEN	_	_
35	_	_	CD	_	_	_
36	T	t	NN	_	_	_
37	_	_	NN	_	_	_
38	3	3	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	sgrS	sgrs	NN	GEN	_	_
41	_	_	CD	_	_	_
42	un	un	NN	_	_	_
43	_	_	NN	_	_	_
44	1	1	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	sgrS	sgrs	NN	GEN	_	_
47	_	_	CD	_	_	_
48	un	un	NN	_	_	_
49	_	_	NN	_	_	_
50	2	2	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	sgrS	sgrs	NN	GEN	_	_
53	_	_	CD	_	_	_
54	un	un	NN	_	_	_
55	_	_	NN	_	_	_
56	3	3	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	strain	strain	NN	_	_	_
59	:	:	:	_	_	_
60	K-12	k-12	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Supplementary	supplementary	JJ	_	_	_
63	_	_	NN	_	_	_
64	files	file	NNS	_	_	_
65	_	_	IN	_	_	_
66	format	format	NN	_	_	_
67	_	_	NN	_	_	_
68	and	and	CC	_	_	_
69	_	_	NN	_	_	_
70	content	content	NN	_	_	_
71	:	:	:	_	_	_
72	Tab	tab	NN	_	_	_
73	delimited	delimit	VBN	_	_	_
74	text	text	NN	_	_	_
75	files	file	NNS	_	_	_
76	containing	contain	VBG	_	_	_
77	transcription	transcription	NN	_	_	_
78	coordinates	coordinate	VBZ	_	_	_
79	and	and	CC	_	_	_
80	abundance	abundance	NN	_	_	_
81	estimates	estimate	NNS	_	_	_
82	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	from	from	IN	_	_	_
5	bacterial	bacterial	JJ	_	_	_
6	culture	culture	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	WT	wt	JJ	_	_	_
9	_	_	NN	_	_	_
10	1	1	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	WT	wt	JJ	_	_	_
13	_	_	NN	_	_	_
14	2	2	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	WT	wt	JJ	_	_	_
17	_	_	NN	_	_	_
18	3	3	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	WT	wt	JJ	_	_	_
21	_	_	NN	_	_	_
22	minus	minus	CC	_	_	_
23	_	_	SYM	_	_	_
24	2DG	2dg	CD	_	_	_
25	_	_	NN	_	_	_
26	1	1	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	WT	wt	JJ	_	_	_
29	_	_	NN	_	_	_
30	minus	minus	CC	_	_	_
31	_	_	SYM	_	_	_
32	2DG	2dg	CD	_	_	_
33	_	_	NN	_	_	_
34	2	2	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	WT	wt	JJ	_	_	_
37	_	_	NN	_	_	_
38	minus	minus	CC	_	_	_
39	_	_	SYM	_	_	_
40	2DG	2dg	CD	_	_	_
41	_	_	SYM	_	_	_
42	3	3	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	WT	wt	JJ	_	_	_
45	_	_	NN	_	_	_
46	plus	plus	CC	_	_	_
47	_	_	SYM	_	_	_
48	2DG	2dg	CD	_	_	_
49	_	_	NN	_	_	_
50	1	1	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	WT	wt	JJ	_	_	_
53	_	_	NN	_	_	_
54	plus	plus	CC	_	_	_
55	_	_	SYM	_	_	_
56	2DG	2dg	CD	_	_	_
57	_	_	NN	_	_	_
58	2	2	CD	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	WT	wt	JJ	_	_	_
61	_	_	NN	_	_	_
62	plus	plus	CC	_	_	_
63	_	_	SYM	_	_	_
64	2DG	2dg	CD	_	_	_
65	_	_	SYM	_	_	_
66	3	3	CD	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	wt	wt	JJ	_	_	_
69	_	_	NN	_	_	_
70	T	t	NN	_	_	_
71	_	_	NN	_	_	_
72	1	1	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	wt	wt	JJ	_	_	_
75	_	_	NN	_	_	_
76	T	t	NN	_	_	_
77	_	_	NN	_	_	_
78	2	2	CD	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	wt	wt	JJ	_	_	_
81	_	_	NN	_	_	_
82	T	t	NN	_	_	_
83	_	_	CD	_	_	_
84	3	3	CD	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	wt	wt	JJ	_	_	_
87	_	_	NN	_	_	_
88	un	un	NN	_	_	_
89	_	_	NN	_	_	_
90	1	1	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	wt	wt	JJ	_	_	_
93	_	_	NN	_	_	_
94	un	un	NN	_	_	_
95	_	_	NN	_	_	_
96	2	2	CD	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	wt	wt	JJ	_	_	_
99	_	_	NN	_	_	_
100	un	un	NN	_	_	_
101	_	_	NN	_	_	_
102	3	3	CD	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	Chemostat	chemostat	NN	_	_	_
105	1	1	CD	_	_	_
106	h	h	NN	_	_	_
107	irradiated	irradiated	JJ	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	Chemostat	chemostat	NN	_	_	_
110	1h	1h	NN	_	_	_
111	irradiated	irradiated	JJ	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	Chemostat	chemostat	NN	_	_	_
114	50	50	CD	_	_	_
115	h	h	NN	_	_	_
116	irradiated	irradiated	JJ	_	_	_
117	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
118	Control	Control	NNP	_	_	_
119	chemostat	chemostat	NN	_	_	_
120	1	1	CD	_	_	_
121	h	h	NN	_	_	_
122	not	not	RB	_	_	_
123	irradiated	irradiated	JJ	_	_	_
124	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
125	Control	Control	NNP	_	_	_
126	chemostat	chemostat	NN	_	_	_
127	1h	1h	NN	_	_	_
128	not	not	RB	_	_	_
129	irradiated	irradiated	JJ	_	_	_
130	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
131	Control	Control	NNP	_	_	_
132	chemostat	chemostat	NN	_	_	_
133	50	50	CD	_	_	_
134	h	h	NN	_	_	_
135	not	not	RB	_	_	_
136	irradiated	irradiated	JJ	_	_	_
137	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
138	E.	E.	NNP	_	_	_
139	coli	coli	NN	_	_	_
140	K12	k12	NN	_	_	_
141	MG1655	mg1655	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	Escherichia	escherichia	FW	Organism	_	_
144	coli	coli	FW	Organism	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	Jaguar	Jaguar	NNP	_	_	_
147	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
148	UVA	UVA	NNP	_	_	_
149	irradiated	irradiate	VBD	_	_	_
150	chemostat	chemostat	NN	_	_	_
151	for	for	IN	_	_	_
152	1	1	CD	_	_	_
153	h	h	NN	_	_	_
154	,	,	,	_	_	_
155	run	run	VBP	_	_	_
156	1	1	CD	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	UVA	uva	NN	_	_	_
159	irradiated	irradiated	JJ	_	_	_
160	chemostat	chemostat	NN	_	_	_
161	for	for	IN	_	_	_
162	1	1	CD	_	_	_
163	h	h	NN	_	_	_
164	,	,	,	_	_	_
165	run	run	NN	_	_	_
166	2	2	CD	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	UVA	uva	NN	_	_	_
169	irradiated	irradiated	JJ	_	_	_
170	chemostat	chemostat	NN	_	_	_
171	for	for	IN	_	_	_
172	1	1	CD	_	_	_
173	h	h	NN	_	_	_
174	,	,	,	_	_	_
175	run	run	NN	_	_	_
176	2	2	CD	_	_	_
177	dye	dye	VBP	_	_	_
178	swap	swap	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	UVA	uva	NN	_	_	_
181	irradiated	irradiated	JJ	_	_	_
182	chemostat	chemostat	NN	_	_	_
183	for	for	IN	_	_	_
184	1	1	CD	_	_	_
185	h	h	NN	_	_	_
186	,	,	,	_	_	_
187	run	run	VBP	_	_	_
188	3	3	CD	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	UVA	uva	NN	_	_	_
191	irradiated	irradiated	JJ	_	_	_
192	chemostat	chemostat	NN	_	_	_
193	for	for	IN	_	_	_
194	50	50	CD	_	_	_
195	h	h	NN	_	_	_
196	,	,	,	_	_	_
197	run	run	VBP	_	_	_
198	1	1	CD	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	UVA	uva	NN	_	_	_
201	irradiated	irradiated	JJ	_	_	_
202	chemostat	chemostat	NN	_	_	_
203	for	for	IN	_	_	_
204	50	50	CD	_	_	_
205	h	h	NN	_	_	_
206	,	,	,	_	_	_
207	run	run	NN	_	_	_
208	2	2	CD	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	UVA	uva	NN	_	_	_
211	irradiated	irradiated	JJ	_	_	_
212	chemostat	chemostat	NN	_	_	_
213	for	for	IN	_	_	_
214	50	50	CD	_	_	_
215	h	h	NN	_	_	_
216	,	,	,	_	_	_
217	run	run	VBP	_	_	_
218	3	3	CD	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	e.coli	e.coli	JJ	_	_	_
221	culture	culture	NN	_	_	_
222	protocol	protocol	NN	_	_	_
223	:	:	:	_	_	_
224	conditioned	condition	VBN	_	_	_
225	Caco-2	caco-2	NN	_	_	_
226	cell	cell	NN	_	_	_
227	medium	medium	NN	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	e.coli	e.coli	JJ	_	_	_
230	culture	culture	NN	_	_	_
231	protocol	protocol	NN	_	_	_
232	:	:	:	_	_	_
233	fresh	fresh	JJ	_	_	_
234	medium	medium	NN	_	_	_
235	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
236	Escherichia	escherichia	FW	Organism	_	_
237	coli	coli	FW	Organism	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
239	STEC	stec	NN	_	_	_
240	EC472	ec472	NN	_	_	_
241	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
242	STEC	STEC	NNP	_	_	_
243	EC472	ec472	NN	_	_	_
244	after	after	IN	_	_	_
245	3	3	CD	_	_	_
246	hrs	hr	NNS	_	_	_
247	incubation	incubation	NN	_	_	_
248	in	in	IN	_	_	_
249	conditioned	conditioned	JJ	_	_	_
250	medium	medium	NN	_	_	_
251	,	,	,	_	_	_
252	replicate	replicate	VB	_	_	_
253	1	1	CD	_	_	_
254	-LSB-	-lsb-	-LRB-	_	_	_
255	COND	cond	NN	_	_	_
256	-RSB-	-rsb-	-RRB-	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	STEC	stec	NN	_	_	_
259	EC472	ec472	NN	_	_	_
260	after	after	IN	_	_	_
261	3	3	CD	_	_	_
262	hrs	hr	NNS	_	_	_
263	incubation	incubation	NN	_	_	_
264	in	in	IN	_	_	_
265	conditioned	conditioned	JJ	_	_	_
266	medium	medium	NN	_	_	_
267	,	,	,	_	_	_
268	replicate	replicate	VB	_	_	_
269	2	2	CD	_	_	_
270	-LSB-	-lsb-	-LRB-	_	_	_
271	COND	cond	NN	_	_	_
272	-RSB-	-rsb-	-RRB-	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	STEC	stec	NN	_	_	_
275	EC472	ec472	NN	_	_	_
276	after	after	IN	_	_	_
277	3	3	CD	_	_	_
278	hrs	hr	NNS	_	_	_
279	incubation	incubation	NN	_	_	_
280	in	in	IN	_	_	_
281	conditioned	conditioned	JJ	_	_	_
282	medium	medium	NN	_	_	_
283	,	,	,	_	_	_
284	replicate	replicate	VB	_	_	_
285	3	3	CD	_	_	_
286	-LSB-	-lsb-	-LRB-	_	_	_
287	COND	cond	NN	_	_	_
288	-RSB-	-rsb-	-RRB-	_	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
290	STEC	stec	NN	_	_	_
291	EC472	ec472	NN	_	_	_
292	after	after	IN	_	_	_
293	3	3	CD	_	_	_
294	hrs	hr	NNS	_	_	_
295	incubation	incubation	NN	_	_	_
296	in	in	IN	_	_	_
297	conditioned	conditioned	JJ	_	_	_
298	medium	medium	NN	_	_	_
299	,	,	,	_	_	_
300	replicate	replicate	VB	_	_	_
301	4	4	CD	_	_	_
302	-LSB-	-lsb-	-LRB-	_	_	_
303	COND	cond	NN	_	_	_
304	-RSB-	-rsb-	-RRB-	_	_	_
305	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
306	STEC	stec	NN	_	_	_
307	EC472	ec472	NN	_	_	_
308	after	after	IN	_	_	_
309	3	3	CD	_	_	_
310	hrs	hr	NNS	_	_	_
311	incubation	incubation	NN	_	_	_
312	in	in	IN	_	_	_
313	fresh	fresh	JJ	_	_	_
314	medium	medium	NN	_	_	_
315	,	,	,	_	_	_
316	replicate	replicate	VB	_	_	_
317	1	1	CD	_	_	_
318	-LSB-	-lsb-	-LRB-	_	_	_
319	FRESH	fresh	JJ	_	_	_
320	-RSB-	-rsb-	-RRB-	_	_	_
321	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
322	STEC	STEC	NNP	_	_	_
323	EC472	ec472	NN	_	_	_
324	after	after	IN	_	_	_
325	3	3	CD	_	_	_
326	hrs	hr	NNS	_	_	_
327	incubation	incubation	NN	_	_	_
328	in	in	IN	_	_	_
329	fresh	fresh	JJ	_	_	_
330	medium	medium	NN	_	_	_
331	,	,	,	_	_	_
332	replicate	replicate	VB	_	_	_
333	2	2	CD	_	_	_
334	-LSB-	-lsb-	-LRB-	_	_	_
335	FRESH	fresh	JJ	_	_	_
336	-RSB-	-rsb-	-RRB-	_	_	_
337	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
338	STEC	STEC	NNP	_	_	_
339	EC472	ec472	NN	_	_	_
340	after	after	IN	_	_	_
341	3	3	CD	_	_	_
342	hrs	hr	NNS	_	_	_
343	incubation	incubation	NN	_	_	_
344	in	in	IN	_	_	_
345	fresh	fresh	JJ	_	_	_
346	medium	medium	NN	_	_	_
347	,	,	,	_	_	_
348	replicate	replicate	VB	_	_	_
349	3	3	CD	_	_	_
350	-LSB-	-lsb-	-LRB-	_	_	_
351	FRESH	fresh	JJ	_	_	_
352	-RSB-	-rsb-	-RRB-	_	_	_
353	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
354	STEC	STEC	NNP	_	_	_
355	EC472	ec472	NN	_	_	_
356	after	after	IN	_	_	_
357	3	3	CD	_	_	_
358	hrs	hr	NNS	_	_	_
359	incubation	incubation	NN	_	_	_
360	in	in	IN	_	_	_
361	fresh	fresh	JJ	_	_	_
362	medium	medium	NN	_	_	_
363	,	,	,	_	_	_
364	replicate	replicate	VB	_	_	_
365	4	4	CD	_	_	_
366	-LSB-	-lsb-	-LRB-	_	_	_
367	FRESH	fresh	JJ	_	_	_
368	-RSB-	-rsb-	-RRB-	_	_	_
369	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
370	STEC	STEC	NNP	_	_	_
371	EH41	eh41	NN	_	_	_
372	after	after	IN	_	_	_
373	3	3	CD	_	_	_
374	hrs	hr	NNS	_	_	_
375	incubation	incubation	NN	_	_	_
376	in	in	IN	_	_	_
377	conditioned	conditioned	JJ	_	_	_
378	medium	medium	NN	_	_	_
379	,	,	,	_	_	_
380	replicate	replicate	VB	_	_	_
381	1	1	CD	_	_	_
382	-LSB-	-lsb-	-LRB-	_	_	_
383	COND	cond	NN	_	_	_
384	-RSB-	-rsb-	-RRB-	_	_	_
385	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
386	STEC	stec	NN	_	_	_
387	EH41	eh41	NN	_	_	_
388	after	after	IN	_	_	_
389	3	3	CD	_	_	_
390	hrs	hr	NNS	_	_	_
391	incubation	incubation	NN	_	_	_
392	in	in	IN	_	_	_
393	conditioned	conditioned	JJ	_	_	_
394	medium	medium	NN	_	_	_
395	,	,	,	_	_	_
396	replicate	replicate	VB	_	_	_
397	2	2	CD	_	_	_
398	-LSB-	-lsb-	-LRB-	_	_	_
399	COND	cond	NN	_	_	_
400	-RSB-	-rsb-	-RRB-	_	_	_
401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
402	STEC	stec	NN	_	_	_
403	EH41	eh41	NN	_	_	_
404	after	after	IN	_	_	_
405	3	3	CD	_	_	_
406	hrs	hr	NNS	_	_	_
407	incubation	incubation	NN	_	_	_
408	in	in	IN	_	_	_
409	conditioned	conditioned	JJ	_	_	_
410	medium	medium	NN	_	_	_
411	,	,	,	_	_	_
412	replicate	replicate	VB	_	_	_
413	3	3	CD	_	_	_
414	-LSB-	-lsb-	-LRB-	_	_	_
415	COND	cond	NN	_	_	_
416	-RSB-	-rsb-	-RRB-	_	_	_
417	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
418	STEC	stec	NN	_	_	_
419	EH41	eh41	NN	_	_	_
420	after	after	IN	_	_	_
421	3	3	CD	_	_	_
422	hrs	hr	NNS	_	_	_
423	incubation	incubation	NN	_	_	_
424	in	in	IN	_	_	_
425	conditioned	conditioned	JJ	_	_	_
426	medium	medium	NN	_	_	_
427	,	,	,	_	_	_
428	replicate	replicate	VB	_	_	_
429	4	4	CD	_	_	_
430	-LSB-	-lsb-	-LRB-	_	_	_
431	COND	cond	NN	_	_	_
432	-RSB-	-rsb-	-RRB-	_	_	_
433	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
434	STEC	stec	NN	_	_	_
435	EH41	eh41	NN	_	_	_
436	after	after	IN	_	_	_
437	3	3	CD	_	_	_
438	hrs	hr	NNS	_	_	_
439	incubation	incubation	NN	_	_	_
440	in	in	IN	_	_	_
441	fresh	fresh	JJ	_	_	_
442	medium	medium	NN	_	_	_
443	,	,	,	_	_	_
444	replicate	replicate	VB	_	_	_
445	1	1	CD	_	_	_
446	-LSB-	-lsb-	-LRB-	_	_	_
447	FRESH	fresh	JJ	_	_	_
448	-RSB-	-rsb-	-RRB-	_	_	_
449	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
450	STEC	STEC	NNP	_	_	_
451	EH41	eh41	NN	_	_	_
452	after	after	IN	_	_	_
453	3	3	CD	_	_	_
454	hrs	hr	NNS	_	_	_
455	incubation	incubation	NN	_	_	_
456	in	in	IN	_	_	_
457	fresh	fresh	JJ	_	_	_
458	medium	medium	NN	_	_	_
459	,	,	,	_	_	_
460	replicate	replicate	VB	_	_	_
461	2	2	CD	_	_	_
462	-LSB-	-lsb-	-LRB-	_	_	_
463	FRESH	fresh	JJ	_	_	_
464	-RSB-	-rsb-	-RRB-	_	_	_
465	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
466	STEC	STEC	NNP	_	_	_
467	EH41	eh41	NN	_	_	_
468	after	after	IN	_	_	_
469	3	3	CD	_	_	_
470	hrs	hr	NNS	_	_	_
471	incubation	incubation	NN	_	_	_
472	in	in	IN	_	_	_
473	fresh	fresh	JJ	_	_	_
474	medium	medium	NN	_	_	_
475	,	,	,	_	_	_
476	replicate	replicate	VB	_	_	_
477	3	3	CD	_	_	_
478	-LSB-	-lsb-	-LRB-	_	_	_
479	FRESH	fresh	JJ	_	_	_
480	-RSB-	-rsb-	-RRB-	_	_	_
481	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
482	STEC	STEC	NNP	_	_	_
483	EH41	eh41	NN	_	_	_
484	after	after	IN	_	_	_
485	3	3	CD	_	_	_
486	hrs	hr	NNS	_	_	_
487	incubation	incubation	NN	_	_	_
488	in	in	IN	_	_	_
489	fresh	fresh	JJ	_	_	_
490	medium	medium	NN	_	_	_
491	,	,	,	_	_	_
492	replicate	replicate	VB	_	_	_
493	4	4	CD	_	_	_
494	-LSB-	-lsb-	-LRB-	_	_	_
495	FRESH	fresh	JJ	_	_	_
496	-RSB-	-rsb-	-RRB-	_	_	_
497	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
498	STEC	STEC	NNP	_	_	_
499	EH41	eh41	NN	_	_	_
500	,	,	,	_	_	_
501	conditioned	conditioned	JJ	_	_	_
502	medium	medium	NN	_	_	_
503	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
504	STEC	STEC	NNP	_	_	_
505	EH41	eh41	NN	_	_	_
506	,	,	,	_	_	_
507	fresh	fresh	JJ	_	_	_
508	medium	medium	NN	_	_	_
509	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
510	STEC	STEC	NNP	_	_	_
511	strains	strain	NNS	_	_	_
512	were	be	VBD	_	_	_
513	lysate	lysate	NN	_	_	_
514	using	use	VBG	_	_	_
515	lysozyme	lysozyme	NN	_	_	_
516	-LRB-	-lrb-	-LRB-	_	_	_
517	1	1	CD	_	_	_
518	mg	mg	NN	_	_	_
519	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
520	strain	strain	NN	_	_	_
521	:	:	:	_	_	_
522	EC472	ec472	NN	_	_	_
523	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
524	strain	strain	NN	_	_	_
525	:	:	:	_	_	_
526	EH41	eh41	NN	_	_	_
527	-LRB-	-lrb-	-LRB-	_	_	_
528	isolated	isolate	VBN	_	_	_
529	from	from	IN	_	_	_
530	patient	patient	NN	_	_	_
531	with	with	IN	_	_	_
532	HUS	hus	NN	_	_	_
533	-RRB-	-rrb-	-RRB-	_	_	_
534	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
535	The	the	DT	_	_	_
536	conditioned	conditioned	JJ	_	_	_
537	medium	medium	NN	_	_	_
538	-LRB-	-lrb-	-LRB-	_	_	_
539	C	c	NN	_	_	_
540	-RRB-	-rrb-	-RRB-	_	_	_
541	was	be	VBD	_	_	_
542	the	the	DT	_	_	_
543	DMEM	DMEM	NNP	_	_	_
544	medium	medium	NN	_	_	_
545	containing	contain	VBG	_	_	_
546	10	10	CD	_	_	_
547	%	%	NN	_	_	_
548	FBS	fbs	NN	_	_	_
549	without	without	IN	_	_	_
550	antibiotics	antibiotic	NNS	_	_	_
551	recovered	recover	VBN	_	_	_
552	after	after	IN	_	_	_
553	24	24	CD	_	_	_
554	hrs	hr	NNS	_	_	_
555	incubation	incubation	NN	_	_	_
556	with	with	IN	_	_	_
557	differentiated	differentiate	VBN	_	_	_
558	Caco-2	caco-2	NN	_	_	_
559	cells	cell	NNS	_	_	_
560	.	.	.	_	_	_

1	400	400	CD	_	_	_
2	µL	µl	NN	_	_	_
3	of	of	IN	_	_	_
4	STEC	stec	NN	_	_	_
5	culture	culture	NN	_	_	_
6	were	be	VBD	_	_	_
7	inoculated	inoculate	VBN	_	_	_
8	in	in	IN	_	_	_
9	4	4	CD	_	_	_
10	mL	ml	NN	_	_	_
11	of	of	IN	_	_	_
12	C	c	NN	_	_	_
13	medium	medium	NN	_	_	_
14	and	and	CC	_	_	_
15	incubated	incubate	VBN	_	_	_
16	for	for	IN	_	_	_
17	3	3	CD	_	_	_
18	hrs	hr	NNS	_	_	_
19	at	at	IN	_	_	_
20	37	37	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	this	this	DT	_	_	_
3	period	period	NN	_	_	_
4	the	the	DT	_	_	_
5	bacteria	bacterium	NNS	_	_	_
6	were	be	VBD	_	_	_
7	recovered	recover	VBN	_	_	_
8	by	by	IN	_	_	_
9	centrifugation	centrifugation	NN	_	_	_
10	for	for	IN	_	_	_
11	10	10	CD	_	_	_
12	min	min	NN	_	_	_
13	at	at	IN	_	_	_
14	5000	5000	CD	_	_	_
15	xg	xg	NN	_	_	_
16	and	and	CC	_	_	_
17	the	the	DT	_	_	_
18	pellet	pellet	NN	_	_	_
19	was	be	VBD	_	_	_
20	ressuspended	ressuspend	VBN	_	_	_
21	in	in	IN	_	_	_
22	600	600	CD	_	_	_
23	µL	µl	NN	_	_	_
24	of	of	IN	_	_	_
25	RNAprotect	rnaprotect	NN	_	_	_
26	Bacteria	bacterium	NNS	_	_	_
27	Reagent	reagent	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Qiagen	Qiagen	NNP	_	_	_
30	cat	cat	NN	_	_	_
31	.	.	.	_	_	_

1	no.	no.	RB	_	_	_
2	76506	76506	CD	_	_	_
3	,	,	,	_	_	_
4	Valencia	Valencia	NNP	_	_	_
5	,	,	,	_	_	_
6	CA	CA	NNP	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	for	for	IN	_	_	_
9	RNA	rna	NN	_	_	_
10	extraction	extraction	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	fresh	fresh	JJ	_	_	_
4	medium	medium	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	F	f	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	was	be	VBD	_	_	_
9	the	the	DT	_	_	_
10	DMEM	DMEM	NNP	_	_	_
11	medium	medium	NN	_	_	_
12	containing	contain	VBG	_	_	_
13	10	10	CD	_	_	_
14	%	%	NN	_	_	_
15	FBS	fbs	NN	_	_	_
16	without	without	IN	_	_	_
17	antibiotics	antibiotic	NNS	_	_	_
18	.	.	.	_	_	_

1	400	400	CD	_	_	_
2	µL	µl	NN	_	_	_
3	of	of	IN	_	_	_
4	STEC	stec	NN	_	_	_
5	culture	culture	NN	_	_	_
6	were	be	VBD	_	_	_
7	inoculated	inoculate	VBN	_	_	_
8	in	in	IN	_	_	_
9	4	4	CD	_	_	_
10	mL	ml	NN	_	_	_
11	of	of	IN	_	_	_
12	F	f	NN	_	_	_
13	medium	medium	NN	_	_	_
14	and	and	CC	_	_	_
15	incubated	incubate	VBN	_	_	_
16	for	for	IN	_	_	_
17	3	3	CD	_	_	_
18	hrs	hr	NNS	_	_	_
19	at	at	IN	_	_	_
20	37	37	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	this	this	DT	_	_	_
3	period	period	NN	_	_	_
4	the	the	DT	_	_	_
5	bacteria	bacterium	NNS	_	_	_
6	were	be	VBD	_	_	_
7	recovered	recover	VBN	_	_	_
8	by	by	IN	_	_	_
9	centrifugation	centrifugation	NN	_	_	_
10	for	for	IN	_	_	_
11	10	10	CD	_	_	_
12	min	min	NN	_	_	_
13	at	at	IN	_	_	_
14	5000	5000	CD	_	_	_
15	xg	xg	NN	_	_	_
16	and	and	CC	_	_	_
17	the	the	DT	_	_	_
18	pellet	pellet	NN	_	_	_
19	was	be	VBD	_	_	_
20	ressuspended	ressuspend	VBN	_	_	_
21	in	in	IN	_	_	_
22	600	600	CD	_	_	_
23	µL	µl	NN	_	_	_
24	of	of	IN	_	_	_
25	RNAprotect	rnaprotect	NN	_	_	_
26	Bacteria	bacterium	NNS	_	_	_
27	Reagent	reagent	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Qiagen	Qiagen	NNP	_	_	_
30	cat	cat	NN	_	_	_
31	.	.	.	_	_	_

1	no.	no.	RB	_	_	_
2	76506	76506	CD	_	_	_
3	,	,	,	_	_	_
4	Valencia	Valencia	NNP	_	_	_
5	,	,	,	_	_	_
6	CA	CA	NNP	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	for	for	IN	_	_	_
9	RNA	rna	NN	_	_	_
10	extraction	extraction	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	scanned	scan	VBN	_	_	_
4	images	image	NNS	_	_	_
5	were	be	VBD	_	_	_
6	analyzed	analyze	VBN	_	_	_
7	with	with	IN	_	_	_
8	Feature	Feature	NNP	_	_	_
9	Extraction	Extraction	NNP	_	_	_
10	Software	Software	NNP	_	_	_
11	version	version	NN	_	_	_
12	9.5.3.1	9.5.3.1	CD	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Agilent	Agilent	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	using	use	VBG	_	_	_
17	default	default	NN	_	_	_
18	parameters	parameter	NNS	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	protocol	protocol	NN	_	_	_
21	GE1-v5	ge1-v5	NN	_	_	_
22	_	_	CD	_	_	_
23	95	95	CD	_	_	_
24	and	and	CC	_	_	_
25	Grid	Grid	NNP	_	_	_
26	:	:	:	_	_	_
27	020097	020097	CD	_	_	_
28	_	_	NN	_	_	_
29	D	d	NN	_	_	_
30	_	_	CD	_	_	_
31	F	f	NN	_	_	_
32	_	_	SYM	_	_	_
33	20080627	20080627	CD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	to	to	TO	_	_	_
36	obtain	obtain	VB	_	_	_
37	background	background	NN	_	_	_
38	subtracted	subtract	VBN	_	_	_
39	and	and	CC	_	_	_
40	spatially	spatially	RB	_	_	_
41	detrended	detrend	VBD	_	_	_
42	Processed	processed	JJ	_	_	_
43	Signal	signal	NN	_	_	_
44	intensities	intensity	NNS	_	_	_
45	but	but	CC	_	_	_
46	not	not	RB	_	_	_
47	included	include	VBD	_	_	_
48	the	the	DT	_	_	_
49	normalization	normalization	NN	_	_	_
50	process	process	NN	_	_	_
51	.	.	.	_	_	_

1	Features	feature	NNS	_	_	_
2	flagged	flag	VBD	_	_	_
3	in	in	IN	_	_	_
4	Feature	Feature	NNP	_	_	_
5	Extraction	Extraction	NNP	_	_	_
6	as	as	IN	_	_	_
7	Feature	Feature	NNP	_	_	_
8	Non-uniform	non-uniform	JJ	_	_	_
9	outliers	outlier	NNS	_	_	_
10	were	be	VBD	_	_	_
11	excluded	exclude	VBN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2	antibody	antibody	NN	_	_	_
3	:	:	:	_	_	_
4	polycolonal	polycolonal	JJ	_	_	_
5	antiserum	antiserum	NN	_	_	_
6	was	be	VBD	_	_	_
7	raised	raise	VBN	_	_	_
8	against	against	IN	_	_	_
9	His6-ArcA	his6-arca	NN	_	_	_
10	then	then	RB	_	_	_
11	Affinity	Affinity	NNP	_	_	_
12	Purified	purify	VBN	_	_	_
13	against	against	IN	_	_	_
14	ArcA	arca	NN	TF	_	_
15	to	to	TO	_	_	_
16	yield	yield	VB	_	_	_
17	the	the	DT	_	_	_
18	polyclonal	polyclonal	JJ	_	_	_
19	antibodies	antibody	NNS	_	_	_
20	used	use	VBN	_	_	_
21	for	for	IN	_	_	_
22	ChIP	chip	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	ArcA	arca	NN	TF	_	_
25	-	-	:	_	_	_
26	Aerobic	aerobic	JJ	_	_	_
27	-	-	:	_	_	_
28	Affinity	affinity	NN	_	_	_
29	Purified	purify	VBN	_	_	_
30	-	-	:	_	_	_
31	A	a	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	ArcA	arca	NN	TF	_	_
34	-	-	:	_	_	_
35	Anaerobic	anaerobic	JJ	_	_	_
36	-	-	:	_	_	_
37	Affinity	affinity	NN	_	_	_
38	Purified	purify	VBN	_	_	_
39	-	-	:	_	_	_
40	biological	biological	JJ	_	_	_
41	rep	rep	NN	GEN	_	_
42	A	a	DT	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	ArcA	arca	NN	TF	_	_
45	-	-	:	_	_	_
46	Anaerobic	anaerobic	JJ	_	_	_
47	-	-	:	_	_	_
48	Affinity	affinity	NN	_	_	_
49	Purified	purify	VBN	_	_	_
50	-	-	:	_	_	_
51	biological	biological	JJ	_	_	_
52	rep	rep	NN	GEN	_	_
53	B	b	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	∆	∆	CD	_	_	_
56	ArcA	arca	NN	TF	_	_
57	-	-	:	_	_	_
58	Anaerobic	anaerobic	JJ	_	_	_
59	-	-	:	_	_	_
60	Affinity	affinity	NN	_	_	_
61	Purified	purify	VBN	_	_	_
62	-	-	:	_	_	_
63	technical	technical	JJ	_	_	_
64	rep	rep	NN	GEN	_	_
65	A	a	DT	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	∆	∆	CD	_	_	_
68	ArcA	arca	NN	TF	_	_
69	-	-	:	_	_	_
70	Anaerobic	anaerobic	JJ	_	_	_
71	-	-	:	_	_	_
72	Affinity	affinity	NN	_	_	_
73	Purified	purify	VBN	_	_	_
74	-	-	:	_	_	_
75	technical	technical	JJ	_	_	_
76	rep	rep	NN	GEN	_	_
77	B	b	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	ArcA	arca	NN	TF	_	_
80	INPUT	input	NN	_	_	_
81	DNA	dna	NN	_	_	_
82	from	from	IN	_	_	_
83	WT	WT	NNP	_	_	_
84	Escherchia	Escherchia	NNP	_	_	_
85	coli	coli	NN	_	_	_
86	MG1655	mg1655	NN	_	_	_
87	K-12	k-12	NN	_	_	_
88	,	,	,	_	_	_
89	no	no	DT	_	_	_
90	antibody	antibody	NN	_	_	_
91	control	control	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
93	ArcA	arca	NN	TF	_	_
94	INPUT	input	NN	_	_	_
95	from	from	IN	_	_	_
96	WT	WT	NNP	_	_	_
97	Escherichia	escherichia	FW	Organism	_	_
98	coli	coli	FW	Organism	_	_
99	MG1655	mg1655	NN	_	_	_
100	K-12	k-12	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	∆	∆	CD	_	_	_
103	arcA	arcA	NNP	GEN	_	_
104	IP	IP	NNP	_	_	_
105	DNA	dna	NN	_	_	_
106	from	from	IN	_	_	_
107	PK9416	pk9416	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	ArcA	arca	NN	TF	_	_
110	IP	IP	NNP	_	_	_
111	DNA	dna	NN	_	_	_
112	from	from	IN	_	_	_
113	WT	WT	NNP	_	_	_
114	Escherichia	escherichia	FW	Organism	_	_
115	coli	coli	FW	Organism	_	_
116	MG1655	mg1655	NN	_	_	_
117	K-12	k-12	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	ArcA	arca	NN	TF	_	_
120	IP	IP	NNP	_	_	_
121	from	from	IN	_	_	_
122	WT	WT	NNP	_	_	_
123	Escherichia	escherichia	FW	Organism	_	_
124	coli	coli	FW	Organism	_	_
125	MG1655	mg1655	NN	_	_	_
126	K-12	k-12	NN	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	Arrays	array	NNS	_	_	_
129	were	be	VBD	_	_	_
130	processed	process	VBN	_	_	_
131	using	use	VBG	_	_	_
132	Nimblegen	Nimblegen	NNP	_	_	_
133	's	's	POS	_	_	_
134	standard	standard	JJ	_	_	_
135	protocol	protocol	NN	_	_	_
136	for	for	IN	_	_	_
137	Nimblescan	nimblescan	JJ	_	_	_
138	2.4	2.4	CD	_	_	_
139	ChIP	chip	NN	_	_	_
140	data	datum	NNS	_	_	_
141	extraction	extraction	NN	_	_	_
142	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cell	cell	NN	_	_	_
3	pellets	pellet	NNS	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	from	from	IN	_	_	_
6	initial	initial	JJ	_	_	_
7	50	50	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	culture	culture	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	were	be	VBD	_	_	_
13	thawed	thaw	VBN	_	_	_
14	and	and	CC	_	_	_
15	resuspended	resuspend	VBN	_	_	_
16	in	in	IN	_	_	_
17	250ul	250ul	NN	_	_	_
18	of	of	IN	_	_	_
19	IP	IP	NNP	_	_	_
20	buffer	buffer	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	100	100	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	Tris	Tris	NNP	_	_	_
25	pH	ph	NN	_	_	_
26	8	8	CD	_	_	_
27	,	,	,	_	_	_
28	300	300	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	NaCl	nacl	NN	_	_	_
31	,	,	,	_	_	_
32	2	2	CD	_	_	_
33	%	%	NN	_	_	_
34	TritonX-100	tritonx-100	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	and	and	CC	_	_	_
37	sonicated	sonicate	VBN	_	_	_
38	using	use	VBG	_	_	_
39	a	a	DT	_	_	_
40	microtip	microtip	NN	_	_	_
41	sonicator	sonicator	NN	_	_	_
42	set	set	VBN	_	_	_
43	at	at	IN	_	_	_
44	10	10	CD	_	_	_
45	%	%	NN	_	_	_
46	output	output	NN	_	_	_
47	for	for	IN	_	_	_
48	20	20	CD	_	_	_
49	second	second	JJ	_	_	_
50	intervals	interval	NNS	_	_	_
51	with	with	IN	_	_	_
52	periods	period	NNS	_	_	_
53	of	of	IN	_	_	_
54	cooling	cool	VBG	_	_	_
55	in	in	IN	_	_	_
56	between	between	IN	_	_	_
57	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	treated	treat	VBN	_	_	_
5	for	for	IN	_	_	_
6	one	one	CD	_	_	_
7	hour	hour	NN	_	_	_
8	at	at	IN	_	_	_
9	4	4	CD	_	_	_
10	°C	°c	NN	_	_	_
11	with	with	IN	_	_	_
12	RNase	rnase	NN	_	_	_
13	A	a	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	2	2	CD	_	_	_
16	ng	ng	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Cells	cell	NNS	_	_	_
19	were	be	VBD	_	_	_
20	grown	grow	VBN	_	_	_
21	aerobically	aerobically	RB	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	25	25	CD	_	_	_
24	%	%	NN	_	_	_
25	O2	o2	CD	_	_	_
26	,	,	,	_	_	_
27	70	70	CD	_	_	_
28	%	%	NN	_	_	_
29	N2	n2	NN	_	_	_
30	and	and	CC	_	_	_
31	5	5	CD	_	_	_
32	%	%	NN	_	_	_
33	CO2	co2	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	until	until	IN	_	_	_
36	mid-log	mid-log	JJ	_	_	_
37	phase	phase	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	OD600	od600	NN	_	_	_
40	of	of	IN	_	_	_
41	0.35	0.35	CD	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	and	and	CC	_	_	_
44	treated	treat	VBN	_	_	_
45	with	with	IN	_	_	_
46	1	1	CD	_	_	_
47	%	%	NN	_	_	_
48	final	final	JJ	_	_	_
49	volumen	voluman	NNS	_	_	_
50	formaldehyde	formaldehyde	NN	_	_	_
51	for	for	IN	_	_	_
52	ten	ten	CD	_	_	_
53	minutes	minute	NNS	_	_	_
54	.	.	.	_	_	_

1	Sodium	sodium	NN	_	_	_
2	phosphate	phosphate	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Cells	cell	NNS	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	anaerobically	anaerobically	RB	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	95	95	CD	_	_	_
12	%	%	NN	_	_	_
13	N2	n2	NN	_	_	_
14	and	and	CC	_	_	_
15	5	5	CD	_	_	_
16	%	%	NN	_	_	_
17	CO2	co2	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	until	until	IN	_	_	_
20	mid-log	mid-log	JJ	_	_	_
21	phase	phase	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	OD600	od600	NN	_	_	_
24	of	of	IN	_	_	_
25	0.3	0.3	CD	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	and	and	CC	_	_	_
28	treated	treat	VBN	_	_	_
29	with	with	IN	_	_	_
30	1	1	CD	_	_	_
31	%	%	NN	_	_	_
32	final	final	JJ	_	_	_
33	volumen	voluman	NNS	_	_	_
34	formaldehyde	formaldehyde	NN	_	_	_
35	for	for	IN	_	_	_
36	ten	ten	CD	_	_	_
37	minutes	minute	NNS	_	_	_
38	.	.	.	_	_	_

1	Sodium	sodium	NN	_	_	_
2	phosphate	phosphate	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Escherichia	escherichia	FW	Organism	_	_
7	coli	coli	FW	Organism	_	_
8	str	str	FW	_	_	_
9	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	INPUT	input	VBP	_	_	_
4	ChIP	chip	NN	_	_	_
5	DNA	dna	NN	_	_	_
6	from	from	IN	_	_	_
7	PK9416	pk9416	NN	_	_	_
8	,	,	,	_	_	_
9	no	no	DT	_	_	_
10	ArcA	arca	NN	TF	_	_
11	control	control	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	strain	strain	NN	_	_	_
14	:	:	:	_	_	_
15	MG1655	mg1655	NN	_	_	_
16	K-12	k-12	NN	_	_	_
17	WT	wt	JJ	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	strain	strain	NN	_	_	_
20	:	:	:	_	_	_
21	PK9416	pk9416	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	10	10	CD	_	_	_
24	ng	ng	NN	_	_	_
25	of	of	IN	_	_	_
26	DNA	dna	NN	_	_	_
27	were	be	VBD	_	_	_
28	submitted	submit	VBN	_	_	_
29	to	to	TO	_	_	_
30	the	the	DT	_	_	_
31	University	University	NNP	_	_	_
32	of	of	IN	_	_	_
33	Wisconsin-Madison	Wisconsin-Madison	NNP	_	_	_
34	DNA	DNA	NNP	_	_	_
35	Sequencing	sequencing	NN	_	_	_
36	Facility	facility	NN	_	_	_
37	for	for	IN	_	_	_
38	ChIP-seq	ChIP-seq	NNP	_	_	_
39	library	library	NN	_	_	_
40	preparation	preparation	NN	_	_	_
41	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	sheared	shear	VBN	_	_	_
4	to	to	TO	_	_	_
5	200-500	200-500	CD	_	_	_
6	nt	nt	NNS	_	_	_
7	during	during	IN	_	_	_
8	the	the	DT	_	_	_
9	IP	IP	NNP	_	_	_
10	process	process	NN	_	_	_
11	to	to	TO	_	_	_
12	facilitate	facilitate	VB	_	_	_
13	library	library	NN	_	_	_
14	preparation	preparation	NN	_	_	_
15	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	libraries	library	NNS	_	_	_
3	were	be	VBD	_	_	_
4	generated	generate	VBN	_	_	_
5	using	use	VBG	_	_	_
6	reagents	reagent	NNS	_	_	_
7	from	from	IN	_	_	_
8	the	the	DT	_	_	_
9	Illumina	Illumina	NNP	_	_	_
10	Paired	Paired	NNP	_	_	_
11	End	End	NNP	_	_	_
12	Sample	Sample	NNP	_	_	_
13	Preparation	Preparation	NNP	_	_	_
14	Kit	kit	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Illumina	Illumina	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	the	the	DT	_	_	_
20	Illumina	Illumina	NNP	_	_	_
21	protocol	protocol	NN	_	_	_
22	``	``	``	_	_	_
23	Preparing	prepare	VBG	_	_	_
24	Samples	sample	NNS	_	_	_
25	for	for	IN	_	_	_
26	ChIP	chip	NN	_	_	_
27	Sequencing	sequencing	NN	_	_	_
28	of	of	IN	_	_	_
29	DNA	dna	NN	_	_	_
30	''	''	''	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Illumina	Illumina	NNP	_	_	_
33	part	part	NN	_	_	_
34	#	#	#	_	_	_
35	11257047	11257047	CD	_	_	_
36	RevA	reva	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	as	as	IN	_	_	_
39	per	per	IN	_	_	_
40	the	the	DT	_	_	_
41	manufacturer	manufacturer	NN	_	_	_
42	's	's	POS	_	_	_
43	instructions	instruction	NNS	_	_	_
44	,	,	,	_	_	_
45	except	except	IN	_	_	_
46	products	product	NNS	_	_	_
47	of	of	IN	_	_	_
48	the	the	DT	_	_	_
49	ligation	ligation	NN	_	_	_
50	reaction	reaction	NN	_	_	_
51	were	be	VBD	_	_	_
52	purified	purify	VBN	_	_	_
53	by	by	IN	_	_	_
54	gel	gel	NN	_	_	_
55	electrophoresis	electrophoresis	NN	_	_	_
56	using	use	VBG	_	_	_
57	2	2	CD	_	_	_
58	%	%	NN	_	_	_
59	SizeSelect	sizeselect	NN	_	_	_
60	agarose	agarose	NN	_	_	_
61	gels	gel	NNS	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	Invitrogen	Invitrogen	NNP	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	targeting	target	VBG	_	_	_
66	400	400	CD	_	_	_
67	bp	bp	NN	_	_	_
68	fragments	fragment	NNS	_	_	_
69	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	library	library	NN	_	_	_
3	construction	construction	NN	_	_	_
4	and	and	CC	_	_	_
5	amplification	amplification	NN	_	_	_
6	,	,	,	_	_	_
7	quality	quality	NN	_	_	_
8	and	and	CC	_	_	_
9	quantity	quantity	NN	_	_	_
10	were	be	VBD	_	_	_
11	assessed	assess	VBN	_	_	_
12	using	use	VBG	_	_	_
13	an	a	DT	_	_	_
14	Agilent	agilent	JJ	_	_	_
15	DNA	dna	NN	_	_	_
16	1000	1000	CD	_	_	_
17	series	series	NN	_	_	_
18	chip	chip	NN	_	_	_
19	assay	assay	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Agilent	agilent	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	and	and	CC	_	_	_
24	QuantIT	quantit	NN	_	_	_
25	PicoGreen	picogreen	NN	_	_	_
26	dsDNA	dsdna	NN	_	_	_
27	Kit	kit	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Invitrogen	invitrogen	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	,	,	,	_	_	_
32	respectively	respectively	RB	_	_	_
33	,	,	,	_	_	_
34	and	and	CC	_	_	_
35	libraries	library	NNS	_	_	_
36	were	be	VBD	_	_	_
37	standardized	standardized	JJ	_	_	_
38	to	to	TO	_	_	_
39	10μM	10μm	NN	_	_	_
40	.	.	.	_	_	_

1	Cluster	cluster	NN	_	_	_
2	generation	generation	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	using	use	VBG	_	_	_
6	a	a	DT	_	_	_
7	cBot	cBot	NNP	_	_	_
8	Single	single	JJ	_	_	_
9	Read	Read	NNP	_	_	_
10	Cluster	Cluster	NNP	_	_	_
11	Generation	Generation	NNP	_	_	_
12	Kit	kit	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	v4	v4	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	and	and	CC	_	_	_
17	placed	place	VBN	_	_	_
18	on	on	IN	_	_	_
19	the	the	DT	_	_	_
20	Illumina	Illumina	NNP	_	_	_
21	cBot	cBot	NNP	_	_	_
22	.	.	.	_	_	_

1	Single	single	JJ	_	_	_
2	read	read	NN	_	_	_
3	,	,	,	_	_	_
4	75	75	CD	_	_	_
5	bp	bp	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	rep	rep	NN	GEN	_	_
8	A	a	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	or	or	CC	_	_	_
11	36	36	CD	_	_	_
12	bp	bp	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	rep	rep	NN	GEN	_	_
15	B	b	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	runs	run	NNS	_	_	_
18	were	be	VBD	_	_	_
19	performed	perform	VBN	_	_	_
20	,	,	,	_	_	_
21	using	use	VBG	_	_	_
22	standard	standard	JJ	_	_	_
23	SBS	SBS	NNP	_	_	_
24	kits	kit	NNS	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	v4	v4	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	and	and	CC	_	_	_
29	SCS	scs	NN	_	_	_
30	2.6	2.6	CD	_	_	_
31	on	on	IN	_	_	_
32	an	a	DT	_	_	_
33	Illumina	Illumina	NNP	_	_	_
34	Genome	Genome	NNP	_	_	_
35	Analyzer	Analyzer	NNP	_	_	_
36	IIx	IIx	NNP	_	_	_
37	.	.	.	_	_	_

1	Basecalling	basecall	VBG	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	using	use	VBG	_	_	_
5	the	the	DT	_	_	_
6	standard	standard	JJ	_	_	_
7	Illumina	Illumina	NNP	_	_	_
8	Pipeline	Pipeline	NNP	_	_	_
9	version	version	NN	_	_	_
10	1.6	1.6	CD	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Anaerobic	anaerobic	JJ	_	_	_
3	Cultures	culture	NNS	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
5	antibody	antibody	NN	_	_	_
6	:	:	:	_	_	_
7	polyclonal	polyclonal	JJ	_	_	_
8	antiserum	antiserum	NN	_	_	_
9	was	be	VBD	_	_	_
10	raised	raise	VBN	_	_	_
11	against	against	IN	_	_	_
12	His6-ArcA	his6-arca	NN	_	_	_
13	then	then	RB	_	_	_
14	Affinity	Affinity	NNP	_	_	_
15	Purified	purify	VBN	_	_	_
16	using	use	VBG	_	_	_
17	purified	purify	VBN	_	_	_
18	ArcA	arca	NN	TF	_	_
19	to	to	TO	_	_	_
20	yield	yield	VB	_	_	_
21	the	the	DT	_	_	_
22	polyclonal	polyclonal	JJ	_	_	_
23	antibodies	antibody	NNS	_	_	_
24	used	use	VBN	_	_	_
25	for	for	IN	_	_	_
26	ChIP	chip	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	ArcA	arca	NN	TF	_	_
29	_	_	NN	_	_	_
30	anaerobic	anaerobic	JJ	_	_	_
31	_	_	NN	_	_	_
32	ChIP-seq	ChIP-seq	NNP	_	_	_
33	_	_	NNP	_	_	_
34	IP	IP	NNP	_	_	_
35	_	_	SYM	_	_	_
36	A.wig	A.wig	NNP	_	_	_
37	:	:	:	_	_	_
38	U00096	u00096	NN	_	_	_
39	.2	.2	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	ArcA	arca	NN	TF	_	_
42	_	_	NN	_	_	_
43	anaerobic	anaerobic	JJ	_	_	_
44	_	_	NN	_	_	_
45	ChIP-seq	ChIP-seq	NNP	_	_	_
46	_	_	NNP	_	_	_
47	IP	IP	NNP	_	_	_
48	_	_	NNP	_	_	_
49	B.wig	B.wig	NNP	_	_	_
50	:	:	:	_	_	_
51	U00096	u00096	NN	_	_	_
52	.2	.2	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	ArcA	arca	NN	TF	_	_
55	IP	IP	NNP	_	_	_
56	ChIP-seq	ChIP-seq	NNP	_	_	_
57	Anaerobic	Anaerobic	NNP	_	_	_
58	Biological	Biological	NNP	_	_	_
59	replicate	replicate	VB	_	_	_
60	1	1	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	ArcA	arca	NN	TF	_	_
63	IP	IP	NNP	_	_	_
64	ChIP-seq	ChIP-seq	NNP	_	_	_
65	Anaerobic	Anaerobic	NNP	_	_	_
66	Biological	Biological	NNP	_	_	_
67	replicate	replicate	VB	_	_	_
68	2	2	CD	_	_	_
69	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
70	Cell	cell	NN	_	_	_
71	pellets	pellet	NNS	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	from	from	IN	_	_	_
74	initial	initial	JJ	_	_	_
75	50	50	CD	_	_	_
76	ml	ml	NN	_	_	_
77	of	of	IN	_	_	_
78	culture	culture	NN	_	_	_
79	-RRB-	-rrb-	-RRB-	_	_	_
80	were	be	VBD	_	_	_
81	thawed	thaw	VBN	_	_	_
82	and	and	CC	_	_	_
83	resuspended	resuspend	VBN	_	_	_
84	in	in	IN	_	_	_
85	250ul	250ul	NN	_	_	_
86	of	of	IN	_	_	_
87	IP	IP	NNP	_	_	_
88	buffer	buffer	NN	_	_	_
89	-LRB-	-lrb-	-LRB-	_	_	_
90	100	100	CD	_	_	_
91	mM	mm	NN	KWSUPP	_	_
92	Tris	Tris	NNP	_	_	_
93	pH	ph	NN	_	_	_
94	8	8	CD	_	_	_
95	,	,	,	_	_	_
96	300	300	CD	_	_	_
97	mM	mm	NN	KWSUPP	_	_
98	NaCl	nacl	NN	_	_	_
99	,	,	,	_	_	_
100	2	2	CD	_	_	_
101	%	%	NN	_	_	_
102	TritonX-100	tritonx-100	NN	_	_	_
103	-RRB-	-rrb-	-RRB-	_	_	_
104	and	and	CC	_	_	_
105	sonicated	sonicate	VBN	_	_	_
106	using	use	VBG	_	_	_
107	a	a	DT	_	_	_
108	microtip	microtip	NN	_	_	_
109	sonicator	sonicator	NN	_	_	_
110	set	set	VBN	_	_	_
111	at	at	IN	_	_	_
112	10	10	CD	_	_	_
113	%	%	NN	_	_	_
114	output	output	NN	_	_	_
115	for	for	IN	_	_	_
116	20	20	CD	_	_	_
117	second	second	JJ	_	_	_
118	intervals	interval	NNS	_	_	_
119	with	with	IN	_	_	_
120	periods	period	NNS	_	_	_
121	of	of	IN	_	_	_
122	cooling	cool	VBG	_	_	_
123	in	in	IN	_	_	_
124	between	between	IN	_	_	_
125	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	treated	treat	VBN	_	_	_
5	for	for	IN	_	_	_
6	one	one	CD	_	_	_
7	hour	hour	NN	_	_	_
8	at	at	IN	_	_	_
9	4	4	CD	_	_	_
10	°C	°c	NN	_	_	_
11	with	with	IN	_	_	_
12	RNase	rnase	NN	_	_	_
13	A	a	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	2	2	CD	_	_	_
16	ng	ng	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Cells	cell	NNS	_	_	_
19	were	be	VBD	_	_	_
20	grown	grow	VBN	_	_	_
21	anaerobically	anaerobically	RB	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	95	95	CD	_	_	_
24	%	%	NN	_	_	_
25	N2	n2	NN	_	_	_
26	and	and	CC	_	_	_
27	5	5	CD	_	_	_
28	%	%	NN	_	_	_
29	CO2	co2	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	until	until	IN	_	_	_
32	mid-log	mid-log	JJ	_	_	_
33	phase	phase	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	OD600	od600	NN	_	_	_
36	of	of	IN	_	_	_
37	0.3	0.3	CD	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	and	and	CC	_	_	_
40	treated	treat	VBN	_	_	_
41	with	with	IN	_	_	_
42	1	1	CD	_	_	_
43	%	%	NN	_	_	_
44	final	final	JJ	_	_	_
45	volumen	voluman	NNS	_	_	_
46	formaldehyde	formaldehyde	NN	_	_	_
47	for	for	IN	_	_	_
48	ten	ten	CD	_	_	_
49	minutes	minute	NNS	_	_	_
50	.	.	.	_	_	_

1	Sodium	sodium	NN	_	_	_
2	phosphate	phosphate	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	ChIP-Seq	chip-seq	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	culture	culture	NN	_	_	_
9	condition	condition	NN	_	_	_
10	:	:	:	_	_	_
11	Anaerobic	anaerobic	JJ	_	_	_
12	Cultures	culture	NNS	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
14	Escherichia	escherichia	FW	Organism	_	_
15	coli	coli	FW	Organism	_	_
16	str	str	FW	_	_	_
17	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Genome	Genome	NNP	_	_	_
4	Build	Build	NNP	_	_	_
5	:	:	:	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	genome	genome	NN	_	_	_
8	build	build	VB	_	_	_
9	:	:	:	_	_	_
10	U00096	u00096	NN	_	_	_
11	.2	.2	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	Sequence	sequence	NN	_	_	_
14	reads	read	VBZ	_	_	_
15	were	be	VBD	_	_	_
16	aligned	align	VBN	_	_	_
17	to	to	TO	_	_	_
18	the	the	DT	_	_	_
19	published	publish	VBN	_	_	_
20	E.	e.	FW	_	_	_
21	coli	coli	FW	_	_	_
22	K-12	k-12	NN	_	_	_
23	MG1655	mg1655	NN	_	_	_
24	genome	genome	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	U00096	u00096	NN	_	_	_
27	.2	.2	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	using	use	VBG	_	_	_
30	the	the	DT	_	_	_
31	software	software	NN	_	_	_
32	packages	package	NNS	_	_	_
33	SOAP	soap	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Li	Li	NNP	_	_	_
36	et	et	FW	_	_	_
37	al	al	FW	_	_	_
38	,	,	,	_	_	_
39	2009	2009	CD	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	and	and	CC	_	_	_
42	ELAND	ELAND	NNP	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	within	within	IN	_	_	_
45	the	the	DT	_	_	_
46	Illumina	Illumina	NNP	_	_	_
47	Genome	Genome	NNP	_	_	_
48	Analyzer	Analyzer	NNP	_	_	_
49	Pipeline	Pipeline	NNP	_	_	_
50	Software	Software	NNP	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	,	,	,	_	_	_
53	allowing	allow	VBG	_	_	_
54	at	at	IN	_	_	_
55	most	most	JJS	_	_	_
56	two	two	CD	_	_	_
57	mismatches	mismatch	NNS	_	_	_
58	.	.	.	_	_	_

1	Sequence	sequence	NN	_	_	_
2	reads	read	VBZ	_	_	_
3	with	with	IN	_	_	_
4	sequences	sequence	NNS	_	_	_
5	that	that	WDT	_	_	_
6	did	do	VBD	_	_	_
7	not	not	RB	_	_	_
8	align	align	VB	_	_	_
9	to	to	TO	_	_	_
10	the	the	DT	_	_	_
11	genome	genome	NN	_	_	_
12	,	,	,	_	_	_
13	aligned	align	VBN	_	_	_
14	to	to	TO	_	_	_
15	multiple	multiple	JJ	_	_	_
16	locations	location	NNS	_	_	_
17	on	on	IN	_	_	_
18	the	the	DT	_	_	_
19	genome	genome	NN	_	_	_
20	,	,	,	_	_	_
21	or	or	CC	_	_	_
22	contained	contain	VBD	_	_	_
23	more	more	JJR	_	_	_
24	than	than	IN	_	_	_
25	two	two	CD	_	_	_
26	mismatches	mismatch	NNS	_	_	_
27	were	be	VBD	_	_	_
28	discarded	discard	VBN	_	_	_
29	from	from	IN	_	_	_
30	further	further	JJ	_	_	_
31	analysis	analysis	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	<	<	JJR	_	_	_
34	10	10	CD	_	_	_
35	%	%	NN	_	_	_
36	of	of	IN	_	_	_
37	reads	read	VBZ	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	Supplemental	Supplemental	NNP	_	_	_
41	Files	Files	NNP	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	visualization	visualization	NN	_	_	_
3	the	the	DT	_	_	_
4	raw	raw	JJ	_	_	_
5	tag	tag	NN	GEN	_	_
6	density	density	NN	_	_	_
7	at	at	IN	_	_	_
8	each	each	DT	_	_	_
9	position	position	NN	_	_	_
10	was	be	VBD	_	_	_
11	calculated	calculate	VBN	_	_	_
12	using	use	VBG	_	_	_
13	QuEST	quest	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Valouev	Valouev	NNP	_	_	_
16	et	et	FW	_	_	_
17	al	al	FW	_	_	_
18	,	,	,	_	_	_
19	2008	2008	CD	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	and	and	CC	_	_	_
22	normalized	normalize	VBD	_	_	_
23	as	as	IN	_	_	_
24	tag	tag	NN	GEN	_	_
25	density	density	NN	_	_	_
26	per	per	IN	_	_	_
27	million	million	CD	_	_	_
28	uniquely	uniquely	RB	_	_	_
29	mapped	map	VBN	_	_	_
30	reads	read	VBZ	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	Wild	Wild	NNP	_	_	_
5	Type	type	NN	_	_	_
6	K-12	k-12	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	BL21	bl21	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	DE3	de3	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	_	_	CD	_	_	_
13	adhE	adhe	NN	GEN	_	_
14	mutant	mutant	JJ	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	BL21	bl21	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	DE3	de3	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	,	,	,	_	_	_
21	adhE	adhe	NN	GEN	_	_
22	mutant	mutant	JJ	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	B	b	NN	_	_	_
25	strain	strain	NN	_	_	_
26	_	_	RB	_	_	_
27	wild	wild	JJ	_	_	_
28	type	type	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	B	b	NN	_	_	_
31	strain	strain	NN	_	_	_
32	,	,	,	_	_	_
33	wild	wild	JJ	_	_	_
34	type	type	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	BW25113	bw25113	NN	_	_	_
37	_	_	CD	_	_	_
38	adhE	adhe	NN	GEN	_	_
39	mutant	mutant	JJ	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	BW25113	bw25113	NN	_	_	_
42	,	,	,	_	_	_
43	adhE	adhe	NN	GEN	_	_
44	mutant	mutant	JJ	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	Data	Data	NNP	_	_	_
47	quantification	quantification	NN	_	_	_
48	was	be	VBD	_	_	_
49	performed	perform	VBN	_	_	_
50	using	use	VBG	_	_	_
51	Agilent	Agilent	NNP	_	_	_
52	Feature	Feature	NNP	_	_	_
53	Extraction	Extraction	NNP	_	_	_
54	software	software	NN	_	_	_
55	9.3.2.1	9.3.2.1	CD	_	_	_
56	-LRB-	-lrb-	-LRB-	_	_	_
57	Agilent	Agilent	NNP	_	_	_
58	Technology	Technology	NNP	_	_	_
59	,	,	,	_	_	_
60	USA	USA	NNP	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	average	average	JJ	_	_	_
3	fluorescence	fluorescence	NN	_	_	_
4	intensity	intensity	NN	_	_	_
5	for	for	IN	_	_	_
6	each	each	DT	_	_	_
7	spot	spot	NN	_	_	_
8	was	be	VBD	_	_	_
9	calculated	calculate	VBN	_	_	_
10	and	and	CC	_	_	_
11	local	local	JJ	_	_	_
12	background	background	NN	_	_	_
13	was	be	VBD	_	_	_
14	subtracted	subtract	VBN	_	_	_
15	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	data	datum	NNS	_	_	_
3	normalization	normalization	NN	_	_	_
4	and	and	CC	_	_	_
5	selection	selection	NN	_	_	_
6	of	of	IN	_	_	_
7	fold-changed	fold-changed	JJ	_	_	_
8	genes	gene	NNS	_	_	_
9	were	be	VBD	_	_	_
10	performed	perform	VBN	_	_	_
11	using	use	VBG	_	_	_
12	GeneSpringGX	GeneSpringGX	NNP	_	_	_
13	7.3.1	7.3.1	CD	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Agilent	Agilent	NNP	_	_	_
16	Technology	Technology	NNP	_	_	_
17	,	,	,	_	_	_
18	USA	USA	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	Normalization	normalization	NN	_	_	_
2	for	for	IN	_	_	_
3	Agilent	Agilent	NNP	_	_	_
4	one-color	one-color	JJ	_	_	_
5	method	method	NN	_	_	_
6	was	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	,	,	,	_	_	_
9	which	which	WDT	_	_	_
10	is	be	VBZ	_	_	_
11	Data	Data	NNP	_	_	_
12	transformation	transformation	NN	_	_	_
13	.	.	.	_	_	_

1	Set	set	VB	_	_	_
2	measurements	measurement	NNS	_	_	_
3	less	less	JJR	_	_	_
4	than	than	IN	_	_	_
5	5.0	5.0	CD	_	_	_
6	to	to	TO	_	_	_
7	5.0	5.0	CD	_	_	_
8	and	and	CC	_	_	_
9	Per	per	IN	_	_	_
10	Chip	chip	NN	_	_	_
11	:	:	:	_	_	_
12	Normalize	normalize	VB	_	_	_
13	to	to	TO	_	_	_
14	50th	50th	JJ	_	_	_
15	percentage	percentage	NN	_	_	_
16	.	.	.	_	_	_

1	Reliable	reliable	JJ	_	_	_
2	genes	gene	NNS	_	_	_
3	were	be	VBD	_	_	_
4	filtered	filter	VBN	_	_	_
5	by	by	IN	_	_	_
6	flag	flag	NN	_	_	_
7	as	as	IN	_	_	_
8	following	follow	VBG	_	_	_
9	the	the	DT	_	_	_
10	Agilent	Agilent	NNP	_	_	_
11	manual	manual	NN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	BL21	bl21	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	DE3	de3	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Escherichia	escherichia	FW	Organism	_	_
10	coli	coli	FW	Organism	_	_
11	BW25113	bw25113	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	For	for	IN	_	_	_
14	control	control	NN	_	_	_
15	and	and	CC	_	_	_
16	test	test	NN	_	_	_
17	RNAs	rna	NNS	_	_	_
18	,	,	,	_	_	_
19	the	the	DT	_	_	_
20	synthesis	synthesis	NN	_	_	_
21	of	of	IN	_	_	_
22	target	target	NN	_	_	_
23	cRNA	crna	NN	_	_	_
24	probes	probe	NNS	_	_	_
25	and	and	CC	_	_	_
26	hybridization	hybridization	NN	_	_	_
27	were	be	VBD	_	_	_
28	performed	perform	VBN	_	_	_
29	using	use	VBG	_	_	_
30	Agilent	Agilent	NNP	_	_	_
31	's	's	POS	_	_	_
32	Low	low	JJ	_	_	_
33	Input	Input	NNP	_	_	_
34	Quick	Quick	NNP	_	_	_
35	Amp	Amp	NNP	_	_	_
36	WT	WT	NNP	_	_	_
37	Labeling	label	VBG	_	_	_
38	Kit	kit	NN	_	_	_
39	,	,	,	_	_	_
40	one	one	CD	_	_	_
41	color	color	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	Agilent	Agilent	NNP	_	_	_
44	Technology	Technology	NNP	_	_	_
45	,	,	,	_	_	_
46	USA	USA	NNP	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	according	accord	VBG	_	_	_
49	to	to	TO	_	_	_
50	the	the	DT	_	_	_
51	manufacturer	manufacturer	NN	_	_	_
52	's	's	POS	_	_	_
53	instructions	instruction	NNS	_	_	_
54	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	each	each	DT	_	_	_
4	0.2	0.2	CD	_	_	_
5	ug	ug	NN	_	_	_
6	total	total	JJ	_	_	_
7	RNA	rna	NN	_	_	_
8	was	be	VBD	_	_	_
9	mixed	mix	VBN	_	_	_
10	with	with	IN	_	_	_
11	WT	wt	JJ	_	_	_
12	primer	primer	NN	_	_	_
13	mix	mix	NN	_	_	_
14	and	and	CC	_	_	_
15	incubated	incubate	VBN	_	_	_
16	at	at	IN	_	_	_
17	65ºC	65ºc	NN	_	_	_
18	for	for	IN	_	_	_
19	10	10	CD	_	_	_
20	min	min	NN	_	_	_
21	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	master	master	NN	_	_	_
3	mix	mix	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	5X	5x	NN	_	_	_
6	First	first	JJ	_	_	_
7	strand	strand	NN	_	_	_
8	buffer	buffer	NN	_	_	_
9	,	,	,	_	_	_
10	0.1	0.1	CD	_	_	_
11	M	m	NN	_	_	_
12	DTT	dtt	NN	_	_	_
13	,	,	,	_	_	_
14	10mM	10mm	NN	_	_	_
15	dNTP	dntp	NN	_	_	_
16	mix	mix	NN	_	_	_
17	,	,	,	_	_	_
18	RNase-Out	rnase-out	NN	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	MMLV-RT	mmlv-rt	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	was	be	VBD	_	_	_
24	prepared	prepare	VBN	_	_	_
25	and	and	CC	_	_	_
26	added	add	VBN	_	_	_
27	to	to	TO	_	_	_
28	the	the	DT	_	_	_
29	reaction	reaction	NN	_	_	_
30	mixer	mixer	NN	_	_	_
31	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	incubated	incubate	VBN	_	_	_
5	at	at	IN	_	_	_
6	40ºC	40ºc	NN	_	_	_
7	for	for	IN	_	_	_
8	2	2	CD	_	_	_
9	hours	hour	NNS	_	_	_
10	and	and	CC	_	_	_
11	then	then	RB	_	_	_
12	the	the	DT	_	_	_
13	RT	rt	NN	_	_	_
14	and	and	CC	_	_	_
15	dsDNA	dsdna	NN	_	_	_
16	synthesis	synthesis	NN	_	_	_
17	was	be	VBD	_	_	_
18	terminated	terminate	VBN	_	_	_
19	by	by	IN	_	_	_
20	incubating	incubate	VBG	_	_	_
21	at	at	IN	_	_	_
22	70ºC	70ºC	NNP	_	_	_
23	for	for	IN	_	_	_
24	15	15	CD	_	_	_
25	min	min	NN	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	genotype	genotype	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	K-12	k-12	NN	_	_	_
5	strain	strain	NN	_	_	_
6	_	_	RB	_	_	_
7	wild	wild	JJ	_	_	_
8	type	type	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	K-12	k-12	NN	_	_	_
11	strain	strain	NN	_	_	_
12	,	,	,	_	_	_
13	wild	wild	JJ	_	_	_
14	type	type	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	strain	strain	NN	_	_	_
17	background	background	NN	_	_	_
18	:	:	:	_	_	_
19	B	b	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	strain	strain	NN	_	_	_
22	background	background	NN	_	_	_
23	:	:	:	_	_	_
24	K-12	k-12	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
26	The	the	DT	_	_	_
27	E.	e.	FW	_	_	_
28	coli	coli	FW	_	_	_
29	strains	strain	NNS	_	_	_
30	were	be	VBD	_	_	_
31	grown	grow	VBN	_	_	_
32	for	for	IN	_	_	_
33	six	six	CD	_	_	_
34	hours	hour	NNS	_	_	_
35	under	under	IN	_	_	_
36	anaerobic	anaerobic	JJ	_	_	_
37	growth	growth	NN	_	_	_
38	condition	condition	NN	_	_	_
39	in	in	IN	_	_	_
40	glucose-containing	glucose-containing	JJ	_	_	_
41	complex	complex	JJ	_	_	_
42	medium	medium	NN	_	_	_
43	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	microarray	microarray	NN	_	_	_
4	experiment	experiment	NN	_	_	_
5	was	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	with	with	IN	_	_	_
8	two	two	CD	_	_	_
9	serotypes	serotype	NNS	_	_	_
10	of	of	IN	_	_	_
11	wild	wild	JJ	_	_	_
12	type	type	NN	_	_	_
13	E.	e.	FW	_	_	_
14	coli	coli	FW	_	_	_
15	and	and	CC	_	_	_
16	their	they	PRP$	_	_	_
17	adhE	adhE	NNP	GEN	_	_
18	mutants	mutant	NNS	_	_	_
19	:	:	:	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	1	1	LS	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	K-12	k-12	NN	_	_	_
24	strain	strain	NN	_	_	_
25	,	,	,	_	_	_
26	wild	wild	JJ	_	_	_
27	type	type	NN	_	_	_
28	;	;	:	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	2	2	LS	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	B	b	NN	_	_	_
33	strain	strain	NN	_	_	_
34	,	,	,	_	_	_
35	wild	wild	JJ	_	_	_
36	type	type	NN	_	_	_
37	;	;	:	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	3	3	LS	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	BW25113	bw25113	NN	_	_	_
42	,	,	,	_	_	_
43	adhE	adhe	NN	GEN	_	_
44	mutants	mutant	NNS	_	_	_
45	;	;	:	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	4	4	LS	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	BL21	bl21	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	DE3	de3	NN	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	,	,	,	_	_	_
54	adhE	adhe	NN	GEN	_	_
55	mutants	mutant	NNS	_	_	_
56	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	A	a	NN	_	_	_
3	single	single	JJ	_	_	_
4	large	large	JJ	_	_	_
5	fastq	fastq	NN	_	_	_
6	format	format	NN	_	_	_
7	file	file	NN	_	_	_
8	of	of	IN	_	_	_
9	high	high	JJ	_	_	_
10	quality	quality	NN	_	_	_
11	reads	read	VBZ	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Q	Q	NNP	_	_	_
14	≥	≥	SYM	_	_	_
15	30	30	CD	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	was	be	VBD	_	_	_
18	split	split	VBN	_	_	_
19	into	into	IN	_	_	_
20	about	about	IN	_	_	_
21	10	10	CD	_	_	_
22	smaller	smaller	JJR	_	_	_
23	files	file	NNS	_	_	_
24	by	by	IN	_	_	_
25	using	use	VBG	_	_	_
26	a	a	DT	_	_	_
27	shell	shell	NN	_	_	_
28	script	script	NN	_	_	_
29	splitReads.sh	splitreads.sh	JJ	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	CASAVA	casava	NN	_	_	_
32	version	version	NN	_	_	_
33	1.4	1.4	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	Cells	cell	NNS	_	_	_
36	were	be	VBD	_	_	_
37	cultured	culture	VBN	_	_	_
38	in	in	IN	_	_	_
39	LB	lb	NN	MED	_	_
40	medium	medium	NN	MED	_	_
41	containing	contain	VBG	_	_	_
42	ampicillin	ampicillin	NN	_	_	_
43	at	at	IN	_	_	_
44	28	28	CD	_	_	_
45	˚C	˚c	NN	_	_	_
46	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	overnight	overnight	JJ	_	_	_
3	cell	cell	NN	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	inoculated	inoculate	VBN	_	_	_
7	into	into	IN	_	_	_
8	the	the	DT	_	_	_
9	fresh	fresh	JJ	_	_	_
10	medium	medium	NN	_	_	_
11	at	at	IN	_	_	_
12	1	1	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Each	each	DT	_	_	_
15	type	type	NN	_	_	_
16	of	of	IN	_	_	_
17	error	error	NN	_	_	_
18	rates	rate	NNS	_	_	_
19	per	per	IN	_	_	_
20	position	position	NN	_	_	_
21	was	be	VBD	_	_	_
22	determined	determine	VBN	_	_	_
23	as	as	IN	_	_	_
24	the	the	DT	_	_	_
25	number	number	NN	_	_	_
26	of	of	IN	_	_	_
27	sequence	sequence	NN	_	_	_
28	reads	read	VBZ	_	_	_
29	with	with	IN	_	_	_
30	a	a	DT	_	_	_
31	particular	particular	JJ	_	_	_
32	type	type	NN	_	_	_
33	of	of	IN	_	_	_
34	base-substitution	base-substitution	NN	_	_	_
35	divided	divide	VBN	_	_	_
36	by	by	IN	_	_	_
37	the	the	DT	_	_	_
38	number	number	NN	_	_	_
39	of	of	IN	_	_	_
40	the	the	DT	_	_	_
41	reads	read	VBZ	_	_	_
42	with	with	IN	_	_	_
43	the	the	DT	_	_	_
44	reference	reference	NN	_	_	_
45	base	base	NN	_	_	_
46	in	in	IN	_	_	_
47	each	each	DT	_	_	_
48	DNA	dna	NN	_	_	_
49	position	position	NN	_	_	_
50	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	E.coli	e.coli	NN	_	_	_
3	strain	strain	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	error-prone	error-prone	NN	_	_	_
7	in	in	FW	_	_	_
8	vitro	vitro	FW	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Mn2	mn2	NN	_	_	_
11	+	+	CC	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
14	error-prone	error-prone	JJ	_	_	_
15	in	in	FW	_	_	_
16	vitro	vitro	FW	_	_	_
17	MnCl2	mncl2	NN	SUPP	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
19	error-proof	error-proof	JJ	_	_	_
20	in	in	FW	_	_	_
21	vitro	vitro	FW	_	_	_
22	1	1	CD	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	GreAB	greab	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	error-proof	error-proof	JJ	_	_	_
27	in	in	FW	_	_	_
28	vitro	vitro	FW	_	_	_
29	2	2	CD	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	GreAB	greab	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	error-proof	error-proof	JJ	_	_	_
34	in	in	FW	_	_	_
35	vitro	vitro	FW	_	_	_
36	MgCl2	mgcl2	NN	_	_	_
37	+	+	CC	_	_	_
38	GreAB	greab	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
40	error-proof	error-proof	JJ	_	_	_
41	in	in	FW	_	_	_
42	vitro	vitro	FW	_	_	_
43	MnCl2	mncl2	NN	SUPP	_	_
44	+	+	CC	_	_	_
45	GreAB	greab	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
47	Escherichia	escherichia	FW	Organism	_	_
48	coli	coli	FW	Organism	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	Genome	Genome	NNP	_	_	_
51	_	_	NNP	_	_	_
52	build	build	VB	_	_	_
53	:	:	:	_	_	_
54	pPR9	ppr9	NN	_	_	_
55	plasmid	plasmid	NN	_	_	_
56	-LRB-	-lrb-	-LRB-	_	_	_
57	ref	ref	NN	_	_	_
58	is	be	VBZ	_	_	_
59	Kashlec	Kashlec	NNP	_	_	_
60	et	et	FW	_	_	_
61	al.	al.	FW	_	_	_
62	,	,	,	_	_	_
63	1989	1989	CD	_	_	_
64	,	,	,	_	_	_
65	PMID	PMID	NNP	_	_	_
66	:	:	:	_	_	_
67	2547695	2547695	CD	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
70	In	in	FW	_	_	_
71	vitro	vitro	FW	_	_	_
72	RNA	rna	NN	_	_	_
73	preparation	preparation	NN	_	_	_
74	:	:	:	_	_	_
75	The	the	DT	_	_	_
76	5.7	5.7	CD	_	_	_
77	kb	kb	NN	_	_	_
78	RNA	rna	NN	_	_	_
79	was	be	VBD	_	_	_
80	purified	purify	VBN	_	_	_
81	from	from	IN	_	_	_
82	the	the	DT	_	_	_
83	digested	digest	VBN	_	_	_
84	DNA	dna	NN	_	_	_
85	,	,	,	_	_	_
86	NTPs	ntp	NNS	_	_	_
87	,	,	,	_	_	_
88	abortive	abortive	JJ	_	_	_
89	oligo-RNA	oligo-rna	JJ	_	_	_
90	products	product	NNS	_	_	_
91	,	,	,	_	_	_
92	and	and	CC	_	_	_
93	proteins	protein	NNS	_	_	_
94	by	by	IN	_	_	_
95	Acidic	acidic	JJ	_	_	_
96	phenol	phenol	NN	_	_	_
97	extraction	extraction	NN	_	_	_
98	,	,	,	_	_	_
99	G50	g50	NN	_	_	_
100	spin	spin	NN	_	_	_
101	column	column	NN	_	_	_
102	,	,	,	_	_	_
103	followed	follow	VBN	_	_	_
104	by	by	IN	_	_	_
105	EtOH	etoh	NN	_	_	_
106	precipitation	precipitation	NN	_	_	_
107	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	in	in	FW	_	_	_
3	vivo	vivo	FW	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	In	in	FW	_	_	_
6	vivo	vivo	FW	_	_	_
7	RNA	rna	NN	_	_	_
8	preparation	preparation	NN	_	_	_
9	:	:	:	_	_	_
10	The	the	DT	_	_	_
11	cells	cell	NNS	_	_	_
12	in	in	IN	_	_	_
13	200	200	CD	_	_	_
14	ml	ml	NN	_	_	_
15	culture	culture	NN	_	_	_
16	were	be	VBD	_	_	_
17	harvested	harvest	VBN	_	_	_
18	and	and	CC	_	_	_
19	resuspended	resuspend	VBN	_	_	_
20	with	with	IN	_	_	_
21	a	a	DT	_	_	_
22	solution	solution	NN	_	_	_
23	containing	contain	VBG	_	_	_
24	0.5	0.5	CD	_	_	_
25	%	%	NN	_	_	_
26	SDS	sds	NN	_	_	_
27	,	,	,	_	_	_
28	20	20	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	sodium	sodium	NN	SUPP	_	_
31	acetate	acetate	NN	SUPP	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	pH	ph	NN	_	_	_
34	5.5	5.5	CD	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	,	,	,	_	_	_
37	and	and	CC	_	_	_
38	10	10	CD	_	_	_
39	mM	mm	NN	KWSUPP	_	_
40	EDTA	edta	NN	_	_	_
41	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	suspended	suspend	VBN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	mixed	mix	VBN	_	_	_
6	with	with	IN	_	_	_
7	an	a	DT	_	_	_
8	equal	equal	JJ	_	_	_
9	volume	volume	NN	_	_	_
10	of	of	IN	_	_	_
11	pre-warmed	pre-warmed	JJ	_	_	_
12	saturated	saturated	JJ	_	_	_
13	phenol	phenol	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	20	20	CD	_	_	_
16	mM	mm	NN	KWSUPP	_	_
17	sodium	sodium	NN	SUPP	_	_
18	acetate	acetate	NN	SUPP	_	_
19	,	,	,	_	_	_
20	10	10	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	EDTA	edta	NN	_	_	_
23	pH	ph	NN	_	_	_
24	5.5	5.5	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	and	and	CC	_	_	_
27	incubated	incubate	VBN	_	_	_
28	for	for	IN	_	_	_
29	5	5	CD	_	_	_
30	min	min	NN	_	_	_
31	at	at	IN	_	_	_
32	60	60	CD	_	_	_
33	C	c	NN	_	_	_
34	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	mixture	mixture	NN	_	_	_
3	was	be	VBD	_	_	_
4	centrifuged	centrifuge	VBN	_	_	_
5	,	,	,	_	_	_
6	and	and	CC	_	_	_
7	RNA	rna	NN	_	_	_
8	and	and	CC	_	_	_
9	DNA	dna	NN	_	_	_
10	were	be	VBD	_	_	_
11	precipitated	precipitate	VBN	_	_	_
12	with	with	IN	_	_	_
13	ethanol	ethanol	NN	_	_	_
14	from	from	IN	_	_	_
15	the	the	DT	_	_	_
16	supernatant	supernatant	NN	_	_	_
17	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	was	be	VBD	_	_	_
4	dissolved	dissolve	VBN	_	_	_
5	in	in	IN	_	_	_
6	DNase	dnase	NN	_	_	_
7	I	i	CD	_	_	_
8	buffer	buffer	NN	_	_	_
9	with	with	IN	_	_	_
10	10U	10u	NN	_	_	_
11	of	of	IN	_	_	_
12	DNaseI	dnasei	NN	_	_	_
13	and	and	CC	_	_	_
14	incubated	incubate	VBN	_	_	_
15	for	for	IN	_	_	_
16	30	30	CD	_	_	_
17	min	min	NN	_	_	_
18	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	separated	separate	VBN	_	_	_
4	from	from	IN	_	_	_
5	the	the	DT	_	_	_
6	digested	digest	VBN	_	_	_
7	DNA	dna	NN	_	_	_
8	by	by	IN	_	_	_
9	acidic	acidic	JJ	_	_	_
10	phenol	phenol	NN	_	_	_
11	extraction	extraction	NN	_	_	_
12	followed	follow	VBN	_	_	_
13	by	by	IN	_	_	_
14	G-50	G-50	NNP	_	_	_
15	Micro	Micro	NNP	_	_	_
16	column	column	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	GE	GE	NNP	_	_	_
19	Healthcare	Healthcare	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	purification	purification	NN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	then	then	RB	_	_	_
25	precipitated	precipitate	VBD	_	_	_
26	with	with	IN	_	_	_
27	ethanol	ethanol	NN	_	_	_
28	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	was	be	VBD	_	_	_
4	dissolved	dissolve	VBN	_	_	_
5	in	in	IN	_	_	_
6	diethylpyrocarbonate-treated	diethylpyrocarbonate-treated	JJ	_	_	_
7	water	water	NN	_	_	_
8	and	and	CC	_	_	_
9	used	use	VBN	_	_	_
10	for	for	IN	_	_	_
11	cDNA	cdna	NN	_	_	_
12	synthesis	synthesis	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	mRNA-seq	mrna-seq	NN	_	_	_
3	with	with	IN	_	_	_
4	barcode	barcode	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	Illumina	Illumina	NNP	_	_	_
7	TruSeq	TruSeq	NNP	_	_	_
8	Index	Index	NNP	_	_	_
9	1-5	1-5	CD	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	mrna	mrna	NN	_	_	_
13	synthesis	synthesis	NN	_	_	_
14	:	:	:	_	_	_
15	in	in	FW	_	_	_
16	vitro	vitro	FW	_	_	_
17	MgCl2	mgcl2	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
19	mrna	mrna	NN	_	_	_
20	synthesis	synthesis	NN	_	_	_
21	:	:	:	_	_	_
22	in	in	FW	_	_	_
23	vitro	vitro	FW	_	_	_
24	MgCl2	mgcl2	NN	_	_	_
25	+	+	CC	_	_	_
26	GreAB	greab	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
28	mrna	mrna	NN	_	_	_
29	synthesis	synthesis	NN	_	_	_
30	:	:	:	_	_	_
31	in	in	FW	_	_	_
32	vitro	vitro	FW	_	_	_
33	MnCl2	mncl2	NN	SUPP	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
35	mrna	mrna	NN	_	_	_
36	synthesis	synthesis	NN	_	_	_
37	:	:	:	_	_	_
38	in	in	FW	_	_	_
39	vitro	vitro	FW	_	_	_
40	MnCl2	mncl2	NN	SUPP	_	_
41	+	+	CC	_	_	_
42	GreAB	greab	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
44	mrna	mrna	NN	_	_	_
45	synthesis	synthesis	NN	_	_	_
46	:	:	:	_	_	_
47	in	in	FW	_	_	_
48	vivo	vivo	FW	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	RNA-Seq	rna-seq	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	standard	standard	NN	_	_	_
53	in	in	FW	_	_	_
54	vitro	vitro	FW	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	Mg2	mg2	NN	_	_	_
57	+	+	CC	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
60	standard	standard	NN	_	_	_
61	in	in	FW	_	_	_
62	vitro	vitro	FW	_	_	_
63	MgCl2	mgcl2	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	strain	strain	NN	_	_	_
66	:	:	:	_	_	_
67	MG1655	mg1655	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	Supplementary	supplementary	JJ	_	_	_
70	_	_	NN	_	_	_
71	files	file	NNS	_	_	_
72	_	_	IN	_	_	_
73	format	format	NN	_	_	_
74	_	_	NN	_	_	_
75	and	and	CC	_	_	_
76	_	_	NN	_	_	_
77	content	content	NN	_	_	_
78	:	:	:	_	_	_
79	tab-delimited	tab-delimited	JJ	_	_	_
80	text	text	NN	_	_	_
81	file	file	NN	_	_	_
82	of	of	IN	_	_	_
83	transition	transition	NN	_	_	_
84	error	error	NN	_	_	_
85	rate	rate	NN	_	_	_
86	per	per	IN	_	_	_
87	position	position	NN	_	_	_
88	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	position	position	NN	_	_	_
3	is	be	VBZ	_	_	_
4	corresponding	correspond	VBG	_	_	_
5	to	to	TO	_	_	_
6	the	the	DT	_	_	_
7	position	position	NN	_	_	_
8	of	of	IN	_	_	_
9	\	\	CD	_	_	_
10	Sequenced	sequence	VBN	_	_	_
11	region	region	NN	_	_	_
12	of	of	IN	_	_	_
13	pPR9	ppr9	NN	_	_	_
14	plasmid	plasmid	NN	_	_	_
15	\	\	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	one	one	CD	_	_	_
18	of	of	IN	_	_	_
19	the	the	DT	_	_	_
20	attached	attach	VBN	_	_	_
21	txt	txt	NN	_	_	_
22	file	file	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cells	cell	NNS	_	_	_
4	culture	culture	NN	_	_	_
5	were	be	VBD	_	_	_
6	harvested	harvest	VBN	_	_	_
7	and	and	CC	_	_	_
8	resuspended	resuspend	VBN	_	_	_
9	with	with	IN	_	_	_
10	a	a	DT	_	_	_
11	solution	solution	NN	_	_	_
12	containing	contain	VBG	_	_	_
13	0.5	0.5	CD	_	_	_
14	%	%	NN	_	_	_
15	SDS	sds	NN	_	_	_
16	,	,	,	_	_	_
17	20	20	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	sodium	sodium	NN	SUPP	_	_
20	acetate	acetate	NN	SUPP	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	pH	ph	NN	_	_	_
23	5.5	5.5	CD	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	,	,	,	_	_	_
26	and	and	CC	_	_	_
27	10	10	CD	_	_	_
28	mM	mm	NN	KWSUPP	_	_
29	EDTA	edta	NN	_	_	_
30	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	suspended	suspend	VBN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	mixed	mix	VBN	_	_	_
6	with	with	IN	_	_	_
7	an	a	DT	_	_	_
8	equal	equal	JJ	_	_	_
9	volume	volume	NN	_	_	_
10	of	of	IN	_	_	_
11	pre-warmed	pre-warmed	JJ	_	_	_
12	saturated	saturated	JJ	_	_	_
13	phenol	phenol	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	20	20	CD	_	_	_
16	mM	mm	NN	KWSUPP	_	_
17	sodium	sodium	NN	SUPP	_	_
18	acetate	acetate	NN	SUPP	_	_
19	,	,	,	_	_	_
20	10	10	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	EDTA	edta	NN	_	_	_
23	pH	ph	NN	_	_	_
24	5.5	5.5	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	and	and	CC	_	_	_
27	incubated	incubate	VBN	_	_	_
28	for	for	IN	_	_	_
29	5	5	CD	_	_	_
30	min	min	NN	_	_	_
31	at	at	IN	_	_	_
32	60	60	CD	_	_	_
33	˚C	˚c	NN	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	numbers	number	NNS	_	_	_
4	of	of	IN	_	_	_
5	4	4	CD	_	_	_
6	bases	basis	NNS	_	_	_
7	A	a	DT	_	_	_
8	,	,	,	_	_	_
9	T	t	NN	_	_	_
10	,	,	,	_	_	_
11	G	g	NN	_	_	_
12	,	,	,	_	_	_
13	C	c	NN	_	_	_
14	,	,	,	_	_	_
15	and	and	CC	_	_	_
16	N	n	NN	_	_	_
17	were	be	VBD	_	_	_
18	counted	count	VBN	_	_	_
19	in	in	IN	_	_	_
20	each	each	DT	_	_	_
21	position	position	NN	_	_	_
22	of	of	IN	_	_	_
23	the	the	DT	_	_	_
24	mapped	map	VBN	_	_	_
25	reads	read	VBZ	_	_	_
26	by	by	IN	_	_	_
27	using	use	VBG	_	_	_
28	the	the	DT	_	_	_
29	program	program	NN	_	_	_
30	SAMtools	samtool	NNS	_	_	_
31	0.1.18	0.1.18	CD	_	_	_
32	with	with	IN	_	_	_
33	supplemental	supplemental	JJ	_	_	_
34	use	use	NN	_	_	_
35	of	of	IN	_	_	_
36	a	a	DT	_	_	_
37	Perl	Perl	NNP	_	_	_
38	script	script	NN	_	_	_
39	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	obtained	obtain	VBN	_	_	_
4	reads	read	VBZ	_	_	_
5	were	be	VBD	_	_	_
6	aligned	align	VBN	_	_	_
7	and	and	CC	_	_	_
8	mapped	map	VBN	_	_	_
9	to	to	TO	_	_	_
10	the	the	DT	_	_	_
11	pPR9	ppr9	NN	_	_	_
12	plasmid	plasmid	NN	_	_	_
13	DNA	dna	NN	_	_	_
14	sequences	sequence	NNS	_	_	_
15	using	use	VBG	_	_	_
16	Bowtie	Bowtie	NNP	_	_	_
17	0.12.7	0.12.7	CD	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	We	we	PRP	_	_	_
3	established	establish	VBD	_	_	_
4	a	a	DT	_	_	_
5	method	method	NN	_	_	_
6	for	for	IN	_	_	_
7	preparing	prepare	VBG	_	_	_
8	five	five	CD	_	_	_
9	different	different	JJ	_	_	_
10	cDNA	cdna	NN	_	_	_
11	libraries	library	NNS	_	_	_
12	each	each	DT	_	_	_
13	with	with	IN	_	_	_
14	its	its	PRP$	_	_	_
15	own	own	JJ	_	_	_
16	barcode	barcode	NN	_	_	_
17	for	for	IN	_	_	_
18	Illumina	Illumina	NNP	_	_	_
19	sequencing	sequencing	NN	_	_	_
20	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	6-nt	6-nt	JJ	_	_	_
3	barcode	barcode	NN	_	_	_
4	allows	allow	VBZ	_	_	_
5	multiplexing	multiplex	VBG	_	_	_
6	all	all	DT	_	_	_
7	five	five	CD	_	_	_
8	in	in	FW	_	_	_
9	vitro	vitro	FW	_	_	_
10	and	and	CC	_	_	_
11	in	in	FW	_	_	_
12	vivo	vivo	FW	_	_	_
13	preparations	preparation	NNS	_	_	_
14	in	in	IN	_	_	_
15	a	a	DT	_	_	_
16	single	single	JJ	_	_	_
17	sequencing	sequencing	NN	_	_	_
18	analysis	analysis	NN	_	_	_
19	.	.	.	_	_	_

1	our	we	PRP$	_	_	_
2	method	method	NN	_	_	_
3	introduces	introduce	VBZ	_	_	_
4	internal	internal	JJ	_	_	_
5	control	control	NN	_	_	_
6	sequences	sequence	NNS	_	_	_
7	to	to	TO	_	_	_
8	the	the	DT	_	_	_
9	library	library	NN	_	_	_
10	that	that	WDT	_	_	_
11	are	be	VBP	_	_	_
12	subjected	subject	VBN	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	artifact	artifact	NN	_	_	_
16	errors	error	NNS	_	_	_
17	,	,	,	_	_	_
18	but	but	CC	_	_	_
19	are	be	VBP	_	_	_
20	not	not	RB	_	_	_
21	for	for	IN	_	_	_
22	RNAP	rnap	NN	_	_	_
23	errors	error	NNS	_	_	_
24	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	5	5	CD	_	_	_
3	'	'	''	_	_	_
4	fragment	fragment	NN	_	_	_
5	of	of	IN	_	_	_
6	the	the	DT	_	_	_
7	5.7	5.7	CD	_	_	_
8	kb	kb	NN	_	_	_
9	RNA	rna	NN	_	_	_
10	transcripts	transcript	NNS	_	_	_
11	was	be	VBD	_	_	_
12	reverse	reverse	JJ	_	_	_
13	transcribed	transcribe	VBN	_	_	_
14	to	to	TO	_	_	_
15	make	make	VB	_	_	_
16	the	the	DT	_	_	_
17	cDNA	cdna	NN	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cDNA	cdna	NN	_	_	_
3	was	be	VBD	_	_	_
4	subjected	subject	VBN	_	_	_
5	to	to	TO	_	_	_
6	PCR	pcr	NN	_	_	_
7	reactions	reaction	NNS	_	_	_
8	that	that	WDT	_	_	_
9	generated	generate	VBD	_	_	_
10	six	six	CD	_	_	_
11	200	200	CD	_	_	_
12	bp	bp	NN	_	_	_
13	segments	segment	NNS	_	_	_
14	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	primers	primer	NNS	_	_	_
3	contained	contain	VBD	_	_	_
4	a	a	DT	_	_	_
5	specific	specific	JJ	_	_	_
6	barcode	barcode	NN	_	_	_
7	for	for	IN	_	_	_
8	each	each	DT	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	five	five	CD	_	_	_
12	starting	start	VBG	_	_	_
13	preparations	preparation	NNS	_	_	_
14	and	and	CC	_	_	_
15	the	the	DT	_	_	_
16	inner	inner	JJ	_	_	_
17	Illuminasequencing	illuminasequencing	NN	_	_	_
18	adapters	adapter	NNS	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	2nd-step	2nd-step	NN	_	_	_
3	of	of	IN	_	_	_
4	PCR	pcr	NN	_	_	_
5	generated	generate	VBD	_	_	_
6	the	the	DT	_	_	_
7	final	final	JJ	_	_	_
8	cDNA	cdna	NN	_	_	_
9	libraries	library	NNS	_	_	_
10	for	for	IN	_	_	_
11	the	the	DT	_	_	_
12	Illumina	Illumina	NNP	_	_	_
13	sequencing	sequencing	NN	_	_	_
14	by	by	IN	_	_	_
15	using	use	VBG	_	_	_
16	the	the	DT	_	_	_
17	1st-step	1st-step	JJ	_	_	_
18	PCR	pcr	NN	_	_	_
19	product	product	NN	_	_	_
20	as	as	IN	_	_	_
21	a	a	DT	_	_	_
22	template	template	NN	_	_	_
23	and	and	CC	_	_	_
24	primers	primer	NNS	_	_	_
25	containing	contain	VBG	_	_	_
26	the	the	DT	_	_	_
27	outer	outer	JJ	_	_	_
28	sequencing	sequencing	NN	_	_	_
29	adapters	adapter	NNS	_	_	_
30	in	in	IN	_	_	_
31	the	the	DT	_	_	_
32	5	5	CD	_	_	_
33	'	'	''	_	_	_
34	tails	tail	NNS	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	At	at	IN	_	_	_
3	the	the	DT	_	_	_
4	appropriate	appropriate	JJ	_	_	_
5	phase	phase	NN	_	_	_
6	of	of	IN	_	_	_
7	growth	growth	NN	_	_	_
8	,	,	,	_	_	_
9	a	a	DT	_	_	_
10	one-eighth	one-eighth	NN	_	_	_
11	volume	volume	NN	_	_	_
12	of	of	IN	_	_	_
13	stop	stop	NN	_	_	_
14	solution	solution	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	95	95	CD	_	_	_
17	%	%	NN	_	_	_
18	-LSB-	-lsb-	-LRB-	_	_	_
19	v	v	LS	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	E.	E.	NNP	_	_	_
22	coli	coli	NN	_	_	_
23	batch	batch	NN	_	_	_
24	culture	culture	NN	_	_	_
25	without	without	IN	_	_	_
26	TAP	tap	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	E.	e.	FW	_	_	_
29	coli	coli	FW	_	_	_
30	batch	batch	NN	_	_	_
31	culture	culture	NN	_	_	_
32	with	with	IN	_	_	_
33	TAP	tap	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	E.	e.	FW	_	_	_
36	coli	coli	FW	_	_	_
37	-	-	:	_	_	_
38	TAP	tap	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	E.	e.	FW	_	_	_
41	coli	coli	FW	_	_	_
42	+	+	CC	_	_	_
43	TAP	tap	FW	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
45	Escherichia	escherichia	FW	Organism	_	_
46	coli	coli	FW	Organism	_	_
47	BW25113	bw25113	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	Escherichia	escherichia	FW	Organism	_	_
50	coli	coli	FW	Organism	_	_
51	K12	k12	NN	_	_	_
52	strain	strain	NN	_	_	_
53	BW25113	bw25113	NN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	Datsenko	Datsenko	NNP	_	_	_
56	&	&	CC	_	_	_
57	Wanner	Wanner	NNP	_	_	_
58	2000	2000	CD	_	_	_
59	.	.	.	_	_	_

1	PNAS	PNAS	NNP	_	_	_
2	97	97	CD	_	_	_
3	:	:	:	_	_	_
4	6640	6640	CD	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	was	be	VBD	_	_	_
7	cultivated	cultivate	VBN	_	_	_
8	in	in	IN	_	_	_
9	100	100	CD	_	_	_
10	mL	ml	NN	_	_	_
11	of	of	IN	_	_	_
12	LB	lb	NN	MED	_	_
13	broth	broth	NN	MED	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Miller	Miller	NNP	_	_	_
16	1972	1972	CD	_	_	_
17	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	:	:	:	_	_	_
3	Experiments	experiment	NNS	_	_	_
4	in	in	IN	_	_	_
5	molecular	molecular	JJ	_	_	_
6	genetics	genetics	NNS	_	_	_
7	.	.	.	_	_	_

1	Cold	Cold	NNP	_	_	_
2	Spring	Spring	NNP	_	_	_
3	Harbor	Harbor	NNP	_	_	_
4	Laboratory	Laboratory	NNP	_	_	_
5	,	,	,	_	_	_
6	NY	NY	NNP	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	in	in	IN	_	_	_
9	a	a	DT	_	_	_
10	250	250	CD	_	_	_
11	mL	ml	NN	_	_	_
12	Erlenmeyer	erlenmeyer	NN	_	_	_
13	flask	flask	NN	_	_	_
14	at	at	IN	_	_	_
15	37	37	CD	_	_	_
16	°C	°c	NN	_	_	_
17	with	with	IN	_	_	_
18	shaking	shake	VBG	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	250	250	CD	_	_	_
21	rpm	rpm	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	to	to	TO	_	_	_
24	an	a	DT	_	_	_
25	O.D.	O.D.	NNP	_	_	_
26	600nm	600nm	NNP	_	_	_
27	of	of	IN	_	_	_
28	0.6	0.6	CD	_	_	_
29	.	.	.	_	_	_

1	S.	S.	NNP	_	_	_
2	coelicolor	coelicolor	NN	_	_	_
3	A3	a3	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	2	2	CD	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	strain	strain	NN	_	_	_
8	M145	m145	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Kieser	Kieser	NNP	_	_	_
11	et	et	FW	_	_	_
12	al.	al.	FW	_	_	_
13	2000	2000	CD	_	_	_
14	.	.	.	_	_	_

1	Practical	Practical	NNP	_	_	_
2	Streptomyces	Streptomyces	NNP	_	_	_
3	Genetics	Genetics	NNP	_	_	_
4	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	John	John	NNP	_	_	_
3	Innes	Innes	NNP	_	_	_
4	Foundation	Foundation	NNP	_	_	_
5	,	,	,	_	_	_
6	Norwich	Norwich	NNP	_	_	_
7	.	.	.	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_

1	was	be	VBD	_	_	_
2	incubated	incubate	VBN	_	_	_
3	in	in	IN	_	_	_
4	YEME	yeme	NN	_	_	_
5	broth	broth	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	Kieser	Kieser	NNP	_	_	_
8	et	et	FW	_	_	_
9	al.	al.	FW	_	_	_
10	2000	2000	CD	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	at	at	IN	_	_	_
13	30	30	CD	_	_	_
14	°C	°c	NN	_	_	_
15	with	with	IN	_	_	_
16	shaking	shake	VBG	_	_	_
17	until	until	IN	_	_	_
18	the	the	DT	_	_	_
19	mycelia	mycelia	NN	_	_	_
20	became	become	VBD	_	_	_
21	pigmented	pigmented	JJ	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	For	for	IN	_	_	_
3	each	each	DT	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	4	4	CD	_	_	_
7	libraries	library	NNS	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	2	2	CD	_	_	_
10	bacterial	bacterial	JJ	_	_	_
11	samples	sample	NNS	_	_	_
12	x	x	CC	_	_	_
13	2	2	CD	_	_	_
14	treatments	treatment	NNS	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	,	,	,	_	_	_
17	we	we	PRP	_	_	_
18	counted	count	VBD	_	_	_
19	the	the	DT	_	_	_
20	number	number	NN	_	_	_
21	of	of	IN	_	_	_
22	times	time	NNS	_	_	_
23	each	each	DT	_	_	_
24	nucleotide	nucleotide	NN	_	_	_
25	position	position	NN	_	_	_
26	was	be	VBD	_	_	_
27	the	the	DT	_	_	_
28	first	first	JJ	_	_	_
29	in	in	IN	_	_	_
30	a	a	DT	_	_	_
31	sequence	sequence	NN	_	_	_
32	read	read	VBN	_	_	_
33	using	use	VBG	_	_	_
34	a	a	DT	_	_	_
35	simple	simple	JJ	_	_	_
36	script	script	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	unpubl	unpubl	NN	_	_	_
39	.	.	.	_	_	_

1	resource	resource	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	forward	forward	JJ	_	_	_
3	and	and	CC	_	_	_
4	reverse	reverse	JJ	_	_	_
5	strands	strand	NNS	_	_	_
6	were	be	VBD	_	_	_
7	then	then	RB	_	_	_
8	processed	process	VBN	_	_	_
9	separately	separately	RB	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	The	the	DT	_	_	_
7	reference	reference	NN	_	_	_
8	genomes	genome	NNS	_	_	_
9	used	use	VBN	_	_	_
10	for	for	IN	_	_	_
11	E.	e.	FW	_	_	_
12	coli	coli	FW	_	_	_
13	K12	k12	NN	_	_	_
14	strain	strain	NN	_	_	_
15	BW25113	bw25113	NN	_	_	_
16	and	and	CC	_	_	_
17	S.	S.	NNP	_	_	_
18	coelicolor	coelicolor	VBP	_	_	_
19	A3	a3	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	2	2	CD	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	strain	strain	NN	_	_	_
24	M145	m145	NN	_	_	_
25	were	be	VBD	_	_	_
26	U00096	u00096	NN	_	_	_
27	.2	.2	NN	_	_	_
28	and	and	CC	_	_	_
29	AL645882	al645882	NN	_	_	_
30	,	,	,	_	_	_
31	respectively	respectively	RB	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	genotype	genotype	NN	_	_	_
3	:	:	:	_	_	_
4	wild-type	wild-type	JJ	_	_	_
5	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
6	Libraries	Libraries	NNPS	_	_	_
7	were	be	VBD	_	_	_
8	constructed	construct	VBN	_	_	_
9	by	by	IN	_	_	_
10	vertis	vertis	NN	_	_	_
11	Biotechnologie	Biotechnologie	NNP	_	_	_
12	AG	AG	NNP	_	_	_
13	,	,	,	_	_	_
14	Germany	Germany	NNP	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	www.vertis-biotech.com	www.vertis-biotech.com	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	as	as	IN	_	_	_
19	a	a	DT	_	_	_
20	service	service	NN	_	_	_
21	that	that	WDT	_	_	_
22	included	include	VBD	_	_	_
23	treating	treat	VBG	_	_	_
24	an	a	DT	_	_	_
25	aliquot	aliquot	NN	_	_	_
26	of	of	IN	_	_	_
27	each	each	DT	_	_	_
28	RNA	rna	NN	_	_	_
29	sample	sample	NN	_	_	_
30	with	with	IN	_	_	_
31	TAP	tap	NN	_	_	_
32	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	5	5	CD	_	_	_
3	'	'	''	_	_	_
4	-	-	:	_	_	_
5	sequencing	sequencing	NN	_	_	_
6	adaptor	adaptor	NN	_	_	_
7	was	be	VBD	_	_	_
8	ligated	ligate	VBN	_	_	_
9	to	to	TO	_	_	_
10	transcripts	transcript	NNS	_	_	_
11	prior	prior	RB	_	_	_
12	to	to	TO	_	_	_
13	fragmentation	fragmentation	NN	_	_	_
14	,	,	,	_	_	_
15	thereby	thereby	RB	_	_	_
16	allowing	allow	VBG	_	_	_
17	the	the	DT	_	_	_
18	5	5	CD	_	_	_
19	'	'	''	_	_	_
20	ends	end	NNS	_	_	_
21	of	of	IN	_	_	_
22	both	both	DT	_	_	_
23	long	long	JJ	_	_	_
24	and	and	CC	_	_	_
25	short	short	JJ	_	_	_
26	transcripts	transcript	NNS	_	_	_
27	to	to	TO	_	_	_
28	be	be	VB	_	_	_
29	detected	detect	VBN	_	_	_
30	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	4	4	CD	_	_	_
5	libraries	library	NNS	_	_	_
6	was	be	VBD	_	_	_
7	constructed	construct	VBN	_	_	_
8	using	use	VBG	_	_	_
9	a	a	DT	_	_	_
10	different	different	JJ	_	_	_
11	barcode	barcode	NN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	RNA	rna	NN	_	_	_
5	sequences	sequence	NNS	_	_	_
6	from	from	IN	_	_	_
7	each	each	DT	_	_	_
8	of	of	IN	_	_	_
9	the	the	DT	_	_	_
10	two	two	CD	_	_	_
11	differential	differential	JJ	_	_	_
12	analyses	analysis	NNS	_	_	_
13	were	be	VBD	_	_	_
14	processed	process	VBN	_	_	_
15	and	and	CC	_	_	_
16	mapped	map	VBN	_	_	_
17	to	to	TO	_	_	_
18	the	the	DT	_	_	_
19	corresponding	corresponding	JJ	_	_	_
20	genomes	genome	NNS	_	_	_
21	as	as	IN	_	_	_
22	a	a	DT	_	_	_
23	service	service	NN	_	_	_
24	provided	provide	VBN	_	_	_
25	by	by	IN	_	_	_
26	vertis	vertis	NN	_	_	_
27	Biotechnologie	Biotechnologie	NNP	_	_	_
28	AG	AG	NNP	_	_	_
29	,	,	,	_	_	_
30	Germany	Germany	NNP	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	www.vertis-biotech.com	www.vertis-biotech.com	NNP	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	involved	involved	JJ	_	_	_
3	trimming	trim	VBG	_	_	_
4	adaptor	adaptor	NN	_	_	_
5	sequence	sequence	NN	_	_	_
6	and	and	CC	_	_	_
7	masking	mask	VBG	_	_	_
8	for	for	IN	_	_	_
9	low-quality	low-quality	JJ	_	_	_
10	sequence	sequence	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	from	from	IN	_	_	_
6	the	the	DT	_	_	_
7	pellet	pellet	NN	_	_	_
8	of	of	IN	_	_	_
9	E.	e.	FW	_	_	_
10	coli	coli	FW	_	_	_
11	cells	cell	NNS	_	_	_
12	using	use	VBG	_	_	_
13	a	a	DT	_	_	_
14	well-established	well-established	JJ	_	_	_
15	,	,	,	_	_	_
16	published	publish	VBN	_	_	_
17	protocol	protocol	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Kime	Kime	NNP	_	_	_
20	et	et	FW	_	_	_
21	al.	al.	FW	_	_	_
22	2008	2008	CD	_	_	_
23	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	RNA	rna	NN	_	_	_
3	Turnover	turnover	NN	_	_	_
4	in	in	IN	_	_	_
5	Bacteria	bacterium	NNS	_	_	_
6	,	,	,	_	_	_
7	Archaea	Archaea	NNP	_	_	_
8	and	and	CC	_	_	_
9	Organelles	Organelles	NNP	_	_	_
10	,	,	,	_	_	_
11	Vol	Vol	NNP	_	_	_
12	447	447	CD	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	ed	ed	VBN	_	_	_
15	.	.	.	_	_	_

1	LE	LE	NNP	_	_	_
2	Maquat	Maquat	NNP	_	_	_
3	,	,	,	_	_	_
4	CM	cm	NN	_	_	_
5	Arraiano	arraiano	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	,	,	,	_	_	_
8	pp.	pp.	NN	_	_	_
9	215	215	CD	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cell	cell	NN	_	_	_
3	pellet	pellet	NN	_	_	_
4	of	of	IN	_	_	_
5	S.	S.	NNP	_	_	_
6	coelicolor	coelicolor	NN	_	_	_
7	was	be	VBD	_	_	_
8	resuspended	resuspend	VBN	_	_	_
9	in	in	IN	_	_	_
10	Kirby	Kirby	NNP	_	_	_
11	mix	mix	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Kieser	Kieser	NNP	_	_	_
14	et	et	FW	_	_	_
15	al.	al.	FW	_	_	_
16	2000	2000	CD	_	_	_
17	.	.	.	_	_	_

1	Practical	Practical	NNP	_	_	_
2	Streptomyces	Streptomyces	NNP	_	_	_
3	Genetics	Genetics	NNP	_	_	_
4	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	John	John	NNP	_	_	_
3	Innes	Innes	NNP	_	_	_
4	Foundation	Foundation	NNP	_	_	_
5	,	,	,	_	_	_
6	Norwich	Norwich	NNP	_	_	_
7	.	.	.	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_

1	,	,	,	_	_	_
2	100	100	CD	_	_	_
3	µL	µl	NN	_	_	_
4	per	per	IN	_	_	_
5	1	1	CD	_	_	_
6	O.D.	O.D.	NNP	_	_	_
7	600nm	600nm	NNP	_	_	_
8	unit	unit	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	transferred	transfer	VBN	_	_	_
12	to	to	TO	_	_	_
13	Lysing	lyse	VBG	_	_	_
14	Matrix	Matrix	NNP	_	_	_
15	B	B	NNP	_	_	_
16	tubes	tube	NNS	_	_	_
17	containing	contain	VBG	_	_	_
18	fine	fine	JJ	_	_	_
19	silica	silica	NN	_	_	_
20	beads	bead	NNS	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	MP	mp	NN	_	_	_
23	Biomedical	biomedical	JJ	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	.	.	.	_	_	_

1	Tubes	tube	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	placed	place	VBN	_	_	_
5	in	in	IN	_	_	_
6	a	a	DT	_	_	_
7	high-speed	high-speed	JJ	_	_	_
8	benchtop	benchtop	NN	_	_	_
9	homogenizer	homogenizer	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Fastprep-24	fastprep-24	NN	_	_	_
12	,	,	,	_	_	_
13	MP	mp	NN	_	_	_
14	Biomedical	biomedical	NN	_	_	_
15	;	;	:	_	_	_
16	set	set	VBN	_	_	_
17	at	at	IN	_	_	_
18	6.5	6.5	CD	_	_	_
19	M	m	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	strain	strain	NN	_	_	_
22	:	:	:	_	_	_
23	BW25113	bw25113	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Supplementary	supplementary	JJ	_	_	_
26	_	_	NN	_	_	_
27	files	file	NNS	_	_	_
28	_	_	IN	_	_	_
29	format	format	NN	_	_	_
30	_	_	NN	_	_	_
31	and	and	CC	_	_	_
32	_	_	NN	_	_	_
33	content	content	NN	_	_	_
34	:	:	:	_	_	_
35	BedGraphs	bedgraph	NNS	_	_	_
36	of	of	IN	_	_	_
37	the	the	DT	_	_	_
38	reads	read	VBZ	_	_	_
39	before	before	IN	_	_	_
40	and	and	CC	_	_	_
41	after	after	IN	_	_	_
42	TAP	tap	NN	_	_	_
43	treatment	treatment	NN	_	_	_
44	for	for	IN	_	_	_
45	each	each	DT	_	_	_
46	of	of	IN	_	_	_
47	the	the	DT	_	_	_
48	samples	sample	NNS	_	_	_
49	.	.	.	_	_	_

1	Separate	separate	JJ	_	_	_
2	files	file	NNS	_	_	_
3	are	be	VBP	_	_	_
4	provided	provide	VBN	_	_	_
5	for	for	IN	_	_	_
6	the	the	DT	_	_	_
7	forward	forward	JJ	_	_	_
8	and	and	CC	_	_	_
9	reverse	reverse	JJ	_	_	_
10	strands	strand	NNS	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	sample	sample	NN	_	_	_
4	sources	source	NNS	_	_	_
5	of	of	IN	_	_	_
6	individual	individual	JJ	_	_	_
7	reads	read	VBZ	_	_	_
8	were	be	VBD	_	_	_
9	determined	determine	VBN	_	_	_
10	by	by	IN	_	_	_
11	the	the	DT	_	_	_
12	barcoding	barcoding	NN	_	_	_
13	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	barcodes	barcode	NNS	_	_	_
3	for	for	IN	_	_	_
4	the	the	DT	_	_	_
5	minus	minus	NN	_	_	_
6	and	and	CC	_	_	_
7	plus	plus	CC	_	_	_
8	TAP	tap	NN	_	_	_
9	treatments	treatment	NNS	_	_	_
10	were	be	VBD	_	_	_
11	ACTTGA	ACTTGA	NNP	_	_	_
12	and	and	CC	_	_	_
13	CGATGT	CGATGT	NNP	_	_	_
14	,	,	,	_	_	_
15	respectively	respectively	RB	_	_	_
16	,	,	,	_	_	_
17	for	for	IN	_	_	_
18	the	the	DT	_	_	_
19	E.	e.	FW	_	_	_
20	coli	coli	FW	_	_	_
21	RNA	rna	NN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	CAGATC	CAGATC	NNP	_	_	_
25	and	and	CC	_	_	_
26	ATCACG	ATCACG	NNP	_	_	_
27	,	,	,	_	_	_
28	respectively	respectively	RB	_	_	_
29	,	,	,	_	_	_
30	for	for	IN	_	_	_
31	the	the	DT	_	_	_
32	S.	S.	NNP	_	_	_
33	coelicolor	coelicolor	NN	_	_	_
34	RNA	rna	NN	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	none	none	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	treatment	treatment	NN	_	_	_
7	:	:	:	_	_	_
8	tobacco	tobacco	NN	_	_	_
9	acid	acid	NN	_	_	_
10	pyrophosphatase	pyrophosphatase	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	TAP	tap	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Cells	cell	NNS	_	_	_
16	at	at	IN	_	_	_
17	appropriate	appropriate	JJ	_	_	_
18	cell	cell	NN	_	_	_
19	density	density	NN	_	_	_
20	were	be	VBD	_	_	_
21	cross-linked	cross-link	VBN	_	_	_
22	by	by	IN	_	_	_
23	1	1	CD	_	_	_
24	%	%	NN	_	_	_
25	formaldehyde	formaldehyde	NN	_	_	_
26	at	at	IN	_	_	_
27	room	room	NN	_	_	_
28	temperature	temperature	NN	_	_	_
29	for	for	IN	_	_	_
30	25	25	CD	_	_	_
31	min	min	NN	_	_	_
32	.	.	.	_	_	_

1	Following	follow	VBG	_	_	_
2	quenching	quench	VBG	_	_	_
3	the	the	DT	_	_	_
4	unused	unused	JJ	_	_	_
5	formaldehyde	formaldehyde	NN	_	_	_
6	with	with	IN	_	_	_
7	a	a	DT	_	_	_
8	final	final	JJ	_	_	_
9	concentration	concentration	NN	_	_	_
10	of	of	IN	_	_	_
11	125	125	CD	_	_	_
12	mM	mm	NN	KWSUPP	_	_
13	glycine	glycine	NN	_	_	_
14	at	at	IN	_	_	_
15	room	room	NN	_	_	_
16	temperature	temperature	NN	_	_	_
17	for	for	IN	_	_	_
18	5	5	CD	_	_	_
19	min	min	NN	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cross-linked	cross-linked	JJ	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	harvested	harvest	VBN	_	_	_
6	and	and	CC	_	_	_
7	washed	wash	VBN	_	_	_
8	three	three	CD	_	_	_
9	times	time	NNS	_	_	_
10	with	with	IN	_	_	_
11	50	50	CD	_	_	_
12	mL	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	ice-cold	ice-cold	JJ	_	_	_
15	TBS	tbs	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Tris	tris	NN	_	_	_
18	Buffered	buffer	VBN	_	_	_
19	Saline	saline	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	washed	wash	VBN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	re-suspended	re-suspended	JJ	_	_	_
6	in	in	IN	_	_	_
7	0.5	0.5	CD	_	_	_
8	mL	ml	NN	_	_	_
9	lysis	lysis	NN	_	_	_
10	buffer	buffer	NN	_	_	_
11	composed	compose	VBN	_	_	_
12	of	of	IN	_	_	_
13	50	50	CD	_	_	_
14	mM	mm	NN	KWSUPP	_	_
15	Tris-HCl	tris-hcl	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	pH	ph	NN	_	_	_
18	7.5	7.5	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	,	,	,	_	_	_
21	100	100	CD	_	_	_
22	mM	mm	NN	KWSUPP	_	_
23	NaCl	nacl	NN	_	_	_
24	,	,	,	_	_	_
25	1	1	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	EDTA	edta	NN	_	_	_
28	,	,	,	_	_	_
29	1	1	CD	_	_	_
30	ug	ug	NN	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	chip	chip	NN	_	_	_
33	antibody	antibody	NN	_	_	_
34	:	:	:	_	_	_
35	anti-c-myc	anti-c-myc	JJ	_	_	_
36	antibody	antibody	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
38	chip	chip	NN	_	_	_
39	antibody	antibody	NN	_	_	_
40	:	:	:	_	_	_
41	anti-FecI	anti-feci	JJ	_	_	_
42	antibody	antibody	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
44	chip	chip	NN	_	_	_
45	antibody	antibody	NN	_	_	_
46	:	:	:	_	_	_
47	anti-RpoB	anti-rpob	JJ	_	_	_
48	antibody	antibody	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
50	chip	chip	NN	_	_	_
51	antibody	antibody	NN	_	_	_
52	:	:	:	_	_	_
53	anti-RpoD	anti-rpod	JJ	_	_	_
54	antibody	antibody	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
56	chip	chip	NN	_	_	_
57	antibody	antibody	NN	_	_	_
58	:	:	:	_	_	_
59	anti-RpoF	anti-rpof	JJ	_	_	_
60	antibody	antibody	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
62	chip	chip	NN	_	_	_
63	antibody	antibody	NN	_	_	_
64	:	:	:	_	_	_
65	anti-RpoN	anti-rpon	JJ	_	_	_
66	antibody	antibody	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
68	chip	chip	NN	_	_	_
69	antibody	antibody	NN	_	_	_
70	:	:	:	_	_	_
71	anti-RpoS	anti-rpos	JJ	_	_	_
72	antibody	antibody	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
74	chip	chip	NN	_	_	_
75	antibody	antibody	NN	_	_	_
76	manufacturer	manufacturer	NN	_	_	_
77	:	:	:	_	_	_
78	Upstate	upstate	JJ	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
80	chip	chip	NN	_	_	_
81	antibody	antibody	NN	_	_	_
82	:	:	:	_	_	_
83	normal	normal	JJ	_	_	_
84	mouse	mouse	NN	_	_	_
85	IgG	igg	NN	_	_	_
86	-LRB-	-lrb-	-LRB-	_	_	_
87	Upstate	upstate	JJ	_	_	_
88	-RRB-	-rrb-	-RRB-	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	Cross-linked	cross-linked	JJ	_	_	_
91	and	and	CC	_	_	_
92	sonicated	sonicated	JJ	_	_	_
93	chromatin	chromatin	NN	_	_	_
94	complex	complex	NN	_	_	_
95	of	of	IN	_	_	_
96	RNAP	rnap	NN	_	_	_
97	and	and	CC	_	_	_
98	DNA	dna	NN	_	_	_
99	was	be	VBD	_	_	_
100	immunoprecipitated	immunoprecipitate	VBN	_	_	_
101	by	by	IN	_	_	_
102	anti-RpoB	anti-rpob	JJ	_	_	_
103	antibody	antibody	NN	_	_	_
104	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cross-linked	cross-linked	JJ	_	_	_
3	and	and	CC	_	_	_
4	sonicated	sonicated	JJ	_	_	_
5	chromatin	chromatin	NN	_	_	_
6	complex	complex	NN	_	_	_
7	of	of	IN	_	_	_
8	RNAP	rnap	NN	_	_	_
9	and	and	CC	_	_	_
10	DNA	dna	NN	_	_	_
11	was	be	VBD	_	_	_
12	immunoprecipitated	immunoprecipitate	VBN	_	_	_
13	by	by	IN	_	_	_
14	using	use	VBG	_	_	_
15	normal	normal	JJ	_	_	_
16	mouse	mouse	NN	_	_	_
17	IgG	igg	NN	_	_	_
18	for	for	IN	_	_	_
19	the	the	DT	_	_	_
20	control	control	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	Coli	Coli	NNP	_	_	_
4	Exponential	Exponential	NNP	_	_	_
5	FecI	FecI	NNP	_	_	_
6	ChIP	ChIP	NNP	_	_	_
7	DNA	dna	NN	_	_	_
8	1	1	CD	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	E.	E.	NNP	_	_	_
11	Coli	Coli	NNP	_	_	_
12	Exponential	Exponential	NNP	_	_	_
13	FecI	FecI	NNP	_	_	_
14	ChIP	ChIP	NNP	_	_	_
15	DNA	dna	NN	_	_	_
16	2	2	CD	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	E.	E.	NNP	_	_	_
19	Coli	Coli	NNP	_	_	_
20	Exponential	Exponential	NNP	_	_	_
21	FecI	FecI	NNP	_	_	_
22	ChIP	ChIP	NNP	_	_	_
23	DNA	DNA	NNP	_	_	_
24	3	3	CD	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	E.	E.	NNP	_	_	_
27	Coli	Coli	NNP	_	_	_
28	Exponential	Exponential	NNP	_	_	_
29	FecI	FecI	NNP	_	_	_
30	ChIP	chip	NN	_	_	_
31	DNA	dna	NN	_	_	_
32	Mock	mock	NN	_	_	_
33	1	1	CD	_	_	_
34	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
35	E.	E.	NNP	_	_	_
36	Coli	Coli	NNP	_	_	_
37	Exponential	Exponential	NNP	_	_	_
38	FecI	FecI	NNP	_	_	_
39	ChIP	chip	NN	_	_	_
40	DNA	dna	NN	_	_	_
41	Mock	mock	NN	_	_	_
42	2	2	CD	_	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	E.	E.	NNP	_	_	_
45	Coli	Coli	NNP	_	_	_
46	Exponential	Exponential	NNP	_	_	_
47	FecI	FecI	NNP	_	_	_
48	ChIP	chip	NN	_	_	_
49	DNA	dna	NN	_	_	_
50	Mock	mock	NN	_	_	_
51	3	3	CD	_	_	_
52	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
53	E.	E.	NNP	_	_	_
54	Coli	Coli	NNP	_	_	_
55	Exponential	Exponential	NNP	_	_	_
56	RpoB	rpob	NN	_	_	_
57	ChIP	chip	NN	_	_	_
58	DNA	dna	NN	_	_	_
59	1	1	CD	_	_	_
60	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
61	E.	E.	NNP	_	_	_
62	Coli	Coli	NNP	_	_	_
63	Exponential	Exponential	NNP	_	_	_
64	RpoB	rpob	NN	_	_	_
65	ChIP	chip	NN	_	_	_
66	DNA	dna	NN	_	_	_
67	2	2	CD	_	_	_
68	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
69	E.	E.	NNP	_	_	_
70	Coli	Coli	NNP	_	_	_
71	Exponential	Exponential	NNP	_	_	_
72	RpoB	rpob	NN	_	_	_
73	ChIP	chip	NN	_	_	_
74	DNA	dna	NN	_	_	_
75	3	3	CD	_	_	_
76	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
77	E.	E.	NNP	_	_	_
78	Coli	Coli	NNP	_	_	_
79	Exponential	Exponential	NNP	_	_	_
80	RpoB	rpob	NN	_	_	_
81	ChIP	chip	NN	_	_	_
82	DNA	dna	NN	_	_	_
83	Mock	mock	NN	_	_	_
84	1	1	CD	_	_	_
85	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
86	E.	E.	NNP	_	_	_
87	Coli	Coli	NNP	_	_	_
88	Exponential	Exponential	NNP	_	_	_
89	RpoB	rpob	NN	_	_	_
90	ChIP	chip	NN	_	_	_
91	DNA	dna	NN	_	_	_
92	Mock	mock	NN	_	_	_
93	2	2	CD	_	_	_
94	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
95	E.	E.	NNP	_	_	_
96	Coli	Coli	NNP	_	_	_
97	Exponential	Exponential	NNP	_	_	_
98	RpoB	rpob	NN	_	_	_
99	ChIP	chip	NN	_	_	_
100	DNA	dna	NN	_	_	_
101	Mock	mock	NN	_	_	_
102	3	3	CD	_	_	_
103	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
104	E.	E.	NNP	_	_	_
105	Coli	Coli	NNP	_	_	_
106	Exponential	Exponential	NNP	_	_	_
107	RpoD	rpod	NN	_	_	_
108	ChIP	chip	NN	_	_	_
109	DNA	dna	NN	_	_	_
110	1	1	CD	_	_	_
111	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
112	E.	E.	NNP	_	_	_
113	Coli	Coli	NNP	_	_	_
114	Exponential	Exponential	NNP	_	_	_
115	RpoD	rpod	NN	_	_	_
116	ChIP	chip	NN	_	_	_
117	DNA	dna	NN	_	_	_
118	2	2	CD	_	_	_
119	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
120	E.	E.	NNP	_	_	_
121	Coli	Coli	NNP	_	_	_
122	Exponential	Exponential	NNP	_	_	_
123	RpoD	rpod	NN	_	_	_
124	ChIP	chip	NN	_	_	_
125	DNA	dna	NN	_	_	_
126	3	3	CD	_	_	_
127	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
128	E.	E.	NNP	_	_	_
129	Coli	Coli	NNP	_	_	_
130	Exponential	Exponential	NNP	_	_	_
131	RpoD	rpod	NN	_	_	_
132	ChIP	chip	NN	_	_	_
133	DNA	dna	NN	_	_	_
134	Mock	mock	NN	_	_	_
135	1	1	CD	_	_	_
136	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
137	E.	E.	NNP	_	_	_
138	Coli	Coli	NNP	_	_	_
139	Exponential	Exponential	NNP	_	_	_
140	RpoD	rpod	NN	_	_	_
141	ChIP	chip	NN	_	_	_
142	DNA	dna	NN	_	_	_
143	Mock	mock	NN	_	_	_
144	2	2	CD	_	_	_
145	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
146	E.	E.	NNP	_	_	_
147	Coli	Coli	NNP	_	_	_
148	Exponential	Exponential	NNP	_	_	_
149	RpoD	rpod	NN	_	_	_
150	ChIP	chip	NN	_	_	_
151	DNA	dna	NN	_	_	_
152	Mock	mock	NN	_	_	_
153	3	3	CD	_	_	_
154	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
155	E.	E.	NNP	_	_	_
156	Coli	Coli	NNP	_	_	_
157	Exponential	Exponential	NNP	_	_	_
158	RpoD	rpod	NN	_	_	_
159	DelN	deln	NN	_	_	_
160	ChIP	chip	NN	_	_	_
161	DNA	dna	NN	_	_	_
162	1	1	CD	_	_	_
163	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
164	E.	E.	NNP	_	_	_
165	Coli	Coli	NNP	_	_	_
166	Exponential	Exponential	NNP	_	_	_
167	RpoD	rpod	NN	_	_	_
168	DelN	deln	NN	_	_	_
169	ChIP	chip	NN	_	_	_
170	DNA	dna	NN	_	_	_
171	2	2	CD	_	_	_
172	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
173	E.	E.	NNP	_	_	_
174	Coli	Coli	NNP	_	_	_
175	Exponential	Exponential	NNP	_	_	_
176	RpoD	rpod	NN	_	_	_
177	DelN	deln	NN	_	_	_
178	ChIP	chip	NN	_	_	_
179	DNA	dna	NN	_	_	_
180	Mock	mock	NN	_	_	_
181	1	1	CD	_	_	_
182	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
183	E.	E.	NNP	_	_	_
184	Coli	Coli	NNP	_	_	_
185	Exponential	Exponential	NNP	_	_	_
186	RpoD	rpod	NN	_	_	_
187	DelN	deln	NN	_	_	_
188	ChIP	chip	NN	_	_	_
189	DNA	dna	NN	_	_	_
190	Mock	mock	NN	_	_	_
191	2	2	CD	_	_	_
192	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
193	E.	E.	NNP	_	_	_
194	Coli	Coli	NNP	_	_	_
195	Exponential	Exponential	NNP	_	_	_
196	RpoF	rpof	NN	_	_	_
197	ChIP	chip	NN	_	_	_
198	DNA	dna	NN	_	_	_
199	1	1	CD	_	_	_
200	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
201	E.	E.	NNP	_	_	_
202	Coli	Coli	NNP	_	_	_
203	Exponential	Exponential	NNP	_	_	_
204	RpoF	rpof	NN	_	_	_
205	ChIP	chip	NN	_	_	_
206	DNA	dna	NN	_	_	_
207	2	2	CD	_	_	_
208	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
209	E.	E.	NNP	_	_	_
210	Coli	Coli	NNP	_	_	_
211	Exponential	Exponential	NNP	_	_	_
212	RpoF	rpof	NN	_	_	_
213	ChIP	chip	NN	_	_	_
214	DNA	dna	NN	_	_	_
215	3	3	CD	_	_	_
216	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
217	E.	E.	NNP	_	_	_
218	Coli	Coli	NNP	_	_	_
219	Exponential	Exponential	NNP	_	_	_
220	RpoF	rpof	NN	_	_	_
221	ChIP	chip	NN	_	_	_
222	DNA	dna	NN	_	_	_
223	Mock	mock	NN	_	_	_
224	1	1	CD	_	_	_
225	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
226	E.	E.	NNP	_	_	_
227	Coli	Coli	NNP	_	_	_
228	Exponential	Exponential	NNP	_	_	_
229	RpoF	rpof	NN	_	_	_
230	ChIP	chip	NN	_	_	_
231	DNA	dna	NN	_	_	_
232	Mock	mock	NN	_	_	_
233	2	2	CD	_	_	_
234	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
235	E.	E.	NNP	_	_	_
236	Coli	Coli	NNP	_	_	_
237	Exponential	Exponential	NNP	_	_	_
238	RpoF	rpof	NN	_	_	_
239	ChIP	chip	NN	_	_	_
240	DNA	dna	NN	_	_	_
241	Mock	mock	NN	_	_	_
242	3	3	CD	_	_	_
243	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
244	E.	E.	NNP	_	_	_
245	Coli	Coli	NNP	_	_	_
246	Exponential	Exponential	NNP	_	_	_
247	RpoH	rpoh	NN	_	_	_
248	ChIP	chip	NN	_	_	_
249	DNA	dna	NN	_	_	_
250	1	1	CD	_	_	_
251	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
252	E.	E.	NNP	_	_	_
253	Coli	Coli	NNP	_	_	_
254	Exponential	Exponential	NNP	_	_	_
255	RpoH	rpoh	NN	_	_	_
256	ChIP	chip	NN	_	_	_
257	DNA	dna	NN	_	_	_
258	2	2	CD	_	_	_
259	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
260	E.	E.	NNP	_	_	_
261	Coli	Coli	NNP	_	_	_
262	Exponential	Exponential	NNP	_	_	_
263	RpoH	rpoh	NN	_	_	_
264	ChIP	chip	NN	_	_	_
265	DNA	dna	NN	_	_	_
266	Mock	mock	NN	_	_	_
267	1	1	CD	_	_	_
268	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
269	E.	E.	NNP	_	_	_
270	Coli	Coli	NNP	_	_	_
271	Exponential	Exponential	NNP	_	_	_
272	RpoH	rpoh	NN	_	_	_
273	ChIP	chip	NN	_	_	_
274	DNA	dna	NN	_	_	_
275	Mock	mock	NN	_	_	_
276	2	2	CD	_	_	_
277	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
278	E.	E.	NNP	_	_	_
279	Coli	Coli	NNP	_	_	_
280	Exponential	Exponential	NNP	_	_	_
281	RpoN	rpon	NN	_	_	_
282	ChIP	chip	NN	_	_	_
283	DNA	dna	NN	_	_	_
284	1	1	CD	_	_	_
285	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
286	E.	E.	NNP	_	_	_
287	Coli	Coli	NNP	_	_	_
288	Exponential	Exponential	NNP	_	_	_
289	RpoN	rpon	NN	_	_	_
290	ChIP	chip	NN	_	_	_
291	DNA	dna	NN	_	_	_
292	2	2	CD	_	_	_
293	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
294	E.	E.	NNP	_	_	_
295	Coli	Coli	NNP	_	_	_
296	Exponential	Exponential	NNP	_	_	_
297	RpoN	rpon	NN	_	_	_
298	ChIP	chip	NN	_	_	_
299	DNA	dna	NN	_	_	_
300	3	3	CD	_	_	_
301	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
302	E.	E.	NNP	_	_	_
303	Coli	Coli	NNP	_	_	_
304	Exponential	Exponential	NNP	_	_	_
305	RpoN	rpon	NN	_	_	_
306	ChIP	chip	NN	_	_	_
307	DNA	dna	NN	_	_	_
308	Mock	mock	NN	_	_	_
309	1	1	CD	_	_	_
310	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
311	E.	E.	NNP	_	_	_
312	Coli	Coli	NNP	_	_	_
313	Exponential	Exponential	NNP	_	_	_
314	RpoN	rpon	NN	_	_	_
315	ChIP	chip	NN	_	_	_
316	DNA	dna	NN	_	_	_
317	Mock	mock	NN	_	_	_
318	2	2	CD	_	_	_
319	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
320	E.	E.	NNP	_	_	_
321	Coli	Coli	NNP	_	_	_
322	Exponential	Exponential	NNP	_	_	_
323	RpoN	rpon	NN	_	_	_
324	ChIP	chip	NN	_	_	_
325	DNA	dna	NN	_	_	_
326	Mock	mock	NN	_	_	_
327	3	3	CD	_	_	_
328	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
329	E.	E.	NNP	_	_	_
330	Coli	Coli	NNP	_	_	_
331	Exponential	Exponential	NNP	_	_	_
332	RpoS	rpos	NN	_	_	_
333	ChIP	chip	NN	_	_	_
334	DNA	dna	NN	_	_	_
335	1	1	CD	_	_	_
336	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
337	E.	E.	NNP	_	_	_
338	Coli	Coli	NNP	_	_	_
339	Exponential	Exponential	NNP	_	_	_
340	RpoS	rpos	NN	_	_	_
341	ChIP	chip	NN	_	_	_
342	DNA	dna	NN	_	_	_
343	2	2	CD	_	_	_
344	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
345	E.	E.	NNP	_	_	_
346	Coli	Coli	NNP	_	_	_
347	Exponential	Exponential	NNP	_	_	_
348	RpoS	rpos	NN	_	_	_
349	ChIP	chip	NN	_	_	_
350	DNA	dna	NN	_	_	_
351	Mock	mock	NN	_	_	_
352	1	1	CD	_	_	_
353	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
354	E.	E.	NNP	_	_	_
355	Coli	Coli	NNP	_	_	_
356	Exponential	Exponential	NNP	_	_	_
357	RpoS	rpos	NN	_	_	_
358	ChIP	chip	NN	_	_	_
359	DNA	dna	NN	_	_	_
360	Mock	mock	NN	_	_	_
361	2	2	CD	_	_	_
362	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
363	E.	E.	NNP	_	_	_
364	Coli	Coli	NNP	_	_	_
365	Glutamine	Glutamine	NNP	_	_	_
366	RpoB	rpob	NN	_	_	_
367	ChIP	chip	NN	_	_	_
368	DNA	dna	NN	_	_	_
369	1	1	CD	_	_	_
370	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
371	E.	E.	NNP	_	_	_
372	Coli	Coli	NNP	_	_	_
373	Glutamine	Glutamine	NNP	_	_	_
374	RpoB	rpob	NN	_	_	_
375	ChIP	chip	NN	_	_	_
376	DNA	dna	NN	_	_	_
377	2	2	CD	_	_	_
378	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
379	E.	E.	NNP	_	_	_
380	Coli	Coli	NNP	_	_	_
381	Glutamine	Glutamine	NNP	_	_	_
382	RpoB	rpob	NN	_	_	_
383	ChIP	chip	NN	_	_	_
384	DNA	dna	NN	_	_	_
385	Mock	mock	NN	_	_	_
386	1	1	CD	_	_	_
387	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
388	E.	E.	NNP	_	_	_
389	Coli	Coli	NNP	_	_	_
390	Glutamine	Glutamine	NNP	_	_	_
391	RpoB	rpob	NN	_	_	_
392	ChIP	chip	NN	_	_	_
393	DNA	dna	NN	_	_	_
394	Mock	mock	NN	_	_	_
395	2	2	CD	_	_	_
396	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
397	E.	E.	NNP	_	_	_
398	Coli	Coli	NNP	_	_	_
399	Glutamine	Glutamine	NNP	_	_	_
400	RpoD	rpod	NN	_	_	_
401	ChIP	chip	NN	_	_	_
402	DNA	dna	NN	_	_	_
403	1	1	CD	_	_	_
404	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
405	E.	E.	NNP	_	_	_
406	Coli	Coli	NNP	_	_	_
407	Glutamine	Glutamine	NNP	_	_	_
408	RpoD	rpod	NN	_	_	_
409	ChIP	chip	NN	_	_	_
410	DNA	dna	NN	_	_	_
411	2	2	CD	_	_	_
412	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
413	E.	E.	NNP	_	_	_
414	Coli	Coli	NNP	_	_	_
415	Glutamine	Glutamine	NNP	_	_	_
416	RpoD	rpod	NN	_	_	_
417	ChIP	chip	NN	_	_	_
418	DNA	dna	NN	_	_	_
419	Mock	mock	NN	_	_	_
420	1	1	CD	_	_	_
421	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
422	E.	E.	NNP	_	_	_
423	Coli	Coli	NNP	_	_	_
424	Glutamine	Glutamine	NNP	_	_	_
425	RpoD	rpod	NN	_	_	_
426	ChIP	chip	NN	_	_	_
427	DNA	dna	NN	_	_	_
428	Mock	mock	NN	_	_	_
429	2	2	CD	_	_	_
430	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
431	E.	E.	NNP	_	_	_
432	Coli	Coli	NNP	_	_	_
433	Glutamine	Glutamine	NNP	_	_	_
434	RpoN	rpon	NN	_	_	_
435	ChIP	chip	NN	_	_	_
436	DNA	dna	NN	_	_	_
437	1	1	CD	_	_	_
438	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
439	E.	E.	NNP	_	_	_
440	Coli	Coli	NNP	_	_	_
441	Glutamine	Glutamine	NNP	_	_	_
442	RpoN	rpon	NN	_	_	_
443	ChIP	chip	NN	_	_	_
444	DNA	dna	NN	_	_	_
445	2	2	CD	_	_	_
446	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
447	E.	E.	NNP	_	_	_
448	Coli	Coli	NNP	_	_	_
449	Glutamine	Glutamine	NNP	_	_	_
450	RpoN	rpon	NN	_	_	_
451	ChIP	chip	NN	_	_	_
452	DNA	dna	NN	_	_	_
453	Mock	mock	NN	_	_	_
454	1	1	CD	_	_	_
455	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
456	E.	E.	NNP	_	_	_
457	Coli	Coli	NNP	_	_	_
458	Glutamine	Glutamine	NNP	_	_	_
459	RpoN	rpon	NN	_	_	_
460	ChIP	chip	NN	_	_	_
461	DNA	dna	NN	_	_	_
462	Mock	mock	NN	_	_	_
463	2	2	CD	_	_	_
464	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
465	E.	E.	NNP	_	_	_
466	Coli	Coli	NNP	_	_	_
467	Heatshock	Heatshock	NNP	_	_	_
468	RpoB	rpob	NN	_	_	_
469	ChIP	chip	NN	_	_	_
470	DNA	dna	NN	_	_	_
471	1	1	CD	_	_	_
472	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
473	E.	E.	NNP	_	_	_
474	Coli	Coli	NNP	_	_	_
475	Heatshock	Heatshock	NNP	_	_	_
476	RpoB	rpob	NN	_	_	_
477	ChIP	chip	NN	_	_	_
478	DNA	dna	NN	_	_	_
479	2	2	CD	_	_	_
480	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
481	E.	E.	NNP	_	_	_
482	Coli	Coli	NNP	_	_	_
483	Heatshock	Heatshock	NNP	_	_	_
484	RpoB	rpob	NN	_	_	_
485	ChIP	chip	NN	_	_	_
486	DNA	dna	NN	_	_	_
487	Mock	mock	NN	_	_	_
488	1	1	CD	_	_	_
489	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
490	E.	E.	NNP	_	_	_
491	Coli	Coli	NNP	_	_	_
492	Heatshock	Heatshock	NNP	_	_	_
493	RpoB	rpob	NN	_	_	_
494	ChIP	chip	NN	_	_	_
495	DNA	dna	NN	_	_	_
496	Mock	mock	NN	_	_	_
497	2	2	CD	_	_	_
498	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
499	E.	E.	NNP	_	_	_
500	Coli	Coli	NNP	_	_	_
501	Heatshock	Heatshock	NNP	_	_	_
502	RpoD	rpod	NN	_	_	_
503	ChIP	chip	NN	_	_	_
504	DNA	dna	NN	_	_	_
505	1	1	CD	_	_	_
506	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
507	E.	E.	NNP	_	_	_
508	Coli	Coli	NNP	_	_	_
509	Heatshock	Heatshock	NNP	_	_	_
510	RpoD	rpod	NN	_	_	_
511	ChIP	chip	NN	_	_	_
512	DNA	dna	NN	_	_	_
513	2	2	CD	_	_	_
514	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
515	E.	E.	NNP	_	_	_
516	Coli	Coli	NNP	_	_	_
517	Heatshock	Heatshock	NNP	_	_	_
518	RpoD	rpod	NN	_	_	_
519	ChIP	chip	NN	_	_	_
520	DNA	dna	NN	_	_	_
521	Mock	mock	NN	_	_	_
522	1	1	CD	_	_	_
523	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
524	E.	E.	NNP	_	_	_
525	Coli	Coli	NNP	_	_	_
526	Heatshock	Heatshock	NNP	_	_	_
527	RpoD	rpod	NN	_	_	_
528	ChIP	chip	NN	_	_	_
529	DNA	dna	NN	_	_	_
530	Mock	mock	NN	_	_	_
531	2	2	CD	_	_	_
532	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
533	E.	E.	NNP	_	_	_
534	Coli	Coli	NNP	_	_	_
535	Heatshock	Heatshock	NNP	_	_	_
536	RpoH	rpoh	NN	_	_	_
537	ChIP	chip	NN	_	_	_
538	DNA	dna	NN	_	_	_
539	1	1	CD	_	_	_
540	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
541	E.	E.	NNP	_	_	_
542	Coli	Coli	NNP	_	_	_
543	Heatshock	Heatshock	NNP	_	_	_
544	RpoH	rpoh	NN	_	_	_
545	ChIP	chip	NN	_	_	_
546	DNA	dna	NN	_	_	_
547	2	2	CD	_	_	_
548	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
549	E.	E.	NNP	_	_	_
550	Coli	Coli	NNP	_	_	_
551	Heatshock	Heatshock	NNP	_	_	_
552	RpoH	rpoh	NN	_	_	_
553	ChIP	chip	NN	_	_	_
554	DNA	dna	NN	_	_	_
555	3	3	CD	_	_	_
556	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
557	E.	E.	NNP	_	_	_
558	Coli	Coli	NNP	_	_	_
559	Heatshock	Heatshock	NNP	_	_	_
560	RpoH	rpoh	NN	_	_	_
561	ChIP	chip	NN	_	_	_
562	DNA	dna	NN	_	_	_
563	Mock	mock	NN	_	_	_
564	1	1	CD	_	_	_
565	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
566	E.	E.	NNP	_	_	_
567	Coli	Coli	NNP	_	_	_
568	Heatshock	Heatshock	NNP	_	_	_
569	RpoH	rpoh	NN	_	_	_
570	ChIP	chip	NN	_	_	_
571	DNA	dna	NN	_	_	_
572	Mock	mock	NN	_	_	_
573	2	2	CD	_	_	_
574	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
575	E.	E.	NNP	_	_	_
576	Coli	Coli	NNP	_	_	_
577	Heatshock	Heatshock	NNP	_	_	_
578	RpoH	rpoh	NN	_	_	_
579	ChIP	chip	NN	_	_	_
580	DNA	dna	NN	_	_	_
581	Mock	mock	NN	_	_	_
582	3	3	CD	_	_	_
583	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
584	E.	E.	NNP	_	_	_
585	Coli	Coli	NNP	_	_	_
586	Iron	Iron	NNP	_	_	_
587	RpoD	rpod	NN	_	_	_
588	ChIP	chip	NN	_	_	_
589	DNA	dna	NN	_	_	_
590	1	1	CD	_	_	_
591	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
592	E.	E.	NNP	_	_	_
593	Coli	Coli	NNP	_	_	_
594	Iron	Iron	NNP	_	_	_
595	RpoD	rpod	NN	_	_	_
596	ChIP	chip	NN	_	_	_
597	DNA	dna	NN	_	_	_
598	2	2	CD	_	_	_
599	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
600	E.	E.	NNP	_	_	_
601	Coli	Coli	NNP	_	_	_
602	Iron	Iron	NNP	_	_	_
603	RpoD	rpod	NN	_	_	_
604	ChIP	chip	NN	_	_	_
605	DNA	dna	NN	_	_	_
606	Mock	mock	NN	_	_	_
607	1	1	CD	_	_	_
608	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
609	E.	E.	NNP	_	_	_
610	Coli	Coli	NNP	_	_	_
611	Iron	Iron	NNP	_	_	_
612	RpoD	rpod	NN	_	_	_
613	ChIP	chip	NN	_	_	_
614	DNA	dna	NN	_	_	_
615	Mock	mock	NN	_	_	_
616	2	2	CD	_	_	_
617	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
618	E.	E.	NNP	_	_	_
619	Coli	Coli	NNP	_	_	_
620	Stationary	Stationary	NNP	_	_	_
621	RpoB	rpob	NN	_	_	_
622	ChIP	chip	NN	_	_	_
623	DNA	dna	NN	_	_	_
624	1	1	CD	_	_	_
625	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
626	E.	E.	NNP	_	_	_
627	Coli	Coli	NNP	_	_	_
628	Stationary	Stationary	NNP	_	_	_
629	RpoB	rpob	NN	_	_	_
630	ChIP	chip	NN	_	_	_
631	DNA	dna	NN	_	_	_
632	2	2	CD	_	_	_
633	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
634	E.	E.	NNP	_	_	_
635	Coli	Coli	NNP	_	_	_
636	Stationary	Stationary	NNP	_	_	_
637	RpoB	rpob	NN	_	_	_
638	ChIP	chip	NN	_	_	_
639	DNA	dna	NN	_	_	_
640	Mock	mock	NN	_	_	_
641	1	1	CD	_	_	_
642	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
643	E.	E.	NNP	_	_	_
644	Coli	Coli	NNP	_	_	_
645	Stationary	Stationary	NNP	_	_	_
646	RpoB	rpob	NN	_	_	_
647	ChIP	chip	NN	_	_	_
648	DNA	dna	NN	_	_	_
649	Mock	mock	NN	_	_	_
650	2	2	CD	_	_	_
651	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
652	E.	E.	NNP	_	_	_
653	Coli	Coli	NNP	_	_	_
654	Stationary	Stationary	NNP	_	_	_
655	RpoD	rpod	NN	_	_	_
656	ChIP	chip	NN	_	_	_
657	DNA	dna	NN	_	_	_
658	1	1	CD	_	_	_
659	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
660	E.	E.	NNP	_	_	_
661	Coli	Coli	NNP	_	_	_
662	Stationary	Stationary	NNP	_	_	_
663	RpoD	rpod	NN	_	_	_
664	ChIP	chip	NN	_	_	_
665	DNA	dna	NN	_	_	_
666	2	2	CD	_	_	_
667	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
668	E.	E.	NNP	_	_	_
669	Coli	Coli	NNP	_	_	_
670	Stationary	Stationary	NNP	_	_	_
671	RpoD	rpod	NN	_	_	_
672	ChIP	chip	NN	_	_	_
673	DNA	dna	NN	_	_	_
674	Mock	mock	NN	_	_	_
675	1	1	CD	_	_	_
676	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
677	E.	E.	NNP	_	_	_
678	Coli	Coli	NNP	_	_	_
679	Stationary	Stationary	NNP	_	_	_
680	RpoD	rpod	NN	_	_	_
681	ChIP	chip	NN	_	_	_
682	DNA	dna	NN	_	_	_
683	Mock	mock	NN	_	_	_
684	2	2	CD	_	_	_
685	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
686	E.	E.	NNP	_	_	_
687	Coli	Coli	NNP	_	_	_
688	Stationary	Stationary	NNP	_	_	_
689	RpoD	rpod	NN	_	_	_
690	DelS	dels	NN	_	_	_
691	ChIP	chip	NN	_	_	_
692	DNA	dna	NN	_	_	_
693	1	1	CD	_	_	_
694	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
695	E.	E.	NNP	_	_	_
696	Coli	Coli	NNP	_	_	_
697	Stationary	Stationary	NNP	_	_	_
698	RpoD	rpod	NN	_	_	_
699	DelS	dels	NN	_	_	_
700	ChIP	chip	NN	_	_	_
701	DNA	dna	NN	_	_	_
702	2	2	CD	_	_	_
703	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
704	E.	E.	NNP	_	_	_
705	Coli	Coli	NNP	_	_	_
706	Stationary	Stationary	NNP	_	_	_
707	RpoD	rpod	NN	_	_	_
708	DelS	dels	NN	_	_	_
709	ChIP	chip	NN	_	_	_
710	DNA	dna	NN	_	_	_
711	Mock	mock	NN	_	_	_
712	1	1	CD	_	_	_
713	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
714	E.	E.	NNP	_	_	_
715	Coli	Coli	NNP	_	_	_
716	Stationary	Stationary	NNP	_	_	_
717	RpoD	rpod	NN	_	_	_
718	DelS	dels	NN	_	_	_
719	ChIP	chip	NN	_	_	_
720	DNA	dna	NN	_	_	_
721	Mock	mock	NN	_	_	_
722	2	2	CD	_	_	_
723	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
724	E.	E.	NNP	_	_	_
725	Coli	Coli	NNP	_	_	_
726	Stationary	Stationary	NNP	_	_	_
727	RpoS	rpos	NN	_	_	_
728	ChIP	chip	NN	_	_	_
729	DNA	dna	NN	_	_	_
730	1	1	CD	_	_	_
731	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
732	E.	E.	NNP	_	_	_
733	Coli	Coli	NNP	_	_	_
734	Stationary	Stationary	NNP	_	_	_
735	RpoS	rpos	NN	_	_	_
736	ChIP	chip	NN	_	_	_
737	DNA	dna	NN	_	_	_
738	2	2	CD	_	_	_
739	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
740	E.	E.	NNP	_	_	_
741	Coli	Coli	NNP	_	_	_
742	Stationary	Stationary	NNP	_	_	_
743	RpoS	rpos	NN	_	_	_
744	ChIP	chip	NN	_	_	_
745	DNA	dna	NN	_	_	_
746	3	3	CD	_	_	_
747	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
748	E.	E.	NNP	_	_	_
749	Coli	Coli	NNP	_	_	_
750	Stationary	Stationary	NNP	_	_	_
751	RpoS	rpos	NN	_	_	_
752	ChIP	chip	NN	_	_	_
753	DNA	dna	NN	_	_	_
754	Mock	mock	NN	_	_	_
755	1	1	CD	_	_	_
756	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
757	E.	E.	NNP	_	_	_
758	Coli	Coli	NNP	_	_	_
759	Stationary	Stationary	NNP	_	_	_
760	RpoS	rpos	NN	_	_	_
761	ChIP	chip	NN	_	_	_
762	DNA	dna	NN	_	_	_
763	Mock	mock	NN	_	_	_
764	2	2	CD	_	_	_
765	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
766	E.	E.	NNP	_	_	_
767	Coli	Coli	NNP	_	_	_
768	Stationary	Stationary	NNP	_	_	_
769	RpoS	rpos	NN	_	_	_
770	ChIP	chip	NN	_	_	_
771	DNA	dna	NN	_	_	_
772	Mock	mock	NN	_	_	_
773	3	3	CD	_	_	_
774	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
775	E.	e.	FW	_	_	_
776	coli	coli	FW	_	_	_
777	strains	strain	NNS	_	_	_
778	were	be	VBD	_	_	_
779	grown	grow	VBN	_	_	_
780	in	in	IN	_	_	_
781	minimal	minimal	JJ	_	_	_
782	M9	m9	NN	_	_	_
783	medium	medium	NN	_	_	_
784	supplemented	supplement	VBN	_	_	_
785	with	with	IN	_	_	_
786	glucose	glucose	NN	SUPP	_	_
787	-LRB-	-lrb-	-LRB-	_	_	_
788	2	2	CD	_	_	_
789	g	g	NN	_	_	_
790	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
791	E.	E.	NNP	_	_	_
792	coli	coli	NN	_	_	_
793	strains	strain	NNS	_	_	_
794	were	be	VBD	_	_	_
795	grown	grow	VBN	_	_	_
796	in	in	IN	_	_	_
797	minimal	minimal	JJ	_	_	_
798	W2	w2	NN	_	_	_
799	medium	medium	NN	_	_	_
800	supplemented	supplement	VBN	_	_	_
801	with	with	IN	_	_	_
802	glucose	glucose	NN	SUPP	_	_
803	-LRB-	-lrb-	-LRB-	_	_	_
804	2	2	CD	_	_	_
805	g	g	NN	_	_	_
806	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
807	Escherichia	escherichia	FW	Organism	_	_
808	coli	coli	FW	Organism	_	_
809	str	str	FW	_	_	_
810	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	genotype	genotype	NN	_	_	_
4	:	:	:	_	_	_
5	rpoH-8myc	rpoh-8myc	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	genotype	genotype	NN	_	_	_
8	:	:	:	_	_	_
9	wild	wild	JJ	_	_	_
10	type	type	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	genotype	genotype	NN	_	_	_
13	:	:	:	_	_	_
14	ΔrpoN	δrpon	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	genotype	genotype	NN	_	_	_
17	:	:	:	_	_	_
18	ΔrpoS	δrpos	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	The	the	DT	_	_	_
21	raw	raw	JJ	_	_	_
22	pair	pair	NN	_	_	_
23	data	datum	NNS	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	.	.	.	_	_	_

1	txt	txt	NN	_	_	_
2	file	file	NN	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	was	be	VBD	_	_	_
5	subjected	subject	VBN	_	_	_
6	to	to	TO	_	_	_
7	per	per	IN	_	_	_
8	channel	channel	NN	_	_	_
9	quantile	quantile	NN	_	_	_
10	normalization	normalization	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Bolstad	Bolstad	NNP	_	_	_
13	et	et	FW	_	_	_
14	al.	al.	FW	_	_	_
15	.	.	.	_	_	_

1	Bioinformatics	bioinformatic	NNS	_	_	_
2	19	19	CD	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	2	2	CD	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	:	:	:	_	_	_
7	185	185	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	,	,	,	_	_	_
10	IP	IP	NNP	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	Among	among	IN	_	_	_
13	potential	potential	JJ	_	_	_
14	TSSs	tsss	NNS	_	_	_
15	,	,	,	_	_	_
16	only	only	RB	_	_	_
17	TSSs	tsss	NNS	_	_	_
18	with	with	IN	_	_	_
19	the	the	DT	_	_	_
20	strongest	strongest	JJS	_	_	_
21	signal	signal	NN	_	_	_
22	within	within	IN	_	_	_
23	10	10	CD	_	_	_
24	bp	bp	NN	_	_	_
25	window	window	NN	_	_	_
26	were	be	VBD	_	_	_
27	kept	keep	VBN	_	_	_
28	to	to	TO	_	_	_
29	remove	remove	VB	_	_	_
30	possible	possible	JJ	_	_	_
31	noise	noise	NN	_	_	_
32	signals	signal	NNS	_	_	_
33	,	,	,	_	_	_
34	and	and	CC	_	_	_
35	TSSs	tsss	NNS	_	_	_
36	with	with	IN	_	_	_
37	greater	greater	JJR	_	_	_
38	than	than	IN	_	_	_
39	or	or	CC	_	_	_
40	equal	equal	JJ	_	_	_
41	to	to	TO	_	_	_
42	40	40	CD	_	_	_
43	%	%	NN	_	_	_
44	of	of	IN	_	_	_
45	the	the	DT	_	_	_
46	strongest	strongest	JJS	_	_	_
47	signal	signal	NN	_	_	_
48	upstream	upstream	RB	_	_	_
49	of	of	IN	_	_	_
50	an	a	DT	_	_	_
51	annotated	annotated	JJ	_	_	_
52	gene	gene	NN	_	_	_
53	were	be	VBD	_	_	_
54	considered	consider	VBN	_	_	_
55	as	as	IN	_	_	_
56	multiple	multiple	JJ	_	_	_
57	TSSs	tsss	NNS	_	_	_
58	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	at	at	IN	_	_	_
4	mid-log	mid-log	JJ	_	_	_
5	phase	phase	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	OD600nm	od600nm	NN	_	_	_
8	0.5	0.5	CD	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	in	in	IN	_	_	_
11	M9	m9	NN	_	_	_
12	glucose	glucose	NN	SUPP	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	0.2	0.2	CD	_	_	_
15	%	%	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	media	media	NNS	_	_	_
18	,	,	,	_	_	_
19	with	with	IN	_	_	_
20	42oC	42oc	NN	_	_	_
21	heatshock	heatshock	NN	_	_	_
22	for	for	IN	_	_	_
23	10	10	CD	_	_	_
24	min	min	NN	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	at	at	IN	_	_	_
4	mid-log	mid-log	JJ	_	_	_
5	phase	phase	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	OD600nm	od600nm	NN	_	_	_
8	0.5	0.5	CD	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	in	in	IN	_	_	_
11	W2	w2	NN	_	_	_
12	media	media	NNS	_	_	_
13	supplemented	supplement	VBN	_	_	_
14	with	with	IN	_	_	_
15	0.2	0.2	CD	_	_	_
16	%	%	NN	_	_	_
17	glucose	glucose	NN	SUPP	_	_
18	and	and	CC	_	_	_
19	0.2	0.2	CD	_	_	_
20	%	%	NN	_	_	_
21	glutamine	glutamine	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Cells	cell	NNS	_	_	_
24	at	at	IN	_	_	_
25	stationary	stationary	JJ	GrowthPhase	_	_
26	phase	phase	NN	GrowthPhase	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	OD600nm	od600nm	NN	_	_	_
29	1.5	1.5	CD	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	in	in	IN	_	_	_
32	M9	m9	NN	_	_	_
33	glucose	glucose	NN	SUPP	_	_
34	media	media	NNS	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	E.	e.	FW	_	_	_
37	coli	coli	FW	_	_	_
38	glutamine	glutamine	NN	_	_	_
39	1	1	CD	_	_	_
40	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
41	E.	E.	NNP	_	_	_
42	coli	coli	NN	_	_	_
43	glutamine	glutamine	NN	_	_	_
44	2	2	CD	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	E.	E.	NNP	_	_	_
47	coli	coli	NN	_	_	_
48	heatshock	heatshock	NN	_	_	_
49	1	1	CD	_	_	_
50	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
51	E.	E.	NNP	_	_	_
52	coli	coli	NN	_	_	_
53	heatshock	heatshock	NN	_	_	_
54	2	2	CD	_	_	_
55	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
56	E.	E.	NNP	_	_	_
57	coli	coli	NN	_	_	_
58	K12	k12	NN	_	_	_
59	MG1655	mg1655	NN	_	_	_
60	was	be	VBD	_	_	_
61	grown	grow	VBN	_	_	_
62	to	to	TO	_	_	_
63	mid-log	mid-log	JJ	_	_	_
64	phase	phase	NN	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	O.D.	o.d.	NN	_	_	_
67	600nm	600nm	CD	_	_	_
68	0.5	0.5	CD	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	or	or	CC	_	_	_
71	to	to	TO	_	_	_
72	stationary	stationary	JJ	GrowthPhase	_	_
73	phase	phase	NN	GrowthPhase	_	_
74	-LRB-	-lrb-	-LRB-	_	_	_
75	O.D.	o.d.	NN	_	_	_
76	600nm	600nm	CD	_	_	_
77	1.5	1.5	CD	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	aerobically	aerobically	RB	_	_	_
80	at	at	IN	_	_	_
81	37	37	CD	_	_	_
82	°C	°c	NN	_	_	_
83	in	in	IN	_	_	_
84	M9	m9	NN	MED	_	_
85	minimal	minimal	JJ	MED	_	_
86	media	media	NNS	MED	_	_
87	supplemented	supplement	VBN	_	_	_
88	with	with	IN	_	_	_
89	0.2	0.2	CD	_	_	_
90	%	%	NN	_	_	_
91	glucose	glucose	NN	SUPP	_	_
92	or	or	CC	_	_	_
93	W2	w2	NN	_	_	_
94	minimal	minimal	JJ	_	_	_
95	media	media	NNS	_	_	_
96	supplemented	supplement	VBN	_	_	_
97	with	with	IN	_	_	_
98	0.2	0.2	CD	_	_	_
99	%	%	NN	_	_	_
100	glucose	glucose	NN	SUPP	_	_
101	and	and	CC	_	_	_
102	0.2	0.2	CD	_	_	_
103	%	%	NN	_	_	_
104	glutamine	glutamine	NN	_	_	_
105	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	heatshock	heatshock	NN	_	_	_
3	conditions	condition	NNS	_	_	_
4	,	,	,	_	_	_
5	cells	cell	NNS	_	_	_
6	were	be	VBD	_	_	_
7	grown	grow	VBN	_	_	_
8	to	to	TO	_	_	_
9	mid-log	mid-log	JJ	_	_	_
10	phase	phase	NN	_	_	_
11	and	and	CC	_	_	_
12	incubated	incubate	VBN	_	_	_
13	at	at	IN	_	_	_
14	42oC	42oc	NN	_	_	_
15	for	for	IN	_	_	_
16	10	10	CD	_	_	_
17	min	min	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	stationary	stationary	JJ	_	_	_
5	1	1	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	E.	e.	FW	_	_	_
8	coli	coli	FW	_	_	_
9	stationary	stationary	JJ	_	_	_
10	2	2	CD	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	Escherichia	escherichia	FW	Organism	_	_
13	coli	coli	FW	Organism	_	_
14	str	str	FW	_	_	_
15	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Genome	Genome	NNP	_	_	_
4	_	_	NNP	_	_	_
5	build	build	VB	_	_	_
6	:	:	:	_	_	_
7	NC	NC	NNP	_	_	_
8	_	_	NNP	_	_	_
9	000913	000913	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	RNA-Seq	rna-seq	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	Sequence	sequence	NN	_	_	_
14	reads	read	VBZ	_	_	_
15	for	for	IN	_	_	_
16	cDNA	cdna	NN	_	_	_
17	libraries	library	NNS	_	_	_
18	were	be	VBD	_	_	_
19	aligned	align	VBN	_	_	_
20	onto	onto	IN	_	_	_
21	E.	e.	FW	_	_	_
22	coli	coli	FW	_	_	_
23	K12	k12	NN	_	_	_
24	MG1655	mg1655	NN	_	_	_
25	genome	genome	NN	_	_	_
26	,	,	,	_	_	_
27	using	use	VBG	_	_	_
28	Mosaik	mosaik	NN	_	_	_
29	with	with	IN	_	_	_
30	following	follow	VBG	_	_	_
31	arguments	argument	NNS	_	_	_
32	:	:	:	_	_	_
33	hash	hash	VB	_	_	_
34	size	size	NN	_	_	_
35	=	=	JJ	_	_	_
36	10	10	CD	_	_	_
37	,	,	,	_	_	_
38	mismatch	mismatch	NN	_	_	_
39	=	=	JJ	_	_	_
40	0	0	CD	_	_	_
41	.	.	.	_	_	_

1	Only	only	RB	_	_	_
2	reads	read	VBZ	_	_	_
3	that	that	IN	_	_	_
4	aligned	align	VBN	_	_	_
5	to	to	TO	_	_	_
6	the	the	DT	_	_	_
7	unique	unique	JJ	_	_	_
8	genomic	genomic	JJ	_	_	_
9	location	location	NN	_	_	_
10	were	be	VBD	_	_	_
11	retained	retain	VBN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Supplementary	supplementary	JJ	_	_	_
7	_	_	NN	_	_	_
8	files	file	NNS	_	_	_
9	_	_	IN	_	_	_
10	format	format	NN	_	_	_
11	_	_	NN	_	_	_
12	and	and	CC	_	_	_
13	_	_	NN	_	_	_
14	content	content	NN	_	_	_
15	:	:	:	_	_	_
16	counts	count	NNS	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
18	The	the	DT	_	_	_
19	amplified	amplify	VBN	_	_	_
20	cDNA	cdna	NN	_	_	_
21	libraries	library	NNS	_	_	_
22	from	from	IN	_	_	_
23	two	two	CD	_	_	_
24	biological	biological	JJ	_	_	_
25	replicates	replicate	VBZ	_	_	_
26	for	for	IN	_	_	_
27	each	each	DT	_	_	_
28	E.	e.	FW	_	_	_
29	coli	coli	FW	_	_	_
30	were	be	VBD	_	_	_
31	sequenced	sequence	VBN	_	_	_
32	on	on	IN	_	_	_
33	an	a	DT	_	_	_
34	Illumina	Illumina	NNP	_	_	_
35	Genome	Genome	NNP	_	_	_
36	Analyzer	Analyzer	NNP	_	_	_
37	.	.	.	_	_	_

1	Sequence	sequence	NN	_	_	_
2	reads	read	VBZ	_	_	_
3	for	for	IN	_	_	_
4	cDNA	cdna	NN	_	_	_
5	libraries	library	NNS	_	_	_
6	were	be	VBD	_	_	_
7	aligned	align	VBN	_	_	_
8	onto	onto	IN	_	_	_
9	E.	e.	FW	_	_	_
10	coli	coli	FW	_	_	_
11	K12	k12	NN	_	_	_
12	MG1655	mg1655	NN	_	_	_
13	genome	genome	NN	_	_	_
14	,	,	,	_	_	_
15	using	use	VBG	_	_	_
16	Mosaik	mosaik	NN	_	_	_
17	with	with	IN	_	_	_
18	following	follow	VBG	_	_	_
19	arguments	argument	NNS	_	_	_
20	:	:	:	_	_	_
21	hash	hash	VB	_	_	_
22	size	size	NN	_	_	_
23	=	=	JJ	_	_	_
24	10	10	CD	_	_	_
25	,	,	,	_	_	_
26	mismatch	mismatch	NN	_	_	_
27	=	=	JJ	_	_	_
28	0	0	CD	_	_	_
29	.	.	.	_	_	_

1	Only	only	RB	_	_	_
2	reads	read	VBZ	_	_	_
3	that	that	IN	_	_	_
4	aligned	align	VBN	_	_	_
5	to	to	TO	_	_	_
6	the	the	DT	_	_	_
7	unique	unique	JJ	_	_	_
8	genomic	genomic	JJ	_	_	_
9	location	location	NN	_	_	_
10	were	be	VBD	_	_	_
11	retained	retain	VBN	_	_	_
12	.	.	.	_	_	_

1	Two	two	CD	_	_	_
2	biological	biological	JJ	_	_	_
3	replicates	replicate	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	processed	process	VBN	_	_	_
6	seperatedly	seperatedly	RB	_	_	_
7	,	,	,	_	_	_
8	and	and	CC	_	_	_
9	only	only	RB	_	_	_
10	sequence	sequence	NN	_	_	_
11	reads	read	VBZ	_	_	_
12	presented	present	VBN	_	_	_
13	in	in	IN	_	_	_
14	both	both	CC	_	_	_
15	biological	biological	JJ	_	_	_
16	replciates	replciate	NNS	_	_	_
17	were	be	VBD	_	_	_
18	considered	consider	VBN	_	_	_
19	for	for	IN	_	_	_
20	further	further	JJ	_	_	_
21	process	process	NN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	genomic	genomic	JJ	_	_	_
3	coordinates	coordinate	VBZ	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	5	5	CD	_	_	_
7	'	'	''	_	_	_
8	-	-	:	_	_	_
9	end	end	NN	_	_	_
10	of	of	IN	_	_	_
11	these	these	DT	_	_	_
12	uniquely	uniquely	RB	_	_	_
13	aligned	align	VBN	_	_	_
14	reads	read	VBZ	_	_	_
15	were	be	VBD	_	_	_
16	defined	define	VBN	_	_	_
17	as	as	IN	_	_	_
18	potential	potential	JJ	_	_	_
19	TSSs	tsss	NNS	_	_	_
20	.	.	.	_	_	_

1	Among	among	IN	_	_	_
2	potential	potential	JJ	_	_	_
3	TSSs	tsss	NNS	_	_	_
4	,	,	,	_	_	_
5	only	only	RB	_	_	_
6	TSSs	tsss	NNS	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	strongest	strongest	JJS	_	_	_
10	signal	signal	NN	_	_	_
11	within	within	IN	_	_	_
12	10	10	CD	_	_	_
13	bp	bp	NN	_	_	_
14	window	window	NN	_	_	_
15	were	be	VBD	_	_	_
16	kept	keep	VBN	_	_	_
17	to	to	TO	_	_	_
18	remove	remove	VB	_	_	_
19	possible	possible	JJ	_	_	_
20	noise	noise	NN	_	_	_
21	signals	signal	NNS	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	TSSs	tsss	NNS	_	_	_
25	with	with	IN	_	_	_
26	greater	greater	JJR	_	_	_
27	than	than	IN	_	_	_
28	or	or	CC	_	_	_
29	equal	equal	JJ	_	_	_
30	to	to	TO	_	_	_
31	40	40	CD	_	_	_
32	%	%	NN	_	_	_
33	of	of	IN	_	_	_
34	the	the	DT	_	_	_
35	strongest	strongest	JJS	_	_	_
36	signal	signal	NN	_	_	_
37	upstream	upstream	RB	_	_	_
38	of	of	IN	_	_	_
39	an	a	DT	_	_	_
40	annotated	annotated	JJ	_	_	_
41	gene	gene	NN	_	_	_
42	were	be	VBD	_	_	_
43	considered	consider	VBN	_	_	_
44	as	as	IN	_	_	_
45	multiple	multiple	JJ	_	_	_
46	TSSs	tsss	NNS	_	_	_
47	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cell	cell	NN	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	treated	treat	VBN	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	RNAprotect	rnaprotect	NN	_	_	_
10	reagent	reagent	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	qiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	mRNA	mrna	NN	_	_	_
4	isolated	isolate	VBN	_	_	_
5	from	from	IN	_	_	_
6	each	each	DT	_	_	_
7	cell	cell	NN	_	_	_
8	culture	culture	NN	_	_	_
9	was	be	VBD	_	_	_
10	treated	treat	VBN	_	_	_
11	with	with	IN	_	_	_
12	Terminator	Terminator	NNP	_	_	_
13	5	5	CD	_	_	_
14	'	'	''	_	_	_
15	Phosphate	Phosphate	NNP	_	_	_
16	Dependent	Dependent	NNP	_	_	_
17	Exonuclease	Exonuclease	NNP	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Epicentre	Epicentre	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	to	to	TO	_	_	_
22	enrich	enrich	VB	_	_	_
23	5	5	CD	_	_	_
24	'	'	''	_	_	_
25	tri-phosphorylated	tri-phosphorylated	JJ	_	_	_
26	mRNAs	mrna	NNS	_	_	_
27	.	.	.	_	_	_

1	Intact	intact	JJ	_	_	_
2	tri-phosphorylated	tri-phosphorylated	JJ	_	_	_
3	RNAs	rna	NNS	_	_	_
4	were	be	VBD	_	_	_
5	then	then	RB	_	_	_
6	treated	treat	VBN	_	_	_
7	with	with	IN	_	_	_
8	RNA	rna	NN	_	_	_
9	5	5	CD	_	_	_
10	'	'	''	_	_	_
11	-	-	:	_	_	_
12	Polyphosphatase	polyphosphatase	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Epicentre	Epicentre	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	to	to	TO	_	_	_
17	generate	generate	VB	_	_	_
18	5	5	CD	_	_	_
19	'	'	''	_	_	_
20	-	-	:	_	_	_
21	end	end	VB	_	_	_
22	monophosphorylated	monophosphorylate	VBN	_	_	_
23	RNA	rna	NN	_	_	_
24	for	for	IN	_	_	_
25	ligation	ligation	NN	_	_	_
26	to	to	TO	_	_	_
27	RNA	rna	NN	_	_	_
28	adaptors	adaptor	NNS	_	_	_
29	.	.	.	_	_	_

1	cDNAs	cdna	NNS	_	_	_
2	were	be	VBD	_	_	_
3	synthesized	synthesize	VBN	_	_	_
4	using	use	VBG	_	_	_
5	the	the	DT	_	_	_
6	adaptor-ligated	adaptor-ligated	JJ	_	_	_
7	mRNAs	mrna	NNS	_	_	_
8	as	as	IN	_	_	_
9	template	template	NN	_	_	_
10	using	use	VBG	_	_	_
11	a	a	DT	_	_	_
12	modified	modify	VBN	_	_	_
13	small	small	JJ	_	_	_
14	RNA	rna	NN	_	_	_
15	RT	rt	NN	_	_	_
16	primer	primer	NN	_	_	_
17	from	from	IN	_	_	_
18	Illumina	Illumina	NNP	_	_	_
19	and	and	CC	_	_	_
20	Superscript	Superscript	NNP	_	_	_
21	II	II	NNP	_	_	_
22	Reverse	reverse	JJ	_	_	_
23	Transcriptase	transcriptase	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Invitrogen	invitrogen	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cDNA	cdna	NN	_	_	_
3	samples	sample	NNS	_	_	_
4	were	be	VBD	_	_	_
5	amplified	amplify	VBN	_	_	_
6	,	,	,	_	_	_
7	and	and	CC	_	_	_
8	size	size	NN	_	_	_
9	fractionated	fractionate	VBN	_	_	_
10	from	from	IN	_	_	_
11	100	100	CD	_	_	_
12	to	to	TO	_	_	_
13	300	300	CD	_	_	_
14	bp	bp	NN	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	glutamine	glutamine	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	treatment	treatment	NN	_	_	_
7	:	:	:	_	_	_
8	heat	heat	NN	_	_	_
9	shock	shock	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	treatment	treatment	NN	_	_	_
12	:	:	:	_	_	_
13	stationary	stationary	JJ	GrowthPhase	_	_
14	phase	phase	NN	GrowthPhase	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Two	two	CD	_	_	_
17	biological	biological	JJ	_	_	_
18	replicates	replicate	VBZ	_	_	_
19	were	be	VBD	_	_	_
20	processed	process	VBN	_	_	_
21	seperatedly	seperatedly	RB	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	only	only	RB	_	_	_
25	sequence	sequence	NN	_	_	_
26	reads	read	VBZ	_	_	_
27	presented	present	VBN	_	_	_
28	in	in	IN	_	_	_
29	both	both	CC	_	_	_
30	biological	biological	JJ	_	_	_
31	replciates	replciate	NNS	_	_	_
32	were	be	VBD	_	_	_
33	considered	consider	VBN	_	_	_
34	for	for	IN	_	_	_
35	further	further	JJ	_	_	_
36	process	process	NN	_	_	_
37	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	genomic	genomic	JJ	_	_	_
3	coordinates	coordinate	VBZ	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	5	5	CD	_	_	_
7	'	'	''	_	_	_
8	-	-	:	_	_	_
9	end	end	NN	_	_	_
10	of	of	IN	_	_	_
11	these	these	DT	_	_	_
12	uniquely	uniquely	RB	_	_	_
13	aligned	align	VBN	_	_	_
14	reads	read	VBZ	_	_	_
15	were	be	VBD	_	_	_
16	defined	define	VBN	_	_	_
17	as	as	IN	_	_	_
18	potential	potential	JJ	_	_	_
19	TSSs	tsss	NNS	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	35381	35381	CD	_	_	_
3	_	_	NN	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	35382	35382	CD	_	_	_
7	_	_	NN	_	_	_
8	2	2	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	DNA	dna	NN	_	_	_
11	were	be	VBD	_	_	_
12	extracted	extract	VBN	_	_	_
13	and	and	CC	_	_	_
14	purified	purify	VBN	_	_	_
15	as	as	IN	_	_	_
16	described	describe	VBN	_	_	_
17	by	by	IN	_	_	_
18	Muniesa	Muniesa	NNP	_	_	_
19	et	et	FW	_	_	_
20	al.	al.	FW	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	2003	2003	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	Shiga	shiga	NN	_	_	_
2	toxin	toxin	NN	_	_	_
3	2-converting	2-converting	JJ	_	_	_
4	bacteriophages	bacteriophage	NNS	_	_	_
5	associated	associate	VBN	_	_	_
6	with	with	IN	_	_	_
7	clonal	clonal	JJ	_	_	_
8	variability	variability	NN	_	_	_
9	in	in	IN	_	_	_
10	Escherichia	escherichia	FW	Organism	_	_
11	coli	coli	FW	Organism	_	_
12	O157	o157	NN	_	_	_
13	:	:	:	_	_	_
14	H7	h7	NN	_	_	_
15	strains	strain	NNS	_	_	_
16	of	of	IN	_	_	_
17	human	human	JJ	_	_	_
18	origin	origin	NN	_	_	_
19	isolated	isolate	VBN	_	_	_
20	from	from	IN	_	_	_
21	a	a	DT	_	_	_
22	single	single	JJ	_	_	_
23	outbreak	outbreak	NN	_	_	_
24	.	.	.	_	_	_

1	Infect	infect	VB	_	_	_
2	Immun	Immun	NNP	_	_	_
3	71	71	CD	_	_	_
4	,	,	,	_	_	_
5	4554-4562	4554-4562	CD	_	_	_
6	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	3538	3538	CD	_	_	_
5	#	#	#	_	_	_
6	1	1	CD	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	E.	E.	NNP	_	_	_
9	coli	coli	NN	_	_	_
10	3538	3538	CD	_	_	_
11	#	#	#	_	_	_
12	2	2	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	ecoli	ecolus	NNS	_	_	_
15	_	_	VBP	_	_	_
16	3538	3538	CD	_	_	_
17	_	_	SYM	_	_	_
18	2x	2x	FW	_	_	_
19	_	_	FW	_	_	_
20	v2	v2	FW	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	E.	e.	FW	_	_	_
23	coli	coli	FW	_	_	_
24	3538	3538	CD	_	_	_
25	#	#	#	_	_	_
26	3	3	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	ecoli	ecolus	NNS	_	_	_
29	_	_	VBP	_	_	_
30	3538	3538	CD	_	_	_
31	_	_	SYM	_	_	_
32	3x	3x	FW	_	_	_
33	_	_	FW	_	_	_
34	v2	v2	FW	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	ecoli	ecolus	NNS	_	_	_
37	_	_	VBP	_	_	_
38	3538	3538	CD	_	_	_
39	_	_	SYM	_	_	_
40	4x	4x	FW	_	_	_
41	_	_	FW	_	_	_
42	v2	v2	FW	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	E.	e.	FW	_	_	_
45	coli	coli	FW	_	_	_
46	D1	d1	NN	_	_	_
47	#	#	#	_	_	_
48	1	1	CD	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	E.	E.	NNP	_	_	_
51	coli	coli	NN	_	_	_
52	D1	d1	NN	_	_	_
53	#	#	#	_	_	_
54	2	2	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	ecoli	ecolus	NNS	_	_	_
57	_	_	VBP	_	_	_
58	D1	d1	NN	_	_	_
59	_	_	SYM	_	_	_
60	2x	2x	FW	_	_	_
61	_	_	FW	_	_	_
62	v2	v2	FW	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	E.	e.	FW	_	_	_
65	coli	coli	FW	_	_	_
66	D1	d1	NN	_	_	_
67	#	#	#	_	_	_
68	3	3	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	ecoli	ecolus	NNS	_	_	_
71	_	_	VBP	_	_	_
72	D1	d1	NN	_	_	_
73	_	_	SYM	_	_	_
74	3x	3x	FW	_	_	_
75	_	_	FW	_	_	_
76	v2	v2	FW	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	ecoli	ecolus	NNS	_	_	_
79	_	_	VBP	_	_	_
80	D1	d1	NN	_	_	_
81	_	_	SYM	_	_	_
82	4x	4x	FW	_	_	_
83	_	_	FW	_	_	_
84	v2	v2	FW	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	E.	e.	FW	_	_	_
87	coli	coli	FW	_	_	_
88	EDL933	edl933	NN	_	_	_
89	#	#	#	_	_	_
90	1	1	CD	_	_	_
91	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
92	E.	E.	NNP	_	_	_
93	coli	coli	NN	_	_	_
94	EDL933	edl933	NN	_	_	_
95	#	#	#	_	_	_
96	2	2	CD	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	ecoli	ecolus	NNS	_	_	_
99	_	_	VBP	_	_	_
100	EDL933	edl933	NN	_	_	_
101	_	_	SYM	_	_	_
102	2x	2x	FW	_	_	_
103	_	_	FW	_	_	_
104	v2	v2	FW	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	E.	e.	FW	_	_	_
107	coli	coli	FW	_	_	_
108	EDL933	edl933	NN	_	_	_
109	#	#	#	_	_	_
110	3	3	CD	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	ecoli	ecolus	NNS	_	_	_
113	_	_	VBP	_	_	_
114	EDL933	edl933	NN	_	_	_
115	_	_	SYM	_	_	_
116	3x	3x	FW	_	_	_
117	_	_	FW	_	_	_
118	v2	v2	FW	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	ecoli	ecolus	NNS	_	_	_
121	_	_	VBP	_	_	_
122	EDL933	edl933	NN	_	_	_
123	_	_	SYM	_	_	_
124	4x	4x	FW	_	_	_
125	_	_	FW	_	_	_
126	v2	v2	FW	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	E.	e.	FW	_	_	_
129	coli	coli	FW	_	_	_
130	K-12	k-12	NN	_	_	_
131	W3110	w3110	NN	_	_	_
132	#	#	#	_	_	_
133	1	1	CD	_	_	_
134	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
135	E.	e.	FW	_	_	_
136	coli	coli	FW	_	_	_
137	K-12	k-12	NN	_	_	_
138	W3110	w3110	NN	_	_	_
139	#	#	#	_	_	_
140	2	2	CD	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
142	E.	e.	FW	_	_	_
143	coli	coli	FW	_	_	_
144	K-12	k-12	NN	_	_	_
145	W3110	w3110	NN	_	_	_
146	#	#	#	_	_	_
147	3	3	CD	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	E.	e.	FW	_	_	_
150	coli	coli	FW	_	_	_
151	phage	phage	NN	_	_	_
152	3538	3538	CD	_	_	_
153	#	#	#	_	_	_
154	1	1	CD	_	_	_
155	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
156	E.	E.	NNP	_	_	_
157	coli	coli	NN	_	_	_
158	phage	phage	NN	_	_	_
159	3538	3538	CD	_	_	_
160	#	#	#	_	_	_
161	2	2	CD	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	ecoli	ecolus	NNS	_	_	_
164	_	_	VBP	_	_	_
165	W3110	w3110	NN	_	_	_
166	_	_	SYM	_	_	_
167	2x	2x	FW	_	_	_
168	_	_	FW	_	_	_
169	v2	v2	FW	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	ecoli	ecolus	NNS	_	_	_
172	_	_	VBP	_	_	_
173	W3110	w3110	NN	_	_	_
174	_	_	SYM	_	_	_
175	3x	3x	FW	_	_	_
176	_	_	FW	_	_	_
177	v2	v2	FW	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	ecoli	ecolus	NNS	_	_	_
180	_	_	VBP	_	_	_
181	W3110	w3110	NN	_	_	_
182	_	_	SYM	_	_	_
183	4x	4x	FW	_	_	_
184	_	_	FW	_	_	_
185	v2	v2	FW	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	Escherichia	escherichia	FW	Organism	_	_
188	coli	coli	FW	Organism	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	Induced	induce	VBN	_	_	_
191	from	from	IN	_	_	_
192	E.	e.	FW	_	_	_
193	coli	coli	FW	_	_	_
194	strain	strain	NN	_	_	_
195	3538	3538	CD	_	_	_
196	with	with	IN	_	_	_
197	mitomycin	mitomycin	NN	_	_	_
198	C	c	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	Isolate	isolate	VB	_	_	_
201	W3110	w3110	NN	_	_	_
202	of	of	IN	_	_	_
203	K-12	k-12	NN	_	_	_
204	strain	strain	NN	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	overnight	overnight	JJ	_	_	_
207	in	in	IN	_	_	_
208	Luria-Bertani	Luria-Bertani	NNP	_	_	_
209	-LRB-	-lrb-	-LRB-	_	_	_
210	LB	LB	NNP	_	_	_
211	-RRB-	-rrb-	-RRB-	_	_	_
212	broth	broth	NN	_	_	_
213	with	with	IN	_	_	_
214	continuous	continuous	JJ	_	_	_
215	agitation	agitation	NN	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	phage	phage	NN	_	_	_
218	DNA	dna	NN	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	Qiagen	Qiagen	NNP	_	_	_
221	Genomic	genomic	JJ	_	_	_
222	Tip	tip	NN	_	_	_
223	500	500	CD	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
225	serotype	serotype	NN	_	_	_
226	O157	o157	NN	_	_	_
227	:	:	:	_	_	_
228	H7	h7	NN	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
230	serotype	serotype	NN	_	_	_
231	O157	o157	NN	_	_	_
232	:	:	:	_	_	_
233	H7	h7	NN	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	serotype	serotype	NN	_	_	_
236	O175	o175	NN	_	_	_
237	:	:	:	_	_	_
238	H16	h16	NN	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
240	Standard	standard	JJ	_	_	_
241	Affymetrix	Affymetrix	NNP	_	_	_
242	procedure	procedure	NN	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	40	40	CD	_	_	_
245	hours	hour	NNS	_	_	_
246	1	1	CD	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	40	40	CD	_	_	_
249	hours	hour	NNS	_	_	_
250	2	2	CD	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
252	40	40	CD	_	_	_
253	hours	hour	NNS	_	_	_
254	3	3	CD	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	40	40	CD	_	_	_
257	hours	hour	NNS	_	_	_
258	cultivation	cultivation	NN	_	_	_
259	in	in	IN	_	_	_
260	continuous	continuous	JJ	_	_	_
261	culture	culture	NN	_	_	_
262	-LRB-	-lrb-	-LRB-	_	_	_
263	mineral	mineral	JJ	_	_	_
264	medium	medium	NN	_	_	_
265	with	with	IN	_	_	_
266	100	100	CD	_	_	_
267	mg	mg	NN	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	40	40	CD	_	_	_
270	hours	hour	NNS	_	_	_
271	of	of	IN	_	_	_
272	cultivation	cultivation	NN	_	_	_
273	in	in	IN	_	_	_
274	continuous	continuous	JJ	_	_	_
275	colture	colture	NN	_	_	_
276	-LRB-	-lrb-	-LRB-	_	_	_
277	mineral	mineral	JJ	_	_	_
278	medium	medium	NN	_	_	_
279	with	with	IN	_	_	_
280	100	100	CD	_	_	_
281	mg	mg	NN	_	_	_
282	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
283	500	500	CD	_	_	_
284	hours	hour	NNS	_	_	_
285	1	1	CD	_	_	_
286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
287	500	500	CD	_	_	_
288	hours	hour	NNS	_	_	_
289	2	2	CD	_	_	_
290	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
291	500	500	CD	_	_	_
292	hours	hour	NNS	_	_	_
293	3	3	CD	_	_	_
294	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
295	500	500	CD	_	_	_
296	hours	hour	NNS	_	_	_
297	of	of	IN	_	_	_
298	cultivation	cultivation	NN	_	_	_
299	in	in	IN	_	_	_
300	continuous	continuous	JJ	_	_	_
301	colture	colture	NN	_	_	_
302	-LRB-	-lrb-	-LRB-	_	_	_
303	mineral	mineral	JJ	_	_	_
304	medium	medium	NN	_	_	_
305	with	with	IN	_	_	_
306	100	100	CD	_	_	_
307	mg	mg	NN	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	Batch	batch	NN	_	_	_
310	growth	growth	NN	_	_	_
311	in	in	IN	_	_	_
312	mineral	mineral	JJ	_	_	_
313	medium	medium	NN	_	_	_
314	supplied	supply	VBN	_	_	_
315	with	with	IN	_	_	_
316	4	4	CD	_	_	_
317	g	g	NN	_	_	_
318	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
319	control	control	NN	_	_	_
320	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
321	Control	Control	NNP	_	_	_
322	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
323	Escherichia	escherichia	FW	Organism	_	_
324	coli	coli	FW	Organism	_	_
325	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
326	Sample	sample	NN	_	_	_
327	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
328	The	the	DT	_	_	_
329	data	datum	NNS	_	_	_
330	provided	provide	VBN	_	_	_
331	are	be	VBP	_	_	_
332	the	the	DT	_	_	_
333	original	original	JJ	_	_	_
334	data	datum	NNS	_	_	_
335	generated	generate	VBN	_	_	_
336	with	with	IN	_	_	_
337	the	the	DT	_	_	_
338	Jaguar	Jaguar	NNP	_	_	_
339	software	software	NN	_	_	_
340	from	from	IN	_	_	_
341	the	the	DT	_	_	_
342	microarray	microarray	NN	_	_	_
343	images	image	NNS	_	_	_
344	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	VALUEs	value	NNS	_	_	_
3	reported	report	VBD	_	_	_
4	represent	represent	VBP	_	_	_
5	log10	log10	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	Cy5	cy5	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Cells	cell	NNS	_	_	_
10	used	use	VBN	_	_	_
11	for	for	IN	_	_	_
12	expression	expression	NN	_	_	_
13	analysis	analysis	NN	_	_	_
14	were	be	VBD	_	_	_
15	grown	grow	VBN	_	_	_
16	in	in	IN	_	_	_
17	minimal	minimal	JJ	_	_	_
18	medium	medium	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Glansdorff	glansdorff	FW	_	_	_
21	,	,	,	_	_	_
22	1965	1965	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	supplemented	supplement	VBN	_	_	_
25	with	with	IN	_	_	_
26	0.5	0.5	CD	_	_	_
27	%	%	NN	_	_	_
28	glucose	glucose	NN	SUPP	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	w	w	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	E.Coli	e.coli	NNS	_	_	_
33	,	,	,	_	_	_
34	strain	strain	NN	_	_	_
35	P4XB2	p4xb2	NN	_	_	_
36	mutant	mutant	NN	_	_	_
37	,	,	,	_	_	_
38	grown	grow	VBN	_	_	_
39	in	in	IN	_	_	_
40	presence	presence	NN	_	_	_
41	of	of	IN	_	_	_
42	arginine	arginine	NN	SUPP	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	100	100	CD	_	_	_
45	ug	ug	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	E.Coli	e.coli	NNS	_	_	_
48	,	,	,	_	_	_
49	strain	strain	NN	_	_	_
50	P4X	p4x	NN	_	_	_
51	,	,	,	_	_	_
52	grown	grow	VBN	_	_	_
53	in	in	IN	_	_	_
54	presence	presence	NN	_	_	_
55	of	of	IN	_	_	_
56	arginine	arginine	NN	SUPP	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	100	100	CD	_	_	_
59	ug	ug	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	E.Coli	e.coli	NNS	_	_	_
62	,	,	,	_	_	_
63	strain	strain	NN	_	_	_
64	P4X	p4x	NN	_	_	_
65	,	,	,	_	_	_
66	grown	grow	VBN	_	_	_
67	on	on	IN	_	_	_
68	minimal	minimal	JJ	_	_	_
69	medium	medium	NN	_	_	_
70	,	,	,	_	_	_
71	reference	reference	NN	_	_	_
72	sample	sample	NN	_	_	_
73	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
74	Escherichia	escherichia	FW	Organism	_	_
75	coli	coli	FW	Organism	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	Initial	initial	JJ	_	_	_
78	data	data	NN	_	_	_
79	analysis	analysis	NN	_	_	_
80	was	be	VBD	_	_	_
81	performed	perform	VBN	_	_	_
82	using	use	VBG	_	_	_
83	the	the	DT	_	_	_
84	GeneChip	GeneChip	NNP	_	_	_
85	®	®	NNP	_	_	_
86	Operating	Operating	NNP	_	_	_
87	Software	Software	NNP	_	_	_
88	.	.	.	_	_	_

1	Microarray	microarray	NN	_	_	_
2	quality	quality	NN	_	_	_
3	control	control	NN	_	_	_
4	parameters	parameter	NNS	_	_	_
5	were	be	VBD	_	_	_
6	as	as	IN	_	_	_
7	follow	follow	VB	_	_	_
8	:	:	:	_	_	_
9	noise	noise	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	RawQ	rawq	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	less	less	JJR	_	_	_
14	than	than	IN	_	_	_
15	5	5	CD	_	_	_
16	,	,	,	_	_	_
17	background	background	NN	_	_	_
18	signal	signal	NN	_	_	_
19	less	less	JJR	_	_	_
20	than	than	IN	_	_	_
21	40	40	CD	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	100	100	CD	_	_	_
24	target	target	NN	_	_	_
25	intensity	intensity	NN	_	_	_
26	for	for	IN	_	_	_
27	array	array	NN	_	_	_
28	scaling	scaling	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	,	,	,	_	_	_
31	consistent	consistent	JJ	_	_	_
32	numbers	number	NNS	_	_	_
33	of	of	IN	_	_	_
34	genes	gene	NNS	_	_	_
35	detected	detect	VBN	_	_	_
36	as	as	IN	_	_	_
37	present	present	JJ	_	_	_
38	across	across	IN	_	_	_
39	arrays	array	NNS	_	_	_
40	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	P4XB2	p4xb2	NN	_	_	_
3	Mutant	mutant	JJ	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	1992	1992	CD	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	in	in	IN	_	_	_
8	Arginine	arginine	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	P4XB2	p4xb2	NN	_	_	_
11	Mutant	mutant	JJ	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	1993	1993	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	in	in	IN	_	_	_
16	Arginine	arginine	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	P4XB2	p4xb2	NN	_	_	_
19	Mutant	mutant	JJ	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	1994	1994	CD	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	in	in	IN	_	_	_
24	Arginine	arginine	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	P4X	p4x	NN	_	_	_
27	Wild	Wild	NNP	_	_	_
28	Type	type	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	1753	1753	CD	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	Reference	Reference	NNP	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	P4X	P4X	NNP	_	_	_
35	Wild	Wild	NNP	_	_	_
36	Type	type	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	1754	1754	CD	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	in	in	IN	_	_	_
41	Arginine	arginine	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	P4X	p4x	NN	_	_	_
44	Wild	Wild	NNP	_	_	_
45	Type	type	NN	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	1765	1765	CD	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	Reference	Reference	NNP	_	_	_
50	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
51	P4X	P4X	NNP	_	_	_
52	Wild	Wild	NNP	_	_	_
53	Type	type	NN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	1766	1766	CD	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	in	in	IN	_	_	_
58	Arginine	arginine	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	P4X	p4x	NN	_	_	_
61	Wild	Wild	NNP	_	_	_
62	Type	type	NN	_	_	_
63	-LRB-	-lrb-	-LRB-	_	_	_
64	1989	1989	CD	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	Reference	Reference	NNP	_	_	_
67	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
68	P4X	P4X	NNP	_	_	_
69	Wild	Wild	NNP	_	_	_
70	Type	type	NN	_	_	_
71	-LRB-	-lrb-	-LRB-	_	_	_
72	1990	1990	CD	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	in	in	IN	_	_	_
75	Arginine	arginine	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	Strain	strain	NN	_	_	_
78	P4X	p4x	NN	_	_	_
79	,	,	,	_	_	_
80	grown	grow	VBN	_	_	_
81	on	on	IN	_	_	_
82	minimal	minimal	JJ	_	_	_
83	medium	medium	NN	_	_	_
84	,	,	,	_	_	_
85	reference	reference	NN	_	_	_
86	sample	sample	NN	_	_	_
87	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
88	Total	Total	NNP	_	_	_
89	RNA	rna	NN	_	_	_
90	was	be	VBD	_	_	_
91	isolated	isolate	VBN	_	_	_
92	using	use	VBG	_	_	_
93	a	a	DT	_	_	_
94	RNeasy	rneasy	NN	_	_	_
95	®	®	NN	_	_	_
96	RNA	rna	NN	_	_	_
97	isolation	isolation	NN	_	_	_
98	kit	kit	NN	_	_	_
99	,	,	,	_	_	_
100	according	accord	VBG	_	_	_
101	to	to	TO	_	_	_
102	the	the	DT	_	_	_
103	manufacturer	manufacturer	NN	_	_	_
104	's	's	POS	_	_	_
105	specifications	specification	NNS	_	_	_
106	-LRB-	-lrb-	-LRB-	_	_	_
107	QIAGEN	QIAGEN	NNP	_	_	_
108	,	,	,	_	_	_
109	Germany	Germany	NNP	_	_	_
110	-RRB-	-rrb-	-RRB-	_	_	_
111	and	and	CC	_	_	_
112	stored	store	VBN	_	_	_
113	in	in	IN	_	_	_
114	RNase-free	rnase-free	JJ	_	_	_
115	water	water	NN	_	_	_
116	at	at	IN	_	_	_
117	--	--	:	_	_	_
118	80	80	CD	_	_	_
119	°C	°c	NN	_	_	_
120	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	concentration	concentration	NN	_	_	_
3	was	be	VBD	_	_	_
4	determined	determine	VBN	_	_	_
5	by	by	IN	_	_	_
6	UV-spectrometry	uv-spectrometry	NN	_	_	_
7	and	and	CC	_	_	_
8	its	its	PRP$	_	_	_
9	quality	quality	NN	_	_	_
10	controlled	control	VBN	_	_	_
11	by	by	IN	_	_	_
12	agarose	agarose	NN	_	_	_
13	gel	gel	NN	_	_	_
14	electrophoresis	electrophoresis	NN	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	BW25113-pCA24N	bw25113-pca24n	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	BW25113-pCA24N	bw25113-pca24n	NN	_	_	_
5	_	_	CD	_	_	_
6	dosP	dosp	NN	GEN	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Cells	cell	NNS	_	_	_
9	were	be	VBD	_	_	_
10	lysed	lyse	VBN	_	_	_
11	using	use	VBG	_	_	_
12	a	a	DT	_	_	_
13	bead	bead	NN	_	_	_
14	beater	beater	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Biospec	biospec	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	mRNA	mrna	NN	_	_	_
20	was	be	VBD	_	_	_
21	isolated	isolate	VBN	_	_	_
22	using	use	VBG	_	_	_
23	a	a	DT	_	_	_
24	Qiagen	Qiagen	NNP	_	_	_
25	RNeasy	RNeasy	NNP	_	_	_
26	mini	minus	NNS	_	_	_
27	kit	kit	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Cat	cat	NN	_	_	_
30	#	#	#	_	_	_
31	74104	74104	CD	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	pelleted	pellete	VBN	_	_	_
5	in	in	IN	_	_	_
6	the	the	DT	_	_	_
7	presence	presence	NN	_	_	_
8	of	of	IN	_	_	_
9	RNALater	rnalater	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Applied	Applied	NNP	_	_	_
12	Biosystems	Biosystems	NNPS	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	and	and	CC	_	_	_
15	flash	flash	NN	_	_	_
16	frozen	freeze	VBN	_	_	_
17	in	in	IN	_	_	_
18	ethanol-dry	ethanol-dry	JJ	_	_	_
19	ice	ice	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	was	be	VBD	_	_	_
4	analyzed	analyze	VBN	_	_	_
5	in	in	IN	_	_	_
6	the	the	DT	_	_	_
7	Affymetrix	Affymetrix	NNP	_	_	_
8	GenomeChipOperating	GenomeChipOperating	NNP	_	_	_
9	Software	Software	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	GCOS	GCOS	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	K-12	k-12	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	genotype	genotype	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	overexpression	overexpression	NN	_	_	_
9	of	of	IN	_	_	_
10	dosP	dosp	NN	GEN	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	pCA24N	pca24n	NN	_	_	_
13	_	_	CD	_	_	_
14	dosP	dosp	NN	GEN	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	overexpression	overexpression	NN	_	_	_
18	of	of	IN	_	_	_
19	empty	empty	JJ	_	_	_
20	vector	vector	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	pCA24N	pca24n	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	strain	strain	NN	_	_	_
26	:	:	:	_	_	_
27	BW25113	bw25113	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Strains	strain	NNS	_	_	_
30	were	be	VBD	_	_	_
31	grown	grow	VBN	_	_	_
32	in	in	IN	_	_	_
33	LBCm30	lbcm30	NN	_	_	_
34	at	at	IN	_	_	_
35	37	37	CD	_	_	_
36	°C	°c	NN	_	_	_
37	with	with	IN	_	_	_
38	shaking	shake	VBG	_	_	_
39	at	at	IN	_	_	_
40	250	250	CD	_	_	_
41	rpm	rpm	NN	_	_	_
42	.	.	.	_	_	_

1	16	16	CD	_	_	_
2	h	h	NN	_	_	_
3	overnight	overnight	JJ	_	_	_
4	cultures	culture	NNS	_	_	_
5	were	be	VBD	_	_	_
6	diluted	dilute	VBN	_	_	_
7	at	at	IN	_	_	_
8	1:1000	1:1000	CD	_	_	_
9	into	into	IN	_	_	_
10	fresh	fresh	JJ	_	_	_
11	LBCm30	lbcm30	NN	_	_	_
12	,	,	,	_	_	_
13	grown	grow	VBN	_	_	_
14	to	to	TO	_	_	_
15	OD600	od600	NN	_	_	_
16	~	~	NN	_	_	_
17	1.0	1.0	CD	_	_	_
18	,	,	,	_	_	_
19	and	and	CC	_	_	_
20	induced	induce	VBN	_	_	_
21	with	with	IN	_	_	_
22	1	1	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	IPTG	iptg	NN	_	_	_
25	for	for	IN	_	_	_
26	90	90	CD	_	_	_
27	min	min	NN	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	1-butanol	1-butanol	NN	_	_	_
3	was	be	VBD	_	_	_
4	added	add	VBN	_	_	_
5	at	at	IN	_	_	_
6	a	a	DT	_	_	_
7	final	final	JJ	_	_	_
8	concentration	concentration	NN	_	_	_
9	of	of	IN	_	_	_
10	0.9	0.9	CD	_	_	_
11	%	%	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	vol	vol	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	A0-A1	a0-a1	NN	_	_	_
16	_	_	CD	_	_	_
17	rep1	rep1	NN	_	_	_
18	_	_	VBD	_	_	_
19	a	a	DT	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	A0-A1	a0-a1	NN	_	_	_
22	_	_	CD	_	_	_
23	rep1	rep1	NN	_	_	_
24	_	_	NN	_	_	_
25	b	b	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	A0-A1	a0-a1	NN	_	_	_
28	_	_	CD	_	_	_
29	rep2	rep2	NN	_	_	_
30	_	_	VBD	_	_	_
31	a	a	DT	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	A0-A1	a0-a1	NN	_	_	_
34	_	_	CD	_	_	_
35	rep2	rep2	NN	_	_	_
36	_	_	NN	_	_	_
37	b	b	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	A0-A1	a0-a1	NN	_	_	_
40	_	_	CD	_	_	_
41	rep3	rep3	NN	_	_	_
42	_	_	VBD	_	_	_
43	a	a	DT	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	A0-A1	a0-a1	NN	_	_	_
46	_	_	CD	_	_	_
47	rep3	rep3	NN	_	_	_
48	_	_	NN	_	_	_
49	b	b	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	A0-E0	a0-e0	NN	_	_	_
52	_	_	CD	_	_	_
53	rep1	rep1	NN	_	_	_
54	_	_	VBD	_	_	_
55	a	a	DT	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	A0-E0	a0-e0	NN	_	_	_
58	_	_	CD	_	_	_
59	rep1	rep1	NN	_	_	_
60	_	_	NN	_	_	_
61	b	b	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	A0-E0	a0-e0	NN	_	_	_
64	_	_	CD	_	_	_
65	rep2	rep2	NN	_	_	_
66	_	_	VBD	_	_	_
67	a	a	DT	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	A0-E0	a0-e0	NN	_	_	_
70	_	_	CD	_	_	_
71	rep2	rep2	NN	_	_	_
72	_	_	NN	_	_	_
73	b	b	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	A0-E0	a0-e0	NN	_	_	_
76	_	_	CD	_	_	_
77	rep3	rep3	NN	_	_	_
78	_	_	VBD	_	_	_
79	a	a	DT	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	A0-E0	a0-e0	NN	_	_	_
82	_	_	CD	_	_	_
83	rep3	rep3	NN	_	_	_
84	_	_	NN	_	_	_
85	b	b	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	Background	background	NN	_	_	_
88	correction	correction	NN	_	_	_
89	and	and	CC	_	_	_
90	normalization	normalization	NN	_	_	_
91	-LRB-	-lrb-	-LRB-	_	_	_
92	print-tip	print-tip	JJ	_	_	_
93	loess	loess	NN	_	_	_
94	and	and	CC	_	_	_
95	quantile	quantile	NN	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	were	be	VBD	_	_	_
98	performed	perform	VBN	_	_	_
99	using	use	VBG	_	_	_
100	the	the	DT	_	_	_
101	limma	limma	NN	_	_	_
102	R	r	NN	_	_	_
103	package	package	NN	_	_	_
104	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	aerobically	aerobically	RB	_	_	_
6	in	in	IN	_	_	_
7	50	50	CD	_	_	_
8	ml	ml	NN	_	_	_
9	LB	lb	NN	MED	_	_
10	medium	medium	NN	MED	_	_
11	until	until	IN	_	_	_
12	OD600	od600	NN	_	_	_
13	reached	reach	VBD	_	_	_
14	~	~	NN	_	_	_
15	1	1	CD	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	late	late	JJ	_	_	_
18	log	log	NN	_	_	_
19	phase	phase	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	E0-E1	e0-e1	NN	_	_	_
3	_	_	CD	_	_	_
4	rep1	rep1	NN	_	_	_
5	_	_	VBD	_	_	_
6	a	a	DT	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	E0-E1	e0-e1	NN	_	_	_
9	_	_	CD	_	_	_
10	rep1	rep1	NN	_	_	_
11	_	_	NN	_	_	_
12	b	b	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	E0-E1	e0-e1	NN	_	_	_
15	_	_	CD	_	_	_
16	rep2	rep2	NN	_	_	_
17	_	_	VBD	_	_	_
18	a	a	DT	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	E0-E1	e0-e1	NN	_	_	_
21	_	_	CD	_	_	_
22	rep2	rep2	NN	_	_	_
23	_	_	NN	_	_	_
24	b	b	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	E0-E1	e0-e1	NN	_	_	_
27	_	_	CD	_	_	_
28	rep3	rep3	NN	_	_	_
29	_	_	VBD	_	_	_
30	a	a	DT	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	E0-E1	e0-e1	NN	_	_	_
33	_	_	CD	_	_	_
34	rep3	rep3	NN	_	_	_
35	_	_	NN	_	_	_
36	b	b	NN	_	_	_
37	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
38	Escherichia	escherichia	FW	Organism	_	_
39	coli	coli	FW	Organism	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	mutant	mutant	JJ	_	_	_
42	E.	e.	FW	_	_	_
43	coli	coli	FW	_	_	_
44	,	,	,	_	_	_
45	after	after	IN	_	_	_
46	butanol	butanol	NN	_	_	_
47	treatment	treatment	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	mutant	mutant	JJ	_	_	_
50	E.	e.	FW	_	_	_
51	coli	coli	FW	_	_	_
52	,	,	,	_	_	_
53	before	before	IN	_	_	_
54	butanol	butanol	NN	_	_	_
55	treatment	treatment	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	protocol	protocol	NN	_	_	_
58	:	:	:	_	_	_
59	late	late	JJ	_	_	_
60	log	log	NN	_	_	_
61	phase	phase	NN	_	_	_
62	,	,	,	_	_	_
63	LB	lb	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	protocol	protocol	NN	_	_	_
66	:	:	:	_	_	_
67	late	late	JJ	_	_	_
68	log	log	NN	_	_	_
69	phase	phase	NN	_	_	_
70	,	,	,	_	_	_
71	LB	lb	NN	_	_	_
72	,	,	,	_	_	_
73	30	30	CD	_	_	_
74	min	min	NN	_	_	_
75	after	after	IN	_	_	_
76	butanol	butanol	NN	_	_	_
77	treatment	treatment	NN	_	_	_
78	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
79	Qiagen	Qiagen	NNP	_	_	_
80	Rneasy	Rneasy	NNP	_	_	_
81	column	column	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	strain	strain	NN	_	_	_
84	:	:	:	_	_	_
85	KCTC	KCTC	NNP	_	_	_
86	2571	2571	CD	_	_	_
87	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
88	strain	strain	NN	_	_	_
89	:	:	:	_	_	_
90	PKH5000	pkh5000	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	wt	wt	JJ	_	_	_
93	E.	e.	FW	_	_	_
94	coli	coli	FW	_	_	_
95	,	,	,	_	_	_
96	after	after	IN	_	_	_
97	butanol	butanol	NN	_	_	_
98	treatment	treatment	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	wt	wt	JJ	_	_	_
101	E.	e.	FW	_	_	_
102	coli	coli	FW	_	_	_
103	,	,	,	_	_	_
104	before	before	IN	_	_	_
105	butanol	butanol	NN	_	_	_
106	treatment	treatment	NN	_	_	_
107	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
108	Algorithm	Algorithm	NNP	_	_	_
109	:	:	:	_	_	_
110	ExpressionStat	ExpressionStat	NNP	_	_	_
111	5.0	5.0	CD	_	_	_
112	-LRB-	-lrb-	-LRB-	_	_	_
113	Affymetrix	Affymetrix	NNP	_	_	_
114	Microarray	Microarray	NNP	_	_	_
115	Suite	Suite	NNP	_	_	_
116	Version	Version	NNP	_	_	_
117	5.0	5.0	CD	_	_	_
118	-RRB-	-rrb-	-RRB-	_	_	_
119	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
120	APEC	APEC	NNP	_	_	_
121	strain	strain	NN	_	_	_
122	O08	o08	NN	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
124	APEC	apec	NN	_	_	_
125	strain	strain	NN	_	_	_
126	SCI-07	sci-07	NN	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	Escherichia	escherichia	FW	Organism	_	_
129	coli	coli	FW	Organism	_	_
130	O08	o08	NN	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	Escherichia	escherichia	FW	Organism	_	_
133	coli	coli	FW	Organism	_	_
134	SCI-07	sci-07	NN	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	growth	growth	NN	_	_	_
137	media	media	NNS	_	_	_
138	:	:	:	_	_	_
139	DMEM	dmem	NN	_	_	_
140	growth	growth	NN	_	_	_
141	media	media	NNS	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	RNA	rna	NN	_	_	_
144	was	be	VBD	_	_	_
145	extracted	extract	VBN	_	_	_
146	using	use	VBG	_	_	_
147	RNAeasy	rnaeasy	NN	_	_	_
148	mini-Kit	mini-kit	NN	_	_	_
149	Qiagen	Qiagen	NNP	_	_	_
150	and	and	CC	_	_	_
151	hybridizated	hybridizate	VBN	_	_	_
152	on	on	IN	_	_	_
153	Affymatrix	Affymatrix	NNP	_	_	_
154	microarrays	microarray	NNS	_	_	_
155	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	APEC	apec	NN	_	_	_
5	SCI-07	sci-07	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	O	o	NN	_	_	_
8	nontypeable	nontypeable	JJ	_	_	_
9	:	:	:	_	_	_
10	H31	h31	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	isolated	isolate	VBN	_	_	_
13	from	from	IN	_	_	_
14	lesions	lesion	NNS	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	gelatinous	gelatinous	JJ	_	_	_
17	edema	edema	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	on	on	IN	_	_	_
20	the	the	DT	_	_	_
21	skin	skin	NN	_	_	_
22	of	of	IN	_	_	_
23	the	the	DT	_	_	_
24	head	head	NN	_	_	_
25	and	and	CC	_	_	_
26	periorbital	periorbital	JJ	_	_	_
27	tissues	tissue	NNS	_	_	_
28	from	from	IN	_	_	_
29	a	a	DT	_	_	_
30	laying	lay	VBG	_	_	_
31	hen	hen	NN	_	_	_
32	showing	show	VBG	_	_	_
33	clinical	clinical	JJ	_	_	_
34	signs	sign	NNS	_	_	_
35	of	of	IN	_	_	_
36	swollen	swollen	JJ	_	_	_
37	head	head	NN	_	_	_
38	syndrome	syndrome	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	strain	strain	NN	_	_	_
41	:	:	:	_	_	_
42	O08	o08	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	O38	o38	NN	_	_	_
45	:	:	:	_	_	_
46	H10	h10	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	obtained	obtain	VBN	_	_	_
49	from	from	IN	_	_	_
50	the	the	DT	_	_	_
51	yolk	yolk	NN	_	_	_
52	of	of	IN	_	_	_
53	the	the	DT	_	_	_
54	abdomen	abdomen	NN	_	_	_
55	of	of	IN	_	_	_
56	a	a	DT	_	_	_
57	diseased	diseased	JJ	_	_	_
58	1-day-old	1-day-old	JJ	_	_	_
59	chick	chick	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	Two	two	CD	_	_	_
62	Avian	avian	JJ	_	_	_
63	Pathogenic	pathogenic	JJ	_	_	_
64	Escherichia	escherichia	FW	Organism	_	_
65	coli	coli	FW	Organism	_	_
66	strains	strain	NNS	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	APEC	apec	NNS	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	were	be	VBD	_	_	_
71	grown	grow	VBN	_	_	_
72	at	at	IN	_	_	_
73	37	37	CD	_	_	_
74	°C	°c	NN	_	_	_
75	in	in	IN	_	_	_
76	Dulbecco	Dulbecco	NNP	_	_	_
77	's	's	POS	_	_	_
78	Modified	modify	VBN	_	_	_
79	Eagle	Eagle	NNP	_	_	_
80	's	's	POS	_	_	_
81	Media	Media	NNP	_	_	_
82	-LRB-	-lrb-	-LRB-	_	_	_
83	DMEM	DMEM	NNP	_	_	_
84	-RRB-	-rrb-	-RRB-	_	_	_
85	media	media	NNS	_	_	_
86	until	until	IN	_	_	_
87	reach	reach	NN	_	_	_
88	O.D	o.d	NN	_	_	_
89	600	600	CD	_	_	_
90	=	=	JJ	_	_	_
91	0.8	0.8	CD	_	_	_
92	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2	culture	culture	NN	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	E.	E.	NNP	_	_	_
5	coli	coli	NN	_	_	_
6	cells	cell	NNS	_	_	_
7	_	_	VBP	_	_	_
8	HS15min	hs15min	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
10	E.	e.	FW	_	_	_
11	coli	coli	FW	_	_	_
12	cells	cell	NNS	_	_	_
13	_	_	VBP	_	_	_
14	HS30min	hs30min	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
16	E.	e.	FW	_	_	_
17	coli	coli	FW	_	_	_
18	cells	cell	NNS	_	_	_
19	_	_	VBP	_	_	_
20	HS60min	hs60min	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
22	E.	e.	FW	_	_	_
23	coli	coli	FW	_	_	_
24	cells	cell	NNS	_	_	_
25	_	_	VBP	_	_	_
26	LB	lb	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	OD	od	NN	_	_	_
29	=	=	JJ	_	_	_
30	0.87	0.87	CD	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	E.	E.	NNP	_	_	_
34	coli	coli	NN	_	_	_
35	cells	cell	NNS	_	_	_
36	_	_	VBP	_	_	_
37	M-P0h	m-p0h	JJ	_	_	_
38	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
39	E.	E.	NNP	_	_	_
40	coli	coli	NN	_	_	_
41	cells	cell	NNS	_	_	_
42	_	_	VBP	_	_	_
43	M-P2h	m-p2h	JJ	_	_	_
44	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
45	E.	E.	NNP	_	_	_
46	coli	coli	NN	_	_	_
47	cells	cell	NNS	_	_	_
48	_	_	VBP	_	_	_
49	M-P4h	m-p4h	JJ	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
51	Escherichia	escherichia	FW	Organism	_	_
52	coli	coli	FW	Organism	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	For	for	IN	_	_	_
55	the	the	DT	_	_	_
56	Illumina	Illumina	NNP	_	_	_
57	GAII	GAII	NNP	_	_	_
58	platform	platform	NN	_	_	_
59	,	,	,	_	_	_
60	the	the	DT	_	_	_
61	directional	directional	JJ	_	_	_
62	RNA-seq	rna-seq	NN	_	_	_
63	libraries	library	NNS	_	_	_
64	were	be	VBD	_	_	_
65	constructed	construct	VBN	_	_	_
66	by	by	IN	_	_	_
67	following	follow	VBG	_	_	_
68	an	a	DT	_	_	_
69	Illumina	Illumina	NNP	_	_	_
70	's	's	POS	_	_	_
71	instruction	instruction	NN	_	_	_
72	using	use	VBG	_	_	_
73	their	they	PRP$	_	_	_
74	Small	small	JJ	_	_	_
75	RNA	rna	NN	_	_	_
76	Sample	sample	NN	_	_	_
77	Prep	Prep	NNP	_	_	_
78	Kit	kit	NN	_	_	_
79	with	with	IN	_	_	_
80	some	some	DT	_	_	_
81	modifications	modification	NNS	_	_	_
82	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	the	the	DT	_	_	_
3	HiSeq	HiSeq	NNP	_	_	_
4	2000	2000	CD	_	_	_
5	platform	platform	NN	_	_	_
6	,	,	,	_	_	_
7	the	the	DT	_	_	_
8	directional	directional	JJ	_	_	_
9	RNA-seq	rna-seq	NN	_	_	_
10	libraries	library	NNS	_	_	_
11	were	be	VBD	_	_	_
12	constructed	construct	VBN	_	_	_
13	using	use	VBG	_	_	_
14	Illumina	Illumina	NNP	_	_	_
15	's	's	POS	_	_	_
16	TruSeq	TruSeq	NNP	_	_	_
17	Small	Small	NNP	_	_	_
18	RNA	rna	NN	_	_	_
19	Sample	sample	NN	_	_	_
20	Prep	Prep	NNP	_	_	_
21	Kit	kit	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	Escherichia	escherichia	FW	Organism	_	_
7	coli	coli	FW	Organism	_	_
8	K12	k12	NN	_	_	_
9	str	str	NN	_	_	_
10	MG1655	mg1655	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	HS15min	hs15min	NN	_	_	_
13	_	_	CD	_	_	_
14	r1	r1	NN	_	_	_
15	_	_	CD	_	_	_
16	HiSeq	hiseq	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	HS15min	hs15min	NN	_	_	_
19	_	_	CD	_	_	_
20	r2	r2	NN	_	_	_
21	_	_	CD	_	_	_
22	HiSeq	hiseq	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	HS15min	hs15min	NN	_	_	_
25	_	_	CD	_	_	_
26	r3	r3	NN	_	_	_
27	_	_	SYM	_	_	_
28	GAII	gaii	CD	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	HS30min	hs30min	NN	_	_	_
31	_	_	CD	_	_	_
32	r1	r1	NN	_	_	_
33	_	_	CD	_	_	_
34	HiSeq	hiseq	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	HS30min	hs30min	NN	_	_	_
37	_	_	CD	_	_	_
38	r2	r2	NN	_	_	_
39	_	_	CD	_	_	_
40	HiSeq	hiseq	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	HS60min	hs60min	NN	_	_	_
43	_	_	CD	_	_	_
44	r1	r1	NN	_	_	_
45	_	_	CD	_	_	_
46	HiSeq	hiseq	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	HS60min	hs60min	NN	_	_	_
49	_	_	CD	_	_	_
50	r2	r2	NN	_	_	_
51	_	_	CD	_	_	_
52	HiSeq	hiseq	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	LB	lb	NN	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	OD	od	NN	_	_	_
57	=	=	JJ	_	_	_
58	0.87	0.87	CD	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
61	Merge	merge	VB	_	_	_
62	the	the	DT	_	_	_
63	replicates	replicate	VBZ	_	_	_
64	for	for	IN	_	_	_
65	each	each	DT	_	_	_
66	sample	sample	NN	_	_	_
67	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	example	example	NN	_	_	_
3	,	,	,	_	_	_
4	for	for	IN	_	_	_
5	sample	sample	NN	_	_	_
6	HS15min	hs15min	NN	_	_	_
7	,	,	,	_	_	_
8	merge	merge	VBP	_	_	_
9	HS15min_r1.HiSeq.fastq.gz	hs15min_r1.hiseq.fastq.gz	NN	_	_	_
10	,	,	,	_	_	_
11	HS15min_r2.HiSeq.fastq.gz	hs15min_r2.hiseq.fastq.gz	NN	_	_	_
12	and	and	CC	_	_	_
13	HS15min_r3.HiSeq.fastq.gz	hs15min_r3.hiseq.fastq.gz	NN	_	_	_
14	to	to	TO	_	_	_
15	one	one	CD	_	_	_
16	fastq	fastq	NN	_	_	_
17	file	file	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	M-P0h	m-p0h	NN	_	_	_
20	_	_	CD	_	_	_
21	r1	r1	NN	_	_	_
22	_	_	CD	_	_	_
23	HiSeq	hiseq	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	M-P0h	m-p0h	NN	_	_	_
26	_	_	CD	_	_	_
27	r2	r2	NN	_	_	_
28	_	_	CD	_	_	_
29	HiSeq	hiseq	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	M-P2h	m-p2h	NN	_	_	_
32	_	_	CD	_	_	_
33	r1	r1	NN	_	_	_
34	_	_	CD	_	_	_
35	HiSeq	hiseq	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	M-P2h	m-p2h	NN	_	_	_
38	_	_	CD	_	_	_
39	r2	r2	NN	_	_	_
40	_	_	CD	_	_	_
41	HiSeq	hiseq	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	M-P4h	m-p4h	NN	_	_	_
44	_	_	CD	_	_	_
45	r1	r1	NN	_	_	_
46	_	_	CD	_	_	_
47	HiSeq	hiseq	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	M-P4h	m-p4h	NN	_	_	_
50	_	_	CD	_	_	_
51	r2	r2	NN	_	_	_
52	_	_	CD	_	_	_
53	HiSeq	hiseq	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	M-P4h	m-p4h	NN	_	_	_
56	_	_	CD	_	_	_
57	r3	r3	NN	_	_	_
58	_	_	CD	_	_	_
59	HiSeq	hiseq	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	RNA-Seq	rna-seq	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	Sequenced	sequence	VBN	_	_	_
64	reads	read	VBZ	_	_	_
65	were	be	VBD	_	_	_
66	trimmed	trim	VBN	_	_	_
67	for	for	IN	_	_	_
68	adaptor	adaptor	NN	_	_	_
69	sequence	sequence	NN	_	_	_
70	,	,	,	_	_	_
71	then	then	RB	_	_	_
72	mapped	map	VBD	_	_	_
73	to	to	TO	_	_	_
74	E.	e.	FW	_	_	_
75	coli	coli	FW	_	_	_
76	K12	k12	NN	_	_	_
77	genome	genome	NN	_	_	_
78	using	use	VBG	_	_	_
79	bowtie	bowtie	NN	_	_	_
80	v0	v0	NN	_	_	_
81	.12.7	.12.7	CD	_	_	_
82	with	with	IN	_	_	_
83	parameters	parameter	NNS	_	_	_
84	bowtie	bowtie	VBP	_	_	_
85	-	-	:	_	_	_
86	t	t	NN	_	_	_
87	-	-	:	_	_	_
88	v	v	LS	_	_	_
89	3	3	LS	_	_	_
90	-	-	:	_	_	_
91	m	m	NN	_	_	_
92	1	1	CD	_	_	_
93	--	--	:	_	_	_
94	best	best	JJS	_	_	_
95	-	-	:	_	_	_
96	S	s	NN	_	_	_
97	-	-	:	_	_	_
98	p	p	NN	_	_	_
99	2	2	CD	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	strain	strain	NN	_	_	_
102	:	:	:	_	_	_
103	K12	k12	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	substrain	substrain	NN	_	_	_
106	:	:	:	_	_	_
107	MG1655	mg1655	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	Supplementary	supplementary	JJ	_	_	_
110	_	_	NN	_	_	_
111	files	file	NNS	_	_	_
112	_	_	IN	_	_	_
113	format	format	NN	_	_	_
114	_	_	NN	_	_	_
115	and	and	CC	_	_	_
116	_	_	NN	_	_	_
117	content	content	NN	_	_	_
118	:	:	:	_	_	_
119	BigWig	BigWig	NNP	_	_	_
120	files	file	VBZ	_	_	_
121	for	for	IN	_	_	_
122	whole-genome	whole-genome	JJ	_	_	_
123	reads	read	VBZ	_	_	_
124	coverage	coverage	NN	_	_	_
125	-LRB-	-lrb-	-LRB-	_	_	_
126	including	include	VBG	_	_	_
127	number	number	NN	_	_	_
128	of	of	IN	_	_	_
129	mapped	map	VBN	_	_	_
130	reads	read	VBZ	_	_	_
131	-RRB-	-rrb-	-RRB-	_	_	_
132	for	for	IN	_	_	_
133	each	each	DT	_	_	_
134	sample	sample	NN	_	_	_
135	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	sample	sample	NN	_	_	_
3	has	have	VBZ	_	_	_
4	two	two	CD	_	_	_
5	files	file	NNS	_	_	_
6	,	,	,	_	_	_
7	one	one	CD	_	_	_
8	for	for	IN	_	_	_
9	plus	plus	CC	_	_	_
10	strand	strand	NN	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	other	other	JJ	_	_	_
15	for	for	IN	_	_	_
16	minus	minus	CC	_	_	_
17	strand	strand	NN	_	_	_
18	.	.	.	_	_	_

1	Therefore	therefore	RB	_	_	_
2	,	,	,	_	_	_
3	there	there	EX	_	_	_
4	are	be	VBP	_	_	_
5	14	14	CD	_	_	_
6	BigWig	BigWig	NNP	_	_	_
7	files	file	NNS	_	_	_
8	for	for	IN	_	_	_
9	7	7	CD	_	_	_
10	samples	sample	NNS	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	To	to	TO	_	_	_
3	enrich	enrich	VB	_	_	_
4	mRNAs	mrna	NNS	_	_	_
5	and	and	CC	_	_	_
6	other	other	JJ	_	_	_
7	transcripts	transcript	NNS	_	_	_
8	,	,	,	_	_	_
9	majority	majority	NN	_	_	_
10	of	of	IN	_	_	_
11	rRNAs	rrna	NNS	_	_	_
12	were	be	VBD	_	_	_
13	removed	remove	VBN	_	_	_
14	from	from	IN	_	_	_
15	the	the	DT	_	_	_
16	DNase-treated	dnase-treated	JJ	_	_	_
17	total	total	JJ	_	_	_
18	RNA	rna	NN	_	_	_
19	using	use	VBG	_	_	_
20	a	a	DT	_	_	_
21	MICROBExpress	microbexpress	NN	_	_	_
22	kit	kit	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Ambion	ambion	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	following	follow	VBG	_	_	_
27	the	the	DT	_	_	_
28	manufacturer	manufacturer	NN	_	_	_
29	's	's	POS	_	_	_
30	instructions	instruction	NNS	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	using	use	VBG	_	_	_
7	a	a	DT	_	_	_
8	RiboPureTM	ribopuretm	NN	_	_	_
9	-	-	:	_	_	_
10	Bacteria	bacterium	NNS	_	_	_
11	Kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Ambion	ambion	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	following	follow	VBG	_	_	_
16	the	the	DT	_	_	_
17	manufacturer	manufacturer	NN	_	_	_
18	's	's	POS	_	_	_
19	instructions	instruction	NNS	_	_	_
20	.	.	.	_	_	_

1	Once	once	RB	_	_	_
2	isolated	isolate	VBN	_	_	_
3	,	,	,	_	_	_
4	~	~	SYM	_	_	_
5	10μg	10μg	CD	_	_	_
6	total	total	JJ	_	_	_
7	RNA	rna	NN	_	_	_
8	was	be	VBD	_	_	_
9	treated	treat	VBN	_	_	_
10	with	with	IN	_	_	_
11	8	8	CD	_	_	_
12	units	unit	NNS	_	_	_
13	DNase	dnase	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Invitrogen	invitrogen	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	twice	twice	RB	_	_	_
18	to	to	TO	_	_	_
19	remove	remove	VB	_	_	_
20	genomic	genomic	JJ	_	_	_
21	DNA	dna	NN	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Transform	transform	VB	_	_	_
3	the	the	DT	_	_	_
4	mapped	map	VBN	_	_	_
5	file	file	NN	_	_	_
6	format	format	NN	_	_	_
7	from	from	IN	_	_	_
8	sam	sam	NN	_	_	_
9	to	to	TO	_	_	_
10	sorted	sort	VBN	_	_	_
11	bam	bam	NN	_	_	_
12	which	which	WDT	_	_	_
13	are	be	VBP	_	_	_
14	later	later	RB	_	_	_
15	tranfered	tranfer	VBN	_	_	_
16	to	to	TO	_	_	_
17	bigWig	bigwig	NN	_	_	_
18	,	,	,	_	_	_
19	and	and	CC	_	_	_
20	separated	separate	VBN	_	_	_
21	by	by	IN	_	_	_
22	the	the	DT	_	_	_
23	strand	strand	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	plus	plus	NN	_	_	_
26	and	and	CC	_	_	_
27	minus	minus	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	basal	basal	JJ	_	_	_
3	media	media	NNS	_	_	_
4	:	:	:	_	_	_
5	M9	m9	NN	_	_	_
6	+	+	CC	_	_	_
7	4	4	CD	_	_	_
8	g	g	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	cra	cra	NN	GEN	_	_
11	KO	ko	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	cra	cra	NN	GEN	_	_
14	KO	ko	NN	_	_	_
15	+	+	CC	_	_	_
16	L-trp	l-trp	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
18	Differential	differential	JJ	_	_	_
19	expression	expression	NN	_	_	_
20	analysis	analysis	NN	_	_	_
21	was	be	VBD	_	_	_
22	carried	carry	VBN	_	_	_
23	out	out	RP	_	_	_
24	using	use	VBG	_	_	_
25	cuffdiff	cuffdiff	JJ	_	_	_
26	v.	v.	CC	_	_	_
27	2.0.2	2.0.2	CD	_	_	_
28	with	with	IN	_	_	_
29	upper-quartile	upper-quartile	JJ	_	_	_
30	normalization	normalization	NN	_	_	_
31	and	and	CC	_	_	_
32	fr-firststrand	fr-firststrand	NN	_	_	_
33	for	for	IN	_	_	_
34	library	library	NN	_	_	_
35	type	type	NN	_	_	_
36	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
37	E.	E.	NNP	_	_	_
38	coli	coli	NN	_	_	_
39	cultures	culture	NNS	_	_	_
40	were	be	VBD	_	_	_
41	grown	grow	VBN	_	_	_
42	at	at	IN	_	_	_
43	37	37	CD	_	_	_
44	°C	°c	NN	_	_	_
45	in	in	IN	_	_	_
46	M9	m9	NN	MED	_	_
47	minimal	minimal	JJ	MED	_	_
48	media	media	NNS	MED	_	_
49	with	with	IN	_	_	_
50	glucose	glucose	NN	SUPP	_	_
51	as	as	IN	_	_	_
52	the	the	DT	_	_	_
53	primary	primary	JJ	_	_	_
54	carbon	carbon	NN	_	_	_
55	source	source	NN	_	_	_
56	and	and	CC	_	_	_
57	harvested	harvest	VBN	_	_	_
58	at	at	IN	_	_	_
59	mid	mid	JJ	_	_	_
60	exponetial	exponetial	JJ	_	_	_
61	phase	phase	NN	_	_	_
62	.	.	.	_	_	_

1	Aerobic	aerobic	JJ	_	_	_
2	E.	e.	FW	_	_	_
3	coli	coli	FW	_	_	_
4	conditions	condition	NNS	_	_	_
5	were	be	VBD	_	_	_
6	grown	grow	VBN	_	_	_
7	in	in	IN	_	_	_
8	shake	shake	NN	_	_	_
9	flasks	flask	NNS	_	_	_
10	and	and	CC	_	_	_
11	anaerobic	anaerobic	JJ	_	_	_
12	conditions	condition	NNS	_	_	_
13	were	be	VBD	_	_	_
14	grown	grow	VBN	_	_	_
15	in	in	IN	_	_	_
16	anoxic	anoxic	JJ	_	_	_
17	serum	serum	NN	_	_	_
18	bottles	bottle	NNS	_	_	_
19	.	.	.	_	_	_

1	Condition	condition	NN	_	_	_
2	specific	specific	JJ	_	_	_
3	media	media	NNS	_	_	_
4	supplementation	supplementation	NN	_	_	_
5	was	be	VBD	_	_	_
6	added	add	VBN	_	_	_
7	as	as	IN	_	_	_
8	described	describe	VBN	_	_	_
9	else	else	RB	_	_	_
10	where	where	WRB	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	K-12	k-12	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	FPKM	fpkm	NN	_	_	_
7	were	be	VBD	_	_	_
8	calculated	calculate	VBN	_	_	_
9	using	use	VBG	_	_	_
10	Cufflinks	Cufflinks	NNP	_	_	_
11	v.	v.	CC	_	_	_
12	2.0.2	2.0.2	CD	_	_	_
13	with	with	IN	_	_	_
14	upper-quartile	upper-quartile	JJ	_	_	_
15	normalization	normalization	NN	_	_	_
16	and	and	CC	_	_	_
17	fr-firststrand	fr-firststrand	NN	_	_	_
18	for	for	IN	_	_	_
19	library	library	NN	_	_	_
20	type	type	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Genome	Genome	NNP	_	_	_
23	_	_	NNP	_	_	_
24	build	build	VB	_	_	_
25	:	:	:	_	_	_
26	NC	NC	NNP	_	_	_
27	_	_	NNP	_	_	_
28	000913	000913	CD	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	genotype	genotype	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	growth	growth	NN	_	_	_
33	stage	stage	NN	_	_	_
34	:	:	:	_	_	_
35	mid	mid	JJ	_	_	_
36	exponetial	exponetial	JJ	_	_	_
37	phase	phase	NN	_	_	_
38	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
39	Illumina	Illumina	NNP	_	_	_
40	read	read	VB	_	_	_
41	were	be	VBD	_	_	_
42	aligned	align	VBN	_	_	_
43	to	to	TO	_	_	_
44	NC	NC	NNP	_	_	_
45	_	_	SYM	_	_	_
46	000913	000913	CD	_	_	_
47	using	use	VBG	_	_	_
48	Bowtie	Bowtie	NNP	_	_	_
49	1	1	CD	_	_	_
50	with	with	IN	_	_	_
51	2	2	CD	_	_	_
52	mismatches	mismatch	NNS	_	_	_
53	allowed	allow	VBD	_	_	_
54	per	per	IN	_	_	_
55	read	read	NN	_	_	_
56	alignment	alignment	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Mid	Mid	NNP	_	_	_
59	log	log	NN	_	_	_
60	_	_	SYM	_	_	_
61	cra	cra	FW	GEN	_	_
62	KO	ko	FW	_	_	_
63	_	_	SYM	_	_	_
64	glc	glc	NN	_	_	_
65	minimal	minimal	JJ	_	_	_
66	media	media	NNS	_	_	_
67	_	_	NN	_	_	_
68	aerobic	aerobic	JJ	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	Mid	Mid	NNP	_	_	_
71	log	log	NN	_	_	_
72	_	_	SYM	_	_	_
73	cra	cra	FW	GEN	_	_
74	KO	ko	FW	_	_	_
75	_	_	SYM	_	_	_
76	glc	glc	NN	_	_	_
77	minimal	minimal	JJ	_	_	_
78	media	media	NNS	_	_	_
79	+	+	CC	_	_	_
80	L-tryptophan	l-tryptophan	JJ	_	_	_
81	_	_	NN	_	_	_
82	aerobic	aerobic	JJ	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	Mid	Mid	NNP	_	_	_
85	log	log	NN	_	_	_
86	cultures	culture	NNS	_	_	_
87	were	be	VBD	_	_	_
88	treated	treat	VBN	_	_	_
89	with	with	IN	_	_	_
90	Qiagen	Qiagen	NNP	_	_	_
91	RNA	rna	NN	_	_	_
92	Protect	protect	VB	_	_	_
93	reagent	reagent	NN	_	_	_
94	following	follow	VBG	_	_	_
95	the	the	DT	_	_	_
96	vendor	vendor	NN	_	_	_
97	's	's	POS	_	_	_
98	protocol	protocol	NN	_	_	_
99	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	centrifuged	centrifuge	VBN	_	_	_
4	and	and	CC	_	_	_
5	stored	store	VBN	_	_	_
6	at	at	IN	_	_	_
7	-80	-80	CD	_	_	_
8	°C	°c	NN	_	_	_
9	for	for	IN	_	_	_
10	<	<	JJR	_	_	_
11	30	30	CD	_	_	_
12	days	day	NNS	_	_	_
13	prior	prior	RB	_	_	_
14	to	to	TO	_	_	_
15	use	use	VB	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Mid	Mid	NNP	_	_	_
3	log	log	NN	_	_	_
4	_	_	CD	_	_	_
5	mntR	mntr	NN	GEN	_	_
6	KO	KO	NNP	_	_	_
7	_	_	NNP	_	_	_
8	glc	glc	NN	_	_	_
9	minimal	minimal	JJ	_	_	_
10	media	media	NNS	_	_	_
11	_	_	NN	_	_	_
12	aerobic	aerobic	JJ	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Mid	Mid	NNP	_	_	_
15	log	log	NN	_	_	_
16	_	_	CD	_	_	_
17	mntR	mntr	NN	GEN	_	_
18	KO	KO	NNP	_	_	_
19	_	_	NNP	_	_	_
20	glc	glc	NN	_	_	_
21	minimal	minimal	JJ	_	_	_
22	media	media	NNS	_	_	_
23	_	_	NN	_	_	_
24	anaerobic	anaerobic	JJ	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Mid	Mid	NNP	_	_	_
27	log	log	NN	_	_	_
28	_	_	CD	_	_	_
29	nac	nac	NN	GEN	_	_
30	KO	KO	NNP	_	_	_
31	_	_	NNP	_	_	_
32	glc	glc	NN	_	_	_
33	minimal	minimal	JJ	_	_	_
34	media	media	NNS	_	_	_
35	+	+	CC	_	_	_
36	adenine	adenine	JJ	_	_	_
37	_	_	NN	_	_	_
38	aerobic	aerobic	JJ	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Mid	Mid	NNP	_	_	_
41	log	log	NN	_	_	_
42	_	_	CD	_	_	_
43	nac	nac	NN	GEN	_	_
44	KO	KO	NNP	_	_	_
45	_	_	NNP	_	_	_
46	glc	glc	NN	_	_	_
47	minimal	minimal	JJ	_	_	_
48	media	media	NNS	_	_	_
49	_	_	NN	_	_	_
50	aerobic	aerobic	JJ	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	Mid	Mid	NNP	_	_	_
53	log	log	NN	_	_	_
54	_	_	NN	_	_	_
55	wildtype	wildtype	JJ	_	_	_
56	_	_	NN	_	_	_
57	glc	glc	NN	_	_	_
58	minimal	minimal	JJ	_	_	_
59	media	media	NNS	_	_	_
60	+	+	CC	_	_	_
61	adenine	adenine	JJ	_	_	_
62	_	_	NN	_	_	_
63	aerobic	aerobic	JJ	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	Mid	Mid	NNP	_	_	_
66	log	log	NN	_	_	_
67	_	_	NN	_	_	_
68	wildtype	wildtype	JJ	_	_	_
69	_	_	NN	_	_	_
70	glc	glc	NN	_	_	_
71	minimal	minimal	JJ	_	_	_
72	media	media	NNS	_	_	_
73	_	_	NN	_	_	_
74	aerobic	aerobic	JJ	_	_	_
75	rep1	rep1	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	Mid	Mid	NNP	_	_	_
78	log	log	NN	_	_	_
79	_	_	NN	_	_	_
80	wildtype	wildtype	JJ	_	_	_
81	_	_	NN	_	_	_
82	glc	glc	NN	_	_	_
83	minimal	minimal	JJ	_	_	_
84	media	media	NNS	_	_	_
85	_	_	NN	_	_	_
86	aerobic	aerobic	JJ	_	_	_
87	rep2	rep2	NN	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	Mid	Mid	NNP	_	_	_
90	log	log	NN	_	_	_
91	_	_	NN	_	_	_
92	wildtype	wildtype	JJ	_	_	_
93	_	_	NN	_	_	_
94	glc	glc	NN	_	_	_
95	minimal	minimal	JJ	_	_	_
96	media	media	NNS	_	_	_
97	_	_	NN	_	_	_
98	aerobic	aerobic	JJ	_	_	_
99	rep3	rep3	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	Mid	Mid	NNP	_	_	_
102	log	log	NN	_	_	_
103	_	_	NN	_	_	_
104	wildtype	wildtype	JJ	_	_	_
105	_	_	NN	_	_	_
106	glc	glc	NN	_	_	_
107	minimal	minimal	JJ	_	_	_
108	media	media	NNS	_	_	_
109	_	_	NN	_	_	_
110	anaerobic	anaerobic	JJ	_	_	_
111	rep1	rep1	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	Mid	Mid	NNP	_	_	_
114	log	log	NN	_	_	_
115	_	_	NN	_	_	_
116	wildtype	wildtype	JJ	_	_	_
117	_	_	NN	_	_	_
118	glc	glc	NN	_	_	_
119	minimal	minimal	JJ	_	_	_
120	media	media	NNS	_	_	_
121	_	_	NN	_	_	_
122	anaerobic	anaerobic	JJ	_	_	_
123	rep2	rep2	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	Mid	Mid	NNP	_	_	_
126	log	log	NN	_	_	_
127	_	_	NN	_	_	_
128	wildtype	wildtype	JJ	_	_	_
129	_	_	NN	_	_	_
130	glc	glc	NN	_	_	_
131	minimal	minimal	JJ	_	_	_
132	media	media	NNS	_	_	_
133	_	_	NN	_	_	_
134	anaerobic	anaerobic	JJ	_	_	_
135	rep3	rep3	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	Mid	Mid	NNP	_	_	_
138	log	log	NN	_	_	_
139	_	_	NN	_	_	_
140	wildtype	wildtype	JJ	_	_	_
141	_	_	NN	_	_	_
142	glc	glc	NN	_	_	_
143	minimal	minimal	JJ	_	_	_
144	media	media	NNS	_	_	_
145	+	+	CC	_	_	_
146	L-tryptophan	l-tryptophan	JJ	_	_	_
147	_	_	NN	_	_	_
148	aerobic	aerobic	JJ	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	mntR	mntr	NN	GEN	_	_
151	KO	ko	NN	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	mntR	mntr	NN	GEN	_	_
154	KO	ko	SYM	_	_	_
155	-	-	:	_	_	_
156	O2	o2	CD	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	nac	nac	NN	GEN	_	_
159	KO	ko	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	nac	nac	NN	GEN	_	_
162	KO	ko	NN	_	_	_
163	+	+	CC	_	_	_
164	ade	ade	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	oxygen	oxygen	NN	_	_	_
167	condition	condition	NN	_	_	_
168	:	:	:	_	_	_
169	aerobic	aerobic	JJ	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	oxygen	oxygen	NN	_	_	_
172	condition	condition	NN	_	_	_
173	:	:	:	_	_	_
174	anaerobic	anaerobic	JJ	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	Paired-end	paired-end	NN	_	_	_
177	,	,	,	_	_	_
178	strand-specific	strand-specific	JJ	_	_	_
179	RNAseq	rnaseq	NN	_	_	_
180	libraries	library	NNS	_	_	_
181	were	be	VBD	_	_	_
182	generated	generate	VBN	_	_	_
183	using	use	VBG	_	_	_
184	the	the	DT	_	_	_
185	dUTP	dutp	NN	_	_	_
186	method	method	NN	_	_	_
187	-LCB-	-lcb-	-LRB-	_	_	_
188	Levin	Levin	NNP	_	_	_
189	JZ	JZ	NNP	_	_	_
190	et	et	FW	_	_	_
191	al.	al.	FW	_	_	_
192	2010	2010	CD	_	_	_
193	,	,	,	_	_	_
194	Nat	Nat	NNP	_	_	_
195	Methods	method	NNS	_	_	_
196	-RCB-	-rcb-	-RRB-	_	_	_
197	with	with	IN	_	_	_
198	the	the	DT	_	_	_
199	following	follow	VBG	_	_	_
200	modifications	modification	NNS	_	_	_
201	.	.	.	_	_	_

1	rRNA	rrna	NN	_	_	_
2	was	be	VBD	_	_	_
3	removed	remove	VBN	_	_	_
4	with	with	IN	_	_	_
5	Epicentre	Epicentre	NNP	_	_	_
6	's	's	POS	_	_	_
7	Ribo-Zero	Ribo-Zero	NNP	_	_	_
8	rRNA	rrna	NN	_	_	_
9	Removal	removal	NN	_	_	_
10	Kit	kit	NN	_	_	_
11	.	.	.	_	_	_

1	Subtracted	subtract	VBN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	fragmented	fragmented	JJ	_	_	_
5	for	for	IN	_	_	_
6	3	3	CD	_	_	_
7	min	min	NN	_	_	_
8	using	use	VBG	_	_	_
9	Ambion	Ambion	NNP	_	_	_
10	's	's	POS	_	_	_
11	RNA	rna	NN	_	_	_
12	Fragmentation	fragmentation	NN	_	_	_
13	Reagents	reagent	NNS	_	_	_
14	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	was	be	VBD	_	_	_
3	generated	generate	VBN	_	_	_
4	using	use	VBG	_	_	_
5	Invitrogen	Invitrogen	NNP	_	_	_
6	's	's	POS	_	_	_
7	SuperScript	SuperScript	NNP	_	_	_
8	III	III	NNP	_	_	_
9	First-Strand	First-Strand	NNP	_	_	_
10	Synthesis	synthesis	NN	_	_	_
11	protocol	protocol	NN	_	_	_
12	with	with	IN	_	_	_
13	random	random	JJ	_	_	_
14	hexamer	hexamer	NN	_	_	_
15	priming	priming	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	strain	strain	NN	_	_	_
5	:	:	:	_	_	_
6	K-12	k-12	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Supplementary	supplementary	JJ	_	_	_
9	_	_	NN	_	_	_
10	files	file	NNS	_	_	_
11	_	_	IN	_	_	_
12	format	format	NN	_	_	_
13	_	_	NN	_	_	_
14	and	and	CC	_	_	_
15	_	_	NN	_	_	_
16	content	content	NN	_	_	_
17	:	:	:	_	_	_
18	csv	csv	NN	_	_	_
19	files	file	NNS	_	_	_
20	,	,	,	_	_	_
21	FPKM	fpkm	NN	_	_	_
22	values	value	NNS	_	_	_
23	from	from	IN	_	_	_
24	pairwise	pairwise	JJ	_	_	_
25	comparisons	comparison	NNS	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	supplementation	supplementation	NN	_	_	_
28	:	:	:	_	_	_
29	adenine	adenine	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	10	10	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	supplementation	supplementation	NN	_	_	_
36	:	:	:	_	_	_
37	L-tryptophan	l-tryptophan	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	20	20	CD	_	_	_
40	mg	mg	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	supplementation	supplementation	NN	_	_	_
43	:	:	:	_	_	_
44	None	none	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	Total	total	JJ	_	_	_
47	RNA	rna	NN	_	_	_
48	was	be	VBD	_	_	_
49	isolated	isolate	VBN	_	_	_
50	using	use	VBG	_	_	_
51	the	the	DT	_	_	_
52	Rneasy	Rneasy	NNP	_	_	_
53	Mini	Mini	NNP	_	_	_
54	Kit	kit	NN	_	_	_
55	procedure	procedure	NN	_	_	_
56	with	with	IN	_	_	_
57	on	on	IN	_	_	_
58	column	column	NN	_	_	_
59	Dnase	dnase	NN	_	_	_
60	treatment	treatment	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	Qiagen	qiagen	NN	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	WT	WT	NNP	_	_	_
3	+	+	CC	_	_	_
4	ade	ade	JJ	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	WT	wt	NN	_	_	_
7	+	+	CC	_	_	_
8	L-trp	l-trp	JJ	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	WT	wt	SYM	_	_	_
11	-	-	:	_	_	_
12	O2	o2	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	23A1	23a1	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	23B1	23b1	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	23C3	23c3	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	39A1	39a1	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	39B1	39b1	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	39C1	39c1	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	DNA	dna	NN	_	_	_
27	was	be	VBD	_	_	_
28	extracted	extract	VBN	_	_	_
29	in	in	IN	_	_	_
30	the	the	DT	_	_	_
31	same	same	JJ	_	_	_
32	manner	manner	NN	_	_	_
33	as	as	IN	_	_	_
34	described	describe	VBN	_	_	_
35	by	by	IN	_	_	_
36	McNulty	McNulty	NNP	_	_	_
37	et	et	FW	_	_	_
38	al.	al.	FW	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	PMID	pmid	NN	_	_	_
41	:	:	:	_	_	_
42	22030749	22030749	CD	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	ecoli	ecolus	NNS	_	_	_
3	NC	NC	NNP	_	_	_
4	_	_	SYM	_	_	_
5	000913.2	000913.2	CD	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	Escherichia	escherichia	FW	Organism	_	_
8	coli	coli	FW	Organism	_	_
9	str	str	FW	_	_	_
10	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Genome	Genome	NNP	_	_	_
4	_	_	NNP	_	_	_
5	build	build	VB	_	_	_
6	:	:	:	_	_	_
7	ASM584v1	asm584v1	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	genotype	genotype	NN	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Illumina	Illumina	NNP	_	_	_
12	Casava	Casava	NNP	_	_	_
13	software	software	NN	_	_	_
14	used	use	VBN	_	_	_
15	for	for	IN	_	_	_
16	basecalling	basecalling	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	prepared	prepare	VBN	_	_	_
6	for	for	IN	_	_	_
7	sequencing	sequencing	NN	_	_	_
8	using	use	VBG	_	_	_
9	standard	standard	JJ	_	_	_
10	Illumina	Illumina	NNP	_	_	_
11	protocols	protocol	NNS	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
13	RNA-Seq	rna-seq	JJ	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Sequenced	sequence	VBN	_	_	_
16	reads	read	VBZ	_	_	_
17	were	be	VBD	_	_	_
18	trimmed	trim	VBN	_	_	_
19	for	for	IN	_	_	_
20	adaptor	adaptor	NN	_	_	_
21	sequence	sequence	NN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	masked	mask	VBN	_	_	_
25	for	for	IN	_	_	_
26	low-complexity	low-complexity	NN	_	_	_
27	or	or	CC	_	_	_
28	low-quality	low-quality	JJ	_	_	_
29	sequence	sequence	NN	_	_	_
30	,	,	,	_	_	_
31	then	then	RB	_	_	_
32	mapped	map	VBD	_	_	_
33	to	to	TO	_	_	_
34	Escherichia	escherichia	FW	Organism	_	_
35	coli	coli	FW	Organism	_	_
36	str	str	FW	_	_	_
37	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	,	,	,	_	_	_
3	complete	complete	JJ	_	_	_
4	genome	genome	NN	_	_	_
5	using	use	VBG	_	_	_
6	bowtie2	bowtie2	NN	_	_	_
7	version	version	NN	_	_	_
8	2.0.5	2.0.5	CD	_	_	_
9	with	with	IN	_	_	_
10	default	default	NN	_	_	_
11	parameters	parameter	NNS	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	K-12	k-12	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Supplementary	supplementary	JJ	_	_	_
7	_	_	NN	_	_	_
8	files	file	NNS	_	_	_
9	_	_	IN	_	_	_
10	format	format	NN	_	_	_
11	_	_	NN	_	_	_
12	and	and	CC	_	_	_
13	_	_	NN	_	_	_
14	content	content	NN	_	_	_
15	:	:	:	_	_	_
16	tab-delimited	tab-delimited	JJ	_	_	_
17	text	text	NN	_	_	_
18	files	file	NNS	_	_	_
19	include	include	VBP	_	_	_
20	count	count	NN	_	_	_
21	values	value	NNS	_	_	_
22	for	for	IN	_	_	_
23	each	each	DT	_	_	_
24	Sample	Sample	NNP	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	WTA1	wta1	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	WTB1	wtb1	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	WTC3	wtc3	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Cells	cell	NNS	_	_	_
9	were	be	VBD	_	_	_
10	grown	grow	VBN	_	_	_
11	in	in	IN	_	_	_
12	the	the	DT	_	_	_
13	minimal	minimal	JJ	_	_	_
14	media	media	NNS	_	_	_
15	,	,	,	_	_	_
16	M63	m63	NN	_	_	_
17	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	final	final	JJ	_	_	_
3	cell	cell	NN	_	_	_
4	concentrations	concentration	NNS	_	_	_
5	were	be	VBD	_	_	_
6	controlled	control	VBN	_	_	_
7	~	~	SYM	_	_	_
8	10	10	CD	_	_	_
9	^	^	SYM	_	_	_
10	8	8	CD	_	_	_
11	cells	cell	NNS	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
13	condition	condition	NN	_	_	_
14	:	:	:	_	_	_
15	osmotic	osmotic	JJ	_	_	_
16	pressure	pressure	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	condition	condition	NN	_	_	_
19	:	:	:	_	_	_
20	regular	regular	JJ	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
22	condition	condition	NN	_	_	_
23	:	:	:	_	_	_
24	starvation	starvation	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	condition	condition	NN	_	_	_
27	:	:	:	_	_	_
28	temperature	temperature	NN	_	_	_
29	change	change	NN	_	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
31	E.	E.	NNP	_	_	_
32	coli	coli	NN	_	_	_
33	MDS42	mds42	NN	_	_	_
34	,	,	,	_	_	_
35	osmotic	osmotic	JJ	_	_	_
36	pressure	pressure	NN	_	_	_
37	NaCl	nacl	NN	_	_	_
38	0.20	0.20	CD	_	_	_
39	M	m	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
41	E.	e.	FW	_	_	_
42	coli	coli	FW	_	_	_
43	MDS42	mds42	NN	_	_	_
44	,	,	,	_	_	_
45	osmotic	osmotic	JJ	_	_	_
46	pressure	pressure	NN	_	_	_
47	,	,	,	_	_	_
48	NaCl	nacl	NN	_	_	_
49	0.20	0.20	CD	_	_	_
50	M	m	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
52	E.	e.	FW	_	_	_
53	coli	coli	FW	_	_	_
54	MDS42	mds42	NN	_	_	_
55	,	,	,	_	_	_
56	osmotic	osmotic	JJ	_	_	_
57	pressure	pressure	NN	_	_	_
58	NaCl	nacl	NN	_	_	_
59	0.20	0.20	CD	_	_	_
60	M	m	NN	_	_	_
61	,	,	,	_	_	_
62	rep	rep	NN	GEN	_	_
63	1	1	CD	_	_	_
64	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
65	E.	E.	NNP	_	_	_
66	coli	coli	NN	_	_	_
67	MDS42	mds42	NN	_	_	_
68	,	,	,	_	_	_
69	osmotic	osmotic	JJ	_	_	_
70	pressure	pressure	NN	_	_	_
71	,	,	,	_	_	_
72	NaCl	nacl	NN	_	_	_
73	0.20	0.20	CD	_	_	_
74	M	m	NN	_	_	_
75	,	,	,	_	_	_
76	rep	rep	NN	GEN	_	_
77	2	2	CD	_	_	_
78	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
79	E.	E.	NNP	_	_	_
80	coli	coli	NN	_	_	_
81	MDS42	mds42	NN	_	_	_
82	,	,	,	_	_	_
83	osmotic	osmotic	JJ	_	_	_
84	pressure	pressure	NN	_	_	_
85	,	,	,	_	_	_
86	NaCl	nacl	NN	_	_	_
87	0.20	0.20	CD	_	_	_
88	M	m	NN	_	_	_
89	,	,	,	_	_	_
90	rep	rep	NN	GEN	_	_
91	3	3	CD	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	E.	e.	FW	_	_	_
94	coli	coli	FW	_	_	_
95	MDS42	mds42	NN	_	_	_
96	,	,	,	_	_	_
97	osmotic	osmotic	JJ	_	_	_
98	pressure	pressure	NN	_	_	_
99	,	,	,	_	_	_
100	NaCl	nacl	NN	_	_	_
101	0.45	0.45	CD	_	_	_
102	M	m	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
104	E.	e.	FW	_	_	_
105	coli	coli	FW	_	_	_
106	MDS42	mds42	NN	_	_	_
107	,	,	,	_	_	_
108	osmotic	osmotic	JJ	_	_	_
109	pressure	pressure	NN	_	_	_
110	,	,	,	_	_	_
111	NaCl	nacl	NN	_	_	_
112	0.45	0.45	CD	_	_	_
113	M	m	NN	_	_	_
114	,	,	,	_	_	_
115	rep	rep	NN	GEN	_	_
116	1	1	CD	_	_	_
117	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
118	E.	E.	NNP	_	_	_
119	coli	coli	NN	_	_	_
120	MDS42	mds42	NN	_	_	_
121	,	,	,	_	_	_
122	osmotic	osmotic	JJ	_	_	_
123	pressure	pressure	NN	_	_	_
124	,	,	,	_	_	_
125	NaCl	nacl	NN	_	_	_
126	0.45	0.45	CD	_	_	_
127	M	m	NN	_	_	_
128	,	,	,	_	_	_
129	rep	rep	NN	GEN	_	_
130	2	2	CD	_	_	_
131	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
132	E.	E.	NNP	_	_	_
133	coli	coli	NN	_	_	_
134	MDS42	mds42	NN	_	_	_
135	,	,	,	_	_	_
136	osmotic	osmotic	JJ	_	_	_
137	pressure	pressure	NN	_	_	_
138	,	,	,	_	_	_
139	NaCl	nacl	NN	_	_	_
140	0.45	0.45	CD	_	_	_
141	M	m	NN	_	_	_
142	,	,	,	_	_	_
143	rep	rep	NN	GEN	_	_
144	3	3	CD	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	E.	e.	FW	_	_	_
147	coli	coli	FW	_	_	_
148	MDS42	mds42	NN	_	_	_
149	,	,	,	_	_	_
150	osmotic	osmotic	JJ	_	_	_
151	pressure	pressure	NN	_	_	_
152	,	,	,	_	_	_
153	NaCl	nacl	NN	_	_	_
154	0.55	0.55	CD	_	_	_
155	M	m	NN	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
157	E.	e.	FW	_	_	_
158	coli	coli	FW	_	_	_
159	MDS42	mds42	NN	_	_	_
160	,	,	,	_	_	_
161	osmotic	osmotic	JJ	_	_	_
162	pressure	pressure	NN	_	_	_
163	,	,	,	_	_	_
164	NaCl	nacl	NN	_	_	_
165	0.55	0.55	CD	_	_	_
166	M	m	NN	_	_	_
167	,	,	,	_	_	_
168	rep	rep	NN	GEN	_	_
169	1	1	CD	_	_	_
170	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
171	E.	E.	NNP	_	_	_
172	coli	coli	NN	_	_	_
173	MDS42	mds42	NN	_	_	_
174	,	,	,	_	_	_
175	osmotic	osmotic	JJ	_	_	_
176	pressure	pressure	NN	_	_	_
177	,	,	,	_	_	_
178	NaCl	nacl	NN	_	_	_
179	0.55	0.55	CD	_	_	_
180	M	m	NN	_	_	_
181	,	,	,	_	_	_
182	rep	rep	NN	GEN	_	_
183	2	2	CD	_	_	_
184	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
185	E.	E.	NNP	_	_	_
186	coli	coli	NN	_	_	_
187	MDS42	mds42	NN	_	_	_
188	,	,	,	_	_	_
189	osmotic	osmotic	JJ	_	_	_
190	pressure	pressure	NN	_	_	_
191	,	,	,	_	_	_
192	NaCl	nacl	NN	_	_	_
193	0.55	0.55	CD	_	_	_
194	M	m	NN	_	_	_
195	,	,	,	_	_	_
196	rep	rep	NN	GEN	_	_
197	3	3	CD	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	E.	e.	FW	_	_	_
200	coli	coli	FW	_	_	_
201	MDS42	mds42	NN	_	_	_
202	,	,	,	_	_	_
203	regular	regular	JJ	_	_	_
204	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
205	E.	e.	FW	_	_	_
206	coli	coli	FW	_	_	_
207	MDS42	mds42	NN	_	_	_
208	,	,	,	_	_	_
209	regular	regular	JJ	_	_	_
210	,	,	,	_	_	_
211	rep	rep	NN	GEN	_	_
212	1	1	CD	_	_	_
213	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
214	E.	E.	NNP	_	_	_
215	coli	coli	NN	_	_	_
216	MDS42	mds42	NN	_	_	_
217	,	,	,	_	_	_
218	regular	regular	JJ	_	_	_
219	,	,	,	_	_	_
220	rep	rep	NN	GEN	_	_
221	2	2	CD	_	_	_
222	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
223	E.	E.	NNP	_	_	_
224	coli	coli	NN	_	_	_
225	MDS42	mds42	NN	_	_	_
226	,	,	,	_	_	_
227	regular	regular	JJ	_	_	_
228	,	,	,	_	_	_
229	rep	rep	NN	GEN	_	_
230	3	3	CD	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	E.	e.	FW	_	_	_
233	coli	coli	FW	_	_	_
234	MDS42	mds42	NN	_	_	_
235	,	,	,	_	_	_
236	starvation	starvation	NN	_	_	_
237	,	,	,	_	_	_
238	SHX	shx	NN	_	_	_
239	100	100	CD	_	_	_
240	ng	ng	NN	_	_	_
241	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
242	E.	E.	NNP	_	_	_
243	coli	coli	NN	_	_	_
244	MDS42	mds42	NN	_	_	_
245	,	,	,	_	_	_
246	starvation	starvation	NN	_	_	_
247	,	,	,	_	_	_
248	SHX	shx	NN	_	_	_
249	150	150	CD	_	_	_
250	ng	ng	NN	_	_	_
251	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
252	E.	E.	NNP	_	_	_
253	coli	coli	NN	_	_	_
254	MDS42	mds42	NN	_	_	_
255	,	,	,	_	_	_
256	starvation	starvation	NN	_	_	_
257	,	,	,	_	_	_
258	SHX	SHX	NNP	_	_	_
259	50	50	CD	_	_	_
260	ng	ng	NN	_	_	_
261	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
262	E.	E.	NNP	_	_	_
263	coli	coli	NN	_	_	_
264	MDS42	mds42	NN	_	_	_
265	,	,	,	_	_	_
266	temperature	temperature	NN	_	_	_
267	change	change	NN	_	_	_
268	,	,	,	_	_	_
269	40.0	40.0	CD	_	_	_
270	deg	deg	NN	_	_	_
271	C	c	NN	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	E.	e.	FW	_	_	_
274	coli	coli	FW	_	_	_
275	MDS42	mds42	NN	_	_	_
276	,	,	,	_	_	_
277	temperature	temperature	NN	_	_	_
278	change	change	NN	_	_	_
279	,	,	,	_	_	_
280	40.0	40.0	CD	_	_	_
281	deg	deg	NN	_	_	_
282	C	c	NN	_	_	_
283	,	,	,	_	_	_
284	rep	rep	NN	GEN	_	_
285	1	1	CD	_	_	_
286	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
287	E.	E.	NNP	_	_	_
288	coli	coli	NN	_	_	_
289	MDS42	mds42	NN	_	_	_
290	,	,	,	_	_	_
291	temperature	temperature	NN	_	_	_
292	change	change	NN	_	_	_
293	,	,	,	_	_	_
294	40.0	40.0	CD	_	_	_
295	deg	deg	NN	_	_	_
296	C	c	NN	_	_	_
297	,	,	,	_	_	_
298	rep	rep	NN	GEN	_	_
299	2	2	CD	_	_	_
300	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
301	E.	E.	NNP	_	_	_
302	coli	coli	NN	_	_	_
303	MDS42	mds42	NN	_	_	_
304	,	,	,	_	_	_
305	temperature	temperature	NN	_	_	_
306	change	change	NN	_	_	_
307	,	,	,	_	_	_
308	40.0	40.0	CD	_	_	_
309	deg	deg	NN	_	_	_
310	C	c	NN	_	_	_
311	,	,	,	_	_	_
312	rep	rep	NN	GEN	_	_
313	3	3	CD	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	E.	e.	FW	_	_	_
316	coli	coli	FW	_	_	_
317	MDS42	mds42	NN	_	_	_
318	,	,	,	_	_	_
319	temperature	temperature	NN	_	_	_
320	change	change	NN	_	_	_
321	,	,	,	_	_	_
322	41.5	41.5	CD	_	_	_
323	deg	deg	NN	_	_	_
324	C	c	NN	_	_	_
325	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
326	E.	e.	FW	_	_	_
327	coli	coli	FW	_	_	_
328	MDS42	mds42	NN	_	_	_
329	,	,	,	_	_	_
330	temperature	temperature	NN	_	_	_
331	change	change	NN	_	_	_
332	,	,	,	_	_	_
333	41.5	41.5	CD	_	_	_
334	deg	deg	NN	_	_	_
335	C	c	NN	_	_	_
336	,	,	,	_	_	_
337	rep	rep	NN	GEN	_	_
338	1	1	CD	_	_	_
339	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
340	E.	E.	NNP	_	_	_
341	coli	coli	NN	_	_	_
342	MDS42	mds42	NN	_	_	_
343	,	,	,	_	_	_
344	temperature	temperature	NN	_	_	_
345	change	change	NN	_	_	_
346	,	,	,	_	_	_
347	41.5	41.5	CD	_	_	_
348	deg	deg	NN	_	_	_
349	C	c	NN	_	_	_
350	,	,	,	_	_	_
351	rep	rep	NN	GEN	_	_
352	2	2	CD	_	_	_
353	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
354	E.	E.	NNP	_	_	_
355	coli	coli	NN	_	_	_
356	MDS42	mds42	NN	_	_	_
357	,	,	,	_	_	_
358	temperature	temperature	NN	_	_	_
359	change	change	NN	_	_	_
360	,	,	,	_	_	_
361	41.5	41.5	CD	_	_	_
362	deg	deg	NN	_	_	_
363	C	c	NN	_	_	_
364	,	,	,	_	_	_
365	rep	rep	NN	GEN	_	_
366	3	3	CD	_	_	_
367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
368	E.	e.	FW	_	_	_
369	coli	coli	FW	_	_	_
370	MDS42	mds42	NN	_	_	_
371	,	,	,	_	_	_
372	temperature	temperature	NN	_	_	_
373	change	change	NN	_	_	_
374	,	,	,	_	_	_
375	41.8	41.8	CD	_	_	_
376	deg	deg	NN	_	_	_
377	C	c	NN	_	_	_
378	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
379	E.	e.	FW	_	_	_
380	coli	coli	FW	_	_	_
381	MDS42	mds42	NN	_	_	_
382	,	,	,	_	_	_
383	temperature	temperature	NN	_	_	_
384	change	change	NN	_	_	_
385	,	,	,	_	_	_
386	41.8	41.8	CD	_	_	_
387	deg	deg	NN	_	_	_
388	C	c	NN	_	_	_
389	,	,	,	_	_	_
390	rep	rep	NN	GEN	_	_
391	1	1	CD	_	_	_
392	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
393	E.	E.	NNP	_	_	_
394	coli	coli	NN	_	_	_
395	MDS42	mds42	NN	_	_	_
396	,	,	,	_	_	_
397	temperature	temperature	NN	_	_	_
398	change	change	NN	_	_	_
399	,	,	,	_	_	_
400	41.8	41.8	CD	_	_	_
401	deg	deg	NN	_	_	_
402	C	c	NN	_	_	_
403	,	,	,	_	_	_
404	rep	rep	NN	GEN	_	_
405	2	2	CD	_	_	_
406	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
407	E.	E.	NNP	_	_	_
408	coli	coli	NN	_	_	_
409	MDS42	mds42	NN	_	_	_
410	,	,	,	_	_	_
411	temperature	temperature	NN	_	_	_
412	change	change	NN	_	_	_
413	,	,	,	_	_	_
414	41.8	41.8	CD	_	_	_
415	deg	deg	NN	_	_	_
416	C	c	NN	_	_	_
417	,	,	,	_	_	_
418	rep	rep	NN	GEN	_	_
419	3	3	CD	_	_	_
420	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
421	Escherichia	escherichia	FW	Organism	_	_
422	coli	coli	FW	Organism	_	_
423	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
424	Microarray	microarray	NN	_	_	_
425	data	datum	NNS	_	_	_
426	were	be	VBD	_	_	_
427	processed	process	VBN	_	_	_
428	using	use	VBG	_	_	_
429	custom	custom	NN	_	_	_
430	scripts	script	NNS	_	_	_
431	written	write	VBN	_	_	_
432	in	in	IN	_	_	_
433	R	r	NN	_	_	_
434	based	base	VBN	_	_	_
435	on	on	IN	_	_	_
436	the	the	DT	_	_	_
437	finite	finite	JJ	_	_	_
438	hybridisation	hybridisation	NN	_	_	_
439	-LRB-	-lrb-	-LRB-	_	_	_
440	FH	fh	NN	_	_	_
441	-RRB-	-rrb-	-RRB-	_	_	_
442	model	model	NN	_	_	_
443	-LRB-	-lrb-	-LRB-	_	_	_
444	Ono	Ono	NNP	_	_	_
445	et	et	FW	_	_	_
446	al	al	FW	_	_	_
447	,	,	,	_	_	_
448	2008	2008	CD	_	_	_
449	-RRB-	-rrb-	-RRB-	_	_	_
450	and	and	CC	_	_	_
451	the	the	DT	_	_	_
452	thermodynamic	thermodynamic	JJ	_	_	_
453	model	model	NN	_	_	_
454	of	of	IN	_	_	_
455	non-specific	non-specific	JJ	_	_	_
456	binding	binding	NN	_	_	_
457	-LRB-	-lrb-	-LRB-	_	_	_
458	NSB	nsb	NN	_	_	_
459	-RRB-	-rrb-	-RRB-	_	_	_
460	on	on	IN	_	_	_
461	short	short	JJ	_	_	_
462	nucleotide	nucleotide	NN	_	_	_
463	microarrays	microarray	NNS	_	_	_
464	-LRB-	-lrb-	-LRB-	_	_	_
465	Furusawa	Furusawa	NNP	_	_	_
466	et	et	FW	_	_	_
467	al	al	FW	_	_	_
468	,	,	,	_	_	_
469	2009	2009	CD	_	_	_
470	-RRB-	-rrb-	-RRB-	_	_	_
471	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MDS42	mds42	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
6	The	the	DT	_	_	_
7	cell	cell	NN	_	_	_
8	culture	culture	NN	_	_	_
9	was	be	VBD	_	_	_
10	put	put	VBN	_	_	_
11	into	into	IN	_	_	_
12	cold	cold	JJ	_	_	_
13	phenol-ethanol	phenol-ethanol	JJ	_	_	_
14	solution	solution	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	1	1	CD	_	_	_
17	g	g	NN	_	_	_
18	of	of	IN	_	_	_
19	phenol	phenol	NN	_	_	_
20	in	in	IN	_	_	_
21	10	10	CD	_	_	_
22	mL	ml	NN	_	_	_
23	of	of	IN	_	_	_
24	ethanol	ethanol	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	prepared	prepare	VBN	_	_	_
27	in	in	IN	_	_	_
28	advance	advance	NN	_	_	_
29	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	collected	collect	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	at	at	IN	_	_	_
8	16,000	16,000	CD	_	_	_
9	×	×	CD	_	_	_
10	g	g	NN	_	_	_
11	for	for	IN	_	_	_
12	5	5	CD	_	_	_
13	min	min	NN	_	_	_
14	at	at	IN	_	_	_
15	4	4	CD	_	_	_
16	°C	°c	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	the	the	DT	_	_	_
20	pelleted	pelleted	JJ	_	_	_
21	cells	cell	NNS	_	_	_
22	were	be	VBD	_	_	_
23	stored	store	VBN	_	_	_
24	at	at	IN	_	_	_
25	--	--	:	_	_	_
26	80	80	CD	_	_	_
27	°C	°c	NN	_	_	_
28	prior	prior	RB	_	_	_
29	to	to	TO	_	_	_
30	use	use	VB	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNAs	rna	NNS	_	_	_
4	were	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	an	a	DT	_	_	_
8	RNeasy	rneasy	NN	_	_	_
9	mini	minus	NNS	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	qiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	in	in	IN	_	_	_
15	accordance	accordance	NN	_	_	_
16	with	with	IN	_	_	_
17	the	the	DT	_	_	_
18	manufacturer	manufacturer	NN	_	_	_
19	's	's	POS	_	_	_
20	instructions	instruction	NNS	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Control	Control	NNP	_	_	_
3	Wild	Wild	NNP	_	_	_
4	type	type	NN	_	_	_
5	E.coli	e.coli	NN	_	_	_
6	SE15	se15	NN	_	_	_
7	vs.	vs.	CC	_	_	_
8	LuxS	luxs	NN	_	_	_
9	mutant	mutant	JJ	_	_	_
10	E.coli	e.coli	NN	_	_	_
11	SE15	se15	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	E.coli	e.coli	NN	_	_	_
14	SE15	se15	NN	_	_	_
15	is	be	VBZ	_	_	_
16	cultured	culture	VBN	_	_	_
17	in	in	IN	_	_	_
18	LB	lb	NN	MED	_	_
19	broth	broth	NN	MED	_	_
20	and	and	CC	_	_	_
21	LuxS	luxs	NN	_	_	_
22	E.coli	e.coli	NN	_	_	_
23	SE15	se15	NN	_	_	_
24	is	be	VBZ	_	_	_
25	cultured	culture	VBN	_	_	_
26	in	in	IN	_	_	_
27	LB	lb	NN	MED	_	_
28	broth	broth	NN	MED	_	_
29	with	with	IN	_	_	_
30	kanamycine	kanamycine	NN	_	_	_
31	at	at	IN	_	_	_
32	37	37	CD	_	_	_
33	℃	℃	NN	_	_	_
34	and	and	CC	_	_	_
35	in	in	IN	_	_	_
36	150rpm	150rpm	NN	_	_	_
37	shaking	shake	VBG	_	_	_
38	incubator	incubator	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	E.coli	e.coli	NN	_	_	_
41	SE15	se15	NN	_	_	_
42	is	be	VBZ	_	_	_
43	isolated	isolate	VBN	_	_	_
44	from	from	IN	_	_	_
45	indwelling	indwell	VBG	_	_	_
46	catheter	catheter	NN	_	_	_
47	of	of	IN	_	_	_
48	patient	patient	NN	_	_	_
49	and	and	CC	_	_	_
50	deleted	delete	VBN	_	_	_
51	LuxS	luxs	NN	_	_	_
52	gene	gene	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	related	related	JJ	_	_	_
55	to	to	TO	_	_	_
56	quorum	quorum	NN	_	_	_
57	sensing	sense	VBG	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	E.coli	e.coli	NN	_	_	_
61	SE15	se15	NN	_	_	_
62	isolated	isolate	VBN	_	_	_
63	from	from	IN	_	_	_
64	indwelling	indwell	VBG	_	_	_
65	catheter	catheter	NN	_	_	_
66	of	of	IN	_	_	_
67	patient	patient	NN	_	_	_
68	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
69	Escherichia	escherichia	FW	Organism	_	_
70	coli	coli	FW	Organism	_	_
71	SE15	se15	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	genotype	genotype	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	Genowiz	genowiz	NN	_	_	_
76	4.0.5.6	4.0.5.6	CD	_	_	_
77	normalized	normalize	VBD	_	_	_
78	,	,	,	_	_	_
79	background	background	NN	_	_	_
80	subtracted	subtract	VBD	_	_	_
81	data	datum	NNS	_	_	_
82	obtained	obtain	VBN	_	_	_
83	from	from	IN	_	_	_
84	log2	log2	NN	_	_	_
85	of	of	IN	_	_	_
86	processed	process	VBN	_	_	_
87	Red	red	JJ	_	_	_
88	signal	signal	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	strain	strain	NN	_	_	_
91	:	:	:	_	_	_
92	SE15	se15	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	Total	total	JJ	_	_	_
95	RNA	rna	NN	_	_	_
96	extracted	extract	VBN	_	_	_
97	using	use	VBG	_	_	_
98	Trizol	Trizol	NNP	_	_	_
99	following	follow	VBG	_	_	_
100	manufacturer	manufacturer	NN	_	_	_
101	's	's	POS	_	_	_
102	instructions	instruction	NNS	_	_	_
103	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
104	Wild	Wild	NNP	_	_	_
105	type	type	NN	_	_	_
106	E.coli	e.coli	NN	_	_	_
107	SE15	se15	NN	_	_	_
108	vs.	vs.	CC	_	_	_
109	LuxS	luxs	NN	_	_	_
110	mutant	mutant	JJ	_	_	_
111	E.coli	e.coli	NN	_	_	_
112	SE15	se15	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	Agilent	Agilent	NNP	_	_	_
115	Feature	Feature	NNP	_	_	_
116	Extraction	Extraction	NNP	_	_	_
117	Software	Software	NNP	_	_	_
118	version	version	NN	_	_	_
119	10.5.1.1	10.5.1.1	CD	_	_	_
120	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	chip	chip	NN	_	_	_
3	antibody	antibody	NN	_	_	_
4	:	:	:	_	_	_
5	Anti-FLAG	anti-flag	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	sigma-aldrich	sigma-aldrich	JJ	_	_	_
8	cat	cat	NN	_	_	_
9	no	no	DT	_	_	_
10	F3165	f3165	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	chip	chip	NN	_	_	_
14	antibody	antibody	NN	_	_	_
15	:	:	:	_	_	_
16	none	none	NN	_	_	_
17	,	,	,	_	_	_
18	input	input	NN	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	chip	chip	NN	_	_	_
21	antibody	antibody	NN	_	_	_
22	:	:	:	_	_	_
23	normal	normal	JJ	_	_	_
24	rabbit	rabbit	NN	_	_	_
25	IgG	igg	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Upstate	upstate	JJ	_	_	_
28	Biotechnology	biotechnology	NN	_	_	_
29	,	,	,	_	_	_
30	Cat	cat	NN	_	_	_
31	.	.	.	_	_	_

1	no.	no.	RB	_	_	_
2	12-370	12-370	CD	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	CSH50	csh50	NN	_	_	_
6	control	control	NN	_	_	_
7	E-minimal	e-minimal	JJ	_	_	_
8	medium	medium	NN	_	_	_
9	90	90	CD	_	_	_
10	min	min	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	CSH50	csh50	NN	_	_	_
13	control	control	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	mock	mock	JJ	_	_	_
16	igG	igg	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	E-minimal	e-minimal	JJ	_	_	_
19	medium	medium	NN	_	_	_
20	replicate	replicate	VB	_	_	_
21	1	1	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	CSH50	csh50	NN	_	_	_
24	control	control	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	mock	mock	JJ	_	_	_
27	igG	igg	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	E-minimal	e-minimal	JJ	_	_	_
30	medium	medium	NN	_	_	_
31	replicate	replicate	VB	_	_	_
32	2	2	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
34	CSH50	csh50	NN	_	_	_
35	E-minimal	e-minimal	JJ	_	_	_
36	medium	medium	NN	_	_	_
37	pH	ph	NN	_	_	_
38	4.5	4.5	CD	_	_	_
39	90	90	CD	_	_	_
40	min	min	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	CSH50	csh50	NN	_	_	_
43	E-minimal	e-minimal	JJ	_	_	_
44	medium	medium	NN	_	_	_
45	pH	ph	NN	_	_	_
46	4.5	4.5	CD	_	_	_
47	90	90	CD	_	_	_
48	min	min	NN	_	_	_
49	replicate	replicate	VBP	_	_	_
50	1	1	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	CSH50	csh50	NN	_	_	_
53	E-minimal	e-minimal	JJ	_	_	_
54	medium	medium	NN	_	_	_
55	pH	ph	NN	_	_	_
56	4.5	4.5	CD	_	_	_
57	90	90	CD	_	_	_
58	min	min	NN	_	_	_
59	replicate	replicate	VBP	_	_	_
60	2	2	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
62	CSH50	csh50	NN	_	_	_
63	E-minimal	e-minimal	JJ	_	_	_
64	medium	medium	NN	_	_	_
65	pH	ph	NN	_	_	_
66	4.5	4.5	CD	_	_	_
67	90	90	CD	_	_	_
68	min	min	NN	_	_	_
69	replicate	replicate	VBP	_	_	_
70	3	3	CD	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	CSH50	csh50	NN	_	_	_
73	E-minimal	e-minimal	JJ	_	_	_
74	medium	medium	NN	_	_	_
75	pH	ph	NN	_	_	_
76	7	7	CD	_	_	_
77	90	90	CD	_	_	_
78	min	min	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	CSH50	csh50	NN	_	_	_
81	E-minimal	e-minimal	JJ	_	_	_
82	medium	medium	NN	_	_	_
83	pH	ph	NN	_	_	_
84	7	7	CD	_	_	_
85	90	90	CD	_	_	_
86	min	min	NN	_	_	_
87	replicate	replicate	VBP	_	_	_
88	1	1	CD	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	CSH50	csh50	NN	_	_	_
91	E-minimal	e-minimal	JJ	_	_	_
92	medium	medium	NN	_	_	_
93	pH	ph	NN	_	_	_
94	7	7	CD	_	_	_
95	90	90	CD	_	_	_
96	min	min	NN	_	_	_
97	replicate	replicate	VBP	_	_	_
98	2	2	CD	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
100	CSH50	csh50	NN	_	_	_
101	E-minimal	e-minimal	JJ	_	_	_
102	medium	medium	NN	_	_	_
103	pH	ph	NN	_	_	_
104	7	7	CD	_	_	_
105	90	90	CD	_	_	_
106	min	min	NN	_	_	_
107	replicate	replicate	VBP	_	_	_
108	3	3	CD	_	_	_
109	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
110	Escherichia	escherichia	FW	Organism	_	_
111	coli	coli	FW	Organism	_	_
112	K-12	k-12	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	OD600	od600	NN	_	_	_
115	15	15	CD	_	_	_
116	units	unit	NNS	_	_	_
117	of	of	IN	_	_	_
118	cells	cell	NNS	_	_	_
119	were	be	VBD	_	_	_
120	harvested	harvest	VBN	_	_	_
121	for	for	IN	_	_	_
122	each	each	DT	_	_	_
123	ChIP	chip	NN	_	_	_
124	procedure	procedure	NN	_	_	_
125	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	harvested	harvest	VBN	_	_	_
4	by	by	IN	_	_	_
5	centrifugation	centrifugation	NN	_	_	_
6	at	at	IN	_	_	_
7	4,000	4,000	CD	_	_	_
8	rpm	rpm	NN	_	_	_
9	for	for	IN	_	_	_
10	8	8	CD	_	_	_
11	min	min	NN	_	_	_
12	at	at	IN	_	_	_
13	room	room	NN	_	_	_
14	temperature	temperature	NN	_	_	_
15	and	and	CC	_	_	_
16	resuspended	resuspend	VBN	_	_	_
17	in	in	IN	_	_	_
18	50	50	CD	_	_	_
19	ml	ml	NN	_	_	_
20	of	of	IN	_	_	_
21	pre-warmed	pre-warmed	JJ	_	_	_
22	PBS	PBS	NNP	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	37	37	CD	_	_	_
25	°C	°c	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	in	in	IN	_	_	_
28	a	a	DT	_	_	_
29	250	250	CD	_	_	_
30	ml	ml	NN	_	_	_
31	flask	flask	NN	_	_	_
32	.	.	.	_	_	_

1	DNA-protein	dna-protein	JJ	_	_	_
2	and	and	CC	_	_	_
3	protein-protein	protein-protein	JJ	_	_	_
4	interactions	interaction	NNS	_	_	_
5	were	be	VBD	_	_	_
6	cross-linked	cross-link	VBN	_	_	_
7	by	by	IN	_	_	_
8	adding	add	VBG	_	_	_
9	1,351	1,351	CD	_	_	_
10	µl	µl	NN	_	_	_
11	of	of	IN	_	_	_
12	formaldehyde	formaldehyde	NN	_	_	_
13	drop-wise	drop-wise	NN	_	_	_
14	to	to	TO	_	_	_
15	a	a	DT	_	_	_
16	final	final	JJ	_	_	_
17	concentration	concentration	NN	_	_	_
18	of	of	IN	_	_	_
19	1	1	CD	_	_	_
20	%	%	NN	_	_	_
21	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	cross-linked	cross-link	VBN	_	_	_
4	at	at	IN	_	_	_
5	room	room	NN	_	_	_
6	temperature	temperature	NN	_	_	_
7	with	with	IN	_	_	_
8	stirring	stir	VBG	_	_	_
9	for	for	IN	_	_	_
10	30	30	CD	_	_	_
11	min	min	NN	_	_	_
12	.	.	.	_	_	_

1	Glycine	glycine	NN	_	_	_
2	was	be	VBD	_	_	_
3	added	add	VBN	_	_	_
4	to	to	TO	_	_	_
5	a	a	DT	_	_	_
6	final	final	JJ	_	_	_
7	concentration	concentration	NN	_	_	_
8	of	of	IN	_	_	_
9	0.125	0.125	CD	_	_	_
10	M	m	NN	_	_	_
11	with	with	IN	_	_	_
12	stirring	stir	VBG	_	_	_
13	for	for	IN	_	_	_
14	5	5	CD	_	_	_
15	min	min	NN	_	_	_
16	at	at	IN	_	_	_
17	room	room	NN	_	_	_
18	temperature	temperature	NN	_	_	_
19	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	centrifuged	centrifuge	VBN	_	_	_
4	at	at	IN	_	_	_
5	4,000	4,000	CD	_	_	_
6	rpm	rpm	NN	_	_	_
7	for	for	IN	_	_	_
8	8	8	CD	_	_	_
9	min	min	NN	_	_	_
10	at	at	IN	_	_	_
11	4	4	CD	_	_	_
12	°C	°c	NN	_	_	_
13	and	and	CC	_	_	_
14	the	the	DT	_	_	_
15	supernatant	supernatant	JJ	_	_	_
16	removed	remove	VBN	_	_	_
17	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	was	be	VBD	_	_	_
4	re-suspended	re-suspended	JJ	_	_	_
5	in	in	IN	_	_	_
6	0.6	0.6	CD	_	_	_
7	ml	ml	NN	_	_	_
8	of	of	IN	_	_	_
9	lysis	lysis	NN	_	_	_
10	buffer	buffer	NN	_	_	_
11	containing	contain	VBG	_	_	_
12	50	50	CD	_	_	_
13	mM	mm	NN	KWSUPP	_	_
14	Tris-HCl	tris-hcl	NN	_	_	_
15	,	,	,	_	_	_
16	10	10	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	EDTA	edta	NN	_	_	_
19	,	,	,	_	_	_
20	1	1	CD	_	_	_
21	%	%	NN	_	_	_
22	SDS	sds	NN	_	_	_
23	and	and	CC	_	_	_
24	incubated	incubate	VBN	_	_	_
25	on	on	IN	_	_	_
26	ice	ice	NN	_	_	_
27	for	for	IN	_	_	_
28	10	10	CD	_	_	_
29	min	min	NN	_	_	_
30	.	.	.	_	_	_

1	1.4	1.4	CD	_	_	_
2	ml	ml	NN	_	_	_
3	of	of	IN	_	_	_
4	IP	IP	NNP	_	_	_
5	dilution	dilution	NN	_	_	_
6	buffer	buffer	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	20	20	CD	_	_	_
9	mM	mm	NN	KWSUPP	_	_
10	Tris-HCl	tris-hcl	NN	_	_	_
11	pH	ph	NN	_	_	_
12	8.1	8.1	CD	_	_	_
13	,	,	,	_	_	_
14	150	150	CD	_	_	_
15	mM	mm	NN	KWSUPP	_	_
16	NaCl	nacl	NN	_	_	_
17	,	,	,	_	_	_
18	2	2	CD	_	_	_
19	mM	mm	NN	KWSUPP	_	_
20	EDTA	edta	NN	_	_	_
21	,	,	,	_	_	_
22	1	1	CD	_	_	_
23	%	%	NN	_	_	_
24	Triton	Triton	NNP	_	_	_
25	X-100	x-100	NN	_	_	_
26	,	,	,	_	_	_
27	0.01	0.01	CD	_	_	_
28	%	%	NN	_	_	_
29	SDS	sds	NN	_	_	_
30	,	,	,	_	_	_
31	Roche	Roche	NNP	_	_	_
32	protease	protease	NN	_	_	_
33	inhibitor	inhibitor	NN	_	_	_
34	cocktail	cocktail	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	was	be	VBD	_	_	_
37	added	add	VBN	_	_	_
38	and	and	CC	_	_	_
39	the	the	DT	_	_	_
40	chromatin	chromatin	NN	_	_	_
41	was	be	VBD	_	_	_
42	sonicated	sonicate	VBN	_	_	_
43	on	on	IN	_	_	_
44	ice	ice	NN	_	_	_
45	in	in	IN	_	_	_
46	a	a	DT	_	_	_
47	5	5	CD	_	_	_
48	ml	ml	NN	_	_	_
49	tube	tube	NN	_	_	_
50	to	to	TO	_	_	_
51	reduce	reduce	VB	_	_	_
52	the	the	DT	_	_	_
53	DNA	dna	NN	_	_	_
54	length	length	NN	_	_	_
55	to	to	TO	_	_	_
56	an	a	DT	_	_	_
57	average	average	JJ	_	_	_
58	size	size	NN	_	_	_
59	of	of	IN	_	_	_
60	approximately	approximately	RB	_	_	_
61	500	500	CD	_	_	_
62	bp	bp	NN	_	_	_
63	using	use	VBG	_	_	_
64	the	the	DT	_	_	_
65	Sanyo	Sanyo	NNP	_	_	_
66	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
67	strain	strain	NN	_	_	_
68	:	:	:	_	_	_
69	CSH50	csh50	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	Strains	strain	NNS	_	_	_
72	were	be	VBD	_	_	_
73	grown	grow	VBN	_	_	_
74	overnight	overnight	RB	_	_	_
75	in	in	IN	_	_	_
76	LB	lb	NN	MED	_	_
77	broth	broth	NN	MED	_	_
78	and	and	CC	_	_	_
79	then	then	RB	_	_	_
80	equalised	equalise	VBD	_	_	_
81	to	to	TO	_	_	_
82	0.15	0.15	CD	_	_	_
83	optical	optical	JJ	_	_	_
84	density	density	NN	_	_	_
85	-LRB-	-lrb-	-LRB-	_	_	_
86	OD600nm	od600nm	NN	_	_	_
87	-RRB-	-rrb-	-RRB-	_	_	_
88	units	unit	NNS	_	_	_
89	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	collected	collect	VBN	_	_	_
4	and	and	CC	_	_	_
5	washed	wash	VBN	_	_	_
6	in	in	IN	_	_	_
7	EG	eg	NN	_	_	_
8	minimal	minimal	JJ	_	_	_
9	medium	medium	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	pH	ph	NN	_	_	_
12	7.2	7.2	CD	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	wash	wash	NN	_	_	_
3	step	step	NN	_	_	_
4	was	be	VBD	_	_	_
5	repeated	repeat	VBN	_	_	_
6	twice	twice	RB	_	_	_
7	more	more	RBR	_	_	_
8	with	with	IN	_	_	_
9	centrifugation	centrifugation	NN	_	_	_
10	to	to	TO	_	_	_
11	collect	collect	VB	_	_	_
12	the	the	DT	_	_	_
13	cells	cell	NNS	_	_	_
14	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	final	final	JJ	_	_	_
3	pellet	pellet	NN	_	_	_
4	was	be	VBD	_	_	_
5	resuspended	resuspend	VBN	_	_	_
6	in	in	IN	_	_	_
7	1	1	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	1X	1x	NN	_	_	_
11	EG	eg	NN	_	_	_
12	minimal	minimal	JJ	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	pH	ph	NN	_	_	_
15	7.2	7.2	CD	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	grown	grow	VBN	_	_	_
4	to	to	TO	_	_	_
5	OD600	od600	NN	_	_	_
6	~	~	NN	_	_	_
7	0.5-0.6	0.5-0.6	CD	_	_	_
8	in	in	IN	_	_	_
9	a	a	DT	_	_	_
10	40	40	CD	_	_	_
11	ml	ml	NN	_	_	_
12	volume	volume	NN	_	_	_
13	in	in	IN	_	_	_
14	a	a	DT	_	_	_
15	250	250	CD	_	_	_
16	ml	ml	NN	_	_	_
17	flask	flask	NN	_	_	_
18	at	at	IN	_	_	_
19	37	37	CD	_	_	_
20	°C	°c	NN	_	_	_
21	and	and	CC	_	_	_
22	200	200	CD	_	_	_
23	rpm	rpm	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	culture	culture	NN	_	_	_
4	was	be	VBD	_	_	_
5	divided	divide	VBN	_	_	_
6	into	into	IN	_	_	_
7	two	two	CD	_	_	_
8	20-ml	20-ml	JJ	_	_	_
9	volumes	volume	NNS	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	cells	cell	NNS	_	_	_
13	collected	collect	VBN	_	_	_
14	by	by	IN	_	_	_
15	centrifugation	centrifugation	NN	_	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	and	and	CC	_	_	_
6	the	the	DT	_	_	_
7	two	two	CD	_	_	_
8	pellets	pellet	NNS	_	_	_
9	were	be	VBD	_	_	_
10	subjected	subject	VBN	_	_	_
11	to	to	TO	_	_	_
12	different	different	JJ	_	_	_
13	treatments	treatment	NNS	_	_	_
14	.	.	.	_	_	_

1	One	one	CD	_	_	_
2	was	be	VBD	_	_	_
3	resuspended	resuspend	VBN	_	_	_
4	in	in	IN	_	_	_
5	1	1	CD	_	_	_
6	ml	ml	NN	_	_	_
7	of	of	IN	_	_	_
8	pre-warmed	pre-warmed	JJ	_	_	_
9	1X	1x	NN	_	_	_
10	EG-minimal	eg-minimal	JJ	_	_	_
11	medium	medium	NN	_	_	_
12	pH	ph	NN	_	_	_
13	7.2	7.2	CD	_	_	_
14	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	second	second	NN	_	_	_
3	was	be	VBD	_	_	_
4	resuspended	resuspend	VBN	_	_	_
5	in	in	IN	_	_	_
6	1	1	CD	_	_	_
7	ml	ml	NN	_	_	_
8	of	of	IN	_	_	_
9	pre-warmed	pre-warmed	JJ	_	_	_
10	1X	1x	NN	_	_	_
11	EG-minimal	eg-minimal	JJ	_	_	_
12	medium	medium	NN	_	_	_
13	pH	ph	NN	_	_	_
14	4.5	4.5	CD	_	_	_
15	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	suspension	suspension	NN	_	_	_
3	was	be	VBD	_	_	_
4	added	add	VBN	_	_	_
5	to	to	TO	_	_	_
6	a	a	DT	_	_	_
7	final	final	JJ	_	_	_
8	volume	volume	NN	_	_	_
9	of	of	IN	_	_	_
10	20	20	CD	_	_	_
11	ml	ml	NN	_	_	_
12	1X	1x	NN	_	_	_
13	EG	eg	NN	_	_	_
14	minimal	minimal	JJ	_	_	_
15	medium	medium	NN	_	_	_
16	of	of	IN	_	_	_
17	the	the	DT	_	_	_
18	same	same	JJ	_	_	_
19	pH	ph	NN	_	_	_
20	in	in	IN	_	_	_
21	a	a	DT	_	_	_
22	250	250	CD	_	_	_
23	ml	ml	NN	_	_	_
24	flask	flask	NN	_	_	_
25	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	grown	grow	VBN	_	_	_
4	at	at	IN	_	_	_
5	37	37	CD	_	_	_
6	°C	°c	NN	_	_	_
7	and	and	CC	_	_	_
8	200	200	CD	_	_	_
9	rpm	rpm	NN	_	_	_
10	shaking	shake	VBG	_	_	_
11	for	for	IN	_	_	_
12	90	90	CD	_	_	_
13	min	min	NN	_	_	_
14	before	before	IN	_	_	_
15	harvesting	harvest	VBG	_	_	_
16	for	for	IN	_	_	_
17	analysis	analysis	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	5	5	CD	_	_	_
3	ml	ml	NN	_	_	_
4	bacterial	bacterial	JJ	_	_	_
5	cultures	culture	NNS	_	_	_
6	with	with	IN	_	_	_
7	a	a	DT	_	_	_
8	known	known	JJ	_	_	_
9	inoculum	inoculum	NN	_	_	_
10	of	of	IN	_	_	_
11	E.	e.	FW	_	_	_
12	coli	coli	FW	_	_	_
13	cells	cell	NNS	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	1.0	1.0	CD	_	_	_
16	×	×	NN	_	_	_
17	109	109	CD	_	_	_
18	cfu	cfu	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	cells	cell	NNS	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	E.	e.	FW	_	_	_
23	coli	coli	FW	_	_	_
24	treated	treat	VBN	_	_	_
25	with	with	IN	_	_	_
26	bicontinious	bicontinious	JJ	_	_	_
27	microemulsion	microemulsion	NN	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	E.	E.	NNP	_	_	_
30	coli	coli	NNS	_	_	_
31	treated	treat	VBN	_	_	_
32	with	with	IN	_	_	_
33	o	o	NN	_	_	_
34	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
35	E.	E.	NNP	_	_	_
36	coli	coli	NNS	_	_	_
37	treated	treat	VBN	_	_	_
38	with	with	IN	_	_	_
39	w	w	NN	_	_	_
40	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
41	E.	E.	NNP	_	_	_
42	coli	coli	NN	_	_	_
43	without	without	IN	_	_	_
44	microemulsion	microemulsion	NN	_	_	_
45	treatment	treatment	NN	_	_	_
46	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
47	Escherichia	escherichia	FW	Organism	_	_
48	coli	coli	FW	Organism	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	Raw	raw	NN	_	_	_
51	microarray	microarray	NN	_	_	_
52	intensity	intensity	NN	_	_	_
53	data	datum	NNS	_	_	_
54	were	be	VBD	_	_	_
55	normalized	normalize	VBN	_	_	_
56	per	per	IN	_	_	_
57	chip	chip	NN	_	_	_
58	to	to	TO	_	_	_
59	the	the	DT	_	_	_
60	same	same	JJ	_	_	_
61	mean	mean	NN	_	_	_
62	value	value	NN	_	_	_
63	,	,	,	_	_	_
64	which	which	WDT	_	_	_
65	is	be	VBZ	_	_	_
66	recommended	recommend	VBN	_	_	_
67	by	by	IN	_	_	_
68	the	the	DT	_	_	_
69	manufacturer	manufacturer	NN	_	_	_
70	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	CMCC	cmcc	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	B	b	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	44102	44102	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
10	The	the	DT	_	_	_
11	strain	strain	NN	_	_	_
12	E.	e.	FW	_	_	_
13	coli	coli	FW	_	_	_
14	CMCC	cmcc	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	B	b	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	44102	44102	CD	_	_	_
19	,	,	,	_	_	_
20	was	be	VBD	_	_	_
21	provided	provide	VBN	_	_	_
22	by	by	IN	_	_	_
23	Institute	Institute	NNP	_	_	_
24	of	of	IN	_	_	_
25	Microbiology	Microbiology	NNP	_	_	_
26	,	,	,	_	_	_
27	Chinese	Chinese	NNP	_	_	_
28	Academy	Academy	NNP	_	_	_
29	of	of	IN	_	_	_
30	Sciences	Sciences	NNPS	_	_	_
31	and	and	CC	_	_	_
32	preserved	preserve	VBN	_	_	_
33	at	at	IN	_	_	_
34	the	the	DT	_	_	_
35	Department	Department	NNP	_	_	_
36	of	of	IN	_	_	_
37	Food	Food	NNP	_	_	_
38	Science	Science	NNP	_	_	_
39	and	and	CC	_	_	_
40	Nutrition	Nutrition	NNP	_	_	_
41	,	,	,	_	_	_
42	Zhejiang	Zhejiang	NNP	_	_	_
43	University	University	NNP	_	_	_
44	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	strain	strain	NN	_	_	_
3	was	be	VBD	_	_	_
4	maintained	maintain	VBN	_	_	_
5	in	in	IN	_	_	_
6	nutrient	nutrient	NN	_	_	_
7	agar	agar	NN	_	_	_
8	medium	medium	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	NA	na	NN	_	_	_
11	,	,	,	_	_	_
12	Hangzhou	Hangzhou	NNP	_	_	_
13	Microbiological	Microbiological	NNP	_	_	_
14	Agents	Agents	NNPS	_	_	_
15	Co.	Co.	NNP	_	_	_
16	,	,	,	_	_	_
17	Ltd.	Ltd.	NNP	_	_	_
18	,	,	,	_	_	_
19	China	China	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	at	at	IN	_	_	_
22	37	37	CD	_	_	_
23	°C	°c	NN	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	cultured	culture	VBN	_	_	_
27	in	in	IN	_	_	_
28	tryptic	tryptic	JJ	_	_	_
29	soy	soy	NN	_	_	_
30	broth	broth	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	TSB	tsb	NN	_	_	_
33	,	,	,	_	_	_
34	Qingdao	Qingdao	NNP	_	_	_
35	Hope	Hope	NNP	_	_	_
36	Biotechnology	Biotechnology	NNP	_	_	_
37	Co.	Co.	NNP	_	_	_
38	,	,	,	_	_	_
39	Ltd.	Ltd.	NNP	_	_	_
40	,	,	,	_	_	_
41	China	China	NNP	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	at	at	IN	_	_	_
44	pH	ph	NN	_	_	_
45	7.0	7.0	CD	_	_	_
46	and	and	CC	_	_	_
47	transferred	transfer	VBN	_	_	_
48	every	every	DT	_	_	_
49	20-24	20-24	CD	_	_	_
50	h	h	NN	_	_	_
51	with	with	IN	_	_	_
52	incubation	incubation	NN	_	_	_
53	at	at	IN	_	_	_
54	37	37	CD	_	_	_
55	°C	°c	NN	_	_	_
56	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	from	from	IN	_	_	_
5	cells	cell	NNS	_	_	_
6	of	of	IN	_	_	_
7	the	the	DT	_	_	_
8	microemulsion-treated	microemulsion-treated	JJ	_	_	_
9	E.	e.	FW	_	_	_
10	coli	coli	FW	_	_	_
11	was	be	VBD	_	_	_
12	extracted	extract	VBN	_	_	_
13	in	in	IN	_	_	_
14	duplicate	duplicate	VB	_	_	_
15	using	use	VBG	_	_	_
16	an	a	DT	_	_	_
17	RNAiso	rnaiso	NN	_	_	_
18	Plus	plus	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Cat	cat	NN	_	_	_
21	.	.	.	_	_	_

1	#	#	#	_	_	_
2	908	908	CD	_	_	_
3	,	,	,	_	_	_
4	Takara	Takara	NNP	_	_	_
5	,	,	,	_	_	_
6	Japan	Japan	NNP	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	according	accord	VBG	_	_	_
9	to	to	TO	_	_	_
10	the	the	DT	_	_	_
11	manufacturer	manufacturer	NN	_	_	_
12	's	's	POS	_	_	_
13	instructions	instruction	NNS	_	_	_
14	,	,	,	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	treatment	treatment	NN	_	_	_
17	:	:	:	_	_	_
18	bicontinious	bicontinious	JJ	_	_	_
19	microemulsion	microemulsion	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	treatment	treatment	NN	_	_	_
22	:	:	:	_	_	_
23	control	control	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	treatment	treatment	NN	_	_	_
26	:	:	:	_	_	_
27	oil	oil	NN	_	_	_
28	in	in	IN	_	_	_
29	water	water	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	treatment	treatment	NN	_	_	_
32	:	:	:	_	_	_
33	water	water	NN	_	_	_
34	in	in	IN	_	_	_
35	oil	oil	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Agilent	Agilent	NNP	_	_	_
38	Feature	Feature	NNP	_	_	_
39	Extraction	Extraction	NNP	_	_	_
40	Software	Software	NNP	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	v	v	LS	_	_	_
43	10.10.1.1	10.10.1.1	CD	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	was	be	VBD	_	_	_
46	used	use	VBN	_	_	_
47	for	for	IN	_	_	_
48	background	background	NN	_	_	_
49	subtraction	subtraction	NN	_	_	_
50	and	and	CC	_	_	_
51	LOWESS	lowess	NN	_	_	_
52	normalization	normalization	NN	_	_	_
53	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Continuous	continuous	JJ	_	_	_
3	aerobically	aerobically	RB	_	_	_
4	grown	grow	VBN	_	_	_
5	cultures	culture	NNS	_	_	_
6	in	in	IN	_	_	_
7	Evans	Evans	NNP	_	_	_
8	medium	medium	NN	_	_	_
9	,	,	,	_	_	_
10	exposed	expose	VBN	_	_	_
11	to	to	TO	_	_	_
12	0.1	0.1	CD	_	_	_
13	L	l	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
15	Continuous	continuous	JJ	_	_	_
16	aerobically	aerobically	RB	_	_	_
17	grown	grow	VBN	_	_	_
18	cultures	culture	NNS	_	_	_
19	in	in	IN	_	_	_
20	Evans	Evans	NNP	_	_	_
21	medium	medium	NN	_	_	_
22	,	,	,	_	_	_
23	exposed	expose	VBN	_	_	_
24	to	to	TO	_	_	_
25	40uM	40um	NN	_	_	_
26	CORM-3	corm-3	NN	_	_	_
27	for	for	IN	_	_	_
28	10	10	CD	_	_	_
29	min	min	NN	_	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
31	Continuous	continuous	JJ	_	_	_
32	aerobically	aerobically	RB	_	_	_
33	grown	grow	VBN	_	_	_
34	cultures	culture	NNS	_	_	_
35	in	in	IN	_	_	_
36	Evans	Evans	NNP	_	_	_
37	medium	medium	NN	_	_	_
38	,	,	,	_	_	_
39	exposed	expose	VBN	_	_	_
40	to	to	TO	_	_	_
41	40uM	40um	NN	_	_	_
42	CORM-3	corm-3	NN	_	_	_
43	for	for	IN	_	_	_
44	20	20	CD	_	_	_
45	min	min	NN	_	_	_
46	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
47	Continuous	continuous	JJ	_	_	_
48	aerobically	aerobically	RB	_	_	_
49	grown	grow	VBN	_	_	_
50	cultures	culture	NNS	_	_	_
51	in	in	IN	_	_	_
52	Evans	Evans	NNP	_	_	_
53	medium	medium	NN	_	_	_
54	,	,	,	_	_	_
55	exposed	expose	VBN	_	_	_
56	to	to	TO	_	_	_
57	40uM	40um	NN	_	_	_
58	CORM-3	corm-3	NN	_	_	_
59	for	for	IN	_	_	_
60	2.5	2.5	CD	_	_	_
61	min	min	NN	_	_	_
62	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
63	Continuous	continuous	JJ	_	_	_
64	aerobically	aerobically	RB	_	_	_
65	grown	grow	VBN	_	_	_
66	cultures	culture	NNS	_	_	_
67	in	in	IN	_	_	_
68	Evans	Evans	NNP	_	_	_
69	medium	medium	NN	_	_	_
70	,	,	,	_	_	_
71	exposed	expose	VBN	_	_	_
72	to	to	TO	_	_	_
73	40uM	40um	NN	_	_	_
74	CORM-3	corm-3	NN	_	_	_
75	for	for	IN	_	_	_
76	40	40	CD	_	_	_
77	min	min	NN	_	_	_
78	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
79	Continuous	continuous	JJ	_	_	_
80	aerobically	aerobically	RB	_	_	_
81	grown	grow	VBN	_	_	_
82	cultures	culture	NNS	_	_	_
83	in	in	IN	_	_	_
84	Evans	Evans	NNP	_	_	_
85	medium	medium	NN	_	_	_
86	,	,	,	_	_	_
87	exposed	expose	VBN	_	_	_
88	to	to	TO	_	_	_
89	40uM	40um	NN	_	_	_
90	CORM-3	corm-3	NN	_	_	_
91	for	for	IN	_	_	_
92	5	5	CD	_	_	_
93	min	min	NN	_	_	_
94	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
95	Continuous	continuous	JJ	_	_	_
96	aerobically	aerobically	RB	_	_	_
97	grown	grow	VBN	_	_	_
98	cultures	culture	NNS	_	_	_
99	in	in	IN	_	_	_
100	Evans	Evans	NNP	_	_	_
101	medium	medium	NN	_	_	_
102	,	,	,	_	_	_
103	exposed	expose	VBN	_	_	_
104	to	to	TO	_	_	_
105	40uM	40um	NN	_	_	_
106	CORM-3	corm-3	NN	_	_	_
107	for	for	IN	_	_	_
108	80	80	CD	_	_	_
109	min	min	NN	_	_	_
110	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
111	Continuous	continuous	JJ	_	_	_
112	aerobically	aerobically	RB	_	_	_
113	grown	grow	VBN	_	_	_
114	cultures	culture	NNS	_	_	_
115	in	in	IN	_	_	_
116	Evans	Evans	NNP	_	_	_
117	medium	medium	NN	_	_	_
118	,	,	,	_	_	_
119	exposed	expose	VBN	_	_	_
120	to	to	TO	_	_	_
121	40uM	40um	NN	_	_	_
122	iCORM-3	icorm-3	NN	_	_	_
123	for	for	IN	_	_	_
124	10	10	CD	_	_	_
125	min	min	NN	_	_	_
126	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
127	Continuous	continuous	JJ	_	_	_
128	aerobically	aerobically	RB	_	_	_
129	grown	grow	VBN	_	_	_
130	cultures	culture	NNS	_	_	_
131	in	in	IN	_	_	_
132	Evans	Evans	NNP	_	_	_
133	medium	medium	NN	_	_	_
134	,	,	,	_	_	_
135	exposed	expose	VBN	_	_	_
136	to	to	TO	_	_	_
137	40uM	40um	NN	_	_	_
138	iCORM-3	icorm-3	NN	_	_	_
139	for	for	IN	_	_	_
140	20	20	CD	_	_	_
141	min	min	NN	_	_	_
142	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
143	Continuous	continuous	JJ	_	_	_
144	aerobically	aerobically	RB	_	_	_
145	grown	grow	VBN	_	_	_
146	cultures	culture	NNS	_	_	_
147	in	in	IN	_	_	_
148	Evans	Evans	NNP	_	_	_
149	medium	medium	NN	_	_	_
150	,	,	,	_	_	_
151	exposed	expose	VBN	_	_	_
152	to	to	TO	_	_	_
153	40uM	40um	NN	_	_	_
154	iCORM-3	icorm-3	NN	_	_	_
155	for	for	IN	_	_	_
156	2.5	2.5	CD	_	_	_
157	min	min	NN	_	_	_
158	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
159	Continuous	continuous	JJ	_	_	_
160	aerobically	aerobically	RB	_	_	_
161	grown	grow	VBN	_	_	_
162	cultures	culture	NNS	_	_	_
163	in	in	IN	_	_	_
164	Evans	Evans	NNP	_	_	_
165	medium	medium	NN	_	_	_
166	,	,	,	_	_	_
167	exposed	expose	VBN	_	_	_
168	to	to	TO	_	_	_
169	40uM	40um	NN	_	_	_
170	iCORM-3	icorm-3	NN	_	_	_
171	for	for	IN	_	_	_
172	40	40	CD	_	_	_
173	min	min	NN	_	_	_
174	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
175	Continuous	continuous	JJ	_	_	_
176	aerobically	aerobically	RB	_	_	_
177	grown	grow	VBN	_	_	_
178	cultures	culture	NNS	_	_	_
179	in	in	IN	_	_	_
180	Evans	Evans	NNP	_	_	_
181	medium	medium	NN	_	_	_
182	,	,	,	_	_	_
183	exposed	expose	VBN	_	_	_
184	to	to	TO	_	_	_
185	40uM	40um	NN	_	_	_
186	iCORM-3	icorm-3	NN	_	_	_
187	for	for	IN	_	_	_
188	5	5	CD	_	_	_
189	min	min	NN	_	_	_
190	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
191	Continuous	continuous	JJ	_	_	_
192	aerobically	aerobically	RB	_	_	_
193	grown	grow	VBN	_	_	_
194	cultures	culture	NNS	_	_	_
195	in	in	IN	_	_	_
196	Evans	Evans	NNP	_	_	_
197	medium	medium	NN	_	_	_
198	,	,	,	_	_	_
199	exposed	expose	VBN	_	_	_
200	to	to	TO	_	_	_
201	40uM	40um	NN	_	_	_
202	iCORM-3	icorm-3	NN	_	_	_
203	for	for	IN	_	_	_
204	80	80	CD	_	_	_
205	min	min	NN	_	_	_
206	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
207	Continuous	continuous	JJ	_	_	_
208	anaerobically	anaerobically	RB	_	_	_
209	grown	grow	VBN	_	_	_
210	cultures	culture	NNS	_	_	_
211	in	in	IN	_	_	_
212	Evans	Evans	NNP	_	_	_
213	medium	medium	NN	_	_	_
214	,	,	,	_	_	_
215	exposed	expose	VBN	_	_	_
216	to	to	TO	_	_	_
217	40uM	40um	NN	_	_	_
218	CORM-3	corm-3	NN	_	_	_
219	for	for	IN	_	_	_
220	10	10	CD	_	_	_
221	min	min	NN	_	_	_
222	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
223	Continuous	continuous	JJ	_	_	_
224	anaerobically	anaerobically	RB	_	_	_
225	grown	grow	VBN	_	_	_
226	cultures	culture	NNS	_	_	_
227	in	in	IN	_	_	_
228	Evans	Evans	NNP	_	_	_
229	medium	medium	NN	_	_	_
230	,	,	,	_	_	_
231	exposed	expose	VBN	_	_	_
232	to	to	TO	_	_	_
233	40uM	40um	NN	_	_	_
234	CORM-3	corm-3	NN	_	_	_
235	for	for	IN	_	_	_
236	20	20	CD	_	_	_
237	min	min	NN	_	_	_
238	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
239	Continuous	continuous	JJ	_	_	_
240	anaerobically	anaerobically	RB	_	_	_
241	grown	grow	VBN	_	_	_
242	cultures	culture	NNS	_	_	_
243	in	in	IN	_	_	_
244	Evans	Evans	NNP	_	_	_
245	medium	medium	NN	_	_	_
246	,	,	,	_	_	_
247	exposed	expose	VBN	_	_	_
248	to	to	TO	_	_	_
249	40uM	40um	NN	_	_	_
250	CORM-3	corm-3	NN	_	_	_
251	for	for	IN	_	_	_
252	2.5	2.5	CD	_	_	_
253	min	min	NN	_	_	_
254	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
255	Continuous	continuous	JJ	_	_	_
256	anaerobically	anaerobically	RB	_	_	_
257	grown	grow	VBN	_	_	_
258	cultures	culture	NNS	_	_	_
259	in	in	IN	_	_	_
260	Evans	Evans	NNP	_	_	_
261	medium	medium	NN	_	_	_
262	,	,	,	_	_	_
263	exposed	expose	VBN	_	_	_
264	to	to	TO	_	_	_
265	40uM	40um	NN	_	_	_
266	CORM-3	corm-3	NN	_	_	_
267	for	for	IN	_	_	_
268	5	5	CD	_	_	_
269	min	min	NN	_	_	_
270	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
271	Continuous	continuous	JJ	_	_	_
272	anaerobically	anaerobically	RB	_	_	_
273	grown	grow	VBN	_	_	_
274	cultures	culture	NNS	_	_	_
275	in	in	IN	_	_	_
276	Evans	Evans	NNP	_	_	_
277	medium	medium	NN	_	_	_
278	,	,	,	_	_	_
279	exposed	expose	VBN	_	_	_
280	to	to	TO	_	_	_
281	CO	CO	NNP	_	_	_
282	gas	gas	NN	_	_	_
283	at	at	IN	_	_	_
284	0.1	0.1	CD	_	_	_
285	L	l	NN	_	_	_
286	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
287	Escherichia	escherichia	FW	Organism	_	_
288	coli	coli	FW	Organism	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
290	Slide	slide	NN	_	_	_
291	31	31	CD	_	_	_
292	_	_	SYM	_	_	_
293	Aerobic	aerobic	JJ	_	_	_
294	culture	culture	NN	_	_	_
295	_	_	CD	_	_	_
296	CO	CO	NNP	_	_	_
297	gas	gas	NN	_	_	_
298	_	_	NN	_	_	_
299	biol	biol	NN	_	_	_
300	rep	rep	NN	GEN	_	_
301	1	1	CD	_	_	_
302	_	_	NN	_	_	_
303	Cy3	cy3	NN	_	_	_
304	0	0	CD	_	_	_
305	Cy5	cy5	NN	_	_	_
306	80	80	CD	_	_	_
307	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
308	Slide	Slide	NNP	_	_	_
309	31	31	CD	_	_	_
310	_	_	SYM	_	_	_
311	Aerobic	aerobic	JJ	_	_	_
312	culture	culture	NN	_	_	_
313	_	_	CD	_	_	_
314	CO	CO	NNP	_	_	_
315	gas	gas	NN	_	_	_
316	_	_	NN	_	_	_
317	biol	biol	NN	_	_	_
318	rep	rep	NN	GEN	_	_
319	1	1	CD	_	_	_
320	_	_	CD	_	_	_
321	Cy3	cy3	NN	_	_	_
322	10	10	CD	_	_	_
323	Cy5	cy5	NN	_	_	_
324	0	0	CD	_	_	_
325	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
326	Slide	Slide	NNP	_	_	_
327	31	31	CD	_	_	_
328	_	_	SYM	_	_	_
329	Aerobic	aerobic	JJ	_	_	_
330	culture	culture	NN	_	_	_
331	_	_	CD	_	_	_
332	CO	CO	NNP	_	_	_
333	gas	gas	NN	_	_	_
334	_	_	NN	_	_	_
335	biol	biol	NN	_	_	_
336	rep	rep	NN	GEN	_	_
337	1	1	CD	_	_	_
338	_	_	CD	_	_	_
339	Cy3	cy3	NN	_	_	_
340	20	20	CD	_	_	_
341	Cy5	cy5	NN	_	_	_
342	0	0	CD	_	_	_
343	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
344	Slide	Slide	NNP	_	_	_
345	31	31	CD	_	_	_
346	_	_	SYM	_	_	_
347	Aerobic	aerobic	JJ	_	_	_
348	culture	culture	NN	_	_	_
349	_	_	CD	_	_	_
350	CO	CO	NNP	_	_	_
351	gas	gas	NN	_	_	_
352	_	_	NN	_	_	_
353	biol	biol	NN	_	_	_
354	rep	rep	NN	GEN	_	_
355	1	1	CD	_	_	_
356	_	_	CD	_	_	_
357	Cy3	cy3	NN	_	_	_
358	40	40	CD	_	_	_
359	Cy5	cy5	NN	_	_	_
360	0	0	CD	_	_	_
361	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
362	Slide	Slide	NNP	_	_	_
363	31	31	CD	_	_	_
364	_	_	SYM	_	_	_
365	Aerobic	aerobic	JJ	_	_	_
366	culture	culture	NN	_	_	_
367	_	_	CD	_	_	_
368	CO	CO	NNP	_	_	_
369	gas	gas	NN	_	_	_
370	_	_	NN	_	_	_
371	biol	biol	NN	_	_	_
372	rep	rep	NN	GEN	_	_
373	2	2	CD	_	_	_
374	_	_	CD	_	_	_
375	Cy3	cy3	NN	_	_	_
376	0	0	CD	_	_	_
377	Cy5	cy5	NN	_	_	_
378	10	10	CD	_	_	_
379	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
380	Slide	Slide	NNP	_	_	_
381	31	31	CD	_	_	_
382	_	_	SYM	_	_	_
383	Aerobic	aerobic	JJ	_	_	_
384	culture	culture	NN	_	_	_
385	_	_	CD	_	_	_
386	CO	CO	NNP	_	_	_
387	gas	gas	NN	_	_	_
388	_	_	NN	_	_	_
389	biol	biol	NN	_	_	_
390	rep	rep	NN	GEN	_	_
391	2	2	CD	_	_	_
392	_	_	CD	_	_	_
393	Cy3	cy3	NN	_	_	_
394	0	0	CD	_	_	_
395	Cy5	cy5	NN	_	_	_
396	20	20	CD	_	_	_
397	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
398	Slide	Slide	NNP	_	_	_
399	31	31	CD	_	_	_
400	_	_	SYM	_	_	_
401	Aerobic	aerobic	JJ	_	_	_
402	culture	culture	NN	_	_	_
403	_	_	CD	_	_	_
404	CO	CO	NNP	_	_	_
405	gas	gas	NN	_	_	_
406	_	_	NN	_	_	_
407	biol	biol	NN	_	_	_
408	rep	rep	NN	GEN	_	_
409	2	2	CD	_	_	_
410	_	_	CD	_	_	_
411	Cy3	cy3	NN	_	_	_
412	0	0	CD	_	_	_
413	Cy5	cy5	NN	_	_	_
414	2.5	2.5	CD	_	_	_
415	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
416	Slide	Slide	NNP	_	_	_
417	31	31	CD	_	_	_
418	_	_	SYM	_	_	_
419	Aerobic	aerobic	JJ	_	_	_
420	culture	culture	NN	_	_	_
421	_	_	CD	_	_	_
422	CO	CO	NNP	_	_	_
423	gas	gas	NN	_	_	_
424	_	_	NN	_	_	_
425	biol	biol	NN	_	_	_
426	rep	rep	NN	GEN	_	_
427	2	2	CD	_	_	_
428	_	_	CD	_	_	_
429	Cy3	cy3	NN	_	_	_
430	0	0	CD	_	_	_
431	Cy5	cy5	NN	_	_	_
432	5	5	CD	_	_	_
433	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
434	Slide	Slide	NNP	_	_	_
435	33	33	CD	_	_	_
436	_	_	SYM	_	_	_
437	Aerobic	aerobic	JJ	_	_	_
438	culture	culture	NN	_	_	_
439	_	_	CD	_	_	_
440	CO	CO	NNP	_	_	_
441	gas	gas	NN	_	_	_
442	_	_	NN	_	_	_
443	biol	biol	NN	_	_	_
444	rep	rep	NN	GEN	_	_
445	2	2	CD	_	_	_
446	_	_	CD	_	_	_
447	Cy3	cy3	NN	_	_	_
448	0	0	CD	_	_	_
449	Cy5	cy5	NN	_	_	_
450	40	40	CD	_	_	_
451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
452	Slide	slide	NN	_	_	_
453	33	33	CD	_	_	_
454	_	_	SYM	_	_	_
455	Aerobic	aerobic	JJ	_	_	_
456	culture	culture	NN	_	_	_
457	_	_	CD	_	_	_
458	CO	CO	NNP	_	_	_
459	gas	gas	NN	_	_	_
460	_	_	NN	_	_	_
461	biol	biol	NN	_	_	_
462	rep	rep	NN	GEN	_	_
463	2	2	CD	_	_	_
464	_	_	CD	_	_	_
465	Cy3	cy3	NN	_	_	_
466	0	0	CD	_	_	_
467	Cy5	cy5	NN	_	_	_
468	80	80	CD	_	_	_
469	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
470	Slide	Slide	NNP	_	_	_
471	33	33	CD	_	_	_
472	_	_	SYM	_	_	_
473	Aerobic	aerobic	JJ	_	_	_
474	culture	culture	NN	_	_	_
475	_	_	CD	_	_	_
476	CO	CO	NNP	_	_	_
477	gas	gas	NN	_	_	_
478	_	_	NN	_	_	_
479	biol	biol	NN	_	_	_
480	rep	rep	NN	GEN	_	_
481	2	2	CD	_	_	_
482	_	_	CD	_	_	_
483	Cy3	cy3	NN	_	_	_
484	10	10	CD	_	_	_
485	Cy5	cy5	NN	_	_	_
486	0	0	CD	_	_	_
487	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
488	Slide	Slide	NNP	_	_	_
489	33	33	CD	_	_	_
490	_	_	SYM	_	_	_
491	Aerobic	aerobic	JJ	_	_	_
492	culture	culture	NN	_	_	_
493	_	_	CD	_	_	_
494	CO	CO	NNP	_	_	_
495	gas	gas	NN	_	_	_
496	_	_	NN	_	_	_
497	biol	biol	NN	_	_	_
498	rep	rep	NN	GEN	_	_
499	2	2	CD	_	_	_
500	_	_	CD	_	_	_
501	Cy3	cy3	NN	_	_	_
502	20	20	CD	_	_	_
503	Cy5	cy5	NN	_	_	_
504	0	0	CD	_	_	_
505	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
506	Slide	Slide	NNP	_	_	_
507	33	33	CD	_	_	_
508	_	_	SYM	_	_	_
509	Aerobic	aerobic	JJ	_	_	_
510	culture	culture	NN	_	_	_
511	_	_	CD	_	_	_
512	CO	CO	NNP	_	_	_
513	gas	gas	NN	_	_	_
514	_	_	NN	_	_	_
515	biol	biol	NN	_	_	_
516	rep	rep	NN	GEN	_	_
517	2	2	CD	_	_	_
518	_	_	CD	_	_	_
519	Cy3	cy3	NN	_	_	_
520	2.5	2.5	CD	_	_	_
521	Cy5	cy5	NN	_	_	_
522	0	0	CD	_	_	_
523	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
524	Slide	Slide	NNP	_	_	_
525	33	33	CD	_	_	_
526	_	_	SYM	_	_	_
527	Aerobic	aerobic	JJ	_	_	_
528	culture	culture	NN	_	_	_
529	_	_	CD	_	_	_
530	CO	CO	NNP	_	_	_
531	gas	gas	NN	_	_	_
532	_	_	NN	_	_	_
533	biol	biol	NN	_	_	_
534	rep	rep	NN	GEN	_	_
535	2	2	CD	_	_	_
536	_	_	CD	_	_	_
537	Cy3	cy3	NN	_	_	_
538	40	40	CD	_	_	_
539	Cy5	cy5	NN	_	_	_
540	0	0	CD	_	_	_
541	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
542	Slide	Slide	NNP	_	_	_
543	33	33	CD	_	_	_
544	_	_	SYM	_	_	_
545	Aerobic	aerobic	JJ	_	_	_
546	culture	culture	NN	_	_	_
547	_	_	CD	_	_	_
548	CO	CO	NNP	_	_	_
549	gas	gas	NN	_	_	_
550	_	_	NN	_	_	_
551	biol	biol	NN	_	_	_
552	rep	rep	NN	GEN	_	_
553	2	2	CD	_	_	_
554	_	_	CD	_	_	_
555	Cy3	cy3	NN	_	_	_
556	5	5	CD	_	_	_
557	Cy5	cy5	NN	_	_	_
558	0	0	CD	_	_	_
559	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
560	Slide	Slide	NNP	_	_	_
561	33	33	CD	_	_	_
562	_	_	SYM	_	_	_
563	Aerobic	aerobic	JJ	_	_	_
564	culture	culture	NN	_	_	_
565	_	_	CD	_	_	_
566	CO	CO	NNP	_	_	_
567	gas	gas	NN	_	_	_
568	_	_	NN	_	_	_
569	biol	biol	NN	_	_	_
570	rep	rep	NN	GEN	_	_
571	2	2	CD	_	_	_
572	_	_	CD	_	_	_
573	Cy3	cy3	NN	_	_	_
574	80	80	CD	_	_	_
575	Cy5	cy5	NN	_	_	_
576	0	0	CD	_	_	_
577	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
578	Slide	Slide	NNP	_	_	_
579	37	37	CD	_	_	_
580	_	_	SYM	_	_	_
581	Aerobic	aerobic	JJ	_	_	_
582	culture	culture	NN	_	_	_
583	_	_	CD	_	_	_
584	CO	CO	NNP	_	_	_
585	gas	gas	NN	_	_	_
586	_	_	NN	_	_	_
587	biol	biol	NN	_	_	_
588	rep	rep	NN	GEN	_	_
589	1	1	CD	_	_	_
590	_	_	NN	_	_	_
591	Cy3	cy3	NN	_	_	_
592	0	0	CD	_	_	_
593	Cy5	cy5	NN	_	_	_
594	10	10	CD	_	_	_
595	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
596	Slide	slide	NN	_	_	_
597	37	37	CD	_	_	_
598	_	_	SYM	_	_	_
599	Aerobic	aerobic	JJ	_	_	_
600	culture	culture	NN	_	_	_
601	_	_	CD	_	_	_
602	CO	CO	NNP	_	_	_
603	gas	gas	NN	_	_	_
604	_	_	NN	_	_	_
605	biol	biol	NN	_	_	_
606	rep	rep	NN	GEN	_	_
607	1	1	CD	_	_	_
608	_	_	NN	_	_	_
609	Cy3	cy3	NN	_	_	_
610	0	0	CD	_	_	_
611	Cy5	cy5	NN	_	_	_
612	20	20	CD	_	_	_
613	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
614	Slide	slide	NN	_	_	_
615	37	37	CD	_	_	_
616	_	_	SYM	_	_	_
617	Aerobic	aerobic	JJ	_	_	_
618	culture	culture	NN	_	_	_
619	_	_	CD	_	_	_
620	CO	CO	NNP	_	_	_
621	gas	gas	NN	_	_	_
622	_	_	NN	_	_	_
623	biol	biol	NN	_	_	_
624	rep	rep	NN	GEN	_	_
625	1	1	CD	_	_	_
626	_	_	NN	_	_	_
627	Cy3	cy3	NN	_	_	_
628	0	0	CD	_	_	_
629	Cy5	cy5	NN	_	_	_
630	2.5	2.5	CD	_	_	_
631	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
632	Slide	slide	NN	_	_	_
633	37	37	CD	_	_	_
634	_	_	SYM	_	_	_
635	Aerobic	aerobic	JJ	_	_	_
636	culture	culture	NN	_	_	_
637	_	_	CD	_	_	_
638	CO	CO	NNP	_	_	_
639	gas	gas	NN	_	_	_
640	_	_	NN	_	_	_
641	biol	biol	NN	_	_	_
642	rep	rep	NN	GEN	_	_
643	1	1	CD	_	_	_
644	_	_	NN	_	_	_
645	Cy3	cy3	NN	_	_	_
646	0	0	CD	_	_	_
647	Cy5	cy5	NN	_	_	_
648	40	40	CD	_	_	_
649	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
650	Slide	slide	NN	_	_	_
651	37	37	CD	_	_	_
652	_	_	SYM	_	_	_
653	Aerobic	aerobic	JJ	_	_	_
654	culture	culture	NN	_	_	_
655	_	_	CD	_	_	_
656	CO	CO	NNP	_	_	_
657	gas	gas	NN	_	_	_
658	_	_	NN	_	_	_
659	biol	biol	NN	_	_	_
660	rep	rep	NN	GEN	_	_
661	1	1	CD	_	_	_
662	_	_	NN	_	_	_
663	Cy3	cy3	NN	_	_	_
664	0	0	CD	_	_	_
665	Cy5	cy5	NN	_	_	_
666	5	5	CD	_	_	_
667	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
668	Slide	slide	NN	_	_	_
669	37	37	CD	_	_	_
670	_	_	SYM	_	_	_
671	Aerobic	aerobic	JJ	_	_	_
672	culture	culture	NN	_	_	_
673	_	_	CD	_	_	_
674	CO	CO	NNP	_	_	_
675	gas	gas	NN	_	_	_
676	_	_	NN	_	_	_
677	biol	biol	NN	_	_	_
678	rep	rep	NN	GEN	_	_
679	1	1	CD	_	_	_
680	_	_	CD	_	_	_
681	Cy3	cy3	NN	_	_	_
682	2.5	2.5	CD	_	_	_
683	Cy5	cy5	NN	_	_	_
684	0	0	CD	_	_	_
685	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
686	Slide	Slide	NNP	_	_	_
687	37	37	CD	_	_	_
688	_	_	SYM	_	_	_
689	Aerobic	aerobic	JJ	_	_	_
690	culture	culture	NN	_	_	_
691	_	_	CD	_	_	_
692	CO	CO	NNP	_	_	_
693	gas	gas	NN	_	_	_
694	_	_	NN	_	_	_
695	biol	biol	NN	_	_	_
696	rep	rep	NN	GEN	_	_
697	1	1	CD	_	_	_
698	_	_	CD	_	_	_
699	Cy3	cy3	NN	_	_	_
700	5	5	CD	_	_	_
701	Cy5	cy5	NN	_	_	_
702	0	0	CD	_	_	_
703	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
704	Slide	Slide	NNP	_	_	_
705	37	37	CD	_	_	_
706	_	_	SYM	_	_	_
707	Aerobic	aerobic	JJ	_	_	_
708	culture	culture	NN	_	_	_
709	_	_	CD	_	_	_
710	CO	CO	NNP	_	_	_
711	gas	gas	NN	_	_	_
712	_	_	NN	_	_	_
713	biol	biol	NN	_	_	_
714	rep	rep	NN	GEN	_	_
715	1	1	CD	_	_	_
716	_	_	CD	_	_	_
717	Cy3	cy3	NN	_	_	_
718	80	80	CD	_	_	_
719	Cy5	cy5	NN	_	_	_
720	0	0	CD	_	_	_
721	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
722	Slide	Slide	NNP	_	_	_
723	39	39	CD	_	_	_
724	_	_	SYM	_	_	_
725	Anaerobic	anaerobic	JJ	_	_	_
726	culture	culture	NN	_	_	_
727	_	_	CD	_	_	_
728	CO	CO	NNP	_	_	_
729	gas	gas	NN	_	_	_
730	_	_	NN	_	_	_
731	biol	biol	NN	_	_	_
732	rep	rep	NN	GEN	_	_
733	1	1	CD	_	_	_
734	_	_	CD	_	_	_
735	Cy3	cy3	NN	_	_	_
736	10	10	CD	_	_	_
737	Cy5	cy5	NN	_	_	_
738	0	0	CD	_	_	_
739	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
740	Slide	Slide	NNP	_	_	_
741	39	39	CD	_	_	_
742	_	_	SYM	_	_	_
743	Anaerobic	anaerobic	JJ	_	_	_
744	culture	culture	NN	_	_	_
745	_	_	CD	_	_	_
746	CO	CO	NNP	_	_	_
747	gas	gas	NN	_	_	_
748	_	_	NN	_	_	_
749	biol	biol	NN	_	_	_
750	rep	rep	NN	GEN	_	_
751	1	1	CD	_	_	_
752	_	_	CD	_	_	_
753	Cy3	cy3	NN	_	_	_
754	20	20	CD	_	_	_
755	Cy5	cy5	NN	_	_	_
756	0	0	CD	_	_	_
757	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
758	Slide	Slide	NNP	_	_	_
759	39	39	CD	_	_	_
760	_	_	SYM	_	_	_
761	Anaerobic	anaerobic	JJ	_	_	_
762	culture	culture	NN	_	_	_
763	_	_	CD	_	_	_
764	CO	CO	NNP	_	_	_
765	gas	gas	NN	_	_	_
766	_	_	NN	_	_	_
767	biol	biol	NN	_	_	_
768	rep	rep	NN	GEN	_	_
769	1	1	CD	_	_	_
770	_	_	CD	_	_	_
771	Cy3	cy3	NN	_	_	_
772	40	40	CD	_	_	_
773	Cy5	cy5	NN	_	_	_
774	0	0	CD	_	_	_
775	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
776	Slide	Slide	NNP	_	_	_
777	39	39	CD	_	_	_
778	_	_	SYM	_	_	_
779	Anaerobic	anaerobic	JJ	_	_	_
780	culture	culture	NN	_	_	_
781	_	_	CD	_	_	_
782	CO	CO	NNP	_	_	_
783	gas	gas	NN	_	_	_
784	_	_	NN	_	_	_
785	biol	biol	NN	_	_	_
786	rep	rep	NN	GEN	_	_
787	1	1	CD	_	_	_
788	_	_	CD	_	_	_
789	Cy3	cy3	NN	_	_	_
790	80	80	CD	_	_	_
791	Cy5	cy5	NN	_	_	_
792	0	0	CD	_	_	_
793	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
794	Slide	Slide	NNP	_	_	_
795	39	39	CD	_	_	_
796	_	_	SYM	_	_	_
797	Anaerobic	anaerobic	JJ	_	_	_
798	culture	culture	NN	_	_	_
799	_	_	CD	_	_	_
800	CO	CO	NNP	_	_	_
801	gas	gas	NN	_	_	_
802	_	_	NN	_	_	_
803	biol	biol	NN	_	_	_
804	rep	rep	NN	GEN	_	_
805	2	2	CD	_	_	_
806	_	_	CD	_	_	_
807	Cy3	cy3	NN	_	_	_
808	10	10	CD	_	_	_
809	Cy5	cy5	NN	_	_	_
810	0	0	CD	_	_	_
811	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
812	Slide	Slide	NNP	_	_	_
813	39	39	CD	_	_	_
814	_	_	SYM	_	_	_
815	Anaerobic	anaerobic	JJ	_	_	_
816	culture	culture	NN	_	_	_
817	_	_	CD	_	_	_
818	CO	CO	NNP	_	_	_
819	gas	gas	NN	_	_	_
820	_	_	NN	_	_	_
821	biol	biol	NN	_	_	_
822	rep	rep	NN	GEN	_	_
823	2	2	CD	_	_	_
824	_	_	CD	_	_	_
825	Cy3	cy3	NN	_	_	_
826	20	20	CD	_	_	_
827	Cy5	cy5	NN	_	_	_
828	0	0	CD	_	_	_
829	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
830	Slide	Slide	NNP	_	_	_
831	39	39	CD	_	_	_
832	_	_	SYM	_	_	_
833	Anaerobic	anaerobic	JJ	_	_	_
834	culture	culture	NN	_	_	_
835	_	_	CD	_	_	_
836	CO	CO	NNP	_	_	_
837	gas	gas	NN	_	_	_
838	_	_	NN	_	_	_
839	biol	biol	NN	_	_	_
840	rep	rep	NN	GEN	_	_
841	2	2	CD	_	_	_
842	_	_	CD	_	_	_
843	Cy3	cy3	NN	_	_	_
844	40	40	CD	_	_	_
845	Cy5	cy5	NN	_	_	_
846	0	0	CD	_	_	_
847	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
848	Slide	Slide	NNP	_	_	_
849	39	39	CD	_	_	_
850	_	_	SYM	_	_	_
851	Anaerobic	anaerobic	JJ	_	_	_
852	culture	culture	NN	_	_	_
853	_	_	CD	_	_	_
854	CO	CO	NNP	_	_	_
855	gas	gas	NN	_	_	_
856	_	_	NN	_	_	_
857	biol	biol	NN	_	_	_
858	rep	rep	NN	GEN	_	_
859	2	2	CD	_	_	_
860	_	_	CD	_	_	_
861	Cy3	cy3	NN	_	_	_
862	80	80	CD	_	_	_
863	Cy5	cy5	NN	_	_	_
864	0	0	CD	_	_	_
865	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
866	Slide	Slide	NNP	_	_	_
867	53	53	CD	_	_	_
868	_	_	SYM	_	_	_
869	Anaerobic	anaerobic	JJ	_	_	_
870	culture	culture	NN	_	_	_
871	_	_	CD	_	_	_
872	CO	CO	NNP	_	_	_
873	gas	gas	NN	_	_	_
874	_	_	NN	_	_	_
875	biol	biol	NN	_	_	_
876	rep	rep	NN	GEN	_	_
877	3	3	CD	_	_	_
878	_	_	NN	_	_	_
879	Cy3	cy3	NN	_	_	_
880	0	0	CD	_	_	_
881	Cy5	cy5	NN	_	_	_
882	2.5	2.5	CD	_	_	_
883	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
884	Slide	Slide	NNP	_	_	_
885	53	53	CD	_	_	_
886	_	_	SYM	_	_	_
887	Anaerobic	anaerobic	JJ	_	_	_
888	culture	culture	NN	_	_	_
889	_	_	CD	_	_	_
890	CO	CO	NNP	_	_	_
891	gas	gas	NN	_	_	_
892	_	_	NN	_	_	_
893	biol	biol	NN	_	_	_
894	rep	rep	NN	GEN	_	_
895	3	3	CD	_	_	_
896	_	_	NN	_	_	_
897	Cy3	cy3	NN	_	_	_
898	0	0	CD	_	_	_
899	Cy5	cy5	NN	_	_	_
900	5	5	CD	_	_	_
901	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
902	Slide	Slide	NNP	_	_	_
903	53	53	CD	_	_	_
904	_	_	SYM	_	_	_
905	Anaerobic	anaerobic	JJ	_	_	_
906	culture	culture	NN	_	_	_
907	_	_	CD	_	_	_
908	CO	CO	NNP	_	_	_
909	gas	gas	NN	_	_	_
910	_	_	NN	_	_	_
911	biol	biol	NN	_	_	_
912	rep	rep	NN	GEN	_	_
913	3	3	CD	_	_	_
914	_	_	NN	_	_	_
915	Cy3	cy3	NN	_	_	_
916	40	40	CD	_	_	_
917	Cy5	cy5	NN	_	_	_
918	0	0	CD	_	_	_
919	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
920	Slide	Slide	NNP	_	_	_
921	53	53	CD	_	_	_
922	_	_	SYM	_	_	_
923	Anaerobic	anaerobic	JJ	_	_	_
924	culture	culture	NN	_	_	_
925	_	_	CD	_	_	_
926	CO	CO	NNP	_	_	_
927	gas	gas	NN	_	_	_
928	_	_	NN	_	_	_
929	biol	biol	NN	_	_	_
930	rep	rep	NN	GEN	_	_
931	3	3	CD	_	_	_
932	_	_	NN	_	_	_
933	Cy3	cy3	NN	_	_	_
934	80	80	CD	_	_	_
935	Cy5	cy5	NN	_	_	_
936	0	0	CD	_	_	_
937	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
938	Slide	Slide	NNP	_	_	_
939	55	55	CD	_	_	_
940	_	_	SYM	_	_	_
941	Anaerobic	anaerobic	JJ	_	_	_
942	culture	culture	NN	_	_	_
943	_	_	CD	_	_	_
944	CO	CO	NNP	_	_	_
945	gas	gas	NN	_	_	_
946	_	_	NN	_	_	_
947	biol	biol	NN	_	_	_
948	rep	rep	NN	GEN	_	_
949	3	3	CD	_	_	_
950	_	_	NN	_	_	_
951	Cy3	cy3	NN	_	_	_
952	0	0	CD	_	_	_
953	Cy5	cy5	NN	_	_	_
954	10	10	CD	_	_	_
955	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
956	Slide	Slide	NNP	_	_	_
957	55	55	CD	_	_	_
958	_	_	SYM	_	_	_
959	Anaerobic	anaerobic	JJ	_	_	_
960	culture	culture	NN	_	_	_
961	_	_	CD	_	_	_
962	CO	CO	NNP	_	_	_
963	gas	gas	NN	_	_	_
964	_	_	NN	_	_	_
965	biol	biol	NN	_	_	_
966	rep	rep	NN	GEN	_	_
967	3	3	CD	_	_	_
968	_	_	NN	_	_	_
969	Cy3	cy3	NN	_	_	_
970	0	0	CD	_	_	_
971	Cy5	cy5	NN	_	_	_
972	10	10	CD	_	_	_
973	2	2	CD	_	_	_
974	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
975	Slide	Slide	NNP	_	_	_
976	55	55	CD	_	_	_
977	_	_	SYM	_	_	_
978	Anaerobic	anaerobic	JJ	_	_	_
979	culture	culture	NN	_	_	_
980	_	_	CD	_	_	_
981	CO	CO	NNP	_	_	_
982	gas	gas	NN	_	_	_
983	_	_	NN	_	_	_
984	biol	biol	NN	_	_	_
985	rep	rep	NN	GEN	_	_
986	3	3	CD	_	_	_
987	_	_	NN	_	_	_
988	Cy3	cy3	NN	_	_	_
989	0	0	CD	_	_	_
990	Cy5	cy5	NN	_	_	_
991	20	20	CD	_	_	_
992	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
993	Slide	Slide	NNP	_	_	_
994	55	55	CD	_	_	_
995	_	_	SYM	_	_	_
996	Anaerobic	anaerobic	JJ	_	_	_
997	culture	culture	NN	_	_	_
998	_	_	CD	_	_	_
999	CO	CO	NNP	_	_	_
1000	gas	gas	NN	_	_	_
1001	_	_	NN	_	_	_
1002	biol	biol	NN	_	_	_
1003	rep	rep	NN	GEN	_	_
1004	3	3	CD	_	_	_
1005	_	_	NN	_	_	_
1006	Cy3	cy3	NN	_	_	_
1007	0	0	CD	_	_	_
1008	Cy5	cy5	NN	_	_	_
1009	2.5	2.5	CD	_	_	_
1010	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1011	Slide	Slide	NNP	_	_	_
1012	55	55	CD	_	_	_
1013	_	_	SYM	_	_	_
1014	Anaerobic	anaerobic	JJ	_	_	_
1015	culture	culture	NN	_	_	_
1016	_	_	CD	_	_	_
1017	CO	CO	NNP	_	_	_
1018	gas	gas	NN	_	_	_
1019	_	_	NN	_	_	_
1020	biol	biol	NN	_	_	_
1021	rep	rep	NN	GEN	_	_
1022	3	3	CD	_	_	_
1023	_	_	NN	_	_	_
1024	Cy3	cy3	NN	_	_	_
1025	0	0	CD	_	_	_
1026	Cy5	cy5	NN	_	_	_
1027	40	40	CD	_	_	_
1028	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1029	Slide	slide	NN	_	_	_
1030	55	55	CD	_	_	_
1031	_	_	SYM	_	_	_
1032	Anaerobic	anaerobic	JJ	_	_	_
1033	culture	culture	NN	_	_	_
1034	_	_	CD	_	_	_
1035	CO	CO	NNP	_	_	_
1036	gas	gas	NN	_	_	_
1037	_	_	NN	_	_	_
1038	biol	biol	NN	_	_	_
1039	rep	rep	NN	GEN	_	_
1040	3	3	CD	_	_	_
1041	_	_	NN	_	_	_
1042	Cy3	cy3	NN	_	_	_
1043	0	0	CD	_	_	_
1044	Cy5	cy5	NN	_	_	_
1045	5	5	CD	_	_	_
1046	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1047	Slide	Slide	NNP	_	_	_
1048	55	55	CD	_	_	_
1049	_	_	SYM	_	_	_
1050	Anaerobic	anaerobic	JJ	_	_	_
1051	culture	culture	NN	_	_	_
1052	_	_	CD	_	_	_
1053	CO	CO	NNP	_	_	_
1054	gas	gas	NN	_	_	_
1055	_	_	NN	_	_	_
1056	biol	biol	NN	_	_	_
1057	rep	rep	NN	GEN	_	_
1058	3	3	CD	_	_	_
1059	_	_	NN	_	_	_
1060	Cy3	cy3	NN	_	_	_
1061	2.5	2.5	CD	_	_	_
1062	Cy5	cy5	NN	_	_	_
1063	0	0	CD	_	_	_
1064	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1065	Slide	Slide	NNP	_	_	_
1066	55	55	CD	_	_	_
1067	_	_	SYM	_	_	_
1068	Anaerobic	anaerobic	JJ	_	_	_
1069	culture	culture	NN	_	_	_
1070	_	_	CD	_	_	_
1071	CO	CO	NNP	_	_	_
1072	gas	gas	NN	_	_	_
1073	_	_	NN	_	_	_
1074	biol	biol	NN	_	_	_
1075	rep	rep	NN	GEN	_	_
1076	3	3	CD	_	_	_
1077	_	_	NN	_	_	_
1078	Cy3	cy3	NN	_	_	_
1079	5	5	CD	_	_	_
1080	Cy5	cy5	NN	_	_	_
1081	0	0	CD	_	_	_
1082	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1083	Slide	Slide	NNP	_	_	_
1084	56	56	CD	_	_	_
1085	_	_	SYM	_	_	_
1086	Anaerobic	anaerobic	JJ	_	_	_
1087	culture	culture	NN	_	_	_
1088	_	_	CD	_	_	_
1089	CO	CO	NNP	_	_	_
1090	gas	gas	NN	_	_	_
1091	_	_	NN	_	_	_
1092	biol	biol	NN	_	_	_
1093	rep	rep	NN	GEN	_	_
1094	1	1	CD	_	_	_
1095	_	_	NN	_	_	_
1096	Cy3	cy3	NN	_	_	_
1097	0	0	CD	_	_	_
1098	Cy5	cy5	NN	_	_	_
1099	10	10	CD	_	_	_
1100	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1101	Slide	Slide	NNP	_	_	_
1102	56	56	CD	_	_	_
1103	_	_	SYM	_	_	_
1104	Anaerobic	anaerobic	JJ	_	_	_
1105	culture	culture	NN	_	_	_
1106	_	_	CD	_	_	_
1107	CO	CO	NNP	_	_	_
1108	gas	gas	NN	_	_	_
1109	_	_	NN	_	_	_
1110	biol	biol	NN	_	_	_
1111	rep	rep	NN	GEN	_	_
1112	1	1	CD	_	_	_
1113	_	_	NN	_	_	_
1114	Cy3	cy3	NN	_	_	_
1115	0	0	CD	_	_	_
1116	Cy5	cy5	NN	_	_	_
1117	20	20	CD	_	_	_
1118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1119	Slide	slide	NN	_	_	_
1120	56	56	CD	_	_	_
1121	_	_	SYM	_	_	_
1122	Anaerobic	anaerobic	JJ	_	_	_
1123	culture	culture	NN	_	_	_
1124	_	_	CD	_	_	_
1125	CO	CO	NNP	_	_	_
1126	gas	gas	NN	_	_	_
1127	_	_	NN	_	_	_
1128	biol	biol	NN	_	_	_
1129	rep	rep	NN	GEN	_	_
1130	1	1	CD	_	_	_
1131	_	_	NN	_	_	_
1132	Cy3	cy3	NN	_	_	_
1133	0	0	CD	_	_	_
1134	Cy5	cy5	NN	_	_	_
1135	2.5	2.5	CD	_	_	_
1136	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1137	Slide	Slide	NNP	_	_	_
1138	56	56	CD	_	_	_
1139	_	_	SYM	_	_	_
1140	Anaerobic	anaerobic	JJ	_	_	_
1141	culture	culture	NN	_	_	_
1142	_	_	CD	_	_	_
1143	CO	CO	NNP	_	_	_
1144	gas	gas	NN	_	_	_
1145	_	_	NN	_	_	_
1146	biol	biol	NN	_	_	_
1147	rep	rep	NN	GEN	_	_
1148	1	1	CD	_	_	_
1149	_	_	NN	_	_	_
1150	Cy3	cy3	NN	_	_	_
1151	0	0	CD	_	_	_
1152	Cy5	cy5	NN	_	_	_
1153	40	40	CD	_	_	_
1154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1155	Slide	slide	NN	_	_	_
1156	56	56	CD	_	_	_
1157	_	_	SYM	_	_	_
1158	Anaerobic	anaerobic	JJ	_	_	_
1159	culture	culture	NN	_	_	_
1160	_	_	CD	_	_	_
1161	CO	CO	NNP	_	_	_
1162	gas	gas	NN	_	_	_
1163	_	_	NN	_	_	_
1164	biol	biol	NN	_	_	_
1165	rep	rep	NN	GEN	_	_
1166	1	1	CD	_	_	_
1167	_	_	NN	_	_	_
1168	Cy3	cy3	NN	_	_	_
1169	0	0	CD	_	_	_
1170	Cy5	cy5	NN	_	_	_
1171	5	5	CD	_	_	_
1172	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1173	Slide	Slide	NNP	_	_	_
1174	56	56	CD	_	_	_
1175	_	_	SYM	_	_	_
1176	Anaerobic	anaerobic	JJ	_	_	_
1177	culture	culture	NN	_	_	_
1178	_	_	CD	_	_	_
1179	CO	CO	NNP	_	_	_
1180	gas	gas	NN	_	_	_
1181	_	_	NN	_	_	_
1182	biol	biol	NN	_	_	_
1183	rep	rep	NN	GEN	_	_
1184	1	1	CD	_	_	_
1185	_	_	NN	_	_	_
1186	Cy3	cy3	NN	_	_	_
1187	0	0	CD	_	_	_
1188	Cy5	cy5	NN	_	_	_
1189	80	80	CD	_	_	_
1190	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1191	Slide	Slide	NNP	_	_	_
1192	56	56	CD	_	_	_
1193	_	_	SYM	_	_	_
1194	Anaerobic	anaerobic	JJ	_	_	_
1195	culture	culture	NN	_	_	_
1196	_	_	CD	_	_	_
1197	CO	CO	NNP	_	_	_
1198	gas	gas	NN	_	_	_
1199	_	_	NN	_	_	_
1200	biol	biol	NN	_	_	_
1201	rep	rep	NN	GEN	_	_
1202	1	1	CD	_	_	_
1203	_	_	CD	_	_	_
1204	Cy3	cy3	NN	_	_	_
1205	2.5	2.5	CD	_	_	_
1206	Cy5	cy5	NN	_	_	_
1207	0	0	CD	_	_	_
1208	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1209	Slide	Slide	NNP	_	_	_
1210	56	56	CD	_	_	_
1211	_	_	SYM	_	_	_
1212	Anaerobic	anaerobic	JJ	_	_	_
1213	culture	culture	NN	_	_	_
1214	_	_	CD	_	_	_
1215	CO	CO	NNP	_	_	_
1216	gas	gas	NN	_	_	_
1217	_	_	NN	_	_	_
1218	biol	biol	NN	_	_	_
1219	rep	rep	NN	GEN	_	_
1220	1	1	CD	_	_	_
1221	_	_	CD	_	_	_
1222	Cy3	cy3	NN	_	_	_
1223	5	5	CD	_	_	_
1224	Cy5	cy5	NN	_	_	_
1225	0	0	CD	_	_	_
1226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1227	strain	strain	NN	_	_	_
1228	:	:	:	_	_	_
1229	Wild	Wild	NNP	_	_	_
1230	type	type	NN	_	_	_
1231	strain	strain	NN	_	_	_
1232	MG1655	mg1655	NN	_	_	_
1233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1234	time	time	NN	_	_	_
1235	:	:	:	_	_	_
1236	10	10	CD	_	_	_
1237	min	min	NN	_	_	_
1238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1239	time	time	NN	_	_	_
1240	:	:	:	_	_	_
1241	10	10	CD	_	_	_
1242	min	min	NN	_	_	_
1243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1244	time	time	NN	_	_	_
1245	:	:	:	_	_	_
1246	20	20	CD	_	_	_
1247	min	min	NN	_	_	_
1248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1249	time	time	NN	_	_	_
1250	:	:	:	_	_	_
1251	2.5	2.5	CD	_	_	_
1252	min	min	NN	_	_	_
1253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1254	time	time	NN	_	_	_
1255	:	:	:	_	_	_
1256	40	40	CD	_	_	_
1257	min	min	NN	_	_	_
1258	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1259	time	time	NN	_	_	_
1260	:	:	:	_	_	_
1261	5	5	CD	_	_	_
1262	min	min	NN	_	_	_
1263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1264	time	time	NN	_	_	_
1265	:	:	:	_	_	_
1266	80	80	CD	_	_	_
1267	min	min	NN	_	_	_
1268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1269	Total	total	JJ	_	_	_
1270	RNA	rna	NN	_	_	_
1271	extracted	extract	VBN	_	_	_
1272	using	use	VBG	_	_	_
1273	Trizol	Trizol	NNP	_	_	_
1274	following	follow	VBG	_	_	_
1275	manufacturer	manufacturer	NN	_	_	_
1276	's	's	POS	_	_	_
1277	instructions	instruction	NNS	_	_	_
1278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1279	treatment	treatment	NN	_	_	_
1280	:	:	:	_	_	_
1281	Continuous	continuous	JJ	_	_	_
1282	aerobically	aerobically	RB	_	_	_
1283	grown	grow	VBN	_	_	_
1284	cultures	culture	NNS	_	_	_
1285	in	in	IN	_	_	_
1286	Evans	Evans	NNP	_	_	_
1287	medium	medium	NN	_	_	_
1288	,	,	,	_	_	_
1289	exposed	expose	VBN	_	_	_
1290	to	to	TO	_	_	_
1291	0.1	0.1	CD	_	_	_
1292	L	l	NN	_	_	_
1293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1294	treatment	treatment	NN	_	_	_
1295	:	:	:	_	_	_
1296	Continuous	continuous	JJ	_	_	_
1297	aerobically	aerobically	RB	_	_	_
1298	grown	grow	VBN	_	_	_
1299	cultures	culture	NNS	_	_	_
1300	in	in	IN	_	_	_
1301	Evans	Evans	NNP	_	_	_
1302	medium	medium	NN	_	_	_
1303	,	,	,	_	_	_
1304	exposed	expose	VBN	_	_	_
1305	to	to	TO	_	_	_
1306	40uM	40um	NN	_	_	_
1307	CORM-3	corm-3	NN	_	_	_
1308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1309	treatment	treatment	NN	_	_	_
1310	:	:	:	_	_	_
1311	Continuous	continuous	JJ	_	_	_
1312	aerobically	aerobically	RB	_	_	_
1313	grown	grow	VBN	_	_	_
1314	cultures	culture	NNS	_	_	_
1315	in	in	IN	_	_	_
1316	Evans	Evans	NNP	_	_	_
1317	medium	medium	NN	_	_	_
1318	,	,	,	_	_	_
1319	exposed	expose	VBN	_	_	_
1320	to	to	TO	_	_	_
1321	40uM	40um	NN	_	_	_
1322	iCORM-3	icorm-3	NN	_	_	_
1323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1324	treatment	treatment	NN	_	_	_
1325	:	:	:	_	_	_
1326	Continuous	continuous	JJ	_	_	_
1327	anaerobically	anaerobically	RB	_	_	_
1328	grown	grow	VBN	_	_	_
1329	cultures	culture	NNS	_	_	_
1330	in	in	IN	_	_	_
1331	Evans	Evans	NNP	_	_	_
1332	medium	medium	NN	_	_	_
1333	,	,	,	_	_	_
1334	exposed	expose	VBN	_	_	_
1335	to	to	TO	_	_	_
1336	40uM	40um	NN	_	_	_
1337	CORM-3	corm-3	NN	_	_	_
1338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1339	treatment	treatment	NN	_	_	_
1340	:	:	:	_	_	_
1341	Continuous	continuous	JJ	_	_	_
1342	anaerobically	anaerobically	RB	_	_	_
1343	grown	grow	VBN	_	_	_
1344	cultures	culture	NNS	_	_	_
1345	in	in	IN	_	_	_
1346	Evans	Evans	NNP	_	_	_
1347	medium	medium	NN	_	_	_
1348	,	,	,	_	_	_
1349	exposed	expose	VBN	_	_	_
1350	to	to	TO	_	_	_
1351	CO	CO	NNP	_	_	_
1352	gas	gas	NN	_	_	_
1353	at	at	IN	_	_	_
1354	0.1	0.1	CD	_	_	_
1355	L	l	NN	_	_	_
1356	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1357	E.coli	e.coli	NNS	_	_	_
1358	,	,	,	_	_	_
1359	grown	grow	VBN	_	_	_
1360	in	in	IN	_	_	_
1361	LB	lb	NN	_	_	_
1362	+	+	CC	_	_	_
1363	glycerol	glycerol	NN	SUPP	_	_
1364	to	to	TO	_	_	_
1365	0.8	0.8	CD	_	_	_
1366	OD	od	NN	_	_	_
1367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1368	E.coli	e.coli	NNS	_	_	_
1369	,	,	,	_	_	_
1370	grown	grow	VBN	_	_	_
1371	in	in	IN	_	_	_
1372	LB	lb	NN	_	_	_
1373	to	to	TO	_	_	_
1374	0.8	0.8	CD	_	_	_
1375	OD	od	NN	_	_	_
1376	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1377	Escherichia	escherichia	FW	Organism	_	_
1378	coli	coli	FW	Organism	_	_
1379	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1380	Escherichia	escherichia	FW	Organism	_	_
1381	coli	coli	FW	Organism	_	_
1382	was	be	VBD	_	_	_
1383	grown	grow	VBN	_	_	_
1384	aerobically	aerobically	RB	_	_	_
1385	in	in	IN	_	_	_
1386	Luria-Bertani	Luria-Bertani	NNP	_	_	_
1387	-LRB-	-lrb-	-LRB-	_	_	_
1388	LB	LB	NNP	_	_	_
1389	-RRB-	-rrb-	-RRB-	_	_	_
1390	broth	broth	NN	_	_	_
1391	and	and	CC	_	_	_
1392	LB	lb	NN	_	_	_
1393	+	+	CC	_	_	_
1394	glycerol	glycerol	NN	SUPP	_	_
1395	at	at	IN	_	_	_
1396	30	30	CD	_	_	_
1397	°C	°c	NN	_	_	_
1398	in	in	IN	_	_	_
1399	an	a	DT	_	_	_
1400	incubator	incubator	NN	_	_	_
1401	shaker	shaker	NN	_	_	_
1402	at	at	IN	_	_	_
1403	150	150	CD	_	_	_
1404	r.p.m.	r.p.m.	NN	_	_	_
1405	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1406	growth	growth	NN	_	_	_
1407	protocol	protocol	NN	_	_	_
1408	:	:	:	_	_	_
1409	grown	grow	VBN	_	_	_
1410	in	in	IN	_	_	_
1411	LB	lb	NN	_	_	_
1412	+	+	CC	_	_	_
1413	glycerol	glycerol	NN	SUPP	_	_
1414	to	to	TO	_	_	_
1415	0.8	0.8	CD	_	_	_
1416	OD	od	NN	_	_	_
1417	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1418	growth	growth	NN	_	_	_
1419	protocol	protocol	NN	_	_	_
1420	:	:	:	_	_	_
1421	grown	grow	VBN	_	_	_
1422	in	in	IN	_	_	_
1423	LB	lb	NN	_	_	_
1424	to	to	TO	_	_	_
1425	0.8	0.8	CD	_	_	_
1426	OD	od	NN	_	_	_
1427	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1428	LB	lb	NN	_	_	_
1429	,	,	,	_	_	_
1430	biological	biological	JJ	_	_	_
1431	rep1	rep1	NN	_	_	_
1432	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1433	LB	lb	NN	_	_	_
1434	,	,	,	_	_	_
1435	biological	biological	JJ	_	_	_
1436	rep2	rep2	NN	_	_	_
1437	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1438	LB	lb	NN	_	_	_
1439	,	,	,	_	_	_
1440	biological	biological	JJ	_	_	_
1441	rep3	rep3	NN	_	_	_
1442	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1443	LB	lb	NN	_	_	_
1444	+	+	CC	_	_	_
1445	glycerol	glycerol	NN	SUPP	_	_
1446	,	,	,	_	_	_
1447	biological	biological	JJ	_	_	_
1448	rep1	rep1	NN	_	_	_
1449	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1450	LB	lb	NN	_	_	_
1451	+	+	CC	_	_	_
1452	glycerol	glycerol	NN	SUPP	_	_
1453	,	,	,	_	_	_
1454	biological	biological	JJ	_	_	_
1455	rep2	rep2	NN	_	_	_
1456	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1457	LB	lb	NN	_	_	_
1458	+	+	CC	_	_	_
1459	glycerol	glycerol	NN	SUPP	_	_
1460	,	,	,	_	_	_
1461	biological	biological	JJ	_	_	_
1462	rep3	rep3	NN	_	_	_
1463	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1464	RNA	rna	NN	_	_	_
1465	was	be	VBD	_	_	_
1466	isolated	isolate	VBN	_	_	_
1467	from	from	IN	_	_	_
1468	the	the	DT	_	_	_
1469	culture	culture	NN	_	_	_
1470	by	by	IN	_	_	_
1471	using	use	VBG	_	_	_
1472	the	the	DT	_	_	_
1473	Qiagen	Qiagen	NNP	_	_	_
1474	RNeasy	RNeasy	NNP	_	_	_
1475	mini-prep	mini-prep	NN	_	_	_
1476	kit.cDNA	kit.cdna	NN	_	_	_
1477	was	be	VBD	_	_	_
1478	synthesized	synthesize	VBN	_	_	_
1479	using	use	VBG	_	_	_
1480	5-10	5-10	CD	_	_	_
1481	µg	µg	NN	_	_	_
1482	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1483	The	the	DT	_	_	_
1484	intensity	intensity	NN	_	_	_
1485	cell	cell	NN	_	_	_
1486	files	file	NNS	_	_	_
1487	were	be	VBD	_	_	_
1488	then	then	RB	_	_	_
1489	imported	import	VBN	_	_	_
1490	,	,	,	_	_	_
1491	normalized	normalize	VBN	_	_	_
1492	for	for	IN	_	_	_
1493	background	background	NN	_	_	_
1494	correction	correction	NN	_	_	_
1495	-LRB-	-lrb-	-LRB-	_	_	_
1496	used	use	VBN	_	_	_
1497	RMA	rma	NN	_	_	_
1498	for	for	IN	_	_	_
1499	normalization	normalization	NN	_	_	_
1500	-RRB-	-rrb-	-RRB-	_	_	_
1501	and	and	CC	_	_	_
1502	data	datum	NNS	_	_	_
1503	analysed	analyse	VBN	_	_	_
1504	using	use	VBG	_	_	_
1505	Gene	Gene	NNP	_	_	_
1506	Spring	Spring	NNP	_	_	_
1507	11.5	11.5	CD	_	_	_
1508	software	software	NN	_	_	_
1509	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	To	to	TO	_	_	_
3	study	study	VB	_	_	_
4	gene	gene	NN	_	_	_
5	expression	expression	NN	_	_	_
6	,	,	,	_	_	_
7	28	28	CD	_	_	_
8	days	day	NNS	_	_	_
9	old	old	JJ	_	_	_
10	E.coli	e.coli	NN	_	_	_
11	cells	cell	NNS	_	_	_
12	were	be	VBD	_	_	_
13	grown	grow	VBN	_	_	_
14	in	in	IN	_	_	_
15	the	the	DT	_	_	_
16	presence	presence	NN	_	_	_
17	of	of	IN	_	_	_
18	LB	lb	NN	MED	_	_
19	broth	broth	NN	MED	_	_
20	and	and	CC	_	_	_
21	LB	lb	NN	MED	_	_
22	broth	broth	NN	MED	_	_
23	supplemented	supplement	VBN	_	_	_
24	with	with	IN	_	_	_
25	10	10	CD	_	_	_
26	%	%	NN	_	_	_
27	v	v	LS	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
29	chip	chip	NN	_	_	_
30	antibody	antibody	NN	_	_	_
31	:	:	:	_	_	_
32	anti-FLAG	anti-flag	JJ	_	_	_
33	antibody	antibody	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Sigma	Sigma	NNP	_	_	_
36	Cat	Cat	NNP	_	_	_
37	#	#	#	_	_	_
38	:	:	:	_	_	_
39	F3165-1MG	f3165-1mg	NN	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	chip	chip	NN	_	_	_
43	antibody	antibody	NN	_	_	_
44	:	:	:	_	_	_
45	none	none	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	ChIP	chip	NN	_	_	_
48	_	_	CD	_	_	_
49	hns-F	hns-f	NN	_	_	_
50	_	_	SYM	_	_	_
51	bcm	bcm	SYM	_	_	_
52	-	-	:	_	_	_
53	#	#	#	_	_	_
54	1	1	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	ChIP	chip	NN	_	_	_
57	_	_	CD	_	_	_
58	hns-F	hns-f	NN	_	_	_
59	_	_	CD	_	_	_
60	bcm	bcm	NN	_	_	_
61	+	+	CC	_	_	_
62	#	#	#	_	_	_
63	1	1	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	ChIP	chip	NN	_	_	_
66	_	_	CD	_	_	_
67	hns-F	hns-f	NN	_	_	_
68	_	_	SYM	_	_	_
69	bcm	bcm	SYM	_	_	_
70	-	-	:	_	_	_
71	#	#	#	_	_	_
72	2	2	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
74	ChIP	chip	NN	_	_	_
75	_	_	SYM	_	_	_
76	hns-F	hns-f	JJ	_	_	_
77	_	_	NN	_	_	_
78	bcm	bcm	NN	_	_	_
79	+	+	CC	_	_	_
80	#	#	#	_	_	_
81	2	2	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
83	ChIP-Seq	chip-seq	JJ	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	consensus	consensus	NN	_	_	_
86	binding	binding	NN	_	_	_
87	regions	region	NNS	_	_	_
88	were	be	VBD	_	_	_
89	obtained	obtain	VBN	_	_	_
90	as	as	IN	_	_	_
91	the	the	DT	_	_	_
92	portion	portion	NN	_	_	_
93	which	which	WDT	_	_	_
94	was	be	VBD	_	_	_
95	covered	cover	VBN	_	_	_
96	by	by	IN	_	_	_
97	replicate	replicate	VB	_	_	_
98	samples	sample	NNS	_	_	_
99	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
100	Escherichia	escherichia	FW	Organism	_	_
101	coli	coli	FW	Organism	_	_
102	str	str	FW	_	_	_
103	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	For	for	IN	_	_	_
4	each	each	DT	_	_	_
5	co-ordinate	co-ordinate	JJ	_	_	_
6	coverage	coverage	NN	_	_	_
7	was	be	VBD	_	_	_
8	calculated	calculate	VBN	_	_	_
9	as	as	IN	_	_	_
10	the	the	DT	_	_	_
11	number	number	NN	_	_	_
12	of	of	IN	_	_	_
13	reads	read	VBZ	_	_	_
14	which	which	WDT	_	_	_
15	was	be	VBD	_	_	_
16	aligned	align	VBN	_	_	_
17	againist	againist	IN	_	_	_
18	the	the	DT	_	_	_
19	position	position	NN	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	coverage	coverage	NN	_	_	_
3	was	be	VBD	_	_	_
4	normalized	normalize	VBN	_	_	_
5	and	and	CC	_	_	_
6	converted	convert	VBN	_	_	_
7	into	into	IN	_	_	_
8	a	a	DT	_	_	_
9	z	z	SYM	_	_	_
10	score	score	NN	_	_	_
11	.	.	.	_	_	_

1	Z	z	NN	_	_	_
2	score	score	NN	_	_	_
3	threshold	threshold	NN	_	_	_
4	of	of	IN	_	_	_
5	12	12	CD	_	_	_
6	was	be	VBD	_	_	_
7	selected	select	VBN	_	_	_
8	to	to	TO	_	_	_
9	identify	identify	VB	_	_	_
10	H-NS	h-ns	NN	_	_	_
11	binding	binding	NN	_	_	_
12	regions	region	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	genome	genome	NN	_	_	_
3	build	build	VB	_	_	_
4	:	:	:	_	_	_
5	ASM584v1	asm584v1	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	H-NS	h-ns	NN	_	_	_
8	flag	flag	NN	_	_	_
9	tagged	tag	VBD	_	_	_
10	cells	cell	NNS	_	_	_
11	with	with	IN	_	_	_
12	bcm	bcm	NN	_	_	_
13	treatment	treatment	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	H-NS	h-ns	NN	_	_	_
16	flag	flag	NN	_	_	_
17	tagged	tag	VBD	_	_	_
18	cells	cell	NNS	_	_	_
19	without	without	IN	_	_	_
20	bcm	bcm	NN	_	_	_
21	treatment	treatment	NN	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	Input	Input	NNP	_	_	_
24	_	_	SYM	_	_	_
25	hns-F	hns-f	JJ	_	_	_
26	_	_	NN	_	_	_
27	bcm	bcm	NN	_	_	_
28	-	-	:	_	_	_
29	#	#	#	_	_	_
30	1	1	CD	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	Input	Input	NNP	_	_	_
33	_	_	SYM	_	_	_
34	hns-F	hns-f	JJ	_	_	_
35	_	_	NN	_	_	_
36	bcm	bcm	NN	_	_	_
37	+	+	CC	_	_	_
38	#	#	#	_	_	_
39	1	1	CD	_	_	_
40	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
41	Input	Input	NNP	_	_	_
42	_	_	SYM	_	_	_
43	hns-F	hns-f	JJ	_	_	_
44	_	_	NN	_	_	_
45	bcm	bcm	NN	_	_	_
46	-	-	:	_	_	_
47	#	#	#	_	_	_
48	2	2	CD	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	Input	Input	NNP	_	_	_
51	_	_	SYM	_	_	_
52	hns-F	hns-f	JJ	_	_	_
53	_	_	NN	_	_	_
54	bcm	bcm	NN	_	_	_
55	+	+	CC	_	_	_
56	#	#	#	_	_	_
57	2	2	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	MG1655	mg1655	NN	_	_	_
60	hns-FLAG	hns-flag	NN	_	_	_
61	cells	cell	NNS	_	_	_
62	were	be	VBD	_	_	_
63	grown	grow	VBN	_	_	_
64	in	in	IN	_	_	_
65	liquid	liquid	JJ	_	_	_
66	LB	lb	NN	MED	_	_
67	medium	medium	NN	MED	_	_
68	with	with	IN	_	_	_
69	and	and	CC	_	_	_
70	without	without	IN	_	_	_
71	bicyclomycin	bicyclomycin	NN	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	BCM	bcm	NN	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	at	at	IN	_	_	_
76	37	37	CD	_	_	_
77	degree	degree	NN	_	_	_
78	with	with	IN	_	_	_
79	shaking	shake	VBG	_	_	_
80	at	at	IN	_	_	_
81	200rpm	200rpm	JJ	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	reads	read	VBZ	_	_	_
84	aligned	align	VBN	_	_	_
85	to	to	TO	_	_	_
86	the	the	DT	_	_	_
87	reference	reference	NN	_	_	_
88	genome	genome	NN	_	_	_
89	of	of	IN	_	_	_
90	E.	e.	FW	_	_	_
91	coli	coli	FW	_	_	_
92	K-12	k-12	NN	_	_	_
93	Mg1655	mg1655	NN	_	_	_
94	using	use	VBG	_	_	_
95	BWA	BWA	NNP	_	_	_
96	,	,	,	_	_	_
97	with	with	IN	_	_	_
98	quality	quality	NN	_	_	_
99	threshold	threshold	NN	_	_	_
100	of	of	IN	_	_	_
101	20	20	CD	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
103	Reads	read	VBZ	_	_	_
104	mapped	map	VBN	_	_	_
105	to	to	TO	_	_	_
106	more	more	JJR	_	_	_
107	than	than	IN	_	_	_
108	one	one	CD	_	_	_
109	locus	locus	NN	_	_	_
110	were	be	VBD	_	_	_
111	discarded	discard	VBN	_	_	_
112	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	mapped	map	VBN	_	_	_
3	position	position	NN	_	_	_
4	obtained	obtain	VBN	_	_	_
5	from	from	IN	_	_	_
6	the	the	DT	_	_	_
7	SAM	SAM	NNP	_	_	_
8	output	output	NN	_	_	_
9	file	file	NN	_	_	_
10	from	from	IN	_	_	_
11	BWA	bwa	NN	_	_	_
12	lists	list	NNS	_	_	_
13	was	be	VBD	_	_	_
14	taken	take	VBN	_	_	_
15	and	and	CC	_	_	_
16	the	the	DT	_	_	_
17	position	position	NN	_	_	_
18	was	be	VBD	_	_	_
19	extended	extend	VBN	_	_	_
20	to	to	TO	_	_	_
21	280	280	CD	_	_	_
22	bp	bp	NN	_	_	_
23	which	which	WDT	_	_	_
24	is	be	VBZ	_	_	_
25	the	the	DT	_	_	_
26	average	average	JJ	_	_	_
27	length	length	NN	_	_	_
28	of	of	IN	_	_	_
29	DNA	dna	NN	_	_	_
30	fragments	fragment	NNS	_	_	_
31	submitted	submit	VBN	_	_	_
32	for	for	IN	_	_	_
33	sequencing	sequencing	NN	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Standard	Standard	NNP	_	_	_
3	illumina	illumina	NNP	_	_	_
4	library	library	NN	_	_	_
5	construction	construction	NN	_	_	_
6	protocol	protocol	NN	_	_	_
7	for	for	IN	_	_	_
8	ChIP	chip	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	strain	strain	NN	_	_	_
11	:	:	:	_	_	_
12	K-12	k-12	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Supplementary	supplementary	JJ	_	_	_
15	_	_	NN	_	_	_
16	files	file	NNS	_	_	_
17	_	_	IN	_	_	_
18	format	format	NN	_	_	_
19	_	_	NN	_	_	_
20	and	and	CC	_	_	_
21	_	_	NN	_	_	_
22	content	content	NN	_	_	_
23	:	:	:	_	_	_
24	contents	contents	NNS	_	_	_
25	:	:	:	_	_	_
26	reference	reference	NN	_	_	_
27	seq,co-ordinate	seq,co-ordinate	JJ	_	_	_
28	start	start	NN	_	_	_
29	position,co-ordinate	position,co-ordinate	JJ	_	_	_
30	end	end	NN	_	_	_
31	position	position	NN	_	_	_
32	,	,	,	_	_	_
33	counts	count	VBZ	_	_	_
34	for	for	IN	_	_	_
35	the	the	DT	_	_	_
36	position	position	NN	_	_	_
37	,	,	,	_	_	_
38	mapping	map	VBG	_	_	_
39	quality	quality	NN	_	_	_
40	,	,	,	_	_	_
41	strand	strand	NN	_	_	_
42	position	position	NN	_	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	Supplementary	Supplementary	NNP	_	_	_
45	_	_	VBD	_	_	_
46	files	file	NNS	_	_	_
47	_	_	IN	_	_	_
48	format	format	NN	_	_	_
49	_	_	NN	_	_	_
50	and	and	CC	_	_	_
51	_	_	NN	_	_	_
52	content	content	NN	_	_	_
53	:	:	:	_	_	_
54	format	format	NN	_	_	_
55	:	:	:	_	_	_
56	bed	bed	NN	_	_	_
57	format	format	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
59	The	the	DT	_	_	_
60	binding	binding	NN	_	_	_
61	regions	region	NNS	_	_	_
62	were	be	VBD	_	_	_
63	considered	consider	VBN	_	_	_
64	by	by	IN	_	_	_
65	taking	take	VBG	_	_	_
66	into	into	IN	_	_	_
67	account	account	NN	_	_	_
68	base	base	NN	_	_	_
69	position	position	NN	_	_	_
70	with	with	IN	_	_	_
71	z-score	z-score	NN	_	_	_
72	greater	greater	JJR	_	_	_
73	than	than	IN	_	_	_
74	threshold	threshold	NN	_	_	_
75	and	and	CC	_	_	_
76	merging	merge	VBG	_	_	_
77	adjacent	adjacent	JJ	_	_	_
78	binding	binding	NN	_	_	_
79	regions	region	NNS	_	_	_
80	seperated	seperate	VBN	_	_	_
81	by	by	IN	_	_	_
82	a	a	DT	_	_	_
83	distance	distance	NN	_	_	_
84	of	of	IN	_	_	_
85	less	less	JJR	_	_	_
86	than	than	IN	_	_	_
87	200bo	200bo	CD	_	_	_
88	into	into	IN	_	_	_
89	the	the	DT	_	_	_
90	single	single	JJ	_	_	_
91	binding	binding	NN	_	_	_
92	regions	region	NNS	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
94	Two	two	CD	_	_	_
95	biological	biological	JJ	_	_	_
96	replicates	replicate	VBZ	_	_	_
97	were	be	VBD	_	_	_
98	performed	perform	VBN	_	_	_
99	for	for	IN	_	_	_
100	samples	sample	NNS	_	_	_
101	with	with	IN	_	_	_
102	and	and	CC	_	_	_
103	without	without	IN	_	_	_
104	treatment	treatment	NN	_	_	_
105	with	with	IN	_	_	_
106	bicyclomycin	bicyclomycin	NN	_	_	_
107	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	samples	sample	NNS	_	_	_
3	without	without	IN	_	_	_
4	BCM	bcm	NN	_	_	_
5	treatment	treatment	NN	_	_	_
6	,	,	,	_	_	_
7	cells	cell	NNS	_	_	_
8	were	be	VBD	_	_	_
9	grown	grow	VBN	_	_	_
10	OD600	od600	NN	_	_	_
11	≈	≈	NN	_	_	_
12	0.8	0.8	CD	_	_	_
13	at	at	IN	_	_	_
14	370	370	CD	_	_	_
15	with	with	IN	_	_	_
16	shaking	shake	VBG	_	_	_
17	at	at	IN	_	_	_
18	200	200	CD	_	_	_
19	rpm	rpm	NN	_	_	_
20	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	samples	sample	NNS	_	_	_
3	with	with	IN	_	_	_
4	BCM	bcm	NN	_	_	_
5	treatment	treatment	NN	_	_	_
6	,	,	,	_	_	_
7	cells	cell	NNS	_	_	_
8	were	be	VBD	_	_	_
9	grown	grow	VBN	_	_	_
10	to	to	TO	_	_	_
11	early	early	JJ	_	_	_
12	log	log	NN	_	_	_
13	phase	phase	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	O.D.	o.d.	NN	_	_	_
16	600	600	CD	_	_	_
17	=	=	JJ	_	_	_
18	0.1	0.1	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	≈	≈	SYM	_	_	_
21	1h	1h	VBP	_	_	_
22	at	at	IN	_	_	_
23	370	370	CD	_	_	_
24	with	with	IN	_	_	_
25	shaking	shake	VBG	_	_	_
26	at	at	IN	_	_	_
27	200	200	CD	_	_	_
28	rpm	rpm	NN	_	_	_
29	.	.	.	_	_	_

1	BCM	BCM	NNP	_	_	_
2	was	be	VBD	_	_	_
3	added	add	VBN	_	_	_
4	to	to	TO	_	_	_
5	a	a	DT	_	_	_
6	final	final	JJ	_	_	_
7	concentration	concentration	NN	_	_	_
8	of	of	IN	_	_	_
9	25ug	25ug	JJ	_	_	_
10	mL-1	ml-1	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	2xOriT	2xorit	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	A2	a2	NN	_	_	_
15	,	,	,	_	_	_
16	osmotolerant	osmotolerant	JJ	_	_	_
17	mutant	mutant	JJ	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	A2	a2	NN	_	_	_
20	Replicate	replicate	VB	_	_	_
21	1	1	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	A2	a2	NN	_	_	_
24	Replicate	replicate	VB	_	_	_
25	2	2	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	A4	a4	NN	_	_	_
28	,	,	,	_	_	_
29	osmotolerant	osmotolerant	JJ	_	_	_
30	mutant	mutant	JJ	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	A4	a4	NN	_	_	_
33	Replicate	replicate	VB	_	_	_
34	1	1	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	A4	a4	NN	_	_	_
37	Replicate	replicate	VB	_	_	_
38	2	2	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
40	average	average	JJ	_	_	_
41	fitness	fitness	NN	_	_	_
42	:	:	:	_	_	_
43	0.196851676684606	0.196851676684606	CD	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
45	average	average	JJ	_	_	_
46	fitness	fitness	NN	_	_	_
47	:	:	:	_	_	_
48	0.296737932583603	0.296737932583603	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
50	average	average	JJ	_	_	_
51	fitness	fitness	NN	_	_	_
52	:	:	:	_	_	_
53	0.344592279464807	0.344592279464807	CD	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
55	average	average	JJ	_	_	_
56	fitness	fitness	NN	_	_	_
57	:	:	:	_	_	_
58	0.353076289611459	0.353076289611459	CD	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
60	average	average	JJ	_	_	_
61	fitness	fitness	NN	_	_	_
62	:	:	:	_	_	_
63	0.434286415079969	0.434286415079969	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
65	average	average	JJ	_	_	_
66	fitness	fitness	NN	_	_	_
67	:	:	:	_	_	_
68	0.502711019240335	0.502711019240335	CD	_	_	_
69	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
70	Data	datum	NNS	_	_	_
71	were	be	VBD	_	_	_
72	normalized	normalize	VBN	_	_	_
73	using	use	VBG	_	_	_
74	the	the	DT	_	_	_
75	LOWESS	LOWESS	NNP	_	_	_
76	algorithm	algorithm	NN	_	_	_
77	and	and	CC	_	_	_
78	analyzed	analyze	VBN	_	_	_
79	for	for	IN	_	_	_
80	statistical	statistical	JJ	_	_	_
81	significance	significance	NN	_	_	_
82	using	use	VBG	_	_	_
83	the	the	DT	_	_	_
84	MeV	mev	NN	_	_	_
85	package	package	NN	_	_	_
86	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
87	Escherichia	escherichia	FW	Organism	_	_
88	coli	coli	FW	Organism	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	Escherichia	escherichia	FW	Organism	_	_
91	coli	coli	FW	Organism	_	_
92	BW25113	bw25113	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	G2	g2	NN	_	_	_
95	,	,	,	_	_	_
96	osmotolerant	osmotolerant	JJ	_	_	_
97	mutant	mutant	JJ	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	G2	g2	NN	_	_	_
100	Replicate	replicate	VB	_	_	_
101	1	1	CD	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	G2	g2	NN	_	_	_
104	Replicate	replicate	VB	_	_	_
105	2	2	CD	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
107	G3	g3	NN	_	_	_
108	,	,	,	_	_	_
109	osmotolerant	osmotolerant	JJ	_	_	_
110	mutant	mutant	JJ	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	G3	g3	NN	_	_	_
113	Replicate	replicate	VB	_	_	_
114	1	1	CD	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	G3	g3	NN	_	_	_
117	Replicate	replicate	VB	_	_	_
118	2	2	CD	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
120	G5	g5	NN	_	_	_
121	,	,	,	_	_	_
122	osmotolerant	osmotolerant	JJ	_	_	_
123	mutant	mutant	JJ	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	G5	g5	NN	_	_	_
126	Replicate	replicate	VB	_	_	_
127	1	1	CD	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	G5	g5	NN	_	_	_
130	Replicate	replicate	VB	_	_	_
131	2	2	CD	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
133	G6	g6	NN	_	_	_
134	,	,	,	_	_	_
135	osmotolerant	osmotolerant	JJ	_	_	_
136	mutant	mutant	JJ	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	G6	g6	NN	_	_	_
139	Replicate	replicate	VB	_	_	_
140	1	1	CD	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	G6	g6	NN	_	_	_
143	Replicate	replicate	VB	_	_	_
144	2	2	CD	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
146	genotype	genotype	NN	_	_	_
147	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
148	Grown	Grown	NNP	_	_	_
149	in	in	IN	_	_	_
150	glucose	glucose	NN	SUPP	_	_
151	M9	m9	NN	_	_	_
152	media	media	NNS	_	_	_
153	supplemented	supplement	VBN	_	_	_
154	with	with	IN	_	_	_
155	0.55	0.55	CD	_	_	_
156	M	m	NN	_	_	_
157	NaCl	nacl	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	Hfr-2xSFX	hfr-2xsfx	NN	_	_	_
160	-	-	:	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	population	population	NN	_	_	_
163	:	:	:	_	_	_
164	A2	a2	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
166	population	population	NN	_	_	_
167	:	:	:	_	_	_
168	A4	a4	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
170	population	population	NN	_	_	_
171	:	:	:	_	_	_
172	G2	g2	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
174	population	population	NN	_	_	_
175	:	:	:	_	_	_
176	G3	g3	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
178	population	population	NN	_	_	_
179	:	:	:	_	_	_
180	G5	g5	NN	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
182	population	population	NN	_	_	_
183	:	:	:	_	_	_
184	G6	g6	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	Samples	sample	NNS	_	_	_
187	were	be	VBD	_	_	_
188	grown	grow	VBN	_	_	_
189	to	to	TO	_	_	_
190	mid	mid	JJ	GrowthPhase	_	_
191	exponential	exponential	JJ	GrowthPhase	_	_
192	phase	phase	NN	GrowthPhase	_	_
193	-LRB-	-lrb-	-LRB-	_	_	_
194	OD	od	NN	_	_	_
195	approx	approx	RB	_	_	_
196	0.5	0.5	CD	_	_	_
197	-RRB-	-rrb-	-RRB-	_	_	_
198	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	harvested	harvest	VBN	_	_	_
5	with	with	IN	_	_	_
6	rapid	rapid	JJ	_	_	_
7	filtration	filtration	NN	_	_	_
8	and	and	CC	_	_	_
9	resuspended	resuspend	VBN	_	_	_
10	in	in	IN	_	_	_
11	RNALater	rnalater	NN	_	_	_
12	to	to	TO	_	_	_
13	stop	stop	VB	_	_	_
14	RNA	rna	NN	_	_	_
15	degradation	degradation	NN	_	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	Zymo	Zymo	NNP	_	_	_
3	Quick-RNA	quick-rna	NN	_	_	_
4	miniprep	miniprep	NN	_	_	_
5	kit	kit	NN	_	_	_
6	was	be	VBD	_	_	_
7	used	use	VBN	_	_	_
8	to	to	TO	_	_	_
9	extract	extract	VB	_	_	_
10	pure	pure	JJ	_	_	_
11	RNA	rna	NN	_	_	_
12	for	for	IN	_	_	_
13	subsequent	subsequent	JJ	_	_	_
14	analysis	analysis	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	strain	strain	NN	_	_	_
17	description	description	NN	_	_	_
18	:	:	:	_	_	_
19	E.	e.	FW	_	_	_
20	coli	coli	FW	_	_	_
21	BW25113	bw25113	NN	_	_	_
22	with	with	IN	_	_	_
23	an	a	DT	_	_	_
24	integrated	integrate	VBN	_	_	_
25	F	f	NN	_	_	_
26	tra	tra	NN	_	_	_
27	operon	operon	NN	_	_	_
28	at	at	IN	_	_	_
29	the	the	DT	_	_	_
30	trp	trp	NN	_	_	_
31	locus	locus	NN	_	_	_
32	,	,	,	_	_	_
33	plus	plus	CC	_	_	_
34	additional	additional	JJ	_	_	_
35	F	f	NN	_	_	_
36	oriT	orit	NN	_	_	_
37	sequences	sequence	NNS	_	_	_
38	integrated	integrate	VBN	_	_	_
39	at	at	IN	_	_	_
40	mbhA	mbha	NN	_	_	_
41	and	and	CC	_	_	_
42	hyfC	hyfc	NN	GEN	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	strain	strain	NN	_	_	_
45	description	description	NN	_	_	_
46	:	:	:	_	_	_
47	E.	e.	FW	_	_	_
48	coli	coli	FW	_	_	_
49	BW25113	bw25113	NN	_	_	_
50	with	with	IN	_	_	_
51	F	f	NN	_	_	_
52	oriTs	orit	NNS	_	_	_
53	integrated	integrate	VBN	_	_	_
54	at	at	IN	_	_	_
55	mbhA	mbha	NN	_	_	_
56	and	and	CC	_	_	_
57	hyfC	hyfc	NN	GEN	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	strain	strain	NN	_	_	_
60	:	:	:	_	_	_
61	unevolved	unevolved	JJ	_	_	_
62	parent	parent	NN	_	_	_
63	strain	strain	NN	_	_	_
64	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
65	All	All	NNP	_	_	_
66	samples	sample	NNS	_	_	_
67	were	be	VBD	_	_	_
68	extracted	extract	VBN	_	_	_
69	using	use	VBG	_	_	_
70	the	the	DT	_	_	_
71	Qiagen	Qiagen	NNP	_	_	_
72	Rnasey	Rnasey	NNP	_	_	_
73	Mini	Mini	NNP	_	_	_
74	Kit	kit	NN	_	_	_
75	,	,	,	_	_	_
76	following	follow	VBG	_	_	_
77	standard	standard	JJ	_	_	_
78	protocol	protocol	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	cDNA	cdna	NN	_	_	_
81	libraries	library	NNS	_	_	_
82	were	be	VBD	_	_	_
83	constructed	construct	VBN	_	_	_
84	at	at	IN	_	_	_
85	Purdue	Purdue	NNP	_	_	_
86	using	use	VBG	_	_	_
87	an	a	DT	_	_	_
88	adapted	adapt	VBN	_	_	_
89	SOLiD	SOLiD	NNP	_	_	_
90	Total	Total	NNP	_	_	_
91	RNA-Seq	RNA-Seq	NNP	_	_	_
92	Kit	kit	NN	_	_	_
93	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	DNase	dnase	NN	_	_	_
5	I	i	CD	_	_	_
6	digested	digest	VBN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	was	be	VBD	_	_	_
9	fragmented	fragment	VBN	_	_	_
10	by	by	IN	_	_	_
11	RNase	rnase	NN	_	_	_
12	III	iii	CD	_	_	_
13	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	samples	sample	NNS	_	_	_
3	labeled	label	VBN	_	_	_
4	as	as	IN	_	_	_
5	TEX	TEX	NNP	_	_	_
6	were	be	VBD	_	_	_
7	also	also	RB	_	_	_
8	subsequently	subsequently	RB	_	_	_
9	digested	digest	VBN	_	_	_
10	with	with	IN	_	_	_
11	Terminator	Terminator	NNP	_	_	_
12	Exonuclease	Exonuclease	NNP	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	TEX	TEX	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	Pyrophosphate	pyrophosphate	NN	_	_	_
2	groups	group	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	from	from	IN	_	_	_
6	the	the	DT	_	_	_
7	5	5	CD	_	_	_
8	′	′	NN	_	_	_
9	terminus	terminus	NN	_	_	_
10	using	use	VBG	_	_	_
11	tobacco	tobacco	NN	_	_	_
12	acid	acid	NN	_	_	_
13	pyrophosphatase	pyrophosphatase	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	TAP	tap	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	an	a	DT	_	_	_
20	RNA	rna	NN	_	_	_
21	adapter	adapter	NN	_	_	_
22	was	be	VBD	_	_	_
23	ligated	ligate	VBN	_	_	_
24	to	to	TO	_	_	_
25	the	the	DT	_	_	_
26	5	5	CD	_	_	_
27	′	′	NN	_	_	_
28	end	end	NN	_	_	_
29	of	of	IN	_	_	_
30	the	the	DT	_	_	_
31	RNA	rna	NN	_	_	_
32	.	.	.	_	_	_

1	First-strand	first-strand	JJ	_	_	_
2	synthesis	synthesis	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	using	use	VBG	_	_	_
6	standard	standard	JJ	_	_	_
7	SOLiD	solid	NN	_	_	_
8	4	4	CD	_	_	_
9	Total	total	JJ	_	_	_
10	RNA-Seq	rna-seq	NN	_	_	_
11	protocol	protocol	NN	_	_	_
12	.	.	.	_	_	_

1	RNA-seq	rna-seq	NN	_	_	_
2	via	via	IN	_	_	_
3	SOLiD	solid	JJ	_	_	_
4	4	4	CD	_	_	_
5	sequencing	sequencing	NN	_	_	_
6	of	of	IN	_	_	_
7	libraries	library	NNS	_	_	_
8	prepared	prepare	VBN	_	_	_
9	by	by	IN	_	_	_
10	ligation	ligation	NN	_	_	_
11	based	base	VBN	_	_	_
12	chemistry	chemistry	NN	_	_	_
13	to	to	TO	_	_	_
14	provide	provide	VB	_	_	_
15	strand-specific	strand-specific	JJ	_	_	_
16	datasets	dataset	NNS	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	K-12	k-12	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	For	for	IN	_	_	_
7	alignment	alignment	NN	_	_	_
8	of	of	IN	_	_	_
9	the	the	DT	_	_	_
10	SAET	SAET	NNP	_	_	_
11	reads	read	VBZ	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	E.	e.	FW	_	_	_
15	coli	coli	FW	_	_	_
16	MG1655	mg1655	NN	_	_	_
17	reference	reference	NN	_	_	_
18	genome	genome	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	RefSeq	refseq	NN	_	_	_
21	NC	nc	NN	_	_	_
22	_	_	SYM	_	_	_
23	000913	000913	CD	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	,	,	,	_	_	_
26	the	the	DT	_	_	_
27	short	short	JJ	_	_	_
28	read	read	NN	_	_	_
29	alignment	alignment	NN	_	_	_
30	tool	tool	NN	_	_	_
31	Bowtie	Bowtie	NNP	_	_	_
32	ver	ver	NN	_	_	_
33	.	.	.	_	_	_

1	1.8	1.8	CD	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	Langmead	Langmead	NNP	_	_	_
4	,	,	,	_	_	_
5	et	et	FW	_	_	_
6	al.	al.	FW	_	_	_
7	,	,	,	_	_	_
8	PMID	pmid	NN	_	_	_
9	19261174	19261174	CD	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	was	be	VBD	_	_	_
12	utilized	utilize	VBN	_	_	_
13	in	in	IN	_	_	_
14	three	three	CD	_	_	_
15	consecutive	consecutive	JJ	_	_	_
16	passes	pass	NNS	_	_	_
17	for	for	IN	_	_	_
18	each	each	DT	_	_	_
19	sample	sample	NN	_	_	_
20	dataset	dataset	NN	_	_	_
21	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	the	the	DT	_	_	_
3	first	first	JJ	_	_	_
4	pass	pass	NN	_	_	_
5	,	,	,	_	_	_
6	we	we	PRP	_	_	_
7	use	use	VBP	_	_	_
8	paired	paired	JJ	_	_	_
9	end	end	NN	_	_	_
10	color	color	NN	_	_	_
11	space	space	NN	_	_	_
12	mapping	mapping	NN	_	_	_
13	with	with	IN	_	_	_
14	a	a	DT	_	_	_
15	distance	distance	NN	_	_	_
16	cutoff	cutoff	NN	_	_	_
17	of	of	IN	_	_	_
18	350	350	CD	_	_	_
19	bases	basis	NNS	_	_	_
20	between	between	IN	_	_	_
21	read	read	NN	_	_	_
22	mates	mate	NNS	_	_	_
23	.	.	.	_	_	_

1	Bowtie	Bowtie	NNP	_	_	_
2	parameters	parameter	NNS	_	_	_
3	were	be	VBD	_	_	_
4	set	set	VBN	_	_	_
5	to	to	TO	_	_	_
6	include	include	VB	_	_	_
7	only	only	RB	_	_	_
8	perfect	perfect	JJ	_	_	_
9	matches	match	NNS	_	_	_
10	and	and	CC	_	_	_
11	suppress	suppress	VBP	_	_	_
12	reads	read	VBZ	_	_	_
13	that	that	IN	_	_	_
14	map	map	NN	GEN	_	_
15	to	to	TO	_	_	_
16	more	more	JJR	_	_	_
17	than	than	IN	_	_	_
18	one	one	CD	_	_	_
19	genome	genome	NN	_	_	_
20	location	location	NN	_	_	_
21	,	,	,	_	_	_
22	i.e.	i.e.	FW	_	_	_
23	,	,	,	_	_	_
24	uniquely	uniquely	RB	_	_	_
25	mapped	map	VBN	_	_	_
26	reads	read	VBZ	_	_	_
27	are	be	VBP	_	_	_
28	retained	retain	VBN	_	_	_
29	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	practice	practice	NN	_	_	_
3	we	we	PRP	_	_	_
4	found	find	VBD	_	_	_
5	the	the	DT	_	_	_
6	efficiency	efficiency	NN	_	_	_
7	of	of	IN	_	_	_
8	paired	paired	JJ	_	_	_
9	end	end	NN	_	_	_
10	mapping	mapping	NN	_	_	_
11	was	be	VBD	_	_	_
12	between	between	IN	_	_	_
13	3	3	CD	_	_	_
14	and	and	CC	_	_	_
15	10	10	CD	_	_	_
16	%	%	NN	_	_	_
17	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	improve	improve	VB	_	_	_
3	the	the	DT	_	_	_
4	overall	overall	JJ	_	_	_
5	alignment	alignment	NN	_	_	_
6	we	we	PRP	_	_	_
7	mapped	map	VBD	_	_	_
8	the	the	DT	_	_	_
9	orphan	orphan	JJ	_	_	_
10	5	5	CD	_	_	_
11	'	'	''	_	_	_
12	and	and	CC	_	_	_
13	3	3	CD	_	_	_
14	'	'	''	_	_	_
15	end	end	NN	_	_	_
16	reads	read	VBZ	_	_	_
17	in	in	IN	_	_	_
18	two	two	CD	_	_	_
19	additional	additional	JJ	_	_	_
20	passes	pass	NNS	_	_	_
21	with	with	IN	_	_	_
22	Bowtie	Bowtie	NNP	_	_	_
23	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	output	output	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	three	three	CD	_	_	_
6	passes	pass	VBZ	_	_	_
7	through	through	IN	_	_	_
8	Bowtie	Bowtie	NNP	_	_	_
9	was	be	VBD	_	_	_
10	three	three	CD	_	_	_
11	SAM	SAM	NNP	_	_	_
12	files	file	NNS	_	_	_
13	for	for	IN	_	_	_
14	each	each	DT	_	_	_
15	sample	sample	NN	_	_	_
16	.	.	.	_	_	_

1	Overall	overall	RB	_	_	_
2	,	,	,	_	_	_
3	we	we	PRP	_	_	_
4	achieved	achieve	VBD	_	_	_
5	40-60	40-60	CD	_	_	_
6	%	%	NN	_	_	_
7	mapping	mapping	NN	_	_	_
8	efficiency	efficiency	NN	_	_	_
9	with	with	IN	_	_	_
10	this	this	DT	_	_	_
11	three-pass	three-pass	JJ	_	_	_
12	strategy	strategy	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	ASM584v1	asm584v1	NN	_	_	_
7	;	;	:	_	_	_
8	Reference	Reference	NNP	_	_	_
9	genome	genome	NN	_	_	_
10	for	for	IN	_	_	_
11	E.	e.	FW	_	_	_
12	coli	coli	FW	_	_	_
13	MG1655	mg1655	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	RefSeq	refseq	NN	_	_	_
16	NC	nc	NN	_	_	_
17	_	_	SYM	_	_	_
18	000913	000913	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	Paper	Paper	NNP	_	_	_
2	title	title	NN	_	_	_
3	:	:	:	_	_	_
4	Escherichia	escherichia	FW	Organism	_	_
5	coli	coli	FW	Organism	_	_
6	K-12	k-12	NN	_	_	_
7	:	:	:	_	_	_
8	a	a	DT	_	_	_
9	cooperatively	cooperatively	RB	_	_	_
10	developed	develop	VBN	_	_	_
11	annotation	annotation	NN	_	_	_
12	snapshot	snapshot	NN	_	_	_
13	--	--	:	_	_	_
14	2005	2005	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
16	phase	phase	NN	_	_	_
17	of	of	IN	_	_	_
18	growth	growth	NN	_	_	_
19	:	:	:	_	_	_
20	15	15	CD	_	_	_
21	min	min	NN	_	_	_
22	post	post	NN	_	_	_
23	stationary	stationary	JJ	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	phase	phase	NN	_	_	_
26	of	of	IN	_	_	_
27	growth	growth	NN	_	_	_
28	:	:	:	_	_	_
29	180	180	CD	_	_	_
30	min	min	NN	_	_	_
31	post	post	NN	_	_	_
32	stationary	stationary	JJ	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	phase	phase	NN	_	_	_
35	of	of	IN	_	_	_
36	growth	growth	NN	_	_	_
37	:	:	:	_	_	_
38	30	30	CD	_	_	_
39	min	min	NN	_	_	_
40	post	post	NN	_	_	_
41	stationary	stationary	JJ	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	phase	phase	NN	_	_	_
44	of	of	IN	_	_	_
45	growth	growth	NN	_	_	_
46	:	:	:	_	_	_
47	Late	late	JJ	_	_	_
48	log	log	NN	_	_	_
49	phase	phase	NN	_	_	_
50	OD	od	NN	_	_	_
51	1.6	1.6	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	phase	phase	NN	_	_	_
54	of	of	IN	_	_	_
55	growth	growth	NN	_	_	_
56	:	:	:	_	_	_
57	Log	log	VB	_	_	_
58	phase	phase	NN	_	_	_
59	OD	od	NN	_	_	_
60	0.1	0.1	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	phase	phase	NN	_	_	_
63	of	of	IN	_	_	_
64	growth	growth	NN	_	_	_
65	:	:	:	_	_	_
66	Log	log	VB	_	_	_
67	phase	phase	NN	_	_	_
68	OD	od	NN	_	_	_
69	0.2	0.2	CD	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	phase	phase	NN	_	_	_
72	of	of	IN	_	_	_
73	growth	growth	NN	_	_	_
74	:	:	:	_	_	_
75	Log	log	VB	_	_	_
76	phase	phase	NN	_	_	_
77	OD	od	NN	_	_	_
78	0.3	0.3	CD	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	phase	phase	NN	_	_	_
81	of	of	IN	_	_	_
82	growth	growth	NN	_	_	_
83	:	:	:	_	_	_
84	Log	log	VB	_	_	_
85	phase	phase	NN	_	_	_
86	OD	od	NN	_	_	_
87	0.4	0.4	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	phase	phase	NN	_	_	_
90	of	of	IN	_	_	_
91	growth	growth	NN	_	_	_
92	:	:	:	_	_	_
93	Log	log	VB	_	_	_
94	phase	phase	NN	_	_	_
95	OD	od	NN	_	_	_
96	0.8	0.8	CD	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	phase	phase	NN	_	_	_
99	of	of	IN	_	_	_
100	growth	growth	NN	_	_	_
101	:	:	:	_	_	_
102	Log	log	VB	_	_	_
103	phase	phase	NN	_	_	_
104	OD	od	NN	_	_	_
105	1.4	1.4	CD	_	_	_
106	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
107	Prior	prior	RB	_	_	_
108	to	to	TO	_	_	_
109	total	total	JJ	_	_	_
110	RNA	rna	NN	_	_	_
111	extraction	extraction	NN	_	_	_
112	harvested	harvest	VBN	_	_	_
113	bacterial	bacterial	JJ	_	_	_
114	cells	cell	NNS	_	_	_
115	were	be	VBD	_	_	_
116	stored	store	VBN	_	_	_
117	at	at	IN	_	_	_
118	-80.0	-80.0	CD	_	_	_
119	°C	°c	NN	_	_	_
120	in	in	IN	_	_	_
121	an	a	DT	_	_	_
122	equal	equal	JJ	_	_	_
123	volume	volume	NN	_	_	_
124	of	of	IN	_	_	_
125	RNAlater	rnalater	NN	_	_	_
126	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	rna	rna	NN	GEN	_	_
5	treatment	treatment	NN	_	_	_
6	:	:	:	_	_	_
7	no	no	DT	_	_	_
8	RNA	rna	NN	_	_	_
9	treatment	treatment	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	rna	rna	NN	GEN	_	_
12	treatment	treatment	NN	_	_	_
13	:	:	:	_	_	_
14	rRNA	rrna	NN	_	_	_
15	depleted	deplete	VBD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	rna	rna	NN	GEN	_	_
18	treatment	treatment	NN	_	_	_
19	:	:	:	_	_	_
20	rRNA	rrna	NN	_	_	_
21	depleted	deplete	VBN	_	_	_
22	;	;	:	_	_	_
23	Terminal	terminal	JJ	_	_	_
24	Exonuclease	exonuclease	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	rpoS	rpos	NN	GEN	_	_
27	_	_	CD	_	_	_
28	04	04	CD	_	_	_
29	_	_	NN	_	_	_
30	rep1	rep1	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	rpoS	rpos	NN	GEN	_	_
33	_	_	CD	_	_	_
34	04	04	CD	_	_	_
35	_	_	NN	_	_	_
36	rep2	rep2	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	rpoS	rpos	NN	GEN	_	_
39	_	_	CD	_	_	_
40	04	04	CD	_	_	_
41	_	_	SYM	_	_	_
42	TEX	TEX	NNP	_	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	rpoS	rpos	NN	GEN	_	_
45	_	_	CD	_	_	_
46	15	15	CD	_	_	_
47	min	min	NN	_	_	_
48	_	_	CD	_	_	_
49	rep1	rep1	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	rpoS	rpos	NN	GEN	_	_
52	_	_	CD	_	_	_
53	16	16	CD	_	_	_
54	_	_	NN	_	_	_
55	rep1	rep1	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	rpoS	rpos	NN	GEN	_	_
58	_	_	NN	_	_	_
59	180	180	CD	_	_	_
60	min	min	NN	_	_	_
61	_	_	CD	_	_	_
62	rep1	rep1	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	rpoS	rpos	NN	GEN	_	_
65	_	_	CD	_	_	_
66	30	30	CD	_	_	_
67	min	min	NN	_	_	_
68	_	_	CD	_	_	_
69	rep1	rep1	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	rpoS	rpos	NN	GEN	_	_
72	_	_	CD	_	_	_
73	30	30	CD	_	_	_
74	min	min	NN	_	_	_
75	_	_	CD	_	_	_
76	rep2	rep2	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	rpoS	rpos	NN	GEN	_	_
79	_	_	CD	_	_	_
80	30	30	CD	_	_	_
81	min	min	NN	_	_	_
82	_	_	CD	_	_	_
83	TEX	TEX	NNP	_	_	_
84	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
85	Sequence	sequence	NN	_	_	_
86	data	datum	NNS	_	_	_
87	was	be	VBD	_	_	_
88	processed	process	VBN	_	_	_
89	by	by	IN	_	_	_
90	conversion	conversion	NN	_	_	_
91	of	of	IN	_	_	_
92	the	the	DT	_	_	_
93	sample	sample	NN	_	_	_
94	alignment	alignment	NN	_	_	_
95	-LRB-	-lrb-	-LRB-	_	_	_
96	BAM	bam	NN	_	_	_
97	-RRB-	-rrb-	-RRB-	_	_	_
98	files	file	VBZ	_	_	_
99	to	to	TO	_	_	_
100	strand-specific	strand-specific	JJ	_	_	_
101	base	base	NN	_	_	_
102	count	count	NN	_	_	_
103	-LRB-	-lrb-	-LRB-	_	_	_
104	WIG	wig	NN	_	_	_
105	-RRB-	-rrb-	-RRB-	_	_	_
106	files	file	NNS	_	_	_
107	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	accomplish	accomplish	VB	_	_	_
3	this	this	DT	_	_	_
4	an	a	DT	_	_	_
5	in-house	in-house	JJ	_	_	_
6	script	script	NN	_	_	_
7	was	be	VBD	_	_	_
8	created	create	VBN	_	_	_
9	to	to	TO	_	_	_
10	extract	extract	VB	_	_	_
11	strand-specific	strand-specific	JJ	_	_	_
12	base	base	NN	_	_	_
13	count	count	NN	_	_	_
14	data	datum	NNS	_	_	_
15	from	from	IN	_	_	_
16	BAM	BAM	NNP	_	_	_
17	files	file	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	outputs	output	NNS	_	_	_
20	are	be	VBP	_	_	_
21	positive	positive	JJ	_	_	_
22	and	and	CC	_	_	_
23	negative	negative	JJ	_	_	_
24	strand	strand	NN	_	_	_
25	WIG	wig	NN	_	_	_
26	files	file	NNS	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	.	.	.	_	_	_

1	First	first	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	script	script	NN	_	_	_
5	reads	read	VBZ	_	_	_
6	in	in	IN	_	_	_
7	the	the	DT	_	_	_
8	paired-end	paired-end	JJ	_	_	_
9	BAM	bam	NN	_	_	_
10	file	file	NN	_	_	_
11	and	and	CC	_	_	_
12	counts	count	VBZ	_	_	_
13	the	the	DT	_	_	_
14	nucleotides	nucleotide	NNS	_	_	_
15	spanning	span	VBG	_	_	_
16	inserts	insert	NNS	_	_	_
17	between	between	IN	_	_	_
18	the	the	DT	_	_	_
19	mated	mate	VBN	_	_	_
20	5	5	CD	_	_	_
21	'	'	''	_	_	_
22	and	and	CC	_	_	_
23	3	3	CD	_	_	_
24	'	'	''	_	_	_
25	reads	read	VBZ	_	_	_
26	.	.	.	_	_	_

1	Next	next	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	script	script	NN	_	_	_
5	pulls	pull	VBZ	_	_	_
6	in	in	IN	_	_	_
7	the	the	DT	_	_	_
8	orphan	orphan	JJ	_	_	_
9	5	5	CD	_	_	_
10	'	'	''	_	_	_
11	and	and	CC	_	_	_
12	3	3	CD	_	_	_
13	'	'	''	_	_	_
14	reads	read	VBZ	_	_	_
15	from	from	IN	_	_	_
16	the	the	DT	_	_	_
17	respective	respective	JJ	_	_	_
18	BAM	BAM	NNP	_	_	_
19	files	file	NNS	_	_	_
20	and	and	CC	_	_	_
21	increments	increment	NNS	_	_	_
22	the	the	DT	_	_	_
23	base	base	NN	_	_	_
24	counts	count	VBZ	_	_	_
25	at	at	IN	_	_	_
26	each	each	DT	_	_	_
27	base	base	NN	_	_	_
28	location	location	NN	_	_	_
29	without	without	IN	_	_	_
30	duplicating	duplicate	VBG	_	_	_
31	the	the	DT	_	_	_
32	reads	read	VBZ	_	_	_
33	already	already	RB	_	_	_
34	incremented	increment	VBN	_	_	_
35	from	from	IN	_	_	_
36	the	the	DT	_	_	_
37	paired	paired	JJ	_	_	_
38	ends	end	NNS	_	_	_
39	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	K-12	k-12	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	sub	sub	NN	_	_	_
7	strain	strain	NN	_	_	_
8	:	:	:	_	_	_
9	BW38028	bw38028	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	sub	sub	NN	_	_	_
12	strain	strain	NN	_	_	_
13	:	:	:	_	_	_
14	BW39452	bw39452	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Supplementary	supplementary	JJ	_	_	_
17	_	_	NN	_	_	_
18	files	file	NNS	_	_	_
19	_	_	IN	_	_	_
20	format	format	NN	_	_	_
21	_	_	NN	_	_	_
22	and	and	CC	_	_	_
23	_	_	NN	_	_	_
24	content	content	NN	_	_	_
25	:	:	:	_	_	_
26	WIG	wig	NN	_	_	_
27	files	file	NNS	_	_	_
28	are	be	VBP	_	_	_
29	provided	provide	VBN	_	_	_
30	showing	show	VBG	_	_	_
31	uniquely	uniquely	RB	_	_	_
32	mapped	map	VBN	_	_	_
33	sequence	sequence	NN	_	_	_
34	reads	read	VBZ	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	normalized	normalize	VBN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	raw	raw	JJ	_	_	_
4	data	datum	NNS	_	_	_
5	output	output	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	XSEQ	xseq	NN	_	_	_
8	files	file	NNS	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	from	from	IN	_	_	_
11	the	the	DT	_	_	_
12	SOLiD	solid	NN	_	_	_
13	4	4	CD	_	_	_
14	Genetic	genetic	JJ	_	_	_
15	Analyzer	Analyzer	NNP	_	_	_
16	System	System	NNP	_	_	_
17	are	be	VBP	_	_	_
18	passed	pass	VBN	_	_	_
19	through	through	IN	_	_	_
20	the	the	DT	_	_	_
21	ABI	ABI	NNP	_	_	_
22	Sequence	sequence	NN	_	_	_
23	Accuracy	Accuracy	NNP	_	_	_
24	Enhancement	enhancement	NN	_	_	_
25	Tool	Tool	NNP	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	SAET	SAET	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	Used	use	VBD	_	_	_
31	SAMTOOLS	samtools	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	Li	Li	NNP	_	_	_
34	,	,	,	_	_	_
35	et	et	FW	_	_	_
36	al.	al.	FW	_	_	_
37	,	,	,	_	_	_
38	PMID	pmid	NN	_	_	_
39	1950593	1950593	CD	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	to	to	TO	_	_	_
42	sort	sort	VB	_	_	_
43	and	and	CC	_	_	_
44	index	index	NN	_	_	_
45	the	the	DT	_	_	_
46	SAM	SAM	NNP	_	_	_
47	files	file	NNS	_	_	_
48	obtained	obtain	VBN	_	_	_
49	from	from	IN	_	_	_
50	Bowtie	Bowtie	NNP	_	_	_
51	and	and	CC	_	_	_
52	convert	convert	VB	_	_	_
53	them	they	PRP	_	_	_
54	to	to	TO	_	_	_
55	BAM	BAM	NNP	_	_	_
56	format	format	NN	_	_	_
57	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	WIG	wig	NN	_	_	_
3	files	file	NNS	_	_	_
4	were	be	VBD	_	_	_
5	normalized	normalize	VBN	_	_	_
6	by	by	IN	_	_	_
7	using	use	VBG	_	_	_
8	an	a	DT	_	_	_
9	in-house	in-house	JJ	_	_	_
10	script	script	NN	_	_	_
11	that	that	WDT	_	_	_
12	reads	read	VBZ	_	_	_
13	in	in	IN	_	_	_
14	the	the	DT	_	_	_
15	raw	raw	JJ	_	_	_
16	WIG	wig	NN	_	_	_
17	files	file	NNS	_	_	_
18	while	while	IN	_	_	_
19	excluding	exclude	VBG	_	_	_
20	counts	count	NNS	_	_	_
21	from	from	IN	_	_	_
22	all	all	DT	_	_	_
23	22	22	CD	_	_	_
24	rRNA	rrna	NN	_	_	_
25	genes	gene	NNS	_	_	_
26	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	simple	simple	JJ	_	_	_
3	global	global	JJ	_	_	_
4	normalization	normalization	NN	_	_	_
5	approach	approach	NN	_	_	_
6	was	be	VBD	_	_	_
7	utilized	utilize	VBN	_	_	_
8	that	that	IN	_	_	_
9	multiplied	multiply	VBD	_	_	_
10	the	the	DT	_	_	_
11	count	count	NN	_	_	_
12	at	at	IN	_	_	_
13	each	each	DT	_	_	_
14	base	base	NN	_	_	_
15	location	location	NN	_	_	_
16	by	by	IN	_	_	_
17	1	1	CD	_	_	_
18	billion	billion	CD	_	_	_
19	and	and	CC	_	_	_
20	divides	divide	VBZ	_	_	_
21	that	that	IN	_	_	_
22	value	value	NN	_	_	_
23	by	by	IN	_	_	_
24	the	the	DT	_	_	_
25	sum	sum	NN	_	_	_
26	of	of	IN	_	_	_
27	base	base	NN	_	_	_
28	counts	count	VBZ	_	_	_
29	at	at	IN	_	_	_
30	all	all	DT	_	_	_
31	base	base	NN	_	_	_
32	locations	location	NNS	_	_	_
33	in	in	IN	_	_	_
34	the	the	DT	_	_	_
35	file	file	NN	_	_	_
36	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	normalization	normalization	NN	_	_	_
3	strategy	strategy	NN	_	_	_
4	is	be	VBZ	_	_	_
5	anlogous	anlogous	JJ	_	_	_
6	to	to	TO	_	_	_
7	the	the	DT	_	_	_
8	Total	total	JJ	_	_	_
9	Count	count	NN	_	_	_
10	approach	approach	NN	_	_	_
11	used	use	VBD	_	_	_
12	for	for	IN	_	_	_
13	normalizing	normalize	VBG	_	_	_
14	gene-specific	gene-specific	JJ	_	_	_
15	read	read	NN	_	_	_
16	alignments	alignment	NNS	_	_	_
17	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	this	this	DT	_	_	_
3	way	way	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	base	base	NN	_	_	_
7	counts	count	NNS	_	_	_
8	are	be	VBP	_	_	_
9	expressed	express	VBN	_	_	_
10	as	as	IN	_	_	_
11	parts	part	NNS	_	_	_
12	per	per	IN	_	_	_
13	billion	billion	CD	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	WIG	wig	NN	_	_	_
3	files	file	NNS	_	_	_
4	were	be	VBD	_	_	_
5	viewed	view	VBN	_	_	_
6	and	and	CC	_	_	_
7	annotated	annotated	JJ	_	_	_
8	using	use	VBG	_	_	_
9	Jbrowse	Jbrowse	NNP	_	_	_
10	and	and	CC	_	_	_
11	Integrated	Integrated	NNP	_	_	_
12	Genome	Genome	NNP	_	_	_
13	Viewer	Viewer	NNP	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Wild	Wild	NNP	_	_	_
3	type	type	NN	_	_	_
4	E.	e.	FW	_	_	_
5	coli	coli	FW	_	_	_
6	K-12	k-12	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	strain	strain	NN	_	_	_
9	BW38038	bw38038	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	and	and	CC	_	_	_
12	BW39452	bw39452	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	ΔrpoS	δrpos	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	cultures	culture	NNS	_	_	_
17	were	be	VBD	_	_	_
18	grown	grow	VBN	_	_	_
19	on	on	IN	_	_	_
20	MOPS	mop	NNS	MED	_	_
21	glucose	glucose	NN	SUPP	_	_
22	minimal	minimal	JJ	_	_	_
23	medium	medium	NN	_	_	_
24	with	with	IN	_	_	_
25	0.2	0.2	CD	_	_	_
26	%	%	NN	_	_	_
27	glucose	glucose	NN	SUPP	_	_
28	as	as	IN	_	_	_
29	sole	sole	JJ	_	_	_
30	carbon	carbon	NN	_	_	_
31	source	source	NN	_	_	_
32	in	in	IN	_	_	_
33	a	a	DT	_	_	_
34	2L	2L	NNP	_	_	_
35	B.	B.	NNP	_	_	_
36	Braun	Braun	NNP	_	_	_
37	Biostat	Biostat	NNP	_	_	_
38	®	®	NN	_	_	_
39	B	b	NN	_	_	_
40	fermenter	fermenter	NN	_	_	_
41	with	with	IN	_	_	_
42	working	work	VBG	_	_	_
43	volume	volume	NN	_	_	_
44	of	of	IN	_	_	_
45	1	1	CD	_	_	_
46	L	l	NN	_	_	_
47	MOPS	mop	NNS	MED	_	_
48	minimal	minimal	JJ	_	_	_
49	medium	medium	NN	_	_	_
50	with	with	IN	_	_	_
51	0.2	0.2	CD	_	_	_
52	%	%	NN	_	_	_
53	glucose	glucose	NN	SUPP	_	_
54	,	,	,	_	_	_
55	at	at	IN	_	_	_
56	37	37	CD	_	_	_
57	°C	°c	NN	_	_	_
58	,	,	,	_	_	_
59	pH	ph	NN	_	_	_
60	was	be	VBD	_	_	_
61	kept	keep	VBN	_	_	_
62	constant	constant	JJ	_	_	_
63	at	at	IN	_	_	_
64	7.4	7.4	CD	_	_	_
65	by	by	IN	_	_	_
66	the	the	DT	_	_	_
67	addition	addition	NN	_	_	_
68	of	of	IN	_	_	_
69	1	1	CD	_	_	_
70	M	m	NN	_	_	_
71	NaOH	naoh	NN	_	_	_
72	,	,	,	_	_	_
73	and	and	CC	_	_	_
74	dissolved	dissolve	VBD	_	_	_
75	oxygen	oxygen	NN	_	_	_
76	was	be	VBD	_	_	_
77	maintained	maintain	VBN	_	_	_
78	above	above	IN	_	_	_
79	40	40	CD	_	_	_
80	%	%	NN	_	_	_
81	of	of	IN	_	_	_
82	saturation	saturation	NN	_	_	_
83	by	by	IN	_	_	_
84	adjusting	adjust	VBG	_	_	_
85	the	the	DT	_	_	_
86	agitation	agitation	NN	_	_	_
87	speeds	speed	NNS	_	_	_
88	in	in	IN	_	_	_
89	the	the	DT	_	_	_
90	range	range	NN	_	_	_
91	of	of	IN	_	_	_
92	270	270	CD	_	_	_
93	--	--	:	_	_	_
94	500	500	CD	_	_	_
95	rpm	rpm	NN	_	_	_
96	with	with	IN	_	_	_
97	fixed	fix	VBN	_	_	_
98	1.5	1.5	CD	_	_	_
99	liter	liter	NN	_	_	_
100	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
101	WT	WT	NNP	_	_	_
102	_	_	SYM	_	_	_
103	01	01	CD	_	_	_
104	_	_	CD	_	_	_
105	rep1	rep1	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	WT	wt	JJ	_	_	_
108	_	_	NN	_	_	_
109	02	02	CD	_	_	_
110	_	_	NN	_	_	_
111	rep1	rep1	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	WT	wt	JJ	_	_	_
114	_	_	NN	_	_	_
115	03	03	CD	_	_	_
116	_	_	NN	_	_	_
117	rep1	rep1	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	WT	wt	JJ	_	_	_
120	_	_	NN	_	_	_
121	04	04	CD	_	_	_
122	_	_	NN	_	_	_
123	rep1	rep1	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	WT	wt	JJ	_	_	_
126	_	_	NN	_	_	_
127	04	04	CD	_	_	_
128	_	_	NN	_	_	_
129	rep2	rep2	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	WT	wt	JJ	_	_	_
132	_	_	NN	_	_	_
133	04-R	04-r	NN	_	_	_
134	_	_	CD	_	_	_
135	rep1	rep1	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	WT	wt	JJ	_	_	_
138	_	_	NN	_	_	_
139	04	04	CD	_	_	_
140	_	_	SYM	_	_	_
141	TEX	TEX	NNP	_	_	_
142	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
143	WT	WT	NNP	_	_	_
144	_	_	SYM	_	_	_
145	08	08	CD	_	_	_
146	_	_	CD	_	_	_
147	rep1	rep1	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	WT	wt	JJ	_	_	_
150	_	_	NN	_	_	_
151	14	14	CD	_	_	_
152	_	_	NN	_	_	_
153	rep1	rep1	NN	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	WT	wt	JJ	_	_	_
156	_	_	NN	_	_	_
157	15	15	CD	_	_	_
158	min	min	NN	_	_	_
159	_	_	CD	_	_	_
160	rep1	rep1	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	WT	wt	JJ	_	_	_
163	_	_	NN	_	_	_
164	16	16	CD	_	_	_
165	_	_	NN	_	_	_
166	rep1	rep1	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	WT	wt	JJ	_	_	_
169	_	_	NN	_	_	_
170	16-R	16-r	NN	_	_	_
171	_	_	CD	_	_	_
172	rep1	rep1	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	WT	wt	JJ	_	_	_
175	_	_	NN	_	_	_
176	180	180	CD	_	_	_
177	min	min	NN	_	_	_
178	_	_	CD	_	_	_
179	rep1	rep1	NN	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	WT	wt	JJ	_	_	_
182	_	_	NN	_	_	_
183	30	30	CD	_	_	_
184	min	min	NN	_	_	_
185	_	_	CD	_	_	_
186	rep1	rep1	NN	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	WT	wt	JJ	_	_	_
189	_	_	NN	_	_	_
190	30	30	CD	_	_	_
191	min	min	NN	_	_	_
192	_	_	CD	_	_	_
193	rep2	rep2	NN	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	WT	wt	JJ	_	_	_
196	_	_	NN	_	_	_
197	30min-R	30min-r	NN	_	_	_
198	_	_	CD	_	_	_
199	rep1	rep1	NN	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	WT	wt	JJ	_	_	_
202	_	_	NN	_	_	_
203	30	30	CD	_	_	_
204	min	min	NN	_	_	_
205	_	_	CD	_	_	_
206	TEX	TEX	NNP	_	_	_
207	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
208	Escherichia	escherichia	FW	Organism	_	_
209	coli	coli	FW	Organism	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	genomic	genomic	JJ	_	_	_
212	dna	dna	NN	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	genomic	genomic	JJ	_	_	_
215	DNA	dna	NN	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	MG1655	mg1655	NN	_	_	_
218	,	,	,	_	_	_
219	SD197	sd197	NN	_	_	_
220	,	,	,	_	_	_
221	SB227	sb227	NN	_	_	_
222	,	,	,	_	_	_
223	SF301	sf301	NN	_	_	_
224	and	and	CC	_	_	_
225	SS046	ss046	NN	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	MG1655	mg1655	NN	_	_	_
228	,	,	,	_	_	_
229	SD197	sd197	NN	_	_	_
230	,	,	,	_	_	_
231	SB227	sb227	NN	_	_	_
232	,	,	,	_	_	_
233	SF301	sf301	NN	_	_	_
234	and	and	CC	_	_	_
235	SS046	ss046	NN	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	ration	ration	NN	_	_	_
238	of	of	IN	_	_	_
239	median	median	NN	_	_	_
240	-LRB-	-lrb-	-LRB-	_	_	_
241	635	635	CD	_	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
243	Ratio	ratio	NN	_	_	_
244	of	of	IN	_	_	_
245	median	median	JJ	_	_	_
246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
247	reference	reference	NN	_	_	_
248	DNA	dna	NN	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	SB10	sb10	NN	_	_	_
251	_	_	NN	_	_	_
252	1	1	CD	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
254	SB10	sb10	NN	_	_	_
255	_	_	NN	_	_	_
256	2	2	CD	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	SB10	sb10	NN	_	_	_
259	_	_	CD	_	_	_
260	3	3	CD	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
262	SB1	sb1	NN	_	_	_
263	_	_	NN	_	_	_
264	1	1	CD	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	SB11	sb11	NN	_	_	_
267	_	_	NN	_	_	_
268	1	1	CD	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	SB11	sb11	NN	_	_	_
271	_	_	NN	_	_	_
272	2	2	CD	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	SB11	sb11	NN	_	_	_
275	_	_	CD	_	_	_
276	3	3	CD	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	SB1	sb1	NN	_	_	_
279	_	_	NN	_	_	_
280	2	2	CD	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	SB12	sb12	NN	_	_	_
283	_	_	NN	_	_	_
284	1	1	CD	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
286	SB12	sb12	NN	_	_	_
287	_	_	NN	_	_	_
288	2	2	CD	_	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
290	SB12	sb12	NN	_	_	_
291	_	_	CD	_	_	_
292	3	3	CD	_	_	_
293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
294	SB1	sb1	NN	_	_	_
295	_	_	CD	_	_	_
296	3	3	CD	_	_	_
297	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
298	SB13	sb13	NN	_	_	_
299	_	_	NN	_	_	_
300	1	1	CD	_	_	_
301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
302	SB13	sb13	NN	_	_	_
303	_	_	NN	_	_	_
304	2	2	CD	_	_	_
305	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
306	SB13	sb13	NN	_	_	_
307	_	_	CD	_	_	_
308	3	3	CD	_	_	_
309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
310	SB14	sb14	NN	_	_	_
311	_	_	NN	_	_	_
312	1	1	CD	_	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
314	SB14	sb14	NN	_	_	_
315	_	_	NN	_	_	_
316	2	2	CD	_	_	_
317	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
318	SB14	sb14	NN	_	_	_
319	_	_	CD	_	_	_
320	3	3	CD	_	_	_
321	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
322	SB15	sb15	NN	_	_	_
323	_	_	NN	_	_	_
324	1	1	CD	_	_	_
325	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
326	SB15	sb15	NN	_	_	_
327	_	_	NN	_	_	_
328	2	2	CD	_	_	_
329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
330	SB15	sb15	NN	_	_	_
331	_	_	CD	_	_	_
332	3	3	CD	_	_	_
333	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
334	SB16	sb16	NN	_	_	_
335	_	_	NN	_	_	_
336	1	1	CD	_	_	_
337	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
338	SB16	sb16	NN	_	_	_
339	_	_	NN	_	_	_
340	2	2	CD	_	_	_
341	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
342	SB16	sb16	NN	_	_	_
343	_	_	CD	_	_	_
344	3	3	CD	_	_	_
345	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
346	SB17	sb17	NN	_	_	_
347	_	_	NN	_	_	_
348	1	1	CD	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	SB17	sb17	NN	_	_	_
351	_	_	NN	_	_	_
352	2	2	CD	_	_	_
353	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
354	SB17	sb17	NN	_	_	_
355	_	_	CD	_	_	_
356	3	3	CD	_	_	_
357	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
358	SB18	sb18	NN	_	_	_
359	_	_	NN	_	_	_
360	1	1	CD	_	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
362	SB18	sb18	NN	_	_	_
363	_	_	NN	_	_	_
364	2	2	CD	_	_	_
365	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
366	SB18	sb18	NN	_	_	_
367	_	_	CD	_	_	_
368	3	3	CD	_	_	_
369	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
370	SB1	sb1	NN	_	_	_
371	genomic	genomic	JJ	_	_	_
372	DNA	dna	NN	_	_	_
373	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
374	SB2	sb2	NN	_	_	_
375	_	_	NN	_	_	_
376	1	1	CD	_	_	_
377	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
378	SB2	sb2	NN	_	_	_
379	_	_	NN	_	_	_
380	2	2	CD	_	_	_
381	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
382	SB2	sb2	NN	_	_	_
383	_	_	CD	_	_	_
384	3	3	CD	_	_	_
385	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
386	SB3	sb3	NN	_	_	_
387	_	_	NN	_	_	_
388	1	1	CD	_	_	_
389	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
390	SB3	sb3	NN	_	_	_
391	_	_	NN	_	_	_
392	2	2	CD	_	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
394	SB3	sb3	NN	_	_	_
395	_	_	CD	_	_	_
396	3	3	CD	_	_	_
397	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
398	SB5	sb5	NN	_	_	_
399	_	_	NN	_	_	_
400	1	1	CD	_	_	_
401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
402	SB5	sb5	NN	_	_	_
403	_	_	NN	_	_	_
404	2	2	CD	_	_	_
405	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
406	SB5	sb5	NN	_	_	_
407	_	_	CD	_	_	_
408	3	3	CD	_	_	_
409	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
410	SB6	sb6	NN	_	_	_
411	_	_	NN	_	_	_
412	1	1	CD	_	_	_
413	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
414	SB6	sb6	NN	_	_	_
415	_	_	NN	_	_	_
416	2	2	CD	_	_	_
417	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
418	SB6	sb6	NN	_	_	_
419	_	_	CD	_	_	_
420	3	3	CD	_	_	_
421	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
422	SB7	sb7	NN	_	_	_
423	_	_	NN	_	_	_
424	1	1	CD	_	_	_
425	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
426	SB7	sb7	NN	_	_	_
427	_	_	NN	_	_	_
428	2	2	CD	_	_	_
429	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
430	SB7	sb7	NN	_	_	_
431	_	_	CD	_	_	_
432	3	3	CD	_	_	_
433	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
434	SB8	sb8	NN	_	_	_
435	_	_	NN	_	_	_
436	1	1	CD	_	_	_
437	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
438	SB8	sb8	NN	_	_	_
439	_	_	NN	_	_	_
440	2	2	CD	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
442	SB8	sb8	NN	_	_	_
443	_	_	CD	_	_	_
444	3	3	CD	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	SB9	sb9	NN	_	_	_
447	_	_	CD	_	_	_
448	1	1	CD	_	_	_
449	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
450	SB9	sb9	NN	_	_	_
451	_	_	NN	_	_	_
452	2	2	CD	_	_	_
453	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
454	SB9	sb9	NN	_	_	_
455	_	_	SYM	_	_	_
456	3	3	CD	_	_	_
457	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
458	SD10	sd10	NN	_	_	_
459	_	_	NN	_	_	_
460	1	1	CD	_	_	_
461	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
462	SD10	sd10	NN	_	_	_
463	_	_	NN	_	_	_
464	2	2	CD	_	_	_
465	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
466	SD10	sd10	NN	_	_	_
467	_	_	CD	_	_	_
468	3	3	CD	_	_	_
469	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
470	SD11	sd11	NN	_	_	_
471	_	_	NN	_	_	_
472	1	1	CD	_	_	_
473	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
474	SD11	sd11	NN	_	_	_
475	_	_	NN	_	_	_
476	2	2	CD	_	_	_
477	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
478	SD11	sd11	NN	_	_	_
479	_	_	CD	_	_	_
480	3	3	CD	_	_	_
481	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
482	SD12	sd12	NN	_	_	_
483	_	_	NN	_	_	_
484	1	1	CD	_	_	_
485	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
486	SD12	sd12	NN	_	_	_
487	_	_	NN	_	_	_
488	2	2	CD	_	_	_
489	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
490	SD12	sd12	NN	_	_	_
491	_	_	CD	_	_	_
492	3	3	CD	_	_	_
493	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
494	SD13	sd13	NN	_	_	_
495	_	_	NN	_	_	_
496	1	1	CD	_	_	_
497	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
498	SD13	sd13	NN	_	_	_
499	_	_	NN	_	_	_
500	2	2	CD	_	_	_
501	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
502	SD13	sd13	NN	_	_	_
503	_	_	CD	_	_	_
504	3	3	CD	_	_	_
505	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
506	SD2	sd2	NN	_	_	_
507	_	_	NN	_	_	_
508	1	1	CD	_	_	_
509	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
510	SD2	sd2	NN	_	_	_
511	_	_	NN	_	_	_
512	2	2	CD	_	_	_
513	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
514	SD2	sd2	NN	_	_	_
515	_	_	CD	_	_	_
516	3	3	CD	_	_	_
517	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
518	SD3	sd3	NN	_	_	_
519	_	_	NN	_	_	_
520	1	1	CD	_	_	_
521	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
522	SD3	sd3	NN	_	_	_
523	_	_	NN	_	_	_
524	2	2	CD	_	_	_
525	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
526	SD3	sd3	NN	_	_	_
527	_	_	CD	_	_	_
528	3	3	CD	_	_	_
529	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
530	SD4	sd4	NN	_	_	_
531	_	_	NN	_	_	_
532	1	1	CD	_	_	_
533	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
534	SD4	sd4	NN	_	_	_
535	_	_	NN	_	_	_
536	2	2	CD	_	_	_
537	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
538	SD4	sd4	NN	_	_	_
539	_	_	CD	_	_	_
540	3	3	CD	_	_	_
541	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
542	SD5	sd5	NN	_	_	_
543	_	_	NN	_	_	_
544	1	1	CD	_	_	_
545	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
546	SD5	sd5	NN	_	_	_
547	_	_	NN	_	_	_
548	2	2	CD	_	_	_
549	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
550	SD5	sd5	NN	_	_	_
551	_	_	CD	_	_	_
552	3	3	CD	_	_	_
553	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
554	SD6	sd6	NN	_	_	_
555	_	_	NN	_	_	_
556	1	1	CD	_	_	_
557	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
558	SD6	sd6	NN	_	_	_
559	_	_	NN	_	_	_
560	2	2	CD	_	_	_
561	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
562	SD6	sd6	NN	_	_	_
563	_	_	CD	_	_	_
564	3	3	CD	_	_	_
565	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
566	SD7	sd7	NN	_	_	_
567	_	_	NN	_	_	_
568	1	1	CD	_	_	_
569	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
570	SD7	sd7	NN	_	_	_
571	_	_	NN	_	_	_
572	2	2	CD	_	_	_
573	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
574	SD7	sd7	NN	_	_	_
575	_	_	CD	_	_	_
576	3	3	CD	_	_	_
577	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
578	SD8	sd8	NN	_	_	_
579	_	_	NN	_	_	_
580	1	1	CD	_	_	_
581	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
582	SD8	sd8	NN	_	_	_
583	_	_	NN	_	_	_
584	2	2	CD	_	_	_
585	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
586	SD8	sd8	NN	_	_	_
587	_	_	CD	_	_	_
588	3	3	CD	_	_	_
589	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
590	SD9	sd9	NN	_	_	_
591	_	_	NN	_	_	_
592	1	1	CD	_	_	_
593	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
594	SD9	sd9	NN	_	_	_
595	_	_	NN	_	_	_
596	2	2	CD	_	_	_
597	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
598	SD9	sd9	NN	_	_	_
599	_	_	CD	_	_	_
600	3	3	CD	_	_	_
601	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
602	SF1a	sf1a	NN	_	_	_
603	_	_	NN	_	_	_
604	1	1	CD	_	_	_
605	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
606	SF1a	sf1a	NN	_	_	_
607	_	_	NN	_	_	_
608	2	2	CD	_	_	_
609	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
610	SF1a	sf1a	NN	_	_	_
611	_	_	CD	_	_	_
612	3	3	CD	_	_	_
613	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
614	SF1b	sf1b	NN	_	_	_
615	_	_	NN	_	_	_
616	1	1	CD	_	_	_
617	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
618	SF1b	sf1b	NN	_	_	_
619	_	_	NN	_	_	_
620	2	2	CD	_	_	_
621	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
622	SF1b	sf1b	NN	_	_	_
623	_	_	CD	_	_	_
624	3	3	CD	_	_	_
625	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
626	SF2b	sf2b	NN	_	_	_
627	_	_	NN	_	_	_
628	1	1	CD	_	_	_
629	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
630	SF2b	sf2b	NN	_	_	_
631	_	_	NN	_	_	_
632	2	2	CD	_	_	_
633	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
634	SF2b	sf2b	NN	_	_	_
635	_	_	CD	_	_	_
636	3	3	CD	_	_	_
637	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
638	SF3	sf3	NN	_	_	_
639	_	_	NN	_	_	_
640	1	1	CD	_	_	_
641	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
642	SF3	sf3	NN	_	_	_
643	_	_	NN	_	_	_
644	2	2	CD	_	_	_
645	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
646	SF3	sf3	NN	_	_	_
647	_	_	CD	_	_	_
648	3	3	CD	_	_	_
649	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
650	SF4a	sf4a	NN	_	_	_
651	_	_	NN	_	_	_
652	1	1	CD	_	_	_
653	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
654	SF4a	sf4a	NN	_	_	_
655	_	_	NN	_	_	_
656	2	2	CD	_	_	_
657	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
658	SF4a	sf4a	NN	_	_	_
659	_	_	CD	_	_	_
660	3	3	CD	_	_	_
661	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
662	SF4b	sf4b	NN	_	_	_
663	_	_	NN	_	_	_
664	1	1	CD	_	_	_
665	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
666	SF4b	sf4b	NN	_	_	_
667	_	_	NN	_	_	_
668	2	2	CD	_	_	_
669	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
670	SF4b	sf4b	NN	_	_	_
671	_	_	CD	_	_	_
672	3	3	CD	_	_	_
673	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
674	SF5	sf5	NN	_	_	_
675	_	_	NN	_	_	_
676	2	2	CD	_	_	_
677	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
678	SF5	sf5	NN	_	_	_
679	_	_	CD	_	_	_
680	3	3	CD	_	_	_
681	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
682	SF6	sf6	NN	_	_	_
683	_	_	NN	_	_	_
684	1	1	CD	_	_	_
685	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
686	SF6	sf6	NN	_	_	_
687	_	_	NN	_	_	_
688	2	2	CD	_	_	_
689	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
690	SF6	sf6	NN	_	_	_
691	_	_	CD	_	_	_
692	3	3	CD	_	_	_
693	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
694	SFx	sfx	NN	_	_	_
695	_	_	NN	_	_	_
696	2	2	CD	_	_	_
697	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
698	SFx	SFx	NNP	_	_	_
699	_	_	SYM	_	_	_
700	3	3	CD	_	_	_
701	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
702	SFy	sfy	NN	_	_	_
703	_	_	NN	_	_	_
704	1	1	CD	_	_	_
705	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
706	SFy	sfy	NN	_	_	_
707	_	_	NN	_	_	_
708	2	2	CD	_	_	_
709	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
710	SFy	sfy	NN	_	_	_
711	_	_	CD	_	_	_
712	3	3	CD	_	_	_
713	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
714	Shigella	shigella	NN	_	_	_
715	boydii	boydii	NN	_	_	_
716	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
717	Shigella	shigella	NN	_	_	_
718	boydii	boydii	NN	_	_	_
719	13	13	CD	_	_	_
720	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
721	Shigella	shigella	NN	_	_	_
722	boydii	boydii	NN	_	_	_
723	14	14	CD	_	_	_
724	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
725	Shigella	shigella	NN	_	_	_
726	boydii	boydii	NN	_	_	_
727	15	15	CD	_	_	_
728	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
729	Shigella	shigella	NN	_	_	_
730	boydii	boydii	NN	_	_	_
731	15	15	CD	_	_	_
732	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
733	Shigella	shigella	NN	_	_	_
734	boydii	boydii	NN	_	_	_
735	16	16	CD	_	_	_
736	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
737	Shigella	shigella	NN	_	_	_
738	boydii	boydii	NN	_	_	_
739	17	17	CD	_	_	_
740	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
741	Shigella	shigella	NN	_	_	_
742	boydii	boydii	NN	_	_	_
743	18	18	CD	_	_	_
744	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
745	Shigella	shigella	NN	_	_	_
746	boydii	boydii	NN	_	_	_
747	serogroup	serogroup	NN	_	_	_
748	1	1	CD	_	_	_
749	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
750	Shigella	shigella	NN	_	_	_
751	boydii	boydii	NN	_	_	_
752	serogroup	serogroup	NN	_	_	_
753	2	2	CD	_	_	_
754	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
755	Shigella	shigella	NN	_	_	_
756	boydii	boydii	NN	_	_	_
757	serotype	serotype	NN	_	_	_
758	1	1	CD	_	_	_
759	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
760	Shigella	shigella	NN	_	_	_
761	boydii	boydii	NN	_	_	_
762	serotype	serotype	NN	_	_	_
763	10	10	CD	_	_	_
764	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
765	Shigella	shigella	NN	_	_	_
766	boydii	boydii	NN	_	_	_
767	serotype	serotype	NN	_	_	_
768	11	11	CD	_	_	_
769	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
770	Shigella	shigella	NN	_	_	_
771	boydii	boydii	NN	_	_	_
772	serotype	serotype	NN	_	_	_
773	12	12	CD	_	_	_
774	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
775	Shigella	shigella	NN	_	_	_
776	boydii	boydii	NN	_	_	_
777	serotype	serotype	NN	_	_	_
778	13	13	CD	_	_	_
779	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
780	Shigella	shigella	NN	_	_	_
781	boydii	boydii	NN	_	_	_
782	serotype2	serotype2	NN	_	_	_
783	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
784	Shigella	shigella	NN	_	_	_
785	boydii	boydii	NN	_	_	_
786	serotype	serotype	NN	_	_	_
787	2	2	CD	_	_	_
788	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
789	Shigella	shigella	NN	_	_	_
790	boydii	boydii	NN	_	_	_
791	serotype3	serotype3	NN	_	_	_
792	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
793	Shigella	shigella	NN	_	_	_
794	boydii	boydii	NN	_	_	_
795	serotype	serotype	NN	_	_	_
796	3	3	CD	_	_	_
797	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
798	Shigella	shigella	NN	_	_	_
799	boydii	boydii	NN	_	_	_
800	serotype	serotype	NN	_	_	_
801	5	5	CD	_	_	_
802	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
803	Shigella	shigella	NN	_	_	_
804	boydii	boydii	NN	_	_	_
805	serotype	serotype	NN	_	_	_
806	6	6	CD	_	_	_
807	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
808	Shigella	shigella	NN	_	_	_
809	boydii	boydii	NN	_	_	_
810	serotype	serotype	NN	_	_	_
811	7	7	CD	_	_	_
812	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
813	Shigella	shigella	NN	_	_	_
814	boydii	boydii	NN	_	_	_
815	serotype	serotype	NN	_	_	_
816	7	7	CD	_	_	_
817	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
818	Shigella	shigella	NN	_	_	_
819	boydii	boydii	NN	_	_	_
820	serotype	serotype	NN	_	_	_
821	8	8	CD	_	_	_
822	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
823	Shigella	shigella	NN	_	_	_
824	boydii	boydii	NN	_	_	_
825	serotype	serotype	NN	_	_	_
826	9	9	CD	_	_	_
827	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
828	Shigella	shigella	NN	_	_	_
829	dysenteriae	dysenteriae	NN	_	_	_
830	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
831	Shigella	shigella	NN	_	_	_
832	dysenteriae	dysenteriae	NN	_	_	_
833	10	10	CD	_	_	_
834	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
835	Shigella	shigella	NN	_	_	_
836	dysenteriae	dysenteriae	NN	_	_	_
837	11	11	CD	_	_	_
838	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
839	Shigella	shigella	NN	_	_	_
840	dysenteriae	dysenteriae	NN	_	_	_
841	12	12	CD	_	_	_
842	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
843	Shigella	shigella	NN	_	_	_
844	dysenteriae	dysenteriae	NN	_	_	_
845	13	13	CD	_	_	_
846	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
847	Shigella	shigella	NN	_	_	_
848	dysenteriae	dysenteriae	NN	_	_	_
849	2	2	CD	_	_	_
850	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
851	Shigella	shigella	NN	_	_	_
852	dysenteriae	dysenteriae	NN	_	_	_
853	3	3	CD	_	_	_
854	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
855	Shigella	shigella	NN	_	_	_
856	dysenteriae	dysenteriae	NN	_	_	_
857	4	4	CD	_	_	_
858	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
859	Shigella	shigella	NN	_	_	_
860	dysenteriae	dysenteriae	NN	_	_	_
861	5	5	CD	_	_	_
862	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
863	Shigella	shigella	NN	_	_	_
864	dysenteriae	dysenteriae	NN	_	_	_
865	6	6	CD	_	_	_
866	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
867	Shigella	shigella	NN	_	_	_
868	dysenteriae	dysenteriae	NN	_	_	_
869	7	7	CD	_	_	_
870	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
871	Shigella	shigella	NN	_	_	_
872	dysenteriae	dysenteriae	NN	_	_	_
873	8	8	CD	_	_	_
874	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
875	Shigella	shigella	NN	_	_	_
876	dysenteriae	dysenteria	NNS	_	_	_
877	9	9	CD	_	_	_
878	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
879	Shigella	shigella	NN	_	_	_
880	flexneri	flexneri	NN	_	_	_
881	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
882	Shigella	shigella	NN	_	_	_
883	flexneri	flexneri	NN	_	_	_
884	1a	1a	NN	_	_	_
885	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
886	Shigella	shigella	NN	_	_	_
887	flexneri	flexneri	NN	_	_	_
888	1b	1b	NN	_	_	_
889	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
890	Shigella	shigella	NN	_	_	_
891	flexneri	flexneri	NN	_	_	_
892	2b	2b	JJ	_	_	_
893	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
894	Shigella	shigella	NN	_	_	_
895	flexneri	flexneri	NN	_	_	_
896	3	3	CD	_	_	_
897	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
898	Shigella	shigella	NN	_	_	_
899	flexneri	flexneri	NN	_	_	_
900	4a	4a	NN	_	_	_
901	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
902	Shigella	shigella	NN	_	_	_
903	flexneri	flexneri	NN	_	_	_
904	4b	4b	NN	_	_	_
905	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
906	Shigella	shigella	NN	_	_	_
907	flexneri	flexneri	NN	_	_	_
908	5	5	CD	_	_	_
909	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
910	Shigella	shigella	NN	_	_	_
911	flexneri	flexneri	NN	_	_	_
912	6	6	CD	_	_	_
913	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
914	Shigella	shigella	NN	_	_	_
915	flexneri	flexneri	NN	_	_	_
916	variant	variant	JJ	_	_	_
917	x	x	NN	_	_	_
918	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
919	Shigella	shigella	NN	_	_	_
920	flexneri	flexneri	NN	_	_	_
921	variant	variant	JJ	_	_	_
922	y	y	NN	_	_	_
923	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
924	All	all	DT	_	_	_
925	cultures	culture	NNS	_	_	_
926	were	be	VBD	_	_	_
927	carried	carry	VBN	_	_	_
928	out	out	RP	_	_	_
929	in	in	IN	_	_	_
930	a	a	DT	_	_	_
931	5	5	CD	_	_	_
932	l	l	NN	_	_	_
933	fermentor	fermentor	JJ	_	_	_
934	BIOSTAT	biostat	NN	_	_	_
935	B-DCU	b-dcu	NN	_	_	_
936	-LRB-	-lrb-	-LRB-	_	_	_
937	Sartorius	Sartorius	NNP	_	_	_
938	BBI	BBI	NNP	_	_	_
939	Systems	Systems	NNPS	_	_	_
940	Inc.	Inc.	NNP	_	_	_
941	.	.	.	_	_	_

1	Melsungen	melsungen	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	at	at	IN	_	_	_
4	controlled	control	VBN	_	_	_
5	temperature	temperature	NN	_	_	_
6	37	37	CD	_	_	_
7	°C	°c	NN	_	_	_
8	,	,	,	_	_	_
9	pH	ph	NN	_	_	_
10	7.0	7.0	CD	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	dissolved	dissolve	VBD	_	_	_
14	oxygen	oxygen	NN	_	_	_
15	tension	tension	NN	_	_	_
16	30	30	CD	_	_	_
17	%	%	NN	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	culture	culture	NN	_	_	_
3	volume	volume	NN	_	_	_
4	was	be	VBD	_	_	_
5	2	2	CD	_	_	_
6	l.	l.	NN	_	_	_
7	All	all	DT	_	_	_
8	reagents	reagent	NNS	_	_	_
9	were	be	VBD	_	_	_
10	purchased	purchase	VBN	_	_	_
11	from	from	IN	_	_	_
12	Sigma-Aldrich	Sigma-Aldrich	NNP	_	_	_
13	,	,	,	_	_	_
14	Inc.	Inc.	NNP	_	_	_
15	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	synthetic	synthetic	JJ	_	_	_
3	culture	culture	NN	_	_	_
4	medium	medium	NN	_	_	_
5	had	have	VBD	_	_	_
6	the	the	DT	_	_	_
7	following	follow	VBG	_	_	_
8	composition	composition	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	g	g	NN	_	_	_
11	l-1	l-1	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	:	:	:	_	_	_
14	8	8	CD	_	_	_
15	,	,	,	_	_	_
16	glucose	glucose	NN	SUPP	_	_
17	;	;	:	_	_	_
18	14.6	14.6	CD	_	_	_
19	,	,	,	_	_	_
20	K2HPO4	k2hpo4	NN	_	_	_
21	;	;	:	_	_	_
22	3.6	3.6	CD	_	_	_
23	,	,	,	_	_	_
24	NaH2PO4	nah2po4	NN	_	_	_
25	·	·	NN	_	_	_
26	H2O	h2o	NN	_	_	_
27	;	;	:	_	_	_
28	2.68	2.68	CD	_	_	_
29	,	,	,	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	NH4	nh4	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	2SO4	2so4	NN	_	_	_
34	;	;	:	_	_	_
35	2	2	CD	_	_	_
36	,	,	,	_	_	_
37	Na2SO4	na2so4	NN	_	_	_
38	;	;	:	_	_	_
39	1	1	CD	_	_	_
40	,	,	,	_	_	_
41	MgSO4	mgso4	NN	_	_	_
42	;	;	:	_	_	_
43	1	1	CD	_	_	_
44	,	,	,	_	_	_
45	Na-citrate	na-citrate	NN	_	_	_
46	;	;	:	_	_	_
47	0.5	0.5	CD	_	_	_
48	,	,	,	_	_	_
49	NH4Cl	nh4cl	NN	_	_	_
50	;	;	:	_	_	_
51	2	2	CD	_	_	_
52	ml	ml	NN	_	_	_
53	of	of	IN	_	_	_
54	10	10	CD	_	_	_
55	mg	mg	NN	_	_	_
56	l-1	l-1	NN	_	_	_
57	of	of	IN	_	_	_
58	thiamine	thiamine	NN	SUPP	_	_
59	;	;	:	_	_	_
60	3	3	CD	_	_	_
61	ml	ml	NN	_	_	_
62	of	of	IN	_	_	_
63	trace	trace	NN	_	_	_
64	element	element	NN	_	_	_
65	solution	solution	NN	_	_	_
66	-LRB-	-lrb-	-LRB-	_	_	_
67	g	g	NN	_	_	_
68	l-1	l-1	NN	_	_	_
69	20.0	20.0	CD	_	_	_
70	,	,	,	_	_	_
71	Na-EDTA	na-edta	NN	_	_	_
72	;	;	:	_	_	_
73	15.0	15.0	CD	_	_	_
74	,	,	,	_	_	_
75	FeCl3	fecl3	NN	_	_	_
76	·	·	NN	_	_	_
77	6H2O	6h2o	NN	_	_	_
78	;	;	:	_	_	_
79	0.5	0.5	CD	_	_	_
80	,	,	,	_	_	_
81	CaCl2	cacl2	NN	_	_	_
82	·	·	NN	_	_	_
83	2H2O	2h2o	NN	_	_	_
84	;	;	:	_	_	_
85	0.2	0.2	CD	_	_	_
86	,	,	,	_	_	_
87	ZnSO4	znso4	NN	_	_	_
88	·	·	NN	_	_	_
89	7H2O	7h2o	NN	_	_	_
90	;	;	:	_	_	_
91	0.2	0.2	CD	_	_	_
92	,	,	,	_	_	_
93	CoCl2	cocl2	NN	_	_	_
94	·	·	NN	_	_	_
95	6H2O	6h2o	NN	_	_	_
96	;	;	:	_	_	_
97	0.2	0.2	CD	_	_	_
98	,	,	,	_	_	_
99	CuSO4	cuso4	NN	_	_	_
100	·	·	NN	_	_	_
101	5H2O	5h2o	NN	_	_	_
102	;	;	:	_	_	_
103	0.2	0.2	CD	_	_	_
104	,	,	,	_	_	_
105	MnSO4	mnso4	NN	_	_	_
106	·	·	NN	_	_	_
107	4H2O	4h2o	NN	_	_	_
108	-RRB-	-rrb-	-RRB-	_	_	_
109	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	chemostat	chemostat	NN	_	_	_
3	culture	culture	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	with	with	IN	_	_	_
7	adding	add	VBG	_	_	_
8	feed	feed	NN	_	_	_
9	medium	medium	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	BL21	bl21	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	BL21	bl21	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	mu	mu	NN	_	_	_
16	=	=	JJ	_	_	_
17	0.20	0.20	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	1	1	LS	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	BL21	bl21	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	mu	mu	NN	_	_	_
26	=	=	JJ	_	_	_
27	0.20	0.20	CD	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	2	2	LS	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	BL21	bl21	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	mu	mu	NN	_	_	_
36	=	=	JJ	_	_	_
37	0.20	0.20	CD	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	3	3	LS	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	BL21	bl21	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	mu	mu	NN	_	_	_
46	=	=	JJ	_	_	_
47	0.20	0.20	CD	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	4	4	LS	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	BL21	bl21	NN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	mu	mu	NN	_	_	_
56	=	=	JJ	_	_	_
57	0.46	0.46	CD	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	1	1	LS	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	BL21	bl21	NN	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	mu	mu	NN	_	_	_
66	=	=	JJ	_	_	_
67	0.46	0.46	CD	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	2	2	LS	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	BL21	bl21	NN	_	_	_
74	-LRB-	-lrb-	-LRB-	_	_	_
75	mu	mu	NN	_	_	_
76	=	=	JJ	_	_	_
77	0.46	0.46	CD	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	3	3	LS	_	_	_
81	-RRB-	-rrb-	-RRB-	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	BL21	bl21	NN	_	_	_
84	-LRB-	-lrb-	-LRB-	_	_	_
85	mu	mu	NN	_	_	_
86	=	=	JJ	_	_	_
87	0.46	0.46	CD	_	_	_
88	-RRB-	-rrb-	-RRB-	_	_	_
89	-LRB-	-lrb-	-LRB-	_	_	_
90	4	4	LS	_	_	_
91	-RRB-	-rrb-	-RRB-	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	E.	e.	FW	_	_	_
94	coli	coli	FW	_	_	_
95	samples	sample	NNS	_	_	_
96	for	for	IN	_	_	_
97	RNA	rna	NN	_	_	_
98	extraction	extraction	NN	_	_	_
99	were	be	VBD	_	_	_
100	taken	take	VBN	_	_	_
101	during	during	IN	_	_	_
102	fermentation	fermentation	NN	_	_	_
103	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	harvested	harvest	VBN	_	_	_
4	by	by	IN	_	_	_
5	centrifugation	centrifugation	NN	_	_	_
6	at	at	IN	_	_	_
7	the	the	DT	_	_	_
8	cultivation	cultivation	NN	_	_	_
9	temperature	temperature	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	37	37	CD	_	_	_
12	°C	°c	NN	_	_	_
13	,	,	,	_	_	_
14	10,000	10,000	CD	_	_	_
15	g	g	NN	_	_	_
16	,	,	,	_	_	_
17	1	1	CD	_	_	_
18	min	min	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	,	,	,	_	_	_
21	separated	separate	VBN	_	_	_
22	from	from	IN	_	_	_
23	the	the	DT	_	_	_
24	supernatant	supernatant	NN	_	_	_
25	,	,	,	_	_	_
26	and	and	CC	_	_	_
27	rapidly	rapidly	RB	_	_	_
28	frozen	freeze	VBN	_	_	_
29	in	in	IN	_	_	_
30	dry	dry	JJ	_	_	_
31	ice	ice	NN	_	_	_
32	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	stored	store	VBN	_	_	_
5	at	at	IN	_	_	_
6	-70	-70	CD	_	_	_
7	°C	°c	NN	_	_	_
8	until	until	IN	_	_	_
9	analysis	analysis	NN	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Escherichia	escherichia	FW	Organism	_	_
12	coli	coli	FW	Organism	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Escherichia	escherichia	FW	Organism	_	_
15	coli	coli	FW	Organism	_	_
16	BL21	bl21	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Escherichia	escherichia	FW	Organism	_	_
19	coli	coli	FW	Organism	_	_
20	BL21	bl21	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	mu	mu	NN	_	_	_
23	=	=	JJ	_	_	_
24	0.20	0.20	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	Escherichia	escherichia	FW	Organism	_	_
28	coli	coli	FW	Organism	_	_
29	BL21	bl21	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	mu	mu	NN	_	_	_
32	=	=	JJ	_	_	_
33	0.46	0.46	CD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	Expression	expression	NN	_	_	_
37	data	datum	NNS	_	_	_
38	were	be	VBD	_	_	_
39	analyzed	analyze	VBN	_	_	_
40	with	with	IN	_	_	_
41	the	the	DT	_	_	_
42	Microarray	Microarray	NNP	_	_	_
43	Analysis	analysis	NN	_	_	_
44	Suite	suite	NN	_	_	_
45	,	,	,	_	_	_
46	version	version	NN	_	_	_
47	5.0	5.0	CD	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	Affymetrix	Affymetrix	NNP	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	.	.	.	_	_	_

1	Global	global	JJ	_	_	_
2	scaling	scaling	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	to	to	TO	_	_	_
6	compare	compare	VB	_	_	_
7	genes	gene	NNS	_	_	_
8	between	between	IN	_	_	_
9	chips	chip	NNS	_	_	_
10	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	chip	chip	NN	_	_	_
3	was	be	VBD	_	_	_
4	normalized	normalize	VBN	_	_	_
5	to	to	TO	_	_	_
6	a	a	DT	_	_	_
7	target	target	NN	_	_	_
8	intensity	intensity	NN	_	_	_
9	value	value	NN	_	_	_
10	of	of	IN	_	_	_
11	2,500	2,500	CD	_	_	_
12	.	.	.	_	_	_

1	Expression	expression	NN	_	_	_
2	analysis	analysis	NN	_	_	_
3	files	file	NNS	_	_	_
4	created	create	VBN	_	_	_
5	by	by	IN	_	_	_
6	Microarray	Microarray	NNP	_	_	_
7	Suite	Suite	NNP	_	_	_
8	,	,	,	_	_	_
9	version	version	NN	_	_	_
10	5.0	5.0	CD	_	_	_
11	,	,	,	_	_	_
12	were	be	VBD	_	_	_
13	exported	export	VBN	_	_	_
14	to	to	TO	_	_	_
15	Microsoft	Microsoft	NNP	_	_	_
16	Excel	Excel	NNP	_	_	_
17	for	for	IN	_	_	_
18	data	datum	NNS	_	_	_
19	formatting	formatting	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genotype	Genotype	NNP	_	_	_
3	:	:	:	_	_	_
4	F	f	NN	_	_	_
5	-	-	:	_	_	_
6	ompT	ompt	NN	GEN	_	_
7	hsdSB	hsdsb	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	rB-mB	rb-mb	NN	_	_	_
10	-	-	:	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	gal	gal	NN	_	_	_
13	dcm	dcm	NN	GEN	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	DE3	de3	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Trizol	trizol	NN	_	_	_
19	extraction	extraction	NN	_	_	_
20	of	of	IN	_	_	_
21	total	total	JJ	_	_	_
22	RNA	rna	NN	_	_	_
23	was	be	VBD	_	_	_
24	performed	perform	VBN	_	_	_
25	according	accord	VBG	_	_	_
26	to	to	TO	_	_	_
27	the	the	DT	_	_	_
28	manufacturer	manufacturer	NN	_	_	_
29	's	's	POS	_	_	_
30	instructions	instruction	NNS	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Cells	cell	NNS	_	_	_
33	were	be	VBD	_	_	_
34	grown	grow	VBN	_	_	_
35	in	in	IN	_	_	_
36	the	the	DT	_	_	_
37	minimal	minimal	JJ	_	_	_
38	media	media	NNS	_	_	_
39	,	,	,	_	_	_
40	M63	m63	NN	_	_	_
41	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	final	final	JJ	_	_	_
3	cell	cell	NN	_	_	_
4	concentrations	concentration	NNS	_	_	_
5	were	be	VBD	_	_	_
6	controlled	control	VBN	_	_	_
7	~	~	SYM	_	_	_
8	10	10	CD	_	_	_
9	^	^	SYM	_	_	_
10	8	8	CD	_	_	_
11	cells	cell	NNS	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
13	condition	condition	NN	_	_	_
14	:	:	:	_	_	_
15	37ºC	37ºc	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	condition	condition	NN	_	_	_
18	:	:	:	_	_	_
19	45ºC	45ºc	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	E.	e.	FW	_	_	_
22	coli	coli	FW	_	_	_
23	Type	type	NN	_	_	_
24	_	_	CD	_	_	_
25	II	ii	CD	_	_	_
26	genotype	genotype	NN	_	_	_
27	strain	strain	NN	_	_	_
28	,	,	,	_	_	_
29	under	under	IN	_	_	_
30	37ºC	37ºc	NN	_	_	_
31	,	,	,	_	_	_
32	rep	rep	NN	GEN	_	_
33	1	1	CD	_	_	_
34	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
35	E.	E.	NNP	_	_	_
36	coli	coli	NN	_	_	_
37	Type	type	NN	_	_	_
38	_	_	CD	_	_	_
39	II	ii	CD	_	_	_
40	genotype	genotype	NN	_	_	_
41	strain	strain	NN	_	_	_
42	,	,	,	_	_	_
43	under	under	IN	_	_	_
44	37ºC	37ºc	NN	_	_	_
45	,	,	,	_	_	_
46	rep	rep	NN	GEN	_	_
47	2	2	CD	_	_	_
48	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
49	E.	E.	NNP	_	_	_
50	coli	coli	NN	_	_	_
51	Type	type	NN	_	_	_
52	_	_	CD	_	_	_
53	II	ii	CD	_	_	_
54	genotype	genotype	NN	_	_	_
55	strain	strain	NN	_	_	_
56	,	,	,	_	_	_
57	under	under	IN	_	_	_
58	37ºC	37ºc	NN	_	_	_
59	,	,	,	_	_	_
60	rep	rep	NN	GEN	_	_
61	3	3	CD	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	E.	e.	FW	_	_	_
64	coli	coli	FW	_	_	_
65	Type	type	NN	_	_	_
66	_	_	CD	_	_	_
67	II	ii	CD	_	_	_
68	genotype	genotype	NN	_	_	_
69	strain	strain	NN	_	_	_
70	,	,	,	_	_	_
71	under	under	IN	_	_	_
72	45ºC	45ºc	NN	_	_	_
73	,	,	,	_	_	_
74	rep	rep	NN	GEN	_	_
75	1	1	CD	_	_	_
76	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
77	E.	E.	NNP	_	_	_
78	coli	coli	NN	_	_	_
79	Type	type	NN	_	_	_
80	_	_	CD	_	_	_
81	II	ii	CD	_	_	_
82	genotype	genotype	NN	_	_	_
83	strain	strain	NN	_	_	_
84	,	,	,	_	_	_
85	under	under	IN	_	_	_
86	45ºC	45ºc	NN	_	_	_
87	,	,	,	_	_	_
88	rep	rep	NN	GEN	_	_
89	2	2	CD	_	_	_
90	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
91	E.	E.	NNP	_	_	_
92	coli	coli	NN	_	_	_
93	Type	type	NN	_	_	_
94	_	_	CD	_	_	_
95	II	ii	CD	_	_	_
96	genotype	genotype	NN	_	_	_
97	strain	strain	NN	_	_	_
98	,	,	,	_	_	_
99	under	under	IN	_	_	_
100	45ºC	45ºc	NN	_	_	_
101	,	,	,	_	_	_
102	rep	rep	NN	GEN	_	_
103	3	3	CD	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	E.	e.	FW	_	_	_
106	coli	coli	FW	_	_	_
107	Type	type	NN	_	_	_
108	_	_	CD	_	_	_
109	III	iii	CD	_	_	_
110	genotype	genotype	NN	_	_	_
111	strain	strain	NN	_	_	_
112	,	,	,	_	_	_
113	under	under	IN	_	_	_
114	37ºC	37ºc	NN	_	_	_
115	,	,	,	_	_	_
116	rep	rep	NN	GEN	_	_
117	1	1	CD	_	_	_
118	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
119	E.	E.	NNP	_	_	_
120	coli	coli	NN	_	_	_
121	Type	type	NN	_	_	_
122	_	_	CD	_	_	_
123	III	iii	CD	_	_	_
124	genotype	genotype	NN	_	_	_
125	strain	strain	NN	_	_	_
126	,	,	,	_	_	_
127	under	under	IN	_	_	_
128	37ºC	37ºc	NN	_	_	_
129	,	,	,	_	_	_
130	rep	rep	NN	GEN	_	_
131	2	2	CD	_	_	_
132	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
133	E.	E.	NNP	_	_	_
134	coli	coli	NN	_	_	_
135	Type	type	NN	_	_	_
136	_	_	CD	_	_	_
137	III	iii	CD	_	_	_
138	genotype	genotype	NN	_	_	_
139	strain	strain	NN	_	_	_
140	,	,	,	_	_	_
141	under	under	IN	_	_	_
142	37ºC	37ºc	NN	_	_	_
143	,	,	,	_	_	_
144	rep	rep	NN	GEN	_	_
145	3	3	CD	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	E.	e.	FW	_	_	_
148	coli	coli	FW	_	_	_
149	Type	type	NN	_	_	_
150	_	_	CD	_	_	_
151	III	iii	CD	_	_	_
152	genotype	genotype	NN	_	_	_
153	strain	strain	NN	_	_	_
154	,	,	,	_	_	_
155	under	under	IN	_	_	_
156	45ºC	45ºc	NN	_	_	_
157	,	,	,	_	_	_
158	rep	rep	NN	GEN	_	_
159	1	1	CD	_	_	_
160	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
161	E.	E.	NNP	_	_	_
162	coli	coli	NN	_	_	_
163	Type	type	NN	_	_	_
164	_	_	CD	_	_	_
165	III	iii	CD	_	_	_
166	genotype	genotype	NN	_	_	_
167	strain	strain	NN	_	_	_
168	,	,	,	_	_	_
169	under	under	IN	_	_	_
170	45ºC	45ºc	NN	_	_	_
171	,	,	,	_	_	_
172	rep	rep	NN	GEN	_	_
173	2	2	CD	_	_	_
174	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
175	E.	E.	NNP	_	_	_
176	coli	coli	NN	_	_	_
177	Type	type	NN	_	_	_
178	_	_	CD	_	_	_
179	III	iii	CD	_	_	_
180	genotype	genotype	NN	_	_	_
181	strain	strain	NN	_	_	_
182	,	,	,	_	_	_
183	under	under	IN	_	_	_
184	45ºC	45ºc	NN	_	_	_
185	,	,	,	_	_	_
186	rep	rep	NN	GEN	_	_
187	3	3	CD	_	_	_
188	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
189	Escherichia	escherichia	FW	Organism	_	_
190	coli	coli	FW	Organism	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	Microarray	microarray	NN	_	_	_
193	data	datum	NNS	_	_	_
194	were	be	VBD	_	_	_
195	processed	process	VBN	_	_	_
196	using	use	VBG	_	_	_
197	custom	custom	NN	_	_	_
198	scripts	script	NNS	_	_	_
199	written	write	VBN	_	_	_
200	in	in	IN	_	_	_
201	R	r	NN	_	_	_
202	based	base	VBN	_	_	_
203	on	on	IN	_	_	_
204	the	the	DT	_	_	_
205	finite	finite	JJ	_	_	_
206	hybridisation	hybridisation	NN	_	_	_
207	-LRB-	-lrb-	-LRB-	_	_	_
208	FH	fh	NN	_	_	_
209	-RRB-	-rrb-	-RRB-	_	_	_
210	model	model	NN	_	_	_
211	-LRB-	-lrb-	-LRB-	_	_	_
212	Ono	Ono	NNP	_	_	_
213	et	et	FW	_	_	_
214	al	al	FW	_	_	_
215	,	,	,	_	_	_
216	2008	2008	CD	_	_	_
217	-RRB-	-rrb-	-RRB-	_	_	_
218	and	and	CC	_	_	_
219	the	the	DT	_	_	_
220	thermodynamic	thermodynamic	JJ	_	_	_
221	model	model	NN	_	_	_
222	of	of	IN	_	_	_
223	non-specific	non-specific	JJ	_	_	_
224	binding	binding	NN	_	_	_
225	-LRB-	-lrb-	-LRB-	_	_	_
226	NSB	nsb	NN	_	_	_
227	-RRB-	-rrb-	-RRB-	_	_	_
228	on	on	IN	_	_	_
229	short	short	JJ	_	_	_
230	nucleotide	nucleotide	NN	_	_	_
231	microarrays	microarray	NNS	_	_	_
232	-LRB-	-lrb-	-LRB-	_	_	_
233	Furusawa	Furusawa	NNP	_	_	_
234	et	et	FW	_	_	_
235	al	al	FW	_	_	_
236	,	,	,	_	_	_
237	2009	2009	CD	_	_	_
238	-RRB-	-rrb-	-RRB-	_	_	_
239	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	DH1ΔleuB	dh1δleub	NN	_	_	_
5	:	:	:	_	_	_
6	:	:	:	_	_	_
7	gfpuv5-kmr	gfpuv5-kmr	JJ	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
9	The	the	DT	_	_	_
10	cell	cell	NN	_	_	_
11	culture	culture	NN	_	_	_
12	was	be	VBD	_	_	_
13	put	put	VBN	_	_	_
14	into	into	IN	_	_	_
15	cold	cold	JJ	_	_	_
16	phenol-ethanol	phenol-ethanol	JJ	_	_	_
17	solution	solution	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	1	1	CD	_	_	_
20	g	g	NN	_	_	_
21	of	of	IN	_	_	_
22	phenol	phenol	NN	_	_	_
23	in	in	IN	_	_	_
24	10	10	CD	_	_	_
25	mL	ml	NN	_	_	_
26	of	of	IN	_	_	_
27	ethanol	ethanol	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	prepared	prepare	VBN	_	_	_
30	in	in	IN	_	_	_
31	advance	advance	NN	_	_	_
32	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	collected	collect	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	at	at	IN	_	_	_
8	7,000	7,000	CD	_	_	_
9	×	×	CD	_	_	_
10	g	g	NN	_	_	_
11	for	for	IN	_	_	_
12	3	3	CD	_	_	_
13	min	min	NN	_	_	_
14	at	at	IN	_	_	_
15	4	4	CD	_	_	_
16	°C	°c	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	the	the	DT	_	_	_
20	pelleted	pelleted	JJ	_	_	_
21	cells	cell	NNS	_	_	_
22	were	be	VBD	_	_	_
23	stored	store	VBN	_	_	_
24	at	at	IN	_	_	_
25	--	--	:	_	_	_
26	80	80	CD	_	_	_
27	°C	°c	NN	_	_	_
28	prior	prior	RB	_	_	_
29	to	to	TO	_	_	_
30	use	use	VB	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNAs	rna	NNS	_	_	_
4	were	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	an	a	DT	_	_	_
8	RNeasy	rneasy	NN	_	_	_
9	mini	minus	NNS	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	qiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	in	in	IN	_	_	_
15	accordance	accordance	NN	_	_	_
16	with	with	IN	_	_	_
17	the	the	DT	_	_	_
18	manufacturer	manufacturer	NN	_	_	_
19	's	's	POS	_	_	_
20	instructions	instruction	NNS	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	centrifuged	centrifuge	VBN	_	_	_
5	and	and	CC	_	_	_
6	the	the	DT	_	_	_
7	cell	cell	NN	_	_	_
8	pellets	pellet	NNS	_	_	_
9	were	be	VBD	_	_	_
10	stored	store	VBN	_	_	_
11	in	in	IN	_	_	_
12	RNA	rna	NN	_	_	_
13	Later	later	RB	_	_	_
14	solution	solution	NN	_	_	_
15	at	at	IN	_	_	_
16	-80	-80	CD	_	_	_
17	ºC	ºc	NN	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	RNeasy	RNeasy	NNP	_	_	_
3	Mini	Mini	NNP	_	_	_
4	Kit	kit	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	Qiagen	Qiagen	NNP	_	_	_
7	,	,	,	_	_	_
8	Venlo	Venlo	NNP	_	_	_
9	,	,	,	_	_	_
10	Netherlands	Netherlands	NNP	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	was	be	VBD	_	_	_
13	used	use	VBN	_	_	_
14	to	to	TO	_	_	_
15	isolate	isolate	VB	_	_	_
16	total	total	JJ	_	_	_
17	RNA	rna	NN	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	incubated	incubate	VBN	_	_	_
6	at	at	IN	_	_	_
7	37ºC	37ºc	NN	_	_	_
8	with	with	IN	_	_	_
9	RNaseOut	rnaseout	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	New	New	NNP	_	_	_
12	England	England	NNP	_	_	_
13	Biolabs	Biolabs	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	and	and	CC	_	_	_
16	DNaseI	dnasei	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	New	New	NNP	_	_	_
19	England	England	NNP	_	_	_
20	Biolabs	Biolabs	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	according	accord	VBG	_	_	_
23	to	to	TO	_	_	_
24	the	the	DT	_	_	_
25	manufacture	manufacture	NN	_	_	_
26	's	's	POS	_	_	_
27	protocol	protocol	NN	_	_	_
28	for	for	IN	_	_	_
29	1	1	CD	_	_	_
30	hour	hour	NN	_	_	_
31	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	mixed	mix	VBN	_	_	_
5	with	with	IN	_	_	_
6	saturated	saturated	JJ	_	_	_
7	phenol	phenol	NN	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	E.	E.	NNP	_	_	_
10	coli	coli	NN	_	_	_
11	MG1655-C8-1	mg1655-c8-1	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	E.	e.	FW	_	_	_
14	coli	coli	FW	_	_	_
15	MG1655-C8-3	mg1655-c8-3	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	E.	e.	FW	_	_	_
18	coli	coli	FW	_	_	_
19	MG1655-control-1	mg1655-control-1	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	E.	e.	FW	_	_	_
22	coli	coli	FW	_	_	_
23	MG1655-control-2	mg1655-control-2	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	E.	e.	FW	_	_	_
26	coli	coli	FW	_	_	_
27	MG1655-control-3	mg1655-control-3	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	E.	e.	FW	_	_	_
30	coli	coli	FW	_	_	_
31	MG1655-MOPS	mg1655-mops	NN	_	_	_
32	+2	+2	CD	_	_	_
33	%	%	NN	_	_	_
34	Dextrose	dextrose	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	E.	e.	FW	_	_	_
37	coli	coli	FW	_	_	_
38	MG1655-MOPS	mg1655-mops	NN	_	_	_
39	+2	+2	CD	_	_	_
40	%	%	NN	_	_	_
41	Dextrose	dextrose	NN	_	_	_
42	+10	+10	CD	_	_	_
43	mM	mm	NN	KWSUPP	_	_
44	C8	c8	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	E.	e.	FW	_	_	_
47	coli	coli	FW	_	_	_
48	MG1655	mg1655	NN	_	_	_
49	was	be	VBD	_	_	_
50	grown	grow	VBN	_	_	_
51	in	in	IN	_	_	_
52	MOPS	MOPS	NNP	MED	_	_
53	+	+	CC	_	_	_
54	2	2	CD	_	_	_
55	%	%	NN	_	_	_
56	Dextrose	dextrose	NN	_	_	_
57	minimal	minimal	JJ	_	_	_
58	media	media	NNS	_	_	_
59	+	+	CC	_	_	_
60	-	-	:	_	_	_
61	10	10	CD	_	_	_
62	mM	mm	NN	KWSUPP	_	_
63	octanoic	octanoic	JJ	_	_	_
64	acid	acid	NN	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	pH	ph	NN	_	_	_
67	=	=	JJ	_	_	_
68	7.0	7.0	CD	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	from	from	IN	_	_	_
71	OD550	od550	NN	_	_	_
72	0.05	0.05	CD	_	_	_
73	to	to	TO	_	_	_
74	~	~	CD	_	_	_
75	0.8	0.8	CD	_	_	_
76	and	and	CC	_	_	_
77	harvested	harvest	VBN	_	_	_
78	at	at	IN	_	_	_
79	Midlog	Midlog	NNP	_	_	_
80	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	MATLAB	MATLAB	NNP	_	_	_
4	v.	v.	CC	_	_	_
5	R2012b	r2012b	NN	_	_	_
6	program	program	NN	_	_	_
7	using	use	VBG	_	_	_
8	GCRMA	GCRMA	NNP	_	_	_
9	algorithm	algorithm	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	strain	strain	NN	_	_	_
12	:	:	:	_	_	_
13	MG1655	mg1655	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
15	The	the	DT	_	_	_
16	treatment	treatment	NN	_	_	_
17	condition	condition	NN	_	_	_
18	includes	include	VBZ	_	_	_
19	adding	add	VBG	_	_	_
20	10	10	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	octanoic	octanoic	JJ	_	_	_
23	acid	acid	NN	_	_	_
24	during	during	IN	_	_	_
25	logarithmic	logarithmic	JJ	_	_	_
26	growth	growth	NN	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	As	as	IN	_	_	_
3	described	describe	VBN	_	_	_
4	in	in	IN	_	_	_
5	description	description	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	As	as	IN	_	_	_
8	described	describe	VBN	_	_	_
9	in	in	IN	_	_	_
10	the	the	DT	_	_	_
11	description	description	NN	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	E.	E.	NNP	_	_	_
14	coli	coli	NN	_	_	_
15	K12	k12	NN	_	_	_
16	grown	grow	VBN	_	_	_
17	in	in	IN	_	_	_
18	minimal	minimal	JJ	_	_	_
19	medium	medium	NN	_	_	_
20	with	with	IN	_	_	_
21	added	add	VBN	_	_	_
22	5	5	CD	_	_	_
23	μM	μm	NN	_	_	_
24	TPEN	tpen	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	E.	e.	FW	_	_	_
27	coli	coli	FW	_	_	_
28	K12	k12	NN	_	_	_
29	grown	grow	VBN	_	_	_
30	in	in	IN	_	_	_
31	minimal	minimal	JJ	_	_	_
32	medium	medium	NN	_	_	_
33	without	without	IN	_	_	_
34	added	add	VBN	_	_	_
35	TPEN	tpen	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
37	Escherichia	escherichia	FW	Organism	_	_
38	coli	coli	FW	Organism	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	mRNA	mrna	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	Transcriptional	transcriptional	JJ	_	_	_
43	response	response	NN	_	_	_
44	of	of	IN	_	_	_
45	E.	e.	FW	_	_	_
46	coli	coli	FW	_	_	_
47	to	to	TO	_	_	_
48	TPEN	tpen	NN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	m1	m1	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	Transcriptional	transcriptional	JJ	_	_	_
54	response	response	NN	_	_	_
55	of	of	IN	_	_	_
56	E.	e.	FW	_	_	_
57	coli	coli	FW	_	_	_
58	to	to	TO	_	_	_
59	TPEN	tpen	NN	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	m2	m2	NN	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	Transcriptional	transcriptional	JJ	_	_	_
65	response	response	NN	_	_	_
66	of	of	IN	_	_	_
67	E.	e.	FW	_	_	_
68	coli	coli	FW	_	_	_
69	to	to	TO	_	_	_
70	TPEN	tpen	NN	_	_	_
71	-LRB-	-lrb-	-LRB-	_	_	_
72	m3	m3	NN	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	Transcriptional	transcriptional	JJ	_	_	_
76	response	response	NN	_	_	_
77	of	of	IN	_	_	_
78	E.	e.	FW	_	_	_
79	coli	coli	FW	_	_	_
80	to	to	TO	_	_	_
81	TPEN	tpen	NN	_	_	_
82	-LRB-	-lrb-	-LRB-	_	_	_
83	t1	t1	NN	_	_	_
84	-RRB-	-rrb-	-RRB-	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	Transcriptional	transcriptional	JJ	_	_	_
87	response	response	NN	_	_	_
88	of	of	IN	_	_	_
89	E.	e.	FW	_	_	_
90	coli	coli	FW	_	_	_
91	to	to	TO	_	_	_
92	TPEN	tpen	NN	_	_	_
93	-LRB-	-lrb-	-LRB-	_	_	_
94	t2	t2	NN	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	Transcriptional	transcriptional	JJ	_	_	_
98	response	response	NN	_	_	_
99	of	of	IN	_	_	_
100	E.	e.	FW	_	_	_
101	coli	coli	FW	_	_	_
102	to	to	TO	_	_	_
103	TPEN	tpen	NN	_	_	_
104	-LRB-	-lrb-	-LRB-	_	_	_
105	t3	t3	NN	_	_	_
106	-RRB-	-rrb-	-RRB-	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	All	all	DT	_	_	_
109	cultures	culture	NNS	_	_	_
110	were	be	VBD	_	_	_
111	based	base	VBN	_	_	_
112	on	on	IN	_	_	_
113	MOPS	mop	NNS	MED	_	_
114	media	media	NNS	_	_	_
115	with	with	IN	_	_	_
116	0.2	0.2	CD	_	_	_
117	%	%	NN	_	_	_
118	glucose	glucose	NN	SUPP	_	_
119	-LRB-	-lrb-	-LRB-	_	_	_
120	Teknova	teknova	NN	_	_	_
121	-RRB-	-rrb-	-RRB-	_	_	_
122	,	,	,	_	_	_
123	with	with	IN	_	_	_
124	either	either	CC	_	_	_
125	full	full	JJ	_	_	_
126	supplement	supplement	NN	_	_	_
127	-LRB-	-lrb-	-LRB-	_	_	_
128	Neidhardt	Neidhardt	NNP	_	_	_
129	et	et	FW	_	_	_
130	al.	al.	FW	_	_	_
131	,	,	,	_	_	_
132	1974	1974	CD	_	_	_
133	-RRB-	-rrb-	-RRB-	_	_	_
134	.	.	.	_	_	_

1	An	a	DT	_	_	_
2	overnight	overnight	JJ	_	_	_
3	liquid	liquid	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	diluted	dilute	VBN	_	_	_
7	400-fold	400-fold	JJ	_	_	_
8	into	into	IN	_	_	_
9	200	200	CD	_	_	_
10	ml	ml	NN	_	_	_
11	fresh	fresh	JJ	_	_	_
12	media	media	NNS	_	_	_
13	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	kept	keep	VBN	_	_	_
5	in	in	IN	_	_	_
6	a	a	DT	_	_	_
7	2.8-liter	2.8-liter	JJ	_	_	_
8	flask	flask	NN	_	_	_
9	at	at	IN	_	_	_
10	37C	37c	NN	_	_	_
11	with	with	IN	_	_	_
12	aeration	aeration	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	180	180	CD	_	_	_
15	rpm	rpm	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	until	until	IN	_	_	_
18	OD600	od600	NN	_	_	_
19	reached	reach	VBD	_	_	_
20	0.3	0.3	CD	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	bacteria	bacterium	NNS	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Basecalls	basecall	NNS	_	_	_
5	performed	perform	VBN	_	_	_
6	using	use	VBG	_	_	_
7	Casava	Casava	NNP	_	_	_
8	versions	version	NNS	_	_	_
9	1.6	1.6	CD	_	_	_
10	or	or	CC	_	_	_
11	1.7	1.7	CD	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Bowtie	Bowtie	NNP	_	_	_
3	alignments	alignment	NNS	_	_	_
4	against	against	IN	_	_	_
5	the	the	DT	_	_	_
6	E	e	NN	_	_	_
7	coli	coli	NN	_	_	_
8	genome	genome	NN	_	_	_
9	were	be	VBD	_	_	_
10	converted	convert	VBN	_	_	_
11	to	to	TO	_	_	_
12	wiggle	wiggle	VB	_	_	_
13	files	file	NNS	_	_	_
14	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	position	position	NN	_	_	_
3	of	of	IN	_	_	_
4	each	each	DT	_	_	_
5	alignment	alignment	NN	_	_	_
6	is	be	VBZ	_	_	_
7	distributed	distribute	VBN	_	_	_
8	into	into	IN	_	_	_
9	several	several	JJ	_	_	_
10	nucleotides	nucleotide	NNS	_	_	_
11	in	in	IN	_	_	_
12	the	the	DT	_	_	_
13	center	center	NN	_	_	_
14	of	of	IN	_	_	_
15	the	the	DT	_	_	_
16	footprint	footprint	NN	_	_	_
17	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	footprint	footprint	NN	_	_	_
4	read	read	NN	_	_	_
5	,	,	,	_	_	_
6	the	the	DT	_	_	_
7	center	center	NN	_	_	_
8	residues	residue	NNS	_	_	_
9	that	that	WDT	_	_	_
10	are	be	VBP	_	_	_
11	at	at	IN	_	_	_
12	least	least	JJS	_	_	_
13	10	10	CD	_	_	_
14	nucleotides	nucleotide	NNS	_	_	_
15	away	away	RB	_	_	_
16	from	from	IN	_	_	_
17	either	either	CC	_	_	_
18	ends	end	NNS	_	_	_
19	were	be	VBD	_	_	_
20	given	give	VBN	_	_	_
21	the	the	DT	_	_	_
22	same	same	JJ	_	_	_
23	score	score	NN	_	_	_
24	,	,	,	_	_	_
25	which	which	WDT	_	_	_
26	is	be	VBZ	_	_	_
27	weighted	weight	VBN	_	_	_
28	by	by	IN	_	_	_
29	the	the	DT	_	_	_
30	length	length	NN	_	_	_
31	of	of	IN	_	_	_
32	the	the	DT	_	_	_
33	fragment	fragment	NN	_	_	_
34	-LSB-	-lsb-	-LRB-	_	_	_
35	Oh	oh	UH	_	_	_
36	et	et	FW	_	_	_
37	al	al	FW	_	_	_
38	,	,	,	_	_	_
39	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	147	147	CD	_	_	_
3	,	,	,	_	_	_
4	1295	1295	CD	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	2011	2011	CD	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	-RSB-	-rsb-	-RRB-	_	_	_
9	.	.	.	_	_	_

1	Scores	score	NNS	_	_	_
2	therefore	therefore	RB	_	_	_
3	represent	represent	VBP	_	_	_
4	the	the	DT	_	_	_
5	number	number	NN	_	_	_
6	of	of	IN	_	_	_
7	read	read	VBN	_	_	_
8	alignments	alignment	NNS	_	_	_
9	attributed	attribute	VBD	_	_	_
10	to	to	TO	_	_	_
11	each	each	DT	_	_	_
12	genomic	genomic	JJ	_	_	_
13	position	position	NN	_	_	_
14	under	under	IN	_	_	_
15	each	each	DT	_	_	_
16	scoring	score	VBG	_	_	_
17	scheme	scheme	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Extraction	extraction	NN	_	_	_
6	was	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	as	as	IN	_	_	_
9	described	describe	VBN	_	_	_
10	in	in	IN	_	_	_
11	detail	detail	NN	_	_	_
12	previously	previously	RB	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Li	Li	NNP	_	_	_
15	et	et	FW	_	_	_
16	al.	al.	FW	_	_	_
17	,	,	,	_	_	_
18	2012	2012	CD	_	_	_
19	;	;	:	_	_	_
20	Oh	oh	UH	_	_	_
21	et	et	FW	_	_	_
22	al.	al.	FW	_	_	_
23	,	,	,	_	_	_
24	2011	2011	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	200	200	CD	_	_	_
2	ml	ml	NN	_	_	_
3	of	of	IN	_	_	_
4	cell	cell	NN	_	_	_
5	culture	culture	NN	_	_	_
6	was	be	VBD	_	_	_
7	rapidly	rapidly	RB	_	_	_
8	filtered	filter	VBN	_	_	_
9	at	at	IN	_	_	_
10	37C	37c	NN	_	_	_
11	by	by	IN	_	_	_
12	passing	pass	VBG	_	_	_
13	through	through	IN	_	_	_
14	a	a	DT	_	_	_
15	nitrocellulose	nitrocellulose	NN	_	_	_
16	filter	filter	NN	_	_	_
17	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	pellets	pellet	NNS	_	_	_
3	was	be	VBD	_	_	_
4	were	be	VBD	_	_	_
5	rapidly	rapidly	RB	_	_	_
6	collected	collect	VBN	_	_	_
7	using	use	VBG	_	_	_
8	a	a	DT	_	_	_
9	pre-warmed	pre-warmed	JJ	_	_	_
10	metal	metal	NN	_	_	_
11	table	table	NN	_	_	_
12	crumber	crumber	NN	_	_	_
13	,	,	,	_	_	_
14	flash	flash	NN	_	_	_
15	frozen	freeze	VBN	_	_	_
16	in	in	IN	_	_	_
17	liquid	liquid	JJ	_	_	_
18	nitrogen	nitrogen	NN	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	combined	combine	VBN	_	_	_
22	with	with	IN	_	_	_
23	frozen	frozen	JJ	_	_	_
24	droplets	droplet	NNS	_	_	_
25	of	of	IN	_	_	_
26	lysis	lysis	NN	_	_	_
27	buffer	buffer	NN	_	_	_
28	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	and	and	CC	_	_	_
3	lysis	lysis	NN	_	_	_
4	buffer	buffer	NN	_	_	_
5	were	be	VBD	_	_	_
6	pulverized	pulverize	VBN	_	_	_
7	in	in	IN	_	_	_
8	10	10	CD	_	_	_
9	ml	ml	NN	_	_	_
10	canisters	canister	NNS	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Retsch	retsch	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	pre-chilled	pre-chilled	JJ	_	_	_
15	in	in	IN	_	_	_
16	liquid	liquid	JJ	_	_	_
17	nitrogen	nitrogen	NN	_	_	_
18	using	use	VBG	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	TissueLyser	TissueLyser	NNP	_	_	_
21	II	II	NNP	_	_	_
22	.	.	.	_	_	_

1	Pulverized	pulverize	VBN	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	thawed	thaw	VBN	_	_	_
5	on	on	IN	_	_	_
6	ice	ice	NN	_	_	_
7	and	and	CC	_	_	_
8	clarified	clarify	VBN	_	_	_
9	by	by	IN	_	_	_
10	centrifugation	centrifugation	NN	_	_	_
11	at	at	IN	_	_	_
12	4C	4c	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	NC000913	nc000913	NN	_	_	_
7	.2	.2	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	media	media	NNS	_	_	_
10	:	:	:	_	_	_
11	fully	fully	RB	_	_	_
12	supplemented	supplement	VBN	_	_	_
13	MOPS	mop	NNS	MED	_	_
14	glucose	glucose	NN	SUPP	_	_
15	media	media	NNS	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	mRNA-seq	mrna-seq	NN	_	_	_
18	in	in	IN	_	_	_
19	rich	rich	JJ	_	_	_
20	defined	define	VBN	_	_	_
21	media	media	NNS	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Ribosome	ribosome	NN	_	_	_
24	protected	protect	VBD	_	_	_
25	mRNA	mrna	NN	_	_	_
26	fragments	fragment	NNS	_	_	_
27	were	be	VBD	_	_	_
28	size	size	NN	_	_	_
29	selected	select	VBN	_	_	_
30	via	via	IN	_	_	_
31	gel	gel	NN	_	_	_
32	purification	purification	NN	_	_	_
33	,	,	,	_	_	_
34	and	and	CC	_	_	_
35	ligated	ligate	VBN	_	_	_
36	to	to	TO	_	_	_
37	5	5	CD	_	_	_
38	'	'	''	_	_	_
39	adenylated	adenylate	VBN	_	_	_
40	DNA	dna	NN	_	_	_
41	oligo	oligo	JJ	_	_	_
42	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	reverse	reverse	JJ	_	_	_
3	transcription	transcription	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	single	single	JJ	_	_	_
7	stranded	stranded	JJ	_	_	_
8	DNA	dna	NN	_	_	_
9	was	be	VBD	_	_	_
10	circularized	circularize	VBN	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	PCR	pcr	NN	_	_	_
14	amplified	amplify	VBD	_	_	_
15	-LSB-	-lsb-	-LRB-	_	_	_
16	Oh	oh	UH	_	_	_
17	et	et	FW	_	_	_
18	al	al	FW	_	_	_
19	,	,	,	_	_	_
20	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	147	147	CD	_	_	_
3	,	,	,	_	_	_
4	1295	1295	CD	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	2011	2011	CD	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	-RSB-	-rsb-	-RRB-	_	_	_
9	.	.	.	_	_	_

1	More	more	RBR	_	_	_
2	at	at	IN	_	_	_
3	G.W.	G.W.	NNP	_	_	_
4	Li	Li	NNP	_	_	_
5	,	,	,	_	_	_
6	D.	D.	NNP	_	_	_
7	Burkhardt	Burkhardt	NNP	_	_	_
8	,	,	,	_	_	_
9	C.A.	C.A.	NNP	_	_	_
10	Gross	Gross	NNP	_	_	_
11	,	,	,	_	_	_
12	J.	J.	NNP	_	_	_
13	S.	S.	NNP	_	_	_
14	Weissman	Weissman	NNP	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Cell	cell	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Sequenced	sequence	VBN	_	_	_
5	reads	read	VBZ	_	_	_
6	were	be	VBD	_	_	_
7	trimmed	trim	VBN	_	_	_
8	for	for	IN	_	_	_
9	adaptor	adaptor	NN	_	_	_
10	sequence	sequence	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Supplementary	supplementary	JJ	_	_	_
7	_	_	NN	_	_	_
8	files	file	NNS	_	_	_
9	_	_	IN	_	_	_
10	format	format	NN	_	_	_
11	_	_	NN	_	_	_
12	and	and	CC	_	_	_
13	_	_	NN	_	_	_
14	content	content	NN	_	_	_
15	:	:	:	_	_	_
16	wiggle	wiggle	NN	_	_	_
17	files	file	NNS	_	_	_
18	with	with	IN	_	_	_
19	two	two	CD	_	_	_
20	columns	column	NNS	_	_	_
21	:	:	:	_	_	_
22	first	first	JJ	_	_	_
23	column	column	NN	_	_	_
24	containing	contain	VBG	_	_	_
25	chromosome	chromosome	NN	_	_	_
26	positions	position	NNS	_	_	_
27	and	and	CC	_	_	_
28	second	second	JJ	_	_	_
29	column	column	NN	_	_	_
30	containing	contain	VBG	_	_	_
31	the	the	DT	_	_	_
32	number	number	NN	_	_	_
33	of	of	IN	_	_	_
34	reads	read	VBZ	_	_	_
35	mapped	map	VBN	_	_	_
36	to	to	TO	_	_	_
37	the	the	DT	_	_	_
38	position	position	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	see	see	VB	_	_	_
41	publication	publication	NN	_	_	_
42	for	for	IN	_	_	_
43	details	detail	NNS	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	remaining	remain	VBG	_	_	_
4	reads	read	VBZ	_	_	_
5	were	be	VBD	_	_	_
6	aligned	align	VBN	_	_	_
7	using	use	VBG	_	_	_
8	Bowtie	Bowtie	NNP	_	_	_
9	v0	v0	NN	_	_	_
10	.12.7	.12.7	CD	_	_	_
11	against	against	IN	_	_	_
12	E.	e.	FW	_	_	_
13	coli	coli	FW	_	_	_
14	MG1655	mg1655	NN	_	_	_
15	genome	genome	NN	_	_	_
16	using	use	VBG	_	_	_
17	parameters	parameter	NNS	_	_	_
18	-	-	:	_	_	_
19	v1	v1	SYM	_	_	_
20	-	-	:	_	_	_
21	m2	m2	SYM	_	_	_
22	-	-	:	_	_	_
23	k1	k1	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Trimmed	trim	VBD	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	sequentially	sequentially	RB	_	_	_
6	aligned	align	VBN	_	_	_
7	using	use	VBG	_	_	_
8	Bowtie	Bowtie	NNP	_	_	_
9	v0	v0	NN	_	_	_
10	.12.7	.12.7	CD	_	_	_
11	to	to	TO	_	_	_
12	E	E	NNP	_	_	_
13	coli	coli	NN	_	_	_
14	rRNA	rrna	NN	_	_	_
15	and	and	CC	_	_	_
16	noncoding	noncoding	JJ	_	_	_
17	RNA	rna	NN	_	_	_
18	allowing	allow	VBG	_	_	_
19	one	one	CD	_	_	_
20	mismatch	mismatch	NN	_	_	_
21	.	.	.	_	_	_

1	Reads	read	VBZ	_	_	_
2	aligning	align	VBG	_	_	_
3	to	to	TO	_	_	_
4	any	any	DT	_	_	_
5	of	of	IN	_	_	_
6	these	these	DT	_	_	_
7	indices	index	NNS	_	_	_
8	were	be	VBD	_	_	_
9	discarded	discard	VBN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	EC	EC	NNP	_	_	_
3	_	_	VBD	_	_	_
4	Cont1	cont1	NN	_	_	_
5	_	_	NN	_	_	_
6	DNA	dna	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	EC	ec	NN	_	_	_
9	_	_	CD	_	_	_
10	Cont1	cont1	NN	_	_	_
11	_	_	NN	_	_	_
12	RNA	rna	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	EC	ec	NN	_	_	_
15	_	_	CD	_	_	_
16	Cont2	cont2	NN	_	_	_
17	_	_	NN	_	_	_
18	DNA	dna	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	EC	ec	NN	_	_	_
21	_	_	CD	_	_	_
22	Cont2	cont2	NN	_	_	_
23	_	_	NN	_	_	_
24	RNA	rna	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	EC	ec	NN	_	_	_
27	_	_	CD	_	_	_
28	Trim1	trim1	NN	_	_	_
29	_	_	NN	_	_	_
30	DNA	dna	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	EC	ec	NN	_	_	_
33	_	_	CD	_	_	_
34	Trim1	trim1	NN	_	_	_
35	_	_	NN	_	_	_
36	RNA	rna	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	EC	ec	NN	_	_	_
39	_	_	CD	_	_	_
40	Trim2	trim2	NN	_	_	_
41	_	_	NN	_	_	_
42	DNA	dna	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	EC	ec	NN	_	_	_
45	_	_	CD	_	_	_
46	Trim2	trim2	NN	_	_	_
47	_	_	NN	_	_	_
48	RNA	rna	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	Escherichia	escherichia	FW	Organism	_	_
51	coli	coli	FW	Organism	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	For	for	IN	_	_	_
54	all	all	PDT	_	_	_
55	the	the	DT	_	_	_
56	samples	sample	NNS	_	_	_
57	;	;	:	_	_	_
58	when	when	WRB	_	_	_
59	1	1	CD	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	Genome	Genome	NNP	_	_	_
62	_	_	NNP	_	_	_
63	build	build	VB	_	_	_
64	:	:	:	_	_	_
65	Escherichia	escherichia	FW	Organism	_	_
66	coli	coli	FW	Organism	_	_
67	K-12	k-12	NN	_	_	_
68	,	,	,	_	_	_
69	substr	substr	NN	_	_	_
70	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	assembly	assembly	NN	_	_	_
4	ASM584v2	asm584v2	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Genome	Genome	NNP	_	_	_
8	_	_	NNP	_	_	_
9	build	build	VB	_	_	_
10	:	:	:	_	_	_
11	Streptococcus	streptococcus	NN	_	_	_
12	pneumoniae	pneumoniae	FW	_	_	_
13	D39	d39	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	assembly	assembly	NN	_	_	_
16	ASM1436v1	asm1436v1	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	genotype	genotype	NN	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	Illumina	Illumina	NNP	_	_	_
22	Casava	Casava	NNP	_	_	_
23	1.8	1.8	CD	_	_	_
24	software	software	NN	_	_	_
25	was	be	VBD	_	_	_
26	used	use	VBN	_	_	_
27	for	for	IN	_	_	_
28	basecalling	basecalling	NN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Library	Library	NNP	_	_	_
3	preparation	preparation	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	by	by	IN	_	_	_
7	vertis	vertis	NN	_	_	_
8	Biotechnologie	Biotechnologie	NNP	_	_	_
9	AG	AG	NNP	_	_	_
10	,	,	,	_	_	_
11	according	accord	VBG	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	following	follow	VBG	_	_	_
15	protocol	protocol	NN	_	_	_
16	:	:	:	_	_	_
17	RNA	rna	NN	_	_	_
18	samples	sample	NNS	_	_	_
19	were	be	VBD	_	_	_
20	first	first	JJ	_	_	_
21	treated	treat	VBN	_	_	_
22	with	with	IN	_	_	_
23	rDNase	rdnase	NN	_	_	_
24	.	.	.	_	_	_

1	From	from	IN	_	_	_
2	the	the	DT	_	_	_
3	total	total	JJ	_	_	_
4	RNA	rna	NN	_	_	_
5	samples	sample	NNS	_	_	_
6	,	,	,	_	_	_
7	ribosomal	ribosomal	JJ	_	_	_
8	RNA	rna	NN	_	_	_
9	molecules	molecule	NNS	_	_	_
10	were	be	VBD	_	_	_
11	depleted	deplete	VBN	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	Ribo-Zero	Ribo-Zero	NNP	_	_	_
15	rRNA	rrna	NN	_	_	_
16	Removal	removal	NN	_	_	_
17	Kit	kit	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Bacteria	bacterium	NNS	_	_	_
20	,	,	,	_	_	_
21	Epicentre	Epicentre	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

1	the	the	DT	_	_	_
2	rRNA	rrna	NN	_	_	_
3	depleted	deplete	VBN	_	_	_
4	RNA	rna	NN	_	_	_
5	samples	sample	NNS	_	_	_
6	were	be	VBD	_	_	_
7	fragmented	fragmented	JJ	_	_	_
8	with	with	IN	_	_	_
9	ultrasound	ultrasound	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	2	2	CD	_	_	_
12	pulses	pulse	NNS	_	_	_
13	of	of	IN	_	_	_
14	30	30	CD	_	_	_
15	sec	sec	NN	_	_	_
16	at	at	IN	_	_	_
17	4	4	CD	_	_	_
18	°C	°c	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	Firststrand	Firststrand	NNP	_	_	_
2	cDNA	cdna	NN	_	_	_
3	synthesis	synthesis	NN	_	_	_
4	was	be	VBD	_	_	_
5	primed	prime	VBN	_	_	_
6	with	with	IN	_	_	_
7	a	a	DT	_	_	_
8	N6	n6	NN	_	_	_
9	randomized	randomize	VBD	_	_	_
10	primer	primer	NN	_	_	_
11	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	,	,	,	_	_	_
3	Illumina	Illumina	NNP	_	_	_
4	TruSeq	TruSeq	NNP	_	_	_
5	sequencing	sequencing	NN	_	_	_
6	adapters	adapter	NNS	_	_	_
7	were	be	VBD	_	_	_
8	ligated	ligate	VBN	_	_	_
9	to	to	TO	_	_	_
10	the	the	DT	_	_	_
11	5	5	CD	_	_	_
12	'	'	''	_	_	_
13	and	and	CC	_	_	_
14	3	3	CD	_	_	_
15	'	'	''	_	_	_
16	ends	end	NNS	_	_	_
17	of	of	IN	_	_	_
18	the	the	DT	_	_	_
19	cDNA	cdna	NN	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cDNA	cdna	NN	_	_	_
3	was	be	VBD	_	_	_
4	finally	finally	RB	_	_	_
5	amplified	amplify	VBN	_	_	_
6	with	with	IN	_	_	_
7	PCR	pcr	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	16-18	16-18	CD	_	_	_
10	cycles	cycle	NNS	_	_	_
11	,	,	,	_	_	_
12	depending	depend	VBG	_	_	_
13	on	on	IN	_	_	_
14	sample	sample	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	using	use	VBG	_	_	_
17	a	a	DT	_	_	_
18	proof	proof	NN	_	_	_
19	reading	reading	NN	_	_	_
20	enzyme	enzyme	NN	_	_	_
21	.	.	.	_	_	_

1	Aliquots	aliquot	NNS	_	_	_
2	of	of	IN	_	_	_
3	each	each	DT	_	_	_
4	library	library	NN	_	_	_
5	were	be	VBD	_	_	_
6	analyzed	analyze	VBN	_	_	_
7	by	by	IN	_	_	_
8	capillary	capillary	JJ	_	_	_
9	electrophoresis	electrophoresis	NN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Library	Library	NNP	_	_	_
3	preparation	preparation	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	by	by	IN	_	_	_
7	vertis	vertis	NN	_	_	_
8	Biotechnologie	Biotechnologie	NNP	_	_	_
9	AG	AG	NNP	_	_	_
10	,	,	,	_	_	_
11	according	accord	VBG	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	following	follow	VBG	_	_	_
15	protocol	protocol	NN	_	_	_
16	:	:	:	_	_	_
17	the	the	DT	_	_	_
18	DNA	dna	NN	_	_	_
19	samples	sample	NNS	_	_	_
20	were	be	VBD	_	_	_
21	treated	treat	VBN	_	_	_
22	with	with	IN	_	_	_
23	ultrasound	ultrasound	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	3-5	3-5	CD	_	_	_
26	pulses	pulse	NNS	_	_	_
27	of	of	IN	_	_	_
28	30	30	CD	_	_	_
29	sec	sec	NN	_	_	_
30	at	at	IN	_	_	_
31	4	4	CD	_	_	_
32	°C	°c	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	end-repair	end-repair	NN	_	_	_
3	,	,	,	_	_	_
4	TruSeq	truseq	NN	_	_	_
5	sequencing	sequencing	NN	_	_	_
6	adapters	adapter	NNS	_	_	_
7	were	be	VBD	_	_	_
8	ligated	ligate	VBN	_	_	_
9	to	to	TO	_	_	_
10	the	the	DT	_	_	_
11	DNA	dna	NN	_	_	_
12	fragments	fragment	NNS	_	_	_
13	.	.	.	_	_	_

1	Finally	finally	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	DNA	dna	NN	_	_	_
5	was	be	VBD	_	_	_
6	PCR-amplified	pcr-amplified	JJ	_	_	_
7	to	to	TO	_	_	_
8	about	about	RB	_	_	_
9	20-30	20-30	CD	_	_	_
10	ng	ng	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	molecule	molecule	NN	_	_	_
13	subtype	subtype	NN	_	_	_
14	:	:	:	_	_	_
15	total	total	JJ	_	_	_
16	RNA	rna	NN	_	_	_
17	,	,	,	_	_	_
18	rRNA	rrna	NN	_	_	_
19	depleted	deplete	VBD	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	OTHER	OTHER	NNP	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	Overnight	overnight	JJ	_	_	_
24	cultures	culture	NNS	_	_	_
25	of	of	IN	_	_	_
26	strain	strain	NN	_	_	_
27	JM83	jm83	NN	_	_	_
28	were	be	VBD	_	_	_
29	diluted	dilute	VBN	_	_	_
30	1	1	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Reads	read	VBZ	_	_	_
33	Per	per	IN	_	_	_
34	Kilobase	kilobase	NN	_	_	_
35	of	of	IN	_	_	_
36	exon	exon	NN	_	_	_
37	per	per	IN	_	_	_
38	Megabase	megabase	NN	_	_	_
39	of	of	IN	_	_	_
40	library	library	NN	_	_	_
41	size	size	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	RPKM	rpkm	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	were	be	VBD	_	_	_
46	calculated	calculate	VBN	_	_	_
47	using	use	VBG	_	_	_
48	a	a	DT	_	_	_
49	protocol	protocol	NN	_	_	_
50	from	from	IN	_	_	_
51	Chepelev	Chepelev	NNP	_	_	_
52	et	et	FW	_	_	_
53	al.	al.	FW	_	_	_
54	,	,	,	_	_	_
55	Nucleic	Nucleic	NNP	_	_	_
56	Acids	Acids	NNP	_	_	_
57	Research	Research	NNP	_	_	_
58	,	,	,	_	_	_
59	2009	2009	CD	_	_	_
60	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	short	short	RB	_	_	_
3	,	,	,	_	_	_
4	exons	exon	NNS	_	_	_
5	from	from	IN	_	_	_
6	all	all	DT	_	_	_
7	isoforms	isoform	NNS	_	_	_
8	of	of	IN	_	_	_
9	a	a	DT	_	_	_
10	gene	gene	NN	_	_	_
11	were	be	VBD	_	_	_
12	merged	merge	VBN	_	_	_
13	to	to	TO	_	_	_
14	create	create	VB	_	_	_
15	one	one	CD	_	_	_
16	meta-transcript	meta-transcript	JJ	_	_	_
17	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	number	number	NN	_	_	_
3	of	of	IN	_	_	_
4	reads	read	VBZ	_	_	_
5	falling	fall	VBG	_	_	_
6	in	in	IN	_	_	_
7	the	the	DT	_	_	_
8	exons	exon	NNS	_	_	_
9	of	of	IN	_	_	_
10	this	this	DT	_	_	_
11	meta-transcript	meta-transcript	JJ	_	_	_
12	were	be	VBD	_	_	_
13	counted	count	VBN	_	_	_
14	and	and	CC	_	_	_
15	normalized	normalize	VBN	_	_	_
16	by	by	IN	_	_	_
17	the	the	DT	_	_	_
18	size	size	NN	_	_	_
19	of	of	IN	_	_	_
20	the	the	DT	_	_	_
21	meta-transcript	meta-transcript	JJ	_	_	_
22	and	and	CC	_	_	_
23	by	by	IN	_	_	_
24	the	the	DT	_	_	_
25	size	size	NN	_	_	_
26	of	of	IN	_	_	_
27	the	the	DT	_	_	_
28	library	library	NN	_	_	_
29	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	the	the	DT	_	_	_
3	S.	S.	NNP	_	_	_
4	pneumoniae	pneumoniae	FW	_	_	_
5	samples	sample	NNS	_	_	_
6	this	this	DT	_	_	_
7	was	be	VBD	_	_	_
8	done	do	VBN	_	_	_
9	internally	internally	RB	_	_	_
10	by	by	IN	_	_	_
11	Rockhopper	Rockhopper	NNP	_	_	_
12	version	version	NN	_	_	_
13	1.21	1.21	CD	_	_	_
14	after	after	IN	_	_	_
15	aligning	align	VBG	_	_	_
16	reads	read	VBZ	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	S.	S.	NNP	_	_	_
5	pneumoniae	pneumoniae	FW	_	_	_
6	reads	read	VBZ	_	_	_
7	were	be	VBD	_	_	_
8	mapped	map	VBN	_	_	_
9	to	to	TO	_	_	_
10	the	the	DT	_	_	_
11	D39	d39	NN	_	_	_
12	whole	whole	JJ	_	_	_
13	genome	genome	NN	_	_	_
14	with	with	IN	_	_	_
15	Rockhopper	rockhopper	JJ	_	_	_
16	version	version	NN	_	_	_
17	1.21	1.21	CD	_	_	_
18	,	,	,	_	_	_
19	using	use	VBG	_	_	_
20	default	default	NN	_	_	_
21	parameters	parameter	NNS	_	_	_
22	.	.	.	_	_	_

1	E.	e.	FW	_	_	_
2	coli	coli	FW	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	mapped	map	VBN	_	_	_
6	to	to	TO	_	_	_
7	the	the	DT	_	_	_
8	K-12	k-12	NN	_	_	_
9	,	,	,	_	_	_
10	substr	substr	NN	_	_	_
11	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	whole	whole	JJ	_	_	_
3	genome	genome	NN	_	_	_
4	with	with	IN	_	_	_
5	Bowtie	bowtie	NN	_	_	_
6	2	2	CD	_	_	_
7	,	,	,	_	_	_
8	using	use	VBG	_	_	_
9	parameters	parameter	NNS	_	_	_
10	--	--	:	_	_	_
11	mixed	mixed	JJ	_	_	_
12	--	--	:	_	_	_
13	discordant	discordant	JJ	_	_	_
14	-	-	:	_	_	_
15	D	d	NN	_	_	_
16	10	10	CD	_	_	_
17	-	-	:	_	_	_
18	R	r	NN	_	_	_
19	2	2	CD	_	_	_
20	-	-	:	_	_	_
21	N	n	NN	_	_	_
22	0	0	CD	_	_	_
23	-	-	:	_	_	_
24	L	l	NN	_	_	_
25	22	22	CD	_	_	_
26	-	-	:	_	_	_
27	i	i	FW	_	_	_
28	S	s	NN	_	_	_
29	,0,2.50	,0,2.50	CD	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	JM83	jm83	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Supplementary	supplementary	JJ	_	_	_
7	_	_	NN	_	_	_
8	files	file	NNS	_	_	_
9	_	_	IN	_	_	_
10	format	format	NN	_	_	_
11	_	_	NN	_	_	_
12	and	and	CC	_	_	_
13	_	_	NN	_	_	_
14	content	content	NN	_	_	_
15	:	:	:	_	_	_
16	tab-delimited	tab-delimited	JJ	_	_	_
17	text	text	NN	_	_	_
18	files	file	NNS	_	_	_
19	include	include	VBP	_	_	_
20	RPKM	rpkm	NN	_	_	_
21	values	value	NNS	_	_	_
22	for	for	IN	_	_	_
23	each	each	DT	_	_	_
24	Sample	Sample	NNP	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	treated	treat	VBN	_	_	_
3	with	with	IN	_	_	_
4	:	:	:	_	_	_
5	0.5	0.5	CD	_	_	_
6	μg	μg	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	treated	treat	VBN	_	_	_
9	with	with	IN	_	_	_
10	:	:	:	_	_	_
11	none	none	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	untreated	untreated	JJ	_	_	_
14	control	control	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Trimethoprim-treated	trimethoprim-treated	JJ	_	_	_
18	E.	e.	FW	_	_	_
19	coli	coli	FW	_	_	_
20	cells	cell	NNS	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
22	Untreated	untreated	JJ	_	_	_
23	E.	e.	FW	_	_	_
24	coli	coli	FW	_	_	_
25	cells	cell	NNS	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	BW25113-pCA24N	bw25113-pca24n	NN	_	_	_
28	_	_	CD	_	_	_
29	arT	art	NN	_	_	_
30	LB	lb	NN	_	_	_
31	90	90	CD	_	_	_
32	min	min	NN	_	_	_
33	1	1	CD	_	_	_
34	mM	mm	NN	KWSUPP	_	_
35	IPTG	iptg	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	BW25113-pCA24N	bw25113-pca24n	NN	_	_	_
38	LB	lb	NN	_	_	_
39	90	90	CD	_	_	_
40	min	min	NN	_	_	_
41	1	1	CD	_	_	_
42	mM	mm	NN	KWSUPP	_	_
43	IPTG	iptg	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	Cells	cell	NNS	_	_	_
46	were	be	VBD	_	_	_
47	lysed	lyse	VBN	_	_	_
48	using	use	VBG	_	_	_
49	a	a	DT	_	_	_
50	bead	bead	NN	_	_	_
51	beater	beater	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	Biospec	biospec	NN	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	and	and	CC	_	_	_
56	mRNA	mrna	NN	_	_	_
57	was	be	VBD	_	_	_
58	isolated	isolate	VBN	_	_	_
59	using	use	VBG	_	_	_
60	a	a	DT	_	_	_
61	Qiagen	Qiagen	NNP	_	_	_
62	RNeasy	RNeasy	NNP	_	_	_
63	mini	minus	NNS	_	_	_
64	kit	kit	NN	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	Cat	cat	NN	_	_	_
67	#	#	#	_	_	_
68	74104	74104	CD	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	pelleted	pellete	VBN	_	_	_
5	in	in	IN	_	_	_
6	the	the	DT	_	_	_
7	presence	presence	NN	_	_	_
8	of	of	IN	_	_	_
9	RNALater	rnalater	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Applied	Applied	NNP	_	_	_
12	Biosystems	Biosystems	NNPS	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	and	and	CC	_	_	_
15	flash	flash	NN	_	_	_
16	frozen	freeze	VBN	_	_	_
17	in	in	IN	_	_	_
18	ethanol-dry	ethanol-dry	JJ	_	_	_
19	ice	ice	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	was	be	VBD	_	_	_
4	analyzed	analyze	VBN	_	_	_
5	in	in	IN	_	_	_
6	the	the	DT	_	_	_
7	Affymetrix	Affymetrix	NNP	_	_	_
8	GenomeChipOperating	GenomeChipOperating	NNP	_	_	_
9	Software	Software	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	GCOS	GCOS	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	BW25113	bw25113	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	genotype	genotype	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	overexpression	overexpression	NN	_	_	_
9	of	of	IN	_	_	_
10	arT	art	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	pCA24N	pca24n	NN	_	_	_
13	_	_	CD	_	_	_
14	arT	art	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	overexpression	overexpression	NN	_	_	_
18	of	of	IN	_	_	_
19	empty	empty	JJ	_	_	_
20	vector	vector	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	pCA24N	pca24n	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Strains	strain	NNS	_	_	_
26	were	be	VBD	_	_	_
27	grown	grow	VBN	_	_	_
28	in	in	IN	_	_	_
29	LBCm30	lbcm30	NN	_	_	_
30	at	at	IN	_	_	_
31	37	37	CD	_	_	_
32	°C	°c	NN	_	_	_
33	with	with	IN	_	_	_
34	shaking	shake	VBG	_	_	_
35	at	at	IN	_	_	_
36	250	250	CD	_	_	_
37	rpm	rpm	NN	_	_	_
38	.	.	.	_	_	_

1	Overnight	overnight	JJ	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	diluted	dilute	VBN	_	_	_
5	into	into	IN	_	_	_
6	fresh	fresh	JJ	_	_	_
7	LBCm30	lbcm30	NN	_	_	_
8	,	,	,	_	_	_
9	grown	grow	VBN	_	_	_
10	for	for	IN	_	_	_
11	2.5	2.5	CD	_	_	_
12	h	h	NN	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	induced	induce	VBN	_	_	_
16	with	with	IN	_	_	_
17	1	1	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	IPTG	iptg	NN	_	_	_
20	for	for	IN	_	_	_
21	90	90	CD	_	_	_
22	min	min	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	final	final	JJ	_	_	_
25	OD600	od600	NN	_	_	_
26	=	=	JJ	_	_	_
27	1.6	1.6	CD	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	2	2	CD	_	_	_
5	%	%	NN	_	_	_
6	NaCl	nacl	NN	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	E.	E.	NNP	_	_	_
9	coli	coli	NN	_	_	_
10	3.5	3.5	CD	_	_	_
11	%	%	NN	_	_	_
12	NaCl	nacl	NN	_	_	_
13	,	,	,	_	_	_
14	replicate	replicate	VB	_	_	_
15	1	1	CD	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	E.	E.	NNP	_	_	_
18	coli	coli	NN	_	_	_
19	3.5	3.5	CD	_	_	_
20	%	%	NN	_	_	_
21	NaCl	nacl	NN	_	_	_
22	,	,	,	_	_	_
23	replicate	replicate	VB	_	_	_
24	2	2	CD	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	E.	E.	NNP	_	_	_
27	coli	coli	NN	_	_	_
28	4.5	4.5	CD	_	_	_
29	%	%	NN	_	_	_
30	NaCl	nacl	NN	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	E.	E.	NNP	_	_	_
33	coli	coli	NN	_	_	_
34	5.5	5.5	CD	_	_	_
35	%	%	NN	_	_	_
36	NaCl	nacl	NN	_	_	_
37	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
38	E.	E.	NNP	_	_	_
39	coli	coli	NN	_	_	_
40	5	5	CD	_	_	_
41	%	%	NN	_	_	_
42	NaCl	nacl	NN	_	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	E.	E.	NNP	_	_	_
45	coli	coli	NN	_	_	_
46	,	,	,	_	_	_
47	stressed	stress	VBN	_	_	_
48	by	by	IN	_	_	_
49	NaCl	nacl	NN	_	_	_
50	,	,	,	_	_	_
51	in	in	IN	_	_	_
52	presence	presence	NN	_	_	_
53	of	of	IN	_	_	_
54	glycine	glycine	NN	_	_	_
55	betaine	betaine	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	E.	e.	FW	_	_	_
58	coli	coli	FW	_	_	_
59	was	be	VBD	_	_	_
60	grown	grow	VBN	_	_	_
61	to	to	TO	_	_	_
62	exponential	exponential	JJ	GrowthPhase	_	_
63	phase	phase	NN	GrowthPhase	_	_
64	in	in	IN	_	_	_
65	glucose	glucose	NN	SUPP	_	_
66	minimal	minimal	JJ	_	_	_
67	medium	medium	NN	_	_	_
68	in	in	IN	_	_	_
69	the	the	DT	_	_	_
70	presence	presence	NN	_	_	_
71	of	of	IN	_	_	_
72	the	the	DT	_	_	_
73	osmoprotectant	osmoprotectant	JJ	_	_	_
74	glycine	glycine	NN	_	_	_
75	beatine	beatine	NN	_	_	_
76	with	with	IN	_	_	_
77	a	a	DT	_	_	_
78	range	range	NN	_	_	_
79	of	of	IN	_	_	_
80	salt	salt	NN	_	_	_
81	concentrations	concentration	NNS	_	_	_
82	at	at	IN	_	_	_
83	2	2	CD	_	_	_
84	,	,	,	_	_	_
85	3.5	3.5	CD	_	_	_
86	-LRB-	-lrb-	-LRB-	_	_	_
87	2	2	CD	_	_	_
88	repeats	repeat	NNS	_	_	_
89	-RRB-	-rrb-	-RRB-	_	_	_
90	,	,	,	_	_	_
91	4.5	4.5	CD	_	_	_
92	,	,	,	_	_	_
93	5	5	CD	_	_	_
94	and	and	CC	_	_	_
95	5.5	5.5	CD	_	_	_
96	%	%	NN	_	_	_
97	NaCl	nacl	NN	_	_	_
98	.	.	.	_	_	_

1	E.	e.	FW	_	_	_
2	coli	coli	FW	_	_	_
3	were	be	VBD	_	_	_
4	inoculated	inoculate	VBN	_	_	_
5	at	at	IN	_	_	_
6	104	104	CD	_	_	_
7	cfu	cfu	NN	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	Escherichia	escherichia	FW	Organism	_	_
10	coli	coli	FW	Organism	_	_
11	K-12	k-12	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
13	Genomic	genomic	JJ	_	_	_
14	DNA	dna	NN	_	_	_
15	was	be	VBD	_	_	_
16	purified	purify	VBN	_	_	_
17	from	from	IN	_	_	_
18	exponentially	exponentially	RB	_	_	_
19	growing	grow	VBG	_	_	_
20	cells	cell	NNS	_	_	_
21	by	by	IN	_	_	_
22	lysis	lysis	NN	_	_	_
23	in	in	IN	_	_	_
24	lysozyme	lysozyme	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	growth	growth	NN	_	_	_
27	phase	phase	NN	_	_	_
28	:	:	:	_	_	_
29	exponential	exponential	JJ	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	growth	growth	NN	_	_	_
32	phase	phase	NN	_	_	_
33	:	:	:	_	_	_
34	Exponential	exponential	JJ	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	strain	strain	NN	_	_	_
37	:	:	:	_	_	_
38	K12	k12	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
40	The	the	DT	_	_	_
41	analysis	analysis	NN	_	_	_
42	of	of	IN	_	_	_
43	the	the	DT	_	_	_
44	data	datum	NNS	_	_	_
45	is	be	VBZ	_	_	_
46	based	base	VBN	_	_	_
47	on	on	IN	_	_	_
48	cross	cross	NN	_	_	_
49	validation	validation	NN	_	_	_
50	with	with	IN	_	_	_
51	datasets	dataset	NNS	_	_	_
52	generated	generate	VBN	_	_	_
53	by	by	IN	_	_	_
54	Monte-Carlo	Monte-Carlo	NNP	_	_	_
55	simulation	simulation	NN	_	_	_
56	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	null	null	JJ	_	_	_
3	hypothesis	hypothesis	NN	_	_	_
4	was	be	VBD	_	_	_
5	that	that	IN	_	_	_
6	the	the	DT	_	_	_
7	gene	gene	NN	_	_	_
8	expression	expression	NN	_	_	_
9	changes	change	NNS	_	_	_
10	monotonously	monotonously	RB	_	_	_
11	as	as	IN	_	_	_
12	a	a	DT	_	_	_
13	function	function	NN	_	_	_
14	of	of	IN	_	_	_
15	NaCl	nacl	NN	_	_	_
16	concentration	concentration	NN	_	_	_
17	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	existence	existence	NN	_	_	_
3	of	of	IN	_	_	_
4	a	a	DT	_	_	_
5	deviation	deviation	NN	_	_	_
6	from	from	IN	_	_	_
7	monotony	monotony	NN	_	_	_
8	was	be	VBD	_	_	_
9	tested	test	VBN	_	_	_
10	by	by	IN	_	_	_
11	F-tests	f-test	NNS	_	_	_
12	for	for	IN	_	_	_
13	each	each	DT	_	_	_
14	gene	gene	NN	_	_	_
15	probe	probe	NN	_	_	_
16	.	.	.	_	_	_

1	By	by	IN	_	_	_
2	comparing	compare	VBG	_	_	_
3	the	the	DT	_	_	_
4	number	number	NN	_	_	_
5	of	of	IN	_	_	_
6	probes	probe	NNS	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	lowest	lowest	JJS	_	_	_
10	p	p	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	F	f	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	values	value	NNS	_	_	_
15	for	for	IN	_	_	_
16	each	each	DT	_	_	_
17	NaCl	nacl	NN	_	_	_
18	concentrations	concentration	NNS	_	_	_
19	with	with	IN	_	_	_
20	analogous	analogous	JJ	_	_	_
21	results	result	NNS	_	_	_
22	generated	generate	VBN	_	_	_
23	from	from	IN	_	_	_
24	Monte-Carlo	Monte-Carlo	NNP	_	_	_
25	sampling	sampling	NN	_	_	_
26	of	of	IN	_	_	_
27	the	the	DT	_	_	_
28	null	null	JJ	_	_	_
29	hypothesis	hypothesis	NN	_	_	_
30	,	,	,	_	_	_
31	we	we	PRP	_	_	_
32	show	show	VBP	_	_	_
33	that	that	IN	_	_	_
34	it	it	PRP	_	_	_
35	is	be	VBZ	_	_	_
36	very	very	RB	_	_	_
37	unlikely	unlikely	JJ	_	_	_
38	that	that	IN	_	_	_
39	a	a	DT	_	_	_
40	switch	switch	NN	_	_	_
41	between	between	IN	_	_	_
42	4.5	4.5	CD	_	_	_
43	and	and	CC	_	_	_
44	5	5	CD	_	_	_
45	%	%	NN	_	_	_
46	NaCl	nacl	NN	_	_	_
47	could	could	MD	_	_	_
48	have	have	VB	_	_	_
49	happened	happen	VBN	_	_	_
50	by	by	IN	_	_	_
51	chance	chance	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	in	in	IN	_	_	_
54	fact	fact	NN	_	_	_
55	p	p	NN	_	_	_
56	<<	<<	CD	_	_	_
57	0.01	0.01	CD	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	normalised	normalised	JJ	_	_	_
6	manually	manually	RB	_	_	_
7	in	in	IN	_	_	_
8	Excel	Excel	NNP	_	_	_
9	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	spot	spot	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	median	median	NN	_	_	_
7	of	of	IN	_	_	_
8	the	the	DT	_	_	_
9	spot	spot	NN	_	_	_
10	intensity	intensity	NN	_	_	_
11	minus	minus	CC	_	_	_
12	the	the	DT	_	_	_
13	background	background	NN	_	_	_
14	were	be	VBD	_	_	_
15	considered	consider	VBN	_	_	_
16	.	.	.	_	_	_

1	Because	because	IN	_	_	_
2	we	we	PRP	_	_	_
3	wanted	want	VBD	_	_	_
4	to	to	TO	_	_	_
5	compare	compare	VB	_	_	_
6	different	different	JJ	_	_	_
7	environmental	environmental	JJ	_	_	_
8	conditions	condition	NNS	_	_	_
9	,	,	,	_	_	_
10	the	the	DT	_	_	_
11	cDNA	cdna	NN	_	_	_
12	signal	signal	NN	_	_	_
13	in	in	IN	_	_	_
14	each	each	DT	_	_	_
15	condition	condition	NN	_	_	_
16	was	be	VBD	_	_	_
17	normalised	normalised	JJ	_	_	_
18	to	to	TO	_	_	_
19	that	that	DT	_	_	_
20	of	of	IN	_	_	_
21	gDNA	gdna	NN	_	_	_
22	with	with	IN	_	_	_
23	M	m	NN	_	_	_
24	=	=	JJ	_	_	_
25	ln	ln	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	cDNA	cdna	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	0.5	0.5	CD	_	_	_
30	mg	mg	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	antibody	antibody	NN	_	_	_
33	:	:	:	_	_	_
34	anti-DksA	anti-dksa	JJ	_	_	_
35	rabbit	rabbit	NN	_	_	_
36	polyclonal	polyclonal	JJ	_	_	_
37	antisera	antisera	NNS	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
39	antibody	antibody	NN	_	_	_
40	:	:	:	_	_	_
41	anti-RNAP	anti-rnap	JJ	_	_	_
42	b	b	NN	_	_	_
43	subunit	subunit	NN	_	_	_
44	NT63	nt63	NN	_	_	_
45	monoclonal	monoclonal	JJ	_	_	_
46	antibodies	antibody	NNS	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
48	antibody	antibody	NN	_	_	_
49	:	:	:	_	_	_
50	anti-s70	anti-s70	JJ	_	_	_
51	monoclonal	monoclonal	JJ	_	_	_
52	antibodies	antibody	NNS	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
54	antibody	antibody	NN	_	_	_
55	:	:	:	_	_	_
56	None	none	NN	_	_	_
57	,	,	,	_	_	_
58	input	input	NN	_	_	_
59	DNA	dna	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	Cells	cell	NNS	_	_	_
62	were	be	VBD	_	_	_
63	fixed	fix	VBN	_	_	_
64	with	with	IN	_	_	_
65	1	1	CD	_	_	_
66	%	%	NN	_	_	_
67	formaldehyde	formaldehyde	NN	_	_	_
68	for	for	IN	_	_	_
69	5	5	CD	_	_	_
70	min	min	NN	_	_	_
71	before	before	IN	_	_	_
72	quenching	quench	VBG	_	_	_
73	with	with	IN	_	_	_
74	ice-cold	ice-cold	JJ	_	_	_
75	glycine	glycine	NN	_	_	_
76	-LRB-	-lrb-	-LRB-	_	_	_
77	100mM	100mm	NN	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	harvested	harvest	VBN	_	_	_
4	,	,	,	_	_	_
5	washed	wash	VBN	_	_	_
6	with	with	IN	_	_	_
7	ice-cold	ice-cold	JJ	_	_	_
8	PBS	PBS	NNP	_	_	_
9	and	and	CC	_	_	_
10	flash-frozen	flash-frozen	JJ	_	_	_
11	in	in	IN	_	_	_
12	liquid	liquid	JJ	_	_	_
13	nitrogen	nitrogen	NN	_	_	_
14	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	pellets	pellet	NNS	_	_	_
3	were	be	VBD	_	_	_
4	resuspended	resuspend	VBN	_	_	_
5	in	in	IN	_	_	_
6	500	500	CD	_	_	_
7	ml	ml	NN	_	_	_
8	of	of	IN	_	_	_
9	IP	IP	NNP	_	_	_
10	buffer	buffer	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	100	100	CD	_	_	_
13	mM	mm	NN	KWSUPP	_	_
14	Tris	Tris	NNP	_	_	_
15	pH	ph	NN	_	_	_
16	8	8	CD	_	_	_
17	,	,	,	_	_	_
18	300mM	300mM	NNP	_	_	_
19	NaCl	nacl	NN	_	_	_
20	,	,	,	_	_	_
21	2	2	CD	_	_	_
22	%	%	NN	_	_	_
23	TritonX-100	tritonx-100	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	and	and	CC	_	_	_
26	sonicated	sonicate	VBN	_	_	_
27	using	use	VBG	_	_	_
28	a	a	DT	_	_	_
29	Misonix	Misonix	NNP	_	_	_
30	sonicator	sonicator	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	S-4000	s-4000	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	with	with	IN	_	_	_
35	a	a	DT	_	_	_
36	cup	cup	NN	_	_	_
37	horn	horn	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	431C	431c	NN	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	set	set	NN	_	_	_
42	at	at	IN	_	_	_
43	60	60	CD	_	_	_
44	%	%	NN	_	_	_
45	output	output	NN	_	_	_
46	,	,	,	_	_	_
47	10	10	CD	_	_	_
48	sec	sec	NN	_	_	_
49	ON	ON	NNP	_	_	_
50	and	and	CC	_	_	_
51	10	10	CD	_	_	_
52	sec	sec	NN	_	_	_
53	OFF	off	NN	_	_	_
54	,	,	,	_	_	_
55	for	for	IN	_	_	_
56	a	a	DT	_	_	_
57	total	total	JJ	_	_	_
58	sonication	sonication	NN	_	_	_
59	time	time	NN	_	_	_
60	of	of	IN	_	_	_
61	16	16	CD	_	_	_
62	min	min	NN	_	_	_
63	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	treated	treat	VBN	_	_	_
5	for	for	IN	_	_	_
6	one	one	CD	_	_	_
7	hour	hour	NN	_	_	_
8	at	at	IN	_	_	_
9	4	4	CD	_	_	_
10	°C	°c	NN	_	_	_
11	with	with	IN	_	_	_
12	RNase	rnase	NN	_	_	_
13	A	a	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	2	2	CD	_	_	_
16	ng	ng	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	DdksA	ddksa	NN	_	_	_
19	cells	cell	NNS	_	_	_
20	were	be	VBD	_	_	_
21	grown	grow	VBN	_	_	_
22	in	in	IN	_	_	_
23	MOPS	MOPS	NNP	MED	_	_
24	medium	medium	NN	_	_	_
25	with	with	IN	_	_	_
26	0.2	0.2	CD	_	_	_
27	%	%	NN	_	_	_
28	glucose	glucose	NN	SUPP	_	_
29	,	,	,	_	_	_
30	leucine	leucine	NN	SUPP	_	_
31	,	,	,	_	_	_
32	isoleucine	isoleucine	NN	_	_	_
33	,	,	,	_	_	_
34	valine	valine	NN	_	_	_
35	,	,	,	_	_	_
36	glycine	glycine	NN	_	_	_
37	,	,	,	_	_	_
38	phenylalanine	phenylalanine	NN	SUPP	_	_
39	,	,	,	_	_	_
40	threonine	threonine	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	40	40	CD	_	_	_
43	mg	mg	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	DksA	dksa	NN	_	_	_
46	ChIP	chip	NN	_	_	_
47	DNA	dna	NN	_	_	_
48	from	from	IN	_	_	_
49	DdksA	ddksa	NN	_	_	_
50	cells	cell	NNS	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
52	DksA	dksa	NN	_	_	_
53	ChIP	chip	NN	_	_	_
54	DNA	dna	NN	_	_	_
55	from	from	IN	_	_	_
56	wt	wt	JJ	_	_	_
57	cells	cell	NNS	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	DksA	dksa	NN	_	_	_
60	_	_	CD	_	_	_
61	DdksA	ddksa	NN	_	_	_
62	_	_	NN	_	_	_
63	untreated	untreated	JJ	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	DksA	dksa	NN	_	_	_
66	_	_	CD	_	_	_
67	wt	wt	JJ	_	_	_
68	_	_	NN	_	_	_
69	untreated	untreated	JJ	_	_	_
70	_	_	NN	_	_	_
71	rep1	rep1	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	DksA	dksa	NN	_	_	_
74	_	_	CD	_	_	_
75	wt	wt	JJ	_	_	_
76	_	_	NN	_	_	_
77	untreated	untreated	JJ	_	_	_
78	_	_	NN	_	_	_
79	rep2	rep2	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	Escherichia	escherichia	FW	Organism	_	_
82	coli	coli	FW	Organism	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	genotype	genotype	NN	_	_	_
85	:	:	:	_	_	_
86	MG1655	mg1655	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	genotype	genotype	NN	_	_	_
89	:	:	:	_	_	_
90	MG1655	mg1655	NN	_	_	_
91	DdksA	ddksa	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	Input	input	NN	_	_	_
94	DNA	dna	NN	_	_	_
95	from	from	IN	_	_	_
96	DdksA	ddksa	NN	_	_	_
97	cells	cell	NNS	_	_	_
98	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
99	Input	Input	NNP	_	_	_
100	DNA	dna	NN	_	_	_
101	from	from	IN	_	_	_
102	starved	starve	VBN	_	_	_
103	DdksA	ddksa	NN	_	_	_
104	cells	cell	NNS	_	_	_
105	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
106	Input	Input	NNP	_	_	_
107	DNA	dna	NN	_	_	_
108	from	from	IN	_	_	_
109	starved	starve	VBN	_	_	_
110	wt	wt	JJ	_	_	_
111	cells	cell	NNS	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
113	Input	input	NN	_	_	_
114	DNA	dna	NN	_	_	_
115	from	from	IN	_	_	_
116	wt	wt	JJ	_	_	_
117	cells	cell	NNS	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
119	None	none	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	RNAP	rnap	NN	_	_	_
122	ChIP	chip	NN	_	_	_
123	DNA	dna	NN	_	_	_
124	from	from	IN	_	_	_
125	DdksA	ddksa	NN	_	_	_
126	cells	cell	NNS	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
128	RNAP	rnap	NN	_	_	_
129	ChIP	chip	NN	_	_	_
130	DNA	dna	NN	_	_	_
131	from	from	IN	_	_	_
132	starved	starve	VBN	_	_	_
133	DdksA	ddksa	NN	_	_	_
134	cells	cell	NNS	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
136	RNAP	rnap	NN	_	_	_
137	ChIP	chip	NN	_	_	_
138	DNA	dna	NN	_	_	_
139	from	from	IN	_	_	_
140	starved	starve	VBN	_	_	_
141	wt	wt	JJ	_	_	_
142	cells	cell	NNS	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
144	RNAP	rnap	NN	_	_	_
145	ChIP	chip	NN	_	_	_
146	DNA	dna	NN	_	_	_
147	from	from	IN	_	_	_
148	wt	wt	JJ	_	_	_
149	cells	cell	NNS	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
151	RNAP	rnap	NN	_	_	_
152	_	_	NN	_	_	_
153	DdksA	ddksa	NN	_	_	_
154	_	_	CD	_	_	_
155	SHX	SHX	NNP	_	_	_
156	_	_	CD	_	_	_
157	rep1	rep1	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	RNAP	rnap	NN	_	_	_
160	_	_	CD	_	_	_
161	DdksA	ddksa	NN	_	_	_
162	_	_	CD	_	_	_
163	SHX	SHX	NNP	_	_	_
164	_	_	CD	_	_	_
165	rep2	rep2	NN	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	RNAP	rnap	NN	_	_	_
168	_	_	CD	_	_	_
169	DdksA	ddksa	NN	_	_	_
170	_	_	NN	_	_	_
171	untreated	untreated	JJ	_	_	_
172	_	_	NN	_	_	_
173	rep1	rep1	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	RNAP	rnap	NN	_	_	_
176	_	_	CD	_	_	_
177	DdksA	ddksa	NN	_	_	_
178	_	_	NN	_	_	_
179	untreated	untreated	JJ	_	_	_
180	_	_	NN	_	_	_
181	rep2	rep2	NN	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	RNAP	rnap	NN	_	_	_
184	_	_	CD	_	_	_
185	wt	wt	JJ	_	_	_
186	_	_	NN	_	_	_
187	SHX	shx	NN	_	_	_
188	_	_	CD	_	_	_
189	rep1	rep1	NN	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	RNAP	rnap	NN	_	_	_
192	_	_	CD	_	_	_
193	wt	wt	JJ	_	_	_
194	_	_	NN	_	_	_
195	SHX	shx	NN	_	_	_
196	_	_	CD	_	_	_
197	rep2	rep2	NN	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	RNAP	rnap	NN	_	_	_
200	_	_	CD	_	_	_
201	wt	wt	JJ	_	_	_
202	_	_	NN	_	_	_
203	untreated	untreated	JJ	_	_	_
204	_	_	NN	_	_	_
205	rep1	rep1	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	RNAP	rnap	NN	_	_	_
208	_	_	CD	_	_	_
209	wt	wt	JJ	_	_	_
210	_	_	NN	_	_	_
211	untreated	untreated	JJ	_	_	_
212	_	_	NN	_	_	_
213	rep2	rep2	NN	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	s70	s70	NN	_	_	_
216	ChIP	chip	NN	_	_	_
217	DNA	dna	NN	_	_	_
218	from	from	IN	_	_	_
219	DdksA	ddksa	NN	_	_	_
220	cells	cell	NNS	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
222	s70	s70	NN	_	_	_
223	ChIP	chip	NN	_	_	_
224	DNA	dna	NN	_	_	_
225	from	from	IN	_	_	_
226	starved	starve	VBN	_	_	_
227	DdksA	ddksa	NN	_	_	_
228	cells	cell	NNS	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
230	s70	s70	NN	_	_	_
231	ChIP	chip	NN	_	_	_
232	DNA	dna	NN	_	_	_
233	from	from	IN	_	_	_
234	starved	starve	VBN	_	_	_
235	wt	wt	JJ	_	_	_
236	cells	cell	NNS	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	s70	s70	NN	_	_	_
239	ChIP	chip	NN	_	_	_
240	DNA	dna	NN	_	_	_
241	from	from	IN	_	_	_
242	wt	wt	JJ	_	_	_
243	cells	cell	NNS	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	s70	s70	NN	_	_	_
246	_	_	CD	_	_	_
247	DdksA	ddksa	NN	_	_	_
248	_	_	CD	_	_	_
249	SHX	SHX	NNP	_	_	_
250	_	_	CD	_	_	_
251	rep1	rep1	NN	_	_	_
252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
253	s70	s70	NN	_	_	_
254	_	_	CD	_	_	_
255	DdksA	ddksa	NN	_	_	_
256	_	_	CD	_	_	_
257	SHX	SHX	NNP	_	_	_
258	_	_	CD	_	_	_
259	rep2	rep2	NN	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	s70	s70	NN	_	_	_
262	_	_	CD	_	_	_
263	DdksA	ddksa	NN	_	_	_
264	_	_	NN	_	_	_
265	untreated	untreated	JJ	_	_	_
266	_	_	NN	_	_	_
267	rep1	rep1	NN	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	s70	s70	NN	_	_	_
270	_	_	CD	_	_	_
271	DdksA	ddksa	NN	_	_	_
272	_	_	NN	_	_	_
273	untreated	untreated	JJ	_	_	_
274	_	_	NN	_	_	_
275	rep2	rep2	NN	_	_	_
276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
277	s70	s70	NN	_	_	_
278	_	_	CD	_	_	_
279	wt	wt	JJ	_	_	_
280	_	_	NN	_	_	_
281	SHX	shx	NN	_	_	_
282	_	_	CD	_	_	_
283	rep1	rep1	NN	_	_	_
284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
285	s70	s70	NN	_	_	_
286	_	_	CD	_	_	_
287	wt	wt	JJ	_	_	_
288	_	_	NN	_	_	_
289	SHX	shx	NN	_	_	_
290	_	_	CD	_	_	_
291	rep2	rep2	NN	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	s70	s70	NN	_	_	_
294	_	_	CD	_	_	_
295	wt	wt	JJ	_	_	_
296	_	_	NN	_	_	_
297	untreated	untreated	JJ	_	_	_
298	_	_	NN	_	_	_
299	rep1	rep1	NN	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	s70	s70	NN	_	_	_
302	_	_	CD	_	_	_
303	wt	wt	JJ	_	_	_
304	_	_	NN	_	_	_
305	untreated	untreated	JJ	_	_	_
306	_	_	NN	_	_	_
307	rep2	rep2	NN	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
309	The	the	DT	_	_	_
310	log2-ratio	log2-ratio	NN	_	_	_
311	is	be	VBZ	_	_	_
312	computed	compute	VBN	_	_	_
313	and	and	CC	_	_	_
314	scaled	scale	VBN	_	_	_
315	to	to	TO	_	_	_
316	center	center	VB	_	_	_
317	the	the	DT	_	_	_
318	ratio	ratio	NN	_	_	_
319	data	datum	NNS	_	_	_
320	around	around	IN	_	_	_
321	zero	zero	CD	_	_	_
322	.	.	.	_	_	_

1	Scaling	scaling	NN	_	_	_
2	is	be	VBZ	_	_	_
3	performed	perform	VBN	_	_	_
4	by	by	IN	_	_	_
5	subtracting	subtract	VBG	_	_	_
6	the	the	DT	_	_	_
7	bi-weight	bi-weight	JJ	_	_	_
8	mean	mean	NN	_	_	_
9	for	for	IN	_	_	_
10	the	the	DT	_	_	_
11	log2-ratio	log2-ratio	JJ	_	_	_
12	values	value	NNS	_	_	_
13	for	for	IN	_	_	_
14	all	all	DT	_	_	_
15	features	feature	NNS	_	_	_
16	on	on	IN	_	_	_
17	the	the	DT	_	_	_
18	array	array	NN	_	_	_
19	from	from	IN	_	_	_
20	each	each	DT	_	_	_
21	log2-ratio	log2-ratio	JJ	_	_	_
22	value	value	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	0.5	0.5	CD	_	_	_
5	mg	mg	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	treatment	treatment	NN	_	_	_
8	:	:	:	_	_	_
9	None	none	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Wild-types	wild-types	JJ	_	_	_
12	cells	cell	NNS	_	_	_
13	were	be	VBD	_	_	_
14	grown	grow	VBN	_	_	_
15	in	in	IN	_	_	_
16	MOPS	MOPS	NNP	MED	_	_
17	medium	medium	NN	_	_	_
18	with	with	IN	_	_	_
19	0.2	0.2	CD	_	_	_
20	%	%	NN	_	_	_
21	glucose	glucose	NN	SUPP	_	_
22	,	,	,	_	_	_
23	leucine	leucine	NN	SUPP	_	_
24	,	,	,	_	_	_
25	isoleucine	isoleucine	NN	_	_	_
26	,	,	,	_	_	_
27	valine	valine	NN	_	_	_
28	,	,	,	_	_	_
29	glycine	glycine	NN	_	_	_
30	,	,	,	_	_	_
31	phenylalanine	phenylalanine	NN	SUPP	_	_
32	,	,	,	_	_	_
33	threonine	threonine	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	40	40	CD	_	_	_
36	mg	mg	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	agent	agent	NN	_	_	_
39	:	:	:	_	_	_
40	DPD	dpd	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
42	agent	agent	NN	_	_	_
43	:	:	:	_	_	_
44	DPD	dpd	NN	_	_	_
45	and	and	CC	_	_	_
46	rifampicin	rifampicin	NN	SUPP	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	agent	agent	NN	_	_	_
49	:	:	:	_	_	_
50	Fe	Fe	NNP	_	_	_
51	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
52	agent	agent	NN	_	_	_
53	:	:	:	_	_	_
54	Fe	Fe	NNP	_	_	_
55	and	and	CC	_	_	_
56	rifampicin	rifampicin	NN	SUPP	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	chip	chip	NN	_	_	_
59	antibody	antibody	NN	_	_	_
60	:	:	:	_	_	_
61	anti-myc	anti-myc	JJ	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	Santa	Santa	NNP	_	_	_
64	Cruz	Cruz	NNP	_	_	_
65	Biotech	Biotech	NNP	_	_	_
66	,	,	,	_	_	_
67	sc-28207	sc-28207	NN	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	chip	chip	NN	_	_	_
71	antibody	antibody	NN	_	_	_
72	:	:	:	_	_	_
73	anti-RpoB	anti-rpob	NN	_	_	_
74	-LRB-	-lrb-	-LRB-	_	_	_
75	Neoclone	Neoclone	NNP	_	_	_
76	,	,	,	_	_	_
77	WP002	wp002	NN	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	ChIP-exo	chip-exo	NN	_	_	_
81	reads	read	VBZ	_	_	_
82	were	be	VBD	_	_	_
83	aligned	align	VBN	_	_	_
84	to	to	TO	_	_	_
85	the	the	DT	_	_	_
86	NC	NC	NNP	_	_	_
87	_	_	SYM	_	_	_
88	000913	000913	CD	_	_	_
89	genome	genome	NN	_	_	_
90	reference	reference	NN	_	_	_
91	sequence	sequence	NN	_	_	_
92	using	use	VBG	_	_	_
93	using	use	VBG	_	_	_
94	bowtie	bowtie	NN	_	_	_
95	v1	v1	NN	_	_	_
96	.0.0	.0.0	CD	_	_	_
97	with	with	IN	_	_	_
98	parameters	parameter	NNS	_	_	_
99	-	-	:	_	_	_
100	S	s	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
102	ChIP-Seq	chip-seq	JJ	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	ChIP-seq	chip-seq	NN	_	_	_
105	libraries	library	NNS	_	_	_
106	were	be	VBD	_	_	_
107	prepared	prepare	VBN	_	_	_
108	for	for	IN	_	_	_
109	sequencing	sequencing	NN	_	_	_
110	using	use	VBG	_	_	_
111	standard	standard	JJ	_	_	_
112	Illumina	Illumina	NNP	_	_	_
113	protocols	protocol	NNS	_	_	_
114	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
115	E.	e.	FW	_	_	_
116	coli	coli	FW	_	_	_
117	K-12	k-12	NN	_	_	_
118	MG1655	mg1655	NN	_	_	_
119	WT	wt	NN	_	_	_
120	and	and	CC	_	_	_
121	Fur-8-myc	fur-8-myc	NN	_	_	_
122	tagged	tag	VBD	_	_	_
123	strains	strain	NNS	_	_	_
124	were	be	VBD	_	_	_
125	grown	grow	VBN	_	_	_
126	to	to	TO	_	_	_
127	mid-log	mid-log	JJ	_	_	_
128	phase	phase	NN	_	_	_
129	aerobically	aerobically	RB	_	_	_
130	at	at	IN	_	_	_
131	37	37	CD	_	_	_
132	°C	°c	NN	_	_	_
133	in	in	IN	_	_	_
134	M9	m9	NN	MED	_	_
135	minimal	minimal	JJ	MED	_	_
136	media	media	NNS	MED	_	_
137	supplemented	supplement	VBN	_	_	_
138	with	with	IN	_	_	_
139	0.2	0.2	CD	_	_	_
140	%	%	NN	_	_	_
141	glucose	glucose	NN	SUPP	_	_
142	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	iron	iron	NN	_	_	_
3	treated	treat	VBN	_	_	_
4	cells	cell	NNS	_	_	_
5	,	,	,	_	_	_
6	0.1	0.1	CD	_	_	_
7	mM	mm	NN	KWSUPP	_	_
8	of	of	IN	_	_	_
9	FeCl2	fecl2	NN	_	_	_
10	were	be	VBD	_	_	_
11	treated	treat	VBN	_	_	_
12	from	from	IN	_	_	_
13	the	the	DT	_	_	_
14	beginning	beginning	NN	_	_	_
15	of	of	IN	_	_	_
16	culture	culture	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	for	for	IN	_	_	_
20	DPD	dpd	NN	_	_	_
21	treated	treat	VBN	_	_	_
22	cells	cell	NNS	_	_	_
23	,	,	,	_	_	_
24	0.2	0.2	CD	_	_	_
25	mM	mm	NN	KWSUPP	_	_
26	of	of	IN	_	_	_
27	DPD	dpd	NN	_	_	_
28	were	be	VBD	_	_	_
29	added	add	VBN	_	_	_
30	at	at	IN	_	_	_
31	early-log	early-log	JJ	_	_	_
32	phase	phase	NN	_	_	_
33	and	and	CC	_	_	_
34	continued	continue	VBD	_	_	_
35	to	to	TO	_	_	_
36	culture	culture	NN	_	_	_
37	for	for	IN	_	_	_
38	additional	additional	JJ	_	_	_
39	2h	2h	NN	_	_	_
40	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	the	the	DT	_	_	_
3	rifampicin-treated	rifampicin-treated	JJ	_	_	_
4	cultures	culture	NNS	_	_	_
5	,	,	,	_	_	_
6	the	the	DT	_	_	_
7	rifampicin	rifampicin	NN	SUPP	_	_
8	dissolved	dissolve	VBN	_	_	_
9	in	in	IN	_	_	_
10	methanol	methanol	NN	_	_	_
11	was	be	VBD	_	_	_
12	added	add	VBN	_	_	_
13	to	to	TO	_	_	_
14	a	a	DT	_	_	_
15	final	final	JJ	_	_	_
16	concentration	concentration	NN	_	_	_
17	of	of	IN	_	_	_
18	150	150	CD	_	_	_
19	mg	mg	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Escherichia	escherichia	FW	Organism	_	_
22	coli	coli	FW	Organism	_	_
23	str	str	FW	_	_	_
24	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Fur	Fur	NNP	TF	_	_
4	with	with	IN	_	_	_
5	DPD	dpd	NN	_	_	_
6	1	1	CD	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	ChIP-exo	chip-exo	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Fur	Fur	NNP	TF	_	_
12	with	with	IN	_	_	_
13	DPD	dpd	NN	_	_	_
14	2	2	CD	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	ChIP-exo	chip-exo	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Fur	Fur	NNP	TF	_	_
20	with	with	IN	_	_	_
21	Fe	Fe	NNP	_	_	_
22	1	1	CD	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	ChIP-exo	chip-exo	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	Fur	Fur	NNP	TF	_	_
28	with	with	IN	_	_	_
29	Fe	Fe	NNP	_	_	_
30	2	2	CD	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	ChIP-exo	chip-exo	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	Genome	Genome	NNP	_	_	_
36	_	_	NNP	_	_	_
37	build	build	VB	_	_	_
38	:	:	:	_	_	_
39	ASM584v2	asm584v2	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	genotype	genotype	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	Immunoprecipitated	immunoprecipitate	VBN	_	_	_
44	DNA	dna	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	library	library	NN	_	_	_
47	strategy	strategy	NN	_	_	_
48	:	:	:	_	_	_
49	ChIP-exo	ChIP-exo	NNP	_	_	_
50	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
51	RpoB	rpob	NN	_	_	_
52	with	with	IN	_	_	_
53	DPD	dpd	NN	_	_	_
54	1	1	CD	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	ChIP-exo	chip-exo	NN	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	RpoB	rpob	NN	_	_	_
60	with	with	IN	_	_	_
61	DPD	dpd	NN	_	_	_
62	2	2	CD	_	_	_
63	-LRB-	-lrb-	-LRB-	_	_	_
64	ChIP-exo	chip-exo	NN	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	RpoB	rpob	NN	_	_	_
68	with	with	IN	_	_	_
69	DPD	dpd	NN	_	_	_
70	and	and	CC	_	_	_
71	rifampicin	rifampicin	NN	SUPP	_	_
72	1	1	CD	_	_	_
73	-LRB-	-lrb-	-LRB-	_	_	_
74	ChIP-exo	chip-exo	NN	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	RpoB	rpob	NN	_	_	_
78	with	with	IN	_	_	_
79	DPD	dpd	NN	_	_	_
80	and	and	CC	_	_	_
81	rifampicin	rifampicin	NN	SUPP	_	_
82	2	2	CD	_	_	_
83	-LRB-	-lrb-	-LRB-	_	_	_
84	ChIP-exo	chip-exo	NN	_	_	_
85	-RRB-	-rrb-	-RRB-	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	RpoB	rpob	NN	_	_	_
88	with	with	IN	_	_	_
89	Fe	Fe	NNP	_	_	_
90	1	1	CD	_	_	_
91	-LRB-	-lrb-	-LRB-	_	_	_
92	ChIP-exo	chip-exo	NN	_	_	_
93	-RRB-	-rrb-	-RRB-	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	RpoB	rpob	NN	_	_	_
96	with	with	IN	_	_	_
97	Fe	Fe	NNP	_	_	_
98	2	2	CD	_	_	_
99	-LRB-	-lrb-	-LRB-	_	_	_
100	ChIP-exo	chip-exo	NN	_	_	_
101	-RRB-	-rrb-	-RRB-	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	RpoB	rpob	NN	_	_	_
104	with	with	IN	_	_	_
105	Fe	Fe	NNP	_	_	_
106	and	and	CC	_	_	_
107	rifampicin	rifampicin	NN	SUPP	_	_
108	1	1	CD	_	_	_
109	-LRB-	-lrb-	-LRB-	_	_	_
110	ChIP-exo	chip-exo	NN	_	_	_
111	-RRB-	-rrb-	-RRB-	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	RpoB	rpob	NN	_	_	_
114	with	with	IN	_	_	_
115	Fe	Fe	NNP	_	_	_
116	and	and	CC	_	_	_
117	rifampicin	rifampicin	NN	SUPP	_	_
118	2	2	CD	_	_	_
119	-LRB-	-lrb-	-LRB-	_	_	_
120	ChIP-exo	chip-exo	NN	_	_	_
121	-RRB-	-rrb-	-RRB-	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	Supplementary	supplementary	JJ	_	_	_
124	_	_	NN	_	_	_
125	files	file	NNS	_	_	_
126	_	_	IN	_	_	_
127	format	format	NN	_	_	_
128	_	_	NN	_	_	_
129	and	and	CC	_	_	_
130	_	_	NN	_	_	_
131	content	content	NN	_	_	_
132	:	:	:	_	_	_
133	Tab-delimited	tab-delimited	JJ	_	_	_
134	text	text	NN	_	_	_
135	files	file	NNS	_	_	_
136	in	in	IN	_	_	_
137	gff	gff	NN	_	_	_
138	format	format	NN	_	_	_
139	which	which	WDT	_	_	_
140	has	have	VBZ	_	_	_
141	8	8	CD	_	_	_
142	columns	column	NNS	_	_	_
143	:	:	:	_	_	_
144	sequence	sequence	NN	_	_	_
145	id	id	NN	_	_	_
146	,	,	,	_	_	_
147	source	source	NN	_	_	_
148	-LRB-	-lrb-	-LRB-	_	_	_
149	empty	empty	JJ	_	_	_
150	-RRB-	-rrb-	-RRB-	_	_	_
151	,	,	,	_	_	_
152	feature	feature	NN	_	_	_
153	-LRB-	-lrb-	-LRB-	_	_	_
154	+	+	CC	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
156	agent	agent	NN	_	_	_
157	:	:	:	_	_	_
158	DPD	dpd	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
160	agent	agent	NN	_	_	_
161	:	:	:	_	_	_
162	Fe	Fe	NNP	_	_	_
163	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
164	E.	E.	NNP	_	_	_
165	coli	coli	NN	_	_	_
166	K-12	k-12	NN	_	_	_
167	MG1655	mg1655	NN	_	_	_
168	WT	wt	NN	_	_	_
169	and	and	CC	_	_	_
170	Δfur	δfur	NN	_	_	_
171	were	be	VBD	_	_	_
172	grown	grow	VBN	_	_	_
173	to	to	TO	_	_	_
174	mid-log	mid-log	JJ	_	_	_
175	phase	phase	NN	_	_	_
176	aerobically	aerobically	RB	_	_	_
177	at	at	IN	_	_	_
178	37	37	CD	_	_	_
179	°C	°c	NN	_	_	_
180	in	in	IN	_	_	_
181	M9	m9	NN	MED	_	_
182	minimal	minimal	JJ	MED	_	_
183	media	media	NNS	MED	_	_
184	supplemented	supplement	VBN	_	_	_
185	with	with	IN	_	_	_
186	0.2	0.2	CD	_	_	_
187	%	%	NN	_	_	_
188	glucose	glucose	NN	SUPP	_	_
189	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	iron	iron	NN	_	_	_
3	treated	treat	VBN	_	_	_
4	cells	cell	NNS	_	_	_
5	,	,	,	_	_	_
6	0.1	0.1	CD	_	_	_
7	mM	mm	NN	KWSUPP	_	_
8	of	of	IN	_	_	_
9	FeCl2	fecl2	NN	_	_	_
10	were	be	VBD	_	_	_
11	treated	treat	VBN	_	_	_
12	from	from	IN	_	_	_
13	the	the	DT	_	_	_
14	beginning	beginning	NN	_	_	_
15	of	of	IN	_	_	_
16	culture	culture	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	for	for	IN	_	_	_
20	DPD	dpd	NN	_	_	_
21	treated	treat	VBN	_	_	_
22	cells	cell	NNS	_	_	_
23	,	,	,	_	_	_
24	0.2	0.2	CD	_	_	_
25	mM	mm	NN	KWSUPP	_	_
26	of	of	IN	_	_	_
27	DPD	dpd	NN	_	_	_
28	were	be	VBD	_	_	_
29	added	add	VBN	_	_	_
30	at	at	IN	_	_	_
31	early-log	early-log	JJ	_	_	_
32	phase	phase	NN	_	_	_
33	and	and	CC	_	_	_
34	continued	continue	VBD	_	_	_
35	to	to	TO	_	_	_
36	culture	culture	NN	_	_	_
37	for	for	IN	_	_	_
38	additional	additional	JJ	_	_	_
39	2h	2h	NN	_	_	_
40	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Genome	Genome	NNP	_	_	_
4	_	_	NNP	_	_	_
5	build	build	VB	_	_	_
6	:	:	:	_	_	_
7	ASM584v2	asm584v2	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	genotype	genotype	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Reads	read	VBZ	_	_	_
12	Per	per	IN	_	_	_
13	Kilobase	kilobase	NN	_	_	_
14	of	of	IN	_	_	_
15	exon	exon	NN	_	_	_
16	per	per	IN	_	_	_
17	Megabase	megabase	NN	_	_	_
18	of	of	IN	_	_	_
19	library	library	NN	_	_	_
20	size	size	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	RPKM	rpkm	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	were	be	VBD	_	_	_
25	calculated	calculate	VBN	_	_	_
26	using	use	VBG	_	_	_
27	cufflinks	cufflink	NNS	_	_	_
28	v.	v.	CC	_	_	_
29	1.3.0	1.3.0	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	RNA	rna	NN	_	_	_
32	libraries	library	NNS	_	_	_
33	were	be	VBD	_	_	_
34	prepared	prepare	VBN	_	_	_
35	for	for	IN	_	_	_
36	sequencing	sequencing	NN	_	_	_
37	using	use	VBG	_	_	_
38	standard	standard	JJ	_	_	_
39	Illumina	Illumina	NNP	_	_	_
40	protocols	protocol	NNS	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
42	RNA-Seq	rna-seq	JJ	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Sequenced	sequence	VBN	_	_	_
45	reads	read	VBZ	_	_	_
46	were	be	VBD	_	_	_
47	mapped	map	VBN	_	_	_
48	onto	onto	IN	_	_	_
49	NC	nc	NN	_	_	_
50	_	_	CD	_	_	_
51	000913	000913	CD	_	_	_
52	reference	reference	NN	_	_	_
53	genome	genome	NN	_	_	_
54	sequence	sequence	NN	_	_	_
55	using	use	VBG	_	_	_
56	bowtie	bowtie	NN	_	_	_
57	v1	v1	NN	_	_	_
58	.0.0	.0.0	CD	_	_	_
59	with	with	IN	_	_	_
60	parameters	parameter	NNS	_	_	_
61	-	-	:	_	_	_
62	X	x	NN	_	_	_
63	1000	1000	CD	_	_	_
64	-	-	:	_	_	_
65	n	n	NN	_	_	_
66	2	2	CD	_	_	_
67	-3	-3	CD	_	_	_
68	3	3	LS	_	_	_
69	-	-	:	_	_	_
70	S	s	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
72	Supplementary	supplementary	JJ	_	_	_
73	_	_	NN	_	_	_
74	files	file	NNS	_	_	_
75	_	_	IN	_	_	_
76	format	format	NN	_	_	_
77	_	_	NN	_	_	_
78	and	and	CC	_	_	_
79	_	_	NN	_	_	_
80	content	content	NN	_	_	_
81	:	:	:	_	_	_
82	Comma-delimited	comma-delimited	JJ	_	_	_
83	text	text	NN	_	_	_
84	file	file	NN	_	_	_
85	includes	include	VBZ	_	_	_
86	RPKM	rpkm	NN	_	_	_
87	values	value	NNS	_	_	_
88	for	for	IN	_	_	_
89	each	each	DT	_	_	_
90	Sample	Sample	NNP	_	_	_
91	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cell	cell	NN	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	treated	treat	VBN	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	RNAprotect	rnaprotect	NN	_	_	_
10	reagent	reagent	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	qiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	isolated	isolate	VBN	_	_	_
5	from	from	IN	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Total	total	JJ	_	_	_
10	RNA	rna	NN	_	_	_
11	was	be	VBD	_	_	_
12	extracted	extract	VBN	_	_	_
13	using	use	VBG	_	_	_
14	the	the	DT	_	_	_
15	RNeasy	RNeasy	NNP	_	_	_
16	Plus	Plus	NNP	_	_	_
17	Mini	Mini	NNP	_	_	_
18	kit	kit	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Qiagen	Qiagen	NNP	_	_	_
21	Inc.	Inc.	NNP	_	_	_
22	,	,	,	_	_	_
23	Valencia	Valencia	NNP	_	_	_
24	,	,	,	_	_	_
25	CA	CA	NNP	_	_	_
26	,	,	,	_	_	_
27	USA	USA	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	and	and	CC	_	_	_
30	genomic	genomic	JJ	_	_	_
31	DNA	dna	NN	_	_	_
32	was	be	VBD	_	_	_
33	removed	remove	VBN	_	_	_
34	by	by	IN	_	_	_
35	gDNA	gdna	NN	_	_	_
36	Eliminator	eliminator	NN	_	_	_
37	spin	spin	NN	_	_	_
38	column	column	NN	_	_	_
39	in	in	IN	_	_	_
40	the	the	DT	_	_	_
41	RNeasy	RNeasy	NNP	_	_	_
42	Plus	Plus	NNP	_	_	_
43	Mini	Mini	NNP	_	_	_
44	Kit	kit	NN	_	_	_
45	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	quality	quality	NN	_	_	_
3	and	and	CC	_	_	_
4	concentration	concentration	NN	_	_	_
5	was	be	VBD	_	_	_
6	determined	determine	VBN	_	_	_
7	by	by	IN	_	_	_
8	analysis	analysis	NN	_	_	_
9	with	with	IN	_	_	_
10	a	a	DT	_	_	_
11	NanoDrop	NanoDrop	NNP	_	_	_
12	1000	1000	CD	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Thermo	Thermo	NNP	_	_	_
15	Scientific	Scientific	NNP	_	_	_
16	Inc.	Inc.	NNP	_	_	_
17	,	,	,	_	_	_
18	Wilmington	Wilmington	NNP	_	_	_
19	,	,	,	_	_	_
20	DE	de	NN	_	_	_
21	,	,	,	_	_	_
22	USA	USA	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	WT	wt	NN	_	_	_
3	with	with	IN	_	_	_
4	DPD	dpd	NN	_	_	_
5	1	1	CD	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	RNA-seq	rna-seq	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	WT	wt	NN	_	_	_
11	with	with	IN	_	_	_
12	DPD	dpd	NN	_	_	_
13	2	2	CD	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	RNA-seq	rna-seq	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	WT	wt	NN	_	_	_
19	with	with	IN	_	_	_
20	Fe	Fe	NNP	_	_	_
21	1	1	CD	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	RNA-seq	rna-seq	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	WT	wt	NN	_	_	_
27	with	with	IN	_	_	_
28	Fe	Fe	NNP	_	_	_
29	2	2	CD	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	RNA-seq	rna-seq	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Δfur	δfur	NN	_	_	_
35	with	with	IN	_	_	_
36	DPD	dpd	NN	_	_	_
37	1	1	CD	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	RNA-seq	rna-seq	NN	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	Δfur	δfur	NN	_	_	_
43	with	with	IN	_	_	_
44	DPD	dpd	NN	_	_	_
45	2	2	CD	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	RNA-seq	rna-seq	NN	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	Δfur	δfur	NN	_	_	_
51	with	with	IN	_	_	_
52	Fe	Fe	NNP	_	_	_
53	1	1	CD	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	RNA-seq	rna-seq	NN	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Δfur	δfur	NN	_	_	_
59	with	with	IN	_	_	_
60	Fe	Fe	NNP	_	_	_
61	2	2	CD	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	RNA-seq	rna-seq	NN	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	Agilent	Agilent	NNP	_	_	_
67	Feature	Feature	NNP	_	_	_
68	Extraction	Extraction	NNP	_	_	_
69	Software	Software	NNP	_	_	_
70	-LRB-	-lrb-	-LRB-	_	_	_
71	v	v	LS	_	_	_
72	10.10.1.1	10.10.1.1	CD	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	was	be	VBD	_	_	_
75	used	use	VBN	_	_	_
76	for	for	IN	_	_	_
77	background	background	NN	_	_	_
78	subtraction	subtraction	NN	_	_	_
79	and	and	CC	_	_	_
80	LOWESS	lowess	NN	_	_	_
81	normalization	normalization	NN	_	_	_
82	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Batch	batch	NN	_	_	_
3	anaerobically	anaerobically	RB	_	_	_
4	grown	grow	VBN	_	_	_
5	cultures	culture	NNS	_	_	_
6	in	in	IN	_	_	_
7	hemA	hema	NN	GEN	_	_
8	defined	define	VBN	_	_	_
9	medium	medium	NN	_	_	_
10	,	,	,	_	_	_
11	exposed	expose	VBN	_	_	_
12	to	to	TO	_	_	_
13	100uM	100um	VB	_	_	_
14	CORM-3	corm-3	NN	_	_	_
15	for	for	IN	_	_	_
16	10	10	CD	_	_	_
17	min	min	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Batch	batch	NN	_	_	_
20	anaerobically	anaerobically	RB	_	_	_
21	grown	grow	VBN	_	_	_
22	cultures	culture	NNS	_	_	_
23	in	in	IN	_	_	_
24	hemA	hema	NN	GEN	_	_
25	defined	define	VBN	_	_	_
26	medium	medium	NN	_	_	_
27	,	,	,	_	_	_
28	exposed	expose	VBN	_	_	_
29	to	to	TO	_	_	_
30	100uM	100um	VB	_	_	_
31	CORM-3	corm-3	NN	_	_	_
32	for	for	IN	_	_	_
33	120	120	CD	_	_	_
34	min	min	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	Batch	batch	NN	_	_	_
37	anaerobically	anaerobically	RB	_	_	_
38	grown	grow	VBN	_	_	_
39	cultures	culture	NNS	_	_	_
40	in	in	IN	_	_	_
41	hemA	hema	NN	GEN	_	_
42	defined	define	VBN	_	_	_
43	medium	medium	NN	_	_	_
44	,	,	,	_	_	_
45	exposed	expose	VBN	_	_	_
46	to	to	TO	_	_	_
47	100uM	100um	VB	_	_	_
48	CORM-3	corm-3	NN	_	_	_
49	for	for	IN	_	_	_
50	20	20	CD	_	_	_
51	min	min	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	Batch	batch	NN	_	_	_
54	anaerobically	anaerobically	RB	_	_	_
55	grown	grow	VBN	_	_	_
56	cultures	culture	NNS	_	_	_
57	in	in	IN	_	_	_
58	hemA	hema	NN	GEN	_	_
59	defined	define	VBN	_	_	_
60	medium	medium	NN	_	_	_
61	,	,	,	_	_	_
62	exposed	expose	VBN	_	_	_
63	to	to	TO	_	_	_
64	100uM	100um	VB	_	_	_
65	CORM-3	corm-3	NN	_	_	_
66	for	for	IN	_	_	_
67	40	40	CD	_	_	_
68	min	min	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	Batch	batch	NN	_	_	_
71	anaerobically	anaerobically	RB	_	_	_
72	grown	grow	VBN	_	_	_
73	cultures	culture	NNS	_	_	_
74	in	in	IN	_	_	_
75	hemA	hema	NN	GEN	_	_
76	defined	define	VBN	_	_	_
77	medium	medium	NN	_	_	_
78	,	,	,	_	_	_
79	exposed	expose	VBN	_	_	_
80	to	to	TO	_	_	_
81	100uM	100um	VB	_	_	_
82	CORM-3	corm-3	NN	_	_	_
83	for	for	IN	_	_	_
84	60	60	CD	_	_	_
85	min	min	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	Batch	batch	NN	_	_	_
88	anaerobically	anaerobically	RB	_	_	_
89	grown	grow	VBN	_	_	_
90	cultures	culture	NNS	_	_	_
91	in	in	IN	_	_	_
92	hemA	hema	NN	GEN	_	_
93	defined	define	VBN	_	_	_
94	medium	medium	NN	_	_	_
95	,	,	,	_	_	_
96	exposed	expose	VBN	_	_	_
97	to	to	TO	_	_	_
98	100uM	100um	VB	_	_	_
99	iCORM-3	icorm-3	NN	_	_	_
100	for	for	IN	_	_	_
101	10	10	CD	_	_	_
102	min	min	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	Batch	batch	NN	_	_	_
105	anaerobically	anaerobically	RB	_	_	_
106	grown	grow	VBN	_	_	_
107	cultures	culture	NNS	_	_	_
108	in	in	IN	_	_	_
109	hemA	hema	NN	GEN	_	_
110	defined	define	VBN	_	_	_
111	medium	medium	NN	_	_	_
112	,	,	,	_	_	_
113	exposed	expose	VBN	_	_	_
114	to	to	TO	_	_	_
115	100uM	100um	VB	_	_	_
116	iCORM-3	icorm-3	NN	_	_	_
117	for	for	IN	_	_	_
118	120	120	CD	_	_	_
119	min	min	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	Batch	batch	NN	_	_	_
122	anaerobically	anaerobically	RB	_	_	_
123	grown	grow	VBN	_	_	_
124	cultures	culture	NNS	_	_	_
125	in	in	IN	_	_	_
126	hemA	hema	NN	GEN	_	_
127	defined	define	VBN	_	_	_
128	medium	medium	NN	_	_	_
129	,	,	,	_	_	_
130	exposed	expose	VBN	_	_	_
131	to	to	TO	_	_	_
132	100uM	100um	VB	_	_	_
133	iCORM-3	icorm-3	NN	_	_	_
134	for	for	IN	_	_	_
135	20	20	CD	_	_	_
136	min	min	NN	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	Batch	batch	NN	_	_	_
139	anaerobically	anaerobically	RB	_	_	_
140	grown	grow	VBN	_	_	_
141	cultures	culture	NNS	_	_	_
142	in	in	IN	_	_	_
143	hemA	hema	NN	GEN	_	_
144	defined	define	VBN	_	_	_
145	medium	medium	NN	_	_	_
146	,	,	,	_	_	_
147	exposed	expose	VBN	_	_	_
148	to	to	TO	_	_	_
149	100uM	100um	VB	_	_	_
150	iCORM-3	icorm-3	NN	_	_	_
151	for	for	IN	_	_	_
152	40	40	CD	_	_	_
153	min	min	NN	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	Batch	batch	NN	_	_	_
156	anaerobically	anaerobically	RB	_	_	_
157	grown	grow	VBN	_	_	_
158	cultures	culture	NNS	_	_	_
159	in	in	IN	_	_	_
160	hemA	hema	NN	GEN	_	_
161	defined	define	VBN	_	_	_
162	medium	medium	NN	_	_	_
163	,	,	,	_	_	_
164	exposed	expose	VBN	_	_	_
165	to	to	TO	_	_	_
166	100uM	100um	VB	_	_	_
167	iCORM-3	icorm-3	NN	_	_	_
168	for	for	IN	_	_	_
169	60	60	CD	_	_	_
170	min	min	NN	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	Batch	batch	NN	_	_	_
173	anaerobically	anaerobically	RB	_	_	_
174	grown	grow	VBN	_	_	_
175	cultures	culture	NNS	_	_	_
176	in	in	IN	_	_	_
177	hemA	hema	NN	GEN	_	_
178	defined	define	VBN	_	_	_
179	medium	medium	NN	_	_	_
180	,	,	,	_	_	_
181	prior	prior	RB	_	_	_
182	to	to	TO	_	_	_
183	CORM-3	corm-3	NN	_	_	_
184	addition	addition	NN	_	_	_
185	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
186	Batch	batch	NN	_	_	_
187	anaerobically	anaerobically	RB	_	_	_
188	grown	grow	VBN	_	_	_
189	cultures	culture	NNS	_	_	_
190	in	in	IN	_	_	_
191	hemA	hema	NN	GEN	_	_
192	defined	define	VBN	_	_	_
193	medium	medium	NN	_	_	_
194	,	,	,	_	_	_
195	prior	prior	RB	_	_	_
196	to	to	TO	_	_	_
197	CORM-3	corm-3	NN	_	_	_
198	addition	addition	NN	_	_	_
199	-LRB-	-lrb-	-LRB-	_	_	_
200	t	t	NN	_	_	_
201	=	=	JJ	_	_	_
202	0	0	CD	_	_	_
203	-RRB-	-rrb-	-RRB-	_	_	_
204	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
205	Batch	batch	NN	_	_	_
206	anaerobically	anaerobically	RB	_	_	_
207	grown	grow	VBN	_	_	_
208	cultures	culture	NNS	_	_	_
209	in	in	IN	_	_	_
210	hemA	hema	NN	GEN	_	_
211	defined	define	VBN	_	_	_
212	medium	medium	NN	_	_	_
213	,	,	,	_	_	_
214	prior	prior	RB	_	_	_
215	to	to	TO	_	_	_
216	iCORM-3	icorm-3	NN	_	_	_
217	addition	addition	NN	_	_	_
218	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
219	Cells	cell	NNS	_	_	_
220	were	be	VBD	_	_	_
221	harvested	harvest	VBN	_	_	_
222	directly	directly	RB	_	_	_
223	into	into	IN	_	_	_
224	phenol	phenol	NN	_	_	_
225	:	:	:	_	_	_
226	ethanol	ethanol	NN	_	_	_
227	to	to	TO	_	_	_
228	stabilize	stabilize	VB	_	_	_
229	RNA	rna	NN	_	_	_
230	and	and	CC	_	_	_
231	total	total	JJ	_	_	_
232	RNA	rna	NN	_	_	_
233	was	be	VBD	_	_	_
234	purified	purify	VBN	_	_	_
235	using	use	VBG	_	_	_
236	Qiagen	Qiagen	NNP	_	_	_
237	's	's	POS	_	_	_
238	RNeasy	RNeasy	NNP	_	_	_
239	Mini	Mini	NNP	_	_	_
240	Kit	kit	NN	_	_	_
241	,	,	,	_	_	_
242	according	accord	VBG	_	_	_
243	to	to	TO	_	_	_
244	the	the	DT	_	_	_
245	manufacturer	manufacturer	NN	_	_	_
246	's	's	POS	_	_	_
247	instructions	instruction	NNS	_	_	_
248	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Slide	slide	NN	_	_	_
6	13	13	CD	_	_	_
7	_	_	CD	_	_	_
8	Wild	Wild	NNP	_	_	_
9	type	type	NN	_	_	_
10	_	_	CD	_	_	_
11	CORM-3	corm-3	NN	_	_	_
12	_	_	NN	_	_	_
13	biol	biol	NN	_	_	_
14	rep	rep	NN	GEN	_	_
15	1	1	CD	_	_	_
16	_	_	NN	_	_	_
17	Cy3	cy3	NN	_	_	_
18	0	0	CD	_	_	_
19	Cy5	cy5	NN	_	_	_
20	120	120	CD	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	Slide	Slide	NNP	_	_	_
23	13	13	CD	_	_	_
24	_	_	CD	_	_	_
25	Wild	Wild	NNP	_	_	_
26	type	type	NN	_	_	_
27	_	_	CD	_	_	_
28	CORM-3	corm-3	NN	_	_	_
29	_	_	NN	_	_	_
30	biol	biol	NN	_	_	_
31	rep	rep	NN	GEN	_	_
32	1	1	CD	_	_	_
33	_	_	CD	_	_	_
34	Cy3	cy3	NN	_	_	_
35	10	10	CD	_	_	_
36	Cy5	cy5	NN	_	_	_
37	0	0	CD	_	_	_
38	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
39	Slide	Slide	NNP	_	_	_
40	13	13	CD	_	_	_
41	_	_	CD	_	_	_
42	Wild	Wild	NNP	_	_	_
43	type	type	NN	_	_	_
44	_	_	CD	_	_	_
45	CORM-3	corm-3	NN	_	_	_
46	_	_	NN	_	_	_
47	biol	biol	NN	_	_	_
48	rep	rep	NN	GEN	_	_
49	1	1	CD	_	_	_
50	_	_	CD	_	_	_
51	Cy3	cy3	NN	_	_	_
52	120	120	CD	_	_	_
53	Cy5	cy5	NN	_	_	_
54	0	0	CD	_	_	_
55	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
56	Slide	Slide	NNP	_	_	_
57	13	13	CD	_	_	_
58	_	_	CD	_	_	_
59	Wild	Wild	NNP	_	_	_
60	type	type	NN	_	_	_
61	_	_	CD	_	_	_
62	CORM-3	corm-3	NN	_	_	_
63	_	_	NN	_	_	_
64	biol	biol	NN	_	_	_
65	rep	rep	NN	GEN	_	_
66	1	1	CD	_	_	_
67	_	_	CD	_	_	_
68	Cy3	cy3	NN	_	_	_
69	20	20	CD	_	_	_
70	Cy5	cy5	NN	_	_	_
71	0	0	CD	_	_	_
72	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
73	Slide	Slide	NNP	_	_	_
74	13	13	CD	_	_	_
75	_	_	CD	_	_	_
76	Wild	Wild	NNP	_	_	_
77	type	type	NN	_	_	_
78	_	_	CD	_	_	_
79	CORM-3	corm-3	NN	_	_	_
80	_	_	NN	_	_	_
81	biol	biol	NN	_	_	_
82	rep	rep	NN	GEN	_	_
83	1	1	CD	_	_	_
84	_	_	CD	_	_	_
85	Cy3	cy3	NN	_	_	_
86	40	40	CD	_	_	_
87	Cy5	cy5	NN	_	_	_
88	0	0	CD	_	_	_
89	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
90	Slide	Slide	NNP	_	_	_
91	13	13	CD	_	_	_
92	_	_	CD	_	_	_
93	Wild	Wild	NNP	_	_	_
94	type	type	NN	_	_	_
95	_	_	CD	_	_	_
96	CORM-3	corm-3	NN	_	_	_
97	_	_	NN	_	_	_
98	biol	biol	NN	_	_	_
99	rep	rep	NN	GEN	_	_
100	1	1	CD	_	_	_
101	_	_	CD	_	_	_
102	Cy3	cy3	NN	_	_	_
103	60	60	CD	_	_	_
104	Cy5	cy5	NN	_	_	_
105	0	0	CD	_	_	_
106	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
107	Slide	Slide	NNP	_	_	_
108	13	13	CD	_	_	_
109	_	_	CD	_	_	_
110	Wild	Wild	NNP	_	_	_
111	type	type	NN	_	_	_
112	_	_	CD	_	_	_
113	CORM-3	corm-3	NN	_	_	_
114	_	_	NN	_	_	_
115	biol	biol	NN	_	_	_
116	rep	rep	NN	GEN	_	_
117	2	2	CD	_	_	_
118	_	_	CD	_	_	_
119	Cy3	cy3	NN	_	_	_
120	0	0	CD	_	_	_
121	Cy5	cy5	NN	_	_	_
122	10	10	CD	_	_	_
123	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
124	Slide	Slide	NNP	_	_	_
125	13	13	CD	_	_	_
126	_	_	CD	_	_	_
127	Wild	Wild	NNP	_	_	_
128	type	type	NN	_	_	_
129	_	_	CD	_	_	_
130	CORM-3	corm-3	NN	_	_	_
131	_	_	NN	_	_	_
132	biol	biol	NN	_	_	_
133	rep	rep	NN	GEN	_	_
134	2	2	CD	_	_	_
135	_	_	CD	_	_	_
136	Cy3	cy3	NN	_	_	_
137	0	0	CD	_	_	_
138	Cy5	cy5	NN	_	_	_
139	20	20	CD	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	Slide	slide	NN	_	_	_
142	14	14	CD	_	_	_
143	_	_	CD	_	_	_
144	Wild	Wild	NNP	_	_	_
145	type	type	NN	_	_	_
146	_	_	CD	_	_	_
147	CORM-3	corm-3	NN	_	_	_
148	_	_	NN	_	_	_
149	biol	biol	NN	_	_	_
150	rep	rep	NN	GEN	_	_
151	2	2	CD	_	_	_
152	_	_	CD	_	_	_
153	Cy3	cy3	NN	_	_	_
154	0	0	CD	_	_	_
155	Cy5	cy5	NN	_	_	_
156	120	120	CD	_	_	_
157	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
158	Slide	Slide	NNP	_	_	_
159	14	14	CD	_	_	_
160	_	_	CD	_	_	_
161	Wild	Wild	NNP	_	_	_
162	type	type	NN	_	_	_
163	_	_	CD	_	_	_
164	CORM-3	corm-3	NN	_	_	_
165	_	_	NN	_	_	_
166	biol	biol	NN	_	_	_
167	rep	rep	NN	GEN	_	_
168	2	2	CD	_	_	_
169	_	_	CD	_	_	_
170	Cy3	cy3	NN	_	_	_
171	0	0	CD	_	_	_
172	Cy5	cy5	NN	_	_	_
173	40	40	CD	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	Slide	slide	NN	_	_	_
176	14	14	CD	_	_	_
177	_	_	CD	_	_	_
178	Wild	Wild	NNP	_	_	_
179	type	type	NN	_	_	_
180	_	_	CD	_	_	_
181	CORM-3	corm-3	NN	_	_	_
182	_	_	NN	_	_	_
183	biol	biol	NN	_	_	_
184	rep	rep	NN	GEN	_	_
185	2	2	CD	_	_	_
186	_	_	CD	_	_	_
187	Cy3	cy3	NN	_	_	_
188	0	0	CD	_	_	_
189	Cy5	cy5	NN	_	_	_
190	60	60	CD	_	_	_
191	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
192	Slide	Slide	NNP	_	_	_
193	14	14	CD	_	_	_
194	_	_	CD	_	_	_
195	Wild	Wild	NNP	_	_	_
196	type	type	NN	_	_	_
197	_	_	CD	_	_	_
198	CORM-3	corm-3	NN	_	_	_
199	_	_	NN	_	_	_
200	biol	biol	NN	_	_	_
201	rep	rep	NN	GEN	_	_
202	2	2	CD	_	_	_
203	_	_	CD	_	_	_
204	Cy3	cy3	NN	_	_	_
205	10	10	CD	_	_	_
206	Cy5	cy5	NN	_	_	_
207	0	0	CD	_	_	_
208	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
209	Slide	Slide	NNP	_	_	_
210	14	14	CD	_	_	_
211	_	_	CD	_	_	_
212	Wild	Wild	NNP	_	_	_
213	type	type	NN	_	_	_
214	_	_	CD	_	_	_
215	CORM-3	corm-3	NN	_	_	_
216	_	_	NN	_	_	_
217	biol	biol	NN	_	_	_
218	rep	rep	NN	GEN	_	_
219	2	2	CD	_	_	_
220	_	_	SYM	_	_	_
221	Cy3	cy3	NN	_	_	_
222	120	120	CD	_	_	_
223	Cy5	cy5	NN	_	_	_
224	0	0	CD	_	_	_
225	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
226	Slide	Slide	NNP	_	_	_
227	14	14	CD	_	_	_
228	_	_	CD	_	_	_
229	Wild	Wild	NNP	_	_	_
230	type	type	NN	_	_	_
231	_	_	CD	_	_	_
232	CORM-3	corm-3	NN	_	_	_
233	_	_	NN	_	_	_
234	biol	biol	NN	_	_	_
235	rep	rep	NN	GEN	_	_
236	2	2	CD	_	_	_
237	_	_	CD	_	_	_
238	Cy3	cy3	NN	_	_	_
239	20	20	CD	_	_	_
240	Cy5	cy5	NN	_	_	_
241	0	0	CD	_	_	_
242	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
243	Slide	Slide	NNP	_	_	_
244	14	14	CD	_	_	_
245	_	_	CD	_	_	_
246	Wild	Wild	NNP	_	_	_
247	type	type	NN	_	_	_
248	_	_	CD	_	_	_
249	CORM-3	corm-3	NN	_	_	_
250	_	_	NN	_	_	_
251	biol	biol	NN	_	_	_
252	rep	rep	NN	GEN	_	_
253	2	2	CD	_	_	_
254	_	_	CD	_	_	_
255	Cy3	cy3	NN	_	_	_
256	40	40	CD	_	_	_
257	Cy5	cy5	NN	_	_	_
258	0	0	CD	_	_	_
259	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
260	Slide	Slide	NNP	_	_	_
261	14	14	CD	_	_	_
262	_	_	CD	_	_	_
263	Wild	Wild	NNP	_	_	_
264	type	type	NN	_	_	_
265	_	_	CD	_	_	_
266	CORM-3	corm-3	NN	_	_	_
267	_	_	NN	_	_	_
268	biol	biol	NN	_	_	_
269	rep	rep	NN	GEN	_	_
270	2	2	CD	_	_	_
271	_	_	CD	_	_	_
272	Cy3	cy3	NN	_	_	_
273	60	60	CD	_	_	_
274	Cy5	cy5	NN	_	_	_
275	0	0	CD	_	_	_
276	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
277	Slide	Slide	NNP	_	_	_
278	15	15	CD	_	_	_
279	_	_	SYM	_	_	_
280	hemA	hema	NN	GEN	_	_
281	_	_	CD	_	_	_
282	CORM-3	corm-3	NN	_	_	_
283	_	_	NN	_	_	_
284	biol	biol	NN	_	_	_
285	rep	rep	NN	GEN	_	_
286	2	2	CD	_	_	_
287	_	_	SYM	_	_	_
288	Cy3	cy3	NN	_	_	_
289	120	120	CD	_	_	_
290	Cy5	cy5	NN	_	_	_
291	0	0	CD	_	_	_
292	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
293	Slide	Slide	NNP	_	_	_
294	15	15	CD	_	_	_
295	_	_	SYM	_	_	_
296	hemA	hema	NN	GEN	_	_
297	_	_	CD	_	_	_
298	CORM-3	corm-3	NN	_	_	_
299	_	_	NN	_	_	_
300	biol	biol	NN	_	_	_
301	rep	rep	NN	GEN	_	_
302	2	2	CD	_	_	_
303	_	_	CD	_	_	_
304	Cy3	cy3	NN	_	_	_
305	20	20	CD	_	_	_
306	Cy5	cy5	NN	_	_	_
307	0	0	CD	_	_	_
308	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
309	Slide	Slide	NNP	_	_	_
310	15	15	CD	_	_	_
311	_	_	SYM	_	_	_
312	hemA	hema	NN	GEN	_	_
313	_	_	CD	_	_	_
314	CORM-3	corm-3	NN	_	_	_
315	_	_	NN	_	_	_
316	biol	biol	NN	_	_	_
317	rep	rep	NN	GEN	_	_
318	2	2	CD	_	_	_
319	_	_	CD	_	_	_
320	Cy3	cy3	NN	_	_	_
321	40	40	CD	_	_	_
322	Cy5	cy5	NN	_	_	_
323	0	0	CD	_	_	_
324	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
325	Slide	Slide	NNP	_	_	_
326	15	15	CD	_	_	_
327	_	_	SYM	_	_	_
328	hemA	hema	NN	GEN	_	_
329	_	_	CD	_	_	_
330	CORM-3	corm-3	NN	_	_	_
331	_	_	NN	_	_	_
332	biol	biol	NN	_	_	_
333	rep	rep	NN	GEN	_	_
334	2	2	CD	_	_	_
335	_	_	CD	_	_	_
336	Cy3	cy3	NN	_	_	_
337	60	60	CD	_	_	_
338	Cy5	cy5	NN	_	_	_
339	0	0	CD	_	_	_
340	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
341	Slide	Slide	NNP	_	_	_
342	15	15	CD	_	_	_
343	_	_	CD	_	_	_
344	Wild	Wild	NNP	_	_	_
345	type	type	NN	_	_	_
346	_	_	CD	_	_	_
347	CORM-3	corm-3	NN	_	_	_
348	_	_	NN	_	_	_
349	biol	biol	NN	_	_	_
350	rep	rep	NN	GEN	_	_
351	1	1	CD	_	_	_
352	_	_	NN	_	_	_
353	Cy3	cy3	NN	_	_	_
354	0	0	CD	_	_	_
355	Cy5	cy5	NN	_	_	_
356	10	10	CD	_	_	_
357	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
358	Slide	Slide	NNP	_	_	_
359	15	15	CD	_	_	_
360	_	_	CD	_	_	_
361	Wild	Wild	NNP	_	_	_
362	type	type	NN	_	_	_
363	_	_	CD	_	_	_
364	CORM-3	corm-3	NN	_	_	_
365	_	_	NN	_	_	_
366	biol	biol	NN	_	_	_
367	rep	rep	NN	GEN	_	_
368	1	1	CD	_	_	_
369	_	_	NN	_	_	_
370	Cy3	cy3	NN	_	_	_
371	0	0	CD	_	_	_
372	Cy5	cy5	NN	_	_	_
373	20	20	CD	_	_	_
374	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
375	Slide	Slide	NNP	_	_	_
376	15	15	CD	_	_	_
377	_	_	CD	_	_	_
378	Wild	Wild	NNP	_	_	_
379	type	type	NN	_	_	_
380	_	_	CD	_	_	_
381	CORM-3	corm-3	NN	_	_	_
382	_	_	NN	_	_	_
383	biol	biol	NN	_	_	_
384	rep	rep	NN	GEN	_	_
385	1	1	CD	_	_	_
386	_	_	NN	_	_	_
387	Cy3	cy3	NN	_	_	_
388	0	0	CD	_	_	_
389	Cy5	cy5	NN	_	_	_
390	40	40	CD	_	_	_
391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
392	Slide	slide	NN	_	_	_
393	15	15	CD	_	_	_
394	_	_	CD	_	_	_
395	Wild	Wild	NNP	_	_	_
396	type	type	NN	_	_	_
397	_	_	CD	_	_	_
398	CORM-3	corm-3	NN	_	_	_
399	_	_	NN	_	_	_
400	biol	biol	NN	_	_	_
401	rep	rep	NN	GEN	_	_
402	1	1	CD	_	_	_
403	_	_	NN	_	_	_
404	Cy3	cy3	NN	_	_	_
405	0	0	CD	_	_	_
406	Cy5	cy5	NN	_	_	_
407	60	60	CD	_	_	_
408	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
409	Slide	slide	NN	_	_	_
410	16	16	CD	_	_	_
411	_	_	NN	_	_	_
412	hemA	hema	NN	GEN	_	_
413	_	_	CD	_	_	_
414	CORM-3	corm-3	NN	_	_	_
415	_	_	NN	_	_	_
416	biol	biol	NN	_	_	_
417	rep	rep	NN	GEN	_	_
418	1	1	CD	_	_	_
419	_	_	CD	_	_	_
420	Cy3	cy3	NN	_	_	_
421	120	120	CD	_	_	_
422	Cy5	cy5	NN	_	_	_
423	0	0	CD	_	_	_
424	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
425	Slide	Slide	NNP	_	_	_
426	16	16	CD	_	_	_
427	_	_	SYM	_	_	_
428	hemA	hema	NN	GEN	_	_
429	_	_	CD	_	_	_
430	CORM-3	corm-3	NN	_	_	_
431	_	_	NN	_	_	_
432	biol	biol	NN	_	_	_
433	rep	rep	NN	GEN	_	_
434	1	1	CD	_	_	_
435	_	_	CD	_	_	_
436	Cy3	cy3	NN	_	_	_
437	60	60	CD	_	_	_
438	Cy5	cy5	NN	_	_	_
439	0	0	CD	_	_	_
440	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
441	Slide	Slide	NNP	_	_	_
442	16	16	CD	_	_	_
443	_	_	SYM	_	_	_
444	hemA	hema	NN	GEN	_	_
445	_	_	CD	_	_	_
446	CORM-3	corm-3	NN	_	_	_
447	_	_	NN	_	_	_
448	biol	biol	NN	_	_	_
449	rep	rep	NN	GEN	_	_
450	2	2	CD	_	_	_
451	_	_	CD	_	_	_
452	Cy3	cy3	NN	_	_	_
453	0	0	CD	_	_	_
454	Cy5	cy5	NN	_	_	_
455	10	10	CD	_	_	_
456	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
457	Slide	slide	NN	_	_	_
458	16	16	CD	_	_	_
459	_	_	NN	_	_	_
460	hemA	hema	NN	GEN	_	_
461	_	_	CD	_	_	_
462	CORM-3	corm-3	NN	_	_	_
463	_	_	NN	_	_	_
464	biol	biol	NN	_	_	_
465	rep	rep	NN	GEN	_	_
466	2	2	CD	_	_	_
467	_	_	CD	_	_	_
468	Cy3	cy3	NN	_	_	_
469	0	0	CD	_	_	_
470	Cy5	cy5	NN	_	_	_
471	120	120	CD	_	_	_
472	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
473	Slide	slide	NN	_	_	_
474	16	16	CD	_	_	_
475	_	_	NN	_	_	_
476	hemA	hema	NN	GEN	_	_
477	_	_	CD	_	_	_
478	CORM-3	corm-3	NN	_	_	_
479	_	_	NN	_	_	_
480	biol	biol	NN	_	_	_
481	rep	rep	NN	GEN	_	_
482	2	2	CD	_	_	_
483	_	_	CD	_	_	_
484	Cy3	cy3	NN	_	_	_
485	0	0	CD	_	_	_
486	Cy5	cy5	NN	_	_	_
487	20	20	CD	_	_	_
488	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
489	Slide	slide	NN	_	_	_
490	16	16	CD	_	_	_
491	_	_	NN	_	_	_
492	hemA	hema	NN	GEN	_	_
493	_	_	CD	_	_	_
494	CORM-3	corm-3	NN	_	_	_
495	_	_	NN	_	_	_
496	biol	biol	NN	_	_	_
497	rep	rep	NN	GEN	_	_
498	2	2	CD	_	_	_
499	_	_	CD	_	_	_
500	Cy3	cy3	NN	_	_	_
501	0	0	CD	_	_	_
502	Cy5	cy5	NN	_	_	_
503	40	40	CD	_	_	_
504	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
505	Slide	slide	NN	_	_	_
506	16	16	CD	_	_	_
507	_	_	NN	_	_	_
508	hemA	hema	NN	GEN	_	_
509	_	_	CD	_	_	_
510	CORM-3	corm-3	NN	_	_	_
511	_	_	NN	_	_	_
512	biol	biol	NN	_	_	_
513	rep	rep	NN	GEN	_	_
514	2	2	CD	_	_	_
515	_	_	CD	_	_	_
516	Cy3	cy3	NN	_	_	_
517	0	0	CD	_	_	_
518	Cy5	cy5	NN	_	_	_
519	60	60	CD	_	_	_
520	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
521	Slide	slide	NN	_	_	_
522	16	16	CD	_	_	_
523	_	_	NN	_	_	_
524	hemA	hema	NN	GEN	_	_
525	_	_	CD	_	_	_
526	CORM-3	corm-3	NN	_	_	_
527	_	_	NN	_	_	_
528	biol	biol	NN	_	_	_
529	rep	rep	NN	GEN	_	_
530	2	2	CD	_	_	_
531	_	_	CD	_	_	_
532	Cy3	cy3	NN	_	_	_
533	10	10	CD	_	_	_
534	Cy5	cy5	NN	_	_	_
535	0	0	CD	_	_	_
536	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
537	Slide	Slide	NNP	_	_	_
538	17	17	CD	_	_	_
539	_	_	SYM	_	_	_
540	hemA	hema	NN	GEN	_	_
541	_	_	CD	_	_	_
542	CORM-3	corm-3	NN	_	_	_
543	_	_	NN	_	_	_
544	biol	biol	NN	_	_	_
545	rep	rep	NN	GEN	_	_
546	1	1	CD	_	_	_
547	_	_	NN	_	_	_
548	Cy3	cy3	NN	_	_	_
549	0	0	CD	_	_	_
550	Cy5	cy5	NN	_	_	_
551	10	10	CD	_	_	_
552	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
553	Slide	slide	NN	_	_	_
554	17	17	CD	_	_	_
555	_	_	NN	_	_	_
556	hemA	hema	NN	GEN	_	_
557	_	_	CD	_	_	_
558	CORM-3	corm-3	NN	_	_	_
559	_	_	NN	_	_	_
560	biol	biol	NN	_	_	_
561	rep	rep	NN	GEN	_	_
562	1	1	CD	_	_	_
563	_	_	NN	_	_	_
564	Cy3	cy3	NN	_	_	_
565	0	0	CD	_	_	_
566	Cy5	cy5	NN	_	_	_
567	120	120	CD	_	_	_
568	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
569	Slide	slide	NN	_	_	_
570	17	17	CD	_	_	_
571	_	_	NN	_	_	_
572	hemA	hema	NN	GEN	_	_
573	_	_	CD	_	_	_
574	CORM-3	corm-3	NN	_	_	_
575	_	_	NN	_	_	_
576	biol	biol	NN	_	_	_
577	rep	rep	NN	GEN	_	_
578	1	1	CD	_	_	_
579	_	_	NN	_	_	_
580	Cy3	cy3	NN	_	_	_
581	0	0	CD	_	_	_
582	Cy5	cy5	NN	_	_	_
583	20	20	CD	_	_	_
584	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
585	Slide	slide	NN	_	_	_
586	17	17	CD	_	_	_
587	_	_	NN	_	_	_
588	hemA	hema	NN	GEN	_	_
589	_	_	CD	_	_	_
590	CORM-3	corm-3	NN	_	_	_
591	_	_	NN	_	_	_
592	biol	biol	NN	_	_	_
593	rep	rep	NN	GEN	_	_
594	1	1	CD	_	_	_
595	_	_	NN	_	_	_
596	Cy3	cy3	NN	_	_	_
597	0	0	CD	_	_	_
598	Cy5	cy5	NN	_	_	_
599	40	40	CD	_	_	_
600	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
601	Slide	slide	NN	_	_	_
602	17	17	CD	_	_	_
603	_	_	NN	_	_	_
604	hemA	hema	NN	GEN	_	_
605	_	_	CD	_	_	_
606	CORM-3	corm-3	NN	_	_	_
607	_	_	NN	_	_	_
608	biol	biol	NN	_	_	_
609	rep	rep	NN	GEN	_	_
610	1	1	CD	_	_	_
611	_	_	NN	_	_	_
612	Cy3	cy3	NN	_	_	_
613	0	0	CD	_	_	_
614	Cy5	cy5	NN	_	_	_
615	60	60	CD	_	_	_
616	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
617	Slide	slide	NN	_	_	_
618	17	17	CD	_	_	_
619	_	_	NN	_	_	_
620	hemA	hema	NN	GEN	_	_
621	_	_	CD	_	_	_
622	CORM-3	corm-3	NN	_	_	_
623	_	_	NN	_	_	_
624	biol	biol	NN	_	_	_
625	rep	rep	NN	GEN	_	_
626	1	1	CD	_	_	_
627	_	_	CD	_	_	_
628	Cy3	cy3	NN	_	_	_
629	10	10	CD	_	_	_
630	Cy5	cy5	NN	_	_	_
631	0	0	CD	_	_	_
632	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
633	Slide	Slide	NNP	_	_	_
634	17	17	CD	_	_	_
635	_	_	SYM	_	_	_
636	hemA	hema	NN	GEN	_	_
637	_	_	CD	_	_	_
638	CORM-3	corm-3	NN	_	_	_
639	_	_	NN	_	_	_
640	biol	biol	NN	_	_	_
641	rep	rep	NN	GEN	_	_
642	1	1	CD	_	_	_
643	_	_	CD	_	_	_
644	Cy3	cy3	NN	_	_	_
645	20	20	CD	_	_	_
646	Cy5	cy5	NN	_	_	_
647	0	0	CD	_	_	_
648	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
649	Slide	Slide	NNP	_	_	_
650	17	17	CD	_	_	_
651	_	_	SYM	_	_	_
652	hemA	hema	NN	GEN	_	_
653	_	_	CD	_	_	_
654	CORM-3	corm-3	NN	_	_	_
655	_	_	NN	_	_	_
656	biol	biol	NN	_	_	_
657	rep	rep	NN	GEN	_	_
658	1	1	CD	_	_	_
659	_	_	CD	_	_	_
660	Cy3	cy3	NN	_	_	_
661	40	40	CD	_	_	_
662	Cy5	cy5	NN	_	_	_
663	0	0	CD	_	_	_
664	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
665	Slide	Slide	NNP	_	_	_
666	34	34	CD	_	_	_
667	_	_	SYM	_	_	_
668	hemA	hema	NN	GEN	_	_
669	_	_	CD	_	_	_
670	iCORM-3	icorm-3	NN	_	_	_
671	_	_	NN	_	_	_
672	biol	biol	NN	_	_	_
673	rep	rep	NN	GEN	_	_
674	1	1	CD	_	_	_
675	_	_	NN	_	_	_
676	Cy3	cy3	NN	_	_	_
677	0	0	CD	_	_	_
678	Cy5	cy5	NN	_	_	_
679	10	10	CD	_	_	_
680	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
681	Slide	slide	NN	_	_	_
682	34	34	CD	_	_	_
683	_	_	NN	_	_	_
684	hemA	hema	NN	GEN	_	_
685	_	_	CD	_	_	_
686	iCORM-3	icorm-3	NN	_	_	_
687	_	_	NN	_	_	_
688	biol	biol	NN	_	_	_
689	rep	rep	NN	GEN	_	_
690	1	1	CD	_	_	_
691	_	_	NN	_	_	_
692	Cy3	cy3	NN	_	_	_
693	0	0	CD	_	_	_
694	Cy5	cy5	NN	_	_	_
695	120	120	CD	_	_	_
696	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
697	Slide	slide	NN	_	_	_
698	34	34	CD	_	_	_
699	_	_	NN	_	_	_
700	hemA	hema	NN	GEN	_	_
701	_	_	CD	_	_	_
702	iCORM-3	icorm-3	NN	_	_	_
703	_	_	NN	_	_	_
704	biol	biol	NN	_	_	_
705	rep	rep	NN	GEN	_	_
706	1	1	CD	_	_	_
707	_	_	NN	_	_	_
708	Cy3	cy3	NN	_	_	_
709	0	0	CD	_	_	_
710	Cy5	cy5	NN	_	_	_
711	20	20	CD	_	_	_
712	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
713	Slide	slide	NN	_	_	_
714	34	34	CD	_	_	_
715	_	_	NN	_	_	_
716	hemA	hema	NN	GEN	_	_
717	_	_	CD	_	_	_
718	iCORM-3	icorm-3	NN	_	_	_
719	_	_	NN	_	_	_
720	biol	biol	NN	_	_	_
721	rep	rep	NN	GEN	_	_
722	1	1	CD	_	_	_
723	_	_	NN	_	_	_
724	Cy3	cy3	NN	_	_	_
725	0	0	CD	_	_	_
726	Cy5	cy5	NN	_	_	_
727	40	40	CD	_	_	_
728	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
729	Slide	slide	NN	_	_	_
730	34	34	CD	_	_	_
731	_	_	NN	_	_	_
732	hemA	hema	NN	GEN	_	_
733	_	_	CD	_	_	_
734	iCORM-3	icorm-3	NN	_	_	_
735	_	_	NN	_	_	_
736	biol	biol	NN	_	_	_
737	rep	rep	NN	GEN	_	_
738	1	1	CD	_	_	_
739	_	_	NN	_	_	_
740	Cy3	cy3	NN	_	_	_
741	0	0	CD	_	_	_
742	Cy5	cy5	NN	_	_	_
743	60	60	CD	_	_	_
744	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
745	Slide	slide	NN	_	_	_
746	34	34	CD	_	_	_
747	_	_	NN	_	_	_
748	hemA	hema	NN	GEN	_	_
749	_	_	CD	_	_	_
750	iCORM-3	icorm-3	NN	_	_	_
751	_	_	NN	_	_	_
752	biol	biol	NN	_	_	_
753	rep	rep	NN	GEN	_	_
754	1	1	CD	_	_	_
755	_	_	CD	_	_	_
756	Cy3	cy3	NN	_	_	_
757	10	10	CD	_	_	_
758	Cy5	cy5	NN	_	_	_
759	0	0	CD	_	_	_
760	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
761	Slide	Slide	NNP	_	_	_
762	34	34	CD	_	_	_
763	_	_	SYM	_	_	_
764	hemA	hema	NN	GEN	_	_
765	_	_	CD	_	_	_
766	iCORM-3	icorm-3	NN	_	_	_
767	_	_	NN	_	_	_
768	biol	biol	NN	_	_	_
769	rep	rep	NN	GEN	_	_
770	1	1	CD	_	_	_
771	_	_	CD	_	_	_
772	Cy3	cy3	NN	_	_	_
773	20	20	CD	_	_	_
774	Cy5	cy5	NN	_	_	_
775	0	0	CD	_	_	_
776	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
777	Slide	Slide	NNP	_	_	_
778	34	34	CD	_	_	_
779	_	_	SYM	_	_	_
780	hemA	hema	NN	GEN	_	_
781	_	_	CD	_	_	_
782	iCORM-3	icorm-3	NN	_	_	_
783	_	_	NN	_	_	_
784	biol	biol	NN	_	_	_
785	rep	rep	NN	GEN	_	_
786	1	1	CD	_	_	_
787	_	_	CD	_	_	_
788	Cy3	cy3	NN	_	_	_
789	40	40	CD	_	_	_
790	Cy5	cy5	NN	_	_	_
791	0	0	CD	_	_	_
792	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
793	Slide	Slide	NNP	_	_	_
794	35	35	CD	_	_	_
795	_	_	SYM	_	_	_
796	hemA	hema	NN	GEN	_	_
797	_	_	CD	_	_	_
798	iCORM-3	icorm-3	NN	_	_	_
799	_	_	NN	_	_	_
800	biol	biol	NN	_	_	_
801	rep	rep	NN	GEN	_	_
802	1	1	CD	_	_	_
803	_	_	CD	_	_	_
804	Cy3	cy3	NN	_	_	_
805	120	120	CD	_	_	_
806	Cy5	cy5	NN	_	_	_
807	0	0	CD	_	_	_
808	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
809	Slide	Slide	NNP	_	_	_
810	35	35	CD	_	_	_
811	_	_	SYM	_	_	_
812	hemA	hema	NN	GEN	_	_
813	_	_	CD	_	_	_
814	iCORM-3	icorm-3	NN	_	_	_
815	_	_	NN	_	_	_
816	biol	biol	NN	_	_	_
817	rep	rep	NN	GEN	_	_
818	1	1	CD	_	_	_
819	_	_	CD	_	_	_
820	Cy3	cy3	NN	_	_	_
821	60	60	CD	_	_	_
822	Cy5	cy5	NN	_	_	_
823	0	0	CD	_	_	_
824	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
825	Slide	Slide	NNP	_	_	_
826	35	35	CD	_	_	_
827	_	_	SYM	_	_	_
828	hemA	hema	NN	GEN	_	_
829	_	_	CD	_	_	_
830	iCORM-3	icorm-3	NN	_	_	_
831	_	_	NN	_	_	_
832	biol	biol	NN	_	_	_
833	rep	rep	NN	GEN	_	_
834	2	2	CD	_	_	_
835	_	_	CD	_	_	_
836	Cy3	cy3	NN	_	_	_
837	0	0	CD	_	_	_
838	Cy5	cy5	NN	_	_	_
839	10	10	CD	_	_	_
840	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
841	Slide	slide	NN	_	_	_
842	35	35	CD	_	_	_
843	_	_	NN	_	_	_
844	hemA	hema	NN	GEN	_	_
845	_	_	CD	_	_	_
846	iCORM-3	icorm-3	NN	_	_	_
847	_	_	NN	_	_	_
848	biol	biol	NN	_	_	_
849	rep	rep	NN	GEN	_	_
850	2	2	CD	_	_	_
851	_	_	CD	_	_	_
852	Cy3	cy3	NN	_	_	_
853	0	0	CD	_	_	_
854	Cy5	cy5	NN	_	_	_
855	120	120	CD	_	_	_
856	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
857	Slide	slide	NN	_	_	_
858	35	35	CD	_	_	_
859	_	_	NN	_	_	_
860	hemA	hema	NN	GEN	_	_
861	_	_	CD	_	_	_
862	iCORM-3	icorm-3	NN	_	_	_
863	_	_	NN	_	_	_
864	biol	biol	NN	_	_	_
865	rep	rep	NN	GEN	_	_
866	2	2	CD	_	_	_
867	_	_	CD	_	_	_
868	Cy3	cy3	NN	_	_	_
869	0	0	CD	_	_	_
870	Cy5	cy5	NN	_	_	_
871	20	20	CD	_	_	_
872	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
873	Slide	slide	NN	_	_	_
874	35	35	CD	_	_	_
875	_	_	NN	_	_	_
876	hemA	hema	NN	GEN	_	_
877	_	_	CD	_	_	_
878	iCORM-3	icorm-3	NN	_	_	_
879	_	_	NN	_	_	_
880	biol	biol	NN	_	_	_
881	rep	rep	NN	GEN	_	_
882	2	2	CD	_	_	_
883	_	_	CD	_	_	_
884	Cy3	cy3	NN	_	_	_
885	0	0	CD	_	_	_
886	Cy5	cy5	NN	_	_	_
887	40	40	CD	_	_	_
888	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
889	Slide	slide	NN	_	_	_
890	35	35	CD	_	_	_
891	_	_	NN	_	_	_
892	hemA	hema	NN	GEN	_	_
893	_	_	CD	_	_	_
894	iCORM-3	icorm-3	NN	_	_	_
895	_	_	NN	_	_	_
896	biol	biol	NN	_	_	_
897	rep	rep	NN	GEN	_	_
898	2	2	CD	_	_	_
899	_	_	CD	_	_	_
900	Cy3	cy3	NN	_	_	_
901	0	0	CD	_	_	_
902	Cy5	cy5	NN	_	_	_
903	60	60	CD	_	_	_
904	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
905	Slide	slide	NN	_	_	_
906	35	35	CD	_	_	_
907	_	_	NN	_	_	_
908	hemA	hema	NN	GEN	_	_
909	_	_	CD	_	_	_
910	iCORM-3	icorm-3	NN	_	_	_
911	_	_	NN	_	_	_
912	biol	biol	NN	_	_	_
913	rep	rep	NN	GEN	_	_
914	2	2	CD	_	_	_
915	_	_	CD	_	_	_
916	Cy3	cy3	NN	_	_	_
917	10	10	CD	_	_	_
918	Cy5	cy5	NN	_	_	_
919	0	0	CD	_	_	_
920	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
921	Slide	Slide	NNP	_	_	_
922	36	36	CD	_	_	_
923	_	_	SYM	_	_	_
924	hemA	hema	NN	GEN	_	_
925	_	_	CD	_	_	_
926	iCORM-3	icorm-3	NN	_	_	_
927	_	_	NN	_	_	_
928	biol	biol	NN	_	_	_
929	rep	rep	NN	GEN	_	_
930	2	2	CD	_	_	_
931	_	_	SYM	_	_	_
932	Cy3	cy3	NN	_	_	_
933	120	120	CD	_	_	_
934	Cy5	cy5	NN	_	_	_
935	0	0	CD	_	_	_
936	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
937	Slide	Slide	NNP	_	_	_
938	36	36	CD	_	_	_
939	_	_	SYM	_	_	_
940	hemA	hema	NN	GEN	_	_
941	_	_	CD	_	_	_
942	iCORM-3	icorm-3	NN	_	_	_
943	_	_	NN	_	_	_
944	biol	biol	NN	_	_	_
945	rep	rep	NN	GEN	_	_
946	2	2	CD	_	_	_
947	_	_	CD	_	_	_
948	Cy3	cy3	NN	_	_	_
949	20	20	CD	_	_	_
950	Cy5	cy5	NN	_	_	_
951	0	0	CD	_	_	_
952	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
953	Slide	Slide	NNP	_	_	_
954	36	36	CD	_	_	_
955	_	_	SYM	_	_	_
956	hemA	hema	NN	GEN	_	_
957	_	_	CD	_	_	_
958	iCORM-3	icorm-3	NN	_	_	_
959	_	_	NN	_	_	_
960	biol	biol	NN	_	_	_
961	rep	rep	NN	GEN	_	_
962	2	2	CD	_	_	_
963	_	_	CD	_	_	_
964	Cy3	cy3	NN	_	_	_
965	40	40	CD	_	_	_
966	Cy5	cy5	NN	_	_	_
967	0	0	CD	_	_	_
968	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
969	Slide	Slide	NNP	_	_	_
970	36	36	CD	_	_	_
971	_	_	SYM	_	_	_
972	hemA	hema	NN	GEN	_	_
973	_	_	CD	_	_	_
974	iCORM-3	icorm-3	NN	_	_	_
975	_	_	NN	_	_	_
976	biol	biol	NN	_	_	_
977	rep	rep	NN	GEN	_	_
978	2	2	CD	_	_	_
979	_	_	CD	_	_	_
980	Cy3	cy3	NN	_	_	_
981	60	60	CD	_	_	_
982	Cy5	cy5	NN	_	_	_
983	0	0	CD	_	_	_
984	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
985	Slide	Slide	NNP	_	_	_
986	36	36	CD	_	_	_
987	_	_	SYM	_	_	_
988	hemA	hema	NN	GEN	_	_
989	vs.	vs.	FW	_	_	_
990	WT	wt	FW	_	_	_
991	t	t	NN	_	_	_
992	=	=	JJ	_	_	_
993	0	0	CD	_	_	_
994	_	_	NN	_	_	_
995	biol	biol	NN	_	_	_
996	rep	rep	NN	GEN	_	_
997	1	1	CD	_	_	_
998	_	_	CD	_	_	_
999	Cy3	cy3	NN	_	_	_
1000	hemA	hema	NN	GEN	_	_
1001	Cy5	cy5	NN	_	_	_
1002	WT	WT	NNP	_	_	_
1003	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1004	Slide	Slide	NNP	_	_	_
1005	36	36	CD	_	_	_
1006	_	_	SYM	_	_	_
1007	hemA	hema	NN	GEN	_	_
1008	vs.	vs.	FW	_	_	_
1009	WT	wt	FW	_	_	_
1010	t	t	NN	_	_	_
1011	=	=	JJ	_	_	_
1012	0	0	CD	_	_	_
1013	_	_	NN	_	_	_
1014	biol	biol	NN	_	_	_
1015	rep	rep	NN	GEN	_	_
1016	2	2	CD	_	_	_
1017	_	_	CD	_	_	_
1018	Cy3	cy3	NN	_	_	_
1019	hemA	hema	NN	GEN	_	_
1020	Cy5	cy5	NN	_	_	_
1021	WT	wt	JJ	_	_	_
1022	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1023	Slide	slide	NN	_	_	_
1024	36	36	CD	_	_	_
1025	_	_	CD	_	_	_
1026	WT	WT	NNP	_	_	_
1027	vs.	vs.	CC	_	_	_
1028	hemA	hemA	NNP	GEN	_	_
1029	t	t	NN	_	_	_
1030	=	=	JJ	_	_	_
1031	0	0	CD	_	_	_
1032	_	_	NN	_	_	_
1033	biol	biol	NN	_	_	_
1034	rep	rep	NN	GEN	_	_
1035	1	1	CD	_	_	_
1036	_	_	CD	_	_	_
1037	Cy3	cy3	NN	_	_	_
1038	WT	WT	NNP	_	_	_
1039	Cy5	Cy5	NNP	_	_	_
1040	hemA	hemA	NNP	GEN	_	_
1041	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1042	Slide	Slide	NNP	_	_	_
1043	36	36	CD	_	_	_
1044	_	_	CD	_	_	_
1045	WT	WT	NNP	_	_	_
1046	vs.	vs.	CC	_	_	_
1047	hemA	hemA	NNP	GEN	_	_
1048	t	t	NN	_	_	_
1049	=	=	JJ	_	_	_
1050	0	0	CD	_	_	_
1051	_	_	NN	_	_	_
1052	biol	biol	NN	_	_	_
1053	rep	rep	NN	GEN	_	_
1054	2	2	CD	_	_	_
1055	_	_	CD	_	_	_
1056	Cy3	cy3	NN	_	_	_
1057	WT	wt	JJ	_	_	_
1058	Cy5	cy5	NN	_	_	_
1059	hemA	hema	NN	GEN	_	_
1060	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1061	strain	strain	NN	_	_	_
1062	:	:	:	_	_	_
1063	hemA	hema	NN	GEN	_	_
1064	strain	strain	NN	_	_	_
1065	MG1655	mg1655	NN	_	_	_
1066	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1067	strain	strain	NN	_	_	_
1068	:	:	:	_	_	_
1069	Wild	Wild	NNP	_	_	_
1070	type	type	NN	_	_	_
1071	strain	strain	NN	_	_	_
1072	MG1655	mg1655	NN	_	_	_
1073	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1074	treatment	treatment	NN	_	_	_
1075	:	:	:	_	_	_
1076	exposed	expose	VBN	_	_	_
1077	to	to	TO	_	_	_
1078	100uM	100um	VB	_	_	_
1079	CORM-3	corm-3	NN	_	_	_
1080	for	for	IN	_	_	_
1081	10	10	CD	_	_	_
1082	min	min	NN	_	_	_
1083	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1084	treatment	treatment	NN	_	_	_
1085	:	:	:	_	_	_
1086	exposed	expose	VBN	_	_	_
1087	to	to	TO	_	_	_
1088	100uM	100um	VB	_	_	_
1089	CORM-3	corm-3	NN	_	_	_
1090	for	for	IN	_	_	_
1091	120	120	CD	_	_	_
1092	min	min	NN	_	_	_
1093	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1094	treatment	treatment	NN	_	_	_
1095	:	:	:	_	_	_
1096	exposed	expose	VBN	_	_	_
1097	to	to	TO	_	_	_
1098	100uM	100um	VB	_	_	_
1099	CORM-3	corm-3	NN	_	_	_
1100	for	for	IN	_	_	_
1101	20	20	CD	_	_	_
1102	min	min	NN	_	_	_
1103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1104	treatment	treatment	NN	_	_	_
1105	:	:	:	_	_	_
1106	exposed	expose	VBN	_	_	_
1107	to	to	TO	_	_	_
1108	100uM	100um	VB	_	_	_
1109	CORM-3	corm-3	NN	_	_	_
1110	for	for	IN	_	_	_
1111	40	40	CD	_	_	_
1112	min	min	NN	_	_	_
1113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1114	treatment	treatment	NN	_	_	_
1115	:	:	:	_	_	_
1116	exposed	expose	VBN	_	_	_
1117	to	to	TO	_	_	_
1118	100uM	100um	VB	_	_	_
1119	CORM-3	corm-3	NN	_	_	_
1120	for	for	IN	_	_	_
1121	60	60	CD	_	_	_
1122	min	min	NN	_	_	_
1123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1124	treatment	treatment	NN	_	_	_
1125	:	:	:	_	_	_
1126	exposed	expose	VBN	_	_	_
1127	to	to	TO	_	_	_
1128	100uM	100um	VB	_	_	_
1129	iCORM-3	icorm-3	NN	_	_	_
1130	for	for	IN	_	_	_
1131	10	10	CD	_	_	_
1132	min	min	NN	_	_	_
1133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1134	treatment	treatment	NN	_	_	_
1135	:	:	:	_	_	_
1136	exposed	expose	VBN	_	_	_
1137	to	to	TO	_	_	_
1138	100uM	100um	VB	_	_	_
1139	iCORM-3	icorm-3	NN	_	_	_
1140	for	for	IN	_	_	_
1141	120	120	CD	_	_	_
1142	min	min	NN	_	_	_
1143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1144	treatment	treatment	NN	_	_	_
1145	:	:	:	_	_	_
1146	exposed	expose	VBN	_	_	_
1147	to	to	TO	_	_	_
1148	100uM	100um	VB	_	_	_
1149	iCORM-3	icorm-3	NN	_	_	_
1150	for	for	IN	_	_	_
1151	20	20	CD	_	_	_
1152	min	min	NN	_	_	_
1153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1154	treatment	treatment	NN	_	_	_
1155	:	:	:	_	_	_
1156	exposed	expose	VBN	_	_	_
1157	to	to	TO	_	_	_
1158	100uM	100um	VB	_	_	_
1159	iCORM-3	icorm-3	NN	_	_	_
1160	for	for	IN	_	_	_
1161	40	40	CD	_	_	_
1162	min	min	NN	_	_	_
1163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1164	treatment	treatment	NN	_	_	_
1165	:	:	:	_	_	_
1166	exposed	expose	VBN	_	_	_
1167	to	to	TO	_	_	_
1168	100uM	100um	VB	_	_	_
1169	iCORM-3	icorm-3	NN	_	_	_
1170	for	for	IN	_	_	_
1171	60	60	CD	_	_	_
1172	min	min	NN	_	_	_
1173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1174	treatment	treatment	NN	_	_	_
1175	:	:	:	_	_	_
1176	prior	prior	RB	_	_	_
1177	to	to	TO	_	_	_
1178	CORM-3	corm-3	NN	_	_	_
1179	addition	addition	NN	_	_	_
1180	-LRB-	-lrb-	-LRB-	_	_	_
1181	t	t	NN	_	_	_
1182	=	=	JJ	_	_	_
1183	0	0	CD	_	_	_
1184	-RRB-	-rrb-	-RRB-	_	_	_
1185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1186	treatment	treatment	NN	_	_	_
1187	:	:	:	_	_	_
1188	prior	prior	RB	_	_	_
1189	to	to	TO	_	_	_
1190	iCORM-3	icorm-3	NN	_	_	_
1191	addition	addition	NN	_	_	_
1192	-LRB-	-lrb-	-LRB-	_	_	_
1193	t	t	NN	_	_	_
1194	=	=	JJ	_	_	_
1195	0	0	CD	_	_	_
1196	-RRB-	-rrb-	-RRB-	_	_	_
1197	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1198	Coverage	Coverage	NNP	_	_	_
1199	calculation	calculation	NN	_	_	_
1200	and	and	CC	_	_	_
1201	normalisation	normalisation	NN	_	_	_
1202	-LRB-	-lrb-	-LRB-	_	_	_
1203	TRAPL	trapl	NN	_	_	_
1204	-RRB-	-rrb-	-RRB-	_	_	_
1205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1206	Demultiplexing	demultiplexing	JJ	_	_	_
1207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1208	Escherichia	escherichia	FW	Organism	_	_
1209	coli	coli	FW	Organism	_	_
1210	MG1655	mg1655	NN	_	_	_
1211	cells	cell	NNS	_	_	_
1212	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1213	Escherichia	escherichia	FW	Organism	_	_
1214	coli	coli	FW	Organism	_	_
1215	str	str	FW	_	_	_
1216	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Fastq	fastq	JJ	_	_	_
4	quality	quality	NN	_	_	_
5	trimming	trim	VBG	_	_	_
6	using	use	VBG	_	_	_
7	FastX	fastx	NN	_	_	_
8	and	and	CC	_	_	_
9	a	a	DT	_	_	_
10	cut-off	cut-off	JJ	_	_	_
11	value	value	NN	_	_	_
12	of	of	IN	_	_	_
13	20	20	CD	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Fastq	fastq	NN	_	_	_
16	to	to	TO	_	_	_
17	fasta	fasta	NN	_	_	_
18	conversion	conversion	NN	_	_	_
19	using	use	VBG	_	_	_
20	FastX	fastx	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Genome	Genome	NNP	_	_	_
23	_	_	NNP	_	_	_
24	build	build	VB	_	_	_
25	:	:	:	_	_	_
26	NC	NC	NNP	_	_	_
27	_	_	NNP	_	_	_
28	000913.2	000913.2	CD	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	growth	growth	NN	_	_	_
31	phase	phase	NN	_	_	_
32	:	:	:	_	_	_
33	exponential	exponential	JJ	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	growth	growth	NN	_	_	_
36	phase	phase	NN	_	_	_
37	:	:	:	_	_	_
38	stationary	stationary	JJ	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Hot	hot	JJ	_	_	_
41	phenol	phenol	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	Sharma	sharma	FW	_	_	_
44	et	et	FW	_	_	_
45	al.	al.	FW	_	_	_
46	2010	2010	CD	_	_	_
47	,	,	,	_	_	_
48	Bloomberg	Bloomberg	NNP	_	_	_
49	1990	1990	CD	_	_	_
50	,	,	,	_	_	_
51	EMBO	EMBO	NNP	_	_	_
52	J	J	NNP	_	_	_
53	-RRB-	-rrb-	-RRB-	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	LB	lb	NN	_	_	_
56	0.4	0.4	CD	_	_	_
57	B1	b1	NN	_	_	_
58	TEX	tex	NN	_	_	_
59	neg	neg	NN	_	_	_
60	L1	l1	NN	_	_	_
61	GA	ga	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	LB	lb	NN	_	_	_
64	0.4	0.4	CD	_	_	_
65	B1	b1	NN	_	_	_
66	TEX	TEX	NNP	_	_	_
67	pos	po	VBZ	_	_	_
68	L1	l1	NN	_	_	_
69	GA	ga	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	LB	lb	NN	_	_	_
72	0.4	0.4	CD	_	_	_
73	B2	b2	NN	_	_	_
74	TEX	TEX	NNP	_	_	_
75	neg	neg	NNP	_	_	_
76	L1	l1	NN	_	_	_
77	HS1	hs1	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	LB	lb	NN	_	_	_
80	0.4	0.4	CD	_	_	_
81	B2	b2	NN	_	_	_
82	TEX	TEX	NNP	_	_	_
83	neg	neg	NNP	_	_	_
84	L1	l1	NN	_	_	_
85	HS2	hs2	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	LB	lb	NN	_	_	_
88	0.4	0.4	CD	_	_	_
89	B2	b2	NN	_	_	_
90	TEX	TEX	NNP	_	_	_
91	pos	po	VBZ	_	_	_
92	L1	l1	NN	_	_	_
93	HS1	hs1	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	LB	lb	NN	_	_	_
96	0.4	0.4	CD	_	_	_
97	B2	b2	NN	_	_	_
98	TEX	TEX	NNP	_	_	_
99	pos	po	VBZ	_	_	_
100	L1	l1	NN	_	_	_
101	HS2	hs2	NN	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	LB	lb	NN	_	_	_
104	2.0	2.0	CD	_	_	_
105	B1	b1	NN	_	_	_
106	TEX	tex	NN	_	_	_
107	neg	neg	NN	_	_	_
108	L1	l1	NN	_	_	_
109	GA	ga	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	LB	lb	NN	_	_	_
112	2.0	2.0	CD	_	_	_
113	B1	b1	NN	_	_	_
114	TEX	TEX	NNP	_	_	_
115	neg	neg	NNP	_	_	_
116	L2	l2	NN	_	_	_
117	HS2	hs2	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	LB	lb	NN	_	_	_
120	2.0	2.0	CD	_	_	_
121	B1	b1	NN	_	_	_
122	TEX	TEX	NNP	_	_	_
123	pos	po	VBZ	_	_	_
124	L1	l1	NN	_	_	_
125	GA	ga	NN	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	LB	lb	NN	_	_	_
128	2.0	2.0	CD	_	_	_
129	B1	b1	NN	_	_	_
130	TEX	TEX	NNP	_	_	_
131	pos	po	VBZ	_	_	_
132	L2	l2	NN	_	_	_
133	HS2	hs2	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	LB	lb	NN	_	_	_
136	2.0	2.0	CD	_	_	_
137	B2	b2	NN	_	_	_
138	TEX	TEX	NNP	_	_	_
139	neg	neg	NNP	_	_	_
140	L1	l1	NN	_	_	_
141	HS1	hs1	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	LB	lb	NN	_	_	_
144	2.0	2.0	CD	_	_	_
145	B2	b2	NN	_	_	_
146	TEX	TEX	NNP	_	_	_
147	neg	neg	NNP	_	_	_
148	L1	l1	NN	_	_	_
149	HS2	hs2	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	LB	lb	NN	_	_	_
152	2.0	2.0	CD	_	_	_
153	B2	b2	NN	_	_	_
154	TEX	TEX	NNP	_	_	_
155	neg	neg	NNP	_	_	_
156	L2	l2	NN	_	_	_
157	HS2	hs2	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	LB	lb	NN	_	_	_
160	2.0	2.0	CD	_	_	_
161	B2	b2	NN	_	_	_
162	TEX	TEX	NNP	_	_	_
163	pos	po	VBZ	_	_	_
164	L1	l1	NN	_	_	_
165	HS1	hs1	NN	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	LB	lb	NN	_	_	_
168	2.0	2.0	CD	_	_	_
169	B2	b2	NN	_	_	_
170	TEX	TEX	NNP	_	_	_
171	pos	po	VBZ	_	_	_
172	L1	l1	NN	_	_	_
173	HS2	hs2	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	LB	lb	NN	_	_	_
176	2.0	2.0	CD	_	_	_
177	B2	b2	NN	_	_	_
178	TEX	TEX	NNP	_	_	_
179	pos	po	VBZ	_	_	_
180	L2	l2	NN	_	_	_
181	HS2	hs2	NN	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	M63	m63	NN	_	_	_
184	0.4	0.4	CD	_	_	_
185	B1	b1	NN	_	_	_
186	TEX	tex	NN	_	_	_
187	neg	neg	NN	_	_	_
188	L1	l1	NN	_	_	_
189	GA	ga	NN	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	M63	m63	NN	_	_	_
192	0.4	0.4	CD	_	_	_
193	B1	b1	NN	_	_	_
194	TEX	TEX	NNP	_	_	_
195	pos	po	VBZ	_	_	_
196	L1	l1	NN	_	_	_
197	GA	ga	NN	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	M63	m63	NN	_	_	_
200	0.4	0.4	CD	_	_	_
201	B2	b2	NN	_	_	_
202	TEX	TEX	NNP	_	_	_
203	neg	neg	NNP	_	_	_
204	L1	l1	NN	_	_	_
205	HS1	hs1	NN	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	M63	m63	NN	_	_	_
208	0.4	0.4	CD	_	_	_
209	B2	b2	NN	_	_	_
210	TEX	TEX	NNP	_	_	_
211	neg	neg	NNP	_	_	_
212	L1	l1	NN	_	_	_
213	HS2	hs2	NN	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	M63	m63	NN	_	_	_
216	0.4	0.4	CD	_	_	_
217	B2	b2	NN	_	_	_
218	TEX	TEX	NNP	_	_	_
219	pos	po	VBZ	_	_	_
220	L1	l1	NN	_	_	_
221	HS1	hs1	NN	_	_	_
222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
223	M63	m63	NN	_	_	_
224	0.4	0.4	CD	_	_	_
225	B2	b2	NN	_	_	_
226	TEX	TEX	NNP	_	_	_
227	pos	po	VBZ	_	_	_
228	L1	l1	NN	_	_	_
229	HS2	hs2	NN	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
231	medium	medium	NN	_	_	_
232	:	:	:	_	_	_
233	LB	lb	NN	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	medium	medium	NN	_	_	_
236	:	:	:	_	_	_
237	M63	m63	NN	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
239	Read	read	VBP	_	_	_
240	mapping	map	VBG	_	_	_
241	using	use	VBG	_	_	_
242	segemehl	segemehl	NN	_	_	_
243	version	version	NN	_	_	_
244	0.13	0.13	CD	_	_	_
245	-LRB-	-lrb-	-LRB-	_	_	_
246	TRAPL	trapl	NN	_	_	_
247	-RRB-	-rrb-	-RRB-	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
249	RNA-Seq	rna-seq	NN	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	Samples	sample	NNS	_	_	_
252	were	be	VBD	_	_	_
253	mixed	mixed	JJ	_	_	_
254	,	,	,	_	_	_
255	incubated	incubate	VBN	_	_	_
256	on	on	IN	_	_	_
257	ice	ice	NN	_	_	_
258	for	for	IN	_	_	_
259	10	10	CD	_	_	_
260	min	min	NN	_	_	_
261	after	after	IN	_	_	_
262	which	which	WDT	_	_	_
263	cells	cell	NNS	_	_	_
264	were	be	VBD	_	_	_
265	collected	collect	VBN	_	_	_
266	by	by	IN	_	_	_
267	centrifugation	centrifugation	NN	_	_	_
268	at	at	IN	_	_	_
269	4150	4150	CD	_	_	_
270	rpm	rpm	NN	_	_	_
271	at	at	IN	_	_	_
272	4	4	CD	_	_	_
273	˚C	˚c	NN	_	_	_
274	for	for	IN	_	_	_
275	10	10	CD	_	_	_
276	min	min	NN	_	_	_
277	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	pellets	pellet	NNS	_	_	_
3	were	be	VBD	_	_	_
4	snap	snap	JJ	_	_	_
5	frozen	freeze	VBN	_	_	_
6	in	in	IN	_	_	_
7	an	a	DT	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Size	size	NN	_	_	_
11	filtering	filter	VBG	_	_	_
12	:	:	:	_	_	_
13	discarding	discard	VBG	_	_	_
14	reads	read	VBZ	_	_	_
15	shorter	shorter	JJR	_	_	_
16	than	than	IN	_	_	_
17	12	12	CD	_	_	_
18	nt	nt	NNS	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	TRAPL	trapl	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	strain	strain	NN	_	_	_
24	:	:	:	_	_	_
25	MG1655	mg1655	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	Supplementary	supplementary	JJ	_	_	_
28	_	_	NN	_	_	_
29	files	file	NNS	_	_	_
30	_	_	IN	_	_	_
31	format	format	NN	_	_	_
32	_	_	NN	_	_	_
33	and	and	CC	_	_	_
34	_	_	NN	_	_	_
35	content	content	NN	_	_	_
36	:	:	:	_	_	_
37	wiggle	wiggle	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
39	The	the	DT	_	_	_
40	libraries	library	NNS	_	_	_
41	were	be	VBD	_	_	_
42	generated	generate	VBN	_	_	_
43	by	by	IN	_	_	_
44	Vertis	Vertis	NNP	_	_	_
45	Biotechnologie	Biotechnologie	NNP	_	_	_
46	AG	AG	NNP	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	Munich	Munich	NNP	_	_	_
49	,	,	,	_	_	_
50	Germany	Germany	NNP	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	poly	poly	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	A	a	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	-	-	:	_	_	_
9	tailed	tail	VBN	_	_	_
10	by	by	IN	_	_	_
11	using	use	VBG	_	_	_
12	poly	poly	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	A	a	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	polymerase	polymerase	NN	_	_	_
17	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	5	5	CD	_	_	_
3	'	'	''	_	_	_
4	-	-	:	_	_	_
5	PPP	ppp	NN	_	_	_
6	were	be	VBD	_	_	_
7	removed	remove	VBN	_	_	_
8	using	use	VBG	_	_	_
9	tobacco	tobacco	NN	_	_	_
10	acid	acid	NN	_	_	_
11	pyrophosphatase	pyrophosphatase	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	TAP	tap	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	followed	follow	VBN	_	_	_
16	by	by	IN	_	_	_
17	the	the	DT	_	_	_
18	ligation	ligation	NN	_	_	_
19	of	of	IN	_	_	_
20	the	the	DT	_	_	_
21	RNA	rna	NN	_	_	_
22	adapter	adapter	NN	_	_	_
23	to	to	TO	_	_	_
24	the	the	DT	_	_	_
25	5	5	CD	_	_	_
26	'	'	''	_	_	_
27	-	-	:	_	_	_
28	monophosphate	monophosphate	NN	_	_	_
29	of	of	IN	_	_	_
30	the	the	DT	_	_	_
31	RNA	rna	NN	_	_	_
32	.	.	.	_	_	_

1	First-strand	first-strand	JJ	_	_	_
2	cDNA	cdna	NN	_	_	_
3	synthesis	synthesis	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	with	with	IN	_	_	_
7	an	a	DT	_	_	_
8	oligo	oligo	JJ	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	dT	dt	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	-	-	:	_	_	_
13	adapter	adapter	NN	_	_	_
14	primer	primer	NN	_	_	_
15	and	and	CC	_	_	_
16	the	the	DT	_	_	_
17	M-MLV	m-mlv	NN	_	_	_
18	reverse	reverse	JJ	_	_	_
19	transcriptase	transcriptase	NN	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	resulting	result	VBG	_	_	_
3	cDNA	cdna	NN	_	_	_
4	was	be	VBD	_	_	_
5	PCR-amplified	pcr-amplified	JJ	_	_	_
6	to	to	TO	_	_	_
7	reach	reach	VB	_	_	_
8	a	a	DT	_	_	_
9	concentration	concentration	NN	_	_	_
10	of	of	IN	_	_	_
11	20-30	20-30	CD	_	_	_
12	ng	ng	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
14	To	to	TO	_	_	_
15	harvest	harvest	VB	_	_	_
16	total	total	JJ	_	_	_
17	RNA	rna	NN	_	_	_
18	samples	sample	NNS	_	_	_
19	,	,	,	_	_	_
20	overnight	overnight	JJ	_	_	_
21	cultures	culture	NNS	_	_	_
22	of	of	IN	_	_	_
23	wild	wild	JJ	_	_	_
24	type	type	NN	_	_	_
25	MG1655	mg1655	NN	_	_	_
26	grown	grow	VBN	_	_	_
27	in	in	IN	_	_	_
28	LB	lb	NN	_	_	_
29	at	at	IN	_	_	_
30	37	37	CD	_	_	_
31	˚C	˚c	NN	_	_	_
32	were	be	VBD	_	_	_
33	diluted	dilute	VBN	_	_	_
34	back	back	RB	_	_	_
35	1:500	1:500	CD	_	_	_
36	in	in	IN	_	_	_
37	either	either	CC	_	_	_
38	fresh	fresh	JJ	_	_	_
39	LB	lb	NN	_	_	_
40	or	or	CC	_	_	_
41	M63	m63	NN	_	_	_
42	minimal	minimal	JJ	_	_	_
43	glucose	glucose	NN	SUPP	_	_
44	medium	medium	NN	_	_	_
45	and	and	CC	_	_	_
46	allowed	allow	VBN	_	_	_
47	to	to	TO	_	_	_
48	grow	grow	VB	_	_	_
49	until	until	IN	_	_	_
50	the	the	DT	_	_	_
51	cultures	culture	NNS	_	_	_
52	reached	reach	VBD	_	_	_
53	an	a	DT	_	_	_
54	OD600	od600	NN	_	_	_
55	of	of	IN	_	_	_
56	~	~	NN	_	_	_
57	0.4	0.4	CD	_	_	_
58	and	and	CC	_	_	_
59	2.0	2.0	CD	_	_	_
60	for	for	IN	_	_	_
61	cultures	culture	NNS	_	_	_
62	grown	grow	VBN	_	_	_
63	in	in	IN	_	_	_
64	LB	lb	NN	_	_	_
65	and	and	CC	_	_	_
66	an	a	DT	_	_	_
67	OD600	od600	NN	_	_	_
68	of	of	IN	_	_	_
69	~	~	NN	_	_	_
70	0.4	0.4	CD	_	_	_
71	for	for	IN	_	_	_
72	cultures	culture	NNS	_	_	_
73	grown	grow	VBN	_	_	_
74	in	in	IN	_	_	_
75	M63	m63	NN	_	_	_
76	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	samples	sample	NNS	_	_	_
3	grown	grow	VBN	_	_	_
4	to	to	TO	_	_	_
5	OD600	od600	NN	_	_	_
6	of	of	IN	_	_	_
7	~	~	NN	_	_	_
8	0.4	0.4	CD	_	_	_
9	a	a	DT	_	_	_
10	total	total	JJ	_	_	_
11	volume	volume	NN	_	_	_
12	of	of	IN	_	_	_
13	25	25	CD	_	_	_
14	ml	ml	NN	_	_	_
15	of	of	IN	_	_	_
16	cells	cell	NNS	_	_	_
17	were	be	VBD	_	_	_
18	harvested	harvest	VBN	_	_	_
19	and	and	CC	_	_	_
20	combined	combine	VBN	_	_	_
21	with	with	IN	_	_	_
22	5	5	CD	_	_	_
23	ml	ml	NN	_	_	_
24	of	of	IN	_	_	_
25	stop	stop	NN	_	_	_
26	solution	solution	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	95	95	CD	_	_	_
29	%	%	NN	_	_	_
30	Ethanol	ethanol	NN	_	_	_
31	,	,	,	_	_	_
32	5	5	CD	_	_	_
33	%	%	NN	_	_	_
34	acid	acid	NN	_	_	_
35	phenol	phenol	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	samples	sample	NNS	_	_	_
3	grown	grow	VBN	_	_	_
4	to	to	TO	_	_	_
5	OD600	od600	NN	_	_	_
6	of	of	IN	_	_	_
7	2.0	2.0	CD	_	_	_
8	a	a	DT	_	_	_
9	total	total	JJ	_	_	_
10	volume	volume	NN	_	_	_
11	of	of	IN	_	_	_
12	5	5	CD	_	_	_
13	ml	ml	NN	_	_	_
14	of	of	IN	_	_	_
15	cells	cell	NNS	_	_	_
16	were	be	VBD	_	_	_
17	harvested	harvest	VBN	_	_	_
18	and	and	CC	_	_	_
19	combined	combine	VBN	_	_	_
20	with	with	IN	_	_	_
21	1	1	CD	_	_	_
22	ml	ml	NN	_	_	_
23	of	of	IN	_	_	_
24	stop	stop	NN	_	_	_
25	solution	solution	NN	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	affyexp	affyexp	NN	_	_	_
3	_	_	CD	_	_	_
4	delta-arcA	delta-arca	NN	_	_	_
5	_	_	NN	_	_	_
6	glucose	glucose	NN	SUPP	_	_
7	_	_	CD	_	_	_
8	NH4CL	nh4cl	NN	_	_	_
9	_	_	NN	_	_	_
10	anaerobic	anaerobic	JJ	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	affyexp	affyexp	NN	_	_	_
13	_	_	CD	_	_	_
14	delta-arcA	delta-arca	NN	_	_	_
15	_	_	NN	_	_	_
16	glucose	glucose	NN	SUPP	_	_
17	_	_	CD	_	_	_
18	NH4CL	nh4cl	NN	_	_	_
19	_	_	NN	_	_	_
20	anaerobic	anaerobic	JJ	_	_	_
21	_	_	NN	_	_	_
22	1	1	CD	_	_	_
23	.	.	.	_	_	_

1	CEL	CEL	NNP	_	_	_
2	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3	affyexp	affyexp	JJ	_	_	_
4	_	_	NN	_	_	_
5	delta-arcA	delta-arca	NN	_	_	_
6	_	_	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	_	_	CD	_	_	_
9	NH4CL	nh4cl	NN	_	_	_
10	_	_	NN	_	_	_
11	anaerobic	anaerobic	JJ	_	_	_
12	_	_	NN	_	_	_
13	2	2	CD	_	_	_
14	.	.	.	_	_	_

1	CEL	CEL	NNP	_	_	_
2	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3	affyexp	affyexp	JJ	_	_	_
4	_	_	NN	_	_	_
5	delta-arcA	delta-arca	NN	_	_	_
6	_	_	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	_	_	CD	_	_	_
9	NH4CL	nh4cl	NN	_	_	_
10	_	_	NN	_	_	_
11	anaerobic	anaerobic	JJ	_	_	_
12	_	_	NN	_	_	_
13	3	3	CD	_	_	_
14	.	.	.	_	_	_

1	CEL	CEL	NNP	_	_	_
2	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3	affyexp	affyexp	JJ	_	_	_
4	_	_	NN	_	_	_
5	delta-arcA	delta-arca	NN	_	_	_
6	_	_	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	_	_	CD	_	_	_
9	NH4Cl	nh4cl	NN	_	_	_
10	_	_	CD	_	_	_
11	NO3	no3	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	affyexp	affyexp	JJ	_	_	_
14	_	_	NN	_	_	_
15	delta-arcA	delta-arca	NN	_	_	_
16	_	_	NN	_	_	_
17	glucose	glucose	NN	SUPP	_	_
18	_	_	CD	_	_	_
19	NH4Cl	nh4cl	NN	_	_	_
20	_	_	CD	_	_	_
21	NO3	no3	NN	_	_	_
22	_	_	NN	_	_	_
23	1	1	CD	_	_	_
24	.	.	.	_	_	_

1	CEL	CEL	NNP	_	_	_
2	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3	affyexp	affyexp	JJ	_	_	_
4	_	_	NN	_	_	_
5	delta-arcA	delta-arca	NN	_	_	_
6	_	_	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	_	_	CD	_	_	_
9	NH4Cl	nh4cl	NN	_	_	_
10	_	_	CD	_	_	_
11	NO3	no3	NN	_	_	_
12	_	_	NN	_	_	_
13	2	2	CD	_	_	_
14	.	.	.	_	_	_

1	CEL	CEL	NNP	_	_	_
2	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3	affyexp	affyexp	JJ	_	_	_
4	_	_	NN	_	_	_
5	delta-arcA	delta-arca	NN	_	_	_
6	_	_	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	_	_	CD	_	_	_
9	NH4Cl	nh4cl	NN	_	_	_
10	_	_	CD	_	_	_
11	NO3	no3	NN	_	_	_
12	_	_	NN	_	_	_
13	3	3	CD	_	_	_
14	.	.	.	_	_	_

1	CEL	cel	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	affyexp	affyexp	NN	_	_	_
4	_	_	CD	_	_	_
5	delta-fnr	delta-fnr	JJ	_	_	_
6	_	_	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	_	_	CD	_	_	_
9	NH4CL	nh4cl	NN	_	_	_
10	_	_	NN	_	_	_
11	anaerobic	anaerobic	JJ	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	affyexp	affyexp	NN	_	_	_
14	_	_	CD	_	_	_
15	delta-fnr	delta-fnr	JJ	_	_	_
16	_	_	NN	_	_	_
17	glucose	glucose	NN	SUPP	_	_
18	_	_	CD	_	_	_
19	NH4CL	nh4cl	NN	_	_	_
20	_	_	NN	_	_	_
21	anaerobic	anaerobic	JJ	_	_	_
22	_	_	NN	_	_	_
23	1	1	CD	_	_	_
24	.	.	.	_	_	_

1	CEL	cel	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	affyexp	affyexp	NN	_	_	_
4	_	_	CD	_	_	_
5	delta-fnr	delta-fnr	JJ	_	_	_
6	_	_	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	_	_	CD	_	_	_
9	NH4CL	nh4cl	NN	_	_	_
10	_	_	NN	_	_	_
11	anaerobic	anaerobic	JJ	_	_	_
12	_	_	NN	_	_	_
13	2	2	CD	_	_	_
14	.	.	.	_	_	_

1	CEL	cel	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	affyexp	affyexp	NN	_	_	_
4	_	_	CD	_	_	_
5	delta-fnr	delta-fnr	JJ	_	_	_
6	_	_	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	_	_	CD	_	_	_
9	NH4CL	nh4cl	NN	_	_	_
10	_	_	NN	_	_	_
11	anaerobic	anaerobic	JJ	_	_	_
12	_	_	NN	_	_	_
13	3	3	CD	_	_	_
14	.	.	.	_	_	_

1	CEL	cel	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	affyexp	affyexp	NN	_	_	_
4	_	_	CD	_	_	_
5	delta-fnr	delta-fnr	JJ	_	_	_
6	_	_	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	_	_	CD	_	_	_
9	NH4Cl	nh4cl	NN	_	_	_
10	_	_	CD	_	_	_
11	NO3	no3	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	affyexp	affyexp	NN	_	_	_
14	_	_	CD	_	_	_
15	delta-fnr	delta-fnr	JJ	_	_	_
16	_	_	NN	_	_	_
17	glucose	glucose	NN	SUPP	_	_
18	_	_	CD	_	_	_
19	NH4Cl	nh4cl	NN	_	_	_
20	_	_	CD	_	_	_
21	NO3	no3	NN	_	_	_
22	_	_	NN	_	_	_
23	1	1	CD	_	_	_
24	.	.	.	_	_	_

1	CEL	cel	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	affyexp	affyexp	NN	_	_	_
4	_	_	CD	_	_	_
5	delta-fnr	delta-fnr	JJ	_	_	_
6	_	_	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	_	_	CD	_	_	_
9	NH4Cl	nh4cl	NN	_	_	_
10	_	_	CD	_	_	_
11	NO3	no3	NN	_	_	_
12	_	_	NN	_	_	_
13	2	2	CD	_	_	_
14	.	.	.	_	_	_

1	CEL	cel	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	affyexp	affyexp	NN	_	_	_
4	_	_	CD	_	_	_
5	delta-fnr	delta-fnr	JJ	_	_	_
6	_	_	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	_	_	CD	_	_	_
9	NH4Cl	nh4cl	NN	_	_	_
10	_	_	CD	_	_	_
11	NO3	no3	NN	_	_	_
12	_	_	NN	_	_	_
13	3	3	CD	_	_	_
14	.	.	.	_	_	_

1	CEL	cel	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	affyexp	affyexp	NN	_	_	_
4	_	_	CD	_	_	_
5	wt	wt	JJ	_	_	_
6	_	_	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	_	_	CD	_	_	_
9	NH4CL	nh4cl	NN	_	_	_
10	_	_	NN	_	_	_
11	anaerobic	anaerobic	JJ	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	affyexp	affyexp	NN	_	_	_
14	_	_	CD	_	_	_
15	wt	wt	JJ	_	_	_
16	_	_	NN	_	_	_
17	glucose	glucose	NN	SUPP	_	_
18	_	_	CD	_	_	_
19	NH4CL	nh4cl	NN	_	_	_
20	_	_	NN	_	_	_
21	anaerobic	anaerobic	JJ	_	_	_
22	_	_	NN	_	_	_
23	1	1	CD	_	_	_
24	.	.	.	_	_	_

1	CEL	cel	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	affyexp	affyexp	NN	_	_	_
4	_	_	CD	_	_	_
5	wt	wt	JJ	_	_	_
6	_	_	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	_	_	CD	_	_	_
9	NH4CL	nh4cl	NN	_	_	_
10	_	_	NN	_	_	_
11	anaerobic	anaerobic	JJ	_	_	_
12	_	_	NN	_	_	_
13	2	2	CD	_	_	_
14	.	.	.	_	_	_

1	CEL	cel	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	affyexp	affyexp	NN	_	_	_
4	_	_	CD	_	_	_
5	wt	wt	JJ	_	_	_
6	_	_	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	_	_	CD	_	_	_
9	NH4CL	nh4cl	NN	_	_	_
10	_	_	NN	_	_	_
11	anaerobic	anaerobic	JJ	_	_	_
12	_	_	NN	_	_	_
13	3	3	CD	_	_	_
14	.	.	.	_	_	_

1	CEL	cel	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	affyexp	affyexp	NN	_	_	_
4	_	_	CD	_	_	_
5	wt	wt	JJ	_	_	_
6	_	_	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	_	_	CD	_	_	_
9	NH4Cl	nh4cl	NN	_	_	_
10	_	_	CD	_	_	_
11	NO3	no3	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	affyexp	affyexp	NN	_	_	_
14	_	_	CD	_	_	_
15	wt	wt	JJ	_	_	_
16	_	_	NN	_	_	_
17	glucose	glucose	NN	SUPP	_	_
18	_	_	CD	_	_	_
19	NH4Cl	nh4cl	NN	_	_	_
20	_	_	CD	_	_	_
21	NO3	no3	NN	_	_	_
22	_	_	NN	_	_	_
23	1	1	CD	_	_	_
24	.	.	.	_	_	_

1	CEL	cel	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	affyexp	affyexp	NN	_	_	_
4	_	_	CD	_	_	_
5	wt	wt	JJ	_	_	_
6	_	_	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	_	_	CD	_	_	_
9	NH4Cl	nh4cl	NN	_	_	_
10	_	_	CD	_	_	_
11	NO3	no3	NN	_	_	_
12	_	_	NN	_	_	_
13	2	2	CD	_	_	_
14	.	.	.	_	_	_

1	CEL	cel	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	affyexp	affyexp	NN	_	_	_
4	_	_	CD	_	_	_
5	wt	wt	JJ	_	_	_
6	_	_	NN	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	_	_	CD	_	_	_
9	NH4Cl	nh4cl	NN	_	_	_
10	_	_	CD	_	_	_
11	NO3	no3	NN	_	_	_
12	_	_	NN	_	_	_
13	3	3	CD	_	_	_
14	.	.	.	_	_	_

1	CEL	CEL	NNP	_	_	_
2	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3	All	All	NNP	_	_	_
4	strains	strain	NNS	_	_	_
5	used	use	VBN	_	_	_
6	in	in	IN	_	_	_
7	this	this	DT	_	_	_
8	study	study	NN	_	_	_
9	were	be	VBD	_	_	_
10	E.	e.	FW	_	_	_
11	coli	coli	FW	_	_	_
12	K-12	k-12	NN	_	_	_
13	MG1655	mg1655	NN	_	_	_
14	and	and	CC	_	_	_
15	its	its	PRP$	_	_	_
16	derivatives	derivative	NNS	_	_	_
17	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	deletion	deletion	NN	_	_	_
3	mutants	mutant	NNS	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	Δfnr	δfnr	NN	_	_	_
6	and	and	CC	_	_	_
7	ΔarcA	δarca	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	were	be	VBD	_	_	_
10	constructed	construct	VBN	_	_	_
11	by	by	IN	_	_	_
12	a	a	DT	_	_	_
13	λ	λ	NN	_	_	_
14	red	red	JJ	_	_	_
15	and	and	CC	_	_	_
16	FLP-mediated	flp-mediated	JJ	_	_	_
17	site-specific	site-specific	JJ	_	_	_
18	recombination	recombination	NN	_	_	_
19	method	method	NN	_	_	_
20	.	.	.	_	_	_

1	Glycerol	glycerol	NN	_	_	_
2	stocks	stock	NNS	_	_	_
3	of	of	IN	_	_	_
4	E.	e.	FW	_	_	_
5	coli	coli	FW	_	_	_
6	strains	strain	NNS	_	_	_
7	were	be	VBD	_	_	_
8	inoculated	inoculate	VBN	_	_	_
9	into	into	IN	_	_	_
10	M9	m9	NN	MED	_	_
11	minimal	minimal	JJ	MED	_	_
12	medium	medium	NN	MED	_	_
13	containing	contain	VBG	_	_	_
14	0.2	0.2	CD	_	_	_
15	%	%	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	w	w	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	culture	culture	NN	_	_	_
20	condition	condition	NN	_	_	_
21	:	:	:	_	_	_
22	anaerobic	anaerobic	JJ	_	_	_
23	fermentive	fermentive	JJ	_	_	_
24	condition	condition	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	culture	culture	NN	_	_	_
27	condition	condition	NN	_	_	_
28	:	:	:	_	_	_
29	nitrate	nitrate	VB	SUPP	_	_
30	respiratory	respiratory	JJ	_	_	_
31	condition	condition	NN	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	Escherichia	escherichia	FW	Organism	_	_
34	coli	coli	FW	Organism	_	_
35	str	str	FW	_	_	_
36	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	genotype	genotype	NN	_	_	_
4	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
5	Raw	raw	NN	_	_	_
6	CEL	cel	NN	_	_	_
7	files	file	NNS	_	_	_
8	were	be	VBD	_	_	_
9	analyzed	analyze	VBN	_	_	_
10	using	use	VBG	_	_	_
11	robust	robust	JJ	_	_	_
12	multi-array	multi-array	JJ	_	_	_
13	average	average	NN	_	_	_
14	for	for	IN	_	_	_
15	normalization	normalization	NN	_	_	_
16	and	and	CC	_	_	_
17	calculation	calculation	NN	_	_	_
18	of	of	IN	_	_	_
19	probe	probe	NN	_	_	_
20	intensities	intensity	NNS	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	processed	process	VBN	_	_	_
3	probe	probe	NN	_	_	_
4	signals	signal	NNS	_	_	_
5	derived	derive	VBN	_	_	_
6	from	from	IN	_	_	_
7	each	each	DT	_	_	_
8	microarray	microarray	NN	_	_	_
9	were	be	VBD	_	_	_
10	averaged	average	VBN	_	_	_
11	for	for	IN	_	_	_
12	both	both	CC	_	_	_
13	the	the	DT	_	_	_
14	wild	wild	JJ	_	_	_
15	type	type	NN	_	_	_
16	and	and	CC	_	_	_
17	deletion	deletion	NN	_	_	_
18	mutant	mutant	JJ	_	_	_
19	strains	strain	NNS	_	_	_
20	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	was	be	VBD	_	_	_
3	done	do	VBN	_	_	_
4	using	use	VBG	_	_	_
5	the	the	DT	_	_	_
6	GCRMA	GCRMA	NNP	_	_	_
7	package	package	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	version	version	NN	_	_	_
10	2.13	2.13	CD	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	from	from	IN	_	_	_
13	Bioconductor	Bioconductor	NNP	_	_	_
14	in	in	IN	_	_	_
15	R.	R.	NNP	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Samples	sample	NNS	_	_	_
18	for	for	IN	_	_	_
19	transcriptome	transcriptome	NN	_	_	_
20	analysis	analysis	NN	_	_	_
21	were	be	VBD	_	_	_
22	taken	take	VBN	_	_	_
23	from	from	IN	_	_	_
24	exponentially	exponentially	RB	_	_	_
25	growing	grow	VBG	_	_	_
26	cells	cell	NNS	_	_	_
27	.	.	.	_	_	_

1	From	from	IN	_	_	_
2	the	the	DT	_	_	_
3	cells	cell	NNS	_	_	_
4	treated	treat	VBN	_	_	_
5	by	by	IN	_	_	_
6	RNAprotect	rnaprotect	NN	_	_	_
7	Bacteria	bacterium	NNS	_	_	_
8	Reagent	reagent	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Qiagen	qiagen	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	,	,	,	_	_	_
13	total	total	JJ	_	_	_
14	RNA	rna	NN	_	_	_
15	samples	sample	NNS	_	_	_
16	were	be	VBD	_	_	_
17	isolated	isolate	VBN	_	_	_
18	using	use	VBG	_	_	_
19	RNeasy	rneasy	JJ	_	_	_
20	columns	column	NNS	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Qiagen	Qiagen	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	in	in	IN	_	_	_
25	accordance	accordance	NN	_	_	_
26	with	with	IN	_	_	_
27	manufacturer	manufacturer	NN	_	_	_
28	's	's	POS	_	_	_
29	instruction	instruction	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	at	at	IN	_	_	_
4	appropriate	appropriate	JJ	_	_	_
5	cell	cell	NN	_	_	_
6	density	density	NN	_	_	_
7	were	be	VBD	_	_	_
8	cross-linked	cross-link	VBN	_	_	_
9	by	by	IN	_	_	_
10	1	1	CD	_	_	_
11	%	%	NN	_	_	_
12	formaldehyde	formaldehyde	NN	_	_	_
13	at	at	IN	_	_	_
14	room	room	NN	_	_	_
15	temperature	temperature	NN	_	_	_
16	for	for	IN	_	_	_
17	25	25	CD	_	_	_
18	min	min	NN	_	_	_
19	.	.	.	_	_	_

1	Following	follow	VBG	_	_	_
2	quenching	quench	VBG	_	_	_
3	the	the	DT	_	_	_
4	unused	unused	JJ	_	_	_
5	formaldehyde	formaldehyde	NN	_	_	_
6	with	with	IN	_	_	_
7	a	a	DT	_	_	_
8	final	final	JJ	_	_	_
9	concentration	concentration	NN	_	_	_
10	of	of	IN	_	_	_
11	125	125	CD	_	_	_
12	mM	mm	NN	KWSUPP	_	_
13	glycine	glycine	NN	_	_	_
14	at	at	IN	_	_	_
15	room	room	NN	_	_	_
16	temperature	temperature	NN	_	_	_
17	for	for	IN	_	_	_
18	5	5	CD	_	_	_
19	min	min	NN	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cross-linked	cross-linked	JJ	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	harvested	harvest	VBN	_	_	_
6	and	and	CC	_	_	_
7	washed	wash	VBN	_	_	_
8	three	three	CD	_	_	_
9	times	time	NNS	_	_	_
10	with	with	IN	_	_	_
11	50	50	CD	_	_	_
12	mL	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	ice-cold	ice-cold	JJ	_	_	_
15	TBS	tbs	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Tris	tris	NN	_	_	_
18	Buffered	buffer	VBN	_	_	_
19	Saline	saline	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	washed	wash	VBN	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	re-suspended	re-suspended	JJ	_	_	_
6	in	in	IN	_	_	_
7	0.5	0.5	CD	_	_	_
8	mL	ml	NN	_	_	_
9	lysis	lysis	NN	_	_	_
10	buffer	buffer	NN	_	_	_
11	composed	compose	VBN	_	_	_
12	of	of	IN	_	_	_
13	50	50	CD	_	_	_
14	mM	mm	NN	KWSUPP	_	_
15	Tris-HCl	tris-hcl	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	pH	ph	NN	_	_	_
18	7.5	7.5	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	,	,	,	_	_	_
21	100	100	CD	_	_	_
22	mM	mm	NN	KWSUPP	_	_
23	NaCl	nacl	NN	_	_	_
24	,	,	,	_	_	_
25	1	1	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	EDTA	edta	NN	_	_	_
28	,	,	,	_	_	_
29	1	1	CD	_	_	_
30	ug	ug	NN	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	chip	chip	NN	_	_	_
33	antibody	antibody	NN	_	_	_
34	:	:	:	_	_	_
35	biotin	biotin	NN	SUPP	_	_
36	conjugated	conjugate	VBN	_	_	_
37	anti-c-myc	anti-c-myc	JJ	_	_	_
38	antibody	antibody	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
40	chip	chip	NN	_	_	_
41	antibody	antibody	NN	_	_	_
42	:	:	:	_	_	_
43	HRP-conjugated	hrp-conjugated	JJ	_	_	_
44	sheep	sheep	NN	_	_	_
45	anti-mouse	anti-mouse	JJ	_	_	_
46	IgG	igg	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
48	chip	chip	NN	_	_	_
49	antibody	antibody	NN	_	_	_
50	vendor	vendor	NN	_	_	_
51	:	:	:	_	_	_
52	Amersham	Amersham	NNP	_	_	_
53	Biosciences	Biosciences	NNP	_	_	_
54	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
55	chip	chip	NN	_	_	_
56	antibody	antibody	NN	_	_	_
57	vendor	vendor	NN	_	_	_
58	:	:	:	_	_	_
59	Santa	Santa	NNP	_	_	_
60	Cruz	Cruz	NNP	_	_	_
61	Biotechnology	Biotechnology	NNP	_	_	_
62	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
63	chip-ArcA	chip-arca	NN	_	_	_
64	_	_	CD	_	_	_
65	ArcA8myc	arca8myc	NN	_	_	_
66	_	_	NN	_	_	_
67	glucose	glucose	NN	SUPP	_	_
68	_	_	CD	_	_	_
69	NH4CL	nh4cl	NN	_	_	_
70	_	_	NN	_	_	_
71	anaerobic	anaerobic	JJ	_	_	_
72	_	_	NN	_	_	_
73	1	1	CD	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	chip-ArcA	chip-arca	NN	_	_	_
76	_	_	CD	_	_	_
77	ArcA8myc	arca8myc	NN	_	_	_
78	_	_	NN	_	_	_
79	glucose	glucose	NN	SUPP	_	_
80	_	_	CD	_	_	_
81	NH4CL	nh4cl	NN	_	_	_
82	_	_	NN	_	_	_
83	anaerobic	anaerobic	JJ	_	_	_
84	_	_	NN	_	_	_
85	2	2	CD	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	chip-ArcA	chip-arca	NN	_	_	_
88	_	_	CD	_	_	_
89	ArcA8myc	arca8myc	NN	_	_	_
90	_	_	NN	_	_	_
91	glucose	glucose	NN	SUPP	_	_
92	_	_	CD	_	_	_
93	NH4CL	nh4cl	NN	_	_	_
94	_	_	NN	_	_	_
95	anaerobic	anaerobic	JJ	_	_	_
96	_	_	NN	_	_	_
97	3	3	CD	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	chip-ArcA	chip-arca	NN	_	_	_
100	_	_	CD	_	_	_
101	ArcA8myc	arca8myc	NN	_	_	_
102	_	_	NN	_	_	_
103	glucose	glucose	NN	SUPP	_	_
104	_	_	CD	_	_	_
105	NH4CL	nh4cl	NN	_	_	_
106	_	_	CD	_	_	_
107	NO3	no3	NN	_	_	_
108	_	_	NN	_	_	_
109	1	1	CD	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	chip-ArcA	chip-arca	NN	_	_	_
112	_	_	CD	_	_	_
113	ArcA8myc	arca8myc	NN	_	_	_
114	_	_	NN	_	_	_
115	glucose	glucose	NN	SUPP	_	_
116	_	_	CD	_	_	_
117	NH4CL	nh4cl	NN	_	_	_
118	_	_	CD	_	_	_
119	NO3	no3	NN	_	_	_
120	_	_	NN	_	_	_
121	2	2	CD	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	chip-ArcA	chip-arca	NN	_	_	_
124	_	_	CD	_	_	_
125	ArcA8myc	arca8myc	NN	_	_	_
126	_	_	NN	_	_	_
127	glucose	glucose	NN	SUPP	_	_
128	_	_	CD	_	_	_
129	NH4CL	nh4cl	NN	_	_	_
130	_	_	CD	_	_	_
131	NO3	no3	NN	_	_	_
132	_	_	NN	_	_	_
133	3	3	CD	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	chip-Fnr	chip-fnr	JJ	_	_	_
136	_	_	NN	_	_	_
137	Fnr8myc	fnr8myc	NN	_	_	_
138	_	_	NN	_	_	_
139	glucose	glucose	NN	SUPP	_	_
140	_	_	CD	_	_	_
141	NH4CL	nh4cl	NN	_	_	_
142	_	_	NN	_	_	_
143	anaerobic	anaerobic	JJ	_	_	_
144	_	_	NN	_	_	_
145	1	1	CD	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	chip-Fnr	chip-fnr	JJ	_	_	_
148	_	_	NN	_	_	_
149	Fnr8myc	fnr8myc	NN	_	_	_
150	_	_	NN	_	_	_
151	glucose	glucose	NN	SUPP	_	_
152	_	_	CD	_	_	_
153	NH4CL	nh4cl	NN	_	_	_
154	_	_	NN	_	_	_
155	anaerobic	anaerobic	JJ	_	_	_
156	_	_	NN	_	_	_
157	2	2	CD	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	chip-Fnr	chip-fnr	JJ	_	_	_
160	_	_	NN	_	_	_
161	Fnr8myc	fnr8myc	NN	_	_	_
162	_	_	NN	_	_	_
163	glucose	glucose	NN	SUPP	_	_
164	_	_	CD	_	_	_
165	NH4CL	nh4cl	NN	_	_	_
166	_	_	NN	_	_	_
167	anaerobic	anaerobic	JJ	_	_	_
168	_	_	NN	_	_	_
169	3	3	CD	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	chip-Fnr	chip-fnr	JJ	_	_	_
172	_	_	NN	_	_	_
173	Fnr8myc	fnr8myc	NN	_	_	_
174	_	_	NN	_	_	_
175	glucose	glucose	NN	SUPP	_	_
176	_	_	CD	_	_	_
177	NH4CL	nh4cl	NN	_	_	_
178	_	_	CD	_	_	_
179	NO3	no3	NN	_	_	_
180	_	_	NN	_	_	_
181	1	1	CD	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	chip-Fnr	chip-fnr	JJ	_	_	_
184	_	_	NN	_	_	_
185	Fnr8myc	fnr8myc	NN	_	_	_
186	_	_	NN	_	_	_
187	glucose	glucose	NN	SUPP	_	_
188	_	_	CD	_	_	_
189	NH4CL	nh4cl	NN	_	_	_
190	_	_	CD	_	_	_
191	NO3	no3	NN	_	_	_
192	_	_	NN	_	_	_
193	2	2	CD	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	chip-Fnr	chip-fnr	JJ	_	_	_
196	_	_	NN	_	_	_
197	Fnr8myc	fnr8myc	NN	_	_	_
198	_	_	NN	_	_	_
199	glucose	glucose	NN	SUPP	_	_
200	_	_	CD	_	_	_
201	NH4CL	nh4cl	NN	_	_	_
202	_	_	CD	_	_	_
203	NO3	no3	NN	_	_	_
204	_	_	NN	_	_	_
205	3	3	CD	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	Cross-linked	cross-linked	JJ	_	_	_
208	and	and	CC	_	_	_
209	sonicated	sonicated	JJ	_	_	_
210	chromatin	chromatin	NN	_	_	_
211	complex	complex	NN	_	_	_
212	of	of	IN	_	_	_
213	ArcA-8myc	arca-8myc	NN	_	_	_
214	and	and	CC	_	_	_
215	DNA	dna	NN	_	_	_
216	was	be	VBD	_	_	_
217	immunoprecipitated	immunoprecipitate	VBN	_	_	_
218	by	by	IN	_	_	_
219	rabbit	rabbit	NN	_	_	_
220	serum	serum	NN	_	_	_
221	containing	contain	VBG	_	_	_
222	myc	myc	NN	_	_	_
223	antibody	antibody	NN	_	_	_
224	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cross-linked	cross-linked	JJ	_	_	_
3	and	and	CC	_	_	_
4	sonicated	sonicated	JJ	_	_	_
5	chromatin	chromatin	NN	_	_	_
6	complex	complex	NN	_	_	_
7	of	of	IN	_	_	_
8	ArgR-8myc	argr-8myc	NN	_	_	_
9	and	and	CC	_	_	_
10	DNA	dna	NN	_	_	_
11	was	be	VBD	_	_	_
12	immunoprecipitated	immunoprecipitate	VBN	_	_	_
13	by	by	IN	_	_	_
14	rabbit	rabbit	NN	_	_	_
15	serum	serum	NN	_	_	_
16	containing	contain	VBG	_	_	_
17	myc	myc	NN	_	_	_
18	antibody	antibody	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cross-linked	cross-linked	JJ	_	_	_
3	and	and	CC	_	_	_
4	sonicated	sonicated	JJ	_	_	_
5	chromatin	chromatin	NN	_	_	_
6	complex	complex	NN	_	_	_
7	of	of	IN	_	_	_
8	Fnr-8myc	fnr-8myc	NN	_	_	_
9	and	and	CC	_	_	_
10	DNA	dna	NN	_	_	_
11	was	be	VBD	_	_	_
12	immunoprecipitated	immunoprecipitate	VBN	_	_	_
13	by	by	IN	_	_	_
14	rabbit	rabbit	NN	_	_	_
15	serum	serum	NN	_	_	_
16	containing	contain	VBG	_	_	_
17	myc	myc	NN	_	_	_
18	antibody	antibody	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	Coli	Coli	NNP	_	_	_
4	ArcA-8myc	ArcA-8myc	NNP	_	_	_
5	ChIP	chip	NN	_	_	_
6	DNA	dna	NN	_	_	_
7	Mock	mock	NN	_	_	_
8	antibody	antibody	NN	_	_	_
9	anaerobic	anaerobic	JJ	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	E.	E.	NNP	_	_	_
12	Coli	Coli	NNP	_	_	_
13	ArcA-8myc	ArcA-8myc	NNP	_	_	_
14	ChIP	chip	NN	_	_	_
15	DNA	dna	NN	_	_	_
16	Mock	mock	NN	_	_	_
17	antibody	antibody	NN	_	_	_
18	NO3	no3	NN	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	E.	E.	NNP	_	_	_
21	Coli	Coli	NNP	_	_	_
22	ArcA	ArcA	NNP	TF	_	_
23	ChIP	chip	NN	_	_	_
24	DNA	dna	NN	_	_	_
25	anaerobic	anaerobic	JJ	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	E.	E.	NNP	_	_	_
28	Coli	Coli	NNP	_	_	_
29	ArcA	ArcA	NNP	TF	_	_
30	ChIP	chip	NN	_	_	_
31	DNA	dna	NN	_	_	_
32	NO3	no3	NN	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	E.	E.	NNP	_	_	_
35	Coli	Coli	NNP	_	_	_
36	Fnr-8myc	fnr-8myc	JJ	_	_	_
37	ChIP	chip	NN	_	_	_
38	DNA	dna	NN	_	_	_
39	Mock	mock	NN	_	_	_
40	antibody	antibody	NN	_	_	_
41	anaerobic	anaerobic	JJ	_	_	_
42	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
43	E.	E.	NNP	_	_	_
44	Coli	Coli	NNP	_	_	_
45	Fnr-8myc	fnr-8myc	JJ	_	_	_
46	ChIP	chip	NN	_	_	_
47	DNA	dna	NN	_	_	_
48	Mock	mock	NN	_	_	_
49	antibody	antibody	NN	_	_	_
50	NO3	no3	NN	_	_	_
51	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
52	E.	E.	NNP	_	_	_
53	Coli	Coli	NNP	_	_	_
54	Fnr	Fnr	NNP	_	_	_
55	ChIP	ChIP	NNP	_	_	_
56	DNA	DNA	NNP	_	_	_
57	anaerobic	anaerobic	JJ	_	_	_
58	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
59	E.	E.	NNP	_	_	_
60	Coli	Coli	NNP	_	_	_
61	Fnr	Fnr	NNP	_	_	_
62	ChIP	ChIP	NNP	_	_	_
63	DNA	DNA	NNP	_	_	_
64	NO3	no3	NN	_	_	_
65	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
66	Escherichia	escherichia	FW	Organism	_	_
67	coli	coli	FW	Organism	_	_
68	str	str	FW	_	_	_
69	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	genotype	genotype	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	The	the	DT	_	_	_
6	raw	raw	JJ	_	_	_
7	data	data	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	.	.	.	_	_	_

1	pair	pair	NN	_	_	_
2	file	file	NN	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	was	be	VBD	_	_	_
5	subjected	subject	VBN	_	_	_
6	to	to	TO	_	_	_
7	per	per	IN	_	_	_
8	channel	channel	NN	_	_	_
9	quantile	quantile	NN	_	_	_
10	normalization	normalization	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Bolstad	Bolstad	NNP	_	_	_
13	et	et	FW	_	_	_
14	al.	al.	FW	_	_	_
15	.	.	.	_	_	_

1	Bioinformatics	bioinformatic	NNS	_	_	_
2	19	19	CD	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	2	2	CD	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	:	:	:	_	_	_
7	185	185	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	,	,	,	_	_	_
10	IP	IP	NNP	_	_	_
11	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
12	background	background	NN	_	_	_
13	strain	strain	NN	_	_	_
14	:	:	:	_	_	_
15	BW25113	bw25113	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
17	CHP	chp	NN	_	_	_
18	files	file	NNS	_	_	_
19	were	be	VBD	_	_	_
20	generated	generate	VBN	_	_	_
21	using	use	VBG	_	_	_
22	Affymetrix	Affymetrix	NNP	_	_	_
23	Expression	expression	NN	_	_	_
24	Control	control	NN	_	_	_
25	.	.	.	_	_	_

1	Downstream	downstream	JJ	_	_	_
2	data	data	NN	_	_	_
3	analysis	analysis	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	in	in	IN	_	_	_
7	GeneSpring	GeneSpring	NNP	_	_	_
8	GX	GX	NNP	_	_	_
9	12	12	CD	_	_	_
10	,	,	,	_	_	_
11	CEL	CEL	NNP	_	_	_
12	files	file	NNS	_	_	_
13	were	be	VBD	_	_	_
14	imported	import	VBN	_	_	_
15	using	use	VBG	_	_	_
16	RMA	RMA	NNP	_	_	_
17	algorithm	algorithm	NN	_	_	_
18	and	and	CC	_	_	_
19	median	median	JJ	_	_	_
20	normalization	normalization	NN	_	_	_
21	was	be	VBD	_	_	_
22	performed	perform	VBN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cirpofloxacin	cirpofloxacin	NN	_	_	_
3	treated	treat	VBN	_	_	_
4	fur	fur	NN	GEN	_	_
5	mutant	mutant	JJ	_	_	_
6	sample	sample	NN	_	_	_
7	at	at	IN	_	_	_
8	T1h	t1h	NN	_	_	_
9	,	,	,	_	_	_
10	biological	biological	JJ	_	_	_
11	rep	rep	NN	GEN	_	_
12	1	1	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Cirpofloxacin	cirpofloxacin	NN	_	_	_
15	treated	treat	VBN	_	_	_
16	fur	fur	NN	GEN	_	_
17	mutant	mutant	JJ	_	_	_
18	sample	sample	NN	_	_	_
19	at	at	IN	_	_	_
20	T1h	t1h	NN	_	_	_
21	,	,	,	_	_	_
22	biological	biological	JJ	_	_	_
23	rep	rep	NN	GEN	_	_
24	2	2	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Cirpofloxacin	cirpofloxacin	NN	_	_	_
27	treated	treat	VBN	_	_	_
28	WT	wt	JJ	_	_	_
29	sample	sample	NN	_	_	_
30	at	at	IN	_	_	_
31	T1h	t1h	NN	_	_	_
32	,	,	,	_	_	_
33	biological	biological	JJ	_	_	_
34	rep	rep	NN	GEN	_	_
35	1	1	CD	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Cirpofloxacin	cirpofloxacin	NN	_	_	_
38	treated	treat	VBN	_	_	_
39	WT	wt	JJ	_	_	_
40	sample	sample	NN	_	_	_
41	at	at	IN	_	_	_
42	T1h	t1h	NN	_	_	_
43	,	,	,	_	_	_
44	biological	biological	JJ	_	_	_
45	rep	rep	NN	GEN	_	_
46	2	2	CD	_	_	_
47	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
48	Escherichia	escherichia	FW	Organism	_	_
49	coli	coli	FW	Organism	_	_
50	BW25113	bw25113	NN	_	_	_
51	and	and	CC	_	_	_
52	fur	fur	NN	GEN	_	_
53	mutant	mutant	JJ	_	_	_
54	strains	strain	NNS	_	_	_
55	were	be	VBD	_	_	_
56	cultivated	cultivate	VBN	_	_	_
57	at	at	IN	_	_	_
58	37Co	37co	NN	_	_	_
59	in	in	IN	_	_	_
60	25	25	CD	_	_	_
61	ml	ml	NN	_	_	_
62	of	of	IN	_	_	_
63	LB	lb	NN	MED	_	_
64	medium	medium	NN	MED	_	_
65	using	use	VBG	_	_	_
66	Erlenmeyer	Erlenmeyer	NNP	_	_	_
67	flasks	flask	NNS	_	_	_
68	.	.	.	_	_	_

1	1	1	CD	_	_	_
2	ml	ml	NN	_	_	_
3	of	of	IN	_	_	_
4	OVN	ovn	NN	_	_	_
5	culture	culture	NN	_	_	_
6	was	be	VBD	_	_	_
7	transferred	transfer	VBN	_	_	_
8	to	to	TO	_	_	_
9	20	20	CD	_	_	_
10	ml	ml	NN	_	_	_
11	of	of	IN	_	_	_
12	fresh	fresh	JJ	_	_	_
13	LB	lb	NN	MED	_	_
14	medium	medium	NN	MED	_	_
15	and	and	CC	_	_	_
16	cells	cell	NNS	_	_	_
17	were	be	VBD	_	_	_
18	incubated	incubate	VBN	_	_	_
19	in	in	IN	_	_	_
20	the	the	DT	_	_	_
21	presence	presence	NN	_	_	_
22	or	or	CC	_	_	_
23	absence	absence	NN	_	_	_
24	of	of	IN	_	_	_
25	ciprofloxacin	ciprofloxacin	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	100	100	CD	_	_	_
28	ng	ng	NN	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	Escherichia	escherichia	FW	Organism	_	_
31	coli	coli	FW	Organism	_	_
32	K-12	k-12	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	FUR	fur	NN	_	_	_
35	_	_	CD	_	_	_
36	CPR	CPR	NNP	_	_	_
37	_	_	SYM	_	_	_
38	1	1	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	FUR	fur	NN	_	_	_
41	_	_	CD	_	_	_
42	CPR	CPR	NNP	_	_	_
43	_	_	SYM	_	_	_
44	2	2	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
46	FUR	fur	NN	_	_	_
47	_	_	CD	_	_	_
48	noCPR	nocpr	NN	_	_	_
49	_	_	NN	_	_	_
50	1	1	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	FUR	fur	NN	_	_	_
53	_	_	CD	_	_	_
54	noCPR	nocpr	NN	_	_	_
55	_	_	NN	_	_	_
56	2	2	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	genotype	genotype	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	Non-treated	non-treated	JJ	_	_	_
61	,	,	,	_	_	_
62	fur	fur	NN	GEN	_	_
63	mutant	mutant	JJ	_	_	_
64	sample	sample	NN	_	_	_
65	at	at	IN	_	_	_
66	T0	t0	NN	_	_	_
67	,	,	,	_	_	_
68	biological	biological	JJ	_	_	_
69	rep	rep	NN	GEN	_	_
70	1	1	CD	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	Non-treated	non-treated	JJ	_	_	_
73	,	,	,	_	_	_
74	fur	fur	NN	GEN	_	_
75	mutant	mutant	JJ	_	_	_
76	sample	sample	NN	_	_	_
77	at	at	IN	_	_	_
78	T0	t0	NN	_	_	_
79	,	,	,	_	_	_
80	biological	biological	JJ	_	_	_
81	rep	rep	NN	GEN	_	_
82	2	2	CD	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
84	Non-treated	non-treated	JJ	_	_	_
85	,	,	,	_	_	_
86	WT	wt	JJ	_	_	_
87	control	control	NN	_	_	_
88	at	at	IN	_	_	_
89	T0	t0	NN	_	_	_
90	,	,	,	_	_	_
91	biological	biological	JJ	_	_	_
92	rep	rep	NN	GEN	_	_
93	1	1	CD	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	Non-treated	non-treated	JJ	_	_	_
96	,	,	,	_	_	_
97	WT	wt	JJ	_	_	_
98	control	control	NN	_	_	_
99	at	at	IN	_	_	_
100	T0	t0	NN	_	_	_
101	,	,	,	_	_	_
102	biological	biological	JJ	_	_	_
103	rep	rep	NN	GEN	_	_
104	2	2	CD	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	Samples	sample	NNS	_	_	_
107	for	for	IN	_	_	_
108	microarray	microarray	NN	_	_	_
109	analyses	analysis	NNS	_	_	_
110	were	be	VBD	_	_	_
111	taken	take	VBN	_	_	_
112	before	before	IN	_	_	_
113	ciprofloxacin	ciprofloxacin	NN	_	_	_
114	treatment	treatment	NN	_	_	_
115	-LRB-	-lrb-	-LRB-	_	_	_
116	t0	t0	NN	_	_	_
117	-RRB-	-rrb-	-RRB-	_	_	_
118	and	and	CC	_	_	_
119	then	then	RB	_	_	_
120	at	at	IN	_	_	_
121	1	1	CD	_	_	_
122	hour	hour	NN	_	_	_
123	post-treatment	post-treatment	JJ	_	_	_
124	-LRB-	-lrb-	-LRB-	_	_	_
125	t1	t1	NN	_	_	_
126	-RRB-	-rrb-	-RRB-	_	_	_
127	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	concentration	concentration	NN	_	_	_
3	was	be	VBD	_	_	_
4	adjusted	adjust	VBN	_	_	_
5	to	to	TO	_	_	_
6	109	109	CD	_	_	_
7	cells	cell	NNS	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	We	we	PRP	_	_	_
10	compared	compare	VBD	_	_	_
11	the	the	DT	_	_	_
12	microarray-determined	microarray-determined	JJ	_	_	_
13	mRNA	mrna	NN	_	_	_
14	profiles	profile	NNS	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Affymetrix	Affymetrix	NNP	_	_	_
17	E.	E.	NNP	_	_	_
18	coli	coli	NN	_	_	_
19	Genome	Genome	NNP	_	_	_
20	2.0	2.0	CD	_	_	_
21	Array	array	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	of	of	IN	_	_	_
24	Δfur	δfur	NN	_	_	_
25	and	and	CC	_	_	_
26	WT	wt	JJ	_	_	_
27	genotypes	genotype	NNS	_	_	_
28	in	in	IN	_	_	_
29	response	response	NN	_	_	_
30	to	to	TO	_	_	_
31	ciprofloxacin	ciprofloxacin	NN	_	_	_
32	treatment	treatment	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	100	100	CD	_	_	_
35	ng	ng	NN	_	_	_
36	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
37	WT	WT	NNP	_	_	_
38	_	_	NNP	_	_	_
39	CPR	CPR	NNP	_	_	_
40	_	_	SYM	_	_	_
41	1	1	CD	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	WT	wt	JJ	_	_	_
44	_	_	NN	_	_	_
45	CPR	CPR	NNP	_	_	_
46	_	_	SYM	_	_	_
47	2	2	CD	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	WT	wt	JJ	_	_	_
50	_	_	NN	_	_	_
51	noCPR	nocpr	NN	_	_	_
52	_	_	NN	_	_	_
53	1	1	CD	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	WT	wt	JJ	_	_	_
56	_	_	NN	_	_	_
57	noCPR	nocpr	NN	_	_	_
58	_	_	NN	_	_	_
59	2	2	CD	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	Cells	cell	NNS	_	_	_
62	were	be	VBD	_	_	_
63	grown	grow	VBN	_	_	_
64	in	in	IN	_	_	_
65	the	the	DT	_	_	_
66	minimal	minimal	JJ	_	_	_
67	media	media	NNS	_	_	_
68	,	,	,	_	_	_
69	modified	modify	VBN	_	_	_
70	M63	m63	NN	_	_	_
71	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	final	final	JJ	_	_	_
3	cell	cell	NN	_	_	_
4	concentrations	concentration	NNS	_	_	_
5	were	be	VBD	_	_	_
6	controlled	control	VBN	_	_	_
7	~	~	SYM	_	_	_
8	10	10	CD	_	_	_
9	^	^	SYM	_	_	_
10	8	8	CD	_	_	_
11	cells	cell	NNS	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
13	condition	condition	NN	_	_	_
14	:	:	:	_	_	_
15	histidine	histidine	NN	_	_	_
16	depleted	deplete	VBD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	condition	condition	NN	_	_	_
19	:	:	:	_	_	_
20	histidine	histidine	NN	_	_	_
21	supplied	supply	VBD	_	_	_
22	,	,	,	_	_	_
23	1	1	CD	_	_	_
24	mM	mm	NN	KWSUPP	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Escherichia	escherichia	FW	Organism	_	_
27	coli	coli	FW	Organism	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Microarray	microarray	NN	_	_	_
30	data	datum	NNS	_	_	_
31	were	be	VBD	_	_	_
32	processed	process	VBN	_	_	_
33	using	use	VBG	_	_	_
34	custom	custom	NN	_	_	_
35	scripts	script	NNS	_	_	_
36	written	write	VBN	_	_	_
37	in	in	IN	_	_	_
38	R	r	NN	_	_	_
39	based	base	VBN	_	_	_
40	on	on	IN	_	_	_
41	the	the	DT	_	_	_
42	finite	finite	JJ	_	_	_
43	hybridisation	hybridisation	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	FH	fh	NN	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	model	model	NN	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	Ono	Ono	NNP	_	_	_
50	et	et	FW	_	_	_
51	al	al	FW	_	_	_
52	,	,	,	_	_	_
53	2008	2008	CD	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	and	and	CC	_	_	_
56	the	the	DT	_	_	_
57	thermodynamic	thermodynamic	JJ	_	_	_
58	model	model	NN	_	_	_
59	of	of	IN	_	_	_
60	non-specific	non-specific	JJ	_	_	_
61	binding	binding	NN	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	NSB	nsb	NN	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	on	on	IN	_	_	_
66	short	short	JJ	_	_	_
67	nucleotide	nucleotide	NN	_	_	_
68	microarrays	microarray	NNS	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	Furusawa	Furusawa	NNP	_	_	_
71	et	et	FW	_	_	_
72	al	al	FW	_	_	_
73	,	,	,	_	_	_
74	2009	2009	CD	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	log10	log10	NN	_	_	_
3	mRNA	mrna	NN	_	_	_
4	concentration	concentration	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	pM	pm	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	data	datum	NNS	_	_	_
9	are	be	VBP	_	_	_
10	provided	provide	VBN	_	_	_
11	as	as	IN	_	_	_
12	a	a	DT	_	_	_
13	supplementary	supplementary	JJ	_	_	_
14	file	file	NN	_	_	_
15	on	on	IN	_	_	_
16	the	the	DT	_	_	_
17	SERIES	series	NN	_	_	_
18	record	record	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	OSU11	osu11	NN	_	_	_
3	,	,	,	_	_	_
4	histidine	histidine	NN	_	_	_
5	depleted	deplete	VBN	_	_	_
6	,	,	,	_	_	_
7	>	>	JJR	_	_	_
8	10	10	CD	_	_	_
9	hrs	hr	NNS	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	OSU11	osu11	NN	_	_	_
12	,	,	,	_	_	_
13	histidine	histidine	NN	_	_	_
14	depleted	deplete	VBN	_	_	_
15	,	,	,	_	_	_
16	>	>	JJR	_	_	_
17	10	10	CD	_	_	_
18	hrs	hr	NNS	_	_	_
19	,	,	,	_	_	_
20	rep	rep	NN	GEN	_	_
21	1	1	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	OSU11	osu11	NN	_	_	_
24	,	,	,	_	_	_
25	histidine	histidine	NN	_	_	_
26	depleted	deplete	VBN	_	_	_
27	,	,	,	_	_	_
28	>	>	JJR	_	_	_
29	10	10	CD	_	_	_
30	hrs	hr	NNS	_	_	_
31	,	,	,	_	_	_
32	rep	rep	NN	GEN	_	_
33	2	2	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	OSU11	osu11	NN	_	_	_
36	,	,	,	_	_	_
37	histidine	histidine	NN	_	_	_
38	depleted	deplete	VBN	_	_	_
39	,	,	,	_	_	_
40	>	>	JJR	_	_	_
41	10	10	CD	_	_	_
42	hrs	hr	NNS	_	_	_
43	,	,	,	_	_	_
44	rep	rep	NN	GEN	_	_
45	3	3	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	OSU11	osu11	NN	_	_	_
48	,	,	,	_	_	_
49	histidine	histidine	NN	_	_	_
50	depleted	deplete	VBN	_	_	_
51	,	,	,	_	_	_
52	10	10	CD	_	_	_
53	min	min	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	OSU11	osu11	NN	_	_	_
56	,	,	,	_	_	_
57	histidine	histidine	NN	_	_	_
58	depleted	deplete	VBN	_	_	_
59	,	,	,	_	_	_
60	10	10	CD	_	_	_
61	min	min	NN	_	_	_
62	,	,	,	_	_	_
63	rep	rep	NN	GEN	_	_
64	1	1	CD	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	OSU11	osu11	NN	_	_	_
67	,	,	,	_	_	_
68	histidine	histidine	NN	_	_	_
69	depleted	deplete	VBN	_	_	_
70	,	,	,	_	_	_
71	10	10	CD	_	_	_
72	min	min	NN	_	_	_
73	,	,	,	_	_	_
74	rep	rep	NN	GEN	_	_
75	2	2	CD	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	OSU11	osu11	NN	_	_	_
78	,	,	,	_	_	_
79	histidine	histidine	NN	_	_	_
80	depleted	deplete	VBN	_	_	_
81	,	,	,	_	_	_
82	10	10	CD	_	_	_
83	min	min	NN	_	_	_
84	,	,	,	_	_	_
85	rep	rep	NN	GEN	_	_
86	3	3	CD	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	OSU11	osu11	NN	_	_	_
89	,	,	,	_	_	_
90	histidine	histidine	NN	_	_	_
91	depleted	deplete	VBN	_	_	_
92	,	,	,	_	_	_
93	2	2	CD	_	_	_
94	hrs	hr	NNS	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	OSU11	osu11	NN	_	_	_
97	,	,	,	_	_	_
98	histidine	histidine	NN	_	_	_
99	depleted	deplete	VBN	_	_	_
100	,	,	,	_	_	_
101	2	2	CD	_	_	_
102	hrs	hr	NNS	_	_	_
103	,	,	,	_	_	_
104	rep	rep	NN	GEN	_	_
105	1	1	CD	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	OSU11	osu11	NN	_	_	_
108	,	,	,	_	_	_
109	histidine	histidine	NN	_	_	_
110	depleted	deplete	VBN	_	_	_
111	,	,	,	_	_	_
112	2	2	CD	_	_	_
113	hrs	hr	NNS	_	_	_
114	,	,	,	_	_	_
115	rep	rep	NN	GEN	_	_
116	2	2	CD	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	OSU11	osu11	NN	_	_	_
119	,	,	,	_	_	_
120	histidine	histidine	NN	_	_	_
121	depleted	deplete	VBN	_	_	_
122	,	,	,	_	_	_
123	2	2	CD	_	_	_
124	hrs	hr	NNS	_	_	_
125	,	,	,	_	_	_
126	rep	rep	NN	GEN	_	_
127	3	3	CD	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	OSU11	osu11	NN	_	_	_
130	,	,	,	_	_	_
131	histidine	histidine	NN	_	_	_
132	supplied	supply	VBD	_	_	_
133	,	,	,	_	_	_
134	1	1	CD	_	_	_
135	mM	mm	NN	KWSUPP	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	OSU11	osu11	NN	_	_	_
138	,	,	,	_	_	_
139	histidine	histidine	NN	_	_	_
140	supplied	supply	VBD	_	_	_
141	,	,	,	_	_	_
142	1	1	CD	_	_	_
143	mM	mm	NN	KWSUPP	_	_
144	,	,	,	_	_	_
145	rep	rep	NN	GEN	_	_
146	1	1	CD	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	OSU11	osu11	NN	_	_	_
149	,	,	,	_	_	_
150	histidine	histidine	NN	_	_	_
151	supplied	supply	VBD	_	_	_
152	,	,	,	_	_	_
153	1	1	CD	_	_	_
154	mM	mm	NN	KWSUPP	_	_
155	,	,	,	_	_	_
156	rep	rep	NN	GEN	_	_
157	2	2	CD	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	OSU11	osu11	NN	_	_	_
160	,	,	,	_	_	_
161	histidine	histidine	NN	_	_	_
162	supplied	supply	VBD	_	_	_
163	,	,	,	_	_	_
164	1	1	CD	_	_	_
165	mM	mm	NN	KWSUPP	_	_
166	,	,	,	_	_	_
167	rep	rep	NN	GEN	_	_
168	3	3	CD	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	OSU12-hisA	osu12-hisa	NN	_	_	_
171	,	,	,	_	_	_
172	histidine	histidine	NN	_	_	_
173	depleted	deplete	VBN	_	_	_
174	,	,	,	_	_	_
175	>	>	JJR	_	_	_
176	10	10	CD	_	_	_
177	hrs	hr	NNS	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	OSU12-hisA	osu12-hisa	NN	_	_	_
180	,	,	,	_	_	_
181	histidine	histidine	NN	_	_	_
182	depleted	deplete	VBN	_	_	_
183	,	,	,	_	_	_
184	>	>	JJR	_	_	_
185	10	10	CD	_	_	_
186	hrs	hr	NNS	_	_	_
187	,	,	,	_	_	_
188	rep	rep	NN	GEN	_	_
189	1	1	CD	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	OSU12-hisA	osu12-hisa	NN	_	_	_
192	,	,	,	_	_	_
193	histidine	histidine	NN	_	_	_
194	depleted	deplete	VBN	_	_	_
195	,	,	,	_	_	_
196	>	>	JJR	_	_	_
197	10	10	CD	_	_	_
198	hrs	hr	NNS	_	_	_
199	,	,	,	_	_	_
200	rep	rep	NN	GEN	_	_
201	2	2	CD	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	OSU12-hisA	osu12-hisa	NN	_	_	_
204	,	,	,	_	_	_
205	histidine	histidine	NN	_	_	_
206	depleted	deplete	VBN	_	_	_
207	,	,	,	_	_	_
208	>	>	JJR	_	_	_
209	10	10	CD	_	_	_
210	hrs	hr	NNS	_	_	_
211	,	,	,	_	_	_
212	rep	rep	NN	GEN	_	_
213	3	3	CD	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	OSU12-hisA	osu12-hisa	NN	_	_	_
216	,	,	,	_	_	_
217	histidine	histidine	NN	_	_	_
218	depleted	deplete	VBN	_	_	_
219	,	,	,	_	_	_
220	10	10	CD	_	_	_
221	min	min	NN	_	_	_
222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
223	OSU12-hisA	osu12-hisa	NN	_	_	_
224	,	,	,	_	_	_
225	histidine	histidine	NN	_	_	_
226	depleted	deplete	VBN	_	_	_
227	,	,	,	_	_	_
228	10	10	CD	_	_	_
229	min	min	NN	_	_	_
230	,	,	,	_	_	_
231	rep	rep	NN	GEN	_	_
232	1	1	CD	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	OSU12-hisA	osu12-hisa	NN	_	_	_
235	,	,	,	_	_	_
236	histidine	histidine	NN	_	_	_
237	depleted	deplete	VBN	_	_	_
238	,	,	,	_	_	_
239	10	10	CD	_	_	_
240	min	min	NN	_	_	_
241	,	,	,	_	_	_
242	rep	rep	NN	GEN	_	_
243	2	2	CD	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	OSU12-hisA	osu12-hisa	NN	_	_	_
246	,	,	,	_	_	_
247	histidine	histidine	NN	_	_	_
248	depleted	deplete	VBN	_	_	_
249	,	,	,	_	_	_
250	10	10	CD	_	_	_
251	min	min	NN	_	_	_
252	,	,	,	_	_	_
253	rep	rep	NN	GEN	_	_
254	3	3	CD	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	OSU12-hisA	osu12-hisa	NN	_	_	_
257	,	,	,	_	_	_
258	histidine	histidine	NN	_	_	_
259	depleted	deplete	VBN	_	_	_
260	,	,	,	_	_	_
261	2	2	CD	_	_	_
262	hrs	hr	NNS	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
264	OSU12-hisA	osu12-hisa	NN	_	_	_
265	,	,	,	_	_	_
266	histidine	histidine	NN	_	_	_
267	depleted	deplete	VBN	_	_	_
268	,	,	,	_	_	_
269	2	2	CD	_	_	_
270	hrs	hr	NNS	_	_	_
271	,	,	,	_	_	_
272	rep	rep	NN	GEN	_	_
273	1	1	CD	_	_	_
274	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
275	OSU12-hisA	osu12-hisa	NN	_	_	_
276	,	,	,	_	_	_
277	histidine	histidine	NN	_	_	_
278	depleted	deplete	VBN	_	_	_
279	,	,	,	_	_	_
280	2	2	CD	_	_	_
281	hrs	hr	NNS	_	_	_
282	,	,	,	_	_	_
283	rep	rep	NN	GEN	_	_
284	2	2	CD	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
286	OSU12-hisA	osu12-hisa	NN	_	_	_
287	,	,	,	_	_	_
288	histidine	histidine	NN	_	_	_
289	depleted	deplete	VBN	_	_	_
290	,	,	,	_	_	_
291	2	2	CD	_	_	_
292	hrs	hr	NNS	_	_	_
293	,	,	,	_	_	_
294	rep	rep	NN	GEN	_	_
295	3	3	CD	_	_	_
296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
297	OSU12-hisA	osu12-hisa	NN	_	_	_
298	,	,	,	_	_	_
299	histidine	histidine	NN	_	_	_
300	supplied	supply	VBD	_	_	_
301	,	,	,	_	_	_
302	1	1	CD	_	_	_
303	mM	mm	NN	KWSUPP	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	OSU12-hisA	osu12-hisa	NN	_	_	_
306	,	,	,	_	_	_
307	histidine	histidine	NN	_	_	_
308	supplied	supply	VBD	_	_	_
309	,	,	,	_	_	_
310	1	1	CD	_	_	_
311	mM	mm	NN	KWSUPP	_	_
312	,	,	,	_	_	_
313	rep	rep	NN	GEN	_	_
314	1	1	CD	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
316	OSU12-hisA	osu12-hisa	NN	_	_	_
317	,	,	,	_	_	_
318	histidine	histidine	NN	_	_	_
319	supplied	supply	VBD	_	_	_
320	,	,	,	_	_	_
321	1	1	CD	_	_	_
322	mM	mm	NN	KWSUPP	_	_
323	,	,	,	_	_	_
324	rep	rep	NN	GEN	_	_
325	2	2	CD	_	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	OSU12-hisA	osu12-hisa	NN	_	_	_
328	,	,	,	_	_	_
329	histidine	histidine	NN	_	_	_
330	supplied	supply	VBD	_	_	_
331	,	,	,	_	_	_
332	1	1	CD	_	_	_
333	mM	mm	NN	KWSUPP	_	_
334	,	,	,	_	_	_
335	rep	rep	NN	GEN	_	_
336	3	3	CD	_	_	_
337	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
338	OSU12-hisB	osu12-hisb	NN	_	_	_
339	,	,	,	_	_	_
340	histidine	histidine	NN	_	_	_
341	depleted	deplete	VBN	_	_	_
342	,	,	,	_	_	_
343	>	>	JJR	_	_	_
344	10	10	CD	_	_	_
345	hrs	hr	NNS	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	OSU12-hisB	osu12-hisb	NN	_	_	_
348	,	,	,	_	_	_
349	histidine	histidine	NN	_	_	_
350	depleted	deplete	VBN	_	_	_
351	,	,	,	_	_	_
352	>	>	JJR	_	_	_
353	10	10	CD	_	_	_
354	hrs	hr	NNS	_	_	_
355	,	,	,	_	_	_
356	rep	rep	NN	GEN	_	_
357	1	1	CD	_	_	_
358	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
359	OSU12-hisB	osu12-hisb	NN	_	_	_
360	,	,	,	_	_	_
361	histidine	histidine	NN	_	_	_
362	depleted	deplete	VBN	_	_	_
363	,	,	,	_	_	_
364	>	>	JJR	_	_	_
365	10	10	CD	_	_	_
366	hrs	hr	NNS	_	_	_
367	,	,	,	_	_	_
368	rep	rep	NN	GEN	_	_
369	2	2	CD	_	_	_
370	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
371	OSU12-hisB	osu12-hisb	NN	_	_	_
372	,	,	,	_	_	_
373	histidine	histidine	NN	_	_	_
374	depleted	deplete	VBN	_	_	_
375	,	,	,	_	_	_
376	>	>	JJR	_	_	_
377	10	10	CD	_	_	_
378	hrs	hr	NNS	_	_	_
379	,	,	,	_	_	_
380	rep	rep	NN	GEN	_	_
381	3	3	CD	_	_	_
382	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
383	OSU12-hisB	osu12-hisb	NN	_	_	_
384	,	,	,	_	_	_
385	histidine	histidine	NN	_	_	_
386	depleted	deplete	VBN	_	_	_
387	,	,	,	_	_	_
388	10	10	CD	_	_	_
389	min	min	NN	_	_	_
390	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
391	OSU12-hisB	osu12-hisb	NN	_	_	_
392	,	,	,	_	_	_
393	histidine	histidine	NN	_	_	_
394	depleted	deplete	VBN	_	_	_
395	,	,	,	_	_	_
396	10	10	CD	_	_	_
397	min	min	NN	_	_	_
398	,	,	,	_	_	_
399	rep	rep	NN	GEN	_	_
400	1	1	CD	_	_	_
401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
402	OSU12-hisB	osu12-hisb	NN	_	_	_
403	,	,	,	_	_	_
404	histidine	histidine	NN	_	_	_
405	depleted	deplete	VBN	_	_	_
406	,	,	,	_	_	_
407	10	10	CD	_	_	_
408	min	min	NN	_	_	_
409	,	,	,	_	_	_
410	rep	rep	NN	GEN	_	_
411	2	2	CD	_	_	_
412	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
413	OSU12-hisB	osu12-hisb	NN	_	_	_
414	,	,	,	_	_	_
415	histidine	histidine	NN	_	_	_
416	depleted	deplete	VBN	_	_	_
417	,	,	,	_	_	_
418	10	10	CD	_	_	_
419	min	min	NN	_	_	_
420	,	,	,	_	_	_
421	rep	rep	NN	GEN	_	_
422	3	3	CD	_	_	_
423	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
424	OSU12-hisB	osu12-hisb	NN	_	_	_
425	,	,	,	_	_	_
426	histidine	histidine	NN	_	_	_
427	depleted	deplete	VBN	_	_	_
428	,	,	,	_	_	_
429	2	2	CD	_	_	_
430	hrs	hr	NNS	_	_	_
431	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
432	OSU12-hisB	osu12-hisb	NN	_	_	_
433	,	,	,	_	_	_
434	histidine	histidine	NN	_	_	_
435	depleted	deplete	VBN	_	_	_
436	,	,	,	_	_	_
437	2	2	CD	_	_	_
438	hrs	hr	NNS	_	_	_
439	,	,	,	_	_	_
440	rep	rep	NN	GEN	_	_
441	1	1	CD	_	_	_
442	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
443	OSU12-hisB	osu12-hisb	NN	_	_	_
444	,	,	,	_	_	_
445	histidine	histidine	NN	_	_	_
446	depleted	deplete	VBN	_	_	_
447	,	,	,	_	_	_
448	2	2	CD	_	_	_
449	hrs	hr	NNS	_	_	_
450	,	,	,	_	_	_
451	rep	rep	NN	GEN	_	_
452	2	2	CD	_	_	_
453	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
454	OSU12-hisB	osu12-hisb	NN	_	_	_
455	,	,	,	_	_	_
456	histidine	histidine	NN	_	_	_
457	depleted	deplete	VBN	_	_	_
458	,	,	,	_	_	_
459	2	2	CD	_	_	_
460	hrs	hr	NNS	_	_	_
461	,	,	,	_	_	_
462	rep	rep	NN	GEN	_	_
463	3	3	CD	_	_	_
464	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
465	OSU12-hisB	osu12-hisb	NN	_	_	_
466	,	,	,	_	_	_
467	histidine	histidine	NN	_	_	_
468	supplied	supply	VBD	_	_	_
469	,	,	,	_	_	_
470	1	1	CD	_	_	_
471	mM	mm	NN	KWSUPP	_	_
472	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
473	OSU12-hisB	osu12-hisb	NN	_	_	_
474	,	,	,	_	_	_
475	histidine	histidine	NN	_	_	_
476	supplied	supply	VBD	_	_	_
477	,	,	,	_	_	_
478	1	1	CD	_	_	_
479	mM	mm	NN	KWSUPP	_	_
480	,	,	,	_	_	_
481	rep	rep	NN	GEN	_	_
482	1	1	CD	_	_	_
483	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
484	OSU12-hisB	osu12-hisb	NN	_	_	_
485	,	,	,	_	_	_
486	histidine	histidine	NN	_	_	_
487	supplied	supply	VBD	_	_	_
488	,	,	,	_	_	_
489	1	1	CD	_	_	_
490	mM	mm	NN	KWSUPP	_	_
491	,	,	,	_	_	_
492	rep	rep	NN	GEN	_	_
493	2	2	CD	_	_	_
494	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
495	OSU12-hisB	osu12-hisb	NN	_	_	_
496	,	,	,	_	_	_
497	histidine	histidine	NN	_	_	_
498	supplied	supply	VBD	_	_	_
499	,	,	,	_	_	_
500	1	1	CD	_	_	_
501	mM	mm	NN	KWSUPP	_	_
502	,	,	,	_	_	_
503	rep	rep	NN	GEN	_	_
504	3	3	CD	_	_	_
505	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
506	OSU12-hisC	osu12-hisc	NN	_	_	_
507	,	,	,	_	_	_
508	histidine	histidine	NN	_	_	_
509	depleted	deplete	VBN	_	_	_
510	,	,	,	_	_	_
511	>	>	JJR	_	_	_
512	10	10	CD	_	_	_
513	hrs	hr	NNS	_	_	_
514	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
515	OSU12-hisC	osu12-hisc	NN	_	_	_
516	,	,	,	_	_	_
517	histidine	histidine	NN	_	_	_
518	depleted	deplete	VBN	_	_	_
519	,	,	,	_	_	_
520	>	>	JJR	_	_	_
521	10	10	CD	_	_	_
522	hrs	hr	NNS	_	_	_
523	,	,	,	_	_	_
524	rep	rep	NN	GEN	_	_
525	1	1	CD	_	_	_
526	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
527	OSU12-hisC	osu12-hisc	NN	_	_	_
528	,	,	,	_	_	_
529	histidine	histidine	NN	_	_	_
530	depleted	deplete	VBN	_	_	_
531	,	,	,	_	_	_
532	>	>	JJR	_	_	_
533	10	10	CD	_	_	_
534	hrs	hr	NNS	_	_	_
535	,	,	,	_	_	_
536	rep	rep	NN	GEN	_	_
537	2	2	CD	_	_	_
538	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
539	OSU12-hisC	osu12-hisc	NN	_	_	_
540	,	,	,	_	_	_
541	histidine	histidine	NN	_	_	_
542	depleted	deplete	VBN	_	_	_
543	,	,	,	_	_	_
544	>	>	JJR	_	_	_
545	10	10	CD	_	_	_
546	hrs	hr	NNS	_	_	_
547	,	,	,	_	_	_
548	rep	rep	NN	GEN	_	_
549	3	3	CD	_	_	_
550	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
551	OSU12-hisC	osu12-hisc	NN	_	_	_
552	,	,	,	_	_	_
553	histidine	histidine	NN	_	_	_
554	depleted	deplete	VBN	_	_	_
555	,	,	,	_	_	_
556	10	10	CD	_	_	_
557	min	min	NN	_	_	_
558	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
559	OSU12-hisC	osu12-hisc	NN	_	_	_
560	,	,	,	_	_	_
561	histidine	histidine	NN	_	_	_
562	depleted	deplete	VBN	_	_	_
563	,	,	,	_	_	_
564	10	10	CD	_	_	_
565	min	min	NN	_	_	_
566	,	,	,	_	_	_
567	rep	rep	NN	GEN	_	_
568	1	1	CD	_	_	_
569	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
570	OSU12-hisC	osu12-hisc	NN	_	_	_
571	,	,	,	_	_	_
572	histidine	histidine	NN	_	_	_
573	depleted	deplete	VBN	_	_	_
574	,	,	,	_	_	_
575	10	10	CD	_	_	_
576	min	min	NN	_	_	_
577	,	,	,	_	_	_
578	rep	rep	NN	GEN	_	_
579	2	2	CD	_	_	_
580	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
581	OSU12-hisC	osu12-hisc	NN	_	_	_
582	,	,	,	_	_	_
583	histidine	histidine	NN	_	_	_
584	depleted	deplete	VBN	_	_	_
585	,	,	,	_	_	_
586	10	10	CD	_	_	_
587	min	min	NN	_	_	_
588	,	,	,	_	_	_
589	rep	rep	NN	GEN	_	_
590	3	3	CD	_	_	_
591	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
592	OSU12-hisC	osu12-hisc	NN	_	_	_
593	,	,	,	_	_	_
594	histidine	histidine	NN	_	_	_
595	depleted	deplete	VBN	_	_	_
596	,	,	,	_	_	_
597	2	2	CD	_	_	_
598	hrs	hr	NNS	_	_	_
599	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
600	OSU12-hisC	osu12-hisc	NN	_	_	_
601	,	,	,	_	_	_
602	histidine	histidine	NN	_	_	_
603	depleted	deplete	VBN	_	_	_
604	,	,	,	_	_	_
605	2	2	CD	_	_	_
606	hrs	hr	NNS	_	_	_
607	,	,	,	_	_	_
608	rep	rep	NN	GEN	_	_
609	1	1	CD	_	_	_
610	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
611	OSU12-hisC	osu12-hisc	NN	_	_	_
612	,	,	,	_	_	_
613	histidine	histidine	NN	_	_	_
614	depleted	deplete	VBN	_	_	_
615	,	,	,	_	_	_
616	2	2	CD	_	_	_
617	hrs	hr	NNS	_	_	_
618	,	,	,	_	_	_
619	rep	rep	NN	GEN	_	_
620	2	2	CD	_	_	_
621	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
622	OSU12-hisC	osu12-hisc	NN	_	_	_
623	,	,	,	_	_	_
624	histidine	histidine	NN	_	_	_
625	depleted	deplete	VBN	_	_	_
626	,	,	,	_	_	_
627	2	2	CD	_	_	_
628	hrs	hr	NNS	_	_	_
629	,	,	,	_	_	_
630	rep	rep	NN	GEN	_	_
631	3	3	CD	_	_	_
632	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
633	OSU12-hisC	osu12-hisc	NN	_	_	_
634	,	,	,	_	_	_
635	histidine	histidine	NN	_	_	_
636	supplied	supply	VBD	_	_	_
637	,	,	,	_	_	_
638	1	1	CD	_	_	_
639	mM	mm	NN	KWSUPP	_	_
640	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
641	OSU12-hisC	osu12-hisc	NN	_	_	_
642	,	,	,	_	_	_
643	histidine	histidine	NN	_	_	_
644	supplied	supply	VBD	_	_	_
645	,	,	,	_	_	_
646	1	1	CD	_	_	_
647	mM	mm	NN	KWSUPP	_	_
648	,	,	,	_	_	_
649	rep	rep	NN	GEN	_	_
650	1	1	CD	_	_	_
651	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
652	OSU12-hisC	osu12-hisc	NN	_	_	_
653	,	,	,	_	_	_
654	histidine	histidine	NN	_	_	_
655	supplied	supply	VBD	_	_	_
656	,	,	,	_	_	_
657	1	1	CD	_	_	_
658	mM	mm	NN	KWSUPP	_	_
659	,	,	,	_	_	_
660	rep	rep	NN	GEN	_	_
661	2	2	CD	_	_	_
662	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
663	OSU12-hisC	osu12-hisc	NN	_	_	_
664	,	,	,	_	_	_
665	histidine	histidine	NN	_	_	_
666	supplied	supply	VBD	_	_	_
667	,	,	,	_	_	_
668	1	1	CD	_	_	_
669	mM	mm	NN	KWSUPP	_	_
670	,	,	,	_	_	_
671	rep	rep	NN	GEN	_	_
672	3	3	CD	_	_	_
673	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
674	OSU12-hisD	osu12-hisd	NN	_	_	_
675	,	,	,	_	_	_
676	histidine	histidine	NN	_	_	_
677	depleted	deplete	VBN	_	_	_
678	,	,	,	_	_	_
679	10	10	CD	_	_	_
680	min	min	NN	_	_	_
681	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
682	OSU12-hisD	osu12-hisd	NN	_	_	_
683	,	,	,	_	_	_
684	histidine	histidine	NN	_	_	_
685	depleted	deplete	VBN	_	_	_
686	,	,	,	_	_	_
687	10	10	CD	_	_	_
688	min	min	NN	_	_	_
689	,	,	,	_	_	_
690	rep	rep	NN	GEN	_	_
691	1	1	CD	_	_	_
692	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
693	OSU12-hisD	osu12-hisd	NN	_	_	_
694	,	,	,	_	_	_
695	histidine	histidine	NN	_	_	_
696	depleted	deplete	VBN	_	_	_
697	,	,	,	_	_	_
698	10	10	CD	_	_	_
699	min	min	NN	_	_	_
700	,	,	,	_	_	_
701	rep	rep	NN	GEN	_	_
702	2	2	CD	_	_	_
703	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
704	OSU12-hisD	osu12-hisd	NN	_	_	_
705	,	,	,	_	_	_
706	histidine	histidine	NN	_	_	_
707	depleted	deplete	VBN	_	_	_
708	,	,	,	_	_	_
709	10	10	CD	_	_	_
710	min	min	NN	_	_	_
711	,	,	,	_	_	_
712	rep	rep	NN	GEN	_	_
713	3	3	CD	_	_	_
714	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
715	OSU12-hisD	osu12-hisd	NN	_	_	_
716	,	,	,	_	_	_
717	histidine	histidine	NN	_	_	_
718	depleted	deplete	VBN	_	_	_
719	,	,	,	_	_	_
720	2	2	CD	_	_	_
721	hrs	hr	NNS	_	_	_
722	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
723	OSU12-hisD	osu12-hisd	NN	_	_	_
724	,	,	,	_	_	_
725	histidine	histidine	NN	_	_	_
726	depleted	deplete	VBN	_	_	_
727	,	,	,	_	_	_
728	2	2	CD	_	_	_
729	hrs	hr	NNS	_	_	_
730	,	,	,	_	_	_
731	rep	rep	NN	GEN	_	_
732	1	1	CD	_	_	_
733	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
734	OSU12-hisD	osu12-hisd	NN	_	_	_
735	,	,	,	_	_	_
736	histidine	histidine	NN	_	_	_
737	depleted	deplete	VBN	_	_	_
738	,	,	,	_	_	_
739	2	2	CD	_	_	_
740	hrs	hr	NNS	_	_	_
741	,	,	,	_	_	_
742	rep	rep	NN	GEN	_	_
743	2	2	CD	_	_	_
744	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
745	OSU12-hisD	osu12-hisd	NN	_	_	_
746	,	,	,	_	_	_
747	histidine	histidine	NN	_	_	_
748	depleted	deplete	VBN	_	_	_
749	,	,	,	_	_	_
750	2	2	CD	_	_	_
751	hrs	hr	NNS	_	_	_
752	,	,	,	_	_	_
753	rep	rep	NN	GEN	_	_
754	3	3	CD	_	_	_
755	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
756	OSU12-hisD	osu12-hisd	NN	_	_	_
757	,	,	,	_	_	_
758	histidine	histidine	NN	_	_	_
759	supplied	supply	VBD	_	_	_
760	,	,	,	_	_	_
761	1	1	CD	_	_	_
762	mM	mm	NN	KWSUPP	_	_
763	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
764	OSU12-hisD	osu12-hisd	NN	_	_	_
765	,	,	,	_	_	_
766	histidine	histidine	NN	_	_	_
767	supplied	supply	VBD	_	_	_
768	,	,	,	_	_	_
769	1	1	CD	_	_	_
770	mM	mm	NN	KWSUPP	_	_
771	,	,	,	_	_	_
772	rep	rep	NN	GEN	_	_
773	1	1	CD	_	_	_
774	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
775	OSU12-hisD	osu12-hisd	NN	_	_	_
776	,	,	,	_	_	_
777	histidine	histidine	NN	_	_	_
778	supplied	supply	VBD	_	_	_
779	,	,	,	_	_	_
780	1	1	CD	_	_	_
781	mM	mm	NN	KWSUPP	_	_
782	,	,	,	_	_	_
783	rep	rep	NN	GEN	_	_
784	2	2	CD	_	_	_
785	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
786	OSU12-hisD	osu12-hisd	NN	_	_	_
787	,	,	,	_	_	_
788	histidine	histidine	NN	_	_	_
789	supplied	supply	VBD	_	_	_
790	,	,	,	_	_	_
791	1	1	CD	_	_	_
792	mM	mm	NN	KWSUPP	_	_
793	,	,	,	_	_	_
794	rep	rep	NN	GEN	_	_
795	3	3	CD	_	_	_
796	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
797	OSU12-hisF	osu12-hisf	NN	_	_	_
798	,	,	,	_	_	_
799	histidine	histidine	NN	_	_	_
800	depleted	deplete	VBN	_	_	_
801	,	,	,	_	_	_
802	>	>	JJR	_	_	_
803	10	10	CD	_	_	_
804	hrs	hr	NNS	_	_	_
805	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
806	OSU12-hisF	osu12-hisf	NN	_	_	_
807	,	,	,	_	_	_
808	histidine	histidine	NN	_	_	_
809	depleted	deplete	VBN	_	_	_
810	,	,	,	_	_	_
811	>	>	JJR	_	_	_
812	10	10	CD	_	_	_
813	hrs	hr	NNS	_	_	_
814	,	,	,	_	_	_
815	rep	rep	NN	GEN	_	_
816	1	1	CD	_	_	_
817	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
818	OSU12-hisF	osu12-hisf	NN	_	_	_
819	,	,	,	_	_	_
820	histidine	histidine	NN	_	_	_
821	depleted	deplete	VBN	_	_	_
822	,	,	,	_	_	_
823	>	>	JJR	_	_	_
824	10	10	CD	_	_	_
825	hrs	hr	NNS	_	_	_
826	,	,	,	_	_	_
827	rep	rep	NN	GEN	_	_
828	2	2	CD	_	_	_
829	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
830	OSU12-hisF	osu12-hisf	NN	_	_	_
831	,	,	,	_	_	_
832	histidine	histidine	NN	_	_	_
833	depleted	deplete	VBN	_	_	_
834	,	,	,	_	_	_
835	>	>	JJR	_	_	_
836	10	10	CD	_	_	_
837	hrs	hr	NNS	_	_	_
838	,	,	,	_	_	_
839	rep	rep	NN	GEN	_	_
840	3	3	CD	_	_	_
841	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
842	OSU12-hisF	osu12-hisf	NN	_	_	_
843	,	,	,	_	_	_
844	histidine	histidine	NN	_	_	_
845	depleted	deplete	VBN	_	_	_
846	,	,	,	_	_	_
847	10	10	CD	_	_	_
848	min	min	NN	_	_	_
849	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
850	OSU12-hisF	osu12-hisf	NN	_	_	_
851	,	,	,	_	_	_
852	histidine	histidine	NN	_	_	_
853	depleted	deplete	VBN	_	_	_
854	,	,	,	_	_	_
855	10	10	CD	_	_	_
856	min	min	NN	_	_	_
857	,	,	,	_	_	_
858	rep	rep	NN	GEN	_	_
859	1	1	CD	_	_	_
860	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
861	OSU12-hisF	osu12-hisf	NN	_	_	_
862	,	,	,	_	_	_
863	histidine	histidine	NN	_	_	_
864	depleted	deplete	VBN	_	_	_
865	,	,	,	_	_	_
866	10	10	CD	_	_	_
867	min	min	NN	_	_	_
868	,	,	,	_	_	_
869	rep	rep	NN	GEN	_	_
870	2	2	CD	_	_	_
871	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
872	OSU12-hisF	osu12-hisf	NN	_	_	_
873	,	,	,	_	_	_
874	histidine	histidine	NN	_	_	_
875	depleted	deplete	VBN	_	_	_
876	,	,	,	_	_	_
877	10	10	CD	_	_	_
878	min	min	NN	_	_	_
879	,	,	,	_	_	_
880	rep	rep	NN	GEN	_	_
881	3	3	CD	_	_	_
882	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
883	OSU12-hisF	osu12-hisf	NN	_	_	_
884	,	,	,	_	_	_
885	histidine	histidine	NN	_	_	_
886	depleted	deplete	VBN	_	_	_
887	,	,	,	_	_	_
888	2	2	CD	_	_	_
889	hrs	hr	NNS	_	_	_
890	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
891	OSU12-hisF	osu12-hisf	NN	_	_	_
892	,	,	,	_	_	_
893	histidine	histidine	NN	_	_	_
894	depleted	deplete	VBN	_	_	_
895	,	,	,	_	_	_
896	2	2	CD	_	_	_
897	hrs	hr	NNS	_	_	_
898	,	,	,	_	_	_
899	rep	rep	NN	GEN	_	_
900	1	1	CD	_	_	_
901	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
902	OSU12-hisF	osu12-hisf	NN	_	_	_
903	,	,	,	_	_	_
904	histidine	histidine	NN	_	_	_
905	depleted	deplete	VBN	_	_	_
906	,	,	,	_	_	_
907	2	2	CD	_	_	_
908	hrs	hr	NNS	_	_	_
909	,	,	,	_	_	_
910	rep	rep	NN	GEN	_	_
911	2	2	CD	_	_	_
912	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
913	OSU12-hisF	osu12-hisf	NN	_	_	_
914	,	,	,	_	_	_
915	histidine	histidine	NN	_	_	_
916	depleted	deplete	VBN	_	_	_
917	,	,	,	_	_	_
918	2	2	CD	_	_	_
919	hrs	hr	NNS	_	_	_
920	,	,	,	_	_	_
921	rep	rep	NN	GEN	_	_
922	3	3	CD	_	_	_
923	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
924	OSU12-hisF	osu12-hisf	NN	_	_	_
925	,	,	,	_	_	_
926	histidine	histidine	NN	_	_	_
927	supplied	supply	VBD	_	_	_
928	,	,	,	_	_	_
929	1	1	CD	_	_	_
930	mM	mm	NN	KWSUPP	_	_
931	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
932	OSU12-hisF	osu12-hisf	NN	_	_	_
933	,	,	,	_	_	_
934	histidine	histidine	NN	_	_	_
935	supplied	supply	VBD	_	_	_
936	,	,	,	_	_	_
937	1	1	CD	_	_	_
938	mM	mm	NN	KWSUPP	_	_
939	,	,	,	_	_	_
940	rep	rep	NN	GEN	_	_
941	1	1	CD	_	_	_
942	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
943	OSU12-hisF	osu12-hisf	NN	_	_	_
944	,	,	,	_	_	_
945	histidine	histidine	NN	_	_	_
946	supplied	supply	VBD	_	_	_
947	,	,	,	_	_	_
948	1	1	CD	_	_	_
949	mM	mm	NN	KWSUPP	_	_
950	,	,	,	_	_	_
951	rep	rep	NN	GEN	_	_
952	2	2	CD	_	_	_
953	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
954	OSU12-hisF	osu12-hisf	NN	_	_	_
955	,	,	,	_	_	_
956	histidine	histidine	NN	_	_	_
957	supplied	supply	VBD	_	_	_
958	,	,	,	_	_	_
959	1	1	CD	_	_	_
960	mM	mm	NN	KWSUPP	_	_
961	,	,	,	_	_	_
962	rep	rep	NN	GEN	_	_
963	3	3	CD	_	_	_
964	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
965	OSU12-hisG	osu12-hisg	NN	_	_	_
966	,	,	,	_	_	_
967	histidine	histidine	NN	_	_	_
968	depleted	deplete	VBN	_	_	_
969	,	,	,	_	_	_
970	10	10	CD	_	_	_
971	min	min	NN	_	_	_
972	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
973	OSU12-hisG	osu12-hisg	NN	_	_	_
974	,	,	,	_	_	_
975	histidine	histidine	NN	_	_	_
976	depleted	deplete	VBN	_	_	_
977	,	,	,	_	_	_
978	10	10	CD	_	_	_
979	min	min	NN	_	_	_
980	,	,	,	_	_	_
981	rep	rep	NN	GEN	_	_
982	1	1	CD	_	_	_
983	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
984	OSU12-hisG	osu12-hisg	NN	_	_	_
985	,	,	,	_	_	_
986	histidine	histidine	NN	_	_	_
987	depleted	deplete	VBN	_	_	_
988	,	,	,	_	_	_
989	10	10	CD	_	_	_
990	min	min	NN	_	_	_
991	,	,	,	_	_	_
992	rep	rep	NN	GEN	_	_
993	2	2	CD	_	_	_
994	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
995	OSU12-hisG	osu12-hisg	NN	_	_	_
996	,	,	,	_	_	_
997	histidine	histidine	NN	_	_	_
998	depleted	deplete	VBN	_	_	_
999	,	,	,	_	_	_
1000	10	10	CD	_	_	_
1001	min	min	NN	_	_	_
1002	,	,	,	_	_	_
1003	rep	rep	NN	GEN	_	_
1004	3	3	CD	_	_	_
1005	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1006	OSU12-hisG	osu12-hisg	NN	_	_	_
1007	,	,	,	_	_	_
1008	histidine	histidine	NN	_	_	_
1009	depleted	deplete	VBN	_	_	_
1010	,	,	,	_	_	_
1011	2	2	CD	_	_	_
1012	hrs	hr	NNS	_	_	_
1013	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1014	OSU12-hisG	osu12-hisg	NN	_	_	_
1015	,	,	,	_	_	_
1016	histidine	histidine	NN	_	_	_
1017	depleted	deplete	VBN	_	_	_
1018	,	,	,	_	_	_
1019	2	2	CD	_	_	_
1020	hrs	hr	NNS	_	_	_
1021	,	,	,	_	_	_
1022	rep	rep	NN	GEN	_	_
1023	1	1	CD	_	_	_
1024	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1025	OSU12-hisG	osu12-hisg	NN	_	_	_
1026	,	,	,	_	_	_
1027	histidine	histidine	NN	_	_	_
1028	depleted	deplete	VBN	_	_	_
1029	,	,	,	_	_	_
1030	2	2	CD	_	_	_
1031	hrs	hr	NNS	_	_	_
1032	,	,	,	_	_	_
1033	rep	rep	NN	GEN	_	_
1034	2	2	CD	_	_	_
1035	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1036	OSU12-hisG	osu12-hisg	NN	_	_	_
1037	,	,	,	_	_	_
1038	histidine	histidine	NN	_	_	_
1039	depleted	deplete	VBN	_	_	_
1040	,	,	,	_	_	_
1041	2	2	CD	_	_	_
1042	hrs	hr	NNS	_	_	_
1043	,	,	,	_	_	_
1044	rep	rep	NN	GEN	_	_
1045	3	3	CD	_	_	_
1046	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1047	OSU12-hisG	osu12-hisg	NN	_	_	_
1048	,	,	,	_	_	_
1049	histidine	histidine	NN	_	_	_
1050	supplied	supply	VBD	_	_	_
1051	,	,	,	_	_	_
1052	1	1	CD	_	_	_
1053	mM	mm	NN	KWSUPP	_	_
1054	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1055	OSU12-hisG	osu12-hisg	NN	_	_	_
1056	,	,	,	_	_	_
1057	histidine	histidine	NN	_	_	_
1058	supplied	supply	VBD	_	_	_
1059	,	,	,	_	_	_
1060	1	1	CD	_	_	_
1061	mM	mm	NN	KWSUPP	_	_
1062	,	,	,	_	_	_
1063	rep	rep	NN	GEN	_	_
1064	1	1	CD	_	_	_
1065	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1066	OSU12-hisG	osu12-hisg	NN	_	_	_
1067	,	,	,	_	_	_
1068	histidine	histidine	NN	_	_	_
1069	supplied	supply	VBD	_	_	_
1070	,	,	,	_	_	_
1071	1	1	CD	_	_	_
1072	mM	mm	NN	KWSUPP	_	_
1073	,	,	,	_	_	_
1074	rep	rep	NN	GEN	_	_
1075	2	2	CD	_	_	_
1076	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1077	OSU12-hisG	osu12-hisg	NN	_	_	_
1078	,	,	,	_	_	_
1079	histidine	histidine	NN	_	_	_
1080	supplied	supply	VBD	_	_	_
1081	,	,	,	_	_	_
1082	1	1	CD	_	_	_
1083	mM	mm	NN	KWSUPP	_	_
1084	,	,	,	_	_	_
1085	rep	rep	NN	GEN	_	_
1086	3	3	CD	_	_	_
1087	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1088	OSU12-hisI	osu12-hisi	NN	_	_	_
1089	,	,	,	_	_	_
1090	histidine	histidine	NN	_	_	_
1091	depleted	deplete	VBN	_	_	_
1092	,	,	,	_	_	_
1093	>	>	JJR	_	_	_
1094	10	10	CD	_	_	_
1095	hrs	hr	NNS	_	_	_
1096	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1097	OSU12-hisI	osu12-hisi	NN	_	_	_
1098	,	,	,	_	_	_
1099	histidine	histidine	NN	_	_	_
1100	depleted	deplete	VBN	_	_	_
1101	,	,	,	_	_	_
1102	>	>	JJR	_	_	_
1103	10	10	CD	_	_	_
1104	hrs	hr	NNS	_	_	_
1105	,	,	,	_	_	_
1106	rep	rep	NN	GEN	_	_
1107	1	1	CD	_	_	_
1108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1109	OSU12-hisI	osu12-hisi	NN	_	_	_
1110	,	,	,	_	_	_
1111	histidine	histidine	NN	_	_	_
1112	depleted	deplete	VBN	_	_	_
1113	,	,	,	_	_	_
1114	>	>	JJR	_	_	_
1115	10	10	CD	_	_	_
1116	hrs	hr	NNS	_	_	_
1117	,	,	,	_	_	_
1118	rep	rep	NN	GEN	_	_
1119	2	2	CD	_	_	_
1120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1121	OSU12-hisI	osu12-hisi	NN	_	_	_
1122	,	,	,	_	_	_
1123	histidine	histidine	NN	_	_	_
1124	depleted	deplete	VBN	_	_	_
1125	,	,	,	_	_	_
1126	>	>	JJR	_	_	_
1127	10	10	CD	_	_	_
1128	hrs	hr	NNS	_	_	_
1129	,	,	,	_	_	_
1130	rep	rep	NN	GEN	_	_
1131	3	3	CD	_	_	_
1132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1133	OSU12-hisI	osu12-hisi	NN	_	_	_
1134	,	,	,	_	_	_
1135	histidine	histidine	NN	_	_	_
1136	depleted	deplete	VBN	_	_	_
1137	,	,	,	_	_	_
1138	10	10	CD	_	_	_
1139	min	min	NN	_	_	_
1140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1141	OSU12-hisI	osu12-hisi	NN	_	_	_
1142	,	,	,	_	_	_
1143	histidine	histidine	NN	_	_	_
1144	depleted	deplete	VBN	_	_	_
1145	,	,	,	_	_	_
1146	10	10	CD	_	_	_
1147	min	min	NN	_	_	_
1148	,	,	,	_	_	_
1149	rep	rep	NN	GEN	_	_
1150	1	1	CD	_	_	_
1151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1152	OSU12-hisI	osu12-hisi	NN	_	_	_
1153	,	,	,	_	_	_
1154	histidine	histidine	NN	_	_	_
1155	depleted	deplete	VBN	_	_	_
1156	,	,	,	_	_	_
1157	10	10	CD	_	_	_
1158	min	min	NN	_	_	_
1159	,	,	,	_	_	_
1160	rep	rep	NN	GEN	_	_
1161	2	2	CD	_	_	_
1162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1163	OSU12-hisI	osu12-hisi	NN	_	_	_
1164	,	,	,	_	_	_
1165	histidine	histidine	NN	_	_	_
1166	depleted	deplete	VBN	_	_	_
1167	,	,	,	_	_	_
1168	10	10	CD	_	_	_
1169	min	min	NN	_	_	_
1170	,	,	,	_	_	_
1171	rep	rep	NN	GEN	_	_
1172	3	3	CD	_	_	_
1173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1174	OSU12-hisI	osu12-hisi	NN	_	_	_
1175	,	,	,	_	_	_
1176	histidine	histidine	NN	_	_	_
1177	depleted	deplete	VBN	_	_	_
1178	,	,	,	_	_	_
1179	2	2	CD	_	_	_
1180	hrs	hr	NNS	_	_	_
1181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1182	OSU12-hisI	osu12-hisi	NN	_	_	_
1183	,	,	,	_	_	_
1184	histidine	histidine	NN	_	_	_
1185	depleted	deplete	VBN	_	_	_
1186	,	,	,	_	_	_
1187	2	2	CD	_	_	_
1188	hrs	hr	NNS	_	_	_
1189	,	,	,	_	_	_
1190	rep	rep	NN	GEN	_	_
1191	1	1	CD	_	_	_
1192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1193	OSU12-hisI	osu12-hisi	NN	_	_	_
1194	,	,	,	_	_	_
1195	histidine	histidine	NN	_	_	_
1196	depleted	deplete	VBN	_	_	_
1197	,	,	,	_	_	_
1198	2	2	CD	_	_	_
1199	hrs	hr	NNS	_	_	_
1200	,	,	,	_	_	_
1201	rep	rep	NN	GEN	_	_
1202	2	2	CD	_	_	_
1203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1204	OSU12-hisI	osu12-hisi	NN	_	_	_
1205	,	,	,	_	_	_
1206	histidine	histidine	NN	_	_	_
1207	depleted	deplete	VBN	_	_	_
1208	,	,	,	_	_	_
1209	2	2	CD	_	_	_
1210	hrs	hr	NNS	_	_	_
1211	,	,	,	_	_	_
1212	rep	rep	NN	GEN	_	_
1213	3	3	CD	_	_	_
1214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1215	OSU12-hisI	osu12-hisi	NN	_	_	_
1216	,	,	,	_	_	_
1217	histidine	histidine	NN	_	_	_
1218	supplied	supply	VBD	_	_	_
1219	,	,	,	_	_	_
1220	1	1	CD	_	_	_
1221	mM	mm	NN	KWSUPP	_	_
1222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1223	OSU12-hisI	osu12-hisi	NN	_	_	_
1224	,	,	,	_	_	_
1225	histidine	histidine	NN	_	_	_
1226	supplied	supply	VBD	_	_	_
1227	,	,	,	_	_	_
1228	1	1	CD	_	_	_
1229	mM	mm	NN	KWSUPP	_	_
1230	,	,	,	_	_	_
1231	rep	rep	NN	GEN	_	_
1232	1	1	CD	_	_	_
1233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1234	OSU12-hisI	osu12-hisi	NN	_	_	_
1235	,	,	,	_	_	_
1236	histidine	histidine	NN	_	_	_
1237	supplied	supply	VBD	_	_	_
1238	,	,	,	_	_	_
1239	1	1	CD	_	_	_
1240	mM	mm	NN	KWSUPP	_	_
1241	,	,	,	_	_	_
1242	rep	rep	NN	GEN	_	_
1243	2	2	CD	_	_	_
1244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1245	OSU12-hisI	osu12-hisi	NN	_	_	_
1246	,	,	,	_	_	_
1247	histidine	histidine	NN	_	_	_
1248	supplied	supply	VBD	_	_	_
1249	,	,	,	_	_	_
1250	1	1	CD	_	_	_
1251	mM	mm	NN	KWSUPP	_	_
1252	,	,	,	_	_	_
1253	rep	rep	NN	GEN	_	_
1254	3	3	CD	_	_	_
1255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1256	strain	strain	NN	_	_	_
1257	:	:	:	_	_	_
1258	DH1	dh1	NN	_	_	_
1259	ΔhisA	δhisa	NN	_	_	_
1260	:	:	:	_	_	_
1261	:	:	:	_	_	_
1262	cat	cat	NN	_	_	_
1263	ΔintC	δintc	NN	_	_	_
1264	:	:	:	_	_	_
1265	:	:	:	_	_	_
1266	Ptrc-dsred	ptrc-dsred	JJ	_	_	_
1267	.	.	.	_	_	_

1	t4-tetR-PEM7-zeo	t4-tetr-pem7-zeo	NN	_	_	_
2	ΔgalK	δgalk	NN	_	_	_
3	:	:	:	_	_	_
4	:	:	:	_	_	_
5	PtetA-gfpuv5	pteta-gfpuv5	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	strain	strain	NN	_	_	_
8	:	:	:	_	_	_
9	DH1	dh1	NN	_	_	_
10	ΔhisB	δhisb	NN	_	_	_
11	:	:	:	_	_	_
12	:	:	:	_	_	_
13	cat	cat	NN	_	_	_
14	ΔintC	δintc	NN	_	_	_
15	:	:	:	_	_	_
16	:	:	:	_	_	_
17	Ptrc-dsred	ptrc-dsred	JJ	_	_	_
18	.	.	.	_	_	_

1	t4-tetR-PEM7-zeo	t4-tetr-pem7-zeo	NN	_	_	_
2	ΔgalK	δgalk	NN	_	_	_
3	:	:	:	_	_	_
4	:	:	:	_	_	_
5	PtetA-gfpuv5	pteta-gfpuv5	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	strain	strain	NN	_	_	_
8	:	:	:	_	_	_
9	DH1	dh1	NN	_	_	_
10	ΔhisC	δhisc	NN	_	_	_
11	:	:	:	_	_	_
12	:	:	:	_	_	_
13	cat	cat	NN	_	_	_
14	ΔintC	δintc	NN	_	_	_
15	:	:	:	_	_	_
16	:	:	:	_	_	_
17	Ptrc-dsred	ptrc-dsred	JJ	_	_	_
18	.	.	.	_	_	_

1	t4-tetR-PEM7-zeo	t4-tetr-pem7-zeo	NN	_	_	_
2	ΔgalK	δgalk	NN	_	_	_
3	:	:	:	_	_	_
4	:	:	:	_	_	_
5	PtetA-gfpuv5	pteta-gfpuv5	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	strain	strain	NN	_	_	_
8	:	:	:	_	_	_
9	DH1	dh1	NN	_	_	_
10	ΔhisD	δhisd	NN	_	_	_
11	:	:	:	_	_	_
12	:	:	:	_	_	_
13	cat	cat	NN	_	_	_
14	ΔintC	δintc	NN	_	_	_
15	:	:	:	_	_	_
16	:	:	:	_	_	_
17	Ptrc-dsred	ptrc-dsred	JJ	_	_	_
18	.	.	.	_	_	_

1	t4-tetR-PEM7-zeo	t4-tetr-pem7-zeo	NN	_	_	_
2	ΔgalK	δgalk	NN	_	_	_
3	:	:	:	_	_	_
4	:	:	:	_	_	_
5	PtetA-gfpuv5	pteta-gfpuv5	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	strain	strain	NN	_	_	_
8	:	:	:	_	_	_
9	DH1	dh1	NN	_	_	_
10	ΔhisF	δhisf	NN	_	_	_
11	:	:	:	_	_	_
12	:	:	:	_	_	_
13	cat	cat	NN	_	_	_
14	ΔintC	δintc	NN	_	_	_
15	:	:	:	_	_	_
16	:	:	:	_	_	_
17	Ptrc-dsred	ptrc-dsred	JJ	_	_	_
18	.	.	.	_	_	_

1	t4-tetR-PEM7-zeo	t4-tetr-pem7-zeo	NN	_	_	_
2	ΔgalK	δgalk	NN	_	_	_
3	:	:	:	_	_	_
4	:	:	:	_	_	_
5	PtetA-gfpuv5	pteta-gfpuv5	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	strain	strain	NN	_	_	_
8	:	:	:	_	_	_
9	DH1	dh1	NN	_	_	_
10	ΔhisG	δhisg	NN	_	_	_
11	:	:	:	_	_	_
12	:	:	:	_	_	_
13	cat	cat	NN	_	_	_
14	ΔintC	δintc	NN	_	_	_
15	:	:	:	_	_	_
16	:	:	:	_	_	_
17	Ptrc-dsred	ptrc-dsred	JJ	_	_	_
18	.	.	.	_	_	_

1	t4-tetR-PEM7-zeo	t4-tetr-pem7-zeo	NN	_	_	_
2	ΔgalK	δgalk	NN	_	_	_
3	:	:	:	_	_	_
4	:	:	:	_	_	_
5	PtetA-gfpuv5	pteta-gfpuv5	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	strain	strain	NN	_	_	_
8	:	:	:	_	_	_
9	DH1	dh1	NN	_	_	_
10	ΔhisI	δhisi	NN	_	_	_
11	:	:	:	_	_	_
12	:	:	:	_	_	_
13	cat	cat	NN	_	_	_
14	ΔintC	δintc	NN	_	_	_
15	:	:	:	_	_	_
16	:	:	:	_	_	_
17	Ptrc-dsred	ptrc-dsred	JJ	_	_	_
18	.	.	.	_	_	_

1	t4-tetR-PEM7-zeo	t4-tetr-pem7-zeo	NN	_	_	_
2	ΔgalK	δgalk	NN	_	_	_
3	:	:	:	_	_	_
4	:	:	:	_	_	_
5	PtetA-gfpuv5	pteta-gfpuv5	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	strain	strain	NN	_	_	_
8	:	:	:	_	_	_
9	DH1	dh1	NN	_	_	_
10	ΔintC	δintc	NN	_	_	_
11	:	:	:	_	_	_
12	:	:	:	_	_	_
13	Ptrc-dsred	ptrc-dsred	JJ	_	_	_
14	.	.	.	_	_	_

1	t4-tetR-PEM7-zeo	t4-tetr-pem7-zeo	NN	_	_	_
2	ΔgalK	δgalk	NN	_	_	_
3	:	:	:	_	_	_
4	:	:	:	_	_	_
5	PtetA-gfpuv5	pteta-gfpuv5	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	The	the	DT	_	_	_
8	cell	cell	NN	_	_	_
9	culture	culture	NN	_	_	_
10	was	be	VBD	_	_	_
11	put	put	VBN	_	_	_
12	into	into	IN	_	_	_
13	cold	cold	JJ	_	_	_
14	phenol-ethanol	phenol-ethanol	JJ	_	_	_
15	solution	solution	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	1	1	CD	_	_	_
18	g	g	NN	_	_	_
19	of	of	IN	_	_	_
20	phenol	phenol	NN	_	_	_
21	in	in	IN	_	_	_
22	10	10	CD	_	_	_
23	mL	ml	NN	_	_	_
24	of	of	IN	_	_	_
25	ethanol	ethanol	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	prepared	prepare	VBN	_	_	_
28	in	in	IN	_	_	_
29	advance	advance	NN	_	_	_
30	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	collected	collect	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	at	at	IN	_	_	_
8	16,000	16,000	CD	_	_	_
9	×	×	CD	_	_	_
10	g	g	NN	_	_	_
11	for	for	IN	_	_	_
12	5	5	CD	_	_	_
13	min	min	NN	_	_	_
14	at	at	IN	_	_	_
15	4	4	CD	_	_	_
16	°C	°c	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	the	the	DT	_	_	_
20	pelleted	pelleted	JJ	_	_	_
21	cells	cell	NNS	_	_	_
22	were	be	VBD	_	_	_
23	stored	store	VBN	_	_	_
24	at	at	IN	_	_	_
25	--	--	:	_	_	_
26	80	80	CD	_	_	_
27	°C	°c	NN	_	_	_
28	prior	prior	RB	_	_	_
29	to	to	TO	_	_	_
30	use	use	VB	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNAs	rna	NNS	_	_	_
4	were	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	an	a	DT	_	_	_
8	RNeasy	rneasy	NN	_	_	_
9	mini	minus	NNS	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	qiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	in	in	IN	_	_	_
15	accordance	accordance	NN	_	_	_
16	with	with	IN	_	_	_
17	the	the	DT	_	_	_
18	manufacturer	manufacturer	NN	_	_	_
19	's	's	POS	_	_	_
20	instructions	instruction	NNS	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	After	after	IN	_	_	_
3	5	5	CD	_	_	_
4	h	h	NN	_	_	_
5	of	of	IN	_	_	_
6	NP-TiO2	np-tio2	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	or	or	CC	_	_	_
9	mQ	mq	NN	_	_	_
10	water	water	NN	_	_	_
11	for	for	IN	_	_	_
12	the	the	DT	_	_	_
13	control	control	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	exposure	exposure	NN	_	_	_
16	,	,	,	_	_	_
17	cells	cell	NNS	_	_	_
18	were	be	VBD	_	_	_
19	incubated	incubate	VBN	_	_	_
20	for	for	IN	_	_	_
21	5	5	CD	_	_	_
22	min	min	NN	_	_	_
23	with	with	IN	_	_	_
24	two	two	CD	_	_	_
25	volumes	volume	NNS	_	_	_
26	of	of	IN	_	_	_
27	RNAprotect	rnaprotect	NN	_	_	_
28	Bacteria	bacterium	NNS	_	_	_
29	Reagent	reagent	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Qiagen	Qiagen	NNP	_	_	_
32	SAS	SAS	NNP	_	_	_
33	,	,	,	_	_	_
34	France	France	NNP	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	at	at	IN	_	_	_
37	room	room	NN	_	_	_
38	temperature	temperature	NN	_	_	_
39	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	pelleted	pellete	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	7,000	7,000	CD	_	_	_
9	g	g	NN	_	_	_
10	,	,	,	_	_	_
11	10	10	CD	_	_	_
12	min	min	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	and	and	CC	_	_	_
15	the	the	DT	_	_	_
16	pellet	pellet	NN	_	_	_
17	stored	store	VBD	_	_	_
18	at	at	IN	_	_	_
19	-80	-80	CD	_	_	_
20	°C	°c	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cell	cell	NN	_	_	_
3	exposure	exposure	NN	_	_	_
4	to	to	TO	_	_	_
5	NP-TiO2	np-tio2	NN	_	_	_
6	was	be	VBD	_	_	_
7	conducted	conduct	VBN	_	_	_
8	in	in	IN	_	_	_
9	50	50	CD	_	_	_
10	ml	ml	NN	_	_	_
11	of	of	IN	_	_	_
12	sterile	sterile	JJ	_	_	_
13	Milli-Q	milli-q	JJ	_	_	_
14	water	water	NN	_	_	_
15	supplemented	supplement	VBN	_	_	_
16	with	with	IN	_	_	_
17	10	10	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	NaCl	nacl	NN	_	_	_
20	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	500	500	CD	_	_	_
4	µl	µl	NN	_	_	_
5	of	of	IN	_	_	_
6	the	the	DT	_	_	_
7	E.	e.	FW	_	_	_
8	coli	coli	FW	_	_	_
9	bacterial	bacterial	JJ	_	_	_
10	suspension	suspension	NN	_	_	_
11	and	and	CC	_	_	_
12	500	500	CD	_	_	_
13	µl	µl	NN	_	_	_
14	of	of	IN	_	_	_
15	the	the	DT	_	_	_
16	NP-TiO2	np-tio2	NN	_	_	_
17	stock	stock	NN	_	_	_
18	suspension	suspension	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	or	or	CC	_	_	_
21	mQ	mq	NN	_	_	_
22	water	water	NN	_	_	_
23	for	for	IN	_	_	_
24	the	the	DT	_	_	_
25	control	control	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	were	be	VBD	_	_	_
28	prepared	prepare	VBN	_	_	_
29	as	as	IN	_	_	_
30	previously	previously	RB	_	_	_
31	described	describe	VBN	_	_	_
32	and	and	CC	_	_	_
33	then	then	RB	_	_	_
34	added	add	VBD	_	_	_
35	to	to	TO	_	_	_
36	the	the	DT	_	_	_
37	NaCl	nacl	NN	_	_	_
38	solution	solution	NN	_	_	_
39	to	to	TO	_	_	_
40	obtain	obtain	VB	_	_	_
41	final	final	JJ	_	_	_
42	concentrations	concentration	NNS	_	_	_
43	of	of	IN	_	_	_
44	10E7	10e7	NN	_	_	_
45	cells	cell	NNS	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
47	Ecoli	ecoli	JJ	_	_	_
48	_	_	NN	_	_	_
49	control	control	NN	_	_	_
50	_	_	CD	_	_	_
51	5h	5h	NN	_	_	_
52	_	_	CD	_	_	_
53	rep1	rep1	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
55	Ecoli	ecoli	JJ	_	_	_
56	_	_	NN	_	_	_
57	control	control	NN	_	_	_
58	_	_	CD	_	_	_
59	5h	5h	NN	_	_	_
60	_	_	CD	_	_	_
61	rep2	rep2	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
63	Ecoli	ecoli	JJ	_	_	_
64	_	_	NN	_	_	_
65	control	control	NN	_	_	_
66	_	_	CD	_	_	_
67	5h	5h	NN	_	_	_
68	_	_	CD	_	_	_
69	rep3	rep3	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
71	Ecoli	ecoli	JJ	_	_	_
72	_	_	NN	_	_	_
73	control	control	NN	_	_	_
74	_	_	CD	_	_	_
75	5h	5h	JJ	_	_	_
76	_	_	NN	_	_	_
77	rep4	rep4	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	E.coli	e.coli	NNS	_	_	_
80	,	,	,	_	_	_
81	control	control	JJ	_	_	_
82	culture	culture	NN	_	_	_
83	,	,	,	_	_	_
84	5h	5h	NN	_	_	_
85	in	in	IN	_	_	_
86	10	10	CD	_	_	_
87	mM	mm	NN	KWSUPP	_	_
88	NaCl	nacl	NN	_	_	_
89	,	,	,	_	_	_
90	replicate	replicate	VB	_	_	_
91	1	1	CD	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	E.coli	e.coli	NNS	_	_	_
94	,	,	,	_	_	_
95	control	control	JJ	_	_	_
96	culture	culture	NN	_	_	_
97	,	,	,	_	_	_
98	5h	5h	NN	_	_	_
99	in	in	IN	_	_	_
100	10	10	CD	_	_	_
101	mM	mm	NN	KWSUPP	_	_
102	NaCl	nacl	NN	_	_	_
103	,	,	,	_	_	_
104	replicate	replicate	VB	_	_	_
105	2	2	CD	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
107	E.coli	e.coli	NNS	_	_	_
108	,	,	,	_	_	_
109	control	control	JJ	_	_	_
110	culture	culture	NN	_	_	_
111	,	,	,	_	_	_
112	5h	5h	NN	_	_	_
113	in	in	IN	_	_	_
114	10	10	CD	_	_	_
115	mM	mm	NN	KWSUPP	_	_
116	NaCl	nacl	NN	_	_	_
117	,	,	,	_	_	_
118	replicate	replicate	VB	_	_	_
119	3	3	CD	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	E.coli	e.coli	NNS	_	_	_
122	,	,	,	_	_	_
123	control	control	JJ	_	_	_
124	culture	culture	NN	_	_	_
125	,	,	,	_	_	_
126	5h	5h	NN	_	_	_
127	in	in	IN	_	_	_
128	10	10	CD	_	_	_
129	mM	mm	NN	KWSUPP	_	_
130	NaCl	nacl	NN	_	_	_
131	,	,	,	_	_	_
132	replicate	replicate	VB	_	_	_
133	4	4	CD	_	_	_
134	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
135	Ecoli	Ecoli	NNP	_	_	_
136	_	_	SYM	_	_	_
137	NP-TiO2	np-tio2	NN	_	_	_
138	_	_	CD	_	_	_
139	5h	5h	JJ	_	_	_
140	_	_	NN	_	_	_
141	rep1	rep1	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	Ecoli	ecolus	NNS	_	_	_
144	_	_	VBP	_	_	_
145	NP-TiO2	np-tio2	NN	_	_	_
146	_	_	CD	_	_	_
147	5h	5h	JJ	_	_	_
148	_	_	NN	_	_	_
149	rep2	rep2	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	Ecoli	ecolus	NNS	_	_	_
152	_	_	VBP	_	_	_
153	NP-TiO2	np-tio2	NN	_	_	_
154	_	_	CD	_	_	_
155	5h	5h	JJ	_	_	_
156	_	_	NN	_	_	_
157	rep3	rep3	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	Ecoli	ecolus	NNS	_	_	_
160	_	_	VBP	_	_	_
161	NP-TiO2	np-tio2	NN	_	_	_
162	_	_	CD	_	_	_
163	5h	5h	JJ	_	_	_
164	_	_	NN	_	_	_
165	rep4	rep4	NN	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	E.coli	e.coli	NNS	_	_	_
168	,	,	,	_	_	_
169	NP-TiO2	np-tio2	NN	_	_	_
170	exposed	expose	VBN	_	_	_
171	culture	culture	NN	_	_	_
172	,	,	,	_	_	_
173	5h	5h	NN	_	_	_
174	in	in	IN	_	_	_
175	10	10	CD	_	_	_
176	mM	mm	NN	KWSUPP	_	_
177	NaCl	nacl	NN	_	_	_
178	100	100	CD	_	_	_
179	mg	mg	NN	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	Escherichia	escherichia	FW	Organism	_	_
182	coli	coli	FW	Organism	_	_
183	str	str	FW	_	_	_
184	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Image	image	NN	_	_	_
4	analysis	analysis	NN	_	_	_
5	was	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	with	with	IN	_	_	_
8	GenePix	GenePix	NNP	_	_	_
9	Pro	pro	FW	_	_	_
10	7	7	CD	_	_	_
11	software	software	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Molecular	molecular	JJ	_	_	_
14	Device	device	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	,	,	,	_	_	_
17	background	background	NN	_	_	_
18	was	be	VBD	_	_	_
19	defined	define	VBN	_	_	_
20	with	with	IN	_	_	_
21	the	the	DT	_	_	_
22	``	``	``	_	_	_
23	Local	local	JJ	_	_	_
24	features	feature	NNS	_	_	_
25	background	background	NN	_	_	_
26	median	median	NN	_	_	_
27	''	''	''	_	_	_
28	method	method	NN	_	_	_
29	.	.	.	_	_	_

1	Quantile	quantile	JJ	_	_	_
2	normalization	normalization	NN	_	_	_
3	was	be	VBD	_	_	_
4	applied	apply	VBN	_	_	_
5	on	on	IN	_	_	_
6	the	the	DT	_	_	_
7	total	total	JJ	_	_	_
8	number	number	NN	_	_	_
9	of	of	IN	_	_	_
10	spots	spot	NNS	_	_	_
11	in	in	IN	_	_	_
12	R	r	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	version	version	NN	_	_	_
15	2.11.1	2.11.1	CD	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	with	with	IN	_	_	_
18	the	the	DT	_	_	_
19	LIMMA	LIMMA	NNP	_	_	_
20	software	software	NN	_	_	_
21	package	package	NN	_	_	_
22	.	.	.	_	_	_

1	Spots	spot	NNS	_	_	_
2	corresponding	correspond	VBG	_	_	_
3	to	to	TO	_	_	_
4	the	the	DT	_	_	_
5	E.	e.	FW	_	_	_
6	coli	coli	FW	_	_	_
7	MG1655	mg1655	NN	_	_	_
8	K12	k12	NN	_	_	_
9	species	species	NNS	_	_	_
10	were	be	VBD	_	_	_
11	extracted	extract	VBN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	incubation	incubation	NN	_	_	_
3	condition	condition	NN	_	_	_
4	:	:	:	_	_	_
5	In	in	IN	_	_	_
6	the	the	DT	_	_	_
7	dark	dark	NN	_	_	_
8	,	,	,	_	_	_
9	5h	5h	NN	_	_	_
10	,	,	,	_	_	_
11	20	20	CD	_	_	_
12	°C	°c	NN	_	_	_
13	,	,	,	_	_	_
14	150	150	CD	_	_	_
15	rpm	rpm	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	incubation	incubation	NN	_	_	_
18	medium	medium	NN	_	_	_
19	:	:	:	_	_	_
20	10	10	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	NaCl	nacl	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	incubation	incubation	NN	_	_	_
25	medium	medium	NN	_	_	_
26	:	:	:	_	_	_
27	10	10	CD	_	_	_
28	mM	mm	NN	KWSUPP	_	_
29	NaCl	nacl	NN	_	_	_
30	+	+	CC	_	_	_
31	100	100	CD	_	_	_
32	mg	mg	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Total	total	JJ	_	_	_
35	RNA	rna	NN	_	_	_
36	was	be	VBD	_	_	_
37	extracted	extract	VBN	_	_	_
38	from	from	IN	_	_	_
39	cells	cell	NNS	_	_	_
40	with	with	IN	_	_	_
41	the	the	DT	_	_	_
42	UltraClean	UltraClean	NNP	_	_	_
43	Microbial	Microbial	NNP	_	_	_
44	RNA	rna	NN	_	_	_
45	isolation	isolation	NN	_	_	_
46	kit	kit	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	MO	MO	NNP	_	_	_
49	BIO	BIO	NNP	_	_	_
50	,	,	,	_	_	_
51	CA	CA	NNP	_	_	_
52	,	,	,	_	_	_
53	USA	USA	NNP	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	extraction	extraction	NN	_	_	_
3	,	,	,	_	_	_
4	contaminating	contaminate	VBG	_	_	_
5	DNA	dna	NN	_	_	_
6	was	be	VBD	_	_	_
7	digested	digest	VBN	_	_	_
8	with	with	IN	_	_	_
9	DNAse	dnase	NN	_	_	_
10	I	i	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Sigma	Sigma	NNP	_	_	_
13	Aldrich	Aldrich	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	and	and	CC	_	_	_
16	total	total	JJ	_	_	_
17	RNA	rna	NN	_	_	_
18	was	be	VBD	_	_	_
19	purified	purify	VBN	_	_	_
20	by	by	IN	_	_	_
21	phenol	phenol	NN	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	E.	E.	NNP	_	_	_
24	coli	coli	NN	_	_	_
25	strain	strain	NN	_	_	_
26	MC4100relA	mc4100rela	NN	_	_	_
27	+	+	CC	_	_	_
28	in	in	IN	_	_	_
29	mid	mid	JJ	_	_	_
30	log	log	NN	_	_	_
31	phase	phase	NN	_	_	_
32	incubated	incubate	VBN	_	_	_
33	at	at	IN	_	_	_
34	37ºC	37ºc	NN	_	_	_
35	for	for	IN	_	_	_
36	4	4	CD	_	_	_
37	hours	hour	NNS	_	_	_
38	with	with	IN	_	_	_
39	100	100	CD	_	_	_
40	μg	μg	NN	_	_	_
41	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
42	E.	E.	NNP	_	_	_
43	coli	coli	NN	_	_	_
44	strain	strain	NN	_	_	_
45	MC4100relA	mc4100rela	NN	_	_	_
46	+	+	CC	_	_	_
47	in	in	IN	_	_	_
48	mid	mid	JJ	_	_	_
49	log	log	NN	_	_	_
50	phase	phase	NN	_	_	_
51	incubated	incubate	VBN	_	_	_
52	at	at	IN	_	_	_
53	37ºC	37ºc	NN	_	_	_
54	for	for	IN	_	_	_
55	4	4	CD	_	_	_
56	hours	hour	NNS	_	_	_
57	with	with	IN	_	_	_
58	10	10	CD	_	_	_
59	μg	μg	NN	_	_	_
60	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
61	E.	E.	NNP	_	_	_
62	coli	coli	NN	_	_	_
63	strain	strain	NN	_	_	_
64	MC4100relA	mc4100rela	NN	_	_	_
65	+	+	CC	_	_	_
66	in	in	IN	_	_	_
67	mid	mid	JJ	_	_	_
68	log	log	NN	_	_	_
69	phase	phase	NN	_	_	_
70	incubated	incubate	VBN	_	_	_
71	at	at	IN	_	_	_
72	37ºC	37ºc	NN	_	_	_
73	for	for	IN	_	_	_
74	4	4	CD	_	_	_
75	hours	hour	NNS	_	_	_
76	without	without	IN	_	_	_
77	treatment	treatment	NN	_	_	_
78	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	strain	strain	NN	_	_	_
5	MC4100relA	mc4100rela	NN	_	_	_
6	+	+	CC	_	_	_
7	∆	∆	SYM	_	_	_
8	mazEF	mazef	NN	_	_	_
9	in	in	IN	_	_	_
10	mid	mid	JJ	_	_	_
11	log	log	NN	_	_	_
12	phase	phase	NN	_	_	_
13	incubated	incubate	VBN	_	_	_
14	at	at	IN	_	_	_
15	37ºC	37ºc	NN	_	_	_
16	for	for	IN	_	_	_
17	4	4	CD	_	_	_
18	hours	hour	NNS	_	_	_
19	with	with	IN	_	_	_
20	100	100	CD	_	_	_
21	μg	μg	NN	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	E.	E.	NNP	_	_	_
24	coli	coli	NN	_	_	_
25	strain	strain	NN	_	_	_
26	MC4100relA	mc4100rela	NN	_	_	_
27	+	+	CC	_	_	_
28	∆	∆	SYM	_	_	_
29	mazEF	mazef	NN	_	_	_
30	in	in	IN	_	_	_
31	mid	mid	JJ	_	_	_
32	log	log	NN	_	_	_
33	phase	phase	NN	_	_	_
34	incubated	incubate	VBN	_	_	_
35	at	at	IN	_	_	_
36	37ºC	37ºc	NN	_	_	_
37	for	for	IN	_	_	_
38	4	4	CD	_	_	_
39	hours	hour	NNS	_	_	_
40	with	with	IN	_	_	_
41	10	10	CD	_	_	_
42	μg	μg	NN	_	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	E.	E.	NNP	_	_	_
45	coli	coli	NN	_	_	_
46	strain	strain	NN	_	_	_
47	MC4100relA	mc4100rela	NN	_	_	_
48	+	+	CC	_	_	_
49	∆	∆	SYM	_	_	_
50	mazEF	mazef	NN	_	_	_
51	in	in	IN	_	_	_
52	mid	mid	JJ	_	_	_
53	log	log	NN	_	_	_
54	phase	phase	NN	_	_	_
55	incubated	incubate	VBN	_	_	_
56	at	at	IN	_	_	_
57	37ºC	37ºc	NN	_	_	_
58	for	for	IN	_	_	_
59	4	4	CD	_	_	_
60	hours	hour	NNS	_	_	_
61	without	without	IN	_	_	_
62	treatment	treatment	NN	_	_	_
63	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
64	E.	E.	NNP	_	_	_
65	coli	coli	NN	_	_	_
66	strain	strain	NN	_	_	_
67	MC4100relA	mc4100rela	NN	_	_	_
68	+	+	CC	_	_	_
69	∆	∆	SYM	_	_	_
70	mazEFlexA3	mazeflexa3	NN	_	_	_
71	in	in	IN	_	_	_
72	mid	mid	JJ	_	_	_
73	log	log	NN	_	_	_
74	phase	phase	NN	_	_	_
75	incubated	incubate	VBN	_	_	_
76	at	at	IN	_	_	_
77	37ºC	37ºc	NN	_	_	_
78	for	for	IN	_	_	_
79	4	4	CD	_	_	_
80	hours	hour	NNS	_	_	_
81	with	with	IN	_	_	_
82	100	100	CD	_	_	_
83	μg	μg	NN	_	_	_
84	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
85	E.	E.	NNP	_	_	_
86	coli	coli	NN	_	_	_
87	strain	strain	NN	_	_	_
88	MC4100relA	mc4100rela	NN	_	_	_
89	+	+	CC	_	_	_
90	∆	∆	SYM	_	_	_
91	mazEFlexA3	mazeflexa3	NN	_	_	_
92	in	in	IN	_	_	_
93	mid	mid	JJ	_	_	_
94	log	log	NN	_	_	_
95	phase	phase	NN	_	_	_
96	incubated	incubate	VBN	_	_	_
97	at	at	IN	_	_	_
98	37ºC	37ºc	NN	_	_	_
99	for	for	IN	_	_	_
100	4	4	CD	_	_	_
101	hours	hour	NNS	_	_	_
102	with	with	IN	_	_	_
103	10	10	CD	_	_	_
104	μg	μg	NN	_	_	_
105	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
106	E.	E.	NNP	_	_	_
107	coli	coli	NN	_	_	_
108	strain	strain	NN	_	_	_
109	MC4100relA	mc4100rela	NN	_	_	_
110	+	+	CC	_	_	_
111	∆	∆	SYM	_	_	_
112	mazEFlexA3	mazeflexa3	NN	_	_	_
113	in	in	IN	_	_	_
114	mid	mid	JJ	_	_	_
115	log	log	NN	_	_	_
116	phase	phase	NN	_	_	_
117	incubated	incubate	VBN	_	_	_
118	at	at	IN	_	_	_
119	37ºC	37ºc	NN	_	_	_
120	for	for	IN	_	_	_
121	4	4	CD	_	_	_
122	hours	hour	NNS	_	_	_
123	without	without	IN	_	_	_
124	treatment	treatment	NN	_	_	_
125	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
126	Escherichia	escherichia	FW	Organism	_	_
127	coli	coli	FW	Organism	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	Gene	gene	NN	_	_	_
130	selection	selection	NN	_	_	_
131	was	be	VBD	_	_	_
132	done	do	VBN	_	_	_
133	using	use	VBG	_	_	_
134	the	the	DT	_	_	_
135	False	False	NNP	_	_	_
136	Discovery	Discovery	NNP	_	_	_
137	Rate	Rate	NNP	_	_	_
138	-LRB-	-lrb-	-LRB-	_	_	_
139	FDR	FDR	NNP	_	_	_
140	-RRB-	-rrb-	-RRB-	_	_	_
141	correction	correction	NN	_	_	_
142	procedure	procedure	NN	_	_	_
143	for	for	IN	_	_	_
144	adjusting	adjust	VBG	_	_	_
145	genes	gene	NNS	_	_	_
146	with	with	IN	_	_	_
147	p-value	p-value	JJ	_	_	_
148	smaller	smaller	JJR	_	_	_
149	than	than	IN	_	_	_
150	0.05	0.05	CD	_	_	_
151	and	and	CC	_	_	_
152	Fold	Fold	NNP	_	_	_
153	Change	Change	NNP	_	_	_
154	greater	greater	JJR	_	_	_
155	than	than	IN	_	_	_
156	2	2	CD	_	_	_
157	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	genotype	genotype	NN	_	_	_
3	:	:	:	_	_	_
4	∆	∆	CD	_	_	_
5	mazEF	mazef	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	genotype	genotype	NN	_	_	_
8	:	:	:	_	_	_
9	∆	∆	SYM	_	_	_
10	mazEFlexA3	mazeflexa3	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	genotype	genotype	NN	_	_	_
13	:	:	:	_	_	_
14	WT	WT	NNP	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	∆	∆	SYM	_	_	_
17	mazEF	mazef	NN	_	_	_
18	0	0	CD	_	_	_
19	μg	μg	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	∆	∆	CD	_	_	_
22	mazEF	mazef	NN	_	_	_
23	100	100	CD	_	_	_
24	μg	μg	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	∆	∆	CD	_	_	_
27	mazEF	mazef	NN	_	_	_
28	10	10	CD	_	_	_
29	μg	μg	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	∆	∆	CD	_	_	_
32	mazEFlexA3	mazeflexa3	NN	_	_	_
33	0	0	CD	_	_	_
34	μg	μg	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	∆	∆	CD	_	_	_
37	mazEFlexA3	mazeflexa3	NN	_	_	_
38	100	100	CD	_	_	_
39	μg	μg	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	∆	∆	CD	_	_	_
42	mazEFlexA3	mazeflexa3	NN	_	_	_
43	10	10	CD	_	_	_
44	μg	μg	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
46	RMA	rma	NN	_	_	_
47	normalization	normalization	NN	_	_	_
48	was	be	VBD	_	_	_
49	performed	perform	VBN	_	_	_
50	on	on	IN	_	_	_
51	CELL	cell	NN	_	_	_
52	files	files	NNS	_	_	_
53	using	use	VBG	_	_	_
54	the	the	DT	_	_	_
55	Partek	Partek	NNP	_	_	_
56	Genomic	genomic	JJ	_	_	_
57	Suite	suite	NN	_	_	_
58	6.5	6.5	CD	_	_	_
59	.	.	.	_	_	_

1	Additional	additional	JJ	_	_	_
2	statistical	statistical	JJ	_	_	_
3	analysis	analysis	NN	_	_	_
4	was	be	VBD	_	_	_
5	carried	carry	VBN	_	_	_
6	out	out	RP	_	_	_
7	using	use	VBG	_	_	_
8	the	the	DT	_	_	_
9	Spotfire	Spotfire	NNP	_	_	_
10	software	software	NN	_	_	_
11	package	package	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Somerville	Somerville	NNP	_	_	_
14	,	,	,	_	_	_
15	MA	MA	NNP	_	_	_
16	,	,	,	_	_	_
17	USA	USA	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	and	and	CC	_	_	_
20	custom	custom	NN	_	_	_
21	Matlab	Matlab	NNP	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	R2010B	r2010b	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	routines	routine	NNS	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	sample	sample	NN	_	_	_
3	type	type	NN	_	_	_
4	:	:	:	_	_	_
5	E.	e.	FW	_	_	_
6	coli	coli	FW	_	_	_
7	strain	strain	NN	_	_	_
8	MC4100relA	mc4100rela	NN	_	_	_
9	+	+	CC	_	_	_
10	in	in	IN	_	_	_
11	mid	mid	JJ	_	_	_
12	log	log	NN	_	_	_
13	phase	phase	NN	_	_	_
14	incubated	incubate	VBN	_	_	_
15	at	at	IN	_	_	_
16	37ºC	37ºc	NN	_	_	_
17	for	for	IN	_	_	_
18	4	4	CD	_	_	_
19	hours	hour	NNS	_	_	_
20	with	with	IN	_	_	_
21	100	100	CD	_	_	_
22	μg	μg	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	sample	sample	NN	_	_	_
25	type	type	NN	_	_	_
26	:	:	:	_	_	_
27	E.	e.	FW	_	_	_
28	coli	coli	FW	_	_	_
29	strain	strain	NN	_	_	_
30	MC4100relA	mc4100rela	NN	_	_	_
31	+	+	CC	_	_	_
32	in	in	IN	_	_	_
33	mid	mid	JJ	_	_	_
34	log	log	NN	_	_	_
35	phase	phase	NN	_	_	_
36	incubated	incubate	VBN	_	_	_
37	at	at	IN	_	_	_
38	37ºC	37ºc	NN	_	_	_
39	for	for	IN	_	_	_
40	4	4	CD	_	_	_
41	hours	hour	NNS	_	_	_
42	with	with	IN	_	_	_
43	10	10	CD	_	_	_
44	μg	μg	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	sample	sample	NN	_	_	_
47	type	type	NN	_	_	_
48	:	:	:	_	_	_
49	E.	e.	FW	_	_	_
50	coli	coli	FW	_	_	_
51	strain	strain	NN	_	_	_
52	MC4100relA	mc4100rela	NN	_	_	_
53	+	+	CC	_	_	_
54	in	in	IN	_	_	_
55	mid	mid	JJ	_	_	_
56	log	log	NN	_	_	_
57	phase	phase	NN	_	_	_
58	incubated	incubate	VBN	_	_	_
59	at	at	IN	_	_	_
60	37ºC	37ºc	NN	_	_	_
61	for	for	IN	_	_	_
62	4	4	CD	_	_	_
63	hours	hour	NNS	_	_	_
64	without	without	IN	_	_	_
65	treatment	treatment	NN	_	_	_
66	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	sample	sample	NN	_	_	_
3	type	type	NN	_	_	_
4	:	:	:	_	_	_
5	E.	e.	FW	_	_	_
6	coli	coli	FW	_	_	_
7	strain	strain	NN	_	_	_
8	MC4100relA	mc4100rela	NN	_	_	_
9	+	+	CC	_	_	_
10	∆	∆	SYM	_	_	_
11	mazEF	mazef	NN	_	_	_
12	in	in	IN	_	_	_
13	mid	mid	JJ	_	_	_
14	log	log	NN	_	_	_
15	phase	phase	NN	_	_	_
16	incubated	incubate	VBN	_	_	_
17	at	at	IN	_	_	_
18	37ºC	37ºc	NN	_	_	_
19	for	for	IN	_	_	_
20	4	4	CD	_	_	_
21	hours	hour	NNS	_	_	_
22	with	with	IN	_	_	_
23	100	100	CD	_	_	_
24	μg	μg	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	sample	sample	NN	_	_	_
27	type	type	NN	_	_	_
28	:	:	:	_	_	_
29	E.	e.	FW	_	_	_
30	coli	coli	FW	_	_	_
31	strain	strain	NN	_	_	_
32	MC4100relA	mc4100rela	NN	_	_	_
33	+	+	CC	_	_	_
34	∆	∆	SYM	_	_	_
35	mazEF	mazef	NN	_	_	_
36	in	in	IN	_	_	_
37	mid	mid	JJ	_	_	_
38	log	log	NN	_	_	_
39	phase	phase	NN	_	_	_
40	incubated	incubate	VBN	_	_	_
41	at	at	IN	_	_	_
42	37ºC	37ºc	NN	_	_	_
43	for	for	IN	_	_	_
44	4	4	CD	_	_	_
45	hours	hour	NNS	_	_	_
46	with	with	IN	_	_	_
47	10	10	CD	_	_	_
48	μg	μg	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	sample	sample	NN	_	_	_
51	type	type	NN	_	_	_
52	:	:	:	_	_	_
53	E.	e.	FW	_	_	_
54	coli	coli	FW	_	_	_
55	strain	strain	NN	_	_	_
56	MC4100relA	mc4100rela	NN	_	_	_
57	+	+	CC	_	_	_
58	∆	∆	SYM	_	_	_
59	mazEF	mazef	NN	_	_	_
60	in	in	IN	_	_	_
61	mid	mid	JJ	_	_	_
62	log	log	NN	_	_	_
63	phase	phase	NN	_	_	_
64	incubated	incubate	VBN	_	_	_
65	at	at	IN	_	_	_
66	37ºC	37ºc	NN	_	_	_
67	for	for	IN	_	_	_
68	4	4	CD	_	_	_
69	hours	hour	NNS	_	_	_
70	without	without	IN	_	_	_
71	treatment	treatment	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	sample	sample	NN	_	_	_
74	type	type	NN	_	_	_
75	:	:	:	_	_	_
76	E.	e.	FW	_	_	_
77	coli	coli	FW	_	_	_
78	strain	strain	NN	_	_	_
79	MC4100relA	mc4100rela	NN	_	_	_
80	+	+	CC	_	_	_
81	∆	∆	SYM	_	_	_
82	mazEFlexA3	mazeflexa3	NN	_	_	_
83	in	in	IN	_	_	_
84	mid	mid	JJ	_	_	_
85	log	log	NN	_	_	_
86	phase	phase	NN	_	_	_
87	incubated	incubate	VBN	_	_	_
88	at	at	IN	_	_	_
89	37ºC	37ºc	NN	_	_	_
90	for	for	IN	_	_	_
91	4	4	CD	_	_	_
92	hours	hour	NNS	_	_	_
93	with	with	IN	_	_	_
94	100	100	CD	_	_	_
95	μg	μg	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	sample	sample	NN	_	_	_
98	type	type	NN	_	_	_
99	:	:	:	_	_	_
100	E.	e.	FW	_	_	_
101	coli	coli	FW	_	_	_
102	strain	strain	NN	_	_	_
103	MC4100relA	mc4100rela	NN	_	_	_
104	+	+	CC	_	_	_
105	∆	∆	SYM	_	_	_
106	mazEFlexA3	mazeflexa3	NN	_	_	_
107	in	in	IN	_	_	_
108	mid	mid	JJ	_	_	_
109	log	log	NN	_	_	_
110	phase	phase	NN	_	_	_
111	incubated	incubate	VBN	_	_	_
112	at	at	IN	_	_	_
113	37ºC	37ºc	NN	_	_	_
114	for	for	IN	_	_	_
115	4	4	CD	_	_	_
116	hours	hour	NNS	_	_	_
117	with	with	IN	_	_	_
118	10	10	CD	_	_	_
119	μg	μg	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	sample	sample	NN	_	_	_
122	type	type	NN	_	_	_
123	:	:	:	_	_	_
124	E.	e.	FW	_	_	_
125	coli	coli	FW	_	_	_
126	strain	strain	NN	_	_	_
127	MC4100relA	mc4100rela	NN	_	_	_
128	+	+	CC	_	_	_
129	∆	∆	SYM	_	_	_
130	mazEFlexA3	mazeflexa3	NN	_	_	_
131	in	in	IN	_	_	_
132	mid	mid	JJ	_	_	_
133	log	log	NN	_	_	_
134	phase	phase	NN	_	_	_
135	incubated	incubate	VBN	_	_	_
136	at	at	IN	_	_	_
137	37ºC	37ºc	NN	_	_	_
138	for	for	IN	_	_	_
139	4	4	CD	_	_	_
140	hours	hour	NNS	_	_	_
141	without	without	IN	_	_	_
142	treatment	treatment	NN	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	treatment	treatment	NN	_	_	_
145	:	:	:	_	_	_
146	0	0	CD	_	_	_
147	μg	μg	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	treatment	treatment	NN	_	_	_
150	:	:	:	_	_	_
151	100	100	CD	_	_	_
152	μg	μg	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	treatment	treatment	NN	_	_	_
155	:	:	:	_	_	_
156	10	10	CD	_	_	_
157	μg	μg	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	We	we	PRP	_	_	_
160	extracted	extract	VBD	_	_	_
161	RNA	rna	NN	_	_	_
162	using	use	VBG	_	_	_
163	RNAprotect	rnaprotect	NN	_	_	_
164	Bacteria	bacterium	NNS	_	_	_
165	reagent	reagent	NN	_	_	_
166	-LRB-	-lrb-	-LRB-	_	_	_
167	Qiagen	qiagen	NN	_	_	_
168	-RRB-	-rrb-	-RRB-	_	_	_
169	and	and	CC	_	_	_
170	RNeasy	RNeasy	NNP	_	_	_
171	Mini	Mini	NNP	_	_	_
172	Kit	kit	NN	_	_	_
173	-LRB-	-lrb-	-LRB-	_	_	_
174	Qiagen	qiagen	NN	_	_	_
175	-RRB-	-rrb-	-RRB-	_	_	_
176	combined	combine	VBN	_	_	_
177	with	with	IN	_	_	_
178	RNase-Free	rnase-free	JJ	_	_	_
179	DNase	dnase	NN	_	_	_
180	Set	set	VB	_	_	_
181	-LRB-	-lrb-	-LRB-	_	_	_
182	Qiagen	Qiagen	NNP	_	_	_
183	-RRB-	-rrb-	-RRB-	_	_	_
184	according	accord	VBG	_	_	_
185	to	to	TO	_	_	_
186	the	the	DT	_	_	_
187	manufacturer	manufacturer	NN	_	_	_
188	's	's	POS	_	_	_
189	instructions	instruction	NNS	_	_	_
190	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	We	we	PRP	_	_	_
3	grew	grow	VBD	_	_	_
4	cells	cell	NNS	_	_	_
5	in	in	IN	_	_	_
6	10	10	CD	_	_	_
7	ml	ml	NN	_	_	_
8	M9	m9	NN	MED	_	_
9	minimal	minimal	JJ	MED	_	_
10	medium	medium	NN	MED	_	_
11	to	to	TO	_	_	_
12	OD600	od600	NN	_	_	_
13	=	=	JJ	_	_	_
14	0.5-0.6	0.5-0.6	CD	_	_	_
15	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	,	,	,	_	_	_
3	we	we	PRP	_	_	_
4	divided	divide	VBD	_	_	_
5	each	each	DT	_	_	_
6	culture	culture	NN	_	_	_
7	into	into	IN	_	_	_
8	500µl	500µl	JJ	_	_	_
9	aliquots	aliquot	NNS	_	_	_
10	to	to	TO	_	_	_
11	which	which	WDT	_	_	_
12	we	we	PRP	_	_	_
13	added	add	VBD	_	_	_
14	the	the	DT	_	_	_
15	appropriate	appropriate	JJ	_	_	_
16	concentration	concentration	NN	_	_	_
17	of	of	IN	_	_	_
18	NA	NA	NNP	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	We	we	PRP	_	_	_
3	incubated	incubate	VBD	_	_	_
4	each	each	DT	_	_	_
5	aliquot	aliquot	NN	_	_	_
6	at	at	IN	_	_	_
7	37ºC	37ºc	NN	_	_	_
8	for	for	IN	_	_	_
9	4	4	CD	_	_	_
10	hours	hour	NNS	_	_	_
11	with	with	IN	_	_	_
12	NA	na	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	WT	wt	NN	_	_	_
15	0	0	CD	_	_	_
16	μg	μg	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	WT	wt	NN	_	_	_
19	100	100	CD	_	_	_
20	μg	μg	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	WT	wt	VBD	_	_	_
23	10	10	CD	_	_	_
24	μg	μg	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Aerobic	aerobic	JJ	_	_	_
27	culture	culture	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Basecalls	basecall	NNS	_	_	_
30	performed	perform	VBN	_	_	_
31	using	use	VBG	_	_	_
32	CASAVA	CASAVA	NNP	_	_	_
33	version	version	NN	_	_	_
34	1.8.2	1.8.2	CD	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	aerobically	aerobically	RB	_	_	_
6	at	at	IN	_	_	_
7	37	37	CD	_	_	_
8	°C	°c	NN	_	_	_
9	in	in	IN	_	_	_
10	1	1	CD	_	_	_
11	L	l	NN	_	_	_
12	volumes	volume	NNS	_	_	_
13	of	of	IN	_	_	_
14	M9	m9	NN	MED	_	_
15	minimal	minimal	JJ	MED	_	_
16	medium	medium	NN	MED	_	_
17	,	,	,	_	_	_
18	supplemented	supplement	VBN	_	_	_
19	with	with	IN	_	_	_
20	MgSO4	mgso4	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	1	1	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	,	,	,	_	_	_
26	CaCl2	cacl2	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	0.1	0.1	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	,	,	,	_	_	_
32	and	and	CC	_	_	_
33	glucose	glucose	NN	SUPP	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	10	10	CD	_	_	_
36	g	g	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
38	Each	each	DT	_	_	_
39	dataset	dataset	NN	_	_	_
40	was	be	VBD	_	_	_
41	normalized	normalize	VBN	_	_	_
42	to	to	TO	_	_	_
43	reads	read	VBZ	_	_	_
44	per	per	IN	_	_	_
45	million	million	CD	_	_	_
46	per	per	IN	_	_	_
47	position	position	NN	_	_	_
48	prior	prior	RB	_	_	_
49	to	to	TO	_	_	_
50	further	further	JJ	_	_	_
51	analysis	analysis	NN	_	_	_
52	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	ethanol	ethanol	NN	_	_	_
6	treatment	treatment	NN	_	_	_
7	:	:	:	_	_	_
8	40	40	CD	_	_	_
9	g	g	NN	_	_	_
10	EtOH	etoh	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	ethanol	ethanol	NN	_	_	_
13	treatment	treatment	NN	_	_	_
14	:	:	:	_	_	_
15	no	no	DT	_	_	_
16	ethanol	ethanol	NN	_	_	_
17	exposure	exposure	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Ethanol	ethanol	NN	_	_	_
20	was	be	VBD	_	_	_
21	added	add	VBN	_	_	_
22	to	to	TO	_	_	_
23	40	40	CD	_	_	_
24	g	g	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	For	for	IN	_	_	_
27	metagene	metagene	NN	_	_	_
28	analyses	analysis	NNS	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	gene-segment	gene-segment	NN	_	_	_
31	analyses	analysis	NNS	_	_	_
32	and	and	CC	_	_	_
33	codon-type	codon-type	JJ	_	_	_
34	analyses	analysis	NNS	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	,	,	,	_	_	_
37	pseudogenes	pseudogene	NNS	_	_	_
38	and	and	CC	_	_	_
39	genes	gene	NNS	_	_	_
40	not	not	RB	_	_	_
41	represented	represent	VBN	_	_	_
42	in	in	IN	_	_	_
43	one	one	CD	_	_	_
44	or	or	CC	_	_	_
45	more	more	JJR	_	_	_
46	datasets	dataset	NNS	_	_	_
47	were	be	VBD	_	_	_
48	excluded	exclude	VBN	_	_	_
49	,	,	,	_	_	_
50	leaving	leave	VBG	_	_	_
51	3048	3048	CD	_	_	_
52	genes	gene	NNS	_	_	_
53	in	in	IN	_	_	_
54	the	the	DT	_	_	_
55	ll	ll	NN	_	_	_
56	genes	gene	NNS	_	_	_
57	\	\	VBP	_	_	_
58	dataset	dataset	NN	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	see	see	VB	_	_	_
61	supplementary	supplementary	JJ	_	_	_
62	file	file	NN	_	_	_
63	for	for	IN	_	_	_
64	list	list	NN	_	_	_
65	of	of	IN	_	_	_
66	genes	gene	NNS	_	_	_
67	in	in	IN	_	_	_
68	ll	ll	NN	_	_	_
69	genes	gene	NNS	_	_	_
70	\	\	VBP	_	_	_
71	,	,	,	_	_	_
72	\	\	VBP	_	_	_
73	low	low	JJ	_	_	_
74	ribosome	ribosome	NN	_	_	_
75	occupancy	occupancy	NN	_	_	_
76	\	\	NN	_	_	_
77	,	,	,	_	_	_
78	and	and	CC	_	_	_
79	\	\	RB	_	_	_
80	high	high	JJ	_	_	_
81	ribosome	ribosome	NN	_	_	_
82	occupancy	occupancy	NN	_	_	_
83	\	\	NN	_	_	_
84	gene	gene	NN	_	_	_
85	sets	set	NNS	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
88	Genome	Genome	NNP	_	_	_
89	_	_	NNP	_	_	_
90	build	build	VB	_	_	_
91	:	:	:	_	_	_
92	NC	NC	NNP	_	_	_
93	_	_	NNP	_	_	_
94	000913.2	000913.2	CD	_	_	_
95	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
96	Library	Library	NNP	_	_	_
97	construction	construction	NN	_	_	_
98	was	be	VBD	_	_	_
99	performed	perform	VBN	_	_	_
100	as	as	IN	_	_	_
101	described	describe	VBN	_	_	_
102	in	in	IN	_	_	_
103	Oh	oh	UH	_	_	_
104	et	et	FW	_	_	_
105	al.	al.	FW	_	_	_
106	2011	2011	CD	_	_	_
107	,	,	,	_	_	_
108	Cell	cell	NN	_	_	_
109	147	147	CD	_	_	_
110	-LRB-	-lrb-	-LRB-	_	_	_
111	6	6	CD	_	_	_
112	-RRB-	-rrb-	-RRB-	_	_	_
113	:	:	:	_	_	_
114	1295-1308	1295-1308	CD	_	_	_
115	-LRB-	-lrb-	-LRB-	_	_	_
116	PMCID	pmcid	NN	_	_	_
117	:	:	:	_	_	_
118	PMC3277850	pmc3277850	NN	_	_	_
119	-RRB-	-rrb-	-RRB-	_	_	_
120	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	fragments	fragment	NNS	_	_	_
4	of	of	IN	_	_	_
5	total	total	NN	_	_	_
6	mRNA	mrna	NN	_	_	_
7	or	or	CC	_	_	_
8	ribosome	ribosome	NN	_	_	_
9	protected	protect	VBD	_	_	_
10	mRNA	mrna	NN	_	_	_
11	fragments	fragment	NNS	_	_	_
12	were	be	VBD	_	_	_
13	size	size	NN	_	_	_
14	selected	select	VBN	_	_	_
15	via	via	IN	_	_	_
16	gel	gel	NN	_	_	_
17	purification	purification	NN	_	_	_
18	,	,	,	_	_	_
19	and	and	CC	_	_	_
20	ligated	ligate	VBN	_	_	_
21	to	to	TO	_	_	_
22	a	a	DT	_	_	_
23	5	5	CD	_	_	_
24	'	'	''	_	_	_
25	adenylated	adenylate	VBN	_	_	_
26	DNA	dna	NN	_	_	_
27	oligo	oligo	JJ	_	_	_
28	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	reverse	reverse	JJ	_	_	_
3	transcription	transcription	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	single	single	JJ	_	_	_
7	stranded	stranded	JJ	_	_	_
8	DNA	dna	NN	_	_	_
9	was	be	VBD	_	_	_
10	circularized	circularize	VBN	_	_	_
11	and	and	CC	_	_	_
12	amplified	amplify	VBN	_	_	_
13	by	by	IN	_	_	_
14	PCR	pcr	NN	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Mutant	mutant	JJ	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	EP61	ep61	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	T0	t0	NN	_	_	_
7	RNA	rna	NN	_	_	_
8	rep	rep	NN	GEN	_	_
9	1	1	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Mutant	mutant	JJ	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	EP61	ep61	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	T0	t0	NN	_	_	_
16	RNA	rna	NN	_	_	_
17	rep	rep	NN	GEN	_	_
18	2	2	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	Mutant	mutant	JJ	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	EP61	ep61	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	T0	t0	NN	_	_	_
25	RP	rp	NN	_	_	_
26	rep	rep	NN	GEN	_	_
27	1	1	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Mutant	mutant	JJ	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	EP61	ep61	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	T0	t0	NN	_	_	_
34	RP	rp	NN	_	_	_
35	rep	rep	NN	GEN	_	_
36	2	2	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
38	Mutant	mutant	JJ	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	EP61	ep61	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	T1	t1	NN	_	_	_
43	RNA	rna	NN	_	_	_
44	rep	rep	NN	GEN	_	_
45	1	1	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	Mutant	mutant	JJ	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	EP61	ep61	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	T1	t1	NN	_	_	_
52	RNA	rna	NN	_	_	_
53	rep	rep	NN	GEN	_	_
54	2	2	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
56	Mutant	mutant	JJ	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	EP61	ep61	NN	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	T1	t1	NN	_	_	_
61	RP	rp	NN	_	_	_
62	rep	rep	NN	GEN	_	_
63	1	1	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	Mutant	mutant	JJ	_	_	_
66	-LRB-	-lrb-	-LRB-	_	_	_
67	EP61	ep61	NN	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	T1	t1	NN	_	_	_
70	RP	rp	NN	_	_	_
71	rep	rep	NN	GEN	_	_
72	2	2	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
74	Mutant	mutant	JJ	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	EP61	ep61	NN	_	_	_
77	-RRB-	-rrb-	-RRB-	_	_	_
78	T2	t2	NN	_	_	_
79	RNA	rna	NN	_	_	_
80	rep	rep	NN	GEN	_	_
81	1	1	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	Mutant	mutant	JJ	_	_	_
84	-LRB-	-lrb-	-LRB-	_	_	_
85	EP61	ep61	NN	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	T2	t2	NN	_	_	_
88	RNA	rna	NN	_	_	_
89	rep	rep	NN	GEN	_	_
90	2	2	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
92	Mutant	mutant	JJ	_	_	_
93	-LRB-	-lrb-	-LRB-	_	_	_
94	EP61	ep61	NN	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	T2	t2	NN	_	_	_
97	RP	rp	NN	_	_	_
98	rep	rep	NN	GEN	_	_
99	1	1	CD	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	Mutant	mutant	JJ	_	_	_
102	-LRB-	-lrb-	-LRB-	_	_	_
103	EP61	ep61	NN	_	_	_
104	-RRB-	-rrb-	-RRB-	_	_	_
105	T2	t2	NN	_	_	_
106	RP	rp	NN	_	_	_
107	rep	rep	NN	GEN	_	_
108	2	2	CD	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
110	Raw	raw	NN	_	_	_
111	reads	read	VBZ	_	_	_
112	were	be	VBD	_	_	_
113	trimmed	trim	VBN	_	_	_
114	by	by	IN	_	_	_
115	two	two	CD	_	_	_
116	nt	nt	NNS	_	_	_
117	from	from	IN	_	_	_
118	the	the	DT	_	_	_
119	5	5	CD	_	_	_
120	'	'	''	_	_	_
121	end	end	NN	_	_	_
122	-LRB-	-lrb-	-LRB-	_	_	_
123	to	to	TO	_	_	_
124	remove	remove	VB	_	_	_
125	any	any	DT	_	_	_
126	non-templated	non-templated	JJ	_	_	_
127	nts	nt	NNS	_	_	_
128	added	add	VBN	_	_	_
129	by	by	IN	_	_	_
130	reverse	reverse	JJ	_	_	_
131	transcriptase	transcriptase	NN	_	_	_
132	-RRB-	-rrb-	-RRB-	_	_	_
133	,	,	,	_	_	_
134	and	and	CC	_	_	_
135	were	be	VBD	_	_	_
136	then	then	RB	_	_	_
137	mapped	map	VBN	_	_	_
138	using	use	VBG	_	_	_
139	the	the	DT	_	_	_
140	Burrows-Wheeler	Burrows-Wheeler	NNP	_	_	_
141	Aligner	Aligner	NNP	_	_	_
142	to	to	TO	_	_	_
143	the	the	DT	_	_	_
144	Escherichia	escherichia	FW	Organism	_	_
145	coli	coli	FW	Organism	_	_
146	MG1655	mg1655	NN	_	_	_
147	genome	genome	NN	_	_	_
148	-LRB-	-lrb-	-LRB-	_	_	_
149	NCBI	ncbi	NN	_	_	_
150	accession	accession	NN	_	_	_
151	NC	nc	NN	_	_	_
152	_	_	SYM	_	_	_
153	000913	000913	CD	_	_	_
154	-RRB-	-rrb-	-RRB-	_	_	_
155	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	ribosome-protected	ribosome-protected	JJ	_	_	_
3	:	:	:	_	_	_
4	No	no	DT	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	ribosome-protected	ribosome-protected	JJ	_	_	_
7	:	:	:	_	_	_
8	Yes	yes	UH	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
10	RNA-Seq	rna-seq	JJ	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	RNA	rna	NN	_	_	_
13	was	be	VBD	_	_	_
14	extracted	extract	VBN	_	_	_
15	from	from	IN	_	_	_
16	samples	sample	NNS	_	_	_
17	using	use	VBG	_	_	_
18	hot	hot	JJ	_	_	_
19	phenol	phenol	NN	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	integrity	integrity	NN	_	_	_
3	of	of	IN	_	_	_
4	total	total	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	was	be	VBD	_	_	_
7	determined	determine	VBN	_	_	_
8	from	from	IN	_	_	_
9	agarose	agarose	NN	_	_	_
10	gels	gel	NNS	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Signals	signal	NNS	_	_	_
3	mapping	map	VBG	_	_	_
4	to	to	TO	_	_	_
5	non-coding	non-coding	JJ	_	_	_
6	RNA	rna	NN	_	_	_
7	regions	region	NNS	_	_	_
8	were	be	VBD	_	_	_
9	removed	remove	VBN	_	_	_
10	from	from	IN	_	_	_
11	the	the	DT	_	_	_
12	datasets	dataset	NNS	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	see	see	VB	_	_	_
15	supplementary	supplementary	JJ	_	_	_
16	file	file	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	EP61	ep61	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	strain	strain	NN	_	_	_
7	:	:	:	_	_	_
8	MG1655	mg1655	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Supplementary	supplementary	JJ	_	_	_
11	_	_	NN	_	_	_
12	files	file	NNS	_	_	_
13	_	_	IN	_	_	_
14	format	format	NN	_	_	_
15	_	_	NN	_	_	_
16	and	and	CC	_	_	_
17	_	_	NN	_	_	_
18	content	content	NN	_	_	_
19	:	:	:	_	_	_
20	Gene	Gene	NNP	_	_	_
21	_	_	NNP	_	_	_
22	lists	list	VBZ	_	_	_
23	_	_	SYM	_	_	_
24	GEO.xls	geo.xls	NNS	_	_	_
25	;	;	:	_	_	_
26	The	the	DT	_	_	_
27	supplementary	supplementary	JJ	_	_	_
28	file	file	NN	_	_	_
29	contains	contain	VBZ	_	_	_
30	gene	gene	NN	_	_	_
31	lists	list	NNS	_	_	_
32	used	use	VBN	_	_	_
33	in	in	IN	_	_	_
34	data	data	NN	_	_	_
35	analysis	analysis	NN	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Supplementary	Supplementary	NNP	_	_	_
3	_	_	VBD	_	_	_
4	files	file	NNS	_	_	_
5	_	_	IN	_	_	_
6	format	format	NN	_	_	_
7	_	_	NN	_	_	_
8	and	and	CC	_	_	_
9	_	_	NN	_	_	_
10	content	content	NN	_	_	_
11	:	:	:	_	_	_
12	Processed	process	VBN	_	_	_
13	data	datum	NNS	_	_	_
14	files	file	NNS	_	_	_
15	are	be	VBP	_	_	_
16	WIG	WIG	NNP	_	_	_
17	files	file	NNS	_	_	_
18	with	with	IN	_	_	_
19	non-coding	non-coding	JJ	_	_	_
20	RNAs	rna	NNS	_	_	_
21	removed	remove	VBD	_	_	_
22	,	,	,	_	_	_
23	normalized	normalize	VBD	_	_	_
24	to	to	TO	_	_	_
25	reads	read	VBZ	_	_	_
26	per	per	IN	_	_	_
27	million	million	CD	_	_	_
28	per	per	IN	_	_	_
29	position	position	NN	_	_	_
30	.	.	.	_	_	_

1	Those	those	DT	_	_	_
2	with	with	IN	_	_	_
3	a	a	DT	_	_	_
4	\	\	SYM	_	_	_
5	-	-	:	_	_	_
6	\	\	SYM	_	_	_
7	as	as	IN	_	_	_
8	the	the	DT	_	_	_
9	final	final	JJ	_	_	_
10	character	character	NN	_	_	_
11	in	in	IN	_	_	_
12	the	the	DT	_	_	_
13	file	file	NN	_	_	_
14	name	name	NN	_	_	_
15	cover	cover	VBP	_	_	_
16	the	the	DT	_	_	_
17	minus	minus	CC	_	_	_
18	strand	strand	NN	_	_	_
19	of	of	IN	_	_	_
20	the	the	DT	_	_	_
21	genome	genome	NN	_	_	_
22	;	;	:	_	_	_
23	those	those	DT	_	_	_
24	with	with	IN	_	_	_
25	a	a	DT	_	_	_
26	\	\	NN	_	_	_
27	+	+	CC	_	_	_
28	\	\	NN	_	_	_
29	as	as	IN	_	_	_
30	the	the	DT	_	_	_
31	final	final	JJ	_	_	_
32	character	character	NN	_	_	_
33	in	in	IN	_	_	_
34	the	the	DT	_	_	_
35	file	file	NN	_	_	_
36	name	name	NN	_	_	_
37	cover	cover	VBP	_	_	_
38	the	the	DT	_	_	_
39	plus	plus	CC	_	_	_
40	strand	strand	NN	_	_	_
41	of	of	IN	_	_	_
42	the	the	DT	_	_	_
43	genome	genome	NN	_	_	_
44	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Wild-type	wild-type	JJ	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	T0	t0	NN	_	_	_
7	RNA	rna	NN	_	_	_
8	rep	rep	NN	GEN	_	_
9	2	2	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
11	Wild-type	wild-type	JJ	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	MG1655	mg1655	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	T0	t0	NN	_	_	_
16	RP	rp	NN	_	_	_
17	rep	rep	NN	GEN	_	_
18	1	1	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Wild-type	wild-type	JJ	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	MG1655	mg1655	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	T0	t0	NN	_	_	_
25	RP	rp	NN	_	_	_
26	rep	rep	NN	GEN	_	_
27	2	2	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
29	Wild-type	wild-type	JJ	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	MG1655	mg1655	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	T1	t1	NN	_	_	_
34	RNA	rna	NN	_	_	_
35	rep	rep	NN	GEN	_	_
36	1	1	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Wild-type	wild-type	JJ	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	MG1655	mg1655	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	T1	t1	NN	_	_	_
43	RNA	rna	NN	_	_	_
44	rep	rep	NN	GEN	_	_
45	2	2	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
47	Wild-type	wild-type	JJ	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	MG1655	mg1655	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	T1	t1	NN	_	_	_
52	RP	rp	NN	_	_	_
53	rep	rep	NN	GEN	_	_
54	1	1	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	Wild-type	wild-type	JJ	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	MG1655	mg1655	NN	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	T1	t1	NN	_	_	_
61	RP	rp	NN	_	_	_
62	rep	rep	NN	GEN	_	_
63	2	2	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
65	Wild-type	wild-type	JJ	_	_	_
66	-LRB-	-lrb-	-LRB-	_	_	_
67	MG1655	mg1655	NN	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	T2	t2	NN	_	_	_
70	RNA	rna	NN	_	_	_
71	rep	rep	NN	GEN	_	_
72	1	1	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	Wild-type	wild-type	JJ	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	MG1655	mg1655	NN	_	_	_
77	-RRB-	-rrb-	-RRB-	_	_	_
78	T2	t2	NN	_	_	_
79	RNA	rna	NN	_	_	_
80	rep	rep	NN	GEN	_	_
81	2	2	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
83	Wild-type	wild-type	JJ	_	_	_
84	-LRB-	-lrb-	-LRB-	_	_	_
85	MG1655	mg1655	NN	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	T2	t2	NN	_	_	_
88	RP	rp	NN	_	_	_
89	rep	rep	NN	GEN	_	_
90	1	1	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	Wild-type	wild-type	JJ	_	_	_
93	-LRB-	-lrb-	-LRB-	_	_	_
94	MG1655	mg1655	NN	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	T2	t2	NN	_	_	_
97	RP	rp	NN	_	_	_
98	rep	rep	NN	GEN	_	_
99	2	2	CD	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
101	Aerobic	aerobic	JJ	_	_	_
102	culture	culture	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	Basecalls	basecall	NNS	_	_	_
105	performed	perform	VBN	_	_	_
106	using	use	VBG	_	_	_
107	CASAVA	CASAVA	NNP	_	_	_
108	version	version	NN	_	_	_
109	1.7	1.7	CD	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
111	Cells	cell	NNS	_	_	_
112	were	be	VBD	_	_	_
113	grown	grow	VBN	_	_	_
114	in	in	IN	_	_	_
115	MOPS	mop	NNS	MED	_	_
116	minimal	minimal	JJ	_	_	_
117	medium	medium	NN	_	_	_
118	with	with	IN	_	_	_
119	0.2	0.2	CD	_	_	_
120	%	%	NN	_	_	_
121	glucose	glucose	NN	SUPP	_	_
122	at	at	IN	_	_	_
123	37	37	CD	_	_	_
124	degrees	degree	NNS	_	_	_
125	C	c	NN	_	_	_
126	in	in	IN	_	_	_
127	gas-sparged	gas-sparged	JJ	_	_	_
128	Roux	Roux	NNP	_	_	_
129	bottles	bottle	NNS	_	_	_
130	to	to	TO	_	_	_
131	mid-log	mid-log	JJ	_	_	_
132	phase	phase	NN	_	_	_
133	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Culture	culture	NN	_	_	_
3	samples	sample	NNS	_	_	_
4	were	be	VBD	_	_	_
5	transferred	transfer	VBN	_	_	_
6	directly	directly	RB	_	_	_
7	into	into	IN	_	_	_
8	an	a	DT	_	_	_
9	ice-cold	ice-cold	JJ	_	_	_
10	ethanol	ethanol	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Each	each	DT	_	_	_
13	dataset	dataset	NN	_	_	_
14	was	be	VBD	_	_	_
15	normalized	normalize	VBN	_	_	_
16	to	to	TO	_	_	_
17	reads	read	VBZ	_	_	_
18	per	per	IN	_	_	_
19	million	million	CD	_	_	_
20	per	per	IN	_	_	_
21	position	position	NN	_	_	_
22	prior	prior	RB	_	_	_
23	to	to	TO	_	_	_
24	further	further	JJ	_	_	_
25	analysis	analysis	NN	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Genome	Genome	NNP	_	_	_
6	_	_	NNP	_	_	_
7	build	build	VB	_	_	_
8	:	:	:	_	_	_
9	ASM584v1	asm584v1	NN	_	_	_
10	,	,	,	_	_	_
11	U00096	u00096	NN	_	_	_
12	.2	.2	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Library	Library	NNP	_	_	_
15	construction	construction	NN	_	_	_
16	was	be	VBD	_	_	_
17	performed	perform	VBN	_	_	_
18	as	as	IN	_	_	_
19	described	describe	VBN	_	_	_
20	in	in	IN	_	_	_
21	Parkhomchuk	Parkhomchuk	NNP	_	_	_
22	et	et	FW	_	_	_
23	al.	al.	FW	_	_	_
24	2009	2009	CD	_	_	_
25	,	,	,	_	_	_
26	Nucleic	Nucleic	NNP	_	_	_
27	Acids	Acids	NNP	_	_	_
28	Res	Res	NNP	_	_	_
29	37	37	CD	_	_	_
30	:	:	:	_	_	_
31	e123	e123	NN	_	_	_
32	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	ribosome-depleted	ribosome-depleted	JJ	_	_	_
4	RNA	rna	NN	_	_	_
5	was	be	VBD	_	_	_
6	fragmented	fragmented	JJ	_	_	_
7	and	and	CC	_	_	_
8	used	use	VBN	_	_	_
9	as	as	IN	_	_	_
10	template	template	NN	_	_	_
11	for	for	IN	_	_	_
12	cDNA	cdna	NN	_	_	_
13	synhtesis	synhtesis	NN	_	_	_
14	.	.	.	_	_	_

1	dUTP	dutp	NN	_	_	_
2	was	be	VBD	_	_	_
3	included	include	VBN	_	_	_
4	in	in	IN	_	_	_
5	the	the	DT	_	_	_
6	second	second	JJ	_	_	_
7	strand	strand	NN	_	_	_
8	synthesis	synthesis	NN	_	_	_
9	reaction	reaction	NN	_	_	_
10	in	in	IN	_	_	_
11	addition	addition	NN	_	_	_
12	to	to	TO	_	_	_
13	dTTP	dttp	NN	_	_	_
14	to	to	TO	_	_	_
15	chemically	chemically	RB	_	_	_
16	mark	mark	VB	_	_	_
17	the	the	DT	_	_	_
18	second	second	JJ	_	_	_
19	strand	strand	NN	_	_	_
20	.	.	.	_	_	_

1	cDNAs	cdna	NNS	_	_	_
2	were	be	VBD	_	_	_
3	size-selected	size-selected	JJ	_	_	_
4	and	and	CC	_	_	_
5	ligated	ligate	VBN	_	_	_
6	to	to	TO	_	_	_
7	sequencing	sequencing	NN	_	_	_
8	adapters	adapter	NNS	_	_	_
9	followed	follow	VBN	_	_	_
10	by	by	IN	_	_	_
11	dUTP	dutp	NN	_	_	_
12	cleavage	cleavage	NN	_	_	_
13	to	to	TO	_	_	_
14	generate	generate	VB	_	_	_
15	adapter-ligated	adapter-ligated	JJ	_	_	_
16	single-stranded	single-stranded	JJ	_	_	_
17	cDNAs	cdna	NNS	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Mutant	mutant	JJ	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	RL2325	rl2325	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	RNA-seq	rna-seq	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	RNA-Seq	rna-seq	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	RNA-seq	rna-seq	NN	_	_	_
11	reads	read	VBZ	_	_	_
12	were	be	VBD	_	_	_
13	mapped	map	VBN	_	_	_
14	to	to	TO	_	_	_
15	the	the	DT	_	_	_
16	E.	e.	FW	_	_	_
17	coli	coli	FW	_	_	_
18	K-12	k-12	NN	_	_	_
19	MG1655	mg1655	NN	_	_	_
20	genome	genome	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	GenBank	genbank	NN	_	_	_
23	ID	id	NN	_	_	_
24	U00096	u00096	NN	_	_	_
25	.2	.2	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	using	use	VBG	_	_	_
28	short	short	JJ	_	_	_
29	oligonucleotide	oligonucleotide	NN	_	_	_
30	alignment	alignment	NN	_	_	_
31	program	program	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	SOAP	soap	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	RNA	rna	NN	_	_	_
37	was	be	VBD	_	_	_
38	extracted	extract	VBN	_	_	_
39	from	from	IN	_	_	_
40	samples	sample	NNS	_	_	_
41	using	use	VBG	_	_	_
42	hot	hot	JJ	_	_	_
43	phenol	phenol	NN	_	_	_
44	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	integrity	integrity	NN	_	_	_
3	of	of	IN	_	_	_
4	total	total	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	was	be	VBD	_	_	_
7	determined	determine	VBN	_	_	_
8	from	from	IN	_	_	_
9	agarose	agarose	NN	_	_	_
10	gels	gel	NNS	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	strain	strain	NN	_	_	_
7	:	:	:	_	_	_
8	RL2325	rl2325	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
10	Supplementary	supplementary	JJ	_	_	_
11	_	_	NN	_	_	_
12	files	file	NNS	_	_	_
13	_	_	IN	_	_	_
14	format	format	NN	_	_	_
15	_	_	NN	_	_	_
16	and	and	CC	_	_	_
17	_	_	NN	_	_	_
18	content	content	NN	_	_	_
19	:	:	:	_	_	_
20	Processed	process	VBN	_	_	_
21	data	datum	NNS	_	_	_
22	files	file	NNS	_	_	_
23	are	be	VBP	_	_	_
24	WIG	WIG	NNP	_	_	_
25	files	file	NNS	_	_	_
26	normalized	normalize	VBD	_	_	_
27	to	to	TO	_	_	_
28	reads	read	VBZ	_	_	_
29	per	per	IN	_	_	_
30	million	million	CD	_	_	_
31	per	per	IN	_	_	_
32	position	position	NN	_	_	_
33	.	.	.	_	_	_

1	Those	those	DT	_	_	_
2	designated	designate	VBN	_	_	_
3	\	\	NN	_	_	_
4	minus	minus	CC	_	_	_
5	\	\	NN	_	_	_
6	cover	cover	VBP	_	_	_
7	the	the	DT	_	_	_
8	minus	minus	CC	_	_	_
9	strand	strand	NN	_	_	_
10	of	of	IN	_	_	_
11	the	the	DT	_	_	_
12	genome	genome	NN	_	_	_
13	;	;	:	_	_	_
14	those	those	DT	_	_	_
15	with	with	IN	_	_	_
16	designated	designate	VBN	_	_	_
17	\	\	NN	_	_	_
18	plus	plus	CC	_	_	_
19	\	\	NN	_	_	_
20	cover	cover	VBP	_	_	_
21	the	the	DT	_	_	_
22	plus	plus	CC	_	_	_
23	strand	strand	NN	_	_	_
24	of	of	IN	_	_	_
25	the	the	DT	_	_	_
26	genome	genome	NN	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Wild-type	wild-type	JJ	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	RNA-seq	rna-seq	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Bacteria	bacterium	NNS	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Basecalls	basecall	NNS	_	_	_
11	performed	perform	VBN	_	_	_
12	using	use	VBG	_	_	_
13	Casava	Casava	NNP	_	_	_
14	versions	version	NNS	_	_	_
15	1.6	1.6	CD	_	_	_
16	or	or	CC	_	_	_
17	1.7	1.7	CD	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Bowtie	Bowtie	NNP	_	_	_
3	alignments	alignment	NNS	_	_	_
4	against	against	IN	_	_	_
5	the	the	DT	_	_	_
6	reference	reference	NN	_	_	_
7	genome	genome	NN	_	_	_
8	were	be	VBD	_	_	_
9	converted	convert	VBN	_	_	_
10	to	to	TO	_	_	_
11	wiggle	wiggle	VB	_	_	_
12	files	file	NNS	_	_	_
13	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	position	position	NN	_	_	_
3	of	of	IN	_	_	_
4	each	each	DT	_	_	_
5	alignment	alignment	NN	_	_	_
6	was	be	VBD	_	_	_
7	mapped	map	VBN	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	3	3	CD	_	_	_
11	'	'	''	_	_	_
12	end	end	NN	_	_	_
13	of	of	IN	_	_	_
14	the	the	DT	_	_	_
15	nascent	nascent	JJ	_	_	_
16	transcript	transcript	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cell	cell	NN	_	_	_
3	culture	culture	NN	_	_	_
4	was	be	VBD	_	_	_
5	rapidly	rapidly	RB	_	_	_
6	filtered	filter	VBN	_	_	_
7	in	in	IN	_	_	_
8	250	250	CD	_	_	_
9	mL	ml	NN	_	_	_
10	increments	increment	NNS	_	_	_
11	at	at	IN	_	_	_
12	37	37	CD	_	_	_
13	°C	°c	NN	_	_	_
14	over	over	IN	_	_	_
15	0.22	0.22	CD	_	_	_
16	μm	μm	NN	_	_	_
17	nitrocellulose	nitrocellulose	NN	_	_	_
18	filters	filters	NNS	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	GE	GE	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	and	and	CC	_	_	_
23	frozen	freeze	VBN	_	_	_
24	in	in	IN	_	_	_
25	liquid	liquid	JJ	_	_	_
26	nitrogen	nitrogen	NN	_	_	_
27	to	to	TO	_	_	_
28	simultaneously	simultaneously	RB	_	_	_
29	halt	halt	VB	_	_	_
30	all	all	DT	_	_	_
31	transcriptional	transcriptional	JJ	_	_	_
32	progress	progress	NN	_	_	_
33	.	.	.	_	_	_

1	Frozen	frozen	JJ	_	_	_
2	cells	cell	NNS	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	100	100	CD	_	_	_
5	μg	μg	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	were	be	VBD	_	_	_
8	pulverized	pulverize	VBN	_	_	_
9	on	on	IN	_	_	_
10	a	a	DT	_	_	_
11	Qiagen	Qiagen	NNP	_	_	_
12	TissueLyser	TissueLyser	NNP	_	_	_
13	II	II	NNP	_	_	_
14	mixer	mixer	NN	_	_	_
15	mill	mill	NN	_	_	_
16	6	6	CD	_	_	_
17	times	time	NNS	_	_	_
18	at	at	IN	_	_	_
19	15	15	CD	_	_	_
20	Hz	hz	NN	_	_	_
21	for	for	IN	_	_	_
22	3	3	CD	_	_	_
23	min	min	NN	_	_	_
24	in	in	IN	_	_	_
25	the	the	DT	_	_	_
26	presence	presence	NN	_	_	_
27	of	of	IN	_	_	_
28	500	500	CD	_	_	_
29	μL	μl	NN	_	_	_
30	frozen	frozen	JJ	_	_	_
31	lysis	lysis	NN	_	_	_
32	buffer	buffer	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	20	20	CD	_	_	_
35	mM	mm	NN	KWSUPP	_	_
36	Tris	Tris	NNP	_	_	_
37	pH	ph	NN	_	_	_
38	8	8	CD	_	_	_
39	,	,	,	_	_	_
40	0.4	0.4	CD	_	_	_
41	%	%	NN	_	_	_
42	Triton	Triton	NNP	_	_	_
43	X-100	x-100	NN	_	_	_
44	,	,	,	_	_	_
45	0.1	0.1	CD	_	_	_
46	%	%	NN	_	_	_
47	NP-40	np-40	NN	_	_	_
48	,	,	,	_	_	_
49	100	100	CD	_	_	_
50	mM	mm	NN	KWSUPP	_	_
51	NH4Cl	nh4cl	NN	_	_	_
52	,	,	,	_	_	_
53	50	50	CD	_	_	_
54	U	U	NNP	_	_	_
55	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
56	Ecoli	Ecoli	NNP	_	_	_
57	_	_	NNP	_	_	_
58	WT	WT	NNP	_	_	_
59	_	_	NNP	_	_	_
60	RNAseq	RNAseq	NNP	_	_	_
61	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
62	Escherichia	escherichia	FW	Organism	_	_
63	coli	coli	FW	Organism	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	For	for	IN	_	_	_
66	each	each	DT	_	_	_
67	sample	sample	NN	_	_	_
68	,	,	,	_	_	_
69	500	500	CD	_	_	_
70	mL	ml	NN	_	_	_
71	liquid	liquid	JJ	_	_	_
72	cultures	culture	NNS	_	_	_
73	were	be	VBD	_	_	_
74	grown	grow	VBN	_	_	_
75	in	in	IN	_	_	_
76	2.8	2.8	CD	_	_	_
77	L	l	NN	_	_	_
78	flasks	flask	NNS	_	_	_
79	with	with	IN	_	_	_
80	shaking	shake	VBG	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	180	180	CD	_	_	_
83	rpm	rpm	NN	_	_	_
84	-RRB-	-rrb-	-RRB-	_	_	_
85	at	at	IN	_	_	_
86	37	37	CD	_	_	_
87	°C	°c	NN	_	_	_
88	from	from	IN	_	_	_
89	an	a	DT	_	_	_
90	OD	od	NN	_	_	_
91	-LRB-	-lrb-	-LRB-	_	_	_
92	600	600	CD	_	_	_
93	nm	nm	NN	_	_	_
94	-RRB-	-rrb-	-RRB-	_	_	_
95	0.05	0.05	CD	_	_	_
96	to	to	TO	_	_	_
97	OD	od	CD	_	_	_
98	0.45	0.45	CD	_	_	_
99	±	±	SYM	_	_	_
100	0.05	0.05	CD	_	_	_
101	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	grown	grow	VBN	_	_	_
4	in	in	IN	_	_	_
5	MOPS	MOPS	NNP	MED	_	_
6	EZ	EZ	NNP	_	_	_
7	rich	rich	JJ	_	_	_
8	defined	define	VBN	_	_	_
9	medium	medium	NN	_	_	_
10	with	with	IN	_	_	_
11	0.2	0.2	CD	_	_	_
12	%	%	NN	_	_	_
13	glucose	glucose	NN	SUPP	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Teknova	teknova	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	:	:	:	_	_	_
9	NC	nc	NN	_	_	_
10	_	_	SYM	_	_	_
11	000913	000913	CD	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
13	genotype	genotype	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	media	media	NNS	_	_	_
16	:	:	:	_	_	_
17	MOPS	MOPS	NNP	MED	_	_
18	EZ	EZ	NNP	_	_	_
19	Rich	Rich	NNP	_	_	_
20	Defined	Defined	NNP	_	_	_
21	Media	Media	NNP	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	molecule	molecule	NN	_	_	_
24	subtype	subtype	NN	_	_	_
25	:	:	:	_	_	_
26	Total	total	JJ	_	_	_
27	RNA	rna	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	RNA-Seq	rna-seq	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Sequenced	sequence	VBN	_	_	_
32	reads	read	VBZ	_	_	_
33	were	be	VBD	_	_	_
34	trimmed	trim	VBN	_	_	_
35	for	for	IN	_	_	_
36	adaptor	adaptor	NN	_	_	_
37	sequence	sequence	NN	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	background	background	NN	_	_	_
4	:	:	:	_	_	_
5	MG1655	mg1655	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Supplementary	supplementary	JJ	_	_	_
8	_	_	NN	_	_	_
9	files	file	NNS	_	_	_
10	_	_	IN	_	_	_
11	format	format	NN	_	_	_
12	_	_	NN	_	_	_
13	and	and	CC	_	_	_
14	_	_	NN	_	_	_
15	content	content	NN	_	_	_
16	:	:	:	_	_	_
17	wiggle	wiggle	NN	_	_	_
18	files	file	NNS	_	_	_
19	with	with	IN	_	_	_
20	two	two	CD	_	_	_
21	columns	column	NNS	_	_	_
22	:	:	:	_	_	_
23	first	first	JJ	_	_	_
24	column	column	NN	_	_	_
25	containing	contain	VBG	_	_	_
26	chromosome	chromosome	NN	_	_	_
27	positions	position	NNS	_	_	_
28	and	and	CC	_	_	_
29	second	second	JJ	_	_	_
30	column	column	NN	_	_	_
31	containing	contain	VBG	_	_	_
32	the	the	DT	_	_	_
33	number	number	NN	_	_	_
34	of	of	IN	_	_	_
35	reads	read	VBZ	_	_	_
36	mapped	map	VBN	_	_	_
37	to	to	TO	_	_	_
38	the	the	DT	_	_	_
39	position	position	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	see	see	VB	_	_	_
42	publication	publication	NN	_	_	_
43	for	for	IN	_	_	_
44	details	detail	NNS	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	full	full	JJ	_	_	_
4	library	library	NN	_	_	_
5	construction	construction	NN	_	_	_
6	protocol	protocol	NN	_	_	_
7	was	be	VBD	_	_	_
8	described	describe	VBN	_	_	_
9	in	in	IN	_	_	_
10	detail	detail	NN	_	_	_
11	previously	previously	RB	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Churchman	Churchman	NNP	_	_	_
14	et	et	FW	_	_	_
15	al.	al.	FW	_	_	_
16	,	,	,	_	_	_
17	Nature	Nature	NNP	_	_	_
18	2011	2011	CD	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	Purified	purify	VBN	_	_	_
2	total	total	JJ	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	fragmented	fragmented	JJ	_	_	_
6	and	and	CC	_	_	_
7	dephosphorylated	dephosphorylate	VBN	_	_	_
8	with	with	IN	_	_	_
9	T4	t4	NN	_	_	_
10	PNK	pnk	NN	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	then	then	RB	_	_	_
14	ligated	ligate	VBD	_	_	_
15	to	to	TO	_	_	_
16	a	a	DT	_	_	_
17	5	5	CD	_	_	_
18	'	'	''	_	_	_
19	adenylated	adenylate	VBN	_	_	_
20	DNA	dna	NN	_	_	_
21	oligo	oligo	JJ	_	_	_
22	to	to	TO	_	_	_
23	generate	generate	VB	_	_	_
24	RNA	rna	NN	_	_	_
25	ranging	range	VBG	_	_	_
26	from	from	IN	_	_	_
27	30-100	30-100	CD	_	_	_
28	nt	nt	NNS	_	_	_
29	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	reverse	reverse	JJ	_	_	_
5	transcribed	transcribe	VBN	_	_	_
6	,	,	,	_	_	_
7	and	and	CC	_	_	_
8	the	the	DT	_	_	_
9	single-stranded	single-stranded	JJ	_	_	_
10	DNA	dna	NN	_	_	_
11	circularized	circularize	VBN	_	_	_
12	and	and	CC	_	_	_
13	PCR	pcr	NN	_	_	_
14	amplified	amplify	VBD	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Trimmed	trim	VBD	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	aligned	align	VBN	_	_	_
6	using	use	VBG	_	_	_
7	Bowtie	Bowtie	NNP	_	_	_
8	v0	v0	NN	_	_	_
9	.12.7	.12.7	CD	_	_	_
10	against	against	IN	_	_	_
11	the	the	DT	_	_	_
12	reference	reference	NN	_	_	_
13	genome	genome	NN	_	_	_
14	using	use	VBG	_	_	_
15	parameters	parameter	NNS	_	_	_
16	-	-	:	_	_	_
17	a	a	SYM	_	_	_
18	-	-	:	_	_	_
19	v	v	LS	_	_	_
20	3	3	LS	_	_	_
21	-	-	:	_	_	_
22	m	m	NN	_	_	_
23	1	1	CD	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	Escherichia	escherichia	FW	Organism	_	_
26	coli	coli	FW	Organism	_	_
27	str	str	FW	_	_	_
28	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	EvgSc	evgsc	NN	_	_	_
4	_	_	NN	_	_	_
5	1	1	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	EvgSc	evgsc	NN	_	_	_
8	_	_	NN	_	_	_
9	2	2	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	EvgSc	evgsc	NN	_	_	_
12	mutant	mutant	JJ	_	_	_
13	rep	rep	NN	GEN	_	_
14	1	1	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	EvgSc	evgsc	NN	_	_	_
17	mutant	mutant	JJ	_	_	_
18	rep	rep	NN	GEN	_	_
19	2	2	CD	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	EvgSc	evgsc	NN	_	_	_
22	_	_	CD	_	_	_
23	ompR	ompr	NN	GEN	_	_
24	_	_	NN	_	_	_
25	1	1	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	EvgSc	evgsc	NN	_	_	_
28	_	_	CD	_	_	_
29	ompR	ompr	NN	GEN	_	_
30	_	_	NN	_	_	_
31	2	2	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	EvgSc	evgsc	NN	_	_	_
34	ompR	ompr	NN	GEN	_	_
35	double	double	JJ	_	_	_
36	mutant	mutant	JJ	_	_	_
37	rep	rep	NN	GEN	_	_
38	1	1	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	EvgSc	evgsc	NN	_	_	_
41	ompR	ompr	NN	GEN	_	_
42	double	double	JJ	_	_	_
43	mutant	mutant	JJ	_	_	_
44	rep	rep	NN	GEN	_	_
45	2	2	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	genotype	genotype	NN	_	_	_
48	:	:	:	_	_	_
49	EvgSc	evgsc	NN	_	_	_
50	KO	ko	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	genotype	genotype	NN	_	_	_
53	:	:	:	_	_	_
54	EvgSc	evgsc	NN	_	_	_
55	ompR	ompr	NN	GEN	_	_
56	KO	ko	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	genotype	genotype	NN	_	_	_
59	:	:	:	_	_	_
60	ompR	ompr	NN	GEN	_	_
61	KO	ko	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	genotype	genotype	NN	_	_	_
64	:	:	:	_	_	_
65	Wild	Wild	NNP	_	_	_
66	Type	type	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	LB	lb	NN	MED	_	_
69	media	media	NNS	MED	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	ompR	ompr	NN	GEN	_	_
72	_	_	NN	_	_	_
73	1	1	CD	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	ompR	ompr	NN	GEN	_	_
76	_	_	NN	_	_	_
77	2	2	CD	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	ompR	ompr	NN	GEN	_	_
80	mutant	mutant	JJ	_	_	_
81	rep	rep	NN	GEN	_	_
82	1	1	CD	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	ompR	ompr	NN	GEN	_	_
85	mutant	mutant	JJ	_	_	_
86	rep	rep	NN	GEN	_	_
87	2	2	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	RNA	rna	NN	_	_	_
90	was	be	VBD	_	_	_
91	extracted	extract	VBN	_	_	_
92	using	use	VBG	_	_	_
93	RNAeasy	rnaeasy	NN	_	_	_
94	columns	column	NNS	_	_	_
95	-LRB-	-lrb-	-LRB-	_	_	_
96	Qiagen	Qiagen	NNP	_	_	_
97	-RRB-	-rrb-	-RRB-	_	_	_
98	following	follow	VBG	_	_	_
99	the	the	DT	_	_	_
100	manufacturer	manufacturer	NN	_	_	_
101	's	's	POS	_	_	_
102	recommendations	recommendation	NNS	_	_	_
103	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	quantified	quantify	VBN	_	_	_
4	using	use	VBG	_	_	_
5	a	a	DT	_	_	_
6	NanoDrop-1000	nanodrop-1000	NN	_	_	_
7	spectrophotometer	spectrophotometer	NN	_	_	_
8	and	and	CC	_	_	_
9	quality	quality	NN	_	_	_
10	was	be	VBD	_	_	_
11	monitored	monitor	VBN	_	_	_
12	with	with	IN	_	_	_
13	the	the	DT	_	_	_
14	Agilent	Agilent	NNP	_	_	_
15	2100	2100	CD	_	_	_
16	Bioanalyzer	Bioanalyzer	NNP	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Agilent	Agilent	NNP	_	_	_
19	Technologies	Technologies	NNPS	_	_	_
20	,	,	,	_	_	_
21	Santa	Santa	NNP	_	_	_
22	Clara	Clara	NNP	_	_	_
23	,	,	,	_	_	_
24	CA	CA	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
6	The	the	DT	_	_	_
7	scanned	scan	VBN	_	_	_
8	images	image	NNS	_	_	_
9	were	be	VBD	_	_	_
10	analyzed	analyze	VBN	_	_	_
11	with	with	IN	_	_	_
12	Feature	Feature	NNP	_	_	_
13	Extraction	Extraction	NNP	_	_	_
14	Software	Software	NNP	_	_	_
15	10.5	10.5	CD	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Agilent	Agilent	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	using	use	VBG	_	_	_
20	default	default	NN	_	_	_
21	parameters	parameter	NNS	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	protocol	protocol	NN	_	_	_
24	GE1	ge1	NN	_	_	_
25	_	_	NN	_	_	_
26	105	105	CD	_	_	_
27	_	_	SYM	_	_	_
28	Dec08	dec08	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	wild	wild	JJ	_	_	_
3	type	type	NN	_	_	_
4	rep	rep	NN	GEN	_	_
5	1	1	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	wild	wild	JJ	_	_	_
8	type	type	NN	_	_	_
9	rep	rep	NN	GEN	_	_
10	2	2	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	WT	wt	JJ	_	_	_
13	_	_	NN	_	_	_
14	1	1	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	WT	wt	JJ	_	_	_
17	_	_	NN	_	_	_
18	2	2	CD	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	Automatic	Automatic	NNP	_	_	_
21	extractor	extractor	NN	_	_	_
22	in	in	IN	_	_	_
23	Verigene	verigene	JJ	_	_	_
24	system	system	NN	_	_	_
25	of	of	IN	_	_	_
26	genomic	genomic	JJ	_	_	_
27	DNA	dna	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Blood	blood	NN	_	_	_
30	culture	culture	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Blood	blood	NN	_	_	_
33	culture	culture	NN	_	_	_
34	bottle	bottle	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	culture	culture	NN	_	_	_
37	system	system	NN	_	_	_
38	:	:	:	_	_	_
39	BACTEC	BACTEC	NNP	_	_	_
40	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
41	Direct	Direct	NNP	_	_	_
42	testing	testing	NN	_	_	_
43	of	of	IN	_	_	_
44	culture	culture	NN	_	_	_
45	broth	broth	NN	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	Standard	standard	JJ	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	or	or	CC	_	_	_
50	after	after	IN	_	_	_
51	centrifugation	centrifugation	NN	_	_	_
52	of	of	IN	_	_	_
53	culture	culture	NN	_	_	_
54	broth	broth	NN	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	Supernatant	supernatant	NN	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	Escherichia	escherichia	FW	Organism	_	_
60	coli	coli	FW	Organism	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	gram	gram	NN	_	_	_
63	status	status	NN	_	_	_
64	:	:	:	_	_	_
65	Gram-negative	gram-negative	JJ	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
67	Sample	sample	VBP	_	_	_
68	79	79	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
70	Scatter	scatter	JJ	_	_	_
71	signal	signal	NN	_	_	_
72	intensity	intensity	NN	_	_	_
73	after	after	IN	_	_	_
74	illumination	illumination	NN	_	_	_
75	at	at	IN	_	_	_
76	150	150	CD	_	_	_
77	ms	m	NNS	_	_	_
78	exposure	exposure	NN	_	_	_
79	without	without	IN	_	_	_
80	normalization	normalization	NN	_	_	_
81	,	,	,	_	_	_
82	without	without	IN	_	_	_
83	transformation	transformation	NN	_	_	_
84	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	non-normalized	non-normalized	JJ	_	_	_
3	signals	signal	NNS	_	_	_
4	form	form	VBP	_	_	_
5	the	the	DT	_	_	_
6	basis	basis	NN	_	_	_
7	of	of	IN	_	_	_
8	conclusions	conclusion	NNS	_	_	_
9	in	in	IN	_	_	_
10	the	the	DT	_	_	_
11	accompanying	accompany	VBG	_	_	_
12	manuscript	manuscript	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	source	source	NN	_	_	_
3	:	:	:	_	_	_
4	Peripheral	peripheral	JJ	_	_	_
5	blood	blood	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	treatment	treatment	NN	_	_	_
8	:	:	:	_	_	_
9	Supernatant	supernatant	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Cells	cell	NNS	_	_	_
12	were	be	VBD	_	_	_
13	grown	grow	VBN	_	_	_
14	at	at	IN	_	_	_
15	30	30	CD	_	_	_
16	°C	°c	NN	_	_	_
17	in	in	IN	_	_	_
18	LB	lb	NN	MED	_	_
19	medium	medium	NN	MED	_	_
20	to	to	TO	_	_	_
21	an	a	DT	_	_	_
22	OD600	od600	NN	_	_	_
23	of	of	IN	_	_	_
24	0.55-0.6	0.55-0.6	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
26	culture	culture	NN	_	_	_
27	denity	denity	NN	_	_	_
28	:	:	:	_	_	_
29	OD600	od600	NN	_	_	_
30	=	=	JJ	_	_	_
31	0.55-0.6	0.55-0.6	CD	_	_	_
32	culture	culture	NN	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	Escherichia	escherichia	FW	Organism	_	_
35	coli	coli	FW	Organism	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	genotype	genotype	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	LOWESS	lowess	NN	_	_	_
40	normalized	normalize	VBD	_	_	_
41	,	,	,	_	_	_
42	background	background	NN	_	_	_
43	subtracted	subtract	VBD	_	_	_
44	data	datum	NNS	_	_	_
45	obtained	obtain	VBN	_	_	_
46	from	from	IN	_	_	_
47	signals	signal	NNS	_	_	_
48	.	.	.	_	_	_

1	Agilent	Agilent	NNP	_	_	_
2	GeneSpring	GeneSpring	NNP	_	_	_
3	GX	GX	NNP	_	_	_
4	7.3	7.3	CD	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	pFlag-only	pflag-only	NN	_	_	_
3	control	control	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	RhIB	rhib	NN	_	_	_
6	wild	wild	JJ	_	_	_
7	type	type	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	RhlBP238L	rhlbp238l	NN	_	_	_
10	mutant	mutant	JJ	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	RhlBP238L	rhlbp238l	NN	_	_	_
13	vs	vs	CC	_	_	_
14	flag	flag	NN	_	_	_
15	only	only	RB	_	_	_
16	1	1	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	RhlBP238L	rhlbp238l	NN	_	_	_
19	vs	vs	CC	_	_	_
20	flag	flag	NN	_	_	_
21	only	only	RB	_	_	_
22	2	2	CD	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	RhlBP238L	rhlbp238l	NN	_	_	_
25	vs	vs	CC	_	_	_
26	flag	flag	NN	_	_	_
27	only	only	RB	_	_	_
28	3	3	CD	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	RhlBwt	rhlbwt	NN	_	_	_
31	vs	vs	CC	_	_	_
32	flag	flag	NN	_	_	_
33	only	only	RB	_	_	_
34	1	1	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	RhlBwt	rhlbwt	NN	_	_	_
37	vs	vs	CC	_	_	_
38	flag	flag	NN	_	_	_
39	only	only	RB	_	_	_
40	2	2	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	RhlBwt	rhlbwt	NN	_	_	_
43	vs	vs	CC	_	_	_
44	flag	flag	NN	_	_	_
45	only	only	RB	_	_	_
46	3	3	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	strain	strain	NN	_	_	_
49	:	:	:	_	_	_
50	BL21	bl21	NN	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	DE3	de3	NN	_	_	_
53	-RRB-	-rrb-	-RRB-	_	_	_
54	rne131	rne131	NN	_	_	_
55	DrhlB	drhlb	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	Total	total	JJ	_	_	_
58	RNA	rna	NN	_	_	_
59	was	be	VBD	_	_	_
60	isolated	isolate	VBN	_	_	_
61	according	accord	VBG	_	_	_
62	to	to	TO	_	_	_
63	the	the	DT	_	_	_
64	RNeasy	RNeasy	NNP	_	_	_
65	Mini	Mini	NNP	_	_	_
66	Kit	kit	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	QIAGEN	qiagen	NN	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	manufacturer	manufacturer	NN	_	_	_
71	's	's	POS	_	_	_
72	protocol	protocol	NN	_	_	_
73	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	All	All	NNP	_	_	_
3	cultures	culture	NNS	_	_	_
4	grown	grow	VBN	_	_	_
5	up	up	RB	_	_	_
6	to	to	TO	_	_	_
7	0.6	0.6	CD	_	_	_
8	OD600	od600	NN	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	at	at	IN	_	_	_
12	200	200	CD	_	_	_
13	rpm	rpm	NN	_	_	_
14	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	1,2,5	1,2,5	CD	_	_	_
3	and	and	CC	_	_	_
4	6	6	CD	_	_	_
5	were	be	VBD	_	_	_
6	grown	grow	VBN	_	_	_
7	at	at	IN	_	_	_
8	30	30	CD	_	_	_
9	°C	°c	NN	_	_	_
10	whereas	whereas	IN	_	_	_
11	samples	sample	NNS	_	_	_
12	3	3	CD	_	_	_
13	and	and	CC	_	_	_
14	4	4	CD	_	_	_
15	were	be	VBD	_	_	_
16	grown	grow	VBN	_	_	_
17	at	at	IN	_	_	_
18	37	37	CD	_	_	_
19	°C	°c	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	analysis	analysis	NN	_	_	_
3	:	:	:	_	_	_
4	in	in	FW	_	_	_
5	vitro	vitro	FW	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	analysis	analysis	NN	_	_	_
8	:	:	:	_	_	_
9	in	in	FW	_	_	_
10	vivo	vivo	FW	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Basecalls	basecall	NNS	_	_	_
13	were	be	VBD	_	_	_
14	performed	perform	VBN	_	_	_
15	using	use	VBG	_	_	_
16	CASAVA	CASAVA	NNP	_	_	_
17	.1.8	.1.8	CD	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Cultures	culture	NNS	_	_	_
20	for	for	IN	_	_	_
21	samples	sample	NNS	_	_	_
22	1	1	CD	_	_	_
23	and	and	CC	_	_	_
24	2	2	CD	_	_	_
25	were	be	VBD	_	_	_
26	incubated	incubate	VBN	_	_	_
27	at	at	IN	_	_	_
28	44	44	CD	_	_	_
29	°C	°c	NN	_	_	_
30	for	for	IN	_	_	_
31	45	45	CD	_	_	_
32	min	min	NN	_	_	_
33	after	after	IN	_	_	_
34	growth	growth	NN	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	cell	cell	NN	_	_	_
5	cultures	culture	NNS	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	Escherichia	escherichia	FW	Organism	_	_
8	coli	coli	FW	Organism	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Genome	Genome	NNP	_	_	_
11	_	_	NNP	_	_	_
12	build	build	VB	_	_	_
13	:	:	:	_	_	_
14	U00096	u00096	NN	_	_	_
15	.2	.2	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	genotype	genotype	NN	_	_	_
18	:	:	:	_	_	_
19	n	n	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	genotype	genotype	NN	_	_	_
22	:	:	:	_	_	_
23	rne-3071	rne-3071	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	ts	t	NNS	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
28	genotype	genotype	NN	_	_	_
29	:	:	:	_	_	_
30	rne	rne	NN	GEN	_	_
31	wild-type	wild-type	JJ	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	genotype	genotype	NN	_	_	_
34	:	:	:	_	_	_
35	rng	rng	NN	GEN	_	_
36	mutant	mutant	JJ	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	genotype	genotype	NN	_	_	_
39	:	:	:	_	_	_
40	rng	rng	NN	GEN	_	_
41	wild-type	wild-type	JJ	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	incubation	incubation	NN	_	_	_
44	time	time	NN	_	_	_
45	:	:	:	_	_	_
46	0	0	CD	_	_	_
47	min	min	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	incubation	incubation	NN	_	_	_
50	time	time	NN	_	_	_
51	:	:	:	_	_	_
52	10	10	CD	_	_	_
53	min	min	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	incubation	incubation	NN	_	_	_
56	time	time	NN	_	_	_
57	:	:	:	_	_	_
58	n	n	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	Libraries	library	NNS	_	_	_
61	were	be	VBD	_	_	_
62	prepared	prepare	VBN	_	_	_
63	for	for	IN	_	_	_
64	sequencing	sequencing	NN	_	_	_
65	using	use	VBG	_	_	_
66	standard	standard	JJ	_	_	_
67	Illumina	Illumina	NNP	_	_	_
68	protocols	protocol	NNS	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
70	RNA-Seq	rna-seq	JJ	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	rne-3071	rne-3071	NN	_	_	_
73	ts	t	NNS	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	rne	rne	NN	GEN	_	_
76	wild-type	wild-type	JJ	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	rng	rng	NN	GEN	_	_
79	mutant	mutant	JJ	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	rng	rng	NN	GEN	_	_
82	wild-type	wild-type	JJ	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	Sequence	sequence	NN	_	_	_
85	reads	read	VBZ	_	_	_
86	were	be	VBD	_	_	_
87	trimmed	trim	VBN	_	_	_
88	for	for	IN	_	_	_
89	adaptor	adaptor	NN	_	_	_
90	reads	read	VBZ	_	_	_
91	and	and	CC	_	_	_
92	mapped	map	VBN	_	_	_
93	to	to	TO	_	_	_
94	E.	e.	FW	_	_	_
95	coli	coli	FW	_	_	_
96	K12	k12	NN	_	_	_
97	MG1655	mg1655	NN	_	_	_
98	genome	genome	NN	_	_	_
99	using	use	VBG	_	_	_
100	CLC	clc	NN	_	_	_
101	Genomics	genomic	NNS	_	_	_
102	Workbench	workbench	JJ	_	_	_
103	6.0.1	6.0.1	CD	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	strain	strain	NN	_	_	_
106	:	:	:	_	_	_
107	BW25113	bw25113	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	strain	strain	NN	_	_	_
110	:	:	:	_	_	_
111	GM11	gm11	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	strain	strain	NN	_	_	_
114	:	:	:	_	_	_
115	MC1061	mc1061	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	strain	strain	NN	_	_	_
118	:	:	:	_	_	_
119	N3431	n3431	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	strain	strain	NN	_	_	_
122	:	:	:	_	_	_
123	N3433	n3433	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	Supplementary	supplementary	JJ	_	_	_
126	_	_	NN	_	_	_
127	files	file	NNS	_	_	_
128	_	_	IN	_	_	_
129	format	format	NN	_	_	_
130	_	_	NN	_	_	_
131	and	and	CC	_	_	_
132	_	_	NN	_	_	_
133	content	content	NN	_	_	_
134	:	:	:	_	_	_
135	Processed	process	VBN	_	_	_
136	files	file	NNS	_	_	_
137	are	be	VBP	_	_	_
138	in	in	IN	_	_	_
139	tab	tab	NN	_	_	_
140	delimited	delimit	VBD	_	_	_
141	format	format	NN	_	_	_
142	.	.	.	_	_	_

1	Separate	separate	JJ	_	_	_
2	files	file	NNS	_	_	_
3	are	be	VBP	_	_	_
4	provided	provide	VBN	_	_	_
5	for	for	IN	_	_	_
6	the	the	DT	_	_	_
7	forward	forward	JJ	_	_	_
8	and	and	CC	_	_	_
9	reverse	reverse	JJ	_	_	_
10	strands	strand	NNS	_	_	_
11	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	start	start	NN	_	_	_
3	and	and	CC	_	_	_
4	end	end	NN	_	_	_
5	coordinates	coordinate	VBZ	_	_	_
6	should	should	MD	_	_	_
7	be	be	VB	_	_	_
8	the	the	DT	_	_	_
9	same	same	JJ	_	_	_
10	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	line	line	NN	_	_	_
3	in	in	IN	_	_	_
4	the	the	DT	_	_	_
5	data	data	NN	_	_	_
6	set	set	NN	_	_	_
7	represents	represent	VBZ	_	_	_
8	the	the	DT	_	_	_
9	position	position	NN	_	_	_
10	of	of	IN	_	_	_
11	the	the	DT	_	_	_
12	first	first	JJ	_	_	_
13	nucleotide	nucleotide	NN	_	_	_
14	at	at	IN	_	_	_
15	the	the	DT	_	_	_
16	5	5	CD	_	_	_
17	'	'	''	_	_	_
18	end	end	NN	_	_	_
19	of	of	IN	_	_	_
20	a	a	DT	_	_	_
21	sequence	sequence	NN	_	_	_
22	that	that	WDT	_	_	_
23	could	could	MD	_	_	_
24	be	be	VB	_	_	_
25	mapped	map	VBN	_	_	_
26	to	to	TO	_	_	_
27	the	the	DT	_	_	_
28	E.	e.	FW	_	_	_
29	coli	coli	FW	_	_	_
30	genome	genome	NN	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	T170V	t170v	NN	_	_	_
3	0	0	CD	_	_	_
4	min	min	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	T170V	t170v	NN	_	_	_
7	10	10	CD	_	_	_
8	min	min	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Total	total	JJ	_	_	_
11	RNA	rna	NN	_	_	_
12	was	be	VBD	_	_	_
13	isolated	isolate	VBN	_	_	_
14	as	as	IN	_	_	_
15	desribed	desribe	VBN	_	_	_
16	in	in	IN	_	_	_
17	Kime	Kime	NNP	_	_	_
18	et	et	FW	_	_	_
19	al.	al.	FW	_	_	_
20	,	,	,	_	_	_
21	2008	2008	CD	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	All	All	NNP	_	_	_
24	samples	sample	NNS	_	_	_
25	were	be	VBD	_	_	_
26	extracted	extract	VBN	_	_	_
27	using	use	VBG	_	_	_
28	the	the	DT	_	_	_
29	hot	hot	JJ	_	_	_
30	phenol	phenol	NN	_	_	_
31	extraction	extraction	NN	_	_	_
32	with	with	IN	_	_	_
33	DNA	dna	NN	_	_	_
34	digestion	digestion	NN	_	_	_
35	,	,	,	_	_	_
36	following	follow	VBG	_	_	_
37	standard	standard	JJ	_	_	_
38	protocol	protocol	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
40	BigWIG	bigwig	NN	_	_	_
41	files	file	NNS	_	_	_
42	were	be	VBD	_	_	_
43	viewed	view	VBN	_	_	_
44	and	and	CC	_	_	_
45	annotated	annotated	JJ	_	_	_
46	using	use	VBG	_	_	_
47	Jbrowse	Jbrowse	NNP	_	_	_
48	and	and	CC	_	_	_
49	Integrated	Integrated	NNP	_	_	_
50	Genome	Genome	NNP	_	_	_
51	Viewer	Viewer	NNP	_	_	_
52	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	cDNA	cdna	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	constructed	construct	VBN	_	_	_
6	at	at	IN	_	_	_
7	Vertis	Vertis	NNP	_	_	_
8	in	in	IN	_	_	_
9	Germany	Germany	NNP	_	_	_
10	using	use	VBG	_	_	_
11	a	a	DT	_	_	_
12	ligation	ligation	NN	_	_	_
13	based	base	VBN	_	_	_
14	stratagey	stratagey	NN	_	_	_
15	for	for	IN	_	_	_
16	Illumina	Illumina	NNP	_	_	_
17	whole	whole	JJ	_	_	_
18	transcriptome	transcriptome	NN	_	_	_
19	sequencing	sequencing	NN	_	_	_
20	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	DNase	dnase	NN	_	_	_
5	I	i	CD	_	_	_
6	digested	digest	VBN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	was	be	VBD	_	_	_
9	fragmented	fragment	VBN	_	_	_
10	by	by	IN	_	_	_
11	RNase	rnase	NN	_	_	_
12	III	iii	CD	_	_	_
13	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	samples	sample	NNS	_	_	_
3	labeled	label	VBN	_	_	_
4	as	as	IN	_	_	_
5	TEX	TEX	NNP	_	_	_
6	were	be	VBD	_	_	_
7	also	also	RB	_	_	_
8	subsequently	subsequently	RB	_	_	_
9	digested	digest	VBN	_	_	_
10	with	with	IN	_	_	_
11	Terminator	Terminator	NNP	_	_	_
12	Exonuclease	Exonuclease	NNP	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	TEX	TEX	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	Pyrophosphate	pyrophosphate	NN	_	_	_
2	groups	group	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	from	from	IN	_	_	_
6	the	the	DT	_	_	_
7	5	5	CD	_	_	_
8	′	′	NN	_	_	_
9	terminus	terminus	NN	_	_	_
10	using	use	VBG	_	_	_
11	tobacco	tobacco	NN	_	_	_
12	acid	acid	NN	_	_	_
13	pyrophosphatase	pyrophosphatase	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	TAP	tap	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	an	a	DT	_	_	_
20	RNA	rna	NN	_	_	_
21	adapter	adapter	NN	_	_	_
22	was	be	VBD	_	_	_
23	ligated	ligate	VBN	_	_	_
24	to	to	TO	_	_	_
25	the	the	DT	_	_	_
26	5	5	CD	_	_	_
27	′	′	NN	_	_	_
28	end	end	NN	_	_	_
29	of	of	IN	_	_	_
30	the	the	DT	_	_	_
31	RNA	rna	NN	_	_	_
32	.	.	.	_	_	_

1	First-strand	first-strand	JJ	_	_	_
2	synthesis	synthesis	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	using	use	VBG	_	_	_
6	standard	standard	JJ	_	_	_
7	Illumina	Illumina	NNP	_	_	_
8	protocols	protocol	NNS	_	_	_
9	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cell	cell	NN	_	_	_
3	culture	culture	NN	_	_	_
4	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
5	Escherichia	escherichia	FW	Organism	_	_
6	coli	coli	FW	Organism	_	_
7	BW38028	bw38028	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	For	for	IN	_	_	_
10	alignment	alignment	NN	_	_	_
11	of	of	IN	_	_	_
12	the	the	DT	_	_	_
13	reads	read	VBZ	_	_	_
14	contained	contain	VBN	_	_	_
15	within	within	IN	_	_	_
16	the	the	DT	_	_	_
17	fastq	fastq	NN	_	_	_
18	files	file	VBZ	_	_	_
19	to	to	TO	_	_	_
20	the	the	DT	_	_	_
21	E.	e.	FW	_	_	_
22	coli	coli	FW	_	_	_
23	MG1655	mg1655	NN	_	_	_
24	reference	reference	NN	_	_	_
25	genome	genome	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	RefSeq	refseq	NN	_	_	_
28	NC	nc	NN	_	_	_
29	_	_	CD	_	_	_
30	U00096	u00096	NN	_	_	_
31	.3	.3	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	,	,	,	_	_	_
34	the	the	DT	_	_	_
35	short	short	JJ	_	_	_
36	read	read	NN	_	_	_
37	alignment	alignment	NN	_	_	_
38	tool	tool	NN	_	_	_
39	Bowtie2	bowtie2	NN	_	_	_
40	was	be	VBD	_	_	_
41	utilized	utilize	VBN	_	_	_
42	under	under	IN	_	_	_
43	default	default	NN	_	_	_
44	settings	setting	NNS	_	_	_
45	.	.	.	_	_	_

1	Bowtie	Bowtie	NNP	_	_	_
2	parameters	parameter	NNS	_	_	_
3	were	be	VBD	_	_	_
4	set	set	VBN	_	_	_
5	to	to	TO	_	_	_
6	include	include	VB	_	_	_
7	only	only	RB	_	_	_
8	perfect	perfect	JJ	_	_	_
9	matches	match	NNS	_	_	_
10	and	and	CC	_	_	_
11	map	map	NN	GEN	_	_
12	once	once	RB	_	_	_
13	reads	read	VBZ	_	_	_
14	that	that	IN	_	_	_
15	map	map	NN	GEN	_	_
16	to	to	TO	_	_	_
17	more	more	JJR	_	_	_
18	than	than	IN	_	_	_
19	one	one	CD	_	_	_
20	genome	genome	NN	_	_	_
21	location	location	NN	_	_	_
22	,	,	,	_	_	_
23	i.e.	i.e.	FW	_	_	_
24	,	,	,	_	_	_
25	uniquely	uniquely	RB	_	_	_
26	mapped	map	VBN	_	_	_
27	reads	read	VBZ	_	_	_
28	are	be	VBP	_	_	_
29	retained	retain	VBN	_	_	_
30	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	output	output	NN	_	_	_
3	Bowtie2	bowtie2	NN	_	_	_
4	was	be	VBD	_	_	_
5	a	a	DT	_	_	_
6	SAM	SAM	NNP	_	_	_
7	files	file	NNS	_	_	_
8	for	for	IN	_	_	_
9	each	each	DT	_	_	_
10	sample	sample	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	Reference	Reference	NNP	_	_	_
7	genome	genome	NN	_	_	_
8	for	for	IN	_	_	_
9	E.	e.	FW	_	_	_
10	coli	coli	FW	_	_	_
11	MG1655	mg1655	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	RefSeq	refseq	NN	_	_	_
14	NC	nc	NN	_	_	_
15	_	_	CD	_	_	_
16	000913.3	000913.3	CD	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	genotype	genotype	NN	_	_	_
3	:	:	:	_	_	_
4	rpoS	rpos	NN	GEN	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	genotype	genotype	NN	_	_	_
7	:	:	:	_	_	_
8	wt	wt	JJ	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	growth	growth	NN	_	_	_
11	phase	phase	NN	_	_	_
12	:	:	:	_	_	_
13	30	30	CD	_	_	_
14	min	min	NN	_	_	_
15	post	post	NN	_	_	_
16	stationary	stationary	JJ	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	growth	growth	NN	_	_	_
19	phase	phase	NN	_	_	_
20	:	:	:	_	_	_
21	Log	log	VB	_	_	_
22	phase	phase	NN	_	_	_
23	OD	od	NN	_	_	_
24	0.4	0.4	CD	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	Prior	prior	RB	_	_	_
27	to	to	TO	_	_	_
28	total	total	JJ	_	_	_
29	RNA	rna	NN	_	_	_
30	extraction	extraction	NN	_	_	_
31	harvested	harvest	VBN	_	_	_
32	bacterial	bacterial	JJ	_	_	_
33	cells	cell	NNS	_	_	_
34	were	be	VBD	_	_	_
35	stored	store	VBN	_	_	_
36	at	at	IN	_	_	_
37	-80.0	-80.0	CD	_	_	_
38	°C	°c	NN	_	_	_
39	in	in	IN	_	_	_
40	an	a	DT	_	_	_
41	equal	equal	JJ	_	_	_
42	volume	volume	NN	_	_	_
43	of	of	IN	_	_	_
44	RNAlater	rnalater	NN	_	_	_
45	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	rpoS	rpos	NN	GEN	_	_
5	_	_	CD	_	_	_
6	N	n	NN	_	_	_
7	_	_	CD	_	_	_
8	strv	strv	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	rpoS	rpos	NN	GEN	_	_
11	_	_	CD	_	_	_
12	N	n	NN	_	_	_
13	_	_	SYM	_	_	_
14	strv	strv	FW	_	_	_
15	_	_	FW	_	_	_
16	TEX	tex	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	sample	sample	NN	_	_	_
19	type	type	NN	_	_	_
20	:	:	:	_	_	_
21	no	no	DT	_	_	_
22	RNA	rna	NN	_	_	_
23	treatment	treatment	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Sequence	sequence	NN	_	_	_
26	data	datum	NNS	_	_	_
27	was	be	VBD	_	_	_
28	processed	process	VBN	_	_	_
29	by	by	IN	_	_	_
30	conversion	conversion	NN	_	_	_
31	of	of	IN	_	_	_
32	the	the	DT	_	_	_
33	sample	sample	NN	_	_	_
34	alignment	alignment	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	BAM	bam	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	files	file	VBZ	_	_	_
39	to	to	TO	_	_	_
40	strand-specific	strand-specific	JJ	_	_	_
41	base	base	NN	_	_	_
42	count	count	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	BigWIG	bigwig	NN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	files	file	NNS	_	_	_
47	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	accomplish	accomplish	VB	_	_	_
3	this	this	DT	_	_	_
4	an	a	DT	_	_	_
5	in-house	in-house	JJ	_	_	_
6	script	script	NN	_	_	_
7	was	be	VBD	_	_	_
8	created	create	VBN	_	_	_
9	to	to	TO	_	_	_
10	extract	extract	VB	_	_	_
11	strand-specific	strand-specific	JJ	_	_	_
12	base	base	NN	_	_	_
13	count	count	NN	_	_	_
14	data	datum	NNS	_	_	_
15	from	from	IN	_	_	_
16	BAM	BAM	NNP	_	_	_
17	files	file	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	outputs	output	NNS	_	_	_
20	are	be	VBP	_	_	_
21	positive	positive	JJ	_	_	_
22	and	and	CC	_	_	_
23	negative	negative	JJ	_	_	_
24	strand	strand	NN	_	_	_
25	BigWIG	bigwig	NN	_	_	_
26	files	file	NNS	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	BW38028	bw38028	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Supplementary	supplementary	JJ	_	_	_
7	_	_	NN	_	_	_
8	files	file	NNS	_	_	_
9	_	_	IN	_	_	_
10	format	format	NN	_	_	_
11	_	_	NN	_	_	_
12	and	and	CC	_	_	_
13	_	_	NN	_	_	_
14	content	content	NN	_	_	_
15	:	:	:	_	_	_
16	BigWIG	bigwig	NN	_	_	_
17	files	file	NNS	_	_	_
18	are	be	VBP	_	_	_
19	provided	provide	VBN	_	_	_
20	showing	show	VBG	_	_	_
21	uniquely	uniquely	RB	_	_	_
22	mapped	map	VBN	_	_	_
23	sequence	sequence	NN	_	_	_
24	reads	read	VBZ	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	data	datum	NNS	_	_	_
4	output	output	NN	_	_	_
5	from	from	IN	_	_	_
6	the	the	DT	_	_	_
7	Illumina	Illumina	NNP	_	_	_
8	Hiseq	Hiseq	NNP	_	_	_
9	System	System	NNP	_	_	_
10	was	be	VBD	_	_	_
11	obtained	obtain	VBN	_	_	_
12	directly	directly	RB	_	_	_
13	from	from	IN	_	_	_
14	Vertis	Vertis	NNP	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	treatment	treatment	NN	_	_	_
17	:	:	:	_	_	_
18	Carbon	Carbon	NNP	_	_	_
19	starvation	starvation	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	treatment	treatment	NN	_	_	_
22	:	:	:	_	_	_
23	log	log	NN	_	_	_
24	phase	phase	NN	_	_	_
25	sample	sample	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	treatment	treatment	NN	_	_	_
28	:	:	:	_	_	_
29	Nitrogen	nitrogen	NN	_	_	_
30	starvation	starvation	NN	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	Used	use	VBD	_	_	_
33	SAMTOOLS	samtools	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Li	Li	NNP	_	_	_
36	,	,	,	_	_	_
37	et	et	FW	_	_	_
38	al.	al.	FW	_	_	_
39	,	,	,	_	_	_
40	PMID	pmid	NN	_	_	_
41	1950593	1950593	CD	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	to	to	TO	_	_	_
44	sort	sort	VB	_	_	_
45	and	and	CC	_	_	_
46	index	index	NN	_	_	_
47	the	the	DT	_	_	_
48	SAM	SAM	NNP	_	_	_
49	files	file	NNS	_	_	_
50	obtained	obtain	VBN	_	_	_
51	from	from	IN	_	_	_
52	Bowtie2	bowtie2	NN	_	_	_
53	and	and	CC	_	_	_
54	convert	convert	VB	_	_	_
55	them	they	PRP	_	_	_
56	to	to	TO	_	_	_
57	BAM	BAM	NNP	_	_	_
58	format	format	NN	_	_	_
59	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Wild	Wild	NNP	_	_	_
3	type	type	NN	_	_	_
4	E.	e.	FW	_	_	_
5	coli	coli	FW	_	_	_
6	K-12	k-12	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	strain	strain	NN	_	_	_
9	BW38038	bw38038	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	and	and	CC	_	_	_
12	BW39452	bw39452	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	ΔrpoS	δrpos	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	cultures	culture	NNS	_	_	_
17	were	be	VBD	_	_	_
18	grown	grow	VBN	_	_	_
19	on	on	IN	_	_	_
20	MOPS	mop	NNS	MED	_	_
21	glucose	glucose	NN	SUPP	_	_
22	minimal	minimal	JJ	_	_	_
23	medium	medium	NN	_	_	_
24	with	with	IN	_	_	_
25	0.2	0.2	CD	_	_	_
26	%	%	NN	_	_	_
27	glucose	glucose	NN	SUPP	_	_
28	as	as	IN	_	_	_
29	sole	sole	JJ	_	_	_
30	carbon	carbon	NN	_	_	_
31	source	source	NN	_	_	_
32	at	at	IN	_	_	_
33	37	37	CD	_	_	_
34	°C	°c	NN	_	_	_
35	,	,	,	_	_	_
36	pH	ph	NN	_	_	_
37	was	be	VBD	_	_	_
38	initially	initially	RB	_	_	_
39	7.4	7.4	CD	_	_	_
40	,	,	,	_	_	_
41	and	and	CC	_	_	_
42	the	the	DT	_	_	_
43	agitation	agitation	NN	_	_	_
44	speed	speed	NN	_	_	_
45	was	be	VBD	_	_	_
46	500	500	CD	_	_	_
47	rpm	rpm	NN	_	_	_
48	.	.	.	_	_	_

1	Culture	culture	NN	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	harvested	harvest	VBN	_	_	_
5	during	during	IN	_	_	_
6	logarithmic	logarithmic	JJ	_	_	_
7	growth	growth	NN	_	_	_
8	and	and	CC	_	_	_
9	following	follow	VBG	_	_	_
10	entry	entry	NN	_	_	_
11	into	into	IN	_	_	_
12	stationary	stationary	JJ	GrowthPhase	_	_
13	phase	phase	NN	GrowthPhase	_	_
14	for	for	IN	_	_	_
15	the	the	DT	_	_	_
16	WT	WT	NNP	_	_	_
17	and	and	CC	_	_	_
18	rpoS	rpos	NN	GEN	_	_
19	mutant	mutant	NN	_	_	_
20	.	.	.	_	_	_

1	OD600	od600	CD	_	_	_
2	measurements	measurement	NNS	_	_	_
3	were	be	VBD	_	_	_
4	made	make	VBN	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	Beckman	Beckman	NNP	_	_	_
8	Coulter	Coulter	NNP	_	_	_
9	DU	DU	NNP	_	_	_
10	800	800	CD	_	_	_
11	spectrophotometer	spectrophotometer	NN	_	_	_
12	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	harvested	harvest	VBN	_	_	_
4	directly	directly	RB	_	_	_
5	into	into	IN	_	_	_
6	ice-cold	ice-cold	JJ	_	_	_
7	RNAlater	rnalater	NN	_	_	_
8	at	at	IN	_	_	_
9	a	a	DT	_	_	_
10	1:1	1:1	CD	_	_	_
11	dilution	dilution	NN	_	_	_
12	to	to	TO	_	_	_
13	protect	protect	VB	_	_	_
14	RNA	rna	NN	_	_	_
15	from	from	IN	_	_	_
16	degradation	degradation	NN	_	_	_
17	and	and	CC	_	_	_
18	cells	cell	NNS	_	_	_
19	then	then	RB	_	_	_
20	were	be	VBD	_	_	_
21	pelleted	pellete	VBN	_	_	_
22	by	by	IN	_	_	_
23	centrifugation	centrifugation	NN	_	_	_
24	at	at	IN	_	_	_
25	8000rpm	8000rpm	CD	_	_	_
26	for	for	IN	_	_	_
27	10	10	CD	_	_	_
28	minutes	minute	NNS	_	_	_
29	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	pellets	pellet	NNS	_	_	_
3	were	be	VBD	_	_	_
4	stored	store	VBN	_	_	_
5	at	at	IN	_	_	_
6	-80	-80	CD	_	_	_
7	°C	°c	NN	_	_	_
8	in	in	IN	_	_	_
9	an	a	DT	_	_	_
10	equal	equal	JJ	_	_	_
11	volume	volume	NN	_	_	_
12	of	of	IN	_	_	_
13	RNAlater	rnalater	NN	_	_	_
14	prior	prior	RB	_	_	_
15	to	to	TO	_	_	_
16	RNA	rna	NN	_	_	_
17	extraction	extraction	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	WT	wt	JJ	_	_	_
3	_	_	NN	_	_	_
4	glucose	glucose	NN	SUPP	_	_
5	_	_	CD	_	_	_
6	log	log	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	WT	wt	JJ	_	_	_
9	_	_	NN	_	_	_
10	glucose	glucose	NN	SUPP	_	_
11	_	_	CD	_	_	_
12	log	log	NN	_	_	_
13	_	_	CD	_	_	_
14	TEX	TEX	NNP	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	WT	WT	NNP	_	_	_
17	_	_	VBD	_	_	_
18	glucose	glucose	NN	SUPP	_	_
19	_	_	CD	_	_	_
20	stat	stat	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	WT	wt	JJ	_	_	_
23	_	_	NN	_	_	_
24	glucose	glucose	NN	SUPP	_	_
25	_	_	CD	_	_	_
26	stat	stat	NN	_	_	_
27	_	_	CD	_	_	_
28	TEX	TEX	NNP	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	WT	WT	NNP	_	_	_
31	_	_	VBD	_	_	_
32	N	n	NN	_	_	_
33	_	_	CD	_	_	_
34	strv	strv	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	WT	wt	JJ	_	_	_
37	_	_	NN	_	_	_
38	N	n	NN	_	_	_
39	_	_	CD	_	_	_
40	strv	strv	NN	_	_	_
41	_	_	CD	_	_	_
42	TEX	TEX	NNP	_	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	10	10	CD	_	_	_
45	mM	mm	NN	KWSUPP	_	_
46	of	of	IN	_	_	_
47	sodium	sodium	NN	_	_	_
48	phosphate	phosphate	NN	_	_	_
49	and	and	CC	_	_	_
50	formaldehyde	formaldehyde	NN	_	_	_
51	to	to	TO	_	_	_
52	a	a	DT	_	_	_
53	final	final	JJ	_	_	_
54	concentration	concentration	NN	_	_	_
55	of	of	IN	_	_	_
56	1	1	CD	_	_	_
57	%	%	NN	_	_	_
58	were	be	VBD	_	_	_
59	then	then	RB	_	_	_
60	added	add	VBN	_	_	_
61	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	10	10	CD	_	_	_
3	min	min	NN	_	_	_
4	of	of	IN	_	_	_
5	incubation	incubation	NN	_	_	_
6	at	at	IN	_	_	_
7	room	room	NN	_	_	_
8	temperature	temperature	NN	_	_	_
9	,	,	,	_	_	_
10	the	the	DT	_	_	_
11	samples	sample	NNS	_	_	_
12	were	be	VBD	_	_	_
13	incubated	incubate	VBN	_	_	_
14	30	30	CD	_	_	_
15	min	min	NN	_	_	_
16	in	in	IN	_	_	_
17	ice	ice	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	bacterial	bacterial	JJ	_	_	_
20	cell	cell	NN	_	_	_
21	culture	culture	NN	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	chip	chip	NN	_	_	_
24	antibody	antibody	NN	_	_	_
25	:	:	:	_	_	_
26	anti-Flag	anti-flag	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Sigma	Sigma	NNP	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	ChIP-Seq	chip-seq	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
33	Cross-linked	cross-linked	JJ	_	_	_
34	cells	cell	NNS	_	_	_
35	were	be	VBD	_	_	_
36	harvested	harvest	VBN	_	_	_
37	and	and	CC	_	_	_
38	washed	wash	VBN	_	_	_
39	two	two	CD	_	_	_
40	times	time	NNS	_	_	_
41	with	with	IN	_	_	_
42	ice-cold	ice-cold	JJ	_	_	_
43	PBS	PBS	NNP	_	_	_
44	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	resuspended	resuspend	VBN	_	_	_
4	in	in	IN	_	_	_
5	450μl	450μl	NN	_	_	_
6	of	of	IN	_	_	_
7	TES	tes	NN	_	_	_
8	buffer	buffer	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	50mM	50mm	NN	_	_	_
11	Tris-HCl	tris-hcl	NN	_	_	_
12	pH	ph	NN	_	_	_
13	7.5	7.5	CD	_	_	_
14	,	,	,	_	_	_
15	150mM	150mm	NN	_	_	_
16	NaCl	nacl	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	20μl	20μl	NN	_	_	_
20	of	of	IN	_	_	_
21	lysis	lysis	NN	_	_	_
22	solution	solution	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	13.6	13.6	CD	_	_	_
25	mg	mg	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	Escherichia	escherichia	FW	Organism	_	_
28	coli	coli	FW	Organism	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Genome	Genome	NNP	_	_	_
31	_	_	NNP	_	_	_
32	build	build	VB	_	_	_
33	:	:	:	_	_	_
34	Reference	Reference	NNP	_	_	_
35	genome	genome	NN	_	_	_
36	used	use	VBN	_	_	_
37	:	:	:	_	_	_
38	Escherichia	escherichia	FW	Organism	_	_
39	coli	coli	FW	Organism	_	_
40	K12	k12	NN	_	_	_
41	MG1655	mg1655	NN	_	_	_
42	,	,	,	_	_	_
43	version	version	NN	_	_	_
44	:	:	:	_	_	_
45	iGenome	iGenome	NNP	_	_	_
46	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
47	genotype	genotype	NN	_	_	_
48	:	:	:	_	_	_
49	wild	wild	JJ	_	_	_
50	type	type	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	genotype	genotype	NN	_	_	_
53	:	:	:	_	_	_
54	ΔbolA	δbola	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	Library	Library	NNP	_	_	_
57	construction	construction	NN	_	_	_
58	was	be	VBD	_	_	_
59	performed	perform	VBN	_	_	_
60	by	by	IN	_	_	_
61	processing	processing	NN	_	_	_
62	in	in	FW	_	_	_
63	vitro	vitro	FW	_	_	_
64	samples	sample	NNS	_	_	_
65	to	to	TO	_	_	_
66	generate	generate	VB	_	_	_
67	a	a	DT	_	_	_
68	library	library	NN	_	_	_
69	of	of	IN	_	_	_
70	short	short	JJ	_	_	_
71	inserts	insert	NNS	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	the	the	DT	_	_	_
74	DNA	dna	NN	_	_	_
75	Colonies	colony	NNS	_	_	_
76	Template	Template	NNP	_	_	_
77	Library	Library	NNP	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	by	by	IN	_	_	_
80	Fasteris	Fasteris	NNP	_	_	_
81	SA	SA	NNP	_	_	_
82	,	,	,	_	_	_
83	Switzerland	Switzerland	NNP	_	_	_
84	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
85	Mapping	mapping	NN	_	_	_
86	was	be	VBD	_	_	_
87	performed	perform	VBN	_	_	_
88	using	use	VBG	_	_	_
89	BWA	BWA	NNP	_	_	_
90	tool	tool	NN	_	_	_
91	-LRB-	-lrb-	-LRB-	_	_	_
92	version	version	NN	_	_	_
93	0.5.9	0.5.9	CD	_	_	_
94	-RRB-	-rrb-	-RRB-	_	_	_
95	against	against	IN	_	_	_
96	the	the	DT	_	_	_
97	reference	reference	NN	_	_	_
98	genome	genome	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	Peak	peak	JJ	_	_	_
101	detection	detection	NN	_	_	_
102	and	and	CC	_	_	_
103	count	count	NN	_	_	_
104	of	of	IN	_	_	_
105	coverage	coverage	NN	_	_	_
106	were	be	VBD	_	_	_
107	done	do	VBN	_	_	_
108	using	use	VBG	_	_	_
109	SEQMONK	SEQMONK	NNP	_	_	_
110	version	version	NN	_	_	_
111	0.21.0	0.21.0	CD	_	_	_
112	by	by	IN	_	_	_
113	Fasteris	Fasteris	NNP	_	_	_
114	SA	SA	NNP	_	_	_
115	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
116	Reference	Reference	NNP	_	_	_
117	genome	genome	NN	_	_	_
118	used	use	VBN	_	_	_
119	:	:	:	_	_	_
120	Escherichia	escherichia	FW	Organism	_	_
121	coli	coli	FW	Organism	_	_
122	K12	k12	NN	_	_	_
123	MG1655	mg1655	NN	_	_	_
124	,	,	,	_	_	_
125	version	version	NN	_	_	_
126	:	:	:	_	_	_
127	iGenome	igenome	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	strain	strain	NN	_	_	_
130	:	:	:	_	_	_
131	no	no	DT	_	_	_
132	tag	tag	NN	GEN	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	strain	strain	NN	_	_	_
135	:	:	:	_	_	_
136	wt	wt	JJ	_	_	_
137	3xflag	3xflag	NN	_	_	_
138	strain	strain	NN	_	_	_
139	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
140	Supplementary	Supplementary	NNP	_	_	_
141	_	_	VBD	_	_	_
142	files	file	NNS	_	_	_
143	_	_	IN	_	_	_
144	format	format	NN	_	_	_
145	_	_	NN	_	_	_
146	and	and	CC	_	_	_
147	_	_	NN	_	_	_
148	content	content	NN	_	_	_
149	:	:	:	_	_	_
150	.	.	.	_	_	_

1	txt	txt	NN	_	_	_
2	file	file	NN	_	_	_
3	file	file	NN	_	_	_
4	with	with	IN	_	_	_
5	raw	raw	JJ	_	_	_
6	and	and	CC	_	_	_
7	normalized	normalize	VBD	_	_	_
8	counts	count	NNS	_	_	_
9	of	of	IN	_	_	_
10	coverage	coverage	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	The	the	DT	_	_	_
13	ΔbolA	δbola	NN	_	_	_
14	and	and	CC	_	_	_
15	wt	wt	JJ	_	_	_
16	3xflag	3xflag	NN	_	_	_
17	strains	strain	NNS	_	_	_
18	were	be	VBD	_	_	_
19	used	use	VBN	_	_	_
20	to	to	TO	_	_	_
21	perform	perform	VB	_	_	_
22	ChIP-seq	chip-seq	JJ	_	_	_
23	experiments	experiment	NNS	_	_	_
24	.	.	.	_	_	_

1	Overnight	overnight	JJ	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	diluted	dilute	VBN	_	_	_
5	1	1	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	wild	wild	JJ	_	_	_
8	type	type	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	ΔbolA	δbola	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	At	at	IN	_	_	_
13	OD	od	NN	_	_	_
14	~	~	NN	_	_	_
15	0.3	0.3	CD	_	_	_
16	,	,	,	_	_	_
17	cultures	culture	NNS	_	_	_
18	were	be	VBD	_	_	_
19	induced	induce	VBN	_	_	_
20	with	with	IN	_	_	_
21	1mM	1mm	NN	_	_	_
22	IPTG	iptg	NN	_	_	_
23	for	for	IN	_	_	_
24	the	the	DT	_	_	_
25	appropriate	appropriate	JJ	_	_	_
26	length	length	NN	_	_	_
27	of	of	IN	_	_	_
28	time	time	NN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	bacteria	bacterium	NNS	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Bacteria	bacterium	NNS	_	_	_
5	were	be	VBD	_	_	_
6	grown	grow	VBN	_	_	_
7	at	at	IN	_	_	_
8	30C	30c	NN	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	~	~	NN	_	_	_
13	200	200	CD	_	_	_
14	rpm	rpm	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	in	in	IN	_	_	_
17	fully	fully	RB	_	_	_
18	supplemented	supplement	VBN	_	_	_
19	MOPS	mop	NNS	MED	_	_
20	glucose	glucose	NN	SUPP	_	_
21	media	media	NNS	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Teknova	teknova	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	to	to	TO	_	_	_
26	OD420	od420	NN	_	_	_
27	~	~	NN	_	_	_
28	0.4	0.4	CD	_	_	_
29	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	split	split	VBN	_	_	_
4	into	into	IN	_	_	_
5	4	4	CD	_	_	_
6	subcultures	subculture	NNS	_	_	_
7	,	,	,	_	_	_
8	and	and	CC	_	_	_
9	grown	grow	VBN	_	_	_
10	to	to	TO	_	_	_
11	OD	od	NN	_	_	_
12	~	~	NN	_	_	_
13	0.3	0.3	CD	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Basecalls	basecall	NNS	_	_	_
3	performed	perform	VBN	_	_	_
4	using	use	VBG	_	_	_
5	Casava	Casava	NNP	_	_	_
6	versions	version	NNS	_	_	_
7	1.6	1.6	CD	_	_	_
8	or	or	CC	_	_	_
9	1.7	1.7	CD	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Bowtie	Bowtie	NNP	_	_	_
3	alignments	alignment	NNS	_	_	_
4	against	against	IN	_	_	_
5	the	the	DT	_	_	_
6	E	e	NN	_	_	_
7	coli	coli	NN	_	_	_
8	genome	genome	NN	_	_	_
9	were	be	VBD	_	_	_
10	converted	convert	VBN	_	_	_
11	to	to	TO	_	_	_
12	wiggle	wiggle	VB	_	_	_
13	files	file	NNS	_	_	_
14	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	position	position	NN	_	_	_
3	of	of	IN	_	_	_
4	each	each	DT	_	_	_
5	alignment	alignment	NN	_	_	_
6	is	be	VBZ	_	_	_
7	distributed	distribute	VBN	_	_	_
8	into	into	IN	_	_	_
9	several	several	JJ	_	_	_
10	nucleotides	nucleotide	NNS	_	_	_
11	in	in	IN	_	_	_
12	the	the	DT	_	_	_
13	center	center	NN	_	_	_
14	of	of	IN	_	_	_
15	the	the	DT	_	_	_
16	footprint	footprint	NN	_	_	_
17	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	footprint	footprint	NN	_	_	_
4	read	read	NN	_	_	_
5	,	,	,	_	_	_
6	the	the	DT	_	_	_
7	center	center	NN	_	_	_
8	residues	residue	NNS	_	_	_
9	that	that	WDT	_	_	_
10	are	be	VBP	_	_	_
11	at	at	IN	_	_	_
12	least	least	JJS	_	_	_
13	10	10	CD	_	_	_
14	nucleotides	nucleotide	NNS	_	_	_
15	away	away	RB	_	_	_
16	from	from	IN	_	_	_
17	either	either	CC	_	_	_
18	ends	end	NNS	_	_	_
19	were	be	VBD	_	_	_
20	given	give	VBN	_	_	_
21	the	the	DT	_	_	_
22	same	same	JJ	_	_	_
23	score	score	NN	_	_	_
24	,	,	,	_	_	_
25	which	which	WDT	_	_	_
26	is	be	VBZ	_	_	_
27	weighted	weight	VBN	_	_	_
28	by	by	IN	_	_	_
29	the	the	DT	_	_	_
30	length	length	NN	_	_	_
31	of	of	IN	_	_	_
32	the	the	DT	_	_	_
33	fragment	fragment	NN	_	_	_
34	-LSB-	-lsb-	-LRB-	_	_	_
35	Oh	oh	UH	_	_	_
36	et	et	FW	_	_	_
37	al	al	FW	_	_	_
38	,	,	,	_	_	_
39	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	147	147	CD	_	_	_
3	,	,	,	_	_	_
4	1295	1295	CD	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	2011	2011	CD	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	-RSB-	-rsb-	-RRB-	_	_	_
9	.	.	.	_	_	_

1	Scores	score	NNS	_	_	_
2	therefore	therefore	RB	_	_	_
3	represent	represent	VBP	_	_	_
4	the	the	DT	_	_	_
5	number	number	NN	_	_	_
6	of	of	IN	_	_	_
7	read	read	VBN	_	_	_
8	alignments	alignment	NNS	_	_	_
9	attributed	attribute	VBD	_	_	_
10	to	to	TO	_	_	_
11	each	each	DT	_	_	_
12	genomic	genomic	JJ	_	_	_
13	position	position	NN	_	_	_
14	under	under	IN	_	_	_
15	each	each	DT	_	_	_
16	scoring	score	VBG	_	_	_
17	scheme	scheme	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Extraction	extraction	NN	_	_	_
6	was	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	as	as	IN	_	_	_
9	described	describe	VBN	_	_	_
10	in	in	IN	_	_	_
11	detail	detail	NN	_	_	_
12	previously	previously	RB	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Li	Li	NNP	_	_	_
15	et	et	FW	_	_	_
16	al.	al.	FW	_	_	_
17	,	,	,	_	_	_
18	2012	2012	CD	_	_	_
19	;	;	:	_	_	_
20	Oh	oh	UH	_	_	_
21	et	et	FW	_	_	_
22	al.	al.	FW	_	_	_
23	,	,	,	_	_	_
24	2011	2011	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	200	200	CD	_	_	_
2	ml	ml	NN	_	_	_
3	of	of	IN	_	_	_
4	cell	cell	NN	_	_	_
5	culture	culture	NN	_	_	_
6	was	be	VBD	_	_	_
7	rapidly	rapidly	RB	_	_	_
8	filtered	filter	VBN	_	_	_
9	at	at	IN	_	_	_
10	37C	37c	NN	_	_	_
11	by	by	IN	_	_	_
12	passing	pass	VBG	_	_	_
13	through	through	IN	_	_	_
14	a	a	DT	_	_	_
15	nitrocellulose	nitrocellulose	NN	_	_	_
16	filter	filter	NN	_	_	_
17	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	pellets	pellet	NNS	_	_	_
3	was	be	VBD	_	_	_
4	were	be	VBD	_	_	_
5	rapidly	rapidly	RB	_	_	_
6	collected	collect	VBN	_	_	_
7	using	use	VBG	_	_	_
8	a	a	DT	_	_	_
9	pre-warmed	pre-warmed	JJ	_	_	_
10	metal	metal	NN	_	_	_
11	table	table	NN	_	_	_
12	crumber	crumber	NN	_	_	_
13	,	,	,	_	_	_
14	flash	flash	NN	_	_	_
15	frozen	freeze	VBN	_	_	_
16	in	in	IN	_	_	_
17	liquid	liquid	JJ	_	_	_
18	nitrogen	nitrogen	NN	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	combined	combine	VBN	_	_	_
22	with	with	IN	_	_	_
23	frozen	frozen	JJ	_	_	_
24	droplets	droplet	NNS	_	_	_
25	of	of	IN	_	_	_
26	lysis	lysis	NN	_	_	_
27	buffer	buffer	NN	_	_	_
28	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	and	and	CC	_	_	_
3	lysis	lysis	NN	_	_	_
4	buffer	buffer	NN	_	_	_
5	were	be	VBD	_	_	_
6	pulverized	pulverize	VBN	_	_	_
7	in	in	IN	_	_	_
8	10	10	CD	_	_	_
9	ml	ml	NN	_	_	_
10	canisters	canister	NNS	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Retsch	retsch	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	pre-chilled	pre-chilled	JJ	_	_	_
15	in	in	IN	_	_	_
16	liquid	liquid	JJ	_	_	_
17	nitrogen	nitrogen	NN	_	_	_
18	using	use	VBG	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	TissueLyser	TissueLyser	NNP	_	_	_
21	II	II	NNP	_	_	_
22	.	.	.	_	_	_

1	Pulverized	pulverize	VBN	_	_	_
2	lysate	lysate	NN	_	_	_
3	was	be	VBD	_	_	_
4	thawed	thaw	VBN	_	_	_
5	on	on	IN	_	_	_
6	ice	ice	NN	_	_	_
7	and	and	CC	_	_	_
8	clarified	clarify	VBN	_	_	_
9	by	by	IN	_	_	_
10	centrifugation	centrifugation	NN	_	_	_
11	at	at	IN	_	_	_
12	4C	4c	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	NC000913	nc000913	NN	_	_	_
7	.2	.2	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	media	media	NNS	_	_	_
10	:	:	:	_	_	_
11	fully	fully	RB	_	_	_
12	supplemented	supplement	VBN	_	_	_
13	MOPS	mop	NNS	MED	_	_
14	glucose	glucose	NN	SUPP	_	_
15	media	media	NNS	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	molecule	molecule	NN	_	_	_
18	subtype	subtype	NN	_	_	_
19	:	:	:	_	_	_
20	mRNA	mrna	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	molecule	molecule	NN	_	_	_
23	subtype	subtype	NN	_	_	_
24	:	:	:	_	_	_
25	ribosome	ribosome	NN	_	_	_
26	protected	protect	VBD	_	_	_
27	mRNA	mrna	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	mRNA-seq	mrna-seq	NN	_	_	_
30	in	in	IN	_	_	_
31	rich	rich	JJ	_	_	_
32	defined	define	VBN	_	_	_
33	media	media	NNS	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	mRNA-seq	mrna-seq	NN	_	_	_
36	MicL-S	micl-s	NN	_	_	_
37	t0	t0	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	mRNA-seq	mrna-seq	NN	_	_	_
40	MicL-S	micl-s	NN	_	_	_
41	t10	t10	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	mRNA-seq	mrna-seq	NN	_	_	_
44	MicL-S	micl-s	NN	_	_	_
45	t20	t20	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	mRNA-seq	mrna-seq	NN	_	_	_
48	MicL-S	micl-s	NN	_	_	_
49	t4	t4	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	mRNA-seq	mrna-seq	NN	_	_	_
52	MicL	micl	NN	_	_	_
53	t0	t0	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	mRNA-seq	mrna-seq	NN	_	_	_
56	MicL	micl	NN	_	_	_
57	t10	t10	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	mRNA-seq	mrna-seq	NN	_	_	_
60	MicL	micl	NN	_	_	_
61	t20	t20	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	mRNA-seq	mrna-seq	NN	_	_	_
64	MicL	micl	NN	_	_	_
65	t4	t4	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	mRNA-seq	mrna-seq	NN	_	_	_
68	Vector	Vector	NNP	_	_	_
69	t0	t0	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	mRNA-seq	mrna-seq	NN	_	_	_
72	Vector	Vector	NNP	_	_	_
73	t20	t20	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	mRNA-seq	mrna-seq	NN	_	_	_
76	WT	wt	JJ	_	_	_
77	t10	t10	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	mRNA-seq	mrna-seq	NN	_	_	_
80	WT	wt	JJ	_	_	_
81	t4	t4	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	plasmid	plasmid	NN	_	_	_
84	:	:	:	_	_	_
85	empty	empty	JJ	_	_	_
86	vector	vector	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	plasmid	plasmid	NN	_	_	_
89	:	:	:	_	_	_
90	pMicL	pmicl	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	plasmid	plasmid	NN	_	_	_
93	:	:	:	_	_	_
94	pMicL-S	pmicl-s	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	ribosome	ribosome	NN	_	_	_
97	profiling	profiling	NN	_	_	_
98	in	in	IN	_	_	_
99	rich	rich	JJ	_	_	_
100	defined	define	VBN	_	_	_
101	media	media	NNS	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	ribosome	ribosome	NN	_	_	_
104	profiling	profile	VBG	_	_	_
105	MicL	micl	NN	_	_	_
106	t0	t0	NN	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	ribosome	ribosome	NN	_	_	_
109	profiling	profile	VBG	_	_	_
110	MicL	micl	NN	_	_	_
111	t20	t20	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	Ribosome	ribosome	NN	_	_	_
114	protected	protect	VBD	_	_	_
115	and	and	CC	_	_	_
116	total	total	JJ	_	_	_
117	mRNA	mrna	NN	_	_	_
118	fragments	fragment	NNS	_	_	_
119	were	be	VBD	_	_	_
120	size	size	NN	_	_	_
121	selected	select	VBN	_	_	_
122	via	via	IN	_	_	_
123	gel	gel	NN	_	_	_
124	purification	purification	NN	_	_	_
125	.	.	.	_	_	_

1	Fragments	fragment	NNS	_	_	_
2	were	be	VBD	_	_	_
3	ligated	ligate	VBN	_	_	_
4	to	to	TO	_	_	_
5	5	5	CD	_	_	_
6	'	'	''	_	_	_
7	adenylated	adenylate	VBN	_	_	_
8	DNA	dna	NN	_	_	_
9	oligo	oligo	JJ	_	_	_
10	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	reverse	reverse	JJ	_	_	_
3	transcription	transcription	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	single	single	JJ	_	_	_
7	stranded	stranded	JJ	_	_	_
8	DNA	dna	NN	_	_	_
9	was	be	VBD	_	_	_
10	circularized	circularize	VBN	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	PCR	pcr	NN	_	_	_
14	amplified	amplify	VBD	_	_	_
15	-LSB-	-lsb-	-LRB-	_	_	_
16	Oh	oh	UH	_	_	_
17	et	et	FW	_	_	_
18	al	al	FW	_	_	_
19	,	,	,	_	_	_
20	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	147	147	CD	_	_	_
3	,	,	,	_	_	_
4	1295	1295	CD	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	2011	2011	CD	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	-RSB-	-rsb-	-RRB-	_	_	_
9	.	.	.	_	_	_

1	More	more	JJR	_	_	_
2	details	detail	NNS	_	_	_
3	at	at	IN	_	_	_
4	MS	ms	NN	_	_	_
5	Guo	Guo	NNP	_	_	_
6	,	,	,	_	_	_
7	TB	tb	NN	_	_	_
8	Updegrove	Updegrove	NNP	_	_	_
9	,	,	,	_	_	_
10	et	et	FW	_	_	_
11	al	al	FW	_	_	_
12	,	,	,	_	_	_
13	Genes	gene	NNS	_	_	_
14	Dev	dev	NN	_	_	_
15	.	.	.	_	_	_

1	-LRB-	-lrb-	-LRB-	_	_	_
2	2014	2014	CD	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Sequenced	sequence	VBN	_	_	_
5	reads	read	VBZ	_	_	_
6	were	be	VBD	_	_	_
7	trimmed	trim	VBN	_	_	_
8	for	for	IN	_	_	_
9	adaptor	adaptor	NN	_	_	_
10	sequence	sequence	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Supplementary	supplementary	JJ	_	_	_
7	_	_	NN	_	_	_
8	files	file	NNS	_	_	_
9	_	_	IN	_	_	_
10	format	format	NN	_	_	_
11	_	_	NN	_	_	_
12	and	and	CC	_	_	_
13	_	_	NN	_	_	_
14	content	content	NN	_	_	_
15	:	:	:	_	_	_
16	wiggle	wiggle	NN	_	_	_
17	files	file	NNS	_	_	_
18	with	with	IN	_	_	_
19	two	two	CD	_	_	_
20	columns	column	NNS	_	_	_
21	:	:	:	_	_	_
22	first	first	JJ	_	_	_
23	column	column	NN	_	_	_
24	containing	contain	VBG	_	_	_
25	chromosome	chromosome	NN	_	_	_
26	positions	position	NNS	_	_	_
27	and	and	CC	_	_	_
28	second	second	JJ	_	_	_
29	column	column	NN	_	_	_
30	containing	contain	VBG	_	_	_
31	the	the	DT	_	_	_
32	number	number	NN	_	_	_
33	of	of	IN	_	_	_
34	reads	read	VBZ	_	_	_
35	mapped	map	VBN	_	_	_
36	to	to	TO	_	_	_
37	the	the	DT	_	_	_
38	position	position	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	see	see	VB	_	_	_
41	publication	publication	NN	_	_	_
42	for	for	IN	_	_	_
43	details	detail	NNS	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Trimmed	trim	VBD	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	sequentially	sequentially	RB	_	_	_
6	aligned	align	VBN	_	_	_
7	using	use	VBG	_	_	_
8	Bowtie	Bowtie	NNP	_	_	_
9	v0	v0	NN	_	_	_
10	.12.7	.12.7	CD	_	_	_
11	to	to	TO	_	_	_
12	E	E	NNP	_	_	_
13	coli	coli	NN	_	_	_
14	genome	genome	NN	_	_	_
15	using	use	VBG	_	_	_
16	parameters	parameter	NNS	_	_	_
17	-	-	:	_	_	_
18	v	v	LS	_	_	_
19	1	1	LS	_	_	_
20	-	-	:	_	_	_
21	m	m	NN	_	_	_
22	1	1	CD	_	_	_
23	--	--	:	_	_	_
24	best	best	JJS	_	_	_
25	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	allows	allow	VBZ	_	_	_
3	one	one	CD	_	_	_
4	mismatch	mismatch	NN	_	_	_
5	and	and	CC	_	_	_
6	reports	report	NNS	_	_	_
7	only	only	RB	_	_	_
8	reads	read	VBZ	_	_	_
9	that	that	IN	_	_	_
10	align	align	NN	_	_	_
11	1	1	CD	_	_	_
12	or	or	CC	_	_	_
13	fewer	fewer	JJR	_	_	_
14	times	time	NNS	_	_	_
15	to	to	TO	_	_	_
16	the	the	DT	_	_	_
17	genome	genome	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	biological	biological	JJ	_	_	_
20	replicate	replicate	VB	_	_	_
21	:	:	:	_	_	_
22	318	318	CD	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
24	biological	biological	JJ	_	_	_
25	replicate	replicate	VB	_	_	_
26	:	:	:	_	_	_
27	320	320	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
29	biological	biological	JJ	_	_	_
30	replicate	replicate	VB	_	_	_
31	:	:	:	_	_	_
32	327	327	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Cells	cell	NNS	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	10	10	CD	_	_	_
37	ml	ml	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	for	for	IN	_	_	_
40	transcriptomic	transcriptomic	JJ	_	_	_
41	analysis	analysis	NN	_	_	_
42	were	be	VBD	_	_	_
43	collected	collect	VBN	_	_	_
44	into	into	IN	_	_	_
45	tubes	tube	NNS	_	_	_
46	containing	contain	VBG	_	_	_
47	1.25	1.25	CD	_	_	_
48	ml	ml	NN	_	_	_
49	ice-cold	ice-cold	JJ	_	_	_
50	5	5	CD	_	_	_
51	%	%	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	vol	vol	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	Escherichia	escherichia	FW	Organism	_	_
56	coli	coli	FW	Organism	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Fermentations	fermentation	NNS	_	_	_
59	were	be	VBD	_	_	_
60	carried	carry	VBN	_	_	_
61	out	out	RP	_	_	_
62	in	in	IN	_	_	_
63	3	3	CD	_	_	_
64	L	l	NN	_	_	_
65	bioreactors	bioreactor	NNS	_	_	_
66	-LRB-	-lrb-	-LRB-	_	_	_
67	Applikon	Applikon	NNP	_	_	_
68	Biotechnology	Biotechnology	NNP	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	containing	contain	VBG	_	_	_
71	2.45	2.45	CD	_	_	_
72	L	l	NN	_	_	_
73	of	of	IN	_	_	_
74	ACSH	acsh	NN	_	_	_
75	or	or	CC	_	_	_
76	SynH	synh	NN	_	_	_
77	media	media	NNS	_	_	_
78	,	,	,	_	_	_
79	and	and	CC	_	_	_
80	cultures	culture	NNS	_	_	_
81	were	be	VBD	_	_	_
82	diluted	dilute	VBN	_	_	_
83	into	into	IN	_	_	_
84	ACSH	acsh	NN	_	_	_
85	or	or	CC	_	_	_
86	SynH	synh	NN	_	_	_
87	with	with	IN	_	_	_
88	initial	initial	JJ	_	_	_
89	OD	od	NN	_	_	_
90	at	at	IN	_	_	_
91	0.2	0.2	CD	_	_	_
92	,	,	,	_	_	_
93	grown	grow	VBN	_	_	_
94	anaerobically	anaerobically	RB	_	_	_
95	overnight	overnight	RB	_	_	_
96	,	,	,	_	_	_
97	and	and	CC	_	_	_
98	then	then	RB	_	_	_
99	inoculated	inoculate	VBN	_	_	_
100	into	into	IN	_	_	_
101	bioreactors	bioreactor	NNS	_	_	_
102	to	to	TO	_	_	_
103	a	a	DT	_	_	_
104	starting	start	VBG	_	_	_
105	OD600	od600	NN	_	_	_
106	of	of	IN	_	_	_
107	0.2	0.2	CD	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	GLBRCE1	glbrce1	NN	_	_	_
110	,	,	,	_	_	_
111	ACSH	ACSH	NNP	_	_	_
112	,	,	,	_	_	_
113	Exp	Exp	NNP	_	_	_
114	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
115	GLBRCE1	GLBRCE1	NNP	_	_	_
116	_	_	NNP	_	_	_
117	ACSH	ACSH	NNP	_	_	_
118	_	_	VBD	_	_	_
119	Exp	Exp	NNP	_	_	_
120	_	_	SYM	_	_	_
121	rep318	rep318	CD	_	_	_
122	_	_	NN	_	_	_
123	1	1	CD	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	GLBRCE1	glbrce1	NN	_	_	_
126	_	_	CD	_	_	_
127	ACSH	ACSH	NNP	_	_	_
128	_	_	NNP	_	_	_
129	Exp	Exp	NNP	_	_	_
130	_	_	SYM	_	_	_
131	rep320	rep320	CD	_	_	_
132	_	_	NN	_	_	_
133	1	1	CD	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	GLBRCE1	glbrce1	NN	_	_	_
136	_	_	CD	_	_	_
137	ACSH	ACSH	NNP	_	_	_
138	_	_	NNP	_	_	_
139	Exp	Exp	NNP	_	_	_
140	_	_	SYM	_	_	_
141	rep327	rep327	CD	_	_	_
142	_	_	NN	_	_	_
143	1	1	CD	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	GLBRCE1	glbrce1	NN	_	_	_
146	,	,	,	_	_	_
147	ACSH	ACSH	NNP	_	_	_
148	,	,	,	_	_	_
149	Stat1	stat1	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	GLBRCE1	glbrce1	NN	_	_	_
152	_	_	CD	_	_	_
153	ACSH	ACSH	NNP	_	_	_
154	_	_	SYM	_	_	_
155	Stat1	stat1	NN	_	_	_
156	_	_	CD	_	_	_
157	rep318	rep318	NN	_	_	_
158	_	_	NN	_	_	_
159	1	1	CD	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	GLBRCE1	glbrce1	NN	_	_	_
162	_	_	CD	_	_	_
163	ACSH	ACSH	NNP	_	_	_
164	_	_	SYM	_	_	_
165	Stat1	stat1	NN	_	_	_
166	_	_	CD	_	_	_
167	rep320	rep320	NN	_	_	_
168	_	_	NN	_	_	_
169	1	1	CD	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	GLBRCE1	glbrce1	NN	_	_	_
172	_	_	CD	_	_	_
173	ACSH	ACSH	NNP	_	_	_
174	_	_	SYM	_	_	_
175	Stat1	stat1	NN	_	_	_
176	_	_	CD	_	_	_
177	rep327	rep327	NN	_	_	_
178	_	_	NN	_	_	_
179	1	1	CD	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	GLBRCE1	glbrce1	NN	_	_	_
182	,	,	,	_	_	_
183	ACSH	ACSH	NNP	_	_	_
184	,	,	,	_	_	_
185	Stat2	stat2	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	GLBRCE1	glbrce1	NN	_	_	_
188	_	_	CD	_	_	_
189	ACSH	ACSH	NNP	_	_	_
190	_	_	SYM	_	_	_
191	Stat2	stat2	NN	_	_	_
192	_	_	CD	_	_	_
193	rep318	rep318	NN	_	_	_
194	_	_	NN	_	_	_
195	1	1	CD	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	GLBRCE1	glbrce1	NN	_	_	_
198	_	_	CD	_	_	_
199	ACSH	ACSH	NNP	_	_	_
200	_	_	SYM	_	_	_
201	Stat2	stat2	NN	_	_	_
202	_	_	CD	_	_	_
203	rep320	rep320	NN	_	_	_
204	_	_	NN	_	_	_
205	1	1	CD	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	GLBRCE1	glbrce1	NN	_	_	_
208	_	_	CD	_	_	_
209	ACSH	ACSH	NNP	_	_	_
210	_	_	SYM	_	_	_
211	Stat2	stat2	NN	_	_	_
212	_	_	CD	_	_	_
213	rep327	rep327	NN	_	_	_
214	_	_	NN	_	_	_
215	1	1	CD	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	GLBRCE1	glbrce1	NN	_	_	_
218	,	,	,	_	_	_
219	ACSH	ACSH	NNP	_	_	_
220	,	,	,	_	_	_
221	Trans	Trans	NNP	_	_	_
222	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
223	GLBRCE1	GLBRCE1	NNP	_	_	_
224	_	_	NNP	_	_	_
225	ACSH	ACSH	NNP	_	_	_
226	_	_	VBD	_	_	_
227	Trans	Trans	NNP	_	_	_
228	_	_	SYM	_	_	_
229	rep318	rep318	CD	_	_	_
230	_	_	NN	_	_	_
231	1	1	CD	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	GLBRCE1	glbrce1	NN	_	_	_
234	_	_	CD	_	_	_
235	ACSH	ACSH	NNP	_	_	_
236	_	_	CD	_	_	_
237	Trans	Trans	NNP	_	_	_
238	_	_	SYM	_	_	_
239	rep318	rep318	CD	_	_	_
240	_	_	NN	_	_	_
241	2	2	CD	_	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
243	GLBRCE1	glbrce1	NN	_	_	_
244	_	_	CD	_	_	_
245	ACSH	ACSH	NNP	_	_	_
246	_	_	CD	_	_	_
247	Trans	Trans	NNP	_	_	_
248	_	_	SYM	_	_	_
249	rep320	rep320	CD	_	_	_
250	_	_	NN	_	_	_
251	1	1	CD	_	_	_
252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
253	GLBRCE1	glbrce1	NN	_	_	_
254	_	_	CD	_	_	_
255	ACSH	ACSH	NNP	_	_	_
256	_	_	CD	_	_	_
257	Trans	Trans	NNP	_	_	_
258	_	_	SYM	_	_	_
259	rep327	rep327	CD	_	_	_
260	_	_	NN	_	_	_
261	1	1	CD	_	_	_
262	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
263	GLBRCE1	glbrce1	NN	_	_	_
264	,	,	,	_	_	_
265	SynH	synh	NN	_	_	_
266	,	,	,	_	_	_
267	Exp	exp	NN	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	GLBRCE1	glbrce1	NN	_	_	_
270	_	_	CD	_	_	_
271	SynH	synh	NN	_	_	_
272	_	_	CD	_	_	_
273	Exp	exp	NN	_	_	_
274	_	_	CD	_	_	_
275	rep318	rep318	NN	_	_	_
276	_	_	NN	_	_	_
277	1	1	CD	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
279	GLBRCE1	glbrce1	NN	_	_	_
280	_	_	CD	_	_	_
281	SynH	synh	NN	_	_	_
282	_	_	CD	_	_	_
283	Exp	exp	NN	_	_	_
284	_	_	CD	_	_	_
285	rep318	rep318	NN	_	_	_
286	_	_	NN	_	_	_
287	2	2	CD	_	_	_
288	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
289	GLBRCE1	glbrce1	NN	_	_	_
290	_	_	CD	_	_	_
291	SynH	synh	NN	_	_	_
292	_	_	CD	_	_	_
293	Exp	exp	NN	_	_	_
294	_	_	CD	_	_	_
295	rep320	rep320	NN	_	_	_
296	_	_	NN	_	_	_
297	1	1	CD	_	_	_
298	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
299	GLBRCE1	glbrce1	NN	_	_	_
300	_	_	CD	_	_	_
301	SynH	synh	NN	_	_	_
302	_	_	CD	_	_	_
303	Exp	exp	NN	_	_	_
304	_	_	CD	_	_	_
305	rep327	rep327	NN	_	_	_
306	_	_	NN	_	_	_
307	1	1	CD	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	GLBRCE1	glbrce1	NN	_	_	_
310	,	,	,	_	_	_
311	SynH	synh	NN	_	_	_
312	_	_	CD	_	_	_
313	LT	lt	NN	_	_	_
314	,	,	,	_	_	_
315	Exp	exp	NN	_	_	_
316	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
317	GLBRCE1	glbrce1	NN	_	_	_
318	_	_	CD	_	_	_
319	SynH	synh	NN	_	_	_
320	_	_	CD	_	_	_
321	LT	lt	NN	_	_	_
322	_	_	CD	_	_	_
323	Exp	exp	NN	_	_	_
324	_	_	CD	_	_	_
325	rep318	rep318	NN	_	_	_
326	_	_	NN	_	_	_
327	1	1	CD	_	_	_
328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
329	GLBRCE1	glbrce1	NN	_	_	_
330	_	_	CD	_	_	_
331	SynH	synh	NN	_	_	_
332	_	_	CD	_	_	_
333	LT	lt	NN	_	_	_
334	_	_	CD	_	_	_
335	Exp	exp	NN	_	_	_
336	_	_	CD	_	_	_
337	rep320	rep320	NN	_	_	_
338	_	_	NN	_	_	_
339	1	1	CD	_	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
341	GLBRCE1	glbrce1	NN	_	_	_
342	_	_	CD	_	_	_
343	SynH	synh	NN	_	_	_
344	_	_	CD	_	_	_
345	LT	lt	NN	_	_	_
346	_	_	CD	_	_	_
347	Exp	exp	NN	_	_	_
348	_	_	CD	_	_	_
349	rep327	rep327	NN	_	_	_
350	_	_	NN	_	_	_
351	1	1	CD	_	_	_
352	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
353	GLBRCE1	glbrce1	NN	_	_	_
354	,	,	,	_	_	_
355	SynH	synh	NN	_	_	_
356	_	_	CD	_	_	_
357	LT	lt	NN	_	_	_
358	,	,	,	_	_	_
359	Stat1	stat1	NN	_	_	_
360	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
361	GLBRCE1	glbrce1	NN	_	_	_
362	_	_	CD	_	_	_
363	SynH	synh	NN	_	_	_
364	_	_	CD	_	_	_
365	LT	lt	NN	_	_	_
366	_	_	CD	_	_	_
367	Stat1	stat1	NN	_	_	_
368	_	_	CD	_	_	_
369	rep318	rep318	NN	_	_	_
370	_	_	NN	_	_	_
371	1	1	CD	_	_	_
372	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
373	GLBRCE1	glbrce1	NN	_	_	_
374	_	_	CD	_	_	_
375	SynH	synh	NN	_	_	_
376	_	_	CD	_	_	_
377	LT	lt	NN	_	_	_
378	_	_	CD	_	_	_
379	Stat1	stat1	NN	_	_	_
380	_	_	CD	_	_	_
381	rep320	rep320	NN	_	_	_
382	_	_	NN	_	_	_
383	1	1	CD	_	_	_
384	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
385	GLBRCE1	glbrce1	NN	_	_	_
386	_	_	CD	_	_	_
387	SynH	synh	NN	_	_	_
388	_	_	CD	_	_	_
389	LT	lt	NN	_	_	_
390	_	_	CD	_	_	_
391	Stat1	stat1	NN	_	_	_
392	_	_	CD	_	_	_
393	rep327	rep327	NN	_	_	_
394	_	_	NN	_	_	_
395	1	1	CD	_	_	_
396	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
397	GLBRCE1	glbrce1	NN	_	_	_
398	,	,	,	_	_	_
399	SynH	synh	NN	_	_	_
400	_	_	CD	_	_	_
401	LT	lt	NN	_	_	_
402	,	,	,	_	_	_
403	Stat2	stat2	NN	_	_	_
404	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
405	GLBRCE1	glbrce1	NN	_	_	_
406	_	_	CD	_	_	_
407	SynH	synh	NN	_	_	_
408	_	_	CD	_	_	_
409	LT	lt	NN	_	_	_
410	_	_	SYM	_	_	_
411	Stat2	stat2	NN	_	_	_
412	_	_	CD	_	_	_
413	rep318	rep318	NN	_	_	_
414	_	_	NN	_	_	_
415	1	1	CD	_	_	_
416	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
417	GLBRCE1	glbrce1	NN	_	_	_
418	_	_	CD	_	_	_
419	SynH	synh	NN	_	_	_
420	_	_	CD	_	_	_
421	LT	lt	NN	_	_	_
422	_	_	SYM	_	_	_
423	Stat2	stat2	NN	_	_	_
424	_	_	CD	_	_	_
425	rep320	rep320	NN	_	_	_
426	_	_	NN	_	_	_
427	1	1	CD	_	_	_
428	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
429	GLBRCE1	glbrce1	NN	_	_	_
430	_	_	CD	_	_	_
431	SynH	synh	NN	_	_	_
432	_	_	CD	_	_	_
433	LT	lt	NN	_	_	_
434	_	_	SYM	_	_	_
435	Stat2	stat2	NN	_	_	_
436	_	_	CD	_	_	_
437	rep327	rep327	NN	_	_	_
438	_	_	NN	_	_	_
439	1	1	CD	_	_	_
440	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
441	GLBRCE1	glbrce1	NN	_	_	_
442	,	,	,	_	_	_
443	SynH	synh	NN	_	_	_
444	_	_	CD	_	_	_
445	LT	lt	NN	_	_	_
446	,	,	,	_	_	_
447	Trans	Trans	NNP	_	_	_
448	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
449	GLBRCE1	glbrce1	NN	_	_	_
450	_	_	CD	_	_	_
451	SynH	synh	NN	_	_	_
452	_	_	CD	_	_	_
453	LT	lt	NN	_	_	_
454	_	_	CD	_	_	_
455	Trans	Trans	NNP	_	_	_
456	_	_	SYM	_	_	_
457	rep318	rep318	CD	_	_	_
458	_	_	NN	_	_	_
459	1	1	CD	_	_	_
460	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
461	GLBRCE1	glbrce1	NN	_	_	_
462	_	_	CD	_	_	_
463	SynH	synh	NN	_	_	_
464	_	_	CD	_	_	_
465	LT	lt	NN	_	_	_
466	_	_	CD	_	_	_
467	Trans	Trans	NNP	_	_	_
468	_	_	SYM	_	_	_
469	rep320	rep320	CD	_	_	_
470	_	_	NN	_	_	_
471	1	1	CD	_	_	_
472	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
473	GLBRCE1	glbrce1	NN	_	_	_
474	_	_	CD	_	_	_
475	SynH	synh	NN	_	_	_
476	_	_	CD	_	_	_
477	LT	lt	NN	_	_	_
478	_	_	CD	_	_	_
479	Trans	Trans	NNP	_	_	_
480	_	_	SYM	_	_	_
481	rep327	rep327	CD	_	_	_
482	_	_	NN	_	_	_
483	1	1	CD	_	_	_
484	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
485	GLBRCE1	glbrce1	NN	_	_	_
486	,	,	,	_	_	_
487	SynH	synh	NN	_	_	_
488	,	,	,	_	_	_
489	Stat1	stat1	NN	_	_	_
490	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
491	GLBRCE1	glbrce1	NN	_	_	_
492	_	_	CD	_	_	_
493	SynH	synh	NN	_	_	_
494	_	_	CD	_	_	_
495	Stat1	stat1	NN	_	_	_
496	_	_	CD	_	_	_
497	rep318	rep318	NN	_	_	_
498	_	_	NN	_	_	_
499	1	1	CD	_	_	_
500	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
501	GLBRCE1	glbrce1	NN	_	_	_
502	_	_	CD	_	_	_
503	SynH	synh	NN	_	_	_
504	_	_	CD	_	_	_
505	Stat1	stat1	NN	_	_	_
506	_	_	CD	_	_	_
507	rep320	rep320	NN	_	_	_
508	_	_	NN	_	_	_
509	1	1	CD	_	_	_
510	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
511	GLBRCE1	glbrce1	NN	_	_	_
512	_	_	CD	_	_	_
513	SynH	synh	NN	_	_	_
514	_	_	CD	_	_	_
515	Stat1	stat1	NN	_	_	_
516	_	_	CD	_	_	_
517	rep327	rep327	NN	_	_	_
518	_	_	NN	_	_	_
519	1	1	CD	_	_	_
520	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
521	GLBRCE1	glbrce1	NN	_	_	_
522	,	,	,	_	_	_
523	SynH	synh	NN	_	_	_
524	,	,	,	_	_	_
525	Stat2	stat2	NN	_	_	_
526	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
527	GLBRCE1	glbrce1	NN	_	_	_
528	_	_	CD	_	_	_
529	SynH	synh	NN	_	_	_
530	_	_	CD	_	_	_
531	Stat2	stat2	NN	_	_	_
532	_	_	CD	_	_	_
533	rep327	rep327	NN	_	_	_
534	_	_	NN	_	_	_
535	1	1	CD	_	_	_
536	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
537	GLBRCE1	glbrce1	NN	_	_	_
538	,	,	,	_	_	_
539	SynH	synh	NN	_	_	_
540	,	,	,	_	_	_
541	Trans	Trans	NNP	_	_	_
542	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
543	GLBRCE1	glbrce1	NN	_	_	_
544	_	_	CD	_	_	_
545	SynH	synh	NN	_	_	_
546	_	_	CD	_	_	_
547	Trans	Trans	NNP	_	_	_
548	_	_	SYM	_	_	_
549	rep318	rep318	CD	_	_	_
550	_	_	NN	_	_	_
551	1	1	CD	_	_	_
552	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
553	GLBRCE1	glbrce1	NN	_	_	_
554	_	_	CD	_	_	_
555	SynH	synh	NN	_	_	_
556	_	_	CD	_	_	_
557	Trans	Trans	NNP	_	_	_
558	_	_	SYM	_	_	_
559	rep320	rep320	CD	_	_	_
560	_	_	NN	_	_	_
561	1	1	CD	_	_	_
562	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
563	GLBRCE1	glbrce1	NN	_	_	_
564	_	_	CD	_	_	_
565	SynH	synh	NN	_	_	_
566	_	_	CD	_	_	_
567	Trans	Trans	NNP	_	_	_
568	_	_	SYM	_	_	_
569	rep327	rep327	CD	_	_	_
570	_	_	NN	_	_	_
571	1	1	CD	_	_	_
572	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
573	growth	growth	NN	_	_	_
574	phase	phase	NN	_	_	_
575	:	:	:	_	_	_
576	Exp	exp	NN	_	_	_
577	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
578	growth	growth	NN	_	_	_
579	phase	phase	NN	_	_	_
580	:	:	:	_	_	_
581	Stat1	stat1	NN	_	_	_
582	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
583	growth	growth	NN	_	_	_
584	phase	phase	NN	_	_	_
585	:	:	:	_	_	_
586	Stat2	stat2	NN	_	_	_
587	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
588	growth	growth	NN	_	_	_
589	phase	phase	NN	_	_	_
590	:	:	:	_	_	_
591	Trans	Trans	NNP	_	_	_
592	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
593	medium	medium	NN	_	_	_
594	:	:	:	_	_	_
595	ACSH	ACSH	NNP	_	_	_
596	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
597	medium	medium	NN	_	_	_
598	:	:	:	_	_	_
599	SynH	synh	NN	_	_	_
600	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
601	medium	medium	NN	_	_	_
602	:	:	:	_	_	_
603	SynH	synh	NN	_	_	_
604	_	_	CD	_	_	_
605	LT	lt	NN	_	_	_
606	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
607	Probe	probe	NN	_	_	_
608	signal	signal	NN	_	_	_
609	intensities	intensity	NNS	_	_	_
610	were	be	VBD	_	_	_
611	preprocessed	preprocess	VBN	_	_	_
612	using	use	VBG	_	_	_
613	robust	robust	JJ	_	_	_
614	multichip	multichip	NN	_	_	_
615	averaging	averaging	NN	_	_	_
616	-LRB-	-lrb-	-LRB-	_	_	_
617	RMA	rma	NN	_	_	_
618	-RRB-	-rrb-	-RRB-	_	_	_
619	in	in	IN	_	_	_
620	the	the	DT	_	_	_
621	program	program	NN	_	_	_
622	ArrayStar	arraystar	NN	_	_	_
623	-LRB-	-lrb-	-LRB-	_	_	_
624	DNASTAR	dnastar	NN	_	_	_
625	-RRB-	-rrb-	-RRB-	_	_	_
626	,	,	,	_	_	_
627	and	and	CC	_	_	_
628	the	the	DT	_	_	_
629	resulting	result	VBG	_	_	_
630	gene	gene	NN	_	_	_
631	expression	expression	NN	_	_	_
632	signals	signal	NNS	_	_	_
633	were	be	VBD	_	_	_
634	quantile-normalized	quantile-normalize	VBN	_	_	_
635	across	across	IN	_	_	_
636	all	all	DT	_	_	_
637	samples	sample	NNS	_	_	_
638	using	use	VBG	_	_	_
639	the	the	DT	_	_	_
640	normalize.quantiles	normalize.quantiles	JJ	_	_	_
641	function	function	NN	_	_	_
642	in	in	IN	_	_	_
643	the	the	DT	_	_	_
644	Bioconductor	Bioconductor	NNP	_	_	_
645	package	package	NN	_	_	_
646	for	for	IN	_	_	_
647	R.	R.	NNP	_	_	_
648	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
649	RNA	rna	NN	_	_	_
650	was	be	VBD	_	_	_
651	obtained	obtain	VBN	_	_	_
652	from	from	IN	_	_	_
653	cells	cell	NNS	_	_	_
654	pellets	pellet	NNS	_	_	_
655	by	by	IN	_	_	_
656	lysozyme	lysozyme	NN	_	_	_
657	treatment	treatment	NN	_	_	_
658	and	and	CC	_	_	_
659	phenol-chloroform	phenol-chloroform	JJ	_	_	_
660	extraction	extraction	NN	_	_	_
661	,	,	,	_	_	_
662	analyzed	analyze	VBN	_	_	_
663	by	by	IN	_	_	_
664	agarose	agarose	NN	_	_	_
665	gel	gel	NN	_	_	_
666	electrophoresis	electrophoresis	NN	_	_	_
667	to	to	TO	_	_	_
668	confirm	confirm	VB	_	_	_
669	integrity	integrity	NN	_	_	_
670	,	,	,	_	_	_
671	quantified	quantify	VBN	_	_	_
672	using	use	VBG	_	_	_
673	a	a	DT	_	_	_
674	Nanodrop	Nanodrop	NNP	_	_	_
675	spectrophotometer	spectrophotometer	NN	_	_	_
676	-LRB-	-lrb-	-LRB-	_	_	_
677	Thermo	Thermo	NNP	_	_	_
678	Scientific	Scientific	NNP	_	_	_
679	-RRB-	-rrb-	-RRB-	_	_	_
680	,	,	,	_	_	_
681	and	and	CC	_	_	_
682	stored	store	VBD	_	_	_
683	at	at	IN	_	_	_
684	-80	-80	CD	_	_	_
685	°C	°c	NN	_	_	_
686	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
687	strain	strain	NN	_	_	_
688	:	:	:	_	_	_
689	GLBRCE1	glbrce1	NN	_	_	_
690	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
691	technical	technical	JJ	_	_	_
692	replicate	replicate	VB	_	_	_
693	:	:	:	_	_	_
694	1	1	CD	_	_	_
695	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
696	technical	technical	JJ	_	_	_
697	replicate	replicate	VB	_	_	_
698	:	:	:	_	_	_
699	2	2	CD	_	_	_
700	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
701	Cells	cell	NNS	_	_	_
702	-LRB-	-lrb-	-LRB-	_	_	_
703	10	10	CD	_	_	_
704	ml	ml	NN	_	_	_
705	-RRB-	-rrb-	-RRB-	_	_	_
706	for	for	IN	_	_	_
707	transcriptomic	transcriptomic	JJ	_	_	_
708	analysis	analysis	NN	_	_	_
709	were	be	VBD	_	_	_
710	collected	collect	VBN	_	_	_
711	into	into	IN	_	_	_
712	tubes	tube	NNS	_	_	_
713	containing	contain	VBG	_	_	_
714	1.25	1.25	CD	_	_	_
715	ml	ml	NN	_	_	_
716	ice-cold	ice-cold	JJ	_	_	_
717	5	5	CD	_	_	_
718	%	%	NN	_	_	_
719	-LRB-	-lrb-	-LRB-	_	_	_
720	vol	vol	NN	_	_	_
721	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
722	E.coli	e.coli	NN	_	_	_
723	ethanologen	ethanologen	NN	_	_	_
724	strain	strain	NN	_	_	_
725	GLBRCE1	glbrce1	NN	_	_	_
726	or	or	CC	_	_	_
727	GLBRCE1	glbrce1	NN	_	_	_
728	lacking	lack	VBG	_	_	_
729	the	the	DT	_	_	_
730	plasmid-borne	plasmid-borne	JJ	_	_	_
731	PET	pet	NN	_	_	_
732	cassette	cassette	NN	_	_	_
733	-LRB-	-lrb-	-LRB-	_	_	_
734	GLBRCE1	glbrce1	NN	_	_	_
735	_	_	CD	_	_	_
736	pBBR	pbbr	NN	_	_	_
737	-RRB-	-rrb-	-RRB-	_	_	_
738	was	be	VBD	_	_	_
739	grown	grow	VBN	_	_	_
740	in	in	IN	_	_	_
741	AFEX	AFEX	NNP	_	_	_
742	corn	corn	NN	_	_	_
743	stover	stover	NN	_	_	_
744	hydrolysate	hydrolysate	NN	_	_	_
745	-LRB-	-lrb-	-LRB-	_	_	_
746	ACSH	acsh	NN	_	_	_
747	-RRB-	-rrb-	-RRB-	_	_	_
748	.	.	.	_	_	_

1	Fermentations	fermentation	NNS	_	_	_
2	were	be	VBD	_	_	_
3	carried	carry	VBN	_	_	_
4	out	out	RP	_	_	_
5	in	in	IN	_	_	_
6	3	3	CD	_	_	_
7	L	l	NN	_	_	_
8	bioreactors	bioreactor	NNS	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Applikon	Applikon	NNP	_	_	_
11	Biotechnology	Biotechnology	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	containing	contain	VBG	_	_	_
14	2.45	2.45	CD	_	_	_
15	L	l	NN	_	_	_
16	of	of	IN	_	_	_
17	ACSH	acsh	NN	_	_	_
18	and	and	CC	_	_	_
19	cultures	culture	NNS	_	_	_
20	were	be	VBD	_	_	_
21	diluted	dilute	VBN	_	_	_
22	into	into	IN	_	_	_
23	ACSH	acsh	NN	_	_	_
24	with	with	IN	_	_	_
25	initial	initial	JJ	_	_	_
26	OD	od	NN	_	_	_
27	at	at	IN	_	_	_
28	0.2	0.2	CD	_	_	_
29	,	,	,	_	_	_
30	grown	grow	VBN	_	_	_
31	anaerobically	anaerobically	RB	_	_	_
32	overnight	overnight	RB	_	_	_
33	,	,	,	_	_	_
34	and	and	CC	_	_	_
35	then	then	RB	_	_	_
36	inoculated	inoculate	VBN	_	_	_
37	into	into	IN	_	_	_
38	bioreactors	bioreactor	NNS	_	_	_
39	to	to	TO	_	_	_
40	a	a	DT	_	_	_
41	starting	start	VBG	_	_	_
42	OD600	od600	NN	_	_	_
43	of	of	IN	_	_	_
44	0.2	0.2	CD	_	_	_
45	.	.	.	_	_	_

1	One	one	CD	_	_	_
2	biological	biological	JJ	_	_	_
3	replicate	replicate	VBP	_	_	_
4	was	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	each	each	DT	_	_	_
8	medium	medium	NN	_	_	_
9	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	obtained	obtain	VBN	_	_	_
5	at	at	IN	_	_	_
6	3	3	CD	_	_	_
7	time	time	NN	_	_	_
8	points	point	NNS	_	_	_
9	,	,	,	_	_	_
10	corresponding	correspond	VBG	_	_	_
11	to	to	TO	_	_	_
12	mid-exponential	mid-exponential	JJ	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Exp	exp	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	,	,	,	_	_	_
17	transitional	transitional	JJ	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Trans	Trans	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	,	,	,	_	_	_
22	and	and	CC	_	_	_
23	stationary	stationary	JJ	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Stat	stat	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	growth	growth	NN	_	_	_
28	phases	phase	NNS	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Escherichia	escherichia	FW	Organism	_	_
6	coli	coli	FW	Organism	_	_
7	GLBRCE1	glbrce1	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Escherichia	escherichia	FW	Organism	_	_
10	coli	coli	FW	Organism	_	_
11	GLBRCE1	glbrce1	NN	_	_	_
12	_	_	CD	_	_	_
13	pBBR	pbbr	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	GLBRCE1	glbrce1	NN	_	_	_
16	_	_	CD	_	_	_
17	ACSH	ACSH	NNP	_	_	_
18	_	_	NNP	_	_	_
19	Exp	Exp	NNP	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	GLBRCE1	GLBRCE1	NNP	_	_	_
22	_	_	NNP	_	_	_
23	ACSH	ACSH	NNP	_	_	_
24	_	_	VBD	_	_	_
25	Stat	stat	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	GLBRCE1	glbrce1	NN	_	_	_
28	_	_	CD	_	_	_
29	ACSH	ACSH	NNP	_	_	_
30	_	_	NNP	_	_	_
31	Trans	Trans	NNP	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	GLBRCE1	glbrce1	NN	_	_	_
34	_	_	CD	_	_	_
35	pBBR	pbbr	NN	_	_	_
36	_	_	CD	_	_	_
37	ACSH	ACSH	NNP	_	_	_
38	_	_	NNP	_	_	_
39	Exp	Exp	NNP	_	_	_
40	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
41	GLBRCE1	glbrce1	NN	_	_	_
42	_	_	CD	_	_	_
43	pBBR	pbbr	NN	_	_	_
44	_	_	SYM	_	_	_
45	ACSH	ACSH	NNP	_	_	_
46	_	_	VBD	_	_	_
47	Stat	stat	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	GLBRCE1	glbrce1	NN	_	_	_
50	_	_	CD	_	_	_
51	pBBR	pbbr	NN	_	_	_
52	_	_	CD	_	_	_
53	ACSH	ACSH	NNP	_	_	_
54	_	_	NNP	_	_	_
55	Trans	Trans	NNP	_	_	_
56	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
57	growth	growth	NN	_	_	_
58	phase	phase	NN	_	_	_
59	:	:	:	_	_	_
60	Exp	exp	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	growth	growth	NN	_	_	_
63	phase	phase	NN	_	_	_
64	:	:	:	_	_	_
65	Stat	stat	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	growth	growth	NN	_	_	_
68	phase	phase	NN	_	_	_
69	:	:	:	_	_	_
70	Trans	Trans	NNP	_	_	_
71	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
72	medium	medium	NN	_	_	_
73	:	:	:	_	_	_
74	ACSH	ACSH	NNP	_	_	_
75	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
76	Probe	Probe	NNP	_	_	_
77	signal	signal	NN	_	_	_
78	intensities	intensity	NNS	_	_	_
79	were	be	VBD	_	_	_
80	preprocessed	preprocess	VBN	_	_	_
81	using	use	VBG	_	_	_
82	robust	robust	JJ	_	_	_
83	multichip	multichip	NN	_	_	_
84	averaging	averaging	NN	_	_	_
85	-LRB-	-lrb-	-LRB-	_	_	_
86	RMA	rma	NN	_	_	_
87	-RRB-	-rrb-	-RRB-	_	_	_
88	in	in	IN	_	_	_
89	the	the	DT	_	_	_
90	program	program	NN	_	_	_
91	ArrayStar	arraystar	NN	_	_	_
92	-LRB-	-lrb-	-LRB-	_	_	_
93	DNASTAR	dnastar	NN	_	_	_
94	-RRB-	-rrb-	-RRB-	_	_	_
95	,	,	,	_	_	_
96	and	and	CC	_	_	_
97	the	the	DT	_	_	_
98	resulting	result	VBG	_	_	_
99	gene	gene	NN	_	_	_
100	expression	expression	NN	_	_	_
101	signals	signal	NNS	_	_	_
102	were	be	VBD	_	_	_
103	quantile-normalized	quantile-normalize	VBN	_	_	_
104	across	across	IN	_	_	_
105	all	all	DT	_	_	_
106	samples	sample	NNS	_	_	_
107	using	use	VBG	_	_	_
108	the	the	DT	_	_	_
109	normalize.quantiles	normalize.quantiles	JJ	_	_	_
110	function	function	NN	_	_	_
111	in	in	IN	_	_	_
112	the	the	DT	_	_	_
113	Bioconductor	Bioconductor	NNP	_	_	_
114	package	package	NN	_	_	_
115	for	for	IN	_	_	_
116	R.	R.	NNP	_	_	_
117	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
118	RNA	rna	NN	_	_	_
119	was	be	VBD	_	_	_
120	obtained	obtain	VBN	_	_	_
121	from	from	IN	_	_	_
122	cells	cell	NNS	_	_	_
123	pellets	pellet	NNS	_	_	_
124	by	by	IN	_	_	_
125	lysozyme	lysozyme	NN	_	_	_
126	treatment	treatment	NN	_	_	_
127	and	and	CC	_	_	_
128	phenol-chloroform	phenol-chloroform	JJ	_	_	_
129	extraction	extraction	NN	_	_	_
130	,	,	,	_	_	_
131	analyzed	analyze	VBN	_	_	_
132	by	by	IN	_	_	_
133	agarose	agarose	NN	_	_	_
134	gel	gel	NN	_	_	_
135	electrophoresis	electrophoresis	NN	_	_	_
136	to	to	TO	_	_	_
137	confirm	confirm	VB	_	_	_
138	integrity	integrity	NN	_	_	_
139	,	,	,	_	_	_
140	quantified	quantify	VBN	_	_	_
141	using	use	VBG	_	_	_
142	a	a	DT	_	_	_
143	Nanodrop	Nanodrop	NNP	_	_	_
144	spectrophotometer	spectrophotometer	NN	_	_	_
145	-LRB-	-lrb-	-LRB-	_	_	_
146	Thermo	Thermo	NNP	_	_	_
147	Scientific	Scientific	NNP	_	_	_
148	-RRB-	-rrb-	-RRB-	_	_	_
149	,	,	,	_	_	_
150	and	and	CC	_	_	_
151	stored	store	VBD	_	_	_
152	at	at	IN	_	_	_
153	-80	-80	CD	_	_	_
154	°C	°c	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	strain	strain	NN	_	_	_
157	:	:	:	_	_	_
158	GLBRCE1	glbrce1	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	strain	strain	NN	_	_	_
161	:	:	:	_	_	_
162	GLBRCE1	glbrce1	NN	_	_	_
163	_	_	CD	_	_	_
164	pBBR	pbbr	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	Cells	cell	NNS	_	_	_
167	-LRB-	-lrb-	-LRB-	_	_	_
168	10	10	CD	_	_	_
169	ml	ml	NN	_	_	_
170	-RRB-	-rrb-	-RRB-	_	_	_
171	for	for	IN	_	_	_
172	transcriptomic	transcriptomic	JJ	_	_	_
173	analysis	analysis	NN	_	_	_
174	were	be	VBD	_	_	_
175	collected	collect	VBN	_	_	_
176	into	into	IN	_	_	_
177	tubes	tube	NNS	_	_	_
178	containing	contain	VBG	_	_	_
179	1.25	1.25	CD	_	_	_
180	ml	ml	NN	_	_	_
181	ice-cold	ice-cold	JJ	_	_	_
182	5	5	CD	_	_	_
183	%	%	NN	_	_	_
184	-LRB-	-lrb-	-LRB-	_	_	_
185	vol	vol	NN	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	Escherichia	escherichia	FW	Organism	_	_
188	coli	coli	FW	Organism	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	Escherichia	escherichia	FW	Organism	_	_
191	coli	coli	FW	Organism	_	_
192	GLBRCE1	glbrce1	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	Fermentations	fermentation	NNS	_	_	_
195	were	be	VBD	_	_	_
196	carried	carry	VBN	_	_	_
197	out	out	RP	_	_	_
198	in	in	IN	_	_	_
199	3	3	CD	_	_	_
200	L	l	NN	_	_	_
201	bioreactors	bioreactor	NNS	_	_	_
202	-LRB-	-lrb-	-LRB-	_	_	_
203	Applikon	Applikon	NNP	_	_	_
204	Biotechnology	Biotechnology	NNP	_	_	_
205	-RRB-	-rrb-	-RRB-	_	_	_
206	containing	contain	VBG	_	_	_
207	2.45	2.45	CD	_	_	_
208	L	l	NN	_	_	_
209	of	of	IN	_	_	_
210	ACSH	acsh	NN	_	_	_
211	or	or	CC	_	_	_
212	SynH	synh	NN	_	_	_
213	media	media	NNS	_	_	_
214	,	,	,	_	_	_
215	and	and	CC	_	_	_
216	cultures	culture	NNS	_	_	_
217	were	be	VBD	_	_	_
218	diluted	dilute	VBN	_	_	_
219	into	into	IN	_	_	_
220	ACSH	acsh	NN	_	_	_
221	or	or	CC	_	_	_
222	SynH	synh	NN	_	_	_
223	with	with	IN	_	_	_
224	initial	initial	JJ	_	_	_
225	OD	od	NN	_	_	_
226	at	at	IN	_	_	_
227	0.2	0.2	CD	_	_	_
228	,	,	,	_	_	_
229	grown	grow	VBN	_	_	_
230	anaerobically	anaerobically	RB	_	_	_
231	overnight	overnight	RB	_	_	_
232	,	,	,	_	_	_
233	and	and	CC	_	_	_
234	then	then	RB	_	_	_
235	inoculated	inoculate	VBN	_	_	_
236	into	into	IN	_	_	_
237	bioreactors	bioreactor	NNS	_	_	_
238	to	to	TO	_	_	_
239	a	a	DT	_	_	_
240	starting	start	VBG	_	_	_
241	OD600	od600	NN	_	_	_
242	of	of	IN	_	_	_
243	0.2	0.2	CD	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	growth	growth	NN	_	_	_
246	phase	phase	NN	_	_	_
247	:	:	:	_	_	_
248	log	log	NN	_	_	_
249	phase	phase	NN	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	growth	growth	NN	_	_	_
252	phase	phase	NN	_	_	_
253	:	:	:	_	_	_
254	stat	stat	NN	_	_	_
255	1	1	CD	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
257	growth	growth	NN	_	_	_
258	phase	phase	NN	_	_	_
259	:	:	:	_	_	_
260	stat	stat	NN	_	_	_
261	2	2	CD	_	_	_
262	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
263	growth	growth	NN	_	_	_
264	phase	phase	NN	_	_	_
265	:	:	:	_	_	_
266	transition	transition	NN	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	LIMS477	lims477	NN	_	_	_
269	_	_	CD	_	_	_
270	S1	s1	NN	_	_	_
271	_	_	CD	_	_	_
272	T10	t10	NN	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	LIMS477	lims477	NN	_	_	_
275	_	_	CD	_	_	_
276	S1	s1	NN	_	_	_
277	_	_	CD	_	_	_
278	T3	t3	NN	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	LIMS477	lims477	NN	_	_	_
281	_	_	CD	_	_	_
282	S1	s1	NN	_	_	_
283	_	_	CD	_	_	_
284	T6	t6	NN	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
286	LIMS477	lims477	NN	_	_	_
287	_	_	CD	_	_	_
288	S2	s2	NN	_	_	_
289	_	_	CD	_	_	_
290	T4	t4	NN	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	LIMS477	lims477	NN	_	_	_
293	_	_	CD	_	_	_
294	S2	s2	NN	_	_	_
295	_	_	CD	_	_	_
296	T6	t6	NN	_	_	_
297	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
298	LIMS477	lims477	NN	_	_	_
299	_	_	CD	_	_	_
300	S2	s2	NN	_	_	_
301	_	_	CD	_	_	_
302	T8	t8	NN	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
304	LIMS477	lims477	NN	_	_	_
305	_	_	CD	_	_	_
306	S3	s3	NN	_	_	_
307	_	_	CD	_	_	_
308	T11	t11	NN	_	_	_
309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
310	LIMS477	lims477	NN	_	_	_
311	_	_	CD	_	_	_
312	S3	s3	NN	_	_	_
313	_	_	CD	_	_	_
314	T3	t3	NN	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
316	LIMS477	lims477	NN	_	_	_
317	_	_	CD	_	_	_
318	S3	s3	NN	_	_	_
319	_	_	CD	_	_	_
320	T6	t6	NN	_	_	_
321	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
322	LIMS477	lims477	NN	_	_	_
323	_	_	CD	_	_	_
324	S5	s5	NN	_	_	_
325	_	_	CD	_	_	_
326	T4	t4	NN	_	_	_
327	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
328	LIMS477	lims477	NN	_	_	_
329	_	_	CD	_	_	_
330	S5	s5	NN	_	_	_
331	_	_	CD	_	_	_
332	T6	t6	NN	_	_	_
333	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
334	LIMS477	lims477	NN	_	_	_
335	_	_	CD	_	_	_
336	S5	s5	NN	_	_	_
337	_	_	CD	_	_	_
338	T8	t8	NN	_	_	_
339	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
340	LIMS484	lims484	NN	_	_	_
341	_	_	CD	_	_	_
342	S1	s1	NN	_	_	_
343	_	_	CD	_	_	_
344	T3	t3	NN	_	_	_
345	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
346	LIMS484	lims484	NN	_	_	_
347	_	_	CD	_	_	_
348	S1	s1	NN	_	_	_
349	_	_	CD	_	_	_
350	T6	t6	NN	_	_	_
351	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
352	LIMS484	lims484	NN	_	_	_
353	_	_	CD	_	_	_
354	S1	s1	NN	_	_	_
355	_	_	CD	_	_	_
356	T8	t8	NN	_	_	_
357	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
358	LIMS484	lims484	NN	_	_	_
359	_	_	CD	_	_	_
360	S2	s2	NN	_	_	_
361	_	_	CD	_	_	_
362	T2	t2	NN	_	_	_
363	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
364	LIMS484	lims484	NN	_	_	_
365	_	_	CD	_	_	_
366	S2	s2	NN	_	_	_
367	_	_	CD	_	_	_
368	T6	t6	NN	_	_	_
369	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
370	LIMS484	lims484	NN	_	_	_
371	_	_	CD	_	_	_
372	S2	s2	NN	_	_	_
373	_	_	CD	_	_	_
374	T8	t8	NN	_	_	_
375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
376	LIMS484	lims484	NN	_	_	_
377	_	_	CD	_	_	_
378	S5	s5	NN	_	_	_
379	_	_	CD	_	_	_
380	T2	t2	NN	_	_	_
381	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
382	LIMS484	lims484	NN	_	_	_
383	_	_	CD	_	_	_
384	S5	s5	NN	_	_	_
385	_	_	CD	_	_	_
386	T6	t6	NN	_	_	_
387	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
388	LIMS484	lims484	NN	_	_	_
389	_	_	CD	_	_	_
390	S5	s5	NN	_	_	_
391	_	_	CD	_	_	_
392	T8	t8	NN	_	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
394	LIMS484	lims484	NN	_	_	_
395	_	_	CD	_	_	_
396	S6	s6	NN	_	_	_
397	_	_	CD	_	_	_
398	T4	t4	NN	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	LIMS484	lims484	NN	_	_	_
401	_	_	CD	_	_	_
402	S6	s6	NN	_	_	_
403	_	_	CD	_	_	_
404	T6	t6	NN	_	_	_
405	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
406	LIMS484	lims484	NN	_	_	_
407	_	_	CD	_	_	_
408	S6	s6	NN	_	_	_
409	_	_	CD	_	_	_
410	T8	t8	NN	_	_	_
411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
412	medium	medium	NN	_	_	_
413	:	:	:	_	_	_
414	SynH	synh	NN	_	_	_
415	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
416	medium	medium	NN	_	_	_
417	:	:	:	_	_	_
418	SynH	synh	NN	_	_	_
419	+	+	CC	_	_	_
420	LTs	lts	NN	_	_	_
421	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
422	medium	medium	NN	_	_	_
423	:	:	:	_	_	_
424	SynH	synh	NN	_	_	_
425	w	w	NN	_	_	_
426	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
427	Probe	Probe	NNP	_	_	_
428	signal	signal	NN	_	_	_
429	intensities	intensity	NNS	_	_	_
430	were	be	VBD	_	_	_
431	preprocessed	preprocess	VBN	_	_	_
432	using	use	VBG	_	_	_
433	robust	robust	JJ	_	_	_
434	multichip	multichip	NN	_	_	_
435	averaging	averaging	NN	_	_	_
436	-LRB-	-lrb-	-LRB-	_	_	_
437	RMA	rma	NN	_	_	_
438	-RRB-	-rrb-	-RRB-	_	_	_
439	in	in	IN	_	_	_
440	the	the	DT	_	_	_
441	program	program	NN	_	_	_
442	ArrayStar	arraystar	NN	_	_	_
443	-LRB-	-lrb-	-LRB-	_	_	_
444	DNASTAR	dnastar	NN	_	_	_
445	-RRB-	-rrb-	-RRB-	_	_	_
446	,	,	,	_	_	_
447	and	and	CC	_	_	_
448	the	the	DT	_	_	_
449	resulting	result	VBG	_	_	_
450	gene	gene	NN	_	_	_
451	expression	expression	NN	_	_	_
452	signals	signal	NNS	_	_	_
453	were	be	VBD	_	_	_
454	quantile-normalized	quantile-normalize	VBN	_	_	_
455	across	across	IN	_	_	_
456	all	all	DT	_	_	_
457	samples	sample	NNS	_	_	_
458	using	use	VBG	_	_	_
459	the	the	DT	_	_	_
460	normalize.quantiles	normalize.quantiles	JJ	_	_	_
461	function	function	NN	_	_	_
462	in	in	IN	_	_	_
463	the	the	DT	_	_	_
464	Bioconductor	Bioconductor	NNP	_	_	_
465	package	package	NN	_	_	_
466	for	for	IN	_	_	_
467	R.	R.	NNP	_	_	_
468	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
469	RNA	rna	NN	_	_	_
470	was	be	VBD	_	_	_
471	obtained	obtain	VBN	_	_	_
472	from	from	IN	_	_	_
473	cells	cell	NNS	_	_	_
474	pellets	pellet	NNS	_	_	_
475	by	by	IN	_	_	_
476	lysozyme	lysozyme	NN	_	_	_
477	treatment	treatment	NN	_	_	_
478	and	and	CC	_	_	_
479	phenol-chloroform	phenol-chloroform	JJ	_	_	_
480	extraction	extraction	NN	_	_	_
481	,	,	,	_	_	_
482	analyzed	analyze	VBN	_	_	_
483	by	by	IN	_	_	_
484	agarose	agarose	NN	_	_	_
485	gel	gel	NN	_	_	_
486	electrophoresis	electrophoresis	NN	_	_	_
487	to	to	TO	_	_	_
488	confirm	confirm	VB	_	_	_
489	integrity	integrity	NN	_	_	_
490	,	,	,	_	_	_
491	quantified	quantify	VBN	_	_	_
492	using	use	VBG	_	_	_
493	a	a	DT	_	_	_
494	Nanodrop	Nanodrop	NNP	_	_	_
495	spectrophotometer	spectrophotometer	NN	_	_	_
496	-LRB-	-lrb-	-LRB-	_	_	_
497	Thermo	Thermo	NNP	_	_	_
498	Scientific	Scientific	NNP	_	_	_
499	-RRB-	-rrb-	-RRB-	_	_	_
500	,	,	,	_	_	_
501	and	and	CC	_	_	_
502	stored	store	VBD	_	_	_
503	at	at	IN	_	_	_
504	-80	-80	CD	_	_	_
505	°C	°c	NN	_	_	_
506	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
507	strain	strain	NN	_	_	_
508	:	:	:	_	_	_
509	GLBRCE1	glbrce1	NN	_	_	_
510	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
511	Cells	cell	NNS	_	_	_
512	-LRB-	-lrb-	-LRB-	_	_	_
513	10	10	CD	_	_	_
514	ml	ml	NN	_	_	_
515	-RRB-	-rrb-	-RRB-	_	_	_
516	for	for	IN	_	_	_
517	transcriptomic	transcriptomic	JJ	_	_	_
518	analysis	analysis	NN	_	_	_
519	were	be	VBD	_	_	_
520	collected	collect	VBN	_	_	_
521	into	into	IN	_	_	_
522	tubes	tube	NNS	_	_	_
523	containing	contain	VBG	_	_	_
524	1.25	1.25	CD	_	_	_
525	ml	ml	NN	_	_	_
526	ice-cold	ice-cold	JJ	_	_	_
527	5	5	CD	_	_	_
528	%	%	NN	_	_	_
529	-LRB-	-lrb-	-LRB-	_	_	_
530	vol	vol	NN	_	_	_
531	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
532	Escherichia	escherichia	FW	Organism	_	_
533	coli	coli	FW	Organism	_	_
534	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
535	Escherichia	escherichia	FW	Organism	_	_
536	coli	coli	FW	Organism	_	_
537	GLBRCE1	glbrce1	NN	_	_	_
538	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
539	Fermentations	fermentation	NNS	_	_	_
540	were	be	VBD	_	_	_
541	carried	carry	VBN	_	_	_
542	out	out	RP	_	_	_
543	in	in	IN	_	_	_
544	3L	3l	NN	_	_	_
545	bioreactors	bioreactor	NNS	_	_	_
546	-LRB-	-lrb-	-LRB-	_	_	_
547	Applikon	Applikon	NNP	_	_	_
548	Biotechnology	Biotechnology	NNP	_	_	_
549	-RRB-	-rrb-	-RRB-	_	_	_
550	containing	contain	VBG	_	_	_
551	2.45	2.45	CD	_	_	_
552	L	l	NN	_	_	_
553	of	of	IN	_	_	_
554	ACSH	ACSH	NNP	_	_	_
555	,	,	,	_	_	_
556	SynH	synh	NN	_	_	_
557	,	,	,	_	_	_
558	SynH	synh	NN	_	_	_
559	+	+	CC	_	_	_
560	LT	lt	NN	_	_	_
561	,	,	,	_	_	_
562	or	or	CC	_	_	_
563	SynH	synh	NN	_	_	_
564	+	+	CC	_	_	_
565	Acid	acid	NN	_	_	_
566	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
567	growth	growth	NN	_	_	_
568	phase	phase	NN	_	_	_
569	:	:	:	_	_	_
570	Exp	exp	NN	_	_	_
571	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
572	growth	growth	NN	_	_	_
573	phase	phase	NN	_	_	_
574	:	:	:	_	_	_
575	Exp1	exp1	NN	_	_	_
576	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
577	growth	growth	NN	_	_	_
578	phase	phase	NN	_	_	_
579	:	:	:	_	_	_
580	Exp2	exp2	NN	_	_	_
581	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
582	growth	growth	NN	_	_	_
583	phase	phase	NN	_	_	_
584	:	:	:	_	_	_
585	Exp3	exp3	NN	_	_	_
586	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
587	growth	growth	NN	_	_	_
588	phase	phase	NN	_	_	_
589	:	:	:	_	_	_
590	Stat	stat	NN	_	_	_
591	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
592	growth	growth	NN	_	_	_
593	phase	phase	NN	_	_	_
594	:	:	:	_	_	_
595	Stat1	stat1	NN	_	_	_
596	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
597	growth	growth	NN	_	_	_
598	phase	phase	NN	_	_	_
599	:	:	:	_	_	_
600	Stat2	stat2	NN	_	_	_
601	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
602	growth	growth	NN	_	_	_
603	phase	phase	NN	_	_	_
604	:	:	:	_	_	_
605	Trans	Trans	NNP	_	_	_
606	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
607	medium	medium	NN	_	_	_
608	:	:	:	_	_	_
609	ACSH	ACSH	NNP	_	_	_
610	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
611	medium	medium	NN	_	_	_
612	:	:	:	_	_	_
613	SynH	synh	NN	_	_	_
614	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
615	medium	medium	NN	_	_	_
616	:	:	:	_	_	_
617	SynH	synh	NN	_	_	_
618	_	_	NN	_	_	_
619	Acids	acid	NNS	_	_	_
620	_	_	VBP	_	_	_
621	Amides	amide	NNS	_	_	_
622	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
623	medium	medium	NN	_	_	_
624	:	:	:	_	_	_
625	SynH	synh	NN	_	_	_
626	_	_	CD	_	_	_
627	LT	lt	NN	_	_	_
628	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
629	Probe	probe	NN	_	_	_
630	signal	signal	NN	_	_	_
631	intensities	intensity	NNS	_	_	_
632	were	be	VBD	_	_	_
633	preprocessed	preprocess	VBN	_	_	_
634	using	use	VBG	_	_	_
635	robust	robust	JJ	_	_	_
636	multichip	multichip	NN	_	_	_
637	averaging	averaging	NN	_	_	_
638	-LRB-	-lrb-	-LRB-	_	_	_
639	RMA	rma	NN	_	_	_
640	-RRB-	-rrb-	-RRB-	_	_	_
641	in	in	IN	_	_	_
642	the	the	DT	_	_	_
643	program	program	NN	_	_	_
644	ArrayStar	arraystar	NN	_	_	_
645	-LRB-	-lrb-	-LRB-	_	_	_
646	DNASTAR	dnastar	NN	_	_	_
647	-RRB-	-rrb-	-RRB-	_	_	_
648	,	,	,	_	_	_
649	and	and	CC	_	_	_
650	the	the	DT	_	_	_
651	resulting	result	VBG	_	_	_
652	gene	gene	NN	_	_	_
653	expression	expression	NN	_	_	_
654	signals	signal	NNS	_	_	_
655	were	be	VBD	_	_	_
656	quantile-normalized	quantile-normalize	VBN	_	_	_
657	across	across	IN	_	_	_
658	all	all	DT	_	_	_
659	samples	sample	NNS	_	_	_
660	using	use	VBG	_	_	_
661	the	the	DT	_	_	_
662	normalize.quantiles	normalize.quantiles	JJ	_	_	_
663	function	function	NN	_	_	_
664	in	in	IN	_	_	_
665	the	the	DT	_	_	_
666	Bioconductor	Bioconductor	NNP	_	_	_
667	package	package	NN	_	_	_
668	for	for	IN	_	_	_
669	R.	R.	NNP	_	_	_
670	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
671	RNA	rna	NN	_	_	_
672	was	be	VBD	_	_	_
673	obtained	obtain	VBN	_	_	_
674	from	from	IN	_	_	_
675	cells	cell	NNS	_	_	_
676	pellets	pellet	NNS	_	_	_
677	by	by	IN	_	_	_
678	lysozyme	lysozyme	NN	_	_	_
679	treatment	treatment	NN	_	_	_
680	and	and	CC	_	_	_
681	phenol-chloroform	phenol-chloroform	JJ	_	_	_
682	extraction	extraction	NN	_	_	_
683	,	,	,	_	_	_
684	analyzed	analyze	VBN	_	_	_
685	by	by	IN	_	_	_
686	agarose	agarose	NN	_	_	_
687	gel	gel	NN	_	_	_
688	electrophoresis	electrophoresis	NN	_	_	_
689	to	to	TO	_	_	_
690	confirm	confirm	VB	_	_	_
691	integrity	integrity	NN	_	_	_
692	,	,	,	_	_	_
693	quantified	quantify	VBN	_	_	_
694	using	use	VBG	_	_	_
695	a	a	DT	_	_	_
696	Nanodrop	Nanodrop	NNP	_	_	_
697	spectrophotometer	spectrophotometer	NN	_	_	_
698	-LRB-	-lrb-	-LRB-	_	_	_
699	Thermo	Thermo	NNP	_	_	_
700	Scientific	Scientific	NNP	_	_	_
701	-RRB-	-rrb-	-RRB-	_	_	_
702	,	,	,	_	_	_
703	and	and	CC	_	_	_
704	stored	store	VBD	_	_	_
705	at	at	IN	_	_	_
706	-80	-80	CD	_	_	_
707	°C	°c	NN	_	_	_
708	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
709	strain	strain	NN	_	_	_
710	:	:	:	_	_	_
711	GLBRCE1	glbrce1	NN	_	_	_
712	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
713	X515	x515	NN	_	_	_
714	_	_	CD	_	_	_
715	V1	v1	NN	_	_	_
716	_	_	CD	_	_	_
717	T4	t4	NN	_	_	_
718	_	_	CD	_	_	_
719	424287A03	424287a03	NN	_	_	_
720	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
721	X515	x515	NN	_	_	_
722	_	_	CD	_	_	_
723	V1	v1	NN	_	_	_
724	_	_	CD	_	_	_
725	T4	t4	NN	_	_	_
726	_	_	CD	_	_	_
727	475655A02	475655a02	NN	_	_	_
728	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
729	X515	x515	NN	_	_	_
730	_	_	CD	_	_	_
731	V1	v1	NN	_	_	_
732	_	_	CD	_	_	_
733	T6	t6	NN	_	_	_
734	_	_	CD	_	_	_
735	475649A04s	475649a04	NNS	_	_	_
736	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
737	X515	x515	NN	_	_	_
738	_	_	CD	_	_	_
739	V1	v1	NN	_	_	_
740	_	_	CD	_	_	_
741	T7	t7	NN	_	_	_
742	_	_	CD	_	_	_
743	475654A02	475654a02	NN	_	_	_
744	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
745	X515	x515	NN	_	_	_
746	_	_	CD	_	_	_
747	V1	v1	NN	_	_	_
748	_	_	CD	_	_	_
749	T8	t8	NN	_	_	_
750	_	_	CD	_	_	_
751	475585A04	475585a04	NN	_	_	_
752	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
753	X515	x515	NN	_	_	_
754	_	_	CD	_	_	_
755	V2	v2	NN	_	_	_
756	_	_	CD	_	_	_
757	T4	t4	NN	_	_	_
758	_	_	CD	_	_	_
759	424219A04	424219a04	NN	_	_	_
760	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
761	X515	x515	NN	_	_	_
762	_	_	CD	_	_	_
763	V2	v2	NN	_	_	_
764	_	_	CD	_	_	_
765	T4	t4	NN	_	_	_
766	_	_	CD	_	_	_
767	475655A03	475655a03	NN	_	_	_
768	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
769	X515	x515	NN	_	_	_
770	_	_	CD	_	_	_
771	V2	v2	NN	_	_	_
772	_	_	CD	_	_	_
773	T6	t6	NN	_	_	_
774	_	_	CD	_	_	_
775	475644A04	475644a04	NN	_	_	_
776	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
777	X515	x515	NN	_	_	_
778	_	_	CD	_	_	_
779	V2	v2	NN	_	_	_
780	_	_	CD	_	_	_
781	T7	t7	NN	_	_	_
782	_	_	CD	_	_	_
783	475649A01	475649a01	NN	_	_	_
784	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
785	X515	x515	NN	_	_	_
786	_	_	CD	_	_	_
787	V2	v2	NN	_	_	_
788	_	_	CD	_	_	_
789	T8	t8	NN	_	_	_
790	_	_	CD	_	_	_
791	424219A01s	424219a01	NNS	_	_	_
792	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
793	X515	x515	NN	_	_	_
794	_	_	CD	_	_	_
795	V3	v3	NN	_	_	_
796	_	_	CD	_	_	_
797	T4	t4	NN	_	_	_
798	_	_	CD	_	_	_
799	475585A02s	475585a02	NNS	_	_	_
800	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
801	X515	x515	NN	_	_	_
802	_	_	CD	_	_	_
803	V3	v3	NN	_	_	_
804	_	_	CD	_	_	_
805	T6	t6	NN	_	_	_
806	_	_	CD	_	_	_
807	424221A04	424221a04	NN	_	_	_
808	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
809	X515	x515	NN	_	_	_
810	_	_	CD	_	_	_
811	V3	v3	NN	_	_	_
812	_	_	CD	_	_	_
813	T7	t7	NN	_	_	_
814	_	_	CD	_	_	_
815	475649A02	475649a02	NN	_	_	_
816	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
817	X515	x515	NN	_	_	_
818	_	_	CD	_	_	_
819	V3	v3	NN	_	_	_
820	_	_	CD	_	_	_
821	T8	t8	NN	_	_	_
822	_	_	CD	_	_	_
823	475641A04	475641a04	NN	_	_	_
824	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
825	X515	x515	NN	_	_	_
826	_	_	CD	_	_	_
827	V4	v4	NN	_	_	_
828	_	_	CD	_	_	_
829	T4	t4	NN	_	_	_
830	_	_	CD	_	_	_
831	475585A03	475585a03	NN	_	_	_
832	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
833	X515	x515	NN	_	_	_
834	_	_	CD	_	_	_
835	V4	v4	NN	_	_	_
836	_	_	CD	_	_	_
837	T4	t4	NN	_	_	_
838	_	_	CD	_	_	_
839	475644A01	475644a01	NN	_	_	_
840	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
841	X515	x515	NN	_	_	_
842	_	_	CD	_	_	_
843	V4	v4	NN	_	_	_
844	_	_	CD	_	_	_
845	T6	t6	NN	_	_	_
846	_	_	CD	_	_	_
847	424221A03	424221a03	NN	_	_	_
848	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
849	X515	x515	NN	_	_	_
850	_	_	CD	_	_	_
851	V4	v4	NN	_	_	_
852	_	_	CD	_	_	_
853	T7	t7	NN	_	_	_
854	_	_	CD	_	_	_
855	424287A04	424287a04	NN	_	_	_
856	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
857	X515	x515	NN	_	_	_
858	_	_	CD	_	_	_
859	V4	v4	NN	_	_	_
860	_	_	CD	_	_	_
861	T8	t8	NN	_	_	_
862	_	_	CD	_	_	_
863	475655A04	475655a04	NN	_	_	_
864	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
865	X520	x520	NN	_	_	_
866	_	_	CD	_	_	_
867	V1	v1	NN	_	_	_
868	_	_	CD	_	_	_
869	T4	t4	NN	_	_	_
870	_	_	CD	_	_	_
871	424221A01	424221a01	NN	_	_	_
872	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
873	X520	x520	NN	_	_	_
874	_	_	CD	_	_	_
875	V1	v1	NN	_	_	_
876	_	_	CD	_	_	_
877	T6	t6	NN	_	_	_
878	_	_	CD	_	_	_
879	475649A03	475649a03	NN	_	_	_
880	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
881	X520	x520	NN	_	_	_
882	_	_	CD	_	_	_
883	V1	v1	NN	_	_	_
884	_	_	CD	_	_	_
885	T7	t7	NN	_	_	_
886	_	_	CD	_	_	_
887	475655A01	475655a01	NN	_	_	_
888	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
889	X520	x520	NN	_	_	_
890	_	_	CD	_	_	_
891	V1	v1	NN	_	_	_
892	_	_	CD	_	_	_
893	T8	t8	NN	_	_	_
894	_	_	CD	_	_	_
895	475641A01	475641a01	NN	_	_	_
896	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
897	X520	x520	NN	_	_	_
898	_	_	CD	_	_	_
899	V2	v2	NN	_	_	_
900	_	_	CD	_	_	_
901	T3	t3	NN	_	_	_
902	_	_	CD	_	_	_
903	424221A02	424221a02	NN	_	_	_
904	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
905	X520	x520	NN	_	_	_
906	_	_	CD	_	_	_
907	V2	v2	NN	_	_	_
908	_	_	CD	_	_	_
909	T4	t4	NN	_	_	_
910	_	_	CD	_	_	_
911	475641A03	475641a03	NN	_	_	_
912	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
913	X520	x520	NN	_	_	_
914	_	_	CD	_	_	_
915	V2	v2	NN	_	_	_
916	_	_	CD	_	_	_
917	T6	t6	NN	_	_	_
918	_	_	CD	_	_	_
919	424287A02	424287a02	NN	_	_	_
920	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
921	X520	x520	NN	_	_	_
922	_	_	CD	_	_	_
923	V2	v2	NN	_	_	_
924	_	_	CD	_	_	_
925	T7	t7	NN	_	_	_
926	_	_	CD	_	_	_
927	475654A01	475654a01	NN	_	_	_
928	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
929	X520	x520	NN	_	_	_
930	_	_	CD	_	_	_
931	V2	v2	NN	_	_	_
932	_	_	CD	_	_	_
933	T8	t8	NN	_	_	_
934	_	_	CD	_	_	_
935	424219A02	424219a02	NN	_	_	_
936	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
937	X520	x520	NN	_	_	_
938	_	_	CD	_	_	_
939	V3	v3	NN	_	_	_
940	_	_	CD	_	_	_
941	T4	t4	NN	_	_	_
942	_	_	CD	_	_	_
943	475654A04	475654a04	NN	_	_	_
944	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
945	X520	x520	NN	_	_	_
946	_	_	CD	_	_	_
947	V3	v3	NN	_	_	_
948	_	_	CD	_	_	_
949	T6	t6	NN	_	_	_
950	_	_	CD	_	_	_
951	475641A02	475641a02	NN	_	_	_
952	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
953	X520	x520	NN	_	_	_
954	_	_	CD	_	_	_
955	V3	v3	NN	_	_	_
956	_	_	CD	_	_	_
957	T7	t7	NN	_	_	_
958	_	_	CD	_	_	_
959	475644A02s	475644a02	NNS	_	_	_
960	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
961	X520	x520	NN	_	_	_
962	_	_	CD	_	_	_
963	V3	v3	NN	_	_	_
964	_	_	CD	_	_	_
965	T8	t8	NN	_	_	_
966	_	_	CD	_	_	_
967	424219A03	424219a03	NN	_	_	_
968	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
969	X520	x520	NN	_	_	_
970	_	_	CD	_	_	_
971	V4	v4	NN	_	_	_
972	_	_	CD	_	_	_
973	T4	t4	NN	_	_	_
974	_	_	CD	_	_	_
975	475654A03	475654a03	NN	_	_	_
976	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
977	X520	x520	NN	_	_	_
978	_	_	CD	_	_	_
979	V4	v4	NN	_	_	_
980	_	_	CD	_	_	_
981	T6	t6	NN	_	_	_
982	_	_	CD	_	_	_
983	424287A01	424287a01	NN	_	_	_
984	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
985	X520	x520	NN	_	_	_
986	_	_	CD	_	_	_
987	V4	v4	NN	_	_	_
988	_	_	CD	_	_	_
989	T7	t7	NN	_	_	_
990	_	_	CD	_	_	_
991	475644A03	475644a03	NN	_	_	_
992	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
993	X520	x520	NN	_	_	_
994	_	_	CD	_	_	_
995	V4	v4	NN	_	_	_
996	_	_	CD	_	_	_
997	T8	t8	NN	_	_	_
998	_	_	CD	_	_	_
999	475585A01	475585a01	NN	_	_	_
1000	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1001	Each	each	DT	_	_	_
1002	strain	strain	NN	_	_	_
1003	was	be	VBD	_	_	_
1004	inoculated	inoculate	VBN	_	_	_
1005	from	from	IN	_	_	_
1006	the	the	DT	_	_	_
1007	frozen	frozen	JJ	_	_	_
1008	stock	stock	NN	_	_	_
1009	into	into	IN	_	_	_
1010	10	10	CD	_	_	_
1011	mL	ml	NN	_	_	_
1012	of	of	IN	_	_	_
1013	M9	m9	NN	_	_	_
1014	medium	medium	NN	_	_	_
1015	for	for	IN	_	_	_
1016	preculture	preculture	NN	_	_	_
1017	.	.	.	_	_	_

1	Five-microliter	five-microliter	NN	_	_	_
2	aliquots	aliquot	NNS	_	_	_
3	of	of	IN	_	_	_
4	preculture	preculture	JJ	_	_	_
5	medium	medium	NN	_	_	_
6	cells	cell	NNS	_	_	_
7	were	be	VBD	_	_	_
8	inoculated	inoculate	VBN	_	_	_
9	into	into	IN	_	_	_
10	the	the	DT	_	_	_
11	fresh	fresh	JJ	_	_	_
12	minimal	minimal	JJ	_	_	_
13	media	media	NNS	_	_	_
14	,	,	,	_	_	_
15	M9	m9	NN	_	_	_
16	with	with	IN	_	_	_
17	5	5	CD	_	_	_
18	%	%	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	v	v	LS	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	Escherichia	escherichia	FW	Organism	_	_
23	coli	coli	FW	Organism	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Evolved	evolve	VBD	_	_	_
26	strain	strain	NN	_	_	_
27	A	a	NN	_	_	_
28	,	,	,	_	_	_
29	time	time	NN	_	_	_
30	point	point	NN	_	_	_
31	1	1	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	Evolved	evolve	VBN	_	_	_
34	strain	strain	NN	_	_	_
35	A	a	NN	_	_	_
36	,	,	,	_	_	_
37	time	time	NN	_	_	_
38	point	point	NN	_	_	_
39	2	2	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
41	Evolved	evolve	VBN	_	_	_
42	strain	strain	NN	_	_	_
43	A	a	NN	_	_	_
44	,	,	,	_	_	_
45	time	time	NN	_	_	_
46	point	point	NN	_	_	_
47	3	3	CD	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	Evolved	evolve	VBN	_	_	_
50	strain	strain	NN	_	_	_
51	A	a	NN	_	_	_
52	,	,	,	_	_	_
53	time	time	NN	_	_	_
54	point	point	NN	_	_	_
55	4	4	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
57	Evolved	evolve	VBN	_	_	_
58	strain	strain	NN	_	_	_
59	A	a	NN	_	_	_
60	,	,	,	_	_	_
61	time	time	NN	_	_	_
62	point	point	NN	_	_	_
63	5	5	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
65	Evolved	evolve	VBN	_	_	_
66	strain	strain	NN	_	_	_
67	B	b	NN	_	_	_
68	,	,	,	_	_	_
69	time	time	NN	_	_	_
70	point	point	NN	_	_	_
71	1	1	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	Evolved	evolve	VBN	_	_	_
74	strain	strain	NN	_	_	_
75	B	b	NN	_	_	_
76	,	,	,	_	_	_
77	time	time	NN	_	_	_
78	point	point	NN	_	_	_
79	2	2	CD	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
81	Evolved	evolve	VBN	_	_	_
82	strain	strain	NN	_	_	_
83	B	b	NN	_	_	_
84	,	,	,	_	_	_
85	time	time	NN	_	_	_
86	point	point	NN	_	_	_
87	3	3	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	Evolved	evolve	VBN	_	_	_
90	strain	strain	NN	_	_	_
91	B	b	NN	_	_	_
92	,	,	,	_	_	_
93	time	time	NN	_	_	_
94	point	point	NN	_	_	_
95	4	4	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
97	Evolved	evolve	VBN	_	_	_
98	strain	strain	NN	_	_	_
99	B	b	NN	_	_	_
100	,	,	,	_	_	_
101	time	time	NN	_	_	_
102	point	point	NN	_	_	_
103	5	5	CD	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
105	Evolved	evolve	VBN	_	_	_
106	strain	strain	NN	_	_	_
107	C	c	NN	_	_	_
108	,	,	,	_	_	_
109	time	time	NN	_	_	_
110	point	point	NN	_	_	_
111	1	1	CD	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	Evolved	evolve	VBN	_	_	_
114	strain	strain	NN	_	_	_
115	C	c	NN	_	_	_
116	,	,	,	_	_	_
117	time	time	NN	_	_	_
118	point	point	NN	_	_	_
119	2	2	CD	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
121	Evolved	evolve	VBN	_	_	_
122	strain	strain	NN	_	_	_
123	C	c	NN	_	_	_
124	,	,	,	_	_	_
125	time	time	NN	_	_	_
126	point	point	NN	_	_	_
127	3	3	CD	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	Evolved	evolve	VBN	_	_	_
130	strain	strain	NN	_	_	_
131	C	c	NN	_	_	_
132	,	,	,	_	_	_
133	time	time	NN	_	_	_
134	point	point	NN	_	_	_
135	4	4	CD	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
137	Evolved	evolve	VBN	_	_	_
138	strain	strain	NN	_	_	_
139	C	c	NN	_	_	_
140	,	,	,	_	_	_
141	time	time	NN	_	_	_
142	point	point	NN	_	_	_
143	5	5	CD	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
145	Evolved	evolve	VBN	_	_	_
146	strain	strain	NN	_	_	_
147	D	d	NN	_	_	_
148	,	,	,	_	_	_
149	time	time	NN	_	_	_
150	point	point	NN	_	_	_
151	1	1	CD	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	Evolved	evolve	VBN	_	_	_
154	strain	strain	NN	_	_	_
155	D	d	NN	_	_	_
156	,	,	,	_	_	_
157	time	time	NN	_	_	_
158	point	point	NN	_	_	_
159	2	2	CD	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
161	Evolved	evolve	VBN	_	_	_
162	strain	strain	NN	_	_	_
163	D	d	NN	_	_	_
164	,	,	,	_	_	_
165	time	time	NN	_	_	_
166	point	point	NN	_	_	_
167	3	3	CD	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	Evolved	evolve	VBN	_	_	_
170	strain	strain	NN	_	_	_
171	D	d	NN	_	_	_
172	,	,	,	_	_	_
173	time	time	NN	_	_	_
174	point	point	NN	_	_	_
175	4	4	CD	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
177	Evolved	evolve	VBN	_	_	_
178	strain	strain	NN	_	_	_
179	D	d	NN	_	_	_
180	,	,	,	_	_	_
181	time	time	NN	_	_	_
182	point	point	NN	_	_	_
183	5	5	CD	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
185	Evolved	evolve	VBN	_	_	_
186	strain	strain	NN	_	_	_
187	E	e	NN	_	_	_
188	,	,	,	_	_	_
189	time	time	NN	_	_	_
190	point	point	NN	_	_	_
191	1	1	CD	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	Evolved	evolve	VBN	_	_	_
194	strain	strain	NN	_	_	_
195	E	e	NN	_	_	_
196	,	,	,	_	_	_
197	time	time	NN	_	_	_
198	point	point	NN	_	_	_
199	2	2	CD	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
201	Evolved	evolve	VBN	_	_	_
202	strain	strain	NN	_	_	_
203	E	e	NN	_	_	_
204	,	,	,	_	_	_
205	time	time	NN	_	_	_
206	point	point	NN	_	_	_
207	3	3	CD	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	Evolved	evolve	VBN	_	_	_
210	strain	strain	NN	_	_	_
211	E	e	NN	_	_	_
212	,	,	,	_	_	_
213	time	time	NN	_	_	_
214	point	point	NN	_	_	_
215	4	4	CD	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
217	Evolved	evolve	VBN	_	_	_
218	strain	strain	NN	_	_	_
219	E	e	NN	_	_	_
220	,	,	,	_	_	_
221	time	time	NN	_	_	_
222	point	point	NN	_	_	_
223	5	5	CD	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
225	Evolved	evolve	VBN	_	_	_
226	strain	strain	NN	_	_	_
227	F	f	NN	_	_	_
228	,	,	,	_	_	_
229	time	time	NN	_	_	_
230	point	point	NN	_	_	_
231	1	1	CD	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	Evolved	evolve	VBN	_	_	_
234	strain	strain	NN	_	_	_
235	F	f	NN	_	_	_
236	,	,	,	_	_	_
237	time	time	NN	_	_	_
238	point	point	NN	_	_	_
239	2	2	CD	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
241	Evolved	evolve	VBN	_	_	_
242	strain	strain	NN	_	_	_
243	F	f	NN	_	_	_
244	,	,	,	_	_	_
245	time	time	NN	_	_	_
246	point	point	NN	_	_	_
247	3	3	CD	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
249	Evolved	evolve	VBN	_	_	_
250	strain	strain	NN	_	_	_
251	F	f	NN	_	_	_
252	,	,	,	_	_	_
253	time	time	NN	_	_	_
254	point	point	NN	_	_	_
255	4	4	CD	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
257	Evolved	evolve	VBN	_	_	_
258	strain	strain	NN	_	_	_
259	F	f	NN	_	_	_
260	,	,	,	_	_	_
261	time	time	NN	_	_	_
262	point	point	NN	_	_	_
263	5	5	CD	_	_	_
264	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
265	Log10	log10	NN	_	_	_
266	mRNA	mrna	NN	_	_	_
267	concentration	concentration	NN	_	_	_
268	-LRB-	-lrb-	-LRB-	_	_	_
269	pM	pm	NN	_	_	_
270	-RRB-	-rrb-	-RRB-	_	_	_
271	data	datum	NNS	_	_	_
272	are	be	VBP	_	_	_
273	provided	provide	VBN	_	_	_
274	as	as	IN	_	_	_
275	a	a	DT	_	_	_
276	supplementary	supplementary	JJ	_	_	_
277	file	file	NN	_	_	_
278	.	.	.	_	_	_

1	Expression	expression	NN	_	_	_
2	levels	level	NNS	_	_	_
3	were	be	VBD	_	_	_
4	normalized	normalize	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	quantile	quantile	JJ	_	_	_
8	normalization	normalization	NN	_	_	_
9	method	method	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Bolstad	Bolstad	NNP	_	_	_
12	et	et	FW	_	_	_
13	al.	al.	FW	_	_	_
14	,	,	,	_	_	_
15	2003	2003	CD	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Parent	Parent	NNP	_	_	_
3	strain	strain	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Parent	Parent	NNP	_	_	_
9	strain	strain	NN	_	_	_
10	of	of	IN	_	_	_
11	experimental	experimental	JJ	_	_	_
12	evolution	evolution	NN	_	_	_
13	as	as	IN	_	_	_
14	adaptive	adaptive	JJ	_	_	_
15	evolved	evolve	VBD	_	_	_
16	E.	e.	FW	_	_	_
17	coli	coli	FW	_	_	_
18	W3110	w3110	NN	_	_	_
19	strain	strain	NN	_	_	_
20	to	to	TO	_	_	_
21	M9	m9	NN	_	_	_
22	synthetic	synthetic	JJ	_	_	_
23	medium	medium	NN	_	_	_
24	without	without	IN	_	_	_
25	ethanol	ethanol	NN	_	_	_
26	stress	stress	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	platform	platform	NN	_	_	_
29	_	_	CD	_	_	_
30	id	id	NN	_	_	_
31	_	_	CD	_	_	_
32	id	id	NN	_	_	_
33	design	design	NN	_	_	_
34	:	:	:	_	_	_
35	EcFS	ecfs	NN	_	_	_
36	_	_	NN	_	_	_
37	1	1	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	platform	platform	NN	_	_	_
40	_	_	CD	_	_	_
41	id	id	NN	_	_	_
42	_	_	CD	_	_	_
43	id	id	NN	_	_	_
44	design	design	NN	_	_	_
45	:	:	:	_	_	_
46	EcFS	ecfs	NN	_	_	_
47	_	_	NN	_	_	_
48	2	2	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	platform	platform	NN	_	_	_
51	_	_	CD	_	_	_
52	id	id	NN	_	_	_
53	_	_	CD	_	_	_
54	id	id	NN	_	_	_
55	design	design	NN	_	_	_
56	:	:	:	_	_	_
57	EcFS	ecfs	NN	_	_	_
58	_	_	NN	_	_	_
59	3	3	CD	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	Strain	strain	NN	_	_	_
62	A	a	NN	_	_	_
63	of	of	IN	_	_	_
64	experimental	experimental	JJ	_	_	_
65	evolution	evolution	NN	_	_	_
66	under	under	IN	_	_	_
67	ethanol	ethanol	NN	_	_	_
68	stress	stress	NN	_	_	_
69	in	in	IN	_	_	_
70	1224	1224	CD	_	_	_
71	hours	hour	NNS	_	_	_
72	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Strain	strain	NN	_	_	_
3	A	a	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	1824	1824	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Strain	strain	NN	_	_	_
3	A	a	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	2496	2496	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Strain	strain	NN	_	_	_
3	A	a	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	384	384	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Strain	strain	NN	_	_	_
3	A	a	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	744	744	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	B	b	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	1224	1224	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	B	b	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	1824	1824	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	B	b	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	2496	2496	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	B	b	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	384	384	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	B	b	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	744	744	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	C	c	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	1224	1224	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	C	c	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	1824	1824	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	C	c	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	2496	2496	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	C	c	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	384	384	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	C	c	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	744	744	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	D	d	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	1224	1224	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	D	d	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	1824	1824	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	D	d	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	2496	2496	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	D	d	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	384	384	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	D	d	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	744	744	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	E	e	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	1224	1224	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	E	e	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	1824	1824	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	E	e	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	2496	2496	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	E	e	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	384	384	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	E	e	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	744	744	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	F	f	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	1224	1224	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	F	f	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	1824	1824	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	F	f	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	2496	2496	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	F	f	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	384	384	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	F	f	NN	_	_	_
4	of	of	IN	_	_	_
5	experimental	experimental	JJ	_	_	_
6	evolution	evolution	NN	_	_	_
7	under	under	IN	_	_	_
8	ethanol	ethanol	NN	_	_	_
9	stress	stress	NN	_	_	_
10	in	in	IN	_	_	_
11	744	744	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	collected	collect	VBN	_	_	_
6	by	by	IN	_	_	_
7	centrifugation	centrifugation	NN	_	_	_
8	at	at	IN	_	_	_
9	8,000	8,000	CD	_	_	_
10	×	×	CD	_	_	_
11	g	g	NN	_	_	_
12	for	for	IN	_	_	_
13	5	5	CD	_	_	_
14	min	min	NN	_	_	_
15	at	at	IN	_	_	_
16	25	25	CD	_	_	_
17	°C	°c	NN	_	_	_
18	,	,	,	_	_	_
19	and	and	CC	_	_	_
20	the	the	DT	_	_	_
21	pelleted	pelleted	JJ	_	_	_
22	cells	cell	NNS	_	_	_
23	were	be	VBD	_	_	_
24	stored	store	VBN	_	_	_
25	at	at	IN	_	_	_
26	--	--	:	_	_	_
27	80	80	CD	_	_	_
28	°C	°c	NN	_	_	_
29	prior	prior	RB	_	_	_
30	to	to	TO	_	_	_
31	use	use	VB	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	To	to	TO	_	_	_
3	obtain	obtain	VB	_	_	_
4	the	the	DT	_	_	_
5	absolute	absolute	JJ	_	_	_
6	expression	expression	NN	_	_	_
7	levels	level	NNS	_	_	_
8	of	of	IN	_	_	_
9	genes	gene	NNS	_	_	_
10	from	from	IN	_	_	_
11	microarray	microarray	NN	_	_	_
12	raw	raw	JJ	_	_	_
13	data	datum	NNS	_	_	_
14	,	,	,	_	_	_
15	we	we	PRP	_	_	_
16	used	use	VBD	_	_	_
17	the	the	DT	_	_	_
18	Finite	Finite	NNP	_	_	_
19	Hybridization	hybridization	NN	_	_	_
20	model	model	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Furusawa	furusawa	NN	_	_	_
23	et	et	FW	_	_	_
24	al	al	FW	_	_	_
25	,	,	,	_	_	_
26	2009	2009	CD	_	_	_
27	;	;	:	_	_	_
28	Ono	Ono	NNP	_	_	_
29	et	et	FW	_	_	_
30	al	al	FW	_	_	_
31	,	,	,	_	_	_
32	2008	2008	CD	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	and	and	CC	_	_	_
7	purified	purify	VBN	_	_	_
8	from	from	IN	_	_	_
9	cells	cell	NNS	_	_	_
10	using	use	VBG	_	_	_
11	an	a	DT	_	_	_
12	RNeasy	rneasy	NN	_	_	_
13	mini	minus	NNS	_	_	_
14	kit	kit	NN	_	_	_
15	with	with	IN	_	_	_
16	on-column	on-column	JJ	_	_	_
17	DNA	dna	NN	_	_	_
18	digestion	digestion	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	ACSH	ACSH	NNP	_	_	_
3	_	_	VBD	_	_	_
4	Exp	Exp	NNP	_	_	_
5	_	_	NNP	_	_	_
6	CIYS	CIYS	NNP	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	ACSH	ACSH	NNP	_	_	_
9	_	_	VBD	_	_	_
10	Exp	Exp	NNP	_	_	_
11	_	_	NNP	_	_	_
12	CNFT	CNFT	NNP	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	ACSH	ACSH	NNP	_	_	_
15	_	_	VBD	_	_	_
16	Stat1	stat1	NN	_	_	_
17	_	_	CD	_	_	_
18	CNFW	CNFW	NNP	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	ACSH	ACSH	NNP	_	_	_
21	_	_	VBD	_	_	_
22	Stat1	stat1	NN	_	_	_
23	_	_	CD	_	_	_
24	CNGG	CNGG	NNP	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	ACSH	ACSH	NNP	_	_	_
27	_	_	VBD	_	_	_
28	Trans	Trans	NNP	_	_	_
29	_	_	NNP	_	_	_
30	CIYT	CIYT	NNP	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	ACSH	ACSH	NNP	_	_	_
33	_	_	VBD	_	_	_
34	Trans	Trans	NNP	_	_	_
35	_	_	NNP	_	_	_
36	CNFU	CNFU	NNP	_	_	_
37	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
38	Basecalling	Basecalling	NNP	_	_	_
39	was	be	VBD	_	_	_
40	done	do	VBN	_	_	_
41	on	on	IN	_	_	_
42	the	the	DT	_	_	_
43	sequencers	sequencer	NNS	_	_	_
44	using	use	VBG	_	_	_
45	the	the	DT	_	_	_
46	sequencer	sequencer	NN	_	_	_
47	's	's	POS	_	_	_
48	Real-Time	Real-Time	NNP	_	_	_
49	Analysis	analysis	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	RTA	rta	NN	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	software	software	NN	_	_	_
54	.	.	.	_	_	_

1	CASAVA	CASAVA	NNP	_	_	_
2	was	be	VBD	_	_	_
3	used	use	VBN	_	_	_
4	to	to	TO	_	_	_
5	process	process	VB	_	_	_
6	the	the	DT	_	_	_
7	basecalled	basecalled	JJ	_	_	_
8	data	datum	NNS	_	_	_
9	into	into	IN	_	_	_
10	FASTQ	fastq	NN	_	_	_
11	format	format	NN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	10	10	CD	_	_	_
5	ml	ml	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	for	for	IN	_	_	_
8	transcriptomic	transcriptomic	JJ	_	_	_
9	analysis	analysis	NN	_	_	_
10	were	be	VBD	_	_	_
11	collected	collect	VBN	_	_	_
12	into	into	IN	_	_	_
13	tubes	tube	NNS	_	_	_
14	containing	contain	VBG	_	_	_
15	1.25	1.25	CD	_	_	_
16	ml	ml	NN	_	_	_
17	ice-cold	ice-cold	JJ	_	_	_
18	5	5	CD	_	_	_
19	%	%	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	vol	vol	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Escherichia	escherichia	FW	Organism	_	_
24	coli	coli	FW	Organism	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Escherichia	escherichia	FW	Organism	_	_
27	coli	coli	FW	Organism	_	_
28	GLBRCE1	glbrce1	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	FASTQ	fastq	NN	_	_	_
31	formatted	format	VBD	_	_	_
32	sequence	sequence	NN	_	_	_
33	files	file	NNS	_	_	_
34	from	from	IN	_	_	_
35	strand-specific	strand-specific	JJ	_	_	_
36	Illumina	Illumina	NNP	_	_	_
37	RNA-Seq	rna-seq	NN	_	_	_
38	reads	read	VBZ	_	_	_
39	were	be	VBD	_	_	_
40	aligned	align	VBN	_	_	_
41	to	to	TO	_	_	_
42	the	the	DT	_	_	_
43	GLBRCE1	glbrce1	NN	_	_	_
44	reference	reference	NN	_	_	_
45	genome	genome	NN	_	_	_
46	NC	nc	NN	_	_	_
47	_	_	CD	_	_	_
48	000913	000913	CD	_	_	_
49	using	use	VBG	_	_	_
50	Bowtie	Bowtie	NNP	_	_	_
51	version	version	NN	_	_	_
52	0.12.7	0.12.7	CD	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	Langmead	Langmead	NNP	_	_	_
55	et	et	FW	_	_	_
56	al.	al.	FW	_	_	_
57	,	,	,	_	_	_
58	2009	2009	CD	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	with	with	IN	_	_	_
61	'	'	''	_	_	_
62	--	--	:	_	_	_
63	nofw	nofw	NN	_	_	_
64	'	'	''	_	_	_
65	strand-specific	strand-specific	JJ	_	_	_
66	parameter	parameter	NN	_	_	_
67	and	and	CC	_	_	_
68	maximal	maximal	JJ	_	_	_
69	distance	distance	NN	_	_	_
70	between	between	IN	_	_	_
71	the	the	DT	_	_	_
72	paired	paired	JJ	_	_	_
73	reads	read	VBZ	_	_	_
74	of	of	IN	_	_	_
75	1000	1000	CD	_	_	_
76	bp	bp	NN	_	_	_
77	.	.	.	_	_	_

1	NOTE	note	VB	_	_	_
2	:	:	:	_	_	_
3	Genome	Genome	NNP	_	_	_
4	NC	NC	NNP	_	_	_
5	_	_	SYM	_	_	_
6	000913	000913	CD	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	ASM584v2	asm584v2	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	represents	represent	VBZ	_	_	_
11	the	the	DT	_	_	_
12	parental	parental	JJ	_	_	_
13	strain	strain	NN	_	_	_
14	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	strain	strain	NN	_	_	_
3	used	use	VBN	_	_	_
4	in	in	IN	_	_	_
5	our	we	PRP$	_	_	_
6	study	study	NN	_	_	_
7	was	be	VBD	_	_	_
8	modified	modify	VBN	_	_	_
9	from	from	IN	_	_	_
10	the	the	DT	_	_	_
11	parental	parental	JJ	_	_	_
12	strain	strain	NN	_	_	_
13	by	by	IN	_	_	_
14	replacing	replace	VBG	_	_	_
15	gene	gene	NN	_	_	_
16	pflB	pflb	NN	GEN	_	_
17	with	with	IN	_	_	_
18	an	a	DT	_	_	_
19	insertion	insertion	NN	_	_	_
20	that	that	WDT	_	_	_
21	contained	contain	VBD	_	_	_
22	3	3	CD	_	_	_
23	different	different	JJ	_	_	_
24	genes	gene	NNS	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Fermentations	Fermentations	NNPS	_	_	_
3	were	be	VBD	_	_	_
4	carried	carry	VBN	_	_	_
5	out	out	RP	_	_	_
6	in	in	IN	_	_	_
7	3	3	CD	_	_	_
8	L	l	NN	_	_	_
9	bioreactors	bioreactor	NNS	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Applikon	Applikon	NNP	_	_	_
12	Biotechnology	Biotechnology	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	containing	contain	VBG	_	_	_
15	2.45	2.45	CD	_	_	_
16	L	l	NN	_	_	_
17	of	of	IN	_	_	_
18	ACSH	acsh	NN	_	_	_
19	or	or	CC	_	_	_
20	SynH	synh	NN	_	_	_
21	media	media	NNS	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	cultures	culture	NNS	_	_	_
25	were	be	VBD	_	_	_
26	diluted	dilute	VBN	_	_	_
27	into	into	IN	_	_	_
28	ACSH	acsh	NN	_	_	_
29	or	or	CC	_	_	_
30	SynH	synh	NN	_	_	_
31	with	with	IN	_	_	_
32	initial	initial	JJ	_	_	_
33	OD	od	NN	_	_	_
34	at	at	IN	_	_	_
35	0.2	0.2	CD	_	_	_
36	,	,	,	_	_	_
37	grown	grow	VBN	_	_	_
38	anaerobically	anaerobically	RB	_	_	_
39	overnight	overnight	RB	_	_	_
40	,	,	,	_	_	_
41	and	and	CC	_	_	_
42	then	then	RB	_	_	_
43	inoculated	inoculate	VBN	_	_	_
44	into	into	IN	_	_	_
45	bioreactors	bioreactor	NNS	_	_	_
46	to	to	TO	_	_	_
47	a	a	DT	_	_	_
48	starting	start	VBG	_	_	_
49	OD600	od600	NN	_	_	_
50	of	of	IN	_	_	_
51	0.2	0.2	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	Genome	Genome	NNP	_	_	_
54	_	_	NNP	_	_	_
55	build	build	VB	_	_	_
56	:	:	:	_	_	_
57	ASM584v2	asm584v2	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	growth	growth	NN	_	_	_
60	phase	phase	NN	_	_	_
61	:	:	:	_	_	_
62	Exp	exp	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	growth	growth	NN	_	_	_
65	phase	phase	NN	_	_	_
66	:	:	:	_	_	_
67	Stat1	stat1	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	growth	growth	NN	_	_	_
70	phase	phase	NN	_	_	_
71	:	:	:	_	_	_
72	Trans	Trans	NNP	_	_	_
73	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
74	medium	medium	NN	_	_	_
75	:	:	:	_	_	_
76	ACSH	ACSH	NNP	_	_	_
77	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
78	medium	medium	NN	_	_	_
79	:	:	:	_	_	_
80	SynH	synh	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	medium	medium	NN	_	_	_
83	:	:	:	_	_	_
84	SynH	synh	NN	_	_	_
85	_	_	CD	_	_	_
86	LT	lt	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
88	Probabilistic	probabilistic	JJ	_	_	_
89	expression	expression	NN	_	_	_
90	counting	counting	NN	_	_	_
91	was	be	VBD	_	_	_
92	performed	perform	VBN	_	_	_
93	using	use	VBG	_	_	_
94	the	the	DT	_	_	_
95	RNA-Seq	rna-seq	NN	_	_	_
96	by	by	IN	_	_	_
97	Expectation-Maximization	expectation-maximization	NN	_	_	_
98	-LRB-	-lrb-	-LRB-	_	_	_
99	RSEM	rsem	NN	_	_	_
100	-RRB-	-rrb-	-RRB-	_	_	_
101	version	version	NN	_	_	_
102	1.2.4	1.2.4	CD	_	_	_
103	-LRB-	-lrb-	-LRB-	_	_	_
104	Li	Li	NNP	_	_	_
105	and	and	CC	_	_	_
106	Dewey	Dewey	NNP	_	_	_
107	,	,	,	_	_	_
108	2011	2011	CD	_	_	_
109	-RRB-	-rrb-	-RRB-	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	RNA-Seq	rna-seq	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	RNA	rna	NN	_	_	_
114	was	be	VBD	_	_	_
115	obtained	obtain	VBN	_	_	_
116	from	from	IN	_	_	_
117	cells	cell	NNS	_	_	_
118	pellets	pellet	NNS	_	_	_
119	by	by	IN	_	_	_
120	lysozyme	lysozyme	NN	_	_	_
121	treatment	treatment	NN	_	_	_
122	and	and	CC	_	_	_
123	phenol-chloroform	phenol-chloroform	JJ	_	_	_
124	extraction	extraction	NN	_	_	_
125	,	,	,	_	_	_
126	analyzed	analyze	VBN	_	_	_
127	by	by	IN	_	_	_
128	agarose	agarose	NN	_	_	_
129	gel	gel	NN	_	_	_
130	electrophoresis	electrophoresis	NN	_	_	_
131	to	to	TO	_	_	_
132	confirm	confirm	VB	_	_	_
133	integrity	integrity	NN	_	_	_
134	,	,	,	_	_	_
135	quantified	quantify	VBN	_	_	_
136	using	use	VBG	_	_	_
137	a	a	DT	_	_	_
138	Nanodrop	Nanodrop	NNP	_	_	_
139	spectrophotometer	spectrophotometer	NN	_	_	_
140	-LRB-	-lrb-	-LRB-	_	_	_
141	Thermo	Thermo	NNP	_	_	_
142	Scientific	Scientific	NNP	_	_	_
143	-RRB-	-rrb-	-RRB-	_	_	_
144	,	,	,	_	_	_
145	and	and	CC	_	_	_
146	stored	store	VBD	_	_	_
147	at	at	IN	_	_	_
148	-80	-80	CD	_	_	_
149	°C	°c	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	strain	strain	NN	_	_	_
152	:	:	:	_	_	_
153	GLBRCE1	glbrce1	NN	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	Supplementary	supplementary	JJ	_	_	_
156	_	_	NN	_	_	_
157	files	file	NNS	_	_	_
158	_	_	IN	_	_	_
159	format	format	NN	_	_	_
160	_	_	NN	_	_	_
161	and	and	CC	_	_	_
162	_	_	NN	_	_	_
163	content	content	NN	_	_	_
164	:	:	:	_	_	_
165	CSV	CSV	NNP	_	_	_
166	file	file	NN	_	_	_
167	contains	contain	VBZ	_	_	_
168	counts	count	NNS	_	_	_
169	generated	generate	VBN	_	_	_
170	using	use	VBG	_	_	_
171	RSEM	rsem	NN	_	_	_
172	software	software	NN	_	_	_
173	.	.	.	_	_	_

1	Ribosomal	ribosomal	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	transcripts	transcript	NNS	_	_	_
4	excluded	exclude	VBN	_	_	_
5	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	SynH	synh	NN	_	_	_
3	_	_	CD	_	_	_
4	Exp	exp	NN	_	_	_
5	_	_	CD	_	_	_
6	BXHU	bxhu	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	SynH	synh	NN	_	_	_
9	_	_	CD	_	_	_
10	Exp	exp	NN	_	_	_
11	_	_	CD	_	_	_
12	CBYS	cbys	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	SynH	synh	NN	_	_	_
15	_	_	CD	_	_	_
16	LT	lt	NN	_	_	_
17	_	_	CD	_	_	_
18	Exp	exp	NN	_	_	_
19	_	_	CD	_	_	_
20	BXNX	bxnx	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	SynH	synh	NN	_	_	_
23	_	_	CD	_	_	_
24	LT	lt	NN	_	_	_
25	_	_	CD	_	_	_
26	Exp	exp	NN	_	_	_
27	_	_	CD	_	_	_
28	CBYU	cbyu	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	SynH	synh	NN	_	_	_
31	_	_	CD	_	_	_
32	LT	lt	NN	_	_	_
33	_	_	CD	_	_	_
34	Exp	exp	NN	_	_	_
35	_	_	CD	_	_	_
36	CCOG	ccog	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	SynH	synh	NN	_	_	_
39	_	_	CD	_	_	_
40	LT	lt	NN	_	_	_
41	_	_	CD	_	_	_
42	Stat1	stat1	NN	_	_	_
43	_	_	CD	_	_	_
44	BXNB	bxnb	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	SynH	synh	NN	_	_	_
47	_	_	CD	_	_	_
48	LT	lt	NN	_	_	_
49	_	_	CD	_	_	_
50	Stat1	stat1	NN	_	_	_
51	_	_	CD	_	_	_
52	BXNZ	bxnz	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	SynH	synh	NN	_	_	_
55	_	_	CD	_	_	_
56	LT	lt	NN	_	_	_
57	_	_	CD	_	_	_
58	Stat1	stat1	NN	_	_	_
59	_	_	CD	_	_	_
60	CHBW	chbw	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	SynH	synh	NN	_	_	_
63	_	_	CD	_	_	_
64	LT	lt	NN	_	_	_
65	_	_	CD	_	_	_
66	Trans	Trans	NNP	_	_	_
67	_	_	CD	_	_	_
68	BXNC	BXNC	NNP	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	SynH	synh	NN	_	_	_
71	_	_	CD	_	_	_
72	LT	lt	NN	_	_	_
73	_	_	CD	_	_	_
74	Trans	Trans	NNP	_	_	_
75	_	_	CD	_	_	_
76	BXXC	BXXC	NNP	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	SynH	synh	NN	_	_	_
79	_	_	CD	_	_	_
80	LT	lt	NN	_	_	_
81	_	_	CD	_	_	_
82	Trans	Trans	NNP	_	_	_
83	_	_	CD	_	_	_
84	CBYW	CBYW	NNP	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	SynH	synh	NN	_	_	_
87	_	_	CD	_	_	_
88	Stat1	stat1	NN	_	_	_
89	_	_	CD	_	_	_
90	CBYN	cbyn	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	SynH	synh	NN	_	_	_
93	_	_	CD	_	_	_
94	Stat1	stat1	NN	_	_	_
95	_	_	CD	_	_	_
96	CUOC	cuoc	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	SynH	synh	NN	_	_	_
99	_	_	CD	_	_	_
100	Trans	Trans	NNP	_	_	_
101	_	_	CD	_	_	_
102	CUNZ	CUNZ	NNP	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	SynH	synh	NN	_	_	_
105	_	_	CD	_	_	_
106	Trans	Trans	NNP	_	_	_
107	_	_	NNP	_	_	_
108	CUOB	CUOB	NNP	_	_	_
109	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
110	Total	Total	NNP	_	_	_
111	RNA	rna	NN	_	_	_
112	-LRB-	-lrb-	-LRB-	_	_	_
113	2ug	2ug	JJ	_	_	_
114	-RRB-	-rrb-	-RRB-	_	_	_
115	was	be	VBD	_	_	_
116	subjected	subject	VBN	_	_	_
117	to	to	TO	_	_	_
118	rRNA	rrna	NN	_	_	_
119	depletion	depletion	NN	_	_	_
120	using	use	VBG	_	_	_
121	Ribozero	Ribozero	NNP	_	_	_
122	rRNA	rrna	NN	_	_	_
123	removal	removal	NN	_	_	_
124	kit	kit	NN	_	_	_
125	--	--	:	_	_	_
126	Bacteria	bacterium	NNS	_	_	_
127	-LRB-	-lrb-	-LRB-	_	_	_
128	Epicenter	epicenter	NN	_	_	_
129	,	,	,	_	_	_
130	illumina	illumina	NN	_	_	_
131	-RRB-	-rrb-	-RRB-	_	_	_
132	.	.	.	_	_	_

1	rRNA-depleted	rrna-depleted	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Ampure	Ampure	NNP	_	_	_
7	XP	xp	NN	_	_	_
8	beads	bead	NNS	_	_	_
9	.	.	.	_	_	_

1	Purified	purify	VBN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	fragmented	fragmented	JJ	_	_	_
6	using	use	VBG	_	_	_
7	RNA	rna	NN	_	_	_
8	Fragmentation	fragmentation	NN	_	_	_
9	Reagents	reagent	NNS	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Ambion	Ambion	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	at	at	IN	_	_	_
14	70C	70C	NNP	_	_	_
15	for	for	IN	_	_	_
16	2	2	CD	_	_	_
17	mins	min	NNS	_	_	_
18	,	,	,	_	_	_
19	targeting	target	VBG	_	_	_
20	fragments	fragment	NNS	_	_	_
21	ranging	range	VBG	_	_	_
22	from	from	IN	_	_	_
23	200-300bp	200-300bp	JJ	_	_	_
24	.	.	.	_	_	_

1	Fragmented	fragmented	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	purified	purify	VBN	_	_	_
6	using	use	VBG	_	_	_
7	Ampure	Ampure	NNP	_	_	_
8	XP	xp	NN	_	_	_
9	beads	bead	NNS	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Agencourt	agencourt	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	.	.	.	_	_	_

1	Reverse	reverse	JJ	_	_	_
2	transcription	transcription	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	using	use	VBG	_	_	_
6	SuperScript	SuperScript	NNP	_	_	_
7	II	II	NNP	_	_	_
8	Reverse	reverse	JJ	_	_	_
9	Transcription	transcription	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Invitrogen	invitrogen	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	with	with	IN	_	_	_
14	an	a	DT	_	_	_
15	initial	initial	JJ	_	_	_
16	annealing	annealing	NN	_	_	_
17	of	of	IN	_	_	_
18	random	random	JJ	_	_	_
19	hexamers	hexamer	NNS	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Fermentas	fermenta	NNS	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	at	at	IN	_	_	_
24	65C	65c	NN	_	_	_
25	for	for	IN	_	_	_
26	5	5	CD	_	_	_
27	mins	min	NNS	_	_	_
28	,	,	,	_	_	_
29	follow	follow	VBP	_	_	_
30	by	by	IN	_	_	_
31	an	a	DT	_	_	_
32	incubation	incubation	NN	_	_	_
33	of	of	IN	_	_	_
34	42C	42c	NN	_	_	_
35	for	for	IN	_	_	_
36	50	50	CD	_	_	_
37	mins	min	NNS	_	_	_
38	and	and	CC	_	_	_
39	an	a	DT	_	_	_
40	inactivation	inactivation	NN	_	_	_
41	step	step	NN	_	_	_
42	at	at	IN	_	_	_
43	70C	70C	NNP	_	_	_
44	for	for	IN	_	_	_
45	10	10	CD	_	_	_
46	mins	min	NNS	_	_	_
47	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	was	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	purified	purify	VBN	_	_	_
5	with	with	IN	_	_	_
6	Ampure	Ampure	NNP	_	_	_
7	XP	xp	NN	_	_	_
8	beads	bead	NNS	_	_	_
9	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	was	be	VBD	_	_	_
3	followed	follow	VBN	_	_	_
4	by	by	IN	_	_	_
5	second	second	JJ	_	_	_
6	strand	strand	NN	_	_	_
7	synthesis	synthesis	NN	_	_	_
8	using	use	VBG	_	_	_
9	dNTP	dntp	NN	_	_	_
10	mix	mix	NN	_	_	_
11	where	where	WRB	_	_	_
12	dTTP	dttp	NN	_	_	_
13	is	be	VBZ	_	_	_
14	replaced	replace	VBN	_	_	_
15	by	by	IN	_	_	_
16	dUTP	dutp	NN	_	_	_
17	.	.	.	_	_	_

1	Reaction	reaction	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	at	at	IN	_	_	_
5	16C	16c	NN	_	_	_
6	for	for	IN	_	_	_
7	1h	1h	NN	_	_	_
8	.	.	.	_	_	_

1	Double	double	JJ	_	_	_
2	stranded	strand	VBN	_	_	_
3	cDNA	cdna	NN	_	_	_
4	fragments	fragment	NNS	_	_	_
5	were	be	VBD	_	_	_
6	purified	purify	VBN	_	_	_
7	and	and	CC	_	_	_
8	selected	select	VBN	_	_	_
9	for	for	IN	_	_	_
10	targeted	target	VBN	_	_	_
11	fragments	fragment	NNS	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	200-300bp	200-300bp	JJ	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	using	use	VBG	_	_	_
16	Ampure	Ampure	NNP	_	_	_
17	XP	xp	NN	_	_	_
18	beads	bead	NNS	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	dscDNA	dscdna	NN	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	blunt-ended	blunt-ended	JJ	_	_	_
6	,	,	,	_	_	_
7	the	the	DT	_	_	_
8	3	3	CD	_	_	_
9	'	'	''	_	_	_
10	ends	end	NNS	_	_	_
11	were	be	VBD	_	_	_
12	adenylated	adenylate	VBN	_	_	_
13	with	with	IN	_	_	_
14	a	a	DT	_	_	_
15	single	single	JJ	_	_	_
16	A	a	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	ligated	ligate	VBN	_	_	_
20	with	with	IN	_	_	_
21	library	library	NN	_	_	_
22	adapters	adapter	NNS	_	_	_
23	using	use	VBG	_	_	_
24	Kapa	Kapa	NNP	_	_	_
25	Library	Library	NNP	_	_	_
26	Amplification	Amplification	NNP	_	_	_
27	Kit	kit	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Kapa	Kapa	NNP	_	_	_
30	Biosystems	Biosystems	NNP	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	.	.	.	_	_	_

1	Adapter-ligated	adapter-ligated	JJ	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Ampure	Ampure	NNP	_	_	_
7	XP	xp	NN	_	_	_
8	beads	bead	NNS	_	_	_
9	.	.	.	_	_	_

1	Digestion	digestion	NN	_	_	_
2	of	of	IN	_	_	_
3	dUTP	dutp	NN	_	_	_
4	was	be	VBD	_	_	_
5	then	then	RB	_	_	_
6	performed	perform	VBN	_	_	_
7	using	use	VBG	_	_	_
8	AmpErase	AmpErase	NNP	_	_	_
9	UNG	UNG	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Applied	Applied	NNP	_	_	_
12	Biosystems	Biosystems	NNPS	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	to	to	TO	_	_	_
15	remove	remove	VB	_	_	_
16	second	second	JJ	_	_	_
17	strand	strand	NN	_	_	_
18	cDNA	cdna	NN	_	_	_
19	.	.	.	_	_	_

1	Digested	digest	VBN	_	_	_
2	cDNA	cdna	NN	_	_	_
3	was	be	VBD	_	_	_
4	again	again	RB	_	_	_
5	cleaned	clean	VBN	_	_	_
6	up	up	RP	_	_	_
7	with	with	IN	_	_	_
8	Ampure	Ampure	NNP	_	_	_
9	SPRI	SPRI	NNP	_	_	_
10	beads	bead	NNS	_	_	_
11	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	was	be	VBD	_	_	_
3	followed	follow	VBN	_	_	_
4	by	by	IN	_	_	_
5	amplification	amplification	NN	_	_	_
6	by	by	IN	_	_	_
7	10	10	CD	_	_	_
8	cycles	cycle	NNS	_	_	_
9	of	of	IN	_	_	_
10	PCR	pcr	NN	_	_	_
11	using	use	VBG	_	_	_
12	Kapa	Kapa	NNP	_	_	_
13	Library	Library	NNP	_	_	_
14	Amplification	Amplification	NNP	_	_	_
15	Kit	kit	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Kapa	Kapa	NNP	_	_	_
18	Biosystems	Biosystems	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	final	final	JJ	_	_	_
3	library	library	NN	_	_	_
4	was	be	VBD	_	_	_
5	cleaned	clean	VBN	_	_	_
6	up	up	RP	_	_	_
7	with	with	IN	_	_	_
8	Ampure	Ampure	NNP	_	_	_
9	SPRI	SPRI	NNP	_	_	_
10	beads	bead	NNS	_	_	_
11	.	.	.	_	_	_

1	Sequencing	sequencing	NN	_	_	_
2	was	be	VBD	_	_	_
3	done	do	VBN	_	_	_
4	on	on	IN	_	_	_
5	the	the	DT	_	_	_
6	Illumina	Illumina	NNP	_	_	_
7	HiSeq	HiSeq	NNP	_	_	_
8	platform	platform	NN	_	_	_
9	generating	generate	VBG	_	_	_
10	paired	paired	JJ	_	_	_
11	end	end	NN	_	_	_
12	reads	read	VBZ	_	_	_
13	of	of	IN	_	_	_
14	100bp	100bp	JJ	_	_	_
15	each	each	DT	_	_	_
16	.	.	.	_	_	_

1	Note	note	VB	_	_	_
2	:	:	:	_	_	_
3	Target	target	NN	_	_	_
4	fragments	fragment	NNS	_	_	_
5	here	here	RB	_	_	_
6	refers	refer	VBZ	_	_	_
7	to	to	TO	_	_	_
8	the	the	DT	_	_	_
9	insert	insert	NN	_	_	_
10	only	only	RB	_	_	_
11	,	,	,	_	_	_
12	that	that	DT	_	_	_
13	is	be	VBZ	_	_	_
14	the	the	DT	_	_	_
15	cDNA	cdna	NN	_	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	actual	actual	JJ	_	_	_
3	size	size	NN	_	_	_
4	we	we	PRP	_	_	_
5	use	use	VBP	_	_	_
6	in	in	IN	_	_	_
7	selection	selection	NN	_	_	_
8	will	will	MD	_	_	_
9	be	be	VB	_	_	_
10	larger	larger	JJR	_	_	_
11	,	,	,	_	_	_
12	typically	typically	RB	_	_	_
13	the	the	DT	_	_	_
14	target	target	NN	_	_	_
15	fragment	fragment	NN	_	_	_
16	size	size	NN	_	_	_
17	+	+	CC	_	_	_
18	125bp	125bp	NN	_	_	_
19	adaptors	adaptor	NNS	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	~	~	CD	_	_	_
22	300-450bp	300-450bp	JJ	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	BW25113	bw25113	NN	_	_	_
3	HEPES-glu	hepes-glu	NN	_	_	_
4	30	30	CD	_	_	_
5	min	min	NN	_	_	_
6	4.5	4.5	CD	_	_	_
7	%	%	NN	_	_	_
8	deoxycholate	deoxycholate	NN	SUPP	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	BW25113	bw25113	NN	_	_	_
11	with	with	IN	_	_	_
12	deoxycholate	deoxycholate	NN	SUPP	_	_
13	stress	stress	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	BW25113	bw25113	NN	_	_	_
16	ΔmqsRA	δmqsra	NN	_	_	_
17	HEPES-glu	hepes-glu	NN	_	_	_
18	30	30	CD	_	_	_
19	min	min	NN	_	_	_
20	4.5	4.5	CD	_	_	_
21	%	%	NN	_	_	_
22	deoxycholate	deoxycholate	NN	SUPP	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	BW25113	bw25113	NN	_	_	_
25	ΔmqsRA	δmqsra	NN	_	_	_
26	with	with	IN	_	_	_
27	deoxycholate	deoxycholate	NN	SUPP	_	_
28	stress	stress	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Cells	cell	NNS	_	_	_
31	were	be	VBD	_	_	_
32	lysed	lyse	VBN	_	_	_
33	using	use	VBG	_	_	_
34	a	a	DT	_	_	_
35	bead	bead	NN	_	_	_
36	beater	beater	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Biospec	biospec	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	and	and	CC	_	_	_
41	mRNA	mrna	NN	_	_	_
42	was	be	VBD	_	_	_
43	isolated	isolate	VBN	_	_	_
44	using	use	VBG	_	_	_
45	a	a	DT	_	_	_
46	Qiagen	Qiagen	NNP	_	_	_
47	RNeasy	RNeasy	NNP	_	_	_
48	mini	minus	NNS	_	_	_
49	kit	kit	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	Cat	cat	NN	_	_	_
52	#	#	#	_	_	_
53	74104	74104	CD	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	pelleted	pellete	VBN	_	_	_
5	in	in	IN	_	_	_
6	the	the	DT	_	_	_
7	presence	presence	NN	_	_	_
8	of	of	IN	_	_	_
9	RNALater	rnalater	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Applied	Applied	NNP	_	_	_
12	Biosystems	Biosystems	NNPS	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	and	and	CC	_	_	_
15	flash	flash	NN	_	_	_
16	frozen	freeze	VBN	_	_	_
17	in	in	IN	_	_	_
18	ethanol-dry	ethanol-dry	JJ	_	_	_
19	ice	ice	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	was	be	VBD	_	_	_
4	analyzed	analyze	VBN	_	_	_
5	in	in	IN	_	_	_
6	the	the	DT	_	_	_
7	Affymetrix	Affymetrix	NNP	_	_	_
8	GenomeChipOperating	GenomeChipOperating	NNP	_	_	_
9	Software	Software	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	GCOS	GCOS	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	BW25113	bw25113	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	genotype	genotype	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Strains	strain	NNS	_	_	_
9	were	be	VBD	_	_	_
10	grown	grow	VBN	_	_	_
11	in	in	IN	_	_	_
12	LB	lb	NN	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	with	with	IN	_	_	_
17	shaking	shake	VBG	_	_	_
18	at	at	IN	_	_	_
19	250	250	CD	_	_	_
20	rpm	rpm	NN	_	_	_
21	.	.	.	_	_	_

1	16	16	CD	_	_	_
2	h	h	NN	_	_	_
3	overnight	overnight	JJ	_	_	_
4	cultures	culture	NNS	_	_	_
5	were	be	VBD	_	_	_
6	diluted	dilute	VBN	_	_	_
7	to	to	TO	_	_	_
8	OD600	od600	NN	_	_	_
9	=	=	JJ	_	_	_
10	0.05	0.05	CD	_	_	_
11	in	in	IN	_	_	_
12	HEPES-glucose	hepes-glucose	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	0.4	0.4	CD	_	_	_
15	%	%	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	,	,	,	_	_	_
18	grown	grow	VBN	_	_	_
19	to	to	TO	_	_	_
20	OD600	od600	NN	_	_	_
21	~	~	NN	_	_	_
22	0.6	0.6	CD	_	_	_
23	,	,	,	_	_	_
24	and	and	CC	_	_	_
25	exposed	expose	VBN	_	_	_
26	to	to	TO	_	_	_
27	4.5	4.5	CD	_	_	_
28	%	%	NN	_	_	_
29	deoxycholate	deoxycholate	NN	SUPP	_	_
30	for	for	IN	_	_	_
31	30	30	CD	_	_	_
32	min	min	NN	_	_	_
33	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	0.2	0.2	CD	_	_	_
3	ppm	ppm	NN	_	_	_
4	deoxynivalenol	deoxynivalenol	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	0.2	0.2	CD	_	_	_
7	ppm	ppm	NN	_	_	_
8	nivalenol	nivalenol	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	1	1	CD	_	_	_
11	ml	ml	NN	_	_	_
12	of	of	IN	_	_	_
13	each	each	DT	_	_	_
14	culture	culture	NN	_	_	_
15	with	with	IN	_	_	_
16	the	the	DT	_	_	_
17	mycotoxin	mycotoxin	NN	_	_	_
18	was	be	VBD	_	_	_
19	centrifuged	centrifuge	VBN	_	_	_
20	and	and	CC	_	_	_
21	total	total	JJ	_	_	_
22	RNA	rna	NN	_	_	_
23	was	be	VBD	_	_	_
24	prepared	prepare	VBN	_	_	_
25	using	use	VBG	_	_	_
26	Hybrid-RTM	hybrid-rtm	JJ	_	_	_
27	kit	kit	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Gene	gene	NN	_	_	_
30	All	all	DT	_	_	_
31	,	,	,	_	_	_
32	Seoul	Seoul	NNP	_	_	_
33	,	,	,	_	_	_
34	Korea	Korea	NNP	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	according	accord	VBG	_	_	_
37	to	to	TO	_	_	_
38	the	the	DT	_	_	_
39	manufacturer	manufacturer	NN	_	_	_
40	's	's	POS	_	_	_
41	protocols	protocol	NNS	_	_	_
42	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	MICOBExpressTM	micobexpresstm	NN	_	_	_
3	bacterial	bacterial	JJ	_	_	_
4	mRNA	mrna	NN	_	_	_
5	enrichment	enrichment	NN	_	_	_
6	kit	kit	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Ambion	Ambion	NNP	_	_	_
9	,	,	,	_	_	_
10	Texas	Texas	NNP	_	_	_
11	,	,	,	_	_	_
12	USA	USA	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	was	be	VBD	_	_	_
15	used	use	VBN	_	_	_
16	to	to	TO	_	_	_
17	remove	remove	VB	_	_	_
18	bacterial	bacterial	JJ	_	_	_
19	rRNA	rrna	NN	_	_	_
20	from	from	IN	_	_	_
21	the	the	DT	_	_	_
22	total	total	JJ	_	_	_
23	RNA	rna	NN	_	_	_
24	samples	sample	NNS	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	2	2	CD	_	_	_
3	ppm	ppm	NN	_	_	_
4	deoxynivalenol	deoxynivalenol	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	2	2	CD	_	_	_
7	ppm	ppm	NN	_	_	_
8	nivalenol	nivalenol	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	acetonitrile	acetonitrile	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Bacterial	bacterial	JJ	_	_	_
13	culture	culture	NN	_	_	_
14	with	with	IN	_	_	_
15	0.2	0.2	CD	_	_	_
16	ppm	ppm	NN	_	_	_
17	deoxynivalenol	deoxynivalenol	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Bacterial	bacterial	JJ	_	_	_
20	culture	culture	NN	_	_	_
21	with	with	IN	_	_	_
22	0.2	0.2	CD	_	_	_
23	ppm	ppm	NN	_	_	_
24	nivalenol	nivalenol	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Bacterial	bacterial	JJ	_	_	_
27	culture	culture	NN	_	_	_
28	with	with	IN	_	_	_
29	2	2	CD	_	_	_
30	ppm	ppm	NN	_	_	_
31	deoxynivalenol	deoxynivalenol	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	Bacterial	bacterial	JJ	_	_	_
34	culture	culture	NN	_	_	_
35	with	with	IN	_	_	_
36	2	2	CD	_	_	_
37	ppm	ppm	NN	_	_	_
38	nivalenol	nivalenol	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Bacterial	bacterial	JJ	_	_	_
41	culture	culture	NN	_	_	_
42	with	with	IN	_	_	_
43	acetonitrile	acetonitrile	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	concentration	concentration	NN	_	_	_
46	:	:	:	_	_	_
47	0.2	0.2	CD	_	_	_
48	ppm	ppm	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	concentration	concentration	NN	_	_	_
51	:	:	:	_	_	_
52	2	2	CD	_	_	_
53	ppm	ppm	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	condition	condition	NN	_	_	_
56	:	:	:	_	_	_
57	acetonitrile	acetonitrile	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	control	control	NN	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	condition	condition	NN	_	_	_
63	:	:	:	_	_	_
64	myxotoxin	myxotoxin	NN	_	_	_
65	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
66	E.	E.	NNP	_	_	_
67	coli	coli	NN	_	_	_
68	K-12	k-12	NN	_	_	_
69	was	be	VBD	_	_	_
70	incubated	incubate	VBN	_	_	_
71	in	in	IN	_	_	_
72	5	5	CD	_	_	_
73	ml	ml	NN	_	_	_
74	LB	lb	NN	_	_	_
75	liquid	liquid	NN	_	_	_
76	for	for	IN	_	_	_
77	16	16	CD	_	_	_
78	h	h	NN	_	_	_
79	at	at	IN	_	_	_
80	37	37	CD	_	_	_
81	°C	°c	NN	_	_	_
82	with	with	IN	_	_	_
83	constant	constant	JJ	_	_	_
84	shaking	shake	VBG	_	_	_
85	,	,	,	_	_	_
86	and	and	CC	_	_	_
87	then	then	RB	_	_	_
88	100	100	CD	_	_	_
89	µl	µl	NN	_	_	_
90	of	of	IN	_	_	_
91	each	each	DT	_	_	_
92	myxotoxin	myxotoxin	NN	_	_	_
93	dissolved	dissolve	VBN	_	_	_
94	in	in	IN	_	_	_
95	acetonitrile	acetonitrile	NN	_	_	_
96	was	be	VBD	_	_	_
97	added	add	VBN	_	_	_
98	to	to	TO	_	_	_
99	each	each	DT	_	_	_
100	culture	culture	NN	_	_	_
101	to	to	TO	_	_	_
102	a	a	DT	_	_	_
103	final	final	JJ	_	_	_
104	concentration	concentration	NN	_	_	_
105	of	of	IN	_	_	_
106	0.2	0.2	CD	_	_	_
107	,	,	,	_	_	_
108	and	and	CC	_	_	_
109	2	2	CD	_	_	_
110	ppm	ppm	NN	_	_	_
111	.	.	.	_	_	_

1	Additional	additional	JJ	_	_	_
2	incubation	incubation	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	for	for	IN	_	_	_
6	2	2	CD	_	_	_
7	h.	h.	NN	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	Escherichia	escherichia	FW	Organism	_	_
10	coli	coli	FW	Organism	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Genome	Genome	NNP	_	_	_
13	_	_	NNP	_	_	_
14	build	build	VB	_	_	_
15	:	:	:	_	_	_
16	Escherichia	escherichia	FW	Organism	_	_
17	coli	coli	FW	Organism	_	_
18	K-12	k-12	NN	_	_	_
19	substr	substr	NN	_	_	_
20	.	.	.	_	_	_

1	DH10B	dh10b	NN	_	_	_
2	ASM1942v1	asm1942v1	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
4	Mapped	map	VBD	_	_	_
5	reads	read	VBZ	_	_	_
6	per	per	IN	_	_	_
7	annotated	annotated	JJ	_	_	_
8	gene	gene	NN	_	_	_
9	were	be	VBD	_	_	_
10	counted	count	VBN	_	_	_
11	by	by	IN	_	_	_
12	Bam2readcount	bam2readcount	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Reads	read	VBZ	_	_	_
3	per	per	IN	_	_	_
4	kilobase	kilobase	NN	_	_	_
5	of	of	IN	_	_	_
6	gene	gene	NN	_	_	_
7	per	per	IN	_	_	_
8	million	million	CD	_	_	_
9	mapped	map	VBN	_	_	_
10	sequence	sequence	NN	_	_	_
11	reads	read	VBZ	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	RPKM	rpkm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	were	be	VBD	_	_	_
16	calculated	calculate	VBN	_	_	_
17	for	for	IN	_	_	_
18	normalization	normalization	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	prepared	prepare	VBN	_	_	_
6	for	for	IN	_	_	_
7	sequencing	sequencing	NN	_	_	_
8	using	use	VBG	_	_	_
9	standard	standard	JJ	_	_	_
10	Illumina	Illumina	NNP	_	_	_
11	protocols	protocol	NNS	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
13	RNA-Seq	rna-seq	JJ	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	strain	strain	NN	_	_	_
16	:	:	:	_	_	_
17	K-12	k-12	NN	_	_	_
18	substr	substr	NN	_	_	_
19	.	.	.	_	_	_

1	DH10B	dh10b	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Supplementary	supplementary	JJ	_	_	_
4	_	_	NN	_	_	_
5	files	file	NNS	_	_	_
6	_	_	IN	_	_	_
7	format	format	NN	_	_	_
8	_	_	NN	_	_	_
9	and	and	CC	_	_	_
10	_	_	NN	_	_	_
11	content	content	NN	_	_	_
12	:	:	:	_	_	_
13	txt	txt	NN	_	_	_
14	:	:	:	_	_	_
15	tab-delimited	tab-delimited	JJ	_	_	_
16	text	text	NN	_	_	_
17	files	file	NNS	_	_	_
18	include	include	VBP	_	_	_
19	RPKM	rpkm	NN	_	_	_
20	values	value	NNS	_	_	_
21	for	for	IN	_	_	_
22	each	each	DT	_	_	_
23	Sample	Sample	NNP	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	The	The	NNP	_	_	_
26	reads	read	VBZ	_	_	_
27	were	be	VBD	_	_	_
28	processed	process	VBN	_	_	_
29	using	use	VBG	_	_	_
30	BWA	BWA	NNP	_	_	_
31	software	software	NN	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	toxin	toxin	NN	_	_	_
3	:	:	:	_	_	_
4	deoxynivalenol	deoxynivalenol	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	toxin	toxin	NN	_	_	_
7	:	:	:	_	_	_
8	nivalenol	nivalenol	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Culture	culture	NN	_	_	_
11	cells	cell	NNS	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	Escherichia	escherichia	FW	Organism	_	_
14	coli	coli	FW	Organism	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Genome	Genome	NNP	_	_	_
17	_	_	NNP	_	_	_
18	build	build	VB	_	_	_
19	:	:	:	_	_	_
20	ASM584v2	asm584v2	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	genotype	genotype	NN	_	_	_
23	:	:	:	_	_	_
24	PNPase	pnpase	NN	_	_	_
25	mutant	mutant	JJ	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	genotype	genotype	NN	_	_	_
28	:	:	:	_	_	_
29	RNase	rnase	NN	_	_	_
30	II	ii	CD	_	_	_
31	mutant	mutant	JJ	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	genotype	genotype	NN	_	_	_
34	:	:	:	_	_	_
35	RNase	rnase	NN	_	_	_
36	R	r	NN	_	_	_
37	mutant	mutant	JJ	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	genotype	genotype	NN	_	_	_
40	:	:	:	_	_	_
41	Wild-type	wild-type	JJ	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	growth	growth	NN	_	_	_
44	phase	phase	NN	_	_	_
45	:	:	:	_	_	_
46	Exponential	Exponential	NNP	_	_	_
47	Phase	phase	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	Overnight	overnight	NN	_	_	_
50	cultures	culture	NNS	_	_	_
51	from	from	IN	_	_	_
52	isolated	isolate	VBN	_	_	_
53	colonies	colony	NNS	_	_	_
54	were	be	VBD	_	_	_
55	diluted	dilute	VBN	_	_	_
56	in	in	IN	_	_	_
57	fresh	fresh	JJ	_	_	_
58	medium	medium	NN	_	_	_
59	to	to	TO	_	_	_
60	an	a	DT	_	_	_
61	initial	initial	JJ	_	_	_
62	OD600	od600	NN	_	_	_
63	~	~	NN	_	_	_
64	0.03	0.03	CD	_	_	_
65	and	and	CC	_	_	_
66	grown	grow	VBN	_	_	_
67	to	to	TO	_	_	_
68	exponential	exponential	JJ	GrowthPhase	_	_
69	phase	phase	NN	GrowthPhase	_	_
70	-LRB-	-lrb-	-LRB-	_	_	_
71	OD600	od600	NN	_	_	_
72	~	~	NN	_	_	_
73	0.3	0.3	CD	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	at	at	IN	_	_	_
76	37ºC	37ºc	NN	_	_	_
77	,	,	,	_	_	_
78	with	with	IN	_	_	_
79	shaking	shake	VBG	_	_	_
80	at	at	IN	_	_	_
81	200	200	CD	_	_	_
82	rpm	rpm	NN	_	_	_
83	in	in	IN	_	_	_
84	Luria-Bertani	Luria-Bertani	NNP	_	_	_
85	-LRB-	-lrb-	-LRB-	_	_	_
86	LB	LB	NNP	_	_	_
87	-RRB-	-rrb-	-RRB-	_	_	_
88	medium	medium	NN	_	_	_
89	supplemented	supplement	VBN	_	_	_
90	with	with	IN	_	_	_
91	thymine	thymine	NN	_	_	_
92	-LRB-	-lrb-	-LRB-	_	_	_
93	50	50	CD	_	_	_
94	mg	mg	NN	_	_	_
95	ml-1	ml-1	NN	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	.	.	.	_	_	_

1	When	when	WRB	_	_	_
2	required	require	VBN	_	_	_
3	,	,	,	_	_	_
4	antibiotics	antibiotic	NNS	_	_	_
5	were	be	VBD	_	_	_
6	present	present	JJ	_	_	_
7	at	at	IN	_	_	_
8	the	the	DT	_	_	_
9	following	follow	VBG	_	_	_
10	concentrations	concentration	NNS	_	_	_
11	:	:	:	_	_	_
12	kanamycin	kanamycin	NN	_	_	_
13	,	,	,	_	_	_
14	50	50	CD	_	_	_
15	mg	mg	NN	_	_	_
16	ml-1	ml-1	NN	_	_	_
17	;	;	:	_	_	_
18	tetracycline	tetracycline	NN	_	_	_
19	,	,	,	_	_	_
20	20	20	CD	_	_	_
21	mg	mg	NN	_	_	_
22	ml-1	ml-1	NN	_	_	_
23	;	;	:	_	_	_
24	streptomycin	streptomycin	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	∆	∆	CD	_	_	_
27	pnp	pnp	NN	GEN	_	_
28	_	_	CD	_	_	_
29	RNA-Seq	rna-seq	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	RNA	rna	NN	_	_	_
32	libraries	library	NNS	_	_	_
33	were	be	VBD	_	_	_
34	prepared	prepare	VBN	_	_	_
35	for	for	IN	_	_	_
36	sequencing	sequencing	NN	_	_	_
37	by	by	IN	_	_	_
38	the	the	DT	_	_	_
39	company	company	NN	_	_	_
40	Vertis	Vertis	NNP	_	_	_
41	Biotechnologie	Biotechnologie	NNP	_	_	_
42	AG	AG	NNP	_	_	_
43	in	in	IN	_	_	_
44	Germany	Germany	NNP	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	RNA-Seq	rna-seq	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	RNA	rna	NN	_	_	_
49	was	be	VBD	_	_	_
50	isolated	isolate	VBN	_	_	_
51	following	follow	VBG	_	_	_
52	cell	cell	NN	_	_	_
53	lysis	lysis	NN	_	_	_
54	and	and	CC	_	_	_
55	phenol	phenol	NN	_	_	_
56	:	:	:	_	_	_
57	chloroform	chloroform	NN	_	_	_
58	extraction	extraction	NN	_	_	_
59	as	as	IN	_	_	_
60	previously	previously	RB	_	_	_
61	described	describe	VBN	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	Andrade	Andrade	NNP	_	_	_
64	,	,	,	_	_	_
65	Pobre	Pobre	NNP	_	_	_
66	et	et	FW	_	_	_
67	al.	al.	FW	_	_	_
68	2012	2012	CD	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	precipitation	precipitation	NN	_	_	_
3	step	step	NN	_	_	_
4	in	in	IN	_	_	_
5	ethanol	ethanol	NN	_	_	_
6	and	and	CC	_	_	_
7	300	300	CD	_	_	_
8	mM	mm	NN	KWSUPP	_	_
9	sodium	sodium	NN	SUPP	_	_
10	acetate	acetate	NN	SUPP	_	_
11	,	,	,	_	_	_
12	RNA	rna	NN	_	_	_
13	was	be	VBD	_	_	_
14	resuspended	resuspend	VBN	_	_	_
15	in	in	IN	_	_	_
16	MilliQ-water	MilliQ-water	NNP	_	_	_
17	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	integrity	integrity	NN	_	_	_
3	of	of	IN	_	_	_
4	RNA	rna	NN	_	_	_
5	samples	sample	NNS	_	_	_
6	was	be	VBD	_	_	_
7	evaluated	evaluate	VBN	_	_	_
8	by	by	IN	_	_	_
9	agarose	agarose	NN	_	_	_
10	gel	gel	NN	_	_	_
11	electrophoresis	electrophoresis	NN	_	_	_
12	.	.	.	_	_	_

1	Turbo	Turbo	NNP	_	_	_
2	DNase	dnase	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	Ambion	ambion	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	treatment	treatment	NN	_	_	_
7	was	be	VBD	_	_	_
8	used	use	VBN	_	_	_
9	to	to	TO	_	_	_
10	remove	remove	VB	_	_	_
11	contaminant	contaminant	NN	_	_	_
12	DNA	dna	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	∆	∆	SYM	_	_	_
3	rnb	rnb	FW	GEN	_	_
4	_	_	FW	_	_	_
5	RNA-Seq	rna-seq	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	∆	∆	CD	_	_	_
8	rnr	rnr	NN	GEN	_	_
9	_	_	CD	_	_	_
10	RNA-Seq	rna-seq	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	strain	strain	NN	_	_	_
13	:	:	:	_	_	_
14	K12-MG1693	k12-mg1693	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Supplementary	supplementary	JJ	_	_	_
17	_	_	NN	_	_	_
18	files	file	NNS	_	_	_
19	_	_	IN	_	_	_
20	format	format	NN	_	_	_
21	_	_	NN	_	_	_
22	and	and	CC	_	_	_
23	_	_	NN	_	_	_
24	content	content	NN	_	_	_
25	:	:	:	_	_	_
26	tab-delimited	tab-delimited	JJ	_	_	_
27	text	text	NN	_	_	_
28	files	file	NNS	_	_	_
29	include	include	VBP	_	_	_
30	RPKM	rpkm	NN	_	_	_
31	values	value	NNS	_	_	_
32	for	for	IN	_	_	_
33	each	each	DT	_	_	_
34	Sample	Sample	NNP	_	_	_
35	...	...	:	_	_	_
36	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
37	Vertis	Vertis	NNP	_	_	_
38	Biotechnologie	Biotechnologie	NNP	_	_	_
39	AG	AG	NNP	_	_	_
40	bioinformatics	bioinformatic	NNS	_	_	_
41	department	department	NN	_	_	_
42	did	do	VBD	_	_	_
43	a	a	DT	_	_	_
44	preliminary	preliminary	JJ	_	_	_
45	analysis	analysis	NN	_	_	_
46	of	of	IN	_	_	_
47	the	the	DT	_	_	_
48	high-throughput	high-throughput	JJ	_	_	_
49	sequencing	sequencing	NN	_	_	_
50	results	result	NNS	_	_	_
51	which	which	WDT	_	_	_
52	included	include	VBD	_	_	_
53	the	the	DT	_	_	_
54	mapping	mapping	NN	_	_	_
55	of	of	IN	_	_	_
56	the	the	DT	_	_	_
57	reads	read	VBZ	_	_	_
58	against	against	IN	_	_	_
59	E.	e.	FW	_	_	_
60	coli	coli	FW	_	_	_
61	genome	genome	NN	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	NC	nc	NN	_	_	_
64	_	_	CD	_	_	_
65	000913	000913	CD	_	_	_
66	downloaded	download	VBN	_	_	_
67	from	from	IN	_	_	_
68	NCBI	NCBI	NNP	_	_	_
69	genome	genome	NN	_	_	_
70	database	database	NN	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	We	we	PRP	_	_	_
3	then	then	RB	_	_	_
4	used	use	VBD	_	_	_
5	the	the	DT	_	_	_
6	mapped	map	VBN	_	_	_
7	files	file	NNS	_	_	_
8	to	to	TO	_	_	_
9	run	run	VB	_	_	_
10	Cufflinks	Cufflinks	NNP	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	estimates	estimate	VBZ	_	_	_
13	the	the	DT	_	_	_
14	relative	relative	JJ	_	_	_
15	abundance	abundance	NN	_	_	_
16	of	of	IN	_	_	_
17	the	the	DT	_	_	_
18	transcripts	transcript	NNS	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	and	and	CC	_	_	_
21	after	after	IN	_	_	_
22	Cuffdiff	Cuffdiff	NNP	_	_	_
23	to	to	TO	_	_	_
24	find	find	VB	_	_	_
25	significant	significant	JJ	_	_	_
26	changes	change	NNS	_	_	_
27	in	in	IN	_	_	_
28	transcript	transcript	NN	_	_	_
29	expression	expression	NN	_	_	_
30	when	when	WRB	_	_	_
31	comparing	compare	VBG	_	_	_
32	two	two	CD	_	_	_
33	samples	sample	NNS	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Trapnell	Trapnell	NNP	_	_	_
36	,	,	,	_	_	_
37	Williams	Williams	NNP	_	_	_
38	et	et	FW	_	_	_
39	al.	al.	FW	_	_	_
40	2010	2010	CD	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	WT	WT	NNP	_	_	_
3	_	_	NNP	_	_	_
4	RNA-Seq	RNA-Seq	NNP	_	_	_
5	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
6	common	common	JJ	_	_	_
7	reference	reference	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	OD600	od600	NN	_	_	_
10	=	=	JJ	_	_	_
11	0.5	0.5	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Escherichia	escherichia	FW	Organism	_	_
15	coli	coli	FW	Organism	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Normalization	normalization	NN	_	_	_
18	is	be	VBZ	_	_	_
19	performed	perform	VBN	_	_	_
20	by	by	IN	_	_	_
21	TREBAX	trebax	NN	_	_	_
22	,	,	,	_	_	_
23	using	use	VBG	_	_	_
24	MA-plots	ma-plot	NNS	_	_	_
25	.	.	.	_	_	_

1	MA-plots	ma-plot	NNS	_	_	_
2	can	can	MD	GEN	_	_
3	reveal	reveal	VB	_	_	_
4	the	the	DT	_	_	_
5	spot	spot	NN	_	_	_
6	artifacts	artifact	NNS	_	_	_
7	globally	globally	RB	_	_	_
8	and	and	CC	_	_	_
9	show	show	VB	_	_	_
10	the	the	DT	_	_	_
11	intensity-dependent	intensity-dependent	JJ	_	_	_
12	logarithmic	logarithmic	JJ	_	_	_
13	ratio	ratio	NN	_	_	_
14	of	of	IN	_	_	_
15	raw	raw	JJ	_	_	_
16	microarray	microarray	NN	_	_	_
17	data	datum	NNS	_	_	_
18	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	MA-plots	ma-plot	NNS	_	_	_
3	,	,	,	_	_	_
4	we	we	PRP	_	_	_
5	calculate	calculate	VBP	_	_	_
6	two	two	CD	_	_	_
7	parameters	parameter	NNS	_	_	_
8	,	,	,	_	_	_
9	average	average	NN	_	_	_
10	of	of	IN	_	_	_
11	logarithmic	logarithmic	JJ	_	_	_
12	transferred	transfer	VBN	_	_	_
13	intensity	intensity	NN	_	_	_
14	As	as	IN	_	_	_
15	=	=	JJ	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	log	log	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Ts	ts	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	+	+	CC	_	_	_
22	log	log	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Rs	rs	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	OD	od	NN	_	_	_
29	:	:	:	_	_	_
30	0.1	0.1	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	OD	od	NN	_	_	_
33	:	:	:	_	_	_
34	0.3	0.3	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	OD	od	NN	_	_	_
37	:	:	:	_	_	_
38	0.4	0.4	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	OD	od	NN	_	_	_
41	:	:	:	_	_	_
42	0.5	0.5	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	OD	od	NN	_	_	_
45	:	:	:	_	_	_
46	0.6	0.6	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	OD	od	NN	_	_	_
49	:	:	:	_	_	_
50	1.0	1.0	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	OD	od	NN	_	_	_
53	:	:	:	_	_	_
54	1.3	1.3	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	OD	od	NN	_	_	_
57	:	:	:	_	_	_
58	1.7	1.7	CD	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	OD	od	NN	_	_	_
61	:	:	:	_	_	_
62	2.7	2.7	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	OD	od	NN	_	_	_
65	:	:	:	_	_	_
66	4.5	4.5	CD	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	OD	od	NN	_	_	_
69	:	:	:	_	_	_
70	4.7	4.7	CD	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	OD	od	NN	_	_	_
73	:	:	:	_	_	_
74	4.8	4.8	CD	_	_	_
75	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
76	Qiagen	Qiagen	NNP	_	_	_
77	RNeasy	RNeasy	NNP	_	_	_
78	mini	minus	NNS	_	_	_
79	Kit	kit	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	Reference	Reference	NNP	_	_	_
82	Design	Design	NNP	_	_	_
83	timecourse	timecourse	NN	_	_	_
84	c	c	NN	_	_	_
85	_	_	CD	_	_	_
86	t10	t10	NN	_	_	_
87	.1	.1	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
89	Reference	Reference	NNP	_	_	_
90	Design	design	NN	_	_	_
91	timecourse	timecourse	NN	_	_	_
92	c	c	NN	_	_	_
93	_	_	CD	_	_	_
94	t10	t10	NN	_	_	_
95	.2	.2	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
97	Reference	Reference	NNP	_	_	_
98	Design	design	NN	_	_	_
99	timecourse	timecourse	NN	_	_	_
100	c	c	NN	_	_	_
101	_	_	CD	_	_	_
102	t1	t1	NN	_	_	_
103	.1	.1	CD	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
105	Reference	Reference	NNP	_	_	_
106	Design	design	NN	_	_	_
107	timecourse	timecourse	NN	_	_	_
108	c	c	NN	_	_	_
109	_	_	CD	_	_	_
110	t11	t11	NN	_	_	_
111	.1	.1	CD	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
113	Reference	Reference	NNP	_	_	_
114	Design	design	NN	_	_	_
115	timecourse	timecourse	NN	_	_	_
116	c	c	NN	_	_	_
117	_	_	CD	_	_	_
118	t11	t11	NN	_	_	_
119	.2	.2	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
121	Reference	Reference	NNP	_	_	_
122	Design	design	NN	_	_	_
123	timecourse	timecourse	NN	_	_	_
124	c	c	NN	_	_	_
125	_	_	CD	_	_	_
126	t1	t1	NN	_	_	_
127	.2	.2	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
129	Reference	Reference	NNP	_	_	_
130	Design	design	NN	_	_	_
131	timecourse	timecourse	NN	_	_	_
132	c	c	NN	_	_	_
133	_	_	CD	_	_	_
134	t2	t2	NN	_	_	_
135	.1	.1	CD	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
137	Reference	Reference	NNP	_	_	_
138	Design	design	NN	_	_	_
139	timecourse	timecourse	NN	_	_	_
140	c	c	NN	_	_	_
141	_	_	CD	_	_	_
142	t2	t2	NN	_	_	_
143	.2	.2	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
145	Reference	Reference	NNP	_	_	_
146	Design	design	NN	_	_	_
147	timecourse	timecourse	NN	_	_	_
148	c	c	NN	_	_	_
149	_	_	CD	_	_	_
150	t3	t3	NN	_	_	_
151	.1	.1	CD	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
153	Reference	Reference	NNP	_	_	_
154	Design	design	NN	_	_	_
155	timecourse	timecourse	NN	_	_	_
156	c	c	NN	_	_	_
157	_	_	CD	_	_	_
158	t3	t3	NN	_	_	_
159	.2	.2	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
161	Reference	Reference	NNP	_	_	_
162	Design	design	NN	_	_	_
163	timecourse	timecourse	NN	_	_	_
164	c	c	NN	_	_	_
165	_	_	CD	_	_	_
166	t4	t4	NN	_	_	_
167	.1	.1	CD	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
169	Reference	Reference	NNP	_	_	_
170	Design	design	NN	_	_	_
171	timecourse	timecourse	NN	_	_	_
172	c	c	NN	_	_	_
173	_	_	CD	_	_	_
174	t4	t4	NN	_	_	_
175	.2	.2	NN	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
177	Reference	Reference	NNP	_	_	_
178	Design	design	NN	_	_	_
179	timecourse	timecourse	NN	_	_	_
180	c	c	NN	_	_	_
181	_	_	CD	_	_	_
182	t5	t5	NN	_	_	_
183	.1	.1	CD	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
185	Reference	Reference	NNP	_	_	_
186	Design	design	NN	_	_	_
187	timecourse	timecourse	NN	_	_	_
188	c	c	NN	_	_	_
189	_	_	CD	_	_	_
190	t5	t5	NN	_	_	_
191	.2	.2	NN	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
193	Reference	Reference	NNP	_	_	_
194	Design	design	NN	_	_	_
195	timecourse	timecourse	NN	_	_	_
196	c	c	NN	_	_	_
197	_	_	CD	_	_	_
198	t6	t6	NN	_	_	_
199	.1	.1	CD	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
201	Reference	Reference	NNP	_	_	_
202	Design	design	NN	_	_	_
203	timecourse	timecourse	NN	_	_	_
204	c	c	NN	_	_	_
205	_	_	CD	_	_	_
206	t6	t6	NN	_	_	_
207	.2	.2	NN	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
209	Reference	Reference	NNP	_	_	_
210	Design	design	NN	_	_	_
211	timecourse	timecourse	NN	_	_	_
212	c	c	NN	_	_	_
213	_	_	CD	_	_	_
214	t7	t7	NN	_	_	_
215	.1	.1	CD	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
217	Reference	Reference	NNP	_	_	_
218	Design	design	NN	_	_	_
219	timecourse	timecourse	NN	_	_	_
220	c	c	NN	_	_	_
221	_	_	CD	_	_	_
222	t7	t7	NN	_	_	_
223	.2	.2	NN	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
225	Reference	Reference	NNP	_	_	_
226	Design	design	NN	_	_	_
227	timecourse	timecourse	NN	_	_	_
228	c	c	NN	_	_	_
229	_	_	CD	_	_	_
230	t8	t8	NN	_	_	_
231	.1	.1	CD	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
233	Reference	Reference	NNP	_	_	_
234	Design	design	NN	_	_	_
235	timecourse	timecourse	NN	_	_	_
236	c	c	NN	_	_	_
237	_	_	CD	_	_	_
238	t8	t8	NN	_	_	_
239	.2	.2	NN	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
241	Reference	Reference	NNP	_	_	_
242	Design	design	NN	_	_	_
243	timecourse	timecourse	NN	_	_	_
244	c	c	NN	_	_	_
245	_	_	CD	_	_	_
246	t9	t9	NN	_	_	_
247	.1	.1	CD	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
249	Reference	Reference	NNP	_	_	_
250	Design	design	NN	_	_	_
251	timecourse	timecourse	NN	_	_	_
252	c	c	NN	_	_	_
253	_	_	CD	_	_	_
254	t9	t9	NN	_	_	_
255	.2	.2	NN	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
257	Strain	strain	NN	_	_	_
258	:	:	:	_	_	_
259	W3110	w3110	NN	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	time	time	NN	_	_	_
262	10	10	CD	_	_	_
263	-LRB-	-lrb-	-LRB-	_	_	_
264	OD600	od600	NN	_	_	_
265	=	=	JJ	_	_	_
266	4.7	4.7	CD	_	_	_
267	-RRB-	-rrb-	-RRB-	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	time	time	NN	_	_	_
270	11	11	CD	_	_	_
271	-LRB-	-lrb-	-LRB-	_	_	_
272	OD600	od600	NN	_	_	_
273	=	=	JJ	_	_	_
274	4.8	4.8	CD	_	_	_
275	-RRB-	-rrb-	-RRB-	_	_	_
276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
277	time	time	NN	_	_	_
278	1	1	CD	_	_	_
279	-LRB-	-lrb-	-LRB-	_	_	_
280	OD600	od600	NN	_	_	_
281	=	=	JJ	_	_	_
282	0.1	0.1	CD	_	_	_
283	-RRB-	-rrb-	-RRB-	_	_	_
284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
285	time	time	NN	_	_	_
286	2	2	CD	_	_	_
287	-LRB-	-lrb-	-LRB-	_	_	_
288	OD600	od600	NN	_	_	_
289	=	=	JJ	_	_	_
290	0.3	0.3	CD	_	_	_
291	-RRB-	-rrb-	-RRB-	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	time	time	NN	_	_	_
294	3	3	CD	_	_	_
295	-LRB-	-lrb-	-LRB-	_	_	_
296	OD600	od600	NN	_	_	_
297	=	=	JJ	_	_	_
298	0.4	0.4	CD	_	_	_
299	-RRB-	-rrb-	-RRB-	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	time	time	NN	_	_	_
302	4	4	CD	_	_	_
303	-LRB-	-lrb-	-LRB-	_	_	_
304	OD600	od600	NN	_	_	_
305	=	=	JJ	_	_	_
306	0.6	0.6	CD	_	_	_
307	-RRB-	-rrb-	-RRB-	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	time	time	NN	_	_	_
310	5	5	CD	_	_	_
311	-LRB-	-lrb-	-LRB-	_	_	_
312	OD600	od600	NN	_	_	_
313	=	=	JJ	_	_	_
314	1.0	1.0	CD	_	_	_
315	-RRB-	-rrb-	-RRB-	_	_	_
316	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
317	time	time	NN	_	_	_
318	6	6	CD	_	_	_
319	-LRB-	-lrb-	-LRB-	_	_	_
320	OD600	od600	NN	_	_	_
321	=	=	JJ	_	_	_
322	1.3	1.3	CD	_	_	_
323	-RRB-	-rrb-	-RRB-	_	_	_
324	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
325	time	time	NN	_	_	_
326	7	7	CD	_	_	_
327	-LRB-	-lrb-	-LRB-	_	_	_
328	OD600	od600	NN	_	_	_
329	=	=	JJ	_	_	_
330	1.7	1.7	CD	_	_	_
331	-RRB-	-rrb-	-RRB-	_	_	_
332	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
333	time	time	NN	_	_	_
334	8	8	CD	_	_	_
335	-LRB-	-lrb-	-LRB-	_	_	_
336	OD600	od600	NN	_	_	_
337	=	=	JJ	_	_	_
338	2.7	2.7	CD	_	_	_
339	-RRB-	-rrb-	-RRB-	_	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
341	time	time	NN	_	_	_
342	9	9	CD	_	_	_
343	-LRB-	-lrb-	-LRB-	_	_	_
344	OD600	od600	NN	_	_	_
345	=	=	JJ	_	_	_
346	4.5	4.5	CD	_	_	_
347	-RRB-	-rrb-	-RRB-	_	_	_
348	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
349	All	all	DT	_	_	_
350	sequencing	sequencing	NN	_	_	_
351	reads	read	VBZ	_	_	_
352	were	be	VBD	_	_	_
353	mapped	map	VBN	_	_	_
354	to	to	TO	_	_	_
355	E.	e.	FW	_	_	_
356	coli	coli	FW	_	_	_
357	MG1655	mg1655	NN	_	_	_
358	reference	reference	NN	_	_	_
359	genome	genome	NN	_	_	_
360	-LRB-	-lrb-	-LRB-	_	_	_
361	NC	nc	NN	_	_	_
362	_	_	CD	_	_	_
363	000913	000913	CD	_	_	_
364	-RRB-	-rrb-	-RRB-	_	_	_
365	using	use	VBG	_	_	_
366	CLC	clc	NN	_	_	_
367	Genomics	genomic	NNS	_	_	_
368	Workbench5	workbench5	NN	_	_	_
369	with	with	IN	_	_	_
370	the	the	DT	_	_	_
371	length	length	NN	_	_	_
372	fraction	fraction	NN	_	_	_
373	of	of	IN	_	_	_
374	0.9	0.9	CD	_	_	_
375	and	and	CC	_	_	_
376	the	the	DT	_	_	_
377	similarity	similarity	NN	_	_	_
378	of	of	IN	_	_	_
379	0.99	0.99	CD	_	_	_
380	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	All	All	NNP	_	_	_
3	strains	strain	NNS	_	_	_
4	used	use	VBN	_	_	_
5	are	be	VBP	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	K-12	k-12	NN	_	_	_
9	MG1655	mg1655	NN	_	_	_
10	and	and	CC	_	_	_
11	its	its	PRP$	_	_	_
12	derivatives	derivative	NNS	_	_	_
13	.	.	.	_	_	_

1	Glycerol	glycerol	NN	_	_	_
2	stock	stock	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	E.	e.	FW	_	_	_
6	coli	coli	FW	_	_	_
7	strain	strain	NN	_	_	_
8	was	be	VBD	_	_	_
9	inoculated	inoculate	VBN	_	_	_
10	into	into	IN	_	_	_
11	3	3	CD	_	_	_
12	mL	ml	NN	_	_	_
13	Luria	Luria	NNP	MED	_	_
14	broth	broth	NN	MED	_	_
15	supplemented	supplement	VBN	_	_	_
16	with	with	IN	_	_	_
17	150	150	CD	_	_	_
18	μg	μg	NN	_	_	_
19	kanamycin	kanamycin	NN	_	_	_
20	and	and	CC	_	_	_
21	cultured	culture	VBN	_	_	_
22	overnight	overnight	JJ	_	_	_
23	at	at	IN	_	_	_
24	37	37	CD	_	_	_
25	°C	°c	NN	_	_	_
26	with	with	IN	_	_	_
27	constant	constant	JJ	_	_	_
28	agitation	agitation	NN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	ArgR	argr	NN	TF	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	-	-	:	_	_	_
5	arg	arg	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	rep1	rep1	NN	_	_	_
8	and	and	CC	_	_	_
9	rep2	rep2	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	ArgR	argr	NN	TF	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	+	+	CC	_	_	_
14	arg	arg	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	rep1	rep1	NN	_	_	_
17	and	and	CC	_	_	_
18	rep2	rep2	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Basecalls	basecall	NNS	_	_	_
21	performed	perform	VBN	_	_	_
22	using	use	VBG	_	_	_
23	CASAVA	CASAVA	NNP	_	_	_
24	version	version	NN	_	_	_
25	1.4	1.4	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	chip	chip	NN	_	_	_
28	antibody	antibody	NN	_	_	_
29	:	:	:	_	_	_
30	Anti-myc	anti-myc	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	9E10	9e10	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Santa	Santa	NNP	_	_	_
36	Cruz	Cruz	NNP	_	_	_
37	,	,	,	_	_	_
38	Dallas	Dallas	NNP	_	_	_
39	,	,	,	_	_	_
40	TX	TX	NNP	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	ChIP-Seq	chip-seq	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	Cultured	culture	VBN	_	_	_
46	cells	cell	NNS	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	50	50	CD	_	_	_
49	mL	ml	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	were	be	VBD	_	_	_
52	cross-linked	cross-link	VBN	_	_	_
53	with	with	IN	_	_	_
54	1	1	CD	_	_	_
55	%	%	NN	_	_	_
56	formaldehyde	formaldehyde	NN	_	_	_
57	at	at	IN	_	_	_
58	room	room	NN	_	_	_
59	temperature	temperature	NN	_	_	_
60	for	for	IN	_	_	_
61	30	30	CD	_	_	_
62	min	min	NN	_	_	_
63	and	and	CC	_	_	_
64	added	add	VBD	_	_	_
65	2	2	CD	_	_	_
66	mL	ml	NN	_	_	_
67	of	of	IN	_	_	_
68	2.5	2.5	CD	_	_	_
69	M	m	NN	_	_	_
70	glycine	glycine	NN	_	_	_
71	to	to	TO	_	_	_
72	quench	quench	VB	_	_	_
73	the	the	DT	_	_	_
74	unused	unused	JJ	_	_	_
75	formaldehyde	formaldehyde	NN	_	_	_
76	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	washing	wash	VBG	_	_	_
3	three	three	CD	_	_	_
4	times	time	NNS	_	_	_
5	with	with	IN	_	_	_
6	50	50	CD	_	_	_
7	mL	ml	NN	_	_	_
8	of	of	IN	_	_	_
9	ice-cold	ice-cold	JJ	_	_	_
10	Tris-buffered	tris-buffered	JJ	_	_	_
11	saline	saline	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	TBS	tbs	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	the	the	DT	_	_	_
17	washed	washed	JJ	_	_	_
18	cells	cell	NNS	_	_	_
19	were	be	VBD	_	_	_
20	resuspended	resuspend	VBN	_	_	_
21	in	in	IN	_	_	_
22	0.5	0.5	CD	_	_	_
23	mL	ml	NN	_	_	_
24	of	of	IN	_	_	_
25	lysis	lysis	NN	_	_	_
26	buffer	buffer	NN	_	_	_
27	composed	compose	VBN	_	_	_
28	of	of	IN	_	_	_
29	50	50	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	Tris-HCl	tris-hcl	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	pH	ph	NN	_	_	_
34	7.5	7.5	CD	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	,	,	,	_	_	_
37	100	100	CD	_	_	_
38	mM	mm	NN	KWSUPP	_	_
39	NaCl	nacl	NN	_	_	_
40	,	,	,	_	_	_
41	1	1	CD	_	_	_
42	mM	mm	NN	KWSUPP	_	_
43	EDTA	edta	NN	_	_	_
44	,	,	,	_	_	_
45	1	1	CD	_	_	_
46	μg	μg	NN	_	_	_
47	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
48	Escherichia	escherichia	FW	Organism	_	_
49	coli	coli	FW	Organism	_	_
50	str	str	FW	_	_	_
51	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	substrain	substrain	NN	_	_	_
4	:	:	:	_	_	_
5	MG1655	mg1655	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Supplementary	supplementary	JJ	_	_	_
8	_	_	NN	_	_	_
9	files	file	NNS	_	_	_
10	_	_	IN	_	_	_
11	format	format	NN	_	_	_
12	_	_	NN	_	_	_
13	and	and	CC	_	_	_
14	_	_	NN	_	_	_
15	content	content	NN	_	_	_
16	:	:	:	_	_	_
17	gff	gff	NN	_	_	_
18	file	file	NN	_	_	_
19	is	be	VBZ	_	_	_
20	generated	generate	VBN	_	_	_
21	by	by	IN	_	_	_
22	in-house	in-house	JJ	_	_	_
23	script	script	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
25	The	the	DT	_	_	_
26	cross-linked	cross-linked	JJ	_	_	_
27	DNA-ArgR	dna-argr	NN	_	_	_
28	complexes	complex	NNS	_	_	_
29	in	in	IN	_	_	_
30	the	the	DT	_	_	_
31	supernatant	supernatant	NN	_	_	_
32	were	be	VBD	_	_	_
33	then	then	RB	_	_	_
34	immunoprecipitated	immunoprecipitate	VBN	_	_	_
35	by	by	IN	_	_	_
36	adding	add	VBG	_	_	_
37	10	10	CD	_	_	_
38	µL	µl	NN	_	_	_
39	of	of	IN	_	_	_
40	Anti-myc	anti-myc	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	9E10	9e10	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	Santa	Santa	NNP	_	_	_
46	Cruz	Cruz	NNP	_	_	_
47	,	,	,	_	_	_
48	Dallas	Dallas	NNP	_	_	_
49	,	,	,	_	_	_
50	TX	TX	NNP	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	mock-IP	mock-ip	JJ	_	_	_
3	control	control	NN	_	_	_
4	,	,	,	_	_	_
5	2	2	CD	_	_	_
6	µg	µg	NN	_	_	_
7	of	of	IN	_	_	_
8	normal	normal	JJ	_	_	_
9	mouse	mouse	NN	_	_	_
10	IgG	igg	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Santa	Santa	NNP	_	_	_
13	Cruz	Cruz	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	was	be	VBD	_	_	_
16	added	add	VBN	_	_	_
17	into	into	IN	_	_	_
18	the	the	DT	_	_	_
19	supernatant	supernatant	NN	_	_	_
20	in	in	IN	_	_	_
21	parallel	parallel	NN	_	_	_
22	.	.	.	_	_	_

1	They	they	PRP	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	incubated	incubate	VBN	_	_	_
5	overnight	overnight	JJ	_	_	_
6	at	at	IN	_	_	_
7	4oC	4oc	NN	_	_	_
8	with	with	IN	_	_	_
9	constant	constant	JJ	_	_	_
10	rotation	rotation	NN	_	_	_
11	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cross-linked	cross-linked	JJ	_	_	_
3	DNA-protein	dna-protein	NN	_	_	_
4	and	and	CC	_	_	_
5	antibody	antibody	NN	_	_	_
6	complexes	complex	NNS	_	_	_
7	were	be	VBD	_	_	_
8	selectively	selectively	RB	_	_	_
9	captured	capture	VBN	_	_	_
10	by	by	IN	_	_	_
11	adding	add	VBG	_	_	_
12	50	50	CD	_	_	_
13	µL	µl	NN	_	_	_
14	of	of	IN	_	_	_
15	Dynabeads	Dynabeads	NNP	_	_	_
16	Pan	Pan	NNP	_	_	_
17	Mouse	Mouse	NNP	_	_	_
18	IgG	igg	NN	_	_	_
19	magnetic	magnetic	JJ	_	_	_
20	beads	bead	NNS	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Invitrogen	Invitrogen	NNP	_	_	_
23	,	,	,	_	_	_
24	Grand	Grand	NNP	_	_	_
25	Island	Island	NNP	_	_	_
26	,	,	,	_	_	_
27	NY	NY	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	,	,	,	_	_	_
3	DNAs	dna	NNS	_	_	_
4	were	be	VBD	_	_	_
5	end-polished	end-polished	JJ	_	_	_
6	using	use	VBG	_	_	_
7	T4	t4	NN	_	_	_
8	DNA	dna	NN	_	_	_
9	polymerase	polymerase	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	NEB	neb	NN	_	_	_
12	,	,	,	_	_	_
13	Ipswich	Ipswich	NNP	_	_	_
14	,	,	,	_	_	_
15	MA	MA	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	,	,	,	_	_	_
18	ligated	ligate	VBN	_	_	_
19	with	with	IN	_	_	_
20	the	the	DT	_	_	_
21	annealed	annealed	JJ	_	_	_
22	adaptor	adaptor	NN	_	_	_
23	1	1	CD	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	5	5	CD	_	_	_
26	'	'	''	_	_	_
27	-	-	:	_	_	_
28	Phospho-AACTGCCCCGGGTTGCTCTTCCGATCT	phospho-aactgccccgggttgctcttccgatct	NN	_	_	_
29	and	and	CC	_	_	_
30	5	5	CD	_	_	_
31	'	'	''	_	_	_
32	-	-	:	_	_	_
33	OH-AGATCGGAAGAGC-OH	oh-agatcggaagagc-oh	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	,	,	,	_	_	_
36	nick-repaired	nick-repaired	JJ	_	_	_
37	using	use	VBG	_	_	_
38	phi29	phi29	NN	_	_	_
39	polymerase	polymerase	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	NEB	neb	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	,	,	,	_	_	_
44	and	and	CC	_	_	_
45	digested	digest	VBN	_	_	_
46	with	with	IN	_	_	_
47	λ	λ	NN	_	_	_
48	exonuclease	exonuclease	NN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	NEB	neb	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	as	as	IN	_	_	_
53	reported	report	VBN	_	_	_
54	previously	previously	RB	_	_	_
55	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	,	,	,	_	_	_
3	protein-DNA	protein-dna	JJ	_	_	_
4	complexes	complex	NNS	_	_	_
5	were	be	VBD	_	_	_
6	reverse-cross-linked	reverse-cross-link	VBN	_	_	_
7	by	by	IN	_	_	_
8	heating	heating	NN	_	_	_
9	at	at	IN	_	_	_
10	65	65	CD	_	_	_
11	°C	°c	NN	_	_	_
12	overnight	overnight	JJ	_	_	_
13	and	and	CC	_	_	_
14	proteins	protein	NNS	_	_	_
15	were	be	VBD	_	_	_
16	degraded	degrade	VBN	_	_	_
17	by	by	IN	_	_	_
18	8	8	CD	_	_	_
19	µg	µg	NN	_	_	_
20	of	of	IN	_	_	_
21	protease	protease	NN	_	_	_
22	K	k	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Invitrogen	invitrogen	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	purified	purify	VBN	_	_	_
3	DNAs	dna	NNS	_	_	_
4	were	be	VBD	_	_	_
5	denatured	denature	VBN	_	_	_
6	at	at	IN	_	_	_
7	95	95	CD	_	_	_
8	°C	°c	NN	_	_	_
9	and	and	CC	_	_	_
10	extended	extend	VBN	_	_	_
11	by	by	IN	_	_	_
12	P1	p1	NN	_	_	_
13	primer	primer	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	5	5	CD	_	_	_
16	'	'	''	_	_	_
17	-	-	:	_	_	_
18	OH-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT	oh-gtgactggagttcagacgtgtgctcttccgatct	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	,	,	,	_	_	_
21	further	further	JJ	_	_	_
22	ligated	ligate	VBN	_	_	_
23	with	with	IN	_	_	_
24	the	the	DT	_	_	_
25	annealed	annealed	JJ	_	_	_
26	adaptor	adaptor	NN	_	_	_
27	2	2	CD	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	5	5	CD	_	_	_
30	'	'	''	_	_	_
31	-	-	:	_	_	_
32	OH-ACACTCTTTCCCTACACGACGCTCTTCCGATCT	oh-acactctttccctacacgacgctcttccgatct	NN	_	_	_
33	and	and	CC	_	_	_
34	5	5	CD	_	_	_
35	'	'	''	_	_	_
36	-	-	:	_	_	_
37	OH-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAG	oh-agatcggaagagcgtcgtgtagggaaagagtgtag	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	ligated	ligate	VBN	_	_	_
3	DNA	dna	NN	_	_	_
4	products	product	NNS	_	_	_
5	were	be	VBD	_	_	_
6	purified	purify	VBN	_	_	_
7	using	use	VBG	_	_	_
8	Qiagen	Qiagen	NNP	_	_	_
9	PCR	pcr	NN	_	_	_
10	purification	purification	NN	_	_	_
11	kit	kit	NN	_	_	_
12	and	and	CC	_	_	_
13	were	be	VBD	_	_	_
14	PCR-amplified	pcr-amplified	JJ	_	_	_
15	by	by	IN	_	_	_
16	P2	p2	NN	_	_	_
17	primer	primer	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	5	5	CD	_	_	_
20	'	'	''	_	_	_
21	-	-	:	_	_	_
22	OH-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT	oh-aatgatacggcgaccaccgagatctacactctttccctacacgacgctcttccgatct	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	and	and	CC	_	_	_
25	P3	p3	NN	_	_	_
26	primer	primer	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	5	5	CD	_	_	_
29	'	'	''	_	_	_
30	-	-	:	_	_	_
31	OH-CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGT	oh-caagcagaagacggcatacgagatnnnnnngtgactggagttcagacgtgt	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	degenerative	degenerative	JJ	_	_	_
3	sequence	sequence	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	the	the	DT	_	_	_
6	underlined	underline	VBN	_	_	_
7	6Ns	6n	NNS	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	in	in	IN	_	_	_
10	the	the	DT	_	_	_
11	P3	p3	NN	_	_	_
12	primer	primer	NN	_	_	_
13	indicates	indicate	VBZ	_	_	_
14	the	the	DT	_	_	_
15	index	index	NN	_	_	_
16	sequence	sequence	NN	_	_	_
17	for	for	IN	_	_	_
18	the	the	DT	_	_	_
19	Illumina	Illumina	NNP	_	_	_
20	next-generation	next-generation	JJ	_	_	_
21	sequencing	sequencing	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Illumina	Illumina	NNP	_	_	_
24	,	,	,	_	_	_
25	San	San	NNP	_	_	_
26	Diego	Diego	NNP	_	_	_
27	,	,	,	_	_	_
28	CA	CA	NNP	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	PCR-amplified	pcr-amplified	JJ	_	_	_
3	DNA	dna	NN	_	_	_
4	products	product	NNS	_	_	_
5	were	be	VBD	_	_	_
6	then	then	RB	_	_	_
7	loaded	load	VBN	_	_	_
8	onto	onto	IN	_	_	_
9	2	2	CD	_	_	_
10	%	%	NN	_	_	_
11	agarose	agarose	NN	_	_	_
12	gel	gel	NN	_	_	_
13	and	and	CC	_	_	_
14	extracted	extract	VBN	_	_	_
15	using	use	VBG	_	_	_
16	QIAquick	qiaquick	NN	_	_	_
17	gel	gel	NN	_	_	_
18	purification	purification	NN	_	_	_
19	columns	column	NNS	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cultured	culture	VBN	_	_	_
4	cells	cell	NNS	_	_	_
5	were	be	VBD	_	_	_
6	inoculated	inoculate	VBN	_	_	_
7	with	with	IN	_	_	_
8	1:100	1:100	CD	_	_	_
9	dilution	dilution	NN	_	_	_
10	into	into	IN	_	_	_
11	50	50	CD	_	_	_
12	mL	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	the	the	DT	_	_	_
15	fresh	fresh	JJ	_	_	_
16	M9	m9	NN	_	_	_
17	medium	medium	NN	_	_	_
18	containing	contain	VBG	_	_	_
19	2	2	CD	_	_	_
20	g	g	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
22	To	to	TO	_	_	_
23	capture	capture	VB	_	_	_
24	target	target	NN	_	_	_
25	protein	protein	NN	_	_	_
26	binding	binding	NN	_	_	_
27	sites	site	NNS	_	_	_
28	corresponding	correspond	VBG	_	_	_
29	genomic	genomic	JJ	_	_	_
30	position	position	NN	_	_	_
31	of	of	IN	_	_	_
32	mapped	map	VBN	_	_	_
33	reads	read	VBZ	_	_	_
34	start	start	NN	_	_	_
35	position	position	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	MRSP	mrsp	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	was	be	VBD	_	_	_
40	counted	count	VBN	_	_	_
41	and	and	CC	_	_	_
42	stored	store	VBN	_	_	_
43	for	for	IN	_	_	_
44	visual	visual	JJ	_	_	_
45	inspection	inspection	NN	_	_	_
46	using	use	VBG	_	_	_
47	in-house	in-house	JJ	_	_	_
48	scripts	script	NNS	_	_	_
49	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	cDNA	cdna	NN	_	_	_
3	_	_	NN	_	_	_
4	A	a	NN	_	_	_
5	_	_	CD	_	_	_
6	cy3	cy3	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	cDNA	cdna	NN	_	_	_
9	_	_	NN	_	_	_
10	B	b	NN	_	_	_
11	_	_	CD	_	_	_
12	cy5	cy5	NN	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	E.	E.	NNP	_	_	_
15	coli	coli	NN	_	_	_
16	MG1655	mg1655	NN	_	_	_
17	genomic	genomic	JJ	_	_	_
18	DNA	dna	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	E.	e.	FW	_	_	_
21	coli	coli	FW	_	_	_
22	MG1655	mg1655	NN	_	_	_
23	RNA	rna	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	Escherichia	escherichia	FW	Organism	_	_
26	coli	coli	FW	Organism	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	gDNA	gdna	NN	_	_	_
29	_	_	CD	_	_	_
30	A	a	DT	_	_	_
31	_	_	NN	_	_	_
32	cy5	cy5	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	gDNA	gdna	NN	_	_	_
35	_	_	NN	_	_	_
36	B	b	NN	_	_	_
37	_	_	CD	_	_	_
38	cy3	cy3	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
40	Genomic	genomic	JJ	_	_	_
41	DNA	dna	NN	_	_	_
42	was	be	VBD	_	_	_
43	purified	purify	VBN	_	_	_
44	using	use	VBG	_	_	_
45	a	a	DT	_	_	_
46	20	20	CD	_	_	_
47	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
48	Linearly	linearly	RB	_	_	_
49	scaled	scale	VBD	_	_	_
50	so	so	RB	_	_	_
51	that	that	IN	_	_	_
52	intensity	intensity	NN	_	_	_
53	values	value	NNS	_	_	_
54	in	in	IN	_	_	_
55	gDNA	gdna	NN	_	_	_
56	_	_	CD	_	_	_
57	A	a	DT	_	_	_
58	_	_	NN	_	_	_
59	cy5	cy5	NN	_	_	_
60	,	,	,	_	_	_
61	cDNA	cdna	NN	_	_	_
62	_	_	NN	_	_	_
63	A	a	NN	_	_	_
64	_	_	NN	_	_	_
65	cy3	cy3	NN	_	_	_
66	,	,	,	_	_	_
67	gDNA	gdna	NN	_	_	_
68	_	_	NN	_	_	_
69	B	b	NN	_	_	_
70	_	_	CD	_	_	_
71	cy3	cy3	NN	_	_	_
72	,	,	,	_	_	_
73	and	and	CC	_	_	_
74	cDNA	cdna	NN	_	_	_
75	_	_	NN	_	_	_
76	B	b	NN	_	_	_
77	_	_	CD	_	_	_
78	cy5	cy5	NN	_	_	_
79	are	be	VBP	_	_	_
80	comparable	comparable	JJ	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
82	Strain	strain	NN	_	_	_
83	MG1655	mg1655	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	Total	total	JJ	_	_	_
86	RNA	rna	NN	_	_	_
87	was	be	VBD	_	_	_
88	purified	purify	VBN	_	_	_
89	on	on	IN	_	_	_
90	a	a	DT	_	_	_
91	RNeasy	rneasy	NN	_	_	_
92	columns	column	NNS	_	_	_
93	-LRB-	-lrb-	-LRB-	_	_	_
94	Qiagen	Qiagen	NNP	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	;	;	:	_	_	_
97	ribosomal	ribosomal	JJ	_	_	_
98	RNAs	rna	NNS	_	_	_
99	were	be	VBD	_	_	_
100	removed	remove	VBN	_	_	_
101	with	with	IN	_	_	_
102	the	the	DT	_	_	_
103	MicroExpress	MicroExpress	NNP	_	_	_
104	kit	kit	NN	_	_	_
105	-LRB-	-lrb-	-LRB-	_	_	_
106	Ambion	ambion	NN	_	_	_
107	-RRB-	-rrb-	-RRB-	_	_	_
108	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	resulting	result	VBG	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	reverse	reverse	JJ	_	_	_
6	transcribed	transcribe	VBN	_	_	_
7	with	with	IN	_	_	_
8	SuperScript	SuperScript	NNP	_	_	_
9	II	II	NNP	_	_	_
10	reverse	reverse	JJ	_	_	_
11	transcriptase	transcriptase	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Invitrogen	invitrogen	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	+	+	CC	_	_	_
16	random	random	JJ	_	_	_
17	hexamers	hexamer	NNS	_	_	_
18	+	+	CC	_	_	_
19	dNTP	dntp	NN	_	_	_
20	mix	mix	NN	_	_	_
21	containing	contain	VBG	_	_	_
22	aminoallyl-dUTP	aminoallyl-dutp	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Beta	Beta	NNP	_	_	_
3	_	_	NNP	_	_	_
4	ChIP	ChIP	NNP	_	_	_
5	_	_	SYM	_	_	_
6	A	a	DT	_	_	_
7	_	_	SYM	_	_	_
8	cy5	cy5	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
10	Beta	beta	JJ	_	_	_
11	_	_	NN	_	_	_
12	ChIP	chip	NN	_	_	_
13	_	_	NN	_	_	_
14	B	b	NN	_	_	_
15	_	_	CD	_	_	_
16	cy5	cy5	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Beta	beta	NN	_	_	_
19	_	_	CD	_	_	_
20	ChIP	chip	NN	_	_	_
21	_	_	NN	_	_	_
22	control	control	NN	_	_	_
23	_	_	CD	_	_	_
24	A	a	DT	_	_	_
25	_	_	NN	_	_	_
26	cy3	cy3	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Beta	beta	NN	_	_	_
29	_	_	CD	_	_	_
30	ChIP	chip	NN	_	_	_
31	_	_	NN	_	_	_
32	control	control	NN	_	_	_
33	_	_	NN	_	_	_
34	B	b	NN	_	_	_
35	_	_	CD	_	_	_
36	cy3	cy3	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Cells	cell	NNS	_	_	_
39	were	be	VBD	_	_	_
40	fixed	fix	VBN	_	_	_
41	in	in	IN	_	_	_
42	1	1	CD	_	_	_
43	%	%	NN	_	_	_
44	formaldehyde	formaldehyde	NN	_	_	_
45	at	at	IN	_	_	_
46	room	room	NN	_	_	_
47	temperature	temperature	NN	_	_	_
48	for	for	IN	_	_	_
49	20	20	CD	_	_	_
50	min	min	NN	_	_	_
51	,	,	,	_	_	_
52	quenched	quench	VBN	_	_	_
53	with	with	IN	_	_	_
54	glycine	glycine	NN	_	_	_
55	,	,	,	_	_	_
56	and	and	CC	_	_	_
57	lysed	lyse	VBN	_	_	_
58	.	.	.	_	_	_

1	Chromatin	chromatin	NN	_	_	_
2	was	be	VBD	_	_	_
3	pelleted	pelleted	JJ	_	_	_
4	and	and	CC	_	_	_
5	solublized	solublize	VBN	_	_	_
6	by	by	IN	_	_	_
7	sonication	sonication	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	fixed	fix	VBN	_	_	_
5	in	in	IN	_	_	_
6	1	1	CD	_	_	_
7	%	%	NN	_	_	_
8	formaldehyde	formaldehyde	NN	_	_	_
9	at	at	IN	_	_	_
10	room	room	NN	_	_	_
11	temperature	temperature	NN	_	_	_
12	for	for	IN	_	_	_
13	20	20	CD	_	_	_
14	min	min	NN	_	_	_
15	,	,	,	_	_	_
16	quenched	quench	VBN	_	_	_
17	with	with	IN	_	_	_
18	glycine	glycine	NN	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	lysed	lyse	VBN	_	_	_
22	.	.	.	_	_	_

1	Chromatin	chromatin	NN	_	_	_
2	was	be	VBD	_	_	_
3	pelleted	pelleted	JJ	_	_	_
4	and	and	CC	_	_	_
5	solublized	solublize	VBN	_	_	_
6	by	by	IN	_	_	_
7	sonication	sonication	NN	_	_	_
8	.	.	.	_	_	_

1	Crosslinked	crosslink	VBN	_	_	_
2	chromatin	chromatin	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	immunoprecipitated	immunoprecipitate	VBN	_	_	_
6	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Escherichia	escherichia	FW	Organism	_	_
7	coli	coli	FW	Organism	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Linearly	linearly	RB	_	_	_
10	scaled	scale	VBN	_	_	_
11	so	so	IN	_	_	_
12	that	that	IN	_	_	_
13	intensity	intensity	NN	_	_	_
14	values	value	NNS	_	_	_
15	in	in	IN	_	_	_
16	Sigma70	sigma70	NN	_	_	_
17	_	_	CD	_	_	_
18	ChIP	chip	NN	_	_	_
19	_	_	NN	_	_	_
20	control	control	NN	_	_	_
21	_	_	CD	_	_	_
22	A	a	DT	_	_	_
23	_	_	NN	_	_	_
24	cy3	cy3	NN	_	_	_
25	,	,	,	_	_	_
26	Sigma70	sigma70	NN	_	_	_
27	_	_	CD	_	_	_
28	ChIP	chip	NN	_	_	_
29	_	_	CD	_	_	_
30	A	a	DT	_	_	_
31	_	_	NN	_	_	_
32	cy5	cy5	NN	_	_	_
33	,	,	,	_	_	_
34	Sigma70	sigma70	NN	_	_	_
35	_	_	CD	_	_	_
36	ChIP	chip	NN	_	_	_
37	_	_	NN	_	_	_
38	control	control	NN	_	_	_
39	_	_	NN	_	_	_
40	B	b	NN	_	_	_
41	_	_	CD	_	_	_
42	cy3	cy3	NN	_	_	_
43	,	,	,	_	_	_
44	Sigma70	sigma70	NN	_	_	_
45	_	_	CD	_	_	_
46	ChIP	chip	NN	_	_	_
47	_	_	NN	_	_	_
48	B	b	NN	_	_	_
49	_	_	CD	_	_	_
50	cy5	cy5	NN	_	_	_
51	,	,	,	_	_	_
52	Beta	beta	NN	_	_	_
53	_	_	CD	_	_	_
54	ChIP	chip	NN	_	_	_
55	_	_	NN	_	_	_
56	control	control	NN	_	_	_
57	_	_	CD	_	_	_
58	A	a	DT	_	_	_
59	_	_	NN	_	_	_
60	cy3	cy3	NN	_	_	_
61	,	,	,	_	_	_
62	Beta	beta	NN	_	_	_
63	_	_	NN	_	_	_
64	ChIP	chip	NN	_	_	_
65	_	_	CD	_	_	_
66	A	a	DT	_	_	_
67	_	_	NN	_	_	_
68	cy5	cy5	NN	_	_	_
69	,	,	,	_	_	_
70	Beta	beta	NN	_	_	_
71	_	_	NN	_	_	_
72	ChIP	chip	NN	_	_	_
73	_	_	CD	_	_	_
74	control	control	NN	_	_	_
75	_	_	NN	_	_	_
76	B	b	NN	_	_	_
77	_	_	CD	_	_	_
78	cy3	cy3	NN	_	_	_
79	,	,	,	_	_	_
80	Beta	beta	NN	_	_	_
81	_	_	NN	_	_	_
82	ChIP	chip	NN	_	_	_
83	_	_	NN	_	_	_
84	B	b	NN	_	_	_
85	_	_	CD	_	_	_
86	cy5	cy5	NN	_	_	_
87	are	be	VBP	_	_	_
88	comparable	comparable	JJ	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
90	Sigma70	sigma70	NN	_	_	_
91	_	_	CD	_	_	_
92	ChIP	chip	NN	_	_	_
93	_	_	CD	_	_	_
94	A	a	DT	_	_	_
95	_	_	NN	_	_	_
96	cy5	cy5	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	Sigma70	sigma70	NN	_	_	_
99	_	_	CD	_	_	_
100	ChIP	chip	NN	_	_	_
101	_	_	NN	_	_	_
102	B	b	NN	_	_	_
103	_	_	CD	_	_	_
104	cy5	cy5	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	Sigma70	sigma70	NN	_	_	_
107	_	_	CD	_	_	_
108	ChIP	chip	NN	_	_	_
109	_	_	NN	_	_	_
110	control	control	NN	_	_	_
111	_	_	CD	_	_	_
112	A	a	DT	_	_	_
113	_	_	NN	_	_	_
114	cy3	cy3	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	Sigma70	sigma70	NN	_	_	_
117	_	_	CD	_	_	_
118	ChIP	chip	NN	_	_	_
119	_	_	NN	_	_	_
120	control	control	NN	_	_	_
121	_	_	NN	_	_	_
122	B	b	NN	_	_	_
123	_	_	CD	_	_	_
124	cy3	cy3	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	Strain	strain	NN	_	_	_
127	MG1655	mg1655	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	Escherichia	escherichia	FW	Organism	_	_
130	coli	coli	FW	Organism	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	Normalization	normalization	NN	_	_	_
133	is	be	VBZ	_	_	_
134	performed	perform	VBN	_	_	_
135	by	by	IN	_	_	_
136	TREBAX	trebax	NN	_	_	_
137	,	,	,	_	_	_
138	using	use	VBG	_	_	_
139	MA-plots	ma-plot	NNS	_	_	_
140	.	.	.	_	_	_

1	MA-plots	ma-plot	NNS	_	_	_
2	can	can	MD	GEN	_	_
3	reveal	reveal	VB	_	_	_
4	the	the	DT	_	_	_
5	spot	spot	NN	_	_	_
6	artifacts	artifact	NNS	_	_	_
7	globally	globally	RB	_	_	_
8	and	and	CC	_	_	_
9	show	show	VB	_	_	_
10	the	the	DT	_	_	_
11	intensity-dependent	intensity-dependent	JJ	_	_	_
12	logarithmic	logarithmic	JJ	_	_	_
13	ratio	ratio	NN	_	_	_
14	of	of	IN	_	_	_
15	raw	raw	JJ	_	_	_
16	microarray	microarray	NN	_	_	_
17	data	datum	NNS	_	_	_
18	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	MA-plots	ma-plot	NNS	_	_	_
3	,	,	,	_	_	_
4	we	we	PRP	_	_	_
5	calculate	calculate	VBP	_	_	_
6	two	two	CD	_	_	_
7	parameters	parameter	NNS	_	_	_
8	,	,	,	_	_	_
9	average	average	NN	_	_	_
10	of	of	IN	_	_	_
11	logarithmic	logarithmic	JJ	_	_	_
12	transferred	transfer	VBN	_	_	_
13	intensity	intensity	NN	_	_	_
14	As	as	IN	_	_	_
15	=	=	JJ	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	log	log	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Ts	ts	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	+	+	CC	_	_	_
22	log	log	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Rs	rs	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	OD	od	NN	_	_	_
29	:	:	:	_	_	_
30	0.1	0.1	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	OD	od	NN	_	_	_
33	:	:	:	_	_	_
34	0.3	0.3	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	OD	od	NN	_	_	_
37	:	:	:	_	_	_
38	0.4	0.4	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	OD	od	NN	_	_	_
41	:	:	:	_	_	_
42	0.6	0.6	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	OD	od	NN	_	_	_
45	:	:	:	_	_	_
46	0.6	0.6	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	OD	od	NN	_	_	_
49	:	:	:	_	_	_
50	1.0	1.0	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	OD	od	NN	_	_	_
53	:	:	:	_	_	_
54	1.3	1.3	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	OD	od	NN	_	_	_
57	:	:	:	_	_	_
58	1.7	1.7	CD	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	OD	od	NN	_	_	_
61	:	:	:	_	_	_
62	2.7	2.7	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	OD	od	NN	_	_	_
65	:	:	:	_	_	_
66	4.5	4.5	CD	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	OD	od	NN	_	_	_
69	4.5	4.5	CD	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	OD	od	NN	_	_	_
72	:	:	:	_	_	_
73	4.7	4.7	CD	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	OD	od	NN	_	_	_
76	:	:	:	_	_	_
77	4.8	4.8	CD	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	OD	od	NN	_	_	_
80	:	:	:	_	_	_
81	OD	od	NN	_	_	_
82	0.1	0.1	CD	_	_	_
83	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
84	Qiagen	Qiagen	NNP	_	_	_
85	RNeasy	RNeasy	NNP	_	_	_
86	mini	minus	NNS	_	_	_
87	Kit	kit	NN	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	Sequential	sequential	JJ	_	_	_
90	Design	design	NN	_	_	_
91	timecourse	timecourse	NN	_	_	_
92	t10	t10	NN	_	_	_
93	_	_	CD	_	_	_
94	t11	t11	NN	_	_	_
95	.1	.1	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
97	Sequential	sequential	JJ	_	_	_
98	Design	design	NN	_	_	_
99	timecourse	timecourse	NN	_	_	_
100	t10	t10	NN	_	_	_
101	_	_	CD	_	_	_
102	t11	t11	NN	_	_	_
103	.2	.2	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
105	Sequential	sequential	JJ	_	_	_
106	Design	design	NN	_	_	_
107	timecourse	timecourse	NN	_	_	_
108	t1	t1	NN	_	_	_
109	_	_	CD	_	_	_
110	t2	t2	NN	_	_	_
111	.1	.1	CD	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
113	Sequential	sequential	JJ	_	_	_
114	Design	design	NN	_	_	_
115	timecourse	timecourse	NN	_	_	_
116	t1	t1	NN	_	_	_
117	_	_	CD	_	_	_
118	t2	t2	NN	_	_	_
119	.2	.2	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
121	Sequential	sequential	JJ	_	_	_
122	Design	design	NN	_	_	_
123	timecourse	timecourse	NN	_	_	_
124	t2	t2	NN	_	_	_
125	_	_	CD	_	_	_
126	t3	t3	NN	_	_	_
127	.1	.1	CD	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
129	Sequential	sequential	JJ	_	_	_
130	Design	design	NN	_	_	_
131	timecourse	timecourse	NN	_	_	_
132	t2	t2	NN	_	_	_
133	_	_	CD	_	_	_
134	t3	t3	NN	_	_	_
135	.2	.2	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
137	Sequential	sequential	JJ	_	_	_
138	Design	design	NN	_	_	_
139	timecourse	timecourse	NN	_	_	_
140	t3	t3	NN	_	_	_
141	_	_	CD	_	_	_
142	t4	t4	NN	_	_	_
143	.1	.1	CD	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
145	Sequential	sequential	JJ	_	_	_
146	Design	design	NN	_	_	_
147	timecourse	timecourse	NN	_	_	_
148	t3	t3	NN	_	_	_
149	_	_	CD	_	_	_
150	t4	t4	NN	_	_	_
151	.2	.2	NN	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
153	Sequential	sequential	JJ	_	_	_
154	Design	design	NN	_	_	_
155	timecourse	timecourse	NN	_	_	_
156	t4	t4	NN	_	_	_
157	_	_	CD	_	_	_
158	t5	t5	NN	_	_	_
159	.1	.1	CD	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
161	Sequential	sequential	JJ	_	_	_
162	Design	design	NN	_	_	_
163	timecourse	timecourse	NN	_	_	_
164	t4	t4	NN	_	_	_
165	_	_	CD	_	_	_
166	t5	t5	NN	_	_	_
167	.2	.2	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
169	Sequential	sequential	JJ	_	_	_
170	Design	design	NN	_	_	_
171	timecourse	timecourse	NN	_	_	_
172	t5	t5	NN	_	_	_
173	_	_	CD	_	_	_
174	t6	t6	NN	_	_	_
175	.1	.1	CD	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
177	Sequential	sequential	JJ	_	_	_
178	Design	design	NN	_	_	_
179	timecourse	timecourse	NN	_	_	_
180	t5	t5	NN	_	_	_
181	_	_	CD	_	_	_
182	t6	t6	NN	_	_	_
183	.2	.2	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
185	Sequential	sequential	JJ	_	_	_
186	Design	design	NN	_	_	_
187	timecourse	timecourse	NN	_	_	_
188	t6	t6	NN	_	_	_
189	_	_	CD	_	_	_
190	t7	t7	NN	_	_	_
191	.1	.1	CD	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
193	Sequential	sequential	JJ	_	_	_
194	Design	design	NN	_	_	_
195	timecourse	timecourse	NN	_	_	_
196	t6	t6	NN	_	_	_
197	_	_	CD	_	_	_
198	t7	t7	NN	_	_	_
199	.2	.2	NN	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
201	Sequential	sequential	JJ	_	_	_
202	Design	design	NN	_	_	_
203	timecourse	timecourse	NN	_	_	_
204	t7	t7	NN	_	_	_
205	_	_	CD	_	_	_
206	t8	t8	NN	_	_	_
207	.1	.1	CD	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
209	Sequential	sequential	JJ	_	_	_
210	Design	design	NN	_	_	_
211	timecourse	timecourse	NN	_	_	_
212	t7	t7	NN	_	_	_
213	_	_	CD	_	_	_
214	t8	t8	NN	_	_	_
215	.2	.2	NN	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
217	Sequential	sequential	JJ	_	_	_
218	Design	design	NN	_	_	_
219	timecourse	timecourse	NN	_	_	_
220	t8	t8	NN	_	_	_
221	_	_	CD	_	_	_
222	t9	t9	NN	_	_	_
223	.1	.1	CD	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
225	Sequential	sequential	JJ	_	_	_
226	Design	design	NN	_	_	_
227	timecourse	timecourse	NN	_	_	_
228	t8	t8	NN	_	_	_
229	_	_	CD	_	_	_
230	t9	t9	NN	_	_	_
231	.2	.2	NN	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
233	Sequential	sequential	JJ	_	_	_
234	Design	design	NN	_	_	_
235	timecourse	timecourse	NN	_	_	_
236	t9	t9	NN	_	_	_
237	_	_	CD	_	_	_
238	t10	t10	NN	_	_	_
239	.1	.1	CD	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
241	Sequential	sequential	JJ	_	_	_
242	Design	design	NN	_	_	_
243	timecourse	timecourse	NN	_	_	_
244	t9	t9	NN	_	_	_
245	_	_	CD	_	_	_
246	t10	t10	NN	_	_	_
247	.2	.2	NN	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
249	Strain	strain	NN	_	_	_
250	W3110	w3110	NN	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	Strain	strain	NN	_	_	_
253	:	:	:	_	_	_
254	W3110	w3110	NN	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	Strain	strain	NN	_	_	_
257	:	:	:	_	_	_
258	W3110	w3110	NN	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	Strain	strain	NN	_	_	_
261	:	:	:	_	_	_
262	W3110	w3110	NN	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
264	Strian	strian	NN	_	_	_
265	:	:	:	_	_	_
266	W3110	w3110	NN	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	time	time	NN	_	_	_
269	10	10	CD	_	_	_
270	-LRB-	-lrb-	-LRB-	_	_	_
271	OD600	od600	NN	_	_	_
272	=	=	JJ	_	_	_
273	4.7	4.7	CD	_	_	_
274	-RRB-	-rrb-	-RRB-	_	_	_
275	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
276	time	time	NN	_	_	_
277	11	11	CD	_	_	_
278	-LRB-	-lrb-	-LRB-	_	_	_
279	OD600	od600	NN	_	_	_
280	=	=	JJ	_	_	_
281	4.8	4.8	CD	_	_	_
282	-RRB-	-rrb-	-RRB-	_	_	_
283	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
284	time	time	NN	_	_	_
285	1	1	CD	_	_	_
286	-LRB-	-lrb-	-LRB-	_	_	_
287	OD600	od600	NN	_	_	_
288	=	=	JJ	_	_	_
289	0.1	0.1	CD	_	_	_
290	-RRB-	-rrb-	-RRB-	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	time	time	NN	_	_	_
293	2	2	CD	_	_	_
294	-LRB-	-lrb-	-LRB-	_	_	_
295	OD600	od600	NN	_	_	_
296	=	=	JJ	_	_	_
297	0.3	0.3	CD	_	_	_
298	-RRB-	-rrb-	-RRB-	_	_	_
299	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
300	time	time	NN	_	_	_
301	3	3	CD	_	_	_
302	-LRB-	-lrb-	-LRB-	_	_	_
303	OD600	od600	NN	_	_	_
304	=	=	JJ	_	_	_
305	0.4	0.4	CD	_	_	_
306	-RRB-	-rrb-	-RRB-	_	_	_
307	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
308	time	time	NN	_	_	_
309	4	4	CD	_	_	_
310	-LRB-	-lrb-	-LRB-	_	_	_
311	OD600	od600	NN	_	_	_
312	=	=	JJ	_	_	_
313	0.6	0.6	CD	_	_	_
314	-RRB-	-rrb-	-RRB-	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
316	time	time	NN	_	_	_
317	5	5	CD	_	_	_
318	-LRB-	-lrb-	-LRB-	_	_	_
319	OD600	od600	NN	_	_	_
320	=	=	JJ	_	_	_
321	1.0	1.0	CD	_	_	_
322	-RRB-	-rrb-	-RRB-	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	time	time	NN	_	_	_
325	6	6	CD	_	_	_
326	-LRB-	-lrb-	-LRB-	_	_	_
327	OD600	od600	NN	_	_	_
328	=	=	JJ	_	_	_
329	1.3	1.3	CD	_	_	_
330	-RRB-	-rrb-	-RRB-	_	_	_
331	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
332	time	time	NN	_	_	_
333	7	7	CD	_	_	_
334	-LRB-	-lrb-	-LRB-	_	_	_
335	OD	od	NN	_	_	_
336	=	=	JJ	_	_	_
337	1.7	1.7	CD	_	_	_
338	-RRB-	-rrb-	-RRB-	_	_	_
339	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
340	time	time	NN	_	_	_
341	7	7	CD	_	_	_
342	-LRB-	-lrb-	-LRB-	_	_	_
343	OD600	od600	NN	_	_	_
344	=	=	JJ	_	_	_
345	1.7	1.7	CD	_	_	_
346	-RRB-	-rrb-	-RRB-	_	_	_
347	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
348	time	time	NN	_	_	_
349	8	8	CD	_	_	_
350	-LRB-	-lrb-	-LRB-	_	_	_
351	OD	od	NN	_	_	_
352	=	=	JJ	_	_	_
353	2.7	2.7	CD	_	_	_
354	-RRB-	-rrb-	-RRB-	_	_	_
355	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
356	time	time	NN	_	_	_
357	8	8	CD	_	_	_
358	-LRB-	-lrb-	-LRB-	_	_	_
359	OD600	od600	NN	_	_	_
360	=	=	JJ	_	_	_
361	2.7	2.7	CD	_	_	_
362	-RRB-	-rrb-	-RRB-	_	_	_
363	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
364	time	time	NN	_	_	_
365	9	9	CD	_	_	_
366	-LRB-	-lrb-	-LRB-	_	_	_
367	OD600	od600	NN	_	_	_
368	=	=	JJ	_	_	_
369	4.5	4.5	CD	_	_	_
370	-RRB-	-rrb-	-RRB-	_	_	_
371	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
372	E.	e.	FW	_	_	_
373	coli	coli	FW	_	_	_
374	HB101	hb101	NN	_	_	_
375	grown	grow	VBN	_	_	_
376	in	in	IN	_	_	_
377	Terrific	Terrific	NNP	_	_	_
378	broth	broth	NN	_	_	_
379	media	media	NNS	_	_	_
380	for	for	IN	_	_	_
381	12	12	CD	_	_	_
382	hours	hour	NNS	_	_	_
383	were	be	VBD	_	_	_
384	washed	wash	VBN	_	_	_
385	three	three	CD	_	_	_
386	times	time	NNS	_	_	_
387	in	in	IN	_	_	_
388	sdH2O	sdh2o	NN	_	_	_
389	and	and	CC	_	_	_
390	re-suspended	re-suspended	JJ	_	_	_
391	in	in	IN	_	_	_
392	S-Basal	s-basal	JJ	_	_	_
393	complete	complete	JJ	_	_	_
394	medium	medium	NN	_	_	_
395	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NNS	_	_	_
4	were	be	VBD	_	_	_
5	incubated	incubate	VBN	_	_	_
6	in	in	IN	_	_	_
7	S-Basal	s-basal	JJ	_	_	_
8	complete	complete	JJ	_	_	_
9	medium	medium	NN	_	_	_
10	alone	alone	RB	_	_	_
11	or	or	CC	_	_	_
12	in	in	IN	_	_	_
13	the	the	DT	_	_	_
14	presence	presence	NN	_	_	_
15	of	of	IN	_	_	_
16	C.	C.	NNP	_	_	_
17	elegans	elegan	NNS	_	_	_
18	,	,	,	_	_	_
19	Giardia	Giardia	NNP	_	_	_
20	conditioned	condition	VBD	_	_	_
21	meida	meida	NN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	both	both	DT	_	_	_
25	C.	c.	FW	_	_	_
26	elegans	elegan	NNS	_	_	_
27	and	and	CC	_	_	_
28	Giardia	Giardia	NNP	_	_	_
29	conditioned	condition	VBN	_	_	_
30	media	media	NNS	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Escherchia	escherchia	FW	_	_	_
3	coli	coli	FW	_	_	_
4	HB101	hb101	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Escherchia	escherchia	FW	_	_	_
7	coli	coli	FW	_	_	_
8	HB101	hb101	NN	_	_	_
9	exposed	expose	VBN	_	_	_
10	to	to	TO	_	_	_
11	C.	C.	NNP	_	_	_
12	elegans	elegan	NNS	_	_	_
13	and	and	CC	_	_	_
14	Giardia	Giardia	NNP	_	_	_
15	for	for	IN	_	_	_
16	24	24	CD	_	_	_
17	hours	hour	NNS	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Escherchia	Escherchia	NNP	_	_	_
20	coli	coli	NN	_	_	_
21	HB101	hb101	NN	_	_	_
22	exposed	expose	VBN	_	_	_
23	to	to	TO	_	_	_
24	C.	C.	NNP	_	_	_
25	elegans	elegan	NNS	_	_	_
26	for	for	IN	_	_	_
27	24	24	CD	_	_	_
28	hours	hour	NNS	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	Escherchia	Escherchia	NNP	_	_	_
31	coli	coli	NN	_	_	_
32	HB101	hb101	NN	_	_	_
33	exposed	expose	VBN	_	_	_
34	to	to	TO	_	_	_
35	Giardia	Giardia	NNP	_	_	_
36	for	for	IN	_	_	_
37	24	24	CD	_	_	_
38	hours	hour	NNS	_	_	_
39	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
40	Escherichia	escherichia	FW	Organism	_	_
41	coli	coli	FW	Organism	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	genotype	genotype	NN	_	_	_
44	:	:	:	_	_	_
45	E.	e.	FW	_	_	_
46	coli	coli	FW	_	_	_
47	-LSB-	-lsb-	-LRB-	_	_	_
48	supE44	supe44	NN	_	_	_
49	hsdS20	hsds20	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	rB-mB	rb-mb	NN	_	_	_
52	-	-	:	_	_	_
53	-RRB-	-rrb-	-RRB-	_	_	_
54	recA13	reca13	NN	_	_	_
55	ara-14	ara-14	NN	_	_	_
56	proA2	proa2	NN	_	_	_
57	lacY1	lacy1	NN	_	_	_
58	galK2	galk2	NN	_	_	_
59	rpsL20	rpsl20	NN	_	_	_
60	xyl-5	xyl-5	NN	_	_	_
61	mtl-1	mtl-1	NN	_	_	_
62	-RSB-	-rsb-	-RRB-	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	HB101	hb101	NN	_	_	_
65	,	,	,	_	_	_
66	biological	biological	JJ	_	_	_
67	rep2	rep2	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	HB101	hb101	NN	_	_	_
70	,	,	,	_	_	_
71	biological	biological	JJ	_	_	_
72	rep3	rep3	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	HB101	hb101	NN	_	_	_
75	,	,	,	_	_	_
76	exposed	expose	VBN	_	_	_
77	to	to	TO	_	_	_
78	C.	C.	NNP	_	_	_
79	elegans	elegan	NNS	_	_	_
80	and	and	CC	_	_	_
81	Giardia	Giardia	NNP	_	_	_
82	,	,	,	_	_	_
83	biological	biological	JJ	_	_	_
84	rep1	rep1	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	HB101	hb101	NN	_	_	_
87	,	,	,	_	_	_
88	exposed	expose	VBN	_	_	_
89	to	to	TO	_	_	_
90	C.	C.	NNP	_	_	_
91	elegans	elegan	NNS	_	_	_
92	and	and	CC	_	_	_
93	Giardia	Giardia	NNP	_	_	_
94	,	,	,	_	_	_
95	biological	biological	JJ	_	_	_
96	rep2	rep2	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	HB101	hb101	NN	_	_	_
99	,	,	,	_	_	_
100	exposed	expose	VBN	_	_	_
101	to	to	TO	_	_	_
102	C.	C.	NNP	_	_	_
103	elegans	elegan	NNS	_	_	_
104	and	and	CC	_	_	_
105	Giardia	Giardia	NNP	_	_	_
106	,	,	,	_	_	_
107	biological	biological	JJ	_	_	_
108	rep3	rep3	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	HB101	hb101	NN	_	_	_
111	,	,	,	_	_	_
112	exposed	expose	VBN	_	_	_
113	to	to	TO	_	_	_
114	C.	C.	NNP	_	_	_
115	elegans	elegan	NNS	_	_	_
116	,	,	,	_	_	_
117	biological	biological	JJ	_	_	_
118	rep1	rep1	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	HB101	hb101	NN	_	_	_
121	,	,	,	_	_	_
122	exposed	expose	VBN	_	_	_
123	to	to	TO	_	_	_
124	C.	C.	NNP	_	_	_
125	elegans	elegan	NNS	_	_	_
126	,	,	,	_	_	_
127	biological	biological	JJ	_	_	_
128	rep2	rep2	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	HB101	hb101	NN	_	_	_
131	,	,	,	_	_	_
132	exposed	expose	VBN	_	_	_
133	to	to	TO	_	_	_
134	C.	C.	NNP	_	_	_
135	elegans	elegan	NNS	_	_	_
136	,	,	,	_	_	_
137	biological	biological	JJ	_	_	_
138	rep3	rep3	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	HB101	hb101	NN	_	_	_
141	,	,	,	_	_	_
142	exposed	expose	VBN	_	_	_
143	to	to	TO	_	_	_
144	Giardia	Giardia	NNP	_	_	_
145	,	,	,	_	_	_
146	biological	biological	JJ	_	_	_
147	rep1	rep1	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	HB101	hb101	NN	_	_	_
150	,	,	,	_	_	_
151	exposed	expose	VBN	_	_	_
152	to	to	TO	_	_	_
153	Giardia	Giardia	NNP	_	_	_
154	,	,	,	_	_	_
155	biological	biological	JJ	_	_	_
156	rep2	rep2	NN	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	HB101	hb101	NN	_	_	_
159	,	,	,	_	_	_
160	exposed	expose	VBN	_	_	_
161	to	to	TO	_	_	_
162	Giardia	Giardia	NNP	_	_	_
163	,	,	,	_	_	_
164	biological	biological	JJ	_	_	_
165	rep3	rep3	NN	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	strain	strain	NN	_	_	_
168	:	:	:	_	_	_
169	HB101	hb101	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
171	The	the	DT	_	_	_
172	microarray	microarray	NN	_	_	_
173	data	datum	NNS	_	_	_
174	files	file	NNS	_	_	_
175	were	be	VBD	_	_	_
176	processed	process	VBN	_	_	_
177	using	use	VBG	_	_	_
178	statistical	statistical	JJ	_	_	_
179	software	software	NN	_	_	_
180	R	r	NN	_	_	_
181	version	version	NN	_	_	_
182	3.0.1	3.0.1	CD	_	_	_
183	and	and	CC	_	_	_
184	Bioconductor	Bioconductor	NNP	_	_	_
185	packages	package	NNS	_	_	_
186	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	Single-Channel	Single-Channel	NNP	_	_	_
3	Array	Array	NNP	_	_	_
4	Normalization	normalization	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	SCAN.UPC	scan.upc	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	package	package	NN	_	_	_
9	was	be	VBD	_	_	_
10	used	use	VBN	_	_	_
11	to	to	TO	_	_	_
12	normalize	normalize	VB	_	_	_
13	the	the	DT	_	_	_
14	microarray	microarray	NN	_	_	_
15	data	datum	NNS	_	_	_
16	.	.	.	_	_	_

1	Batch	batch	NN	_	_	_
2	effects	effect	NNS	_	_	_
3	were	be	VBD	_	_	_
4	adjusted	adjust	VBN	_	_	_
5	by	by	IN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	Empirical	Empirical	NNP	_	_	_
9	Bayes	Bayes	NNP	_	_	_
10	method	method	NN	_	_	_
11	implemented	implement	VBN	_	_	_
12	in	in	IN	_	_	_
13	COMBAT	COMBAT	NNP	_	_	_
14	software	software	NN	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	RNeasy	RNeasy	NNP	_	_	_
8	Mini	Mini	NNP	_	_	_
9	Kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Qiagen	qiagen	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	according	accord	VBG	_	_	_
14	to	to	TO	_	_	_
15	instructions	instruction	NNS	_	_	_
16	in	in	IN	_	_	_
17	the	the	DT	_	_	_
18	kit	kit	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	CEL	cel	NN	_	_	_
3	files	file	NNS	_	_	_
4	were	be	VBD	_	_	_
5	quantified	quantify	VBN	_	_	_
6	with	with	IN	_	_	_
7	Distribution	distribution	NN	_	_	_
8	Free	Free	NNP	_	_	_
9	Weighted	Weighted	NNP	_	_	_
10	method	method	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	DFW	dfw	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	,	,	,	_	_	_
15	using	use	VBG	_	_	_
16	the	the	DT	_	_	_
17	statistical	statistical	JJ	_	_	_
18	language	language	NN	_	_	_
19	R	r	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	R-2.7.2	r-2.7.2	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	and	and	CC	_	_	_
24	Bioconductor	Bioconductor	NNP	_	_	_
25	2.2	2.2	CD	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	BW25113	bw25113	NN	_	_	_
5	were	be	VBD	_	_	_
6	maintained	maintain	VBN	_	_	_
7	in	in	IN	_	_	_
8	Luria-Bertani	luria-bertani	JJ	_	_	_
9	medium	medium	NN	_	_	_
10	at	at	IN	_	_	_
11	37ºC	37ºc	NN	_	_	_
12	for	for	IN	_	_	_
13	about	about	RB	_	_	_
14	14	14	CD	_	_	_
15	h	h	NN	_	_	_
16	until	until	IN	_	_	_
17	they	they	PRP	_	_	_
18	reached	reach	VBD	_	_	_
19	the	the	DT	_	_	_
20	stationary	stationary	JJ	GrowthPhase	_	_
21	phase	phase	NN	GrowthPhase	_	_
22	of	of	IN	_	_	_
23	cell	cell	NN	_	_	_
24	growth	growth	NN	_	_	_
25	before	before	IN	_	_	_
26	treatment	treatment	NN	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	incubated	incubate	VBN	_	_	_
5	with	with	IN	_	_	_
6	GST-fused	gst-fused	JJ	_	_	_
7	Drosophila	drosophila	NN	_	_	_
8	immune	immune	JJ	_	_	_
9	proteins	protein	NNS	_	_	_
10	for	for	IN	_	_	_
11	10	10	CD	_	_	_
12	min	min	NN	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	E.	E.	NNP	_	_	_
15	coli	coli	NN	_	_	_
16	incubated	incubate	VBN	_	_	_
17	with	with	IN	_	_	_
18	GST-fused	gst-fused	JJ	_	_	_
19	Drosophila	drosophila	NN	_	_	_
20	immune	immune	JJ	_	_	_
21	proteins	protein	NNS	_	_	_
22	for	for	IN	_	_	_
23	10	10	CD	_	_	_
24	min	min	NN	_	_	_
25	,	,	,	_	_	_
26	biological	biological	JJ	_	_	_
27	rep1	rep1	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	E.	e.	FW	_	_	_
30	coli	coli	FW	_	_	_
31	incubated	incubate	VBN	_	_	_
32	with	with	IN	_	_	_
33	GST-fused	gst-fused	JJ	_	_	_
34	Drosophila	drosophila	NN	_	_	_
35	immune	immune	JJ	_	_	_
36	proteins	protein	NNS	_	_	_
37	for	for	IN	_	_	_
38	10	10	CD	_	_	_
39	min	min	NN	_	_	_
40	,	,	,	_	_	_
41	biological	biological	JJ	_	_	_
42	rep2	rep2	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	E.	e.	FW	_	_	_
45	coli	coli	FW	_	_	_
46	incubated	incubate	VBN	_	_	_
47	with	with	IN	_	_	_
48	GST-fused	gst-fused	JJ	_	_	_
49	Drosophila	drosophila	NN	_	_	_
50	immune	immune	JJ	_	_	_
51	proteins	protein	NNS	_	_	_
52	for	for	IN	_	_	_
53	10	10	CD	_	_	_
54	min	min	NN	_	_	_
55	,	,	,	_	_	_
56	biological	biological	JJ	_	_	_
57	rep3	rep3	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	E.	e.	FW	_	_	_
60	coli	coli	FW	_	_	_
61	incubated	incubate	VBN	_	_	_
62	with	with	IN	_	_	_
63	GST	gst	NN	_	_	_
64	protein	protein	NN	_	_	_
65	alone	alone	RB	_	_	_
66	for	for	IN	_	_	_
67	10	10	CD	_	_	_
68	min	min	NN	_	_	_
69	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
70	E.	E.	NNP	_	_	_
71	coli	coli	NN	_	_	_
72	incubated	incubate	VBN	_	_	_
73	with	with	IN	_	_	_
74	GST	gst	NN	_	_	_
75	protein	protein	NN	_	_	_
76	for	for	IN	_	_	_
77	10	10	CD	_	_	_
78	min	min	NN	_	_	_
79	,	,	,	_	_	_
80	biological	biological	JJ	_	_	_
81	rep1	rep1	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	E.	e.	FW	_	_	_
84	coli	coli	FW	_	_	_
85	incubated	incubate	VBN	_	_	_
86	with	with	IN	_	_	_
87	GST	gst	NN	_	_	_
88	protein	protein	NN	_	_	_
89	for	for	IN	_	_	_
90	10	10	CD	_	_	_
91	min	min	NN	_	_	_
92	,	,	,	_	_	_
93	biological	biological	JJ	_	_	_
94	rep2	rep2	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	E.	e.	FW	_	_	_
97	coli	coli	FW	_	_	_
98	incubated	incubate	VBN	_	_	_
99	with	with	IN	_	_	_
100	GST	gst	NN	_	_	_
101	protein	protein	NN	_	_	_
102	for	for	IN	_	_	_
103	10	10	CD	_	_	_
104	min	min	NN	_	_	_
105	,	,	,	_	_	_
106	biological	biological	JJ	_	_	_
107	rep3	rep3	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	Escherichia	escherichia	FW	Organism	_	_
110	coli	coli	FW	Organism	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	genotype	genotype	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	incubated	incubate	VBN	_	_	_
115	with	with	IN	_	_	_
116	:	:	:	_	_	_
117	Drosophila	drosophila	FW	_	_	_
118	immune	immune	JJ	_	_	_
119	proteins	protein	NNS	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	incubated	incubate	VBN	_	_	_
122	with	with	IN	_	_	_
123	:	:	:	_	_	_
124	GST	gst	NN	_	_	_
125	alone	alone	RB	_	_	_
126	-LRB-	-lrb-	-LRB-	_	_	_
127	3	3	CD	_	_	_
128	μM	μm	NN	_	_	_
129	;	;	:	_	_	_
130	control	control	NN	_	_	_
131	-RRB-	-rrb-	-RRB-	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	incubation	incubation	NN	_	_	_
134	duration	duration	NN	_	_	_
135	:	:	:	_	_	_
136	10	10	CD	_	_	_
137	min	min	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	strain	strain	NN	_	_	_
140	:	:	:	_	_	_
141	BW25113	bw25113	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
143	The	the	DT	_	_	_
144	E.	e.	FW	_	_	_
145	coli	coli	FW	_	_	_
146	strain	strain	NN	_	_	_
147	BW25113	bw25113	NN	_	_	_
148	-LRB-	-lrb-	-LRB-	_	_	_
149	2	2	CD	_	_	_
150	x	x	CC	_	_	_
151	10	10	CD	_	_	_
152	^	^	SYM	_	_	_
153	9	9	CD	_	_	_
154	-RRB-	-rrb-	-RRB-	_	_	_
155	suspended	suspend	VBN	_	_	_
156	with	with	IN	_	_	_
157	insect	insect	JJ	_	_	_
158	saline	saline	NN	_	_	_
159	-LRB-	-lrb-	-LRB-	_	_	_
160	0.13	0.13	CD	_	_	_
161	M	m	NN	_	_	_
162	NaCl	nacl	NN	_	_	_
163	,	,	,	_	_	_
164	4.7	4.7	CD	_	_	_
165	mM	mm	NN	KWSUPP	_	_
166	KCl	kcl	NN	_	_	_
167	,	,	,	_	_	_
168	1.9	1.9	CD	_	_	_
169	mM	mm	NN	KWSUPP	_	_
170	CaCl2	cacl2	NN	_	_	_
171	-RRB-	-rrb-	-RRB-	_	_	_
172	,	,	,	_	_	_
173	was	be	VBD	_	_	_
174	incubated	incubate	VBN	_	_	_
175	with	with	IN	_	_	_
176	GST	gst	NN	_	_	_
177	or	or	CC	_	_	_
178	GST-fused	gst-fused	JJ	_	_	_
179	Drosophila	drosophila	FW	_	_	_
180	immune	immune	JJ	_	_	_
181	proteins	protein	NNS	_	_	_
182	for	for	IN	_	_	_
183	10	10	CD	_	_	_
184	min	min	NN	_	_	_
185	at	at	IN	_	_	_
186	room	room	NN	_	_	_
187	temperature	temperature	NN	_	_	_
188	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	purified	purify	VBN	_	_	_
6	with	with	IN	_	_	_
7	an	a	DT	_	_	_
8	RNeasy	rneasy	NN	_	_	_
9	micro	micro	JJ	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	Qiagen	NNP	_	_	_
13	K.K.	K.K.	NNP	_	_	_
14	,	,	,	_	_	_
15	Tokyo	Tokyo	NNP	_	_	_
16	,	,	,	_	_	_
17	Japan	Japan	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	cDNA	cdna	NN	_	_	_
3	were	be	VBD	_	_	_
4	synthesized	synthesize	VBN	_	_	_
5	from	from	IN	_	_	_
6	the	the	DT	_	_	_
7	reverse	reverse	JJ	_	_	_
8	transcription	transcription	NN	_	_	_
9	of	of	IN	_	_	_
10	Total	total	JJ	_	_	_
11	RNA	rna	NN	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	Life	Life	NNP	_	_	_
15	Technologies	Technologies	NNPS	_	_	_
16	SuperScript	SuperScript	NNP	_	_	_
17	II	II	NNP	_	_	_
18	Double-Strand	Double-Strand	NNP	_	_	_
19	Synthesis	synthesis	NN	_	_	_
20	Kit	kit	NN	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	E.	E.	NNP	_	_	_
23	coli	coli	NN	_	_	_
24	MG1655	mg1655	NN	_	_	_
25	Cold	Cold	NNP	_	_	_
26	Shock	shock	NN	_	_	_
27	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
28	E.	E.	NNP	_	_	_
29	coli	coli	NN	_	_	_
30	MG1655	mg1655	NN	_	_	_
31	Cold	Cold	NNP	_	_	_
32	Shock	shock	NN	_	_	_
33	was	be	VBD	_	_	_
34	grown	grow	VBN	_	_	_
35	at	at	IN	_	_	_
36	15	15	CD	_	_	_
37	°C	°c	NN	_	_	_
38	for	for	IN	_	_	_
39	4	4	CD	_	_	_
40	hour	hour	NN	_	_	_
41	then	then	RB	_	_	_
42	grown	grow	VBN	_	_	_
43	untill	untill	JJ	_	_	_
44	reach	reach	NN	_	_	_
45	to	to	TO	_	_	_
46	half	half	NN	_	_	_
47	of	of	IN	_	_	_
48	O.D.	O.D.	NNP	_	_	_
49	600nm	600nm	NNP	_	_	_
50	of	of	IN	_	_	_
51	Standard	Standard	NNP	_	_	_
52	sample	sample	NN	_	_	_
53	at	at	IN	_	_	_
54	37	37	CD	_	_	_
55	°C	°c	NN	_	_	_
56	in	in	IN	_	_	_
57	LB	LB	NNP	MED	_	_
58	media	media	NNS	MED	_	_
59	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	Heat	heat	NN	_	_	_
6	Shock	shock	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	E.	e.	FW	_	_	_
9	coli	coli	FW	_	_	_
10	MG1655	mg1655	NN	_	_	_
11	Heat	heat	NN	_	_	_
12	Shock	shock	NN	_	_	_
13	was	be	VBD	_	_	_
14	grown	grow	VBN	_	_	_
15	at	at	IN	_	_	_
16	50	50	CD	_	_	_
17	°C	°c	NN	_	_	_
18	for	for	IN	_	_	_
19	4	4	CD	_	_	_
20	hour	hour	NN	_	_	_
21	then	then	RB	_	_	_
22	grown	grow	VBN	_	_	_
23	untill	untill	JJ	_	_	_
24	reach	reach	NN	_	_	_
25	to	to	TO	_	_	_
26	half	half	NN	_	_	_
27	of	of	IN	_	_	_
28	O.D.	O.D.	NNP	_	_	_
29	600nm	600nm	NNP	_	_	_
30	of	of	IN	_	_	_
31	Standard	Standard	NNP	_	_	_
32	sample	sample	NN	_	_	_
33	at	at	IN	_	_	_
34	37	37	CD	_	_	_
35	°C	°c	NN	_	_	_
36	in	in	IN	_	_	_
37	LB	LB	NNP	MED	_	_
38	media	media	NNS	MED	_	_
39	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	Low	low	JJ	_	_	_
6	pH	ph	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	E.	e.	FW	_	_	_
9	coli	coli	FW	_	_	_
10	MG1655	mg1655	NN	_	_	_
11	Low	low	JJ	_	_	_
12	pH	ph	NN	_	_	_
13	was	be	VBD	_	_	_
14	grown	grow	VBN	_	_	_
15	at	at	IN	_	_	_
16	37	37	CD	_	_	_
17	°C	°c	NN	_	_	_
18	for	for	IN	_	_	_
19	1	1	CD	_	_	_
20	hour	hour	NN	_	_	_
21	in	in	IN	_	_	_
22	LB	LB	NNP	MED	_	_
23	media	media	NNS	MED	_	_
24	with	with	IN	_	_	_
25	pH4	ph4	NN	_	_	_
26	.5	.5	CD	_	_	_
27	then	then	RB	_	_	_
28	grown	grow	VBN	_	_	_
29	untill	untill	JJ	_	_	_
30	reach	reach	NN	_	_	_
31	to	to	TO	_	_	_
32	half	half	NN	_	_	_
33	of	of	IN	_	_	_
34	O.D.	O.D.	NNP	_	_	_
35	600nm	600nm	NNP	_	_	_
36	of	of	IN	_	_	_
37	Standard	Standard	NNP	_	_	_
38	sample	sample	NN	_	_	_
39	at	at	IN	_	_	_
40	37	37	CD	_	_	_
41	°C	°c	NN	_	_	_
42	in	in	IN	_	_	_
43	LB	LB	NNP	MED	_	_
44	media	media	NNS	MED	_	_
45	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	minimal	minimal	JJ	_	_	_
6	C	c	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	E.	e.	FW	_	_	_
9	coli	coli	FW	_	_	_
10	MG1655	mg1655	NN	_	_	_
11	minimal	minimal	JJ	_	_	_
12	C&N	c&n	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	E.	e.	FW	_	_	_
15	coli	coli	FW	_	_	_
16	MG1655	mg1655	NN	_	_	_
17	minimal	minimal	JJ	_	_	_
18	C&N	C&N	NNP	_	_	_
19	Source	Source	NNP	_	_	_
20	was	be	VBD	_	_	_
21	grown	grow	VBN	_	_	_
22	untill	untill	JJ	_	_	_
23	reach	reach	NN	_	_	_
24	to	to	TO	_	_	_
25	quater	quater	NN	_	_	_
26	of	of	IN	_	_	_
27	O.D.	O.D.	NNP	_	_	_
28	600nm	600nm	NNP	_	_	_
29	of	of	IN	_	_	_
30	Standard	Standard	NNP	_	_	_
31	sample	sample	NN	_	_	_
32	at	at	IN	_	_	_
33	37	37	CD	_	_	_
34	°C	°c	NN	_	_	_
35	in	in	IN	_	_	_
36	minimal	minimal	JJ	_	_	_
37	C	c	NN	_	_	_
38	and	and	CC	_	_	_
39	N	n	NN	_	_	_
40	source	source	NN	_	_	_
41	MOPS	mop	NNS	MED	_	_
42	media	media	NNS	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	C-N	c-n	NN	_	_	_
45	-	-	:	_	_	_
46	MOPS	mop	NNS	MED	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	minimal	minimal	JJ	_	_	_
6	C	c	NN	_	_	_
7	Source	source	NN	_	_	_
8	was	be	VBD	_	_	_
9	grown	grow	VBN	_	_	_
10	untill	untill	JJ	_	_	_
11	reach	reach	NN	_	_	_
12	to	to	TO	_	_	_
13	half	half	NN	_	_	_
14	of	of	IN	_	_	_
15	O.D.	O.D.	NNP	_	_	_
16	600nm	600nm	NNP	_	_	_
17	of	of	IN	_	_	_
18	Standard	Standard	NNP	_	_	_
19	sample	sample	NN	_	_	_
20	at	at	IN	_	_	_
21	37	37	CD	_	_	_
22	°C	°c	NN	_	_	_
23	in	in	IN	_	_	_
24	minimal	minimal	JJ	_	_	_
25	C	c	NN	_	_	_
26	source	source	NN	_	_	_
27	MOPS	mop	NNS	MED	_	_
28	media	media	NNS	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	C	c	NN	_	_	_
31	-	-	:	_	_	_
32	MOPS	mop	NNS	MED	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	minimal	minimal	JJ	_	_	_
6	N	n	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	E.	e.	FW	_	_	_
9	coli	coli	FW	_	_	_
10	MG1655	mg1655	NN	_	_	_
11	minimal	minimal	JJ	_	_	_
12	N	n	NN	_	_	_
13	Source	source	NN	_	_	_
14	was	be	VBD	_	_	_
15	grown	grow	VBN	_	_	_
16	untill	untill	JJ	_	_	_
17	reach	reach	NN	_	_	_
18	to	to	TO	_	_	_
19	half	half	NN	_	_	_
20	of	of	IN	_	_	_
21	O.D.	O.D.	NNP	_	_	_
22	600nm	600nm	NNP	_	_	_
23	of	of	IN	_	_	_
24	Standard	Standard	NNP	_	_	_
25	sample	sample	NN	_	_	_
26	at	at	IN	_	_	_
27	37	37	CD	_	_	_
28	°C	°c	NN	_	_	_
29	in	in	IN	_	_	_
30	minimal	minimal	JJ	_	_	_
31	N	n	NN	_	_	_
32	source	source	NN	_	_	_
33	MOPS	mop	NNS	MED	_	_
34	media	media	NNS	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	N	n	NN	_	_	_
37	-	-	:	_	_	_
38	MOPS	mop	NNS	MED	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	Osmotic	osmotic	JJ	_	_	_
6	stress	stress	NN	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	E.	E.	NNP	_	_	_
9	coli	coli	NN	_	_	_
10	MG1655	mg1655	NN	_	_	_
11	Osmotic	osmotic	JJ	_	_	_
12	Stress	stress	NN	_	_	_
13	was	be	VBD	_	_	_
14	grown	grow	VBN	_	_	_
15	untill	untill	JJ	_	_	_
16	reach	reach	NN	_	_	_
17	to	to	TO	_	_	_
18	half	half	NN	_	_	_
19	of	of	IN	_	_	_
20	O.D.	O.D.	NNP	_	_	_
21	600nm	600nm	NNP	_	_	_
22	of	of	IN	_	_	_
23	Standard	Standard	NNP	_	_	_
24	sample	sample	NN	_	_	_
25	at	at	IN	_	_	_
26	37	37	CD	_	_	_
27	°C	°c	NN	_	_	_
28	in	in	IN	_	_	_
29	45	45	CD	_	_	_
30	ml	ml	NN	_	_	_
31	MOPS	mop	NNS	MED	_	_
32	media	media	NNS	_	_	_
33	with	with	IN	_	_	_
34	6	6	CD	_	_	_
35	ml	ml	NN	_	_	_
36	4M	4m	NN	_	_	_
37	Sodium	sodium	NN	_	_	_
38	Chloride	chloride	NN	_	_	_
39	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	Oxidative	oxidative	JJ	_	_	_
6	stress	stress	NN	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	E.	E.	NNP	_	_	_
9	coli	coli	NN	_	_	_
10	MG1655	mg1655	NN	_	_	_
11	Oxidative	oxidative	JJ	_	_	_
12	Stress	stress	NN	_	_	_
13	was	be	VBD	_	_	_
14	grown	grow	VBN	_	_	_
15	untill	untill	JJ	_	_	_
16	reach	reach	NN	_	_	_
17	to	to	TO	_	_	_
18	half	half	NN	_	_	_
19	of	of	IN	_	_	_
20	O.D.	O.D.	NNP	_	_	_
21	600nm	600nm	NNP	_	_	_
22	of	of	IN	_	_	_
23	Standard	Standard	NNP	_	_	_
24	sample	sample	NN	_	_	_
25	at	at	IN	_	_	_
26	37	37	CD	_	_	_
27	°C	°c	NN	_	_	_
28	in	in	IN	_	_	_
29	49	49	CD	_	_	_
30	ml	ml	NN	_	_	_
31	MOPS	mop	NNS	MED	_	_
32	media	media	NNS	_	_	_
33	with	with	IN	_	_	_
34	400μl	400μl	NN	_	_	_
35	7	7	CD	_	_	_
36	%	%	NN	_	_	_
37	Hydrogen	hydrogen	NN	_	_	_
38	peroxide	peroxide	NN	_	_	_
39	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655	MG1655	NNP	_	_	_
5	Standard	Standard	NNP	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	E.	E.	NNP	_	_	_
8	coli	coli	NN	_	_	_
9	MG1655	mg1655	NN	_	_	_
10	Standard	Standard	NNP	_	_	_
11	was	be	VBD	_	_	_
12	grown	grow	VBN	_	_	_
13	to	to	TO	_	_	_
14	mid-log	mid-log	JJ	_	_	_
15	phase	phase	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	O.D.	o.d.	NN	_	_	_
18	600nm	600nm	CD	_	_	_
19	0.6	0.6	CD	_	_	_
20	~	~	NN	_	_	_
21	0.8	0.8	CD	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	at	at	IN	_	_	_
24	37	37	CD	_	_	_
25	°C	°c	NN	_	_	_
26	in	in	IN	_	_	_
27	LB	LB	NNP	MED	_	_
28	media	media	NNS	MED	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	UV	uv	NN	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	E.	E.	NNP	_	_	_
8	coli	coli	NN	_	_	_
9	MG1655	mg1655	NN	_	_	_
10	UV	uv	NN	_	_	_
11	was	be	VBD	_	_	_
12	exposed	expose	VBN	_	_	_
13	to	to	TO	_	_	_
14	UV	uv	NN	_	_	_
15	light	light	NN	_	_	_
16	for	for	IN	_	_	_
17	15	15	CD	_	_	_
18	minutes	minute	NNS	_	_	_
19	then	then	RB	_	_	_
20	grown	grow	VBN	_	_	_
21	untill	untill	JJ	_	_	_
22	reach	reach	NN	_	_	_
23	to	to	TO	_	_	_
24	half	half	NN	_	_	_
25	of	of	IN	_	_	_
26	O.D.	O.D.	NNP	_	_	_
27	600nm	600nm	NNP	_	_	_
28	of	of	IN	_	_	_
29	Standard	Standard	NNP	_	_	_
30	sample	sample	NN	_	_	_
31	at	at	IN	_	_	_
32	37	37	CD	_	_	_
33	°C	°c	NN	_	_	_
34	in	in	IN	_	_	_
35	LB	LB	NNP	MED	_	_
36	media	media	NNS	MED	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	MG1655	mg1655	NN	_	_	_
4	_	_	CD	_	_	_
5	standard	standard	JJ	_	_	_
6	_	_	NN	_	_	_
7	condition	condition	NN	_	_	_
8	_	_	CD	_	_	_
9	rep1	rep1	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	MG1655	mg1655	NN	_	_	_
12	_	_	CD	_	_	_
13	standard	standard	JJ	_	_	_
14	_	_	NN	_	_	_
15	condition	condition	NN	_	_	_
16	_	_	CD	_	_	_
17	rep2	rep2	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	MG1655	mg1655	NN	_	_	_
20	_	_	NN	_	_	_
21	under	under	IN	_	_	_
22	_	_	CD	_	_	_
23	ColdShock	ColdShock	NNP	_	_	_
24	_	_	CD	_	_	_
25	rep1	rep1	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	MG1655	mg1655	NN	_	_	_
28	_	_	NN	_	_	_
29	under	under	IN	_	_	_
30	_	_	CD	_	_	_
31	ColdShock	ColdShock	NNP	_	_	_
32	_	_	CD	_	_	_
33	rep2	rep2	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	MG1655	mg1655	NN	_	_	_
36	_	_	NN	_	_	_
37	under	under	IN	_	_	_
38	_	_	NN	_	_	_
39	HeatShock	heatshock	NN	_	_	_
40	_	_	CD	_	_	_
41	rep2	rep2	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	MG1655	mg1655	NN	_	_	_
44	_	_	NN	_	_	_
45	under	under	IN	_	_	_
46	_	_	NNP	_	_	_
47	Low	Low	NNP	_	_	_
48	_	_	NNP	_	_	_
49	pH	ph	NN	_	_	_
50	_	_	CD	_	_	_
51	rep1	rep1	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	MG1655	mg1655	NN	_	_	_
54	_	_	NN	_	_	_
55	under	under	IN	_	_	_
56	_	_	NN	_	_	_
57	minimal	minimal	JJ	_	_	_
58	_	_	NN	_	_	_
59	C&N	c&n	NN	_	_	_
60	_	_	NN	_	_	_
61	source	source	NN	_	_	_
62	_	_	CD	_	_	_
63	rep1	rep1	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	MG1655	mg1655	NN	_	_	_
66	_	_	NN	_	_	_
67	under	under	IN	_	_	_
68	_	_	NN	_	_	_
69	minimal	minimal	JJ	_	_	_
70	_	_	NN	_	_	_
71	C&N	c&n	NN	_	_	_
72	_	_	NN	_	_	_
73	source	source	NN	_	_	_
74	_	_	CD	_	_	_
75	rep2	rep2	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	MG1655	mg1655	NN	_	_	_
78	_	_	NN	_	_	_
79	under	under	IN	_	_	_
80	_	_	NN	_	_	_
81	minimal	minimal	JJ	_	_	_
82	_	_	NN	_	_	_
83	C	c	NN	_	_	_
84	_	_	NN	_	_	_
85	source	source	NN	_	_	_
86	_	_	CD	_	_	_
87	rep1	rep1	NN	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	MG1655	mg1655	NN	_	_	_
90	_	_	NN	_	_	_
91	under	under	IN	_	_	_
92	_	_	NN	_	_	_
93	minimal	minimal	JJ	_	_	_
94	_	_	NN	_	_	_
95	C	c	NN	_	_	_
96	_	_	NN	_	_	_
97	source	source	NN	_	_	_
98	_	_	CD	_	_	_
99	rep2	rep2	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	MG1655	mg1655	NN	_	_	_
102	_	_	NN	_	_	_
103	under	under	IN	_	_	_
104	_	_	NN	_	_	_
105	minimal	minimal	JJ	_	_	_
106	_	_	CD	_	_	_
107	N	n	NN	_	_	_
108	_	_	NN	_	_	_
109	source	source	NN	_	_	_
110	_	_	CD	_	_	_
111	rep1	rep1	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	MG1655	mg1655	NN	_	_	_
114	_	_	NN	_	_	_
115	under	under	IN	_	_	_
116	_	_	NN	_	_	_
117	minimal	minimal	JJ	_	_	_
118	_	_	CD	_	_	_
119	N	n	NN	_	_	_
120	_	_	NN	_	_	_
121	source	source	NN	_	_	_
122	_	_	CD	_	_	_
123	rep2	rep2	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	MG1655	mg1655	NN	_	_	_
126	_	_	NN	_	_	_
127	under	under	IN	_	_	_
128	_	_	NNP	_	_	_
129	Osmotic	Osmotic	NNP	_	_	_
130	_	_	NNP	_	_	_
131	Stress	stress	NN	_	_	_
132	_	_	NN	_	_	_
133	rep1	rep1	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	MG1655	mg1655	NN	_	_	_
136	_	_	NN	_	_	_
137	under	under	IN	_	_	_
138	_	_	CD	_	_	_
139	Osmotic	osmotic	JJ	_	_	_
140	_	_	NN	_	_	_
141	Stress	stress	NN	_	_	_
142	_	_	CD	_	_	_
143	rep2	rep2	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	MG1655	mg1655	NN	_	_	_
146	_	_	NN	_	_	_
147	under	under	IN	_	_	_
148	_	_	NNP	_	_	_
149	Oxidative	oxidative	JJ	_	_	_
150	_	_	NN	_	_	_
151	Stress	stress	NN	_	_	_
152	_	_	CD	_	_	_
153	rep1	rep1	NN	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	MG1655	mg1655	NN	_	_	_
156	_	_	NN	_	_	_
157	under	under	IN	_	_	_
158	_	_	NNP	_	_	_
159	Oxidative	oxidative	JJ	_	_	_
160	_	_	NN	_	_	_
161	Stress	stress	NN	_	_	_
162	_	_	CD	_	_	_
163	rep2	rep2	NN	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	MG1655	mg1655	NN	_	_	_
166	_	_	CD	_	_	_
167	UV	uv	NN	_	_	_
168	_	_	NN	_	_	_
169	Treatment	treatment	NN	_	_	_
170	_	_	CD	_	_	_
171	rep1	rep1	NN	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	MG1655	mg1655	NN	_	_	_
174	_	_	CD	_	_	_
175	UV	uv	NN	_	_	_
176	_	_	NN	_	_	_
177	Treatment	treatment	NN	_	_	_
178	_	_	CD	_	_	_
179	rep2	rep2	NN	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	strain	strain	NN	_	_	_
182	:	:	:	_	_	_
183	MG1655	mg1655	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
185	The	the	DT	_	_	_
186	raw	raw	JJ	_	_	_
187	data	data	NN	_	_	_
188	-LRB-	-lrb-	-LRB-	_	_	_
189	.	.	.	_	_	_

1	pair	pair	NN	_	_	_
2	file	file	NN	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	was	be	VBD	_	_	_
5	subjected	subject	VBN	_	_	_
6	to	to	TO	_	_	_
7	RMA	rma	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Robust	robust	JJ	_	_	_
10	Multi-Array	multi-array	JJ	_	_	_
11	Analysis	analysis	NN	_	_	_
12	;	;	:	_	_	_
13	Irizarry	Irizarry	NNP	_	_	_
14	et	et	FW	_	_	_
15	al.	al.	FW	_	_	_
16	.	.	.	_	_	_

1	Biostatistics	biostatistic	NNS	_	_	_
2	4	4	CD	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	2	2	CD	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	:	:	:	_	_	_
7	249	249	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	,	,	,	_	_	_
10	quantile	quantile	JJ	_	_	_
11	normalization	normalization	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Bolstad	Bolstad	NNP	_	_	_
14	et	et	FW	_	_	_
15	al.	al.	FW	_	_	_
16	.	.	.	_	_	_

1	Bioinformatics	bioinformatic	NNS	_	_	_
2	19	19	CD	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	2	2	CD	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	:	:	:	_	_	_
7	185	185	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	background	background	NN	_	_	_
12	correction	correction	NN	_	_	_
13	as	as	IN	_	_	_
14	implemented	implement	VBN	_	_	_
15	in	in	IN	_	_	_
16	the	the	DT	_	_	_
17	NimbleGen	NimbleGen	NNP	_	_	_
18	Deva	Deva	NNP	_	_	_
19	software	software	NN	_	_	_
20	,	,	,	_	_	_
21	version	version	NN	_	_	_
22	1.2	1.2	CD	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Roche	Roche	NNP	_	_	_
25	NimbleGen	NimbleGen	NNP	_	_	_
26	,	,	,	_	_	_
27	Inc.	Inc.	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	RNeasy	RNeasy	NNP	_	_	_
9	Mini	Mini	NNP	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	qiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	and	and	CC	_	_	_
15	DNA	dna	NN	_	_	_
16	was	be	VBD	_	_	_
17	removed	remove	VBN	_	_	_
18	by	by	IN	_	_	_
19	on-column	on-column	JJ	_	_	_
20	DNase	dnase	NN	_	_	_
21	digestion	digestion	NN	_	_	_
22	with	with	IN	_	_	_
23	the	the	DT	_	_	_
24	RNase-Free	rnase-free	JJ	_	_	_
25	DNase	dnase	NN	_	_	_
26	set	set	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Qiagen	qiagen	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	concentration	concentration	NN	_	_	_
3	was	be	VBD	_	_	_
4	measured	measure	VBN	_	_	_
5	by	by	IN	_	_	_
6	SpectorPhotometer	spectorphotometer	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	NonoDrop	nonodrop	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	Cold	Cold	NNP	_	_	_
5	Shock	shock	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	treatment	treatment	NN	_	_	_
8	:	:	:	_	_	_
9	Heat	Heat	NNP	_	_	_
10	Shock	shock	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	treatment	treatment	NN	_	_	_
13	:	:	:	_	_	_
14	Low	low	JJ	_	_	_
15	pH	ph	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	treatment	treatment	NN	_	_	_
18	:	:	:	_	_	_
19	minimal	minimal	JJ	_	_	_
20	C&N	c&n	NN	_	_	_
21	source	source	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	treatment	treatment	NN	_	_	_
24	:	:	:	_	_	_
25	minimal	minimal	JJ	_	_	_
26	C	c	NN	_	_	_
27	source	source	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	treatment	treatment	NN	_	_	_
30	:	:	:	_	_	_
31	minimal	minimal	JJ	_	_	_
32	N	n	NN	_	_	_
33	source	source	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	treatment	treatment	NN	_	_	_
36	:	:	:	_	_	_
37	Osmotic	osmotic	JJ	_	_	_
38	stress	stress	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	treatment	treatment	NN	_	_	_
41	:	:	:	_	_	_
42	Oxidative	oxidative	JJ	_	_	_
43	stress	stress	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	treatment	treatment	NN	_	_	_
46	:	:	:	_	_	_
47	Standard	Standard	NNP	_	_	_
48	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
49	treatment	treatment	NN	_	_	_
50	:	:	:	_	_	_
51	UV	uv	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	Cells	cell	NNS	_	_	_
54	were	be	VBD	_	_	_
55	grown	grow	VBN	_	_	_
56	in	in	IN	_	_	_
57	the	the	DT	_	_	_
58	minimal	minimal	JJ	_	_	_
59	media	media	NNS	_	_	_
60	,	,	,	_	_	_
61	M63	m63	NN	_	_	_
62	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	final	final	JJ	_	_	_
3	cell	cell	NN	_	_	_
4	concentrations	concentration	NNS	_	_	_
5	were	be	VBD	_	_	_
6	controlled	control	VBN	_	_	_
7	~	~	SYM	_	_	_
8	10	10	CD	_	_	_
9	^	^	SYM	_	_	_
10	8	8	CD	_	_	_
11	cells	cell	NNS	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
13	condition	condition	NN	_	_	_
14	:	:	:	_	_	_
15	exponential	exponential	JJ	_	_	_
16	growth	growth	NN	_	_	_
17	,	,	,	_	_	_
18	36.9	36.9	CD	_	_	_
19	ºC	ºc	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	condition	condition	NN	_	_	_
22	:	:	:	_	_	_
23	exponential	exponential	JJ	_	_	_
24	growth	growth	NN	_	_	_
25	,	,	,	_	_	_
26	41.2	41.2	CD	_	_	_
27	ºC	ºc	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	condition	condition	NN	_	_	_
30	:	:	:	_	_	_
31	exponential	exponential	JJ	_	_	_
32	growth	growth	NN	_	_	_
33	,	,	,	_	_	_
34	43.2	43.2	CD	_	_	_
35	ºC	ºc	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	condition	condition	NN	_	_	_
38	:	:	:	_	_	_
39	exponential	exponential	JJ	_	_	_
40	growth	growth	NN	_	_	_
41	,	,	,	_	_	_
42	44.8	44.8	CD	_	_	_
43	ºC	ºc	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	condition	condition	NN	_	_	_
46	:	:	:	_	_	_
47	heat	heat	NN	_	_	_
48	shock	shock	NN	_	_	_
49	response	response	NN	_	_	_
50	,	,	,	_	_	_
51	44.8	44.8	CD	_	_	_
52	ºC	ºc	NN	_	_	_
53	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
54	E.	E.	NNP	_	_	_
55	coli	coli	NN	_	_	_
56	37L	37l	NN	_	_	_
57	evolved	evolve	VBD	_	_	_
58	strain	strain	NN	_	_	_
59	,	,	,	_	_	_
60	under	under	IN	_	_	_
61	37ºC	37ºc	NN	_	_	_
62	,	,	,	_	_	_
63	rep	rep	NN	GEN	_	_
64	1	1	CD	_	_	_
65	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
66	E.	E.	NNP	_	_	_
67	coli	coli	NN	_	_	_
68	37L	37l	NN	_	_	_
69	evolved	evolve	VBD	_	_	_
70	strain	strain	NN	_	_	_
71	,	,	,	_	_	_
72	under	under	IN	_	_	_
73	37ºC	37ºc	NN	_	_	_
74	,	,	,	_	_	_
75	rep	rep	NN	GEN	_	_
76	2	2	CD	_	_	_
77	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
78	E.	E.	NNP	_	_	_
79	coli	coli	NN	_	_	_
80	37L	37l	NN	_	_	_
81	evolved	evolve	VBD	_	_	_
82	strain	strain	NN	_	_	_
83	,	,	,	_	_	_
84	under	under	IN	_	_	_
85	37ºC	37ºc	NN	_	_	_
86	,	,	,	_	_	_
87	rep	rep	NN	GEN	_	_
88	3	3	CD	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	E.	e.	FW	_	_	_
91	coli	coli	FW	_	_	_
92	41B	41b	NN	_	_	_
93	evolved	evolve	VBD	_	_	_
94	strain	strain	NN	_	_	_
95	,	,	,	_	_	_
96	evolutionary	evolutionary	JJ	_	_	_
97	temperature	temperature	NN	_	_	_
98	,	,	,	_	_	_
99	rep	rep	NN	GEN	_	_
100	1	1	CD	_	_	_
101	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
102	E.	E.	NNP	_	_	_
103	coli	coli	NN	_	_	_
104	41B	41b	NN	_	_	_
105	evolved	evolve	VBD	_	_	_
106	strain	strain	NN	_	_	_
107	,	,	,	_	_	_
108	evolutionary	evolutionary	JJ	_	_	_
109	temperature	temperature	NN	_	_	_
110	,	,	,	_	_	_
111	rep	rep	NN	GEN	_	_
112	2	2	CD	_	_	_
113	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
114	E.	E.	NNP	_	_	_
115	coli	coli	NN	_	_	_
116	41B	41b	NN	_	_	_
117	evolved	evolve	VBD	_	_	_
118	strain	strain	NN	_	_	_
119	,	,	,	_	_	_
120	evolutionary	evolutionary	JJ	_	_	_
121	temperature	temperature	NN	_	_	_
122	,	,	,	_	_	_
123	rep	rep	NN	GEN	_	_
124	3	3	CD	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	E.	e.	FW	_	_	_
127	coli	coli	FW	_	_	_
128	41B	41b	NN	_	_	_
129	evolved	evolve	VBD	_	_	_
130	strain	strain	NN	_	_	_
131	,	,	,	_	_	_
132	regular	regular	JJ	_	_	_
133	temperature	temperature	NN	_	_	_
134	,	,	,	_	_	_
135	rep	rep	NN	GEN	_	_
136	1	1	CD	_	_	_
137	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
138	E.	E.	NNP	_	_	_
139	coli	coli	NN	_	_	_
140	41B	41b	NN	_	_	_
141	evolved	evolve	VBD	_	_	_
142	strain	strain	NN	_	_	_
143	,	,	,	_	_	_
144	regular	regular	JJ	_	_	_
145	temperature	temperature	NN	_	_	_
146	,	,	,	_	_	_
147	rep	rep	NN	GEN	_	_
148	2	2	CD	_	_	_
149	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
150	E.	E.	NNP	_	_	_
151	coli	coli	NN	_	_	_
152	41B	41b	NN	_	_	_
153	evolved	evolve	VBD	_	_	_
154	strain	strain	NN	_	_	_
155	,	,	,	_	_	_
156	regular	regular	JJ	_	_	_
157	temperature	temperature	NN	_	_	_
158	,	,	,	_	_	_
159	rep	rep	NN	GEN	_	_
160	3	3	CD	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	E.	e.	FW	_	_	_
163	coli	coli	FW	_	_	_
164	41B	41b	NN	_	_	_
165	evolved	evolve	VBD	_	_	_
166	strain	strain	NN	_	_	_
167	,	,	,	_	_	_
168	under	under	IN	_	_	_
169	37ºC	37ºc	NN	_	_	_
170	,	,	,	_	_	_
171	rep	rep	NN	GEN	_	_
172	1	1	CD	_	_	_
173	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
174	E.	E.	NNP	_	_	_
175	coli	coli	NN	_	_	_
176	41B	41b	NN	_	_	_
177	evolved	evolve	VBD	_	_	_
178	strain	strain	NN	_	_	_
179	,	,	,	_	_	_
180	under	under	IN	_	_	_
181	37ºC	37ºc	NN	_	_	_
182	,	,	,	_	_	_
183	rep	rep	NN	GEN	_	_
184	2	2	CD	_	_	_
185	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
186	E.	E.	NNP	_	_	_
187	coli	coli	NN	_	_	_
188	41B	41b	NN	_	_	_
189	evolved	evolve	VBD	_	_	_
190	strain	strain	NN	_	_	_
191	,	,	,	_	_	_
192	under	under	IN	_	_	_
193	37ºC	37ºc	NN	_	_	_
194	,	,	,	_	_	_
195	rep	rep	NN	GEN	_	_
196	3	3	CD	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	E.	e.	FW	_	_	_
199	coli	coli	FW	_	_	_
200	41B	41b	NN	_	_	_
201	evolved	evolve	VBD	_	_	_
202	strain	strain	NN	_	_	_
203	,	,	,	_	_	_
204	under	under	IN	_	_	_
205	41ºC	41ºc	NN	_	_	_
206	,	,	,	_	_	_
207	rep	rep	NN	GEN	_	_
208	1	1	CD	_	_	_
209	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
210	E.	E.	NNP	_	_	_
211	coli	coli	NN	_	_	_
212	41B	41b	NN	_	_	_
213	evolved	evolve	VBD	_	_	_
214	strain	strain	NN	_	_	_
215	,	,	,	_	_	_
216	under	under	IN	_	_	_
217	41ºC	41ºc	NN	_	_	_
218	,	,	,	_	_	_
219	rep	rep	NN	GEN	_	_
220	2	2	CD	_	_	_
221	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
222	E.	E.	NNP	_	_	_
223	coli	coli	NN	_	_	_
224	41B	41b	NN	_	_	_
225	evolved	evolve	VBD	_	_	_
226	strain	strain	NN	_	_	_
227	,	,	,	_	_	_
228	under	under	IN	_	_	_
229	41ºC	41ºc	NN	_	_	_
230	,	,	,	_	_	_
231	rep	rep	NN	GEN	_	_
232	3	3	CD	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	E.	e.	FW	_	_	_
235	coli	coli	FW	_	_	_
236	41B	41b	NN	_	_	_
237	strain	strain	NN	_	_	_
238	,	,	,	_	_	_
239	30	30	CD	_	_	_
240	min	min	NN	_	_	_
241	heat	heat	NN	_	_	_
242	shock	shock	NN	_	_	_
243	at	at	IN	_	_	_
244	45ºC	45ºc	NN	_	_	_
245	,	,	,	_	_	_
246	rep	rep	NN	GEN	_	_
247	1	1	CD	_	_	_
248	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
249	E.	E.	NNP	_	_	_
250	coli	coli	NN	_	_	_
251	41B	41b	NN	_	_	_
252	strain	strain	NN	_	_	_
253	,	,	,	_	_	_
254	30	30	CD	_	_	_
255	min	min	NN	_	_	_
256	heat	heat	NN	_	_	_
257	shock	shock	NN	_	_	_
258	at	at	IN	_	_	_
259	45ºC	45ºc	NN	_	_	_
260	,	,	,	_	_	_
261	rep	rep	NN	GEN	_	_
262	2	2	CD	_	_	_
263	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
264	E.	E.	NNP	_	_	_
265	coli	coli	NN	_	_	_
266	41B	41b	NN	_	_	_
267	strain	strain	NN	_	_	_
268	,	,	,	_	_	_
269	5	5	CD	_	_	_
270	min	min	NN	_	_	_
271	heat	heat	NN	_	_	_
272	shock	shock	NN	_	_	_
273	at	at	IN	_	_	_
274	45ºC	45ºc	NN	_	_	_
275	,	,	,	_	_	_
276	rep	rep	NN	GEN	_	_
277	1	1	CD	_	_	_
278	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
279	E.	E.	NNP	_	_	_
280	coli	coli	NN	_	_	_
281	41B	41b	NN	_	_	_
282	strain	strain	NN	_	_	_
283	,	,	,	_	_	_
284	5	5	CD	_	_	_
285	min	min	NN	_	_	_
286	heat	heat	NN	_	_	_
287	shock	shock	NN	_	_	_
288	at	at	IN	_	_	_
289	45ºC	45ºc	NN	_	_	_
290	,	,	,	_	_	_
291	rep	rep	NN	GEN	_	_
292	2	2	CD	_	_	_
293	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
294	E.	E.	NNP	_	_	_
295	coli	coli	NN	_	_	_
296	41B	41b	NN	_	_	_
297	strain	strain	NN	_	_	_
298	,	,	,	_	_	_
299	heat	heat	NN	_	_	_
300	shock	shock	NN	_	_	_
301	,	,	,	_	_	_
302	long	long	RB	_	_	_
303	,	,	,	_	_	_
304	rep	rep	NN	GEN	_	_
305	1	1	CD	_	_	_
306	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
307	E.	E.	NNP	_	_	_
308	coli	coli	NN	_	_	_
309	41B	41b	NN	_	_	_
310	strain	strain	NN	_	_	_
311	,	,	,	_	_	_
312	heat	heat	NN	_	_	_
313	shock	shock	NN	_	_	_
314	,	,	,	_	_	_
315	long	long	RB	_	_	_
316	,	,	,	_	_	_
317	rep	rep	NN	GEN	_	_
318	2	2	CD	_	_	_
319	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
320	E.	E.	NNP	_	_	_
321	coli	coli	NN	_	_	_
322	41B	41b	NN	_	_	_
323	strain	strain	NN	_	_	_
324	,	,	,	_	_	_
325	heat	heat	NN	_	_	_
326	shock	shock	NN	_	_	_
327	,	,	,	_	_	_
328	rep	rep	NN	GEN	_	_
329	1	1	CD	_	_	_
330	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
331	E.	E.	NNP	_	_	_
332	coli	coli	NN	_	_	_
333	41B	41b	NN	_	_	_
334	strain	strain	NN	_	_	_
335	,	,	,	_	_	_
336	heat	heat	NN	_	_	_
337	shock	shock	NN	_	_	_
338	,	,	,	_	_	_
339	rep	rep	NN	GEN	_	_
340	2	2	CD	_	_	_
341	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
342	E.	E.	NNP	_	_	_
343	coli	coli	NN	_	_	_
344	43B	43b	NN	_	_	_
345	evolved	evolve	VBD	_	_	_
346	strain	strain	NN	_	_	_
347	,	,	,	_	_	_
348	evolutionary	evolutionary	JJ	_	_	_
349	temperature	temperature	NN	_	_	_
350	,	,	,	_	_	_
351	rep	rep	NN	GEN	_	_
352	1	1	CD	_	_	_
353	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
354	E.	E.	NNP	_	_	_
355	coli	coli	NN	_	_	_
356	43B	43b	NN	_	_	_
357	evolved	evolve	VBD	_	_	_
358	strain	strain	NN	_	_	_
359	,	,	,	_	_	_
360	evolutionary	evolutionary	JJ	_	_	_
361	temperature	temperature	NN	_	_	_
362	,	,	,	_	_	_
363	rep	rep	NN	GEN	_	_
364	2	2	CD	_	_	_
365	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
366	E.	E.	NNP	_	_	_
367	coli	coli	NN	_	_	_
368	43B	43b	NN	_	_	_
369	evolved	evolve	VBD	_	_	_
370	strain	strain	NN	_	_	_
371	,	,	,	_	_	_
372	evolutionary	evolutionary	JJ	_	_	_
373	temperature	temperature	NN	_	_	_
374	,	,	,	_	_	_
375	rep	rep	NN	GEN	_	_
376	3	3	CD	_	_	_
377	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
378	E.	e.	FW	_	_	_
379	coli	coli	FW	_	_	_
380	43B	43b	NN	_	_	_
381	evolved	evolve	VBD	_	_	_
382	strain	strain	NN	_	_	_
383	,	,	,	_	_	_
384	regular	regular	JJ	_	_	_
385	temperature	temperature	NN	_	_	_
386	,	,	,	_	_	_
387	rep	rep	NN	GEN	_	_
388	1	1	CD	_	_	_
389	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
390	E.	E.	NNP	_	_	_
391	coli	coli	NN	_	_	_
392	43B	43b	NN	_	_	_
393	evolved	evolve	VBD	_	_	_
394	strain	strain	NN	_	_	_
395	,	,	,	_	_	_
396	regular	regular	JJ	_	_	_
397	temperature	temperature	NN	_	_	_
398	,	,	,	_	_	_
399	rep	rep	NN	GEN	_	_
400	2	2	CD	_	_	_
401	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
402	E.	E.	NNP	_	_	_
403	coli	coli	NN	_	_	_
404	43B	43b	NN	_	_	_
405	evolved	evolve	VBD	_	_	_
406	strain	strain	NN	_	_	_
407	,	,	,	_	_	_
408	regular	regular	JJ	_	_	_
409	temperature	temperature	NN	_	_	_
410	,	,	,	_	_	_
411	rep	rep	NN	GEN	_	_
412	3	3	CD	_	_	_
413	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
414	E.	e.	FW	_	_	_
415	coli	coli	FW	_	_	_
416	43B	43b	NN	_	_	_
417	evolved	evolve	VBD	_	_	_
418	strain	strain	NN	_	_	_
419	,	,	,	_	_	_
420	under	under	IN	_	_	_
421	37ºC	37ºc	NN	_	_	_
422	,	,	,	_	_	_
423	rep	rep	NN	GEN	_	_
424	1	1	CD	_	_	_
425	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
426	E.	E.	NNP	_	_	_
427	coli	coli	NN	_	_	_
428	43B	43b	NN	_	_	_
429	evolved	evolve	VBD	_	_	_
430	strain	strain	NN	_	_	_
431	,	,	,	_	_	_
432	under	under	IN	_	_	_
433	37ºC	37ºc	NN	_	_	_
434	,	,	,	_	_	_
435	rep	rep	NN	GEN	_	_
436	2	2	CD	_	_	_
437	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
438	E.	E.	NNP	_	_	_
439	coli	coli	NN	_	_	_
440	43B	43b	NN	_	_	_
441	evolved	evolve	VBD	_	_	_
442	strain	strain	NN	_	_	_
443	,	,	,	_	_	_
444	under	under	IN	_	_	_
445	37ºC	37ºc	NN	_	_	_
446	,	,	,	_	_	_
447	rep	rep	NN	GEN	_	_
448	3	3	CD	_	_	_
449	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
450	E.	e.	FW	_	_	_
451	coli	coli	FW	_	_	_
452	43B	43b	NN	_	_	_
453	evolved	evolve	VBD	_	_	_
454	strain	strain	NN	_	_	_
455	,	,	,	_	_	_
456	under	under	IN	_	_	_
457	43ºC	43ºc	NN	_	_	_
458	,	,	,	_	_	_
459	rep	rep	NN	GEN	_	_
460	1	1	CD	_	_	_
461	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
462	E.	E.	NNP	_	_	_
463	coli	coli	NN	_	_	_
464	43B	43b	NN	_	_	_
465	evolved	evolve	VBD	_	_	_
466	strain	strain	NN	_	_	_
467	,	,	,	_	_	_
468	under	under	IN	_	_	_
469	43ºC	43ºc	NN	_	_	_
470	,	,	,	_	_	_
471	rep	rep	NN	GEN	_	_
472	2	2	CD	_	_	_
473	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
474	E.	E.	NNP	_	_	_
475	coli	coli	NN	_	_	_
476	43B	43b	NN	_	_	_
477	evolved	evolve	VBD	_	_	_
478	strain	strain	NN	_	_	_
479	,	,	,	_	_	_
480	under	under	IN	_	_	_
481	43ºC	43ºc	NN	_	_	_
482	,	,	,	_	_	_
483	rep	rep	NN	GEN	_	_
484	3	3	CD	_	_	_
485	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
486	E.	e.	FW	_	_	_
487	coli	coli	FW	_	_	_
488	43B	43b	NN	_	_	_
489	strain	strain	NN	_	_	_
490	,	,	,	_	_	_
491	30	30	CD	_	_	_
492	min	min	NN	_	_	_
493	heat	heat	NN	_	_	_
494	shock	shock	NN	_	_	_
495	at	at	IN	_	_	_
496	45ºC	45ºc	NN	_	_	_
497	,	,	,	_	_	_
498	rep	rep	NN	GEN	_	_
499	1	1	CD	_	_	_
500	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
501	E.	E.	NNP	_	_	_
502	coli	coli	NN	_	_	_
503	43B	43b	NN	_	_	_
504	strain	strain	NN	_	_	_
505	,	,	,	_	_	_
506	30	30	CD	_	_	_
507	min	min	NN	_	_	_
508	heat	heat	NN	_	_	_
509	shock	shock	NN	_	_	_
510	at	at	IN	_	_	_
511	45ºC	45ºc	NN	_	_	_
512	,	,	,	_	_	_
513	rep	rep	NN	GEN	_	_
514	2	2	CD	_	_	_
515	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
516	E.	E.	NNP	_	_	_
517	coli	coli	NN	_	_	_
518	43B	43b	NN	_	_	_
519	strain	strain	NN	_	_	_
520	,	,	,	_	_	_
521	5	5	CD	_	_	_
522	min	min	NN	_	_	_
523	heat	heat	NN	_	_	_
524	shock	shock	NN	_	_	_
525	at	at	IN	_	_	_
526	45ºC	45ºc	NN	_	_	_
527	,	,	,	_	_	_
528	rep	rep	NN	GEN	_	_
529	1	1	CD	_	_	_
530	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
531	E.	E.	NNP	_	_	_
532	coli	coli	NN	_	_	_
533	43B	43b	NN	_	_	_
534	strain	strain	NN	_	_	_
535	,	,	,	_	_	_
536	5	5	CD	_	_	_
537	min	min	NN	_	_	_
538	heat	heat	NN	_	_	_
539	shock	shock	NN	_	_	_
540	at	at	IN	_	_	_
541	45ºC	45ºc	NN	_	_	_
542	,	,	,	_	_	_
543	rep	rep	NN	GEN	_	_
544	2	2	CD	_	_	_
545	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
546	E.	E.	NNP	_	_	_
547	coli	coli	NN	_	_	_
548	43B	43b	NN	_	_	_
549	strain	strain	NN	_	_	_
550	,	,	,	_	_	_
551	heat	heat	NN	_	_	_
552	shock	shock	NN	_	_	_
553	,	,	,	_	_	_
554	long	long	RB	_	_	_
555	,	,	,	_	_	_
556	rep	rep	NN	GEN	_	_
557	1	1	CD	_	_	_
558	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
559	E.	E.	NNP	_	_	_
560	coli	coli	NN	_	_	_
561	43B	43b	NN	_	_	_
562	strain	strain	NN	_	_	_
563	,	,	,	_	_	_
564	heat	heat	NN	_	_	_
565	shock	shock	NN	_	_	_
566	,	,	,	_	_	_
567	long	long	RB	_	_	_
568	,	,	,	_	_	_
569	rep	rep	NN	GEN	_	_
570	2	2	CD	_	_	_
571	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
572	E.	E.	NNP	_	_	_
573	coli	coli	NN	_	_	_
574	43B	43b	NN	_	_	_
575	strain	strain	NN	_	_	_
576	,	,	,	_	_	_
577	heat	heat	NN	_	_	_
578	shock	shock	NN	_	_	_
579	,	,	,	_	_	_
580	rep	rep	NN	GEN	_	_
581	1	1	CD	_	_	_
582	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
583	E.	E.	NNP	_	_	_
584	coli	coli	NN	_	_	_
585	43B	43b	NN	_	_	_
586	strain	strain	NN	_	_	_
587	,	,	,	_	_	_
588	heat	heat	NN	_	_	_
589	shock	shock	NN	_	_	_
590	,	,	,	_	_	_
591	rep	rep	NN	GEN	_	_
592	2	2	CD	_	_	_
593	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
594	E.	E.	NNP	_	_	_
595	coli	coli	NN	_	_	_
596	45L	45l	NN	_	_	_
597	evolved	evolve	VBD	_	_	_
598	strain	strain	NN	_	_	_
599	,	,	,	_	_	_
600	evolutionary	evolutionary	JJ	_	_	_
601	temperature	temperature	NN	_	_	_
602	,	,	,	_	_	_
603	rep	rep	NN	GEN	_	_
604	1	1	CD	_	_	_
605	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
606	E.	E.	NNP	_	_	_
607	coli	coli	NN	_	_	_
608	45L	45l	NN	_	_	_
609	evolved	evolve	VBD	_	_	_
610	strain	strain	NN	_	_	_
611	,	,	,	_	_	_
612	evolutionary	evolutionary	JJ	_	_	_
613	temperature	temperature	NN	_	_	_
614	,	,	,	_	_	_
615	rep	rep	NN	GEN	_	_
616	2	2	CD	_	_	_
617	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
618	E.	E.	NNP	_	_	_
619	coli	coli	NN	_	_	_
620	45L	45l	NN	_	_	_
621	evolved	evolve	VBD	_	_	_
622	strain	strain	NN	_	_	_
623	,	,	,	_	_	_
624	evolutionary	evolutionary	JJ	_	_	_
625	temperature	temperature	NN	_	_	_
626	,	,	,	_	_	_
627	rep	rep	NN	GEN	_	_
628	3	3	CD	_	_	_
629	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
630	E.	e.	FW	_	_	_
631	coli	coli	FW	_	_	_
632	45L	45l	NN	_	_	_
633	evolved	evolve	VBD	_	_	_
634	strain	strain	NN	_	_	_
635	,	,	,	_	_	_
636	regular	regular	JJ	_	_	_
637	temperature	temperature	NN	_	_	_
638	,	,	,	_	_	_
639	rep	rep	NN	GEN	_	_
640	1	1	CD	_	_	_
641	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
642	E.	E.	NNP	_	_	_
643	coli	coli	NN	_	_	_
644	45L	45l	NN	_	_	_
645	evolved	evolve	VBD	_	_	_
646	strain	strain	NN	_	_	_
647	,	,	,	_	_	_
648	regular	regular	JJ	_	_	_
649	temperature	temperature	NN	_	_	_
650	,	,	,	_	_	_
651	rep	rep	NN	GEN	_	_
652	2	2	CD	_	_	_
653	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
654	E.	E.	NNP	_	_	_
655	coli	coli	NN	_	_	_
656	45L	45l	NN	_	_	_
657	evolved	evolve	VBD	_	_	_
658	strain	strain	NN	_	_	_
659	,	,	,	_	_	_
660	regular	regular	JJ	_	_	_
661	temperature	temperature	NN	_	_	_
662	,	,	,	_	_	_
663	rep	rep	NN	GEN	_	_
664	3	3	CD	_	_	_
665	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
666	E.	e.	FW	_	_	_
667	coli	coli	FW	_	_	_
668	45L	45l	NN	_	_	_
669	evolved	evolve	VBD	_	_	_
670	strain	strain	NN	_	_	_
671	,	,	,	_	_	_
672	under	under	IN	_	_	_
673	37ºC	37ºc	NN	_	_	_
674	,	,	,	_	_	_
675	rep	rep	NN	GEN	_	_
676	1	1	CD	_	_	_
677	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
678	E.	E.	NNP	_	_	_
679	coli	coli	NN	_	_	_
680	45L	45l	NN	_	_	_
681	evolved	evolve	VBD	_	_	_
682	strain	strain	NN	_	_	_
683	,	,	,	_	_	_
684	under	under	IN	_	_	_
685	37ºC	37ºc	NN	_	_	_
686	,	,	,	_	_	_
687	rep	rep	NN	GEN	_	_
688	2	2	CD	_	_	_
689	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
690	E.	E.	NNP	_	_	_
691	coli	coli	NN	_	_	_
692	45L	45l	NN	_	_	_
693	evolved	evolve	VBD	_	_	_
694	strain	strain	NN	_	_	_
695	,	,	,	_	_	_
696	under	under	IN	_	_	_
697	37ºC	37ºc	NN	_	_	_
698	,	,	,	_	_	_
699	rep	rep	NN	GEN	_	_
700	3	3	CD	_	_	_
701	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
702	E.	e.	FW	_	_	_
703	coli	coli	FW	_	_	_
704	45L	45l	NN	_	_	_
705	evolved	evolve	VBD	_	_	_
706	strain	strain	NN	_	_	_
707	,	,	,	_	_	_
708	under	under	IN	_	_	_
709	45ºC	45ºc	NN	_	_	_
710	,	,	,	_	_	_
711	rep	rep	NN	GEN	_	_
712	1	1	CD	_	_	_
713	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
714	E.	E.	NNP	_	_	_
715	coli	coli	NN	_	_	_
716	45L	45l	NN	_	_	_
717	evolved	evolve	VBD	_	_	_
718	strain	strain	NN	_	_	_
719	,	,	,	_	_	_
720	under	under	IN	_	_	_
721	45ºC	45ºc	NN	_	_	_
722	,	,	,	_	_	_
723	rep	rep	NN	GEN	_	_
724	2	2	CD	_	_	_
725	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
726	E.	E.	NNP	_	_	_
727	coli	coli	NN	_	_	_
728	45L	45l	NN	_	_	_
729	evolved	evolve	VBD	_	_	_
730	strain	strain	NN	_	_	_
731	,	,	,	_	_	_
732	under	under	IN	_	_	_
733	45ºC	45ºc	NN	_	_	_
734	,	,	,	_	_	_
735	rep	rep	NN	GEN	_	_
736	3	3	CD	_	_	_
737	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
738	E.	e.	FW	_	_	_
739	coli	coli	FW	_	_	_
740	45L	45l	NN	_	_	_
741	strain	strain	NN	_	_	_
742	,	,	,	_	_	_
743	30	30	CD	_	_	_
744	min	min	NN	_	_	_
745	heat	heat	NN	_	_	_
746	shock	shock	NN	_	_	_
747	at	at	IN	_	_	_
748	45ºC	45ºc	NN	_	_	_
749	,	,	,	_	_	_
750	rep	rep	NN	GEN	_	_
751	1	1	CD	_	_	_
752	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
753	E.	E.	NNP	_	_	_
754	coli	coli	NN	_	_	_
755	45L	45l	NN	_	_	_
756	strain	strain	NN	_	_	_
757	,	,	,	_	_	_
758	30	30	CD	_	_	_
759	min	min	NN	_	_	_
760	heat	heat	NN	_	_	_
761	shock	shock	NN	_	_	_
762	at	at	IN	_	_	_
763	45ºC	45ºc	NN	_	_	_
764	,	,	,	_	_	_
765	rep	rep	NN	GEN	_	_
766	2	2	CD	_	_	_
767	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
768	E.	E.	NNP	_	_	_
769	coli	coli	NN	_	_	_
770	45L	45l	NN	_	_	_
771	strain	strain	NN	_	_	_
772	,	,	,	_	_	_
773	5	5	CD	_	_	_
774	min	min	NN	_	_	_
775	heat	heat	NN	_	_	_
776	shock	shock	NN	_	_	_
777	at	at	IN	_	_	_
778	45ºC	45ºc	NN	_	_	_
779	,	,	,	_	_	_
780	rep	rep	NN	GEN	_	_
781	1	1	CD	_	_	_
782	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
783	E.	E.	NNP	_	_	_
784	coli	coli	NN	_	_	_
785	45L	45l	NN	_	_	_
786	strain	strain	NN	_	_	_
787	,	,	,	_	_	_
788	5	5	CD	_	_	_
789	min	min	NN	_	_	_
790	heat	heat	NN	_	_	_
791	shock	shock	NN	_	_	_
792	at	at	IN	_	_	_
793	45ºC	45ºc	NN	_	_	_
794	,	,	,	_	_	_
795	rep	rep	NN	GEN	_	_
796	2	2	CD	_	_	_
797	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
798	E.	E.	NNP	_	_	_
799	coli	coli	NN	_	_	_
800	45L	45l	NN	_	_	_
801	strain	strain	NN	_	_	_
802	,	,	,	_	_	_
803	heat	heat	NN	_	_	_
804	shock	shock	NN	_	_	_
805	,	,	,	_	_	_
806	long	long	RB	_	_	_
807	,	,	,	_	_	_
808	rep	rep	NN	GEN	_	_
809	1	1	CD	_	_	_
810	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
811	E.	E.	NNP	_	_	_
812	coli	coli	NN	_	_	_
813	45L	45l	NN	_	_	_
814	strain	strain	NN	_	_	_
815	,	,	,	_	_	_
816	heat	heat	NN	_	_	_
817	shock	shock	NN	_	_	_
818	,	,	,	_	_	_
819	long	long	RB	_	_	_
820	,	,	,	_	_	_
821	rep	rep	NN	GEN	_	_
822	2	2	CD	_	_	_
823	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
824	E.	E.	NNP	_	_	_
825	coli	coli	NN	_	_	_
826	45L	45l	NN	_	_	_
827	strain	strain	NN	_	_	_
828	,	,	,	_	_	_
829	heat	heat	NN	_	_	_
830	shock	shock	NN	_	_	_
831	,	,	,	_	_	_
832	rep	rep	NN	GEN	_	_
833	1	1	CD	_	_	_
834	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
835	E.	E.	NNP	_	_	_
836	coli	coli	NN	_	_	_
837	45L	45l	NN	_	_	_
838	strain	strain	NN	_	_	_
839	,	,	,	_	_	_
840	heat	heat	NN	_	_	_
841	shock	shock	NN	_	_	_
842	,	,	,	_	_	_
843	rep	rep	NN	GEN	_	_
844	2	2	CD	_	_	_
845	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
846	E.	E.	NNP	_	_	_
847	coli	coli	NN	_	_	_
848	ancestor	ancestor	NN	_	_	_
849	strain	strain	NN	_	_	_
850	,	,	,	_	_	_
851	30	30	CD	_	_	_
852	min	min	NN	_	_	_
853	heat	heat	NN	_	_	_
854	shock	shock	NN	_	_	_
855	at	at	IN	_	_	_
856	45ºC	45ºc	NN	_	_	_
857	,	,	,	_	_	_
858	rep	rep	NN	GEN	_	_
859	1	1	CD	_	_	_
860	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
861	E.	E.	NNP	_	_	_
862	coli	coli	NN	_	_	_
863	ancestor	ancestor	NN	_	_	_
864	strain	strain	NN	_	_	_
865	,	,	,	_	_	_
866	30	30	CD	_	_	_
867	min	min	NN	_	_	_
868	heat	heat	NN	_	_	_
869	shock	shock	NN	_	_	_
870	at	at	IN	_	_	_
871	45ºC	45ºc	NN	_	_	_
872	,	,	,	_	_	_
873	rep	rep	NN	GEN	_	_
874	2	2	CD	_	_	_
875	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
876	E.	E.	NNP	_	_	_
877	coli	coli	NN	_	_	_
878	ancestor	ancestor	NN	_	_	_
879	strain	strain	NN	_	_	_
880	,	,	,	_	_	_
881	5	5	CD	_	_	_
882	min	min	NN	_	_	_
883	heat	heat	NN	_	_	_
884	shock	shock	NN	_	_	_
885	at	at	IN	_	_	_
886	45ºC	45ºc	NN	_	_	_
887	,	,	,	_	_	_
888	rep	rep	NN	GEN	_	_
889	1	1	CD	_	_	_
890	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
891	E.	E.	NNP	_	_	_
892	coli	coli	NN	_	_	_
893	ancestor	ancestor	NN	_	_	_
894	strain	strain	NN	_	_	_
895	,	,	,	_	_	_
896	5	5	CD	_	_	_
897	min	min	NN	_	_	_
898	heat	heat	NN	_	_	_
899	shock	shock	NN	_	_	_
900	at	at	IN	_	_	_
901	45ºC	45ºc	NN	_	_	_
902	,	,	,	_	_	_
903	rep	rep	NN	GEN	_	_
904	2	2	CD	_	_	_
905	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
906	E.	E.	NNP	_	_	_
907	coli	coli	NN	_	_	_
908	ancestor	ancestor	NN	_	_	_
909	strain	strain	NN	_	_	_
910	,	,	,	_	_	_
911	under	under	IN	_	_	_
912	37ºC	37ºc	NN	_	_	_
913	,	,	,	_	_	_
914	rep	rep	NN	GEN	_	_
915	1	1	CD	_	_	_
916	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
917	E.	E.	NNP	_	_	_
918	coli	coli	NN	_	_	_
919	ancestor	ancestor	NN	_	_	_
920	strain	strain	NN	_	_	_
921	,	,	,	_	_	_
922	under	under	IN	_	_	_
923	37ºC	37ºc	NN	_	_	_
924	,	,	,	_	_	_
925	rep	rep	NN	GEN	_	_
926	2	2	CD	_	_	_
927	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
928	E.	E.	NNP	_	_	_
929	coli	coli	NN	_	_	_
930	ancestor	ancestor	NN	_	_	_
931	strain	strain	NN	_	_	_
932	,	,	,	_	_	_
933	under	under	IN	_	_	_
934	37ºC	37ºc	NN	_	_	_
935	,	,	,	_	_	_
936	rep	rep	NN	GEN	_	_
937	3	3	CD	_	_	_
938	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
939	E.	e.	FW	_	_	_
940	coli	coli	FW	_	_	_
941	Anc	anc	NN	_	_	_
942	strain	strain	NN	_	_	_
943	,	,	,	_	_	_
944	heat	heat	NN	_	_	_
945	shock	shock	NN	_	_	_
946	,	,	,	_	_	_
947	long	long	RB	_	_	_
948	,	,	,	_	_	_
949	rep	rep	NN	GEN	_	_
950	1	1	CD	_	_	_
951	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
952	E.	e.	FW	_	_	_
953	coli	coli	FW	_	_	_
954	Anc	anc	NN	_	_	_
955	strain	strain	NN	_	_	_
956	,	,	,	_	_	_
957	heat	heat	NN	_	_	_
958	shock	shock	NN	_	_	_
959	,	,	,	_	_	_
960	long	long	RB	_	_	_
961	,	,	,	_	_	_
962	rep	rep	NN	GEN	_	_
963	2	2	CD	_	_	_
964	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
965	E.	e.	FW	_	_	_
966	coli	coli	FW	_	_	_
967	Anc	anc	NN	_	_	_
968	strain	strain	NN	_	_	_
969	,	,	,	_	_	_
970	heat	heat	NN	_	_	_
971	shock	shock	NN	_	_	_
972	,	,	,	_	_	_
973	rep	rep	NN	GEN	_	_
974	1	1	CD	_	_	_
975	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
976	E.	e.	FW	_	_	_
977	coli	coli	FW	_	_	_
978	Anc	anc	NN	_	_	_
979	strain	strain	NN	_	_	_
980	,	,	,	_	_	_
981	heat	heat	NN	_	_	_
982	shock	shock	NN	_	_	_
983	,	,	,	_	_	_
984	rep	rep	NN	GEN	_	_
985	2	2	CD	_	_	_
986	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
987	E.	e.	FW	_	_	_
988	coli	coli	FW	_	_	_
989	Anc	anc	NN	_	_	_
990	strain	strain	NN	_	_	_
991	,	,	,	_	_	_
992	regular	regular	JJ	_	_	_
993	temperature	temperature	NN	_	_	_
994	,	,	,	_	_	_
995	rep	rep	NN	GEN	_	_
996	1	1	CD	_	_	_
997	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
998	E.	e.	FW	_	_	_
999	coli	coli	FW	_	_	_
1000	Anc	anc	NN	_	_	_
1001	strain	strain	NN	_	_	_
1002	,	,	,	_	_	_
1003	regular	regular	JJ	_	_	_
1004	temperature	temperature	NN	_	_	_
1005	,	,	,	_	_	_
1006	rep	rep	NN	GEN	_	_
1007	2	2	CD	_	_	_
1008	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1009	E.	e.	FW	_	_	_
1010	coli	coli	FW	_	_	_
1011	Anc	anc	NN	_	_	_
1012	strain	strain	NN	_	_	_
1013	,	,	,	_	_	_
1014	regular	regular	JJ	_	_	_
1015	temperature	temperature	NN	_	_	_
1016	,	,	,	_	_	_
1017	rep	rep	NN	GEN	_	_
1018	3	3	CD	_	_	_
1019	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1020	Escherichia	escherichia	FW	Organism	_	_
1021	coli	coli	FW	Organism	_	_
1022	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1023	Microarray	microarray	NN	_	_	_
1024	data	datum	NNS	_	_	_
1025	were	be	VBD	_	_	_
1026	processed	process	VBN	_	_	_
1027	using	use	VBG	_	_	_
1028	custom	custom	NN	_	_	_
1029	scripts	script	NNS	_	_	_
1030	written	write	VBN	_	_	_
1031	in	in	IN	_	_	_
1032	R	r	NN	_	_	_
1033	based	base	VBN	_	_	_
1034	on	on	IN	_	_	_
1035	the	the	DT	_	_	_
1036	finite	finite	JJ	_	_	_
1037	hybridisation	hybridisation	NN	_	_	_
1038	-LRB-	-lrb-	-LRB-	_	_	_
1039	FH	fh	NN	_	_	_
1040	-RRB-	-rrb-	-RRB-	_	_	_
1041	model	model	NN	_	_	_
1042	-LRB-	-lrb-	-LRB-	_	_	_
1043	Ono	Ono	NNP	_	_	_
1044	et	et	FW	_	_	_
1045	al	al	FW	_	_	_
1046	,	,	,	_	_	_
1047	2008	2008	CD	_	_	_
1048	-RRB-	-rrb-	-RRB-	_	_	_
1049	and	and	CC	_	_	_
1050	the	the	DT	_	_	_
1051	thermodynamic	thermodynamic	JJ	_	_	_
1052	model	model	NN	_	_	_
1053	of	of	IN	_	_	_
1054	non-specific	non-specific	JJ	_	_	_
1055	binding	binding	NN	_	_	_
1056	-LRB-	-lrb-	-LRB-	_	_	_
1057	NSB	nsb	NN	_	_	_
1058	-RRB-	-rrb-	-RRB-	_	_	_
1059	on	on	IN	_	_	_
1060	short	short	JJ	_	_	_
1061	nucleotide	nucleotide	NN	_	_	_
1062	microarrays	microarray	NNS	_	_	_
1063	-LRB-	-lrb-	-LRB-	_	_	_
1064	Furusawa	Furusawa	NNP	_	_	_
1065	et	et	FW	_	_	_
1066	al	al	FW	_	_	_
1067	,	,	,	_	_	_
1068	2009	2009	CD	_	_	_
1069	-RRB-	-rrb-	-RRB-	_	_	_
1070	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	DH1ΔleuB	dh1δleub	NN	_	_	_
5	:	:	:	_	_	_
6	:	:	:	_	_	_
7	gfpuv5-kmr	gfpuv5-kmr	JJ	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
9	The	the	DT	_	_	_
10	cell	cell	NN	_	_	_
11	culture	culture	NN	_	_	_
12	was	be	VBD	_	_	_
13	put	put	VBN	_	_	_
14	into	into	IN	_	_	_
15	cold	cold	JJ	_	_	_
16	phenol-ethanol	phenol-ethanol	JJ	_	_	_
17	solution	solution	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	1	1	CD	_	_	_
20	g	g	NN	_	_	_
21	of	of	IN	_	_	_
22	phenol	phenol	NN	_	_	_
23	in	in	IN	_	_	_
24	10	10	CD	_	_	_
25	mL	ml	NN	_	_	_
26	of	of	IN	_	_	_
27	ethanol	ethanol	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	prepared	prepare	VBN	_	_	_
30	in	in	IN	_	_	_
31	advance	advance	NN	_	_	_
32	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	collected	collect	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	at	at	IN	_	_	_
8	7,000	7,000	CD	_	_	_
9	×	×	CD	_	_	_
10	g	g	NN	_	_	_
11	for	for	IN	_	_	_
12	3	3	CD	_	_	_
13	min	min	NN	_	_	_
14	at	at	IN	_	_	_
15	4	4	CD	_	_	_
16	°C	°c	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	the	the	DT	_	_	_
20	pelleted	pelleted	JJ	_	_	_
21	cells	cell	NNS	_	_	_
22	were	be	VBD	_	_	_
23	stored	store	VBN	_	_	_
24	at	at	IN	_	_	_
25	--	--	:	_	_	_
26	80	80	CD	_	_	_
27	°C	°c	NN	_	_	_
28	prior	prior	RB	_	_	_
29	to	to	TO	_	_	_
30	use	use	VB	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	normalized	normalize	VBN	_	_	_
4	data	datum	NNS	_	_	_
5	can	can	MD	GEN	_	_
6	be	be	VB	_	_	_
7	found	find	VBN	_	_	_
8	on	on	IN	_	_	_
9	the	the	DT	_	_	_
10	series	series	NN	_	_	_
11	record	record	NN	_	_	_
12	in	in	IN	_	_	_
13	the	the	DT	_	_	_
14	file	file	NN	_	_	_
15	\	\	NN	_	_	_
16	GSE61749	gse61749	NN	_	_	_
17	_	_	CD	_	_	_
18	Normalized	normalize	VBN	_	_	_
19	_	_	SYM	_	_	_
20	data.txt	data.txt	FW	_	_	_
21	\	\	FW	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	data	datum	NNS	_	_	_
3	values	value	NNS	_	_	_
4	presented	present	VBN	_	_	_
5	in	in	IN	_	_	_
6	this	this	DT	_	_	_
7	file	file	NN	_	_	_
8	are	be	VBP	_	_	_
9	log10	log10	NN	_	_	_
10	mRNA	mrna	NN	_	_	_
11	concentration	concentration	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	pM	pm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNAs	rna	NNS	_	_	_
4	were	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	an	a	DT	_	_	_
8	RNeasy	rneasy	NN	_	_	_
9	mini	minus	NNS	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	qiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	in	in	IN	_	_	_
15	accordance	accordance	NN	_	_	_
16	with	with	IN	_	_	_
17	the	the	DT	_	_	_
18	manufacturer	manufacturer	NN	_	_	_
19	's	's	POS	_	_	_
20	instructions	instruction	NNS	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	7	7	CD	_	_	_
3	h	h	NN	_	_	_
4	7HI	7HI	NNP	_	_	_
5	biofilm	biofilm	NN	_	_	_
6	cells	cell	NNS	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	7	7	CD	_	_	_
9	h	h	NN	_	_	_
10	biofilm	biofilm	NN	_	_	_
11	cells	cell	NNS	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	7	7	CD	_	_	_
14	h	h	NN	_	_	_
15	isatin	isatin	NN	_	_	_
16	biofilm	biofilm	NN	_	_	_
17	cells	cell	NNS	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	7	7	CD	_	_	_
20	h	h	NN	_	_	_
21	suspension	suspension	NN	_	_	_
22	cells	cell	NNS	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
24	EHEC	ehec	NN	_	_	_
25	LB	lb	NN	_	_	_
26	7	7	CD	_	_	_
27	h	h	NN	_	_	_
28	7HI	7HI	NNP	_	_	_
29	biofilm	biofilm	NN	_	_	_
30	cells	cell	NNS	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
32	EHEC	ehec	NN	_	_	_
33	LB	lb	NN	_	_	_
34	7	7	CD	_	_	_
35	h	h	NN	_	_	_
36	biofilm	biofilm	NN	_	_	_
37	cells	cell	NNS	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
39	EHEC	ehec	NN	_	_	_
40	LB	lb	NN	_	_	_
41	7	7	CD	_	_	_
42	h	h	NN	_	_	_
43	isatin	isatin	NN	_	_	_
44	biofilm	biofilm	NN	_	_	_
45	cells	cell	NNS	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
47	EHEC	ehec	NN	_	_	_
48	LB	lb	NN	_	_	_
49	7	7	CD	_	_	_
50	h	h	NN	_	_	_
51	suspension	suspension	NN	_	_	_
52	cells	cell	NNS	_	_	_
53	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
54	Escherichia	escherichia	FW	Organism	_	_
55	coli	coli	FW	Organism	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
57	MAS	mas	FW	_	_	_
58	5.0	5.0	CD	_	_	_
59	Expression	expression	NN	_	_	_
60	Analysis	analysis	NN	_	_	_
61	Default	Default	NNP	_	_	_
62	Setting	set	VBG	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	RNA	rna	NN	_	_	_
65	extracted	extract	VBN	_	_	_
66	from	from	IN	_	_	_
67	biofilm	biofilm	NN	_	_	_
68	cells	cell	NNS	_	_	_
69	of	of	IN	_	_	_
70	EHEC	ehec	NN	_	_	_
71	wild	wild	JJ	_	_	_
72	type	type	NN	_	_	_
73	after	after	IN	_	_	_
74	7h	7h	NN	_	_	_
75	of	of	IN	_	_	_
76	growth	growth	NN	_	_	_
77	in	in	IN	_	_	_
78	LB	lb	NN	_	_	_
79	and	and	CC	_	_	_
80	0.1	0.1	CD	_	_	_
81	%	%	NN	_	_	_
82	DMF	dmf	NN	_	_	_
83	with	with	IN	_	_	_
84	glass	glass	NN	_	_	_
85	wool	wool	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	RNA	rna	NN	_	_	_
88	extracted	extract	VBN	_	_	_
89	from	from	IN	_	_	_
90	biofilm	biofilm	NN	_	_	_
91	cells	cell	NNS	_	_	_
92	of	of	IN	_	_	_
93	EHEC	ehec	NN	_	_	_
94	wild	wild	JJ	_	_	_
95	type	type	NN	_	_	_
96	after	after	IN	_	_	_
97	7h	7h	NN	_	_	_
98	of	of	IN	_	_	_
99	growth	growth	NN	_	_	_
100	in	in	IN	_	_	_
101	LB	lb	NN	_	_	_
102	and	and	CC	_	_	_
103	1000	1000	CD	_	_	_
104	micro	micro	JJ	_	_	_
105	M	m	NN	_	_	_
106	7-hydroxyindole	7-hydroxyindole	NN	_	_	_
107	with	with	IN	_	_	_
108	glass	glass	NN	_	_	_
109	wool	wool	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	RNA	rna	NN	_	_	_
112	extracted	extract	VBN	_	_	_
113	from	from	IN	_	_	_
114	biofilm	biofilm	NN	_	_	_
115	cells	cell	NNS	_	_	_
116	of	of	IN	_	_	_
117	EHEC	ehec	NN	_	_	_
118	wild	wild	JJ	_	_	_
119	type	type	NN	_	_	_
120	after	after	IN	_	_	_
121	7h	7h	NN	_	_	_
122	of	of	IN	_	_	_
123	growth	growth	NN	_	_	_
124	in	in	IN	_	_	_
125	LB	lb	NN	_	_	_
126	and	and	CC	_	_	_
127	250	250	CD	_	_	_
128	micro	micro	JJ	_	_	_
129	M	m	NN	_	_	_
130	isatin	isatin	NN	_	_	_
131	with	with	IN	_	_	_
132	glass	glass	NN	_	_	_
133	wool	wool	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	RNA	rna	NN	_	_	_
136	extracted	extract	VBN	_	_	_
137	from	from	IN	_	_	_
138	suspension	suspension	NN	_	_	_
139	cells	cell	NNS	_	_	_
140	of	of	IN	_	_	_
141	EHEC	ehec	NN	_	_	_
142	wild	wild	JJ	_	_	_
143	type	type	NN	_	_	_
144	after	after	IN	_	_	_
145	7	7	CD	_	_	_
146	h	h	NN	_	_	_
147	of	of	IN	_	_	_
148	growth	growth	NN	_	_	_
149	in	in	IN	_	_	_
150	LB	lb	NN	_	_	_
151	and	and	CC	_	_	_
152	0.1	0.1	CD	_	_	_
153	%	%	NN	_	_	_
154	DMF	dmf	NN	_	_	_
155	with	with	IN	_	_	_
156	glass	glass	NN	_	_	_
157	wool	wool	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
159	To	to	TO	_	_	_
160	lyse	lyse	VB	_	_	_
161	the	the	DT	_	_	_
162	cells	cell	NNS	_	_	_
163	,	,	,	_	_	_
164	1.0	1.0	CD	_	_	_
165	mL	ml	NN	_	_	_
166	RLT	rlt	NN	_	_	_
167	buffer	buffer	NN	_	_	_
168	-LRB-	-lrb-	-LRB-	_	_	_
169	Qiagen	Qiagen	NNP	_	_	_
170	,	,	,	_	_	_
171	Inc.	Inc.	NNP	_	_	_
172	,	,	,	_	_	_
173	Valencia	Valencia	NNP	_	_	_
174	,	,	,	_	_	_
175	CA	CA	NNP	_	_	_
176	-RRB-	-rrb-	-RRB-	_	_	_
177	and	and	CC	_	_	_
178	0.2	0.2	CD	_	_	_
179	mL	ml	NN	_	_	_
180	0.1	0.1	CD	_	_	_
181	mm	mm	NN	_	_	_
182	zirconia	zirconia	NN	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	cDNA	cdna	NN	_	_	_
185	library	library	NN	_	_	_
186	of	of	IN	_	_	_
187	the	the	DT	_	_	_
188	nascent	nascent	JJ	_	_	_
189	RNA	rna	NN	_	_	_
190	was	be	VBD	_	_	_
191	constructed	construct	VBN	_	_	_
192	according	accord	VBG	_	_	_
193	to	to	TO	_	_	_
194	Churchman	Churchman	NNP	_	_	_
195	and	and	CC	_	_	_
196	Weissman	Weissman	NNP	_	_	_
197	,	,	,	_	_	_
198	Nature	Nature	NNP	_	_	_
199	2011	2011	CD	_	_	_
200	-LRB-	-lrb-	-LRB-	_	_	_
201	PMID	pmid	NN	_	_	_
202	:	:	:	_	_	_
203	21248844	21248844	CD	_	_	_
204	-RRB-	-rrb-	-RRB-	_	_	_
205	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Each	each	DT	_	_	_
3	tube	tube	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	cell	cell	NN	_	_	_
7	pellet	pellet	NN	_	_	_
8	stored	store	VBD	_	_	_
9	at	at	IN	_	_	_
10	-80	-80	CD	_	_	_
11	˚C	˚c	NN	_	_	_
12	was	be	VBD	_	_	_
13	resuspended	resuspend	VBN	_	_	_
14	in	in	IN	_	_	_
15	650	650	CD	_	_	_
16	ml	ml	NN	_	_	_
17	TES	tes	NN	_	_	_
18	buffer	buffer	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	10	10	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	Tris-HCl	tris-hcl	NN	_	_	_
23	,	,	,	_	_	_
24	pH	ph	NN	_	_	_
25	7.5	7.5	CD	_	_	_
26	,	,	,	_	_	_
27	1	1	CD	_	_	_
28	mM	mm	NN	KWSUPP	_	_
29	EDTA	edta	NN	_	_	_
30	,	,	,	_	_	_
31	100	100	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	NaCl	nacl	NN	_	_	_
34	,	,	,	_	_	_
35	0.1	0.1	CD	_	_	_
36	%	%	NN	_	_	_
37	TritonX	tritonx	NN	_	_	_
38	100	100	CD	_	_	_
39	,	,	,	_	_	_
40	0.3	0.3	CD	_	_	_
41	mM	mm	NN	KWSUPP	_	_
42	PMSF	pmsf	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	at	at	IN	_	_	_
45	room	room	NN	_	_	_
46	temperature	temperature	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	RT	rt	NN	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cell	cell	NN	_	_	_
3	suspension	suspension	NN	_	_	_
4	was	be	VBD	_	_	_
5	mixed	mix	VBN	_	_	_
6	with	with	IN	_	_	_
7	100	100	CD	_	_	_
8	kU	ku	NN	_	_	_
9	Ready-Lyse	Ready-Lyse	NNP	_	_	_
10	Lysozyme	Lysozyme	NNP	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Epicentre	Epicentre	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	and	and	CC	_	_	_
15	50	50	CD	_	_	_
16	µg	µg	NN	_	_	_
17	RNaseA	rnasea	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Sigma	Sigma	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	and	and	CC	_	_	_
22	incubated	incubate	VBN	_	_	_
23	for	for	IN	_	_	_
24	5	5	CD	_	_	_
25	min	min	NN	_	_	_
26	,	,	,	_	_	_
27	allowing	allow	VBG	_	_	_
28	rapid	rapid	JJ	_	_	_
29	cell	cell	NN	_	_	_
30	lysis	lysis	NN	_	_	_
31	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	digest	digest	VB	_	_	_
3	the	the	DT	_	_	_
4	nucleoide	nucleoide	NN	_	_	_
5	,	,	,	_	_	_
6	62.5	62.5	CD	_	_	_
7	U	U	NNP	_	_	_
8	DNaseI	dnasei	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Roche	Roche	NNP	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	and	and	CC	_	_	_
13	250	250	CD	_	_	_
14	µg	µg	NN	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	Escherichia	escherichia	FW	Organism	_	_
17	coli	coli	FW	Organism	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	genotype	genotype	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	molecule	molecule	NN	_	_	_
22	subtype	subtype	NN	_	_	_
23	:	:	:	_	_	_
24	nascent	nascent	JJ	_	_	_
25	3	3	CD	_	_	_
26	'	'	''	_	_	_
27	RNA	rna	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Pause	pause	NN	_	_	_
30	sites	site	NNS	_	_	_
31	in	in	IN	_	_	_
32	E.	e.	FW	_	_	_
33	coli	coli	FW	_	_	_
34	wild-type	wild-type	JJ	_	_	_
35	strain	strain	NN	_	_	_
36	identified	identify	VBN	_	_	_
37	by	by	IN	_	_	_
38	RNET-seq	rnet-seq	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Pause	pause	NN	_	_	_
41	sites	site	NNS	_	_	_
42	in	in	IN	_	_	_
43	E.	e.	FW	_	_	_
44	coli	coli	FW	_	_	_
45	ΔgreAB	δgreab	NN	_	_	_
46	strain	strain	NN	_	_	_
47	identified	identify	VBN	_	_	_
48	by	by	IN	_	_	_
49	RNET-seq	rnet-seq	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	RNA-Seq	rna-seq	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
53	The	the	DT	_	_	_
54	200	200	CD	_	_	_
55	ml	ml	NN	_	_	_
56	eluate	eluate	NN	_	_	_
57	from	from	IN	_	_	_
58	the	the	DT	_	_	_
59	Ni-NTA	ni-nta	NN	_	_	_
60	agarose	agarose	NN	_	_	_
61	was	be	VBD	_	_	_
62	mixed	mix	VBN	_	_	_
63	with	with	IN	_	_	_
64	equal	equal	JJ	_	_	_
65	volume	volume	NN	_	_	_
66	of	of	IN	_	_	_
67	pre-warmed	pre-warmed	JJ	_	_	_
68	PCI	pci	NN	_	_	_
69	and	and	CC	_	_	_
70	incubated	incubate	VBN	_	_	_
71	for	for	IN	_	_	_
72	2	2	CD	_	_	_
73	min	min	NN	_	_	_
74	at	at	IN	_	_	_
75	70	70	CD	_	_	_
76	˚C	˚c	NN	_	_	_
77	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	mixture	mixture	NN	_	_	_
3	was	be	VBD	_	_	_
4	centrifuged	centrifuge	VBN	_	_	_
5	,	,	,	_	_	_
6	and	and	CC	_	_	_
7	RNA	rna	NN	_	_	_
8	and	and	CC	_	_	_
9	DNA	dna	NN	_	_	_
10	were	be	VBD	_	_	_
11	precipitated	precipitate	VBN	_	_	_
12	with	with	IN	_	_	_
13	isopropanol	isopropanol	NN	_	_	_
14	from	from	IN	_	_	_
15	the	the	DT	_	_	_
16	supernatant	supernatant	NN	_	_	_
17	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	was	be	VBD	_	_	_
4	dissolved	dissolve	VBN	_	_	_
5	in	in	IN	_	_	_
6	30	30	CD	_	_	_
7	ml	ml	NN	_	_	_
8	DNase	dnase	NN	_	_	_
9	I	i	CD	_	_	_
10	buffer	buffer	NN	_	_	_
11	with	with	IN	_	_	_
12	5	5	CD	_	_	_
13	U	U	NNP	_	_	_
14	DNaseI	dnasei	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Takara	Takara	NNP	_	_	_
17	Bio	Bio	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	and	and	CC	_	_	_
20	20	20	CD	_	_	_
21	U	U	NNP	_	_	_
22	SUPERase	SUPERase	NNP	_	_	_
23	,	,	,	_	_	_
24	incubated	incubate	VBN	_	_	_
25	for	for	IN	_	_	_
26	10	10	CD	_	_	_
27	min	min	NN	_	_	_
28	at	at	IN	_	_	_
29	RT.	RT.	NNP	_	_	_
30	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	separated	separate	VBN	_	_	_
4	from	from	IN	_	_	_
5	the	the	DT	_	_	_
6	digested	digest	VBN	_	_	_
7	DNA	dna	NN	_	_	_
8	by	by	IN	_	_	_
9	the	the	DT	_	_	_
10	PCI	pci	NN	_	_	_
11	extraction	extraction	NN	_	_	_
12	and	and	CC	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	precipitated	precipitate	VBN	_	_	_
16	with	with	IN	_	_	_
17	isopropanol	isopropanol	NN	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	was	be	VBD	_	_	_
4	dissolved	dissolve	VBN	_	_	_
5	in	in	IN	_	_	_
6	diethylpyrocarbonate-treated	diethylpyrocarbonate-treated	JJ	_	_	_
7	water	water	NN	_	_	_
8	and	and	CC	_	_	_
9	used	use	VBN	_	_	_
10	for	for	IN	_	_	_
11	cDNA	cdna	NN	_	_	_
12	synthesis	synthesis	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	~	~	NN	_	_	_
8	300	300	CD	_	_	_
9	ml	ml	NN	_	_	_
10	LB	lb	NN	MED	_	_
11	broth	broth	NN	MED	_	_
12	+25	+25	CD	_	_	_
13	mg	mg	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	The	the	DT	_	_	_
16	fastq	fastq	NN	_	_	_
17	files	file	NNS	_	_	_
18	of	of	IN	_	_	_
19	36-bp	36-bp	JJ	_	_	_
20	sequenced	sequence	VBN	_	_	_
21	reads	read	VBZ	_	_	_
22	were	be	VBD	_	_	_
23	generated	generate	VBN	_	_	_
24	with	with	IN	_	_	_
25	the	the	DT	_	_	_
26	CASAVA	CASAVA	NNP	_	_	_
27	v1	v1	NN	_	_	_
28	.8	.8	CD	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Illumina	Illumina	NNP	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	the	the	DT	_	_	_
3	bulk	bulk	NN	_	_	_
4	RNET-seq	rnet-seq	NN	_	_	_
5	analysis	analysis	NN	_	_	_
6	,	,	,	_	_	_
7	the	the	DT	_	_	_
8	specific	specific	JJ	_	_	_
9	adapter	adapter	NN	_	_	_
10	sequences	sequence	NNS	_	_	_
11	were	be	VBD	_	_	_
12	trimmed	trim	VBN	_	_	_
13	with	with	IN	_	_	_
14	the	the	DT	_	_	_
15	Trimmomatic	trimmomatic	JJ	_	_	_
16	v0	v0	NN	_	_	_
17	.25	.25	CD	_	_	_
18	to	to	TO	_	_	_
19	obtain	obtain	VB	_	_	_
20	reads	read	VBZ	_	_	_
21	≥	≥	SYM	_	_	_
22	21-nt	21-nt	CD	_	_	_
23	from	from	IN	_	_	_
24	the	the	DT	_	_	_
25	5	5	CD	_	_	_
26	'	'	''	_	_	_
27	end	end	NN	_	_	_
28	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	reads	read	VBZ	_	_	_
3	≥	≥	SYM	_	_	_
4	21-nt	21-nt	JJ	_	_	_
5	were	be	VBD	_	_	_
6	mapped	map	VBN	_	_	_
7	to	to	TO	_	_	_
8	the	the	DT	_	_	_
9	reference	reference	NN	_	_	_
10	genome	genome	NN	_	_	_
11	of	of	IN	_	_	_
12	E.	e.	FW	_	_	_
13	coli	coli	FW	_	_	_
14	K-12	k-12	NN	_	_	_
15	strain	strain	NN	_	_	_
16	W3110	w3110	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	NC	nc	NN	_	_	_
19	_	_	CD	_	_	_
20	007779.1	007779.1	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	using	use	VBG	_	_	_
23	the	the	DT	_	_	_
24	Bowtie2	bowtie2	NN	_	_	_
25	v2	v2	NN	_	_	_
26	.1.0	.1.0	CD	_	_	_
27	with	with	IN	_	_	_
28	the	the	DT	_	_	_
29	default	default	NN	_	_	_
30	parameter	parameter	NN	_	_	_
31	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	gene	gene	NN	_	_	_
3	annotation	annotation	NN	_	_	_
4	file	file	NN	_	_	_
5	of	of	IN	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	W3110	w3110	NN	_	_	_
9	was	be	VBD	_	_	_
10	downloaded	download	VBN	_	_	_
11	from	from	IN	_	_	_
12	the	the	DT	_	_	_
13	ftp	ftp	NN	GEN	_	_
14	server	server	NN	_	_	_
15	of	of	IN	_	_	_
16	Ensembl	ensembl	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	processed	process	VBN	_	_	_
4	data	datum	NNS	_	_	_
5	file	file	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	csv	csv	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	includes	include	VBZ	_	_	_
10	information	information	NN	_	_	_
11	about	about	IN	_	_	_
12	genomic	genomic	JJ	_	_	_
13	position	position	NN	_	_	_
14	,	,	,	_	_	_
15	reference	reference	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
17	To	to	TO	_	_	_
18	analyze	analyze	VB	_	_	_
19	RNAP	rnap	NN	_	_	_
20	pausing	pause	VBG	_	_	_
21	on	on	IN	_	_	_
22	the	the	DT	_	_	_
23	E.	e.	FW	_	_	_
24	coli	coli	FW	_	_	_
25	chromosome	chromosome	NN	_	_	_
26	,	,	,	_	_	_
27	we	we	PRP	_	_	_
28	counted	count	VBD	_	_	_
29	the	the	DT	_	_	_
30	number	number	NN	_	_	_
31	of	of	IN	_	_	_
32	reads	read	VBZ	_	_	_
33	at	at	IN	_	_	_
34	every	every	DT	_	_	_
35	genomic	genomic	JJ	_	_	_
36	nucleotide	nucleotide	NN	_	_	_
37	position	position	NN	_	_	_
38	using	use	VBG	_	_	_
39	the	the	DT	_	_	_
40	mpileup	mpileup	NN	_	_	_
41	command	command	NN	_	_	_
42	of	of	IN	_	_	_
43	SAM	SAM	NNP	_	_	_
44	tools	tool	NNS	_	_	_
45	v0	v0	VBP	_	_	_
46	.1.18	.1.18	CD	_	_	_
47	with	with	IN	_	_	_
48	--	--	:	_	_	_
49	A	a	DT	_	_	_
50	--	--	:	_	_	_
51	B	b	NN	_	_	_
52	parameters	parameter	NNS	_	_	_
53	.	.	.	_	_	_

1	Pausing	pause	VBG	_	_	_
2	sites	site	NNS	_	_	_
3	were	be	VBD	_	_	_
4	defined	define	VBN	_	_	_
5	P	p	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	φ	φ	NN	_	_	_
8	,	,	,	_	_	_
9	δ	δ	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	,	,	,	_	_	_
12	where	where	WRB	_	_	_
13	φ	φ	NN	_	_	_
14	is	be	VBZ	_	_	_
15	the	the	DT	_	_	_
16	minimal	minimal	JJ	_	_	_
17	fraction	fraction	NN	_	_	_
18	of	of	IN	_	_	_
19	having	have	VBG	_	_	_
20	3	3	CD	_	_	_
21	'	'	''	_	_	_
22	RNA	rna	NN	_	_	_
23	ends	end	VBZ	_	_	_
24	in	in	IN	_	_	_
25	the	the	DT	_	_	_
26	mapped	map	VBN	_	_	_
27	reads	read	VBZ	_	_	_
28	and	and	CC	_	_	_
29	δ	δ	NN	_	_	_
30	is	be	VBZ	_	_	_
31	the	the	DT	_	_	_
32	minimal	minimal	JJ	_	_	_
33	read	read	NN	_	_	_
34	depth	depth	NN	_	_	_
35	for	for	IN	_	_	_
36	any	any	DT	_	_	_
37	genomic	genomic	JJ	_	_	_
38	position	position	NN	_	_	_
39	.	.	.	_	_	_

1	We	we	PRP	_	_	_
2	chose	choose	VBD	_	_	_
3	δ	δ	NN	_	_	_
4	to	to	TO	_	_	_
5	be	be	VB	_	_	_
6	100	100	CD	_	_	_
7	for	for	IN	_	_	_
8	WT	WT	NNP	_	_	_
9	and	and	CC	_	_	_
10	160	160	CD	_	_	_
11	for	for	IN	_	_	_
12	ΔgreAB	δgreab	NN	_	_	_
13	,	,	,	_	_	_
14	which	which	WDT	_	_	_
15	normalized	normalize	VBD	_	_	_
16	these	these	DT	_	_	_
17	respective	respective	JJ	_	_	_
18	numbers	number	NNS	_	_	_
19	for	for	IN	_	_	_
20	each	each	DT	_	_	_
21	strain	strain	NN	_	_	_
22	since	since	IN	_	_	_
23	there	there	EX	_	_	_
24	were	be	VBD	_	_	_
25	1.6-fold	1.6-fold	RB	_	_	_
26	more	more	RBR	_	_	_
27	total	total	JJ	_	_	_
28	reads	read	VBZ	_	_	_
29	in	in	IN	_	_	_
30	the	the	DT	_	_	_
31	ΔgreAB	δgreab	NN	_	_	_
32	strain	strain	NN	_	_	_
33	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	high	high	JJ	_	_	_
3	φ	φ	NN	_	_	_
4	parameter	parameter	NN	_	_	_
5	allowed	allow	VBD	_	_	_
6	us	we	PRP	_	_	_
7	to	to	TO	_	_	_
8	define	define	VB	_	_	_
9	a	a	DT	_	_	_
10	reliable	reliable	JJ	_	_	_
11	pause-inducing	pause-inducing	JJ	_	_	_
12	element	element	NN	_	_	_
13	for	for	IN	_	_	_
14	WT	WT	NNP	_	_	_
15	or	or	CC	_	_	_
16	ΔgreAB	δgreab	NN	_	_	_
17	cells	cell	NNS	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	W3110	w3110	NN	_	_	_
3	rpoC-6xHis	rpoc-6xhis	NN	_	_	_
4	:	:	:	_	_	_
5	:	:	:	_	_	_
6	kan	kan	FW	_	_	_
7	gal490	gal490	FW	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	W3110	w3110	NN	_	_	_
10	rpoC-6xHis	rpoc-6xhis	NN	_	_	_
11	:	:	:	_	_	_
12	:	:	:	_	_	_
13	kan	kan	NN	_	_	_
14	greA	grea	NN	GEN	_	_
15	:	:	:	_	_	_
16	:	:	:	_	_	_
17	tet	tet	NN	_	_	_
18	,	,	,	_	_	_
19	greB	greb	NN	GEN	_	_
20	:	:	:	_	_	_
21	:	:	:	_	_	_
22	amp	amp	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	10	10	CD	_	_	_
25	μg	μg	NN	_	_	_
26	of	of	IN	_	_	_
27	total	total	JJ	_	_	_
28	RNA	rna	NN	_	_	_
29	sample	sample	NN	_	_	_
30	was	be	VBD	_	_	_
31	subjected	subject	VBN	_	_	_
32	to	to	TO	_	_	_
33	purification	purification	NN	_	_	_
34	for	for	IN	_	_	_
35	discarding	discard	VBG	_	_	_
36	rRNA	rrna	NN	_	_	_
37	via	via	IN	_	_	_
38	the	the	DT	_	_	_
39	MICROBExpress	microbexpress	NN	_	_	_
40	kit	kit	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	Ambion	ambion	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	according	accord	VBG	_	_	_
45	to	to	TO	_	_	_
46	the	the	DT	_	_	_
47	manufacturer	manufacturer	NN	_	_	_
48	's	's	POS	_	_	_
49	protocol	protocol	NN	_	_	_
50	.	.	.	_	_	_

1	Following	follow	VBG	_	_	_
2	purification	purification	NN	_	_	_
3	,	,	,	_	_	_
4	the	the	DT	_	_	_
5	RNA	rna	NN	_	_	_
6	was	be	VBD	_	_	_
7	interrupted	interrupt	VBN	_	_	_
8	into	into	IN	_	_	_
9	short	short	JJ	_	_	_
10	fragments	fragment	NNS	_	_	_
11	using	use	VBG	_	_	_
12	divalent	divalent	JJ	_	_	_
13	cations	cation	NNS	_	_	_
14	under	under	IN	_	_	_
15	elevated	elevated	JJ	_	_	_
16	temperature	temperature	NN	_	_	_
17	and	and	CC	_	_	_
18	the	the	DT	_	_	_
19	short	short	JJ	_	_	_
20	fragments	fragment	NNS	_	_	_
21	were	be	VBD	_	_	_
22	used	use	VBN	_	_	_
23	for	for	IN	_	_	_
24	the	the	DT	_	_	_
25	cDNA	cdna	NN	_	_	_
26	synthesis	synthesis	NN	_	_	_
27	using	use	VBG	_	_	_
28	a	a	DT	_	_	_
29	SuperScript	SuperScript	NNP	_	_	_
30	Double-Stranded	Double-Stranded	NNP	_	_	_
31	cDNA	cdna	NN	_	_	_
32	Synthesis	synthesis	NN	_	_	_
33	Kit	kit	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Invitrogen	invitrogen	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	according	accord	VBG	_	_	_
38	to	to	TO	_	_	_
39	the	the	DT	_	_	_
40	manufacturer	manufacturer	NN	_	_	_
41	's	's	POS	_	_	_
42	instructions	instruction	NNS	_	_	_
43	.	.	.	_	_	_

1	These	these	DT	_	_	_
2	cDNA	cdna	NN	_	_	_
3	fragments	fragment	NNS	_	_	_
4	were	be	VBD	_	_	_
5	purified	purify	VBN	_	_	_
6	with	with	IN	_	_	_
7	a	a	DT	_	_	_
8	QIAquick	qiaquick	NN	_	_	_
9	PCR	pcr	NN	_	_	_
10	purification	purification	NN	_	_	_
11	kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Qiagen	qiagen	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	and	and	CC	_	_	_
17	then	then	RB	_	_	_
18	went	go	VBD	_	_	_
19	through	through	IN	_	_	_
20	end	end	NN	_	_	_
21	reparation	reparation	NN	_	_	_
22	,	,	,	_	_	_
23	adding	add	VBG	_	_	_
24	poly	poly	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	A	a	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	and	and	CC	_	_	_
29	ligation	ligation	NN	_	_	_
30	of	of	IN	_	_	_
31	sequencing	sequencing	NN	_	_	_
32	adaptors	adaptor	NNS	_	_	_
33	.	.	.	_	_	_

1	These	these	DT	_	_	_
2	products	product	NNS	_	_	_
3	were	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	with	with	IN	_	_	_
6	agarose	agarose	NN	_	_	_
7	gel	gel	NN	_	_	_
8	electrophoresis	electrophoresis	NN	_	_	_
9	and	and	CC	_	_	_
10	fragments	fragment	NNS	_	_	_
11	in	in	IN	_	_	_
12	the	the	DT	_	_	_
13	size	size	NN	_	_	_
14	of	of	IN	_	_	_
15	200-250	200-250	CD	_	_	_
16	bp	bp	NN	_	_	_
17	were	be	VBD	_	_	_
18	selected	select	VBN	_	_	_
19	for	for	IN	_	_	_
20	PCR	pcr	NN	_	_	_
21	amplification	amplification	NN	_	_	_
22	to	to	TO	_	_	_
23	construct	construct	VB	_	_	_
24	the	the	DT	_	_	_
25	cDNA	cdna	NN	_	_	_
26	library	library	NN	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	All	all	PDT	_	_	_
3	those	those	DT	_	_	_
4	uniquely	uniquely	RB	_	_	_
5	mapped	map	VBN	_	_	_
6	reads	read	VBZ	_	_	_
7	were	be	VBD	_	_	_
8	used	use	VBN	_	_	_
9	to	to	TO	_	_	_
10	calculate	calculate	VB	_	_	_
11	the	the	DT	_	_	_
12	gene	gene	NN	_	_	_
13	expression	expression	NN	_	_	_
14	level	level	NN	_	_	_
15	by	by	IN	_	_	_
16	the	the	DT	_	_	_
17	RPKM	rpkm	NN	_	_	_
18	method	method	NN	_	_	_
19	,	,	,	_	_	_
20	which	which	WDT	_	_	_
21	is	be	VBZ	_	_	_
22	able	able	JJ	_	_	_
23	to	to	TO	_	_	_
24	eliminate	eliminate	VB	_	_	_
25	the	the	DT	_	_	_
26	influence	influence	NN	_	_	_
27	of	of	IN	_	_	_
28	different	different	JJ	_	_	_
29	gene	gene	NN	_	_	_
30	length	length	NN	_	_	_
31	and	and	CC	_	_	_
32	sequencing	sequencing	NN	_	_	_
33	discrepancy	discrepancy	NN	_	_	_
34	on	on	IN	_	_	_
35	the	the	DT	_	_	_
36	calculation	calculation	NN	_	_	_
37	of	of	IN	_	_	_
38	gene	gene	NN	_	_	_
39	expression	expression	NN	_	_	_
40	and	and	CC	_	_	_
41	thus	thus	RB	_	_	_
42	the	the	DT	_	_	_
43	calculated	calculate	VBN	_	_	_
44	gene	gene	NN	_	_	_
45	expression	expression	NN	_	_	_
46	level	level	NN	_	_	_
47	can	can	MD	GEN	_	_
48	be	be	VB	_	_	_
49	directly	directly	RB	_	_	_
50	used	use	VBN	_	_	_
51	for	for	IN	_	_	_
52	comparing	compare	VBG	_	_	_
53	the	the	DT	_	_	_
54	difference	difference	NN	_	_	_
55	of	of	IN	_	_	_
56	gene	gene	NN	_	_	_
57	expression	expression	NN	_	_	_
58	among	among	IN	_	_	_
59	samples	sample	NNS	_	_	_
60	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Bacterium	Bacterium	NNP	_	_	_
3	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
4	Base	Base	NNP	_	_	_
5	calling	call	VBG	_	_	_
6	performed	perform	VBN	_	_	_
7	using	use	VBG	_	_	_
8	Illumina	Illumina	NNP	_	_	_
9	GA	GA	NNP	_	_	_
10	pipeline	pipeline	NN	_	_	_
11	1.6	1.6	CD	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	cas	ca	NNS	_	_	_
3	_	_	VBP	_	_	_
4	RNAA	rnaa	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	con	con	NN	_	_	_
7	_	_	CD	_	_	_
8	RNAA	rnaa	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Escherichia	escherichia	FW	Organism	_	_
11	coli	coli	FW	Organism	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	Genome	Genome	NNP	_	_	_
14	_	_	NNP	_	_	_
15	build	build	VB	_	_	_
16	:	:	:	_	_	_
17	ASM666v1	asm666v1	NN	_	_	_
18	;	;	:	_	_	_
19	NC	NC	NNP	_	_	_
20	_	_	NNP	_	_	_
21	002655.2	002655.2	CD	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	In	in	IN	_	_	_
24	order	order	NN	_	_	_
25	to	to	TO	_	_	_
26	generate	generate	VB	_	_	_
27	the	the	DT	_	_	_
28	VBNC	vbnc	JJ	_	_	_
29	state	state	NN	_	_	_
30	in	in	IN	_	_	_
31	E.	e.	FW	_	_	_
32	coli	coli	FW	_	_	_
33	O157	o157	NN	_	_	_
34	:	:	:	_	_	_
35	H7	h7	NN	_	_	_
36	,	,	,	_	_	_
37	20	20	CD	_	_	_
38	mL	ml	NN	_	_	_
39	of	of	IN	_	_	_
40	the	the	DT	_	_	_
41	exponential-phase	exponential-phase	NN	_	_	_
42	cell	cell	NN	_	_	_
43	suspensions	suspension	NNS	_	_	_
44	in	in	IN	_	_	_
45	a	a	DT	_	_	_
46	50	50	CD	_	_	_
47	mL	ml	NN	_	_	_
48	sterile	sterile	JJ	_	_	_
49	glass	glass	NN	_	_	_
50	tube	tube	NN	_	_	_
51	was	be	VBD	_	_	_
52	treated	treat	VBN	_	_	_
53	by	by	IN	_	_	_
54	HPCD	hpcd	NN	_	_	_
55	at	at	IN	_	_	_
56	5	5	CD	_	_	_
57	MPa	mpa	NN	_	_	_
58	and	and	CC	_	_	_
59	25	25	CD	_	_	_
60	℃	℃	NN	_	_	_
61	for	for	IN	_	_	_
62	40	40	CD	_	_	_
63	min	min	NN	_	_	_
64	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	strain	strain	NN	_	_	_
5	:	:	:	_	_	_
6	O157	o157	NN	_	_	_
7	:	:	:	_	_	_
8	H7	h7	NN	_	_	_
9	NCTC	nctc	NN	_	_	_
10	12900	12900	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	Supplementary	supplementary	JJ	_	_	_
13	_	_	NN	_	_	_
14	files	file	NNS	_	_	_
15	_	_	IN	_	_	_
16	format	format	NN	_	_	_
17	_	_	NN	_	_	_
18	and	and	CC	_	_	_
19	_	_	NN	_	_	_
20	content	content	NN	_	_	_
21	:	:	:	_	_	_
22	Microsoft	Microsoft	NNP	_	_	_
23	excel	excel	VB	_	_	_
24	spreadsheet	spreadsheet	NN	_	_	_
25	files	file	NNS	_	_	_
26	include	include	VBP	_	_	_
27	RPKM	rpkm	NN	_	_	_
28	values	value	NNS	_	_	_
29	for	for	IN	_	_	_
30	each	each	DT	_	_	_
31	gene	gene	NN	_	_	_
32	of	of	IN	_	_	_
33	sample	sample	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
35	The	the	DT	_	_	_
36	clean	clean	JJ	_	_	_
37	reads	read	VBZ	_	_	_
38	obtained	obtain	VBN	_	_	_
39	were	be	VBD	_	_	_
40	aligned	align	VBN	_	_	_
41	to	to	TO	_	_	_
42	the	the	DT	_	_	_
43	genome	genome	NN	_	_	_
44	sequence	sequence	NN	_	_	_
45	of	of	IN	_	_	_
46	E.	e.	FW	_	_	_
47	coli	coli	FW	_	_	_
48	O157	o157	NN	_	_	_
49	:	:	:	_	_	_
50	H7	h7	NN	_	_	_
51	EDL933	edl933	NN	_	_	_
52	using	use	VBG	_	_	_
53	SOAP2	soap2	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
55	The	the	DT	_	_	_
56	raw	raw	JJ	_	_	_
57	reads	read	VBZ	_	_	_
58	were	be	VBD	_	_	_
59	filtered	filtered	VBN	_	_	_
60	for	for	IN	_	_	_
61	removing	remove	VBG	_	_	_
62	dirty	dirty	JJ	_	_	_
63	raw	raw	JJ	_	_	_
64	reads	read	VBZ	_	_	_
65	which	which	WDT	_	_	_
66	contain	contain	VBP	_	_	_
67	adapters	adapter	NNS	_	_	_
68	,	,	,	_	_	_
69	unknown	unknown	JJ	_	_	_
70	or	or	CC	_	_	_
71	low	low	JJ	_	_	_
72	quality	quality	NN	_	_	_
73	bases	basis	NNS	_	_	_
74	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	strain	strain	NN	_	_	_
4	was	be	VBD	_	_	_
5	stocked	stock	VBN	_	_	_
6	in	in	IN	_	_	_
7	tryptic	tryptic	JJ	_	_	_
8	soy	soy	NN	_	_	_
9	broth	broth	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	TSB	tsb	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	with	with	IN	_	_	_
14	25	25	CD	_	_	_
15	%	%	NN	_	_	_
16	glycerol	glycerol	NN	SUPP	_	_
17	at	at	IN	_	_	_
18	-80	-80	CD	_	_	_
19	℃	℃	NN	_	_	_
20	,	,	,	_	_	_
21	and	and	CC	_	_	_
22	was	be	VBD	_	_	_
23	activated	activate	VBN	_	_	_
24	by	by	IN	_	_	_
25	streaking	streak	VBG	_	_	_
26	onto	onto	IN	_	_	_
27	TSA	TSA	NNP	_	_	_
28	plate	plate	NN	_	_	_
29	and	and	CC	_	_	_
30	incubating	incubate	VBG	_	_	_
31	at	at	IN	_	_	_
32	37	37	CD	_	_	_
33	℃	℃	NN	_	_	_
34	for	for	IN	_	_	_
35	24	24	CD	_	_	_
36	h.	h.	NN	_	_	_
37	And	and	CC	_	_	_
38	then	then	RB	_	_	_
39	,	,	,	_	_	_
40	a	a	DT	_	_	_
41	single	single	JJ	_	_	_
42	colony	colony	NN	_	_	_
43	was	be	VBD	_	_	_
44	picked	pick	VBN	_	_	_
45	and	and	CC	_	_	_
46	used	use	VBN	_	_	_
47	to	to	TO	_	_	_
48	inoculate	inoculate	VB	_	_	_
49	TSB	TSB	NNP	_	_	_
50	and	and	CC	_	_	_
51	incubated	incubate	VBN	_	_	_
52	at	at	IN	_	_	_
53	37	37	CD	_	_	_
54	℃	℃	NN	_	_	_
55	for	for	IN	_	_	_
56	12	12	CD	_	_	_
57	h	h	NN	_	_	_
58	with	with	IN	_	_	_
59	shaking	shake	VBG	_	_	_
60	at	at	IN	_	_	_
61	200	200	CD	_	_	_
62	rpm	rpm	NN	_	_	_
63	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	overnight	overnight	JJ	_	_	_
3	culture	culture	NN	_	_	_
4	was	be	VBD	_	_	_
5	transferred	transfer	VBN	_	_	_
6	to	to	TO	_	_	_
7	TSB	tsb	NN	_	_	_
8	at	at	IN	_	_	_
9	a	a	DT	_	_	_
10	dilution	dilution	NN	_	_	_
11	of	of	IN	_	_	_
12	1:100	1:100	CD	_	_	_
13	and	and	CC	_	_	_
14	grew	grow	VBD	_	_	_
15	to	to	TO	_	_	_
16	the	the	DT	_	_	_
17	exponential	exponential	JJ	GrowthPhase	_	_
18	phase	phase	NN	GrowthPhase	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	OD550	od550	NN	_	_	_
21	=	=	JJ	_	_	_
22	0.93	0.93	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	from	from	IN	_	_	_
7	the	the	DT	_	_	_
8	VBNC	vbnc	NN	_	_	_
9	cells	cell	NNS	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	exponential-phase	exponential-phase	NN	_	_	_
13	cells	cell	NNS	_	_	_
14	using	use	VBG	_	_	_
15	TRIzol	trizol	NN	_	_	_
16	reagent	reagent	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Invitrogen	invitrogen	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	according	accord	VBG	_	_	_
21	to	to	TO	_	_	_
22	the	the	DT	_	_	_
23	manufacturer	manufacturer	NN	_	_	_
24	's	's	POS	_	_	_
25	instructions	instruction	NNS	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	RNA	rna	NN	_	_	_
3	samples	sample	NNS	_	_	_
4	were	be	VBD	_	_	_
5	treated	treat	VBN	_	_	_
6	with	with	IN	_	_	_
7	DNase	dnase	NN	_	_	_
8	Ⅰ	ⅰ	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Invitrogen	invitrogen	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	to	to	TO	_	_	_
13	remove	remove	VB	_	_	_
14	residual	residual	JJ	_	_	_
15	genomic	genomic	JJ	_	_	_
16	DNA	dna	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	None	none	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	treatment	treatment	NN	_	_	_
7	:	:	:	_	_	_
8	Treated	treat	VBN	_	_	_
9	by	by	IN	_	_	_
10	HPCD	hpcd	NN	_	_	_
11	at	at	IN	_	_	_
12	5	5	CD	_	_	_
13	MPa	mpa	NN	_	_	_
14	and	and	CC	_	_	_
15	25	25	CD	_	_	_
16	℃	℃	NN	_	_	_
17	for	for	IN	_	_	_
18	40	40	CD	_	_	_
19	min	min	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	bacterial	bacterial	JJ	_	_	_
22	cells	cell	NNS	_	_	_
23	grown	grow	VBN	_	_	_
24	to	to	TO	_	_	_
25	OD600	od600	NN	_	_	_
26	=	=	JJ	_	_	_
27	0.5	0.5	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Bacterial	bacterial	JJ	_	_	_
30	strains	strain	NNS	_	_	_
31	were	be	VBD	_	_	_
32	grown	grow	VBN	_	_	_
33	in	in	IN	_	_	_
34	LB	lb	NN	_	_	_
35	.	.	.	_	_	_

1	Overnight	overnight	JJ	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	diluted	dilute	VBN	_	_	_
5	1:100	1:100	CD	_	_	_
6	in	in	IN	_	_	_
7	fresh	fresh	JJ	_	_	_
8	LB	lb	NN	_	_	_
9	and	and	CC	_	_	_
10	grown	grow	VBN	_	_	_
11	at	at	IN	_	_	_
12	37	37	CD	_	_	_
13	°C	°c	NN	_	_	_
14	with	with	IN	_	_	_
15	shaking	shake	VBG	_	_	_
16	to	to	TO	_	_	_
17	an	a	DT	_	_	_
18	OD600	od600	NN	_	_	_
19	=	=	JJ	_	_	_
20	0.5	0.5	CD	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	GPR	gpr	NN	_	_	_
6	files	file	NNS	_	_	_
7	were	be	VBD	_	_	_
8	analyzed	analyze	VBN	_	_	_
9	further	further	RB	_	_	_
10	with	with	IN	_	_	_
11	Acuity	acuity	NN	_	_	_
12	4.0	4.0	CD	_	_	_
13	software	software	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Molecular	molecular	JJ	_	_	_
16	Devices	Devices	NNPS	_	_	_
17	,	,	,	_	_	_
18	USA	USA	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	starting	start	VBG	_	_	_
21	with	with	IN	_	_	_
22	lowess	lowess	NN	_	_	_
23	normalization	normalization	NN	_	_	_
24	.	.	.	_	_	_

1	Normalized	normalize	VBN	_	_	_
2	log2	log2	NN	_	_	_
3	ratio	ratio	NN	_	_	_
4	data	datum	NNS	_	_	_
5	from	from	IN	_	_	_
6	biological	biological	JJ	_	_	_
7	replicates	replicate	VBZ	_	_	_
8	and	and	CC	_	_	_
9	technical	technical	JJ	_	_	_
10	replicates	replicate	VBZ	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	dye	dye	VB	_	_	_
13	swap	swap	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	were	be	VBD	_	_	_
16	averaged	average	VBN	_	_	_
17	and	and	CC	_	_	_
18	the	the	DT	_	_	_
19	statistical	statistical	JJ	_	_	_
20	significance	significance	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	p-value	p-value	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	was	be	VBD	_	_	_
25	calculated	calculate	VBN	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	recA730	reca730	NN	_	_	_
3	_	_	CD	_	_	_
4	vs	vs	CC	_	_	_
5	_	_	CD	_	_	_
6	recA730	reca730	NN	_	_	_
7	,	,	,	_	_	_
8	dcd	dcd	NN	GEN	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	recA730	reca730	NN	_	_	_
11	_	_	CD	_	_	_
12	vs	vs	CC	_	_	_
13	_	_	CD	_	_	_
14	recA730	reca730	NN	_	_	_
15	,	,	,	_	_	_
16	ndk	ndk	NN	GEN	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	RNA	rna	NN	_	_	_
19	was	be	VBD	_	_	_
20	isolated	isolate	VBN	_	_	_
21	using	use	VBG	_	_	_
22	the	the	DT	_	_	_
23	RNeasy	RNeasy	NNP	_	_	_
24	Protect	Protect	NNP	_	_	_
25	Bacteria	bacterium	NNS	_	_	_
26	Mini	Mini	NNP	_	_	_
27	Kit	kit	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Qiagen	qiagen	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	,	,	,	_	_	_
32	following	follow	VBG	_	_	_
33	manufacturer	manufacturer	NN	_	_	_
34	's	's	POS	_	_	_
35	instructions	instruction	NNS	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MC4100	mc4100	NN	_	_	_
5	derivative	derivative	JJ	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	strain	strain	NN	_	_	_
8	:	:	:	_	_	_
9	MC4100	mc4100	NN	_	_	_
10	derivative	derivative	NN	_	_	_
11	,	,	,	_	_	_
12	dcd	dcd	NN	GEN	_	_
13	:	:	:	_	_	_
14	:	:	:	_	_	_
15	kan	kan	FW	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
17	strain	strain	NN	_	_	_
18	:	:	:	_	_	_
19	MC4100	mc4100	NN	_	_	_
20	derivative	derivative	NN	_	_	_
21	,	,	,	_	_	_
22	ndk	ndk	NN	GEN	_	_
23	:	:	:	_	_	_
24	:	:	:	_	_	_
25	cam	cam	FW	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
27	strain	strain	NN	_	_	_
28	:	:	:	_	_	_
29	MC4100	mc4100	NN	_	_	_
30	derivative	derivative	NN	_	_	_
31	,	,	,	_	_	_
32	recA730	reca730	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	strain	strain	NN	_	_	_
35	:	:	:	_	_	_
36	MC4100	mc4100	NN	_	_	_
37	derivative	derivative	NN	_	_	_
38	,	,	,	_	_	_
39	recA730	reca730	NN	_	_	_
40	,	,	,	_	_	_
41	dcd	dcd	NN	GEN	_	_
42	:	:	:	_	_	_
43	:	:	:	_	_	_
44	kan	kan	FW	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
46	strain	strain	NN	_	_	_
47	:	:	:	_	_	_
48	MC4100	mc4100	NN	_	_	_
49	derivative	derivative	NN	_	_	_
50	,	,	,	_	_	_
51	recA730	reca730	NN	_	_	_
52	,	,	,	_	_	_
53	ndk	ndk	NN	GEN	_	_
54	:	:	:	_	_	_
55	:	:	:	_	_	_
56	cam	cam	FW	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
58	WT	wt	FW	_	_	_
59	_	_	FW	_	_	_
60	vs	vs	CC	_	_	_
61	_	_	FW	_	_	_
62	dcd	dcd	FW	GEN	_	_
63	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
64	WT	WT	NNP	_	_	_
65	_	_	CD	_	_	_
66	vs	vs	CC	_	_	_
67	_	_	CD	_	_	_
68	ndk	ndk	NN	GEN	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	WT	wt	VBD	_	_	_
71	_	_	CD	_	_	_
72	vs	vs	CC	_	_	_
73	_	_	CD	_	_	_
74	recA730	reca730	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	50	50	CD	_	_	_
77	OD600	od600	NN	_	_	_
78	of	of	IN	_	_	_
79	bacteria	bacterium	NNS	_	_	_
80	have	have	VBP	_	_	_
81	been	be	VBN	_	_	_
82	grown	grow	VBN	_	_	_
83	to	to	TO	_	_	_
84	the	the	DT	_	_	_
85	desired	desire	VBN	_	_	_
86	growth	growth	NN	_	_	_
87	stage	stage	NN	_	_	_
88	and	and	CC	_	_	_
89	harvested	harvest	VBN	_	_	_
90	by	by	IN	_	_	_
91	centrifugation	centrifugation	NN	_	_	_
92	.	.	.	_	_	_

1	They	they	PRP	_	_	_
2	were	be	VBD	_	_	_
3	lysed	lyse	VBN	_	_	_
4	in	in	IN	_	_	_
5	500	500	CD	_	_	_
6	µl	µl	NN	_	_	_
7	of	of	IN	_	_	_
8	the	the	DT	_	_	_
9	lysis	lysis	NN	_	_	_
10	buffer	buffer	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	20	20	CD	_	_	_
13	mM	mm	NN	KWSUPP	_	_
14	Tris-HCl	tris-hcl	NN	_	_	_
15	,	,	,	_	_	_
16	pH7	ph7	NN	_	_	_
17	.5	.5	CD	_	_	_
18	,	,	,	_	_	_
19	150	150	CD	_	_	_
20	mM	mm	NN	KWSUPP	_	_
21	KCl	kcl	NN	_	_	_
22	,	,	,	_	_	_
23	1	1	CD	_	_	_
24	mM	mm	NN	KWSUPP	_	_
25	MgCl2	mgcl2	NN	_	_	_
26	,	,	,	_	_	_
27	1	1	CD	_	_	_
28	mM	mm	NN	KWSUPP	_	_
29	DTT	dtt	NN	_	_	_
30	,	,	,	_	_	_
31	1	1	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	PMSF	pmsf	NN	_	_	_
34	,	,	,	_	_	_
35	0.2	0.2	CD	_	_	_
36	%	%	NN	_	_	_
37	Triton	Triton	NNP	_	_	_
38	X100	x100	NN	_	_	_
39	,	,	,	_	_	_
40	20	20	CD	_	_	_
41	U	U	NNP	_	_	_
42	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
43	bacterial	bacterial	JJ	_	_	_
44	cells	cell	NNS	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	Coverage	Coverage	NNP	_	_	_
47	calculation	calculation	NN	_	_	_
48	and	and	CC	_	_	_
49	normalisation	normalisation	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	via	via	IN	_	_	_
52	READemption	reademption	NN	_	_	_
53	-RRB-	-rrb-	-RRB-	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	Demultiplexing	demultiplexing	JJ	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	Escherichia	escherichia	FW	Organism	_	_
58	coli	coli	FW	Organism	_	_
59	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
60	Escherichia	escherichia	FW	_	_	_
61	ProQ	ProQ	NNP	_	_	_
62	coIP	coIP	NNP	_	_	_
63	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
64	Escherichia	escherichia	FW	_	_	_
65	ProQ	ProQ	NNP	_	_	_
66	Lysate	Lysate	NNP	_	_	_
67	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
68	Escherichia	escherichia	FW	_	_	_
69	WT	WT	NNP	_	_	_
70	coIP	coIP	NNP	_	_	_
71	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
72	Escherichia	escherichia	FW	_	_	_
73	WT	WT	NNP	_	_	_
74	Lysate	Lysate	NNP	_	_	_
75	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
76	Fastq	Fastq	NNP	_	_	_
77	quality	quality	NN	_	_	_
78	trimming	trim	VBG	_	_	_
79	using	use	VBG	_	_	_
80	FastX	fastx	NN	_	_	_
81	and	and	CC	_	_	_
82	a	a	DT	_	_	_
83	cut-off	cut-off	JJ	_	_	_
84	value	value	NN	_	_	_
85	of	of	IN	_	_	_
86	20	20	CD	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	Fastq	fastq	NN	_	_	_
89	to	to	TO	_	_	_
90	fasta	fasta	NN	_	_	_
91	conversion	conversion	NN	_	_	_
92	using	use	VBG	_	_	_
93	FastX	fastx	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	Genome	Genome	NNP	_	_	_
96	_	_	NNP	_	_	_
97	build	build	VB	_	_	_
98	:	:	:	_	_	_
99	NC	NC	NNP	_	_	_
100	_	_	NNP	_	_	_
101	007779.1	007779.1	CD	_	_	_
102	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
103	LB	LB	NNP	_	_	_
104	,	,	,	_	_	_
105	37	37	CD	_	_	_
106	°C	°c	NN	_	_	_
107	,	,	,	_	_	_
108	220	220	CD	_	_	_
109	rpm	rpm	NN	_	_	_
110	,	,	,	_	_	_
111	OD600	od600	NN	_	_	_
112	=	=	JJ	_	_	_
113	0.5	0.5	CD	_	_	_
114	,	,	,	_	_	_
115	2.0	2.0	CD	_	_	_
116	,	,	,	_	_	_
117	2.0	2.0	CD	_	_	_
118	+6	+6	CD	_	_	_
119	h	h	NN	_	_	_
120	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
121	Read	Read	NNP	_	_	_
122	mapping	mapping	NN	_	_	_
123	using	use	VBG	_	_	_
124	segemehl	segemehl	NN	_	_	_
125	-LRB-	-lrb-	-LRB-	_	_	_
126	via	via	IN	_	_	_
127	READemption	reademption	NN	_	_	_
128	-RRB-	-rrb-	-RRB-	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
130	rip	rip	JJ	_	_	_
131	antibody	antibody	NN	_	_	_
132	:	:	:	_	_	_
133	Monoclonal	monoclonal	JJ	_	_	_
134	ANTI-FLAG	anti-flag	NN	_	_	_
135	^	^	NN	_	_	_
136	=	=	JJ	_	_	_
137	AE	ae	NN	_	_	_
138	M2	m2	NN	_	_	_
139	antibody	antibody	NN	_	_	_
140	produced	produce	VBN	_	_	_
141	in	in	IN	_	_	_
142	mouse	mouse	NN	_	_	_
143	,	,	,	_	_	_
144	Sigma	Sigma	NNP	_	_	_
145	,	,	,	_	_	_
146	F1804-200UG	f1804-200ug	NN	_	_	_
147	,	,	,	_	_	_
148	SLBG5673V	slbg5673v	NN	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	RIP-Seq	rip-seq	JJ	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	RNA-seq	rna-seq	NN	_	_	_
153	libraries	library	NNS	_	_	_
154	were	be	VBD	_	_	_
155	prepared	prepare	VBN	_	_	_
156	by	by	IN	_	_	_
157	Vertis	Vertis	NNP	_	_	_
158	AG	AG	NNP	_	_	_
159	-LRB-	-lrb-	-LRB-	_	_	_
160	Freising-Weihenstephan	Freising-Weihenstephan	NNP	_	_	_
161	,	,	,	_	_	_
162	Germany	Germany	NNP	_	_	_
163	-RRB-	-rrb-	-RRB-	_	_	_
164	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	polyadenylated	polyadenylated	JJ	_	_	_
6	with	with	IN	_	_	_
7	poly	poly	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	A	a	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	polymerase	polymerase	NN	_	_	_
12	,	,	,	_	_	_
13	5	5	CD	_	_	_
14	'	'	''	_	_	_
15	-	-	:	_	_	_
16	triphosphates	triphosphate	NNS	_	_	_
17	were	be	VBD	_	_	_
18	removed	remove	VBN	_	_	_
19	with	with	IN	_	_	_
20	tobacco	tobacco	NN	_	_	_
21	acid	acid	NN	_	_	_
22	pyrophosphatase	pyrophosphatase	NN	_	_	_
23	followed	follow	VBN	_	_	_
24	by	by	IN	_	_	_
25	ligation	ligation	NN	_	_	_
26	of	of	IN	_	_	_
27	a	a	DT	_	_	_
28	5	5	CD	_	_	_
29	'	'	''	_	_	_
30	-	-	:	_	_	_
31	adapter	adapter	NN	_	_	_
32	.	.	.	_	_	_

1	First-strand	first-strand	JJ	_	_	_
2	cDNA	cdna	NN	_	_	_
3	synthesis	synthesis	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	with	with	IN	_	_	_
7	the	the	DT	_	_	_
8	use	use	NN	_	_	_
9	of	of	IN	_	_	_
10	an	a	DT	_	_	_
11	oligo	oligo	JJ	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	dT	dt	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	barcoded	barcoded	JJ	_	_	_
16	adapter	adapter	NN	_	_	_
17	primer	primer	NN	_	_	_
18	and	and	CC	_	_	_
19	the	the	DT	_	_	_
20	M-MVL	m-mvl	NN	_	_	_
21	reverse	reverse	JJ	_	_	_
22	transcriptase	transcriptase	NN	_	_	_
23	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	resulting	result	VBG	_	_	_
3	cDNA	cdna	NN	_	_	_
4	was	be	VBD	_	_	_
5	PCR-amplified	pcr-amplified	JJ	_	_	_
6	with	with	IN	_	_	_
7	a	a	DT	_	_	_
8	high	high	JJ	_	_	_
9	fidelity	fidelity	NN	_	_	_
10	DNA	dna	NN	_	_	_
11	polymerase	polymerase	NN	_	_	_
12	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	was	be	VBD	_	_	_
3	purified	purify	VBN	_	_	_
4	with	with	IN	_	_	_
5	the	the	DT	_	_	_
6	Agencourt	Agencourt	NNP	_	_	_
7	AMPure	AMPure	NNP	_	_	_
8	XP	xp	NN	_	_	_
9	kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Beckman	Beckman	NNP	_	_	_
12	Coulter	Coulter	NNP	_	_	_
13	Genomics	Genomics	NNPS	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Size	size	NN	_	_	_
3	filtering	filter	VBG	_	_	_
4	:	:	:	_	_	_
5	discarding	discard	VBG	_	_	_
6	reads	read	VBZ	_	_	_
7	shorter	shorter	JJR	_	_	_
8	than	than	IN	_	_	_
9	12	12	CD	_	_	_
10	nt	nt	NNS	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	via	via	IN	_	_	_
13	READemption	reademption	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	strain	strain	NN	_	_	_
17	:	:	:	_	_	_
18	W3110	w3110	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Supplementary	supplementary	JJ	_	_	_
21	_	_	NN	_	_	_
22	files	file	NNS	_	_	_
23	_	_	IN	_	_	_
24	format	format	NN	_	_	_
25	_	_	NN	_	_	_
26	and	and	CC	_	_	_
27	_	_	NN	_	_	_
28	content	content	NN	_	_	_
29	:	:	:	_	_	_
30	wiggle	wiggle	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
32	The	the	DT	_	_	_
33	equivalent	equivalent	NN	_	_	_
34	of	of	IN	_	_	_
35	5	5	CD	_	_	_
36	OD600	od600	NN	_	_	_
37	was	be	VBD	_	_	_
38	saved	save	VBN	_	_	_
39	for	for	IN	_	_	_
40	RNA	rna	NN	_	_	_
41	extraction	extraction	NN	_	_	_
42	with	with	IN	_	_	_
43	TriZOL	trizol	NN	_	_	_
44	before	before	IN	_	_	_
45	adding	add	VBG	_	_	_
46	antibodies	antibody	NNS	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	lysate	lysate	NN	_	_	_
49	RNA	rna	NN	_	_	_
50	sample	sample	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	coIP	coip	NN	_	_	_
3	samples	sample	NNS	_	_	_
4	,	,	,	_	_	_
5	beads	bead	NNS	_	_	_
6	were	be	VBD	_	_	_
7	resuspended	resuspend	VBN	_	_	_
8	in	in	IN	_	_	_
9	the	the	DT	_	_	_
10	lysis	lysis	NN	_	_	_
11	buffer	buffer	NN	_	_	_
12	,	,	,	_	_	_
13	mixed	mix	VBN	_	_	_
14	with	with	IN	_	_	_
15	an	a	DT	_	_	_
16	equal	equal	JJ	_	_	_
17	volume	volume	NN	_	_	_
18	of	of	IN	_	_	_
19	phenol	phenol	NN	_	_	_
20	:	:	:	_	_	_
21	chloroform	chloroform	NN	_	_	_
22	:	:	:	_	_	_
23	isopropanol	isopropanol	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	25:24:1	25:24:1	CD	_	_	_
26	,	,	,	_	_	_
27	pH4	ph4	NN	_	_	_
28	.5	.5	CD	_	_	_
29	,	,	,	_	_	_
30	Roth	Roth	NNP	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	for	for	IN	_	_	_
33	20	20	CD	_	_	_
34	s	s	NNS	_	_	_
35	and	and	CC	_	_	_
36	incubated	incubate	VBN	_	_	_
37	at	at	IN	_	_	_
38	room	room	NN	_	_	_
39	temperature	temperature	NN	_	_	_
40	for	for	IN	_	_	_
41	3	3	CD	_	_	_
42	min	min	NN	_	_	_
43	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	centrifugation	centrifugation	NN	_	_	_
3	,	,	,	_	_	_
4	the	the	DT	_	_	_
5	aqueous	aqueous	JJ	_	_	_
6	phase	phase	NN	_	_	_
7	was	be	VBD	_	_	_
8	precipitated	precipitate	VBN	_	_	_
9	with	with	IN	_	_	_
10	isopropanol	isopropanol	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	coIP	coip	NN	_	_	_
13	RNA	rna	NN	_	_	_
14	sample	sample	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	purified	purify	VBN	_	_	_
3	RNA	rna	NN	_	_	_
4	coIP	coip	NN	_	_	_
5	sample	sample	NN	_	_	_
6	was	be	VBD	_	_	_
7	treated	treat	VBN	_	_	_
8	with	with	IN	_	_	_
9	DNase	dnase	NN	_	_	_
10	I	i	CD	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Thermo	Thermo	NNP	_	_	_
13	Scientific	Scientific	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	to	to	TO	_	_	_
16	remove	remove	VB	_	_	_
17	the	the	DT	_	_	_
18	residual	residual	JJ	_	_	_
19	DNA	dna	NN	_	_	_
20	and	and	CC	_	_	_
21	reisolated	reisolate	VBN	_	_	_
22	with	with	IN	_	_	_
23	phenol	phenol	NN	_	_	_
24	:	:	:	_	_	_
25	chloroform	chloroform	NN	_	_	_
26	:	:	:	_	_	_
27	isopropanol	isopropanol	NN	_	_	_
28	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	spike-in	spike-in	JJ	_	_	_
3	RNA	rna	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	5	5	CD	_	_	_
6	'	'	''	_	_	_
7	P-CUCGUCCGACGUCACCUAGA	p-cucguccgacgucaccuaga	NN	_	_	_
8	,	,	,	_	_	_
9	IBA	iba	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	had	have	VBD	_	_	_
12	been	be	VBN	_	_	_
13	added	add	VBN	_	_	_
14	to	to	TO	_	_	_
15	40	40	CD	_	_	_
16	pg	pg	NN	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	Adapter	Adapter	NNP	_	_	_
19	cutting	cut	VBG	_	_	_
20	using	use	VBG	_	_	_
21	cutadapt	cutadapt	NN	_	_	_
22	,	,	,	_	_	_
23	version	version	NN	_	_	_
24	1.2.1	1.2.1	CD	_	_	_
25	,	,	,	_	_	_
26	parameters	parameter	NNS	_	_	_
27	-	-	:	_	_	_
28	e	e	SYM	_	_	_
29	0.1	0.1	CD	_	_	_
30	-	-	:	_	_	_
31	O	o	NN	_	_	_
32	1	1	CD	_	_	_
33	-	-	:	_	_	_
34	m	m	NN	_	_	_
35	12	12	CD	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	AT1	at1	NN	_	_	_
38	biological	biological	JJ	_	_	_
39	replicate	replicate	VB	_	_	_
40	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
41	E.	e.	FW	_	_	_
42	coli	coli	FW	_	_	_
43	MC4100	mc4100	NN	_	_	_
44	strain	strain	NN	_	_	_
45	was	be	VBD	_	_	_
46	cultured	culture	VBN	_	_	_
47	at	at	IN	_	_	_
48	37	37	CD	_	_	_
49	°C	°c	NN	_	_	_
50	to	to	TO	_	_	_
51	mid-log	mid-log	JJ	_	_	_
52	phase	phase	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	OD600	od600	NN	_	_	_
55	~	~	NN	_	_	_
56	0.4	0.4	CD	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	in	in	IN	_	_	_
59	LB	LB	NNP	MED	_	_
60	media	media	NNS	MED	_	_
61	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
62	Escherichia	escherichia	FW	Organism	_	_
63	coli	coli	FW	Organism	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	Genome	Genome	NNP	_	_	_
66	_	_	NNP	_	_	_
67	build	build	VB	_	_	_
68	:	:	:	_	_	_
69	strain	strain	NN	_	_	_
70	MG1655	mg1655	NN	_	_	_
71	,	,	,	_	_	_
72	version	version	NN	_	_	_
73	U00096	u00096	NN	_	_	_
74	.2	.2	NN	_	_	_
75	,	,	,	_	_	_
76	downloaded	download	VBN	_	_	_
77	from	from	IN	_	_	_
78	NCBI	NCBI	NNP	_	_	_
79	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
80	Genome	Genome	NNP	_	_	_
81	mapping	mapping	NN	_	_	_
82	using	use	VBG	_	_	_
83	Bowtie	Bowtie	NNP	_	_	_
84	,	,	,	_	_	_
85	version	version	NN	_	_	_
86	0.12.9	0.12.9	CD	_	_	_
87	,	,	,	_	_	_
88	parameters	parameter	NNS	_	_	_
89	for	for	IN	_	_	_
90	samples	sample	NNS	_	_	_
91	1-5	1-5	CD	_	_	_
92	:	:	:	_	_	_
93	-	-	:	_	_	_
94	v	v	LS	_	_	_
95	2	2	CD	_	_	_
96	--	--	:	_	_	_
97	best	best	JJS	_	_	_
98	--	--	:	_	_	_
99	strata	strata	SYM	_	_	_
100	-	-	:	_	_	_
101	m	m	NN	_	_	_
102	1	1	CD	_	_	_
103	,	,	,	_	_	_
104	parameters	parameter	NNS	_	_	_
105	for	for	IN	_	_	_
106	samples	sample	NNS	_	_	_
107	6-9	6-9	CD	_	_	_
108	:	:	:	_	_	_
109	-	-	:	_	_	_
110	v	v	LS	_	_	_
111	3	3	CD	_	_	_
112	--	--	:	_	_	_
113	best	best	JJS	_	_	_
114	--	--	:	_	_	_
115	strata	strata	SYM	_	_	_
116	-	-	:	_	_	_
117	m	m	NN	_	_	_
118	1	1	CD	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	LB	lb	NN	_	_	_
121	mRNA	mrna	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	LB	lb	NN	_	_	_
124	mRNA	mrna	NN	_	_	_
125	biological	biological	JJ	_	_	_
126	replicate	replicate	VBP	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	LB	lb	NN	_	_	_
129	mRNA	mrna	NN	_	_	_
130	technical	technical	JJ	_	_	_
131	replicate	replicate	VB	_	_	_
132	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
133	LB	LB	NNP	_	_	_
134	RPF	RPF	NNP	_	_	_
135	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
136	LB	LB	NNP	_	_	_
137	RPF	RPF	NNP	_	_	_
138	biological	biological	JJ	_	_	_
139	replicate	replicate	VBP	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	media	media	NNS	_	_	_
142	:	:	:	_	_	_
143	LB	lb	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	Quality	quality	JJ	_	_	_
146	trimming	trim	VBG	_	_	_
147	using	use	VBG	_	_	_
148	FASTX-toolkit	fastx-toolkit	NN	_	_	_
149	,	,	,	_	_	_
150	version	version	NN	_	_	_
151	0.0.13.2	0.0.13.2	CD	_	_	_
152	,	,	,	_	_	_
153	parameters	parameter	NNS	_	_	_
154	-	-	:	_	_	_
155	v	v	LS	_	_	_
156	-	-	:	_	_	_
157	t	t	NN	_	_	_
158	20	20	CD	_	_	_
159	-	-	:	_	_	_
160	l	l	NN	_	_	_
161	10	10	CD	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
163	Read	read	VBP	_	_	_
164	counts	count	NNS	_	_	_
165	were	be	VBD	_	_	_
166	normalized	normalize	VBN	_	_	_
167	by	by	IN	_	_	_
168	million	million	CD	_	_	_
169	mapped	map	VBD	_	_	_
170	reads	read	VBZ	_	_	_
171	for	for	IN	_	_	_
172	each	each	DT	_	_	_
173	nucleotide	nucleotide	NN	_	_	_
174	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
175	Read	Read	NNP	_	_	_
176	using	use	VBG	_	_	_
177	bedtools	bedtool	NNS	_	_	_
178	,	,	,	_	_	_
179	version	version	NN	_	_	_
180	2.17.0	2.17.0	CD	_	_	_
181	,	,	,	_	_	_
182	parameter	parameter	NN	_	_	_
183	:	:	:	_	_	_
184	-	-	:	_	_	_
185	s	s	NNS	_	_	_
186	,	,	,	_	_	_
187	for	for	IN	_	_	_
188	samples	sample	NNS	_	_	_
189	1-5	1-5	CD	_	_	_
190	the	the	DT	_	_	_
191	middle	middle	NN	_	_	_
192	nucleotide	nucleotide	NN	_	_	_
193	of	of	IN	_	_	_
194	each	each	DT	_	_	_
195	read	read	NN	_	_	_
196	was	be	VBD	_	_	_
197	taken	take	VBN	_	_	_
198	,	,	,	_	_	_
199	for	for	IN	_	_	_
200	samples	sample	NNS	_	_	_
201	6-9	6-9	CD	_	_	_
202	the	the	DT	_	_	_
203	first	first	JJ	_	_	_
204	nucleotide	nucleotide	NN	_	_	_
205	was	be	VBD	_	_	_
206	taken	take	VBN	_	_	_
207	and	and	CC	_	_	_
208	the	the	DT	_	_	_
209	read	read	NN	_	_	_
210	count	count	NN	_	_	_
211	was	be	VBD	_	_	_
212	assigned	assign	VBN	_	_	_
213	to	to	TO	_	_	_
214	the	the	DT	_	_	_
215	nucleotide	nucleotide	NN	_	_	_
216	5	5	CD	_	_	_
217	'	'	''	_	_	_
218	of	of	IN	_	_	_
219	the	the	DT	_	_	_
220	first	first	JJ	_	_	_
221	nucleotide	nucleotide	NN	_	_	_
222	see	see	VB	_	_	_
223	-LCB-	-lcb-	-LRB-	_	_	_
224	Kertesz	Kertesz	NNP	_	_	_
225	,	,	,	_	_	_
226	2010	2010	CD	_	_	_
227	-RCB-	-rcb-	-RRB-	_	_	_
228	for	for	IN	_	_	_
229	details	detail	NNS	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
231	RNA-Seq	rna-seq	JJ	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	RNA-size	rna-size	NN	_	_	_
234	selection	selection	NN	_	_	_
235	and	and	CC	_	_	_
236	generation	generation	NN	_	_	_
237	of	of	IN	_	_	_
238	the	the	DT	_	_	_
239	cDNA	cdna	NN	_	_	_
240	libraries	library	NNS	_	_	_
241	was	be	VBD	_	_	_
242	performed	perform	VBN	_	_	_
243	as	as	IN	_	_	_
244	described	describe	VBN	_	_	_
245	-LCB-	-lcb-	-LRB-	_	_	_
246	Ingolia	Ingolia	NNP	_	_	_
247	,	,	,	_	_	_
248	2009	2009	CD	_	_	_
249	-RCB-	-rcb-	-RRB-	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	sample	sample	NN	_	_	_
252	type	type	NN	_	_	_
253	:	:	:	_	_	_
254	AT1	at1	NN	_	_	_
255	digested	digest	VBD	_	_	_
256	total	total	JJ	_	_	_
257	RNA	rna	NN	_	_	_
258	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
259	sample	sample	NN	_	_	_
260	type	type	NN	_	_	_
261	:	:	:	_	_	_
262	ribosome	ribosome	NN	_	_	_
263	protected	protect	VBD	_	_	_
264	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
265	sample	sample	NN	_	_	_
266	type	type	NN	_	_	_
267	:	:	:	_	_	_
268	V1	v1	NN	_	_	_
269	digested	digest	VBD	_	_	_
270	total	total	JJ	_	_	_
271	RNA	rna	NN	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	strain	strain	NN	_	_	_
274	:	:	:	_	_	_
275	MC4100	mc4100	NN	_	_	_
276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
277	strain	strain	NN	_	_	_
278	:	:	:	_	_	_
279	MC4101	mc4101	NN	_	_	_
280	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
281	strain	strain	NN	_	_	_
282	:	:	:	_	_	_
283	MC4102	mc4102	NN	_	_	_
284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
285	strain	strain	NN	_	_	_
286	:	:	:	_	_	_
287	MC4103	mc4103	NN	_	_	_
288	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
289	strain	strain	NN	_	_	_
290	:	:	:	_	_	_
291	MC4104	mc4104	NN	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	strain	strain	NN	_	_	_
294	:	:	:	_	_	_
295	MC4105	mc4105	NN	_	_	_
296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
297	strain	strain	NN	_	_	_
298	:	:	:	_	_	_
299	MC4106	mc4106	NN	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	strain	strain	NN	_	_	_
302	:	:	:	_	_	_
303	MC4107	mc4107	NN	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	Supplementary	supplementary	JJ	_	_	_
306	_	_	NN	_	_	_
307	files	file	NNS	_	_	_
308	_	_	IN	_	_	_
309	format	format	NN	_	_	_
310	_	_	NN	_	_	_
311	and	and	CC	_	_	_
312	_	_	NN	_	_	_
313	content	content	NN	_	_	_
314	:	:	:	_	_	_
315	Column	Column	NNP	_	_	_
316	1	1	CD	_	_	_
317	names	name	NNS	_	_	_
318	the	the	DT	_	_	_
319	nucleotide	nucleotide	NN	_	_	_
320	in	in	IN	_	_	_
321	the	the	DT	_	_	_
322	genome	genome	NN	_	_	_
323	,	,	,	_	_	_
324	column	column	NN	_	_	_
325	2	2	CD	_	_	_
326	gives	give	VBZ	_	_	_
327	counts	count	NNS	_	_	_
328	for	for	IN	_	_	_
329	the	the	DT	_	_	_
330	forward	forward	JJ	_	_	_
331	strand	strand	NN	_	_	_
332	,	,	,	_	_	_
333	column	column	NN	_	_	_
334	3	3	CD	_	_	_
335	for	for	IN	_	_	_
336	the	the	DT	_	_	_
337	reverse	reverse	JJ	_	_	_
338	strand	strand	NN	_	_	_
339	,	,	,	_	_	_
340	columns	column	NNS	_	_	_
341	are	be	VBP	_	_	_
342	tab	tab	NN	_	_	_
343	separated	separated	JJ	_	_	_
344	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
345	Total	total	JJ	_	_	_
346	RNA	rna	NN	_	_	_
347	was	be	VBD	_	_	_
348	extracted	extract	VBN	_	_	_
349	using	use	VBG	_	_	_
350	TRIzol	trizol	NN	_	_	_
351	reagent	reagent	NN	_	_	_
352	-LRB-	-lrb-	-LRB-	_	_	_
353	Invitrogen	invitrogen	NN	_	_	_
354	-RRB-	-rrb-	-RRB-	_	_	_
355	and	and	CC	_	_	_
356	the	the	DT	_	_	_
357	sample	sample	NN	_	_	_
358	was	be	VBD	_	_	_
359	enriched	enrich	VBN	_	_	_
360	in	in	IN	_	_	_
361	mRNA	mrna	NN	_	_	_
362	,	,	,	_	_	_
363	depleting	deplete	VBG	_	_	_
364	small	small	JJ	_	_	_
365	RNAs	rna	NNS	_	_	_
366	with	with	IN	_	_	_
367	GeneJET	genejet	NN	_	_	_
368	™	™	NN	_	_	_
369	RNA	rna	NN	_	_	_
370	Purification	purification	NN	_	_	_
371	Kit	kit	NN	_	_	_
372	-LRB-	-lrb-	-LRB-	_	_	_
373	Fermentas	fermentas	NN	_	_	_
374	-RRB-	-rrb-	-RRB-	_	_	_
375	and	and	CC	_	_	_
376	ribosomal	ribosomal	JJ	_	_	_
377	RNA	rna	NN	_	_	_
378	with	with	IN	_	_	_
379	two	two	CD	_	_	_
380	cycle	cycle	NN	_	_	_
381	of	of	IN	_	_	_
382	MICROBExpress	microbexpress	NN	_	_	_
383	™	™	CD	_	_	_
384	Bacterial	bacterial	JJ	_	_	_
385	mRNA	mrna	NN	_	_	_
386	Enrichment	Enrichment	NNP	_	_	_
387	Kit	kit	NN	_	_	_
388	-LRB-	-lrb-	-LRB-	_	_	_
389	Ambion	ambion	NN	_	_	_
390	-RRB-	-rrb-	-RRB-	_	_	_
391	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	probe	probe	VB	_	_	_
3	the	the	DT	_	_	_
4	RNA	rna	NN	_	_	_
5	structure	structure	NN	_	_	_
6	two	two	CD	_	_	_
7	µg	µg	NN	_	_	_
8	of	of	IN	_	_	_
9	enriched	enriched	JJ	_	_	_
10	mRNA	mrna	NN	_	_	_
11	were	be	VBD	_	_	_
12	resuspended	resuspend	VBN	_	_	_
13	in	in	IN	_	_	_
14	45	45	CD	_	_	_
15	µl	µl	NN	_	_	_
16	of	of	IN	_	_	_
17	DEPC	depc	NN	_	_	_
18	water	water	NN	_	_	_
19	and	and	CC	_	_	_
20	denatured	denature	VBN	_	_	_
21	for	for	IN	_	_	_
22	3	3	CD	_	_	_
23	min	min	NN	_	_	_
24	at	at	IN	_	_	_
25	95	95	CD	_	_	_
26	°C	°c	NN	_	_	_
27	,	,	,	_	_	_
28	refolded	refold	VBN	_	_	_
29	at	at	IN	_	_	_
30	37	37	CD	_	_	_
31	°C	°c	NN	_	_	_
32	,	,	,	_	_	_
33	after	after	IN	_	_	_
34	addition	addition	NN	_	_	_
35	of	of	IN	_	_	_
36	10x	10x	CD	_	_	_
37	RNA-structure	rna-structure	NN	_	_	_
38	buffer	buffer	NN	_	_	_
39	with	with	IN	_	_	_
40	pH	ph	NN	_	_	_
41	7.0	7.0	CD	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	100	100	CD	_	_	_
44	mM	mm	NN	KWSUPP	_	_
45	Tris	Tris	NNP	_	_	_
46	,	,	,	_	_	_
47	1	1	CD	_	_	_
48	M	m	NN	_	_	_
49	KCl	kcl	NN	_	_	_
50	,	,	,	_	_	_
51	100	100	CD	_	_	_
52	mM	mm	NN	KWSUPP	_	_
53	MgCl2	mgcl2	NN	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	and	and	CC	_	_	_
56	digested	digest	VBN	_	_	_
57	for	for	IN	_	_	_
58	1	1	CD	_	_	_
59	min	min	NN	_	_	_
60	at	at	IN	_	_	_
61	37	37	CD	_	_	_
62	°C	°c	NN	_	_	_
63	with	with	IN	_	_	_
64	either	either	CC	_	_	_
65	0.05	0.05	CD	_	_	_
66	U	U	NNP	_	_	_
67	RNase	rnase	NN	_	_	_
68	V1	v1	NN	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	Life	Life	NNP	_	_	_
71	Technologies	Technologies	NNPS	_	_	_
72	-RRB-	-rrb-	-RRB-	_	_	_
73	or	or	CC	_	_	_
74	a	a	DT	_	_	_
75	combination	combination	NN	_	_	_
76	of	of	IN	_	_	_
77	2	2	CD	_	_	_
78	µg	µg	NN	_	_	_
79	RNase	rnase	NN	_	_	_
80	A	a	NN	_	_	_
81	and	and	CC	_	_	_
82	5	5	CD	_	_	_
83	U	U	NNP	_	_	_
84	RNase	rnase	NN	_	_	_
85	T1	t1	NN	_	_	_
86	-LRB-	-lrb-	-LRB-	_	_	_
87	Thermo	Thermo	NNP	_	_	_
88	Scientific	Scientific	NNP	_	_	_
89	-RRB-	-rrb-	-RRB-	_	_	_
90	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	reaction	reaction	NN	_	_	_
3	was	be	VBD	_	_	_
4	stopped	stop	VBN	_	_	_
5	by	by	IN	_	_	_
6	extracting	extract	VBG	_	_	_
7	the	the	DT	_	_	_
8	RNA	rna	NN	_	_	_
9	with	with	IN	_	_	_
10	phenol-chlorophorm	phenol-chlorophorm	NN	_	_	_
11	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	RNase	rnase	NN	_	_	_
3	A	a	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	V1	v1	NN	_	_	_
6	biological	biological	JJ	_	_	_
7	replicate	replicate	VBP	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
9	At	at	IN	_	_	_
10	OD450	od450	NN	_	_	_
11	=	=	JJ	_	_	_
12	0.3	0.3	CD	_	_	_
13	,	,	,	_	_	_
14	cultures	culture	NNS	_	_	_
15	induced	induce	VBN	_	_	_
16	with	with	IN	_	_	_
17	1	1	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	IPTG	iptg	NN	_	_	_
20	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	harvested	harvest	VBN	_	_	_
3	20	20	CD	_	_	_
4	min	min	NN	_	_	_
5	after	after	IN	_	_	_
6	induction	induction	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Cells	cell	NNS	_	_	_
9	harvested	harvest	VBN	_	_	_
10	at	at	IN	_	_	_
11	OD450	od450	NN	_	_	_
12	=	=	JJ	_	_	_
13	0.3	0.3	CD	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Culture	culture	NN	_	_	_
16	samples	sample	NNS	_	_	_
17	for	for	IN	_	_	_
18	microarray	microarray	NN	_	_	_
19	analysis	analysis	NN	_	_	_
20	were	be	VBD	_	_	_
21	added	add	VBN	_	_	_
22	to	to	TO	_	_	_
23	ice-cold	ice-cold	JJ	_	_	_
24	5	5	CD	_	_	_
25	%	%	NN	_	_	_
26	water-saturated	water-saturated	JJ	_	_	_
27	phenol	phenol	NN	_	_	_
28	in	in	IN	_	_	_
29	ethanol	ethanol	NN	_	_	_
30	solution	solution	NN	_	_	_
31	,	,	,	_	_	_
32	centrifuged	centrifuge	VBN	_	_	_
33	at	at	IN	_	_	_
34	6,600	6,600	CD	_	_	_
35	g	g	NN	_	_	_
36	and	and	CC	_	_	_
37	the	the	DT	_	_	_
38	cell	cell	NN	_	_	_
39	pellets	pellet	NNS	_	_	_
40	flash	flash	VBP	_	_	_
41	frozen	freeze	VBN	_	_	_
42	in	in	IN	_	_	_
43	liquid	liquid	JJ	_	_	_
44	N2	n2	NN	_	_	_
45	before	before	IN	_	_	_
46	storing	store	VBG	_	_	_
47	at	at	IN	_	_	_
48	-80	-80	CD	_	_	_
49	degrees	degree	NNS	_	_	_
50	C	c	NN	_	_	_
51	until	until	IN	_	_	_
52	required	require	VBN	_	_	_
53	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	from	from	IN	_	_	_
6	the	the	DT	_	_	_
7	stored	store	VBN	_	_	_
8	cell	cell	NN	_	_	_
9	pellets	pellet	NNS	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	hot	hot	JJ	_	_	_
13	phenol	phenol	NN	_	_	_
14	method	method	NN	_	_	_
15	,	,	,	_	_	_
16	and	and	CC	_	_	_
17	labeled	label	VBN	_	_	_
18	Cy3	cy3	NN	_	_	_
19	and	and	CC	_	_	_
20	Cy5	cy5	NN	_	_	_
21	cDNA	cdna	NN	_	_	_
22	was	be	VBD	_	_	_
23	prepared	prepare	VBN	_	_	_
24	from	from	IN	_	_	_
25	16	16	CD	_	_	_
26	ug	ug	NN	_	_	_
27	total	total	JJ	_	_	_
28	RNA	rna	NN	_	_	_
29	with	with	IN	_	_	_
30	10	10	CD	_	_	_
31	ug	ug	NN	_	_	_
32	random	random	JJ	_	_	_
33	hexamer	hexamer	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Integrated	Integrated	NNP	_	_	_
36	DNA	DNA	NNP	_	_	_
37	Technologies	Technologies	NNPS	_	_	_
38	,	,	,	_	_	_
39	Inc.	Inc.	NNP	_	_	_
40	,	,	,	_	_	_
41	Coralville	Coralville	NNP	_	_	_
42	,	,	,	_	_	_
43	IA	IA	NNP	_	_	_
44	,	,	,	_	_	_
45	USA	USA	NNP	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	filtered	filter	VBD	_	_	_
4	for	for	IN	_	_	_
5	PCR	pcr	NN	_	_	_
6	success	success	NN	_	_	_
7	,	,	,	_	_	_
8	>	>	JJR	_	_	_
9	3x	3x	NN	_	_	_
10	local	local	JJ	_	_	_
11	background	background	NN	_	_	_
12	and	and	CC	_	_	_
13	spot	spot	NN	_	_	_
14	quality	quality	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	GenePix	GenePix	NNP	_	_	_
17	Flag	Flag	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	Normalized	normalize	VBN	_	_	_
2	using	use	VBG	_	_	_
3	Lowess	Lowess	NNP	_	_	_
4	smoothing	smooth	VBG	_	_	_
5	from	from	IN	_	_	_
6	MA	MA	NNP	_	_	_
7	plot	plot	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	delta	delta	NN	_	_	_
10	hfq	hfq	NN	GEN	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Delta	delta	NN	_	_	_
13	hfq	hfq	NN	GEN	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Delta	delta	NN	_	_	_
16	rseA	rsea	NN	GEN	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	EC12n097	ec12n097	NN	_	_	_
19	delta	delta	NN	_	_	_
20	rseA	rsea	NN	GEN	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	EC12n098	ec12n098	NN	_	_	_
23	delta	delta	NN	_	_	_
24	rseA	rsea	NN	GEN	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	EC12n099	ec12n099	NN	_	_	_
27	delta	delta	NN	_	_	_
28	rseA	rsea	NN	GEN	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	EC18n018	ec18n018	NN	_	_	_
31	hfq	hfq	NN	GEN	_	_
32	+	+	CC	_	_	_
33	rpoE	rpoe	NN	GEN	_	_
34	overexpression	overexpression	NN	_	_	_
35	20	20	CD	_	_	_
36	min	min	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	EC18n019	ec18n019	NN	_	_	_
39	hfq	hfq	NN	GEN	_	_
40	-	-	:	_	_	_
41	rpoE	rpoe	NN	GEN	_	_
42	overexpression	overexpression	NN	_	_	_
43	20	20	CD	_	_	_
44	min	min	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	EC18n035	ec18n035	NN	_	_	_
47	delta	delta	NN	_	_	_
48	rseA	rsea	NN	GEN	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	EC18n036	ec18n036	NN	_	_	_
51	delta	delta	NN	_	_	_
52	rseA	rsea	NN	GEN	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	EC18n037	ec18n037	NN	_	_	_
55	delta	delta	NN	_	_	_
56	hfq	hfq	NN	GEN	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	EC18n038	ec18n038	NN	_	_	_
59	delta	delta	NN	_	_	_
60	hfq	hfq	NN	GEN	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	EC18n039	ec18n039	NN	_	_	_
63	delta	delta	NN	_	_	_
64	hfq	hfq	NN	GEN	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	EC18n040	ec18n040	NN	_	_	_
67	delta	delta	NN	_	_	_
68	hfq	hfq	NN	GEN	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	EC18n136	ec18n136	NN	_	_	_
71	hfq	hfq	NN	GEN	_	_
72	+	+	CC	_	_	_
73	rpoE	rpoe	NN	GEN	_	_
74	overexpression	overexpression	NN	_	_	_
75	20	20	CD	_	_	_
76	min	min	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	Ec18n137	ec18n137	NN	_	_	_
79	hfq	hfq	NN	GEN	_	_
80	-	-	:	_	_	_
81	rpoE	rpoe	NN	GEN	_	_
82	overexpression	overexpression	NN	_	_	_
83	20	20	CD	_	_	_
84	min	min	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	EC18n139	ec18n139	NN	_	_	_
87	hfq	hfq	NN	GEN	_	_
88	+	+	CC	_	_	_
89	rpoE	rpoe	NN	GEN	_	_
90	overexpression	overexpression	NN	_	_	_
91	20	20	CD	_	_	_
92	min	min	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	EC18n140	ec18n140	NN	_	_	_
95	hfq	hfq	NN	GEN	_	_
96	-	-	:	_	_	_
97	rpoE	rpoe	NN	GEN	_	_
98	overexpression	overexpression	NN	_	_	_
99	20	20	CD	_	_	_
100	min	min	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	EC19n075	ec19n075	NN	_	_	_
103	delta	delta	NN	_	_	_
104	hfq	hfq	NN	GEN	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	EC19n076	ec19n076	NN	_	_	_
107	delta	delta	NN	_	_	_
108	hfq	hfq	NN	GEN	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	EC19n098	ec19n098	NN	_	_	_
111	delta	delta	NN	_	_	_
112	hfq	hfq	NN	GEN	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	EC19n099	ec19n099	NN	_	_	_
115	delta	delta	NN	_	_	_
116	hfq	hfq	NN	GEN	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	EC19n100	ec19n100	NN	_	_	_
119	delta	delta	NN	_	_	_
120	rseA	rsea	NN	GEN	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	EC19n101	ec19n101	NN	_	_	_
123	delta	delta	NN	_	_	_
124	rseA	rsea	NN	GEN	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	Escherichia	escherichia	FW	Organism	_	_
127	coli	coli	FW	Organism	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	Hfq	hfq	NN	_	_	_
130	-	-	:	_	_	_
131	RpoE	rpoe	NN	_	_	_
132	overexpression	overexpression	NN	_	_	_
133	-LRB-	-lrb-	-LRB-	_	_	_
134	20	20	CD	_	_	_
135	min	min	NN	_	_	_
136	-RRB-	-rrb-	-RRB-	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	hfq	hfq	NN	GEN	_	_
139	+	+	CC	_	_	_
140	Wild	Wild	NNP	_	_	_
141	type	type	NN	_	_	_
142	control	control	NN	_	_	_
143	-LRB-	-lrb-	-LRB-	_	_	_
144	20	20	CD	_	_	_
145	min	min	NN	_	_	_
146	-RRB-	-rrb-	-RRB-	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	M9	m9	NN	_	_	_
149	minimal	minimal	JJ	_	_	_
150	complete	complete	JJ	_	_	_
151	media	media	NNS	_	_	_
152	,	,	,	_	_	_
153	cultures	culture	NNS	_	_	_
154	grown	grow	VBN	_	_	_
155	aerobically	aerobically	RB	_	_	_
156	at	at	IN	_	_	_
157	30	30	CD	_	_	_
158	degrees	degree	NNS	_	_	_
159	C	c	NN	_	_	_
160	in	in	IN	_	_	_
161	a	a	DT	_	_	_
162	gyratory	gyratory	JJ	_	_	_
163	water	water	NN	_	_	_
164	bath	bath	NN	_	_	_
165	shaking	shake	VBG	_	_	_
166	at	at	IN	_	_	_
167	240	240	CD	_	_	_
168	rpm	rpm	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	MG1655	mg1655	NN	_	_	_
171	rpoHp3	rpohp3	NN	Pr	_	_
172	:	:	:	_	_	_
173	:	:	:	_	_	_
174	lacZ	lacz	NN	GEN	_	_
175	delta	delta	NN	_	_	_
176	lacX74	lacx74	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	MG1655	mg1655	NN	_	_	_
179	rpoHp3	rpohp3	NN	Pr	_	_
180	:	:	:	_	_	_
181	:	:	:	_	_	_
182	lacZ	lacz	NN	GEN	_	_
183	delta	delta	NN	_	_	_
184	lacX74	lacx74	NN	_	_	_
185	hfq1	hfq1	NN	_	_	_
186	:	:	:	_	_	_
187	:	:	:	_	_	_
188	omega	omega	NN	_	_	_
189	-LRB-	-lrb-	-LRB-	_	_	_
190	Km	km	NN	_	_	_
191	;	;	:	_	_	_
192	BclI	bcli	NN	_	_	_
193	-RRB-	-rrb-	-RRB-	_	_	_
194	-LRB-	-lrb-	-LRB-	_	_	_
195	hfq	hfq	SYM	GEN	_	_
196	-	-	:	_	_	_
197	-RRB-	-rrb-	-RRB-	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	MG1655	mg1655	NN	_	_	_
200	rpoHp3	rpohp3	NN	Pr	_	_
201	:	:	:	_	_	_
202	:	:	:	_	_	_
203	lacZ	lacz	NN	GEN	_	_
204	delta	delta	NN	_	_	_
205	lacX74	lacx74	NN	_	_	_
206	hfq2	hfq2	NN	_	_	_
207	:	:	:	_	_	_
208	:	:	:	_	_	_
209	omega	omega	NN	_	_	_
210	-LRB-	-lrb-	-LRB-	_	_	_
211	Km	km	NN	_	_	_
212	;	;	:	_	_	_
213	KpnI	kpni	NN	_	_	_
214	-RRB-	-rrb-	-RRB-	_	_	_
215	-LRB-	-lrb-	-LRB-	_	_	_
216	hfq	hfq	NN	GEN	_	_
217	+	+	CC	_	_	_
218	-RRB-	-rrb-	-RRB-	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	MG1655	mg1655	NN	_	_	_
221	rpoHp3	rpohp3	NN	Pr	_	_
222	:	:	:	_	_	_
223	:	:	:	_	_	_
224	lacZ	lacz	NN	GEN	_	_
225	delta	delta	NN	_	_	_
226	lacX74	lacx74	NN	_	_	_
227	nadB	nadb	NN	GEN	_	_
228	:	:	:	_	_	_
229	:	:	:	_	_	_
230	Tn10	tn10	NN	_	_	_
231	drseA	drsea	NN	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	RpoE	rpoe	NN	_	_	_
234	induced	induce	VBN	_	_	_
235	-LRB-	-lrb-	-LRB-	_	_	_
236	20	20	CD	_	_	_
237	min	min	NN	_	_	_
238	-RRB-	-rrb-	-RRB-	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	Wild	Wild	NNP	_	_	_
241	type	type	NN	_	_	_
242	control	control	NN	_	_	_
243	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
244	Wild	Wild	NNP	_	_	_
245	type	type	NN	_	_	_
246	control	control	NN	_	_	_
247	-LRB-	-lrb-	-LRB-	_	_	_
248	20	20	CD	_	_	_
249	min	min	NN	_	_	_
250	-RRB-	-rrb-	-RRB-	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	bowtie2	bowtie2	NN	_	_	_
253	v2	v2	NN	_	_	_
254	.2.3	.2.3	CD	_	_	_
255	was	be	VBD	_	_	_
256	used	use	VBN	_	_	_
257	for	for	IN	_	_	_
258	alignment	alignment	NN	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	Cells	cell	NNS	_	_	_
261	were	be	VBD	_	_	_
262	crosslinked	crosslink	VBN	_	_	_
263	in	in	IN	_	_	_
264	1	1	CD	_	_	_
265	%	%	NN	_	_	_
266	formadehyde	formadehyde	NN	_	_	_
267	for	for	IN	_	_	_
268	25	25	CD	_	_	_
269	min	min	NN	_	_	_
270	at	at	IN	_	_	_
271	room	room	NN	_	_	_
272	temperature	temperature	NN	_	_	_
273	followed	follow	VBN	_	_	_
274	by	by	IN	_	_	_
275	5	5	CD	_	_	_
276	minutes	minute	NNS	_	_	_
277	of	of	IN	_	_	_
278	quenching	quench	VBG	_	_	_
279	with	with	IN	_	_	_
280	glycine	glycine	NN	_	_	_
281	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	washed	wash	VBN	_	_	_
4	3X	3x	NN	_	_	_
5	with	with	IN	_	_	_
6	ice	ice	NN	_	_	_
7	cold	cold	JJ	_	_	_
8	TBS	tbs	NN	_	_	_
9	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	pellets	pellet	NNS	_	_	_
3	were	be	VBD	_	_	_
4	stored	store	VBN	_	_	_
5	at	at	IN	_	_	_
6	-80	-80	CD	_	_	_
7	C.	C.	NNP	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	Cells	cell	NNS	_	_	_
10	were	be	VBD	_	_	_
11	enyzmatically	enyzmatically	RB	_	_	_
12	lysed	lyse	VBN	_	_	_
13	in	in	IN	_	_	_
14	the	the	DT	_	_	_
15	presence	presence	NN	_	_	_
16	of	of	IN	_	_	_
17	protease	protease	NN	_	_	_
18	inhibitors	inhibitor	NNS	_	_	_
19	prior	prior	RB	_	_	_
20	to	to	TO	_	_	_
21	fragmentation	fragmentation	NN	_	_	_
22	using	use	VBG	_	_	_
23	sonication	sonication	NN	_	_	_
24	.	.	.	_	_	_

1	Protein	protein	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	in	in	IN	_	_	_
7	shake	shake	NN	_	_	_
8	flasks	flask	NNS	_	_	_
9	to	to	TO	_	_	_
10	mid-exponential	mid-exponential	JJ	_	_	_
11	phase	phase	NN	_	_	_
12	under	under	IN	_	_	_
13	either	either	CC	_	_	_
14	aerobic	aerobic	JJ	_	_	_
15	or	or	CC	_	_	_
16	anaerobic	anaerobic	JJ	_	_	_
17	conditions	condition	NNS	_	_	_
18	depending	depend	VBG	_	_	_
19	on	on	IN	_	_	_
20	the	the	DT	_	_	_
21	sample	sample	NN	_	_	_
22	.	.	.	_	_	_

1	M9	m9	NN	MED	_	_
2	minimal	minimal	JJ	MED	_	_
3	media	media	NNS	MED	_	_
4	supplement	supplement	NN	_	_	_
5	with	with	IN	_	_	_
6	either	either	CC	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	,	,	,	_	_	_
9	fructose	fructose	NN	_	_	_
10	,	,	,	_	_	_
11	or	or	CC	_	_	_
12	glycerol	glycerol	NN	SUPP	_	_
13	as	as	IN	_	_	_
14	the	the	DT	_	_	_
15	sole	sole	JJ	_	_	_
16	carbon	carbon	NN	_	_	_
17	source	source	NN	_	_	_
18	was	be	VBD	_	_	_
19	used	use	VBN	_	_	_
20	depending	depend	VBG	_	_	_
21	on	on	IN	_	_	_
22	the	the	DT	_	_	_
23	sample	sample	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	chip	chip	NN	_	_	_
3	antibody	antibody	NN	_	_	_
4	:	:	:	_	_	_
5	c-Myc	c-myc	NN	_	_	_
6	Antibody	antibody	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	9E10	9e10	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	,	,	,	_	_	_
11	Santa	Santa	NNP	_	_	_
12	Cruz	Cruz	NNP	_	_	_
13	Biotech	Biotech	NNP	_	_	_
14	,	,	,	_	_	_
15	sc-40	sc-40	JJ	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
17	chip	chip	NN	_	_	_
18	antibody	antibody	NN	_	_	_
19	:	:	:	_	_	_
20	E.	e.	FW	_	_	_
21	coli	coli	FW	_	_	_
22	CRP	crp	NN	TF	_	_
23	Monoclonal	monoclonal	JJ	_	_	_
24	Antibody	antibody	NN	_	_	_
25	,	,	,	_	_	_
26	Neoclone	neoclone	NN	_	_	_
27	,	,	,	_	_	_
28	#N0004	#n0004	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
30	chip	chip	NN	_	_	_
31	antibody	antibody	NN	_	_	_
32	:	:	:	_	_	_
33	E.	e.	FW	_	_	_
34	coli	coli	FW	_	_	_
35	RNA	rna	NN	_	_	_
36	Sigma	Sigma	NNP	_	_	_
37	70	70	CD	_	_	_
38	Monoclonal	monoclonal	JJ	_	_	_
39	Antibody	antibody	NN	_	_	_
40	,	,	,	_	_	_
41	Neoclone	neoclone	NN	_	_	_
42	,	,	,	_	_	_
43	#WP004	#wp004	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	ChIPExo-ArcA	chipexo-arca	NN	_	_	_
46	_	_	CD	_	_	_
47	ArcA8myc	arca8myc	NN	_	_	_
48	_	_	NN	_	_	_
49	glucose	glucose	NN	SUPP	_	_
50	_	_	CD	_	_	_
51	NH4Cl	nh4cl	NN	_	_	_
52	_	_	NN	_	_	_
53	anaerobic	anaerobic	JJ	_	_	_
54	_	_	NN	_	_	_
55	1	1	CD	_	_	_
56	_	_	NN	_	_	_
57	anti-myc	anti-myc	JJ	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	ChIPExo-ArcA	chipexo-arca	NN	_	_	_
60	_	_	CD	_	_	_
61	ArcA8myc	arca8myc	NN	_	_	_
62	_	_	NN	_	_	_
63	glucose	glucose	NN	SUPP	_	_
64	_	_	CD	_	_	_
65	NH4Cl	nh4cl	NN	_	_	_
66	_	_	NN	_	_	_
67	anaerobic	anaerobic	JJ	_	_	_
68	_	_	NN	_	_	_
69	2	2	CD	_	_	_
70	_	_	SYM	_	_	_
71	anti-myc	anti-myc	JJ	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	ChIPExo-ArcA	chipexo-arca	NN	_	_	_
74	_	_	CD	_	_	_
75	ArcA8myc	arca8myc	NN	_	_	_
76	_	_	NN	_	_	_
77	glucose	glucose	NN	SUPP	_	_
78	_	_	CD	_	_	_
79	NH4Cl	nh4cl	NN	_	_	_
80	_	_	NN	_	_	_
81	anaerobic	anaerobic	JJ	_	_	_
82	_	_	NN	_	_	_
83	3	3	CD	_	_	_
84	_	_	NN	_	_	_
85	anti-myc	anti-myc	JJ	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
88	_	_	NN	_	_	_
89	delAr1delAr2	delar1delar2	NN	_	_	_
90	_	_	CD	_	_	_
91	glycerol	glycerol	NN	SUPP	_	_
92	_	_	NN	_	_	_
93	NH4Cl	nh4cl	NN	_	_	_
94	_	_	CD	_	_	_
95	O2	o2	CD	_	_	_
96	_	_	NN	_	_	_
97	1	1	CD	_	_	_
98	_	_	NN	_	_	_
99	anti-crp	anti-crp	JJ	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
102	_	_	NN	_	_	_
103	delAr1delAr2	delar1delar2	NN	_	_	_
104	_	_	CD	_	_	_
105	glycerol	glycerol	NN	SUPP	_	_
106	_	_	NN	_	_	_
107	NH4Cl	nh4cl	NN	_	_	_
108	_	_	CD	_	_	_
109	O2	o2	CD	_	_	_
110	_	_	NN	_	_	_
111	2	2	CD	_	_	_
112	_	_	SYM	_	_	_
113	anti-crp	anti-crp	JJ	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
116	_	_	NN	_	_	_
117	delAr1delAr2	delar1delar2	NN	_	_	_
118	_	_	CD	_	_	_
119	glycerol	glycerol	NN	SUPP	_	_
120	_	_	NN	_	_	_
121	NH4Cl	nh4cl	NN	_	_	_
122	_	_	CD	_	_	_
123	O2	o2	CD	_	_	_
124	_	_	NN	_	_	_
125	3	3	CD	_	_	_
126	_	_	NN	_	_	_
127	anti-crp	anti-crp	JJ	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
130	_	_	NN	_	_	_
131	delAr1	delar1	NN	_	_	_
132	_	_	CD	_	_	_
133	glycerol	glycerol	NN	SUPP	_	_
134	_	_	NN	_	_	_
135	NH4Cl	nh4cl	NN	_	_	_
136	_	_	CD	_	_	_
137	O2	o2	CD	_	_	_
138	_	_	NN	_	_	_
139	1	1	CD	_	_	_
140	_	_	NN	_	_	_
141	anti-crp	anti-crp	JJ	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
144	_	_	NN	_	_	_
145	delAr1	delar1	NN	_	_	_
146	_	_	CD	_	_	_
147	glycerol	glycerol	NN	SUPP	_	_
148	_	_	NN	_	_	_
149	NH4Cl	nh4cl	NN	_	_	_
150	_	_	CD	_	_	_
151	O2	o2	CD	_	_	_
152	_	_	NN	_	_	_
153	2	2	CD	_	_	_
154	_	_	SYM	_	_	_
155	anti-crp	anti-crp	JJ	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
157	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
158	_	_	NN	_	_	_
159	delAr1	delar1	NN	_	_	_
160	_	_	CD	_	_	_
161	glycerol	glycerol	NN	SUPP	_	_
162	_	_	NN	_	_	_
163	NH4Cl	nh4cl	NN	_	_	_
164	_	_	CD	_	_	_
165	O2	o2	CD	_	_	_
166	_	_	NN	_	_	_
167	3	3	CD	_	_	_
168	_	_	NN	_	_	_
169	anti-crp	anti-crp	JJ	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
172	_	_	NN	_	_	_
173	delAr2	delar2	NN	_	_	_
174	_	_	CD	_	_	_
175	glycerol	glycerol	NN	SUPP	_	_
176	_	_	NN	_	_	_
177	NH4Cl	nh4cl	NN	_	_	_
178	_	_	CD	_	_	_
179	O2	o2	CD	_	_	_
180	_	_	NN	_	_	_
181	1	1	CD	_	_	_
182	_	_	NN	_	_	_
183	anti-crp	anti-crp	JJ	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
186	_	_	NN	_	_	_
187	delAr2	delar2	NN	_	_	_
188	_	_	CD	_	_	_
189	glycerol	glycerol	NN	SUPP	_	_
190	_	_	NN	_	_	_
191	NH4Cl	nh4cl	NN	_	_	_
192	_	_	CD	_	_	_
193	O2	o2	CD	_	_	_
194	_	_	NN	_	_	_
195	2	2	CD	_	_	_
196	_	_	SYM	_	_	_
197	anti-crp	anti-crp	JJ	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
200	_	_	NN	_	_	_
201	delAr2	delar2	NN	_	_	_
202	_	_	CD	_	_	_
203	glycerol	glycerol	NN	SUPP	_	_
204	_	_	NN	_	_	_
205	NH4Cl	nh4cl	NN	_	_	_
206	_	_	CD	_	_	_
207	O2	o2	CD	_	_	_
208	_	_	NN	_	_	_
209	3	3	CD	_	_	_
210	_	_	NN	_	_	_
211	anti-crp	anti-crp	JJ	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
214	_	_	NN	_	_	_
215	delta-crp	delta-crp	JJ	_	_	_
216	_	_	NN	_	_	_
217	glycerol	glycerol	NN	SUPP	_	_
218	_	_	CD	_	_	_
219	NH4Cl	nh4cl	NN	_	_	_
220	_	_	CD	_	_	_
221	O2	o2	CD	_	_	_
222	_	_	NN	_	_	_
223	1	1	CD	_	_	_
224	_	_	NN	_	_	_
225	anti-crp	anti-crp	JJ	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
228	_	_	NN	_	_	_
229	delta-crp	delta-crp	JJ	_	_	_
230	_	_	NN	_	_	_
231	glycerol	glycerol	NN	SUPP	_	_
232	_	_	CD	_	_	_
233	NH4Cl	nh4cl	NN	_	_	_
234	_	_	CD	_	_	_
235	O2	o2	CD	_	_	_
236	_	_	NN	_	_	_
237	2	2	CD	_	_	_
238	_	_	SYM	_	_	_
239	anti-crp	anti-crp	JJ	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
241	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
242	_	_	NN	_	_	_
243	delta-crp	delta-crp	JJ	_	_	_
244	_	_	NN	_	_	_
245	glycerol	glycerol	NN	SUPP	_	_
246	_	_	CD	_	_	_
247	NH4Cl	nh4cl	NN	_	_	_
248	_	_	CD	_	_	_
249	O2	o2	CD	_	_	_
250	_	_	NN	_	_	_
251	3	3	CD	_	_	_
252	_	_	NN	_	_	_
253	anti-crp	anti-crp	JJ	_	_	_
254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
255	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
256	_	_	NN	_	_	_
257	wt	wt	JJ	_	_	_
258	_	_	NN	_	_	_
259	fructose	fructose	NN	_	_	_
260	_	_	CD	_	_	_
261	NH4Cl	nh4cl	NN	_	_	_
262	_	_	CD	_	_	_
263	O2	o2	CD	_	_	_
264	_	_	NN	_	_	_
265	1	1	CD	_	_	_
266	_	_	CD	_	_	_
267	anti-crp	anti-crp	JJ	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
269	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
270	_	_	NN	_	_	_
271	wt	wt	JJ	_	_	_
272	_	_	NN	_	_	_
273	fructose	fructose	NN	_	_	_
274	_	_	CD	_	_	_
275	NH4Cl	nh4cl	NN	_	_	_
276	_	_	CD	_	_	_
277	O2	o2	CD	_	_	_
278	_	_	NN	_	_	_
279	2	2	CD	_	_	_
280	_	_	CD	_	_	_
281	anti-crp	anti-crp	JJ	_	_	_
282	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
283	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
284	_	_	NN	_	_	_
285	wt	wt	JJ	_	_	_
286	_	_	NN	_	_	_
287	fructose	fructose	NN	_	_	_
288	_	_	CD	_	_	_
289	NH4Cl	nh4cl	NN	_	_	_
290	_	_	CD	_	_	_
291	O2	o2	CD	_	_	_
292	_	_	NN	_	_	_
293	3	3	CD	_	_	_
294	_	_	NN	_	_	_
295	anti-crp	anti-crp	JJ	_	_	_
296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
297	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
298	_	_	NN	_	_	_
299	wt	wt	JJ	_	_	_
300	_	_	NN	_	_	_
301	fructose	fructose	NN	_	_	_
302	_	_	CD	_	_	_
303	NH4Cl	nh4cl	NN	_	_	_
304	_	_	CD	_	_	_
305	O2	o2	CD	_	_	_
306	_	_	NN	_	_	_
307	4	4	CD	_	_	_
308	_	_	SYM	_	_	_
309	anti-crp	anti-crp	JJ	_	_	_
310	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
311	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
312	_	_	NN	_	_	_
313	wt	wt	JJ	_	_	_
314	_	_	NN	_	_	_
315	fructose	fructose	NN	_	_	_
316	_	_	CD	_	_	_
317	NH4Cl	nh4cl	NN	_	_	_
318	_	_	SYM	_	_	_
319	O2	o2	CD	_	_	_
320	_	_	SYM	_	_	_
321	5	5	CD	_	_	_
322	_	_	SYM	_	_	_
323	anti-crp	anti-crp	JJ	_	_	_
324	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
325	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
326	_	_	NN	_	_	_
327	wt	wt	JJ	_	_	_
328	_	_	NN	_	_	_
329	glucose	glucose	NN	SUPP	_	_
330	_	_	CD	_	_	_
331	NH4Cl	nh4cl	NN	_	_	_
332	_	_	CD	_	_	_
333	O2	o2	CD	_	_	_
334	_	_	NN	_	_	_
335	1	1	CD	_	_	_
336	_	_	CD	_	_	_
337	anti-crp	anti-crp	JJ	_	_	_
338	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
339	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
340	_	_	NN	_	_	_
341	wt	wt	JJ	_	_	_
342	_	_	NN	_	_	_
343	glucose	glucose	NN	SUPP	_	_
344	_	_	CD	_	_	_
345	NH4Cl	nh4cl	NN	_	_	_
346	_	_	CD	_	_	_
347	O2	o2	CD	_	_	_
348	_	_	NN	_	_	_
349	2	2	CD	_	_	_
350	_	_	CD	_	_	_
351	anti-crp	anti-crp	JJ	_	_	_
352	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
353	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
354	_	_	NN	_	_	_
355	wt	wt	JJ	_	_	_
356	_	_	NN	_	_	_
357	glycerol	glycerol	NN	SUPP	_	_
358	_	_	CD	_	_	_
359	NH4Cl	nh4cl	NN	_	_	_
360	_	_	CD	_	_	_
361	O2	o2	CD	_	_	_
362	_	_	NN	_	_	_
363	1	1	CD	_	_	_
364	_	_	CD	_	_	_
365	anti-crp	anti-crp	JJ	_	_	_
366	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
367	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
368	_	_	NN	_	_	_
369	wt	wt	JJ	_	_	_
370	_	_	NN	_	_	_
371	glycerol	glycerol	NN	SUPP	_	_
372	_	_	CD	_	_	_
373	NH4Cl	nh4cl	NN	_	_	_
374	_	_	CD	_	_	_
375	O2	o2	CD	_	_	_
376	_	_	NN	_	_	_
377	1	1	CD	_	_	_
378	_	_	CD	_	_	_
379	anti-crp	anti-crp	JJ	_	_	_
380	_	_	NN	_	_	_
381	rif	rif	NN	_	_	_
382	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
383	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
384	_	_	NN	_	_	_
385	wt	wt	JJ	_	_	_
386	_	_	NN	_	_	_
387	glycerol	glycerol	NN	SUPP	_	_
388	_	_	CD	_	_	_
389	NH4Cl	nh4cl	NN	_	_	_
390	_	_	CD	_	_	_
391	O2	o2	CD	_	_	_
392	_	_	NN	_	_	_
393	2	2	CD	_	_	_
394	_	_	CD	_	_	_
395	anti-crp	anti-crp	JJ	_	_	_
396	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
397	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
398	_	_	NN	_	_	_
399	wt	wt	JJ	_	_	_
400	_	_	NN	_	_	_
401	glycerol	glycerol	NN	SUPP	_	_
402	_	_	CD	_	_	_
403	NH4Cl	nh4cl	NN	_	_	_
404	_	_	CD	_	_	_
405	O2	o2	CD	_	_	_
406	_	_	NN	_	_	_
407	2	2	CD	_	_	_
408	_	_	CD	_	_	_
409	anti-crp	anti-crp	JJ	_	_	_
410	_	_	NN	_	_	_
411	rif	rif	NN	_	_	_
412	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
413	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
414	_	_	NN	_	_	_
415	wt	wt	JJ	_	_	_
416	_	_	NN	_	_	_
417	glycerol	glycerol	NN	SUPP	_	_
418	_	_	CD	_	_	_
419	NH4Cl	nh4cl	NN	_	_	_
420	_	_	CD	_	_	_
421	O2	o2	CD	_	_	_
422	_	_	NN	_	_	_
423	3	3	CD	_	_	_
424	_	_	NN	_	_	_
425	anti-crp	anti-crp	JJ	_	_	_
426	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
427	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
428	_	_	NN	_	_	_
429	wt	wt	JJ	_	_	_
430	_	_	NN	_	_	_
431	glycerol	glycerol	NN	SUPP	_	_
432	_	_	CD	_	_	_
433	NH4Cl	nh4cl	NN	_	_	_
434	_	_	CD	_	_	_
435	O2	o2	CD	_	_	_
436	_	_	NN	_	_	_
437	3	3	CD	_	_	_
438	_	_	NN	_	_	_
439	anti-crp	anti-crp	JJ	_	_	_
440	_	_	NN	_	_	_
441	rif	rif	NN	_	_	_
442	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
443	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
444	_	_	NN	_	_	_
445	wt	wt	JJ	_	_	_
446	_	_	NN	_	_	_
447	glycerol	glycerol	NN	SUPP	_	_
448	_	_	CD	_	_	_
449	NH4Cl	nh4cl	NN	_	_	_
450	_	_	CD	_	_	_
451	O2	o2	CD	_	_	_
452	_	_	NN	_	_	_
453	4	4	CD	_	_	_
454	_	_	SYM	_	_	_
455	anti-crp	anti-crp	JJ	_	_	_
456	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
457	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
458	_	_	NN	_	_	_
459	wt	wt	JJ	_	_	_
460	_	_	NN	_	_	_
461	glycerol	glycerol	NN	SUPP	_	_
462	_	_	CD	_	_	_
463	NH4Cl	nh4cl	NN	_	_	_
464	_	_	SYM	_	_	_
465	O2	o2	CD	_	_	_
466	_	_	SYM	_	_	_
467	5	5	CD	_	_	_
468	_	_	SYM	_	_	_
469	anti-crp	anti-crp	JJ	_	_	_
470	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
471	ChIPExo-Crp	chipexo-crp	JJ	_	_	_
472	_	_	NN	_	_	_
473	wt	wt	JJ	_	_	_
474	_	_	NN	_	_	_
475	glycerol	glycerol	NN	SUPP	_	_
476	_	_	CD	_	_	_
477	NH4Cl	nh4cl	NN	_	_	_
478	_	_	CD	_	_	_
479	O2	o2	CD	_	_	_
480	_	_	NN	_	_	_
481	6	6	CD	_	_	_
482	_	_	NN	_	_	_
483	anti-crp	anti-crp	JJ	_	_	_
484	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
485	ChIPExo-Fnr	chipexo-fnr	JJ	_	_	_
486	_	_	NN	_	_	_
487	Fnr8myc	fnr8myc	NN	_	_	_
488	_	_	NN	_	_	_
489	glucose	glucose	NN	SUPP	_	_
490	_	_	CD	_	_	_
491	NH4Cl	nh4cl	NN	_	_	_
492	_	_	NN	_	_	_
493	anaerobic	anaerobic	JJ	_	_	_
494	_	_	NN	_	_	_
495	1	1	CD	_	_	_
496	_	_	CD	_	_	_
497	anti-myc	anti-myc	JJ	_	_	_
498	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
499	ChIPExo-Fnr	chipexo-fnr	JJ	_	_	_
500	_	_	NN	_	_	_
501	Fnr8myc	fnr8myc	NN	_	_	_
502	_	_	NN	_	_	_
503	glucose	glucose	NN	SUPP	_	_
504	_	_	CD	_	_	_
505	NH4Cl	nh4cl	NN	_	_	_
506	_	_	NN	_	_	_
507	anaerobic	anaerobic	JJ	_	_	_
508	_	_	NN	_	_	_
509	2	2	CD	_	_	_
510	_	_	CD	_	_	_
511	anti-myc	anti-myc	JJ	_	_	_
512	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
513	ChIPExo-Fnr	chipexo-fnr	JJ	_	_	_
514	_	_	NN	_	_	_
515	Fnr8myc	fnr8myc	NN	_	_	_
516	_	_	NN	_	_	_
517	glucose	glucose	NN	SUPP	_	_
518	_	_	CD	_	_	_
519	NH4Cl	nh4cl	NN	_	_	_
520	_	_	NN	_	_	_
521	anaerobic	anaerobic	JJ	_	_	_
522	_	_	NN	_	_	_
523	3	3	CD	_	_	_
524	_	_	NN	_	_	_
525	anti-myc	anti-myc	JJ	_	_	_
526	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
527	ChIPExo-RpoD	chipexo-rpod	NN	_	_	_
528	_	_	CD	_	_	_
529	wt	wt	JJ	_	_	_
530	_	_	NN	_	_	_
531	fructose	fructose	NN	_	_	_
532	_	_	CD	_	_	_
533	NH4Cl	nh4cl	NN	_	_	_
534	_	_	CD	_	_	_
535	O2	o2	CD	_	_	_
536	_	_	NN	_	_	_
537	1	1	CD	_	_	_
538	_	_	NN	_	_	_
539	anti-rpod	anti-rpod	JJ	_	_	_
540	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
541	ChIPExo-RpoD	chipexo-rpod	NN	_	_	_
542	_	_	CD	_	_	_
543	wt	wt	JJ	_	_	_
544	_	_	NN	_	_	_
545	fructose	fructose	NN	_	_	_
546	_	_	CD	_	_	_
547	NH4Cl	nh4cl	NN	_	_	_
548	_	_	CD	_	_	_
549	O2	o2	CD	_	_	_
550	_	_	NN	_	_	_
551	2	2	CD	_	_	_
552	_	_	SYM	_	_	_
553	anti-rpod	anti-rpod	JJ	_	_	_
554	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
555	ChIPExo-RpoD	chipexo-rpod	NN	_	_	_
556	_	_	CD	_	_	_
557	wt	wt	JJ	_	_	_
558	_	_	NN	_	_	_
559	fructose	fructose	NN	_	_	_
560	_	_	CD	_	_	_
561	NH4Cl	nh4cl	NN	_	_	_
562	_	_	CD	_	_	_
563	O2	o2	CD	_	_	_
564	_	_	NN	_	_	_
565	3	3	CD	_	_	_
566	_	_	NN	_	_	_
567	anti-rpod	anti-rpod	JJ	_	_	_
568	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
569	ChIPExo-RpoD	chipexo-rpod	NN	_	_	_
570	_	_	CD	_	_	_
571	wt	wt	JJ	_	_	_
572	_	_	NN	_	_	_
573	glucose	glucose	NN	SUPP	_	_
574	_	_	CD	_	_	_
575	NH4Cl	nh4cl	NN	_	_	_
576	_	_	CD	_	_	_
577	O2	o2	CD	_	_	_
578	_	_	NN	_	_	_
579	1	1	CD	_	_	_
580	_	_	NN	_	_	_
581	anti-rpod	anti-rpod	JJ	_	_	_
582	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
583	ChIPExo-RpoD	chipexo-rpod	NN	_	_	_
584	_	_	CD	_	_	_
585	wt	wt	JJ	_	_	_
586	_	_	NN	_	_	_
587	glucose	glucose	NN	SUPP	_	_
588	_	_	CD	_	_	_
589	NH4Cl	nh4cl	NN	_	_	_
590	_	_	CD	_	_	_
591	O2	o2	CD	_	_	_
592	_	_	NN	_	_	_
593	2	2	CD	_	_	_
594	_	_	SYM	_	_	_
595	anti-rpod	anti-rpod	JJ	_	_	_
596	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
597	ChIPExo-RpoD	chipexo-rpod	NN	_	_	_
598	_	_	CD	_	_	_
599	wt	wt	JJ	_	_	_
600	_	_	NN	_	_	_
601	glucose	glucose	NN	SUPP	_	_
602	_	_	CD	_	_	_
603	NH4Cl	nh4cl	NN	_	_	_
604	_	_	CD	_	_	_
605	O2	o2	CD	_	_	_
606	_	_	NN	_	_	_
607	3	3	CD	_	_	_
608	_	_	NN	_	_	_
609	anti-rpod	anti-rpod	JJ	_	_	_
610	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
611	ChIPExo-RpoD	chipexo-rpod	NN	_	_	_
612	_	_	CD	_	_	_
613	wt	wt	JJ	_	_	_
614	_	_	NN	_	_	_
615	glycerol	glycerol	NN	SUPP	_	_
616	_	_	CD	_	_	_
617	NH4Cl	nh4cl	NN	_	_	_
618	_	_	CD	_	_	_
619	O2	o2	CD	_	_	_
620	_	_	NN	_	_	_
621	1	1	CD	_	_	_
622	_	_	NN	_	_	_
623	anti-rpod	anti-rpod	JJ	_	_	_
624	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
625	ChIPExo-RpoD	chipexo-rpod	NN	_	_	_
626	_	_	CD	_	_	_
627	wt	wt	JJ	_	_	_
628	_	_	NN	_	_	_
629	glycerol	glycerol	NN	SUPP	_	_
630	_	_	CD	_	_	_
631	NH4Cl	nh4cl	NN	_	_	_
632	_	_	CD	_	_	_
633	O2	o2	CD	_	_	_
634	_	_	NN	_	_	_
635	2	2	CD	_	_	_
636	_	_	SYM	_	_	_
637	anti-rpod	anti-rpod	JJ	_	_	_
638	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
639	ChIPExo-RpoD	chipexo-rpod	NN	_	_	_
640	_	_	CD	_	_	_
641	wt	wt	JJ	_	_	_
642	_	_	NN	_	_	_
643	glycerol	glycerol	NN	SUPP	_	_
644	_	_	CD	_	_	_
645	NH4Cl	nh4cl	NN	_	_	_
646	_	_	CD	_	_	_
647	O2	o2	CD	_	_	_
648	_	_	NN	_	_	_
649	3	3	CD	_	_	_
650	_	_	NN	_	_	_
651	anti-rpod	anti-rpod	JJ	_	_	_
652	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
653	ChIP-Seq	chip-seq	NN	_	_	_
654	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
655	Chromosomal	chromosomal	JJ	_	_	_
656	DNA	dna	NN	_	_	_
657	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
658	Escherichia	escherichia	FW	Organism	_	_
659	coli	coli	FW	Organism	_	_
660	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
661	Genome	Genome	NNP	_	_	_
662	_	_	NNP	_	_	_
663	build	build	VB	_	_	_
664	:	:	:	_	_	_
665	NC	NC	NNP	_	_	_
666	_	_	NNP	_	_	_
667	000913.2	000913.2	CD	_	_	_
668	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
669	Library	Library	NNP	_	_	_
670	construction	construction	NN	_	_	_
671	was	be	VBD	_	_	_
672	based	base	VBN	_	_	_
673	on	on	IN	_	_	_
674	the	the	DT	_	_	_
675	method	method	NN	_	_	_
676	described	describe	VBN	_	_	_
677	by	by	IN	_	_	_
678	Rhee	Rhee	NNP	_	_	_
679	et	et	FW	_	_	_
680	al.	al.	FW	_	_	_
681	-LRB-	-lrb-	-LRB-	_	_	_
682	doi	doi	FW	_	_	_
683	:	:	:	_	_	_
684	10.1016	10.1016	CD	_	_	_
685	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
686	Peak-calls	peak-call	NNS	_	_	_
687	were	be	VBD	_	_	_
688	done	do	VBN	_	_	_
689	using	use	VBG	_	_	_
690	GPS	gps	NN	_	_	_
691	within	within	IN	_	_	_
692	the	the	DT	_	_	_
693	GEMS	gem	NNS	_	_	_
694	software	software	NN	_	_	_
695	package	package	NN	_	_	_
696	-LRB-	-lrb-	-LRB-	_	_	_
697	v2	v2	NN	_	_	_
698	.3	.3	NN	_	_	_
699	-RRB-	-rrb-	-RRB-	_	_	_
700	adapted	adapt	VBD	_	_	_
701	for	for	IN	_	_	_
702	ChIP-exo	ChIP-exo	NNP	_	_	_
703	data	datum	NNS	_	_	_
704	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
705	strain	strain	NN	_	_	_
706	:	:	:	_	_	_
707	ArcA8myc	arca8myc	NN	_	_	_
708	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
709	strain	strain	NN	_	_	_
710	:	:	:	_	_	_
711	Crp	Crp	NNP	_	_	_
712	_	_	SYM	_	_	_
713	delAr1	delar1	NN	_	_	_
714	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
715	strain	strain	NN	_	_	_
716	:	:	:	_	_	_
717	Crp	Crp	NNP	_	_	_
718	_	_	SYM	_	_	_
719	delAr1delAr2	delar1delar2	NN	_	_	_
720	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
721	strain	strain	NN	_	_	_
722	:	:	:	_	_	_
723	Crp	Crp	NNP	_	_	_
724	_	_	SYM	_	_	_
725	delAr2	delar2	NN	_	_	_
726	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
727	strain	strain	NN	_	_	_
728	:	:	:	_	_	_
729	delta	delta	NN	_	_	_
730	Crp	crp	NN	_	_	_
731	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
732	strain	strain	NN	_	_	_
733	:	:	:	_	_	_
734	Fnr8myc	fnr8myc	NN	_	_	_
735	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
736	strain	strain	NN	_	_	_
737	:	:	:	_	_	_
738	wt	wt	JJ	_	_	_
739	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
740	Supplementary	supplementary	JJ	_	_	_
741	_	_	NN	_	_	_
742	files	file	NNS	_	_	_
743	_	_	IN	_	_	_
744	format	format	NN	_	_	_
745	_	_	NN	_	_	_
746	and	and	CC	_	_	_
747	_	_	NN	_	_	_
748	content	content	NN	_	_	_
749	:	:	:	_	_	_
750	Processed	process	VBN	_	_	_
751	data	datum	NNS	_	_	_
752	is	be	VBZ	_	_	_
753	presented	present	VBN	_	_	_
754	in	in	IN	_	_	_
755	gff	gff	NN	_	_	_
756	files	file	NNS	_	_	_
757	containing	contain	VBG	_	_	_
758	a	a	DT	_	_	_
759	pileup	pileup	NN	_	_	_
760	of	of	IN	_	_	_
761	5	5	CD	_	_	_
762	'	'	''	_	_	_
763	tags	tag	NNS	_	_	_
764	.	.	.	_	_	_

1	GFF	gff	NN	_	_	_
2	column	column	NN	_	_	_
3	headers	header	NNS	_	_	_
4	\	\	VBP	_	_	_
5	Genbank	Genbank	NNP	_	_	_
6	fna	fna	NNP	_	_	_
7	ID	ID	NNP	_	_	_
8	,	,	,	_	_	_
9	file	file	NN	_	_	_
10	name	name	NN	_	_	_
11	,	,	,	_	_	_
12	left	leave	VBD	_	_	_
13	genomic	genomic	JJ	_	_	_
14	position	position	NN	_	_	_
15	,	,	,	_	_	_
16	right	right	JJ	_	_	_
17	genomic	genomic	JJ	_	_	_
18	position	position	NN	_	_	_
19	,	,	,	_	_	_
20	value	value	NN	_	_	_
21	,	,	,	_	_	_
22	strand	strand	NN	_	_	_
23	,	,	,	_	_	_
24	extra	extra	JJ	_	_	_
25	value	value	NN	_	_	_
26	,	,	,	_	_	_
27	information	information	NN	_	_	_
28	\	\	SYM	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
30	The	the	DT	_	_	_
31	MiSeq	MiSeq	NNP	_	_	_
32	Reporter	reporter	NN	_	_	_
33	MiSeq	miseq	NN	_	_	_
34	Reporter	reporter	NN	_	_	_
35	2.4.60.8	2.4.60.8	CD	_	_	_
36	was	be	VBD	_	_	_
37	used	use	VBN	_	_	_
38	for	for	IN	_	_	_
39	basecalling	basecalling	NN	_	_	_
40	and	and	CC	_	_	_
41	demultiplexing	demultiplex	VBG	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	bowtie2	bowtie2	NN	_	_	_
44	v2	v2	NN	_	_	_
45	.2.3	.2.3	CD	_	_	_
46	was	be	VBD	_	_	_
47	used	use	VBN	_	_	_
48	for	for	IN	_	_	_
49	alignment	alignment	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	Cells	cell	NNS	_	_	_
52	were	be	VBD	_	_	_
53	grown	grow	VBN	_	_	_
54	in	in	IN	_	_	_
55	shake	shake	NN	_	_	_
56	flasks	flask	NNS	_	_	_
57	to	to	TO	_	_	_
58	mid-exponential	mid-exponential	JJ	_	_	_
59	phase	phase	NN	_	_	_
60	under	under	IN	_	_	_
61	either	either	CC	_	_	_
62	aerobic	aerobic	JJ	_	_	_
63	or	or	CC	_	_	_
64	anaerobic	anaerobic	JJ	_	_	_
65	conditions	condition	NNS	_	_	_
66	depending	depend	VBG	_	_	_
67	on	on	IN	_	_	_
68	the	the	DT	_	_	_
69	sample	sample	NN	_	_	_
70	.	.	.	_	_	_

1	M9	m9	NN	MED	_	_
2	minimal	minimal	JJ	MED	_	_
3	media	media	NNS	MED	_	_
4	supplement	supplement	NN	_	_	_
5	with	with	IN	_	_	_
6	either	either	CC	_	_	_
7	glucose	glucose	NN	SUPP	_	_
8	,	,	,	_	_	_
9	fructose	fructose	NN	_	_	_
10	,	,	,	_	_	_
11	or	or	CC	_	_	_
12	glycerol	glycerol	NN	SUPP	_	_
13	as	as	IN	_	_	_
14	the	the	DT	_	_	_
15	sole	sole	JJ	_	_	_
16	carbon	carbon	NN	_	_	_
17	source	source	NN	_	_	_
18	was	be	VBD	_	_	_
19	used	use	VBN	_	_	_
20	depending	depend	VBG	_	_	_
21	on	on	IN	_	_	_
22	the	the	DT	_	_	_
23	sample	sample	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	K12	k12	NN	_	_	_
5	MG1655	mg1655	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Escherichia	escherichia	FW	Organism	_	_
8	coli	coli	FW	Organism	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Gene	gene	NN	_	_	_
11	expression	expression	NN	_	_	_
12	analysis	analysis	NN	_	_	_
13	was	be	VBD	_	_	_
14	performed	perform	VBN	_	_	_
15	using	use	VBG	_	_	_
16	a	a	DT	_	_	_
17	strand-specific	strand-specific	JJ	_	_	_
18	,	,	,	_	_	_
19	paired-end	paired-end	JJ	_	_	_
20	RNA-seq	rna-seq	NN	_	_	_
21	protocol	protocol	NN	_	_	_
22	using	use	VBG	_	_	_
23	the	the	DT	_	_	_
24	dUTP	dutp	NN	_	_	_
25	method	method	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Levin	Levin	NNP	_	_	_
28	et	et	FW	_	_	_
29	al.	al.	FW	_	_	_
30	,	,	,	_	_	_
31	2010	2010	CD	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	and	and	CC	_	_	_
6	purified	purify	VBN	_	_	_
7	using	use	VBG	_	_	_
8	the	the	DT	_	_	_
9	Qiagen	Qiagen	NNP	_	_	_
10	Rneasy	Rneasy	NNP	_	_	_
11	Kit	kit	NN	_	_	_
12	with	with	IN	_	_	_
13	on-column	on-column	JJ	_	_	_
14	DNase	dnase	NN	_	_	_
15	treatment	treatment	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	NC	NC	NNP	_	_	_
7	_	_	NNP	_	_	_
8	000913.2	000913.2	CD	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	Reads	Reads	NNPS	_	_	_
11	were	be	VBD	_	_	_
12	mapped	map	VBN	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	NC	NC	NNP	_	_	_
16	_	_	SYM	_	_	_
17	000913.2	000913.2	CD	_	_	_
18	reference	reference	NN	_	_	_
19	genome	genome	NN	_	_	_
20	using	use	VBG	_	_	_
21	the	the	DT	_	_	_
22	default	default	NN	_	_	_
23	settings	setting	NNS	_	_	_
24	in	in	IN	_	_	_
25	bowtie2	bowtie2	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Langmead	langmead	NN	_	_	_
28	and	and	CC	_	_	_
29	Salzberg	Salzberg	NNP	_	_	_
30	,	,	,	_	_	_
31	2012	2012	CD	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Datasets	dataset	NNS	_	_	_
2	were	be	VBD	_	_	_
3	quantified	quantify	VBN	_	_	_
4	using	use	VBG	_	_	_
5	cuffdiff	cuffdiff	NN	_	_	_
6	in	in	IN	_	_	_
7	the	the	DT	_	_	_
8	cufflinks	cufflink	NNS	_	_	_
9	package	package	NN	_	_	_
10	to	to	TO	_	_	_
11	generate	generate	VB	_	_	_
12	FPKM	fpkm	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Framents	Framents	NNP	_	_	_
15	Per	per	IN	_	_	_
16	Kilobase	Kilobase	NNP	_	_	_
17	per	per	IN	_	_	_
18	Million	Million	NNP	_	_	_
19	reads	read	VBZ	_	_	_
20	mapped	map	VBN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	values	value	NNS	_	_	_
23	for	for	IN	_	_	_
24	all	all	DT	_	_	_
25	genes	gene	NNS	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Trapnell	Trapnell	NNP	_	_	_
28	et	et	FW	_	_	_
29	al.	al.	FW	_	_	_
30	,	,	,	_	_	_
31	2013	2013	CD	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	RNAseq	rnaseq	NN	_	_	_
5	_	_	CD	_	_	_
6	delAr1delAr2	delar1delar2	NN	_	_	_
7	_	_	NN	_	_	_
8	glycerol	glycerol	NN	SUPP	_	_
9	_	_	CD	_	_	_
10	NH4Cl	nh4cl	NN	_	_	_
11	_	_	CD	_	_	_
12	O2	o2	CD	_	_	_
13	_	_	NN	_	_	_
14	1	1	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	RNAseq	rnaseq	NN	_	_	_
17	_	_	CD	_	_	_
18	delAr1delAr2	delar1delar2	NN	_	_	_
19	_	_	NN	_	_	_
20	glycerol	glycerol	NN	SUPP	_	_
21	_	_	CD	_	_	_
22	NH4Cl	nh4cl	NN	_	_	_
23	_	_	CD	_	_	_
24	O2	o2	CD	_	_	_
25	_	_	NN	_	_	_
26	2	2	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	RNAseq	rnaseq	NN	_	_	_
29	_	_	CD	_	_	_
30	delAr1delAr2	delar1delar2	NN	_	_	_
31	_	_	NN	_	_	_
32	glycerol	glycerol	NN	SUPP	_	_
33	_	_	CD	_	_	_
34	NH4Cl	nh4cl	NN	_	_	_
35	_	_	CD	_	_	_
36	O2	o2	CD	_	_	_
37	_	_	NN	_	_	_
38	3	3	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	RNAseq	rnaseq	NN	_	_	_
41	_	_	CD	_	_	_
42	delAr1	delar1	NN	_	_	_
43	_	_	NN	_	_	_
44	glycerol	glycerol	NN	SUPP	_	_
45	_	_	CD	_	_	_
46	NH4Cl	nh4cl	NN	_	_	_
47	_	_	CD	_	_	_
48	O2	o2	CD	_	_	_
49	_	_	NN	_	_	_
50	1	1	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	RNAseq	rnaseq	NN	_	_	_
53	_	_	CD	_	_	_
54	delAr1	delar1	NN	_	_	_
55	_	_	NN	_	_	_
56	glycerol	glycerol	NN	SUPP	_	_
57	_	_	CD	_	_	_
58	NH4Cl	nh4cl	NN	_	_	_
59	_	_	CD	_	_	_
60	O2	o2	CD	_	_	_
61	_	_	NN	_	_	_
62	2	2	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	RNAseq	rnaseq	NN	_	_	_
65	_	_	CD	_	_	_
66	delAr1	delar1	NN	_	_	_
67	_	_	NN	_	_	_
68	glycerol	glycerol	NN	SUPP	_	_
69	_	_	CD	_	_	_
70	NH4Cl	nh4cl	NN	_	_	_
71	_	_	CD	_	_	_
72	O2	o2	CD	_	_	_
73	_	_	NN	_	_	_
74	3	3	CD	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	RNAseq	rnaseq	NN	_	_	_
77	_	_	CD	_	_	_
78	delAr2	delar2	NN	_	_	_
79	_	_	NN	_	_	_
80	glycerol	glycerol	NN	SUPP	_	_
81	_	_	CD	_	_	_
82	NH4Cl	nh4cl	NN	_	_	_
83	_	_	CD	_	_	_
84	O2	o2	CD	_	_	_
85	_	_	NN	_	_	_
86	1	1	CD	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	RNAseq	rnaseq	NN	_	_	_
89	_	_	CD	_	_	_
90	delAr2	delar2	NN	_	_	_
91	_	_	NN	_	_	_
92	glycerol	glycerol	NN	SUPP	_	_
93	_	_	CD	_	_	_
94	NH4Cl	nh4cl	NN	_	_	_
95	_	_	CD	_	_	_
96	O2	o2	CD	_	_	_
97	_	_	NN	_	_	_
98	2	2	CD	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	RNAseq	rnaseq	NN	_	_	_
101	_	_	CD	_	_	_
102	delAr2	delar2	NN	_	_	_
103	_	_	NN	_	_	_
104	glycerol	glycerol	NN	SUPP	_	_
105	_	_	CD	_	_	_
106	NH4Cl	nh4cl	NN	_	_	_
107	_	_	CD	_	_	_
108	O2	o2	CD	_	_	_
109	_	_	NN	_	_	_
110	3	3	CD	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	RNAseq	rnaseq	NN	_	_	_
113	_	_	CD	_	_	_
114	delta-crp	delta-crp	JJ	_	_	_
115	_	_	NN	_	_	_
116	fructose	fructose	NN	_	_	_
117	_	_	CD	_	_	_
118	NH4Cl	nh4cl	NN	_	_	_
119	_	_	CD	_	_	_
120	O2	o2	CD	_	_	_
121	_	_	NN	_	_	_
122	1	1	CD	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	RNAseq	rnaseq	NN	_	_	_
125	_	_	CD	_	_	_
126	delta-crp	delta-crp	JJ	_	_	_
127	_	_	NN	_	_	_
128	fructose	fructose	NN	_	_	_
129	_	_	CD	_	_	_
130	NH4Cl	nh4cl	NN	_	_	_
131	_	_	CD	_	_	_
132	O2	o2	CD	_	_	_
133	_	_	NN	_	_	_
134	2	2	CD	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	RNAseq	rnaseq	NN	_	_	_
137	_	_	CD	_	_	_
138	delta-crp	delta-crp	JJ	_	_	_
139	_	_	NN	_	_	_
140	fructose	fructose	NN	_	_	_
141	_	_	CD	_	_	_
142	NH4Cl	nh4cl	NN	_	_	_
143	_	_	CD	_	_	_
144	O2	o2	CD	_	_	_
145	_	_	NN	_	_	_
146	3	3	CD	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	RNAseq	rnaseq	NN	_	_	_
149	_	_	CD	_	_	_
150	delta-crp	delta-crp	JJ	_	_	_
151	_	_	NN	_	_	_
152	glucose	glucose	NN	SUPP	_	_
153	_	_	CD	_	_	_
154	NH4Cl	nh4cl	NN	_	_	_
155	_	_	CD	_	_	_
156	O2	o2	CD	_	_	_
157	_	_	NN	_	_	_
158	1	1	CD	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	RNAseq	rnaseq	NN	_	_	_
161	_	_	CD	_	_	_
162	delta-crp	delta-crp	JJ	_	_	_
163	_	_	NN	_	_	_
164	glucose	glucose	NN	SUPP	_	_
165	_	_	CD	_	_	_
166	NH4Cl	nh4cl	NN	_	_	_
167	_	_	CD	_	_	_
168	O2	o2	CD	_	_	_
169	_	_	NN	_	_	_
170	2	2	CD	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	RNAseq	rnaseq	NN	_	_	_
173	_	_	CD	_	_	_
174	delta-crp	delta-crp	JJ	_	_	_
175	_	_	NN	_	_	_
176	glucose	glucose	NN	SUPP	_	_
177	_	_	CD	_	_	_
178	NH4Cl	nh4cl	NN	_	_	_
179	_	_	CD	_	_	_
180	O2	o2	CD	_	_	_
181	_	_	NN	_	_	_
182	3	3	CD	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	RNAseq	rnaseq	NN	_	_	_
185	_	_	CD	_	_	_
186	delta-crp	delta-crp	JJ	_	_	_
187	_	_	NN	_	_	_
188	glycerol	glycerol	NN	SUPP	_	_
189	_	_	CD	_	_	_
190	NH4Cl	nh4cl	NN	_	_	_
191	_	_	CD	_	_	_
192	O2	o2	CD	_	_	_
193	_	_	NN	_	_	_
194	1	1	CD	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	RNAseq	rnaseq	NN	_	_	_
197	_	_	CD	_	_	_
198	delta-crp	delta-crp	JJ	_	_	_
199	_	_	NN	_	_	_
200	glycerol	glycerol	NN	SUPP	_	_
201	_	_	CD	_	_	_
202	NH4Cl	nh4cl	NN	_	_	_
203	_	_	CD	_	_	_
204	O2	o2	CD	_	_	_
205	_	_	NN	_	_	_
206	2	2	CD	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	RNAseq	rnaseq	NN	_	_	_
209	_	_	CD	_	_	_
210	delta-crp	delta-crp	JJ	_	_	_
211	_	_	NN	_	_	_
212	glycerol	glycerol	NN	SUPP	_	_
213	_	_	CD	_	_	_
214	NH4Cl	nh4cl	NN	_	_	_
215	_	_	CD	_	_	_
216	O2	o2	CD	_	_	_
217	_	_	NN	_	_	_
218	3	3	CD	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	RNAseq	rnaseq	NN	_	_	_
221	_	_	CD	_	_	_
222	wt	wt	JJ	_	_	_
223	_	_	NN	_	_	_
224	fructose	fructose	NN	_	_	_
225	_	_	CD	_	_	_
226	NH4Cl	nh4cl	NN	_	_	_
227	_	_	CD	_	_	_
228	O2	o2	CD	_	_	_
229	_	_	NN	_	_	_
230	1	1	CD	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	RNAseq	rnaseq	NN	_	_	_
233	_	_	CD	_	_	_
234	wt	wt	JJ	_	_	_
235	_	_	NN	_	_	_
236	fructose	fructose	NN	_	_	_
237	_	_	CD	_	_	_
238	NH4Cl	nh4cl	NN	_	_	_
239	_	_	CD	_	_	_
240	O2	o2	CD	_	_	_
241	_	_	NN	_	_	_
242	2	2	CD	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	RNAseq	rnaseq	NN	_	_	_
245	_	_	CD	_	_	_
246	wt	wt	JJ	_	_	_
247	_	_	NN	_	_	_
248	glucose	glucose	NN	SUPP	_	_
249	_	_	CD	_	_	_
250	NH4Cl	nh4cl	NN	_	_	_
251	_	_	CD	_	_	_
252	O2	o2	CD	_	_	_
253	_	_	NN	_	_	_
254	1	1	CD	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	RNAseq	rnaseq	NN	_	_	_
257	_	_	CD	_	_	_
258	wt	wt	JJ	_	_	_
259	_	_	NN	_	_	_
260	glucose	glucose	NN	SUPP	_	_
261	_	_	CD	_	_	_
262	NH4Cl	nh4cl	NN	_	_	_
263	_	_	CD	_	_	_
264	O2	o2	CD	_	_	_
265	_	_	NN	_	_	_
266	2	2	CD	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	RNAseq	rnaseq	NN	_	_	_
269	_	_	CD	_	_	_
270	wt	wt	JJ	_	_	_
271	_	_	NN	_	_	_
272	glucose	glucose	NN	SUPP	_	_
273	_	_	CD	_	_	_
274	NH4Cl	nh4cl	NN	_	_	_
275	_	_	CD	_	_	_
276	O2	o2	CD	_	_	_
277	_	_	NN	_	_	_
278	3	3	CD	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	RNAseq	rnaseq	NN	_	_	_
281	_	_	CD	_	_	_
282	wt	wt	JJ	_	_	_
283	_	_	NN	_	_	_
284	glycerol	glycerol	NN	SUPP	_	_
285	_	_	CD	_	_	_
286	NH4Cl	nh4cl	NN	_	_	_
287	_	_	CD	_	_	_
288	O2	o2	CD	_	_	_
289	_	_	NN	_	_	_
290	1	1	CD	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	RNAseq	rnaseq	NN	_	_	_
293	_	_	CD	_	_	_
294	wt	wt	JJ	_	_	_
295	_	_	NN	_	_	_
296	glycerol	glycerol	NN	SUPP	_	_
297	_	_	CD	_	_	_
298	NH4Cl	nh4cl	NN	_	_	_
299	_	_	CD	_	_	_
300	O2	o2	CD	_	_	_
301	_	_	NN	_	_	_
302	2	2	CD	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
304	rRNA	rrna	NN	_	_	_
305	depleted	deplete	VBN	_	_	_
306	RNA	rna	NN	_	_	_
307	was	be	VBD	_	_	_
308	then	then	RB	_	_	_
309	primed	prime	VBN	_	_	_
310	using	use	VBG	_	_	_
311	random	random	JJ	_	_	_
312	hexamers	hexamer	NNS	_	_	_
313	and	and	CC	_	_	_
314	reverse	reverse	VB	_	_	_
315	transcribed	transcribe	VBN	_	_	_
316	using	use	VBG	_	_	_
317	SuperScript	SuperScript	NNP	_	_	_
318	III	III	NNP	_	_	_
319	-LRB-	-lrb-	-LRB-	_	_	_
320	Life	Life	NNP	_	_	_
321	Technologies	Technologies	NNPS	_	_	_
322	-RRB-	-rrb-	-RRB-	_	_	_
323	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	Crp	Crp	NNP	_	_	_
5	_	_	SYM	_	_	_
6	delAr1	delar1	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	strain	strain	NN	_	_	_
9	:	:	:	_	_	_
10	Crp	Crp	NNP	_	_	_
11	_	_	SYM	_	_	_
12	delAr1delAr2	delar1delar2	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	strain	strain	NN	_	_	_
15	:	:	:	_	_	_
16	Crp	Crp	NNP	_	_	_
17	_	_	SYM	_	_	_
18	delAr2	delar2	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	strain	strain	NN	_	_	_
21	:	:	:	_	_	_
22	delta	delta	NN	_	_	_
23	Crp	crp	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	strain	strain	NN	_	_	_
26	:	:	:	_	_	_
27	wt	wt	JJ	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
29	Supplementary	supplementary	JJ	_	_	_
30	_	_	NN	_	_	_
31	files	file	NNS	_	_	_
32	_	_	IN	_	_	_
33	format	format	NN	_	_	_
34	_	_	NN	_	_	_
35	and	and	CC	_	_	_
36	_	_	NN	_	_	_
37	content	content	NN	_	_	_
38	:	:	:	_	_	_
39	Processed	process	VBN	_	_	_
40	data	datum	NNS	_	_	_
41	is	be	VBZ	_	_	_
42	presented	present	VBN	_	_	_
43	in	in	IN	_	_	_
44	a	a	DT	_	_	_
45	cuff	cuff	NN	_	_	_
46	diff	diff	NN	_	_	_
47	analysis	analysis	NN	_	_	_
48	format	format	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
50	The	the	DT	_	_	_
51	MiSeq	MiSeq	NNP	_	_	_
52	Reporter	reporter	NN	_	_	_
53	MiSeq	miseq	NN	_	_	_
54	Reporter	reporter	NN	_	_	_
55	2.4.60.8	2.4.60.8	CD	_	_	_
56	was	be	VBD	_	_	_
57	used	use	VBN	_	_	_
58	for	for	IN	_	_	_
59	basecalling	basecalling	NN	_	_	_
60	and	and	CC	_	_	_
61	demultiplexing	demultiplex	VBG	_	_	_
62	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
63	Total	Total	NNP	_	_	_
64	RNA	rna	NN	_	_	_
65	was	be	VBD	_	_	_
66	depleted	deplete	VBN	_	_	_
67	of	of	IN	_	_	_
68	ribosomal	ribosomal	JJ	_	_	_
69	RNAs	rna	NNS	_	_	_
70	using	use	VBG	_	_	_
71	Epicentre	Epicentre	NNP	_	_	_
72	's	's	POS	_	_	_
73	RiboZero	RiboZero	NNP	_	_	_
74	rRNA	rrna	NN	_	_	_
75	removal	removal	NN	_	_	_
76	kit	kit	NN	_	_	_
77	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	DNeasy	dneasy	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	Qiagen	qiagen	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Escherichia	escherichia	FW	Organism	_	_
8	coli	coli	FW	Organism	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Escherichia	escherichia	FW	Organism	_	_
11	coli	coli	FW	Organism	_	_
12	K-12	k-12	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	gDNA	gdna	NN	_	_	_
15	520	520	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	gDNA	gdna	NN	_	_	_
18	521	521	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	gDNA	gdna	NN	_	_	_
21	B02	b02	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	gDNA	gdna	NN	_	_	_
24	B05	b05	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	gDNA	gdna	NN	_	_	_
27	C01	c01	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	gDNA	gdna	NN	_	_	_
30	C02	c02	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	gDNA	gdna	NN	_	_	_
33	_	_	CD	_	_	_
34	EColi	ecolus	NNS	_	_	_
35	_	_	SYM	_	_	_
36	520	520	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	gDNA	gdna	NN	_	_	_
39	_	_	CD	_	_	_
40	EColi	ecolus	NNS	_	_	_
41	_	_	SYM	_	_	_
42	521	521	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	gDNA	gdna	NN	_	_	_
45	_	_	CD	_	_	_
46	EColi	ecolus	NNS	_	_	_
47	_	_	VBP	_	_	_
48	B02	b02	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	gDNA	gdna	NN	_	_	_
51	_	_	CD	_	_	_
52	EColi	ecolus	NNS	_	_	_
53	_	_	VBP	_	_	_
54	B05	b05	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	gDNA	gdna	NN	_	_	_
57	_	_	CD	_	_	_
58	EColi	ecolus	NNS	_	_	_
59	_	_	VBP	_	_	_
60	C01	c01	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	gDNA	gdna	NN	_	_	_
63	_	_	CD	_	_	_
64	EColi	ecolus	NNS	_	_	_
65	_	_	VBP	_	_	_
66	C02	c02	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	gDNA	gdna	NN	_	_	_
69	_	_	CD	_	_	_
70	EColi	ecolus	NNS	_	_	_
71	_	_	VBP	_	_	_
72	F01	f01	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	gDNA	gdna	NN	_	_	_
75	_	_	CD	_	_	_
76	EColi	ecolus	NNS	_	_	_
77	_	_	VBP	_	_	_
78	F02	f02	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	gDNA	gdna	NN	_	_	_
81	_	_	CD	_	_	_
82	EColi	ecolus	NNS	_	_	_
83	_	_	VBP	_	_	_
84	H01	h01	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	gDNA	gdna	NN	_	_	_
87	_	_	CD	_	_	_
88	EColi	ecolus	NNS	_	_	_
89	_	_	VBP	_	_	_
90	H02	h02	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	gDNA	gdna	NN	_	_	_
93	_	_	CD	_	_	_
94	EColi	ecolus	NNS	_	_	_
95	_	_	VBP	_	_	_
96	H03	h03	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	gDNA	gdna	NN	_	_	_
99	_	_	CD	_	_	_
100	EColi	ecolus	NNS	_	_	_
101	_	_	VBP	_	_	_
102	H04	h04	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	gDNA	gdna	NN	_	_	_
105	_	_	CD	_	_	_
106	EColi	ecolus	NNS	_	_	_
107	_	_	VBP	_	_	_
108	H05	h05	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	gDNA	gdna	NN	_	_	_
111	_	_	CD	_	_	_
112	EColi	ecolus	NNS	_	_	_
113	_	_	VBP	_	_	_
114	H12	h12	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	gDNA	gdna	NN	_	_	_
117	_	_	CD	_	_	_
118	EColi	ecolus	NNS	_	_	_
119	_	_	VBP	_	_	_
120	H23	h23	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	gDNA	gdna	NN	_	_	_
123	_	_	CD	_	_	_
124	EColi	ecolus	NNS	_	_	_
125	_	_	VBP	_	_	_
126	H27	h27	NN	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	gDNA	gdna	NN	_	_	_
129	_	_	CD	_	_	_
130	EColi	ecolus	NNS	_	_	_
131	_	_	VBP	_	_	_
132	S04	s04	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	gDNA	gdna	NN	_	_	_
135	_	_	CD	_	_	_
136	EColi	ecolus	NNS	_	_	_
137	_	_	VBP	_	_	_
138	S05	s05	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	gDNA	gdna	NN	_	_	_
141	_	_	CD	_	_	_
142	EColi	ecolus	NNS	_	_	_
143	_	_	VBP	_	_	_
144	S13	s13	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	gDNA	gdna	NN	_	_	_
147	F01	f01	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	gDNA	gdna	NN	_	_	_
150	F02	f02	NN	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	gDNA	gdna	NN	_	_	_
153	from	from	IN	_	_	_
154	E.coli	e.coli	JJ	_	_	_
155	K12	k12	NN	_	_	_
156	cyanine	cyanine	NN	_	_	_
157	3	3	CD	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	gDNA	gdna	NN	_	_	_
160	H01	h01	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	gDNA	gdna	NN	_	_	_
163	H02	h02	NN	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	gDNA	gdna	NN	_	_	_
166	H03	h03	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	gDNA	gdna	NN	_	_	_
169	H04	h04	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	gDNA	gdna	NN	_	_	_
172	H05	h05	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	gDNA	gdna	NN	_	_	_
175	H12	h12	NN	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	gDNA	gdna	NN	_	_	_
178	H23	h23	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	gDNA	gdna	NN	_	_	_
181	H27	h27	NN	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	gDNA	gdna	NN	_	_	_
184	K12	k12	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	gDNA	gdna	NN	_	_	_
187	S04	s04	NN	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	gDNA	gdna	NN	_	_	_
190	S05	s05	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	gDNA	gdna	NN	_	_	_
193	S13	s13	NN	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	Local	local	JJ	_	_	_
196	Background	background	NN	_	_	_
197	Substracted	Substracted	NNP	_	_	_
198	Signal	Signal	NNP	_	_	_
199	Corrected	Corrected	NNP	_	_	_
200	for	for	IN	_	_	_
201	unequal	unequal	JJ	_	_	_
202	Dye	dye	NN	_	_	_
203	incorporation	incorporation	NN	_	_	_
204	or	or	CC	_	_	_
205	unequal	unequal	JJ	_	_	_
206	load	load	NN	_	_	_
207	of	of	IN	_	_	_
208	labelled	label	VBN	_	_	_
209	product	product	NN	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	strain	strain	NN	_	_	_
212	520	520	CD	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	strain	strain	NN	_	_	_
215	521	521	CD	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	strain	strain	NN	_	_	_
218	B02	b02	NN	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	strain	strain	NN	_	_	_
221	B05	b05	NN	_	_	_
222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
223	strain	strain	NN	_	_	_
224	C01	c01	NN	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	strain	strain	NN	_	_	_
227	C02	c02	NN	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	strain	strain	NN	_	_	_
230	F01	f01	NN	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	strain	strain	NN	_	_	_
233	F02	f02	NN	_	_	_
234	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
235	strain	strain	NN	_	_	_
236	H01	h01	NN	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	strain	strain	NN	_	_	_
239	H02	h02	NN	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
241	strain	strain	NN	_	_	_
242	H03	h03	NN	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	strain	strain	NN	_	_	_
245	H04	h04	NN	_	_	_
246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
247	strain	strain	NN	_	_	_
248	H05	h05	NN	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	strain	strain	NN	_	_	_
251	H12	h12	NN	_	_	_
252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
253	strain	strain	NN	_	_	_
254	H23	h23	NN	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	strain	strain	NN	_	_	_
257	H27	h27	NN	_	_	_
258	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
259	strain	strain	NN	_	_	_
260	S04	s04	NN	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
262	strain	strain	NN	_	_	_
263	S05	s05	NN	_	_	_
264	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
265	strain	strain	NN	_	_	_
266	S13	s13	NN	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	Escherichia	escherichia	FW	Organism	_	_
269	coli	coli	FW	Organism	_	_
270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
271	Escherichia	escherichia	FW	Organism	_	_
272	coli	coli	FW	Organism	_	_
273	CSH50	csh50	NN	_	_	_
274	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
275	Escherichia	escherichia	FW	Organism	_	_
276	coli	coli	FW	Organism	_	_
277	CSH50	csh50	NN	_	_	_
278	Δfis	Δfis	NNP	_	_	_
279	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
280	Escherichia	escherichia	FW	Organism	_	_
281	coli	coli	FW	Organism	_	_
282	CSH50	csh50	NN	_	_	_
283	Δhns	δhns	NNS	_	_	_
284	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
285	Fis	Fis	NNP	TF	_	_
286	--	--	:	_	_	_
287	120	120	CD	_	_	_
288	min	min	NN	_	_	_
289	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
290	Fis	Fis	NNP	TF	_	_
291	--	--	:	_	_	_
292	180	180	CD	_	_	_
293	min	min	NN	_	_	_
294	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
295	Fis	Fis	NNP	TF	_	_
296	--	--	:	_	_	_
297	420	420	CD	_	_	_
298	min	min	NN	_	_	_
299	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
300	Fis	Fis	NNP	TF	_	_
301	--	--	:	_	_	_
302	60	60	CD	_	_	_
303	min	min	NN	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	GATC	gatc	NN	_	_	_
306	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
307	GATC	gatc	NN	_	_	_
308	software	software	NN	_	_	_
309	for	for	IN	_	_	_
310	read	read	NN	_	_	_
311	mapping	mapping	NN	_	_	_
312	on	on	IN	_	_	_
313	MG1655	mg1655	NN	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	gene	gene	NN	_	_	_
316	expression	expression	NN	_	_	_
317	sum	sum	NN	_	_	_
318	normalized	normalize	VBD	_	_	_
319	to	to	TO	_	_	_
320	1	1	CD	_	_	_
321	at	at	IN	_	_	_
322	each	each	DT	_	_	_
323	time	time	NN	_	_	_
324	point	point	NN	_	_	_
325	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
326	Gene	Gene	NNP	_	_	_
327	wise	wise	JJ	_	_	_
328	natural	natural	JJ	_	_	_
329	spline	spline	NN	_	_	_
330	interpolation	interpolation	NN	_	_	_
331	of	of	IN	_	_	_
332	temporal	temporal	JJ	_	_	_
333	data	datum	NNS	_	_	_
334	from	from	IN	_	_	_
335	initial	initial	JJ	_	_	_
336	time	time	NN	_	_	_
337	points	point	NNS	_	_	_
338	to	to	TO	_	_	_
339	a	a	DT	_	_	_
340	dataset	dataset	NN	_	_	_
341	of	of	IN	_	_	_
342	10	10	CD	_	_	_
343	minutes	minute	NNS	_	_	_
344	steps	step	NNS	_	_	_
345	-LRB-	-lrb-	-LRB-	_	_	_
346	see	see	VB	_	_	_
347	processed	process	VBN	_	_	_
348	data	datum	NNS	_	_	_
349	files	file	NNS	_	_	_
350	-RRB-	-rrb-	-RRB-	_	_	_
351	.	.	.	_	_	_

1	Expression	expression	NN	_	_	_
2	values	value	NNS	_	_	_
3	at	at	IN	_	_	_
4	the	the	DT	_	_	_
5	time	time	NN	_	_	_
6	points	point	NNS	_	_	_
7	of	of	IN	_	_	_
8	the	the	DT	_	_	_
9	raw	raw	JJ	_	_	_
10	data	datum	NNS	_	_	_
11	are	be	VBP	_	_	_
12	not	not	RB	_	_	_
13	affected	affect	VBN	_	_	_
14	by	by	IN	_	_	_
15	the	the	DT	_	_	_
16	interpolation	interpolation	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	genotype	genotype	NN	_	_	_
3	:	:	:	_	_	_
4	delta-fis	delta-fis	JJ	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	genotype	genotype	NN	_	_	_
7	:	:	:	_	_	_
8	delta-hns	delta-hn	NNS	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	genotype	genotype	NN	_	_	_
11	:	:	:	_	_	_
12	wildtype	wildtype	JJ	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
14	Hns	hn	NNS	_	_	_
15	--	--	:	_	_	_
16	120	120	CD	_	_	_
17	min	min	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
19	Hns	hn	VBZ	_	_	_
20	-180	-180	CD	_	_	_
21	min	min	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Hns	hn	NNS	_	_	_
24	--	--	:	_	_	_
25	420	420	CD	_	_	_
26	min	min	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Hns	hn	NNS	_	_	_
29	--	--	:	_	_	_
30	60	60	CD	_	_	_
31	min	min	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	LB	lb	NN	MED	_	_
34	medium	medium	NN	MED	_	_
35	,	,	,	_	_	_
36	37	37	CD	_	_	_
37	°C	°c	NN	_	_	_
38	,	,	,	_	_	_
39	airated	airate	VBN	_	_	_
40	,	,	,	_	_	_
41	constant	constant	JJ	_	_	_
42	pH	ph	NN	_	_	_
43	7.5	7.5	CD	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	RNA	rna	NN	_	_	_
46	extraction	extraction	NN	_	_	_
47	Kit	kit	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	RNA-Seq	rna-seq	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	strain	strain	NN	_	_	_
52	:	:	:	_	_	_
53	CSH50	csh50	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	Supplementary	supplementary	JJ	_	_	_
56	_	_	NN	_	_	_
57	files	file	NNS	_	_	_
58	_	_	IN	_	_	_
59	format	format	NN	_	_	_
60	_	_	NN	_	_	_
61	and	and	CC	_	_	_
62	_	_	NN	_	_	_
63	content	content	NN	_	_	_
64	:	:	:	_	_	_
65	expression	expression	NN	_	_	_
66	of	of	IN	_	_	_
67	genes	gene	NNS	_	_	_
68	in	in	IN	_	_	_
69	time	time	NN	_	_	_
70	,	,	,	_	_	_
71	rows	row	NNS	_	_	_
72	=	=	JJ	_	_	_
73	genes	gene	NNS	_	_	_
74	,	,	,	_	_	_
75	cols	col	NNS	_	_	_
76	=	=	JJ	_	_	_
77	time	time	NN	_	_	_
78	points	point	NNS	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
80	time	time	NN	_	_	_
81	:	:	:	_	_	_
82	120	120	CD	_	_	_
83	minutes	minute	NNS	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
85	time	time	NN	_	_	_
86	:	:	:	_	_	_
87	180	180	CD	_	_	_
88	minutes	minute	NNS	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
90	time	time	NN	_	_	_
91	:	:	:	_	_	_
92	300	300	CD	_	_	_
93	minutes	minute	NNS	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
95	time	time	NN	_	_	_
96	:	:	:	_	_	_
97	420	420	CD	_	_	_
98	minutes	minute	NNS	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
100	time	time	NN	_	_	_
101	:	:	:	_	_	_
102	60	60	CD	_	_	_
103	minutes	minute	NNS	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	verified	verify	VBN	_	_	_
106	with	with	IN	_	_	_
107	in-house	in-house	JJ	_	_	_
108	pipeline	pipeline	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	Wt	wt	NN	_	_	_
111	--	--	:	_	_	_
112	120	120	CD	_	_	_
113	min	min	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	Wt	wt	NN	_	_	_
116	--	--	:	_	_	_
117	180	180	CD	_	_	_
118	min	min	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	Wt	wt	NN	_	_	_
121	--	--	:	_	_	_
122	300	300	CD	_	_	_
123	min	min	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	Wt	wt	NN	_	_	_
126	--	--	:	_	_	_
127	420	420	CD	_	_	_
128	min	min	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	Wt	wt	NN	_	_	_
131	--	--	:	_	_	_
132	60	60	CD	_	_	_
133	min	min	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	Bacteria	bacterium	NNS	_	_	_
136	were	be	VBD	_	_	_
137	cultured	culture	VBN	_	_	_
138	in	in	IN	_	_	_
139	an	a	DT	_	_	_
140	M9	m9	NN	MED	_	_
141	minimal	minimal	JJ	MED	_	_
142	medium	medium	NN	MED	_	_
143	supplemented	supplement	VBN	_	_	_
144	with	with	IN	_	_	_
145	2	2	CD	_	_	_
146	g	g	NN	_	_	_
147	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
148	Data	Data	NNP	_	_	_
149	analysis	analysis	NN	_	_	_
150	was	be	VBD	_	_	_
151	done	do	VBN	_	_	_
152	using	use	VBG	_	_	_
153	R	r	NN	_	_	_
154	language	language	NN	_	_	_
155	and	and	CC	_	_	_
156	environment	environment	NN	_	_	_
157	for	for	IN	_	_	_
158	a	a	DT	_	_	_
159	statistical	statistical	JJ	_	_	_
160	computing	computing	NN	_	_	_
161	and	and	CC	_	_	_
162	Bioconductor	bioconductor	NN	_	_	_
163	.	.	.	_	_	_

1	Array	array	NN	_	_	_
2	data	datum	NNS	_	_	_
3	were	be	VBD	_	_	_
4	normalized	normalize	VBN	_	_	_
5	with	with	IN	_	_	_
6	gcRMA	gcrma	NN	_	_	_
7	method	method	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Escherichia	escherichia	FW	Organism	_	_
6	coli	coli	FW	Organism	_	_
7	K-12	k-12	NN	_	_	_
8	tynA	tyna	NN	GEN	_	_
9	-	-	:	_	_	_
10	1h	1h	NN	_	_	_
11	after	after	IN	_	_	_
12	induction	induction	NN	_	_	_
13	of	of	IN	_	_	_
14	tynA	tyna	NN	GEN	_	_
15	expression	expression	NN	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Escherichia	escherichia	FW	Organism	_	_
18	coli	coli	FW	Organism	_	_
19	K-12	k-12	NN	_	_	_
20	tynA	tyna	NN	GEN	_	_
21	-	-	:	_	_	_
22	4h	4h	NN	_	_	_
23	after	after	IN	_	_	_
24	the	the	DT	_	_	_
25	induction	induction	NN	_	_	_
26	of	of	IN	_	_	_
27	tynA	tyna	NN	GEN	_	_
28	expression	expression	NN	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	Escherichia	escherichia	FW	Organism	_	_
31	coli	coli	FW	Organism	_	_
32	K-12	k-12	NN	_	_	_
33	tynA	tyna	NN	GEN	_	_
34	-	-	:	_	_	_
35	at	at	IN	_	_	_
36	time	time	NN	_	_	_
37	of	of	IN	_	_	_
38	induction	induction	NN	_	_	_
39	of	of	IN	_	_	_
40	tynA	tyna	NN	GEN	_	_
41	expression	expression	NN	_	_	_
42	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
43	Escherichia	escherichia	FW	Organism	_	_
44	coli	coli	FW	Organism	_	_
45	K-12	k-12	NN	_	_	_
46	wt	wt	JJ	_	_	_
47	1h	1h	NN	_	_	_
48	after	after	IN	_	_	_
49	the	the	DT	_	_	_
50	induction	induction	NN	_	_	_
51	of	of	IN	_	_	_
52	tynA	tyna	NN	GEN	_	_
53	expression	expression	NN	_	_	_
54	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
55	Escherichia	escherichia	FW	Organism	_	_
56	coli	coli	FW	Organism	_	_
57	K-12	k-12	NN	_	_	_
58	wt	wt	JJ	_	_	_
59	4h	4h	NN	_	_	_
60	after	after	IN	_	_	_
61	the	the	DT	_	_	_
62	induction	induction	NN	_	_	_
63	of	of	IN	_	_	_
64	tynA	tyna	NN	GEN	_	_
65	expression	expression	NN	_	_	_
66	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
67	Escherichia	escherichia	FW	Organism	_	_
68	coli	coli	FW	Organism	_	_
69	K-12	k-12	NN	_	_	_
70	wt	wt	JJ	_	_	_
71	at	at	IN	_	_	_
72	time	time	NN	_	_	_
73	of	of	IN	_	_	_
74	induction	induction	NN	_	_	_
75	of	of	IN	_	_	_
76	tynA	tyna	NN	GEN	_	_
77	expression	expression	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	genotype	genotype	NN	_	_	_
80	:	:	:	_	_	_
81	tynA	tyna	NN	GEN	_	_
82	-	-	:	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	genotype	genotype	NN	_	_	_
85	:	:	:	_	_	_
86	wild	wild	JJ	_	_	_
87	type	type	NN	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	Samples	sample	NNS	_	_	_
90	were	be	VBD	_	_	_
91	treated	treat	VBN	_	_	_
92	with	with	IN	_	_	_
93	Prokaryotic	Prokaryotic	NNP	_	_	_
94	Target	target	NN	_	_	_
95	Preparation	preparation	NN	_	_	_
96	protocol	protocol	NN	_	_	_
97	-LRB-	-lrb-	-LRB-	_	_	_
98	GeneChip	genechip	NN	_	_	_
99	Expression	expression	NN	_	_	_
100	Analysis	analysis	NN	_	_	_
101	Technical	Technical	NNP	_	_	_
102	Manual	Manual	NNP	_	_	_
103	-RRB-	-rrb-	-RRB-	_	_	_
104	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	K12	k12	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Total	total	JJ	_	_	_
7	RNA	rna	NN	_	_	_
8	was	be	VBD	_	_	_
9	isolated	isolate	VBN	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	RNeasy	rneasy	NN	_	_	_
13	Mini-Kit	mini-kit	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Qiagen	qiagen	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	according	accord	VBG	_	_	_
18	to	to	TO	_	_	_
19	the	the	DT	_	_	_
20	manufacturer	manufacturer	NN	_	_	_
21	`	`	``	_	_	_
22	s	be	VBZ	_	_	_
23	instruction	instruction	NN	_	_	_
24	and	and	CC	_	_	_
25	DNA	dna	NN	_	_	_
26	was	be	VBD	_	_	_
27	removed	remove	VBN	_	_	_
28	by	by	IN	_	_	_
29	using	use	VBG	_	_	_
30	RNAse-Free	rnase-free	JJ	_	_	_
31	DNAse	dnase	NN	_	_	_
32	Set	set	VB	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	Qiagen	Qiagen	NNP	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	tynA	tyna	SYM	GEN	_	_
3	-	-	:	_	_	_
4	at	at	IN	_	_	_
5	T0	t0	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	tynA	tyna	NN	GEN	_	_
8	-	-	:	_	_	_
9	at	at	IN	_	_	_
10	T1h	t1h	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	tynA	tyna	NN	GEN	_	_
13	-	-	:	_	_	_
14	at	at	IN	_	_	_
15	T4h	t4h	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	wt	wt	JJ	_	_	_
18	at	at	IN	_	_	_
19	T0	t0	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	wt	wt	JJ	_	_	_
22	at	at	IN	_	_	_
23	T1h	t1h	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	wt	wt	JJ	_	_	_
26	at	at	IN	_	_	_
27	T4h	t4h	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	acetate	acetate	NN	SUPP	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
31	chip	chip	NN	_	_	_
32	antibody	antibody	NN	_	_	_
33	:	:	:	_	_	_
34	anti-myc	anti-myc	JJ	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
36	chip	chip	NN	_	_	_
37	antibody	antibody	NN	_	_	_
38	:	:	:	_	_	_
39	anti-rpoB	anti-rpob	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	Santa	Santa	NNP	_	_	_
42	Cruz	Cruz	NNP	_	_	_
43	Biotech	Biotech	NNP	_	_	_
44	,	,	,	_	_	_
45	sc-56766	sc-56766	NN	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	chip	chip	NN	_	_	_
49	antibody	antibody	NN	_	_	_
50	cat	cat	NN	_	_	_
51	.	.	.	_	_	_

1	#	#	#	_	_	_
2	:	:	:	_	_	_
3	sc-28207	sc-28207	JJ	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
5	chip	chip	NN	_	_	_
6	antibody	antibody	NN	_	_	_
7	vendor	vendor	NN	_	_	_
8	:	:	:	_	_	_
9	Santa	Santa	NNP	_	_	_
10	Cruz	Cruz	NNP	_	_	_
11	Biotech	Biotech	NNP	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	ChIP-exo	ChIP-exo	NNP	_	_	_
14	reads	read	VBZ	_	_	_
15	were	be	VBD	_	_	_
16	aligned	align	VBN	_	_	_
17	to	to	TO	_	_	_
18	the	the	DT	_	_	_
19	ASM584v2	asm584v2	NN	_	_	_
20	genome	genome	NN	_	_	_
21	reference	reference	NN	_	_	_
22	sequence	sequence	NN	_	_	_
23	using	use	VBG	_	_	_
24	using	use	VBG	_	_	_
25	bowtie	bowtie	NN	_	_	_
26	v1	v1	NN	_	_	_
27	.0.0	.0.0	CD	_	_	_
28	with	with	IN	_	_	_
29	parameters	parameter	NNS	_	_	_
30	-	-	:	_	_	_
31	S	s	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
33	ChIP-Seq	chip-seq	JJ	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	ChIP-seq	chip-seq	NN	_	_	_
36	libraries	library	NNS	_	_	_
37	were	be	VBD	_	_	_
38	prepared	prepare	VBN	_	_	_
39	for	for	IN	_	_	_
40	sequencing	sequencing	NN	_	_	_
41	using	use	VBG	_	_	_
42	standard	standard	JJ	_	_	_
43	Illumina	Illumina	NNP	_	_	_
44	protocols	protocol	NNS	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	cra-8myc	cra-8myc	NN	_	_	_
47	tagged	tag	VBD	_	_	_
48	strain	strain	NN	_	_	_
49	_	_	NN	_	_	_
50	acetate	acetate	NN	SUPP	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	cra-8myc	cra-8myc	NN	_	_	_
53	tagged	tag	VBD	_	_	_
54	strain	strain	NN	_	_	_
55	_	_	NN	_	_	_
56	fructose	fructose	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	cra-8myc	cra-8myc	NN	_	_	_
59	tagged	tag	VBD	_	_	_
60	strain	strain	NN	_	_	_
61	_	_	NN	_	_	_
62	glucose	glucose	NN	SUPP	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
64	Cra	Cra	NNP	TF	_	_
65	acetate	acetate	NN	SUPP	_	_
66	1	1	CD	_	_	_
67	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
68	Cra	Cra	NNP	TF	_	_
69	acetate	acetate	NN	SUPP	_	_
70	2	2	CD	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
72	Cra	Cra	NNP	TF	_	_
73	fructose	fructose	NN	_	_	_
74	1	1	CD	_	_	_
75	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
76	Cra	Cra	NNP	TF	_	_
77	fructose	fructose	NN	_	_	_
78	2	2	CD	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
80	Cra	cra	NN	TF	_	_
81	glucose	glucose	NN	SUPP	_	_
82	1	1	CD	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	Cra	cra	NN	TF	_	_
85	glucose	glucose	NN	SUPP	_	_
86	2	2	CD	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	Crosslinked	crosslink	VBN	_	_	_
89	cells	cell	NNS	_	_	_
90	were	be	VBD	_	_	_
91	then	then	RB	_	_	_
92	resuspended	resuspend	VBN	_	_	_
93	in	in	IN	_	_	_
94	500	500	CD	_	_	_
95	ul	ul	NN	_	_	_
96	of	of	IN	_	_	_
97	lysis	lysis	NN	_	_	_
98	buffer	buffer	NN	_	_	_
99	-LRB-	-lrb-	-LRB-	_	_	_
100	10	10	CD	_	_	_
101	mM	mm	NN	KWSUPP	_	_
102	Tris-HCl	tris-hcl	NN	_	_	_
103	-LRB-	-lrb-	-LRB-	_	_	_
104	pH	ph	NN	_	_	_
105	7.5	7.5	CD	_	_	_
106	-RRB-	-rrb-	-RRB-	_	_	_
107	,	,	,	_	_	_
108	100	100	CD	_	_	_
109	mM	mm	NN	KWSUPP	_	_
110	NaCl	nacl	NN	_	_	_
111	and	and	CC	_	_	_
112	1	1	CD	_	_	_
113	mM	mm	NN	KWSUPP	_	_
114	EDTA	edta	NN	_	_	_
115	-RRB-	-rrb-	-RRB-	_	_	_
116	with	with	IN	_	_	_
117	40	40	CD	_	_	_
118	ul	ul	NN	_	_	_
119	of	of	IN	_	_	_
120	protease	protease	NN	_	_	_
121	inhibitor	inhibitor	NN	_	_	_
122	cocktail	cocktail	NN	_	_	_
123	-LRB-	-lrb-	-LRB-	_	_	_
124	50	50	CD	_	_	_
125	mg	mg	NN	_	_	_
126	in	in	IN	_	_	_
127	0.25	0.25	CD	_	_	_
128	ml	ml	NN	_	_	_
129	of	of	IN	_	_	_
130	DMSO	dmso	NN	_	_	_
131	and	and	CC	_	_	_
132	0.75	0.75	CD	_	_	_
133	ml	ml	NN	_	_	_
134	of	of	IN	_	_	_
135	TDW	tdw	NN	_	_	_
136	-RRB-	-rrb-	-RRB-	_	_	_
137	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	lyzed	lyze	VBN	_	_	_
4	with	with	IN	_	_	_
5	1	1	CD	_	_	_
6	ul	ul	NN	_	_	_
7	of	of	IN	_	_	_
8	lysozyme	lysozyme	NN	_	_	_
9	for	for	IN	_	_	_
10	30	30	CD	_	_	_
11	min	min	NN	_	_	_
12	at	at	IN	_	_	_
13	37C	37c	NN	_	_	_
14	on	on	IN	_	_	_
15	a	a	DT	_	_	_
16	rocker	rocker	NN	_	_	_
17	.	.	.	_	_	_

1	0.55	0.55	CD	_	_	_
2	ml	ml	NN	_	_	_
3	of	of	IN	_	_	_
4	2X	2x	NN	_	_	_
5	IP	IP	NNP	_	_	_
6	buffer	buffer	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	100	100	CD	_	_	_
9	mM	mm	NN	KWSUPP	_	_
10	Tris-HCl	tris-hcl	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	pH	ph	NN	_	_	_
13	7.5	7.5	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	200	200	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	NaCl	nacl	NN	_	_	_
19	,	,	,	_	_	_
20	2	2	CD	_	_	_
21	%	%	NN	_	_	_
22	Triton	Triton	NNP	_	_	_
23	X-100	x-100	NN	_	_	_
24	and	and	CC	_	_	_
25	1	1	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	EDTA	edta	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	were	be	VBD	_	_	_
30	added	add	VBN	_	_	_
31	to	to	TO	_	_	_
32	the	the	DT	_	_	_
33	sample	sample	NN	_	_	_
34	,	,	,	_	_	_
35	and	and	CC	_	_	_
36	then	then	RB	_	_	_
37	was	be	VBD	_	_	_
38	sonicated	sonicate	VBN	_	_	_
39	to	to	TO	_	_	_
40	fragmentize	fragmentize	VB	_	_	_
41	genomic	genomic	JJ	_	_	_
42	DNA	dna	NN	_	_	_
43	.	.	.	_	_	_

1	0.3	0.3	CD	_	_	_
2	ml	ml	NN	_	_	_
3	of	of	IN	_	_	_
4	Wash	Wash	NNP	_	_	_
5	buffer	buffer	NN	_	_	_
6	I	i	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	50	50	CD	_	_	_
9	mM	mm	NN	KWSUPP	_	_
10	Tris-HCl	tris-hcl	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	pH	ph	NN	_	_	_
13	7.5	7.5	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	140	140	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	NaCl	nacl	NN	_	_	_
19	,	,	,	_	_	_
20	1	1	CD	_	_	_
21	%	%	NN	_	_	_
22	Triton	Triton	NNP	_	_	_
23	X-100	x-100	NN	_	_	_
24	and	and	CC	_	_	_
25	1mM	1mm	NN	_	_	_
26	EDTA	edta	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	was	be	VBD	_	_	_
29	added	add	VBN	_	_	_
30	to	to	TO	_	_	_
31	make	make	VB	_	_	_
32	the	the	DT	_	_	_
33	volume	volume	NN	_	_	_
34	up	up	IN	_	_	_
35	to	to	TO	_	_	_
36	1.4	1.4	CD	_	_	_
37	ml	ml	NN	_	_	_
38	.	.	.	_	_	_

1	Only	only	RB	_	_	_
2	0.7	0.7	CD	_	_	_
3	ml	ml	NN	_	_	_
4	was	be	VBD	_	_	_
5	taken	take	VBN	_	_	_
6	and	and	CC	_	_	_
7	transfered	transfer	VBN	_	_	_
8	to	to	TO	_	_	_
9	a	a	DT	_	_	_
10	new	new	JJ	_	_	_
11	tube	tube	NN	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	15	15	CD	_	_	_
15	ul	ul	NN	_	_	_
16	of	of	IN	_	_	_
17	Anti-c-myc	anti-c-myc	JJ	_	_	_
18	mouse	mouse	NN	_	_	_
19	antibody	antibody	NN	_	_	_
20	was	be	VBD	_	_	_
21	added	add	VBN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	the	the	DT	_	_	_
25	sample	sample	NN	_	_	_
26	was	be	VBD	_	_	_
27	incubated	incubate	VBN	_	_	_
28	overnight	overnight	RB	_	_	_
29	at	at	IN	_	_	_
30	4C	4c	NN	_	_	_
31	to	to	TO	_	_	_
32	make	make	VB	_	_	_
33	Antibody-TF	antibody-tf	NN	_	_	_
34	complex	complex	NN	_	_	_
35	.	.	.	_	_	_

1	50	50	CD	_	_	_
2	ul	ul	NN	_	_	_
3	of	of	IN	_	_	_
4	Dynabeads	Dynabeads	NNP	_	_	_
5	Pan	Pan	NNP	_	_	_
6	mouse	mouse	NN	_	_	_
7	IgG	igg	NN	_	_	_
8	were	be	VBD	_	_	_
9	washed	wash	VBN	_	_	_
10	3	3	CD	_	_	_
11	times	time	NNS	_	_	_
12	with	with	IN	_	_	_
13	bead	bead	NN	_	_	_
14	washing	wash	VBG	_	_	_
15	solution	solution	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	250	250	CD	_	_	_
18	mg	mg	NN	_	_	_
19	BSA	bsa	NN	_	_	_
20	in	in	IN	_	_	_
21	50	50	CD	_	_	_
22	ml	ml	NN	_	_	_
23	of	of	IN	_	_	_
24	PBS	PBS	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	,	,	,	_	_	_
27	and	and	CC	_	_	_
28	were	be	VBD	_	_	_
29	added	add	VBN	_	_	_
30	to	to	TO	_	_	_
31	the	the	DT	_	_	_
32	sample	sample	NN	_	_	_
33	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	lysate	lysate	NN	_	_	_
3	with	with	IN	_	_	_
4	beads	bead	NNS	_	_	_
5	were	be	VBD	_	_	_
6	incubated	incubate	VBN	_	_	_
7	for	for	IN	_	_	_
8	6	6	CD	_	_	_
9	hours	hour	NNS	_	_	_
10	or	or	CC	_	_	_
11	overnight	overnight	JJ	_	_	_
12	at	at	IN	_	_	_
13	4C	4c	NN	_	_	_
14	to	to	TO	_	_	_
15	make	make	VB	_	_	_
16	Dynabead-antibody-TF	dynabead-antibody-tf	NN	_	_	_
17	complex	complex	NN	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	beads	bead	NNS	_	_	_
3	were	be	VBD	_	_	_
4	pulled	pull	VBN	_	_	_
5	down	down	RP	_	_	_
6	on	on	IN	_	_	_
7	a	a	DT	_	_	_
8	magnet	magnet	NN	_	_	_
9	stand	stand	NN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	washed	wash	VBN	_	_	_
13	2	2	CD	_	_	_
14	times	time	NNS	_	_	_
15	with	with	IN	_	_	_
16	wash	wash	NN	_	_	_
17	buffer	buffer	NN	_	_	_
18	I	i	NN	_	_	_
19	and	and	CC	_	_	_
20	with	with	IN	_	_	_
21	wash	wash	NN	_	_	_
22	buffer	buffer	NN	_	_	_
23	II	ii	CD	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	50	50	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	Tris-HCl	tris-hcl	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	pH	ph	NN	_	_	_
30	7.5	7.5	CD	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	,	,	,	_	_	_
33	500	500	CD	_	_	_
34	mM	mm	NN	KWSUPP	_	_
35	NaCl	nacl	NN	_	_	_
36	,	,	,	_	_	_
37	1	1	CD	_	_	_
38	%	%	NN	_	_	_
39	Triton	Triton	NNP	_	_	_
40	X-100	x-100	NN	_	_	_
41	and	and	CC	_	_	_
42	1mM	1mm	NN	_	_	_
43	EDTA	edta	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	,	,	,	_	_	_
46	wash	wash	NN	_	_	_
47	buffer	buffer	NN	_	_	_
48	III	iii	CD	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	10	10	CD	_	_	_
51	mM	mm	NN	KWSUPP	_	_
52	Tris-HCl	tris-hcl	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	pH	ph	NN	_	_	_
55	8.0	8.0	CD	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	,	,	,	_	_	_
58	250	250	CD	_	_	_
59	mM	mm	NN	KWSUPP	_	_
60	LiCl	licl	NN	_	_	_
61	,	,	,	_	_	_
62	1	1	CD	_	_	_
63	%	%	NN	_	_	_
64	Triton	Triton	NNP	_	_	_
65	X-100	x-100	NN	_	_	_
66	and	and	CC	_	_	_
67	1mM	1mm	NN	_	_	_
68	EDTA	edta	NN	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	,	,	,	_	_	_
71	and	and	CC	_	_	_
72	wash	wash	NN	_	_	_
73	buffer	buffer	NN	_	_	_
74	IV	iv	CD	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	10	10	CD	_	_	_
77	mM	mm	NN	KWSUPP	_	_
78	Tris-HCl	tris-hcl	NN	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	pH	ph	NN	_	_	_
81	8.0	8.0	CD	_	_	_
82	-RRB-	-rrb-	-RRB-	_	_	_
83	,	,	,	_	_	_
84	1mM	1mm	NN	_	_	_
85	EDTA	edta	NN	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	bead-bound	bead-bound	JJ	_	_	_
3	TF-DNA	tf-dna	NN	_	_	_
4	complex	complex	NN	_	_	_
5	was	be	VBD	_	_	_
6	then	then	RB	_	_	_
7	end-repaired	end-repaired	JJ	_	_	_
8	,	,	,	_	_	_
9	dA-tailed	da-tailed	JJ	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	ligated	ligate	VBN	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	first	first	JJ	_	_	_
16	adapter	adapter	NN	_	_	_
17	.	.	.	_	_	_

1	Adapter-ligated	adapter-ligated	JJ	_	_	_
2	sample	sample	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	treated	treat	VBN	_	_	_
6	with	with	IN	_	_	_
7	nick-repair	nick-repair	JJ	_	_	_
8	reagent	reagent	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	was	be	VBD	_	_	_
12	treated	treat	VBN	_	_	_
13	with	with	IN	_	_	_
14	lambda	lambda	NN	_	_	_
15	exonuclease	exonuclease	NN	_	_	_
16	and	and	CC	_	_	_
17	RecJ	recj	NN	_	_	_
18	exonuclease	exonuclease	NN	_	_	_
19	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	eluted	elute	VBN	_	_	_
5	away	away	RB	_	_	_
6	from	from	IN	_	_	_
7	Dynabeads	Dynabeads	NNPS	_	_	_
8	by	by	IN	_	_	_
9	incubating	incubate	VBG	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	ul	ul	NN	_	_	_
13	of	of	IN	_	_	_
14	elution	elution	NN	_	_	_
15	buffer	buffer	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	50	50	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	Tris-HCl	tris-hcl	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	pH	ph	NN	_	_	_
22	8.0	8.0	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	,	,	,	_	_	_
25	1	1	CD	_	_	_
26	%	%	NN	_	_	_
27	SDS	sds	NN	_	_	_
28	and	and	CC	_	_	_
29	1	1	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	EDTA	edta	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	at	at	IN	_	_	_
34	65C	65c	CD	_	_	_
35	overnight	overnight	JJ	_	_	_
36	.	.	.	_	_	_

1	Protein	protein	NN	_	_	_
2	was	be	VBD	_	_	_
3	removed	remove	VBN	_	_	_
4	by	by	IN	_	_	_
5	treating	treat	VBG	_	_	_
6	4	4	CD	_	_	_
7	ul	ul	NN	_	_	_
8	of	of	IN	_	_	_
9	protease	protease	NN	_	_	_
10	K	k	NN	_	_	_
11	and	and	CC	_	_	_
12	being	be	VBG	_	_	_
13	incubated	incubate	VBN	_	_	_
14	at	at	IN	_	_	_
15	55C	55c	NN	_	_	_
16	for	for	IN	_	_	_
17	2	2	CD	_	_	_
18	hours	hour	NNS	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	by	by	IN	_	_	_
22	Phenol-Chloroform-IAA	phenol-chloroform-iaa	NN	_	_	_
23	extraction	extraction	NN	_	_	_
24	.	.	.	_	_	_

1	Purified	purify	VBN	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	used	use	VBN	_	_	_
5	to	to	TO	_	_	_
6	bulid	bulid	VB	_	_	_
7	the	the	DT	_	_	_
8	second	second	JJ	_	_	_
9	strand	strand	NN	_	_	_
10	synthesis	synthesis	NN	_	_	_
11	,	,	,	_	_	_
12	followed	follow	VBN	_	_	_
13	by	by	IN	_	_	_
14	another	another	DT	_	_	_
15	dA-tailing	da-tailing	NN	_	_	_
16	,	,	,	_	_	_
17	second	second	JJ	_	_	_
18	strand	strand	NN	_	_	_
19	ligation	ligation	NN	_	_	_
20	,	,	,	_	_	_
21	and	and	CC	_	_	_
22	3	3	CD	_	_	_
23	'	'	''	_	_	_
24	overhang	overhang	NN	_	_	_
25	removal	removal	NN	_	_	_
26	stpes	stpe	NNS	_	_	_
27	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	the	the	DT	_	_	_
3	sequencing	sequencing	NN	_	_	_
4	library	library	NN	_	_	_
5	was	be	VBD	_	_	_
6	amplified	amplify	VBN	_	_	_
7	with	with	IN	_	_	_
8	PCR	pcr	NN	_	_	_
9	enrichment	enrichment	NN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Crosslinked	crosslinked	JJ	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	then	then	RB	_	_	_
6	resuspended	resuspend	VBN	_	_	_
7	in	in	IN	_	_	_
8	500	500	CD	_	_	_
9	ul	ul	NN	_	_	_
10	of	of	IN	_	_	_
11	lysis	lysis	NN	_	_	_
12	buffer	buffer	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	10	10	CD	_	_	_
15	mM	mm	NN	KWSUPP	_	_
16	Tris-HCl	tris-hcl	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	pH	ph	NN	_	_	_
19	7.5	7.5	CD	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	,	,	,	_	_	_
22	100	100	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	NaCl	nacl	NN	_	_	_
25	and	and	CC	_	_	_
26	1	1	CD	_	_	_
27	mM	mm	NN	KWSUPP	_	_
28	EDTA	edta	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	with	with	IN	_	_	_
31	40	40	CD	_	_	_
32	ul	ul	NN	_	_	_
33	of	of	IN	_	_	_
34	protease	protease	NN	_	_	_
35	inhibitor	inhibitor	NN	_	_	_
36	cocktail	cocktail	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	50	50	CD	_	_	_
39	mg	mg	NN	_	_	_
40	in	in	IN	_	_	_
41	0.25	0.25	CD	_	_	_
42	ml	ml	NN	_	_	_
43	of	of	IN	_	_	_
44	DMSO	dmso	NN	_	_	_
45	and	and	CC	_	_	_
46	0.75	0.75	CD	_	_	_
47	ml	ml	NN	_	_	_
48	of	of	IN	_	_	_
49	TDW	tdw	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	lyzed	lyze	VBN	_	_	_
4	with	with	IN	_	_	_
5	1	1	CD	_	_	_
6	ul	ul	NN	_	_	_
7	of	of	IN	_	_	_
8	lysozyme	lysozyme	NN	_	_	_
9	for	for	IN	_	_	_
10	30	30	CD	_	_	_
11	min	min	NN	_	_	_
12	at	at	IN	_	_	_
13	37oC	37oc	NN	_	_	_
14	on	on	IN	_	_	_
15	a	a	DT	_	_	_
16	rocker	rocker	NN	_	_	_
17	.	.	.	_	_	_

1	0.55	0.55	CD	_	_	_
2	ml	ml	NN	_	_	_
3	of	of	IN	_	_	_
4	2X	2x	NN	_	_	_
5	IP	IP	NNP	_	_	_
6	buffer	buffer	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	100	100	CD	_	_	_
9	mM	mm	NN	KWSUPP	_	_
10	Tris-HCl	tris-hcl	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	pH	ph	NN	_	_	_
13	7.5	7.5	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	200	200	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	NaCl	nacl	NN	_	_	_
19	,	,	,	_	_	_
20	2	2	CD	_	_	_
21	%	%	NN	_	_	_
22	Triton	Triton	NNP	_	_	_
23	X-100	x-100	NN	_	_	_
24	and	and	CC	_	_	_
25	1	1	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	EDTA	edta	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	were	be	VBD	_	_	_
30	added	add	VBN	_	_	_
31	to	to	TO	_	_	_
32	the	the	DT	_	_	_
33	sample	sample	NN	_	_	_
34	,	,	,	_	_	_
35	and	and	CC	_	_	_
36	then	then	RB	_	_	_
37	was	be	VBD	_	_	_
38	sonicated	sonicate	VBN	_	_	_
39	to	to	TO	_	_	_
40	fragmentize	fragmentize	VB	_	_	_
41	genomic	genomic	JJ	_	_	_
42	DNA	dna	NN	_	_	_
43	.	.	.	_	_	_

1	0.3	0.3	CD	_	_	_
2	ml	ml	NN	_	_	_
3	of	of	IN	_	_	_
4	Wash	Wash	NNP	_	_	_
5	buffer	buffer	NN	_	_	_
6	I	i	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	50	50	CD	_	_	_
9	mM	mm	NN	KWSUPP	_	_
10	Tris-HCl	tris-hcl	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	pH	ph	NN	_	_	_
13	7.5	7.5	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	140	140	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	NaCl	nacl	NN	_	_	_
19	,	,	,	_	_	_
20	1	1	CD	_	_	_
21	%	%	NN	_	_	_
22	Triton	Triton	NNP	_	_	_
23	X-100	x-100	NN	_	_	_
24	and	and	CC	_	_	_
25	1mM	1mm	NN	_	_	_
26	EDTA	edta	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	was	be	VBD	_	_	_
29	added	add	VBN	_	_	_
30	to	to	TO	_	_	_
31	make	make	VB	_	_	_
32	the	the	DT	_	_	_
33	volume	volume	NN	_	_	_
34	up	up	IN	_	_	_
35	to	to	TO	_	_	_
36	1.4	1.4	CD	_	_	_
37	ml	ml	NN	_	_	_
38	.	.	.	_	_	_

1	Only	only	RB	_	_	_
2	0.7	0.7	CD	_	_	_
3	ml	ml	NN	_	_	_
4	was	be	VBD	_	_	_
5	taken	take	VBN	_	_	_
6	and	and	CC	_	_	_
7	transfered	transfer	VBN	_	_	_
8	to	to	TO	_	_	_
9	a	a	DT	_	_	_
10	new	new	JJ	_	_	_
11	tube	tube	NN	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	10	10	CD	_	_	_
15	ul	ul	NN	_	_	_
16	of	of	IN	_	_	_
17	Anti-rpoB	anti-rpob	JJ	_	_	_
18	mouse	mouse	NN	_	_	_
19	antibody	antibody	NN	_	_	_
20	was	be	VBD	_	_	_
21	added	add	VBN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	the	the	DT	_	_	_
25	sample	sample	NN	_	_	_
26	was	be	VBD	_	_	_
27	incubated	incubate	VBN	_	_	_
28	overnight	overnight	RB	_	_	_
29	at	at	IN	_	_	_
30	4	4	CD	_	_	_
31	oC	oc	NN	_	_	_
32	to	to	TO	_	_	_
33	make	make	VB	_	_	_
34	Antibody-TF	antibody-tf	NN	_	_	_
35	complex	complex	NN	_	_	_
36	.	.	.	_	_	_

1	50	50	CD	_	_	_
2	ul	ul	NN	_	_	_
3	of	of	IN	_	_	_
4	Dynabeads	Dynabeads	NNP	_	_	_
5	Pan	Pan	NNP	_	_	_
6	mouse	mouse	NN	_	_	_
7	IgG	igg	NN	_	_	_
8	were	be	VBD	_	_	_
9	washed	wash	VBN	_	_	_
10	3	3	CD	_	_	_
11	times	time	NNS	_	_	_
12	with	with	IN	_	_	_
13	bead	bead	NN	_	_	_
14	washing	wash	VBG	_	_	_
15	solution	solution	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	250	250	CD	_	_	_
18	mg	mg	NN	_	_	_
19	BSA	bsa	NN	_	_	_
20	in	in	IN	_	_	_
21	50	50	CD	_	_	_
22	ml	ml	NN	_	_	_
23	of	of	IN	_	_	_
24	PBS	PBS	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	,	,	,	_	_	_
27	and	and	CC	_	_	_
28	were	be	VBD	_	_	_
29	added	add	VBN	_	_	_
30	to	to	TO	_	_	_
31	the	the	DT	_	_	_
32	sample	sample	NN	_	_	_
33	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	lysate	lysate	NN	_	_	_
3	with	with	IN	_	_	_
4	beads	bead	NNS	_	_	_
5	were	be	VBD	_	_	_
6	incubated	incubate	VBN	_	_	_
7	for	for	IN	_	_	_
8	6	6	CD	_	_	_
9	hours	hour	NNS	_	_	_
10	or	or	CC	_	_	_
11	overnight	overnight	JJ	_	_	_
12	at	at	IN	_	_	_
13	4oC	4oc	NN	_	_	_
14	to	to	TO	_	_	_
15	make	make	VB	_	_	_
16	Dynabead-antibody-TF	dynabead-antibody-tf	NN	_	_	_
17	complex	complex	NN	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	beads	bead	NNS	_	_	_
3	were	be	VBD	_	_	_
4	pulled	pull	VBN	_	_	_
5	down	down	RP	_	_	_
6	on	on	IN	_	_	_
7	a	a	DT	_	_	_
8	magnet	magnet	NN	_	_	_
9	stand	stand	NN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	washed	wash	VBN	_	_	_
13	2	2	CD	_	_	_
14	times	time	NNS	_	_	_
15	with	with	IN	_	_	_
16	wash	wash	NN	_	_	_
17	buffer	buffer	NN	_	_	_
18	I	i	NN	_	_	_
19	and	and	CC	_	_	_
20	with	with	IN	_	_	_
21	wash	wash	NN	_	_	_
22	buffer	buffer	NN	_	_	_
23	II	ii	CD	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	50	50	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	Tris-HCl	tris-hcl	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	pH	ph	NN	_	_	_
30	7.5	7.5	CD	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	,	,	,	_	_	_
33	500	500	CD	_	_	_
34	mM	mm	NN	KWSUPP	_	_
35	NaCl	nacl	NN	_	_	_
36	,	,	,	_	_	_
37	1	1	CD	_	_	_
38	%	%	NN	_	_	_
39	Triton	Triton	NNP	_	_	_
40	X-100	x-100	NN	_	_	_
41	and	and	CC	_	_	_
42	1mM	1mm	NN	_	_	_
43	EDTA	edta	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	,	,	,	_	_	_
46	wash	wash	NN	_	_	_
47	buffer	buffer	NN	_	_	_
48	III	iii	CD	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	10	10	CD	_	_	_
51	mM	mm	NN	KWSUPP	_	_
52	Tris-HCl	tris-hcl	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	pH	ph	NN	_	_	_
55	8.0	8.0	CD	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	,	,	,	_	_	_
58	250	250	CD	_	_	_
59	mM	mm	NN	KWSUPP	_	_
60	LiCl	licl	NN	_	_	_
61	,	,	,	_	_	_
62	1	1	CD	_	_	_
63	%	%	NN	_	_	_
64	Triton	Triton	NNP	_	_	_
65	X-100	x-100	NN	_	_	_
66	and	and	CC	_	_	_
67	1mM	1mm	NN	_	_	_
68	EDTA	edta	NN	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	,	,	,	_	_	_
71	and	and	CC	_	_	_
72	wash	wash	NN	_	_	_
73	buffer	buffer	NN	_	_	_
74	IV	iv	CD	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	10	10	CD	_	_	_
77	mM	mm	NN	KWSUPP	_	_
78	Tris-HCl	tris-hcl	NN	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	pH	ph	NN	_	_	_
81	8.0	8.0	CD	_	_	_
82	-RRB-	-rrb-	-RRB-	_	_	_
83	,	,	,	_	_	_
84	1mM	1mm	NN	_	_	_
85	EDTA	edta	NN	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	bead-bound	bead-bound	JJ	_	_	_
3	TF-DNA	tf-dna	NN	_	_	_
4	complex	complex	NN	_	_	_
5	was	be	VBD	_	_	_
6	then	then	RB	_	_	_
7	end-repaired	end-repaired	JJ	_	_	_
8	,	,	,	_	_	_
9	dA-tailed	da-tailed	JJ	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	ligated	ligate	VBN	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	first	first	JJ	_	_	_
16	adapter	adapter	NN	_	_	_
17	.	.	.	_	_	_

1	Adapter-ligated	adapter-ligated	JJ	_	_	_
2	sample	sample	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	treated	treat	VBN	_	_	_
6	with	with	IN	_	_	_
7	nick-repair	nick-repair	JJ	_	_	_
8	reagent	reagent	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	was	be	VBD	_	_	_
12	treated	treat	VBN	_	_	_
13	with	with	IN	_	_	_
14	lambda	lambda	NN	_	_	_
15	exonuclease	exonuclease	NN	_	_	_
16	and	and	CC	_	_	_
17	RecJ	recj	NN	_	_	_
18	exonuclease	exonuclease	NN	_	_	_
19	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	eluted	elute	VBN	_	_	_
5	away	away	RB	_	_	_
6	from	from	IN	_	_	_
7	Dynabeads	Dynabeads	NNPS	_	_	_
8	by	by	IN	_	_	_
9	incubating	incubate	VBG	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	ul	ul	NN	_	_	_
13	of	of	IN	_	_	_
14	elution	elution	NN	_	_	_
15	buffer	buffer	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	50	50	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	Tris-HCl	tris-hcl	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	pH	ph	NN	_	_	_
22	8.0	8.0	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	,	,	,	_	_	_
25	1	1	CD	_	_	_
26	%	%	NN	_	_	_
27	SDS	sds	NN	_	_	_
28	and	and	CC	_	_	_
29	1	1	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	EDTA	edta	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	at	at	IN	_	_	_
34	65oC	65oc	NN	_	_	_
35	overnight	overnight	JJ	_	_	_
36	.	.	.	_	_	_

1	Protein	protein	NN	_	_	_
2	was	be	VBD	_	_	_
3	removed	remove	VBN	_	_	_
4	by	by	IN	_	_	_
5	treating	treat	VBG	_	_	_
6	4	4	CD	_	_	_
7	ul	ul	NN	_	_	_
8	of	of	IN	_	_	_
9	protease	protease	NN	_	_	_
10	K	k	NN	_	_	_
11	and	and	CC	_	_	_
12	being	be	VBG	_	_	_
13	incubated	incubate	VBN	_	_	_
14	at	at	IN	_	_	_
15	55	55	CD	_	_	_
16	oC	oc	NN	_	_	_
17	for	for	IN	_	_	_
18	2	2	CD	_	_	_
19	hours	hour	NNS	_	_	_
20	,	,	,	_	_	_
21	and	and	CC	_	_	_
22	by	by	IN	_	_	_
23	Phenol-Chloroform-IAA	phenol-chloroform-iaa	NN	_	_	_
24	extraction	extraction	NN	_	_	_
25	.	.	.	_	_	_

1	Purified	purify	VBN	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	used	use	VBN	_	_	_
5	to	to	TO	_	_	_
6	bulid	bulid	VB	_	_	_
7	the	the	DT	_	_	_
8	second	second	JJ	_	_	_
9	strand	strand	NN	_	_	_
10	synthesis	synthesis	NN	_	_	_
11	,	,	,	_	_	_
12	followed	follow	VBN	_	_	_
13	by	by	IN	_	_	_
14	another	another	DT	_	_	_
15	dA-tailing	da-tailing	NN	_	_	_
16	,	,	,	_	_	_
17	second	second	JJ	_	_	_
18	strand	strand	NN	_	_	_
19	ligation	ligation	NN	_	_	_
20	,	,	,	_	_	_
21	and	and	CC	_	_	_
22	3	3	CD	_	_	_
23	'	'	''	_	_	_
24	overhang	overhang	NN	_	_	_
25	removal	removal	NN	_	_	_
26	stpes	stpe	NNS	_	_	_
27	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	the	the	DT	_	_	_
3	sequencing	sequencing	NN	_	_	_
4	library	library	NN	_	_	_
5	was	be	VBD	_	_	_
6	amplified	amplify	VBN	_	_	_
7	with	with	IN	_	_	_
8	PCR	pcr	NN	_	_	_
9	enrichment	enrichment	NN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	cultured	culture	VBN	_	_	_
3	in	in	IN	_	_	_
4	:	:	:	_	_	_
5	M9	m9	NN	MED	_	_
6	minimal	minimal	JJ	MED	_	_
7	media	media	NNS	MED	_	_
8	with	with	IN	_	_	_
9	0.2	0.2	CD	_	_	_
10	%	%	NN	_	_	_
11	acetate	acetate	NN	SUPP	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	cultured	culture	VBN	_	_	_
14	in	in	IN	_	_	_
15	:	:	:	_	_	_
16	M9	m9	NN	MED	_	_
17	minimal	minimal	JJ	MED	_	_
18	media	media	NNS	MED	_	_
19	with	with	IN	_	_	_
20	0.2	0.2	CD	_	_	_
21	%	%	NN	_	_	_
22	fructose	fructose	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	cultured	culture	VBN	_	_	_
25	in	in	IN	_	_	_
26	:	:	:	_	_	_
27	M9	m9	NN	MED	_	_
28	minimal	minimal	JJ	MED	_	_
29	media	media	NNS	MED	_	_
30	with	with	IN	_	_	_
31	0.2	0.2	CD	_	_	_
32	%	%	NN	_	_	_
33	glucose	glucose	NN	SUPP	_	_
34	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
35	E.	E.	NNP	_	_	_
36	coli	coli	NN	_	_	_
37	cells	cell	NNS	_	_	_
38	were	be	VBD	_	_	_
39	crosslinked	crosslink	VBN	_	_	_
40	in	in	IN	_	_	_
41	1	1	CD	_	_	_
42	%	%	NN	_	_	_
43	formaldehyde	formaldehyde	NN	_	_	_
44	for	for	IN	_	_	_
45	25	25	CD	_	_	_
46	minutes	minute	NNS	_	_	_
47	at	at	IN	_	_	_
48	RT	rt	NN	_	_	_
49	on	on	IN	_	_	_
50	a	a	DT	_	_	_
51	rocker	rocker	NN	_	_	_
52	,	,	,	_	_	_
53	then	then	RB	_	_	_
54	washed	wash	VBN	_	_	_
55	3	3	CD	_	_	_
56	times	time	NNS	_	_	_
57	with	with	IN	_	_	_
58	50	50	CD	_	_	_
59	ml	ml	NN	_	_	_
60	of	of	IN	_	_	_
61	ice-cold	ice-cold	JJ	_	_	_
62	TBS	tbs	NN	_	_	_
63	-LRB-	-lrb-	-LRB-	_	_	_
64	Tris	tris	NN	_	_	_
65	buffered	buffer	VBN	_	_	_
66	saline	saline	NN	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	each	each	DT	_	_	_
69	time	time	NN	_	_	_
70	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	K-12	k-12	NN	_	_	_
5	MG1655	mg1655	NN	_	_	_
6	cra-8myc	cra-8myc	NN	_	_	_
7	tagged	tag	VBD	_	_	_
8	strains	strain	NNS	_	_	_
9	was	be	VBD	_	_	_
10	grown	grow	VBN	_	_	_
11	to	to	TO	_	_	_
12	mid-log	mid-log	JJ	_	_	_
13	phase	phase	NN	_	_	_
14	aerobically	aerobically	RB	_	_	_
15	at	at	IN	_	_	_
16	37	37	CD	_	_	_
17	°C	°c	NN	_	_	_
18	in	in	IN	_	_	_
19	M9	m9	NN	MED	_	_
20	minimal	minimal	JJ	MED	_	_
21	media	media	NNS	MED	_	_
22	supplemented	supplement	VBN	_	_	_
23	with	with	IN	_	_	_
24	0.2	0.2	CD	_	_	_
25	%	%	NN	_	_	_
26	glucose	glucose	NN	SUPP	_	_
27	,	,	,	_	_	_
28	fructose	fructose	NN	_	_	_
29	and	and	CC	_	_	_
30	acetate	acetate	NN	SUPP	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	For	for	IN	_	_	_
6	each	each	DT	_	_	_
7	peak	peak	NN	_	_	_
8	detected	detect	VBN	_	_	_
9	with	with	IN	_	_	_
10	MACE	MACE	NNP	_	_	_
11	,	,	,	_	_	_
12	binding	bind	VBG	_	_	_
13	intensity	intensity	NN	_	_	_
14	was	be	VBD	_	_	_
15	calculated	calculate	VBN	_	_	_
16	by	by	IN	_	_	_
17	averaging	average	VBG	_	_	_
18	read	read	VBN	_	_	_
19	counts	count	NNS	_	_	_
20	from	from	IN	_	_	_
21	two	two	CD	_	_	_
22	biological	biological	JJ	_	_	_
23	replicates	replicate	VBZ	_	_	_
24	and	and	CC	_	_	_
25	dividing	divide	VBG	_	_	_
26	by	by	IN	_	_	_
27	background	background	NN	_	_	_
28	intensity	intensity	NN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	ASM584v2	asm584v2	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	genotype	genotype	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	genotype	genotype	NN	_	_	_
11	:	:	:	_	_	_
12	delta-cra	delta-cra	NN	_	_	_
13	Knock-out	knock-out	JJ	_	_	_
14	strain	strain	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	genotype	genotype	NN	_	_	_
17	:	:	:	_	_	_
18	delta-crp	delta-crp	JJ	_	_	_
19	Knock-out	knock-out	JJ	_	_	_
20	strain	strain	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	genotype	genotype	NN	_	_	_
23	:	:	:	_	_	_
24	Wildtype	wildtype	JJ	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	growth	growth	NN	_	_	_
27	phase	phase	NN	_	_	_
28	:	:	:	_	_	_
29	mid-log	mid-log	JJ	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
31	MACE	mace	VBP	_	_	_
32	software	software	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	https	http	NNS	_	_	_
35	:	:	:	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
37	Read	read	VBP	_	_	_
38	count	count	NN	_	_	_
39	was	be	VBD	_	_	_
40	calculated	calculate	VBN	_	_	_
41	for	for	IN	_	_	_
42	each	each	DT	_	_	_
43	genomic	genomic	JJ	_	_	_
44	position	position	NN	_	_	_
45	from	from	IN	_	_	_
46	sequence	sequence	NN	_	_	_
47	alignment	alignment	NN	_	_	_
48	,	,	,	_	_	_
49	and	and	CC	_	_	_
50	95	95	CD	_	_	_
51	%	%	NN	_	_	_
52	strongest	strongest	JJS	_	_	_
53	intensity	intensity	NN	_	_	_
54	was	be	VBD	_	_	_
55	used	use	VBN	_	_	_
56	as	as	IN	_	_	_
57	background	background	NN	_	_	_
58	intensity	intensity	NN	_	_	_
59	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RpoB	rpob	NN	_	_	_
3	∆	∆	CD	_	_	_
4	cra	cra	NN	GEN	_	_
5	1	1	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	RpoB	rpob	NN	_	_	_
8	∆	∆	CD	_	_	_
9	cra	cra	NN	GEN	_	_
10	2	2	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	RpoB	rpob	NN	_	_	_
13	∆	∆	CD	_	_	_
14	crp	crp	NN	GEN	_	_
15	1	1	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	RpoB	rpob	NN	_	_	_
18	∆	∆	CD	_	_	_
19	crp	crp	NN	GEN	_	_
20	2	2	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	RpoB	rpob	NN	_	_	_
23	WT	wt	NN	_	_	_
24	1	1	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	RpoB	rpob	NN	_	_	_
27	WT	wt	NN	_	_	_
28	2	2	CD	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	strain	strain	NN	_	_	_
31	:	:	:	_	_	_
32	K-12	k-12	NN	_	_	_
33	MG1655	mg1655	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	Supplementary	supplementary	JJ	_	_	_
36	_	_	NN	_	_	_
37	files	file	NNS	_	_	_
38	_	_	IN	_	_	_
39	format	format	NN	_	_	_
40	_	_	NN	_	_	_
41	and	and	CC	_	_	_
42	_	_	NN	_	_	_
43	content	content	NN	_	_	_
44	:	:	:	_	_	_
45	Tab-delimited	tab-delimited	JJ	_	_	_
46	text	text	NN	_	_	_
47	files	file	NNS	_	_	_
48	in	in	IN	_	_	_
49	gff	gff	NN	_	_	_
50	format	format	NN	_	_	_
51	which	which	WDT	_	_	_
52	has	have	VBZ	_	_	_
53	8	8	CD	_	_	_
54	columns	column	NNS	_	_	_
55	:	:	:	_	_	_
56	sequence	sequence	NN	_	_	_
57	id	id	NN	_	_	_
58	,	,	,	_	_	_
59	source	source	NN	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	empty	empty	JJ	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	,	,	,	_	_	_
64	feature	feature	NN	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	+	+	CC	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
68	carbon	carbon	NN	_	_	_
69	source	source	NN	_	_	_
70	:	:	:	_	_	_
71	acetate	acetate	NN	SUPP	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
73	carbon	carbon	NN	_	_	_
74	source	source	NN	_	_	_
75	:	:	:	_	_	_
76	fructose	fructose	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	carbon	carbon	NN	_	_	_
79	source	source	NN	_	_	_
80	:	:	:	_	_	_
81	glucose	glucose	NN	SUPP	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	E.	e.	FW	_	_	_
84	coli	coli	FW	_	_	_
85	K-12	k-12	NN	_	_	_
86	MG1655	mg1655	NN	_	_	_
87	WT	WT	NNP	_	_	_
88	,	,	,	_	_	_
89	and	and	CC	_	_	_
90	Δcra	Δcra	NNP	_	_	_
91	were	be	VBD	_	_	_
92	grown	grow	VBN	_	_	_
93	to	to	TO	_	_	_
94	mid-log	mid-log	JJ	_	_	_
95	phase	phase	NN	_	_	_
96	aerobically	aerobically	RB	_	_	_
97	at	at	IN	_	_	_
98	37	37	CD	_	_	_
99	°C	°c	NN	_	_	_
100	in	in	IN	_	_	_
101	M9	m9	NN	MED	_	_
102	minimal	minimal	JJ	MED	_	_
103	media	media	NNS	MED	_	_
104	supplemented	supplement	VBN	_	_	_
105	with	with	IN	_	_	_
106	0.2	0.2	CD	_	_	_
107	%	%	NN	_	_	_
108	glucose	glucose	NN	SUPP	_	_
109	,	,	,	_	_	_
110	fructose	fructose	NN	_	_	_
111	and	and	CC	_	_	_
112	acetate	acetate	NN	SUPP	_	_
113	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Fragments	fragment	NNS	_	_	_
6	Per	per	IN	_	_	_
7	Kilobase	kilobase	NN	_	_	_
8	of	of	IN	_	_	_
9	exon	exon	NN	_	_	_
10	per	per	IN	_	_	_
11	Megabase	megabase	NN	_	_	_
12	of	of	IN	_	_	_
13	library	library	NN	_	_	_
14	size	size	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	FPKM	fpkm	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	were	be	VBD	_	_	_
19	calculated	calculate	VBN	_	_	_
20	using	use	VBG	_	_	_
21	cufflinks	cufflink	NNS	_	_	_
22	v.	v.	CC	_	_	_
23	1.3.0	1.3.0	CD	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
25	Genome	Genome	NNP	_	_	_
26	_	_	NNP	_	_	_
27	build	build	VB	_	_	_
28	:	:	:	_	_	_
29	NC	NC	NNP	_	_	_
30	_	_	NNP	_	_	_
31	000913	000913	CD	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	genotype	genotype	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	RNA	rna	NN	_	_	_
36	libraries	library	NNS	_	_	_
37	were	be	VBD	_	_	_
38	prepared	prepare	VBN	_	_	_
39	for	for	IN	_	_	_
40	sequencing	sequencing	NN	_	_	_
41	using	use	VBG	_	_	_
42	standard	standard	JJ	_	_	_
43	Illumina	Illumina	NNP	_	_	_
44	protocols	protocol	NNS	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
46	RNA-Seq	rna-seq	JJ	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	Sequenced	sequence	VBN	_	_	_
49	reads	read	VBZ	_	_	_
50	were	be	VBD	_	_	_
51	mapped	map	VBN	_	_	_
52	onto	onto	IN	_	_	_
53	NC	nc	NN	_	_	_
54	_	_	CD	_	_	_
55	000913	000913	CD	_	_	_
56	reference	reference	NN	_	_	_
57	genome	genome	NN	_	_	_
58	sequence	sequence	NN	_	_	_
59	using	use	VBG	_	_	_
60	bowtie	bowtie	NN	_	_	_
61	v1	v1	NN	_	_	_
62	.0.0	.0.0	CD	_	_	_
63	with	with	IN	_	_	_
64	parameters	parameter	NNS	_	_	_
65	-	-	:	_	_	_
66	X	x	NN	_	_	_
67	1000	1000	CD	_	_	_
68	-	-	:	_	_	_
69	n	n	NN	_	_	_
70	2	2	CD	_	_	_
71	-3	-3	CD	_	_	_
72	3	3	LS	_	_	_
73	-	-	:	_	_	_
74	S	s	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	strain	strain	NN	_	_	_
77	:	:	:	_	_	_
78	K-12	k-12	NN	_	_	_
79	MG1655	mg1655	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	Supplementary	supplementary	JJ	_	_	_
82	_	_	NN	_	_	_
83	files	file	NNS	_	_	_
84	_	_	IN	_	_	_
85	format	format	NN	_	_	_
86	_	_	NN	_	_	_
87	and	and	CC	_	_	_
88	_	_	NN	_	_	_
89	content	content	NN	_	_	_
90	:	:	:	_	_	_
91	comma-delimited	comma-delimited	JJ	_	_	_
92	text	text	NN	_	_	_
93	files	file	NNS	_	_	_
94	include	include	VBP	_	_	_
95	FPKM	fpkm	NN	_	_	_
96	values	value	NNS	_	_	_
97	for	for	IN	_	_	_
98	each	each	DT	_	_	_
99	Sample	Sample	NNP	_	_	_
100	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cell	cell	NN	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	treated	treat	VBN	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	RNAprotect	rnaprotect	NN	_	_	_
10	reagent	reagent	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	qiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	RNeasy	RNeasy	NNP	_	_	_
9	Plus	Plus	NNP	_	_	_
10	Mini	Mini	NNP	_	_	_
11	kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Qiagen	Qiagen	NNP	_	_	_
14	Inc.	Inc.	NNP	_	_	_
15	,	,	,	_	_	_
16	Valencia	Valencia	NNP	_	_	_
17	,	,	,	_	_	_
18	CA	CA	NNP	_	_	_
19	,	,	,	_	_	_
20	USA	USA	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	and	and	CC	_	_	_
23	genomic	genomic	JJ	_	_	_
24	DNA	dna	NN	_	_	_
25	was	be	VBD	_	_	_
26	removed	remove	VBN	_	_	_
27	by	by	IN	_	_	_
28	gDNA	gdna	NN	_	_	_
29	Eliminator	eliminator	NN	_	_	_
30	spin	spin	NN	_	_	_
31	column	column	NN	_	_	_
32	in	in	IN	_	_	_
33	the	the	DT	_	_	_
34	RNeasy	RNeasy	NNP	_	_	_
35	Plus	Plus	NNP	_	_	_
36	Mini	Mini	NNP	_	_	_
37	Kit	kit	NN	_	_	_
38	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	quality	quality	NN	_	_	_
3	and	and	CC	_	_	_
4	concentration	concentration	NN	_	_	_
5	was	be	VBD	_	_	_
6	determined	determine	VBN	_	_	_
7	by	by	IN	_	_	_
8	analysis	analysis	NN	_	_	_
9	with	with	IN	_	_	_
10	a	a	DT	_	_	_
11	NanoDrop	NanoDrop	NNP	_	_	_
12	1000	1000	CD	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Thermo	Thermo	NNP	_	_	_
15	Scientific	Scientific	NNP	_	_	_
16	Inc.	Inc.	NNP	_	_	_
17	,	,	,	_	_	_
18	Wilmington	Wilmington	NNP	_	_	_
19	,	,	,	_	_	_
20	DE	de	NN	_	_	_
21	,	,	,	_	_	_
22	USA	USA	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	WT	WT	NNP	_	_	_
3	_	_	NNP	_	_	_
4	acetate	acetate	NN	SUPP	_	_
5	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
6	WT	WT	NNP	_	_	_
7	acetate	acetate	NN	SUPP	_	_
8	1	1	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	WT	wt	JJ	_	_	_
11	acetate	acetate	NN	SUPP	_	_
12	2	2	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	WT	wt	JJ	_	_	_
15	_	_	NN	_	_	_
16	fructose	fructose	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	WT	wt	JJ	_	_	_
19	fructose	fructose	NN	_	_	_
20	1	1	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	WT	wt	JJ	_	_	_
23	fructose	fructose	NN	_	_	_
24	2	2	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	WT	wt	JJ	_	_	_
27	_	_	NN	_	_	_
28	glucose	glucose	NN	SUPP	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	WT	wt	JJ	_	_	_
31	glucose	glucose	NN	SUPP	_	_
32	1	1	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	WT	wt	JJ	_	_	_
35	glucose	glucose	NN	SUPP	_	_
36	2	2	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Δcra	δcra	NN	_	_	_
39	_	_	NN	_	_	_
40	acetate	acetate	NN	SUPP	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	Δcra	δcra	NN	_	_	_
43	acetate	acetate	NN	SUPP	_	_
44	1	1	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	Δcra	δcra	NN	_	_	_
47	acetate	acetate	NN	SUPP	_	_
48	2	2	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	Δcra	δcra	NN	_	_	_
51	_	_	NN	_	_	_
52	fructose	fructose	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Δcra	δcra	NN	_	_	_
55	fructose	fructose	NN	_	_	_
56	1	1	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Δcra	δcra	NN	_	_	_
59	fructose	fructose	NN	_	_	_
60	2	2	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Δcra	δcra	NN	_	_	_
63	_	_	NN	_	_	_
64	glucose	glucose	NN	SUPP	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	Δcra	δcra	NN	_	_	_
67	glucose	glucose	NN	SUPP	_	_
68	1	1	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	Δcra	δcra	NN	_	_	_
71	glucose	glucose	NN	SUPP	_	_
72	2	2	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	A	a	DT	_	_	_
75	total	total	NN	_	_	_
76	of	of	IN	_	_	_
77	six	six	CD	_	_	_
78	samples	sample	NNS	_	_	_
79	were	be	VBD	_	_	_
80	analyzed	analyze	VBN	_	_	_
81	.	.	.	_	_	_

1	oxyR-8myc	oxyr-8myc	NN	_	_	_
2	,	,	,	_	_	_
3	soxR-8myc	soxr-8myc	NN	_	_	_
4	,	,	,	_	_	_
5	and	and	CC	_	_	_
6	soxS-8myc	soxs-8myc	NN	_	_	_
7	tagged	tag	VBD	_	_	_
8	cells	cell	NNS	_	_	_
9	were	be	VBD	_	_	_
10	cultured	culture	VBN	_	_	_
11	in	in	IN	_	_	_
12	M9	m9	NN	MED	_	_
13	minimal	minimal	JJ	MED	_	_
14	media	media	NNS	MED	_	_
15	with	with	IN	_	_	_
16	0.2	0.2	CD	_	_	_
17	%	%	NN	_	_	_
18	glucose	glucose	NN	SUPP	_	_
19	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	treated	treat	VBN	_	_	_
5	with	with	IN	_	_	_
6	250	250	CD	_	_	_
7	uM	um	NN	_	_	_
8	of	of	IN	_	_	_
9	paraquat	paraquat	NN	SUPP	_	_
10	at	at	IN	_	_	_
11	mid-log	mid-log	JJ	_	_	_
12	pahse	pahse	NN	_	_	_
13	for	for	IN	_	_	_
14	20	20	CD	_	_	_
15	min	min	NN	_	_	_
16	with	with	IN	_	_	_
17	agitation	agitation	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	chip	chip	NN	_	_	_
3	antibody	antibody	NN	_	_	_
4	:	:	:	_	_	_
5	anti-myc	anti-myc	JJ	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	chip	chip	NN	_	_	_
8	antibody	antibody	NN	_	_	_
9	cat	cat	NN	_	_	_
10	.	.	.	_	_	_

1	#	#	#	_	_	_
2	:	:	:	_	_	_
3	sc-28207	sc-28207	JJ	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
5	chip	chip	NN	_	_	_
6	antibody	antibody	NN	_	_	_
7	vendor	vendor	NN	_	_	_
8	:	:	:	_	_	_
9	Santa	Santa	NNP	_	_	_
10	Cruz	Cruz	NNP	_	_	_
11	Biotech	Biotech	NNP	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	ChIP-exo	ChIP-exo	NNP	_	_	_
14	reads	read	VBZ	_	_	_
15	were	be	VBD	_	_	_
16	aligned	align	VBN	_	_	_
17	to	to	TO	_	_	_
18	the	the	DT	_	_	_
19	ASM584v2	asm584v2	NN	_	_	_
20	genome	genome	NN	_	_	_
21	reference	reference	NN	_	_	_
22	sequence	sequence	NN	_	_	_
23	using	use	VBG	_	_	_
24	using	use	VBG	_	_	_
25	bowtie	bowtie	NN	_	_	_
26	v1	v1	NN	_	_	_
27	.0.0	.0.0	CD	_	_	_
28	with	with	IN	_	_	_
29	parameters	parameter	NNS	_	_	_
30	-	-	:	_	_	_
31	S	s	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
33	ChIP-Seq	chip-seq	JJ	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	ChIP-seq	chip-seq	NN	_	_	_
36	libraries	library	NNS	_	_	_
37	were	be	VBD	_	_	_
38	prepared	prepare	VBN	_	_	_
39	for	for	IN	_	_	_
40	sequencing	sequencing	NN	_	_	_
41	using	use	VBG	_	_	_
42	standard	standard	JJ	_	_	_
43	Illumina	Illumina	NNP	_	_	_
44	protocols	protocol	NNS	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	Crosslinked	crosslink	VBN	_	_	_
47	cells	cell	NNS	_	_	_
48	were	be	VBD	_	_	_
49	then	then	RB	_	_	_
50	resuspended	resuspend	VBN	_	_	_
51	in	in	IN	_	_	_
52	500	500	CD	_	_	_
53	ul	ul	NN	_	_	_
54	of	of	IN	_	_	_
55	lysis	lysis	NN	_	_	_
56	buffer	buffer	NN	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	10	10	CD	_	_	_
59	mM	mm	NN	KWSUPP	_	_
60	Tris-HCl	tris-hcl	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	pH	ph	NN	_	_	_
63	7.5	7.5	CD	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	,	,	,	_	_	_
66	100	100	CD	_	_	_
67	mM	mm	NN	KWSUPP	_	_
68	NaCl	nacl	NN	_	_	_
69	and	and	CC	_	_	_
70	1	1	CD	_	_	_
71	mM	mm	NN	KWSUPP	_	_
72	EDTA	edta	NN	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	with	with	IN	_	_	_
75	40	40	CD	_	_	_
76	ul	ul	NN	_	_	_
77	of	of	IN	_	_	_
78	protease	protease	NN	_	_	_
79	inhibitor	inhibitor	NN	_	_	_
80	cocktail	cocktail	NN	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	50	50	CD	_	_	_
83	mg	mg	NN	_	_	_
84	in	in	IN	_	_	_
85	0.25	0.25	CD	_	_	_
86	ml	ml	NN	_	_	_
87	of	of	IN	_	_	_
88	DMSO	dmso	NN	_	_	_
89	and	and	CC	_	_	_
90	0.75	0.75	CD	_	_	_
91	ml	ml	NN	_	_	_
92	of	of	IN	_	_	_
93	TDW	tdw	NN	_	_	_
94	-RRB-	-rrb-	-RRB-	_	_	_
95	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	lyzed	lyze	VBN	_	_	_
4	with	with	IN	_	_	_
5	1	1	CD	_	_	_
6	ul	ul	NN	_	_	_
7	of	of	IN	_	_	_
8	lysozyme	lysozyme	NN	_	_	_
9	for	for	IN	_	_	_
10	30	30	CD	_	_	_
11	min	min	NN	_	_	_
12	at	at	IN	_	_	_
13	37oC	37oc	NN	_	_	_
14	on	on	IN	_	_	_
15	a	a	DT	_	_	_
16	rocker	rocker	NN	_	_	_
17	.	.	.	_	_	_

1	0.55	0.55	CD	_	_	_
2	ml	ml	NN	_	_	_
3	of	of	IN	_	_	_
4	2X	2x	NN	_	_	_
5	IP	IP	NNP	_	_	_
6	buffer	buffer	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	100	100	CD	_	_	_
9	mM	mm	NN	KWSUPP	_	_
10	Tris-HCl	tris-hcl	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	pH	ph	NN	_	_	_
13	7.5	7.5	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	200	200	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	NaCl	nacl	NN	_	_	_
19	,	,	,	_	_	_
20	2	2	CD	_	_	_
21	%	%	NN	_	_	_
22	Triton	Triton	NNP	_	_	_
23	X-100	x-100	NN	_	_	_
24	and	and	CC	_	_	_
25	1	1	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	EDTA	edta	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	were	be	VBD	_	_	_
30	added	add	VBN	_	_	_
31	to	to	TO	_	_	_
32	the	the	DT	_	_	_
33	sample	sample	NN	_	_	_
34	,	,	,	_	_	_
35	and	and	CC	_	_	_
36	then	then	RB	_	_	_
37	was	be	VBD	_	_	_
38	sonicated	sonicate	VBN	_	_	_
39	to	to	TO	_	_	_
40	fragmentize	fragmentize	VB	_	_	_
41	genomic	genomic	JJ	_	_	_
42	DNA	dna	NN	_	_	_
43	.	.	.	_	_	_

1	0.3	0.3	CD	_	_	_
2	ml	ml	NN	_	_	_
3	of	of	IN	_	_	_
4	Wash	Wash	NNP	_	_	_
5	buffer	buffer	NN	_	_	_
6	I	i	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	50	50	CD	_	_	_
9	mM	mm	NN	KWSUPP	_	_
10	Tris-HCl	tris-hcl	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	pH	ph	NN	_	_	_
13	7.5	7.5	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	140	140	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	NaCl	nacl	NN	_	_	_
19	,	,	,	_	_	_
20	1	1	CD	_	_	_
21	%	%	NN	_	_	_
22	Triton	Triton	NNP	_	_	_
23	X-100	x-100	NN	_	_	_
24	and	and	CC	_	_	_
25	1mM	1mm	NN	_	_	_
26	EDTA	edta	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	was	be	VBD	_	_	_
29	added	add	VBN	_	_	_
30	to	to	TO	_	_	_
31	make	make	VB	_	_	_
32	the	the	DT	_	_	_
33	volume	volume	NN	_	_	_
34	up	up	IN	_	_	_
35	to	to	TO	_	_	_
36	1.4	1.4	CD	_	_	_
37	ml	ml	NN	_	_	_
38	.	.	.	_	_	_

1	Only	only	RB	_	_	_
2	0.7	0.7	CD	_	_	_
3	ml	ml	NN	_	_	_
4	was	be	VBD	_	_	_
5	taken	take	VBN	_	_	_
6	and	and	CC	_	_	_
7	transfered	transfer	VBN	_	_	_
8	to	to	TO	_	_	_
9	a	a	DT	_	_	_
10	new	new	JJ	_	_	_
11	tube	tube	NN	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	15	15	CD	_	_	_
15	ul	ul	NN	_	_	_
16	of	of	IN	_	_	_
17	Anti-c-myc	anti-c-myc	JJ	_	_	_
18	mouse	mouse	NN	_	_	_
19	antibody	antibody	NN	_	_	_
20	was	be	VBD	_	_	_
21	added	add	VBN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	the	the	DT	_	_	_
25	sample	sample	NN	_	_	_
26	was	be	VBD	_	_	_
27	incubated	incubate	VBN	_	_	_
28	overnight	overnight	RB	_	_	_
29	at	at	IN	_	_	_
30	4	4	CD	_	_	_
31	oC	oc	NN	_	_	_
32	to	to	TO	_	_	_
33	make	make	VB	_	_	_
34	Antibody-TF	antibody-tf	NN	_	_	_
35	complex	complex	NN	_	_	_
36	.	.	.	_	_	_

1	50	50	CD	_	_	_
2	ul	ul	NN	_	_	_
3	of	of	IN	_	_	_
4	Dynabeads	Dynabeads	NNP	_	_	_
5	Pan	Pan	NNP	_	_	_
6	mouse	mouse	NN	_	_	_
7	IgG	igg	NN	_	_	_
8	were	be	VBD	_	_	_
9	washed	wash	VBN	_	_	_
10	3	3	CD	_	_	_
11	times	time	NNS	_	_	_
12	with	with	IN	_	_	_
13	bead	bead	NN	_	_	_
14	washing	wash	VBG	_	_	_
15	solution	solution	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	250	250	CD	_	_	_
18	mg	mg	NN	_	_	_
19	BSA	bsa	NN	_	_	_
20	in	in	IN	_	_	_
21	50	50	CD	_	_	_
22	ml	ml	NN	_	_	_
23	of	of	IN	_	_	_
24	PBS	PBS	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	,	,	,	_	_	_
27	and	and	CC	_	_	_
28	were	be	VBD	_	_	_
29	added	add	VBN	_	_	_
30	to	to	TO	_	_	_
31	the	the	DT	_	_	_
32	sample	sample	NN	_	_	_
33	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	lysate	lysate	NN	_	_	_
3	with	with	IN	_	_	_
4	beads	bead	NNS	_	_	_
5	were	be	VBD	_	_	_
6	incubated	incubate	VBN	_	_	_
7	for	for	IN	_	_	_
8	6	6	CD	_	_	_
9	hours	hour	NNS	_	_	_
10	or	or	CC	_	_	_
11	overnight	overnight	JJ	_	_	_
12	at	at	IN	_	_	_
13	4oC	4oc	NN	_	_	_
14	to	to	TO	_	_	_
15	make	make	VB	_	_	_
16	Dynabead-antibody-TF	dynabead-antibody-tf	NN	_	_	_
17	complex	complex	NN	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	beads	bead	NNS	_	_	_
3	were	be	VBD	_	_	_
4	pulled	pull	VBN	_	_	_
5	down	down	RP	_	_	_
6	on	on	IN	_	_	_
7	a	a	DT	_	_	_
8	magnet	magnet	NN	_	_	_
9	stand	stand	NN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	washed	wash	VBN	_	_	_
13	2	2	CD	_	_	_
14	times	time	NNS	_	_	_
15	with	with	IN	_	_	_
16	wash	wash	NN	_	_	_
17	buffer	buffer	NN	_	_	_
18	I	i	NN	_	_	_
19	and	and	CC	_	_	_
20	with	with	IN	_	_	_
21	wash	wash	NN	_	_	_
22	buffer	buffer	NN	_	_	_
23	II	ii	CD	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	50	50	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	Tris-HCl	tris-hcl	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	pH	ph	NN	_	_	_
30	7.5	7.5	CD	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	,	,	,	_	_	_
33	500	500	CD	_	_	_
34	mM	mm	NN	KWSUPP	_	_
35	NaCl	nacl	NN	_	_	_
36	,	,	,	_	_	_
37	1	1	CD	_	_	_
38	%	%	NN	_	_	_
39	Triton	Triton	NNP	_	_	_
40	X-100	x-100	NN	_	_	_
41	and	and	CC	_	_	_
42	1mM	1mm	NN	_	_	_
43	EDTA	edta	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	,	,	,	_	_	_
46	wash	wash	NN	_	_	_
47	buffer	buffer	NN	_	_	_
48	III	iii	CD	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	10	10	CD	_	_	_
51	mM	mm	NN	KWSUPP	_	_
52	Tris-HCl	tris-hcl	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	pH	ph	NN	_	_	_
55	8.0	8.0	CD	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	,	,	,	_	_	_
58	250	250	CD	_	_	_
59	mM	mm	NN	KWSUPP	_	_
60	LiCl	licl	NN	_	_	_
61	,	,	,	_	_	_
62	1	1	CD	_	_	_
63	%	%	NN	_	_	_
64	Triton	Triton	NNP	_	_	_
65	X-100	x-100	NN	_	_	_
66	and	and	CC	_	_	_
67	1mM	1mm	NN	_	_	_
68	EDTA	edta	NN	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	,	,	,	_	_	_
71	and	and	CC	_	_	_
72	wash	wash	NN	_	_	_
73	buffer	buffer	NN	_	_	_
74	IV	iv	CD	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	10	10	CD	_	_	_
77	mM	mm	NN	KWSUPP	_	_
78	Tris-HCl	tris-hcl	NN	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	pH	ph	NN	_	_	_
81	8.0	8.0	CD	_	_	_
82	-RRB-	-rrb-	-RRB-	_	_	_
83	,	,	,	_	_	_
84	1mM	1mm	NN	_	_	_
85	EDTA	edta	NN	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	bead-bound	bead-bound	JJ	_	_	_
3	TF-DNA	tf-dna	NN	_	_	_
4	complex	complex	NN	_	_	_
5	was	be	VBD	_	_	_
6	then	then	RB	_	_	_
7	end-repaired	end-repaired	JJ	_	_	_
8	,	,	,	_	_	_
9	dA-tailed	da-tailed	JJ	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	ligated	ligate	VBN	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	first	first	JJ	_	_	_
16	adapter	adapter	NN	_	_	_
17	.	.	.	_	_	_

1	Adapter-ligated	adapter-ligated	JJ	_	_	_
2	sample	sample	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	treated	treat	VBN	_	_	_
6	with	with	IN	_	_	_
7	nick-repair	nick-repair	JJ	_	_	_
8	reagent	reagent	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	was	be	VBD	_	_	_
12	treated	treat	VBN	_	_	_
13	with	with	IN	_	_	_
14	lambda	lambda	NN	_	_	_
15	exonuclease	exonuclease	NN	_	_	_
16	and	and	CC	_	_	_
17	RecJ	recj	NN	_	_	_
18	exonuclease	exonuclease	NN	_	_	_
19	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	eluted	elute	VBN	_	_	_
5	away	away	RB	_	_	_
6	from	from	IN	_	_	_
7	Dynabeads	Dynabeads	NNPS	_	_	_
8	by	by	IN	_	_	_
9	incubating	incubate	VBG	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	ul	ul	NN	_	_	_
13	of	of	IN	_	_	_
14	elution	elution	NN	_	_	_
15	buffer	buffer	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	50	50	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	Tris-HCl	tris-hcl	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	pH	ph	NN	_	_	_
22	8.0	8.0	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	,	,	,	_	_	_
25	1	1	CD	_	_	_
26	%	%	NN	_	_	_
27	SDS	sds	NN	_	_	_
28	and	and	CC	_	_	_
29	1	1	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	EDTA	edta	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	at	at	IN	_	_	_
34	65oC	65oc	NN	_	_	_
35	overnight	overnight	JJ	_	_	_
36	.	.	.	_	_	_

1	Protein	protein	NN	_	_	_
2	was	be	VBD	_	_	_
3	removed	remove	VBN	_	_	_
4	by	by	IN	_	_	_
5	treating	treat	VBG	_	_	_
6	4	4	CD	_	_	_
7	ul	ul	NN	_	_	_
8	of	of	IN	_	_	_
9	protease	protease	NN	_	_	_
10	K	k	NN	_	_	_
11	and	and	CC	_	_	_
12	being	be	VBG	_	_	_
13	incubated	incubate	VBN	_	_	_
14	at	at	IN	_	_	_
15	55	55	CD	_	_	_
16	oC	oc	NN	_	_	_
17	for	for	IN	_	_	_
18	2	2	CD	_	_	_
19	hours	hour	NNS	_	_	_
20	,	,	,	_	_	_
21	and	and	CC	_	_	_
22	by	by	IN	_	_	_
23	Phenol-Chloroform-IAA	phenol-chloroform-iaa	NN	_	_	_
24	extraction	extraction	NN	_	_	_
25	.	.	.	_	_	_

1	Purified	purify	VBN	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	used	use	VBN	_	_	_
5	to	to	TO	_	_	_
6	bulid	bulid	VB	_	_	_
7	the	the	DT	_	_	_
8	second	second	JJ	_	_	_
9	strand	strand	NN	_	_	_
10	synthesis	synthesis	NN	_	_	_
11	,	,	,	_	_	_
12	followed	follow	VBN	_	_	_
13	by	by	IN	_	_	_
14	another	another	DT	_	_	_
15	dA-tailing	da-tailing	NN	_	_	_
16	,	,	,	_	_	_
17	second	second	JJ	_	_	_
18	strand	strand	NN	_	_	_
19	ligation	ligation	NN	_	_	_
20	,	,	,	_	_	_
21	and	and	CC	_	_	_
22	3	3	CD	_	_	_
23	'	'	''	_	_	_
24	overhang	overhang	NN	_	_	_
25	removal	removal	NN	_	_	_
26	stpes	stpe	NNS	_	_	_
27	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	the	the	DT	_	_	_
3	sequencing	sequencing	NN	_	_	_
4	library	library	NN	_	_	_
5	was	be	VBD	_	_	_
6	amplified	amplify	VBN	_	_	_
7	with	with	IN	_	_	_
8	PCR	pcr	NN	_	_	_
9	enrichment	enrichment	NN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	cells	cell	NNS	_	_	_
5	were	be	VBD	_	_	_
6	crosslinked	crosslink	VBN	_	_	_
7	in	in	IN	_	_	_
8	1	1	CD	_	_	_
9	%	%	NN	_	_	_
10	formaldehyde	formaldehyde	NN	_	_	_
11	for	for	IN	_	_	_
12	25	25	CD	_	_	_
13	minutes	minute	NNS	_	_	_
14	at	at	IN	_	_	_
15	RT	rt	NN	_	_	_
16	on	on	IN	_	_	_
17	a	a	DT	_	_	_
18	rocker	rocker	NN	_	_	_
19	,	,	,	_	_	_
20	then	then	RB	_	_	_
21	washed	wash	VBN	_	_	_
22	3	3	CD	_	_	_
23	times	time	NNS	_	_	_
24	with	with	IN	_	_	_
25	50	50	CD	_	_	_
26	ml	ml	NN	_	_	_
27	of	of	IN	_	_	_
28	ice-cold	ice-cold	JJ	_	_	_
29	TBS	tbs	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Tris	tris	NN	_	_	_
32	buffered	buffer	VBN	_	_	_
33	saline	saline	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	each	each	DT	_	_	_
36	time	time	NN	_	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	For	for	IN	_	_	_
6	each	each	DT	_	_	_
7	peak	peak	NN	_	_	_
8	detected	detect	VBN	_	_	_
9	with	with	IN	_	_	_
10	MACE	MACE	NNP	_	_	_
11	,	,	,	_	_	_
12	binding	bind	VBG	_	_	_
13	intensity	intensity	NN	_	_	_
14	was	be	VBD	_	_	_
15	calculated	calculate	VBN	_	_	_
16	by	by	IN	_	_	_
17	averaging	average	VBG	_	_	_
18	read	read	VBN	_	_	_
19	counts	count	NNS	_	_	_
20	from	from	IN	_	_	_
21	two	two	CD	_	_	_
22	biological	biological	JJ	_	_	_
23	replicates	replicate	VBZ	_	_	_
24	and	and	CC	_	_	_
25	dividing	divide	VBG	_	_	_
26	by	by	IN	_	_	_
27	background	background	NN	_	_	_
28	intensity	intensity	NN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	ASM584v2	asm584v2	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	genotype	genotype	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	library	library	NN	_	_	_
11	strategy	strategy	NN	_	_	_
12	:	:	:	_	_	_
13	ChIP-seq	ChIP-seq	NNP	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	ChIP-exo	ChIP-exo	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	MACE	MACE	NNP	_	_	_
19	software	software	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	https	http	NNS	_	_	_
22	:	:	:	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	oxyR-8myc-tagged	oxyr-8myc-tagged	JJ	_	_	_
25	_	_	NN	_	_	_
26	PQ	pq	NN	_	_	_
27	treated	treat	VBN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	OxyR	oxyr	NN	TF	_	_
30	PQ	pq	NN	_	_	_
31	1	1	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	OxyR	oxyr	NN	TF	_	_
34	PQ	pq	NN	_	_	_
35	2	2	CD	_	_	_
36	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
37	Read	Read	NNP	_	_	_
38	count	count	NN	_	_	_
39	was	be	VBD	_	_	_
40	calculated	calculate	VBN	_	_	_
41	for	for	IN	_	_	_
42	each	each	DT	_	_	_
43	genomic	genomic	JJ	_	_	_
44	position	position	NN	_	_	_
45	from	from	IN	_	_	_
46	sequence	sequence	NN	_	_	_
47	alignment	alignment	NN	_	_	_
48	,	,	,	_	_	_
49	and	and	CC	_	_	_
50	95	95	CD	_	_	_
51	%	%	NN	_	_	_
52	strongest	strongest	JJS	_	_	_
53	intensity	intensity	NN	_	_	_
54	was	be	VBD	_	_	_
55	used	use	VBN	_	_	_
56	as	as	IN	_	_	_
57	background	background	NN	_	_	_
58	intensity	intensity	NN	_	_	_
59	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	soxR-8myc-tagged	soxr-8myc-tagged	JJ	_	_	_
3	_	_	NN	_	_	_
4	PQ	pq	NN	_	_	_
5	treated	treat	VBN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	SoxR	soxr	NN	TF	_	_
8	PQ	pq	NN	_	_	_
9	1	1	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	SoxR	soxr	NN	TF	_	_
12	PQ	pq	NN	_	_	_
13	2	2	CD	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	soxS-8myc-tagged	soxs-8myc-tagged	JJ	_	_	_
16	_	_	NN	_	_	_
17	PQ	pq	NN	_	_	_
18	treated	treat	VBN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	SoxS	soxs	NN	TF	_	_
21	PQ	pq	NN	_	_	_
22	1	1	CD	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	SoxS	soxs	NN	TF	_	_
25	PQ	pq	NN	_	_	_
26	2	2	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	strain	strain	NN	_	_	_
29	:	:	:	_	_	_
30	K-12	k-12	NN	_	_	_
31	MG1655	mg1655	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	Supplementary	supplementary	JJ	_	_	_
34	_	_	NN	_	_	_
35	files	file	NNS	_	_	_
36	_	_	IN	_	_	_
37	format	format	NN	_	_	_
38	_	_	NN	_	_	_
39	and	and	CC	_	_	_
40	_	_	NN	_	_	_
41	content	content	NN	_	_	_
42	:	:	:	_	_	_
43	Tab-delimited	tab-delimited	JJ	_	_	_
44	text	text	NN	_	_	_
45	files	file	NNS	_	_	_
46	in	in	IN	_	_	_
47	gff	gff	NN	_	_	_
48	format	format	NN	_	_	_
49	which	which	WDT	_	_	_
50	has	have	VBZ	_	_	_
51	8	8	CD	_	_	_
52	columns	column	NNS	_	_	_
53	:	:	:	_	_	_
54	sequence	sequence	NN	_	_	_
55	id	id	NN	_	_	_
56	,	,	,	_	_	_
57	source	source	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	empty	empty	JJ	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	,	,	,	_	_	_
62	feature	feature	NN	_	_	_
63	-LRB-	-lrb-	-LRB-	_	_	_
64	+	+	CC	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	treated	treat	VBN	_	_	_
67	with	with	IN	_	_	_
68	:	:	:	_	_	_
69	250	250	CD	_	_	_
70	uM	um	NN	_	_	_
71	of	of	IN	_	_	_
72	paraquat	paraquat	NN	SUPP	_	_
73	at	at	IN	_	_	_
74	mid-log	mid-log	JJ	_	_	_
75	phase	phase	NN	_	_	_
76	for	for	IN	_	_	_
77	20	20	CD	_	_	_
78	min	min	NN	_	_	_
79	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
80	E.	E.	NNP	_	_	_
81	coli	coli	NN	_	_	_
82	K-12	k-12	NN	_	_	_
83	MG1655	mg1655	NN	_	_	_
84	WT	wt	NN	_	_	_
85	,	,	,	_	_	_
86	ΔoxyR	δoxyr	NN	_	_	_
87	,	,	,	_	_	_
88	ΔsoxR	δsoxr	NN	_	_	_
89	,	,	,	_	_	_
90	and	and	CC	_	_	_
91	ΔsoxS	δsoxs	NN	_	_	_
92	were	be	VBD	_	_	_
93	grown	grow	VBN	_	_	_
94	to	to	TO	_	_	_
95	mid-log	mid-log	JJ	_	_	_
96	phase	phase	NN	_	_	_
97	aerobically	aerobically	RB	_	_	_
98	at	at	IN	_	_	_
99	37	37	CD	_	_	_
100	°C	°c	NN	_	_	_
101	in	in	IN	_	_	_
102	M9	m9	NN	MED	_	_
103	minimal	minimal	JJ	MED	_	_
104	media	media	NNS	MED	_	_
105	supplemented	supplement	VBN	_	_	_
106	with	with	IN	_	_	_
107	0.2	0.2	CD	_	_	_
108	%	%	NN	_	_	_
109	glucose	glucose	NN	SUPP	_	_
110	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	treated	treat	VBN	_	_	_
5	with	with	IN	_	_	_
6	250	250	CD	_	_	_
7	uM	um	NN	_	_	_
8	of	of	IN	_	_	_
9	paraquat	paraquat	NN	SUPP	_	_
10	at	at	IN	_	_	_
11	mid-log	mid-log	JJ	_	_	_
12	pahse	pahse	NN	_	_	_
13	for	for	IN	_	_	_
14	20	20	CD	_	_	_
15	min	min	NN	_	_	_
16	with	with	IN	_	_	_
17	agitation	agitation	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Fragments	fragment	NNS	_	_	_
6	Per	per	IN	_	_	_
7	Kilobase	kilobase	NN	_	_	_
8	of	of	IN	_	_	_
9	exon	exon	NN	_	_	_
10	per	per	IN	_	_	_
11	Megabase	megabase	NN	_	_	_
12	of	of	IN	_	_	_
13	library	library	NN	_	_	_
14	size	size	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	FPKM	fpkm	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	were	be	VBD	_	_	_
19	calculated	calculate	VBN	_	_	_
20	using	use	VBG	_	_	_
21	cufflinks	cufflink	NNS	_	_	_
22	v.	v.	CC	_	_	_
23	1.3.0	1.3.0	CD	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
25	Genome	Genome	NNP	_	_	_
26	_	_	NNP	_	_	_
27	build	build	VB	_	_	_
28	:	:	:	_	_	_
29	NC	NC	NNP	_	_	_
30	_	_	NNP	_	_	_
31	000913	000913	CD	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	genotype	genotype	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	RNA	rna	NN	_	_	_
36	libraries	library	NNS	_	_	_
37	were	be	VBD	_	_	_
38	prepared	prepare	VBN	_	_	_
39	for	for	IN	_	_	_
40	sequencing	sequencing	NN	_	_	_
41	using	use	VBG	_	_	_
42	standard	standard	JJ	_	_	_
43	Illumina	Illumina	NNP	_	_	_
44	protocols	protocol	NNS	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
46	RNA-Seq	rna-seq	JJ	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	Sequenced	sequence	VBN	_	_	_
49	reads	read	VBZ	_	_	_
50	were	be	VBD	_	_	_
51	mapped	map	VBN	_	_	_
52	onto	onto	IN	_	_	_
53	NC	nc	NN	_	_	_
54	_	_	CD	_	_	_
55	000913	000913	CD	_	_	_
56	reference	reference	NN	_	_	_
57	genome	genome	NN	_	_	_
58	sequence	sequence	NN	_	_	_
59	using	use	VBG	_	_	_
60	bowtie	bowtie	NN	_	_	_
61	v1	v1	NN	_	_	_
62	.0.0	.0.0	CD	_	_	_
63	with	with	IN	_	_	_
64	parameters	parameter	NNS	_	_	_
65	-	-	:	_	_	_
66	X	x	NN	_	_	_
67	1000	1000	CD	_	_	_
68	-	-	:	_	_	_
69	n	n	NN	_	_	_
70	2	2	CD	_	_	_
71	-3	-3	CD	_	_	_
72	3	3	LS	_	_	_
73	-	-	:	_	_	_
74	S	s	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	strain	strain	NN	_	_	_
77	:	:	:	_	_	_
78	K-12	k-12	NN	_	_	_
79	MG1655	mg1655	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	Supplementary	supplementary	JJ	_	_	_
82	_	_	NN	_	_	_
83	files	file	NNS	_	_	_
84	_	_	IN	_	_	_
85	format	format	NN	_	_	_
86	_	_	NN	_	_	_
87	and	and	CC	_	_	_
88	_	_	NN	_	_	_
89	content	content	NN	_	_	_
90	:	:	:	_	_	_
91	comma-delimited	comma-delimited	JJ	_	_	_
92	text	text	NN	_	_	_
93	files	file	NNS	_	_	_
94	include	include	VBP	_	_	_
95	FPKM	fpkm	NN	_	_	_
96	values	value	NNS	_	_	_
97	for	for	IN	_	_	_
98	each	each	DT	_	_	_
99	Sample	Sample	NNP	_	_	_
100	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cell	cell	NN	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	treated	treat	VBN	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	RNAprotect	rnaprotect	NN	_	_	_
10	reagent	reagent	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	qiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	RNeasy	RNeasy	NNP	_	_	_
9	Plus	Plus	NNP	_	_	_
10	Mini	Mini	NNP	_	_	_
11	kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Qiagen	Qiagen	NNP	_	_	_
14	Inc.	Inc.	NNP	_	_	_
15	,	,	,	_	_	_
16	Valencia	Valencia	NNP	_	_	_
17	,	,	,	_	_	_
18	CA	CA	NNP	_	_	_
19	,	,	,	_	_	_
20	USA	USA	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	and	and	CC	_	_	_
23	genomic	genomic	JJ	_	_	_
24	DNA	dna	NN	_	_	_
25	was	be	VBD	_	_	_
26	removed	remove	VBN	_	_	_
27	by	by	IN	_	_	_
28	gDNA	gdna	NN	_	_	_
29	Eliminator	eliminator	NN	_	_	_
30	spin	spin	NN	_	_	_
31	column	column	NN	_	_	_
32	in	in	IN	_	_	_
33	the	the	DT	_	_	_
34	RNeasy	RNeasy	NNP	_	_	_
35	Plus	Plus	NNP	_	_	_
36	Mini	Mini	NNP	_	_	_
37	Kit	kit	NN	_	_	_
38	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	quality	quality	NN	_	_	_
3	and	and	CC	_	_	_
4	concentration	concentration	NN	_	_	_
5	was	be	VBD	_	_	_
6	determined	determine	VBN	_	_	_
7	by	by	IN	_	_	_
8	analysis	analysis	NN	_	_	_
9	with	with	IN	_	_	_
10	a	a	DT	_	_	_
11	NanoDrop	NanoDrop	NNP	_	_	_
12	1000	1000	CD	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Thermo	Thermo	NNP	_	_	_
15	Scientific	Scientific	NNP	_	_	_
16	Inc.	Inc.	NNP	_	_	_
17	,	,	,	_	_	_
18	Wilmington	Wilmington	NNP	_	_	_
19	,	,	,	_	_	_
20	DE	de	NN	_	_	_
21	,	,	,	_	_	_
22	USA	USA	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	treated	treat	VBN	_	_	_
3	with	with	IN	_	_	_
4	:	:	:	_	_	_
5	250	250	CD	_	_	_
6	uM	um	NN	_	_	_
7	of	of	IN	_	_	_
8	paraquat	paraquat	NN	SUPP	_	_
9	at	at	IN	_	_	_
10	mid-log	mid-log	JJ	_	_	_
11	pahse	pahse	NN	_	_	_
12	for	for	IN	_	_	_
13	20	20	CD	_	_	_
14	min	min	NN	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	WT	WT	NNP	_	_	_
17	PQ	PQ	NNP	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	WT	WT	NNP	_	_	_
20	PQ	PQ	NNP	_	_	_
21	1	1	CD	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	WT	WT	NNP	_	_	_
24	PQ	PQ	NNP	_	_	_
25	2	2	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	ΔoxyR	δoxyr	NN	_	_	_
28	PQ	pq	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	ΔoxyR	δoxyr	NN	_	_	_
31	PQ	pq	NN	_	_	_
32	1	1	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	ΔoxyR	δoxyr	NN	_	_	_
35	PQ	pq	NN	_	_	_
36	2	2	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	ΔsoxR	δsoxr	NN	_	_	_
39	PQ	pq	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	ΔsoxR	δsoxr	NN	_	_	_
42	PQ	pq	NN	_	_	_
43	1	1	CD	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	ΔsoxR	δsoxr	NN	_	_	_
46	PQ	pq	NN	_	_	_
47	2	2	CD	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	ΔsoxS	δsoxs	NN	_	_	_
50	PQ	pq	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	ΔsoxS	δsoxs	VBZ	_	_	_
53	PQ	pq	NN	_	_	_
54	1	1	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	ΔsoxS	δsoxs	NN	_	_	_
57	PQ	pq	NN	_	_	_
58	2	2	CD	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	16,000	16,000	CD	_	_	_
61	g	g	NN	_	_	_
62	for	for	IN	_	_	_
63	40	40	CD	_	_	_
64	s	s	NNS	_	_	_
65	at	at	IN	_	_	_
66	room	room	NN	_	_	_
67	temperature	temperature	NN	_	_	_
68	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	discarded	discard	VBN	_	_	_
5	,	,	,	_	_	_
6	and	and	CC	_	_	_
7	cell	cell	NN	_	_	_
8	pellets	pellet	NNS	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	1.8	1.8	CD	_	_	_
11	ml	ml	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	ca.	ca.	FW	_	_	_
14	3E	3e	FW	_	_	_
15	+9	+9	NN	_	_	_
16	cells	cell	NNS	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	were	be	VBD	_	_	_
19	pipetted	pipet	VBN	_	_	_
20	into	into	IN	_	_	_
21	2.0	2.0	CD	_	_	_
22	ml	ml	NN	_	_	_
23	tubes	tube	NNS	_	_	_
24	and	and	CC	_	_	_
25	immediately	immediately	RB	_	_	_
26	centrifuged	centrifuge	VBN	_	_	_
27	at	at	IN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	68908	68908	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	68909	68909	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	68910	68910	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	68911	68911	CD	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	68912	68912	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	68913	68913	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	68915	68915	CD	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	68916	68916	CD	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	68917	68917	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	68919	68919	CD	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	68920	68920	CD	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	68921	68921	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	68922	68922	CD	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	68923	68923	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	68924	68924	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	68925	68925	CD	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	68926	68926	CD	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	68927	68927	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	68928	68928	CD	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	68929	68929	CD	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	68930	68930	CD	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	68931	68931	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	68932	68932	CD	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	68933	68933	CD	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	Cells	cell	NNS	_	_	_
78	were	be	VBD	_	_	_
79	harvested	harvest	VBN	_	_	_
80	on	on	IN	_	_	_
81	days	day	NNS	_	_	_
82	1	1	CD	_	_	_
83	and	and	CC	_	_	_
84	3	3	CD	_	_	_
85	of	of	IN	_	_	_
86	glucose	glucose	NN	SUPP	_	_
87	starvation	starvation	NN	_	_	_
88	,	,	,	_	_	_
89	with	with	IN	_	_	_
90	samples	sample	NNS	_	_	_
91	taken	take	VBN	_	_	_
92	from	from	IN	_	_	_
93	the	the	DT	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	chilled	chill	VBN	_	_	_
96	in	in	IN	_	_	_
97	a	a	DT	_	_	_
98	dry	dry	JJ	_	_	_
99	ice	ice	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	D1-ae10	d1-ae10	NN	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	D1-ae11	d1-ae11	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	D1-ae12	d1-ae12	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	D1	d1	NN	_	_	_
108	+	+	CC	_	_	_
109	ae7	ae7	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	D1	d1	NN	_	_	_
112	+	+	CC	_	_	_
113	ae8	ae8	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	D1	d1	NN	_	_	_
116	+	+	CC	_	_	_
117	ae9	ae9	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	D1	d1	NN	_	_	_
120	+	+	CC	_	_	_
121	AN	a	DT	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	D1	d1	NN	_	_	_
124	+	+	CC	_	_	_
125	AN2	an2	NN	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	D1	d1	NN	_	_	_
128	+	+	CC	_	_	_
129	AN3	an3	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	D1-AN4	d1-an4	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	D1-AN5	d1-an5	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	D1-AN6	d1-an6	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	D3	d3	NN	_	_	_
138	+	+	CC	_	_	_
139	ae19	ae19	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	D3	d3	NN	_	_	_
142	+	+	CC	_	_	_
143	ae20	ae20	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	D3	d3	NN	_	_	_
146	+	+	CC	_	_	_
147	ae21	ae21	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	D3-ae22	d3-ae22	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	D3-ae23	d3-ae23	NN	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	D3-ae24	d3-ae24	NN	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	D3	d3	NN	_	_	_
156	+	+	CC	_	_	_
157	AN13	an13	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	D3	d3	NN	_	_	_
160	+	+	CC	_	_	_
161	AN14	an14	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	D3	d3	NN	_	_	_
164	+	+	CC	_	_	_
165	AN15	an15	NN	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	D3-AN16	d3-an16	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	D3-AN17	d3-an17	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	D3-AN18	d3-an18	NN	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	day	day	NN	_	_	_
174	:	:	:	_	_	_
175	.	.	.	_	_	_

1	strain	strain	NN	_	_	_
2	:	:	:	_	_	_
3	.	.	.	_	_	_

1	oxygen	oxygen	NN	_	_	_
2	:	:	:	_	_	_
3	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Feature	feature	NN	_	_	_
6	pixel	pixel	NN	_	_	_
7	median	median	NN	_	_	_
8	minus	minus	CC	_	_	_
9	background	background	NN	_	_	_
10	pixel	pixel	NN	_	_	_
11	mean	mean	NN	_	_	_
12	;	;	:	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
14	further	further	RB	_	_	_
15	processing	process	VBG	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	isolated	isolate	VBN	_	_	_
18	by	by	IN	_	_	_
19	chloroform	chloroform	NN	_	_	_
20	extraction	extraction	NN	_	_	_
21	and	and	CC	_	_	_
22	precipitation	precipitation	NN	_	_	_
23	by	by	IN	_	_	_
24	isopropanol	isopropanol	NN	_	_	_
25	.	.	.	_	_	_

1	Precipitated	precipitate	VBN	_	_	_
2	RNA	rna	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	normalization	normalization	NN	_	_	_
5	subtracting	subtract	VBG	_	_	_
6	array-median	array-median	JJ	_	_	_
7	log2	log2	NN	_	_	_
8	ratio	ratio	NN	_	_	_
9	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	pool	pool	NN	_	_	_
3	of	of	IN	_	_	_
4	aliquots	aliquot	NNS	_	_	_
5	from	from	IN	_	_	_
6	all	all	DT	_	_	_
7	samples	sample	NNS	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
9	ratio	ratio	NN	_	_	_
10	set	set	VBN	_	_	_
11	to	to	TO	_	_	_
12	missing	miss	VBG	_	_	_
13	where	where	WRB	_	_	_
14	SNR	snr	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	feature	feature	NN	_	_	_
17	mean	mean	NN	_	_	_
18	-	-	:	_	_	_
19	backround	backround	NN	_	_	_
20	mean	mean	VB	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	Reference	Reference	NNP	_	_	_
23	Pool	Pool	NNP	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	re-suspended	re-suspended	JJ	_	_	_
26	in	in	IN	_	_	_
27	200	200	CD	_	_	_
28	ul	ul	NN	_	_	_
29	Trizol	trizol	NN	_	_	_
30	and	and	CC	_	_	_
31	combined	combine	VBN	_	_	_
32	for	for	IN	_	_	_
33	a	a	DT	_	_	_
34	total	total	JJ	_	_	_
35	volume	volume	NN	_	_	_
36	of	of	IN	_	_	_
37	1	1	CD	_	_	_
38	ml	ml	NN	_	_	_
39	,	,	,	_	_	_
40	then	then	RB	_	_	_
41	promptly	promptly	RB	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
43	same	same	JJ	_	_	_
44	cultures	culture	NNS	_	_	_
45	used	use	VBN	_	_	_
46	for	for	IN	_	_	_
47	the	the	DT	_	_	_
48	viability	viability	NN	_	_	_
49	assay	assay	NN	_	_	_
50	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	experimental	experimental	JJ	_	_	_
4	condition	condition	NN	_	_	_
5	,	,	,	_	_	_
6	15	15	CD	_	_	_
7	aliquots	aliquot	NNS	_	_	_
8	of	of	IN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	triplicate	triplicate	NN	_	_	_
11	samples	sample	NNS	_	_	_
12	were	be	VBD	_	_	_
13	prepared	prepare	VBN	_	_	_
14	by	by	IN	_	_	_
15	combining	combine	VBG	_	_	_
16	cells	cell	NNS	_	_	_
17	from	from	IN	_	_	_
18	5	5	CD	_	_	_
19	tubes	tube	NNS	_	_	_
20	each	each	DT	_	_	_
21	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	was	be	VBD	_	_	_
4	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
5	was	be	VBD	_	_	_
6	washed	wash	VBN	_	_	_
7	with	with	IN	_	_	_
8	70	70	CD	_	_	_
9	percent	percent	NN	_	_	_
10	ethanol	ethanol	NN	_	_	_
11	,	,	,	_	_	_
12	resuspended	resuspend	VBN	_	_	_
13	in	in	IN	_	_	_
14	30	30	CD	_	_	_
15	ul	ul	NN	_	_	_
16	water	water	NN	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	held	hold	VBN	_	_	_
20	at	at	IN	_	_	_
21	4	4	CD	_	_	_
22	deg	deg	NN	_	_	_
23	.	.	.	_	_	_

1	C	c	NN	_	_	_
2	for	for	IN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
4	were	be	VBD	_	_	_
5	immediately	immediately	RB	_	_	_
6	frozen	freeze	VBN	_	_	_
7	in	in	IN	_	_	_
8	liquid	liquid	JJ	_	_	_
9	nitrogen	nitrogen	NN	_	_	_
10	and	and	CC	_	_	_
11	stored	store	VBD	_	_	_
12	at	at	IN	_	_	_
13	-80	-80	CD	_	_	_
14	deg	deg	NN	_	_	_
15	.	.	.	_	_	_

1	C.	c.	NN	_	_	_
2	For	for	IN	_	_	_
3	RNA	rna	NN	_	_	_
4	isolation	isolation	NN	_	_	_
5	,	,	,	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	chip	chip	NN	_	_	_
8	antibody	antibody	NN	_	_	_
9	:	:	:	_	_	_
10	anti-myc	anti-myc	JJ	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Santa	Santa	NNP	_	_	_
13	Cruz	Cruz	NNP	_	_	_
14	Biotech	Biotech	NNP	_	_	_
15	,	,	,	_	_	_
16	sc-28207	sc-28207	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	chip	chip	NN	_	_	_
20	antibody	antibody	NN	_	_	_
21	:	:	:	_	_	_
22	anti-RpoS	anti-rpos	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	neoclone	neoclone	NN	_	_	_
25	,	,	,	_	_	_
26	WP009	wp009	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	ChIP-exo	ChIP-exo	NNP	_	_	_
30	GadE	GadE	NNP	TF	_	_
31	pH5	ph5	NN	_	_	_
32	.5	.5	CD	_	_	_
33	1	1	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	ChIP-exo	ChIP-exo	NNP	_	_	_
36	GadE	GadE	NNP	TF	_	_
37	pH5	ph5	NN	_	_	_
38	.5	.5	CD	_	_	_
39	2	2	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
41	ChIP-exo	chip-exo	JJ	_	_	_
42	GadW	gadw	NN	TF	_	_
43	pH5	ph5	NN	_	_	_
44	.5	.5	CD	_	_	_
45	1	1	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	ChIP-exo	chip-exo	JJ	_	_	_
48	GadW	gadw	NN	TF	_	_
49	pH5	ph5	NN	_	_	_
50	.5	.5	CD	_	_	_
51	2	2	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
53	ChIP-exo	chip-exo	JJ	_	_	_
54	GadX	gadx	NN	TF	_	_
55	pH5	ph5	NN	_	_	_
56	.5	.5	CD	_	_	_
57	1	1	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	ChIP-exo	chip-exo	JJ	_	_	_
60	GadX	gadx	NN	TF	_	_
61	pH5	ph5	NN	_	_	_
62	.5	.5	CD	_	_	_
63	2	2	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	ChIP-exo	chip-exo	NN	_	_	_
66	reads	read	VBZ	_	_	_
67	were	be	VBD	_	_	_
68	aligned	align	VBN	_	_	_
69	to	to	TO	_	_	_
70	the	the	DT	_	_	_
71	ASM584v2	asm584v2	NN	_	_	_
72	genome	genome	NN	_	_	_
73	reference	reference	NN	_	_	_
74	sequence	sequence	NN	_	_	_
75	using	use	VBG	_	_	_
76	using	use	VBG	_	_	_
77	bowtie	bowtie	NN	_	_	_
78	v1	v1	NN	_	_	_
79	.0.0	.0.0	CD	_	_	_
80	with	with	IN	_	_	_
81	parameters	parameter	NNS	_	_	_
82	-	-	:	_	_	_
83	S	s	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
85	ChIP-exo	chip-exo	JJ	_	_	_
86	RpoS	rpos	NN	_	_	_
87	pH5	ph5	NN	_	_	_
88	.5	.5	CD	_	_	_
89	1	1	CD	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	ChIP-exo	chip-exo	JJ	_	_	_
92	RpoS	rpos	NN	_	_	_
93	pH5	ph5	NN	_	_	_
94	.5	.5	CD	_	_	_
95	2	2	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
97	ChIP-Seq	chip-seq	JJ	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	ChIP-seq	chip-seq	NN	_	_	_
100	libraries	library	NNS	_	_	_
101	were	be	VBD	_	_	_
102	prepared	prepare	VBN	_	_	_
103	for	for	IN	_	_	_
104	sequencing	sequencing	NN	_	_	_
105	using	use	VBG	_	_	_
106	standard	standard	JJ	_	_	_
107	Illumina	Illumina	NNP	_	_	_
108	protocols	protocol	NNS	_	_	_
109	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
110	E.	e.	FW	_	_	_
111	coli	coli	FW	_	_	_
112	K-12	k-12	NN	_	_	_
113	MG1655	mg1655	NN	_	_	_
114	WT	WT	NNP	_	_	_
115	,	,	,	_	_	_
116	GadE-8-myc	gade-8-myc	NN	_	_	_
117	,	,	,	_	_	_
118	GadW-8-myc	gadw-8-myc	NN	_	_	_
119	,	,	,	_	_	_
120	and	and	CC	_	_	_
121	GadX-8-myc	gadx-8-myc	NN	_	_	_
122	tagged	tag	VBD	_	_	_
123	strains	strain	NNS	_	_	_
124	were	be	VBD	_	_	_
125	grown	grow	VBN	_	_	_
126	to	to	TO	_	_	_
127	mid-log	mid-log	JJ	_	_	_
128	phase	phase	NN	_	_	_
129	-LRB-	-lrb-	-LRB-	_	_	_
130	OD600	od600	NN	_	_	_
131	=	=	JJ	_	_	_
132	0.3	0.3	CD	_	_	_
133	-RRB-	-rrb-	-RRB-	_	_	_
134	aerobically	aerobically	RB	_	_	_
135	-LRB-	-lrb-	-LRB-	_	_	_
136	250	250	CD	_	_	_
137	rpm	rpm	NN	_	_	_
138	-RRB-	-rrb-	-RRB-	_	_	_
139	at	at	IN	_	_	_
140	37	37	CD	_	_	_
141	°C	°c	NN	_	_	_
142	in	in	IN	_	_	_
143	M9	m9	NN	MED	_	_
144	minimal	minimal	JJ	MED	_	_
145	media	media	NNS	MED	_	_
146	supplemented	supplement	VBN	_	_	_
147	with	with	IN	_	_	_
148	0.2	0.2	CD	_	_	_
149	%	%	NN	_	_	_
150	glucose	glucose	NN	SUPP	_	_
151	at	at	IN	_	_	_
152	pH	ph	NN	_	_	_
153	5.5	5.5	CD	_	_	_
154	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	For	for	IN	_	_	_
4	each	each	DT	_	_	_
5	peak	peak	NN	_	_	_
6	detected	detect	VBN	_	_	_
7	with	with	IN	_	_	_
8	MACE	MACE	NNP	_	_	_
9	,	,	,	_	_	_
10	binding	bind	VBG	_	_	_
11	intensity	intensity	NN	_	_	_
12	was	be	VBD	_	_	_
13	calculated	calculate	VBN	_	_	_
14	by	by	IN	_	_	_
15	averaging	average	VBG	_	_	_
16	read	read	VBN	_	_	_
17	counts	count	NNS	_	_	_
18	from	from	IN	_	_	_
19	two	two	CD	_	_	_
20	biological	biological	JJ	_	_	_
21	replicates	replicate	VBZ	_	_	_
22	and	and	CC	_	_	_
23	dividing	divide	VBG	_	_	_
24	by	by	IN	_	_	_
25	background	background	NN	_	_	_
26	intensity	intensity	NN	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	ASM584v2	asm584v2	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	genotype	genotype	NN	_	_	_
9	:	:	:	_	_	_
10	gadE-8myc	gade-8myc	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	genotype	genotype	NN	_	_	_
13	:	:	:	_	_	_
14	gadW-8myc	gadw-8myc	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	genotype	genotype	NN	_	_	_
17	:	:	:	_	_	_
18	gadX-8myc	gadx-8myc	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	genotype	genotype	NN	_	_	_
21	:	:	:	_	_	_
22	WT	WT	NNP	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	Immunoprecipitated	immunoprecipitate	VBD	_	_	_
25	DNA	dna	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	MACE	mace	NN	_	_	_
28	software	software	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	https	http	NNS	_	_	_
31	:	:	:	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
33	Read	read	VBP	_	_	_
34	count	count	NN	_	_	_
35	was	be	VBD	_	_	_
36	calculated	calculate	VBN	_	_	_
37	for	for	IN	_	_	_
38	each	each	DT	_	_	_
39	genomic	genomic	JJ	_	_	_
40	position	position	NN	_	_	_
41	from	from	IN	_	_	_
42	sequence	sequence	NN	_	_	_
43	alignment	alignment	NN	_	_	_
44	,	,	,	_	_	_
45	and	and	CC	_	_	_
46	95	95	CD	_	_	_
47	%	%	NN	_	_	_
48	strongest	strongest	JJS	_	_	_
49	intensity	intensity	NN	_	_	_
50	was	be	VBD	_	_	_
51	used	use	VBN	_	_	_
52	as	as	IN	_	_	_
53	background	background	NN	_	_	_
54	intensity	intensity	NN	_	_	_
55	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	K-12	k-12	NN	_	_	_
5	MG1655	mg1655	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Supplementary	supplementary	JJ	_	_	_
8	_	_	NN	_	_	_
9	files	file	NNS	_	_	_
10	_	_	IN	_	_	_
11	format	format	NN	_	_	_
12	_	_	NN	_	_	_
13	and	and	CC	_	_	_
14	_	_	NN	_	_	_
15	content	content	NN	_	_	_
16	:	:	:	_	_	_
17	Tab-delimited	tab-delimited	JJ	_	_	_
18	text	text	NN	_	_	_
19	files	file	NNS	_	_	_
20	in	in	IN	_	_	_
21	gff	gff	NN	_	_	_
22	format	format	NN	_	_	_
23	which	which	WDT	_	_	_
24	has	have	VBZ	_	_	_
25	8	8	CD	_	_	_
26	columns	column	NNS	_	_	_
27	:	:	:	_	_	_
28	sequence	sequence	NN	_	_	_
29	id	id	NN	_	_	_
30	,	,	,	_	_	_
31	source	source	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	empty	empty	JJ	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	,	,	,	_	_	_
36	feature	feature	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	+	+	CC	_	_	_
39	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
40	E.	E.	NNP	_	_	_
41	coli	coli	NN	_	_	_
42	K-12	k-12	NN	_	_	_
43	MG1655	mg1655	NN	_	_	_
44	WT	wt	NN	_	_	_
45	,	,	,	_	_	_
46	gadE	gade	NN	GEN	_	_
47	,	,	,	_	_	_
48	gadW	gadw	NN	GEN	_	_
49	and	and	CC	_	_	_
50	gadX	gadx	NN	GEN	_	_
51	mutant	mutant	JJ	_	_	_
52	cells	cell	NNS	_	_	_
53	were	be	VBD	_	_	_
54	grown	grow	VBN	_	_	_
55	to	to	TO	_	_	_
56	mid-log	mid-log	JJ	_	_	_
57	phase	phase	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	OD600	od600	NN	_	_	_
60	=	=	JJ	_	_	_
61	0.3	0.3	CD	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	aerobically	aerobically	RB	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	250	250	CD	_	_	_
66	rpm	rpm	NN	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	at	at	IN	_	_	_
69	37	37	CD	_	_	_
70	°C	°c	NN	_	_	_
71	in	in	IN	_	_	_
72	M9	m9	NN	MED	_	_
73	minimal	minimal	JJ	MED	_	_
74	media	media	NNS	MED	_	_
75	supplemented	supplement	VBN	_	_	_
76	with	with	IN	_	_	_
77	0.2	0.2	CD	_	_	_
78	%	%	NN	_	_	_
79	glucose	glucose	NN	SUPP	_	_
80	at	at	IN	_	_	_
81	pH	ph	NN	_	_	_
82	5.5	5.5	CD	_	_	_
83	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Fragments	fragment	NNS	_	_	_
6	Per	per	IN	_	_	_
7	Kilobase	kilobase	NN	_	_	_
8	of	of	IN	_	_	_
9	exon	exon	NN	_	_	_
10	per	per	IN	_	_	_
11	Megabase	megabase	NN	_	_	_
12	of	of	IN	_	_	_
13	library	library	NN	_	_	_
14	size	size	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	FPKM	fpkm	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	were	be	VBD	_	_	_
19	calculated	calculate	VBN	_	_	_
20	using	use	VBG	_	_	_
21	cufflinks	cufflink	NNS	_	_	_
22	v.	v.	CC	_	_	_
23	1.3.0	1.3.0	CD	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
25	Genome	Genome	NNP	_	_	_
26	_	_	NNP	_	_	_
27	build	build	VB	_	_	_
28	:	:	:	_	_	_
29	NC	NC	NNP	_	_	_
30	_	_	NNP	_	_	_
31	000913	000913	CD	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	genotype	genotype	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	growth	growth	NN	_	_	_
36	phase	phase	NN	_	_	_
37	:	:	:	_	_	_
38	mid-log	mid-log	JJ	_	_	_
39	phase	phase	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	OD600	od600	NN	_	_	_
42	=	=	JJ	_	_	_
43	0.3	0.3	CD	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	RNA	rna	NN	_	_	_
47	libraries	library	NNS	_	_	_
48	were	be	VBD	_	_	_
49	prepared	prepare	VBN	_	_	_
50	for	for	IN	_	_	_
51	sequencing	sequencing	NN	_	_	_
52	using	use	VBG	_	_	_
53	standard	standard	JJ	_	_	_
54	Illumina	Illumina	NNP	_	_	_
55	protocols	protocol	NNS	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
57	RNA-Seq	rna-seq	JJ	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	Sequenced	sequence	VBN	_	_	_
60	reads	read	VBZ	_	_	_
61	were	be	VBD	_	_	_
62	mapped	map	VBN	_	_	_
63	onto	onto	IN	_	_	_
64	NC	nc	NN	_	_	_
65	_	_	CD	_	_	_
66	000913	000913	CD	_	_	_
67	reference	reference	NN	_	_	_
68	genome	genome	NN	_	_	_
69	sequence	sequence	NN	_	_	_
70	using	use	VBG	_	_	_
71	bowtie	bowtie	NN	_	_	_
72	v1	v1	NN	_	_	_
73	.0.0	.0.0	CD	_	_	_
74	with	with	IN	_	_	_
75	parameters	parameter	NNS	_	_	_
76	-	-	:	_	_	_
77	X	x	NN	_	_	_
78	1000	1000	CD	_	_	_
79	-	-	:	_	_	_
80	n	n	NN	_	_	_
81	2	2	CD	_	_	_
82	-3	-3	CD	_	_	_
83	3	3	LS	_	_	_
84	-	-	:	_	_	_
85	S	s	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	strain	strain	NN	_	_	_
88	:	:	:	_	_	_
89	K-12	k-12	NN	_	_	_
90	MG1655	mg1655	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	Supplementary	supplementary	JJ	_	_	_
93	_	_	NN	_	_	_
94	files	file	NNS	_	_	_
95	_	_	IN	_	_	_
96	format	format	NN	_	_	_
97	_	_	NN	_	_	_
98	and	and	CC	_	_	_
99	_	_	NN	_	_	_
100	content	content	NN	_	_	_
101	:	:	:	_	_	_
102	comma-delimited	comma-delimited	JJ	_	_	_
103	text	text	NN	_	_	_
104	files	file	NNS	_	_	_
105	include	include	VBP	_	_	_
106	FPKM	fpkm	NN	_	_	_
107	values	value	NNS	_	_	_
108	for	for	IN	_	_	_
109	each	each	DT	_	_	_
110	Sample	Sample	NNP	_	_	_
111	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cell	cell	NN	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	treated	treat	VBN	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	RNAprotect	rnaprotect	NN	_	_	_
10	reagent	reagent	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	qiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	RNeasy	RNeasy	NNP	_	_	_
9	Plus	Plus	NNP	_	_	_
10	Mini	Mini	NNP	_	_	_
11	kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Qiagen	Qiagen	NNP	_	_	_
14	Inc.	Inc.	NNP	_	_	_
15	,	,	,	_	_	_
16	Valencia	Valencia	NNP	_	_	_
17	,	,	,	_	_	_
18	CA	CA	NNP	_	_	_
19	,	,	,	_	_	_
20	USA	USA	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	and	and	CC	_	_	_
23	genomic	genomic	JJ	_	_	_
24	DNA	dna	NN	_	_	_
25	was	be	VBD	_	_	_
26	removed	remove	VBN	_	_	_
27	by	by	IN	_	_	_
28	gDNA	gdna	NN	_	_	_
29	Eliminator	eliminator	NN	_	_	_
30	spin	spin	NN	_	_	_
31	column	column	NN	_	_	_
32	in	in	IN	_	_	_
33	the	the	DT	_	_	_
34	RNeasy	RNeasy	NNP	_	_	_
35	Plus	Plus	NNP	_	_	_
36	Mini	Mini	NNP	_	_	_
37	Kit	kit	NN	_	_	_
38	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	quality	quality	NN	_	_	_
3	and	and	CC	_	_	_
4	concentration	concentration	NN	_	_	_
5	was	be	VBD	_	_	_
6	determined	determine	VBN	_	_	_
7	by	by	IN	_	_	_
8	analysis	analysis	NN	_	_	_
9	with	with	IN	_	_	_
10	a	a	DT	_	_	_
11	NanoDrop	NanoDrop	NNP	_	_	_
12	1000	1000	CD	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Thermo	Thermo	NNP	_	_	_
15	Scientific	Scientific	NNP	_	_	_
16	Inc.	Inc.	NNP	_	_	_
17	,	,	,	_	_	_
18	Wilmington	Wilmington	NNP	_	_	_
19	,	,	,	_	_	_
20	DE	de	NN	_	_	_
21	,	,	,	_	_	_
22	USA	USA	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	WT	WT	NNP	_	_	_
3	pH5	ph5	NN	_	_	_
4	.5	.5	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	WT	wt	JJ	_	_	_
7	pH5	ph5	NN	_	_	_
8	.5	.5	CD	_	_	_
9	1	1	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	WT	wt	JJ	_	_	_
12	pH5	ph5	NN	_	_	_
13	.5	.5	NN	_	_	_
14	2	2	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	ΔgadE	δgade	NN	_	_	_
17	pH5	ph5	NN	_	_	_
18	.5	.5	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	ΔgadE	δgade	NN	_	_	_
21	pH5	ph5	NN	_	_	_
22	.5	.5	CD	_	_	_
23	1	1	CD	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	ΔgadE	δgade	NN	_	_	_
26	pH5	ph5	NN	_	_	_
27	.5	.5	CD	_	_	_
28	2	2	CD	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	ΔgadW	δgadw	NN	_	_	_
31	pH5	ph5	NN	_	_	_
32	.5	.5	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	ΔgadW	δgadw	NN	_	_	_
35	pH5	ph5	NN	_	_	_
36	.5	.5	CD	_	_	_
37	1	1	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	ΔgadW	δgadw	NN	_	_	_
40	pH5	ph5	NN	_	_	_
41	.5	.5	CD	_	_	_
42	2	2	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	ΔgadX	δgadx	NN	_	_	_
45	pH5	ph5	NN	_	_	_
46	.5	.5	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	ΔgadX	δgadx	NN	_	_	_
49	pH5	ph5	NN	_	_	_
50	.5	.5	CD	_	_	_
51	1	1	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	ΔgadX	δgadx	NN	_	_	_
54	pH5	ph5	NN	_	_	_
55	.5	.5	CD	_	_	_
56	2	2	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
58	Background	background	NN	_	_	_
59	subtractions	subtraction	NNS	_	_	_
60	and	and	CC	_	_	_
61	normalization	normalization	NN	_	_	_
62	of	of	IN	_	_	_
63	extracted	extract	VBN	_	_	_
64	data	datum	NNS	_	_	_
65	were	be	VBD	_	_	_
66	performed	perform	VBN	_	_	_
67	through	through	IN	_	_	_
68	R	r	NN	_	_	_
69	using	use	VBG	_	_	_
70	the	the	DT	_	_	_
71	Bioconductor	Bioconductor	NNP	_	_	_
72	package	package	NN	_	_	_
73	as	as	IN	_	_	_
74	described	describe	VBN	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	Yang	Yang	NNP	_	_	_
77	,	,	,	_	_	_
78	Y.H.	Y.H.	NNP	_	_	_
79	et	et	FW	_	_	_
80	al.	al.	FW	_	_	_
81	.	.	.	_	_	_

1	Normalization	normalization	NN	_	_	_
2	for	for	IN	_	_	_
3	cDNA	cdna	NN	_	_	_
4	microarray	microarray	NN	_	_	_
5	data	datum	NNS	_	_	_
6	:	:	:	_	_	_
7	a	a	DT	_	_	_
8	robust	robust	JJ	_	_	_
9	composite	composite	JJ	_	_	_
10	method	method	NN	_	_	_
11	addressing	address	VBG	_	_	_
12	single	single	JJ	_	_	_
13	and	and	CC	_	_	_
14	multiple	multiple	JJ	_	_	_
15	slide	slide	NN	_	_	_
16	systematic	systematic	JJ	_	_	_
17	variation	variation	NN	_	_	_
18	,	,	,	_	_	_
19	Nucleic	nucleic	JJ	_	_	_
20	Acid	acid	NN	_	_	_
21	Res	Res	NNP	_	_	_
22	30	30	CD	_	_	_
23	,	,	,	_	_	_
24	e15	e15	NN	_	_	_
25	,	,	,	_	_	_
26	2002	2002	CD	_	_	_
27	;	;	:	_	_	_
28	Smyth	Smyth	NNP	_	_	_
29	,	,	,	_	_	_
30	G.K.	G.K.	NNP	_	_	_
31	in	in	IN	_	_	_
32	Bioinformatics	Bioinformatics	NNP	_	_	_
33	and	and	CC	_	_	_
34	Computational	Computational	NNP	_	_	_
35	Biology	Biology	NNP	_	_	_
36	Solutions	Solutions	NNPS	_	_	_
37	using	use	VBG	_	_	_
38	R	r	NN	_	_	_
39	and	and	CC	_	_	_
40	Bioconductor	bioconductor	NN	_	_	_
41	.	.	.	_	_	_

1	397-420	397-420	CD	_	_	_
2	,	,	,	_	_	_
3	Springer	Springer	NNP	_	_	_
4	,	,	,	_	_	_
5	New	New	NNP	_	_	_
6	York	York	NNP	_	_	_
7	,	,	,	_	_	_
8	2005	2005	CD	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Cultures	culture	NNS	_	_	_
3	of	of	IN	_	_	_
4	both	both	DT	_	_	_
5	strains	strain	NNS	_	_	_
6	were	be	VBD	_	_	_
7	started	start	VBN	_	_	_
8	with	with	IN	_	_	_
9	a	a	DT	_	_	_
10	2	2	CD	_	_	_
11	%	%	NN	_	_	_
12	overnight	overnight	JJ	_	_	_
13	inoculum	inoculum	NN	_	_	_
14	in	in	IN	_	_	_
15	LB	LB	NNP	MED	_	_
16	media	media	NNS	MED	_	_
17	containing	contain	VBG	_	_	_
18	35ug	35ug	JJ	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	Escherichia	escherichia	FW	Organism	_	_
21	coli	coli	FW	Organism	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	growth	growth	NN	_	_	_
24	phase	phase	NN	_	_	_
25	:	:	:	_	_	_
26	exponential	exponential	JJ	_	_	_
27	growth	growth	NN	_	_	_
28	phase	phase	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	growth	growth	NN	_	_	_
31	phase	phase	NN	_	_	_
32	:	:	:	_	_	_
33	stationary	stationary	JJ	_	_	_
34	growth	growth	NN	_	_	_
35	phase	phase	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	growth	growth	NN	_	_	_
38	phase	phase	NN	_	_	_
39	:	:	:	_	_	_
40	transition	transition	NN	_	_	_
41	growth	growth	NN	_	_	_
42	phase	phase	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	pControl	pcontrol	NN	_	_	_
45	_	_	CD	_	_	_
46	exponential	exponential	JJ	_	_	_
47	growth	growth	NN	_	_	_
48	phase	phase	NN	_	_	_
49	_	_	NN	_	_	_
50	1	1	CD	_	_	_
51	ml	ml	NN	_	_	_
52	cell	cell	NN	_	_	_
53	pellet	pellet	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	pControl	pcontrol	NN	_	_	_
56	_	_	CD	_	_	_
57	stationary	stationary	JJ	_	_	_
58	growth	growth	NN	_	_	_
59	phase	phase	NN	_	_	_
60	_	_	NN	_	_	_
61	1	1	CD	_	_	_
62	ml	ml	NN	_	_	_
63	cell	cell	NN	_	_	_
64	pellet	pellet	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	pControl	pcontrol	NN	_	_	_
67	_	_	CD	_	_	_
68	transition	transition	NN	_	_	_
69	growth	growth	NN	_	_	_
70	phase	phase	NN	_	_	_
71	_	_	NN	_	_	_
72	1	1	CD	_	_	_
73	ml	ml	NN	_	_	_
74	cell	cell	NN	_	_	_
75	pellet	pellet	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	plasmid	plasmid	NN	_	_	_
78	:	:	:	_	_	_
79	pControl	pcontrol	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	plasmid	plasmid	NN	_	_	_
82	:	:	:	_	_	_
83	pLPLσ	plplσ	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	pLPLσ	plplσ	NN	_	_	_
86	_	_	CD	_	_	_
87	exponential	exponential	JJ	_	_	_
88	growth	growth	NN	_	_	_
89	phase	phase	NN	_	_	_
90	_	_	NN	_	_	_
91	1	1	CD	_	_	_
92	ml	ml	NN	_	_	_
93	cell	cell	NN	_	_	_
94	pellet	pellet	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	pLPLσ	plplσ	NN	_	_	_
97	_	_	CD	_	_	_
98	stationary	stationary	JJ	_	_	_
99	growth	growth	NN	_	_	_
100	phase	phase	NN	_	_	_
101	_	_	NN	_	_	_
102	1	1	CD	_	_	_
103	ml	ml	NN	_	_	_
104	cell	cell	NN	_	_	_
105	pellet	pellet	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	pLPLσ	plplσ	NN	_	_	_
108	_	_	CD	_	_	_
109	transition	transition	NN	_	_	_
110	growth	growth	NN	_	_	_
111	phase	phase	NN	_	_	_
112	_	_	NN	_	_	_
113	1	1	CD	_	_	_
114	ml	ml	NN	_	_	_
115	cell	cell	NN	_	_	_
116	pellet	pellet	NN	_	_	_
117	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
118	Replicate	replicate	VB	_	_	_
119	1	1	LS	_	_	_
120	-	-	:	_	_	_
121	timepoint	timepoint	NN	_	_	_
122	1	1	CD	_	_	_
123	-LRB-	-lrb-	-LRB-	_	_	_
124	4.5	4.5	CD	_	_	_
125	h	h	NN	_	_	_
126	-RRB-	-rrb-	-RRB-	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	Replicate	replicate	VB	_	_	_
129	1	1	LS	_	_	_
130	-	-	:	_	_	_
131	timepoint	timepoint	NN	_	_	_
132	1	1	CD	_	_	_
133	-LRB-	-lrb-	-LRB-	_	_	_
134	4.5	4.5	CD	_	_	_
135	h	h	NN	_	_	_
136	-RRB-	-rrb-	-RRB-	_	_	_
137	-	-	:	_	_	_
138	dye	dye	VB	_	_	_
139	swap	swap	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	Replicate	replicate	VB	_	_	_
142	1	1	LS	_	_	_
143	-	-	:	_	_	_
144	timepoint	timepoint	NN	_	_	_
145	2	2	CD	_	_	_
146	-LRB-	-lrb-	-LRB-	_	_	_
147	6h	6h	NN	_	_	_
148	-RRB-	-rrb-	-RRB-	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	Replicate	replicate	VB	_	_	_
151	1	1	LS	_	_	_
152	-	-	:	_	_	_
153	timepoint	timepoint	NN	_	_	_
154	2	2	CD	_	_	_
155	-LRB-	-lrb-	-LRB-	_	_	_
156	6h	6h	NN	_	_	_
157	-RRB-	-rrb-	-RRB-	_	_	_
158	-	-	:	_	_	_
159	dye	dye	VB	_	_	_
160	swap	swap	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	Replicate	replicate	VB	_	_	_
163	1	1	LS	_	_	_
164	-	-	:	_	_	_
165	timepoint	timepoint	NN	_	_	_
166	3	3	CD	_	_	_
167	-LRB-	-lrb-	-LRB-	_	_	_
168	9h	9h	NN	_	_	_
169	-RRB-	-rrb-	-RRB-	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	Replicate	replicate	VB	_	_	_
172	1	1	LS	_	_	_
173	-	-	:	_	_	_
174	timepoint	timepoint	NN	_	_	_
175	3	3	CD	_	_	_
176	-LRB-	-lrb-	-LRB-	_	_	_
177	9h	9h	NN	_	_	_
178	-RRB-	-rrb-	-RRB-	_	_	_
179	-	-	:	_	_	_
180	dye	dye	VB	_	_	_
181	swap	swap	NN	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	Replicate	replicate	VB	_	_	_
184	2	2	LS	_	_	_
185	-	-	:	_	_	_
186	timepoint	timepoint	NN	_	_	_
187	1	1	CD	_	_	_
188	-LRB-	-lrb-	-LRB-	_	_	_
189	4.5	4.5	CD	_	_	_
190	h	h	NN	_	_	_
191	-RRB-	-rrb-	-RRB-	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	Replicate	replicate	VB	_	_	_
194	2	2	LS	_	_	_
195	-	-	:	_	_	_
196	timepoint	timepoint	NN	_	_	_
197	1	1	CD	_	_	_
198	-LRB-	-lrb-	-LRB-	_	_	_
199	4.5	4.5	CD	_	_	_
200	h	h	NN	_	_	_
201	-RRB-	-rrb-	-RRB-	_	_	_
202	-	-	:	_	_	_
203	dye	dye	VB	_	_	_
204	swap	swap	NN	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	Replicate	replicate	VB	_	_	_
207	2	2	LS	_	_	_
208	-	-	:	_	_	_
209	timepoint	timepoint	NN	_	_	_
210	2	2	CD	_	_	_
211	-LRB-	-lrb-	-LRB-	_	_	_
212	6h	6h	NN	_	_	_
213	-RRB-	-rrb-	-RRB-	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	Replicate	replicate	VB	_	_	_
216	2	2	LS	_	_	_
217	-	-	:	_	_	_
218	timepoint	timepoint	NN	_	_	_
219	2	2	CD	_	_	_
220	-LRB-	-lrb-	-LRB-	_	_	_
221	6h	6h	NN	_	_	_
222	-RRB-	-rrb-	-RRB-	_	_	_
223	-	-	:	_	_	_
224	dye	dye	VB	_	_	_
225	swap	swap	NN	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	Replicate	replicate	VB	_	_	_
228	2	2	LS	_	_	_
229	-	-	:	_	_	_
230	timepoint	timepoint	NN	_	_	_
231	3	3	CD	_	_	_
232	-LRB-	-lrb-	-LRB-	_	_	_
233	9h	9h	NN	_	_	_
234	-RRB-	-rrb-	-RRB-	_	_	_
235	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
236	Replicate	replicate	VB	_	_	_
237	2	2	LS	_	_	_
238	-	-	:	_	_	_
239	timepoint	timepoint	NN	_	_	_
240	3	3	CD	_	_	_
241	-LRB-	-lrb-	-LRB-	_	_	_
242	9h	9h	NN	_	_	_
243	-RRB-	-rrb-	-RRB-	_	_	_
244	-	-	:	_	_	_
245	dye	dye	VB	_	_	_
246	swap	swap	NN	_	_	_
247	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
248	strain	strain	NN	_	_	_
249	:	:	:	_	_	_
250	MG1655	mg1655	NN	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
252	The	the	DT	_	_	_
253	optical	optical	JJ	_	_	_
254	density	density	NN	_	_	_
255	was	be	VBD	_	_	_
256	measured	measure	VBN	_	_	_
257	every	every	DT	_	_	_
258	30	30	CD	_	_	_
259	min	min	NN	_	_	_
260	and	and	CC	_	_	_
261	expression	expression	NN	_	_	_
262	of	of	IN	_	_	_
263	the	the	DT	_	_	_
264	heterologous	heterologous	JJ	_	_	_
265	sigma	sigma	NN	_	_	_
266	factor	factor	NN	_	_	_
267	was	be	VBD	_	_	_
268	induced	induce	VBN	_	_	_
269	with	with	IN	_	_	_
270	1mM	1mm	NN	_	_	_
271	IPTG	iptg	NN	_	_	_
272	at	at	IN	_	_	_
273	an	a	DT	_	_	_
274	optical	optical	JJ	_	_	_
275	density	density	NN	_	_	_
276	of	of	IN	_	_	_
277	0.1	0.1	CD	_	_	_
278	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	for	for	IN	_	_	_
3	RNA	rna	NN	_	_	_
4	extractions	extraction	NNS	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	1	1	CD	_	_	_
7	ml	ml	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	were	be	VBD	_	_	_
10	taken	take	VBN	_	_	_
11	after	after	IN	_	_	_
12	4.5	4.5	CD	_	_	_
13	,	,	,	_	_	_
14	6	6	CD	_	_	_
15	and	and	CC	_	_	_
16	9	9	CD	_	_	_
17	hours	hour	NNS	_	_	_
18	after	after	IN	_	_	_
19	induction	induction	NN	_	_	_
20	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	pellets	pellet	NNS	_	_	_
3	were	be	VBD	_	_	_
4	stored	store	VBN	_	_	_
5	at	at	IN	_	_	_
6	-80	-80	CD	_	_	_
7	°C	°c	NN	_	_	_
8	until	until	IN	_	_	_
9	total	total	JJ	_	_	_
10	RNA	rna	NN	_	_	_
11	extraction	extraction	NN	_	_	_
12	was	be	VBD	_	_	_
13	performed	perform	VBN	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	time	time	NN	_	_	_
3	point	point	NN	_	_	_
4	:	:	:	_	_	_
5	4.5	4.5	CD	_	_	_
6	hrs	hr	NNS	_	_	_
7	after	after	IN	_	_	_
8	induction	induction	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	time	time	NN	_	_	_
11	point	point	NN	_	_	_
12	:	:	:	_	_	_
13	6	6	CD	_	_	_
14	hrs	hr	NNS	_	_	_
15	after	after	IN	_	_	_
16	induction	induction	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	time	time	NN	_	_	_
19	point	point	NN	_	_	_
20	:	:	:	_	_	_
21	9	9	CD	_	_	_
22	hrs	hr	NNS	_	_	_
23	after	after	IN	_	_	_
24	induction	induction	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Total	total	JJ	_	_	_
27	RNA	rna	NN	_	_	_
28	was	be	VBD	_	_	_
29	extracted	extract	VBN	_	_	_
30	using	use	VBG	_	_	_
31	the	the	DT	_	_	_
32	RNeasy	RNeasy	NNP	_	_	_
33	Mini	Mini	NNP	_	_	_
34	kit	kit	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	Qiagen	Qiagen	NNP	_	_	_
37	,	,	,	_	_	_
38	Hilden	Hilden	NNP	_	_	_
39	,	,	,	_	_	_
40	Germany	Germany	NNP	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	according	accord	VBG	_	_	_
43	to	to	TO	_	_	_
44	the	the	DT	_	_	_
45	manufactures	manufacture	VBZ	_	_	_
46	recommendations	recommendation	NNS	_	_	_
47	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	10-HT874-PS-60min1	10-ht874-ps-60min1	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	11-HT874-PS-60min2	11-ht874-ps-60min2	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	12-HT874-PS-60min3	12-ht874-ps-60min3	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	1-HT873-PA1	1-ht873-pa1	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	1-HT873-PA1	1-ht873-pa1	NN	_	_	_
11	-	-	:	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	2-HT873-PA2	2-ht873-pa2	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	2-HT873-PA2	2-ht873-pa2	NN	_	_	_
16	-	-	:	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	3-HT873-PA3	3-ht873-pa3	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	3-HT873-PA3	3-ht873-pa3	NN	_	_	_
21	-	-	:	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	4-HT873-PS-60min1	4-ht873-ps-60min1	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	5-HT873-PS-60min2	5-ht873-ps-60min2	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	6-HT873-PS-60min3	6-ht873-ps-60min3	JJ	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	7-HT874-PA1	7-ht874-pa1	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	7-HT874-PA1	7-ht874-pa1	NN	_	_	_
32	-	-	:	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	873-Con1	873-con1	NN	_	_	_
35	--	--	:	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	873-Con2	873-con2	NN	_	_	_
38	--	--	:	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	873-Con3	873-con3	NN	_	_	_
41	--	--	:	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	873-PA1	873-pa1	NN	_	_	_
44	--	--	:	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	873-PA2	873-pa2	NN	_	_	_
47	--	--	:	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	873-PA3	873-pa3	NN	_	_	_
50	--	--	:	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	875-Con1	875-con1	NN	_	_	_
53	--	--	:	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	875-Con2	875-con2	NN	_	_	_
56	--	--	:	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	875-Con3	875-con3	NN	_	_	_
59	--	--	:	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	875-PA1	875-pa1	NN	_	_	_
62	--	--	:	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	875-PA2	875-pa2	NN	_	_	_
65	--	--	:	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	875-PA3	875-pa3	NN	_	_	_
68	--	--	:	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	8-HT874-PA2	8-ht874-pa2	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	8-HT874-PA2	8-ht874-pa2	NN	_	_	_
73	-	-	:	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	9-HT874-PA3	9-ht874-pa3	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	9-HT874-PA3	9-ht874-pa3	NN	_	_	_
78	-	-	:	_	_	_
79	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
80	Data	Data	NNP	_	_	_
81	was	be	VBD	_	_	_
82	analyzed	analyze	VBN	_	_	_
83	with	with	IN	_	_	_
84	RMA	rma	NN	_	_	_
85	using	use	VBG	_	_	_
86	the	the	DT	_	_	_
87	program	program	NN	_	_	_
88	Partek	Partek	NNP	_	_	_
89	6.6	6.6	CD	_	_	_
90	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
91	E.	E.	NNP	_	_	_
92	coli	coli	NN	_	_	_
93	strains	strain	NNS	_	_	_
94	HT874	ht874	NN	_	_	_
95	,	,	,	_	_	_
96	HT873	ht873	NN	_	_	_
97	,	,	,	_	_	_
98	HT875	ht875	NN	_	_	_
99	,	,	,	_	_	_
100	HT873	ht873	NN	_	_	_
101	treated	treat	VBN	_	_	_
102	with	with	IN	_	_	_
103	or	or	CC	_	_	_
104	no	no	DT	_	_	_
105	polyamines	polyamine	NNS	_	_	_
106	by	by	IN	_	_	_
107	Trizol	trizol	NN	_	_	_
108	protocol	protocol	NN	_	_	_
109	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	HT873-Con1	ht873-con1	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	HT873-Con2	ht873-con2	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	HT873-Con3	ht873-con3	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	HT873-PA1	ht873-pa1	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	HT873-PA2	ht873-pa2	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	HT873-PA3	ht873-pa3	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	HT875-Con1	ht875-con1	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	HT875-Con2	ht875-con2	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	HT875-Con3	ht875-con3	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	HT875-PA1	ht875-pa1	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	HT875-PA2	ht875-pa2	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	HT875-PA3	ht875-pa3	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	RNA	rna	NN	_	_	_
30	were	be	VBD	_	_	_
31	isolated	isolate	VBN	_	_	_
32	from	from	IN	_	_	_
33	wild	wild	JJ	_	_	_
34	type	type	NN	_	_	_
35	and	and	CC	_	_	_
36	mutants	mutant	NNS	_	_	_
37	.	.	.	_	_	_

1	Trizol	trizol	NN	_	_	_
2	extraction	extraction	NN	_	_	_
3	of	of	IN	_	_	_
4	total	total	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	was	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	according	accord	VBG	_	_	_
9	to	to	TO	_	_	_
10	standard	standard	JJ	_	_	_
11	affymetrix	affymetrix	NN	_	_	_
12	labeling	labeling	NN	_	_	_
13	protocols	protocol	NNS	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	HT873	ht873	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	strain	strain	NN	_	_	_
7	:	:	:	_	_	_
8	HT874	ht874	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	strain	strain	NN	_	_	_
11	:	:	:	_	_	_
12	HT875	ht875	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	treatment	treatment	NN	_	_	_
15	:	:	:	_	_	_
16	Con1	con1	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	treatment	treatment	NN	_	_	_
19	:	:	:	_	_	_
20	Con2	con2	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	treatment	treatment	NN	_	_	_
23	:	:	:	_	_	_
24	Con3	con3	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	treatment	treatment	NN	_	_	_
27	:	:	:	_	_	_
28	PA1	pa1	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	treatment	treatment	NN	_	_	_
31	:	:	:	_	_	_
32	PA2	pa2	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	treatment	treatment	NN	_	_	_
35	:	:	:	_	_	_
36	PA3	pa3	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	treatment	treatment	NN	_	_	_
39	:	:	:	_	_	_
40	PS-60min	ps-60min	JJ	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	50	50	CD	_	_	_
43	ng	ng	NN	_	_	_
44	of	of	IN	_	_	_
45	the	the	DT	_	_	_
46	fragmented	fragmented	JJ	_	_	_
47	RNA	rna	NN	_	_	_
48	was	be	VBD	_	_	_
49	converted	convert	VBN	_	_	_
50	to	to	TO	_	_	_
51	sequencing	sequencing	NN	_	_	_
52	library	library	NN	_	_	_
53	using	use	VBG	_	_	_
54	TruSeq	TruSeq	NNP	_	_	_
55	®	®	NNP	_	_	_
56	Stranded	Stranded	NNP	_	_	_
57	mRNA	mrna	NN	_	_	_
58	Sample	Sample	NNP	_	_	_
59	Prep	Prep	NNP	_	_	_
60	Kit	kit	NN	_	_	_
61	in	in	IN	_	_	_
62	accordance	accordance	NN	_	_	_
63	with	with	IN	_	_	_
64	manufacturer	manufacturer	NN	_	_	_
65	's	's	POS	_	_	_
66	instruction	instruction	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	Illumina	Illumina	NNP	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	All	All	NNP	_	_	_
3	sequencing	sequencing	NN	_	_	_
4	reads	read	VBZ	_	_	_
5	were	be	VBD	_	_	_
6	mapped	map	VBN	_	_	_
7	to	to	TO	_	_	_
8	E.	e.	FW	_	_	_
9	coli	coli	FW	_	_	_
10	MG1655	mg1655	NN	_	_	_
11	reference	reference	NN	_	_	_
12	genome	genome	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	NC	nc	NN	_	_	_
15	_	_	CD	_	_	_
16	000913	000913	CD	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	using	use	VBG	_	_	_
19	CLC	clc	NN	_	_	_
20	Genomics	genomic	NNS	_	_	_
21	Workbench5	workbench5	NN	_	_	_
22	with	with	IN	_	_	_
23	the	the	DT	_	_	_
24	length	length	NN	_	_	_
25	fraction	fraction	NN	_	_	_
26	of	of	IN	_	_	_
27	0.9	0.9	CD	_	_	_
28	and	and	CC	_	_	_
29	the	the	DT	_	_	_
30	similarity	similarity	NN	_	_	_
31	of	of	IN	_	_	_
32	0.99	0.99	CD	_	_	_
33	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Basecalls	basecall	NNS	_	_	_
3	performed	perform	VBN	_	_	_
4	using	use	VBG	_	_	_
5	CASAVA	CASAVA	NNP	_	_	_
6	version	version	NN	_	_	_
7	1.4	1.4	CD	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	cell	cell	NN	_	_	_
10	type	type	NN	_	_	_
11	:	:	:	_	_	_
12	Escherichia	escherichia	FW	Organism	_	_
13	coli	coli	FW	Organism	_	_
14	str	str	FW	_	_	_
15	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Escherichia	escherichia	FW	Organism	_	_
4	coli	coli	FW	Organism	_	_
5	str	str	FW	_	_	_
6	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	From	from	IN	_	_	_
4	the	the	DT	_	_	_
5	cells	cell	NNS	_	_	_
6	cultured	culture	VBN	_	_	_
7	in	in	IN	_	_	_
8	LB	LB	NNP	MED	_	_
9	media	media	NNS	MED	_	_
10	at	at	IN	_	_	_
11	37	37	CD	_	_	_
12	℃	℃	CD	_	_	_
13	,	,	,	_	_	_
14	total	total	JJ	_	_	_
15	RNA	rna	NN	_	_	_
16	was	be	VBD	_	_	_
17	extracted	extract	VBN	_	_	_
18	using	use	VBG	_	_	_
19	RNAsnapTM	rnasnaptm	NN	_	_	_
20	method	method	NN	_	_	_
21	,	,	,	_	_	_
22	followed	follow	VBN	_	_	_
23	by	by	IN	_	_	_
24	the	the	DT	_	_	_
25	ethanol	ethanol	NN	_	_	_
26	precipitation	precipitation	NN	_	_	_
27	.	.	.	_	_	_

1	rRNA	rrna	NN	_	_	_
2	was	be	VBD	_	_	_
3	removed	remove	VBN	_	_	_
4	using	use	VBG	_	_	_
5	ribo-zeroTM	ribo-zerotm	JJ	_	_	_
6	magnetic	magnetic	JJ	_	_	_
7	kit	kit	NN	_	_	_
8	for	for	IN	_	_	_
9	bacteria	bacterium	NNS	_	_	_
10	in	in	IN	_	_	_
11	accordance	accordance	NN	_	_	_
12	with	with	IN	_	_	_
13	manufacturer	manufacturer	NN	_	_	_
14	's	's	POS	_	_	_
15	instruction	instruction	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Epicentre	Epicentre	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	rRNA	rrna	NN	_	_	_
2	removal	removal	NN	_	_	_
3	was	be	VBD	_	_	_
4	confirmed	confirm	VBN	_	_	_
5	using	use	VBG	_	_	_
6	ExperionTM	experiontm	NN	_	_	_
7	system	system	NN	_	_	_
8	.	.	.	_	_	_

1	Subsequently	subsequently	RB	_	_	_
2	,	,	,	_	_	_
3	4	4	CD	_	_	_
4	µg	µg	NN	_	_	_
5	of	of	IN	_	_	_
6	the	the	DT	_	_	_
7	purified	purify	VBN	_	_	_
8	RNA	rna	NN	_	_	_
9	was	be	VBD	_	_	_
10	fragmented	fragmented	JJ	_	_	_
11	to	to	TO	_	_	_
12	sizes	size	NNS	_	_	_
13	of	of	IN	_	_	_
14	~	~	NN	_	_	_
15	300	300	CD	_	_	_
16	bp	bp	NN	_	_	_
17	using	use	VBG	_	_	_
18	RNA	rna	NN	_	_	_
19	fragmentation	fragmentation	NN	_	_	_
20	reagent	reagent	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Ambion	Ambion	NNP	_	_	_
23	,	,	,	_	_	_
24	Grand	Grand	NNP	_	_	_
25	Island	Island	NNP	_	_	_
26	,	,	,	_	_	_
27	NY	NY	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Glycerol	Glycerol	NNP	_	_	_
3	stocks	stock	NNS	_	_	_
4	of	of	IN	_	_	_
5	E.	e.	FW	_	_	_
6	coli	coli	FW	_	_	_
7	K12	k12	NN	_	_	_
8	strain	strain	NN	_	_	_
9	MG1655	mg1655	NN	_	_	_
10	were	be	VBD	_	_	_
11	inoculated	inoculate	VBN	_	_	_
12	into	into	IN	_	_	_
13	LB	lb	NN	MED	_	_
14	media	media	NNS	MED	_	_
15	grown	grow	VBN	_	_	_
16	at	at	IN	_	_	_
17	37	37	CD	_	_	_
18	℃	℃	NN	_	_	_
19	with	with	IN	_	_	_
20	constant	constant	JJ	_	_	_
21	agitation	agitation	NN	_	_	_
22	overnight	overnight	JJ	_	_	_
23	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	diluted	dilute	VBN	_	_	_
4	1:100	1:100	CD	_	_	_
5	into	into	IN	_	_	_
6	fresh	fresh	JJ	_	_	_
7	minimal	minimal	JJ	_	_	_
8	medium	medium	NN	_	_	_
9	and	and	CC	_	_	_
10	then	then	RB	_	_	_
11	cultured	culture	VBN	_	_	_
12	at	at	IN	_	_	_
13	37	37	CD	_	_	_
14	℃	℃	CD	_	_	_
15	to	to	TO	_	_	_
16	mid-exponential	mid-exponential	JJ	_	_	_
17	phase	phase	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	OD600	od600	NN	_	_	_
20	nm	nm	NN	_	_	_
21	~	~	NN	_	_	_
22	0.6	0.6	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	No	no	DT	_	_	_
3	treatment	treatment	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	RNA-Seq	rna-seq	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	RNA-seq	rna-seq	NN	_	_	_
8	37C	37c	NN	_	_	_
9	LB	lb	NN	_	_	_
10	rep1	rep1	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	RNA-seq	rna-seq	NN	_	_	_
13	37C	37c	NN	_	_	_
14	LB	lb	NN	_	_	_
15	rep2	rep2	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Supplementary	supplementary	JJ	_	_	_
18	_	_	NN	_	_	_
19	files	file	NNS	_	_	_
20	_	_	IN	_	_	_
21	format	format	NN	_	_	_
22	_	_	NN	_	_	_
23	and	and	CC	_	_	_
24	_	_	NN	_	_	_
25	content	content	NN	_	_	_
26	:	:	:	_	_	_
27	RPKM	rpkm	NN	_	_	_
28	is	be	VBZ	_	_	_
29	generated	generate	VBN	_	_	_
30	by	by	IN	_	_	_
31	in-house	in-house	JJ	_	_	_
32	script	script	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
34	The	the	DT	_	_	_
35	expression	expression	NN	_	_	_
36	levels	level	NNS	_	_	_
37	were	be	VBD	_	_	_
38	based	base	VBN	_	_	_
39	upon	upon	IN	_	_	_
40	the	the	DT	_	_	_
41	RPKM	RPKM	NNP	_	_	_
42	metric	metric	JJ	_	_	_
43	obtained	obtain	VBN	_	_	_
44	from	from	IN	_	_	_
45	strand-specific	strand-specific	JJ	_	_	_
46	manner	manner	NN	_	_	_
47	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	LB	lb	NN	_	_	_
7	at	at	IN	_	_	_
8	22	22	CD	_	_	_
9	°C	°c	NN	_	_	_
10	or	or	CC	_	_	_
11	37	37	CD	_	_	_
12	°C	°c	NN	_	_	_
13	,	,	,	_	_	_
14	as	as	IN	_	_	_
15	indicated	indicate	VBN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	resuspended	resuspend	VBN	_	_	_
5	in	in	IN	_	_	_
6	Lysis	lysis	NN	_	_	_
7	buffer	buffer	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	10mM	10mm	NN	_	_	_
10	tris	tris	NN	_	_	_
11	,	,	,	_	_	_
12	20	20	CD	_	_	_
13	%	%	NN	_	_	_
14	sucrose	sucrose	NN	_	_	_
15	,	,	,	_	_	_
16	50mM	50mm	NN	_	_	_
17	NaCl	nacl	NN	_	_	_
18	,	,	,	_	_	_
19	10mM	10mm	NN	_	_	_
20	EDTA	edta	NN	_	_	_
21	,	,	,	_	_	_
22	10	10	CD	_	_	_
23	mg	mg	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	chip	chip	NN	_	_	_
26	antibody	antibody	NN	_	_	_
27	:	:	:	_	_	_
28	anti-Flag	anti-flag	JJ	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	ChIP-Seq	chip-seq	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Crosslinking	crosslinking	NN	_	_	_
33	was	be	VBD	_	_	_
34	performed	perform	VBN	_	_	_
35	using	use	VBG	_	_	_
36	1	1	CD	_	_	_
37	%	%	NN	_	_	_
38	of	of	IN	_	_	_
39	forlmaldehyde	forlmaldehyde	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	deltamatP	deltamatp	NN	_	_	_
42	22	22	CD	_	_	_
43	°C	°c	NN	_	_	_
44	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
45	E.	E.	NNP	_	_	_
46	coli	coli	NN	_	_	_
47	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
48	Escherichia	escherichia	FW	Organism	_	_
49	coli	coli	FW	Organism	_	_
50	K-12	k-12	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	Genome	Genome	NNP	_	_	_
53	_	_	NNP	_	_	_
54	build	build	VB	_	_	_
55	:	:	:	_	_	_
56	NC	NC	NNP	_	_	_
57	_	_	NNP	_	_	_
58	000913.2	000913.2	CD	_	_	_
59	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
60	genotype	genotype	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	growth	growth	NN	_	_	_
63	temperature	temperature	NN	_	_	_
64	:	:	:	_	_	_
65	22	22	CD	_	_	_
66	°C	°c	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	growth	growth	NN	_	_	_
69	temperature	temperature	NN	_	_	_
70	:	:	:	_	_	_
71	37	37	CD	_	_	_
72	°C	°c	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	Illumina	Illumina	NNP	_	_	_
75	Casava	Casava	NNP	_	_	_
76	v1	v1	NN	_	_	_
77	.8	.8	CD	_	_	_
78	used	use	VBN	_	_	_
79	for	for	IN	_	_	_
80	basecalling	basecalling	NN	_	_	_
81	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	MACS	mac	NNS	_	_	_
3	v2	v2	VBP	_	_	_
4	.0.10.20131216	.0.10.20131216	CD	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	for	for	IN	_	_	_
8	peak	peak	JJ	_	_	_
9	calling	call	VBG	_	_	_
10	with	with	IN	_	_	_
11	parameters	parameter	NNS	_	_	_
12	--	--	:	_	_	_
13	llocal	llocal	JJ	_	_	_
14	=	=	JJ	_	_	_
15	10000	10000	CD	_	_	_
16	-	-	:	_	_	_
17	g	g	NN	_	_	_
18	4639675	4639675	CD	_	_	_
19	--	--	:	_	_	_
20	bw	bw	NN	_	_	_
21	300	300	CD	_	_	_
22	-	-	:	_	_	_
23	p	p	NN	_	_	_
24	0.05	0.05	CD	_	_	_
25	--	--	:	_	_	_
26	slocal	slocal	JJ	_	_	_
27	=	=	JJ	_	_	_
28	1000	1000	CD	_	_	_
29	--	--	:	_	_	_
30	keep-dup	keep-dup	NN	_	_	_
31	=	=	JJ	_	_	_
32	20	20	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	MatP	matp	NN	_	_	_
35	37	37	CD	_	_	_
36	°C	°c	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	MukB	mukb	NN	_	_	_
39	22	22	CD	_	_	_
40	°C	°c	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	MukB	mukb	NN	_	_	_
43	37	37	CD	_	_	_
44	°C	°c	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	MukBDA	mukbda	NN	_	_	_
47	22	22	CD	_	_	_
48	°C	°c	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	MukB	mukb	NN	_	_	_
51	deltamatP	deltamatp	NN	_	_	_
52	22	22	CD	_	_	_
53	°C	°c	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	MukBEQ	mukbeq	NN	_	_	_
56	22	22	CD	_	_	_
57	°C	°c	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	MukBEQ	mukbeq	NN	_	_	_
60	deltamatP	deltamatp	NN	_	_	_
61	22	22	CD	_	_	_
62	°C	°c	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	Reads	read	NNS	_	_	_
65	were	be	VBD	_	_	_
66	adapter	adapter	NN	_	_	_
67	removed	remove	VBN	_	_	_
68	and	and	CC	_	_	_
69	trimmed	trim	VBN	_	_	_
70	to	to	TO	_	_	_
71	40Bp	40bp	NN	_	_	_
72	using	use	VBG	_	_	_
73	trimmomatic	trimmomatic	JJ	_	_	_
74	0.32	0.32	CD	_	_	_
75	with	with	IN	_	_	_
76	parameters	parameter	NNS	_	_	_
77	ILLUMINACLIP	ILLUMINACLIP	NNP	_	_	_
78	:	:	:	_	_	_
79	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
80	Sequences	sequence	NNS	_	_	_
81	were	be	VBD	_	_	_
82	mapped	map	VBN	_	_	_
83	to	to	TO	_	_	_
84	NC	NC	NNP	_	_	_
85	_	_	SYM	_	_	_
86	000913.2	000913.2	CD	_	_	_
87	using	use	VBG	_	_	_
88	bowtie2	bowtie2	NN	_	_	_
89	v2	v2	NN	_	_	_
90	.2.2	.2.2	CD	_	_	_
91	with	with	IN	_	_	_
92	parameters	parameter	NNS	_	_	_
93	-	-	:	_	_	_
94	N	n	NN	_	_	_
95	0	0	CD	_	_	_
96	--	--	:	_	_	_
97	sensitive	sensitive	JJ	_	_	_
98	--	--	:	_	_	_
99	minins	minin	NNS	_	_	_
100	130	130	CD	_	_	_
101	--	--	:	_	_	_
102	maxins	maxin	NNS	_	_	_
103	780	780	CD	_	_	_
104	-	-	:	_	_	_
105	q	q	NN	_	_	_
106	--	--	:	_	_	_
107	no-mixed	no-mixed	JJ	_	_	_
108	--	--	:	_	_	_
109	no-discordant	no-discordant	JJ	_	_	_
110	--	--	:	_	_	_
111	no-unal	no-unal	JJ	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
113	Sequencing	sequencing	NN	_	_	_
114	libraries	library	NNS	_	_	_
115	were	be	VBD	_	_	_
116	constructed	construct	VBN	_	_	_
117	using	use	VBG	_	_	_
118	the	the	DT	_	_	_
119	NEBNext	nebnext	NN	_	_	_
120	Ultra	ultra	NN	_	_	_
121	DNA	dna	NN	_	_	_
122	Library	Library	NNP	_	_	_
123	Prep	Prep	NNP	_	_	_
124	Kit	kit	NN	_	_	_
125	for	for	IN	_	_	_
126	Illumina	Illumina	NNP	_	_	_
127	-LRB-	-lrb-	-LRB-	_	_	_
128	#E7370	#E7370	NNP	_	_	_
129	,	,	,	_	_	_
130	NEB	NEB	NNP	_	_	_
131	-RRB-	-rrb-	-RRB-	_	_	_
132	for	for	IN	_	_	_
133	samples	sample	NNS	_	_	_
134	1	1	CD	_	_	_
135	to	to	TO	_	_	_
136	3	3	CD	_	_	_
137	-LRB-	-lrb-	-LRB-	_	_	_
138	37	37	CD	_	_	_
139	C	c	NN	_	_	_
140	-RRB-	-rrb-	-RRB-	_	_	_
141	and	and	CC	_	_	_
142	the	the	DT	_	_	_
143	WaferGen	WaferGen	NNP	_	_	_
144	PrepX	PrepX	NNP	_	_	_
145	ILM	ILM	NNP	_	_	_
146	ChiP-Seq	ChiP-Seq	NNP	_	_	_
147	Library	Library	NNP	_	_	_
148	Kit	kit	NN	_	_	_
149	-LRB-	-lrb-	-LRB-	_	_	_
150	#	#	#	_	_	_
151	400075	400075	CD	_	_	_
152	,	,	,	_	_	_
153	WaferGen	WaferGen	NNP	_	_	_
154	-RRB-	-rrb-	-RRB-	_	_	_
155	on	on	IN	_	_	_
156	the	the	DT	_	_	_
157	Apollo	Apollo	NNP	_	_	_
158	324	324	CD	_	_	_
159	System	System	NNP	_	_	_
160	for	for	IN	_	_	_
161	samples	sample	NNS	_	_	_
162	4	4	CD	_	_	_
163	to	to	TO	_	_	_
164	10	10	CD	_	_	_
165	-LRB-	-lrb-	-LRB-	_	_	_
166	22	22	CD	_	_	_
167	C	c	NN	_	_	_
168	-RRB-	-rrb-	-RRB-	_	_	_
169	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Supplementary	Supplementary	NNP	_	_	_
3	_	_	VBD	_	_	_
4	files	file	NNS	_	_	_
5	_	_	IN	_	_	_
6	format	format	NN	_	_	_
7	_	_	NN	_	_	_
8	and	and	CC	_	_	_
9	_	_	NN	_	_	_
10	content	content	NN	_	_	_
11	:	:	:	_	_	_
12	MACS	macs	NN	_	_	_
13	v2	v2	NN	_	_	_
14	.0.10.20131216	.0.10.20131216	CD	_	_	_
15	peaks	peak	VBZ	_	_	_
16	file	file	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	WT	wt	NN	_	_	_
19	22	22	CD	_	_	_
20	°C	°c	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	WT	wt	NN	_	_	_
23	37	37	CD	_	_	_
24	°C	°c	NN	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	Escherichia	escherichia	FW	Organism	_	_
27	coli	coli	FW	Organism	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Escherichia	escherichia	FW	Organism	_	_
30	coli	coli	FW	Organism	_	_
31	B	b	NN	_	_	_
32	strain	strain	NN	_	_	_
33	REL606	rel606	NN	_	_	_
34	was	be	VBD	_	_	_
35	revived	revive	VBN	_	_	_
36	from	from	IN	_	_	_
37	a	a	DT	_	_	_
38	freezer	freezer	NN	_	_	_
39	stock	stock	NN	_	_	_
40	via	via	IN	_	_	_
41	overnight	overnight	JJ	_	_	_
42	growth	growth	NN	_	_	_
43	in	in	IN	_	_	_
44	10	10	CD	_	_	_
45	ml	ml	NN	_	_	_
46	Davis	Davis	NNP	_	_	_
47	Minimal	minimal	JJ	_	_	_
48	medium	medium	NN	_	_	_
49	supplemented	supplement	VBN	_	_	_
50	with	with	IN	_	_	_
51	limiting	limit	VBG	_	_	_
52	glucose	glucose	NN	SUPP	_	_
53	at	at	IN	_	_	_
54	0.5	0.5	CD	_	_	_
55	g	g	NN	_	_	_
56	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
57	Exact	exact	JJ	_	_	_
58	details	detail	NNS	_	_	_
59	for	for	IN	_	_	_
60	the	the	DT	_	_	_
61	full	full	JJ	_	_	_
62	computational	computational	JJ	_	_	_
63	pipeline	pipeline	NN	_	_	_
64	are	be	VBP	_	_	_
65	available	available	JJ	_	_	_
66	at	at	IN	_	_	_
67	https	http	NNS	_	_	_
68	:	:	:	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
70	Genome	Genome	NNP	_	_	_
71	_	_	NNP	_	_	_
72	build	build	VB	_	_	_
73	:	:	:	_	_	_
74	NC	NC	NNP	_	_	_
75	_	_	NNP	_	_	_
76	012967.1	012967.1	CD	_	_	_
77	plus	plus	CC	_	_	_
78	small	small	JJ	_	_	_
79	RNAs	rna	NNS	_	_	_
80	as	as	IN	_	_	_
81	annotated	annotated	JJ	_	_	_
82	in	in	IN	_	_	_
83	Rfam	Rfam	NNP	_	_	_
84	11.0	11.0	CD	_	_	_
85	database	database	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	Glucose	glucose	NN	_	_	_
88	time	time	NN	_	_	_
89	course	course	NN	_	_	_
90	,	,	,	_	_	_
91	168	168	CD	_	_	_
92	hour	hour	NN	_	_	_
93	time	time	NN	_	_	_
94	point	point	NN	_	_	_
95	,	,	,	_	_	_
96	biological	biological	JJ	_	_	_
97	replicate	replicate	VBP	_	_	_
98	1	1	CD	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	Glucose	glucose	NN	_	_	_
101	time	time	NN	_	_	_
102	course	course	NN	_	_	_
103	,	,	,	_	_	_
104	168	168	CD	_	_	_
105	hour	hour	NN	_	_	_
106	time	time	NN	_	_	_
107	point	point	NN	_	_	_
108	,	,	,	_	_	_
109	biological	biological	JJ	_	_	_
110	replicate	replicate	VB	_	_	_
111	2	2	CD	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
113	Glucose	glucose	NN	_	_	_
114	time	time	NN	_	_	_
115	course	course	NN	_	_	_
116	,	,	,	_	_	_
117	168	168	CD	_	_	_
118	hour	hour	NN	_	_	_
119	time	time	NN	_	_	_
120	point	point	NN	_	_	_
121	,	,	,	_	_	_
122	biological	biological	JJ	_	_	_
123	replicate	replicate	VBP	_	_	_
124	3	3	CD	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	Glucose	glucose	NN	_	_	_
127	time	time	NN	_	_	_
128	course	course	NN	_	_	_
129	,	,	,	_	_	_
130	168	168	CD	_	_	_
131	hour	hour	NN	_	_	_
132	time	time	NN	_	_	_
133	point	point	NN	_	_	_
134	,	,	,	_	_	_
135	biological	biological	JJ	_	_	_
136	replicate	replicate	VBP	_	_	_
137	3	3	CD	_	_	_
138	,	,	,	_	_	_
139	rRNA	rrna	NN	_	_	_
140	not	not	RB	_	_	_
141	depleted	deplete	VBN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	Glucose	glucose	NN	_	_	_
144	time	time	NN	_	_	_
145	course	course	NN	_	_	_
146	,	,	,	_	_	_
147	24	24	CD	_	_	_
148	hour	hour	NN	_	_	_
149	time	time	NN	_	_	_
150	point	point	NN	_	_	_
151	,	,	,	_	_	_
152	biological	biological	JJ	_	_	_
153	replicate	replicate	VBP	_	_	_
154	1	1	CD	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	Glucose	glucose	NN	_	_	_
157	time	time	NN	_	_	_
158	course	course	NN	_	_	_
159	,	,	,	_	_	_
160	24	24	CD	_	_	_
161	hour	hour	NN	_	_	_
162	time	time	NN	_	_	_
163	point	point	NN	_	_	_
164	,	,	,	_	_	_
165	biological	biological	JJ	_	_	_
166	replicate	replicate	VB	_	_	_
167	2	2	CD	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
169	Glucose	glucose	NN	_	_	_
170	time	time	NN	_	_	_
171	course	course	NN	_	_	_
172	,	,	,	_	_	_
173	24	24	CD	_	_	_
174	hour	hour	NN	_	_	_
175	time	time	NN	_	_	_
176	point	point	NN	_	_	_
177	,	,	,	_	_	_
178	biological	biological	JJ	_	_	_
179	replicate	replicate	VBP	_	_	_
180	3	3	CD	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	Glucose	glucose	NN	_	_	_
183	time	time	NN	_	_	_
184	course	course	NN	_	_	_
185	,	,	,	_	_	_
186	24	24	CD	_	_	_
187	hour	hour	NN	_	_	_
188	time	time	NN	_	_	_
189	point	point	NN	_	_	_
190	,	,	,	_	_	_
191	biological	biological	JJ	_	_	_
192	replicate	replicate	VBP	_	_	_
193	3	3	CD	_	_	_
194	,	,	,	_	_	_
195	rRNA	rrna	NN	_	_	_
196	not	not	RB	_	_	_
197	depleted	deplete	VBN	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	Glucose	glucose	NN	_	_	_
200	time	time	NN	_	_	_
201	course	course	NN	_	_	_
202	,	,	,	_	_	_
203	336	336	CD	_	_	_
204	hour	hour	NN	_	_	_
205	time	time	NN	_	_	_
206	point	point	NN	_	_	_
207	,	,	,	_	_	_
208	biological	biological	JJ	_	_	_
209	replicate	replicate	VBP	_	_	_
210	1	1	CD	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	Glucose	glucose	NN	_	_	_
213	time	time	NN	_	_	_
214	course	course	NN	_	_	_
215	,	,	,	_	_	_
216	336	336	CD	_	_	_
217	hour	hour	NN	_	_	_
218	time	time	NN	_	_	_
219	point	point	NN	_	_	_
220	,	,	,	_	_	_
221	biological	biological	JJ	_	_	_
222	replicate	replicate	VB	_	_	_
223	2	2	CD	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
225	Glucose	glucose	NN	_	_	_
226	time	time	NN	_	_	_
227	course	course	NN	_	_	_
228	,	,	,	_	_	_
229	336	336	CD	_	_	_
230	hour	hour	NN	_	_	_
231	time	time	NN	_	_	_
232	point	point	NN	_	_	_
233	,	,	,	_	_	_
234	biological	biological	JJ	_	_	_
235	replicate	replicate	VBP	_	_	_
236	3	3	CD	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	Glucose	glucose	NN	_	_	_
239	time	time	NN	_	_	_
240	course	course	NN	_	_	_
241	,	,	,	_	_	_
242	336	336	CD	_	_	_
243	hour	hour	NN	_	_	_
244	time	time	NN	_	_	_
245	point	point	NN	_	_	_
246	,	,	,	_	_	_
247	biological	biological	JJ	_	_	_
248	replicate	replicate	VBP	_	_	_
249	3	3	CD	_	_	_
250	,	,	,	_	_	_
251	rRNA	rrna	NN	_	_	_
252	not	not	RB	_	_	_
253	depleted	deplete	VBN	_	_	_
254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
255	Glucose	glucose	NN	_	_	_
256	time	time	NN	_	_	_
257	course	course	NN	_	_	_
258	,	,	,	_	_	_
259	3	3	CD	_	_	_
260	hour	hour	NN	_	_	_
261	time	time	NN	_	_	_
262	point	point	NN	_	_	_
263	,	,	,	_	_	_
264	biological	biological	JJ	_	_	_
265	replicate	replicate	VBP	_	_	_
266	1	1	CD	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	Glucose	glucose	NN	_	_	_
269	time	time	NN	_	_	_
270	course	course	NN	_	_	_
271	,	,	,	_	_	_
272	3	3	CD	_	_	_
273	hour	hour	NN	_	_	_
274	time	time	NN	_	_	_
275	point	point	NN	_	_	_
276	,	,	,	_	_	_
277	biological	biological	JJ	_	_	_
278	replicate	replicate	VB	_	_	_
279	2	2	CD	_	_	_
280	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
281	Glucose	glucose	NN	_	_	_
282	time	time	NN	_	_	_
283	course	course	NN	_	_	_
284	,	,	,	_	_	_
285	3	3	CD	_	_	_
286	hour	hour	NN	_	_	_
287	time	time	NN	_	_	_
288	point	point	NN	_	_	_
289	,	,	,	_	_	_
290	biological	biological	JJ	_	_	_
291	replicate	replicate	VBP	_	_	_
292	3	3	CD	_	_	_
293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
294	Glucose	glucose	NN	_	_	_
295	time	time	NN	_	_	_
296	course	course	NN	_	_	_
297	,	,	,	_	_	_
298	3	3	CD	_	_	_
299	hour	hour	NN	_	_	_
300	time	time	NN	_	_	_
301	point	point	NN	_	_	_
302	,	,	,	_	_	_
303	biological	biological	JJ	_	_	_
304	replicate	replicate	VBP	_	_	_
305	3	3	CD	_	_	_
306	,	,	,	_	_	_
307	rRNA	rrna	NN	_	_	_
308	not	not	RB	_	_	_
309	depleted	deplete	VBN	_	_	_
310	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
311	Glucose	glucose	NN	_	_	_
312	time	time	NN	_	_	_
313	course	course	NN	_	_	_
314	,	,	,	_	_	_
315	48	48	CD	_	_	_
316	hour	hour	NN	_	_	_
317	time	time	NN	_	_	_
318	point	point	NN	_	_	_
319	,	,	,	_	_	_
320	biological	biological	JJ	_	_	_
321	replicate	replicate	VBP	_	_	_
322	1	1	CD	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	Glucose	glucose	NN	_	_	_
325	time	time	NN	_	_	_
326	course	course	NN	_	_	_
327	,	,	,	_	_	_
328	48	48	CD	_	_	_
329	hour	hour	NN	_	_	_
330	time	time	NN	_	_	_
331	point	point	NN	_	_	_
332	,	,	,	_	_	_
333	biological	biological	JJ	_	_	_
334	replicate	replicate	VB	_	_	_
335	2	2	CD	_	_	_
336	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
337	Glucose	glucose	NN	_	_	_
338	time	time	NN	_	_	_
339	course	course	NN	_	_	_
340	,	,	,	_	_	_
341	48	48	CD	_	_	_
342	hour	hour	NN	_	_	_
343	time	time	NN	_	_	_
344	point	point	NN	_	_	_
345	,	,	,	_	_	_
346	biological	biological	JJ	_	_	_
347	replicate	replicate	VBP	_	_	_
348	3	3	CD	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	Glucose	glucose	NN	_	_	_
351	time	time	NN	_	_	_
352	course	course	NN	_	_	_
353	,	,	,	_	_	_
354	48	48	CD	_	_	_
355	hour	hour	NN	_	_	_
356	time	time	NN	_	_	_
357	point	point	NN	_	_	_
358	,	,	,	_	_	_
359	biological	biological	JJ	_	_	_
360	replicate	replicate	VBP	_	_	_
361	3	3	CD	_	_	_
362	,	,	,	_	_	_
363	rRNA	rrna	NN	_	_	_
364	not	not	RB	_	_	_
365	depleted	deplete	VBN	_	_	_
366	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
367	Glucose	glucose	NN	_	_	_
368	time	time	NN	_	_	_
369	course	course	NN	_	_	_
370	,	,	,	_	_	_
371	4	4	CD	_	_	_
372	hour	hour	NN	_	_	_
373	time	time	NN	_	_	_
374	point	point	NN	_	_	_
375	,	,	,	_	_	_
376	biological	biological	JJ	_	_	_
377	replicate	replicate	VBP	_	_	_
378	1	1	CD	_	_	_
379	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
380	Glucose	glucose	NN	_	_	_
381	time	time	NN	_	_	_
382	course	course	NN	_	_	_
383	,	,	,	_	_	_
384	4	4	CD	_	_	_
385	hour	hour	NN	_	_	_
386	time	time	NN	_	_	_
387	point	point	NN	_	_	_
388	,	,	,	_	_	_
389	biological	biological	JJ	_	_	_
390	replicate	replicate	VB	_	_	_
391	2	2	CD	_	_	_
392	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
393	Glucose	glucose	NN	_	_	_
394	time	time	NN	_	_	_
395	course	course	NN	_	_	_
396	,	,	,	_	_	_
397	4	4	CD	_	_	_
398	hour	hour	NN	_	_	_
399	time	time	NN	_	_	_
400	point	point	NN	_	_	_
401	,	,	,	_	_	_
402	biological	biological	JJ	_	_	_
403	replicate	replicate	VBP	_	_	_
404	3	3	CD	_	_	_
405	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
406	Glucose	glucose	NN	_	_	_
407	time	time	NN	_	_	_
408	course	course	NN	_	_	_
409	,	,	,	_	_	_
410	4	4	CD	_	_	_
411	hour	hour	NN	_	_	_
412	time	time	NN	_	_	_
413	point	point	NN	_	_	_
414	,	,	,	_	_	_
415	biological	biological	JJ	_	_	_
416	replicate	replicate	VBP	_	_	_
417	3	3	CD	_	_	_
418	,	,	,	_	_	_
419	rRNA	rrna	NN	_	_	_
420	not	not	RB	_	_	_
421	depleted	deplete	VBN	_	_	_
422	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
423	Glucose	glucose	NN	_	_	_
424	time	time	NN	_	_	_
425	course	course	NN	_	_	_
426	,	,	,	_	_	_
427	5	5	CD	_	_	_
428	hour	hour	NN	_	_	_
429	time	time	NN	_	_	_
430	point	point	NN	_	_	_
431	,	,	,	_	_	_
432	biological	biological	JJ	_	_	_
433	replicate	replicate	VBP	_	_	_
434	1	1	CD	_	_	_
435	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
436	Glucose	glucose	NN	_	_	_
437	time	time	NN	_	_	_
438	course	course	NN	_	_	_
439	,	,	,	_	_	_
440	5	5	CD	_	_	_
441	hour	hour	NN	_	_	_
442	time	time	NN	_	_	_
443	point	point	NN	_	_	_
444	,	,	,	_	_	_
445	biological	biological	JJ	_	_	_
446	replicate	replicate	VB	_	_	_
447	2	2	CD	_	_	_
448	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
449	Glucose	glucose	NN	_	_	_
450	time	time	NN	_	_	_
451	course	course	NN	_	_	_
452	,	,	,	_	_	_
453	5	5	CD	_	_	_
454	hour	hour	NN	_	_	_
455	time	time	NN	_	_	_
456	point	point	NN	_	_	_
457	,	,	,	_	_	_
458	biological	biological	JJ	_	_	_
459	replicate	replicate	VBP	_	_	_
460	3	3	CD	_	_	_
461	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
462	Glucose	glucose	NN	_	_	_
463	time	time	NN	_	_	_
464	course	course	NN	_	_	_
465	,	,	,	_	_	_
466	5	5	CD	_	_	_
467	hour	hour	NN	_	_	_
468	time	time	NN	_	_	_
469	point	point	NN	_	_	_
470	,	,	,	_	_	_
471	biological	biological	JJ	_	_	_
472	replicate	replicate	VBP	_	_	_
473	3	3	CD	_	_	_
474	,	,	,	_	_	_
475	rRNA	rrna	NN	_	_	_
476	not	not	RB	_	_	_
477	depleted	deplete	VBN	_	_	_
478	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
479	Glucose	glucose	NN	_	_	_
480	time	time	NN	_	_	_
481	course	course	NN	_	_	_
482	,	,	,	_	_	_
483	6	6	CD	_	_	_
484	hour	hour	NN	_	_	_
485	time	time	NN	_	_	_
486	point	point	NN	_	_	_
487	,	,	,	_	_	_
488	biological	biological	JJ	_	_	_
489	replicate	replicate	VBP	_	_	_
490	1	1	CD	_	_	_
491	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
492	Glucose	glucose	NN	_	_	_
493	time	time	NN	_	_	_
494	course	course	NN	_	_	_
495	,	,	,	_	_	_
496	6	6	CD	_	_	_
497	hour	hour	NN	_	_	_
498	time	time	NN	_	_	_
499	point	point	NN	_	_	_
500	,	,	,	_	_	_
501	biological	biological	JJ	_	_	_
502	replicate	replicate	VB	_	_	_
503	2	2	CD	_	_	_
504	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
505	Glucose	glucose	NN	_	_	_
506	time	time	NN	_	_	_
507	course	course	NN	_	_	_
508	,	,	,	_	_	_
509	6	6	CD	_	_	_
510	hour	hour	NN	_	_	_
511	time	time	NN	_	_	_
512	point	point	NN	_	_	_
513	,	,	,	_	_	_
514	biological	biological	JJ	_	_	_
515	replicate	replicate	VBP	_	_	_
516	3	3	CD	_	_	_
517	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
518	Glucose	glucose	NN	_	_	_
519	time	time	NN	_	_	_
520	course	course	NN	_	_	_
521	,	,	,	_	_	_
522	6	6	CD	_	_	_
523	hour	hour	NN	_	_	_
524	time	time	NN	_	_	_
525	point	point	NN	_	_	_
526	,	,	,	_	_	_
527	biological	biological	JJ	_	_	_
528	replicate	replicate	VBP	_	_	_
529	3	3	CD	_	_	_
530	,	,	,	_	_	_
531	rRNA	rrna	NN	_	_	_
532	not	not	RB	_	_	_
533	depleted	deplete	VBN	_	_	_
534	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
535	Glucose	glucose	NN	_	_	_
536	time	time	NN	_	_	_
537	course	course	NN	_	_	_
538	,	,	,	_	_	_
539	8	8	CD	_	_	_
540	hour	hour	NN	_	_	_
541	time	time	NN	_	_	_
542	point	point	NN	_	_	_
543	,	,	,	_	_	_
544	biological	biological	JJ	_	_	_
545	replicate	replicate	VBP	_	_	_
546	1	1	CD	_	_	_
547	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
548	Glucose	glucose	NN	_	_	_
549	time	time	NN	_	_	_
550	course	course	NN	_	_	_
551	,	,	,	_	_	_
552	8	8	CD	_	_	_
553	hour	hour	NN	_	_	_
554	time	time	NN	_	_	_
555	point	point	NN	_	_	_
556	,	,	,	_	_	_
557	biological	biological	JJ	_	_	_
558	replicate	replicate	VB	_	_	_
559	2	2	CD	_	_	_
560	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
561	Glucose	glucose	NN	_	_	_
562	time	time	NN	_	_	_
563	course	course	NN	_	_	_
564	,	,	,	_	_	_
565	8	8	CD	_	_	_
566	hourt	hourt	NN	_	_	_
567	ime	ime	NN	_	_	_
568	point	point	NN	_	_	_
569	,	,	,	_	_	_
570	biological	biological	JJ	_	_	_
571	replicate	replicate	VBP	_	_	_
572	3	3	CD	_	_	_
573	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
574	Glucose	glucose	NN	_	_	_
575	time	time	NN	_	_	_
576	course	course	NN	_	_	_
577	,	,	,	_	_	_
578	8	8	CD	_	_	_
579	hourt	hourt	NN	_	_	_
580	ime	ime	NN	_	_	_
581	point	point	NN	_	_	_
582	,	,	,	_	_	_
583	biological	biological	JJ	_	_	_
584	replicate	replicate	VBP	_	_	_
585	3	3	CD	_	_	_
586	,	,	,	_	_	_
587	rRNA	rrna	NN	_	_	_
588	not	not	RB	_	_	_
589	depleted	deplete	VBN	_	_	_
590	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
591	Mapped	map	VBD	_	_	_
592	R1	r1	NN	_	_	_
593	reads	read	VBZ	_	_	_
594	in	in	IN	_	_	_
595	single-end	single-end	JJ	_	_	_
596	mode	mode	NN	_	_	_
597	using	use	VBG	_	_	_
598	Bowtie2	bowtie2	NN	_	_	_
599	2.1.0	2.1.0	CD	_	_	_
600	with	with	IN	_	_	_
601	the	the	DT	_	_	_
602	--	--	:	_	_	_
603	k	k	NN	_	_	_
604	1	1	CD	_	_	_
605	option	option	NN	_	_	_
606	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
607	molecule	molecule	NN	_	_	_
608	subtype	subtype	NN	_	_	_
609	:	:	:	_	_	_
610	rRNA-depleted	rrna-depleted	JJ	_	_	_
611	total	total	JJ	_	_	_
612	RNA	rna	NN	_	_	_
613	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
614	molecule	molecule	NN	_	_	_
615	subtype	subtype	NN	_	_	_
616	:	:	:	_	_	_
617	total	total	JJ	_	_	_
618	RNA	rna	NN	_	_	_
619	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
620	REL606	rel606	NN	_	_	_
621	_	_	CD	_	_	_
622	glucose-limited	glucose-limited	JJ	_	_	_
623	minimal	minimal	JJ	_	_	_
624	medium	medium	NN	_	_	_
625	_	_	NN	_	_	_
626	168	168	CD	_	_	_
627	hr	hr	NN	_	_	_
628	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
629	REL606	rel606	NN	_	_	_
630	_	_	CD	_	_	_
631	glucose-limited	glucose-limited	JJ	_	_	_
632	minimal	minimal	JJ	_	_	_
633	medium	medium	NN	_	_	_
634	_	_	NN	_	_	_
635	168	168	CD	_	_	_
636	hr	hr	NN	_	_	_
637	_	_	NN	_	_	_
638	rRNA	rrna	NN	_	_	_
639	not	not	RB	_	_	_
640	depleted	deplete	VBN	_	_	_
641	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
642	REL606	rel606	NN	_	_	_
643	_	_	CD	_	_	_
644	glucose-limited	glucose-limited	JJ	_	_	_
645	minimal	minimal	JJ	_	_	_
646	medium	medium	NN	_	_	_
647	_	_	NN	_	_	_
648	24	24	CD	_	_	_
649	hr	hr	NN	_	_	_
650	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
651	REL606	rel606	NN	_	_	_
652	_	_	CD	_	_	_
653	glucose-limited	glucose-limited	JJ	_	_	_
654	minimal	minimal	JJ	_	_	_
655	medium	medium	NN	_	_	_
656	_	_	NN	_	_	_
657	24	24	CD	_	_	_
658	hr	hr	NN	_	_	_
659	_	_	NN	_	_	_
660	rRNA	rrna	NN	_	_	_
661	not	not	RB	_	_	_
662	depleted	deplete	VBN	_	_	_
663	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
664	REL606	rel606	NN	_	_	_
665	_	_	CD	_	_	_
666	glucose-limited	glucose-limited	JJ	_	_	_
667	minimal	minimal	JJ	_	_	_
668	medium	medium	NN	_	_	_
669	_	_	NN	_	_	_
670	336	336	CD	_	_	_
671	hr	hr	NN	_	_	_
672	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
673	REL606	rel606	NN	_	_	_
674	_	_	CD	_	_	_
675	glucose-limited	glucose-limited	JJ	_	_	_
676	minimal	minimal	JJ	_	_	_
677	medium	medium	NN	_	_	_
678	_	_	NN	_	_	_
679	336	336	CD	_	_	_
680	hr	hr	NN	_	_	_
681	_	_	NN	_	_	_
682	rRNA	rrna	NN	_	_	_
683	not	not	RB	_	_	_
684	depleted	deplete	VBN	_	_	_
685	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
686	REL606	rel606	NN	_	_	_
687	_	_	CD	_	_	_
688	glucose-limited	glucose-limited	JJ	_	_	_
689	minimal	minimal	JJ	_	_	_
690	medium	medium	NN	_	_	_
691	_	_	NN	_	_	_
692	3	3	CD	_	_	_
693	hr	hr	NN	_	_	_
694	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
695	REL606	rel606	NN	_	_	_
696	_	_	CD	_	_	_
697	glucose-limited	glucose-limited	JJ	_	_	_
698	minimal	minimal	JJ	_	_	_
699	medium	medium	NN	_	_	_
700	_	_	NN	_	_	_
701	3	3	CD	_	_	_
702	hr	hr	NN	_	_	_
703	_	_	NN	_	_	_
704	rRNA	rrna	NN	_	_	_
705	not	not	RB	_	_	_
706	depleted	deplete	VBN	_	_	_
707	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
708	REL606	rel606	NN	_	_	_
709	_	_	CD	_	_	_
710	glucose-limited	glucose-limited	JJ	_	_	_
711	minimal	minimal	JJ	_	_	_
712	medium	medium	NN	_	_	_
713	_	_	NN	_	_	_
714	48	48	CD	_	_	_
715	hr	hr	NN	_	_	_
716	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
717	REL606	rel606	NN	_	_	_
718	_	_	CD	_	_	_
719	glucose-limited	glucose-limited	JJ	_	_	_
720	minimal	minimal	JJ	_	_	_
721	medium	medium	NN	_	_	_
722	_	_	NN	_	_	_
723	48	48	CD	_	_	_
724	hr	hr	NN	_	_	_
725	_	_	NN	_	_	_
726	rRNA	rrna	NN	_	_	_
727	not	not	RB	_	_	_
728	depleted	deplete	VBN	_	_	_
729	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
730	REL606	rel606	NN	_	_	_
731	_	_	CD	_	_	_
732	glucose-limited	glucose-limited	JJ	_	_	_
733	minimal	minimal	JJ	_	_	_
734	medium	medium	NN	_	_	_
735	_	_	NN	_	_	_
736	4	4	CD	_	_	_
737	hr	hr	NN	_	_	_
738	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
739	REL606	rel606	NN	_	_	_
740	_	_	CD	_	_	_
741	glucose-limited	glucose-limited	JJ	_	_	_
742	minimal	minimal	JJ	_	_	_
743	medium	medium	NN	_	_	_
744	_	_	NN	_	_	_
745	4	4	CD	_	_	_
746	hr	hr	NN	_	_	_
747	_	_	NN	_	_	_
748	rRNA	rrna	NN	_	_	_
749	not	not	RB	_	_	_
750	depleted	deplete	VBN	_	_	_
751	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
752	REL606	rel606	NN	_	_	_
753	_	_	CD	_	_	_
754	glucose-limited	glucose-limited	JJ	_	_	_
755	minimal	minimal	JJ	_	_	_
756	medium	medium	NN	_	_	_
757	_	_	SYM	_	_	_
758	5	5	CD	_	_	_
759	hr	hr	NN	_	_	_
760	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
761	REL606	rel606	NN	_	_	_
762	_	_	CD	_	_	_
763	glucose-limited	glucose-limited	JJ	_	_	_
764	minimal	minimal	JJ	_	_	_
765	medium	medium	NN	_	_	_
766	_	_	SYM	_	_	_
767	5	5	CD	_	_	_
768	hr	hr	NN	_	_	_
769	_	_	NN	_	_	_
770	rRNA	rrna	NN	_	_	_
771	not	not	RB	_	_	_
772	depleted	deplete	VBN	_	_	_
773	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
774	REL606	rel606	NN	_	_	_
775	_	_	CD	_	_	_
776	glucose-limited	glucose-limited	JJ	_	_	_
777	minimal	minimal	JJ	_	_	_
778	medium	medium	NN	_	_	_
779	_	_	NN	_	_	_
780	6	6	CD	_	_	_
781	hr	hr	NN	_	_	_
782	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
783	REL606	rel606	NN	_	_	_
784	_	_	CD	_	_	_
785	glucose-limited	glucose-limited	JJ	_	_	_
786	minimal	minimal	JJ	_	_	_
787	medium	medium	NN	_	_	_
788	_	_	NN	_	_	_
789	6	6	CD	_	_	_
790	hr	hr	NN	_	_	_
791	_	_	NN	_	_	_
792	rRNA	rrna	NN	_	_	_
793	not	not	RB	_	_	_
794	depleted	deplete	VBN	_	_	_
795	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
796	REL606	rel606	NN	_	_	_
797	_	_	CD	_	_	_
798	glucose-limited	glucose-limited	JJ	_	_	_
799	minimal	minimal	JJ	_	_	_
800	medium	medium	NN	_	_	_
801	_	_	NN	_	_	_
802	8	8	CD	_	_	_
803	hr	hr	NN	_	_	_
804	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
805	REL606	rel606	NN	_	_	_
806	_	_	CD	_	_	_
807	glucose-limited	glucose-limited	JJ	_	_	_
808	minimal	minimal	JJ	_	_	_
809	medium	medium	NN	_	_	_
810	_	_	NN	_	_	_
811	8	8	CD	_	_	_
812	hr	hr	NN	_	_	_
813	_	_	NN	_	_	_
814	rRNA	rrna	NN	_	_	_
815	not	not	RB	_	_	_
816	depleted	deplete	VBN	_	_	_
817	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
818	RNA-Seq	rna-seq	NN	_	_	_
819	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
820	RNAsnap	rnasnap	NN	_	_	_
821	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
822	RNAsnap	rnasnap	NN	_	_	_
823	followed	follow	VBN	_	_	_
824	by	by	IN	_	_	_
825	RiboZero	RiboZero	NNP	_	_	_
826	rRNA	rrna	NN	_	_	_
827	removal	removal	NN	_	_	_
828	kit	kit	NN	_	_	_
829	for	for	IN	_	_	_
830	gram-negative	gram-negative	JJ	_	_	_
831	bacteria	bacterium	NNS	_	_	_
832	-LRB-	-lrb-	-LRB-	_	_	_
833	Epicentre	Epicentre	NNP	_	_	_
834	-RRB-	-rrb-	-RRB-	_	_	_
835	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
836	RNA	rna	NN	_	_	_
837	was	be	VBD	_	_	_
838	fragmented	fragmented	JJ	_	_	_
839	using	use	VBG	_	_	_
840	the	the	DT	_	_	_
841	NEBNext	nebnext	NN	_	_	_
842	Magnesium	magnesium	NN	_	_	_
843	RNA	rna	NN	_	_	_
844	Fragmentation	fragmentation	NN	_	_	_
845	Module	module	NN	_	_	_
846	-LRB-	-lrb-	-LRB-	_	_	_
847	New	New	NNP	_	_	_
848	England	England	NNP	_	_	_
849	Biolabs	Biolabs	NNP	_	_	_
850	-RRB-	-rrb-	-RRB-	_	_	_
851	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	,	,	,	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	phosphorylated	phosphorylate	VBN	_	_	_
6	using	use	VBG	_	_	_
7	T4	t4	NN	_	_	_
8	polynucleotide	polynucleotide	NN	_	_	_
9	kinase	kinase	NN	_	_	_
10	and	and	CC	_	_	_
11	prepared	prepare	VBN	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	NEBNext	nebnext	NN	_	_	_
15	Small	small	JJ	_	_	_
16	RNA	rna	NN	_	_	_
17	Library	Library	NNP	_	_	_
18	Prep	Prep	NNP	_	_	_
19	Set	set	VB	_	_	_
20	for	for	IN	_	_	_
21	Illumina	Illumina	NNP	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Multiplex	Multiplex	NNP	_	_	_
24	Compatible	Compatible	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	fragments	fragment	NNS	_	_	_
3	greater	greater	JJR	_	_	_
4	than	than	IN	_	_	_
5	100	100	CD	_	_	_
6	bp	bp	NN	_	_	_
7	were	be	VBD	_	_	_
8	excised	excise	VBN	_	_	_
9	from	from	IN	_	_	_
10	a	a	DT	_	_	_
11	4	4	CD	_	_	_
12	%	%	NN	_	_	_
13	agarose	agarose	NN	_	_	_
14	gel	gel	NN	_	_	_
15	after	after	IN	_	_	_
16	library	library	NN	_	_	_
17	preparation	preparation	NN	_	_	_
18	and	and	CC	_	_	_
19	recovered	recover	VBD	_	_	_
20	using	use	VBG	_	_	_
21	the	the	DT	_	_	_
22	Zymoclean	Zymoclean	NNP	_	_	_
23	Gel	gel	NN	_	_	_
24	DNA	dna	NN	_	_	_
25	Recovery	recovery	NN	_	_	_
26	Kit	kit	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Zymo	Zymo	NNP	_	_	_
29	Research	Research	NNP	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	REL606	rel606	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Supplementary	supplementary	JJ	_	_	_
7	_	_	NN	_	_	_
8	files	file	NNS	_	_	_
9	_	_	IN	_	_	_
10	format	format	NN	_	_	_
11	_	_	NN	_	_	_
12	and	and	CC	_	_	_
13	_	_	NN	_	_	_
14	content	content	NN	_	_	_
15	:	:	:	_	_	_
16	Read	Read	NNP	_	_	_
17	counts	count	VBZ	_	_	_
18	aligned	align	VBN	_	_	_
19	to	to	TO	_	_	_
20	genes	gene	NNS	_	_	_
21	and	and	CC	_	_	_
22	noncoding	noncoding	JJ	_	_	_
23	Rfam	rfam	NN	_	_	_
24	features	feature	NNS	_	_	_
25	in	in	IN	_	_	_
26	CSV	CSV	NNP	_	_	_
27	format	format	NN	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	The	the	DT	_	_	_
30	number	number	NN	_	_	_
31	of	of	IN	_	_	_
32	R1	r1	NN	_	_	_
33	reads	read	VBZ	_	_	_
34	mapping	map	VBG	_	_	_
35	to	to	TO	_	_	_
36	each	each	DT	_	_	_
37	gene	gene	NN	_	_	_
38	were	be	VBD	_	_	_
39	counted	count	VBN	_	_	_
40	using	use	VBG	_	_	_
41	HTSeq	htseq	NN	_	_	_
42	0.6.0	0.6.0	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
44	time	time	NN	_	_	_
45	point	point	NN	_	_	_
46	:	:	:	_	_	_
47	168	168	CD	_	_	_
48	hours	hour	NNS	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
50	time	time	NN	_	_	_
51	point	point	NN	_	_	_
52	:	:	:	_	_	_
53	24	24	CD	_	_	_
54	hours	hour	NNS	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
56	time	time	NN	_	_	_
57	point	point	NN	_	_	_
58	:	:	:	_	_	_
59	336	336	CD	_	_	_
60	hours	hour	NNS	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
62	time	time	NN	_	_	_
63	point	point	NN	_	_	_
64	:	:	:	_	_	_
65	3	3	CD	_	_	_
66	hours	hour	NNS	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
68	time	time	NN	_	_	_
69	point	point	NN	_	_	_
70	:	:	:	_	_	_
71	48	48	CD	_	_	_
72	hours	hour	NNS	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
74	time	time	NN	_	_	_
75	point	point	NN	_	_	_
76	:	:	:	_	_	_
77	4	4	CD	_	_	_
78	hours	hour	NNS	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
80	time	time	NN	_	_	_
81	point	point	NN	_	_	_
82	:	:	:	_	_	_
83	5	5	CD	_	_	_
84	hours	hour	NNS	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
86	time	time	NN	_	_	_
87	point	point	NN	_	_	_
88	:	:	:	_	_	_
89	6	6	CD	_	_	_
90	hours	hour	NNS	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
92	time	time	NN	_	_	_
93	point	point	NN	_	_	_
94	:	:	:	_	_	_
95	8	8	CD	_	_	_
96	hours	hour	NNS	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	Trimmed	trim	VBD	_	_	_
99	adaptor	adaptor	NN	_	_	_
100	sequences	sequence	NNS	_	_	_
101	from	from	IN	_	_	_
102	reads	read	VBZ	_	_	_
103	using	use	VBG	_	_	_
104	Flexbar	Flexbar	NNP	_	_	_
105	2.31	2.31	CD	_	_	_
106	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
107	After	after	IN	_	_	_
108	normalization	normalization	NN	_	_	_
109	,	,	,	_	_	_
110	the	the	DT	_	_	_
111	expression	expression	NN	_	_	_
112	of	of	IN	_	_	_
113	a	a	DT	_	_	_
114	gene	gene	NN	_	_	_
115	was	be	VBD	_	_	_
116	calculated	calculate	VBN	_	_	_
117	by	by	IN	_	_	_
118	a	a	DT	_	_	_
119	RMA-summarization	rma-summarization	NN	_	_	_
120	procedure	procedure	NN	_	_	_
121	within	within	IN	_	_	_
122	each	each	DT	_	_	_
123	growth	growth	NN	_	_	_
124	condition	condition	NN	_	_	_
125	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	agno3	agno3	NN	_	_	_
3	concentration	concentration	NN	_	_	_
4	in	in	IN	_	_	_
5	µm	µm	NN	_	_	_
6	:	:	:	_	_	_
7	0	0	CD	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	agno3	agno3	NN	_	_	_
10	concentration	concentration	NN	_	_	_
11	in	in	IN	_	_	_
12	µm	µm	NN	_	_	_
13	:	:	:	_	_	_
14	5	5	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	agno3	agno3	NN	_	_	_
17	concentration	concentration	NN	_	_	_
18	in	in	IN	_	_	_
19	µm	µm	NN	_	_	_
20	:	:	:	_	_	_
21	6.5	6.5	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	agno3	agno3	NN	_	_	_
24	concentration	concentration	NN	_	_	_
25	in	in	IN	_	_	_
26	µm	µm	NN	_	_	_
27	:	:	:	_	_	_
28	8.5	8.5	CD	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
30	At	at	IN	_	_	_
31	3	3	CD	_	_	_
32	h	h	NN	_	_	_
33	of	of	IN	_	_	_
34	culture	culture	NN	_	_	_
35	,	,	,	_	_	_
36	60	60	CD	_	_	_
37	mL	ml	NN	_	_	_
38	of	of	IN	_	_	_
39	culture	culture	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	at	at	IN	_	_	_
42	OD595	od595	CD	_	_	_
43	nm	nm	NN	_	_	_
44	=	=	JJ	_	_	_
45	0.73	0.73	CD	_	_	_
46	±	±	SYM	_	_	_
47	0.07	0.07	CD	_	_	_
48	,	,	,	_	_	_
49	0.63	0.63	CD	_	_	_
50	±	±	SYM	_	_	_
51	0.02	0.02	CD	_	_	_
52	,	,	,	_	_	_
53	0.12	0.12	CD	_	_	_
54	±	±	SYM	_	_	_
55	0.01	0.01	CD	_	_	_
56	and	and	CC	_	_	_
57	0.11	0.11	CD	_	_	_
58	±	±	NN	_	_	_
59	0.02	0.02	CD	_	_	_
60	for	for	IN	_	_	_
61	cultures	culture	NNS	_	_	_
62	subjected	subject	VBN	_	_	_
63	to	to	TO	_	_	_
64	0	0	CD	_	_	_
65	,	,	,	_	_	_
66	5.0	5.0	CD	_	_	_
67	,	,	,	_	_	_
68	6.5	6.5	CD	_	_	_
69	and	and	CC	_	_	_
70	8.5	8.5	CD	_	_	_
71	µM	µm	NN	_	_	_
72	AgNO3	agno3	NN	_	_	_
73	,	,	,	_	_	_
74	respectively	respectively	RB	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	were	be	VBD	_	_	_
77	sampled	sample	VBN	_	_	_
78	and	and	CC	_	_	_
79	centrifuged	centrifuge	VBN	_	_	_
80	-LRB-	-lrb-	-LRB-	_	_	_
81	4000	4000	CD	_	_	_
82	rpm	rpm	NN	_	_	_
83	,	,	,	_	_	_
84	5	5	CD	_	_	_
85	min	min	NN	_	_	_
86	,	,	,	_	_	_
87	4	4	CD	_	_	_
88	°C	°c	NN	_	_	_
89	-RRB-	-rrb-	-RRB-	_	_	_
90	,	,	,	_	_	_
91	then	then	RB	_	_	_
92	the	the	DT	_	_	_
93	pellet	pellet	NN	_	_	_
94	was	be	VBD	_	_	_
95	frozen	freeze	VBN	_	_	_
96	in	in	IN	_	_	_
97	liquid	liquid	JJ	_	_	_
98	nitrogen	nitrogen	NN	_	_	_
99	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	was	be	VBD	_	_	_
4	resuspended	resuspend	VBN	_	_	_
5	with	with	IN	_	_	_
6	1	1	CD	_	_	_
7	mL	ml	NN	_	_	_
8	of	of	IN	_	_	_
9	TE	TE	NNP	_	_	_
10	buffer	buffer	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Tris-HCl	tris-hcl	NN	_	_	_
13	10	10	CD	_	_	_
14	mM	mm	NN	KWSUPP	_	_
15	,	,	,	_	_	_
16	pH	ph	NN	_	_	_
17	8	8	CD	_	_	_
18	,	,	,	_	_	_
19	EDTA	edta	NN	_	_	_
20	1	1	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	,	,	,	_	_	_
23	1	1	CD	_	_	_
24	mg	mg	NN	_	_	_
25	lysozyme	lysozyme	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	and	and	CC	_	_	_
28	incubated	incubate	VBN	_	_	_
29	5	5	CD	_	_	_
30	min	min	NN	_	_	_
31	at	at	IN	_	_	_
32	room	room	NN	_	_	_
33	temperature	temperature	NN	_	_	_
34	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	RNeasy	rneasy	NN	_	_	_
8	midi	midi	JJ	_	_	_
9	kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Qiagen	qiagen	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	,	,	,	_	_	_
14	including	include	VBG	_	_	_
15	the	the	DT	_	_	_
16	DNase	dnase	NN	_	_	_
17	I	i	CD	_	_	_
18	treatment	treatment	NN	_	_	_
19	described	describe	VBN	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	manufacturer	manufacturer	NN	_	_	_
23	's	's	POS	_	_	_
24	instructions	instruction	NNS	_	_	_
25	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	quantity	quantity	NN	_	_	_
4	and	and	CC	_	_	_
5	integrity	integrity	NN	_	_	_
6	were	be	VBD	_	_	_
7	checked	check	VBN	_	_	_
8	by	by	IN	_	_	_
9	Nanodrop	Nanodrop	NNP	_	_	_
10	®	®	NNP	_	_	_
11	and	and	CC	_	_	_
12	Agilent	Agilent	NNP	_	_	_
13	BioAnalyzer	BioAnalyzer	NNP	_	_	_
14	,	,	,	_	_	_
15	respectively	respectively	RB	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Ecoli	Ecoli	NNP	_	_	_
3	_	_	SYM	_	_	_
4	Ag0	ag0	NN	_	_	_
5	.0	.0	CD	_	_	_
6	_	_	NN	_	_	_
7	rep1	rep1	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Ecoli	ecolus	NNS	_	_	_
10	_	_	VBP	_	_	_
11	Ag0	ag0	NN	_	_	_
12	.0	.0	CD	_	_	_
13	_	_	NN	_	_	_
14	rep2	rep2	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Ecoli	ecolus	NNS	_	_	_
17	_	_	VBP	_	_	_
18	Ag0	ag0	NN	_	_	_
19	.0	.0	CD	_	_	_
20	_	_	NN	_	_	_
21	rep3	rep3	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Ecoli	ecolus	NNS	_	_	_
24	_	_	VBP	_	_	_
25	Ag5	ag5	NN	_	_	_
26	.0	.0	CD	_	_	_
27	_	_	NN	_	_	_
28	rep1	rep1	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Ecoli	ecolus	NNS	_	_	_
31	_	_	VBP	_	_	_
32	Ag5	ag5	NN	_	_	_
33	.0	.0	CD	_	_	_
34	_	_	NN	_	_	_
35	rep2	rep2	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Ecoli	ecolus	NNS	_	_	_
38	_	_	VBP	_	_	_
39	Ag5	ag5	NN	_	_	_
40	.0	.0	CD	_	_	_
41	_	_	NN	_	_	_
42	rep3	rep3	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Ecoli	ecolus	NNS	_	_	_
45	_	_	VBP	_	_	_
46	Ag6	ag6	NN	_	_	_
47	.5	.5	CD	_	_	_
48	_	_	NN	_	_	_
49	rep1	rep1	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	Ecoli	ecolus	NNS	_	_	_
52	_	_	VBP	_	_	_
53	Ag6	ag6	NN	_	_	_
54	.5	.5	CD	_	_	_
55	_	_	NN	_	_	_
56	rep2	rep2	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Ecoli	ecolus	NNS	_	_	_
59	_	_	VBP	_	_	_
60	Ag6	ag6	NN	_	_	_
61	.5	.5	CD	_	_	_
62	_	_	NN	_	_	_
63	rep3	rep3	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	Ecoli	ecolus	NNS	_	_	_
66	_	_	VBP	_	_	_
67	Ag8	ag8	NN	_	_	_
68	.5	.5	CD	_	_	_
69	_	_	NN	_	_	_
70	rep1	rep1	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	Ecoli	ecolus	NNS	_	_	_
73	_	_	VBP	_	_	_
74	Ag8	ag8	NN	_	_	_
75	.5	.5	CD	_	_	_
76	_	_	NN	_	_	_
77	rep2	rep2	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	Ecoli	ecolus	NNS	_	_	_
80	_	_	VBP	_	_	_
81	Ag8	ag8	NN	_	_	_
82	.5	.5	CD	_	_	_
83	_	_	NN	_	_	_
84	rep3	rep3	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	Escherichia	escherichia	FW	Organism	_	_
87	coli	coli	FW	Organism	_	_
88	,	,	,	_	_	_
89	0	0	CD	_	_	_
90	µM	µm	NN	_	_	_
91	AgNO3	agno3	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	Escherichia	escherichia	FW	Organism	_	_
94	coli	coli	FW	Organism	_	_
95	,	,	,	_	_	_
96	0	0	CD	_	_	_
97	µM	µm	NN	_	_	_
98	AgNO3	agno3	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	Escherichia	escherichia	FW	Organism	_	_
101	coli	coli	FW	Organism	_	_
102	,	,	,	_	_	_
103	5	5	CD	_	_	_
104	µM	µm	NN	_	_	_
105	AgNO3	agno3	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	Escherichia	escherichia	FW	Organism	_	_
108	coli	coli	FW	Organism	_	_
109	,	,	,	_	_	_
110	6.5	6.5	CD	_	_	_
111	µM	µm	NN	_	_	_
112	AgNO3	agno3	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	Escherichia	escherichia	FW	Organism	_	_
115	coli	coli	FW	Organism	_	_
116	,	,	,	_	_	_
117	8.5	8.5	CD	_	_	_
118	µM	µm	NN	_	_	_
119	AgNO3	agno3	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	Escherichia	escherichia	FW	Organism	_	_
122	coli	coli	FW	Organism	_	_
123	str	str	FW	_	_	_
124	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Ionic	ionic	JJ	_	_	_
4	silver	silver	NN	_	_	_
5	stock	stock	NN	_	_	_
6	solutions	solution	NNS	_	_	_
7	were	be	VBD	_	_	_
8	prepared	prepare	VBN	_	_	_
9	from	from	IN	_	_	_
10	AgNO3	agno3	NN	_	_	_
11	powder	powder	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Fisher	Fisher	NNP	_	_	_
14	Scientific	Scientific	NNP	_	_	_
15	Bioblock	Bioblock	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	as	as	IN	_	_	_
18	previously	previously	RB	_	_	_
19	described	describe	VBN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Saulou	Saulou	NNP	_	_	_
22	,	,	,	_	_	_
23	Jamme	Jamme	NNP	_	_	_
24	et	et	FW	_	_	_
25	al.	al.	FW	_	_	_
26	,	,	,	_	_	_
27	2013	2013	CD	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	and	and	CC	_	_	_
30	stored	store	VBN	_	_	_
31	in	in	IN	_	_	_
32	darkness	darkness	NN	_	_	_
33	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	final	final	JJ	_	_	_
3	tested	test	VBN	_	_	_
4	concentrations	concentration	NNS	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	5.0	5.0	CD	_	_	_
7	,	,	,	_	_	_
8	6.5	6.5	CD	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	8.5	8.5	CD	_	_	_
12	µM	µm	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	were	be	VBD	_	_	_
15	obtained	obtain	VBN	_	_	_
16	by	by	IN	_	_	_
17	diluting	dilute	VBG	_	_	_
18	the	the	DT	_	_	_
19	corresponding	corresponding	JJ	_	_	_
20	AgNO3	agno3	NN	_	_	_
21	stock	stock	NN	_	_	_
22	solution	solution	NN	_	_	_
23	directly	directly	RB	_	_	_
24	into	into	IN	_	_	_
25	the	the	DT	_	_	_
26	M9	m9	NN	_	_	_
27	growth	growth	NN	_	_	_
28	medium	medium	NN	_	_	_
29	.	.	.	_	_	_

1	Control	Control	NNP	_	_	_
2	experiment	experiment	NN	_	_	_
3	was	be	VBD	_	_	_
4	simultaneously	simultaneously	RB	_	_	_
5	performed	perform	VBN	_	_	_
6	by	by	IN	_	_	_
7	adding	add	VBG	_	_	_
8	deionised	deionised	JJ	_	_	_
9	water	water	NN	_	_	_
10	into	into	IN	_	_	_
11	the	the	DT	_	_	_
12	M9	m9	NN	_	_	_
13	broth	broth	NN	_	_	_
14	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	both	both	DT	_	_	_
3	cases	case	NNS	_	_	_
4	,	,	,	_	_	_
5	a	a	DT	_	_	_
6	stabilization	stabilization	NN	_	_	_
7	period	period	NN	_	_	_
8	of	of	IN	_	_	_
9	24	24	CD	_	_	_
10	h	h	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	at	at	IN	_	_	_
13	37	37	CD	_	_	_
14	°C	°c	NN	_	_	_
15	and	and	CC	_	_	_
16	120	120	CD	_	_	_
17	rpm	rpm	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	was	be	VBD	_	_	_
20	carried	carry	VBN	_	_	_
21	out	out	RP	_	_	_
22	before	before	IN	_	_	_
23	cell	cell	NN	_	_	_
24	inoculation	inoculation	NN	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	probe	probe	NN	_	_	_
4	intensities	intensity	NNS	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	.	.	.	_	_	_

1	pair	pair	NN	_	_	_
2	files	file	NNS	_	_	_
3	three	three	CD	_	_	_
4	replicates	replicate	VBZ	_	_	_
5	for	for	IN	_	_	_
6	each	each	DT	_	_	_
7	growth	growth	NN	_	_	_
8	condition	condition	NN	_	_	_
9	with	with	IN	_	_	_
10	respectively	respectively	RB	_	_	_
11	0	0	CD	_	_	_
12	,	,	,	_	_	_
13	5.0	5.0	CD	_	_	_
14	,	,	,	_	_	_
15	6.5	6.5	CD	_	_	_
16	and	and	CC	_	_	_
17	8.5	8.5	CD	_	_	_
18	µM	µm	NN	_	_	_
19	of	of	IN	_	_	_
20	AgNO3	agno3	NN	_	_	_
21	in	in	IN	_	_	_
22	the	the	DT	_	_	_
23	medium	medium	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	was	be	VBD	_	_	_
26	processed	process	VBN	_	_	_
27	and	and	CC	_	_	_
28	analyzed	analyze	VBN	_	_	_
29	with	with	IN	_	_	_
30	R	r	NN	_	_	_
31	computing	computing	NN	_	_	_
32	environment	environment	NN	_	_	_
33	using	use	VBG	_	_	_
34	the	the	DT	_	_	_
35	affy	affy	NN	_	_	_
36	and	and	CC	_	_	_
37	limma	limma	NN	_	_	_
38	package	package	NN	_	_	_
39	of	of	IN	_	_	_
40	Bioconductor	Bioconductor	NNP	_	_	_
41	.	.	.	_	_	_

1	Raw	raw	NN	_	_	_
2	data	datum	NNS	_	_	_
3	were	be	VBD	_	_	_
4	submitted	submit	VBN	_	_	_
5	to	to	TO	_	_	_
6	a	a	DT	_	_	_
7	RMA-base	rma-base	NN	_	_	_
8	background	background	NN	_	_	_
9	correction	correction	NN	_	_	_
10	-LSB-	-lsb-	-LRB-	_	_	_
11	Irizarry	Irizarry	NNP	_	_	_
12	et	et	FW	_	_	_
13	al	al	FW	_	_	_
14	,	,	,	_	_	_
15	2003	2003	CD	_	_	_
16	,	,	,	_	_	_
17	Biostatistics	biostatistic	NNS	_	_	_
18	4	4	CD	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	2	2	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	:	:	:	_	_	_
23	249-264	249-264	CD	_	_	_
24	-RSB-	-rsb-	-RRB-	_	_	_
25	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	background	background	NN	_	_	_
3	correction	correction	NN	_	_	_
4	,	,	,	_	_	_
5	intra-replicate	intra-replicate	JJ	_	_	_
6	quantil	quantil	NN	_	_	_
7	normalization	normalization	NN	_	_	_
8	was	be	VBD	_	_	_
9	performed	perform	VBN	_	_	_
10	for	for	IN	_	_	_
11	each	each	DT	_	_	_
12	growth	growth	NN	_	_	_
13	condition	condition	NN	_	_	_
14	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	set	set	NN	_	_	_
3	of	of	IN	_	_	_
4	probes	probe	NNS	_	_	_
5	in	in	IN	_	_	_
6	the	the	DT	_	_	_
7	background	background	NN	_	_	_
8	for	for	IN	_	_	_
9	which	which	WDT	_	_	_
10	the	the	DT	_	_	_
11	ranks	rank	NNS	_	_	_
12	were	be	VBD	_	_	_
13	roughly	roughly	RB	_	_	_
14	invariant	invariant	JJ	_	_	_
15	across	across	IN	_	_	_
16	all	all	PDT	_	_	_
17	the	the	DT	_	_	_
18	twelve	twelve	CD	_	_	_
19	arrays	array	NNS	_	_	_
20	was	be	VBD	_	_	_
21	selected	select	VBN	_	_	_
22	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	median	median	JJ	_	_	_
3	value	value	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	invariant	invariant	JJ	_	_	_
7	probeset	probeset	NN	_	_	_
8	intensities	intensity	NNS	_	_	_
9	on	on	IN	_	_	_
10	each	each	DT	_	_	_
11	array	array	NN	_	_	_
12	was	be	VBD	_	_	_
13	used	use	VBN	_	_	_
14	as	as	IN	_	_	_
15	a	a	DT	_	_	_
16	scaling	scaling	NN	_	_	_
17	factor	factor	NN	_	_	_
18	for	for	IN	_	_	_
19	normalization	normalization	NN	_	_	_
20	between	between	IN	_	_	_
21	growth	growth	NN	_	_	_
22	conditions	condition	NNS	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	laboratory	laboratory	NN	_	_	_
4	strain	strain	NN	_	_	_
5	E.	e.	FW	_	_	_
6	coli	coli	FW	_	_	_
7	K12	k12	NN	_	_	_
8	MG1655	mg1655	NN	_	_	_
9	was	be	VBD	_	_	_
10	grown	grow	VBN	_	_	_
11	for	for	IN	_	_	_
12	24	24	CD	_	_	_
13	h	h	NN	_	_	_
14	at	at	IN	_	_	_
15	37	37	CD	_	_	_
16	°C	°c	NN	_	_	_
17	under	under	IN	_	_	_
18	continuous	continuous	JJ	_	_	_
19	shaking	shake	VBG	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	120	120	CD	_	_	_
22	rpm	rpm	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	,	,	,	_	_	_
25	in	in	IN	_	_	_
26	200	200	CD	_	_	_
27	mL	ml	NN	_	_	_
28	M9	m9	NN	_	_	_
29	medium	medium	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Merck	Merck	NNP	_	_	_
32	Prolabo	Prolabo	NNP	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	complemented	complement	VBN	_	_	_
35	with	with	IN	_	_	_
36	2.5	2.5	CD	_	_	_
37	g	g	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	15	15	CD	_	_	_
40	ml	ml	NN	_	_	_
41	of	of	IN	_	_	_
42	culture	culture	NN	_	_	_
43	was	be	VBD	_	_	_
44	mixed	mix	VBN	_	_	_
45	with	with	IN	_	_	_
46	30	30	CD	_	_	_
47	ml	ml	NN	_	_	_
48	of	of	IN	_	_	_
49	RNAprotect	rnaprotect	NN	_	_	_
50	bacterial	bacterial	JJ	_	_	_
51	reagent	reagent	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	QIAGEN	QIAGEN	NNP	_	_	_
54	Ltd	Ltd	NNP	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	An	a	DT	_	_	_
3	RNeasy	rneasy	NN	_	_	_
4	midikit	midikit	NN	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	to	to	TO	_	_	_
8	prepare	prepare	VB	_	_	_
9	total	total	JJ	_	_	_
10	RNA	rna	NN	_	_	_
11	according	accord	VBG	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	manufacturer	manufacturer	NN	_	_	_
15	's	's	POS	_	_	_
16	instructions	instruction	NNS	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	QIAGEN	QIAGEN	NNP	_	_	_
19	Ltd.	Ltd.	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	Any	any	DT	_	_	_
2	contaminating	contaminate	VBG	_	_	_
3	DNA	dna	NN	_	_	_
4	was	be	VBD	_	_	_
5	removed	remove	VBN	_	_	_
6	using	use	VBG	_	_	_
7	a	a	DT	_	_	_
8	DNAase	dnaase	NN	_	_	_
9	column	column	NN	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	QIAGEN	QIAGEN	NNP	_	_	_
13	Ltd	Ltd	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	was	be	VBD	_	_	_
4	analysed	analyse	VBN	_	_	_
5	using	use	VBG	_	_	_
6	GeneSpring	GeneSpring	NNP	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	Escherichia	escherichia	FW	Organism	_	_
9	coli	coli	FW	Organism	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Growth	growth	NN	_	_	_
12	:	:	:	_	_	_
13	Anaerobic	anaerobic	JJ	_	_	_
14	to	to	TO	_	_	_
15	early	early	JJ	_	_	_
16	exponential	exponential	JJ	_	_	_
17	growth	growth	NN	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Media	Media	NNP	_	_	_
20	:	:	:	_	_	_
21	Minimal	minimal	JJ	_	_	_
22	salts	salt	NNS	_	_	_
23	+	+	CC	_	_	_
24	20	20	CD	_	_	_
25	mM	mm	NN	KWSUPP	_	_
26	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Media	Media	NNP	_	_	_
29	:	:	:	_	_	_
30	Minimal	minimal	JJ	_	_	_
31	salts	salt	NNS	_	_	_
32	+	+	CC	_	_	_
33	20	20	CD	_	_	_
34	mM	mm	NN	KWSUPP	_	_
35	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
36	+2.5	+2.5	CD	_	_	_
37	mM	mm	NN	KWSUPP	_	_
38	sodium	sodium	NN	_	_	_
39	nitrite	nitrite	JJ	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	pGIT1	pgit1	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	pGIT1	pgit1	NN	_	_	_
44	.1	.1	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	pGIT1	pgit1	NN	_	_	_
47	.1	.1	NN	_	_	_
48	+	+	CC	_	_	_
49	NO2	no2	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	pGIT1	pgit1	NN	_	_	_
52	.2	.2	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	pGIT1	pgit1	NN	_	_	_
55	.2	.2	NN	_	_	_
56	+	+	CC	_	_	_
57	NO2	no2	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	pGIT1	pgit1	NN	_	_	_
60	.3	.3	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	pGIT1	pgit1	NN	_	_	_
63	.3	.3	NN	_	_	_
64	+	+	CC	_	_	_
65	NO2	no2	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	pGIT1	pgit1	NN	_	_	_
68	.4	.4	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	pGIT1	pgit1	NN	_	_	_
71	.4	.4	NN	_	_	_
72	+	+	CC	_	_	_
73	NO2	no2	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	pGIT1	pgit1	NN	_	_	_
76	+	+	CC	_	_	_
77	NO2	no2	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	pGIT8	pgit8	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	pGIT8	pgit8	NN	_	_	_
82	.1	.1	NN	_	_	_
83	+	+	CC	_	_	_
84	NO2	no2	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	pGIT8	pgit8	NN	_	_	_
87	.2	.2	NN	_	_	_
88	+	+	CC	_	_	_
89	NO2	no2	NN	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	pGIT8	pgit8	NN	_	_	_
92	.3	.3	NN	_	_	_
93	+	+	CC	_	_	_
94	NO2	no2	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	pGIT8	pgit8	NN	_	_	_
97	.4	.4	NN	_	_	_
98	+	+	CC	_	_	_
99	NO2	no2	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	pGIT8	pgit8	NN	_	_	_
102	+	+	CC	_	_	_
103	NO2	no2	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
105	Pool	Pool	NNP	_	_	_
106	of	of	IN	_	_	_
107	eight	eight	CD	_	_	_
108	independent	independent	JJ	_	_	_
109	cultures	culture	NNS	_	_	_
110	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
111	Strain	Strain	NNP	_	_	_
112	:	:	:	_	_	_
113	MG1655	mg1655	NN	_	_	_
114	pGIT1	pgit1	NN	_	_	_
115	-LRB-	-lrb-	-LRB-	_	_	_
116	carries	carry	VBZ	_	_	_
117	the	the	DT	_	_	_
118	ytfE	ytfe	NN	GEN	_	_
119	promoter	promoter	NN	_	_	_
120	in	in	IN	_	_	_
121	multicopy	multicopy	JJ	_	_	_
122	,	,	,	_	_	_
123	titrates	titrate	VBZ	_	_	_
124	out	out	RP	_	_	_
125	NsrR	nsrr	NN	TF	_	_
126	to	to	TO	_	_	_
127	phenocopy	phenocopy	VB	_	_	_
128	an	a	DT	_	_	_
129	NsrR	nsrr	NN	TF	_	_
130	-	-	:	_	_	_
131	mutation	mutation	NN	_	_	_
132	-RRB-	-rrb-	-RRB-	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	Strain	strain	NN	_	_	_
135	:	:	:	_	_	_
136	MG1655	mg1655	NN	_	_	_
137	pGIT1	pgit1	NN	_	_	_
138	-LRB-	-lrb-	-LRB-	_	_	_
139	carries	carry	VBZ	_	_	_
140	the	the	DT	_	_	_
141	ytfE	ytfe	NN	GEN	_	_
142	promoter	promoter	NN	_	_	_
143	in	in	IN	_	_	_
144	multicopy	multicopy	JJ	_	_	_
145	,	,	,	_	_	_
146	titrates	titrate	VBZ	_	_	_
147	out	out	RP	_	_	_
148	NsrR	nsrr	NN	TF	_	_
149	to	to	TO	_	_	_
150	phenocopy	phenocopy	VB	_	_	_
151	an	a	DT	_	_	_
152	NsrR	nsrr	NN	TF	_	_
153	-	-	:	_	_	_
154	mutation	mutation	NN	_	_	_
155	-RRB-	-rrb-	-RRB-	_	_	_
156	Growth	growth	NN	_	_	_
157	:	:	:	_	_	_
158	Anaerobic	anaerobic	JJ	_	_	_
159	to	to	TO	_	_	_
160	early	early	JJ	_	_	_
161	exponential	exponential	JJ	_	_	_
162	growth	growth	NN	_	_	_
163	Media	Media	NNP	_	_	_
164	:	:	:	_	_	_
165	Minimal	minimal	JJ	_	_	_
166	salts	salt	NNS	_	_	_
167	+	+	CC	_	_	_
168	20	20	CD	_	_	_
169	mM	mm	NN	KWSUPP	_	_
170	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	Strain	strain	NN	_	_	_
173	:	:	:	_	_	_
174	MG1655	mg1655	NN	_	_	_
175	pGIT1	pgit1	NN	_	_	_
176	-LRB-	-lrb-	-LRB-	_	_	_
177	carries	carry	VBZ	_	_	_
178	the	the	DT	_	_	_
179	ytfE	ytfe	NN	GEN	_	_
180	promoter	promoter	NN	_	_	_
181	in	in	IN	_	_	_
182	multicopy	multicopy	JJ	_	_	_
183	,	,	,	_	_	_
184	titrates	titrate	VBZ	_	_	_
185	out	out	RP	_	_	_
186	NsrR	nsrr	NN	TF	_	_
187	to	to	TO	_	_	_
188	phenocopy	phenocopy	VB	_	_	_
189	an	a	DT	_	_	_
190	NsrR	nsrr	NN	TF	_	_
191	-	-	:	_	_	_
192	mutation	mutation	NN	_	_	_
193	-RRB-	-rrb-	-RRB-	_	_	_
194	Growth	growth	NN	_	_	_
195	:	:	:	_	_	_
196	Anaerobic	anaerobic	JJ	_	_	_
197	to	to	TO	_	_	_
198	early	early	JJ	_	_	_
199	exponential	exponential	JJ	_	_	_
200	growth	growth	NN	_	_	_
201	Media	Media	NNP	_	_	_
202	:	:	:	_	_	_
203	Minimal	minimal	JJ	_	_	_
204	salts	salt	NNS	_	_	_
205	+	+	CC	_	_	_
206	20	20	CD	_	_	_
207	mM	mm	NN	KWSUPP	_	_
208	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	Strain	strain	NN	_	_	_
211	:	:	:	_	_	_
212	MG1655	mg1655	NN	_	_	_
213	pGIT1	pgit1	NN	_	_	_
214	-LRB-	-lrb-	-LRB-	_	_	_
215	carries	carry	VBZ	_	_	_
216	the	the	DT	_	_	_
217	ytfE	ytfe	NN	GEN	_	_
218	promoter	promoter	NN	_	_	_
219	in	in	IN	_	_	_
220	multicopy	multicopy	JJ	_	_	_
221	,	,	,	_	_	_
222	titrates	titrate	VBZ	_	_	_
223	out	out	RP	_	_	_
224	NsrR	nsrr	NN	TF	_	_
225	to	to	TO	_	_	_
226	phenocopy	phenocopy	VB	_	_	_
227	an	a	DT	_	_	_
228	NsrR	nsrr	NN	TF	_	_
229	-	-	:	_	_	_
230	mutation	mutation	NN	_	_	_
231	-RRB-	-rrb-	-RRB-	_	_	_
232	Growth	growth	NN	_	_	_
233	:	:	:	_	_	_
234	Anaerobic	anaerobic	JJ	_	_	_
235	to	to	TO	_	_	_
236	early	early	JJ	_	_	_
237	exponential	exponential	JJ	_	_	_
238	growth	growth	NN	_	_	_
239	Media	Media	NNP	_	_	_
240	:	:	:	_	_	_
241	Minimal	minimal	JJ	_	_	_
242	salts	salt	NNS	_	_	_
243	+	+	CC	_	_	_
244	20	20	CD	_	_	_
245	mM	mm	NN	KWSUPP	_	_
246	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
247	+2.5	+2.5	CD	_	_	_
248	mM	mm	NN	KWSUPP	_	_
249	sodium	sodium	NN	_	_	_
250	nitrite	nitrite	JJ	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	Strain	strain	NN	_	_	_
253	:	:	:	_	_	_
254	MG1655	mg1655	NN	_	_	_
255	pGIT8	pgit8	NN	_	_	_
256	-LRB-	-lrb-	-LRB-	_	_	_
257	carries	carry	VBZ	_	_	_
258	1	1	CD	_	_	_
259	base	base	NN	_	_	_
260	pair	pair	NN	_	_	_
261	deletion	deletion	NN	_	_	_
262	in	in	IN	_	_	_
263	the	the	DT	_	_	_
264	NsrR-binding	nsrr-binding	JJ	_	_	_
265	site	site	NN	_	_	_
266	of	of	IN	_	_	_
267	the	the	DT	_	_	_
268	ytfE	ytfe	NN	GEN	_	_
269	promoter	promoter	NN	_	_	_
270	-RRB-	-rrb-	-RRB-	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	Strain	strain	NN	_	_	_
273	:	:	:	_	_	_
274	MG1655	mg1655	NN	_	_	_
275	pGIT8	pgit8	NN	_	_	_
276	-LRB-	-lrb-	-LRB-	_	_	_
277	carries	carry	VBZ	_	_	_
278	1	1	CD	_	_	_
279	base	base	NN	_	_	_
280	pair	pair	NN	_	_	_
281	deletion	deletion	NN	_	_	_
282	in	in	IN	_	_	_
283	the	the	DT	_	_	_
284	NsrR-binding	nsrr-binding	JJ	_	_	_
285	site	site	NN	_	_	_
286	of	of	IN	_	_	_
287	the	the	DT	_	_	_
288	ytfE	ytfe	NN	GEN	_	_
289	promoter	promoter	NN	_	_	_
290	-RRB-	-rrb-	-RRB-	_	_	_
291	Growth	growth	NN	_	_	_
292	:	:	:	_	_	_
293	Anaerobic	anaerobic	JJ	_	_	_
294	to	to	TO	_	_	_
295	early	early	JJ	_	_	_
296	exponential	exponential	JJ	_	_	_
297	growth	growth	NN	_	_	_
298	Media	Media	NNP	_	_	_
299	:	:	:	_	_	_
300	Minimal	minimal	JJ	_	_	_
301	salts	salt	NNS	_	_	_
302	+	+	CC	_	_	_
303	20	20	CD	_	_	_
304	mM	mm	NN	KWSUPP	_	_
305	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
306	+	+	CC	_	_	_
307	2.5	2.5	CD	_	_	_
308	mM	mm	NN	KWSUPP	_	_
309	sodium	sodium	NN	_	_	_
310	nitrite	nitrite	JJ	_	_	_
311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
312	Strain	strain	NN	_	_	_
313	:	:	:	_	_	_
314	MG1655	mg1655	NN	_	_	_
315	pGIT8	pgit8	NN	_	_	_
316	-LRB-	-lrb-	-LRB-	_	_	_
317	carries	carry	VBZ	_	_	_
318	1	1	CD	_	_	_
319	base	base	NN	_	_	_
320	pair	pair	NN	_	_	_
321	deletion	deletion	NN	_	_	_
322	in	in	IN	_	_	_
323	the	the	DT	_	_	_
324	NsrR-binding	nsrr-binding	JJ	_	_	_
325	site	site	NN	_	_	_
326	of	of	IN	_	_	_
327	the	the	DT	_	_	_
328	ytfE	ytfe	NN	GEN	_	_
329	promoter	promoter	NN	_	_	_
330	-RRB-	-rrb-	-RRB-	_	_	_
331	Growth	growth	NN	_	_	_
332	:	:	:	_	_	_
333	Anaerobic	anaerobic	JJ	_	_	_
334	to	to	TO	_	_	_
335	early	early	JJ	_	_	_
336	exponential	exponential	JJ	_	_	_
337	growth	growth	NN	_	_	_
338	Media	Media	NNP	_	_	_
339	:	:	:	_	_	_
340	Minimal	minimal	JJ	_	_	_
341	salts	salt	NNS	_	_	_
342	+	+	CC	_	_	_
343	20	20	CD	_	_	_
344	mM	mm	NN	KWSUPP	_	_
345	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
346	+2.5	+2.5	CD	_	_	_
347	mM	mm	NN	KWSUPP	_	_
348	sodium	sodium	NN	_	_	_
349	nitrite	nitrite	JJ	_	_	_
350	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
351	Strain	strain	NN	_	_	_
352	:	:	:	_	_	_
353	MG1655	mg1655	NN	_	_	_
354	pGIT8	pgit8	NN	_	_	_
355	-LRB-	-lrb-	-LRB-	_	_	_
356	carries	carry	VBZ	_	_	_
357	1	1	CD	_	_	_
358	base	base	NN	_	_	_
359	pair	pair	NN	_	_	_
360	deletion	deletion	NN	_	_	_
361	in	in	IN	_	_	_
362	the	the	DT	_	_	_
363	NsrR-binding	nsrr-binding	JJ	_	_	_
364	site	site	NN	_	_	_
365	of	of	IN	_	_	_
366	the	the	DT	_	_	_
367	ytfE	ytfe	NN	GEN	_	_
368	promoter	promoter	NN	_	_	_
369	-RRB-	-rrb-	-RRB-	_	_	_
370	Growth	growth	NN	_	_	_
371	:	:	:	_	_	_
372	Anaerobic	anaerobic	JJ	_	_	_
373	to	to	TO	_	_	_
374	early	early	JJ	_	_	_
375	exponential	exponential	JJ	_	_	_
376	growth	growth	NN	_	_	_
377	Media	Media	NNP	_	_	_
378	:	:	:	_	_	_
379	Minimal	minimal	JJ	_	_	_
380	salts	salt	NNS	_	_	_
381	+	+	CC	_	_	_
382	20	20	CD	_	_	_
383	mM	mm	NN	KWSUPP	_	_
384	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
385	+	+	CC	_	_	_
386	.5	.5	CD	_	_	_
387	mM	mm	NN	KWSUPP	_	_
388	sodium	sodium	NN	_	_	_
389	nitrite	nitrite	JJ	_	_	_
390	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
391	Strain	strain	NN	_	_	_
392	:	:	:	_	_	_
393	MG1655	mg1655	NN	_	_	_
394	pGIT8	pgit8	NN	_	_	_
395	-LRB-	-lrb-	-LRB-	_	_	_
396	carries	carry	VBZ	_	_	_
397	1	1	CD	_	_	_
398	base	base	NN	_	_	_
399	pair	pair	NN	_	_	_
400	deletion	deletion	NN	_	_	_
401	in	in	IN	_	_	_
402	the	the	DT	_	_	_
403	NsrR-binding	nsrr-binding	JJ	_	_	_
404	site	site	NN	_	_	_
405	of	of	IN	_	_	_
406	the	the	DT	_	_	_
407	ytfE	ytfe	NN	GEN	_	_
408	promoter	promoter	NN	_	_	_
409	-RRB-	-rrb-	-RRB-	_	_	_
410	Growth	growth	NN	_	_	_
411	:	:	:	_	_	_
412	Anaerobic	anaerobic	JJ	_	_	_
413	to	to	TO	_	_	_
414	early	early	JJ	_	_	_
415	exponential	exponential	JJ	_	_	_
416	growth	growth	NN	_	_	_
417	Media	Media	NNP	_	_	_
418	:	:	:	_	_	_
419	Minimal	minimal	JJ	_	_	_
420	salts	salt	NNS	_	_	_
421	+	+	CC	_	_	_
422	20	20	CD	_	_	_
423	mM	mm	NN	KWSUPP	_	_
424	trimethylamine-N-oxide	trimethylamine-n-oxide	NN	_	_	_
425	Pool	Pool	NNP	_	_	_
426	of	of	IN	_	_	_
427	eight	eight	CD	_	_	_
428	independent	independent	JJ	_	_	_
429	cultures	culture	NNS	_	_	_
430	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
431	b2618	b2618	NN	_	_	_
432	_	_	CD	_	_	_
433	U	U	NNP	_	_	_
434	_	_	NNP	_	_	_
435	N0075	N0075	NNP	_	_	_
436	_	_	VBD	_	_	_
437	r1	r1	NN	_	_	_
438	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
439	b2618	b2618	NN	_	_	_
440	_	_	CD	_	_	_
441	U	U	NNP	_	_	_
442	_	_	NNP	_	_	_
443	N0075	N0075	NNP	_	_	_
444	_	_	VBD	_	_	_
445	r2	r2	NN	_	_	_
446	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
447	b2618	b2618	NN	_	_	_
448	_	_	CD	_	_	_
449	U	U	NNP	_	_	_
450	_	_	NNP	_	_	_
451	N0075	N0075	NNP	_	_	_
452	_	_	VBD	_	_	_
453	r3	r3	NN	_	_	_
454	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
455	b2618	b2618	NN	_	_	_
456	upregulation	upregulation	NN	_	_	_
457	,	,	,	_	_	_
458	0.075	0.075	CD	_	_	_
459	ug	ug	NN	_	_	_
460	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
461	bcp	bcp	NN	GEN	_	_
462	___	___	CD	_	_	_
463	U	U	NNP	_	_	_
464	_	_	NNP	_	_	_
465	N0075	N0075	NNP	_	_	_
466	_	_	NNP	_	_	_
467	r1	r1	NN	_	_	_
468	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
469	bcp	bcp	NN	GEN	_	_
470	___	___	CD	_	_	_
471	U	U	NNP	_	_	_
472	_	_	NNP	_	_	_
473	N0075	N0075	NNP	_	_	_
474	_	_	NNP	_	_	_
475	r2	r2	NN	_	_	_
476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
477	bcp	bcp	NN	GEN	_	_
478	___	___	CD	_	_	_
479	U	U	NNP	_	_	_
480	_	_	NNP	_	_	_
481	N0075	N0075	NNP	_	_	_
482	_	_	NNP	_	_	_
483	r3	r3	NN	_	_	_
484	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
485	bcp	bcp	NN	GEN	_	_
486	upregulation	upregulation	NN	_	_	_
487	,	,	,	_	_	_
488	0.075	0.075	CD	_	_	_
489	ug	ug	NN	_	_	_
490	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
491	ccdB	ccdb	NN	_	_	_
492	_	_	CD	_	_	_
493	K12	k12	NN	_	_	_
494	_	_	NN	_	_	_
495	0	0	CD	_	_	_
496	_	_	NN	_	_	_
497	r1	r1	NN	_	_	_
498	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
499	ccdB	ccdb	NN	_	_	_
500	_	_	CD	_	_	_
501	K12	k12	NN	_	_	_
502	_	_	NN	_	_	_
503	120	120	CD	_	_	_
504	_	_	NN	_	_	_
505	r1	r1	NN	_	_	_
506	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
507	ccdB	ccdb	NN	_	_	_
508	_	_	CD	_	_	_
509	K12	k12	NN	_	_	_
510	_	_	CD	_	_	_
511	30	30	CD	_	_	_
512	_	_	NN	_	_	_
513	r1	r1	NN	_	_	_
514	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
515	ccdB	ccdb	NN	_	_	_
516	_	_	CD	_	_	_
517	K12	k12	NN	_	_	_
518	_	_	NN	_	_	_
519	60	60	CD	_	_	_
520	_	_	NN	_	_	_
521	r1	r1	NN	_	_	_
522	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
523	ccdB	ccdb	NN	_	_	_
524	_	_	CD	_	_	_
525	K12	k12	NN	_	_	_
526	_	_	NN	_	_	_
527	90	90	CD	_	_	_
528	_	_	NN	_	_	_
529	r1	r1	NN	_	_	_
530	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
531	ccdB	ccdb	NN	_	_	_
532	_	_	CD	_	_	_
533	MG1063	mg1063	NN	_	_	_
534	_	_	NN	_	_	_
535	0	0	CD	_	_	_
536	_	_	NN	_	_	_
537	r1	r1	NN	_	_	_
538	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
539	ccdB	ccdb	NN	_	_	_
540	_	_	CD	_	_	_
541	MG1063	mg1063	NN	_	_	_
542	_	_	NN	_	_	_
543	0	0	CD	_	_	_
544	_	_	NN	_	_	_
545	r2	r2	NN	_	_	_
546	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
547	ccdB	ccdb	NN	_	_	_
548	_	_	CD	_	_	_
549	MG1063	mg1063	NN	_	_	_
550	_	_	NN	_	_	_
551	120	120	CD	_	_	_
552	_	_	NN	_	_	_
553	r1	r1	NN	_	_	_
554	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
555	ccdB	ccdb	NN	_	_	_
556	_	_	CD	_	_	_
557	MG1063	mg1063	NN	_	_	_
558	_	_	CD	_	_	_
559	30	30	CD	_	_	_
560	_	_	NN	_	_	_
561	r1	r1	NN	_	_	_
562	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
563	ccdB	ccdb	NN	_	_	_
564	_	_	CD	_	_	_
565	MG1063	mg1063	NN	_	_	_
566	_	_	CD	_	_	_
567	30	30	CD	_	_	_
568	_	_	NN	_	_	_
569	r2	r2	NN	_	_	_
570	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
571	ccdB	ccdb	NN	_	_	_
572	_	_	CD	_	_	_
573	MG1063	mg1063	NN	_	_	_
574	_	_	NN	_	_	_
575	60	60	CD	_	_	_
576	_	_	NN	_	_	_
577	r1	r1	NN	_	_	_
578	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
579	ccdB	ccdb	NN	_	_	_
580	_	_	CD	_	_	_
581	MG1063	mg1063	NN	_	_	_
582	_	_	NN	_	_	_
583	60	60	CD	_	_	_
584	_	_	NN	_	_	_
585	r2	r2	NN	_	_	_
586	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
587	ccdB	ccdb	NN	_	_	_
588	_	_	CD	_	_	_
589	MG1063	mg1063	NN	_	_	_
590	_	_	NN	_	_	_
591	90	90	CD	_	_	_
592	_	_	NN	_	_	_
593	r1	r1	NN	_	_	_
594	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
595	ccdB	ccdb	NN	_	_	_
596	_	_	CD	_	_	_
597	MG1063	mg1063	NN	_	_	_
598	_	_	NN	_	_	_
599	90	90	CD	_	_	_
600	_	_	NN	_	_	_
601	r2	r2	NN	_	_	_
602	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
603	ccdB	ccdb	NN	_	_	_
604	_	_	CD	_	_	_
605	W1863	w1863	NN	_	_	_
606	_	_	NN	_	_	_
607	0	0	CD	_	_	_
608	_	_	NN	_	_	_
609	r1	r1	NN	_	_	_
610	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
611	ccdB	ccdb	NN	_	_	_
612	_	_	CD	_	_	_
613	W1863	w1863	NN	_	_	_
614	_	_	CD	_	_	_
615	30	30	CD	_	_	_
616	_	_	NN	_	_	_
617	r1	r1	NN	_	_	_
618	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
619	ccdB	ccdb	NN	_	_	_
620	_	_	CD	_	_	_
621	W1863	w1863	NN	_	_	_
622	_	_	NN	_	_	_
623	60	60	CD	_	_	_
624	_	_	NN	_	_	_
625	r1	r1	NN	_	_	_
626	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
627	ccdB	ccdb	NN	_	_	_
628	_	_	CD	_	_	_
629	W1863	w1863	NN	_	_	_
630	_	_	NN	_	_	_
631	90	90	CD	_	_	_
632	_	_	NN	_	_	_
633	r1	r1	NN	_	_	_
634	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
635	cells	cell	NNS	_	_	_
636	12	12	CD	_	_	_
637	min	min	NN	_	_	_
638	after	after	IN	_	_	_
639	treatment	treatment	NN	_	_	_
640	by	by	IN	_	_	_
641	norfloxacin	norfloxacin	NN	_	_	_
642	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
643	cells	cell	NNS	_	_	_
644	24	24	CD	_	_	_
645	min	min	NN	_	_	_
646	after	after	IN	_	_	_
647	treatment	treatment	NN	_	_	_
648	by	by	IN	_	_	_
649	norfloxacin	norfloxacin	NN	_	_	_
650	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
651	cells	cell	NNS	_	_	_
652	36	36	CD	_	_	_
653	min	min	NN	_	_	_
654	after	after	IN	_	_	_
655	treatment	treatment	NN	_	_	_
656	by	by	IN	_	_	_
657	norfloxacin	norfloxacin	NN	_	_	_
658	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
659	cells	cell	NNS	_	_	_
660	48	48	CD	_	_	_
661	min	min	NN	_	_	_
662	after	after	IN	_	_	_
663	treatment	treatment	NN	_	_	_
664	by	by	IN	_	_	_
665	norfloxacin	norfloxacin	NN	_	_	_
666	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
667	cells	cell	NNS	_	_	_
668	60	60	CD	_	_	_
669	min	min	NN	_	_	_
670	after	after	IN	_	_	_
671	treatment	treatment	NN	_	_	_
672	by	by	IN	_	_	_
673	norfloxacin	norfloxacin	NN	_	_	_
674	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
675	cells	cell	NNS	_	_	_
676	prior	prior	RB	_	_	_
677	to	to	TO	_	_	_
678	treatment	treatment	NN	_	_	_
679	by	by	IN	_	_	_
680	norfloxacin	norfloxacin	NN	_	_	_
681	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
682	cpxR	cpxr	NN	GEN	_	_
683	__	__	CD	_	_	_
684	U	U	NNP	_	_	_
685	_	_	NNP	_	_	_
686	N0075	N0075	NNP	_	_	_
687	_	_	VBD	_	_	_
688	r1	r1	NN	_	_	_
689	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
690	cpxR	cpxr	NN	GEN	_	_
691	__	__	CD	_	_	_
692	U	U	NNP	_	_	_
693	_	_	NNP	_	_	_
694	N0075	N0075	NNP	_	_	_
695	_	_	VBD	_	_	_
696	r2	r2	NN	_	_	_
697	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
698	cpxR	cpxr	NN	GEN	_	_
699	__	__	CD	_	_	_
700	U	U	NNP	_	_	_
701	_	_	NNP	_	_	_
702	N0075	N0075	NNP	_	_	_
703	_	_	SYM	_	_	_
704	r3	r3	FW	_	_	_
705	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
706	cpxR	cpxr	NN	GEN	_	_
707	upregulation	upregulation	NN	_	_	_
708	,	,	,	_	_	_
709	0.075	0.075	CD	_	_	_
710	ug	ug	NN	_	_	_
711	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
712	crcB	crcb	NN	GEN	_	_
713	__	__	CD	_	_	_
714	U	U	NNP	_	_	_
715	_	_	NNP	_	_	_
716	N0075	N0075	NNP	_	_	_
717	_	_	VBD	_	_	_
718	r1	r1	NN	_	_	_
719	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
720	crcB	crcb	NN	GEN	_	_
721	__	__	CD	_	_	_
722	U	U	NNP	_	_	_
723	_	_	NNP	_	_	_
724	N0075	N0075	NNP	_	_	_
725	_	_	VBD	_	_	_
726	r2	r2	NN	_	_	_
727	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
728	crcB	crcb	NN	GEN	_	_
729	__	__	CD	_	_	_
730	U	U	NNP	_	_	_
731	_	_	NNP	_	_	_
732	N0075	N0075	NNP	_	_	_
733	_	_	SYM	_	_	_
734	r3	r3	FW	_	_	_
735	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
736	crcB	crcb	NN	GEN	_	_
737	upregulation	upregulation	NN	_	_	_
738	,	,	,	_	_	_
739	0.075	0.075	CD	_	_	_
740	ug	ug	NN	_	_	_
741	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
742	crp	crp	NN	GEN	_	_
743	___	___	CD	_	_	_
744	U	U	NNP	_	_	_
745	_	_	NNP	_	_	_
746	N0075	N0075	NNP	_	_	_
747	_	_	VBD	_	_	_
748	r1	r1	NN	_	_	_
749	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
750	crp	crp	VBP	GEN	_	_
751	___	___	CD	_	_	_
752	U	U	NNP	_	_	_
753	_	_	NNP	_	_	_
754	N0075	N0075	NNP	_	_	_
755	_	_	VBD	_	_	_
756	r2	r2	NN	_	_	_
757	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
758	crp	crp	VBP	GEN	_	_
759	___	___	CD	_	_	_
760	U	U	NNP	_	_	_
761	_	_	NNP	_	_	_
762	N0075	N0075	NNP	_	_	_
763	_	_	SYM	_	_	_
764	r3	r3	FW	_	_	_
765	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
766	crp	crp	NN	GEN	_	_
767	upregulation	upregulation	NN	_	_	_
768	,	,	,	_	_	_
769	0.075	0.075	CD	_	_	_
770	ug	ug	NN	_	_	_
771	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
772	cspF	cspf	NN	GEN	_	_
773	__	__	CD	_	_	_
774	U	U	NNP	_	_	_
775	_	_	NNP	_	_	_
776	N0075	N0075	NNP	_	_	_
777	_	_	VBD	_	_	_
778	r1	r1	NN	_	_	_
779	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
780	cspF	cspf	NN	GEN	_	_
781	__	__	CD	_	_	_
782	U	U	NNP	_	_	_
783	_	_	NNP	_	_	_
784	N0075	N0075	NNP	_	_	_
785	_	_	VBD	_	_	_
786	r2	r2	NN	_	_	_
787	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
788	cspF	cspf	NN	GEN	_	_
789	__	__	CD	_	_	_
790	U	U	NNP	_	_	_
791	_	_	NNP	_	_	_
792	N0075	N0075	NNP	_	_	_
793	_	_	SYM	_	_	_
794	r3	r3	FW	_	_	_
795	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
796	cspF	cspf	NN	GEN	_	_
797	upregulation	upregulation	NN	_	_	_
798	,	,	,	_	_	_
799	0.075	0.075	CD	_	_	_
800	ug	ug	NN	_	_	_
801	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
802	dam	dam	NN	GEN	_	_
803	___	___	CD	_	_	_
804	U	U	NNP	_	_	_
805	_	_	NNP	_	_	_
806	N0075	N0075	NNP	_	_	_
807	_	_	NNP	_	_	_
808	r1	r1	NN	_	_	_
809	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
810	dam	dam	NN	GEN	_	_
811	___	___	CD	_	_	_
812	U	U	NNP	_	_	_
813	_	_	NNP	_	_	_
814	N0075	N0075	NNP	_	_	_
815	_	_	NNP	_	_	_
816	r2	r2	NN	_	_	_
817	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
818	dam	dam	NN	GEN	_	_
819	___	___	CD	_	_	_
820	U	U	NNP	_	_	_
821	_	_	NNP	_	_	_
822	N0075	N0075	NNP	_	_	_
823	_	_	NNP	_	_	_
824	r3	r3	NN	_	_	_
825	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
826	dam	dam	NN	GEN	_	_
827	upregulation	upregulation	NN	_	_	_
828	,	,	,	_	_	_
829	0.075	0.075	CD	_	_	_
830	ug	ug	NN	_	_	_
831	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
832	dinI	dini	NN	GEN	_	_
833	___	___	CD	_	_	_
834	U	U	NNP	_	_	_
835	_	_	NNP	_	_	_
836	N0025	N0025	NNP	_	_	_
837	_	_	NNP	_	_	_
838	r1	r1	NN	_	_	_
839	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
840	dinI	dini	NN	GEN	_	_
841	___	___	CD	_	_	_
842	U	U	NNP	_	_	_
843	_	_	NNP	_	_	_
844	N0025	N0025	NNP	_	_	_
845	_	_	SYM	_	_	_
846	r2	r2	FW	_	_	_
847	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
848	dinI	dini	NN	GEN	_	_
849	___	___	CD	_	_	_
850	U	U	NNP	_	_	_
851	_	_	NNP	_	_	_
852	N0025	N0025	NNP	_	_	_
853	_	_	SYM	_	_	_
854	r3	r3	FW	_	_	_
855	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
856	dinI	dini	NN	GEN	_	_
857	upregulation	upregulation	NN	_	_	_
858	,	,	,	_	_	_
859	amp	amp	NN	_	_	_
860	50ug	50ug	JJ	_	_	_
861	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
862	dinP	dinp	NN	_	_	_
863	___	___	CD	_	_	_
864	U	U	NNP	_	_	_
865	_	_	NNP	_	_	_
866	N0025	N0025	NNP	_	_	_
867	_	_	SYM	_	_	_
868	r1	r1	FW	_	_	_
869	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
870	dinP	dinp	NN	_	_	_
871	___	___	CD	_	_	_
872	U	U	NNP	_	_	_
873	_	_	NNP	_	_	_
874	N0025	N0025	NNP	_	_	_
875	_	_	SYM	_	_	_
876	r2	r2	FW	_	_	_
877	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
878	dinP	dinp	NN	_	_	_
879	___	___	CD	_	_	_
880	U	U	NNP	_	_	_
881	_	_	NNP	_	_	_
882	N0025	N0025	NNP	_	_	_
883	_	_	SYM	_	_	_
884	r3	r3	FW	_	_	_
885	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
886	dinP	dinp	NN	_	_	_
887	upregulation	upregulation	NN	_	_	_
888	,	,	,	_	_	_
889	amp	amp	NN	_	_	_
890	50ug	50ug	JJ	_	_	_
891	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
892	dnaA	dnaa	NN	GEN	_	_
893	__	__	CD	_	_	_
894	U	U	NNP	_	_	_
895	_	_	NNP	_	_	_
896	N0075	N0075	NNP	_	_	_
897	_	_	VBD	_	_	_
898	r1	r1	NN	_	_	_
899	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
900	dnaA	dnaa	NN	GEN	_	_
901	__	__	CD	_	_	_
902	U	U	NNP	_	_	_
903	_	_	NNP	_	_	_
904	N0075	N0075	NNP	_	_	_
905	_	_	VBD	_	_	_
906	r2	r2	NN	_	_	_
907	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
908	dnaA	dnaa	NN	GEN	_	_
909	__	__	CD	_	_	_
910	U	U	NNP	_	_	_
911	_	_	NNP	_	_	_
912	N0075	N0075	NNP	_	_	_
913	_	_	VBD	_	_	_
914	r3	r3	NN	_	_	_
915	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
916	dnaA	dnaa	NN	GEN	_	_
917	upregulation	upregulation	NN	_	_	_
918	,	,	,	_	_	_
919	0.075	0.075	CD	_	_	_
920	ug	ug	NN	_	_	_
921	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
922	dnaN	dnan	NN	GEN	_	_
923	__	__	CD	_	_	_
924	U	U	NNP	_	_	_
925	_	_	NNP	_	_	_
926	N0075	N0075	NNP	_	_	_
927	_	_	VBD	_	_	_
928	r1	r1	NN	_	_	_
929	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
930	dnaN	dnan	NN	GEN	_	_
931	__	__	CD	_	_	_
932	U	U	NNP	_	_	_
933	_	_	NNP	_	_	_
934	N0075	N0075	NNP	_	_	_
935	_	_	VBD	_	_	_
936	r2	r2	NN	_	_	_
937	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
938	dnaN	dnan	NN	GEN	_	_
939	__	__	CD	_	_	_
940	U	U	NNP	_	_	_
941	_	_	NNP	_	_	_
942	N0075	N0075	NNP	_	_	_
943	_	_	VBD	_	_	_
944	r3	r3	NN	_	_	_
945	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
946	dnaN	dnan	NN	GEN	_	_
947	upregulation	upregulation	NN	_	_	_
948	,	,	,	_	_	_
949	0.075	0.075	CD	_	_	_
950	ug	ug	NN	_	_	_
951	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
952	dnaT	dnat	NN	GEN	_	_
953	__	__	CD	_	_	_
954	U	U	NNP	_	_	_
955	_	_	NNP	_	_	_
956	N0075	N0075	NNP	_	_	_
957	_	_	VBD	_	_	_
958	r1	r1	NN	_	_	_
959	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
960	dnaT	dnat	NN	GEN	_	_
961	__	__	CD	_	_	_
962	U	U	NNP	_	_	_
963	_	_	NNP	_	_	_
964	N0075	N0075	NNP	_	_	_
965	_	_	VBD	_	_	_
966	r2	r2	NN	_	_	_
967	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
968	dnaT	dnat	NN	GEN	_	_
969	__	__	CD	_	_	_
970	U	U	NNP	_	_	_
971	_	_	NNP	_	_	_
972	N0075	N0075	NNP	_	_	_
973	_	_	VBD	_	_	_
974	r3	r3	NN	_	_	_
975	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
976	dnaT	dnat	NN	GEN	_	_
977	upregulation	upregulation	NN	_	_	_
978	,	,	,	_	_	_
979	0.075	0.075	CD	_	_	_
980	ug	ug	NN	_	_	_
981	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
982	E.coli	e.coli	NN	_	_	_
983	K12	k12	NN	_	_	_
984	with	with	IN	_	_	_
985	ccdB	ccdb	NN	_	_	_
986	upregulation	upregulation	NN	_	_	_
987	0	0	CD	_	_	_
988	minutes	minute	NNS	_	_	_
989	after	after	IN	_	_	_
990	induction	induction	NN	_	_	_
991	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
992	E.coli	e.coli	NN	_	_	_
993	K12	k12	NN	_	_	_
994	with	with	IN	_	_	_
995	ccdB	ccdb	NN	_	_	_
996	upregulation	upregulation	NN	_	_	_
997	120	120	CD	_	_	_
998	minutes	minute	NNS	_	_	_
999	after	after	IN	_	_	_
1000	induction	induction	NN	_	_	_
1001	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1002	E.coli	e.coli	NN	_	_	_
1003	K12	k12	NN	_	_	_
1004	with	with	IN	_	_	_
1005	ccdB	ccdb	NN	_	_	_
1006	upregulation	upregulation	NN	_	_	_
1007	30	30	CD	_	_	_
1008	minutes	minute	NNS	_	_	_
1009	after	after	IN	_	_	_
1010	induction	induction	NN	_	_	_
1011	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1012	E.coli	e.coli	NN	_	_	_
1013	K12	k12	NN	_	_	_
1014	with	with	IN	_	_	_
1015	ccdB	ccdb	NN	_	_	_
1016	upregulation	upregulation	NN	_	_	_
1017	60	60	CD	_	_	_
1018	minutes	minute	NNS	_	_	_
1019	after	after	IN	_	_	_
1020	induction	induction	NN	_	_	_
1021	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1022	E.coli	e.coli	NN	_	_	_
1023	K12	k12	NN	_	_	_
1024	with	with	IN	_	_	_
1025	ccdB	ccdb	NN	_	_	_
1026	upregulation	upregulation	NN	_	_	_
1027	90	90	CD	_	_	_
1028	minutes	minute	NNS	_	_	_
1029	after	after	IN	_	_	_
1030	induction	induction	NN	_	_	_
1031	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1032	E.coli	e.coli	NN	_	_	_
1033	K12	k12	NN	_	_	_
1034	with	with	IN	_	_	_
1035	lacZ	lacz	NN	GEN	_	_
1036	upregulation	upregulation	NN	_	_	_
1037	0	0	CD	_	_	_
1038	minutes	minute	NNS	_	_	_
1039	after	after	IN	_	_	_
1040	induction	induction	NN	_	_	_
1041	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1042	E.coli	e.coli	NN	_	_	_
1043	K12	k12	NN	_	_	_
1044	with	with	IN	_	_	_
1045	lacZ	lacz	NN	GEN	_	_
1046	upregulation	upregulation	NN	_	_	_
1047	120	120	CD	_	_	_
1048	minutes	minute	NNS	_	_	_
1049	after	after	IN	_	_	_
1050	induction	induction	NN	_	_	_
1051	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1052	E.coli	e.coli	NN	_	_	_
1053	K12	k12	NN	_	_	_
1054	with	with	IN	_	_	_
1055	lacZ	lacz	NN	GEN	_	_
1056	upregulation	upregulation	NN	_	_	_
1057	30	30	CD	_	_	_
1058	minutes	minute	NNS	_	_	_
1059	after	after	IN	_	_	_
1060	induction	induction	NN	_	_	_
1061	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1062	E.coli	e.coli	NN	_	_	_
1063	K12	k12	NN	_	_	_
1064	with	with	IN	_	_	_
1065	lacZ	lacz	NN	GEN	_	_
1066	upregulation	upregulation	NN	_	_	_
1067	60	60	CD	_	_	_
1068	minutes	minute	NNS	_	_	_
1069	after	after	IN	_	_	_
1070	induction	induction	NN	_	_	_
1071	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1072	E.coli	e.coli	NN	_	_	_
1073	K12	k12	NN	_	_	_
1074	with	with	IN	_	_	_
1075	lacZ	lacz	NN	GEN	_	_
1076	upregulation	upregulation	NN	_	_	_
1077	90	90	CD	_	_	_
1078	minutes	minute	NNS	_	_	_
1079	after	after	IN	_	_	_
1080	induction	induction	NN	_	_	_
1081	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1082	E.coli	e.coli	NN	_	_	_
1083	MG1063	mg1063	NN	_	_	_
1084	-LRB-	-lrb-	-LRB-	_	_	_
1085	recA56	reca56	NN	_	_	_
1086	=	=	JJ	_	_	_
1087	recA	reca	NN	GEN	_	_
1088	-	-	:	_	_	_
1089	-RRB-	-rrb-	-RRB-	_	_	_
1090	with	with	IN	_	_	_
1091	ccdB	ccdb	NN	_	_	_
1092	upregulation	upregulation	NN	_	_	_
1093	0	0	CD	_	_	_
1094	minutes	minute	NNS	_	_	_
1095	after	after	IN	_	_	_
1096	induction	induction	NN	_	_	_
1097	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1098	E.coli	e.coli	NN	_	_	_
1099	MG1063	mg1063	NN	_	_	_
1100	-LRB-	-lrb-	-LRB-	_	_	_
1101	recA56	reca56	NN	_	_	_
1102	=	=	JJ	_	_	_
1103	recA	reca	NN	GEN	_	_
1104	-	-	:	_	_	_
1105	-RRB-	-rrb-	-RRB-	_	_	_
1106	with	with	IN	_	_	_
1107	ccdB	ccdb	NN	_	_	_
1108	upregulation	upregulation	NN	_	_	_
1109	120	120	CD	_	_	_
1110	minutes	minute	NNS	_	_	_
1111	after	after	IN	_	_	_
1112	induction	induction	NN	_	_	_
1113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1114	E.coli	e.coli	NN	_	_	_
1115	MG1063	mg1063	NN	_	_	_
1116	-LRB-	-lrb-	-LRB-	_	_	_
1117	recA56	reca56	NN	_	_	_
1118	=	=	JJ	_	_	_
1119	recA	reca	NN	GEN	_	_
1120	-	-	:	_	_	_
1121	-RRB-	-rrb-	-RRB-	_	_	_
1122	with	with	IN	_	_	_
1123	ccdB	ccdb	NN	_	_	_
1124	upregulation	upregulation	NN	_	_	_
1125	30	30	CD	_	_	_
1126	minutes	minute	NNS	_	_	_
1127	after	after	IN	_	_	_
1128	induction	induction	NN	_	_	_
1129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1130	E.coli	e.coli	NN	_	_	_
1131	MG1063	mg1063	NN	_	_	_
1132	-LRB-	-lrb-	-LRB-	_	_	_
1133	recA56	reca56	NN	_	_	_
1134	=	=	JJ	_	_	_
1135	recA	reca	NN	GEN	_	_
1136	-	-	:	_	_	_
1137	-RRB-	-rrb-	-RRB-	_	_	_
1138	with	with	IN	_	_	_
1139	ccdB	ccdb	NN	_	_	_
1140	upregulation	upregulation	NN	_	_	_
1141	60	60	CD	_	_	_
1142	minutes	minute	NNS	_	_	_
1143	after	after	IN	_	_	_
1144	induction	induction	NN	_	_	_
1145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1146	E.coli	e.coli	NN	_	_	_
1147	MG1063	mg1063	NN	_	_	_
1148	-LRB-	-lrb-	-LRB-	_	_	_
1149	recA56	reca56	NN	_	_	_
1150	=	=	JJ	_	_	_
1151	recA	reca	NN	GEN	_	_
1152	-	-	:	_	_	_
1153	-RRB-	-rrb-	-RRB-	_	_	_
1154	with	with	IN	_	_	_
1155	ccdB	ccdb	NN	_	_	_
1156	upregulation	upregulation	NN	_	_	_
1157	90	90	CD	_	_	_
1158	minutes	minute	NNS	_	_	_
1159	after	after	IN	_	_	_
1160	induction	induction	NN	_	_	_
1161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1162	E.coli	e.coli	NN	_	_	_
1163	MG1063	mg1063	NN	_	_	_
1164	-LRB-	-lrb-	-LRB-	_	_	_
1165	recA56	reca56	NN	_	_	_
1166	=	=	JJ	_	_	_
1167	recA	reca	NN	GEN	_	_
1168	-	-	:	_	_	_
1169	-RRB-	-rrb-	-RRB-	_	_	_
1170	with	with	IN	_	_	_
1171	lacZ	lacz	NN	GEN	_	_
1172	upregulation	upregulation	NN	_	_	_
1173	0	0	CD	_	_	_
1174	minutes	minute	NNS	_	_	_
1175	after	after	IN	_	_	_
1176	induction	induction	NN	_	_	_
1177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1178	E.coli	e.coli	NN	_	_	_
1179	MG1063	mg1063	NN	_	_	_
1180	-LRB-	-lrb-	-LRB-	_	_	_
1181	recA56	reca56	NN	_	_	_
1182	=	=	JJ	_	_	_
1183	recA	reca	NN	GEN	_	_
1184	-	-	:	_	_	_
1185	-RRB-	-rrb-	-RRB-	_	_	_
1186	with	with	IN	_	_	_
1187	lacZ	lacz	NN	GEN	_	_
1188	upregulation	upregulation	NN	_	_	_
1189	120	120	CD	_	_	_
1190	minutes	minute	NNS	_	_	_
1191	after	after	IN	_	_	_
1192	induction	induction	NN	_	_	_
1193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1194	E.coli	e.coli	NN	_	_	_
1195	MG1063	mg1063	NN	_	_	_
1196	-LRB-	-lrb-	-LRB-	_	_	_
1197	recA56	reca56	NN	_	_	_
1198	=	=	JJ	_	_	_
1199	recA	reca	NN	GEN	_	_
1200	-	-	:	_	_	_
1201	-RRB-	-rrb-	-RRB-	_	_	_
1202	with	with	IN	_	_	_
1203	lacZ	lacz	NN	GEN	_	_
1204	upregulation	upregulation	NN	_	_	_
1205	30	30	CD	_	_	_
1206	minutes	minute	NNS	_	_	_
1207	after	after	IN	_	_	_
1208	induction	induction	NN	_	_	_
1209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1210	E.coli	e.coli	NN	_	_	_
1211	MG1063	mg1063	NN	_	_	_
1212	-LRB-	-lrb-	-LRB-	_	_	_
1213	recA56	reca56	NN	_	_	_
1214	=	=	JJ	_	_	_
1215	recA	reca	NN	GEN	_	_
1216	-	-	:	_	_	_
1217	-RRB-	-rrb-	-RRB-	_	_	_
1218	with	with	IN	_	_	_
1219	lacZ	lacz	NN	GEN	_	_
1220	upregulation	upregulation	NN	_	_	_
1221	60	60	CD	_	_	_
1222	minutes	minute	NNS	_	_	_
1223	after	after	IN	_	_	_
1224	induction	induction	NN	_	_	_
1225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1226	E.coli	e.coli	NN	_	_	_
1227	MG1063	mg1063	NN	_	_	_
1228	-LRB-	-lrb-	-LRB-	_	_	_
1229	recA56	reca56	NN	_	_	_
1230	=	=	JJ	_	_	_
1231	recA	reca	NN	GEN	_	_
1232	-	-	:	_	_	_
1233	-RRB-	-rrb-	-RRB-	_	_	_
1234	with	with	IN	_	_	_
1235	lacZ	lacz	NN	GEN	_	_
1236	upregulation	upregulation	NN	_	_	_
1237	90	90	CD	_	_	_
1238	minutes	minute	NNS	_	_	_
1239	after	after	IN	_	_	_
1240	induction	induction	NN	_	_	_
1241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1242	E.coli	e.coli	NN	_	_	_
1243	W1863	w1863	NN	_	_	_
1244	wt	wt	JJ	_	_	_
1245	lambda	lambda	NN	_	_	_
1246	-	-	:	_	_	_
1247	with	with	IN	_	_	_
1248	ccdB	ccdb	NN	_	_	_
1249	upregulation	upregulation	NN	_	_	_
1250	0	0	CD	_	_	_
1251	minutes	minute	NNS	_	_	_
1252	after	after	IN	_	_	_
1253	induction	induction	NN	_	_	_
1254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1255	E.coli	e.coli	NN	_	_	_
1256	W1863	w1863	NN	_	_	_
1257	wt	wt	JJ	_	_	_
1258	lambda	lambda	NN	_	_	_
1259	-	-	:	_	_	_
1260	with	with	IN	_	_	_
1261	ccdB	ccdb	NN	_	_	_
1262	upregulation	upregulation	NN	_	_	_
1263	30	30	CD	_	_	_
1264	minutes	minute	NNS	_	_	_
1265	after	after	IN	_	_	_
1266	induction	induction	NN	_	_	_
1267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1268	E.coli	e.coli	NN	_	_	_
1269	W1863	w1863	NN	_	_	_
1270	wt	wt	JJ	_	_	_
1271	lambda	lambda	NN	_	_	_
1272	-	-	:	_	_	_
1273	with	with	IN	_	_	_
1274	ccdB	ccdb	NN	_	_	_
1275	upregulation	upregulation	NN	_	_	_
1276	60	60	CD	_	_	_
1277	minutes	minute	NNS	_	_	_
1278	after	after	IN	_	_	_
1279	induction	induction	NN	_	_	_
1280	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1281	E.coli	e.coli	NN	_	_	_
1282	W1863	w1863	NN	_	_	_
1283	wt	wt	JJ	_	_	_
1284	lambda	lambda	NN	_	_	_
1285	-	-	:	_	_	_
1286	with	with	IN	_	_	_
1287	ccdB	ccdb	NN	_	_	_
1288	upregulation	upregulation	NN	_	_	_
1289	90	90	CD	_	_	_
1290	minutes	minute	NNS	_	_	_
1291	after	after	IN	_	_	_
1292	induction	induction	NN	_	_	_
1293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1294	E.coli	e.coli	NN	_	_	_
1295	W1863	w1863	NN	_	_	_
1296	wt	wt	JJ	_	_	_
1297	lambda	lambda	NN	_	_	_
1298	-	-	:	_	_	_
1299	with	with	IN	_	_	_
1300	lacZ	lacz	NN	GEN	_	_
1301	upregulation	upregulation	NN	_	_	_
1302	0	0	CD	_	_	_
1303	minutes	minute	NNS	_	_	_
1304	after	after	IN	_	_	_
1305	induction	induction	NN	_	_	_
1306	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1307	E.coli	e.coli	NN	_	_	_
1308	W1863	w1863	NN	_	_	_
1309	wt	wt	JJ	_	_	_
1310	lambda	lambda	NN	_	_	_
1311	-	-	:	_	_	_
1312	with	with	IN	_	_	_
1313	lacZ	lacz	NN	GEN	_	_
1314	upregulation	upregulation	NN	_	_	_
1315	30	30	CD	_	_	_
1316	minutes	minute	NNS	_	_	_
1317	after	after	IN	_	_	_
1318	induction	induction	NN	_	_	_
1319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1320	E.coli	e.coli	NN	_	_	_
1321	W1863	w1863	NN	_	_	_
1322	wt	wt	JJ	_	_	_
1323	lambda	lambda	NN	_	_	_
1324	-	-	:	_	_	_
1325	with	with	IN	_	_	_
1326	lacZ	lacz	NN	GEN	_	_
1327	upregulation	upregulation	NN	_	_	_
1328	60	60	CD	_	_	_
1329	minutes	minute	NNS	_	_	_
1330	after	after	IN	_	_	_
1331	induction	induction	NN	_	_	_
1332	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1333	E.coli	e.coli	NN	_	_	_
1334	W1863	w1863	NN	_	_	_
1335	wt	wt	JJ	_	_	_
1336	lambda	lambda	NN	_	_	_
1337	-	-	:	_	_	_
1338	with	with	IN	_	_	_
1339	lacZ	lacz	NN	GEN	_	_
1340	upregulation	upregulation	NN	_	_	_
1341	90	90	CD	_	_	_
1342	minutes	minute	NNS	_	_	_
1343	after	after	IN	_	_	_
1344	induction	induction	NN	_	_	_
1345	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1346	emrR	emrr	NN	_	_	_
1347	__	__	CD	_	_	_
1348	U	U	NNP	_	_	_
1349	_	_	NNP	_	_	_
1350	N0075	N0075	NNP	_	_	_
1351	_	_	VBD	_	_	_
1352	r1	r1	NN	_	_	_
1353	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1354	emrR	emrr	NN	_	_	_
1355	__	__	CD	_	_	_
1356	U	U	NNP	_	_	_
1357	_	_	NNP	_	_	_
1358	N0075	N0075	NNP	_	_	_
1359	_	_	VBD	_	_	_
1360	r3	r3	NN	_	_	_
1361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1362	emrR	emrr	NN	_	_	_
1363	upregulation	upregulation	NN	_	_	_
1364	,	,	,	_	_	_
1365	0.075	0.075	CD	_	_	_
1366	ug	ug	NN	_	_	_
1367	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1368	era	era	NN	GEN	_	_
1369	___	___	CD	_	_	_
1370	U	U	NNP	_	_	_
1371	_	_	NNP	_	_	_
1372	N0075	N0075	NNP	_	_	_
1373	_	_	NNP	_	_	_
1374	r1	r1	NN	_	_	_
1375	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1376	era	era	NN	GEN	_	_
1377	___	___	CD	_	_	_
1378	U	U	NNP	_	_	_
1379	_	_	NNP	_	_	_
1380	N0075	N0075	NNP	_	_	_
1381	_	_	NNP	_	_	_
1382	r2	r2	NN	_	_	_
1383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1384	era	era	NN	GEN	_	_
1385	___	___	CD	_	_	_
1386	U	U	NNP	_	_	_
1387	_	_	NNP	_	_	_
1388	N0075	N0075	NNP	_	_	_
1389	_	_	SYM	_	_	_
1390	r3	r3	FW	_	_	_
1391	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
1392	era	era	NN	GEN	_	_
1393	upregulation	upregulation	NN	_	_	_
1394	,	,	,	_	_	_
1395	0.075	0.075	CD	_	_	_
1396	ug	ug	NN	_	_	_
1397	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1398	Escherichia	escherichia	FW	Organism	_	_
1399	coli	coli	FW	Organism	_	_
1400	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1401	fis	fi	VBZ	GEN	_	_
1402	___	___	CD	_	_	_
1403	U	U	NNP	_	_	_
1404	_	_	NNP	_	_	_
1405	N0075	N0075	NNP	_	_	_
1406	_	_	VBD	_	_	_
1407	r1	r1	NN	_	_	_
1408	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1409	fis	fi	VBZ	GEN	_	_
1410	___	___	CD	_	_	_
1411	U	U	NNP	_	_	_
1412	_	_	NNP	_	_	_
1413	N0075	N0075	NNP	_	_	_
1414	_	_	VBD	_	_	_
1415	r2	r2	NN	_	_	_
1416	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1417	fis	fi	VBZ	GEN	_	_
1418	___	___	CD	_	_	_
1419	U	U	NNP	_	_	_
1420	_	_	NNP	_	_	_
1421	N0075	N0075	NNP	_	_	_
1422	_	_	SYM	_	_	_
1423	r3	r3	FW	_	_	_
1424	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
1425	fis	fis	FW	GEN	_	_
1426	upregulation	upregulation	NN	_	_	_
1427	,	,	,	_	_	_
1428	0.075	0.075	CD	_	_	_
1429	ug	ug	NN	_	_	_
1430	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1431	fklB	fklb	NN	GEN	_	_
1432	__	__	CD	_	_	_
1433	U	U	NNP	_	_	_
1434	_	_	NNP	_	_	_
1435	N0075	N0075	NNP	_	_	_
1436	_	_	VBD	_	_	_
1437	r1	r1	NN	_	_	_
1438	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1439	fklB	fklb	NN	GEN	_	_
1440	__	__	CD	_	_	_
1441	U	U	NNP	_	_	_
1442	_	_	NNP	_	_	_
1443	N0075	N0075	NNP	_	_	_
1444	_	_	VBD	_	_	_
1445	r2	r2	NN	_	_	_
1446	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1447	fklB	fklb	NN	GEN	_	_
1448	__	__	CD	_	_	_
1449	U	U	NNP	_	_	_
1450	_	_	NNP	_	_	_
1451	N0075	N0075	NNP	_	_	_
1452	_	_	SYM	_	_	_
1453	r3	r3	FW	_	_	_
1454	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
1455	fklB	fklb	NN	GEN	_	_
1456	upregulation	upregulation	NN	_	_	_
1457	,	,	,	_	_	_
1458	0.075	0.075	CD	_	_	_
1459	ug	ug	NN	_	_	_
1460	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1461	folA	fola	NN	GEN	_	_
1462	__	__	CD	_	_	_
1463	U	U	NNP	_	_	_
1464	_	_	NNP	_	_	_
1465	N0075	N0075	NNP	_	_	_
1466	_	_	NNP	_	_	_
1467	r1	r1	NN	_	_	_
1468	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1469	folA	fola	NN	GEN	_	_
1470	__	__	CD	_	_	_
1471	U	U	NNP	_	_	_
1472	_	_	NNP	_	_	_
1473	N0075	N0075	NNP	_	_	_
1474	_	_	SYM	_	_	_
1475	r2	r2	FW	_	_	_
1476	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
1477	folA	fola	NN	GEN	_	_
1478	__	__	CD	_	_	_
1479	U	U	NNP	_	_	_
1480	_	_	NNP	_	_	_
1481	N0075	N0075	NNP	_	_	_
1482	_	_	SYM	_	_	_
1483	r3	r3	FW	_	_	_
1484	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
1485	folA	fola	NN	GEN	_	_
1486	upregulation	upregulation	NN	_	_	_
1487	,	,	,	_	_	_
1488	0.075	0.075	CD	_	_	_
1489	ug	ug	NN	_	_	_
1490	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1491	galF	galf	NN	GEN	_	_
1492	__	__	CD	_	_	_
1493	U	U	NNP	_	_	_
1494	_	_	NNP	_	_	_
1495	N0075	N0075	NNP	_	_	_
1496	_	_	VBD	_	_	_
1497	r1	r1	NN	_	_	_
1498	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1499	galF	galf	NN	GEN	_	_
1500	__	__	CD	_	_	_
1501	U	U	NNP	_	_	_
1502	_	_	NNP	_	_	_
1503	N0075	N0075	NNP	_	_	_
1504	_	_	VBD	_	_	_
1505	r2	r2	NN	_	_	_
1506	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1507	galF	galf	NN	GEN	_	_
1508	__	__	CD	_	_	_
1509	U	U	NNP	_	_	_
1510	_	_	NNP	_	_	_
1511	N0075	N0075	NNP	_	_	_
1512	_	_	SYM	_	_	_
1513	r3	r3	FW	_	_	_
1514	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
1515	galF	galf	NN	GEN	_	_
1516	upregulation	upregulation	NN	_	_	_
1517	,	,	,	_	_	_
1518	0.075	0.075	CD	_	_	_
1519	ug	ug	NN	_	_	_
1520	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1521	gcvR	gcvr	NN	GEN	_	_
1522	__	__	CD	_	_	_
1523	U	U	NNP	_	_	_
1524	_	_	NNP	_	_	_
1525	N0075	N0075	NNP	_	_	_
1526	_	_	VBD	_	_	_
1527	r1	r1	NN	_	_	_
1528	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1529	gcvR	gcvr	NN	GEN	_	_
1530	__	__	CD	_	_	_
1531	U	U	NNP	_	_	_
1532	_	_	NNP	_	_	_
1533	N0075	N0075	NNP	_	_	_
1534	_	_	VBD	_	_	_
1535	r2	r2	NN	_	_	_
1536	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1537	gcvR	gcvr	NN	GEN	_	_
1538	__	__	CD	_	_	_
1539	U	U	NNP	_	_	_
1540	_	_	NNP	_	_	_
1541	N0075	N0075	NNP	_	_	_
1542	_	_	SYM	_	_	_
1543	r3	r3	FW	_	_	_
1544	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
1545	gcvR	gcvr	NN	GEN	_	_
1546	upregulation	upregulation	NN	_	_	_
1547	,	,	,	_	_	_
1548	0.075	0.075	CD	_	_	_
1549	mg	mg	NN	_	_	_
1550	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1551	GeneChips	genechip	NNS	_	_	_
1552	were	be	VBD	_	_	_
1553	washed	wash	VBN	_	_	_
1554	and	and	CC	_	_	_
1555	stained	stain	VBN	_	_	_
1556	with	with	IN	_	_	_
1557	an	a	DT	_	_	_
1558	FS450	fs450	NN	_	_	_
1559	fluidics	fluidic	NNS	_	_	_
1560	machine	machine	NN	_	_	_
1561	and	and	CC	_	_	_
1562	scanned	scan	VBN	_	_	_
1563	using	use	VBG	_	_	_
1564	a	a	DT	_	_	_
1565	GeneChip	GeneChip	NNP	_	_	_
1566	Scanner	Scanner	NNP	_	_	_
1567	3000	3000	CD	_	_	_
1568	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
1569	gyrA	gyrA	NNP	GEN	_	_
1570	__	__	VBD	_	_	_
1571	U	U	NNP	_	_	_
1572	_	_	NNP	_	_	_
1573	N0075	N0075	NNP	_	_	_
1574	_	_	NNP	_	_	_
1575	r1	r1	NN	_	_	_
1576	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1577	gyrA	gyra	NN	GEN	_	_
1578	__	__	CD	_	_	_
1579	U	U	NNP	_	_	_
1580	_	_	NNP	_	_	_
1581	N0075	N0075	NNP	_	_	_
1582	_	_	SYM	_	_	_
1583	r2	r2	FW	_	_	_
1584	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
1585	gyrA	gyra	NN	GEN	_	_
1586	__	__	CD	_	_	_
1587	U	U	NNP	_	_	_
1588	_	_	NNP	_	_	_
1589	N0075	N0075	NNP	_	_	_
1590	_	_	SYM	_	_	_
1591	r3	r3	FW	_	_	_
1592	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
1593	gyrA	gyra	NN	GEN	_	_
1594	upregulation	upregulation	NN	_	_	_
1595	,	,	,	_	_	_
1596	0.075	0.075	CD	_	_	_
1597	mg	mg	NN	_	_	_
1598	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1599	gyrI	gyri	NN	_	_	_
1600	__	__	CD	_	_	_
1601	U	U	NNP	_	_	_
1602	_	_	NNP	_	_	_
1603	N0075	N0075	NNP	_	_	_
1604	_	_	VBD	_	_	_
1605	r1	r1	NN	_	_	_
1606	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1607	gyrI	gyri	NN	_	_	_
1608	__	__	CD	_	_	_
1609	U	U	NNP	_	_	_
1610	_	_	NNP	_	_	_
1611	N0075	N0075	NNP	_	_	_
1612	_	_	VBD	_	_	_
1613	r2	r2	NN	_	_	_
1614	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1615	gyrI	gyri	NN	_	_	_
1616	__	__	CD	_	_	_
1617	U	U	NNP	_	_	_
1618	_	_	NNP	_	_	_
1619	N0075	N0075	NNP	_	_	_
1620	_	_	VBD	_	_	_
1621	r3	r3	NN	_	_	_
1622	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1623	gyrI	gyri	NN	_	_	_
1624	upregulation	upregulation	NN	_	_	_
1625	,	,	,	_	_	_
1626	0.075	0.075	CD	_	_	_
1627	mg	mg	NN	_	_	_
1628	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1629	hlpA	hlpa	NN	_	_	_
1630	__	__	CD	_	_	_
1631	U	U	NNP	_	_	_
1632	_	_	NNP	_	_	_
1633	N0075	N0075	NNP	_	_	_
1634	_	_	VBD	_	_	_
1635	r1	r1	NN	_	_	_
1636	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1637	hlpA	hlpa	NN	_	_	_
1638	__	__	CD	_	_	_
1639	U	U	NNP	_	_	_
1640	_	_	NNP	_	_	_
1641	N0075	N0075	NNP	_	_	_
1642	_	_	VBD	_	_	_
1643	r2	r2	NN	_	_	_
1644	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1645	hlpA	hlpa	NN	_	_	_
1646	__	__	CD	_	_	_
1647	U	U	NNP	_	_	_
1648	_	_	NNP	_	_	_
1649	N0075	N0075	NNP	_	_	_
1650	_	_	SYM	_	_	_
1651	r3	r3	FW	_	_	_
1652	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
1653	hlpA	hlpa	NN	_	_	_
1654	upregulation	upregulation	NN	_	_	_
1655	,	,	,	_	_	_
1656	0.075	0.075	CD	_	_	_
1657	mg	mg	NN	_	_	_
1658	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1659	holD	hold	VBP	GEN	_	_
1660	__	__	CD	_	_	_
1661	U	U	NNP	_	_	_
1662	_	_	NNP	_	_	_
1663	N0075	N0075	NNP	_	_	_
1664	_	_	VBD	_	_	_
1665	r1	r1	NN	_	_	_
1666	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1667	holD	hold	VBP	GEN	_	_
1668	__	__	CD	_	_	_
1669	U	U	NNP	_	_	_
1670	_	_	NNP	_	_	_
1671	N0075	N0075	NNP	_	_	_
1672	_	_	VBD	_	_	_
1673	r2	r2	NN	_	_	_
1674	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1675	holD	hold	VBP	GEN	_	_
1676	__	__	CD	_	_	_
1677	U	U	NNP	_	_	_
1678	_	_	NNP	_	_	_
1679	N0075	N0075	NNP	_	_	_
1680	_	_	VBD	_	_	_
1681	r3	r3	NN	_	_	_
1682	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
1683	holD	hold	VBP	GEN	_	_
1684	upregulation	upregulation	NN	_	_	_
1685	,	,	,	_	_	_
1686	0.075	0.075	CD	_	_	_
1687	mg	mg	NN	_	_	_
1688	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1689	hscA	hsca	NN	GEN	_	_
1690	__	__	CD	_	_	_
1691	U	U	NNP	_	_	_
1692	_	_	NNP	_	_	_
1693	N0075	N0075	NNP	_	_	_
1694	_	_	SYM	_	_	_
1695	r1	r1	FW	_	_	_
1696	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
1697	hscA	hsca	NN	GEN	_	_
1698	__	__	CD	_	_	_
1699	U	U	NNP	_	_	_
1700	_	_	NNP	_	_	_
1701	N0075	N0075	NNP	_	_	_
1702	_	_	SYM	_	_	_
1703	r2	r2	FW	_	_	_
1704	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
1705	hscA	hsca	NN	GEN	_	_
1706	__	__	CD	_	_	_
1707	U	U	NNP	_	_	_
1708	_	_	NNP	_	_	_
1709	N0075	N0075	NNP	_	_	_
1710	_	_	SYM	_	_	_
1711	r3	r3	FW	_	_	_
1712	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
1713	hscA	hsca	NN	GEN	_	_
1714	upregulation	upregulation	NN	_	_	_
1715	,	,	,	_	_	_
1716	0.075	0.075	CD	_	_	_
1717	mg	mg	NN	_	_	_
1718	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1719	IHF	ihf	NN	TF	_	_
1720	___	___	CD	_	_	_
1721	U	U	NNP	_	_	_
1722	_	_	NNP	_	_	_
1723	N0075	N0075	NNP	_	_	_
1724	_	_	SYM	_	_	_
1725	r1	r1	FW	_	_	_
1726	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
1727	IHF	ihf	NN	TF	_	_
1728	___	___	CD	_	_	_
1729	U	U	NNP	_	_	_
1730	_	_	NNP	_	_	_
1731	N0075	N0075	NNP	_	_	_
1732	_	_	SYM	_	_	_
1733	r3	r3	FW	_	_	_
1734	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
1735	IHF	ihf	NN	TF	_	_
1736	upregulation	upregulation	NN	_	_	_
1737	,	,	,	_	_	_
1738	0.075	0.075	CD	_	_	_
1739	mg	mg	NN	_	_	_
1740	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1741	ik	ik	NN	_	_	_
1742	_	_	NN	_	_	_
1743	H2	h2	NN	_	_	_
1744	_	_	CD	_	_	_
1745	T2	t2	NN	_	_	_
1746	.5	.5	CD	_	_	_
1747	_	_	NN	_	_	_
1748	r1	r1	NN	_	_	_
1749	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1750	ik	ik	NN	_	_	_
1751	_	_	NN	_	_	_
1752	H2	h2	NN	_	_	_
1753	_	_	CD	_	_	_
1754	T3	t3	NN	_	_	_
1755	.5	.5	CD	_	_	_
1756	_	_	NN	_	_	_
1757	r1	r1	NN	_	_	_
1758	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1759	ik	ik	NN	_	_	_
1760	_	_	NN	_	_	_
1761	H2	h2	NN	_	_	_
1762	_	_	CD	_	_	_
1763	T3	t3	NN	_	_	_
1764	_	_	CD	_	_	_
1765	r1	r1	NN	_	_	_
1766	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1767	ik	ik	NN	_	_	_
1768	_	_	NN	_	_	_
1769	H2	h2	NN	_	_	_
1770	_	_	CD	_	_	_
1771	T4	t4	NN	_	_	_
1772	.5	.5	CD	_	_	_
1773	_	_	NN	_	_	_
1774	r1	r1	NN	_	_	_
1775	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1776	ik	ik	NN	_	_	_
1777	_	_	NN	_	_	_
1778	H2	h2	NN	_	_	_
1779	_	_	CD	_	_	_
1780	T4	t4	NN	_	_	_
1781	_	_	CD	_	_	_
1782	r1	r1	NN	_	_	_
1783	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1784	ik	ik	NN	_	_	_
1785	_	_	NN	_	_	_
1786	H2	h2	NN	_	_	_
1787	_	_	CD	_	_	_
1788	T5	t5	NN	_	_	_
1789	.5	.5	CD	_	_	_
1790	_	_	NN	_	_	_
1791	r1	r1	NN	_	_	_
1792	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1793	ik	ik	NN	_	_	_
1794	_	_	NN	_	_	_
1795	H2	h2	NN	_	_	_
1796	_	_	CD	_	_	_
1797	T5	t5	NN	_	_	_
1798	_	_	CD	_	_	_
1799	r1	r1	NN	_	_	_
1800	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1801	ik	ik	NN	_	_	_
1802	_	_	NN	_	_	_
1803	H2	h2	NN	_	_	_
1804	_	_	CD	_	_	_
1805	T6	t6	NN	_	_	_
1806	_	_	CD	_	_	_
1807	r1	r1	NN	_	_	_
1808	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1809	ik	ik	NN	_	_	_
1810	_	_	NN	_	_	_
1811	H2	h2	NN	_	_	_
1812	_	_	CD	_	_	_
1813	T8	t8	NN	_	_	_
1814	_	_	CD	_	_	_
1815	r1	r1	NN	_	_	_
1816	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1817	ik	ik	NN	_	_	_
1818	_	_	NN	_	_	_
1819	L2	l2	NN	_	_	_
1820	_	_	CD	_	_	_
1821	T2	t2	NN	_	_	_
1822	.5	.5	CD	_	_	_
1823	_	_	NN	_	_	_
1824	r1	r1	NN	_	_	_
1825	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1826	ik	ik	NN	_	_	_
1827	_	_	NN	_	_	_
1828	L2	l2	NN	_	_	_
1829	_	_	CD	_	_	_
1830	T3	t3	NN	_	_	_
1831	.5	.5	CD	_	_	_
1832	_	_	NN	_	_	_
1833	r1	r1	NN	_	_	_
1834	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1835	ik	ik	NN	_	_	_
1836	_	_	NN	_	_	_
1837	L2	l2	NN	_	_	_
1838	_	_	CD	_	_	_
1839	T3	t3	NN	_	_	_
1840	_	_	CD	_	_	_
1841	r1	r1	NN	_	_	_
1842	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1843	ik	ik	NN	_	_	_
1844	_	_	NN	_	_	_
1845	L2	l2	NN	_	_	_
1846	_	_	CD	_	_	_
1847	T4	t4	NN	_	_	_
1848	.5	.5	CD	_	_	_
1849	_	_	NN	_	_	_
1850	r1	r1	NN	_	_	_
1851	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1852	ik	ik	NN	_	_	_
1853	_	_	NN	_	_	_
1854	L2	l2	NN	_	_	_
1855	_	_	CD	_	_	_
1856	T4	t4	NN	_	_	_
1857	_	_	CD	_	_	_
1858	r1	r1	NN	_	_	_
1859	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1860	ik	ik	NN	_	_	_
1861	_	_	NN	_	_	_
1862	L2	l2	NN	_	_	_
1863	_	_	CD	_	_	_
1864	T5	t5	NN	_	_	_
1865	.5	.5	CD	_	_	_
1866	_	_	NN	_	_	_
1867	r1	r1	NN	_	_	_
1868	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1869	ik	ik	NN	_	_	_
1870	_	_	NN	_	_	_
1871	L2	l2	NN	_	_	_
1872	_	_	CD	_	_	_
1873	T5	t5	NN	_	_	_
1874	_	_	CD	_	_	_
1875	r1	r1	NN	_	_	_
1876	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1877	ik	ik	NN	_	_	_
1878	_	_	NN	_	_	_
1879	L2	l2	NN	_	_	_
1880	_	_	CD	_	_	_
1881	T6	t6	NN	_	_	_
1882	_	_	CD	_	_	_
1883	r1	r1	NN	_	_	_
1884	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1885	ik	ik	NN	_	_	_
1886	_	_	NN	_	_	_
1887	L2	l2	NN	_	_	_
1888	_	_	CD	_	_	_
1889	T8	t8	NN	_	_	_
1890	_	_	CD	_	_	_
1891	r1	r1	NN	_	_	_
1892	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1893	K12	k12	NN	_	_	_
1894	EMG2	emg2	NN	_	_	_
1895	on	on	IN	_	_	_
1896	LB	lb	NN	_	_	_
1897	with	with	IN	_	_	_
1898	0.2	0.2	CD	_	_	_
1899	percent	percent	NN	_	_	_
1900	glucose	glucose	NN	SUPP	_	_
1901	,	,	,	_	_	_
1902	2.5	2.5	CD	_	_	_
1903	hours	hour	NNS	_	_	_
1904	post-incubation	post-incubation	JJ	_	_	_
1905	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1906	K12	k12	NN	_	_	_
1907	EMG2	emg2	NN	_	_	_
1908	on	on	IN	_	_	_
1909	LB	lb	NN	_	_	_
1910	with	with	IN	_	_	_
1911	0.2	0.2	CD	_	_	_
1912	percent	percent	NN	_	_	_
1913	glucose	glucose	NN	SUPP	_	_
1914	,	,	,	_	_	_
1915	3.5	3.5	CD	_	_	_
1916	hours	hour	NNS	_	_	_
1917	post-incubation	post-incubation	JJ	_	_	_
1918	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1919	K12	k12	NN	_	_	_
1920	EMG2	emg2	NN	_	_	_
1921	on	on	IN	_	_	_
1922	LB	lb	NN	_	_	_
1923	with	with	IN	_	_	_
1924	0.2	0.2	CD	_	_	_
1925	percent	percent	NN	_	_	_
1926	glucose	glucose	NN	SUPP	_	_
1927	,	,	,	_	_	_
1928	3	3	CD	_	_	_
1929	hours	hour	NNS	_	_	_
1930	post-incubation	post-incubation	JJ	_	_	_
1931	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1932	K12	k12	NN	_	_	_
1933	EMG2	emg2	NN	_	_	_
1934	on	on	IN	_	_	_
1935	LB	lb	NN	_	_	_
1936	with	with	IN	_	_	_
1937	0.2	0.2	CD	_	_	_
1938	percent	percent	NN	_	_	_
1939	glucose	glucose	NN	SUPP	_	_
1940	,	,	,	_	_	_
1941	4.5	4.5	CD	_	_	_
1942	hours	hour	NNS	_	_	_
1943	post-incubation	post-incubation	JJ	_	_	_
1944	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1945	K12	k12	NN	_	_	_
1946	EMG2	emg2	NN	_	_	_
1947	on	on	IN	_	_	_
1948	LB	lb	NN	_	_	_
1949	with	with	IN	_	_	_
1950	0.2	0.2	CD	_	_	_
1951	percent	percent	NN	_	_	_
1952	glucose	glucose	NN	SUPP	_	_
1953	,	,	,	_	_	_
1954	4	4	CD	_	_	_
1955	hours	hour	NNS	_	_	_
1956	post-incubation	post-incubation	JJ	_	_	_
1957	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1958	K12	k12	NN	_	_	_
1959	EMG2	emg2	NN	_	_	_
1960	on	on	IN	_	_	_
1961	LB	lb	NN	_	_	_
1962	with	with	IN	_	_	_
1963	0.2	0.2	CD	_	_	_
1964	percent	percent	NN	_	_	_
1965	glucose	glucose	NN	SUPP	_	_
1966	,	,	,	_	_	_
1967	5.5	5.5	CD	_	_	_
1968	hours	hour	NNS	_	_	_
1969	post-incubation	post-incubation	JJ	_	_	_
1970	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1971	K12	k12	NN	_	_	_
1972	EMG2	emg2	NN	_	_	_
1973	on	on	IN	_	_	_
1974	LB	lb	NN	_	_	_
1975	with	with	IN	_	_	_
1976	0.2	0.2	CD	_	_	_
1977	percent	percent	NN	_	_	_
1978	glucose	glucose	NN	SUPP	_	_
1979	,	,	,	_	_	_
1980	5	5	CD	_	_	_
1981	hours	hour	NNS	_	_	_
1982	post-incubation	post-incubation	JJ	_	_	_
1983	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1984	K12	k12	NN	_	_	_
1985	EMG2	emg2	NN	_	_	_
1986	on	on	IN	_	_	_
1987	LB	lb	NN	_	_	_
1988	with	with	IN	_	_	_
1989	0.2	0.2	CD	_	_	_
1990	percent	percent	NN	_	_	_
1991	glucose	glucose	NN	SUPP	_	_
1992	,	,	,	_	_	_
1993	6	6	CD	_	_	_
1994	hours	hour	NNS	_	_	_
1995	post-incubation	post-incubation	JJ	_	_	_
1996	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1997	K12	k12	NN	_	_	_
1998	EMG2	emg2	NN	_	_	_
1999	on	on	IN	_	_	_
2000	LB	lb	NN	_	_	_
2001	with	with	IN	_	_	_
2002	0.2	0.2	CD	_	_	_
2003	percent	percent	NN	_	_	_
2004	glucose	glucose	NN	SUPP	_	_
2005	,	,	,	_	_	_
2006	8	8	CD	_	_	_
2007	hours	hour	NNS	_	_	_
2008	post-incubation	post-incubation	JJ	_	_	_
2009	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2010	K12	k12	NN	_	_	_
2011	EMG2	emg2	NN	_	_	_
2012	on	on	IN	_	_	_
2013	LB	lb	NN	_	_	_
2014	with	with	IN	_	_	_
2015	0.4	0.4	CD	_	_	_
2016	percent	percent	NN	_	_	_
2017	glucose	glucose	NN	SUPP	_	_
2018	,	,	,	_	_	_
2019	2.5	2.5	CD	_	_	_
2020	hours	hour	NNS	_	_	_
2021	post-incubation	post-incubation	JJ	_	_	_
2022	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2023	K12	k12	NN	_	_	_
2024	EMG2	emg2	NN	_	_	_
2025	on	on	IN	_	_	_
2026	LB	lb	NN	_	_	_
2027	with	with	IN	_	_	_
2028	0.4	0.4	CD	_	_	_
2029	percent	percent	NN	_	_	_
2030	glucose	glucose	NN	SUPP	_	_
2031	,	,	,	_	_	_
2032	3.5	3.5	CD	_	_	_
2033	hours	hour	NNS	_	_	_
2034	post-incubation	post-incubation	JJ	_	_	_
2035	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2036	K12	k12	NN	_	_	_
2037	EMG2	emg2	NN	_	_	_
2038	on	on	IN	_	_	_
2039	LB	lb	NN	_	_	_
2040	with	with	IN	_	_	_
2041	0.4	0.4	CD	_	_	_
2042	percent	percent	NN	_	_	_
2043	glucose	glucose	NN	SUPP	_	_
2044	,	,	,	_	_	_
2045	3	3	CD	_	_	_
2046	hours	hour	NNS	_	_	_
2047	post-incubation	post-incubation	JJ	_	_	_
2048	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2049	K12	k12	NN	_	_	_
2050	EMG2	emg2	NN	_	_	_
2051	on	on	IN	_	_	_
2052	LB	lb	NN	_	_	_
2053	with	with	IN	_	_	_
2054	0.4	0.4	CD	_	_	_
2055	percent	percent	NN	_	_	_
2056	glucose	glucose	NN	SUPP	_	_
2057	,	,	,	_	_	_
2058	4.5	4.5	CD	_	_	_
2059	hours	hour	NNS	_	_	_
2060	post-incubation	post-incubation	JJ	_	_	_
2061	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2062	K12	k12	NN	_	_	_
2063	EMG2	emg2	NN	_	_	_
2064	on	on	IN	_	_	_
2065	LB	lb	NN	_	_	_
2066	with	with	IN	_	_	_
2067	0.4	0.4	CD	_	_	_
2068	percent	percent	NN	_	_	_
2069	glucose	glucose	NN	SUPP	_	_
2070	,	,	,	_	_	_
2071	4	4	CD	_	_	_
2072	hours	hour	NNS	_	_	_
2073	post-incubation	post-incubation	JJ	_	_	_
2074	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2075	K12	k12	NN	_	_	_
2076	EMG2	emg2	NN	_	_	_
2077	on	on	IN	_	_	_
2078	LB	lb	NN	_	_	_
2079	with	with	IN	_	_	_
2080	0.4	0.4	CD	_	_	_
2081	percent	percent	NN	_	_	_
2082	glucose	glucose	NN	SUPP	_	_
2083	,	,	,	_	_	_
2084	5.5	5.5	CD	_	_	_
2085	hours	hour	NNS	_	_	_
2086	post-incubation	post-incubation	JJ	_	_	_
2087	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2088	K12	k12	NN	_	_	_
2089	EMG2	emg2	NN	_	_	_
2090	on	on	IN	_	_	_
2091	LB	lb	NN	_	_	_
2092	with	with	IN	_	_	_
2093	0.4	0.4	CD	_	_	_
2094	percent	percent	NN	_	_	_
2095	glucose	glucose	NN	SUPP	_	_
2096	,	,	,	_	_	_
2097	5	5	CD	_	_	_
2098	hours	hour	NNS	_	_	_
2099	post-incubation	post-incubation	JJ	_	_	_
2100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2101	K12	k12	NN	_	_	_
2102	EMG2	emg2	NN	_	_	_
2103	on	on	IN	_	_	_
2104	LB	lb	NN	_	_	_
2105	with	with	IN	_	_	_
2106	0.4	0.4	CD	_	_	_
2107	percent	percent	NN	_	_	_
2108	glucose	glucose	NN	SUPP	_	_
2109	,	,	,	_	_	_
2110	6	6	CD	_	_	_
2111	hours	hour	NNS	_	_	_
2112	post-incubation	post-incubation	JJ	_	_	_
2113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2114	K12	k12	NN	_	_	_
2115	EMG2	emg2	NN	_	_	_
2116	on	on	IN	_	_	_
2117	LB	lb	NN	_	_	_
2118	with	with	IN	_	_	_
2119	0.4	0.4	CD	_	_	_
2120	percent	percent	NN	_	_	_
2121	glucose	glucose	NN	SUPP	_	_
2122	,	,	,	_	_	_
2123	8	8	CD	_	_	_
2124	hours	hour	NNS	_	_	_
2125	post-incubation	post-incubation	JJ	_	_	_
2126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2127	lacZ	lacz	NN	GEN	_	_
2128	_	_	CD	_	_	_
2129	K12	k12	NN	_	_	_
2130	_	_	NN	_	_	_
2131	0	0	CD	_	_	_
2132	_	_	NN	_	_	_
2133	r1	r1	NN	_	_	_
2134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2135	lacZ	lacz	NN	GEN	_	_
2136	_	_	CD	_	_	_
2137	K12	k12	NN	_	_	_
2138	_	_	NN	_	_	_
2139	120	120	CD	_	_	_
2140	_	_	NN	_	_	_
2141	r1	r1	NN	_	_	_
2142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2143	lacZ	lacz	NN	GEN	_	_
2144	_	_	CD	_	_	_
2145	K12	k12	NN	_	_	_
2146	_	_	CD	_	_	_
2147	30	30	CD	_	_	_
2148	_	_	NN	_	_	_
2149	r1	r1	NN	_	_	_
2150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2151	lacZ	lacz	NN	GEN	_	_
2152	_	_	CD	_	_	_
2153	K12	k12	NN	_	_	_
2154	_	_	NN	_	_	_
2155	60	60	CD	_	_	_
2156	_	_	NN	_	_	_
2157	r1	r1	NN	_	_	_
2158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2159	lacZ	lacz	NN	GEN	_	_
2160	_	_	CD	_	_	_
2161	K12	k12	NN	_	_	_
2162	_	_	NN	_	_	_
2163	90	90	CD	_	_	_
2164	_	_	NN	_	_	_
2165	r1	r1	NN	_	_	_
2166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2167	lacZ	lacz	NN	GEN	_	_
2168	_	_	CD	_	_	_
2169	MG1063	mg1063	NN	_	_	_
2170	_	_	NN	_	_	_
2171	0	0	CD	_	_	_
2172	_	_	NN	_	_	_
2173	r1	r1	NN	_	_	_
2174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2175	lacZ	lacz	NN	GEN	_	_
2176	_	_	CD	_	_	_
2177	MG1063	mg1063	NN	_	_	_
2178	_	_	NN	_	_	_
2179	0	0	CD	_	_	_
2180	_	_	NN	_	_	_
2181	r2	r2	NN	_	_	_
2182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2183	lacZ	lacz	NN	GEN	_	_
2184	_	_	CD	_	_	_
2185	MG1063	mg1063	NN	_	_	_
2186	_	_	NN	_	_	_
2187	120	120	CD	_	_	_
2188	_	_	NN	_	_	_
2189	r1	r1	NN	_	_	_
2190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2191	lacZ	lacz	NN	GEN	_	_
2192	_	_	CD	_	_	_
2193	MG1063	mg1063	NN	_	_	_
2194	_	_	CD	_	_	_
2195	30	30	CD	_	_	_
2196	_	_	NN	_	_	_
2197	r1	r1	NN	_	_	_
2198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2199	lacZ	lacz	NN	GEN	_	_
2200	_	_	CD	_	_	_
2201	MG1063	mg1063	NN	_	_	_
2202	_	_	CD	_	_	_
2203	30	30	CD	_	_	_
2204	_	_	NN	_	_	_
2205	r2	r2	NN	_	_	_
2206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2207	lacZ	lacz	NN	GEN	_	_
2208	_	_	CD	_	_	_
2209	MG1063	mg1063	NN	_	_	_
2210	_	_	NN	_	_	_
2211	60	60	CD	_	_	_
2212	_	_	NN	_	_	_
2213	r1	r1	NN	_	_	_
2214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2215	lacZ	lacz	NN	GEN	_	_
2216	_	_	CD	_	_	_
2217	MG1063	mg1063	NN	_	_	_
2218	_	_	NN	_	_	_
2219	60	60	CD	_	_	_
2220	_	_	NN	_	_	_
2221	r2	r2	NN	_	_	_
2222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2223	lacZ	lacz	NN	GEN	_	_
2224	_	_	CD	_	_	_
2225	MG1063	mg1063	NN	_	_	_
2226	_	_	NN	_	_	_
2227	90	90	CD	_	_	_
2228	_	_	NN	_	_	_
2229	r1	r1	NN	_	_	_
2230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2231	lacZ	lacz	NN	GEN	_	_
2232	_	_	CD	_	_	_
2233	MG1063	mg1063	NN	_	_	_
2234	_	_	NN	_	_	_
2235	90	90	CD	_	_	_
2236	_	_	NN	_	_	_
2237	r2	r2	NN	_	_	_
2238	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2239	lacZ	lacz	NN	GEN	_	_
2240	_	_	CD	_	_	_
2241	W1863	w1863	NN	_	_	_
2242	_	_	NN	_	_	_
2243	0	0	CD	_	_	_
2244	_	_	NN	_	_	_
2245	r1	r1	NN	_	_	_
2246	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2247	lacZ	lacz	NN	GEN	_	_
2248	_	_	CD	_	_	_
2249	W1863	w1863	NN	_	_	_
2250	_	_	CD	_	_	_
2251	30	30	CD	_	_	_
2252	_	_	NN	_	_	_
2253	r1	r1	NN	_	_	_
2254	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2255	lacZ	lacz	NN	GEN	_	_
2256	_	_	CD	_	_	_
2257	W1863	w1863	NN	_	_	_
2258	_	_	NN	_	_	_
2259	60	60	CD	_	_	_
2260	_	_	NN	_	_	_
2261	r1	r1	NN	_	_	_
2262	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2263	lacZ	lacz	NN	GEN	_	_
2264	_	_	CD	_	_	_
2265	W1863	w1863	NN	_	_	_
2266	_	_	NN	_	_	_
2267	90	90	CD	_	_	_
2268	_	_	NN	_	_	_
2269	r1	r1	NN	_	_	_
2270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2271	ldrA	ldra	NN	GEN	_	_
2272	__	__	CD	_	_	_
2273	U	U	NNP	_	_	_
2274	_	_	NNP	_	_	_
2275	N0075	N0075	NNP	_	_	_
2276	_	_	VBD	_	_	_
2277	r1	r1	NN	_	_	_
2278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2279	ldrA	ldra	NN	GEN	_	_
2280	__	__	CD	_	_	_
2281	U	U	NNP	_	_	_
2282	_	_	NNP	_	_	_
2283	N0075	N0075	NNP	_	_	_
2284	_	_	VBD	_	_	_
2285	r2	r2	NN	_	_	_
2286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2287	ldrA	ldra	NN	GEN	_	_
2288	__	__	CD	_	_	_
2289	U	U	NNP	_	_	_
2290	_	_	NNP	_	_	_
2291	N0075	N0075	NNP	_	_	_
2292	_	_	VBD	_	_	_
2293	r3	r3	NN	_	_	_
2294	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2295	ldrA	ldra	NN	GEN	_	_
2296	upregulation	upregulation	NN	_	_	_
2297	,	,	,	_	_	_
2298	0.075	0.075	CD	_	_	_
2299	mg	mg	NN	_	_	_
2300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2301	lexA	lexa	NN	GEN	_	_
2302	___	___	CD	_	_	_
2303	U	U	NNP	_	_	_
2304	_	_	NNP	_	_	_
2305	N0025	N0025	NNP	_	_	_
2306	_	_	SYM	_	_	_
2307	r1	r1	FW	_	_	_
2308	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2309	lexA	lexa	NN	GEN	_	_
2310	___	___	CD	_	_	_
2311	U	U	NNP	_	_	_
2312	_	_	NNP	_	_	_
2313	N0025	N0025	NNP	_	_	_
2314	_	_	SYM	_	_	_
2315	r2	r2	FW	_	_	_
2316	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2317	lexA	lexa	NN	GEN	_	_
2318	___	___	CD	_	_	_
2319	U	U	NNP	_	_	_
2320	_	_	NNP	_	_	_
2321	N0025	N0025	NNP	_	_	_
2322	_	_	SYM	_	_	_
2323	r3	r3	FW	_	_	_
2324	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2325	lexA	lexa	NN	GEN	_	_
2326	upregulation	upregulation	NN	_	_	_
2327	,	,	,	_	_	_
2328	amp	amp	NN	_	_	_
2329	50ug	50ug	JJ	_	_	_
2330	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2331	lon	lon	NN	GEN	_	_
2332	___	___	CD	_	_	_
2333	U	U	NNP	_	_	_
2334	_	_	NNP	_	_	_
2335	N0025	N0025	NNP	_	_	_
2336	_	_	NNP	_	_	_
2337	r1	r1	NN	_	_	_
2338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2339	lon	lon	NN	GEN	_	_
2340	___	___	CD	_	_	_
2341	U	U	NNP	_	_	_
2342	_	_	NNP	_	_	_
2343	N0025	N0025	NNP	_	_	_
2344	_	_	NNP	_	_	_
2345	r2	r2	NN	_	_	_
2346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2347	lon	lon	NN	GEN	_	_
2348	___	___	CD	_	_	_
2349	U	U	NNP	_	_	_
2350	_	_	NNP	_	_	_
2351	N0025	N0025	NNP	_	_	_
2352	_	_	NNP	_	_	_
2353	r3	r3	NN	_	_	_
2354	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2355	lon	lon	NN	GEN	_	_
2356	upregulation	upregulation	NN	_	_	_
2357	,	,	,	_	_	_
2358	amp	amp	NN	_	_	_
2359	50ug	50ug	JJ	_	_	_
2360	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2361	luc2	luc2	NN	_	_	_
2362	_	_	CD	_	_	_
2363	U	U	NNP	_	_	_
2364	_	_	NNP	_	_	_
2365	N0000	N0000	NNP	_	_	_
2366	_	_	VBD	_	_	_
2367	r1	r1	NN	_	_	_
2368	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2369	luc2	luc2	NN	_	_	_
2370	_	_	CD	_	_	_
2371	U	U	NNP	_	_	_
2372	_	_	NNP	_	_	_
2373	N0000	N0000	NNP	_	_	_
2374	_	_	VBD	_	_	_
2375	r2	r2	NN	_	_	_
2376	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2377	luc2	luc2	NN	_	_	_
2378	_	_	CD	_	_	_
2379	U	U	NNP	_	_	_
2380	_	_	NNP	_	_	_
2381	N0025	N0025	NNP	_	_	_
2382	_	_	VBD	_	_	_
2383	r1	r1	NN	_	_	_
2384	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2385	luc2	luc2	NN	_	_	_
2386	_	_	CD	_	_	_
2387	U	U	NNP	_	_	_
2388	_	_	NNP	_	_	_
2389	N0025	N0025	NNP	_	_	_
2390	_	_	VBD	_	_	_
2391	r2	r2	NN	_	_	_
2392	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2393	luciferase	luciferase	NN	_	_	_
2394	0.025	0.025	CD	_	_	_
2395	ug	ug	NN	_	_	_
2396	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2397	luciferase	luciferase	NN	_	_	_
2398	no	no	DT	_	_	_
2399	drug	drug	NN	_	_	_
2400	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2401	luc	luc	NN	_	_	_
2402	___	___	CD	_	_	_
2403	U	U	NNP	_	_	_
2404	_	_	NNP	_	_	_
2405	N0000	N0000	NNP	_	_	_
2406	_	_	NNP	_	_	_
2407	r1	r1	NN	_	_	_
2408	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2409	luc	luc	NN	_	_	_
2410	___	___	CD	_	_	_
2411	U	U	NNP	_	_	_
2412	_	_	NNP	_	_	_
2413	N0000	N0000	NNP	_	_	_
2414	_	_	NNP	_	_	_
2415	r2	r2	NN	_	_	_
2416	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2417	luc	luc	NN	_	_	_
2418	___	___	CD	_	_	_
2419	U	U	NNP	_	_	_
2420	_	_	NNP	_	_	_
2421	N0000	N0000	NNP	_	_	_
2422	_	_	NNP	_	_	_
2423	r3	r3	NN	_	_	_
2424	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2425	luc	luc	NN	_	_	_
2426	___	___	CD	_	_	_
2427	U	U	NNP	_	_	_
2428	_	_	NNP	_	_	_
2429	N0025	N0025	NNP	_	_	_
2430	_	_	NNP	_	_	_
2431	r1	r1	NN	_	_	_
2432	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2433	luc	luc	NN	_	_	_
2434	___	___	CD	_	_	_
2435	U	U	NNP	_	_	_
2436	_	_	NNP	_	_	_
2437	N0025	N0025	NNP	_	_	_
2438	_	_	NNP	_	_	_
2439	r2	r2	NN	_	_	_
2440	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2441	luc	luc	NN	_	_	_
2442	___	___	CD	_	_	_
2443	U	U	NNP	_	_	_
2444	_	_	NNP	_	_	_
2445	N0025	N0025	NNP	_	_	_
2446	_	_	NNP	_	_	_
2447	r3	r3	NN	_	_	_
2448	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2449	luc	luc	NN	_	_	_
2450	___	___	CD	_	_	_
2451	U	U	NNP	_	_	_
2452	_	_	NNP	_	_	_
2453	N0075	N0075	NNP	_	_	_
2454	_	_	NNP	_	_	_
2455	r1	r1	NN	_	_	_
2456	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2457	luc	luc	NN	_	_	_
2458	___	___	CD	_	_	_
2459	U	U	NNP	_	_	_
2460	_	_	NNP	_	_	_
2461	N0075	N0075	NNP	_	_	_
2462	_	_	NNP	_	_	_
2463	r2	r2	NN	_	_	_
2464	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2465	luc	luc	NN	_	_	_
2466	___	___	CD	_	_	_
2467	U	U	NNP	_	_	_
2468	_	_	NNP	_	_	_
2469	N0075	N0075	NNP	_	_	_
2470	_	_	NNP	_	_	_
2471	r3	r3	NN	_	_	_
2472	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2473	luc	luc	NN	_	_	_
2474	upregulation	upregulation	NN	_	_	_
2475	,	,	,	_	_	_
2476	0.000	0.000	CD	_	_	_
2477	ug	ug	NN	_	_	_
2478	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2479	luc	luc	NN	_	_	_
2480	upregulation	upregulation	NN	_	_	_
2481	,	,	,	_	_	_
2482	0.075	0.075	CD	_	_	_
2483	ug	ug	NN	_	_	_
2484	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2485	luc	luc	NN	_	_	_
2486	upregulation	upregulation	NN	_	_	_
2487	,	,	,	_	_	_
2488	amp	amp	NN	_	_	_
2489	50ug	50ug	JJ	_	_	_
2490	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2491	mazF	mazf	NN	GEN	_	_
2492	_	_	CD	_	_	_
2493	chpA	chpa	NN	_	_	_
2494	upregulation	upregulation	NN	_	_	_
2495	,	,	,	_	_	_
2496	amp	amp	NN	_	_	_
2497	50ug	50ug	JJ	_	_	_
2498	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2499	mazF	mazf	NN	GEN	_	_
2500	___	___	CD	_	_	_
2501	U	U	NNP	_	_	_
2502	_	_	NNP	_	_	_
2503	N0025	N0025	NNP	_	_	_
2504	_	_	VBD	_	_	_
2505	r1	r1	NN	_	_	_
2506	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2507	mazF	mazf	NN	GEN	_	_
2508	___	___	CD	_	_	_
2509	U	U	NNP	_	_	_
2510	_	_	NNP	_	_	_
2511	N0025	N0025	NNP	_	_	_
2512	_	_	VBD	_	_	_
2513	r2	r2	NN	_	_	_
2514	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2515	mazF	mazf	NN	GEN	_	_
2516	___	___	CD	_	_	_
2517	U	U	NNP	_	_	_
2518	_	_	NNP	_	_	_
2519	N0025	N0025	NNP	_	_	_
2520	_	_	VBD	_	_	_
2521	r3	r3	NN	_	_	_
2522	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2523	mcrB	mcrb	NN	GEN	_	_
2524	__	__	CD	_	_	_
2525	U	U	NNP	_	_	_
2526	_	_	NNP	_	_	_
2527	N0075	N0075	NNP	_	_	_
2528	_	_	VBD	_	_	_
2529	r1	r1	NN	_	_	_
2530	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2531	mcrB	mcrb	NN	GEN	_	_
2532	__	__	CD	_	_	_
2533	U	U	NNP	_	_	_
2534	_	_	NNP	_	_	_
2535	N0075	N0075	NNP	_	_	_
2536	_	_	VBD	_	_	_
2537	r2	r2	NN	_	_	_
2538	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2539	mcrB	mcrb	NN	GEN	_	_
2540	__	__	CD	_	_	_
2541	U	U	NNP	_	_	_
2542	_	_	NNP	_	_	_
2543	N0075	N0075	NNP	_	_	_
2544	_	_	VBD	_	_	_
2545	r3	r3	NN	_	_	_
2546	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2547	mcrB	mcrb	NN	GEN	_	_
2548	upregulation	upregulation	NN	_	_	_
2549	,	,	,	_	_	_
2550	0.075	0.075	CD	_	_	_
2551	mg	mg	NN	_	_	_
2552	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2553	mcrC	mcrc	NN	GEN	_	_
2554	__	__	CD	_	_	_
2555	U	U	NNP	_	_	_
2556	_	_	NNP	_	_	_
2557	N0075	N0075	NNP	_	_	_
2558	_	_	VBD	_	_	_
2559	r1	r1	NN	_	_	_
2560	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2561	mcrC	mcrc	NN	GEN	_	_
2562	__	__	CD	_	_	_
2563	U	U	NNP	_	_	_
2564	_	_	NNP	_	_	_
2565	N0075	N0075	NNP	_	_	_
2566	_	_	VBD	_	_	_
2567	r2	r2	NN	_	_	_
2568	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2569	mcrC	mcrc	NN	GEN	_	_
2570	__	__	CD	_	_	_
2571	U	U	NNP	_	_	_
2572	_	_	NNP	_	_	_
2573	N0075	N0075	NNP	_	_	_
2574	_	_	VBD	_	_	_
2575	r3	r3	NN	_	_	_
2576	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2577	mcrC	mcrc	NN	GEN	_	_
2578	upregulation	upregulation	NN	_	_	_
2579	,	,	,	_	_	_
2580	0.075	0.075	CD	_	_	_
2581	mg	mg	NN	_	_	_
2582	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2583	menB	menb	NN	GEN	_	_
2584	__	__	CD	_	_	_
2585	U	U	NNP	_	_	_
2586	_	_	NNP	_	_	_
2587	N0075	N0075	NNP	_	_	_
2588	_	_	VBD	_	_	_
2589	r1	r1	NN	_	_	_
2590	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2591	menB	menb	NN	GEN	_	_
2592	__	__	CD	_	_	_
2593	U	U	NNP	_	_	_
2594	_	_	NNP	_	_	_
2595	N0075	N0075	NNP	_	_	_
2596	_	_	VBD	_	_	_
2597	r2	r2	NN	_	_	_
2598	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2599	menB	menb	NN	GEN	_	_
2600	__	__	CD	_	_	_
2601	U	U	NNP	_	_	_
2602	_	_	NNP	_	_	_
2603	N0075	N0075	NNP	_	_	_
2604	_	_	VBD	_	_	_
2605	r3	r3	NN	_	_	_
2606	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2607	menB	menb	NN	GEN	_	_
2608	upregulation	upregulation	NN	_	_	_
2609	,	,	,	_	_	_
2610	0.075	0.075	CD	_	_	_
2611	mg	mg	NN	_	_	_
2612	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2613	menC	menc	NN	GEN	_	_
2614	__	__	CD	_	_	_
2615	U	U	NNP	_	_	_
2616	_	_	NNP	_	_	_
2617	N0075	N0075	NNP	_	_	_
2618	_	_	NNP	_	_	_
2619	r1	r1	NN	_	_	_
2620	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2621	menC	menc	NN	GEN	_	_
2622	__	__	CD	_	_	_
2623	U	U	NNP	_	_	_
2624	_	_	NNP	_	_	_
2625	N0075	N0075	NNP	_	_	_
2626	_	_	SYM	_	_	_
2627	r2	r2	FW	_	_	_
2628	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2629	menC	menc	NN	GEN	_	_
2630	__	__	CD	_	_	_
2631	U	U	NNP	_	_	_
2632	_	_	NNP	_	_	_
2633	N0075	N0075	NNP	_	_	_
2634	_	_	SYM	_	_	_
2635	r3	r3	FW	_	_	_
2636	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2637	menC	menc	NN	GEN	_	_
2638	upregulation	upregulation	NN	_	_	_
2639	,	,	,	_	_	_
2640	0.075	0.075	CD	_	_	_
2641	mg	mg	NN	_	_	_
2642	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2643	minD	mind	NN	GEN	_	_
2644	__	__	CD	_	_	_
2645	U	U	NNP	_	_	_
2646	_	_	NNP	_	_	_
2647	N0075	N0075	NNP	_	_	_
2648	_	_	NNP	_	_	_
2649	r1	r1	NN	_	_	_
2650	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2651	minD	mind	NN	GEN	_	_
2652	__	__	CD	_	_	_
2653	U	U	NNP	_	_	_
2654	_	_	NNP	_	_	_
2655	N0075	N0075	NNP	_	_	_
2656	_	_	SYM	_	_	_
2657	r2	r2	FW	_	_	_
2658	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2659	minD	mind	NN	GEN	_	_
2660	__	__	CD	_	_	_
2661	U	U	NNP	_	_	_
2662	_	_	NNP	_	_	_
2663	N0075	N0075	NNP	_	_	_
2664	_	_	SYM	_	_	_
2665	r3	r3	FW	_	_	_
2666	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2667	minD	mind	NN	GEN	_	_
2668	upregulation	upregulation	NN	_	_	_
2669	,	,	,	_	_	_
2670	0.075	0.075	CD	_	_	_
2671	mg	mg	NN	_	_	_
2672	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2673	minE	mine	NN	GEN	_	_
2674	__	__	CD	_	_	_
2675	U	U	NNP	_	_	_
2676	_	_	NNP	_	_	_
2677	N0075	N0075	NNP	_	_	_
2678	_	_	NNP	_	_	_
2679	r1	r1	NN	_	_	_
2680	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2681	minE	mine	NN	GEN	_	_
2682	__	__	CD	_	_	_
2683	U	U	NNP	_	_	_
2684	_	_	NNP	_	_	_
2685	N0075	N0075	NNP	_	_	_
2686	_	_	NNP	_	_	_
2687	r2	r2	NN	_	_	_
2688	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2689	minE	mine	NN	GEN	_	_
2690	__	__	CD	_	_	_
2691	U	U	NNP	_	_	_
2692	_	_	NNP	_	_	_
2693	N0075	N0075	NNP	_	_	_
2694	_	_	SYM	_	_	_
2695	r3	r3	FW	_	_	_
2696	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2697	minE	mine	NN	GEN	_	_
2698	upregulation	upregulation	NN	_	_	_
2699	,	,	,	_	_	_
2700	0.075	0.075	CD	_	_	_
2701	mg	mg	NN	_	_	_
2702	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2703	murI	muri	NN	GEN	_	_
2704	__	__	CD	_	_	_
2705	U	U	NNP	_	_	_
2706	_	_	NNP	_	_	_
2707	N0075	N0075	NNP	_	_	_
2708	_	_	SYM	_	_	_
2709	r1	r1	FW	_	_	_
2710	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2711	murI	muri	NN	GEN	_	_
2712	__	__	CD	_	_	_
2713	U	U	NNP	_	_	_
2714	_	_	NNP	_	_	_
2715	N0075	N0075	NNP	_	_	_
2716	_	_	SYM	_	_	_
2717	r2	r2	FW	_	_	_
2718	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2719	murI	muri	NN	GEN	_	_
2720	__	__	CD	_	_	_
2721	U	U	NNP	_	_	_
2722	_	_	NNP	_	_	_
2723	N0075	N0075	NNP	_	_	_
2724	_	_	SYM	_	_	_
2725	r3	r3	FW	_	_	_
2726	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2727	murI	muri	NN	GEN	_	_
2728	upregulation	upregulation	NN	_	_	_
2729	,	,	,	_	_	_
2730	0.075	0.075	CD	_	_	_
2731	mg	mg	NN	_	_	_
2732	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2733	nrdA	nrda	NN	GEN	_	_
2734	__	__	CD	_	_	_
2735	U	U	NNP	_	_	_
2736	_	_	NNP	_	_	_
2737	N0075	N0075	NNP	_	_	_
2738	_	_	VBD	_	_	_
2739	r1	r1	NN	_	_	_
2740	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2741	nrdA	nrda	NN	GEN	_	_
2742	__	__	CD	_	_	_
2743	U	U	NNP	_	_	_
2744	_	_	NNP	_	_	_
2745	N0075	N0075	NNP	_	_	_
2746	_	_	VBD	_	_	_
2747	r2	r2	NN	_	_	_
2748	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2749	nrdA	nrda	NN	GEN	_	_
2750	__	__	CD	_	_	_
2751	U	U	NNP	_	_	_
2752	_	_	NNP	_	_	_
2753	N0075	N0075	NNP	_	_	_
2754	_	_	VBD	_	_	_
2755	r3	r3	NN	_	_	_
2756	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2757	nrdA	nrda	NN	GEN	_	_
2758	upregulation	upregulation	NN	_	_	_
2759	,	,	,	_	_	_
2760	0.075	0.075	CD	_	_	_
2761	mg	mg	NN	_	_	_
2762	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2763	nrdB	nrdb	NN	GEN	_	_
2764	__	__	CD	_	_	_
2765	U	U	NNP	_	_	_
2766	_	_	NNP	_	_	_
2767	N0075	N0075	NNP	_	_	_
2768	_	_	VBD	_	_	_
2769	r1	r1	NN	_	_	_
2770	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2771	nrdB	nrdb	NN	GEN	_	_
2772	__	__	CD	_	_	_
2773	U	U	NNP	_	_	_
2774	_	_	NNP	_	_	_
2775	N0075	N0075	NNP	_	_	_
2776	_	_	SYM	_	_	_
2777	r3	r3	FW	_	_	_
2778	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2779	nrdB	nrdb	NN	GEN	_	_
2780	upregulation	upregulation	NN	_	_	_
2781	,	,	,	_	_	_
2782	0.075	0.075	CD	_	_	_
2783	mg	mg	NN	_	_	_
2784	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2785	nupC	nupc	NN	GEN	_	_
2786	__	__	CD	_	_	_
2787	U	U	NNP	_	_	_
2788	_	_	NNP	_	_	_
2789	N0075	N0075	NNP	_	_	_
2790	_	_	VBD	_	_	_
2791	r1	r1	NN	_	_	_
2792	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2793	nupC	nupc	NN	GEN	_	_
2794	__	__	CD	_	_	_
2795	U	U	NNP	_	_	_
2796	_	_	NNP	_	_	_
2797	N0075	N0075	NNP	_	_	_
2798	_	_	VBD	_	_	_
2799	r2	r2	NN	_	_	_
2800	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2801	nupC	nupc	NN	GEN	_	_
2802	__	__	CD	_	_	_
2803	U	U	NNP	_	_	_
2804	_	_	NNP	_	_	_
2805	N0075	N0075	NNP	_	_	_
2806	_	_	VBD	_	_	_
2807	r3	r3	NN	_	_	_
2808	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2809	nupC	nupc	NN	GEN	_	_
2810	upregulation	upregulation	NN	_	_	_
2811	,	,	,	_	_	_
2812	0.075	0.075	CD	_	_	_
2813	mg	mg	NN	_	_	_
2814	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2815	pyrC	pyrc	NN	GEN	_	_
2816	__	__	CD	_	_	_
2817	U	U	NNP	_	_	_
2818	_	_	NNP	_	_	_
2819	N0075	N0075	NNP	_	_	_
2820	_	_	VBD	_	_	_
2821	r1	r1	NN	_	_	_
2822	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2823	pyrC	pyrc	NN	GEN	_	_
2824	__	__	CD	_	_	_
2825	U	U	NNP	_	_	_
2826	_	_	NNP	_	_	_
2827	N0075	N0075	NNP	_	_	_
2828	_	_	VBD	_	_	_
2829	r2	r2	NN	_	_	_
2830	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2831	pyrC	pyrc	NN	GEN	_	_
2832	__	__	CD	_	_	_
2833	U	U	NNP	_	_	_
2834	_	_	NNP	_	_	_
2835	N0075	N0075	NNP	_	_	_
2836	_	_	SYM	_	_	_
2837	r3	r3	FW	_	_	_
2838	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2839	pyrC	pyrc	NN	GEN	_	_
2840	upregulation	upregulation	NN	_	_	_
2841	,	,	,	_	_	_
2842	0.075	0.075	CD	_	_	_
2843	mg	mg	NN	_	_	_
2844	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2845	recA	reca	NN	GEN	_	_
2846	deletion	deletion	NN	_	_	_
2847	0.05	0.05	CD	_	_	_
2848	ug	ug	NN	_	_	_
2849	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2850	recA	reca	NN	GEN	_	_
2851	deletion	deletion	NN	_	_	_
2852	0	0	CD	_	_	_
2853	ug	ug	NN	_	_	_
2854	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2855	recA	reca	NN	GEN	_	_
2856	deletion	deletion	NN	_	_	_
2857	1.0	1.0	CD	_	_	_
2858	ug	ug	NN	_	_	_
2859	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2860	recA	reca	NN	GEN	_	_
2861	_	_	NN	_	_	_
2862	D	d	NN	_	_	_
2863	_	_	CD	_	_	_
2864	N0000	n0000	NN	_	_	_
2865	_	_	CD	_	_	_
2866	r1	r1	NN	_	_	_
2867	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2868	recA	reca	NN	GEN	_	_
2869	_	_	NN	_	_	_
2870	D	d	NN	_	_	_
2871	_	_	CD	_	_	_
2872	N0000	n0000	NN	_	_	_
2873	_	_	CD	_	_	_
2874	r2	r2	NN	_	_	_
2875	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2876	recA	reca	NN	GEN	_	_
2877	_	_	NN	_	_	_
2878	D	d	NN	_	_	_
2879	_	_	CD	_	_	_
2880	N0050	n0050	NN	_	_	_
2881	_	_	CD	_	_	_
2882	r1	r1	NN	_	_	_
2883	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2884	recA	reca	NN	GEN	_	_
2885	_	_	NN	_	_	_
2886	D	d	NN	_	_	_
2887	_	_	CD	_	_	_
2888	N0050	n0050	NN	_	_	_
2889	_	_	CD	_	_	_
2890	r2	r2	NN	_	_	_
2891	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2892	recA	reca	NN	GEN	_	_
2893	_	_	NN	_	_	_
2894	D	d	NN	_	_	_
2895	_	_	CD	_	_	_
2896	N1000	n1000	NN	_	_	_
2897	_	_	CD	_	_	_
2898	r1	r1	NN	_	_	_
2899	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2900	recA	reca	NN	GEN	_	_
2901	_	_	NN	_	_	_
2902	D	d	NN	_	_	_
2903	_	_	CD	_	_	_
2904	N1000	n1000	NN	_	_	_
2905	_	_	CD	_	_	_
2906	r2	r2	NN	_	_	_
2907	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2908	recA	reca	NN	GEN	_	_
2909	___	___	CD	_	_	_
2910	U	U	NNP	_	_	_
2911	_	_	NNP	_	_	_
2912	N0025	N0025	NNP	_	_	_
2913	_	_	NNP	_	_	_
2914	r1	r1	NN	_	_	_
2915	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2916	recA	reca	NN	GEN	_	_
2917	___	___	CD	_	_	_
2918	U	U	NNP	_	_	_
2919	_	_	NNP	_	_	_
2920	N0025	N0025	NNP	_	_	_
2921	_	_	SYM	_	_	_
2922	r2	r2	FW	_	_	_
2923	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2924	recA	reca	NN	GEN	_	_
2925	___	___	CD	_	_	_
2926	U	U	NNP	_	_	_
2927	_	_	NNP	_	_	_
2928	N0025	N0025	NNP	_	_	_
2929	_	_	SYM	_	_	_
2930	r3	r3	FW	_	_	_
2931	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2932	recA	reca	NN	GEN	_	_
2933	upregulation	upregulation	NN	_	_	_
2934	,	,	,	_	_	_
2935	amp	amp	NN	_	_	_
2936	50ug	50ug	JJ	_	_	_
2937	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2938	relE	rele	NN	GEN	_	_
2939	___	___	CD	_	_	_
2940	U	U	NNP	_	_	_
2941	_	_	NNP	_	_	_
2942	N0025	N0025	NNP	_	_	_
2943	_	_	VBD	_	_	_
2944	r1	r1	NN	_	_	_
2945	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2946	relE	rele	NN	GEN	_	_
2947	___	___	CD	_	_	_
2948	U	U	NNP	_	_	_
2949	_	_	NNP	_	_	_
2950	N0025	N0025	NNP	_	_	_
2951	_	_	VBD	_	_	_
2952	r2	r2	NN	_	_	_
2953	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2954	relE	rele	NN	GEN	_	_
2955	___	___	CD	_	_	_
2956	U	U	NNP	_	_	_
2957	_	_	NNP	_	_	_
2958	N0025	N0025	NNP	_	_	_
2959	_	_	VBD	_	_	_
2960	r3	r3	NN	_	_	_
2961	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2962	relE	rele	NN	GEN	_	_
2963	upregulation	upregulation	NN	_	_	_
2964	,	,	,	_	_	_
2965	amp	amp	NN	_	_	_
2966	50ug	50ug	JJ	_	_	_
2967	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2968	rimI	rimi	NN	GEN	_	_
2969	__	__	CD	_	_	_
2970	U	U	NNP	_	_	_
2971	_	_	NNP	_	_	_
2972	N0075	N0075	NNP	_	_	_
2973	_	_	SYM	_	_	_
2974	r1	r1	FW	_	_	_
2975	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2976	rimI	rimi	NN	GEN	_	_
2977	__	__	CD	_	_	_
2978	U	U	NNP	_	_	_
2979	_	_	NNP	_	_	_
2980	N0075	N0075	NNP	_	_	_
2981	_	_	SYM	_	_	_
2982	r2	r2	FW	_	_	_
2983	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2984	rimI	rimi	NN	GEN	_	_
2985	__	__	CD	_	_	_
2986	U	U	NNP	_	_	_
2987	_	_	NNP	_	_	_
2988	N0075	N0075	NNP	_	_	_
2989	_	_	SYM	_	_	_
2990	r3	r3	FW	_	_	_
2991	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
2992	rimI	rimi	NN	GEN	_	_
2993	upregulation	upregulation	NN	_	_	_
2994	,	,	,	_	_	_
2995	0.075	0.075	CD	_	_	_
2996	mg	mg	NN	_	_	_
2997	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2998	RNAEasy	rnaeasy	NN	_	_	_
2999	with	with	IN	_	_	_
3000	RNAProtect	rnaprotect	NN	_	_	_
3001	-LRB-	-lrb-	-LRB-	_	_	_
3002	Qiagen	qiagen	NN	_	_	_
3003	-RRB-	-rrb-	-RRB-	_	_	_
3004	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3005	rstB	rstb	NN	GEN	_	_
3006	__	__	CD	_	_	_
3007	U	U	NNP	_	_	_
3008	_	_	NNP	_	_	_
3009	N0075	N0075	NNP	_	_	_
3010	_	_	VBD	_	_	_
3011	r1	r1	NN	_	_	_
3012	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3013	rstB	rstb	NN	GEN	_	_
3014	__	__	CD	_	_	_
3015	U	U	NNP	_	_	_
3016	_	_	NNP	_	_	_
3017	N0075	N0075	NNP	_	_	_
3018	_	_	VBD	_	_	_
3019	r2	r2	NN	_	_	_
3020	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3021	rstB	rstb	NN	GEN	_	_
3022	__	__	CD	_	_	_
3023	U	U	NNP	_	_	_
3024	_	_	NNP	_	_	_
3025	N0075	N0075	NNP	_	_	_
3026	_	_	SYM	_	_	_
3027	r3	r3	FW	_	_	_
3028	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3029	rstB	rstb	NN	GEN	_	_
3030	upregulation	upregulation	NN	_	_	_
3031	,	,	,	_	_	_
3032	0.075	0.075	CD	_	_	_
3033	mg	mg	NN	_	_	_
3034	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3035	ruvA	ruva	NN	GEN	_	_
3036	___	___	CD	_	_	_
3037	U	U	NNP	_	_	_
3038	_	_	NNP	_	_	_
3039	N0025	N0025	NNP	_	_	_
3040	_	_	VBD	_	_	_
3041	r1	r1	NN	_	_	_
3042	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3043	ruvA	ruva	NN	GEN	_	_
3044	___	___	CD	_	_	_
3045	U	U	NNP	_	_	_
3046	_	_	NNP	_	_	_
3047	N0025	N0025	NNP	_	_	_
3048	_	_	VBD	_	_	_
3049	r2	r2	NN	_	_	_
3050	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3051	ruvA	ruva	NN	GEN	_	_
3052	___	___	CD	_	_	_
3053	U	U	NNP	_	_	_
3054	_	_	NNP	_	_	_
3055	N0025	N0025	NNP	_	_	_
3056	_	_	SYM	_	_	_
3057	r3	r3	FW	_	_	_
3058	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3059	ruvA	ruva	NN	GEN	_	_
3060	upregulation	upregulation	NN	_	_	_
3061	,	,	,	_	_	_
3062	amp	amp	NN	_	_	_
3063	50ug	50ug	JJ	_	_	_
3064	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3065	ruvC	ruvc	NN	GEN	_	_
3066	__	__	CD	_	_	_
3067	U	U	NNP	_	_	_
3068	_	_	NNP	_	_	_
3069	N0075	N0075	NNP	_	_	_
3070	_	_	VBD	_	_	_
3071	r1	r1	NN	_	_	_
3072	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3073	ruvC	ruvc	NN	GEN	_	_
3074	__	__	CD	_	_	_
3075	U	U	NNP	_	_	_
3076	_	_	NNP	_	_	_
3077	N0075	N0075	NNP	_	_	_
3078	_	_	VBD	_	_	_
3079	r2	r2	NN	_	_	_
3080	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3081	ruvC	ruvc	NN	GEN	_	_
3082	__	__	CD	_	_	_
3083	U	U	NNP	_	_	_
3084	_	_	NNP	_	_	_
3085	N0075	N0075	NNP	_	_	_
3086	_	_	SYM	_	_	_
3087	r3	r3	FW	_	_	_
3088	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3089	ruvC	ruvc	NN	GEN	_	_
3090	upregulation	upregulation	NN	_	_	_
3091	,	,	,	_	_	_
3092	0.075	0.075	CD	_	_	_
3093	mg	mg	NN	_	_	_
3094	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3095	sbcB	sbcb	NN	GEN	_	_
3096	__	__	CD	_	_	_
3097	U	U	NNP	_	_	_
3098	_	_	NNP	_	_	_
3099	N0075	N0075	NNP	_	_	_
3100	_	_	VBD	_	_	_
3101	r1	r1	NN	_	_	_
3102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3103	sbcB	sbcb	NN	GEN	_	_
3104	__	__	CD	_	_	_
3105	U	U	NNP	_	_	_
3106	_	_	NNP	_	_	_
3107	N0075	N0075	NNP	_	_	_
3108	_	_	VBD	_	_	_
3109	r2	r2	NN	_	_	_
3110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3111	sbcB	sbcb	NN	GEN	_	_
3112	__	__	CD	_	_	_
3113	U	U	NNP	_	_	_
3114	_	_	NNP	_	_	_
3115	N0075	N0075	NNP	_	_	_
3116	_	_	SYM	_	_	_
3117	r3	r3	FW	_	_	_
3118	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3119	sbcB	sbcb	NN	GEN	_	_
3120	upregulation	upregulation	NN	_	_	_
3121	,	,	,	_	_	_
3122	0.075	0.075	CD	_	_	_
3123	mg	mg	NN	_	_	_
3124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3125	sulA	sula	NN	GEN	_	_
3126	___	___	CD	_	_	_
3127	U	U	NNP	_	_	_
3128	_	_	NNP	_	_	_
3129	N0025	N0025	NNP	_	_	_
3130	_	_	SYM	_	_	_
3131	r1	r1	FW	_	_	_
3132	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3133	sulA	sula	NN	GEN	_	_
3134	___	___	CD	_	_	_
3135	U	U	NNP	_	_	_
3136	_	_	NNP	_	_	_
3137	N0025	N0025	NNP	_	_	_
3138	_	_	SYM	_	_	_
3139	r2	r2	FW	_	_	_
3140	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3141	sulA	sula	NN	GEN	_	_
3142	___	___	CD	_	_	_
3143	U	U	NNP	_	_	_
3144	_	_	NNP	_	_	_
3145	N0025	N0025	NNP	_	_	_
3146	_	_	SYM	_	_	_
3147	r3	r3	FW	_	_	_
3148	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3149	sulA	sula	NN	GEN	_	_
3150	upregulation	upregulation	NN	_	_	_
3151	,	,	,	_	_	_
3152	amp	amp	NN	_	_	_
3153	50ug	50ug	JJ	_	_	_
3154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3155	T0	t0	NN	_	_	_
3156	_	_	SYM	_	_	_
3157	N0025	n0025	CD	_	_	_
3158	_	_	CD	_	_	_
3159	r1	r1	NN	_	_	_
3160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3161	T0	t0	NN	_	_	_
3162	_	_	SYM	_	_	_
3163	N0025	n0025	CD	_	_	_
3164	_	_	CD	_	_	_
3165	r2	r2	NN	_	_	_
3166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3167	T0	t0	NN	_	_	_
3168	_	_	SYM	_	_	_
3169	N0025	n0025	CD	_	_	_
3170	_	_	CD	_	_	_
3171	r3	r3	NN	_	_	_
3172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3173	T12	t12	NN	_	_	_
3174	_	_	SYM	_	_	_
3175	N0025	n0025	CD	_	_	_
3176	_	_	CD	_	_	_
3177	r1	r1	NN	_	_	_
3178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3179	T12	t12	NN	_	_	_
3180	_	_	SYM	_	_	_
3181	N0025	n0025	CD	_	_	_
3182	_	_	CD	_	_	_
3183	r2	r2	NN	_	_	_
3184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3185	T12	t12	NN	_	_	_
3186	_	_	SYM	_	_	_
3187	N0025	n0025	CD	_	_	_
3188	_	_	CD	_	_	_
3189	r3	r3	NN	_	_	_
3190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3191	T24	t24	NN	_	_	_
3192	_	_	CD	_	_	_
3193	N0000	n0000	NN	_	_	_
3194	_	_	CD	_	_	_
3195	r1	r1	NN	_	_	_
3196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3197	T24	t24	NN	_	_	_
3198	_	_	CD	_	_	_
3199	N0000	n0000	NN	_	_	_
3200	_	_	CD	_	_	_
3201	r2	r2	NN	_	_	_
3202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3203	T24	t24	NN	_	_	_
3204	_	_	CD	_	_	_
3205	N0000	n0000	NN	_	_	_
3206	_	_	CD	_	_	_
3207	r3	r3	NN	_	_	_
3208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3209	T24	t24	NN	_	_	_
3210	_	_	SYM	_	_	_
3211	N0025	n0025	CD	_	_	_
3212	_	_	CD	_	_	_
3213	r1	r1	NN	_	_	_
3214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3215	T24	t24	NN	_	_	_
3216	_	_	SYM	_	_	_
3217	N0025	n0025	CD	_	_	_
3218	_	_	CD	_	_	_
3219	r2	r2	NN	_	_	_
3220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3221	T24	t24	NN	_	_	_
3222	_	_	SYM	_	_	_
3223	N0025	n0025	CD	_	_	_
3224	_	_	SYM	_	_	_
3225	r3	r3	FW	_	_	_
3226	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3227	T36	t36	FW	_	_	_
3228	_	_	SYM	_	_	_
3229	N0025	n0025	CD	_	_	_
3230	_	_	CD	_	_	_
3231	r1	r1	NN	_	_	_
3232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3233	T36	t36	NN	_	_	_
3234	_	_	SYM	_	_	_
3235	N0025	n0025	CD	_	_	_
3236	_	_	SYM	_	_	_
3237	r2	r2	FW	_	_	_
3238	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3239	T36	t36	FW	_	_	_
3240	_	_	SYM	_	_	_
3241	N0025	n0025	CD	_	_	_
3242	_	_	CD	_	_	_
3243	r3	r3	NN	_	_	_
3244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3245	T48	t48	NN	_	_	_
3246	_	_	SYM	_	_	_
3247	N0025	n0025	CD	_	_	_
3248	_	_	CD	_	_	_
3249	r1	r1	NN	_	_	_
3250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3251	T48	t48	NN	_	_	_
3252	_	_	SYM	_	_	_
3253	N0025	n0025	CD	_	_	_
3254	_	_	CD	_	_	_
3255	r2	r2	NN	_	_	_
3256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3257	T48	t48	NN	_	_	_
3258	_	_	SYM	_	_	_
3259	N0025	n0025	CD	_	_	_
3260	_	_	CD	_	_	_
3261	r3	r3	NN	_	_	_
3262	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3263	T60	t60	NN	_	_	_
3264	_	_	CD	_	_	_
3265	N0000	n0000	NN	_	_	_
3266	_	_	CD	_	_	_
3267	r1	r1	NN	_	_	_
3268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3269	T60	t60	NN	_	_	_
3270	_	_	CD	_	_	_
3271	N0000	n0000	NN	_	_	_
3272	_	_	CD	_	_	_
3273	r2	r2	NN	_	_	_
3274	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3275	T60	t60	NN	_	_	_
3276	_	_	CD	_	_	_
3277	N0000	n0000	NN	_	_	_
3278	_	_	CD	_	_	_
3279	r3	r3	NN	_	_	_
3280	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3281	T60	t60	NN	_	_	_
3282	_	_	SYM	_	_	_
3283	N0025	n0025	CD	_	_	_
3284	_	_	CD	_	_	_
3285	r1	r1	NN	_	_	_
3286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3287	T60	t60	NN	_	_	_
3288	_	_	SYM	_	_	_
3289	N0025	n0025	CD	_	_	_
3290	_	_	CD	_	_	_
3291	r2	r2	NN	_	_	_
3292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3293	T60	t60	NN	_	_	_
3294	_	_	SYM	_	_	_
3295	N0025	n0025	CD	_	_	_
3296	_	_	CD	_	_	_
3297	r3	r3	NN	_	_	_
3298	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3299	umuD	umud	NN	GEN	_	_
3300	___	___	CD	_	_	_
3301	U	U	NNP	_	_	_
3302	_	_	NNP	_	_	_
3303	N0025	N0025	NNP	_	_	_
3304	_	_	VBD	_	_	_
3305	r1	r1	NN	_	_	_
3306	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3307	umuD	umud	NN	GEN	_	_
3308	___	___	CD	_	_	_
3309	U	U	NNP	_	_	_
3310	_	_	NNP	_	_	_
3311	N0025	N0025	NNP	_	_	_
3312	_	_	VBD	_	_	_
3313	r2	r2	NN	_	_	_
3314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3315	umuD	umud	NN	GEN	_	_
3316	___	___	CD	_	_	_
3317	U	U	NNP	_	_	_
3318	_	_	NNP	_	_	_
3319	N0025	N0025	NNP	_	_	_
3320	_	_	VBD	_	_	_
3321	r3	r3	NN	_	_	_
3322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3323	umuD	umud	NN	GEN	_	_
3324	upregulation	upregulation	NN	_	_	_
3325	,	,	,	_	_	_
3326	amp	amp	NN	_	_	_
3327	50ug	50ug	JJ	_	_	_
3328	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3329	untreated	untreated	JJ	_	_	_
3330	cells	cell	NNS	_	_	_
3331	after	after	IN	_	_	_
3332	24	24	CD	_	_	_
3333	min	min	NN	_	_	_
3334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3335	untreated	untreated	JJ	_	_	_
3336	cells	cell	NNS	_	_	_
3337	after	after	IN	_	_	_
3338	60	60	CD	_	_	_
3339	min	min	NN	_	_	_
3340	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3341	uspA	uspa	NN	GEN	_	_
3342	__	__	CD	_	_	_
3343	U	U	NNP	_	_	_
3344	_	_	NNP	_	_	_
3345	N0075	N0075	NNP	_	_	_
3346	_	_	SYM	_	_	_
3347	r1	r1	FW	_	_	_
3348	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3349	uspA	uspa	NN	GEN	_	_
3350	__	__	CD	_	_	_
3351	U	U	NNP	_	_	_
3352	_	_	NNP	_	_	_
3353	N0075	N0075	NNP	_	_	_
3354	_	_	SYM	_	_	_
3355	r2	r2	FW	_	_	_
3356	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3357	uspA	uspa	NN	GEN	_	_
3358	__	__	CD	_	_	_
3359	U	U	NNP	_	_	_
3360	_	_	NNP	_	_	_
3361	N0075	N0075	NNP	_	_	_
3362	_	_	SYM	_	_	_
3363	r3	r3	FW	_	_	_
3364	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3365	uspA	uspa	NN	GEN	_	_
3366	upregulation	upregulation	NN	_	_	_
3367	,	,	,	_	_	_
3368	0.075	0.075	CD	_	_	_
3369	mg	mg	NN	_	_	_
3370	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3371	uvrA	uvra	NN	GEN	_	_
3372	___	___	CD	_	_	_
3373	U	U	NNP	_	_	_
3374	_	_	NNP	_	_	_
3375	N0025	N0025	NNP	_	_	_
3376	_	_	VBD	_	_	_
3377	r1	r1	NN	_	_	_
3378	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3379	uvrA	uvra	NN	GEN	_	_
3380	___	___	CD	_	_	_
3381	U	U	NNP	_	_	_
3382	_	_	NNP	_	_	_
3383	N0025	N0025	NNP	_	_	_
3384	_	_	VBD	_	_	_
3385	r2	r2	NN	_	_	_
3386	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3387	uvrA	uvra	NN	GEN	_	_
3388	___	___	CD	_	_	_
3389	U	U	NNP	_	_	_
3390	_	_	NNP	_	_	_
3391	N0025	N0025	NNP	_	_	_
3392	_	_	SYM	_	_	_
3393	r3	r3	FW	_	_	_
3394	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3395	uvrA	uvra	NN	GEN	_	_
3396	upregulation	upregulation	NN	_	_	_
3397	,	,	,	_	_	_
3398	amp	amp	NN	_	_	_
3399	50ug	50ug	JJ	_	_	_
3400	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3401	wild-type	wild-type	JJ	_	_	_
3402	1.0	1.0	CD	_	_	_
3403	ug	ug	NN	_	_	_
3404	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3405	wild-type	wild-type	JJ	_	_	_
3406	cells	cell	NNS	_	_	_
3407	with	with	IN	_	_	_
3408	0.025	0.025	CD	_	_	_
3409	ug	ug	NN	_	_	_
3410	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3411	wild-type	wild-type	JJ	_	_	_
3412	cells	cell	NNS	_	_	_
3413	with	with	IN	_	_	_
3414	0.050	0.050	CD	_	_	_
3415	ug	ug	NN	_	_	_
3416	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3417	wild-type	wild-type	JJ	_	_	_
3418	cells	cell	NNS	_	_	_
3419	with	with	IN	_	_	_
3420	0.075	0.075	CD	_	_	_
3421	ug	ug	NN	_	_	_
3422	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3423	wild-type	wild-type	JJ	_	_	_
3424	cells	cell	NNS	_	_	_
3425	without	without	IN	_	_	_
3426	norfloxacin	norfloxacin	JJ	_	_	_
3427	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3428	WT	wt	JJ	_	_	_
3429	_	_	NN	_	_	_
3430	D	d	NN	_	_	_
3431	_	_	CD	_	_	_
3432	N1000	n1000	NN	_	_	_
3433	_	_	CD	_	_	_
3434	r1	r1	NN	_	_	_
3435	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3436	WT	wt	JJ	_	_	_
3437	_	_	NN	_	_	_
3438	D	d	NN	_	_	_
3439	_	_	CD	_	_	_
3440	N1000	n1000	NN	_	_	_
3441	_	_	CD	_	_	_
3442	r2	r2	NN	_	_	_
3443	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3444	WT	wt	JJ	_	_	_
3445	_	_	NN	_	_	_
3446	N0000	n0000	NN	_	_	_
3447	_	_	CD	_	_	_
3448	r1	r1	NN	_	_	_
3449	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3450	WT	wt	JJ	_	_	_
3451	_	_	NN	_	_	_
3452	N0000	n0000	NN	_	_	_
3453	_	_	CD	_	_	_
3454	r2	r2	NN	_	_	_
3455	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3456	WT	wt	JJ	_	_	_
3457	_	_	SYM	_	_	_
3458	N0025	n0025	CD	_	_	_
3459	_	_	SYM	_	_	_
3460	r1	r1	FW	_	_	_
3461	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3462	WT	wt	FW	_	_	_
3463	_	_	SYM	_	_	_
3464	N0025	n0025	CD	_	_	_
3465	_	_	CD	_	_	_
3466	r2	r2	NN	_	_	_
3467	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3468	WT	wt	JJ	_	_	_
3469	_	_	NN	_	_	_
3470	N0050	n0050	NN	_	_	_
3471	_	_	CD	_	_	_
3472	r1	r1	NN	_	_	_
3473	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3474	WT	wt	JJ	_	_	_
3475	_	_	NN	_	_	_
3476	N0050	n0050	NN	_	_	_
3477	_	_	CD	_	_	_
3478	r2	r2	NN	_	_	_
3479	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3480	WT	wt	JJ	_	_	_
3481	_	_	NN	_	_	_
3482	N0075	n0075	NN	_	_	_
3483	_	_	CD	_	_	_
3484	r1	r1	NN	_	_	_
3485	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3486	WT	wt	JJ	_	_	_
3487	_	_	NN	_	_	_
3488	N0075	n0075	NN	_	_	_
3489	_	_	CD	_	_	_
3490	r2	r2	NN	_	_	_
3491	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3492	yebF	yebf	NN	GEN	_	_
3493	__	__	CD	_	_	_
3494	U	U	NNP	_	_	_
3495	_	_	NNP	_	_	_
3496	N0075	N0075	NNP	_	_	_
3497	_	_	VBD	_	_	_
3498	r1	r1	NN	_	_	_
3499	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3500	yebF	yebf	NN	GEN	_	_
3501	__	__	CD	_	_	_
3502	U	U	NNP	_	_	_
3503	_	_	NNP	_	_	_
3504	N0075	N0075	NNP	_	_	_
3505	_	_	VBD	_	_	_
3506	r2	r2	NN	_	_	_
3507	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3508	yebF	yebf	NN	GEN	_	_
3509	__	__	CD	_	_	_
3510	U	U	NNP	_	_	_
3511	_	_	NNP	_	_	_
3512	N0075	N0075	NNP	_	_	_
3513	_	_	SYM	_	_	_
3514	r3	r3	FW	_	_	_
3515	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3516	yebF	yebf	NN	GEN	_	_
3517	upregulation	upregulation	NN	_	_	_
3518	,	,	,	_	_	_
3519	0.075	0.075	CD	_	_	_
3520	ug	ug	NN	_	_	_
3521	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3522	yoeB	yoeb	NN	GEN	_	_
3523	__	__	CD	_	_	_
3524	U	U	NNP	_	_	_
3525	_	_	NNP	_	_	_
3526	N0075	N0075	NNP	_	_	_
3527	_	_	VBD	_	_	_
3528	r1	r1	NN	_	_	_
3529	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3530	yoeB	yoeb	NN	GEN	_	_
3531	__	__	CD	_	_	_
3532	U	U	NNP	_	_	_
3533	_	_	NNP	_	_	_
3534	N0075	N0075	NNP	_	_	_
3535	_	_	VBD	_	_	_
3536	r2	r2	NN	_	_	_
3537	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3538	yoeB	yoeb	NN	GEN	_	_
3539	__	__	CD	_	_	_
3540	U	U	NNP	_	_	_
3541	_	_	NNP	_	_	_
3542	N0075	N0075	NNP	_	_	_
3543	_	_	SYM	_	_	_
3544	r3	r3	FW	_	_	_
3545	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3546	yoeB	yoeb	NN	GEN	_	_
3547	upregulation	upregulation	NN	_	_	_
3548	,	,	,	_	_	_
3549	0.075	0.075	CD	_	_	_
3550	mg	mg	NN	_	_	_
3551	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3552	zipA	zipa	NN	GEN	_	_
3553	__	__	CD	_	_	_
3554	U	U	NNP	_	_	_
3555	_	_	NNP	_	_	_
3556	N0075	N0075	NNP	_	_	_
3557	_	_	VBD	_	_	_
3558	r1	r1	NN	_	_	_
3559	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3560	zipA	zipa	NN	GEN	_	_
3561	__	__	CD	_	_	_
3562	U	U	NNP	_	_	_
3563	_	_	NNP	_	_	_
3564	N0075	N0075	NNP	_	_	_
3565	_	_	SYM	_	_	_
3566	r2	r2	FW	_	_	_
3567	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3568	zipA	zipa	NN	GEN	_	_
3569	__	__	CD	_	_	_
3570	U	U	NNP	_	_	_
3571	_	_	NNP	_	_	_
3572	N0075	N0075	NNP	_	_	_
3573	_	_	SYM	_	_	_
3574	r3	r3	FW	_	_	_
3575	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3576	zipA	zipa	NN	GEN	_	_
3577	upregulation	upregulation	NN	_	_	_
3578	,	,	,	_	_	_
3579	0.075	0.075	CD	_	_	_
3580	ug	ug	NN	_	_	_
3581	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3582	BW25113	bw25113	NN	_	_	_
3583	W	w	NN	_	_	_
3584	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3585	BW25113	bw25113	NN	_	_	_
3586	ymgB	ymgb	NN	_	_	_
3587	LBglu	lbglu	NN	_	_	_
3588	24h	24h	JJ	_	_	_
3589	biofilm	biofilm	NN	_	_	_
3590	cells	cell	NNS	_	_	_
3591	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3592	channel	channel	NN	_	_	_
3593	1	1	CD	_	_	_
3594	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3595	Channel	Channel	NNP	_	_	_
3596	1	1	CD	_	_	_
3597	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3598	Escherichia	escherichia	FW	Organism	_	_
3599	coli	coli	FW	Organism	_	_
3600	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
3601	MAS	mas	FW	_	_	_
3602	5.0	5.0	CD	_	_	_
3603	Expression	expression	NN	_	_	_
3604	Analysis	analysis	NN	_	_	_
3605	Default	Default	NNP	_	_	_
3606	Setting	set	VBG	_	_	_
3607	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3608	RNA	rna	NN	_	_	_
3609	extracted	extract	VBN	_	_	_
3610	from	from	IN	_	_	_
3611	biofilm	biofilm	NN	_	_	_
3612	cells	cell	NNS	_	_	_
3613	of	of	IN	_	_	_
3614	BW25113	bw25113	NN	_	_	_
3615	wild	wild	JJ	_	_	_
3616	type	type	NN	_	_	_
3617	after	after	IN	_	_	_
3618	24h	24h	NN	_	_	_
3619	of	of	IN	_	_	_
3620	growth	growth	NN	_	_	_
3621	in	in	IN	_	_	_
3622	LBglu	lbglu	NN	_	_	_
3623	with	with	IN	_	_	_
3624	glass	glass	NN	_	_	_
3625	wool	wool	NN	_	_	_
3626	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3627	RNA	rna	NN	_	_	_
3628	extracted	extract	VBN	_	_	_
3629	from	from	IN	_	_	_
3630	biofilm	biofilm	NN	_	_	_
3631	cells	cell	NNS	_	_	_
3632	of	of	IN	_	_	_
3633	BW25113	bw25113	NN	_	_	_
3634	ymgB	ymgb	NN	_	_	_
3635	mutant	mutant	NN	_	_	_
3636	after	after	IN	_	_	_
3637	24h	24h	NN	_	_	_
3638	of	of	IN	_	_	_
3639	growth	growth	NN	_	_	_
3640	in	in	IN	_	_	_
3641	LBglu	lbglu	NN	_	_	_
3642	with	with	IN	_	_	_
3643	glass	glass	NN	_	_	_
3644	wool	wool	NN	_	_	_
3645	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3646	To	to	TO	_	_	_
3647	lyse	lyse	VB	_	_	_
3648	the	the	DT	_	_	_
3649	cells	cell	NNS	_	_	_
3650	,	,	,	_	_	_
3651	1.0	1.0	CD	_	_	_
3652	mL	ml	NN	_	_	_
3653	RLT	rlt	NN	_	_	_
3654	buffer	buffer	NN	_	_	_
3655	-LRB-	-lrb-	-LRB-	_	_	_
3656	Qiagen	Qiagen	NNP	_	_	_
3657	,	,	,	_	_	_
3658	Inc.	Inc.	NNP	_	_	_
3659	,	,	,	_	_	_
3660	Valencia	Valencia	NNP	_	_	_
3661	,	,	,	_	_	_
3662	CA	CA	NNP	_	_	_
3663	-RRB-	-rrb-	-RRB-	_	_	_
3664	and	and	CC	_	_	_
3665	0.2	0.2	CD	_	_	_
3666	mL	ml	NN	_	_	_
3667	0.1	0.1	CD	_	_	_
3668	mm	mm	NN	_	_	_
3669	zirconia	zirconia	NN	_	_	_
3670	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3671	agent	agent	NN	_	_	_
3672	:	:	:	_	_	_
3673	control	control	NN	_	_	_
3674	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3675	agent	agent	NN	_	_	_
3676	:	:	:	_	_	_
3677	glycolaldehyde	glycolaldehyde	NN	_	_	_
3678	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
3679	Data	Data	NNP	_	_	_
3680	were	be	VBD	_	_	_
3681	analyzed	analyze	VBN	_	_	_
3682	by	by	IN	_	_	_
3683	Feature	Feature	NNP	_	_	_
3684	Extraction	Extraction	NNP	_	_	_
3685	V.	V.	NNP	_	_	_
3686	11.5.1.1	11.5.1.1	CD	_	_	_
3687	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Escherichia	escherichia	FW	Organism	_	_
4	coli	coli	FW	Organism	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	genotype	genotype	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	M9	m9	NN	_	_	_
9	mineral	mineral	NN	_	_	_
10	medium	medium	NN	_	_	_
11	containing	contain	VBG	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	D	d	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	-	-	:	_	_	_
16	xylose	xylose	NN	_	_	_
17	as	as	IN	_	_	_
18	the	the	DT	_	_	_
19	only	only	JJ	_	_	_
20	carbon	carbon	NN	_	_	_
21	source	source	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	100	100	CD	_	_	_
24	ml	ml	NN	_	_	_
25	in	in	IN	_	_	_
26	500	500	CD	_	_	_
27	ml	ml	NN	_	_	_
28	shake	shake	NN	_	_	_
29	flasks	flask	NNS	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	was	be	VBD	_	_	_
32	inoculated	inoculate	VBN	_	_	_
33	from	from	IN	_	_	_
34	exponentially	exponentially	RB	_	_	_
35	growing	grow	VBG	_	_	_
36	wild-type	wild-type	JJ	_	_	_
37	cells	cell	NNS	_	_	_
38	or	or	CC	_	_	_
39	synthetic	synthetic	JJ	_	_	_
40	cells	cell	NNS	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	cultivated	cultivate	VBN	_	_	_
43	on	on	IN	_	_	_
44	xylose	xylose	NN	_	_	_
45	M9	m9	NN	_	_	_
46	medium	medium	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	to	to	TO	_	_	_
49	adjust	adjust	VB	_	_	_
50	an	a	DT	_	_	_
51	OD	od	NN	_	_	_
52	of	of	IN	_	_	_
53	~	~	NN	_	_	_
54	0.1	0.1	CD	_	_	_
55	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	incubated	incubate	VBN	_	_	_
4	at	at	IN	_	_	_
5	37	37	CD	_	_	_
6	°C	°c	NN	_	_	_
7	under	under	IN	_	_	_
8	shaking	shake	VBG	_	_	_
9	until	until	IN	_	_	_
10	OD	od	NN	_	_	_
11	reached	reach	VBD	_	_	_
12	~	~	NN	_	_	_
13	1	1	CD	_	_	_
14	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	they	they	PRP	_	_	_
3	were	be	VBD	_	_	_
4	split	split	VBN	_	_	_
5	into	into	IN	_	_	_
6	two	two	CD	_	_	_
7	50	50	CD	_	_	_
8	ml	ml	NN	_	_	_
9	aliquots	aliquot	NNS	_	_	_
10	and	and	CC	_	_	_
11	further	further	JJ	_	_	_
12	cultivated	cultivate	VBN	_	_	_
13	in	in	IN	_	_	_
14	250	250	CD	_	_	_
15	ml	ml	NN	_	_	_
16	shake	shake	NN	_	_	_
17	flasks	flask	NNS	_	_	_
18	in	in	IN	_	_	_
19	the	the	DT	_	_	_
20	presence	presence	NN	_	_	_
21	or	or	CC	_	_	_
22	absence	absence	NN	_	_	_
23	of	of	IN	_	_	_
24	10	10	CD	_	_	_
25	mM	mm	NN	KWSUPP	_	_
26	glycolaldehyde	glycolaldehyde	NN	_	_	_
27	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	30	30	CD	_	_	_
3	min	min	NN	_	_	_
4	of	of	IN	_	_	_
5	incubation	incubation	NN	_	_	_
6	,	,	,	_	_	_
7	1	1	CD	_	_	_
8	ml	ml	NN	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	cell	cell	NN	_	_	_
12	suspension	suspension	NN	_	_	_
13	was	be	VBD	_	_	_
14	withdrawn	withdraw	VBN	_	_	_
15	and	and	CC	_	_	_
16	centrifuged	centrifuge	VBN	_	_	_
17	at	at	IN	_	_	_
18	1500	1500	CD	_	_	_
19	x	x	CC	_	_	_
20	g	g	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Eppendorf	eppendorf	NN	_	_	_
23	5415D	5415d	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	for	for	IN	_	_	_
26	5	5	CD	_	_	_
27	min	min	NN	_	_	_
28	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	and	and	CC	_	_	_
6	the	the	DT	_	_	_
7	cell	cell	NN	_	_	_
8	pellets	pellet	NNS	_	_	_
9	were	be	VBD	_	_	_
10	directly	directly	RB	_	_	_
11	subject	subject	JJ	_	_	_
12	to	to	TO	_	_	_
13	RNA	rna	NN	_	_	_
14	extraction	extraction	NN	_	_	_
15	.	.	.	_	_	_

1	Experiment	experiment	NN	_	_	_
2	were	be	VBD	_	_	_
3	repeated	repeat	VBN	_	_	_
4	three	three	CD	_	_	_
5	times	time	NNS	_	_	_
6	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	PEN205	pen205	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	PEN205	pen205	NN	_	_	_
5	strain	strain	NN	_	_	_
6	first	first	JJ	_	_	_
7	repetition	repetition	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	PEN205	pen205	NN	_	_	_
10	strain	strain	NN	_	_	_
11	second	second	JJ	_	_	_
12	repetition	repetition	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	PEN205	pen205	NN	_	_	_
15	strain	strain	NN	_	_	_
16	third	third	JJ	_	_	_
17	repetition	repetition	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	strain	strain	NN	_	_	_
20	:	:	:	_	_	_
21	MG1655	mg1655	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	The	the	DT	_	_	_
24	RNeasy	rneasy	NN	_	_	_
25	Mini	Mini	NNP	_	_	_
26	Kit	kit	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	QIAGEN	qiagen	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	was	be	VBD	_	_	_
31	used	use	VBN	_	_	_
32	to	to	TO	_	_	_
33	extract	extract	NN	_	_	_
34	RNA	rna	NN	_	_	_
35	.	.	.	_	_	_

1	Quantity	quantity	NN	_	_	_
2	and	and	CC	_	_	_
3	quality	quality	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	samples	sample	NNS	_	_	_
7	were	be	VBD	_	_	_
8	determined	determine	VBN	_	_	_
9	by	by	IN	_	_	_
10	NanoDrop	NanoDrop	NNP	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Thermo	Thermo	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	and	and	CC	_	_	_
15	Bioanalyzer	bioanalyzer	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Agilent	Agilent	NNP	_	_	_
18	Technologies	Technologies	NNPS	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	,	,	,	_	_	_
21	respectively	respectively	RB	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	wild-type	wild-type	JJ	_	_	_
24	MG1655	mg1655	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	wild-type	wild-type	JJ	_	_	_
27	MG1655	mg1655	NN	_	_	_
28	+	+	CC	_	_	_
29	glycolaldehyde	glycolaldehyde	NN	_	_	_
30	10	10	CD	_	_	_
31	mM	mm	NN	KWSUPP	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	WT	wt	JJ	_	_	_
34	cells	cell	NNS	_	_	_
35	were	be	VBD	_	_	_
36	treated	treat	VBN	_	_	_
37	with	with	IN	_	_	_
38	10	10	CD	_	_	_
39	mM	mm	NN	KWSUPP	_	_
40	Glycolaldehyde	glycolaldehyde	NN	_	_	_
41	for	for	IN	_	_	_
42	30	30	CD	_	_	_
43	min	min	NN	_	_	_
44	whenever	whenever	WRB	_	_	_
45	the	the	DT	_	_	_
46	culture	culture	NN	_	_	_
47	OD600nm	od600nm	NN	_	_	_
48	reached	reach	VBD	_	_	_
49	~	~	NN	_	_	_
50	1	1	CD	_	_	_
51	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	WT	WT	NNP	_	_	_
3	strain	strain	NN	_	_	_
4	treated	treat	VBN	_	_	_
5	with	with	IN	_	_	_
6	glycolaldehyde	glycolaldehyde	NN	_	_	_
7	first	first	JJ	_	_	_
8	repetition	repetition	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	WT	wt	JJ	_	_	_
11	strain	strain	NN	_	_	_
12	treated	treat	VBN	_	_	_
13	with	with	IN	_	_	_
14	glycolaldehyde	glycolaldehyde	NN	_	_	_
15	second	second	JJ	_	_	_
16	repetition	repetition	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	WT	wt	JJ	_	_	_
19	strain	strain	NN	_	_	_
20	treated	treat	VBN	_	_	_
21	with	with	IN	_	_	_
22	glycolaldehyde	glycolaldehyde	NN	_	_	_
23	third	third	JJ	_	_	_
24	repetition	repetition	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	WT	wt	JJ	_	_	_
27	strain	strain	NN	_	_	_
28	without	without	IN	_	_	_
29	glycolaldehyde	glycolaldehyde	NN	_	_	_
30	first	first	JJ	_	_	_
31	repetition	repetition	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	WT	wt	JJ	_	_	_
34	strain	strain	NN	_	_	_
35	without	without	IN	_	_	_
36	glycolaldehyde	glycolaldehyde	NN	_	_	_
37	second	second	JJ	_	_	_
38	repetition	repetition	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	WT	wt	JJ	_	_	_
41	strain	strain	NN	_	_	_
42	without	without	IN	_	_	_
43	glycolaldehyde	glycolaldehyde	NN	_	_	_
44	third	third	JJ	_	_	_
45	repetition	repetition	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	Cells	cell	NNS	_	_	_
48	were	be	VBD	_	_	_
49	disrupted	disrupt	VBN	_	_	_
50	by	by	IN	_	_	_
51	sonication	sonication	NN	_	_	_
52	and	and	CC	_	_	_
53	NsrR	nsrr	NN	TF	_	_
54	bound	bind	VBD	_	_	_
55	DNA	dna	NN	_	_	_
56	was	be	VBD	_	_	_
57	isolated	isolate	VBN	_	_	_
58	with	with	IN	_	_	_
59	anti-Flag	anti-flag	JJ	_	_	_
60	antibody	antibody	NN	_	_	_
61	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	chip	chip	NN	_	_	_
3	antibody	antibody	NN	_	_	_
4	:	:	:	_	_	_
5	Monoclonal	monoclonal	JJ	_	_	_
6	ANTI-FLAG	anti-flag	NN	_	_	_
7	M5	m5	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Sigma-Aldrich	Sigma-Aldrich	NNP	_	_	_
10	,	,	,	_	_	_
11	catalog	catalog	NN	_	_	_
12	number	number	NN	_	_	_
13	:	:	:	_	_	_
14	F4042	f4042	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	chip	chip	NN	_	_	_
18	antibody	antibody	NN	_	_	_
19	:	:	:	_	_	_
20	none	none	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	ChIP-Seq	chip-seq	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	ChIP-seq	chip-seq	NN	_	_	_
25	reads	read	VBZ	_	_	_
26	were	be	VBD	_	_	_
27	aligned	align	VBN	_	_	_
28	to	to	TO	_	_	_
29	the	the	DT	_	_	_
30	CFT073	cft073	NN	_	_	_
31	genome	genome	NN	_	_	_
32	using	use	VBG	_	_	_
33	bowtie	bowtie	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	version	version	NN	_	_	_
36	0.12.8	0.12.8	CD	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	DNA	dna	NN	_	_	_
40	fragments	fragment	NNS	_	_	_
41	were	be	VBD	_	_	_
42	treated	treat	VBN	_	_	_
43	with	with	IN	_	_	_
44	Epicentre	Epicentre	NNP	_	_	_
45	End-It	end-it	JJ	_	_	_
46	DNA	dna	NN	_	_	_
47	End	end	NN	_	_	_
48	Repair	Repair	NNP	_	_	_
49	Kit	kit	NN	_	_	_
50	and	and	CC	_	_	_
51	3	3	CD	_	_	_
52	'	'	''	_	_	_
53	A	a	DT	_	_	_
54	overhangs	overhang	NNS	_	_	_
55	were	be	VBD	_	_	_
56	added	add	VBN	_	_	_
57	with	with	IN	_	_	_
58	DNA	dna	NN	_	_	_
59	polymerase	polymerase	NN	_	_	_
60	I	i	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	Klenow	klenow	NN	_	_	_
63	fragment	fragment	NN	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	.	.	.	_	_	_

1	Adapters	adapter	NNS	_	_	_
2	from	from	IN	_	_	_
3	the	the	DT	_	_	_
4	IlluminaTruSeq	illuminatruseq	NN	_	_	_
5	DNA	dna	NN	_	_	_
6	sample	sample	NN	_	_	_
7	preparation	preparation	NN	_	_	_
8	kit	kit	NN	_	_	_
9	were	be	VBD	_	_	_
10	ligated	ligate	VBN	_	_	_
11	using	use	VBG	_	_	_
12	LigFast	LigFast	NNP	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Promega	Promega	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	and	and	CC	_	_	_
17	DNAs	dna	NNS	_	_	_
18	were	be	VBD	_	_	_
19	amplified	amplify	VBN	_	_	_
20	by	by	IN	_	_	_
21	PCR	pcr	NN	_	_	_
22	using	use	VBG	_	_	_
23	primers	primer	NNS	_	_	_
24	provided	provide	VBN	_	_	_
25	in	in	IN	_	_	_
26	the	the	DT	_	_	_
27	IlluminaTruSeq	illuminatruseq	NN	_	_	_
28	DNA	dna	NN	_	_	_
29	sample	sample	NN	_	_	_
30	preparation	preparation	NN	_	_	_
31	kit	kit	NN	_	_	_
32	and	and	CC	_	_	_
33	Phusion	phusion	NN	_	_	_
34	DNA	dna	NN	_	_	_
35	polymerase	polymerase	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	NEB	neb	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	.	.	.	_	_	_

1	Products	Products	NNPS	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	ligation	ligation	NN	_	_	_
5	reaction	reaction	NN	_	_	_
6	and	and	CC	_	_	_
7	PCR	pcr	NN	_	_	_
8	amplification	amplification	NN	_	_	_
9	in	in	IN	_	_	_
10	the	the	DT	_	_	_
11	range	range	NN	_	_	_
12	300-400	300-400	CD	_	_	_
13	bp	bp	NN	_	_	_
14	were	be	VBD	_	_	_
15	purified	purify	VBN	_	_	_
16	by	by	IN	_	_	_
17	2	2	CD	_	_	_
18	%	%	NN	_	_	_
19	agarose	agarose	NN	_	_	_
20	gel	gel	NN	_	_	_
21	electrophoresis	electrophoresis	NN	_	_	_
22	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	concentrations	concentration	NNS	_	_	_
3	were	be	VBD	_	_	_
4	measured	measure	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Qubit	Qubit	NNP	_	_	_
7	™	™	SYM	_	_	_
8	dsDNA	dsdna	NN	_	_	_
9	HS	hs	NN	_	_	_
10	Assay	assay	NN	_	_	_
11	Kits	kit	NNS	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Invitrogen	Invitrogen	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	CFT073	cft073	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Genome	Genome	NNP	_	_	_
7	_	_	NNP	_	_	_
8	build	build	VB	_	_	_
9	:	:	:	_	_	_
10	CFT073	cft073	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	AE014075	ae014075	NN	_	_	_
13	.1	.1	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	NsrR	nsrr	NN	TF	_	_
17	_	_	NN	_	_	_
18	ChIPSeq	chipseq	NN	_	_	_
19	_	_	CD	_	_	_
20	rep1	rep1	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	NsrR	nsrr	NN	TF	_	_
23	_	_	NN	_	_	_
24	ChIPSeq	chipseq	NN	_	_	_
25	_	_	CD	_	_	_
26	rep2	rep2	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	NsrR	nsrr	NN	TF	_	_
29	_	_	NN	_	_	_
30	ChIPSeq	chipseq	NN	_	_	_
31	_	_	CD	_	_	_
32	rep3	rep3	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	NsrR	nsrr	NN	TF	_	_
35	_	_	NN	_	_	_
36	input	input	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	peaks	peak	NNS	_	_	_
39	were	be	VBD	_	_	_
40	called	call	VBN	_	_	_
41	using	use	VBG	_	_	_
42	MACS2	macs2	NN	_	_	_
43	with	with	IN	_	_	_
44	default	default	NN	_	_	_
45	parameters	parameter	NNS	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	samples	sample	NNS	_	_	_
48	were	be	VBD	_	_	_
49	grown	grow	VBN	_	_	_
50	aerobically	aerobically	RB	_	_	_
51	in	in	IN	_	_	_
52	rich	rich	JJ	MED	_	_
53	media	media	NNS	MED	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	strain	strain	NN	_	_	_
56	:	:	:	_	_	_
57	CFT073	cft073	NN	_	_	_
58	nsrR	nsrr	NN	GEN	_	_
59	:	:	:	_	_	_
60	:	:	:	_	_	_
61	3X-Flag	3x-flag	NN	_	_	_
62	tag	tag	NN	GEN	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	Supplementary	supplementary	JJ	_	_	_
65	_	_	NN	_	_	_
66	files	file	NNS	_	_	_
67	_	_	IN	_	_	_
68	format	format	NN	_	_	_
69	_	_	NN	_	_	_
70	and	and	CC	_	_	_
71	_	_	NN	_	_	_
72	content	content	NN	_	_	_
73	:	:	:	_	_	_
74	bed	bed	NN	_	_	_
75	format	format	NN	_	_	_
76	peak	peak	NN	_	_	_
77	file	file	NN	_	_	_
78	generated	generate	VBN	_	_	_
79	from	from	IN	_	_	_
80	MACS2	macs2	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	uropathogenic	uropathogenic	JJ	_	_	_
83	Escherichia	escherichia	FW	Organism	_	_
84	coli	coli	FW	Organism	_	_
85	-LRB-	-lrb-	-LRB-	_	_	_
86	UPEC	upec	NN	_	_	_
87	-RRB-	-rrb-	-RRB-	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	Escherichia	escherichia	FW	Organism	_	_
90	coli	coli	FW	Organism	_	_
91	CFT073	cft073	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	Genome	Genome	NNP	_	_	_
94	_	_	NNP	_	_	_
95	build	build	VB	_	_	_
96	:	:	:	_	_	_
97	CFT073	cft073	NN	_	_	_
98	-LRB-	-lrb-	-LRB-	_	_	_
99	AE014075	ae014075	NN	_	_	_
100	.1	.1	NN	_	_	_
101	-RRB-	-rrb-	-RRB-	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	genotype	genotype	NN	_	_	_
104	:	:	:	_	_	_
105	deltahmp	deltahmp	JJ	_	_	_
106	deltanrfA	deltanrfa	NN	_	_	_
107	deltanorVW	deltanorvw	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	-LRB-	-lrb-	-LRB-	_	_	_
110	-	-	:	_	_	_
111	NO	no	NN	_	_	_
112	-RRB-	-rrb-	-RRB-	_	_	_
113	1	1	CD	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	-LRB-	-lrb-	-LRB-	_	_	_
116	+	+	CC	_	_	_
117	NO	no	NN	_	_	_
118	-RRB-	-rrb-	-RRB-	_	_	_
119	1	1	CD	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	-LRB-	-lrb-	-LRB-	_	_	_
122	-	-	:	_	_	_
123	NO	no	NN	_	_	_
124	-RRB-	-rrb-	-RRB-	_	_	_
125	2	2	CD	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	-LRB-	-lrb-	-LRB-	_	_	_
128	+	+	CC	_	_	_
129	NO	no	NN	_	_	_
130	-RRB-	-rrb-	-RRB-	_	_	_
131	2	2	CD	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	-LRB-	-lrb-	-LRB-	_	_	_
134	-	-	:	_	_	_
135	NO	no	NN	_	_	_
136	-RRB-	-rrb-	-RRB-	_	_	_
137	3	3	CD	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	-LRB-	-lrb-	-LRB-	_	_	_
140	+	+	CC	_	_	_
141	NO	no	NN	_	_	_
142	-RRB-	-rrb-	-RRB-	_	_	_
143	3	3	CD	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	RNA	rna	NN	_	_	_
146	libraries	library	NNS	_	_	_
147	were	be	VBD	_	_	_
148	prepared	prepare	VBN	_	_	_
149	for	for	IN	_	_	_
150	sequencing	sequencing	NN	_	_	_
151	using	use	VBG	_	_	_
152	standard	standard	JJ	_	_	_
153	Illumina	Illumina	NNP	_	_	_
154	protocols	protocol	NNS	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
156	RNA-Seq	rna-seq	JJ	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	RNA-seq	rna-seq	NN	_	_	_
159	reads	read	VBZ	_	_	_
160	were	be	VBD	_	_	_
161	aligned	align	VBN	_	_	_
162	to	to	TO	_	_	_
163	the	the	DT	_	_	_
164	CFT073	cft073	NN	_	_	_
165	genome	genome	NN	_	_	_
166	using	use	VBG	_	_	_
167	bowtie	bowtie	NN	_	_	_
168	-LRB-	-lrb-	-LRB-	_	_	_
169	version	version	NN	_	_	_
170	0.12.8	0.12.8	CD	_	_	_
171	-RRB-	-rrb-	-RRB-	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	Samples	sample	NNS	_	_	_
174	were	be	VBD	_	_	_
175	grown	grow	VBN	_	_	_
176	anaerobically	anaerobically	RB	_	_	_
177	in	in	IN	_	_	_
178	MOPS	mop	NNS	MED	_	_
179	minimal	minimal	JJ	_	_	_
180	media	media	NNS	_	_	_
181	supplemented	supplement	VBN	_	_	_
182	with	with	IN	_	_	_
183	casamino	casamino	NN	SUPP	_	_
184	acids	acid	NNS	SUPP	_	_
185	using	use	VBG	_	_	_
186	glucose	glucose	NN	SUPP	_	_
187	as	as	IN	_	_	_
188	the	the	DT	_	_	_
189	carbon	carbon	NN	_	_	_
190	source	source	NN	_	_	_
191	.	.	.	_	_	_

1	20mM	20mm	NN	_	_	_
2	nitrate	nitrate	NN	SUPP	_	_
3	was	be	VBD	_	_	_
4	added	add	VBN	_	_	_
5	to	to	TO	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	+	+	CC	_	_	_
8	NO	no	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	cultures	culture	NNS	_	_	_
11	for	for	IN	_	_	_
12	inducing	induce	VBG	_	_	_
13	nitrosative	nitrosative	JJ	_	_	_
14	stress	stress	NN	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	CFT073	cft073	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Supplementary	supplementary	JJ	_	_	_
7	_	_	NN	_	_	_
8	files	file	NNS	_	_	_
9	_	_	IN	_	_	_
10	format	format	NN	_	_	_
11	_	_	NN	_	_	_
12	and	and	CC	_	_	_
13	_	_	NN	_	_	_
14	content	content	NN	_	_	_
15	:	:	:	_	_	_
16	tab-delimited	tab-delimited	JJ	_	_	_
17	text	text	NN	_	_	_
18	files	file	NNS	_	_	_
19	include	include	VBP	_	_	_
20	TPM	tpm	NN	_	_	_
21	values	value	NNS	_	_	_
22	for	for	IN	_	_	_
23	each	each	DT	_	_	_
24	Sample	sample	NN	_	_	_
25	;	;	:	_	_	_
26	column1	column1	NN	_	_	_
27	:	:	:	_	_	_
28	transcript	transcript	NN	_	_	_
29	id	id	NN	_	_	_
30	;	;	:	_	_	_
31	column2	column2	NN	_	_	_
32	:	:	:	_	_	_
33	TPM	tpm	NN	_	_	_
34	value	value	NN	_	_	_
35	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
36	Total	Total	NNP	_	_	_
37	Rna	Rna	NNP	_	_	_
38	was	be	VBD	_	_	_
39	extracted	extract	VBN	_	_	_
40	from	from	IN	_	_	_
41	cultures	culture	NNS	_	_	_
42	using	use	VBG	_	_	_
43	Qiagen	Qiagen	NNP	_	_	_
44	RNeasy	RNeasy	NNP	_	_	_
45	Protect	protect	VB	_	_	_
46	Bacteria	bacterium	NNS	_	_	_
47	Mini	Mini	NNP	_	_	_
48	Kit	kit	NN	_	_	_
49	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	rRNA	rrna	NN	_	_	_
3	depletion	depletion	NN	_	_	_
4	,	,	,	_	_	_
5	samples	sample	NNS	_	_	_
6	were	be	VBD	_	_	_
7	treated	treat	VBN	_	_	_
8	with	with	IN	_	_	_
9	the	the	DT	_	_	_
10	MICROBExpressTM	MICROBExpressTM	NNP	_	_	_
11	Bacterial	bacterial	JJ	_	_	_
12	mRNA	mrna	NN	_	_	_
13	Enrichment	Enrichment	NNP	_	_	_
14	Kit	kit	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Life	Life	NNP	_	_	_
17	Technologies	Technologies	NNPS	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	according	accord	VBG	_	_	_
20	to	to	TO	_	_	_
21	the	the	DT	_	_	_
22	manufacturer	manufacturer	NN	_	_	_
23	's	's	POS	_	_	_
24	instructions	instruction	NNS	_	_	_
25	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	cleaned	clean	VBN	_	_	_
4	with	with	IN	_	_	_
5	the	the	DT	_	_	_
6	Zymo	Zymo	NNP	_	_	_
7	RNA	rna	NN	_	_	_
8	Clean	clean	JJ	_	_	_
9	and	and	CC	_	_	_
10	ConcentratorTM	concentratortm	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Zymo	Zymo	NNP	_	_	_
13	Research	Research	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	and	and	CC	_	_	_
16	then	then	RB	_	_	_
17	subjected	subject	VBN	_	_	_
18	to	to	TO	_	_	_
19	a	a	DT	_	_	_
20	second	second	JJ	_	_	_
21	cycle	cycle	NN	_	_	_
22	of	of	IN	_	_	_
23	rRNA	rrna	NN	_	_	_
24	depletion	depletion	NN	_	_	_
25	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	recovered	recover	VBN	_	_	_
4	by	by	IN	_	_	_
5	ethanol	ethanol	NN	_	_	_
6	precipitation	precipitation	NN	_	_	_
7	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	TPM	tpm	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	transcripts	transcript	NNS	_	_	_
5	per	per	IN	_	_	_
6	million	million	CD	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	was	be	VBD	_	_	_
9	calculated	calculate	VBN	_	_	_
10	by	by	IN	_	_	_
11	RSEM	rsem	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	version	version	NN	_	_	_
14	1.2.19	1.2.19	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	uropathogenic	uropathogenic	JJ	_	_	_
18	Escherichia	escherichia	FW	Organism	_	_
19	coli	coli	FW	Organism	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	UPEC	upec	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	grown	grow	VBN	_	_	_
24	with	with	IN	_	_	_
25	nitrosative	nitrosative	JJ	_	_	_
26	stress	stress	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	uropathogenic	uropathogenic	JJ	_	_	_
29	Escherichia	escherichia	FW	Organism	_	_
30	coli	coli	FW	Organism	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	UPEC	upec	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	grown	grow	VBN	_	_	_
35	without	without	IN	_	_	_
36	nitrosative	nitrosative	JJ	_	_	_
37	stress	stress	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	DnaK	dnak	NN	_	_	_
40	deletant	deletant	JJ	_	_	_
41	_	_	NN	_	_	_
42	37C	37c	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	E.coli	e.coli	NN	_	_	_
45	gene	gene	NN	_	_	_
46	expression	expression	NN	_	_	_
47	data	datum	NNS	_	_	_
48	in	in	IN	_	_	_
49	deletion	deletion	NN	_	_	_
50	of	of	IN	_	_	_
51	chaperone	chaperone	NN	_	_	_
52	DnaK	dnak	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Escherichia	escherichia	FW	Organism	_	_
55	coli	coli	FW	Organism	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	genotype	genotype	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	strain	strain	NN	_	_	_
60	background	background	NN	_	_	_
61	:	:	:	_	_	_
62	BW25113	bw25113	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
64	The	the	DT	_	_	_
65	signal	signal	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	Total	total	JJ	_	_	_
68	RNA	rna	NN	_	_	_
69	was	be	VBD	_	_	_
70	isolated	isolate	VBN	_	_	_
71	from	from	IN	_	_	_
72	strains	strain	NNS	_	_	_
73	using	use	VBG	_	_	_
74	NucleoSpin	NucleoSpin	NNP	_	_	_
75	RNAII	RNAII	NNP	_	_	_
76	kit	kit	NN	_	_	_
77	-LRB-	-lrb-	-LRB-	_	_	_
78	Macherey-Nagel	Macherey-Nagel	NNP	_	_	_
79	Corporation	Corporation	NNP	_	_	_
80	-RRB-	-rrb-	-RRB-	_	_	_
81	following	follow	VBG	_	_	_
82	the	the	DT	_	_	_
83	instruction	instruction	NN	_	_	_
84	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	examined	examine	VBN	_	_	_
5	in	in	IN	_	_	_
6	a	a	DT	_	_	_
7	1.5	1.5	CD	_	_	_
8	%	%	NN	_	_	_
9	denaturing	denature	VBG	_	_	_
10	agarose	agarose	NN	_	_	_
11	gel	gel	NN	_	_	_
12	,	,	,	_	_	_
13	quantitated	quantitate	VBN	_	_	_
14	by	by	IN	_	_	_
15	absorbance	absorbance	NN	_	_	_
16	at	at	IN	_	_	_
17	260	260	CD	_	_	_
18	nm	nm	NN	_	_	_
19	and	and	CC	_	_	_
20	stored	store	VBN	_	_	_
21	until	until	IN	_	_	_
22	further	further	JJ	_	_	_
23	use	use	NN	_	_	_
24	for	for	IN	_	_	_
25	microarray	microarray	NN	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	WT	WT	NNP	_	_	_
3	_	_	NNP	_	_	_
4	37C	37C	NNP	_	_	_
5	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
6	Escherichia	escherichia	FW	Organism	_	_
7	coli	coli	FW	Organism	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Escherichia	escherichia	FW	Organism	_	_
10	coli	coli	FW	Organism	_	_
11	MG1655	mg1655	NN	_	_	_
12	10	10	CD	_	_	_
13	minutes	minute	NNS	_	_	_
14	paraquat	paraquat	NN	SUPP	_	_
15	treatment	treatment	NN	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Escherichia	escherichia	FW	Organism	_	_
18	coli	coli	FW	Organism	_	_
19	MG1655	mg1655	NN	_	_	_
20	2	2	CD	_	_	_
21	minutes	minute	NNS	_	_	_
22	paraquat	paraquat	NN	SUPP	_	_
23	treatment	treatment	NN	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	Escherichia	escherichia	FW	Organism	_	_
26	coli	coli	FW	Organism	_	_
27	MG1655	mg1655	NN	_	_	_
28	4	4	CD	_	_	_
29	minutes	minute	NNS	_	_	_
30	paraquat	paraquat	NN	SUPP	_	_
31	treatment	treatment	NN	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	Escherichia	escherichia	FW	Organism	_	_
34	coli	coli	FW	Organism	_	_
35	MG1655	mg1655	NN	_	_	_
36	6	6	CD	_	_	_
37	minutes	minute	NNS	_	_	_
38	paraquat	paraquat	NN	SUPP	_	_
39	treatment	treatment	NN	_	_	_
40	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
41	Escherichia	escherichia	FW	Organism	_	_
42	coli	coli	FW	Organism	_	_
43	MG1655	mg1655	NN	_	_	_
44	8	8	CD	_	_	_
45	minutes	minute	NNS	_	_	_
46	paraquat	paraquat	NN	SUPP	_	_
47	treatment	treatment	NN	_	_	_
48	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
49	Escherichia	escherichia	FW	Organism	_	_
50	coli	coli	FW	Organism	_	_
51	MG1655	mg1655	NN	_	_	_
52	before	before	IN	_	_	_
53	paraquat	paraquat	NN	SUPP	_	_
54	treatment	treatment	NN	_	_	_
55	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
56	Escherichia	escherichia	FW	Organism	_	_
57	coli	coli	FW	Organism	_	_
58	MG1655	mg1655	NN	_	_	_
59	with	with	IN	_	_	_
60	a	a	DT	_	_	_
61	precise	precise	JJ	_	_	_
62	deletion	deletion	NN	_	_	_
63	in	in	IN	_	_	_
64	soxR	soxr	NN	GEN	_	_
65	and	and	CC	_	_	_
66	10	10	CD	_	_	_
67	minutes	minute	NNS	_	_	_
68	paraquat	paraquat	NN	SUPP	_	_
69	treatment	treatment	NN	_	_	_
70	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
71	Escherichia	escherichia	FW	Organism	_	_
72	coli	coli	FW	Organism	_	_
73	MG1655	mg1655	NN	_	_	_
74	with	with	IN	_	_	_
75	a	a	DT	_	_	_
76	precise	precise	JJ	_	_	_
77	deletion	deletion	NN	_	_	_
78	in	in	IN	_	_	_
79	soxR	soxr	NN	GEN	_	_
80	and	and	CC	_	_	_
81	2	2	CD	_	_	_
82	minutes	minute	NNS	_	_	_
83	paraquat	paraquat	NN	SUPP	_	_
84	treatment	treatment	NN	_	_	_
85	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
86	Escherichia	escherichia	FW	Organism	_	_
87	coli	coli	FW	Organism	_	_
88	MG1655	mg1655	NN	_	_	_
89	with	with	IN	_	_	_
90	a	a	DT	_	_	_
91	precise	precise	JJ	_	_	_
92	deletion	deletion	NN	_	_	_
93	in	in	IN	_	_	_
94	soxR	soxr	NN	GEN	_	_
95	and	and	CC	_	_	_
96	4	4	CD	_	_	_
97	minutes	minute	NNS	_	_	_
98	paraquat	paraquat	NN	SUPP	_	_
99	treatment	treatment	NN	_	_	_
100	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
101	Escherichia	escherichia	FW	Organism	_	_
102	coli	coli	FW	Organism	_	_
103	MG1655	mg1655	NN	_	_	_
104	with	with	IN	_	_	_
105	a	a	DT	_	_	_
106	precise	precise	JJ	_	_	_
107	deletion	deletion	NN	_	_	_
108	in	in	IN	_	_	_
109	soxR	soxr	NN	GEN	_	_
110	and	and	CC	_	_	_
111	6	6	CD	_	_	_
112	minutes	minute	NNS	_	_	_
113	paraquat	paraquat	NN	SUPP	_	_
114	treatment	treatment	NN	_	_	_
115	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
116	Escherichia	escherichia	FW	Organism	_	_
117	coli	coli	FW	Organism	_	_
118	MG1655	mg1655	NN	_	_	_
119	with	with	IN	_	_	_
120	a	a	DT	_	_	_
121	precise	precise	JJ	_	_	_
122	deletion	deletion	NN	_	_	_
123	in	in	IN	_	_	_
124	soxR	soxr	NN	GEN	_	_
125	and	and	CC	_	_	_
126	8	8	CD	_	_	_
127	minutes	minute	NNS	_	_	_
128	paraquat	paraquat	NN	SUPP	_	_
129	treatment	treatment	NN	_	_	_
130	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
131	Escherichia	escherichia	FW	Organism	_	_
132	coli	coli	FW	Organism	_	_
133	MG1655	mg1655	NN	_	_	_
134	with	with	IN	_	_	_
135	a	a	DT	_	_	_
136	precise	precise	JJ	_	_	_
137	deletion	deletion	NN	_	_	_
138	in	in	IN	_	_	_
139	soxR	soxr	NN	GEN	_	_
140	before	before	IN	_	_	_
141	paraquat	paraquat	NN	SUPP	_	_
142	treatment	treatment	NN	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	M1655	m1655	NN	_	_	_
145	wild	wild	JJ	_	_	_
146	type	type	NN	_	_	_
147	at	at	IN	_	_	_
148	t0	t0	NN	_	_	_
149	,	,	,	_	_	_
150	rep1	rep1	NN	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	M1655	m1655	NN	_	_	_
153	wild	wild	JJ	_	_	_
154	type	type	NN	_	_	_
155	at	at	IN	_	_	_
156	t0	t0	NN	_	_	_
157	,	,	,	_	_	_
158	rep2	rep2	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	M1655	m1655	NN	_	_	_
161	wild	wild	JJ	_	_	_
162	type	type	NN	_	_	_
163	at	at	IN	_	_	_
164	t10	t10	NN	_	_	_
165	,	,	,	_	_	_
166	rep1	rep1	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	M1655	m1655	NN	_	_	_
169	wild	wild	JJ	_	_	_
170	type	type	NN	_	_	_
171	at	at	IN	_	_	_
172	t10	t10	NN	_	_	_
173	,	,	,	_	_	_
174	rep2	rep2	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	M1655	m1655	NN	_	_	_
177	wild	wild	JJ	_	_	_
178	type	type	NN	_	_	_
179	at	at	IN	_	_	_
180	t2	t2	NN	_	_	_
181	,	,	,	_	_	_
182	rep1	rep1	NN	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	M1655	m1655	NN	_	_	_
185	wild	wild	JJ	_	_	_
186	type	type	NN	_	_	_
187	at	at	IN	_	_	_
188	t2	t2	NN	_	_	_
189	,	,	,	_	_	_
190	rep2	rep2	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	M1655	m1655	NN	_	_	_
193	wild	wild	JJ	_	_	_
194	type	type	NN	_	_	_
195	at	at	IN	_	_	_
196	t4	t4	NN	_	_	_
197	,	,	,	_	_	_
198	rep1	rep1	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	M1655	m1655	NN	_	_	_
201	wild	wild	JJ	_	_	_
202	type	type	NN	_	_	_
203	at	at	IN	_	_	_
204	t4	t4	NN	_	_	_
205	,	,	,	_	_	_
206	rep2	rep2	NN	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	M1655	m1655	NN	_	_	_
209	wild	wild	JJ	_	_	_
210	type	type	NN	_	_	_
211	at	at	IN	_	_	_
212	t6	t6	NN	_	_	_
213	,	,	,	_	_	_
214	rep1	rep1	NN	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	M1655	m1655	NN	_	_	_
217	wild	wild	JJ	_	_	_
218	type	type	NN	_	_	_
219	at	at	IN	_	_	_
220	t6	t6	NN	_	_	_
221	,	,	,	_	_	_
222	rep2	rep2	NN	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	M1655	m1655	NN	_	_	_
225	wild	wild	JJ	_	_	_
226	type	type	NN	_	_	_
227	at	at	IN	_	_	_
228	t8	t8	NN	_	_	_
229	,	,	,	_	_	_
230	rep1	rep1	NN	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	M1655	m1655	NN	_	_	_
233	wild	wild	JJ	_	_	_
234	type	type	NN	_	_	_
235	at	at	IN	_	_	_
236	t8	t8	NN	_	_	_
237	,	,	,	_	_	_
238	rep2	rep2	NN	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	M1655	m1655	NN	_	_	_
241	with	with	IN	_	_	_
242	deletion	deletion	NN	_	_	_
243	in	in	IN	_	_	_
244	soxR	soxr	NN	GEN	_	_
245	at	at	IN	_	_	_
246	t0	t0	NN	_	_	_
247	,	,	,	_	_	_
248	rep1	rep1	NN	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	M1655	m1655	NN	_	_	_
251	with	with	IN	_	_	_
252	deletion	deletion	NN	_	_	_
253	in	in	IN	_	_	_
254	soxR	soxr	NN	GEN	_	_
255	at	at	IN	_	_	_
256	t10	t10	NN	_	_	_
257	,	,	,	_	_	_
258	rep1	rep1	NN	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	M1655	m1655	NN	_	_	_
261	with	with	IN	_	_	_
262	deletion	deletion	NN	_	_	_
263	in	in	IN	_	_	_
264	soxR	soxr	NN	GEN	_	_
265	at	at	IN	_	_	_
266	t2	t2	NN	_	_	_
267	,	,	,	_	_	_
268	rep1	rep1	NN	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	M1655	m1655	NN	_	_	_
271	with	with	IN	_	_	_
272	deletion	deletion	NN	_	_	_
273	in	in	IN	_	_	_
274	soxR	soxr	NN	GEN	_	_
275	at	at	IN	_	_	_
276	t4	t4	NN	_	_	_
277	,	,	,	_	_	_
278	rep1	rep1	NN	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	M1655	m1655	NN	_	_	_
281	with	with	IN	_	_	_
282	deletion	deletion	NN	_	_	_
283	in	in	IN	_	_	_
284	soxR	soxr	NN	GEN	_	_
285	at	at	IN	_	_	_
286	t6	t6	NN	_	_	_
287	,	,	,	_	_	_
288	rep1	rep1	NN	_	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
290	M1655	m1655	NN	_	_	_
291	with	with	IN	_	_	_
292	deletion	deletion	NN	_	_	_
293	in	in	IN	_	_	_
294	soxR	soxr	NN	GEN	_	_
295	at	at	IN	_	_	_
296	t8	t8	NN	_	_	_
297	,	,	,	_	_	_
298	rep1	rep1	NN	_	_	_
299	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
300	Overnight	overnight	JJ	_	_	_
301	cultures	culture	NNS	_	_	_
302	were	be	VBD	_	_	_
303	inoculated	inoculate	VBN	_	_	_
304	1:100	1:100	CD	_	_	_
305	into	into	IN	_	_	_
306	20	20	CD	_	_	_
307	ml	ml	NN	_	_	_
308	of	of	IN	_	_	_
309	EZ	ez	NN	_	_	_
310	Rich	rich	JJ	_	_	_
311	Defined	defined	JJ	_	_	_
312	Medium	medium	NN	_	_	_
313	-LRB-	-lrb-	-LRB-	_	_	_
314	Neidhardt	Neidhardt	NNP	_	_	_
315	et	et	FW	_	_	_
316	al.	al.	FW	_	_	_
317	,	,	,	_	_	_
318	1974	1974	CD	_	_	_
319	-RRB-	-rrb-	-RRB-	_	_	_
320	in	in	IN	_	_	_
321	125	125	CD	_	_	_
322	ml	ml	NN	_	_	_
323	Erlenmeyer	erlenmeyer	NN	_	_	_
324	flasks	flask	NNS	_	_	_
325	and	and	CC	_	_	_
326	grown	grow	VBN	_	_	_
327	at	at	IN	_	_	_
328	37oC	37oc	NN	_	_	_
329	and	and	CC	_	_	_
330	250	250	CD	_	_	_
331	rpm	rpm	NN	_	_	_
332	in	in	IN	_	_	_
333	a	a	DT	_	_	_
334	reciprocating	reciprocate	VBG	_	_	_
335	water	water	NN	_	_	_
336	bath	bath	NN	_	_	_
337	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Paraquat	Paraquat	NNP	_	_	_
3	was	be	VBD	_	_	_
4	added	add	VBN	_	_	_
5	to	to	TO	_	_	_
6	growing	grow	VBG	_	_	_
7	cultures	culture	NNS	_	_	_
8	at	at	IN	_	_	_
9	a	a	DT	_	_	_
10	final	final	JJ	_	_	_
11	concentration	concentration	NN	_	_	_
12	of	of	IN	_	_	_
13	250	250	CD	_	_	_
14	?	?	.	_	_	_

1	M.	M.	NNP	_	_	_
2	Samples	Samples	NNP	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	1.4	1.4	CD	_	_	_
5	ml	ml	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	were	be	VBD	_	_	_
8	taken	take	VBN	_	_	_
9	every	every	DT	_	_	_
10	2	2	CD	_	_	_
11	minutes	minute	NNS	_	_	_
12	following	follow	VBG	_	_	_
13	paraquat	paraquat	NN	SUPP	_	_
14	treatment	treatment	NN	_	_	_
15	for	for	IN	_	_	_
16	the	the	DT	_	_	_
17	length	length	NN	_	_	_
18	of	of	IN	_	_	_
19	the	the	DT	_	_	_
20	time	time	NN	_	_	_
21	course	course	NN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	flash-frozen	flash-frozen	JJ	_	_	_
25	by	by	IN	_	_	_
26	immersion	immersion	NN	_	_	_
27	of	of	IN	_	_	_
28	the	the	DT	_	_	_
29	tubes	tube	NNS	_	_	_
30	in	in	IN	_	_	_
31	liquid	liquid	JJ	_	_	_
32	nitrogen	nitrogen	NN	_	_	_
33	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	collected	collect	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	for	for	IN	_	_	_
8	1	1	CD	_	_	_
9	minute	minute	NN	_	_	_
10	at	at	IN	_	_	_
11	13,000	13,000	CD	_	_	_
12	rpm	rpm	NN	_	_	_
13	,	,	,	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	The	the	DT	_	_	_
16	data	datum	NNS	_	_	_
17	were	be	VBD	_	_	_
18	analyzed	analyze	VBN	_	_	_
19	using	use	VBG	_	_	_
20	Robust	robust	JJ	_	_	_
21	Multi-Array	multi-array	JJ	_	_	_
22	average	average	NN	_	_	_
23	as	as	IN	_	_	_
24	implemented	implement	VBN	_	_	_
25	in	in	IN	_	_	_
26	Bioconductor	Bioconductor	NNP	_	_	_
27	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
28	Total	Total	NNP	_	_	_
29	RNA	rna	NN	_	_	_
30	was	be	VBD	_	_	_
31	isolated	isolate	VBN	_	_	_
32	using	use	VBG	_	_	_
33	Qiagen	Qiagen	NNP	_	_	_
34	RNeasy	RNeasy	NNP	_	_	_
35	Mini	Mini	NNP	_	_	_
36	Kit	kit	NN	_	_	_
37	and	and	CC	_	_	_
38	treated	treat	VBN	_	_	_
39	with	with	IN	_	_	_
40	DNase	dnase	NN	_	_	_
41	I	i	CD	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	agitation	agitation	NN	_	_	_
44	speed	speed	NN	_	_	_
45	:	:	:	_	_	_
46	1200	1200	CD	_	_	_
47	rpm	rpm	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	agitation	agitation	NN	_	_	_
50	speed	speed	NN	_	_	_
51	:	:	:	_	_	_
52	600	600	CD	_	_	_
53	rpm	rpm	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	bacterial	bacterial	JJ	_	_	_
56	cells	cell	NNS	_	_	_
57	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
58	Data	Data	NNP	_	_	_
59	filtering	filter	VBG	_	_	_
60	was	be	VBD	_	_	_
61	done	do	VBN	_	_	_
62	with	with	IN	_	_	_
63	in-house	in-house	JJ	_	_	_
64	script	script	NN	_	_	_
65	with	with	IN	_	_	_
66	the	the	DT	_	_	_
67	set	set	VBN	_	_	_
68	value	value	NN	_	_	_
69	as	as	IN	_	_	_
70	follows	follow	VBZ	_	_	_
71	:	:	:	_	_	_
72	Removal	removal	NN	_	_	_
73	if	if	IN	_	_	_
74	%	%	NN	_	_	_
75	of	of	IN	_	_	_
76	N	n	NN	_	_	_
77	nucleotide	nucleotide	NN	_	_	_
78	is	be	VBZ	_	_	_
79	more	more	JJR	_	_	_
80	than	than	IN	_	_	_
81	10	10	CD	_	_	_
82	%	%	NN	_	_	_
83	,	,	,	_	_	_
84	if	if	IN	_	_	_
85	more	more	JJR	_	_	_
86	than	than	IN	_	_	_
87	40	40	CD	_	_	_
88	%	%	NN	_	_	_
89	of	of	IN	_	_	_
90	the	the	DT	_	_	_
91	nucleotide	nucleotide	NN	_	_	_
92	is	be	VBZ	_	_	_
93	Q20	q20	NN	_	_	_
94	or	or	CC	_	_	_
95	less	less	JJR	_	_	_
96	,	,	,	_	_	_
97	if	if	IN	_	_	_
98	average	average	JJ	_	_	_
99	quality	quality	NN	_	_	_
100	of	of	IN	_	_	_
101	the	the	DT	_	_	_
102	reads	read	VBZ	_	_	_
103	is	be	VBZ	_	_	_
104	less	less	JJR	_	_	_
105	than	than	IN	_	_	_
106	Q20	q20	NN	_	_	_
107	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Expression	expression	NN	_	_	_
6	of	of	IN	_	_	_
7	introduced	introduce	VBN	_	_	_
8	enzymes	enzyme	NNS	_	_	_
9	for	for	IN	_	_	_
10	3-HP	3-hp	NN	_	_	_
11	productionm	productionm	NN	_	_	_
12	was	be	VBD	_	_	_
13	induced	induce	VBN	_	_	_
14	by	by	IN	_	_	_
15	0.05	0.05	CD	_	_	_
16	mM	mm	NN	KWSUPP	_	_
17	IPTG	iptg	NN	_	_	_
18	and	and	CC	_	_	_
19	50	50	CD	_	_	_
20	µM	µm	NN	_	_	_
21	vitamin	vitamin	NN	_	_	_
22	B12	b12	NN	_	_	_
23	when	when	WRB	_	_	_
24	the	the	DT	_	_	_
25	cell	cell	NN	_	_	_
26	reached	reach	VBN	_	_	_
27	at	at	IN	_	_	_
28	the	the	DT	_	_	_
29	early-exponential	early-exponential	JJ	_	_	_
30	growth	growth	NN	_	_	_
31	phase	phase	NN	_	_	_
32	.	.	.	_	_	_

1	T	t	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	fermentation	fermentation	NN	_	_	_
4	time	time	NN	_	_	_
5	:	:	:	_	_	_
6	20h	20h	JJ	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	fermentation	fermentation	NN	_	_	_
9	time	time	NN	_	_	_
10	:	:	:	_	_	_
11	30h	30h	CD	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	fermentation	fermentation	NN	_	_	_
14	time	time	NN	_	_	_
15	:	:	:	_	_	_
16	40h	40h	JJ	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Genome	Genome	NNP	_	_	_
19	_	_	NNP	_	_	_
20	build	build	VB	_	_	_
21	:	:	:	_	_	_
22	http	http	NN	_	_	_
23	:	:	:	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	Illumina	Illumina	NNP	_	_	_
26	Casava	Casava	NNP	_	_	_
27	1.8.2	1.8.2	CD	_	_	_
28	software	software	NN	_	_	_
29	used	use	VBN	_	_	_
30	for	for	IN	_	_	_
31	basecalling	basecall	VBG	_	_	_
32	with	with	IN	_	_	_
33	default	default	NN	_	_	_
34	parameter	parameter	NN	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Read	Read	NNP	_	_	_
3	alignment	alignment	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	with	with	IN	_	_	_
7	BWA	bwa	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	version	version	NN	_	_	_
10	0.6.2	0.6.2	CD	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	with	with	IN	_	_	_
13	default	default	NN	_	_	_
14	parameter	parameter	NN	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Sequenced	sequence	VBN	_	_	_
5	reads	read	VBZ	_	_	_
6	were	be	VBD	_	_	_
7	trimmed	trim	VBN	_	_	_
8	for	for	IN	_	_	_
9	adaptor	adaptor	NN	_	_	_
10	sequence	sequence	NN	_	_	_
11	and	and	CC	_	_	_
12	masked	mask	VBN	_	_	_
13	for	for	IN	_	_	_
14	low-complexity	low-complexity	JJ	_	_	_
15	sequence	sequence	NN	_	_	_
16	,	,	,	_	_	_
17	then	then	RB	_	_	_
18	mapped	map	VBD	_	_	_
19	to	to	TO	_	_	_
20	E.coli	e.coli	VB	_	_	_
21	W3110	w3110	NN	_	_	_
22	whole	whole	JJ	_	_	_
23	genome	genome	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	SH0003	sh0003	NN	_	_	_
3	30h	30h	CD	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	SH0012	sh0012	NN	_	_	_
6	20h	20h	JJ	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	SH0012	sh0012	NN	_	_	_
9	30h	30h	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Sh0012	sh0012	NN	_	_	_
12	40h	40h	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	SH0012	sh0012	NN	_	_	_
15	and	and	CC	_	_	_
16	SH0003	sh0003	NN	_	_	_
17	were	be	VBD	_	_	_
18	fermented	ferment	VBN	_	_	_
19	in	in	IN	_	_	_
20	a	a	DT	_	_	_
21	5.0	5.0	CD	_	_	_
22	L	l	NN	_	_	_
23	jar-fermenter	jar-fermenter	NN	_	_	_
24	with	with	IN	_	_	_
25	a	a	DT	_	_	_
26	2.0	2.0	CD	_	_	_
27	working	work	VBG	_	_	_
28	voulume	voulume	NN	_	_	_
29	of	of	IN	_	_	_
30	modified	modify	VBN	_	_	_
31	R	r	NN	_	_	_
32	medium	medium	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	20g	20g	JJ	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	SH0012	sh0012	NN	_	_	_
37	no	no	DT	_	_	_
38	rpm	rpm	NN	_	_	_
39	change	change	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	SH0012	sh0012	NN	_	_	_
42	no	no	DT	_	_	_
43	vitamin	vitamin	NN	_	_	_
44	B12	b12	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	strain	strain	NN	_	_	_
47	:	:	:	_	_	_
48	SH0003	sh0003	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	strain	strain	NN	_	_	_
51	:	:	:	_	_	_
52	SH0012	sh0012	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Supplementary	supplementary	JJ	_	_	_
55	_	_	NN	_	_	_
56	files	file	NNS	_	_	_
57	_	_	IN	_	_	_
58	format	format	NN	_	_	_
59	_	_	NN	_	_	_
60	and	and	CC	_	_	_
61	_	_	NN	_	_	_
62	content	content	NN	_	_	_
63	:	:	:	_	_	_
64	Excel	Excel	NNP	_	_	_
65	files	file	NNS	_	_	_
66	include	include	VBP	_	_	_
67	FPKM	fpkm	NN	_	_	_
68	values	value	NNS	_	_	_
69	for	for	IN	_	_	_
70	each	each	DT	_	_	_
71	sample	sample	NN	_	_	_
72	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	bacterial	bacterial	JJ	_	_	_
4	cells	cell	NNS	_	_	_
5	from	from	IN	_	_	_
6	5L	5l	NN	_	_	_
7	fermentation	fermentation	NN	_	_	_
8	were	be	VBD	_	_	_
9	collected	collect	VBN	_	_	_
10	at	at	IN	_	_	_
11	20h	20h	CD	_	_	_
12	,	,	,	_	_	_
13	30h	30h	CD	_	_	_
14	,	,	,	_	_	_
15	40h	40h	NN	_	_	_
16	and	and	CC	_	_	_
17	centrifuged	centrifuge	VBN	_	_	_
18	for	for	IN	_	_	_
19	5	5	CD	_	_	_
20	min	min	NN	_	_	_
21	to	to	TO	_	_	_
22	pellet	pellet	VB	_	_	_
23	the	the	DT	_	_	_
24	cells	cell	NNS	_	_	_
25	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	then	then	RB	_	_	_
4	mixed	mix	VBN	_	_	_
5	with	with	IN	_	_	_
6	500mL	500ml	NN	_	_	_
7	of	of	IN	_	_	_
8	RNA	rna	NN	_	_	_
9	protectant	protectant	NN	_	_	_
10	bacterial	bacterial	JJ	_	_	_
11	reagents	reagent	NNS	_	_	_
12	to	to	TO	_	_	_
13	stabilize	stabilize	VB	_	_	_
14	RNA	rna	NN	_	_	_
15	and	and	CC	_	_	_
16	stored	store	VBD	_	_	_
17	at	at	IN	_	_	_
18	-80	-80	CD	_	_	_
19	°C	°c	NN	_	_	_
20	until	until	IN	_	_	_
21	use	use	NN	_	_	_
22	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNAs	rna	NNS	_	_	_
3	were	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	using	use	VBG	_	_	_
6	RNeasy	RNeasy	NNP	_	_	_
7	mini	minus	NNS	_	_	_
8	kit	kit	NN	_	_	_
9	and	and	CC	_	_	_
10	were	be	VBD	_	_	_
11	treated	treat	VBN	_	_	_
12	with	with	IN	_	_	_
13	DNase	dnase	NN	_	_	_
14	to	to	TO	_	_	_
15	remove	remove	VB	_	_	_
16	DNA	dna	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	RNA-Seq	rna-seq	JJ	_	_	_
4	library	library	NN	_	_	_
5	was	be	VBD	_	_	_
6	constructed	construct	VBN	_	_	_
7	with	with	IN	_	_	_
8	TruSeq	truseq	NN	_	_	_
9	RNA	rna	NN	_	_	_
10	Preparation	preparation	NN	_	_	_
11	Kit	kit	NN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Transcript	Transcript	NNP	_	_	_
3	assembly	assembly	NN	_	_	_
4	an	a	DT	_	_	_
5	quantification	quantification	NN	_	_	_
6	was	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	using	use	VBG	_	_	_
9	a	a	DT	_	_	_
10	protocols	protocol	NNS	_	_	_
11	from	from	IN	_	_	_
12	Trapnell	Trapnell	NNP	_	_	_
13	et	et	FW	_	_	_
14	al.	al.	FW	_	_	_
15	,	,	,	_	_	_
16	and	and	CC	_	_	_
17	Li	Li	NNP	_	_	_
18	et	et	FW	_	_	_
19	al.	al.	FW	_	_	_
20	.	.	.	_	_	_

1	Fragments	fragment	NNS	_	_	_
2	Per	per	IN	_	_	_
3	Kilobases	kilobase	NNS	_	_	_
4	of	of	IN	_	_	_
5	exon	exon	NN	_	_	_
6	per	per	IN	_	_	_
7	million	million	CD	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	FPKM	fpkm	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	were	be	VBD	_	_	_
12	calculated	calculate	VBN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	grown	grow	VBN	_	_	_
4	aerobically	aerobically	RB	_	_	_
5	to	to	TO	_	_	_
6	exponential	exponential	JJ	GrowthPhase	_	_
7	phase	phase	NN	GrowthPhase	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	OD600	od600	NN	_	_	_
10	=	=	JJ	_	_	_
11	0.8	0.8	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	in	in	IN	_	_	_
14	LB	lb	NN	MED	_	_
15	media	media	NNS	MED	_	_
16	at	at	IN	_	_	_
17	37C	37c	NN	_	_	_
18	were	be	VBD	_	_	_
19	harvested	harvest	VBN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	expressing	express	VBG	_	_	_
5	dr1558	dr1558	NN	_	_	_
6	replicate	replicate	VB	_	_	_
7	1	1	CD	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	E.	E.	NNP	_	_	_
10	coli	coli	NN	_	_	_
11	expressing	express	VBG	_	_	_
12	dr1558	dr1558	NN	_	_	_
13	replicate	replicate	VB	_	_	_
14	2	2	CD	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	E.	E.	NNP	_	_	_
17	coli	coli	NN	_	_	_
18	expressing	express	VBG	_	_	_
19	dr1558	dr1558	NN	_	_	_
20	replicate	replicate	VB	_	_	_
21	3	3	CD	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	E.	E.	NNP	_	_	_
24	coli	coli	NN	_	_	_
25	harboring	harboring	NN	_	_	_
26	pRadGro	pradgro	NN	_	_	_
27	replicate	replicate	VBP	_	_	_
28	1	1	CD	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	E.	E.	NNP	_	_	_
31	coli	coli	NN	_	_	_
32	harboring	harboring	NN	_	_	_
33	pRadGro	pradgro	NN	_	_	_
34	replicate	replicate	VBP	_	_	_
35	2	2	CD	_	_	_
36	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
37	E.	E.	NNP	_	_	_
38	coli	coli	NN	_	_	_
39	harboring	harboring	NN	_	_	_
40	pRadGro	pradgro	NN	_	_	_
41	replicate	replicate	VBP	_	_	_
42	3	3	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Ec-pR	ec-pr	NN	_	_	_
45	VS	vs	NN	_	_	_
46	Ec-1558	ec-1558	NN	_	_	_
47	rep1	rep1	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	Ec-pR	ec-pr	NN	_	_	_
50	VS	vs	NN	_	_	_
51	Ec-1558	ec-1558	NN	_	_	_
52	rep2	rep2	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Ec-pR	ec-pr	NN	_	_	_
55	VS	vs	NN	_	_	_
56	Ec-1558	ec-1558	NN	_	_	_
57	rep3	rep3	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	Escherichia	escherichia	FW	Organism	_	_
60	coli	coli	FW	Organism	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Non-treatment	non-treatment	JJ	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	strain	strain	NN	_	_	_
65	information	information	NN	_	_	_
66	:	:	:	_	_	_
67	E.	e.	FW	_	_	_
68	coli	coli	FW	_	_	_
69	harboring	harboring	NN	_	_	_
70	empty	empty	JJ	_	_	_
71	vector	vector	NN	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	pRADgro	pradgro	NN	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	,	,	,	_	_	_
76	used	use	VBN	_	_	_
77	as	as	IN	_	_	_
78	a	a	DT	_	_	_
79	control	control	NN	_	_	_
80	strain	strain	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	strain	strain	NN	_	_	_
83	information	information	NN	_	_	_
84	:	:	:	_	_	_
85	E.	e.	FW	_	_	_
86	coli	coli	FW	_	_	_
87	harboring	harbor	VBG	_	_	_
88	pRADgro	pradgro	NN	_	_	_
89	:	:	:	_	_	_
90	:	:	:	_	_	_
91	dr1558	dr1558	CD	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
93	The	the	DT	_	_	_
94	genes	gene	NNS	_	_	_
95	were	be	VBD	_	_	_
96	considered	consider	VBN	_	_	_
97	differentially	differentially	RB	_	_	_
98	expressed	express	VBN	_	_	_
99	when	when	WRB	_	_	_
100	the	the	DT	_	_	_
101	logarithmic	logarithmic	JJ	_	_	_
102	gene	gene	NN	_	_	_
103	expression	expression	NN	_	_	_
104	ratios	ratio	NNS	_	_	_
105	had	have	VBD	_	_	_
106	a	a	DT	_	_	_
107	2-fold	2-fold	JJ	_	_	_
108	difference	difference	NN	_	_	_
109	in	in	IN	_	_	_
110	the	the	DT	_	_	_
111	expression	expression	NN	_	_	_
112	level	level	NN	_	_	_
113	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	significance	significance	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	data	datum	NNS	_	_	_
6	was	be	VBD	_	_	_
7	determined	determine	VBN	_	_	_
8	using	use	VBG	_	_	_
9	Student	student	NN	_	_	_
10	's	's	POS	_	_	_
11	t	t	NN	_	_	_
12	test	test	NN	_	_	_
13	.	.	.	_	_	_

1	P-values	p-value	NNS	_	_	_
2	of	of	IN	_	_	_
3	less	less	JJR	_	_	_
4	than	than	IN	_	_	_
5	0.01	0.01	CD	_	_	_
6	were	be	VBD	_	_	_
7	considered	consider	VBN	_	_	_
8	significant	significant	JJ	_	_	_
9	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	genes	gene	NNS	_	_	_
4	were	be	VBD	_	_	_
5	filtered	filter	VBN	_	_	_
6	by	by	IN	_	_	_
7	removing	remove	VBG	_	_	_
8	the	the	DT	_	_	_
9	flag-out	flag-out	JJ	_	_	_
10	genes	gene	NNS	_	_	_
11	in	in	IN	_	_	_
12	each	each	DT	_	_	_
13	experiment	experiment	NN	_	_	_
14	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	gene	gene	NN	_	_	_
3	expression	expression	NN	_	_	_
4	was	be	VBD	_	_	_
5	normalized	normalize	VBN	_	_	_
6	through	through	IN	_	_	_
7	LOWESS	lowess	NN	_	_	_
8	regression	regression	NN	_	_	_
9	for	for	IN	_	_	_
10	3	3	CD	_	_	_
11	datasets	dataset	NNS	_	_	_
12	obtained	obtain	VBN	_	_	_
13	from	from	IN	_	_	_
14	3	3	CD	_	_	_
15	biological	biological	JJ	_	_	_
16	replicates	replicate	VBZ	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Total	total	JJ	_	_	_
3	RNA	rna	NN	_	_	_
4	extracted	extract	VBN	_	_	_
5	using	use	VBG	_	_	_
6	RiboEX	RiboEX	NNP	_	_	_
7	reagent	reagent	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	GeneAll	GeneAll	NNP	_	_	_
10	,	,	,	_	_	_
11	Korea	Korea	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	,	,	,	_	_	_
14	treated	treat	VBN	_	_	_
15	with	with	IN	_	_	_
16	Dnase	Dnase	NNP	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	purified	purify	VBN	_	_	_
20	using	use	VBG	_	_	_
21	the	the	DT	_	_	_
22	Rneasy	Rneasy	NNP	_	_	_
23	Mini	Mini	NNP	_	_	_
24	kit	kit	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	Qiagen	Qiagen	NNP	_	_	_
27	,	,	,	_	_	_
28	Germany	Germany	NNP	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	according	accord	VBG	_	_	_
31	to	to	TO	_	_	_
32	the	the	DT	_	_	_
33	manufacturer	manufacturer	NN	_	_	_
34	's	's	POS	_	_	_
35	instructions	instruction	NNS	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	0	0	CD	_	_	_
3	'	'	''	_	_	_
4	in	in	IN	_	_	_
5	minimal	minimal	JJ	_	_	_
6	medium	medium	NN	_	_	_
7	+0.2	+0.2	CD	_	_	_
8	%	%	NN	_	_	_
9	glu	glu	NN	_	_	_
10	,	,	,	_	_	_
11	25	25	CD	_	_	_
12	ug	ug	NN	_	_	_
13	total	total	JJ	_	_	_
14	RNA	rna	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	0	0	CD	_	_	_
17	'	'	''	_	_	_
18	in	in	IN	_	_	_
19	min	min	NN	_	_	_
20	med	med	VBD	_	_	_
21	+0.2	+0.2	CD	_	_	_
22	%	%	NN	_	_	_
23	glu	glu	NN	_	_	_
24	,	,	,	_	_	_
25	25ug	25ug	JJ	_	_	_
26	total	total	JJ	_	_	_
27	RNA	rna	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	0	0	CD	_	_	_
30	'	'	''	_	_	_
31	minimal	minimal	JJ	_	_	_
32	+	+	CC	_	_	_
33	0.2	0.2	CD	_	_	_
34	%	%	NN	_	_	_
35	glu	glu	NN	_	_	_
36	,	,	,	_	_	_
37	25	25	CD	_	_	_
38	ug	ug	NN	_	_	_
39	total	total	JJ	_	_	_
40	RNA	rna	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	0	0	CD	_	_	_
43	'	'	''	_	_	_
44	minimal	minimal	JJ	_	_	_
45	+02	+02	CD	_	_	_
46	%	%	NN	_	_	_
47	glu	glu	NN	_	_	_
48	,	,	,	_	_	_
49	25	25	CD	_	_	_
50	ug	ug	NN	_	_	_
51	total	total	JJ	_	_	_
52	RNA	rna	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	0	0	CD	_	_	_
55	'	'	''	_	_	_
56	minimal	minimal	JJ	_	_	_
57	medium	medium	NN	_	_	_
58	+	+	CC	_	_	_
59	0.2	0.2	CD	_	_	_
60	%	%	NN	_	_	_
61	glu	glu	NN	_	_	_
62	,	,	,	_	_	_
63	25	25	CD	_	_	_
64	ug	ug	NN	_	_	_
65	total	total	JJ	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
67	Adaptor	adaptor	NN	_	_	_
68	Sequences	sequence	NNS	_	_	_
69	were	be	VBD	_	_	_
70	removed	remove	VBN	_	_	_
71	using	use	VBG	_	_	_
72	fastx	fastx	NN	_	_	_
73	_	_	NN	_	_	_
74	clipper	clipper	NN	_	_	_
75	.	.	.	_	_	_

1	-LRB-	-lrb-	-LRB-	_	_	_
2	http	http	NN	_	_	_
3	:	:	:	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
5	All	all	DT	_	_	_
6	samples	sample	NNS	_	_	_
7	were	be	VBD	_	_	_
8	processed	process	VBN	_	_	_
9	following	follow	VBG	_	_	_
10	NEB	NEB	NNP	_	_	_
11	's	's	POS	_	_	_
12	protocol	protocol	NN	_	_	_
13	from	from	IN	_	_	_
14	the	the	DT	_	_	_
15	NEBNext	nebnext	NN	_	_	_
16	®	®	NN	_	_	_
17	ChIP-Seq	chip-seq	JJ	_	_	_
18	library	library	NN	_	_	_
19	preparation	preparation	NN	_	_	_
20	kit	kit	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	bacterial	bacterial	JJ	_	_	_
3	cell	cell	NN	_	_	_
4	lysates	lysate	NNS	_	_	_
5	_	_	VBP	_	_	_
6	input	input	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	bacterial	bacterial	JJ	_	_	_
9	cell	cell	NN	_	_	_
10	lysates	lysate	NNS	_	_	_
11	_	_	VBP	_	_	_
12	RecA-ChIP-seq	reca-chip-seq	JJ	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Cells	cell	NNS	_	_	_
15	were	be	VBD	_	_	_
16	collected	collect	VBN	_	_	_
17	by	by	IN	_	_	_
18	centrifugation	centrifugation	NN	_	_	_
19	and	and	CC	_	_	_
20	washed	wash	VBN	_	_	_
21	three	three	CD	_	_	_
22	times	time	NNS	_	_	_
23	in	in	IN	_	_	_
24	ice-cold	ice-cold	JJ	_	_	_
25	1X	1x	NN	_	_	_
26	PBS	PBS	NNP	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	re-suspended	re-suspended	JJ	_	_	_
6	in	in	IN	_	_	_
7	250	250	CD	_	_	_
8	μl	μl	NN	_	_	_
9	ChIP	chip	NN	_	_	_
10	buffer	buffer	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	200	200	CD	_	_	_
13	mM	mm	NN	KWSUPP	_	_
14	Tris-HCl	tris-hcl	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	pH	ph	NN	_	_	_
17	8.0	8.0	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	600	600	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	NaCl	nacl	NN	_	_	_
23	4	4	CD	_	_	_
24	%	%	NN	_	_	_
25	Triton	Triton	NNP	_	_	_
26	X	X	NNP	_	_	_
27	,	,	,	_	_	_
28	Complete	complete	JJ	_	_	_
29	protease	protease	NN	_	_	_
30	inhibitor	inhibitor	NN	_	_	_
31	cocktail	cocktail	NN	_	_	_
32	EDTA-free	edta-free	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	Roche	Roche	NNP	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	.	.	.	_	_	_

1	Sonication	sonication	NN	_	_	_
2	of	of	IN	_	_	_
3	crosslinked	crosslink	VBN	_	_	_
4	samples	sample	NNS	_	_	_
5	was	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	using	use	VBG	_	_	_
8	the	the	DT	_	_	_
9	Diagenode	Diagenode	NNP	_	_	_
10	Bioruptor	Bioruptor	NNP	_	_	_
11	®	®	NN	_	_	_
12	at	at	IN	_	_	_
13	30s	30s	CD	_	_	_
14	intervals	interval	NNS	_	_	_
15	for	for	IN	_	_	_
16	10	10	CD	_	_	_
17	min	min	NN	_	_	_
18	at	at	IN	_	_	_
19	high	high	JJ	_	_	_
20	amplitude	amplitude	NN	_	_	_
21	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	sonication	sonication	NN	_	_	_
3	,	,	,	_	_	_
4	350	350	CD	_	_	_
5	μl	μl	NN	_	_	_
6	of	of	IN	_	_	_
7	ChIP	chip	NN	_	_	_
8	buffer	buffer	NN	_	_	_
9	was	be	VBD	_	_	_
10	added	add	VBN	_	_	_
11	to	to	TO	_	_	_
12	each	each	DT	_	_	_
13	sample	sample	NN	_	_	_
14	,	,	,	_	_	_
15	the	the	DT	_	_	_
16	samples	sample	NNS	_	_	_
17	were	be	VBD	_	_	_
18	mixed	mix	VBN	_	_	_
19	by	by	IN	_	_	_
20	gentle	gentle	JJ	_	_	_
21	pipetting	pipetting	NN	_	_	_
22	and	and	CC	_	_	_
23	100	100	CD	_	_	_
24	μl	μl	NN	_	_	_
25	of	of	IN	_	_	_
26	each	each	DT	_	_	_
27	lysate	lysate	NN	_	_	_
28	was	be	VBD	_	_	_
29	removed	remove	VBN	_	_	_
30	and	and	CC	_	_	_
31	stored	store	VBN	_	_	_
32	as	as	IN	_	_	_
33	`	`	``	_	_	_
34	input	input	NN	_	_	_
35	'	'	''	_	_	_
36	.	.	.	_	_	_

1	Immunoprecipitation	immunoprecipitation	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	overnight	overnight	RB	_	_	_
5	at	at	IN	_	_	_
6	4	4	CD	_	_	_
7	°C	°c	NN	_	_	_
8	using	use	VBG	_	_	_
9	1	1	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Cells	cell	NNS	_	_	_
12	were	be	VBD	_	_	_
13	grown	grow	VBN	_	_	_
14	in	in	IN	_	_	_
15	M9	m9	NN	MED	_	_
16	minimal	minimal	JJ	MED	_	_
17	media	media	NNS	MED	_	_
18	supplemented	supplement	VBN	_	_	_
19	with	with	IN	_	_	_
20	0.2	0.2	CD	_	_	_
21	%	%	NN	_	_	_
22	casamino	casamino	NN	SUPP	_	_
23	acids	acid	NNS	SUPP	_	_
24	,	,	,	_	_	_
25	0.5	0.5	CD	_	_	_
26	%	%	NN	_	_	_
27	glucose	glucose	NN	SUPP	_	_
28	5μM	5μm	NN	_	_	_
29	CaCl2	cacl2	NN	_	_	_
30	and	and	CC	_	_	_
31	1mM	1mm	NN	_	_	_
32	MgSO4	mgso4	NN	_	_	_
33	at	at	IN	_	_	_
34	37	37	CD	_	_	_
35	°C	°c	NN	_	_	_
36	to	to	TO	_	_	_
37	and	and	CC	_	_	_
38	OD600nm	od600nm	NN	_	_	_
39	of	of	IN	_	_	_
40	0.2-0.25	0.2-0.25	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
42	chip	chip	NN	_	_	_
43	antibody	antibody	NN	_	_	_
44	:	:	:	_	_	_
45	anti-RecA	anti-reca	JJ	_	_	_
46	antibody	antibody	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
48	chip	chip	NN	_	_	_
49	antibody	antibody	NN	_	_	_
50	cat	cat	NN	_	_	_
51	.	.	.	_	_	_

1	#	#	#	_	_	_
2	:	:	:	_	_	_
3	ab63797	ab63797	CD	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
5	chip	chip	NN	_	_	_
6	antibody	antibody	NN	_	_	_
7	vendor	vendor	NN	_	_	_
8	:	:	:	_	_	_
9	Abcam	Abcam	NNP	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	ChIP-Seq	ChIP-Seq	NNP	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	Data	Data	NNP	_	_	_
14	collapsed	collapse	VBD	_	_	_
15	using	use	VBG	_	_	_
16	fastx	fastx	NN	_	_	_
17	collapser	collapser	NN	_	_	_
18	to	to	TO	_	_	_
19	remove	remove	VB	_	_	_
20	identical	identical	JJ	_	_	_
21	sequencing	sequencing	NN	_	_	_
22	reads	read	VBZ	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	http	http	NN	_	_	_
25	:	:	:	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	DL4899	dl4899	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	DL4900	dl4900	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	DL4900	dl4900	NN	_	_	_
32	_	_	NN	_	_	_
33	input	input	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	DL5215	dl5215	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	DL5322	dl5322	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	DL5324	dl5324	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	DL5326	dl5326	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	DL5328	dl5328	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	DL5330	dl5330	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	Escherichia	escherichia	FW	Organism	_	_
48	coli	coli	FW	Organism	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	Genome	Genome	NNP	_	_	_
51	_	_	NNP	_	_	_
52	build	build	VB	_	_	_
53	:	:	:	_	_	_
54	Escherichia	escherichia	FW	Organism	_	_
55	coli	coli	FW	Organism	_	_
56	K12	k12	NN	_	_	_
57	MG1655	mg1655	NN	_	_	_
58	NC000913	nc000913	NN	_	_	_
59	.3	.3	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	Protein	protein	NN	_	_	_
62	DNA	dna	NN	_	_	_
63	interactions	interaction	NNS	_	_	_
64	were	be	VBD	_	_	_
65	crosslinked	crosslink	VBN	_	_	_
66	for	for	IN	_	_	_
67	10	10	CD	_	_	_
68	min	min	NN	_	_	_
69	at	at	IN	_	_	_
70	22.5	22.5	CD	_	_	_
71	C	c	NN	_	_	_
72	with	with	IN	_	_	_
73	1	1	CD	_	_	_
74	%	%	NN	_	_	_
75	formaldehyde	formaldehyde	NN	_	_	_
76	and	and	CC	_	_	_
77	quenched	quench	VBN	_	_	_
78	using	use	VBG	_	_	_
79	glycine	glycine	NN	_	_	_
80	to	to	TO	_	_	_
81	a	a	DT	_	_	_
82	final	final	JJ	_	_	_
83	concentration	concentration	NN	_	_	_
84	of	of	IN	_	_	_
85	0.5	0.5	CD	_	_	_
86	M	m	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	reads	read	VBZ	_	_	_
89	were	be	VBD	_	_	_
90	mapped	map	VBN	_	_	_
91	to	to	TO	_	_	_
92	the	the	DT	_	_	_
93	E.	e.	FW	_	_	_
94	coli	coli	FW	_	_	_
95	K12	k12	NN	_	_	_
96	MG1655	mg1655	NN	_	_	_
97	-LRB-	-lrb-	-LRB-	_	_	_
98	NC000913	nc000913	NN	_	_	_
99	.3	.3	NN	_	_	_
100	-RRB-	-rrb-	-RRB-	_	_	_
101	genome	genome	NN	_	_	_
102	using	use	VBG	_	_	_
103	Novoalign	novoalign	JJ	_	_	_
104	version	version	NN	_	_	_
105	2.07	2.07	CD	_	_	_
106	-LRB-	-lrb-	-LRB-	_	_	_
107	www.novocraft.com	www.novocraft.com	NN	_	_	_
108	-RRB-	-rrb-	-RRB-	_	_	_
109	-	-	:	_	_	_
110	Example	example	NN	_	_	_
111	:	:	:	_	_	_
112	-LRB-	-lrb-	-LRB-	_	_	_
113	novoalign	novoalign	JJ	_	_	_
114	-	-	:	_	_	_
115	f	f	FW	_	_	_
116	DL4900	dl4900	FW	_	_	_
117	_	_	SYM	_	_	_
118	clip	clip	VB	_	_	_
119	_	_	SYM	_	_	_
120	clp.fasta	clp.fasta	SYM	_	_	_
121	-	-	:	_	_	_
122	d	d	NN	_	_	_
123	NC000913	nc000913	NN	_	_	_
124	.3	.3	NN	_	_	_
125	.	.	.	_	_	_

1	nix	nix	SYM	_	_	_
2	-	-	:	_	_	_
3	r	r	NN	_	_	_
4	Random	Random	NNP	_	_	_
5	>	>	JJR	_	_	_
6	DL4900.novo	dl4900.novo	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	strain	strain	NN	_	_	_
10	details	detail	NNS	_	_	_
11	:	:	:	_	_	_
12	lacIq	laciq	NN	_	_	_
13	lacZχ	laczχ	NN	_	_	_
14	-	-	:	_	_	_
15	cynX	cynx	NN	GEN	_	_
16	:	:	:	_	_	_
17	:	:	:	_	_	_
18	GmR	gmr	NN	_	_	_
19	lacZY	laczy	NN	_	_	_
20	:	:	:	_	_	_
21	:	:	:	_	_	_
22	χχχ	χχχ	NN	_	_	_
23	mhpA	mhpa	NN	GEN	_	_
24	:	:	:	_	_	_
25	:	:	:	_	_	_
26	χχχ	χχχ	NN	_	_	_
27	rph	rph	NN	GEN	_	_
28	+	+	CC	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	strain	strain	NN	_	_	_
31	details	detail	NNS	_	_	_
32	:	:	:	_	_	_
33	lacIq	laciq	NN	_	_	_
34	lacZχ	laczχ	NN	_	_	_
35	-	-	:	_	_	_
36	lacZ	lacz	NN	GEN	_	_
37	:	:	:	_	_	_
38	:	:	:	_	_	_
39	246pal	246pal	JJ	_	_	_
40	cynX	cynx	NN	GEN	_	_
41	:	:	:	_	_	_
42	:	:	:	_	_	_
43	GmR	gmr	NN	_	_	_
44	lacZY	laczy	NN	_	_	_
45	:	:	:	_	_	_
46	:	:	:	_	_	_
47	χ	χ	NN	_	_	_
48	mhpA	mhpa	NN	GEN	_	_
49	:	:	:	_	_	_
50	:	:	:	_	_	_
51	χχχ	χχχ	NN	_	_	_
52	codBχ	codbχ	NN	_	_	_
53	-	-	:	_	_	_
54	prpEχ	prpeχ	NN	_	_	_
55	-	-	:	_	_	_
56	mhpCχ	mhpcχ	NN	_	_	_
57	-	-	:	_	_	_
58	cynXχ	cynxχ	NN	_	_	_
59	-	-	:	_	_	_
60	rph	rph	NN	GEN	_	_
61	+	+	CC	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	strain	strain	NN	_	_	_
64	details	detail	NNS	_	_	_
65	:	:	:	_	_	_
66	lacIq	laciq	NN	_	_	_
67	lacZχ	laczχ	NN	_	_	_
68	-	-	:	_	_	_
69	lacZ	lacz	NN	GEN	_	_
70	:	:	:	_	_	_
71	:	:	:	_	_	_
72	246pal	246pal	JJ	_	_	_
73	cynX	cynx	NN	GEN	_	_
74	:	:	:	_	_	_
75	:	:	:	_	_	_
76	GmR	gmr	NN	_	_	_
77	lacZY	laczy	NN	_	_	_
78	:	:	:	_	_	_
79	:	:	:	_	_	_
80	χχ	χχ	NN	_	_	_
81	mhpA	mhpa	NN	GEN	_	_
82	:	:	:	_	_	_
83	:	:	:	_	_	_
84	χχχ	χχχ	NN	_	_	_
85	codBχ	codbχ	NN	_	_	_
86	-	-	:	_	_	_
87	prpEχ	prpeχ	NN	_	_	_
88	-	-	:	_	_	_
89	mhpCχ	mhpcχ	NN	_	_	_
90	-	-	:	_	_	_
91	cynXχ	cynxχ	NN	_	_	_
92	-	-	:	_	_	_
93	rph	rph	NN	GEN	_	_
94	+	+	CC	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	strain	strain	NN	_	_	_
97	details	detail	NNS	_	_	_
98	:	:	:	_	_	_
99	lacIq	laciq	NN	_	_	_
100	lacZχ	laczχ	NN	_	_	_
101	-	-	:	_	_	_
102	lacZ	lacz	NN	GEN	_	_
103	:	:	:	_	_	_
104	:	:	:	_	_	_
105	246pal	246pal	JJ	_	_	_
106	cynX	cynx	NN	GEN	_	_
107	:	:	:	_	_	_
108	:	:	:	_	_	_
109	GmR	gmr	NN	_	_	_
110	lacZY	laczy	NN	_	_	_
111	:	:	:	_	_	_
112	:	:	:	_	_	_
113	χχχ	χχχ	NN	_	_	_
114	mhpA	mhpa	NN	GEN	_	_
115	:	:	:	_	_	_
116	:	:	:	_	_	_
117	χχχ	χχχ	NN	_	_	_
118	codBχ	codbχ	NN	_	_	_
119	-	-	:	_	_	_
120	prpEχ	prpeχ	NN	_	_	_
121	-	-	:	_	_	_
122	mhpCχ	mhpcχ	NN	_	_	_
123	-	-	:	_	_	_
124	cynXχ	cynxχ	NN	_	_	_
125	-	-	:	_	_	_
126	rph	rph	NN	GEN	_	_
127	+	+	CC	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	strain	strain	NN	_	_	_
130	details	detail	NNS	_	_	_
131	:	:	:	_	_	_
132	lacIq	laciq	NN	_	_	_
133	lacZχ	laczχ	NN	_	_	_
134	-	-	:	_	_	_
135	lacZ	lacz	NN	GEN	_	_
136	:	:	:	_	_	_
137	:	:	:	_	_	_
138	246pal	246pal	JJ	_	_	_
139	cynX	cynx	NN	GEN	_	_
140	:	:	:	_	_	_
141	:	:	:	_	_	_
142	GmR	gmr	NN	_	_	_
143	lacZY	laczy	NN	_	_	_
144	:	:	:	_	_	_
145	:	:	:	_	_	_
146	χχχ	χχχ	NN	_	_	_
147	mhpA	mhpa	NN	GEN	_	_
148	:	:	:	_	_	_
149	:	:	:	_	_	_
150	χχχ	χχχ	NN	_	_	_
151	rph	rph	NN	GEN	_	_
152	+	+	CC	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	strain	strain	NN	_	_	_
155	details	detail	NNS	_	_	_
156	:	:	:	_	_	_
157	lacIq	laciq	NN	_	_	_
158	lacZχ	laczχ	NN	_	_	_
159	-	-	:	_	_	_
160	lacZ	lacz	NN	GEN	_	_
161	:	:	:	_	_	_
162	:	:	:	_	_	_
163	246pal	246pal	JJ	_	_	_
164	cynX	cynx	NN	GEN	_	_
165	:	:	:	_	_	_
166	:	:	:	_	_	_
167	GmR	gmr	NN	_	_	_
168	lacZY	laczy	NN	_	_	_
169	:	:	:	_	_	_
170	:	:	:	_	_	_
171	χχχχ	χχχχ	NN	_	_	_
172	mhpA	mhpa	NN	GEN	_	_
173	:	:	:	_	_	_
174	:	:	:	_	_	_
175	χχχ	χχχ	NN	_	_	_
176	codBχ	codbχ	NN	_	_	_
177	-	-	:	_	_	_
178	prpEχ	prpeχ	NN	_	_	_
179	-	-	:	_	_	_
180	mhpCχ	mhpcχ	NN	_	_	_
181	-	-	:	_	_	_
182	cynXχ	cynxχ	NN	_	_	_
183	-	-	:	_	_	_
184	rph	rph	NN	GEN	_	_
185	+	+	CC	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	strain	strain	NN	_	_	_
188	details	detail	NNS	_	_	_
189	:	:	:	_	_	_
190	lacIq	laciq	NN	_	_	_
191	lacZχ	laczχ	NN	_	_	_
192	-	-	:	_	_	_
193	lacZ	lacz	NN	GEN	_	_
194	:	:	:	_	_	_
195	:	:	:	_	_	_
196	246pal	246pal	JJ	_	_	_
197	cynX	cynx	NN	GEN	_	_
198	:	:	:	_	_	_
199	:	:	:	_	_	_
200	GmR	gmr	NN	_	_	_
201	lacZY	laczy	NN	_	_	_
202	:	:	:	_	_	_
203	:	:	:	_	_	_
204	χχχχχ	χχχχχ	NN	_	_	_
205	mhpA	mhpa	NN	GEN	_	_
206	:	:	:	_	_	_
207	:	:	:	_	_	_
208	χχχ	χχχ	NN	_	_	_
209	codBχ	codbχ	NN	_	_	_
210	-	-	:	_	_	_
211	prpEχ	prpeχ	NN	_	_	_
212	-	-	:	_	_	_
213	mhpCχ	mhpcχ	NN	_	_	_
214	-	-	:	_	_	_
215	cynXχ	cynxχ	NN	_	_	_
216	-	-	:	_	_	_
217	rph	rph	NN	GEN	_	_
218	+	+	CC	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	strain	strain	NN	_	_	_
221	details	detail	NNS	_	_	_
222	:	:	:	_	_	_
223	lacIq	laciq	NN	_	_	_
224	lacZχ	laczχ	NN	_	_	_
225	-	-	:	_	_	_
226	lacZ	lacz	NN	GEN	_	_
227	:	:	:	_	_	_
228	:	:	:	_	_	_
229	246pal	246pal	JJ	_	_	_
230	cynX	cynx	NN	GEN	_	_
231	:	:	:	_	_	_
232	:	:	:	_	_	_
233	GmR	gmr	NN	_	_	_
234	lacZY	laczy	NN	_	_	_
235	:	:	:	_	_	_
236	:	:	:	_	_	_
237	χχχχχχ	χχχχχχ	NN	_	_	_
238	mhpA	mhpa	NN	GEN	_	_
239	:	:	:	_	_	_
240	:	:	:	_	_	_
241	χχχ	χχχ	NN	_	_	_
242	codBχ	codbχ	NN	_	_	_
243	-	-	:	_	_	_
244	prpEχ	prpeχ	NN	_	_	_
245	-	-	:	_	_	_
246	mhpCχ	mhpcχ	NN	_	_	_
247	-	-	:	_	_	_
248	cynXχ	cynxχ	NN	_	_	_
249	-	-	:	_	_	_
250	rph	rph	NN	GEN	_	_
251	+	+	CC	_	_	_
252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
253	strain	strain	NN	_	_	_
254	:	:	:	_	_	_
255	K-12	k-12	NN	_	_	_
256	MG1655	mg1655	NN	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	Supplementary	supplementary	JJ	_	_	_
259	_	_	NN	_	_	_
260	files	file	NNS	_	_	_
261	_	_	IN	_	_	_
262	format	format	NN	_	_	_
263	_	_	NN	_	_	_
264	and	and	CC	_	_	_
265	_	_	NN	_	_	_
266	content	content	NN	_	_	_
267	:	:	:	_	_	_
268	txt	txt	NN	_	_	_
269	files	file	NNS	_	_	_
270	including	include	VBG	_	_	_
271	count	count	NN	_	_	_
272	data	datum	NNS	_	_	_
273	for	for	IN	_	_	_
274	the	the	DT	_	_	_
275	whole	whole	JJ	_	_	_
276	genome	genome	NN	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	yPileup	ypileup	NN	_	_	_
279	was	be	VBD	_	_	_
280	used	use	VBN	_	_	_
281	to	to	TO	_	_	_
282	generate	generate	VB	_	_	_
283	count	count	NN	_	_	_
284	data	datum	NNS	_	_	_
285	for	for	IN	_	_	_
286	the	the	DT	_	_	_
287	whole	whole	JJ	_	_	_
288	genome	genome	NN	_	_	_
289	-	-	:	_	_	_
290	Example	example	NN	_	_	_
291	:	:	:	_	_	_
292	pyPileup.py	pypileup.py	NN	_	_	_
293	--	--	:	_	_	_
294	file	file	NN	_	_	_
295	_	_	NN	_	_	_
296	type	type	NN	_	_	_
297	=	=	JJ	_	_	_
298	novo	novo	FW	_	_	_
299	-	-	:	_	_	_
300	f	f	LS	_	_	_
301	DL4900.novo	dl4900.novo	NN	_	_	_
302	--	--	:	_	_	_
303	tab	tab	NN	_	_	_
304	=	=	JJ	_	_	_
305	NC000913	nc000913	NN	_	_	_
306	.3	.3	NN	_	_	_
307	.	.	.	_	_	_

1	tab	tab	NN	_	_	_
2	--	--	:	_	_	_
3	chr	chr	NN	_	_	_
4	=	=	JJ	_	_	_
5	Wholechom.txt.gz	wholechom.txt.gz	NN	_	_	_
6	--	--	:	_	_	_
7	ignorestrand	ignorestrand	JJ	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	15	15	CD	_	_	_
10	'	'	''	_	_	_
11	10	10	CD	_	_	_
12	ug	ug	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	15	15	CD	_	_	_
15	'	'	''	_	_	_
16	15	15	CD	_	_	_
17	ug	ug	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	15	15	CD	_	_	_
20	'	'	''	_	_	_
21	+50	+50	CD	_	_	_
22	ug	ug	NN	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	Aeration	Aeration	NNP	_	_	_
25	was	be	VBD	_	_	_
26	initiated	initiate	VBN	_	_	_
27	at	at	IN	_	_	_
28	1	1	CD	_	_	_
29	l	l	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	alignment	alignment	NN	_	_	_
32	:	:	:	_	_	_
33	STAR	star	NN	_	_	_
34	2.4.0	2.4.0	CD	_	_	_
35	i	i	FW	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
37	batch	batch	NN	_	_	_
38	culture	culture	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	batch	batch	NN	_	_	_
41	culture	culture	NN	_	_	_
42	rep1	rep1	NN	_	_	_
43	,	,	,	_	_	_
44	0.5	0.5	CD	_	_	_
45	min	min	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	batch	batch	NN	_	_	_
48	culture	culture	NN	_	_	_
49	rep1	rep1	NN	_	_	_
50	,	,	,	_	_	_
51	0	0	CD	_	_	_
52	min	min	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	batch	batch	NN	_	_	_
55	culture	culture	NN	_	_	_
56	rep1	rep1	NN	_	_	_
57	,	,	,	_	_	_
58	10	10	CD	_	_	_
59	min	min	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	batch	batch	NN	_	_	_
62	culture	culture	NN	_	_	_
63	rep1	rep1	NN	_	_	_
64	,	,	,	_	_	_
65	1	1	CD	_	_	_
66	min	min	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	batch	batch	NN	_	_	_
69	culture	culture	NN	_	_	_
70	rep1	rep1	NN	_	_	_
71	,	,	,	_	_	_
72	2	2	CD	_	_	_
73	min	min	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	batch	batch	NN	_	_	_
76	culture	culture	NN	_	_	_
77	rep1	rep1	NN	_	_	_
78	,	,	,	_	_	_
79	5	5	CD	_	_	_
80	min	min	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	batch	batch	NN	_	_	_
83	culture	culture	NN	_	_	_
84	rep2	rep2	NN	_	_	_
85	,	,	,	_	_	_
86	0.5	0.5	CD	_	_	_
87	min	min	NN	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	batch	batch	NN	_	_	_
90	culture	culture	NN	_	_	_
91	rep2	rep2	NN	_	_	_
92	,	,	,	_	_	_
93	0	0	CD	_	_	_
94	min	min	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	batch	batch	NN	_	_	_
97	culture	culture	NN	_	_	_
98	rep2	rep2	NN	_	_	_
99	,	,	,	_	_	_
100	10	10	CD	_	_	_
101	min	min	NN	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	batch	batch	NN	_	_	_
104	culture	culture	NN	_	_	_
105	rep2	rep2	NN	_	_	_
106	,	,	,	_	_	_
107	1	1	CD	_	_	_
108	min	min	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	batch	batch	NN	_	_	_
111	culture	culture	NN	_	_	_
112	rep2	rep2	NN	_	_	_
113	,	,	,	_	_	_
114	2	2	CD	_	_	_
115	min	min	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	batch	batch	NN	_	_	_
118	culture	culture	NN	_	_	_
119	rep2	rep2	NN	_	_	_
120	,	,	,	_	_	_
121	5	5	CD	_	_	_
122	min	min	NN	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	batch	batch	NN	_	_	_
125	culture	culture	NN	_	_	_
126	rep3	rep3	NN	_	_	_
127	,	,	,	_	_	_
128	0.5	0.5	CD	_	_	_
129	min	min	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	batch	batch	NN	_	_	_
132	culture	culture	NN	_	_	_
133	rep3	rep3	NN	_	_	_
134	,	,	,	_	_	_
135	0	0	CD	_	_	_
136	min	min	NN	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	batch	batch	NN	_	_	_
139	culture	culture	NN	_	_	_
140	rep3	rep3	NN	_	_	_
141	,	,	,	_	_	_
142	10	10	CD	_	_	_
143	min	min	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	batch	batch	NN	_	_	_
146	culture	culture	NN	_	_	_
147	rep3	rep3	NN	_	_	_
148	,	,	,	_	_	_
149	1	1	CD	_	_	_
150	min	min	NN	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	batch	batch	NN	_	_	_
153	culture	culture	NN	_	_	_
154	rep3	rep3	NN	_	_	_
155	,	,	,	_	_	_
156	2	2	CD	_	_	_
157	min	min	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	batch	batch	NN	_	_	_
160	culture	culture	NN	_	_	_
161	rep3	rep3	NN	_	_	_
162	,	,	,	_	_	_
163	5	5	CD	_	_	_
164	min	min	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	Cell	cell	NN	_	_	_
167	were	be	VBD	_	_	_
168	grown	grow	VBN	_	_	_
169	in	in	IN	_	_	_
170	3-liter	3-liter	NN	_	_	_
171	stirred	stir	VBD	_	_	_
172	tank	tank	NN	_	_	_
173	bioreactor	bioreactor	NN	_	_	_
174	anaerobically	anaerobically	RB	_	_	_
175	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	growth	growth	NN	_	_	_
3	medium	medium	NN	_	_	_
4	contained	contain	VBD	_	_	_
5	Na2H2PO4	na2h2po4	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	1.1	1.1	CD	_	_	_
8	g	g	NN	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	Escherichia	escherichia	FW	Organism	_	_
11	coli	coli	FW	Organism	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	gene	gene	NN	_	_	_
14	counting	counting	NN	_	_	_
15	:	:	:	_	_	_
16	HTSeq-Count	htseq-count	JJ	_	_	_
17	0.6.0	0.6.0	CD	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Genome	Genome	NNP	_	_	_
20	_	_	NNP	_	_	_
21	build	build	VB	_	_	_
22	:	:	:	_	_	_
23	NC007779	nc007779	NN	_	_	_
24	.1	.1	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	UCSC	ucsc	NN	_	_	_
27	Archaeal	archaeal	NN	_	_	_
28	Genome	Genome	NNP	_	_	_
29	Browser	Browser	NNP	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
32	replicate	replicate	VBP	_	_	_
33	:	:	:	_	_	_
34	1	1	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	replicate	replicate	VB	_	_	_
37	:	:	:	_	_	_
38	2	2	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
40	replicate	replicate	VBP	_	_	_
41	:	:	:	_	_	_
42	3	3	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	RNA	rna	NN	_	_	_
45	libraries	library	NNS	_	_	_
46	were	be	VBD	_	_	_
47	prepared	prepare	VBN	_	_	_
48	for	for	IN	_	_	_
49	sequencing	sequencing	NN	_	_	_
50	using	use	VBG	_	_	_
51	standard	standard	JJ	_	_	_
52	Illumina	Illumina	NNP	_	_	_
53	protocols	protocol	NNS	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
55	RNA-Seq	rna-seq	JJ	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	Samples	sample	NNS	_	_	_
58	were	be	VBD	_	_	_
59	treated	treat	VBN	_	_	_
60	with	with	IN	_	_	_
61	RNAprotect	rnaprotect	NN	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	Qiagen	Qiagen	NNP	_	_	_
64	,	,	,	_	_	_
65	Hilden	Hilden	NNP	_	_	_
66	,	,	,	_	_	_
67	Germany	Germany	NNP	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	and	and	CC	_	_	_
70	stored	store	VBN	_	_	_
71	at	at	IN	_	_	_
72	-80	-80	CD	_	_	_
73	°C	°c	NN	_	_	_
74	until	until	IN	_	_	_
75	preparation	preparation	NN	_	_	_
76	.	.	.	_	_	_

1	rRNA	rrna	NN	_	_	_
2	was	be	VBD	_	_	_
3	removed	remove	VBN	_	_	_
4	using	use	VBG	_	_	_
5	RiboZero	RiboZero	NNP	_	_	_
6	rRNA	rrna	NN	_	_	_
7	Removal	removal	NN	_	_	_
8	Kit	kit	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Illumina	Illumina	NNP	_	_	_
11	,	,	,	_	_	_
12	San	San	NNP	_	_	_
13	Diego	Diego	NNP	_	_	_
14	,	,	,	_	_	_
15	CA	CA	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	sequencing	sequencing	NN	_	_	_
20	libraries	library	NNS	_	_	_
21	were	be	VBD	_	_	_
22	prepared	prepare	VBN	_	_	_
23	with	with	IN	_	_	_
24	TruSeq	truseq	NN	_	_	_
25	™	™	CD	_	_	_
26	RNA	rna	NN	_	_	_
27	Sample	sample	NN	_	_	_
28	Preparation	preparation	NN	_	_	_
29	Kitv2	kitv2	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Illumina	Illumina	NNP	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	strain	strain	NN	_	_	_
35	:	:	:	_	_	_
36	K12	k12	NN	_	_	_
37	W3110	w3110	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	Supplementary	supplementary	JJ	_	_	_
40	_	_	NN	_	_	_
41	files	file	NNS	_	_	_
42	_	_	IN	_	_	_
43	format	format	NN	_	_	_
44	_	_	NN	_	_	_
45	and	and	CC	_	_	_
46	_	_	NN	_	_	_
47	content	content	NN	_	_	_
48	:	:	:	_	_	_
49	The	the	DT	_	_	_
50	file	file	NN	_	_	_
51	format	format	NN	_	_	_
52	is	be	VBZ	_	_	_
53	.	.	.	_	_	_

1	xlsx	xlsx	NN	_	_	_
2	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	file	file	NN	_	_	_
3	contains	contain	VBZ	_	_	_
4	the	the	DT	_	_	_
5	raw	raw	JJ	_	_	_
6	gene	gene	NN	_	_	_
7	counts	count	NNS	_	_	_
8	of	of	IN	_	_	_
9	all	all	DT	_	_	_
10	samples	sample	NNS	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	time	time	NN	_	_	_
3	:	:	:	_	_	_
4	0.5	0.5	CD	_	_	_
5	min	min	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	time	time	NN	_	_	_
8	:	:	:	_	_	_
9	0	0	CD	_	_	_
10	min	min	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	time	time	NN	_	_	_
13	:	:	:	_	_	_
14	10	10	CD	_	_	_
15	min	min	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	time	time	NN	_	_	_
18	:	:	:	_	_	_
19	1	1	CD	_	_	_
20	min	min	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	time	time	NN	_	_	_
23	:	:	:	_	_	_
24	2	2	CD	_	_	_
25	min	min	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	time	time	NN	_	_	_
28	:	:	:	_	_	_
29	5	5	CD	_	_	_
30	min	min	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	15	15	CD	_	_	_
33	'	'	''	_	_	_
34	in	in	IN	_	_	_
35	minimal	minimal	JJ	_	_	_
36	medium	medium	NN	_	_	_
37	+0.2	+0.2	CD	_	_	_
38	%	%	NN	_	_	_
39	glu	glu	NN	_	_	_
40	,	,	,	_	_	_
41	25	25	CD	_	_	_
42	ug	ug	NN	_	_	_
43	total	total	JJ	_	_	_
44	RNA	rna	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	15	15	CD	_	_	_
47	'	'	''	_	_	_
48	in	in	IN	_	_	_
49	min	min	NN	_	_	_
50	med	med	VBD	_	_	_
51	+0.2	+0.2	CD	_	_	_
52	%	%	NN	_	_	_
53	glu	glu	NN	_	_	_
54	+50	+50	CD	_	_	_
55	ug	ug	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	15	15	CD	_	_	_
58	'	'	''	_	_	_
59	vs	vs	CC	_	_	_
60	0	0	CD	_	_	_
61	'	'	''	_	_	_
62	in	in	IN	_	_	_
63	minimal	minimal	JJ	_	_	_
64	medium	medium	NN	_	_	_
65	+0.2	+0.2	CD	_	_	_
66	%	%	NN	_	_	_
67	glu	glu	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	agent	agent	NN	_	_	_
70	:	:	:	_	_	_
71	control	control	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
73	agent	agent	NN	_	_	_
74	:	:	:	_	_	_
75	CORM-401	corm-401	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	Agilent	Agilent	NNP	_	_	_
78	Feature	Feature	NNP	_	_	_
79	Extraction	Extraction	NNP	_	_	_
80	Software	Software	NNP	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	v	v	LS	_	_	_
83	10.10.1.1	10.10.1.1	CD	_	_	_
84	-RRB-	-rrb-	-RRB-	_	_	_
85	was	be	VBD	_	_	_
86	used	use	VBN	_	_	_
87	for	for	IN	_	_	_
88	background	background	NN	_	_	_
89	subtraction	subtraction	NN	_	_	_
90	and	and	CC	_	_	_
91	LOWESS	lowess	NN	_	_	_
92	normalization	normalization	NN	_	_	_
93	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Continuous	continuous	JJ	_	_	_
3	aerobically	aerobically	RB	_	_	_
4	grown	grow	VBN	_	_	_
5	cultures	culture	NNS	_	_	_
6	in	in	IN	_	_	_
7	Evans	Evans	NNP	_	_	_
8	medium	medium	NN	_	_	_
9	,	,	,	_	_	_
10	CORM-401	corm-401	NN	_	_	_
11	samples	sample	NNS	_	_	_
12	or	or	CC	_	_	_
13	samples	sample	NNS	_	_	_
14	prior	prior	RB	_	_	_
15	to	to	TO	_	_	_
16	addition	addition	NN	_	_	_
17	of	of	IN	_	_	_
18	CORM-401	corm-401	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	Continuous	continuous	JJ	_	_	_
21	anaerobically	anaerobically	RB	_	_	_
22	grown	grow	VBN	_	_	_
23	cultures	culture	NNS	_	_	_
24	in	in	IN	_	_	_
25	Evans	Evans	NNP	_	_	_
26	medium	medium	NN	_	_	_
27	,	,	,	_	_	_
28	CORM-401	corm-401	NN	_	_	_
29	samples	sample	NNS	_	_	_
30	or	or	CC	_	_	_
31	samples	sample	NNS	_	_	_
32	prior	prior	RB	_	_	_
33	to	to	TO	_	_	_
34	addition	addition	NN	_	_	_
35	of	of	IN	_	_	_
36	CORM-401	corm-401	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	culture	culture	NN	_	_	_
39	conditions	condition	NNS	_	_	_
40	:	:	:	_	_	_
41	aerobic	aerobic	JJ	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	culture	culture	NN	_	_	_
44	conditions	condition	NNS	_	_	_
45	:	:	:	_	_	_
46	anaerobic	anaerobic	JJ	_	_	_
47	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
48	Escherichia	escherichia	FW	Organism	_	_
49	coli	coli	FW	Organism	_	_
50	str	str	FW	_	_	_
51	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Slide	slide	VBP	_	_	_
4	46	46	CD	_	_	_
5	_	_	SYM	_	_	_
6	Aerobic	aerobic	JJ	_	_	_
7	culture	culture	NN	_	_	_
8	_	_	NN	_	_	_
9	CORM-401	corm-401	NN	_	_	_
10	_	_	CD	_	_	_
11	biol	biol	NN	_	_	_
12	rep	rep	NN	GEN	_	_
13	2	2	CD	_	_	_
14	_	_	CD	_	_	_
15	Cy3	cy3	NN	_	_	_
16	0	0	CD	_	_	_
17	Cy5	cy5	NN	_	_	_
18	10	10	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Slide	slide	NN	_	_	_
21	46	46	CD	_	_	_
22	_	_	SYM	_	_	_
23	Aerobic	aerobic	JJ	_	_	_
24	culture	culture	NN	_	_	_
25	_	_	NN	_	_	_
26	CORM-401	corm-401	NN	_	_	_
27	_	_	CD	_	_	_
28	biol	biol	NN	_	_	_
29	rep	rep	NN	GEN	_	_
30	2	2	CD	_	_	_
31	_	_	CD	_	_	_
32	Cy3	cy3	NN	_	_	_
33	0	0	CD	_	_	_
34	Cy5	cy5	NN	_	_	_
35	20	20	CD	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Slide	slide	NN	_	_	_
38	46	46	CD	_	_	_
39	_	_	SYM	_	_	_
40	Aerobic	aerobic	JJ	_	_	_
41	culture	culture	NN	_	_	_
42	_	_	NN	_	_	_
43	CORM-401	corm-401	NN	_	_	_
44	_	_	CD	_	_	_
45	biol	biol	NN	_	_	_
46	rep	rep	NN	GEN	_	_
47	2	2	CD	_	_	_
48	_	_	CD	_	_	_
49	Cy3	cy3	NN	_	_	_
50	2.5	2.5	CD	_	_	_
51	Cy5	cy5	NN	_	_	_
52	0	0	CD	_	_	_
53	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
54	Slide	Slide	NNP	_	_	_
55	46	46	CD	_	_	_
56	_	_	SYM	_	_	_
57	Aerobic	aerobic	JJ	_	_	_
58	culture	culture	NN	_	_	_
59	_	_	NN	_	_	_
60	CORM-401	corm-401	NN	_	_	_
61	_	_	CD	_	_	_
62	biol	biol	NN	_	_	_
63	rep	rep	NN	GEN	_	_
64	2	2	CD	_	_	_
65	_	_	CD	_	_	_
66	Cy3	cy3	NN	_	_	_
67	5	5	CD	_	_	_
68	Cy5	cy5	NN	_	_	_
69	0	0	CD	_	_	_
70	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
71	Slide	Slide	NNP	_	_	_
72	48	48	CD	_	_	_
73	_	_	SYM	_	_	_
74	Aerobic	aerobic	JJ	_	_	_
75	culture	culture	NN	_	_	_
76	_	_	NN	_	_	_
77	CORM-401	corm-401	NN	_	_	_
78	_	_	CD	_	_	_
79	biol	biol	NN	_	_	_
80	rep	rep	NN	GEN	_	_
81	2	2	CD	_	_	_
82	_	_	CD	_	_	_
83	Cy3	cy3	NN	_	_	_
84	0	0	CD	_	_	_
85	Cy5	cy5	NN	_	_	_
86	2.5	2.5	CD	_	_	_
87	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
88	Slide	Slide	NNP	_	_	_
89	48	48	CD	_	_	_
90	_	_	SYM	_	_	_
91	Aerobic	aerobic	JJ	_	_	_
92	culture	culture	NN	_	_	_
93	_	_	NN	_	_	_
94	CORM-401	corm-401	NN	_	_	_
95	_	_	CD	_	_	_
96	biol	biol	NN	_	_	_
97	rep	rep	NN	GEN	_	_
98	2	2	CD	_	_	_
99	_	_	CD	_	_	_
100	Cy3	cy3	NN	_	_	_
101	0	0	CD	_	_	_
102	Cy5	cy5	NN	_	_	_
103	40	40	CD	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	Slide	slide	NN	_	_	_
106	48	48	CD	_	_	_
107	_	_	SYM	_	_	_
108	Aerobic	aerobic	JJ	_	_	_
109	culture	culture	NN	_	_	_
110	_	_	NN	_	_	_
111	CORM-401	corm-401	NN	_	_	_
112	_	_	CD	_	_	_
113	biol	biol	NN	_	_	_
114	rep	rep	NN	GEN	_	_
115	2	2	CD	_	_	_
116	_	_	CD	_	_	_
117	Cy3	cy3	NN	_	_	_
118	0	0	CD	_	_	_
119	Cy5	cy5	NN	_	_	_
120	5	5	CD	_	_	_
121	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
122	Slide	Slide	NNP	_	_	_
123	48	48	CD	_	_	_
124	_	_	SYM	_	_	_
125	Aerobic	aerobic	JJ	_	_	_
126	culture	culture	NN	_	_	_
127	_	_	NN	_	_	_
128	CORM-401	corm-401	NN	_	_	_
129	_	_	CD	_	_	_
130	biol	biol	NN	_	_	_
131	rep	rep	NN	GEN	_	_
132	2	2	CD	_	_	_
133	_	_	CD	_	_	_
134	Cy3	cy3	NN	_	_	_
135	0	0	CD	_	_	_
136	Cy5	cy5	NN	_	_	_
137	80	80	CD	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
139	Slide	slide	VBP	_	_	_
140	48	48	CD	_	_	_
141	_	_	SYM	_	_	_
142	Aerobic	aerobic	JJ	_	_	_
143	culture	culture	NN	_	_	_
144	_	_	NN	_	_	_
145	CORM-401	corm-401	NN	_	_	_
146	_	_	CD	_	_	_
147	biol	biol	NN	_	_	_
148	rep	rep	NN	GEN	_	_
149	2	2	CD	_	_	_
150	_	_	CD	_	_	_
151	Cy3	cy3	NN	_	_	_
152	10	10	CD	_	_	_
153	Cy5	cy5	NN	_	_	_
154	0	0	CD	_	_	_
155	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
156	Slide	Slide	NNP	_	_	_
157	48	48	CD	_	_	_
158	_	_	SYM	_	_	_
159	Aerobic	aerobic	JJ	_	_	_
160	culture	culture	NN	_	_	_
161	_	_	NN	_	_	_
162	CORM-401	corm-401	NN	_	_	_
163	_	_	CD	_	_	_
164	biol	biol	NN	_	_	_
165	rep	rep	NN	GEN	_	_
166	2	2	CD	_	_	_
167	_	_	CD	_	_	_
168	Cy3	cy3	NN	_	_	_
169	20	20	CD	_	_	_
170	Cy5	cy5	NN	_	_	_
171	0	0	CD	_	_	_
172	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
173	Slide	Slide	NNP	_	_	_
174	48	48	CD	_	_	_
175	_	_	SYM	_	_	_
176	Aerobic	aerobic	JJ	_	_	_
177	culture	culture	NN	_	_	_
178	_	_	NN	_	_	_
179	CORM-401	corm-401	NN	_	_	_
180	_	_	CD	_	_	_
181	biol	biol	NN	_	_	_
182	rep	rep	NN	GEN	_	_
183	2	2	CD	_	_	_
184	_	_	CD	_	_	_
185	Cy3	cy3	NN	_	_	_
186	40	40	CD	_	_	_
187	Cy5	cy5	NN	_	_	_
188	0	0	CD	_	_	_
189	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
190	Slide	Slide	NNP	_	_	_
191	48	48	CD	_	_	_
192	_	_	SYM	_	_	_
193	Aerobic	aerobic	JJ	_	_	_
194	culture	culture	NN	_	_	_
195	_	_	NN	_	_	_
196	CORM-401	corm-401	NN	_	_	_
197	_	_	CD	_	_	_
198	biol	biol	NN	_	_	_
199	rep	rep	NN	GEN	_	_
200	2	2	CD	_	_	_
201	_	_	CD	_	_	_
202	Cy3	cy3	NN	_	_	_
203	80	80	CD	_	_	_
204	Cy5	cy5	NN	_	_	_
205	0	0	CD	_	_	_
206	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
207	Slide	Slide	NNP	_	_	_
208	53	53	CD	_	_	_
209	_	_	SYM	_	_	_
210	Aerobic	aerobic	JJ	_	_	_
211	culture	culture	NN	_	_	_
212	_	_	NN	_	_	_
213	CORM-401	corm-401	NN	_	_	_
214	_	_	CD	_	_	_
215	biol	biol	NN	_	_	_
216	rep	rep	NN	GEN	_	_
217	1	1	CD	_	_	_
218	_	_	NN	_	_	_
219	Cy3	cy3	NN	_	_	_
220	0	0	CD	_	_	_
221	Cy5	cy5	NN	_	_	_
222	10	10	CD	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	Slide	slide	NN	_	_	_
225	53	53	CD	_	_	_
226	_	_	SYM	_	_	_
227	Aerobic	aerobic	JJ	_	_	_
228	culture	culture	NN	_	_	_
229	_	_	NN	_	_	_
230	CORM-401	corm-401	NN	_	_	_
231	_	_	CD	_	_	_
232	biol	biol	NN	_	_	_
233	rep	rep	NN	GEN	_	_
234	1	1	CD	_	_	_
235	_	_	NN	_	_	_
236	Cy3	cy3	NN	_	_	_
237	0	0	CD	_	_	_
238	Cy5	cy5	NN	_	_	_
239	20	20	CD	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
241	Slide	slide	NN	_	_	_
242	53	53	CD	_	_	_
243	_	_	SYM	_	_	_
244	Aerobic	aerobic	JJ	_	_	_
245	culture	culture	NN	_	_	_
246	_	_	NN	_	_	_
247	CORM-401	corm-401	NN	_	_	_
248	_	_	CD	_	_	_
249	biol	biol	NN	_	_	_
250	rep	rep	NN	GEN	_	_
251	1	1	CD	_	_	_
252	_	_	NN	_	_	_
253	Cy3	cy3	NN	_	_	_
254	0	0	CD	_	_	_
255	Cy5	cy5	NN	_	_	_
256	2.5	2.5	CD	_	_	_
257	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
258	Slide	Slide	NNP	_	_	_
259	53	53	CD	_	_	_
260	_	_	SYM	_	_	_
261	Aerobic	aerobic	JJ	_	_	_
262	culture	culture	NN	_	_	_
263	_	_	NN	_	_	_
264	CORM-401	corm-401	NN	_	_	_
265	_	_	CD	_	_	_
266	biol	biol	NN	_	_	_
267	rep	rep	NN	GEN	_	_
268	1	1	CD	_	_	_
269	_	_	NN	_	_	_
270	Cy3	cy3	NN	_	_	_
271	0	0	CD	_	_	_
272	Cy5	cy5	NN	_	_	_
273	5	5	CD	_	_	_
274	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
275	Slide	Slide	NNP	_	_	_
276	54	54	CD	_	_	_
277	_	_	SYM	_	_	_
278	Aerobic	aerobic	JJ	_	_	_
279	culture	culture	NN	_	_	_
280	_	_	NN	_	_	_
281	CORM-401	corm-401	NN	_	_	_
282	_	_	CD	_	_	_
283	biol	biol	NN	_	_	_
284	rep	rep	NN	GEN	_	_
285	1	1	CD	_	_	_
286	_	_	NN	_	_	_
287	Cy3	cy3	NN	_	_	_
288	0	0	CD	_	_	_
289	Cy5	cy5	NN	_	_	_
290	40	40	CD	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	Slide	slide	NN	_	_	_
293	54	54	CD	_	_	_
294	_	_	SYM	_	_	_
295	Aerobic	aerobic	JJ	_	_	_
296	culture	culture	NN	_	_	_
297	_	_	NN	_	_	_
298	CORM-401	corm-401	NN	_	_	_
299	_	_	CD	_	_	_
300	biol	biol	NN	_	_	_
301	rep	rep	NN	GEN	_	_
302	1	1	CD	_	_	_
303	_	_	NN	_	_	_
304	Cy3	cy3	NN	_	_	_
305	0	0	CD	_	_	_
306	Cy5	cy5	NN	_	_	_
307	80	80	CD	_	_	_
308	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
309	Slide	Slide	NNP	_	_	_
310	54	54	CD	_	_	_
311	_	_	SYM	_	_	_
312	Aerobic	aerobic	JJ	_	_	_
313	culture	culture	NN	_	_	_
314	_	_	NN	_	_	_
315	CORM-401	corm-401	NN	_	_	_
316	_	_	CD	_	_	_
317	biol	biol	NN	_	_	_
318	rep	rep	NN	GEN	_	_
319	1	1	CD	_	_	_
320	_	_	CD	_	_	_
321	Cy3	cy3	NN	_	_	_
322	10	10	CD	_	_	_
323	Cy5	cy5	NN	_	_	_
324	0	0	CD	_	_	_
325	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
326	Slide	Slide	NNP	_	_	_
327	54	54	CD	_	_	_
328	_	_	SYM	_	_	_
329	Aerobic	aerobic	JJ	_	_	_
330	culture	culture	NN	_	_	_
331	_	_	NN	_	_	_
332	CORM-401	corm-401	NN	_	_	_
333	_	_	CD	_	_	_
334	biol	biol	NN	_	_	_
335	rep	rep	NN	GEN	_	_
336	1	1	CD	_	_	_
337	_	_	CD	_	_	_
338	Cy3	cy3	NN	_	_	_
339	20	20	CD	_	_	_
340	Cy5	cy5	NN	_	_	_
341	0	0	CD	_	_	_
342	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
343	Slide	Slide	NNP	_	_	_
344	54	54	CD	_	_	_
345	_	_	SYM	_	_	_
346	Aerobic	aerobic	JJ	_	_	_
347	culture	culture	NN	_	_	_
348	_	_	NN	_	_	_
349	CORM-401	corm-401	NN	_	_	_
350	_	_	CD	_	_	_
351	biol	biol	NN	_	_	_
352	rep	rep	NN	GEN	_	_
353	1	1	CD	_	_	_
354	_	_	CD	_	_	_
355	Cy3	cy3	NN	_	_	_
356	2.5	2.5	CD	_	_	_
357	Cy5	cy5	NN	_	_	_
358	0	0	CD	_	_	_
359	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
360	Slide	Slide	NNP	_	_	_
361	54	54	CD	_	_	_
362	_	_	SYM	_	_	_
363	Aerobic	aerobic	JJ	_	_	_
364	culture	culture	NN	_	_	_
365	_	_	NN	_	_	_
366	CORM-401	corm-401	NN	_	_	_
367	_	_	CD	_	_	_
368	biol	biol	NN	_	_	_
369	rep	rep	NN	GEN	_	_
370	1	1	CD	_	_	_
371	_	_	CD	_	_	_
372	Cy3	cy3	NN	_	_	_
373	40	40	CD	_	_	_
374	Cy5	cy5	NN	_	_	_
375	0	0	CD	_	_	_
376	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
377	Slide	Slide	NNP	_	_	_
378	54	54	CD	_	_	_
379	_	_	SYM	_	_	_
380	Aerobic	aerobic	JJ	_	_	_
381	culture	culture	NN	_	_	_
382	_	_	NN	_	_	_
383	CORM-401	corm-401	NN	_	_	_
384	_	_	CD	_	_	_
385	biol	biol	NN	_	_	_
386	rep	rep	NN	GEN	_	_
387	1	1	CD	_	_	_
388	_	_	CD	_	_	_
389	Cy3	cy3	NN	_	_	_
390	5	5	CD	_	_	_
391	Cy5	cy5	NN	_	_	_
392	0	0	CD	_	_	_
393	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
394	Slide	Slide	NNP	_	_	_
395	54	54	CD	_	_	_
396	_	_	SYM	_	_	_
397	Aerobic	aerobic	JJ	_	_	_
398	culture	culture	NN	_	_	_
399	_	_	NN	_	_	_
400	CORM-401	corm-401	NN	_	_	_
401	_	_	CD	_	_	_
402	biol	biol	NN	_	_	_
403	rep	rep	NN	GEN	_	_
404	1	1	CD	_	_	_
405	_	_	CD	_	_	_
406	Cy3	cy3	NN	_	_	_
407	80	80	CD	_	_	_
408	Cy5	cy5	NN	_	_	_
409	0	0	CD	_	_	_
410	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
411	Slide	Slide	NNP	_	_	_
412	58	58	CD	_	_	_
413	_	_	SYM	_	_	_
414	Anaerobic	anaerobic	JJ	_	_	_
415	culture	culture	NN	_	_	_
416	_	_	NN	_	_	_
417	CORM-401	corm-401	NN	_	_	_
418	_	_	CD	_	_	_
419	biol	biol	NN	_	_	_
420	rep	rep	NN	GEN	_	_
421	1	1	CD	_	_	_
422	_	_	CD	_	_	_
423	Cy3	cy3	NN	_	_	_
424	10	10	CD	_	_	_
425	Cy5	cy5	NN	_	_	_
426	0	0	CD	_	_	_
427	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
428	Slide	Slide	NNP	_	_	_
429	58	58	CD	_	_	_
430	_	_	SYM	_	_	_
431	Anaerobic	anaerobic	JJ	_	_	_
432	culture	culture	NN	_	_	_
433	_	_	NN	_	_	_
434	CORM-401	corm-401	NN	_	_	_
435	_	_	CD	_	_	_
436	biol	biol	NN	_	_	_
437	rep	rep	NN	GEN	_	_
438	1	1	CD	_	_	_
439	_	_	CD	_	_	_
440	Cy3	cy3	NN	_	_	_
441	20	20	CD	_	_	_
442	Cy5	cy5	NN	_	_	_
443	0	0	CD	_	_	_
444	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
445	Slide	Slide	NNP	_	_	_
446	58	58	CD	_	_	_
447	_	_	SYM	_	_	_
448	Anaerobic	anaerobic	JJ	_	_	_
449	culture	culture	NN	_	_	_
450	_	_	NN	_	_	_
451	CORM-401	corm-401	NN	_	_	_
452	_	_	CD	_	_	_
453	biol	biol	NN	_	_	_
454	rep	rep	NN	GEN	_	_
455	1	1	CD	_	_	_
456	_	_	CD	_	_	_
457	Cy3	cy3	NN	_	_	_
458	40	40	CD	_	_	_
459	Cy5	cy5	NN	_	_	_
460	0	0	CD	_	_	_
461	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
462	Slide	Slide	NNP	_	_	_
463	58	58	CD	_	_	_
464	_	_	SYM	_	_	_
465	Anaerobic	anaerobic	JJ	_	_	_
466	culture	culture	NN	_	_	_
467	_	_	NN	_	_	_
468	CORM-401	corm-401	NN	_	_	_
469	_	_	CD	_	_	_
470	biol	biol	NN	_	_	_
471	rep	rep	NN	GEN	_	_
472	1	1	CD	_	_	_
473	_	_	CD	_	_	_
474	Cy3	cy3	NN	_	_	_
475	80	80	CD	_	_	_
476	Cy5	cy5	NN	_	_	_
477	0	0	CD	_	_	_
478	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
479	Slide	Slide	NNP	_	_	_
480	58	58	CD	_	_	_
481	_	_	SYM	_	_	_
482	Anaerobic	anaerobic	JJ	_	_	_
483	culture	culture	NN	_	_	_
484	_	_	NN	_	_	_
485	CORM-401	corm-401	NN	_	_	_
486	_	_	CD	_	_	_
487	biol	biol	NN	_	_	_
488	rep	rep	NN	GEN	_	_
489	2	2	CD	_	_	_
490	_	_	CD	_	_	_
491	Cy3	cy3	NN	_	_	_
492	0	0	CD	_	_	_
493	Cy5	cy5	NN	_	_	_
494	10	10	CD	_	_	_
495	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
496	Slide	Slide	NNP	_	_	_
497	58	58	CD	_	_	_
498	_	_	SYM	_	_	_
499	Anaerobic	anaerobic	JJ	_	_	_
500	culture	culture	NN	_	_	_
501	_	_	NN	_	_	_
502	CORM-401	corm-401	NN	_	_	_
503	_	_	CD	_	_	_
504	biol	biol	NN	_	_	_
505	rep	rep	NN	GEN	_	_
506	2	2	CD	_	_	_
507	_	_	CD	_	_	_
508	Cy3	cy3	NN	_	_	_
509	0	0	CD	_	_	_
510	Cy5	cy5	NN	_	_	_
511	20	20	CD	_	_	_
512	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
513	Slide	Slide	NNP	_	_	_
514	58	58	CD	_	_	_
515	_	_	SYM	_	_	_
516	Anaerobic	anaerobic	JJ	_	_	_
517	culture	culture	NN	_	_	_
518	_	_	NN	_	_	_
519	CORM-401	corm-401	NN	_	_	_
520	_	_	CD	_	_	_
521	biol	biol	NN	_	_	_
522	rep	rep	NN	GEN	_	_
523	2	2	CD	_	_	_
524	_	_	CD	_	_	_
525	Cy3	cy3	NN	_	_	_
526	0	0	CD	_	_	_
527	Cy5	cy5	NN	_	_	_
528	2.5	2.5	CD	_	_	_
529	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
530	Slide	Slide	NNP	_	_	_
531	58	58	CD	_	_	_
532	_	_	SYM	_	_	_
533	Anaerobic	anaerobic	JJ	_	_	_
534	culture	culture	NN	_	_	_
535	_	_	NN	_	_	_
536	CORM-401	corm-401	NN	_	_	_
537	_	_	CD	_	_	_
538	biol	biol	NN	_	_	_
539	rep	rep	NN	GEN	_	_
540	2	2	CD	_	_	_
541	_	_	CD	_	_	_
542	Cy3	cy3	NN	_	_	_
543	0	0	CD	_	_	_
544	Cy5	cy5	NN	_	_	_
545	5	5	CD	_	_	_
546	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
547	Slide	Slide	NNP	_	_	_
548	59	59	CD	_	_	_
549	_	_	SYM	_	_	_
550	Anaerobic	anaerobic	JJ	_	_	_
551	culture	culture	NN	_	_	_
552	_	_	NN	_	_	_
553	CORM-401	corm-401	NN	_	_	_
554	_	_	CD	_	_	_
555	biol	biol	NN	_	_	_
556	rep	rep	NN	GEN	_	_
557	2	2	CD	_	_	_
558	_	_	CD	_	_	_
559	Cy3	cy3	NN	_	_	_
560	0	0	CD	_	_	_
561	Cy5	cy5	NN	_	_	_
562	40	40	CD	_	_	_
563	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
564	Slide	slide	NN	_	_	_
565	59	59	CD	_	_	_
566	_	_	SYM	_	_	_
567	Anaerobic	anaerobic	JJ	_	_	_
568	culture	culture	NN	_	_	_
569	_	_	NN	_	_	_
570	CORM-401	corm-401	NN	_	_	_
571	_	_	CD	_	_	_
572	biol	biol	NN	_	_	_
573	rep	rep	NN	GEN	_	_
574	2	2	CD	_	_	_
575	_	_	CD	_	_	_
576	Cy3	cy3	NN	_	_	_
577	0	0	CD	_	_	_
578	Cy5	cy5	NN	_	_	_
579	80	80	CD	_	_	_
580	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
581	Slide	Slide	NNP	_	_	_
582	59	59	CD	_	_	_
583	_	_	SYM	_	_	_
584	Anaerobic	anaerobic	JJ	_	_	_
585	culture	culture	NN	_	_	_
586	_	_	NN	_	_	_
587	CORM-401	corm-401	NN	_	_	_
588	_	_	CD	_	_	_
589	biol	biol	NN	_	_	_
590	rep	rep	NN	GEN	_	_
591	2	2	CD	_	_	_
592	_	_	CD	_	_	_
593	Cy3	cy3	NN	_	_	_
594	10	10	CD	_	_	_
595	Cy5	cy5	NN	_	_	_
596	0	0	CD	_	_	_
597	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
598	Slide	Slide	NNP	_	_	_
599	59	59	CD	_	_	_
600	_	_	SYM	_	_	_
601	Anaerobic	anaerobic	JJ	_	_	_
602	culture	culture	NN	_	_	_
603	_	_	NN	_	_	_
604	CORM-401	corm-401	NN	_	_	_
605	_	_	CD	_	_	_
606	biol	biol	NN	_	_	_
607	rep	rep	NN	GEN	_	_
608	2	2	CD	_	_	_
609	_	_	CD	_	_	_
610	Cy3	cy3	NN	_	_	_
611	20	20	CD	_	_	_
612	Cy5	cy5	NN	_	_	_
613	0	0	CD	_	_	_
614	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
615	Slide	Slide	NNP	_	_	_
616	59	59	CD	_	_	_
617	_	_	SYM	_	_	_
618	Anaerobic	anaerobic	JJ	_	_	_
619	culture	culture	NN	_	_	_
620	_	_	NN	_	_	_
621	CORM-401	corm-401	NN	_	_	_
622	_	_	CD	_	_	_
623	biol	biol	NN	_	_	_
624	rep	rep	NN	GEN	_	_
625	2	2	CD	_	_	_
626	_	_	CD	_	_	_
627	Cy3	cy3	NN	_	_	_
628	2.5	2.5	CD	_	_	_
629	Cy5	cy5	NN	_	_	_
630	0	0	CD	_	_	_
631	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
632	Slide	Slide	NNP	_	_	_
633	59	59	CD	_	_	_
634	_	_	SYM	_	_	_
635	Anaerobic	anaerobic	JJ	_	_	_
636	culture	culture	NN	_	_	_
637	_	_	NN	_	_	_
638	CORM-401	corm-401	NN	_	_	_
639	_	_	CD	_	_	_
640	biol	biol	NN	_	_	_
641	rep	rep	NN	GEN	_	_
642	2	2	CD	_	_	_
643	_	_	CD	_	_	_
644	Cy3	cy3	NN	_	_	_
645	40	40	CD	_	_	_
646	Cy5	cy5	NN	_	_	_
647	0	0	CD	_	_	_
648	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
649	Slide	Slide	NNP	_	_	_
650	59	59	CD	_	_	_
651	_	_	SYM	_	_	_
652	Anaerobic	anaerobic	JJ	_	_	_
653	culture	culture	NN	_	_	_
654	_	_	NN	_	_	_
655	CORM-401	corm-401	NN	_	_	_
656	_	_	CD	_	_	_
657	biol	biol	NN	_	_	_
658	rep	rep	NN	GEN	_	_
659	2	2	CD	_	_	_
660	_	_	CD	_	_	_
661	Cy3	cy3	NN	_	_	_
662	5	5	CD	_	_	_
663	Cy5	cy5	NN	_	_	_
664	0	0	CD	_	_	_
665	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
666	Slide	Slide	NNP	_	_	_
667	59	59	CD	_	_	_
668	_	_	SYM	_	_	_
669	Anaerobic	anaerobic	JJ	_	_	_
670	culture	culture	NN	_	_	_
671	_	_	NN	_	_	_
672	CORM-401	corm-401	NN	_	_	_
673	_	_	CD	_	_	_
674	biol	biol	NN	_	_	_
675	rep	rep	NN	GEN	_	_
676	2	2	CD	_	_	_
677	_	_	CD	_	_	_
678	Cy3	cy3	NN	_	_	_
679	80	80	CD	_	_	_
680	Cy5	cy5	NN	_	_	_
681	0	0	CD	_	_	_
682	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
683	Slide	Slide	NNP	_	_	_
684	70	70	CD	_	_	_
685	_	_	SYM	_	_	_
686	Anaerobic	anaerobic	JJ	_	_	_
687	culture	culture	NN	_	_	_
688	_	_	NN	_	_	_
689	CORM-401	corm-401	NN	_	_	_
690	_	_	CD	_	_	_
691	biol	biol	NN	_	_	_
692	rep	rep	NN	GEN	_	_
693	1	1	CD	_	_	_
694	_	_	NN	_	_	_
695	Cy3	cy3	NN	_	_	_
696	0	0	CD	_	_	_
697	Cy5	cy5	NN	_	_	_
698	10	10	CD	_	_	_
699	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
700	Slide	Slide	NNP	_	_	_
701	70	70	CD	_	_	_
702	_	_	SYM	_	_	_
703	Anaerobic	anaerobic	JJ	_	_	_
704	culture	culture	NN	_	_	_
705	_	_	NN	_	_	_
706	CORM-401	corm-401	NN	_	_	_
707	_	_	CD	_	_	_
708	biol	biol	NN	_	_	_
709	rep	rep	NN	GEN	_	_
710	1	1	CD	_	_	_
711	_	_	NN	_	_	_
712	Cy3	cy3	NN	_	_	_
713	0	0	CD	_	_	_
714	Cy5	cy5	NN	_	_	_
715	20	20	CD	_	_	_
716	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
717	Slide	Slide	NNP	_	_	_
718	70	70	CD	_	_	_
719	_	_	SYM	_	_	_
720	Anaerobic	anaerobic	JJ	_	_	_
721	culture	culture	NN	_	_	_
722	_	_	NN	_	_	_
723	CORM-401	corm-401	NN	_	_	_
724	_	_	CD	_	_	_
725	biol	biol	NN	_	_	_
726	rep	rep	NN	GEN	_	_
727	1	1	CD	_	_	_
728	_	_	NN	_	_	_
729	Cy3	cy3	NN	_	_	_
730	0	0	CD	_	_	_
731	Cy5	cy5	NN	_	_	_
732	2.5	2.5	CD	_	_	_
733	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
734	Slide	Slide	NNP	_	_	_
735	70	70	CD	_	_	_
736	_	_	SYM	_	_	_
737	Anaerobic	anaerobic	JJ	_	_	_
738	culture	culture	NN	_	_	_
739	_	_	NN	_	_	_
740	CORM-401	corm-401	NN	_	_	_
741	_	_	CD	_	_	_
742	biol	biol	NN	_	_	_
743	rep	rep	NN	GEN	_	_
744	1	1	CD	_	_	_
745	_	_	NN	_	_	_
746	Cy3	cy3	NN	_	_	_
747	0	0	CD	_	_	_
748	Cy5	cy5	NN	_	_	_
749	40	40	CD	_	_	_
750	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
751	Slide	slide	NN	_	_	_
752	70	70	CD	_	_	_
753	_	_	SYM	_	_	_
754	Anaerobic	anaerobic	JJ	_	_	_
755	culture	culture	NN	_	_	_
756	_	_	NN	_	_	_
757	CORM-401	corm-401	NN	_	_	_
758	_	_	CD	_	_	_
759	biol	biol	NN	_	_	_
760	rep	rep	NN	GEN	_	_
761	1	1	CD	_	_	_
762	_	_	NN	_	_	_
763	Cy3	cy3	NN	_	_	_
764	0	0	CD	_	_	_
765	Cy5	cy5	NN	_	_	_
766	5	5	CD	_	_	_
767	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
768	Slide	Slide	NNP	_	_	_
769	70	70	CD	_	_	_
770	_	_	SYM	_	_	_
771	Anaerobic	anaerobic	JJ	_	_	_
772	culture	culture	NN	_	_	_
773	_	_	NN	_	_	_
774	CORM-401	corm-401	NN	_	_	_
775	_	_	CD	_	_	_
776	biol	biol	NN	_	_	_
777	rep	rep	NN	GEN	_	_
778	1	1	CD	_	_	_
779	_	_	NN	_	_	_
780	Cy3	cy3	NN	_	_	_
781	0	0	CD	_	_	_
782	Cy5	cy5	NN	_	_	_
783	80	80	CD	_	_	_
784	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
785	Slide	Slide	NNP	_	_	_
786	70	70	CD	_	_	_
787	_	_	SYM	_	_	_
788	Anaerobic	anaerobic	JJ	_	_	_
789	culture	culture	NN	_	_	_
790	_	_	NN	_	_	_
791	CORM-401	corm-401	NN	_	_	_
792	_	_	CD	_	_	_
793	biol	biol	NN	_	_	_
794	rep	rep	NN	GEN	_	_
795	1	1	CD	_	_	_
796	_	_	CD	_	_	_
797	Cy3	cy3	NN	_	_	_
798	2.5	2.5	CD	_	_	_
799	Cy5	cy5	NN	_	_	_
800	0	0	CD	_	_	_
801	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
802	Slide	Slide	NNP	_	_	_
803	70	70	CD	_	_	_
804	_	_	SYM	_	_	_
805	Anaerobic	anaerobic	JJ	_	_	_
806	culture	culture	NN	_	_	_
807	_	_	NN	_	_	_
808	CORM-401	corm-401	NN	_	_	_
809	_	_	CD	_	_	_
810	biol	biol	NN	_	_	_
811	rep	rep	NN	GEN	_	_
812	1	1	CD	_	_	_
813	_	_	CD	_	_	_
814	Cy3	cy3	NN	_	_	_
815	5	5	CD	_	_	_
816	Cy5	cy5	NN	_	_	_
817	0	0	CD	_	_	_
818	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
819	strain	strain	NN	_	_	_
820	:	:	:	_	_	_
821	Wild	Wild	NNP	_	_	_
822	type	type	NN	_	_	_
823	strain	strain	NN	_	_	_
824	MG1655	mg1655	NN	_	_	_
825	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
826	time	time	NN	_	_	_
827	:	:	:	_	_	_
828	0	0	CD	_	_	_
829	min	min	NN	_	_	_
830	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
831	time	time	NN	_	_	_
832	:	:	:	_	_	_
833	10	10	CD	_	_	_
834	min	min	NN	_	_	_
835	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
836	time	time	NN	_	_	_
837	:	:	:	_	_	_
838	20	20	CD	_	_	_
839	min	min	NN	_	_	_
840	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
841	time	time	NN	_	_	_
842	:	:	:	_	_	_
843	2.5	2.5	CD	_	_	_
844	min	min	NN	_	_	_
845	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
846	time	time	NN	_	_	_
847	:	:	:	_	_	_
848	40	40	CD	_	_	_
849	min	min	NN	_	_	_
850	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
851	time	time	NN	_	_	_
852	:	:	:	_	_	_
853	5	5	CD	_	_	_
854	min	min	NN	_	_	_
855	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
856	time	time	NN	_	_	_
857	:	:	:	_	_	_
858	80	80	CD	_	_	_
859	min	min	NN	_	_	_
860	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
861	Total	total	JJ	_	_	_
862	RNA	rna	NN	_	_	_
863	extracted	extract	VBN	_	_	_
864	using	use	VBG	_	_	_
865	Trizol	Trizol	NNP	_	_	_
866	following	follow	VBG	_	_	_
867	manufacturer	manufacturer	NN	_	_	_
868	's	's	POS	_	_	_
869	instructions	instruction	NNS	_	_	_
870	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
871	Escherichia	escherichia	FW	Organism	_	_
872	coli	coli	FW	Organism	_	_
873	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
874	K12	k12	NN	_	_	_
875	WT	wt	JJ	_	_	_
876	3110	3110	CD	_	_	_
877	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
878	MasterPure	masterpure	NN	_	_	_
879	RNA	rna	NN	_	_	_
880	purification	purification	NN	_	_	_
881	Kit	kit	NN	_	_	_
882	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
883	Overnight	overnight	JJ	_	_	_
884	culture	culture	NN	_	_	_
885	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
886	phoU	phou	NN	GEN	_	_
887	_	_	NN	_	_	_
888	1	1	CD	_	_	_
889	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
890	phoU	phou	NN	GEN	_	_
891	_	_	NN	_	_	_
892	2	2	CD	_	_	_
893	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
894	phoU	phou	NN	GEN	_	_
895	_	_	CD	_	_	_
896	3	3	CD	_	_	_
897	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
898	phoU	phou	NN	GEN	_	_
899	gene	gene	NN	_	_	_
900	mutant	mutant	JJ	_	_	_
901	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
902	phoU	phou	NN	GEN	_	_
903	gene	gene	NN	_	_	_
904	mutant	mutant	NN	_	_	_
905	;	;	:	_	_	_
906	minimal	minimal	JJ	_	_	_
907	medium	medium	NN	_	_	_
908	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
909	The	the	DT	_	_	_
910	data	datum	NNS	_	_	_
911	were	be	VBD	_	_	_
912	analyzed	analyze	VBN	_	_	_
913	with	with	IN	_	_	_
914	GCOS	gcos	NN	_	_	_
915	1.4	1.4	CD	_	_	_
916	software	software	NN	_	_	_
917	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	probe	probe	NN	_	_	_
3	sets	set	VBZ	_	_	_
4	scaling	scale	VBG	_	_	_
5	was	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	with	with	IN	_	_	_
8	a	a	DT	_	_	_
9	target	target	NN	_	_	_
10	signal	signal	NN	_	_	_
11	value	value	NN	_	_	_
12	of	of	IN	_	_	_
13	500	500	CD	_	_	_
14	.	.	.	_	_	_

1	No	no	DT	_	_	_
2	normalization	normalization	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	wildtype	wildtype	JJ	_	_	_
3	strain	strain	NN	_	_	_
4	;	;	:	_	_	_
5	minimal	minimal	JJ	_	_	_
6	medium	medium	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	WT3110	wt3110	NN	_	_	_
9	_	_	NN	_	_	_
10	1	1	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	WT3110	wt3110	NN	_	_	_
13	_	_	NN	_	_	_
14	2	2	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	WT3110	wt3110	NN	_	_	_
17	_	_	CD	_	_	_
18	3	3	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	30	30	CD	_	_	_
21	'	'	''	_	_	_
22	10	10	CD	_	_	_
23	ug	ug	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	30	30	CD	_	_	_
26	'	'	''	_	_	_
27	15	15	CD	_	_	_
28	ug	ug	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	30	30	CD	_	_	_
31	'	'	''	_	_	_
32	+50	+50	CD	_	_	_
33	ug	ug	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	30	30	CD	_	_	_
36	'	'	''	_	_	_
37	in	in	IN	_	_	_
38	minimal	minimal	JJ	_	_	_
39	medium	medium	NN	_	_	_
40	+0.2	+0.2	CD	_	_	_
41	%	%	NN	_	_	_
42	glu	glu	NN	_	_	_
43	,	,	,	_	_	_
44	25	25	CD	_	_	_
45	ug	ug	NN	_	_	_
46	total	total	JJ	_	_	_
47	RNA	rna	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	30	30	CD	_	_	_
50	'	'	''	_	_	_
51	in	in	IN	_	_	_
52	min	min	NN	_	_	_
53	med	med	VBD	_	_	_
54	+0.2	+0.2	CD	_	_	_
55	%	%	NN	_	_	_
56	glu	glu	NN	_	_	_
57	+50	+50	CD	_	_	_
58	ug	ug	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	30	30	CD	_	_	_
61	'	'	''	_	_	_
62	vs	vs	CC	_	_	_
63	0	0	CD	_	_	_
64	'	'	''	_	_	_
65	in	in	IN	_	_	_
66	minimal	minimal	JJ	_	_	_
67	medium	medium	NN	_	_	_
68	+0.2	+0.2	CD	_	_	_
69	%	%	NN	_	_	_
70	glu	glu	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	BL21	bl21	NN	_	_	_
73	-LRB-	-lrb-	-LRB-	_	_	_
74	DE3	de3	NN	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	HPA	hpa	NN	_	_	_
77	0mM	0mm	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	BL21	bl21	NN	_	_	_
80	-LRB-	-lrb-	-LRB-	_	_	_
81	DE3	de3	NN	_	_	_
82	-RRB-	-rrb-	-RRB-	_	_	_
83	HPA	hpa	NN	_	_	_
84	3mM	3mm	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	BL21	bl21	NN	_	_	_
87	-LRB-	-lrb-	-LRB-	_	_	_
88	DE3	de3	NN	_	_	_
89	-RRB-	-rrb-	-RRB-	_	_	_
90	with	with	IN	_	_	_
91	3	3	CD	_	_	_
92	mM	mm	NN	KWSUPP	_	_
93	of	of	IN	_	_	_
94	heptanoic	heptanoic	JJ	_	_	_
95	acid	acid	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	BL21	bl21	NN	_	_	_
98	-LRB-	-lrb-	-LRB-	_	_	_
99	DE3	de3	NN	_	_	_
100	-RRB-	-rrb-	-RRB-	_	_	_
101	without	without	IN	_	_	_
102	heptanoic	heptanoic	JJ	_	_	_
103	acid	acid	NN	_	_	_
104	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
105	Escherichia	escherichia	FW	Organism	_	_
106	coli	coli	FW	Organism	_	_
107	BL21	bl21	NN	_	_	_
108	-LRB-	-lrb-	-LRB-	_	_	_
109	DE3	de3	NN	_	_	_
110	-RRB-	-rrb-	-RRB-	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	Escherichia	escherichia	FW	Organism	_	_
113	coli	coli	FW	Organism	_	_
114	str	str	FW	_	_	_
115	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	K12	k12	NN	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	with	with	IN	_	_	_
6	10	10	CD	_	_	_
7	mM	mm	NN	KWSUPP	_	_
8	of	of	IN	_	_	_
9	heptanoic	heptanoic	JJ	_	_	_
10	acid	acid	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	K12	k12	NN	_	_	_
13	MG1655	mg1655	NN	_	_	_
14	without	without	IN	_	_	_
15	heptanoic	heptanoic	JJ	_	_	_
16	acid	acid	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	metabolic	metabolic	JJ	_	_	_
19	response	response	NN	_	_	_
20	:	:	:	_	_	_
21	BL21	bl21	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	DE3	de3	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	is	be	VBZ	_	_	_
26	very	very	RB	_	_	_
27	susceptible	susceptible	JJ	_	_	_
28	to	to	TO	_	_	_
29	heptanoic	heptanoic	JJ	_	_	_
30	acid	acid	NN	_	_	_
31	,	,	,	_	_	_
32	because	because	IN	_	_	_
33	several	several	JJ	_	_	_
34	acid	acid	NN	_	_	_
35	resistance	resistance	NN	_	_	_
36	systems	system	NNS	_	_	_
37	stay	stay	VBP	_	_	_
38	inactive	inactive	JJ	_	_	_
39	under	under	IN	_	_	_
40	this	this	DT	_	_	_
41	stress	stress	NN	_	_	_
42	condition	condition	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	metabolic	metabolic	JJ	_	_	_
45	response	response	NN	_	_	_
46	:	:	:	_	_	_
47	K12	k12	NN	_	_	_
48	MG1655	mg1655	NN	_	_	_
49	activates	activate	VBZ	_	_	_
50	various	various	JJ	_	_	_
51	acid	acid	NN	_	_	_
52	resistance	resistance	NN	_	_	_
53	systems	system	NNS	_	_	_
54	under	under	IN	_	_	_
55	heptanoic	heptanoic	JJ	_	_	_
56	acid	acid	NN	_	_	_
57	stress	stress	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	MG1655	mg1655	NN	_	_	_
60	HPA	hpa	NN	_	_	_
61	0mM	0mm	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	MG1655	mg1655	NN	_	_	_
64	HPA	hpa	NN	_	_	_
65	10mM	10mm	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	strain	strain	NN	_	_	_
68	:	:	:	_	_	_
69	BL21	bl21	NN	_	_	_
70	-LRB-	-lrb-	-LRB-	_	_	_
71	DE3	de3	NN	_	_	_
72	-RRB-	-rrb-	-RRB-	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	strain	strain	NN	_	_	_
75	:	:	:	_	_	_
76	K12	k12	NN	_	_	_
77	MG1655	mg1655	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	stress	stress	NN	_	_	_
80	:	:	:	_	_	_
81	control	control	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
83	stress	stress	NN	_	_	_
84	:	:	:	_	_	_
85	heptanoic	heptanoic	JJ	_	_	_
86	acid	acid	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
88	The	the	DT	_	_	_
89	average	average	JJ	_	_	_
90	fluorescence	fluorescence	NN	_	_	_
91	intensity	intensity	NN	_	_	_
92	for	for	IN	_	_	_
93	each	each	DT	_	_	_
94	spot	spot	NN	_	_	_
95	was	be	VBD	_	_	_
96	calculated	calculate	VBN	_	_	_
97	and	and	CC	_	_	_
98	local	local	JJ	_	_	_
99	background	background	NN	_	_	_
100	was	be	VBD	_	_	_
101	subtracted	subtract	VBN	_	_	_
102	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	data	datum	NNS	_	_	_
3	normalization	normalization	NN	_	_	_
4	and	and	CC	_	_	_
5	selection	selection	NN	_	_	_
6	of	of	IN	_	_	_
7	fold-changed	fold-changed	JJ	_	_	_
8	genes	gene	NNS	_	_	_
9	were	be	VBD	_	_	_
10	performed	perform	VBN	_	_	_
11	using	use	VBG	_	_	_
12	GeneSpringGX	GeneSpringGX	NNP	_	_	_
13	7.3.1	7.3.1	CD	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Agilent	Agilent	NNP	_	_	_
16	Technology	Technology	NNP	_	_	_
17	,	,	,	_	_	_
18	USA	USA	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	Normalization	normalization	NN	_	_	_
2	for	for	IN	_	_	_
3	Agilent	Agilent	NNP	_	_	_
4	one-color	one-color	JJ	_	_	_
5	method	method	NN	_	_	_
6	was	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	,	,	,	_	_	_
9	which	which	WDT	_	_	_
10	is	be	VBZ	_	_	_
11	Data	Data	NNP	_	_	_
12	transformation	transformation	NN	_	_	_
13	:	:	:	_	_	_
14	Set	set	VB	_	_	_
15	measurements	measurement	NNS	_	_	_
16	less	less	JJR	_	_	_
17	than	than	IN	_	_	_
18	5.0	5.0	CD	_	_	_
19	to	to	TO	_	_	_
20	5.0	5.0	CD	_	_	_
21	and	and	CC	_	_	_
22	Per	per	IN	_	_	_
23	Chip	chip	NN	_	_	_
24	:	:	:	_	_	_
25	Normalize	normalize	VB	_	_	_
26	to	to	TO	_	_	_
27	50th	50th	JJ	_	_	_
28	percentage	percentage	NN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	using	use	VBG	_	_	_
7	TRIzol	trizol	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Invitrogen	invitrogen	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	When	when	WRB	_	_	_
13	E.	e.	FW	_	_	_
14	coli	coli	FW	_	_	_
15	cells	cell	NNS	_	_	_
16	were	be	VBD	_	_	_
17	cultivated	cultivate	VBN	_	_	_
18	to	to	TO	_	_	_
19	the	the	DT	_	_	_
20	exponential	exponential	JJ	_	_	_
21	growth	growth	NN	_	_	_
22	phase	phase	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	OD600	od600	NN	_	_	_
25	=	=	JJ	_	_	_
26	0.5	0.5	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	in	in	IN	_	_	_
29	Riesenberg	Riesenberg	NNP	_	_	_
30	medium	medium	NN	_	_	_
31	,	,	,	_	_	_
32	3	3	CD	_	_	_
33	or	or	CC	_	_	_
34	10	10	CD	_	_	_
35	mM	mm	NN	KWSUPP	_	_
36	heptanoic	heptanoic	JJ	_	_	_
37	acid	acid	NN	_	_	_
38	was	be	VBD	_	_	_
39	treated	treat	VBN	_	_	_
40	to	to	TO	_	_	_
41	BL21	bl21	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	DE3	de3	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	and	and	CC	_	_	_
46	K-12	k-12	NN	_	_	_
47	MG1655	mg1655	NN	_	_	_
48	,	,	,	_	_	_
49	respectively	respectively	RB	_	_	_
50	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	3	3	CD	_	_	_
3	h	h	NN	_	_	_
4	incubation	incubation	NN	_	_	_
5	,	,	,	_	_	_
6	the	the	DT	_	_	_
7	E.	e.	FW	_	_	_
8	coli	coli	FW	_	_	_
9	cells	cell	NNS	_	_	_
10	were	be	VBD	_	_	_
11	harvested	harvest	VBN	_	_	_
12	for	for	IN	_	_	_
13	transcriptome	transcriptome	NN	_	_	_
14	analysis	analysis	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	aspC	aspc	NN	GEN	_	_
17	KO	ko	NN	_	_	_
18	rep1	rep1	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	aspC	aspc	NN	GEN	_	_
21	KO	ko	NN	_	_	_
22	rep2	rep2	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	aspC	aspc	NN	GEN	_	_
25	KO	ko	NN	_	_	_
26	rep3	rep3	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Bacteria	bacterium	NNS	_	_	_
29	were	be	VBD	_	_	_
30	harvested	harvest	VBN	_	_	_
31	with	with	IN	_	_	_
32	0.5	0.5	CD	_	_	_
33	Vol	vol	NN	_	_	_
34	of	of	IN	_	_	_
35	5	5	CD	_	_	_
36	%	%	NN	_	_	_
37	phenol	phenol	NN	_	_	_
38	in	in	IN	_	_	_
39	ethanol	ethanol	NN	_	_	_
40	and	and	CC	_	_	_
41	frozen	freeze	VBN	_	_	_
42	at	at	IN	_	_	_
43	-80	-80	CD	_	_	_
44	C.	C.	NNP	_	_	_
45	Total	Total	NNP	_	_	_
46	RNA	rna	NN	_	_	_
47	was	be	VBD	_	_	_
48	extracted	extract	VBN	_	_	_
49	from	from	IN	_	_	_
50	frozen	frozen	JJ	_	_	_
51	cultures	culture	NNS	_	_	_
52	using	use	VBG	_	_	_
53	RNeasy	RNeasy	NNP	_	_	_
54	kit	kit	NN	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	Qiagen	qiagen	NN	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	cysA	cysa	NN	GEN	_	_
3	KO	ko	NN	_	_	_
4	rep1	rep1	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	cysA	cysa	NN	GEN	_	_
7	KO	ko	NN	_	_	_
8	rep2	rep2	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	cysA	cysa	NN	GEN	_	_
11	KO	ko	NN	_	_	_
12	rep3	rep3	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	cysG	cysg	NN	GEN	_	_
15	KO	ko	NN	_	_	_
16	LB	lb	NN	_	_	_
17	rep1	rep1	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	cysG	cysg	NN	GEN	_	_
20	KO	ko	NN	_	_	_
21	LB	lb	NN	_	_	_
22	rep2	rep2	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	cysH	cysh	NN	GEN	_	_
25	KO	ko	NN	_	_	_
26	LB	lb	NN	_	_	_
27	rep1	rep1	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	cysH	cysh	NN	GEN	_	_
30	KO	ko	NN	_	_	_
31	LB	lb	NN	_	_	_
32	rep2	rep2	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	dcd	dcd	NN	GEN	_	_
35	KO	KO	NNP	_	_	_
36	LB	LB	NNP	_	_	_
37	rep1	rep1	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	dcd	dcd	NN	GEN	_	_
40	KO	KO	NNP	_	_	_
41	LB	LB	NNP	_	_	_
42	rep2	rep2	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	dcd	dcd	NN	GEN	_	_
45	KO	ko	NN	_	_	_
46	M9	m9	NN	_	_	_
47	rep1	rep1	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	dcd	dcd	NN	GEN	_	_
50	KO	ko	NN	_	_	_
51	M9	m9	NN	_	_	_
52	rep2	rep2	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	entF	entf	NN	GEN	_	_
55	KO	ko	NN	_	_	_
56	rep1	rep1	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	entF	entf	NN	GEN	_	_
59	KO	ko	NN	_	_	_
60	rep2	rep2	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	entF	entf	NN	GEN	_	_
63	KO	ko	NN	_	_	_
64	rep3	rep3	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	Escherichia	escherichia	FW	Organism	_	_
67	coli	coli	FW	Organism	_	_
68	BW25113	bw25113	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	fadr	fadr	NN	_	_	_
71	KO	ko	NN	_	_	_
72	LB	lb	NN	_	_	_
73	rep1	rep1	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	fadr	fadr	NN	_	_	_
76	KO	ko	NN	_	_	_
77	LB	lb	NN	_	_	_
78	rep2	rep2	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	fadr	fadr	NN	_	_	_
81	KO	ko	NN	_	_	_
82	M9	m9	NN	_	_	_
83	rep1	rep1	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	fadr	fadr	NN	_	_	_
86	KO	ko	NN	_	_	_
87	M9	m9	NN	_	_	_
88	rep2	rep2	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
90	fepA	fepa	NN	GEN	_	_
91	KO	ko	NN	_	_	_
92	LB	lb	NN	_	_	_
93	rep1	rep1	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
95	fepA	fepa	NN	GEN	_	_
96	KO	ko	NN	_	_	_
97	LB	lb	NN	_	_	_
98	rep2	rep2	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
100	fepA	fepa	NN	GEN	_	_
101	KO	ko	NN	_	_	_
102	M9	m9	NN	_	_	_
103	rep1	rep1	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
105	fepA	fepa	NN	GEN	_	_
106	KO	ko	NN	_	_	_
107	M9	m9	NN	_	_	_
108	rep2	rep2	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	fliY	fliy	NN	_	_	_
111	KO	ko	NN	_	_	_
112	rep1	rep1	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	fliY	fliy	NN	_	_	_
115	KO	ko	NN	_	_	_
116	rep2	rep2	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	fliY	fliy	NN	_	_	_
119	KO	ko	NN	_	_	_
120	rep3	rep3	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	For	for	IN	_	_	_
123	RNA-Seq	rna-seq	NN	_	_	_
124	analysis	analysis	NN	_	_	_
125	,	,	,	_	_	_
126	the	the	DT	_	_	_
127	fastq	fastq	NN	_	_	_
128	file	file	NN	_	_	_
129	produced	produce	VBN	_	_	_
130	from	from	IN	_	_	_
131	the	the	DT	_	_	_
132	machine	machine	NN	_	_	_
133	was	be	VBD	_	_	_
134	demultiplexed	demultiplex	VBN	_	_	_
135	into	into	IN	_	_	_
136	a	a	DT	_	_	_
137	separate	separate	JJ	_	_	_
138	file	file	NN	_	_	_
139	for	for	IN	_	_	_
140	each	each	DT	_	_	_
141	sample	sample	NN	_	_	_
142	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	For	for	IN	_	_	_
3	the	the	DT	_	_	_
4	first	first	JJ	_	_	_
5	batch	batch	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	from	from	IN	_	_	_
8	WT	WT	NNP	_	_	_
9	_	_	NNP	_	_	_
10	LB	LB	NNP	_	_	_
11	_	_	SYM	_	_	_
12	1	1	CD	_	_	_
13	to	to	TO	_	_	_
14	lacA	lacA	NNP	GEN	_	_
15	_	_	NNP	_	_	_
16	M9	M9	NNP	_	_	_
17	_	_	SYM	_	_	_
18	2	2	LS	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	,	,	,	_	_	_
21	fresh	fresh	JJ	_	_	_
22	colonies	colony	NNS	_	_	_
23	of	of	IN	_	_	_
24	E.	e.	FW	_	_	_
25	coli	coli	FW	_	_	_
26	cells	cell	NNS	_	_	_
27	were	be	VBD	_	_	_
28	taken	take	VBN	_	_	_
29	and	and	CC	_	_	_
30	inoculated	inoculate	VBN	_	_	_
31	in	in	IN	_	_	_
32	1	1	CD	_	_	_
33	ml	ml	NN	_	_	_
34	LB	lb	NN	_	_	_
35	and	and	CC	_	_	_
36	grown	grow	VBN	_	_	_
37	for	for	IN	_	_	_
38	8	8	CD	_	_	_
39	h	h	NN	_	_	_
40	at	at	IN	_	_	_
41	37	37	CD	_	_	_
42	°C	°c	NN	_	_	_
43	.	.	.	_	_	_

1	20	20	CD	_	_	_
2	µL	µl	NN	_	_	_
3	of	of	IN	_	_	_
4	grown	grown	JJ	_	_	_
5	culture	culture	NN	_	_	_
6	was	be	VBD	_	_	_
7	taken	take	VBN	_	_	_
8	and	and	CC	_	_	_
9	transferred	transfer	VBN	_	_	_
10	to	to	TO	_	_	_
11	3	3	CD	_	_	_
12	ml	ml	NN	_	_	_
13	LB	lb	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	gabT	gabt	NN	GEN	_	_
16	KO	ko	NN	_	_	_
17	rep1	rep1	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	gabT	gabt	NN	GEN	_	_
20	KO	ko	NN	_	_	_
21	rep2	rep2	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	gabT	gabt	NN	GEN	_	_
24	KO	ko	NN	_	_	_
25	rep3	rep3	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	galE	gale	NN	GEN	_	_
28	KO	ko	NN	_	_	_
29	rep1	rep1	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	galE	gale	NN	GEN	_	_
32	KO	ko	NN	_	_	_
33	rep2	rep2	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	galE	gale	NN	GEN	_	_
36	KO	ko	NN	_	_	_
37	rep3	rep3	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	Genome	Genome	NNP	_	_	_
40	_	_	NNP	_	_	_
41	build	build	VB	_	_	_
42	:	:	:	_	_	_
43	RefSeq	RefSeq	NNP	_	_	_
44	NC	NC	NNP	_	_	_
45	_	_	SYM	_	_	_
46	000913.3	000913.3	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
48	genotype	genotype	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	HTSeq	htseq	NN	_	_	_
51	is	be	VBZ	_	_	_
52	used	use	VBN	_	_	_
53	to	to	TO	_	_	_
54	generate	generate	VB	_	_	_
55	expression	expression	NN	_	_	_
56	count	count	NN	_	_	_
57	for	for	IN	_	_	_
58	each	each	DT	_	_	_
59	gene	gene	NN	_	_	_
60	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Index	Index	NNP	_	_	_
3	sequences	sequence	NNS	_	_	_
4	accompanying	accompany	VBG	_	_	_
5	with	with	IN	_	_	_
6	reads	read	VBZ	_	_	_
7	were	be	VBD	_	_	_
8	compared	compare	VBN	_	_	_
9	with	with	IN	_	_	_
10	pre-designed	pre-designed	JJ	_	_	_
11	barcodes	barcode	NNS	_	_	_
12	,	,	,	_	_	_
13	allowing	allow	VBG	_	_	_
14	two	two	CD	_	_	_
15	base	base	NN	_	_	_
16	mismatches	mismatch	NNS	_	_	_
17	at	at	IN	_	_	_
18	most	most	JJS	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	kefB	kefb	NN	GEN	_	_
3	KO	ko	NN	_	_	_
4	rep1	rep1	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	kefB	kefb	NN	GEN	_	_
7	KO	ko	NN	_	_	_
8	rep2	rep2	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	kefB	kefb	NN	GEN	_	_
11	KO	ko	NN	_	_	_
12	rep3	rep3	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	khc	khc	NN	_	_	_
15	KO	ko	NN	_	_	_
16	rep1	rep1	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	khc	khc	NN	_	_	_
19	KO	ko	NN	_	_	_
20	rep2	rep2	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	khc	khc	NN	_	_	_
23	KO	ko	NN	_	_	_
24	rep3	rep3	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	lacA	laca	NN	GEN	_	_
27	KO	ko	NN	_	_	_
28	LB	lb	NN	_	_	_
29	rep1	rep1	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	lacA	laca	NN	GEN	_	_
32	KO	ko	NN	_	_	_
33	LB	lb	NN	_	_	_
34	rep2	rep2	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	lacA	laca	NN	GEN	_	_
37	KO	ko	NN	_	_	_
38	M9	m9	NN	_	_	_
39	rep1	rep1	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	lacA	laca	NN	GEN	_	_
42	KO	ko	NN	_	_	_
43	M9	m9	NN	_	_	_
44	rep2	rep2	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	Library	Library	NNP	_	_	_
47	constructed	construct	VBN	_	_	_
48	using	use	VBG	_	_	_
49	KAPA	KAPA	NNP	_	_	_
50	Kit	kit	NN	_	_	_
51	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	lplA	lpla	NN	GEN	_	_
3	KO	ko	NN	_	_	_
4	rep1	rep1	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	lplA	lpla	NN	GEN	_	_
7	KO	ko	NN	_	_	_
8	rep2	rep2	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	lplA	lpla	NN	GEN	_	_
11	KO	ko	NN	_	_	_
12	rep3	rep3	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	media	media	NNS	_	_	_
15	:	:	:	_	_	_
16	LB	lb	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	media	media	NNS	_	_	_
19	:	:	:	_	_	_
20	M9	m9	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	mgtA	mgta	NN	GEN	_	_
23	KO	ko	NN	_	_	_
24	rep1	rep1	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	mgtA	mgta	NN	GEN	_	_
27	KO	ko	NN	_	_	_
28	rep2	rep2	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	mgtA	mgta	NN	GEN	_	_
31	KO	ko	NN	_	_	_
32	rep3	rep3	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	mhpD	mhpd	NN	GEN	_	_
35	KO	ko	NN	_	_	_
36	rep1	rep1	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	mhpD	mhpd	NN	GEN	_	_
39	KO	ko	NN	_	_	_
40	rep2	rep2	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	mhpD	mhpd	NN	GEN	_	_
43	KO	ko	NN	_	_	_
44	rep3	rep3	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	Parent	Parent	NNP	_	_	_
47	LB	LB	NNP	_	_	_
48	rep1	rep1	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	Parent	Parent	NNP	_	_	_
51	LB	LB	NNP	_	_	_
52	rep2	rep2	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Parent	Parent	NNP	_	_	_
55	M9	M9	NNP	_	_	_
56	rep1	rep1	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Parent	Parent	NNP	_	_	_
59	M9	M9	NNP	_	_	_
60	rep2	rep2	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	ppk	ppk	NN	GEN	_	_
63	KO	KO	NNP	_	_	_
64	LB	LB	NNP	_	_	_
65	rep1	rep1	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	ppk	ppk	NN	GEN	_	_
68	KO	KO	NNP	_	_	_
69	LB	LB	NNP	_	_	_
70	rep2	rep2	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	ppk	ppk	NN	GEN	_	_
73	KO	ko	NN	_	_	_
74	M9	m9	NN	_	_	_
75	rep1	rep1	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	ppk	ppk	NN	GEN	_	_
78	KO	ko	NN	_	_	_
79	M9	m9	NN	_	_	_
80	rep2	rep2	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	putP	putp	NN	GEN	_	_
83	KO	ko	NN	_	_	_
84	rep1	rep1	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	putP	putp	NN	GEN	_	_
87	KO	ko	NN	_	_	_
88	rep2	rep2	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	putP	putp	NN	GEN	_	_
91	KO	ko	NN	_	_	_
92	rep3	rep3	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	rfbA	rfba	NN	GEN	_	_
95	KO	ko	NN	_	_	_
96	rep1	rep1	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	rfbA	rfba	NN	GEN	_	_
99	KO	ko	NN	_	_	_
100	rep2	rep2	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	rfbA	rfba	NN	GEN	_	_
103	KO	ko	NN	_	_	_
104	rep3	rep3	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	RNA-Seq	rna-seq	NN	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	sdhC	sdhc	NN	GEN	_	_
109	KO	ko	NN	_	_	_
110	rep1	rep1	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	sdhC	sdhc	NN	GEN	_	_
113	KO	ko	NN	_	_	_
114	rep2	rep2	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	sdhC	sdhc	NN	GEN	_	_
117	KO	ko	NN	_	_	_
118	rep3	rep3	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	strain	strain	NN	_	_	_
121	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
122	Supplementary	Supplementary	NNP	_	_	_
123	_	_	VBD	_	_	_
124	files	file	NNS	_	_	_
125	_	_	IN	_	_	_
126	format	format	NN	_	_	_
127	_	_	NN	_	_	_
128	and	and	CC	_	_	_
129	_	_	NN	_	_	_
130	content	content	NN	_	_	_
131	:	:	:	_	_	_
132	htcount	htcount	NN	_	_	_
133	:	:	:	_	_	_
134	expression	expression	NN	_	_	_
135	count	count	NN	_	_	_
136	for	for	IN	_	_	_
137	each	each	DT	_	_	_
138	gene	gene	NN	_	_	_
139	and	and	CC	_	_	_
140	its	its	PRP$	_	_	_
141	name	name	NN	_	_	_
142	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	low-quality	low-quality	NN	_	_	_
4	of	of	IN	_	_	_
5	raw	raw	JJ	_	_	_
6	reads	read	VBZ	_	_	_
7	were	be	VBD	_	_	_
8	trimmed	trim	VBN	_	_	_
9	using	use	VBG	_	_	_
10	Trimmomatic	trimmomatic	JJ	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	v0	v0	JJ	_	_	_
13	.30	.30	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	with	with	IN	_	_	_
16	default	default	NN	_	_	_
17	settings	setting	NNS	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	0.3	0.3	CD	_	_	_
5	%	%	NN	_	_	_
6	glucose	glucose	NN	SUPP	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	treatment	treatment	NN	_	_	_
9	:	:	:	_	_	_
10	0.4	0.4	CD	_	_	_
11	%	%	NN	_	_	_
12	glucose	glucose	NN	SUPP	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Trimmed	trim	VBD	_	_	_
15	reads	read	VBZ	_	_	_
16	were	be	VBD	_	_	_
17	aligned	align	VBN	_	_	_
18	on	on	IN	_	_	_
19	most	most	JJS	_	_	_
20	recent	recent	JJ	_	_	_
21	reference	reference	NN	_	_	_
22	genome	genome	NN	_	_	_
23	of	of	IN	_	_	_
24	Escherichia	escherichia	FW	Organism	_	_
25	coli	coli	FW	Organism	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	GenBank	genbank	NN	_	_	_
28	U00096	u00096	NN	_	_	_
29	.3	.3	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	by	by	IN	_	_	_
32	using	use	VBG	_	_	_
33	TopHat	TopHat	NNP	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	v2	v2	NN	_	_	_
36	.0.10	.0.10	CD	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	coupled	couple	VBN	_	_	_
39	with	with	IN	_	_	_
40	bowtie	bowtie	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	v1	v1	NN	_	_	_
43	.0.0	.0.0	CD	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	trpD	trpd	NN	GEN	_	_
3	KO	ko	NN	_	_	_
4	rep1	rep1	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	trpD	trpd	NN	GEN	_	_
7	KO	ko	NN	_	_	_
8	rep2	rep2	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	trpD	trpd	NN	GEN	_	_
11	KO	ko	NN	_	_	_
12	rep3	rep3	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	ugpC	ugpc	NN	GEN	_	_
15	KO	ko	NN	_	_	_
16	rep1	rep1	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	ugpC	ugpc	NN	GEN	_	_
19	KO	ko	NN	_	_	_
20	rep2	rep2	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	ugpC	ugpc	NN	GEN	_	_
23	KO	ko	NN	_	_	_
24	rep3	rep3	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
26	Whole	whole	JJ	_	_	_
27	cell	cell	NN	_	_	_
28	,	,	,	_	_	_
29	aspC	aspc	NN	GEN	_	_
30	KO	ko	NN	_	_	_
31	,	,	,	_	_	_
32	M9	m9	NN	_	_	_
33	and	and	CC	_	_	_
34	0.4	0.4	CD	_	_	_
35	%	%	NN	_	_	_
36	glucose	glucose	NN	SUPP	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Whole	whole	JJ	_	_	_
39	cell	cell	NN	_	_	_
40	,	,	,	_	_	_
41	cysA	cysa	NN	GEN	_	_
42	KO	ko	NN	_	_	_
43	,	,	,	_	_	_
44	M9	m9	NN	_	_	_
45	and	and	CC	_	_	_
46	0.4	0.4	CD	_	_	_
47	%	%	NN	_	_	_
48	glucose	glucose	NN	SUPP	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	Whole	whole	JJ	_	_	_
51	cell	cell	NN	_	_	_
52	,	,	,	_	_	_
53	cysG	cysg	NN	GEN	_	_
54	KO	ko	NN	_	_	_
55	,	,	,	_	_	_
56	LB	lb	NN	_	_	_
57	and	and	CC	_	_	_
58	0.3	0.3	CD	_	_	_
59	%	%	NN	_	_	_
60	glucose	glucose	NN	SUPP	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Whole	whole	JJ	_	_	_
63	cell	cell	NN	_	_	_
64	,	,	,	_	_	_
65	cysH	cysh	NN	GEN	_	_
66	KO	ko	NN	_	_	_
67	,	,	,	_	_	_
68	LB	lb	NN	_	_	_
69	and	and	CC	_	_	_
70	0.3	0.3	CD	_	_	_
71	%	%	NN	_	_	_
72	glucose	glucose	NN	SUPP	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	Whole	whole	JJ	_	_	_
75	cell	cell	NN	_	_	_
76	,	,	,	_	_	_
77	dcd	dcd	NN	GEN	_	_
78	KO	ko	NN	_	_	_
79	,	,	,	_	_	_
80	LB	lb	NN	_	_	_
81	and	and	CC	_	_	_
82	0.3	0.3	CD	_	_	_
83	%	%	NN	_	_	_
84	glucose	glucose	NN	SUPP	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	Whole	whole	JJ	_	_	_
87	cell	cell	NN	_	_	_
88	,	,	,	_	_	_
89	dcd	dcd	NN	GEN	_	_
90	KO	ko	NN	_	_	_
91	,	,	,	_	_	_
92	M9	m9	NN	_	_	_
93	and	and	CC	_	_	_
94	0.3	0.3	CD	_	_	_
95	%	%	NN	_	_	_
96	glucose	glucose	NN	SUPP	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	Whole	whole	JJ	_	_	_
99	cell	cell	NN	_	_	_
100	,	,	,	_	_	_
101	entF	entf	NN	GEN	_	_
102	KO	ko	NN	_	_	_
103	,	,	,	_	_	_
104	M9	m9	NN	_	_	_
105	and	and	CC	_	_	_
106	0.4	0.4	CD	_	_	_
107	%	%	NN	_	_	_
108	glucose	glucose	NN	SUPP	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	Whole	whole	JJ	_	_	_
111	cell	cell	NN	_	_	_
112	,	,	,	_	_	_
113	fadR	fadr	NN	GEN	_	_
114	KO	ko	NN	_	_	_
115	,	,	,	_	_	_
116	LB	lb	NN	_	_	_
117	and	and	CC	_	_	_
118	0.3	0.3	CD	_	_	_
119	%	%	NN	_	_	_
120	glucose	glucose	NN	SUPP	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	Whole	whole	JJ	_	_	_
123	cell	cell	NN	_	_	_
124	,	,	,	_	_	_
125	fadR	fadr	NN	GEN	_	_
126	KO	ko	NN	_	_	_
127	,	,	,	_	_	_
128	M9	m9	NN	_	_	_
129	and	and	CC	_	_	_
130	0.3	0.3	CD	_	_	_
131	%	%	NN	_	_	_
132	glucose	glucose	NN	SUPP	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	Whole	whole	JJ	_	_	_
135	cell	cell	NN	_	_	_
136	,	,	,	_	_	_
137	fepA	fepa	NN	GEN	_	_
138	KO	ko	NN	_	_	_
139	,	,	,	_	_	_
140	LB	lb	NN	_	_	_
141	and	and	CC	_	_	_
142	0.3	0.3	CD	_	_	_
143	%	%	NN	_	_	_
144	glucose	glucose	NN	SUPP	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	Whole	whole	JJ	_	_	_
147	cell	cell	NN	_	_	_
148	,	,	,	_	_	_
149	fepA	fepa	NN	GEN	_	_
150	KO	ko	NN	_	_	_
151	,	,	,	_	_	_
152	M9	m9	NN	_	_	_
153	and	and	CC	_	_	_
154	0.3	0.3	CD	_	_	_
155	%	%	NN	_	_	_
156	glucose	glucose	NN	SUPP	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	Whole	whole	JJ	_	_	_
159	cell	cell	NN	_	_	_
160	,	,	,	_	_	_
161	fliY	fliy	NN	_	_	_
162	KO	ko	NN	_	_	_
163	,	,	,	_	_	_
164	M9	m9	NN	_	_	_
165	and	and	CC	_	_	_
166	0.4	0.4	CD	_	_	_
167	%	%	NN	_	_	_
168	glucose	glucose	NN	SUPP	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	Whole	whole	JJ	_	_	_
171	cell	cell	NN	_	_	_
172	,	,	,	_	_	_
173	gabT	gabt	NN	GEN	_	_
174	KO	ko	NN	_	_	_
175	,	,	,	_	_	_
176	M9	m9	NN	_	_	_
177	and	and	CC	_	_	_
178	0.4	0.4	CD	_	_	_
179	%	%	NN	_	_	_
180	glucose	glucose	NN	SUPP	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	Whole	whole	JJ	_	_	_
183	cell	cell	NN	_	_	_
184	,	,	,	_	_	_
185	galE	gale	NN	GEN	_	_
186	KO	KO	NNP	_	_	_
187	,	,	,	_	_	_
188	M9	m9	NN	_	_	_
189	and	and	CC	_	_	_
190	0.4	0.4	CD	_	_	_
191	%	%	NN	_	_	_
192	glucose	glucose	NN	SUPP	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	Whole	whole	JJ	_	_	_
195	cell	cell	NN	_	_	_
196	,	,	,	_	_	_
197	kefB	kefb	NN	GEN	_	_
198	KO	ko	NN	_	_	_
199	,	,	,	_	_	_
200	M9	m9	NN	_	_	_
201	and	and	CC	_	_	_
202	0.4	0.4	CD	_	_	_
203	%	%	NN	_	_	_
204	glucose	glucose	NN	SUPP	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	Whole	whole	JJ	_	_	_
207	cell	cell	NN	_	_	_
208	,	,	,	_	_	_
209	khc	khc	NN	_	_	_
210	KO	ko	NN	_	_	_
211	,	,	,	_	_	_
212	M9	m9	NN	_	_	_
213	and	and	CC	_	_	_
214	0.4	0.4	CD	_	_	_
215	%	%	NN	_	_	_
216	glucose	glucose	NN	SUPP	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	Whole	whole	JJ	_	_	_
219	cell	cell	NN	_	_	_
220	,	,	,	_	_	_
221	lacA	laca	NN	GEN	_	_
222	KO	ko	NN	_	_	_
223	,	,	,	_	_	_
224	LB	lb	NN	_	_	_
225	and	and	CC	_	_	_
226	0.3	0.3	CD	_	_	_
227	%	%	NN	_	_	_
228	glucose	glucose	NN	SUPP	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
230	Whole	whole	JJ	_	_	_
231	cell	cell	NN	_	_	_
232	,	,	,	_	_	_
233	lacA	laca	NN	GEN	_	_
234	KO	ko	NN	_	_	_
235	,	,	,	_	_	_
236	M9	m9	NN	_	_	_
237	and	and	CC	_	_	_
238	0.3	0.3	CD	_	_	_
239	%	%	NN	_	_	_
240	glucose	glucose	NN	SUPP	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	Whole	whole	JJ	_	_	_
243	cell	cell	NN	_	_	_
244	,	,	,	_	_	_
245	lplA	lpla	NN	GEN	_	_
246	KO	ko	NN	_	_	_
247	,	,	,	_	_	_
248	M9	m9	NN	_	_	_
249	and	and	CC	_	_	_
250	0.4	0.4	CD	_	_	_
251	%	%	NN	_	_	_
252	glucose	glucose	NN	SUPP	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
254	Whole	whole	JJ	_	_	_
255	cell	cell	NN	_	_	_
256	,	,	,	_	_	_
257	mgtA	mgta	NN	GEN	_	_
258	KO	ko	NN	_	_	_
259	,	,	,	_	_	_
260	M9	m9	NN	_	_	_
261	and	and	CC	_	_	_
262	0.4	0.4	CD	_	_	_
263	%	%	NN	_	_	_
264	glucose	glucose	NN	SUPP	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	Whole	whole	JJ	_	_	_
267	cell	cell	NN	_	_	_
268	,	,	,	_	_	_
269	mhpD	mhpd	NN	GEN	_	_
270	KO	ko	NN	_	_	_
271	,	,	,	_	_	_
272	M9	m9	NN	_	_	_
273	and	and	CC	_	_	_
274	0.4	0.4	CD	_	_	_
275	%	%	NN	_	_	_
276	glucose	glucose	NN	SUPP	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	Whole	whole	JJ	_	_	_
279	cell	cell	NN	_	_	_
280	,	,	,	_	_	_
281	ppk	ppk	NN	GEN	_	_
282	KO	ko	NN	_	_	_
283	,	,	,	_	_	_
284	LB	lb	NN	_	_	_
285	and	and	CC	_	_	_
286	0.3	0.3	CD	_	_	_
287	%	%	NN	_	_	_
288	glucose	glucose	NN	SUPP	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
290	Whole	whole	JJ	_	_	_
291	cell	cell	NN	_	_	_
292	,	,	,	_	_	_
293	ppk	ppk	NN	GEN	_	_
294	KO	ko	NN	_	_	_
295	,	,	,	_	_	_
296	M9	m9	NN	_	_	_
297	and	and	CC	_	_	_
298	0.3	0.3	CD	_	_	_
299	%	%	NN	_	_	_
300	glucose	glucose	NN	SUPP	_	_
301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
302	Whole	whole	JJ	_	_	_
303	cell	cell	NN	_	_	_
304	,	,	,	_	_	_
305	putP	putp	NN	GEN	_	_
306	KO	ko	NN	_	_	_
307	,	,	,	_	_	_
308	M9	m9	NN	_	_	_
309	and	and	CC	_	_	_
310	0.4	0.4	CD	_	_	_
311	%	%	NN	_	_	_
312	glucose	glucose	NN	SUPP	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
314	Whole	whole	JJ	_	_	_
315	cell	cell	NN	_	_	_
316	,	,	,	_	_	_
317	rfbA	rfba	NN	GEN	_	_
318	KO	ko	NN	_	_	_
319	,	,	,	_	_	_
320	M9	m9	NN	_	_	_
321	and	and	CC	_	_	_
322	0.4	0.4	CD	_	_	_
323	%	%	NN	_	_	_
324	glucose	glucose	NN	SUPP	_	_
325	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
326	Whole	whole	JJ	_	_	_
327	cell	cell	NN	_	_	_
328	,	,	,	_	_	_
329	sdhC	sdhc	NN	GEN	_	_
330	KO	ko	NN	_	_	_
331	,	,	,	_	_	_
332	M9	m9	NN	_	_	_
333	and	and	CC	_	_	_
334	0.4	0.4	CD	_	_	_
335	%	%	NN	_	_	_
336	glucose	glucose	NN	SUPP	_	_
337	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
338	Whole	whole	JJ	_	_	_
339	cell	cell	NN	_	_	_
340	,	,	,	_	_	_
341	trpD	trpd	NN	GEN	_	_
342	KO	ko	NN	_	_	_
343	,	,	,	_	_	_
344	M9	m9	NN	_	_	_
345	and	and	CC	_	_	_
346	0.4	0.4	CD	_	_	_
347	%	%	NN	_	_	_
348	glucose	glucose	NN	SUPP	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	Whole	whole	JJ	_	_	_
351	cell	cell	NN	_	_	_
352	,	,	,	_	_	_
353	ugpC	ugpc	NN	GEN	_	_
354	KO	ko	NN	_	_	_
355	,	,	,	_	_	_
356	M9	m9	NN	_	_	_
357	and	and	CC	_	_	_
358	0.4	0.4	CD	_	_	_
359	%	%	NN	_	_	_
360	glucose	glucose	NN	SUPP	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
362	Whole	whole	JJ	_	_	_
363	cell	cell	NN	_	_	_
364	,	,	,	_	_	_
365	WT	WT	NNP	_	_	_
366	,	,	,	_	_	_
367	LB	LB	NNP	_	_	_
368	and	and	CC	_	_	_
369	0.3	0.3	CD	_	_	_
370	%	%	NN	_	_	_
371	glucose	glucose	NN	SUPP	_	_
372	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
373	Whole	whole	JJ	_	_	_
374	cell	cell	NN	_	_	_
375	,	,	,	_	_	_
376	WT	WT	NNP	_	_	_
377	,	,	,	_	_	_
378	M9	m9	NN	_	_	_
379	and	and	CC	_	_	_
380	0.3	0.3	CD	_	_	_
381	%	%	NN	_	_	_
382	glucose	glucose	NN	SUPP	_	_
383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
384	Whole	whole	JJ	_	_	_
385	cell	cell	NN	_	_	_
386	,	,	,	_	_	_
387	WT	WT	NNP	_	_	_
388	,	,	,	_	_	_
389	M9	m9	NN	_	_	_
390	and	and	CC	_	_	_
391	0.4	0.4	CD	_	_	_
392	%	%	NN	_	_	_
393	glucose	glucose	NN	SUPP	_	_
394	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
395	Whole	whole	JJ	_	_	_
396	cell	cell	NN	_	_	_
397	,	,	,	_	_	_
398	wzc	wzc	NN	GEN	_	_
399	KO	ko	NN	_	_	_
400	,	,	,	_	_	_
401	LB	lb	NN	_	_	_
402	and	and	CC	_	_	_
403	0.3	0.3	CD	_	_	_
404	%	%	NN	_	_	_
405	glucose	glucose	NN	SUPP	_	_
406	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
407	Whole	whole	JJ	_	_	_
408	cell	cell	NN	_	_	_
409	,	,	,	_	_	_
410	wzc	wzc	NN	GEN	_	_
411	KO	ko	NN	_	_	_
412	,	,	,	_	_	_
413	M9	m9	NN	_	_	_
414	and	and	CC	_	_	_
415	0.3	0.3	CD	_	_	_
416	%	%	NN	_	_	_
417	glucose	glucose	NN	SUPP	_	_
418	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
419	Whole	whole	JJ	_	_	_
420	cell	cell	NN	_	_	_
421	,	,	,	_	_	_
422	yghD	yghd	NN	GEN	_	_
423	KO	ko	NN	_	_	_
424	,	,	,	_	_	_
425	LB	lb	NN	_	_	_
426	and	and	CC	_	_	_
427	0.3	0.3	CD	_	_	_
428	%	%	NN	_	_	_
429	glucose	glucose	NN	SUPP	_	_
430	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
431	Whole	whole	JJ	_	_	_
432	cell	cell	NN	_	_	_
433	,	,	,	_	_	_
434	yghD	yghd	NN	GEN	_	_
435	KO	ko	NN	_	_	_
436	,	,	,	_	_	_
437	M9	m9	NN	_	_	_
438	and	and	CC	_	_	_
439	0.3	0.3	CD	_	_	_
440	%	%	NN	_	_	_
441	glucose	glucose	NN	SUPP	_	_
442	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
443	WT	wt	JJ	_	_	_
444	rep1	rep1	NN	_	_	_
445	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
446	WT	wt	JJ	_	_	_
447	rep2	rep2	NN	_	_	_
448	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
449	WT	wt	JJ	_	_	_
450	rep3	rep3	NN	_	_	_
451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
452	wzc	wzc	NN	GEN	_	_
453	KO	ko	NN	_	_	_
454	LB	lb	NN	_	_	_
455	rep1	rep1	NN	_	_	_
456	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
457	wzc	wzc	NN	GEN	_	_
458	KO	ko	NN	_	_	_
459	LB	lb	NN	_	_	_
460	rep2	rep2	NN	_	_	_
461	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
462	wzc	wzc	NN	GEN	_	_
463	KO	ko	NN	_	_	_
464	M9	m9	NN	_	_	_
465	rep1	rep1	NN	_	_	_
466	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
467	wzc	wzc	NN	GEN	_	_
468	KO	ko	NN	_	_	_
469	M9	m9	NN	_	_	_
470	rep2	rep2	NN	_	_	_
471	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
472	yghD	yghd	NN	GEN	_	_
473	KO	ko	NN	_	_	_
474	LB	lb	NN	_	_	_
475	rep1	rep1	NN	_	_	_
476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
477	yghD	yghd	NN	GEN	_	_
478	KO	ko	NN	_	_	_
479	LB	lb	NN	_	_	_
480	rep2	rep2	NN	_	_	_
481	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
482	yghD	yghd	NN	GEN	_	_
483	KO	ko	NN	_	_	_
484	M9	m9	NN	_	_	_
485	rep1	rep1	NN	_	_	_
486	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
487	yghD	yghd	NN	GEN	_	_
488	KO	ko	NN	_	_	_
489	M9	m9	NN	_	_	_
490	rep2	rep2	NN	_	_	_
491	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
492	5-azacytidine-treated	5-azacytidine-treated	JJ	_	_	_
493	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
494	Agilent	Agilent	NNP	_	_	_
495	Feature	Feature	NNP	_	_	_
496	Extract	extract	NN	_	_	_
497	software	software	NN	_	_	_
498	performed	perform	VBN	_	_	_
499	background	background	NN	_	_	_
500	normalization	normalization	NN	_	_	_
501	and	and	CC	_	_	_
502	LOWESS	lowess	NN	_	_	_
503	correction	correction	NN	_	_	_
504	for	for	IN	_	_	_
505	dye	dye	VB	_	_	_
506	bias	bias	NN	_	_	_
507	.	.	.	_	_	_

1	Non-E	non-e	NN	_	_	_
2	.	.	.	_	_	_

1	coli	coli	NN	_	_	_
2	K-12	k-12	NN	_	_	_
3	probes	probe	NNS	_	_	_
4	were	be	VBD	_	_	_
5	removed	remove	VBN	_	_	_
6	from	from	IN	_	_	_
7	the	the	DT	_	_	_
8	dataset	dataset	NN	_	_	_
9	,	,	,	_	_	_
10	as	as	IN	_	_	_
11	the	the	DT	_	_	_
12	BW25113	bw25113	NN	_	_	_
13	strain	strain	NN	_	_	_
14	is	be	VBZ	_	_	_
15	a	a	DT	_	_	_
16	K-12	k-12	NN	_	_	_
17	strain	strain	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	the	the	DT	_	_	_
7	absence	absence	NN	_	_	_
8	and	and	CC	_	_	_
9	presence	presence	NN	_	_	_
10	of	of	IN	_	_	_
11	0.005	0.005	CD	_	_	_
12	mg	mg	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	early	early	JJ	GrowthPhase	_	_
15	stationary	stationary	JJ	GrowthPhase	_	_
16	phase	phase	NN	GrowthPhase	_	_
17	1	1	CD	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	early	early	JJ	GrowthPhase	_	_
20	stationary	stationary	JJ	GrowthPhase	_	_
21	phase	phase	NN	GrowthPhase	_	_
22	2	2	CD	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	early	early	JJ	GrowthPhase	_	_
25	stationary	stationary	JJ	GrowthPhase	_	_
26	phase	phase	NN	GrowthPhase	_	_
27	3	3	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	early	early	JJ	GrowthPhase	_	_
30	stationary	stationary	JJ	GrowthPhase	_	_
31	phase	phase	NN	GrowthPhase	_	_
32	4	4	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	early	early	JJ	GrowthPhase	_	_
35	stationary	stationary	JJ	GrowthPhase	_	_
36	phase	phase	NN	GrowthPhase	_	_
37	5	5	CD	_	_	_
38	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
39	Escherichia	escherichia	FW	Organism	_	_
40	coli	coli	FW	Organism	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	Escherichia	escherichia	FW	Organism	_	_
43	coli	coli	FW	Organism	_	_
44	cells	cell	NNS	_	_	_
45	were	be	VBD	_	_	_
46	grown	grow	VBN	_	_	_
47	in	in	IN	_	_	_
48	LB	lb	NN	_	_	_
49	at	at	IN	_	_	_
50	37oC	37oc	NN	_	_	_
51	with	with	IN	_	_	_
52	shaking	shake	VBG	_	_	_
53	at	at	IN	_	_	_
54	250	250	CD	_	_	_
55	RPM	rpm	NNS	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
57	log	log	VBP	_	_	_
58	phase	phase	NN	_	_	_
59	1	1	CD	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	log	log	NN	_	_	_
62	phase	phase	NN	_	_	_
63	2	2	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
65	log	log	VBP	_	_	_
66	phase	phase	NN	_	_	_
67	3	3	CD	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	log	log	NN	_	_	_
70	phase	phase	NN	_	_	_
71	4	4	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
73	log	log	VBP	_	_	_
74	phase	phase	NN	_	_	_
75	5	5	CD	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	phase	phase	NN	_	_	_
78	:	:	:	_	_	_
79	early	early	JJ	GrowthPhase	_	_
80	stationary	stationary	JJ	GrowthPhase	_	_
81	phase	phase	NN	GrowthPhase	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	phase	phase	NN	_	_	_
84	:	:	:	_	_	_
85	log	log	NN	_	_	_
86	phase	phase	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	strain	strain	NN	_	_	_
89	:	:	:	_	_	_
90	BW25113	bw25113	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	Total	total	JJ	_	_	_
93	RNA	rna	NN	_	_	_
94	was	be	VBD	_	_	_
95	isolated	isolate	VBN	_	_	_
96	with	with	IN	_	_	_
97	the	the	DT	_	_	_
98	MasterPure	masterpure	NN	_	_	_
99	RNA	rna	NN	_	_	_
100	Isolation	isolation	NN	_	_	_
101	Kit	kit	NN	_	_	_
102	-LRB-	-lrb-	-LRB-	_	_	_
103	Epicentre	Epicentre	NNP	_	_	_
104	-RRB-	-rrb-	-RRB-	_	_	_
105	,	,	,	_	_	_
106	enriched	enriched	JJ	_	_	_
107	for	for	IN	_	_	_
108	mRNA	mrna	NN	_	_	_
109	using	use	VBG	_	_	_
110	the	the	DT	_	_	_
111	mRNA	mrna	NN	_	_	_
112	Prokaryotic	prokaryotic	JJ	_	_	_
113	mRNA	mrna	NN	_	_	_
114	Isolation	isolation	NN	_	_	_
115	Kit	kit	NN	_	_	_
116	-LRB-	-lrb-	-LRB-	_	_	_
117	Epicentre	Epicentre	NNP	_	_	_
118	-RRB-	-rrb-	-RRB-	_	_	_
119	,	,	,	_	_	_
120	and	and	CC	_	_	_
121	polyadenylated	polyadenylated	JJ	_	_	_
122	with	with	IN	_	_	_
123	kit	kit	NN	_	_	_
124	all	all	DT	_	_	_
125	based	base	VBN	_	_	_
126	on	on	IN	_	_	_
127	the	the	DT	_	_	_
128	manufacturer	manufacturer	NN	_	_	_
129	's	's	POS	_	_	_
130	instructions	instruction	NNS	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
132	untreated	untreated	JJ	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	150	150	CD	_	_	_
135	minutes	minute	NNS	_	_	_
136	growth	growth	NN	_	_	_
137	in	in	IN	_	_	_
138	LB	lb	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	240	240	CD	_	_	_
141	minutes	minute	NNS	_	_	_
142	growth	growth	NN	_	_	_
143	in	in	IN	_	_	_
144	LB	lb	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	360	360	CD	_	_	_
147	minutes	minute	NNS	_	_	_
148	growth	growth	NN	_	_	_
149	in	in	IN	_	_	_
150	LB	LB	NNP	_	_	_
151	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
152	90	90	CD	_	_	_
153	minutes	minute	NNS	_	_	_
154	growth	growth	NN	_	_	_
155	in	in	IN	_	_	_
156	LB	LB	NNP	_	_	_
157	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
158	Cells	cell	NNS	_	_	_
159	were	be	VBD	_	_	_
160	grown	grow	VBN	_	_	_
161	in	in	IN	_	_	_
162	LB	lb	NN	_	_	_
163	at	at	IN	_	_	_
164	37	37	CD	_	_	_
165	degrees	degree	NNS	_	_	_
166	celsius	celsius	NN	_	_	_
167	with	with	IN	_	_	_
168	shaking	shake	VBG	_	_	_
169	for	for	IN	_	_	_
170	150	150	CD	_	_	_
171	minutes	minute	NNS	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	Cells	cell	NNS	_	_	_
174	were	be	VBD	_	_	_
175	grown	grow	VBN	_	_	_
176	in	in	IN	_	_	_
177	LB	lb	NN	_	_	_
178	at	at	IN	_	_	_
179	37	37	CD	_	_	_
180	degrees	degree	NNS	_	_	_
181	celsius	celsius	NN	_	_	_
182	with	with	IN	_	_	_
183	shaking	shake	VBG	_	_	_
184	for	for	IN	_	_	_
185	240	240	CD	_	_	_
186	minutes	minute	NNS	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	Cells	cell	NNS	_	_	_
189	were	be	VBD	_	_	_
190	grown	grow	VBN	_	_	_
191	in	in	IN	_	_	_
192	LB	lb	NN	_	_	_
193	at	at	IN	_	_	_
194	37	37	CD	_	_	_
195	degrees	degree	NNS	_	_	_
196	celsius	celsius	NN	_	_	_
197	with	with	IN	_	_	_
198	shaking	shake	VBG	_	_	_
199	for	for	IN	_	_	_
200	360	360	CD	_	_	_
201	minutes	minute	NNS	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	Cells	cell	NNS	_	_	_
204	were	be	VBD	_	_	_
205	grown	grow	VBN	_	_	_
206	in	in	IN	_	_	_
207	LB	lb	NN	_	_	_
208	at	at	IN	_	_	_
209	37	37	CD	_	_	_
210	degrees	degree	NNS	_	_	_
211	celsius	celsius	NN	_	_	_
212	with	with	IN	_	_	_
213	shaking	shake	VBG	_	_	_
214	for	for	IN	_	_	_
215	90	90	CD	_	_	_
216	minutes	minute	NNS	_	_	_
217	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
218	Escherichia	escherichia	FW	Organism	_	_
219	coli	coli	FW	Organism	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	Escherichia	escherichia	FW	Organism	_	_
222	coli	coli	FW	Organism	_	_
223	MG1655	mg1655	NN	_	_	_
224	fis	fis	NN	GEN	_	_
225	:	:	:	_	_	_
226	:	:	:	_	_	_
227	kan	kan	NN	_	_	_
228	grown	grow	VBN	_	_	_
229	150	150	CD	_	_	_
230	minutes	minute	NNS	_	_	_
231	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
232	Escherichia	escherichia	FW	Organism	_	_
233	coli	coli	FW	Organism	_	_
234	MG1655	mg1655	NN	_	_	_
235	fis	fis	NN	GEN	_	_
236	:	:	:	_	_	_
237	:	:	:	_	_	_
238	kan	kan	NN	_	_	_
239	grown	grow	VBN	_	_	_
240	240	240	CD	_	_	_
241	minutes	minute	NNS	_	_	_
242	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
243	Escherichia	escherichia	FW	Organism	_	_
244	coli	coli	FW	Organism	_	_
245	MG1655	mg1655	NN	_	_	_
246	fis	fis	NN	GEN	_	_
247	:	:	:	_	_	_
248	:	:	:	_	_	_
249	kan	kan	NN	_	_	_
250	grown	grow	VBN	_	_	_
251	360	360	CD	_	_	_
252	minutes	minute	NNS	_	_	_
253	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
254	Escherichia	escherichia	FW	Organism	_	_
255	coli	coli	FW	Organism	_	_
256	MG1655	mg1655	NN	_	_	_
257	fis	fis	NN	GEN	_	_
258	:	:	:	_	_	_
259	:	:	:	_	_	_
260	kan	kan	NN	_	_	_
261	grown	grow	VBN	_	_	_
262	90	90	CD	_	_	_
263	minutes	minute	NNS	_	_	_
264	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
265	fis	fis	NN	GEN	_	_
266	150	150	CD	_	_	_
267	minutes	minute	NNS	_	_	_
268	growth	growth	NN	_	_	_
269	rep1	rep1	NN	_	_	_
270	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
271	fis	fi	VBZ	GEN	_	_
272	150	150	CD	_	_	_
273	minutes	minute	NNS	_	_	_
274	growth	growth	NN	_	_	_
275	rep2	rep2	NN	_	_	_
276	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
277	fis	fi	VBZ	GEN	_	_
278	150	150	CD	_	_	_
279	minutes	minute	NNS	_	_	_
280	growth	growth	NN	_	_	_
281	rep3	rep3	NN	_	_	_
282	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
283	fis	fi	VBZ	GEN	_	_
284	240	240	CD	_	_	_
285	minutes	minute	NNS	_	_	_
286	growth	growth	NN	_	_	_
287	rep1	rep1	NN	_	_	_
288	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
289	fis	fi	VBZ	GEN	_	_
290	240	240	CD	_	_	_
291	minutes	minute	NNS	_	_	_
292	growth	growth	NN	_	_	_
293	rep2	rep2	NN	_	_	_
294	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
295	fis	fi	VBZ	GEN	_	_
296	240	240	CD	_	_	_
297	minutes	minute	NNS	_	_	_
298	growth	growth	NN	_	_	_
299	rep3	rep3	NN	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
301	fis	fi	VBZ	GEN	_	_
302	360	360	CD	_	_	_
303	minutes	minute	NNS	_	_	_
304	growth	growth	NN	_	_	_
305	rep1	rep1	NN	_	_	_
306	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
307	fis	fi	VBZ	GEN	_	_
308	360	360	CD	_	_	_
309	minutes	minute	NNS	_	_	_
310	growth	growth	NN	_	_	_
311	rep2	rep2	NN	_	_	_
312	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
313	fis	fi	VBZ	GEN	_	_
314	360	360	CD	_	_	_
315	minutes	minute	NNS	_	_	_
316	growth	growth	NN	_	_	_
317	rep3	rep3	NN	_	_	_
318	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
319	fis	fi	VBZ	GEN	_	_
320	90	90	CD	_	_	_
321	minutes	minute	NNS	_	_	_
322	growth	growth	NN	_	_	_
323	rep1	rep1	NN	_	_	_
324	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
325	fis	fi	VBZ	GEN	_	_
326	90	90	CD	_	_	_
327	minutes	minute	NNS	_	_	_
328	growth	growth	NN	_	_	_
329	rep2	rep2	NN	_	_	_
330	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
331	fis	fi	VBZ	GEN	_	_
332	90	90	CD	_	_	_
333	minutes	minute	NNS	_	_	_
334	growth	growth	NN	_	_	_
335	rep3	rep3	NN	_	_	_
336	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
337	fis	fi	VBZ	GEN	_	_
338	Escherichia	escherichia	FW	Organism	_	_
339	coli	coli	FW	Organism	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
341	MasterPure	masterpure	NN	_	_	_
342	RNA	rna	NN	_	_	_
343	purification	purification	NN	_	_	_
344	Kit	kit	NN	_	_	_
345	per	per	IN	_	_	_
346	manufacturers	manufacturer	NNS	_	_	_
347	protocol	protocol	NN	_	_	_
348	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
349	Saturated	Saturated	NNP	_	_	_
350	E.	E.	NNP	_	_	_
351	coli	coli	NN	_	_	_
352	cultures	culture	NNS	_	_	_
353	were	be	VBD	_	_	_
354	diluted	dilute	VBN	_	_	_
355	in	in	IN	_	_	_
356	LB	LB	NNP	_	_	_
357	toan	toan	NN	_	_	_
358	OD.of	od.of	NN	_	_	_
359	0.05	0.05	CD	_	_	_
360	OD600	od600	NN	_	_	_
361	,	,	,	_	_	_
362	grown	grow	VBN	_	_	_
363	at	at	IN	_	_	_
364	37	37	CD	_	_	_
365	degrees	degree	NNS	_	_	_
366	Celsius	Celsius	NNP	_	_	_
367	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
368	The	the	DT	_	_	_
369	data	datum	NNS	_	_	_
370	were	be	VBD	_	_	_
371	analyzed	analyze	VBN	_	_	_
372	with	with	IN	_	_	_
373	Microarray	Microarray	NNP	_	_	_
374	Suite	Suite	NNP	_	_	_
375	version	version	NN	_	_	_
376	5.0	5.0	CD	_	_	_
377	-LRB-	-lrb-	-LRB-	_	_	_
378	MAS	mas	NN	_	_	_
379	5.0	5.0	CD	_	_	_
380	-RRB-	-rrb-	-RRB-	_	_	_
381	using	use	VBG	_	_	_
382	Affymetrix	Affymetrix	NNP	_	_	_
383	default	default	NN	_	_	_
384	analysis	analysis	NN	_	_	_
385	settings	setting	NNS	_	_	_
386	and	and	CC	_	_	_
387	global	global	JJ	_	_	_
388	scaling	scaling	NN	_	_	_
389	as	as	IN	_	_	_
390	normalization	normalization	NN	_	_	_
391	method	method	NN	_	_	_
392	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	analyzed	analyze	VBN	_	_	_
6	with	with	IN	_	_	_
7	Microarray	Microarray	NNP	_	_	_
8	Suite	Suite	NNP	_	_	_
9	version	version	NN	_	_	_
10	5.0	5.0	CD	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	MAS	mas	NN	_	_	_
13	5.0	5.0	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	using	use	VBG	_	_	_
16	Affymetrix	Affymetrix	NNP	_	_	_
17	default	default	NN	_	_	_
18	analysis	analysis	NN	_	_	_
19	settings	setting	NNS	_	_	_
20	and	and	CC	_	_	_
21	global	global	JJ	_	_	_
22	scaling	scaling	NN	_	_	_
23	as	as	IN	_	_	_
24	normalization	normalization	NN	_	_	_
25	method	method	NN	_	_	_
26	.	.	.	_	_	_

1	Data	datum	NNS	_	_	_
2	from	from	IN	_	_	_
3	this	this	DT	_	_	_
4	sample	sample	NN	_	_	_
5	were	be	VBD	_	_	_
6	collected	collect	VBN	_	_	_
7	using	use	VBG	_	_	_
8	Affy	Affy	NNP	_	_	_
9	Ecoli	Ecoli	NNP	_	_	_
10	anti-sense	anti-sense	JJ	_	_	_
11	chip	chip	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	2001	2001	CD	_	_	_
14	;	;	:	_	_	_
15	platform	platform	NN	_	_	_
16	ID	id	NN	_	_	_
17	GPL4940	gpl4940	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	but	but	CC	_	_	_
21	because	because	IN	_	_	_
22	the	the	DT	_	_	_
23	analysis	analysis	NN	_	_	_
24	software	software	NN	_	_	_
25	failed	fail	VBD	_	_	_
26	to	to	TO	_	_	_
27	recognize	recognize	VB	_	_	_
28	the	the	DT	_	_	_
29	correct	correct	JJ	_	_	_
30	platform	platform	NN	_	_	_
31	,	,	,	_	_	_
32	we	we	PRP	_	_	_
33	reformatted	reformat	VBD	_	_	_
34	the	the	DT	_	_	_
35	data	datum	NNS	_	_	_
36	to	to	TO	_	_	_
37	match	match	VB	_	_	_
38	the	the	DT	_	_	_
39	newer	newer	JJR	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	and	and	CC	_	_	_
42	mostly	mostly	RB	_	_	_
43	equivalent	equivalent	JJ	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	platform	platform	NN	_	_	_
46	GPL199	gpl199	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	Affy	Affy	NNP	_	_	_
49	Ecoli	Ecoli	NNP	_	_	_
50	anti-sense	anti-sense	JJ	_	_	_
51	chip	chip	NN	_	_	_
52	version	version	NN	_	_	_
53	2	2	CD	_	_	_
54	,	,	,	_	_	_
55	2002	2002	CD	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	.	.	.	_	_	_

1	Because	because	IN	_	_	_
2	,	,	,	_	_	_
3	however	however	RB	_	_	_
4	,	,	,	_	_	_
5	not	not	RB	_	_	_
6	all	all	DT	_	_	_
7	of	of	IN	_	_	_
8	the	the	DT	_	_	_
9	probes	probe	NNS	_	_	_
10	on	on	IN	_	_	_
11	the	the	DT	_	_	_
12	new	new	JJ	_	_	_
13	platform	platform	NN	_	_	_
14	were	be	VBD	_	_	_
15	present	present	JJ	_	_	_
16	on	on	IN	_	_	_
17	the	the	DT	_	_	_
18	old	old	JJ	_	_	_
19	platform	platform	NN	_	_	_
20	,	,	,	_	_	_
21	data	datum	NNS	_	_	_
22	for	for	IN	_	_	_
23	some	some	DT	_	_	_
24	probes	probe	NNS	_	_	_
25	were	be	VBD	_	_	_
26	unavailable	unavailable	JJ	_	_	_
27	and	and	CC	_	_	_
28	labeled	label	VBN	_	_	_
29	in	in	IN	_	_	_
30	the	the	DT	_	_	_
31	`	`	``	_	_	_
32	remapped	remapped	NN	_	_	_
33	'	'	''	_	_	_
34	dataset	dataset	NN	_	_	_
35	as	as	IN	_	_	_
36	`	`	``	_	_	_
37	NULL	NULL	NNP	_	_	_
38	'	'	''	_	_	_
39	to	to	TO	_	_	_
40	indicate	indicate	VB	_	_	_
41	they	they	PRP	_	_	_
42	were	be	VBD	_	_	_
43	missing	miss	VBG	_	_	_
44	.	.	.	_	_	_

1	While	while	IN	_	_	_
2	the	the	DT	_	_	_
3	following	follow	VBG	_	_	_
4	data	datum	NNS	_	_	_
5	are	be	VBP	_	_	_
6	therefore	therefore	RB	_	_	_
7	formatted	format	VBN	_	_	_
8	using	use	VBG	_	_	_
9	ID	ID	NNP	_	_	_
10	_	_	SYM	_	_	_
11	REFs	ref	NNS	_	_	_
12	that	that	WDT	_	_	_
13	match	match	VBP	_	_	_
14	GPL199	gpl199	NN	_	_	_
15	,	,	,	_	_	_
16	the	the	DT	_	_	_
17	CEL	CEL	NNP	_	_	_
18	file	file	NN	_	_	_
19	contains	contain	VBZ	_	_	_
20	the	the	DT	_	_	_
21	raw	raw	JJ	_	_	_
22	data	data	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	not	not	RB	_	_	_
25	`	`	``	_	_	_
26	remapped	remap	VBN	_	_	_
27	'	'	''	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	and	and	CC	_	_	_
30	thus	thus	RB	_	_	_
31	corresponds	correspond	VBZ	_	_	_
32	to	to	TO	_	_	_
33	the	the	DT	_	_	_
34	actual	actual	JJ	_	_	_
35	array	array	NN	_	_	_
36	used	use	VBN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	GPL4940	gpl4940	NN	_	_	_
39	,	,	,	_	_	_
40	Ecoli	ecoli	JJ	_	_	_
41	antisense	antisense	JJ	_	_	_
42	chip	chip	NN	_	_	_
43	,	,	,	_	_	_
44	2001	2001	CD	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	150	150	CD	_	_	_
3	minutes	minute	NNS	_	_	_
4	growth	growth	NN	_	_	_
5	in	in	IN	_	_	_
6	LB	lb	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	240	240	CD	_	_	_
9	minutes	minute	NNS	_	_	_
10	growth	growth	NN	_	_	_
11	in	in	IN	_	_	_
12	LB	lb	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	360	360	CD	_	_	_
15	minutes	minute	NNS	_	_	_
16	growth	growth	NN	_	_	_
17	in	in	IN	_	_	_
18	LB	LB	NNP	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	90	90	CD	_	_	_
21	minutes	minute	NNS	_	_	_
22	growth	growth	NN	_	_	_
23	in	in	IN	_	_	_
24	LB	LB	NNP	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	Cells	cell	NNS	_	_	_
27	were	be	VBD	_	_	_
28	grown	grow	VBN	_	_	_
29	in	in	IN	_	_	_
30	LB	lb	NN	_	_	_
31	at	at	IN	_	_	_
32	37	37	CD	_	_	_
33	degrees	degree	NNS	_	_	_
34	celsius	celsius	NN	_	_	_
35	with	with	IN	_	_	_
36	shaking	shake	VBG	_	_	_
37	for	for	IN	_	_	_
38	150	150	CD	_	_	_
39	minutes	minute	NNS	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	Cells	cell	NNS	_	_	_
42	were	be	VBD	_	_	_
43	grown	grow	VBN	_	_	_
44	in	in	IN	_	_	_
45	LB	lb	NN	_	_	_
46	at	at	IN	_	_	_
47	37	37	CD	_	_	_
48	degrees	degree	NNS	_	_	_
49	celsius	celsius	NN	_	_	_
50	with	with	IN	_	_	_
51	shaking	shake	VBG	_	_	_
52	for	for	IN	_	_	_
53	240	240	CD	_	_	_
54	minutes	minute	NNS	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	Cells	cell	NNS	_	_	_
57	were	be	VBD	_	_	_
58	grown	grow	VBN	_	_	_
59	in	in	IN	_	_	_
60	LB	lb	NN	_	_	_
61	at	at	IN	_	_	_
62	37	37	CD	_	_	_
63	degrees	degree	NNS	_	_	_
64	celsius	celsius	NN	_	_	_
65	with	with	IN	_	_	_
66	shaking	shake	VBG	_	_	_
67	for	for	IN	_	_	_
68	360	360	CD	_	_	_
69	minutes	minute	NNS	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	Cells	cell	NNS	_	_	_
72	were	be	VBD	_	_	_
73	grown	grow	VBN	_	_	_
74	in	in	IN	_	_	_
75	LB	lb	NN	_	_	_
76	at	at	IN	_	_	_
77	37	37	CD	_	_	_
78	degrees	degree	NNS	_	_	_
79	celsius	celsius	NN	_	_	_
80	with	with	IN	_	_	_
81	shaking	shake	VBG	_	_	_
82	for	for	IN	_	_	_
83	90	90	CD	_	_	_
84	minutes	minute	NNS	_	_	_
85	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
86	Escherichia	escherichia	FW	Organism	_	_
87	coli	coli	FW	Organism	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	Escherichia	escherichia	FW	Organism	_	_
90	coli	coli	FW	Organism	_	_
91	MG1655	mg1655	NN	_	_	_
92	wt	wt	JJ	_	_	_
93	grown	grown	JJ	_	_	_
94	150	150	CD	_	_	_
95	minutes	minute	NNS	_	_	_
96	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
97	Escherichia	escherichia	FW	Organism	_	_
98	coli	coli	FW	Organism	_	_
99	MG1655	mg1655	NN	_	_	_
100	wt	wt	JJ	_	_	_
101	grown	grown	JJ	_	_	_
102	240	240	CD	_	_	_
103	minutes	minute	NNS	_	_	_
104	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
105	Escherichia	escherichia	FW	Organism	_	_
106	coli	coli	FW	Organism	_	_
107	MG1655	mg1655	NN	_	_	_
108	wt	wt	JJ	_	_	_
109	grown	grown	JJ	_	_	_
110	360	360	CD	_	_	_
111	minutes	minute	NNS	_	_	_
112	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
113	Escherichia	escherichia	FW	Organism	_	_
114	coli	coli	FW	Organism	_	_
115	MG1655	mg1655	NN	_	_	_
116	wt	wt	JJ	_	_	_
117	grown	grown	JJ	_	_	_
118	90	90	CD	_	_	_
119	minutes	minute	NNS	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	MasterPure	masterpure	NN	_	_	_
122	RNA	rna	NN	_	_	_
123	purification	purification	NN	_	_	_
124	Kit	kit	NN	_	_	_
125	per	per	IN	_	_	_
126	manufacturers	manufacturer	NNS	_	_	_
127	protocol	protocol	NN	_	_	_
128	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
129	Saturated	Saturated	NNP	_	_	_
130	E.	E.	NNP	_	_	_
131	coli	coli	NN	_	_	_
132	cultures	culture	NNS	_	_	_
133	were	be	VBD	_	_	_
134	diluted	dilute	VBN	_	_	_
135	in	in	IN	_	_	_
136	LB	lb	NN	_	_	_
137	to	to	TO	_	_	_
138	an	a	DT	_	_	_
139	OD.of	od.of	JJ	_	_	_
140	0.05	0.05	CD	_	_	_
141	OD600	od600	NN	_	_	_
142	,	,	,	_	_	_
143	grown	grow	VBN	_	_	_
144	at	at	IN	_	_	_
145	37	37	CD	_	_	_
146	degrees	degree	NNS	_	_	_
147	Celsius	Celsius	NNP	_	_	_
148	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
149	Saturated	Saturated	NNP	_	_	_
150	E.	E.	NNP	_	_	_
151	coli	coli	NN	_	_	_
152	cultures	culture	NNS	_	_	_
153	were	be	VBD	_	_	_
154	diluted	dilute	VBN	_	_	_
155	in	in	IN	_	_	_
156	LB	LB	NNP	_	_	_
157	toan	toan	NN	_	_	_
158	OD.of	od.of	NN	_	_	_
159	0.05	0.05	CD	_	_	_
160	OD600	od600	NN	_	_	_
161	,	,	,	_	_	_
162	grown	grow	VBN	_	_	_
163	at	at	IN	_	_	_
164	37	37	CD	_	_	_
165	degrees	degree	NNS	_	_	_
166	Celsius	Celsius	NNP	_	_	_
167	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
168	The	the	DT	_	_	_
169	data	datum	NNS	_	_	_
170	were	be	VBD	_	_	_
171	analyzed	analyze	VBN	_	_	_
172	with	with	IN	_	_	_
173	Microarray	Microarray	NNP	_	_	_
174	Suite	Suite	NNP	_	_	_
175	version	version	NN	_	_	_
176	5.0	5.0	CD	_	_	_
177	-LRB-	-lrb-	-LRB-	_	_	_
178	MAS	mas	NN	_	_	_
179	5.0	5.0	CD	_	_	_
180	-RRB-	-rrb-	-RRB-	_	_	_
181	using	use	VBG	_	_	_
182	Affymetrix	Affymetrix	NNP	_	_	_
183	default	default	NN	_	_	_
184	analysis	analysis	NN	_	_	_
185	settings	setting	NNS	_	_	_
186	and	and	CC	_	_	_
187	global	global	JJ	_	_	_
188	scaling	scaling	NN	_	_	_
189	as	as	IN	_	_	_
190	normalization	normalization	NN	_	_	_
191	method	method	NN	_	_	_
192	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	data	datum	NNS	_	_	_
4	were	be	VBD	_	_	_
5	analyzed	analyze	VBN	_	_	_
6	with	with	IN	_	_	_
7	Microarray	Microarray	NNP	_	_	_
8	Suite	Suite	NNP	_	_	_
9	version	version	NN	_	_	_
10	5.0	5.0	CD	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	MAS	mas	NN	_	_	_
13	5.0	5.0	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	using	use	VBG	_	_	_
16	Affymetrix	Affymetrix	NNP	_	_	_
17	default	default	NN	_	_	_
18	analysis	analysis	NN	_	_	_
19	settings	setting	NNS	_	_	_
20	and	and	CC	_	_	_
21	global	global	JJ	_	_	_
22	scaling	scaling	NN	_	_	_
23	as	as	IN	_	_	_
24	normalization	normalization	NN	_	_	_
25	method	method	NN	_	_	_
26	.	.	.	_	_	_

1	Data	datum	NNS	_	_	_
2	from	from	IN	_	_	_
3	this	this	DT	_	_	_
4	sample	sample	NN	_	_	_
5	were	be	VBD	_	_	_
6	collected	collect	VBN	_	_	_
7	using	use	VBG	_	_	_
8	Affy	Affy	NNP	_	_	_
9	Ecoli	Ecoli	NNP	_	_	_
10	anti-sense	anti-sense	JJ	_	_	_
11	chip	chip	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	2001	2001	CD	_	_	_
14	;	;	:	_	_	_
15	platform	platform	NN	_	_	_
16	ID	id	NN	_	_	_
17	GPL4940	gpl4940	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	but	but	CC	_	_	_
21	because	because	IN	_	_	_
22	the	the	DT	_	_	_
23	analysis	analysis	NN	_	_	_
24	software	software	NN	_	_	_
25	failed	fail	VBD	_	_	_
26	to	to	TO	_	_	_
27	recognize	recognize	VB	_	_	_
28	the	the	DT	_	_	_
29	correct	correct	JJ	_	_	_
30	platform	platform	NN	_	_	_
31	,	,	,	_	_	_
32	we	we	PRP	_	_	_
33	reformatted	reformat	VBD	_	_	_
34	the	the	DT	_	_	_
35	data	datum	NNS	_	_	_
36	to	to	TO	_	_	_
37	match	match	VB	_	_	_
38	the	the	DT	_	_	_
39	newer	newer	JJR	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	and	and	CC	_	_	_
42	mostly	mostly	RB	_	_	_
43	equivalent	equivalent	JJ	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	platform	platform	NN	_	_	_
46	GPL199	gpl199	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	Affy	Affy	NNP	_	_	_
49	Ecoli	Ecoli	NNP	_	_	_
50	anti-sense	anti-sense	JJ	_	_	_
51	chip	chip	NN	_	_	_
52	version	version	NN	_	_	_
53	2	2	CD	_	_	_
54	,	,	,	_	_	_
55	2002	2002	CD	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	.	.	.	_	_	_

1	Because	because	IN	_	_	_
2	,	,	,	_	_	_
3	however	however	RB	_	_	_
4	,	,	,	_	_	_
5	not	not	RB	_	_	_
6	all	all	DT	_	_	_
7	of	of	IN	_	_	_
8	the	the	DT	_	_	_
9	probes	probe	NNS	_	_	_
10	on	on	IN	_	_	_
11	the	the	DT	_	_	_
12	new	new	JJ	_	_	_
13	platform	platform	NN	_	_	_
14	were	be	VBD	_	_	_
15	present	present	JJ	_	_	_
16	on	on	IN	_	_	_
17	the	the	DT	_	_	_
18	old	old	JJ	_	_	_
19	platform	platform	NN	_	_	_
20	,	,	,	_	_	_
21	data	datum	NNS	_	_	_
22	for	for	IN	_	_	_
23	some	some	DT	_	_	_
24	probes	probe	NNS	_	_	_
25	were	be	VBD	_	_	_
26	unavailable	unavailable	JJ	_	_	_
27	and	and	CC	_	_	_
28	labeled	label	VBN	_	_	_
29	in	in	IN	_	_	_
30	the	the	DT	_	_	_
31	`	`	``	_	_	_
32	remapped	remapped	NN	_	_	_
33	'	'	''	_	_	_
34	dataset	dataset	NN	_	_	_
35	as	as	IN	_	_	_
36	`	`	``	_	_	_
37	NULL	NULL	NNP	_	_	_
38	'	'	''	_	_	_
39	to	to	TO	_	_	_
40	indicate	indicate	VB	_	_	_
41	they	they	PRP	_	_	_
42	were	be	VBD	_	_	_
43	missing	miss	VBG	_	_	_
44	.	.	.	_	_	_

1	While	while	IN	_	_	_
2	the	the	DT	_	_	_
3	following	follow	VBG	_	_	_
4	data	datum	NNS	_	_	_
5	are	be	VBP	_	_	_
6	therefore	therefore	RB	_	_	_
7	formatted	format	VBN	_	_	_
8	using	use	VBG	_	_	_
9	ID	ID	NNP	_	_	_
10	_	_	SYM	_	_	_
11	REFs	ref	NNS	_	_	_
12	that	that	WDT	_	_	_
13	match	match	VBP	_	_	_
14	GPL199	gpl199	NN	_	_	_
15	,	,	,	_	_	_
16	the	the	DT	_	_	_
17	CEL	CEL	NNP	_	_	_
18	file	file	NN	_	_	_
19	contains	contain	VBZ	_	_	_
20	the	the	DT	_	_	_
21	raw	raw	JJ	_	_	_
22	data	data	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	not	not	RB	_	_	_
25	`	`	``	_	_	_
26	remapped	remap	VBN	_	_	_
27	'	'	''	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	and	and	CC	_	_	_
30	thus	thus	RB	_	_	_
31	corresponds	correspond	VBZ	_	_	_
32	to	to	TO	_	_	_
33	the	the	DT	_	_	_
34	actual	actual	JJ	_	_	_
35	array	array	NN	_	_	_
36	used	use	VBN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	GPL4940	gpl4940	NN	_	_	_
39	,	,	,	_	_	_
40	Ecoli	ecoli	JJ	_	_	_
41	antisense	antisense	JJ	_	_	_
42	chip	chip	NN	_	_	_
43	,	,	,	_	_	_
44	2001	2001	CD	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	wildtype	wildtype	JJ	_	_	_
3	Escherichia	escherichia	FW	Organism	_	_
4	coli	coli	FW	Organism	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	wt	wt	JJ	_	_	_
7	150	150	CD	_	_	_
8	minutes	minute	NNS	_	_	_
9	growth	growth	NN	_	_	_
10	rep1	rep1	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	wt	wt	JJ	_	_	_
13	150	150	CD	_	_	_
14	minutes	minute	NNS	_	_	_
15	growth	growth	NN	_	_	_
16	rep2	rep2	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	wt	wt	JJ	_	_	_
19	150	150	CD	_	_	_
20	minutes	minute	NNS	_	_	_
21	growth	growth	NN	_	_	_
22	rep3	rep3	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	wt	wt	JJ	_	_	_
25	240	240	CD	_	_	_
26	minutes	minute	NNS	_	_	_
27	growth	growth	NN	_	_	_
28	rep1	rep1	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	wt	wt	JJ	_	_	_
31	240	240	CD	_	_	_
32	minutes	minute	NNS	_	_	_
33	growth	growth	NN	_	_	_
34	rep2	rep2	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	wt	wt	JJ	_	_	_
37	240	240	CD	_	_	_
38	minutes	minute	NNS	_	_	_
39	growth	growth	NN	_	_	_
40	rep3	rep3	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	wt	wt	JJ	_	_	_
43	360	360	CD	_	_	_
44	minutes	minute	NNS	_	_	_
45	growth	growth	NN	_	_	_
46	rep1	rep1	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	wt	wt	JJ	_	_	_
49	360	360	CD	_	_	_
50	minutes	minute	NNS	_	_	_
51	growth	growth	NN	_	_	_
52	rep2	rep2	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	wt	wt	JJ	_	_	_
55	360	360	CD	_	_	_
56	minutes	minute	NNS	_	_	_
57	growth	growth	NN	_	_	_
58	rep3	rep3	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	wt	wt	JJ	_	_	_
61	90	90	CD	_	_	_
62	minutes	minute	NNS	_	_	_
63	growth	growth	NN	_	_	_
64	rep1	rep1	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	wt	wt	JJ	_	_	_
67	90	90	CD	_	_	_
68	minutes	minute	NNS	_	_	_
69	growth	growth	NN	_	_	_
70	rep2	rep2	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	wt	wt	JJ	_	_	_
73	90	90	CD	_	_	_
74	minutes	minute	NNS	_	_	_
75	growth	growth	NN	_	_	_
76	rep3	rep3	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
78	All	all	DT	_	_	_
79	raw	raw	JJ	_	_	_
80	FastQ	fastq	NN	_	_	_
81	files	file	NNS	_	_	_
82	generated	generate	VBN	_	_	_
83	were	be	VBD	_	_	_
84	filtered	filter	VBN	_	_	_
85	using	use	VBG	_	_	_
86	FASTX-Toolkit	fastx-toolkit	NN	_	_	_
87	-LRB-	-lrb-	-LRB-	_	_	_
88	http	http	NN	_	_	_
89	:	:	:	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	Enterohemorrhagic	enterohemorrhagic	JJ	_	_	_
92	Escherichia	escherichia	FW	Organism	_	_
93	coli	coli	FW	Organism	_	_
94	O157	o157	NN	_	_	_
95	:	:	:	_	_	_
96	H7	h7	NN	_	_	_
97	strain	strain	NN	_	_	_
98	EDL933	edl933	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	Escherichia	escherichia	FW	Organism	_	_
101	coli	coli	FW	Organism	_	_
102	O157	o157	NN	_	_	_
103	:	:	:	_	_	_
104	H7	h7	NN	_	_	_
105	str	str	NN	_	_	_
106	.	.	.	_	_	_

1	EDL933	edl933	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Genome	Genome	NNP	_	_	_
4	_	_	NNP	_	_	_
5	build	build	VB	_	_	_
6	:	:	:	_	_	_
7	NC	NC	NNP	_	_	_
8	_	_	NNP	_	_	_
9	002655.2	002655.2	CD	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	genotype	genotype	NN	_	_	_
12	:	:	:	_	_	_
13	-LCB-	-lcb-	-LRB-	_	_	_
14	delta	delta	NN	_	_	_
15	-RCB-	-rcb-	-RRB-	_	_	_
16	hns	hn	VBZ	GEN	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	genotype	genotype	NN	_	_	_
19	:	:	:	_	_	_
20	wild	wild	JJ	_	_	_
21	type	type	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	hns	hn	NNS	GEN	_	_
24	_	_	VBP	_	_	_
25	1	1	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	hns	hn	NNS	GEN	_	_
28	_	_	VBP	_	_	_
29	2	2	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
31	Illumina	Illumina	NNP	_	_	_
32	Casava1	Casava1	NNP	_	_	_
33	.7	.7	CD	_	_	_
34	software	software	NN	_	_	_
35	used	use	VBN	_	_	_
36	for	for	IN	_	_	_
37	basecalling	basecalling	NN	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Overnight	Overnight	NNP	_	_	_
3	cultures	culture	NNS	_	_	_
4	of	of	IN	_	_	_
5	bacteria	bacterium	NNS	_	_	_
6	were	be	VBD	_	_	_
7	diluted	dilute	VBN	_	_	_
8	1:100	1:100	CD	_	_	_
9	in	in	IN	_	_	_
10	fresh	fresh	JJ	_	_	_
11	LB	lb	NN	MED	_	_
12	broth	broth	NN	MED	_	_
13	and	and	CC	_	_	_
14	grown	grow	VBN	_	_	_
15	to	to	TO	_	_	_
16	logarithmic	logarithmic	JJ	_	_	_
17	phase	phase	NN	_	_	_
18	at	at	IN	_	_	_
19	an	a	DT	_	_	_
20	OD600	od600	NN	_	_	_
21	of	of	IN	_	_	_
22	about	about	IN	_	_	_
23	0.8	0.8	CD	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	phase	phase	NN	_	_	_
3	:	:	:	_	_	_
4	logarithmic	logarithmic	JJ	_	_	_
5	phase	phase	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Reads	read	VBZ	_	_	_
8	per	per	IN	_	_	_
9	kilobase	kilobase	NN	_	_	_
10	of	of	IN	_	_	_
11	exon	exon	NN	_	_	_
12	model	model	NN	_	_	_
13	per	per	IN	_	_	_
14	million	million	CD	_	_	_
15	mapped	map	VBD	_	_	_
16	reads	read	VBZ	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	RPKM	rpkm	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	was	be	VBD	_	_	_
21	used	use	VBN	_	_	_
22	as	as	IN	_	_	_
23	a	a	DT	_	_	_
24	normalized	normalize	VBN	_	_	_
25	metric	metric	JJ	_	_	_
26	to	to	TO	_	_	_
27	present	present	VB	_	_	_
28	the	the	DT	_	_	_
29	gene	gene	NN	_	_	_
30	expression	expression	NN	_	_	_
31	levels	level	NNS	_	_	_
32	.	.	.	_	_	_

1	-LRB-	-lrb-	-LRB-	_	_	_
2	Nature	Nature	NNP	_	_	_
3	methods	method	NNS	_	_	_
4	2008	2008	CD	_	_	_
5	,	,	,	_	_	_
6	5	5	CD	_	_	_
7	:	:	:	_	_	_
8	621-628	621-628	CD	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	RNA	rna	NN	_	_	_
12	extraction	extraction	NN	_	_	_
13	was	be	VBD	_	_	_
14	performed	perform	VBN	_	_	_
15	using	use	VBG	_	_	_
16	RiboPure-BacteriaTM	RiboPure-BacteriaTM	NNP	_	_	_
17	Bacteria	bacterium	NNS	_	_	_
18	kit	kit	NN	_	_	_
19	according	accord	VBG	_	_	_
20	to	to	TO	_	_	_
21	the	the	DT	_	_	_
22	manufacturer	manufacturer	NN	_	_	_
23	's	's	POS	_	_	_
24	protocol	protocol	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	Ambion	Ambion	NNP	_	_	_
27	,	,	,	_	_	_
28	Life	Life	NNP	_	_	_
29	Technologies	Technologies	NNPS	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	DNase	dnase	NN	_	_	_
2	I	i	CD	_	_	_
3	treatment	treatment	NN	_	_	_
4	was	be	VBD	_	_	_
5	applied	apply	VBN	_	_	_
6	to	to	TO	_	_	_
7	eliminate	eliminate	VB	_	_	_
8	genomic	genomic	JJ	_	_	_
9	DNA	dna	NN	_	_	_
10	contamination	contamination	NN	_	_	_
11	as	as	IN	_	_	_
12	per	per	IN	_	_	_
13	the	the	DT	_	_	_
14	manufacturer	manufacturer	NN	_	_	_
15	's	's	POS	_	_	_
16	recommendations	recommendation	NNS	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	prepared	prepare	VBN	_	_	_
6	for	for	IN	_	_	_
7	sequencing	sequencing	NN	_	_	_
8	using	use	VBG	_	_	_
9	standard	standard	JJ	_	_	_
10	Illumina	Illumina	NNP	_	_	_
11	protocols	protocol	NNS	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBP	_	_	_
13	RNA-Seq	rna-seq	JJ	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
15	Supplementary	supplementary	JJ	_	_	_
16	_	_	NN	_	_	_
17	files	file	NNS	_	_	_
18	_	_	IN	_	_	_
19	format	format	NN	_	_	_
20	_	_	NN	_	_	_
21	and	and	CC	_	_	_
22	_	_	NN	_	_	_
23	content	content	NN	_	_	_
24	:	:	:	_	_	_
25	RPKM	rpkm	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	The	the	DT	_	_	_
28	bacteria	bacterium	NNS	_	_	_
29	were	be	VBD	_	_	_
30	centrifuged	centrifuge	VBN	_	_	_
31	at	at	IN	_	_	_
32	4000	4000	CD	_	_	_
33	×	×	CD	_	_	_
34	g	g	NN	_	_	_
35	at	at	IN	_	_	_
36	4	4	CD	_	_	_
37	°C	°c	NN	_	_	_
38	for	for	IN	_	_	_
39	5	5	CD	_	_	_
40	min	min	NN	_	_	_
41	and	and	CC	_	_	_
42	then	then	RB	_	_	_
43	washed	wash	VBN	_	_	_
44	with	with	IN	_	_	_
45	PBS	PBS	NNP	_	_	_
46	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Transcripts	transcript	NNS	_	_	_
3	evaluation	evaluation	NN	_	_	_
4	of	of	IN	_	_	_
5	differential	differential	JJ	_	_	_
6	expression	expression	NN	_	_	_
7	were	be	VBD	_	_	_
8	accomplished	accomplish	VBN	_	_	_
9	using	use	VBG	_	_	_
10	MARS	mars	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	MA-plot-based	ma-plot-based	JJ	_	_	_
13	method	method	NN	_	_	_
14	with	with	IN	_	_	_
15	Random	Random	NNP	_	_	_
16	sampling	sampling	NN	_	_	_
17	model	model	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	in	in	IN	_	_	_
20	DEGseq	degseq	NN	_	_	_
21	package	package	NN	_	_	_
22	.	.	.	_	_	_

1	-LRB-	-lrb-	-LRB-	_	_	_
2	Bioinformatics	bioinformatic	NNS	_	_	_
3	2010	2010	CD	_	_	_
4	,	,	,	_	_	_
5	26	26	CD	_	_	_
6	:	:	:	_	_	_
7	136-138	136-138	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	wt	wt	JJ	_	_	_
11	_	_	NN	_	_	_
12	1	1	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	wt	wt	JJ	_	_	_
15	_	_	NN	_	_	_
16	2	2	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
18	Bacterial	bacterial	JJ	_	_	_
19	cells	cell	NNS	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	Escherichia	escherichia	FW	Organism	_	_
22	coli	coli	FW	Organism	_	_
23	str	str	FW	_	_	_
24	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Genome	Genome	NNP	_	_	_
4	_	_	NNP	_	_	_
5	build	build	VB	_	_	_
6	:	:	:	_	_	_
7	NC	NC	NNP	_	_	_
8	_	_	NNP	_	_	_
9	000913.2	000913.2	CD	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	genotype	genotype	NN	_	_	_
12	:	:	:	_	_	_
13	del	del	DT	_	_	_
14	rpoS	rpos	NN	GEN	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	genotype	genotype	NN	_	_	_
17	:	:	:	_	_	_
18	del	del	DT	_	_	_
19	rsd	rsd	NN	GEN	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	genotype	genotype	NN	_	_	_
22	:	:	:	_	_	_
23	del	del	DT	_	_	_
24	rsd	rsd	NN	GEN	_	_
25	;	;	:	_	_	_
26	del	del	DT	_	_	_
27	ssrS	ssrs	NN	GEN	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	genotype	genotype	NN	_	_	_
30	:	:	:	_	_	_
31	del	del	DT	_	_	_
32	ssrS	ssrs	NN	GEN	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	genotype	genotype	NN	_	_	_
35	:	:	:	_	_	_
36	Wild-type	wild-type	JJ	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	growth	growth	NN	_	_	_
39	phase	phase	NN	_	_	_
40	:	:	:	_	_	_
41	Early	early	JJ	_	_	_
42	Exponential	exponential	JJ	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	growth	growth	NN	_	_	_
45	phase	phase	NN	_	_	_
46	:	:	:	_	_	_
47	Late	late	JJ	_	_	_
48	Stationary	stationary	JJ	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	growth	growth	NN	_	_	_
51	phase	phase	NN	_	_	_
52	:	:	:	_	_	_
53	Mid-Exponential	mid-exponential	JJ	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	growth	growth	NN	_	_	_
56	phase	phase	NN	_	_	_
57	:	:	:	_	_	_
58	Stationary	stationary	JJ	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	growth	growth	NN	_	_	_
61	phase	phase	NN	_	_	_
62	:	:	:	_	_	_
63	Transition	transition	NN	_	_	_
64	to	to	TO	_	_	_
65	Stationary	stationary	JJ	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	Libraries	library	NNS	_	_	_
68	for	for	IN	_	_	_
69	Illumina	Illumina	NNP	_	_	_
70	HiSeq	HiSeq	NNP	_	_	_
71	1000	1000	CD	_	_	_
72	sequencing	sequencing	NN	_	_	_
73	using	use	VBG	_	_	_
74	the	the	DT	_	_	_
75	Truseq	Truseq	NNP	_	_	_
76	kit	kit	NN	_	_	_
77	were	be	VBD	_	_	_
78	prepared	prepare	VBN	_	_	_
79	using	use	VBG	_	_	_
80	protocols	protocol	NNS	_	_	_
81	recommended	recommend	VBN	_	_	_
82	by	by	IN	_	_	_
83	the	the	DT	_	_	_
84	manufacturer	manufacturer	NN	_	_	_
85	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	M9	m9	NN	_	_	_
3	defined	define	VBN	_	_	_
4	medium	medium	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	0.6	0.6	CD	_	_	_
7	%	%	NN	_	_	_
8	Na2HPO4	na2hpo4	NN	_	_	_
9	,	,	,	_	_	_
10	0.3	0.3	CD	_	_	_
11	%	%	NN	_	_	_
12	KH2PO4	kh2po4	NN	_	_	_
13	,	,	,	_	_	_
14	0.05	0.05	CD	_	_	_
15	%	%	NN	_	_	_
16	NaCl	nacl	NN	_	_	_
17	,	,	,	_	_	_
18	0.01	0.01	CD	_	_	_
19	%	%	NN	_	_	_
20	NH4Cl	nh4cl	NN	_	_	_
21	,	,	,	_	_	_
22	0.1	0.1	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	CaCl2	cacl2	NN	_	_	_
25	,	,	,	_	_	_
26	1	1	CD	_	_	_
27	mM	mm	NN	KWSUPP	_	_
28	MgSO4	mgso4	NN	_	_	_
29	,	,	,	_	_	_
30	5	5	CD	_	_	_
31	x	x	CC	_	_	_
32	10	10	CD	_	_	_
33	−	−	NN	_	_	_
34	4	4	CD	_	_	_
35	%	%	NN	_	_	_
36	Thiamin	thiamin	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	supplemented	supplement	VBN	_	_	_
39	with	with	IN	_	_	_
40	0.5	0.5	CD	_	_	_
41	%	%	NN	_	_	_
42	glucose	glucose	NN	SUPP	_	_
43	and	and	CC	_	_	_
44	0.1	0.1	CD	_	_	_
45	%	%	NN	_	_	_
46	amino	amino	NN	SUPP	_	_
47	acids	acid	NNS	SUPP	_	_
48	was	be	VBD	_	_	_
49	used	use	VBN	_	_	_
50	for	for	IN	_	_	_
51	RNA-seq	rna-seq	NN	_	_	_
52	experiments	experiment	NNS	_	_	_
53	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Overnight	Overnight	NNP	_	_	_
3	cultures	culture	NNS	_	_	_
4	in	in	IN	_	_	_
5	M9	m9	NN	_	_	_
6	glucose	glucose	NN	SUPP	_	_
7	were	be	VBD	_	_	_
8	inoculated	inoculate	VBN	_	_	_
9	into	into	IN	_	_	_
10	100	100	CD	_	_	_
11	mL	ml	NN	_	_	_
12	fresh	fresh	JJ	_	_	_
13	M9	m9	NN	_	_	_
14	glucose	glucose	NN	SUPP	_	_
15	to	to	TO	_	_	_
16	a	a	DT	_	_	_
17	final	final	JJ	_	_	_
18	OD600	od600	NN	_	_	_
19	of	of	IN	_	_	_
20	0.02	0.02	CD	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	flasks	flask	NNS	_	_	_
3	were	be	VBD	_	_	_
4	incubated	incubate	VBN	_	_	_
5	at	at	IN	_	_	_
6	37	37	CD	_	_	_
7	°C	°c	NN	_	_	_
8	with	with	IN	_	_	_
9	shaking	shake	VBG	_	_	_
10	at	at	IN	_	_	_
11	200	200	CD	_	_	_
12	rpm	rpm	NN	_	_	_
13	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	collected	collect	VBN	_	_	_
4	by	by	IN	_	_	_
5	centrifugation	centrifugation	NN	_	_	_
6	at	at	IN	_	_	_
7	the	the	DT	_	_	_
8	early	early	JJ	_	_	_
9	exponential	exponential	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	OD600	od600	NN	_	_	_
12	~	~	NN	_	_	_
13	0.3	0.3	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	mid-exponential	mid-exponential	JJ	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	OD600	od600	NN	_	_	_
19	~	~	NN	_	_	_
20	0.8	0.8	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	,	,	,	_	_	_
23	transition	transition	NN	_	_	_
24	to	to	TO	_	_	_
25	stationary	stationary	JJ	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	OD600	od600	NN	_	_	_
28	~	~	NN	_	_	_
29	1.6	1.6	CD	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	,	,	,	_	_	_
32	stationary	stationary	JJ	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	16	16	CD	_	_	_
35	hrs	hr	NNS	_	_	_
36	,	,	,	_	_	_
37	OD600	od600	NN	_	_	_
38	~	~	NN	_	_	_
39	2	2	CD	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	,	,	,	_	_	_
42	and	and	CC	_	_	_
43	late	late	JJ	_	_	_
44	stationary	stationary	JJ	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	48	48	CD	_	_	_
47	hrs	hr	NNS	_	_	_
48	,	,	,	_	_	_
49	OD600	od600	NN	_	_	_
50	~	~	NN	_	_	_
51	1.6	1.6	CD	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	phases	phase	NNS	_	_	_
54	of	of	IN	_	_	_
55	growth	growth	NN	_	_	_
56	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	sequence	sequence	NN	_	_	_
4	data	datum	NNS	_	_	_
5	obtained	obtain	VBN	_	_	_
6	in	in	IN	_	_	_
7	the	the	DT	_	_	_
8	fastq	fastq	NN	_	_	_
9	format	format	NN	_	_	_
10	were	be	VBD	_	_	_
11	aligned	align	VBN	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	genome	genome	NN	_	_	_
15	of	of	IN	_	_	_
16	E.	e.	FW	_	_	_
17	coli	coli	FW	_	_	_
18	K12	k12	NN	_	_	_
19	MG1655	mg1655	NN	_	_	_
20	using	use	VBG	_	_	_
21	the	the	DT	_	_	_
22	Burrows-Wheeler	Burrows-Wheeler	NNP	_	_	_
23	matching	match	VBG	_	_	_
24	program	program	NN	_	_	_
25	BWA	bwa	NN	_	_	_
26	.	.	.	_	_	_

1	Reads	read	NNS	_	_	_
2	mapping	map	VBG	_	_	_
3	uniquely	uniquely	RB	_	_	_
4	to	to	TO	_	_	_
5	the	the	DT	_	_	_
6	genome	genome	NN	_	_	_
7	were	be	VBD	_	_	_
8	selected	select	VBN	_	_	_
9	and	and	CC	_	_	_
10	the	the	DT	_	_	_
11	number	number	NN	_	_	_
12	of	of	IN	_	_	_
13	reads	read	VBZ	_	_	_
14	mapping	map	VBG	_	_	_
15	to	to	TO	_	_	_
16	each	each	DT	_	_	_
17	gene	gene	NN	_	_	_
18	was	be	VBD	_	_	_
19	computed	compute	VBN	_	_	_
20	using	use	VBG	_	_	_
21	custom	custom	NN	_	_	_
22	scripts	script	NNS	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	RNA	rna	NN	_	_	_
5	was	be	VBD	_	_	_
6	extracted	extract	VBN	_	_	_
7	using	use	VBG	_	_	_
8	TRIzol	trizol	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Invitrogen	invitrogen	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	,	,	,	_	_	_
13	following	follow	VBG	_	_	_
14	the	the	DT	_	_	_
15	manufacturer	manufacturer	NN	_	_	_
16	's	's	POS	_	_	_
17	protocol	protocol	NN	_	_	_
18	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	treated	treat	VBN	_	_	_
5	with	with	IN	_	_	_
6	DNAse	dnase	NN	_	_	_
7	I	i	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	Invitrogen	Invitrogen	NNP	_	_	_
10	,	,	,	_	_	_
11	Cat	Cat	NNP	_	_	_
12	No.	No.	NNP	_	_	_
13	18068-015	18068-015	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	according	accord	VBG	_	_	_
16	to	to	TO	_	_	_
17	the	the	DT	_	_	_
18	manufacturer	manufacturer	NN	_	_	_
19	's	's	POS	_	_	_
20	protocol	protocol	NN	_	_	_
21	.	.	.	_	_	_

1	Further	further	JJ	_	_	_
2	precipitation	precipitation	NN	_	_	_
3	of	of	IN	_	_	_
4	RNA	rna	NN	_	_	_
5	and	and	CC	_	_	_
6	ribosomal	ribosomal	JJ	_	_	_
7	RNA	rna	NN	_	_	_
8	cleanup	cleanup	NN	_	_	_
9	was	be	VBD	_	_	_
10	achieved	achieve	VBN	_	_	_
11	by	by	IN	_	_	_
12	Ambion	Ambion	NNP	_	_	_
13	MICROBExpress	MICROBExpress	NNPS	_	_	_
14	bacterial	bacterial	JJ	_	_	_
15	mRNA	mrna	NN	_	_	_
16	purification	purification	NN	_	_	_
17	Kit	kit	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	cat	cat	NN	_	_	_
20	.	.	.	_	_	_

1	no	no	DT	_	_	_
2	.	.	.	_	_	_

1	AM1905	am1905	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	according	accord	VBG	_	_	_
4	to	to	TO	_	_	_
5	the	the	DT	_	_	_
6	manufacturer	manufacturer	NN	_	_	_
7	's	's	POS	_	_	_
8	protocol	protocol	NN	_	_	_
9	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	finally	finally	RB	_	_	_
5	suspended	suspend	VBN	_	_	_
6	in	in	IN	_	_	_
7	10	10	CD	_	_	_
8	μL	μl	NN	_	_	_
9	RNAse	rnase	NN	_	_	_
10	free	free	JJ	_	_	_
11	water	water	NN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	rpoS	rpos	NN	GEN	_	_
3	_	_	CD	_	_	_
4	EE	ee	NN	_	_	_
5	_	_	NN	_	_	_
6	1	1	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	rpoS	rpos	NN	GEN	_	_
9	_	_	CD	_	_	_
10	EE	ee	NN	_	_	_
11	_	_	NN	_	_	_
12	2	2	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	rpoS	rpos	NN	GEN	_	_
15	_	_	NN	_	_	_
16	LS	ls	NN	_	_	_
17	_	_	NN	_	_	_
18	1	1	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	rpoS	rpos	NN	GEN	_	_
21	_	_	NN	_	_	_
22	LS	ls	NN	_	_	_
23	_	_	NN	_	_	_
24	2	2	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	rpoS	rpos	NN	GEN	_	_
27	_	_	CD	_	_	_
28	ME	me	NN	_	_	_
29	_	_	NN	_	_	_
30	1	1	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	rpoS	rpos	NN	GEN	_	_
33	_	_	CD	_	_	_
34	ME	me	NN	_	_	_
35	_	_	NN	_	_	_
36	2	2	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	rpoS	rpos	NN	GEN	_	_
39	_	_	CD	_	_	_
40	S	s	NN	_	_	_
41	_	_	NN	_	_	_
42	1	1	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	rpoS	rpos	NN	GEN	_	_
45	_	_	CD	_	_	_
46	S	s	NN	_	_	_
47	_	_	NN	_	_	_
48	2	2	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	rpoS	rpos	NN	GEN	_	_
51	_	_	CD	_	_	_
52	TS	ts	NN	_	_	_
53	_	_	NN	_	_	_
54	1	1	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	rpoS	rpos	NN	GEN	_	_
57	_	_	CD	_	_	_
58	TS	ts	NN	_	_	_
59	_	_	NN	_	_	_
60	2	2	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	rsd	rsd	NN	GEN	_	_
63	_	_	CD	_	_	_
64	EE	ee	NN	_	_	_
65	_	_	NN	_	_	_
66	1	1	CD	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	rsd	rsd	NN	GEN	_	_
69	_	_	CD	_	_	_
70	EE	ee	NN	_	_	_
71	_	_	NN	_	_	_
72	2	2	CD	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	rsd	rsd	NN	GEN	_	_
75	_	_	NN	_	_	_
76	LS	ls	NN	_	_	_
77	_	_	NN	_	_	_
78	1	1	CD	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	rsd	rsd	NN	GEN	_	_
81	_	_	NN	_	_	_
82	LS	ls	NN	_	_	_
83	_	_	NN	_	_	_
84	2	2	CD	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	rsd	rsd	NN	GEN	_	_
87	_	_	CD	_	_	_
88	ME	me	NN	_	_	_
89	_	_	NN	_	_	_
90	1	1	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	rsd	rsd	NN	GEN	_	_
93	_	_	CD	_	_	_
94	ME	me	NN	_	_	_
95	_	_	NN	_	_	_
96	2	2	CD	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	rsd	rsd	NN	GEN	_	_
99	_	_	CD	_	_	_
100	S	s	NN	_	_	_
101	_	_	NN	_	_	_
102	1	1	CD	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	rsd	rsd	NN	GEN	_	_
105	_	_	CD	_	_	_
106	S	s	NN	_	_	_
107	_	_	NN	_	_	_
108	2	2	CD	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	rsdssrS	rsdssrs	NN	_	_	_
111	_	_	CD	_	_	_
112	EE	ee	NN	_	_	_
113	_	_	NN	_	_	_
114	1	1	CD	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	rsdssrS	rsdssrs	NN	_	_	_
117	_	_	CD	_	_	_
118	EE	ee	NN	_	_	_
119	_	_	NN	_	_	_
120	2	2	CD	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	rsdssrS	rsdssrs	NN	_	_	_
123	_	_	NN	_	_	_
124	LS	ls	NN	_	_	_
125	_	_	NN	_	_	_
126	1	1	CD	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	rsdssrS	rsdssrs	NN	_	_	_
129	_	_	NN	_	_	_
130	LS	ls	NN	_	_	_
131	_	_	NN	_	_	_
132	2	2	CD	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	rsdssrS	rsdssrs	NN	_	_	_
135	_	_	CD	_	_	_
136	ME	me	NN	_	_	_
137	_	_	NN	_	_	_
138	1	1	CD	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	rsdssrS	rsdssrs	NN	_	_	_
141	_	_	CD	_	_	_
142	ME	me	NN	_	_	_
143	_	_	NN	_	_	_
144	2	2	CD	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	rsdssrS	rsdssrs	NN	_	_	_
147	_	_	CD	_	_	_
148	S	s	NN	_	_	_
149	_	_	NN	_	_	_
150	1	1	CD	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	rsdssrS	rsdssrs	NN	_	_	_
153	_	_	CD	_	_	_
154	S	s	NN	_	_	_
155	_	_	NN	_	_	_
156	2	2	CD	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	rsdssrS	rsdssrs	NN	_	_	_
159	_	_	CD	_	_	_
160	TS	ts	NN	_	_	_
161	_	_	NN	_	_	_
162	1	1	CD	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	rsdssrS	rsdssrs	NN	_	_	_
165	_	_	CD	_	_	_
166	TS	ts	NN	_	_	_
167	_	_	NN	_	_	_
168	2	2	CD	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	rsd	rsd	NN	GEN	_	_
171	_	_	CD	_	_	_
172	TS	ts	NN	_	_	_
173	_	_	NN	_	_	_
174	1	1	CD	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	rsd	rsd	NN	GEN	_	_
177	_	_	CD	_	_	_
178	TS	ts	NN	_	_	_
179	_	_	NN	_	_	_
180	2	2	CD	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	ssrS	ssrs	NN	GEN	_	_
183	_	_	CD	_	_	_
184	EE	ee	NN	_	_	_
185	_	_	NN	_	_	_
186	1	1	CD	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	ssrS	ssrs	NN	GEN	_	_
189	_	_	CD	_	_	_
190	EE	ee	NN	_	_	_
191	_	_	NN	_	_	_
192	2	2	CD	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	ssrS	ssrs	NN	GEN	_	_
195	_	_	NN	_	_	_
196	LS	ls	NN	_	_	_
197	_	_	NN	_	_	_
198	1	1	CD	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	ssrS	ssrs	NN	GEN	_	_
201	_	_	NN	_	_	_
202	LS	ls	NN	_	_	_
203	_	_	NN	_	_	_
204	2	2	CD	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	ssrS	ssrs	NN	GEN	_	_
207	_	_	CD	_	_	_
208	ME	me	NN	_	_	_
209	_	_	NN	_	_	_
210	1	1	CD	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	ssrS	ssrs	NN	GEN	_	_
213	_	_	CD	_	_	_
214	ME	me	NN	_	_	_
215	_	_	NN	_	_	_
216	2	2	CD	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	ssrS	ssrs	NN	GEN	_	_
219	_	_	CD	_	_	_
220	S	s	NN	_	_	_
221	_	_	NN	_	_	_
222	1	1	CD	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	ssrS	ssrs	NN	GEN	_	_
225	_	_	CD	_	_	_
226	S	s	NN	_	_	_
227	_	_	NN	_	_	_
228	2	2	CD	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
230	ssrS	ssrs	NN	GEN	_	_
231	_	_	CD	_	_	_
232	TS	ts	NN	_	_	_
233	_	_	NN	_	_	_
234	1	1	CD	_	_	_
235	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
236	ssrS	ssrs	NN	GEN	_	_
237	_	_	CD	_	_	_
238	TS	ts	NN	_	_	_
239	_	_	NN	_	_	_
240	2	2	CD	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
242	Supplementary	supplementary	JJ	_	_	_
243	_	_	NN	_	_	_
244	files	file	NNS	_	_	_
245	_	_	IN	_	_	_
246	format	format	NN	_	_	_
247	_	_	NN	_	_	_
248	and	and	CC	_	_	_
249	_	_	NN	_	_	_
250	content	content	NN	_	_	_
251	:	:	:	_	_	_
252	Tab-delimited	tab-delimited	JJ	_	_	_
253	text	text	NN	_	_	_
254	file	file	NN	_	_	_
255	;	;	:	_	_	_
256	genes	gene	NNS	_	_	_
257	in	in	IN	_	_	_
258	rows	row	NNS	_	_	_
259	and	and	CC	_	_	_
260	samples	sample	NNS	_	_	_
261	in	in	IN	_	_	_
262	columns	column	NNS	_	_	_
263	;	;	:	_	_	_
264	each	each	DT	_	_	_
265	entry	entry	NN	_	_	_
266	corresponds	correspond	VBZ	_	_	_
267	to	to	TO	_	_	_
268	the	the	DT	_	_	_
269	number	number	NN	_	_	_
270	of	of	IN	_	_	_
271	reads	read	VBZ	_	_	_
272	mapping	map	VBG	_	_	_
273	to	to	TO	_	_	_
274	the	the	DT	_	_	_
275	given	give	VBN	_	_	_
276	gene	gene	NN	_	_	_
277	in	in	IN	_	_	_
278	the	the	DT	_	_	_
279	given	give	VBN	_	_	_
280	sample	sample	NN	_	_	_
281	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	These	these	DT	_	_	_
3	counts	count	NNS	_	_	_
4	were	be	VBD	_	_	_
5	fed	feed	VBN	_	_	_
6	into	into	IN	_	_	_
7	the	the	DT	_	_	_
8	DESeq	deseq	NN	_	_	_
9	package	package	NN	_	_	_
10	in	in	IN	_	_	_
11	Bioconductor	Bioconductor	NNP	_	_	_
12	to	to	TO	_	_	_
13	estimate	estimate	VB	_	_	_
14	differential	differential	JJ	_	_	_
15	expression	expression	NN	_	_	_
16	between	between	IN	_	_	_
17	the	the	DT	_	_	_
18	mutants	mutant	NNS	_	_	_
19	and	and	CC	_	_	_
20	the	the	DT	_	_	_
21	wildtype	wildtype	JJ	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	wt	wt	JJ	_	_	_
3	_	_	NN	_	_	_
4	EE	ee	NN	_	_	_
5	_	_	NN	_	_	_
6	1	1	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	wt	wt	JJ	_	_	_
9	_	_	NN	_	_	_
10	EE	ee	NN	_	_	_
11	_	_	NN	_	_	_
12	2	2	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	wt	wt	JJ	_	_	_
15	_	_	NN	_	_	_
16	LS	ls	NN	_	_	_
17	_	_	NN	_	_	_
18	1	1	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	wt	wt	JJ	_	_	_
21	_	_	NN	_	_	_
22	LS	ls	NN	_	_	_
23	_	_	NN	_	_	_
24	2	2	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	wt	wt	JJ	_	_	_
27	_	_	CD	_	_	_
28	ME	me	NN	_	_	_
29	_	_	NN	_	_	_
30	1	1	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	wt	wt	JJ	_	_	_
33	_	_	CD	_	_	_
34	ME	me	NN	_	_	_
35	_	_	NN	_	_	_
36	2	2	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	wt	wt	JJ	_	_	_
39	_	_	NN	_	_	_
40	S	s	NN	_	_	_
41	_	_	NN	_	_	_
42	1	1	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	wt	wt	JJ	_	_	_
45	_	_	NN	_	_	_
46	S	s	NN	_	_	_
47	_	_	NN	_	_	_
48	2	2	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	wt	wt	JJ	_	_	_
51	_	_	NN	_	_	_
52	TS	ts	NN	_	_	_
53	_	_	NN	_	_	_
54	1	1	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	wt	wt	JJ	_	_	_
57	_	_	NN	_	_	_
58	TS	ts	NN	_	_	_
59	_	_	NN	_	_	_
60	2	2	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
62	chip	chip	NN	_	_	_
63	antibody	antibody	NN	_	_	_
64	manufacturer	manufacturer	NN	_	_	_
65	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
66	chip	chip	NN	_	_	_
67	antibody	antibody	NN	_	_	_
68	:	:	:	_	_	_
69	Monoclonal	monoclonal	JJ	_	_	_
70	anti-FLAG	anti-flag	JJ	_	_	_
71	antibody	antibody	NN	_	_	_
72	,	,	,	_	_	_
73	Murine	murine	JJ	_	_	_
74	IgG	igg	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	ChIP-exo	chip-exo	NN	_	_	_
77	reads	read	VBZ	_	_	_
78	were	be	VBD	_	_	_
79	aligned	align	VBN	_	_	_
80	using	use	VBG	_	_	_
81	BWA	bwa	NN	_	_	_
82	with	with	IN	_	_	_
83	default	default	NN	_	_	_
84	parameters	parameter	NNS	_	_	_
85	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
86	E.	E.	NNP	_	_	_
87	coli	coli	NN	_	_	_
88	and	and	CC	_	_	_
89	S.	S.	NNP	_	_	_
90	Typhimurium	Typhimurium	NNP	_	_	_
91	cells	cell	NNS	_	_	_
92	-LRB-	-lrb-	-LRB-	_	_	_
93	at	at	IN	_	_	_
94	mid-exponential	mid-exponential	JJ	_	_	_
95	growth	growth	NN	_	_	_
96	phase	phase	NN	_	_	_
97	-RRB-	-rrb-	-RRB-	_	_	_
98	were	be	VBD	_	_	_
99	fixed	fix	VBN	_	_	_
100	with	with	IN	_	_	_
101	formaldehyde	formaldehyde	NN	_	_	_
102	-LRB-	-lrb-	-LRB-	_	_	_
103	1	1	CD	_	_	_
104	%	%	NN	_	_	_
105	final	final	JJ	_	_	_
106	concentration	concentration	NN	_	_	_
107	-RRB-	-rrb-	-RRB-	_	_	_
108	for	for	IN	_	_	_
109	20	20	CD	_	_	_
110	min	min	NN	_	_	_
111	at	at	IN	_	_	_
112	30	30	CD	_	_	_
113	°C	°c	NN	_	_	_
114	with	with	IN	_	_	_
115	shaking	shake	VBG	_	_	_
116	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	crosslinking	crosslinking	NN	_	_	_
3	reaction	reaction	NN	_	_	_
4	was	be	VBD	_	_	_
5	then	then	RB	_	_	_
6	quenched	quench	VBN	_	_	_
7	by	by	IN	_	_	_
8	the	the	DT	_	_	_
9	addition	addition	NN	_	_	_
10	of	of	IN	_	_	_
11	glycine	glycine	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	0.33	0.33	CD	_	_	_
14	M	m	NN	_	_	_
15	final	final	JJ	_	_	_
16	concentrationg	concentrationg	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	for	for	IN	_	_	_
19	5	5	CD	_	_	_
20	minutes	minute	NNS	_	_	_
21	at	at	IN	_	_	_
22	room	room	NN	_	_	_
23	temperature	temperature	NN	_	_	_
24	with	with	IN	_	_	_
25	gentle	gentle	JJ	_	_	_
26	mixing	mix	VBG	_	_	_
27	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	where	where	WRB	_	_	_
3	then	then	RB	_	_	_
4	lysed	lyse	VBN	_	_	_
5	on	on	IN	_	_	_
6	ice	ice	NN	_	_	_
7	with	with	IN	_	_	_
8	lysozyme	lysozyme	NN	_	_	_
9	and	and	CC	_	_	_
10	sonication	sonication	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	cells	cell	NNS	_	_	_
5	were	be	VBD	_	_	_
6	grown	grow	VBN	_	_	_
7	in	in	IN	_	_	_
8	Kornberg	Kornberg	NNP	_	_	_
9	medium	medium	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	1.1	1.1	CD	_	_	_
12	%	%	NN	_	_	_
13	-LSB-	-lsb-	-LRB-	_	_	_
14	wt	wt	JJ	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	Escherichia	escherichia	FW	Organism	_	_
17	coli	coli	FW	Organism	_	_
18	str	str	FW	_	_	_
19	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Genome	Genome	NNP	_	_	_
4	_	_	NNP	_	_	_
5	build	build	VB	_	_	_
6	:	:	:	_	_	_
7	NC	NC	NNP	_	_	_
8	_	_	NNP	_	_	_
9	000913.3	000913.3	CD	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Genome	Genome	NNP	_	_	_
12	_	_	NNP	_	_	_
13	build	build	VB	_	_	_
14	:	:	:	_	_	_
15	NC	NC	NNP	_	_	_
16	_	_	NNP	_	_	_
17	016856.1	016856.1	CD	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Library	Library	NNP	_	_	_
20	strategy	strategy	NN	_	_	_
21	:	:	:	_	_	_
22	ChIP-exo	ChIP-exo	NNP	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	OTHER	OTHER	NNP	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	Peaks	Peaks	NNPS	_	_	_
27	on	on	IN	_	_	_
28	opposing	oppose	VBG	_	_	_
29	strands	strand	NNS	_	_	_
30	were	be	VBD	_	_	_
31	paired	pair	VBN	_	_	_
32	with	with	IN	_	_	_
33	Genetrack	genetrack	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	u	u	NN	_	_	_
36	=	=	JJ	_	_	_
37	0	0	CD	_	_	_
38	,	,	,	_	_	_
39	d	d	NN	_	_	_
40	=	=	JJ	_	_	_
41	80	80	CD	_	_	_
42	,	,	,	_	_	_
43	b	b	NN	_	_	_
44	=	=	JJ	_	_	_
45	2	2	CD	_	_	_
46	,	,	,	_	_	_
47	m	m	NN	_	_	_
48	=	=	JJ	_	_	_
49	mode	mode	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	Peaks	peak	NNS	_	_	_
53	were	be	VBD	_	_	_
54	called	call	VBN	_	_	_
55	with	with	IN	_	_	_
56	GeneTrack	genetrack	NN	_	_	_
57	1.0.3	1.0.3	CD	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	s	s	NN	_	_	_
60	=	=	JJ	_	_	_
61	5	5	CD	_	_	_
62	,	,	,	_	_	_
63	e	e	SYM	_	_	_
64	=	=	JJ	_	_	_
65	10	10	CD	_	_	_
66	-RRB-	-rrb-	-RRB-	_	_	_
67	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
68	Peconic	Peconic	NNP	_	_	_
69	LLC	LLC	NNP	_	_	_
70	performed	perform	VBD	_	_	_
71	data	datum	NNS	_	_	_
72	processing	processing	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	Samples	sample	NNS	_	_	_
75	were	be	VBD	_	_	_
76	used	use	VBN	_	_	_
77	for	for	IN	_	_	_
78	on-bead	on-bead	JJ	_	_	_
79	enzymatic	enzymatic	JJ	_	_	_
80	reactions	reaction	NNS	_	_	_
81	of	of	IN	_	_	_
82	the	the	DT	_	_	_
83	ChIP-exo	ChIP-exo	NNP	_	_	_
84	procedure	procedure	NN	_	_	_
85	and	and	CC	_	_	_
86	Illumina	Illumina	NNP	_	_	_
87	Tru-seq	tru-seq	JJ	_	_	_
88	sequencing	sequencing	NN	_	_	_
89	libraries	library	NNS	_	_	_
90	were	be	VBD	_	_	_
91	construction	construction	NN	_	_	_
92	as	as	IN	_	_	_
93	described	describe	VBN	_	_	_
94	in	in	IN	_	_	_
95	Rhee	Rhee	NNP	_	_	_
96	and	and	CC	_	_	_
97	Pugh	Pugh	NNP	_	_	_
98	,	,	,	_	_	_
99	2012	2012	CD	_	_	_
100	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
101	Singleton	Singleton	NNP	_	_	_
102	peaks	peak	VBZ	_	_	_
103	-LRB-	-lrb-	-LRB-	_	_	_
104	standard	standard	JJ	_	_	_
105	deviation	deviation	NN	_	_	_
106	=	=	JJ	_	_	_
107	0	0	CD	_	_	_
108	-RRB-	-rrb-	-RRB-	_	_	_
109	and	and	CC	_	_	_
110	peaks	peak	VBZ	_	_	_
111	without	without	IN	_	_	_
112	matched	match	VBN	_	_	_
113	peaks	peak	NNS	_	_	_
114	on	on	IN	_	_	_
115	the	the	DT	_	_	_
116	opposing	oppose	VBG	_	_	_
117	strand	strand	NN	_	_	_
118	where	where	WRB	_	_	_
119	discarded	discard	VBN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	strain	strain	NN	_	_	_
122	:	:	:	_	_	_
123	MG1655	mg1655	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	S.	S.	NNP	_	_	_
126	Typhimurium	Typhimurium	NNP	_	_	_
127	cells	cell	NNS	_	_	_
128	were	be	VBD	_	_	_
129	grown	grow	VBN	_	_	_
130	in	in	IN	_	_	_
131	LB	lb	NN	_	_	_
132	-LRB-	-lrb-	-LRB-	_	_	_
133	supplemented	supplement	VBN	_	_	_
134	with	with	IN	_	_	_
135	10mM	10mm	NN	_	_	_
136	glucose	glucose	NN	SUPP	_	_
137	-RRB-	-rrb-	-RRB-	_	_	_
138	to	to	TO	_	_	_
139	mid-exponential	mid-exponential	JJ	_	_	_
140	phase	phase	NN	_	_	_
141	-LRB-	-lrb-	-LRB-	_	_	_
142	OD600	od600	NN	_	_	_
143	=	=	JJ	_	_	_
144	~	~	NN	_	_	_
145	0.6	0.6	CD	_	_	_
146	-RRB-	-rrb-	-RRB-	_	_	_
147	at	at	IN	_	_	_
148	37C	37c	NN	_	_	_
149	and	and	CC	_	_	_
150	shaking	shake	VBG	_	_	_
151	250rpm	250rpm	JJ	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
153	Supplementary	supplementary	JJ	_	_	_
154	_	_	NN	_	_	_
155	files	file	NNS	_	_	_
156	_	_	IN	_	_	_
157	format	format	NN	_	_	_
158	_	_	NN	_	_	_
159	and	and	CC	_	_	_
160	_	_	NN	_	_	_
161	content	content	NN	_	_	_
162	:	:	:	_	_	_
163	Bedgraphs	bedgraph	NNS	_	_	_
164	files	file	NNS	_	_	_
165	representing	represent	VBG	_	_	_
166	the	the	DT	_	_	_
167	extracted	extract	VBN	_	_	_
168	peak	peak	NN	_	_	_
169	data	datum	NNS	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	Supplementary	supplementary	JJ	_	_	_
172	_	_	NN	_	_	_
173	files	file	NNS	_	_	_
174	_	_	IN	_	_	_
175	format	format	NN	_	_	_
176	_	_	NN	_	_	_
177	and	and	CC	_	_	_
178	_	_	NN	_	_	_
179	content	content	NN	_	_	_
180	:	:	:	_	_	_
181	chromosome	chromosome	NN	_	_	_
182	chromosomeStartPosition	chromosomestartposition	NN	_	_	_
183	chromosomeStopPosition	chromosomestopposition	NN	_	_	_
184	readCoverage	readcoverage	NN	_	_	_
185	-LRB-	-lrb-	-LRB-	_	_	_
186	positive	positive	JJ	_	_	_
187	values	value	NNS	_	_	_
188	on	on	IN	_	_	_
189	+	+	CC	_	_	_
190	strand	strand	NN	_	_	_
191	,	,	,	_	_	_
192	negative	negative	JJ	_	_	_
193	on	on	IN	_	_	_
194	-	-	:	_	_	_
195	strand	strand	NN	_	_	_
196	-RRB-	-rrb-	-RRB-	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	UvrY	uvry	NN	TF	_	_
199	-	-	:	_	_	_
200	ChIP-exo	ChIP-exo	NNP	_	_	_
201	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
202	UvrY	uvry	NN	TF	_	_
203	-LRB-	-lrb-	-LRB-	_	_	_
204	Response	response	NN	_	_	_
205	regulator	regulator	NN	_	_	_
206	of	of	IN	_	_	_
207	the	the	DT	_	_	_
208	BarA	bara	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	Bacterial	bacterial	JJ	_	_	_
211	cells	cell	NNS	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
213	Cells	cell	NNS	_	_	_
214	were	be	VBD	_	_	_
215	grown	grow	VBN	_	_	_
216	at	at	IN	_	_	_
217	37	37	CD	_	_	_
218	°C	°c	NN	_	_	_
219	,	,	,	_	_	_
220	200	200	CD	_	_	_
221	rpm	rpm	NN	_	_	_
222	in	in	IN	_	_	_
223	M9	m9	NN	_	_	_
224	glucose	glucose	NN	SUPP	_	_
225	,	,	,	_	_	_
226	for	for	IN	_	_	_
227	16	16	CD	_	_	_
228	hours	hour	NNS	_	_	_
229	-LRB-	-lrb-	-LRB-	_	_	_
230	stationary	stationary	JJ	GrowthPhase	_	_
231	phase	phase	NN	GrowthPhase	_	_
232	-RRB-	-rrb-	-RRB-	_	_	_
233	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	chip	chip	NN	_	_	_
3	antibody	antibody	NN	_	_	_
4	:	:	:	_	_	_
5	None	none	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	chip	chip	NN	_	_	_
8	antibody	antibody	NN	_	_	_
9	:	:	:	_	_	_
10	RpoS	rpos	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Neoclone	neoclone	JJ	_	_	_
13	cat	cat	NN	_	_	_
14	.	.	.	_	_	_

1	no	no	DT	_	_	_
2	.	.	.	_	_	_

1	WP009	wp009	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	ChIP-Seq	chip-seq	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
6	Cross-linked	cross-linked	JJ	_	_	_
7	cells	cell	NNS	_	_	_
8	were	be	VBD	_	_	_
9	harvested	harvest	VBN	_	_	_
10	by	by	IN	_	_	_
11	centrifugation	centrifugation	NN	_	_	_
12	,	,	,	_	_	_
13	washed	wash	VBN	_	_	_
14	thrice	thrice	RB	_	_	_
15	with	with	IN	_	_	_
16	ice-cold	ice-cold	JJ	_	_	_
17	TBS	tbs	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	pH	ph	NN	_	_	_
20	7.5	7.5	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	,	,	,	_	_	_
23	resuspended	resuspend	VBN	_	_	_
24	in	in	IN	_	_	_
25	1	1	CD	_	_	_
26	ml	ml	NN	_	_	_
27	lysis	lysis	NN	_	_	_
28	buffer	buffer	NN	_	_	_
29	-LSB-	-lsb-	-LRB-	_	_	_
30	10	10	CD	_	_	_
31	mM	mm	NN	KWSUPP	_	_
32	Tris	tris	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	pH	ph	NN	_	_	_
35	8.0	8.0	CD	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	,	,	,	_	_	_
38	20	20	CD	_	_	_
39	%	%	NN	_	_	_
40	sucrose	sucrose	NN	_	_	_
41	,	,	,	_	_	_
42	50	50	CD	_	_	_
43	mM	mm	NN	KWSUPP	_	_
44	NaCl	nacl	NN	_	_	_
45	,	,	,	_	_	_
46	10	10	CD	_	_	_
47	mM	mm	NN	KWSUPP	_	_
48	EDTA	edta	NN	_	_	_
49	,	,	,	_	_	_
50	20	20	CD	_	_	_
51	mg	mg	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	Escherichia	escherichia	FW	Organism	_	_
54	coli	coli	FW	Organism	_	_
55	str	str	FW	_	_	_
56	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Files	file	NNS	_	_	_
4	were	be	VBD	_	_	_
5	coverted	covert	VBN	_	_	_
6	to	to	TO	_	_	_
7	.	.	.	_	_	_

1	bam	bam	NN	_	_	_
2	format	format	NN	_	_	_
3	using	use	VBG	_	_	_
4	samtools	samtool	NNS	_	_	_
5	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
6	Formaldehyde	Formaldehyde	NNP	_	_	_
7	was	be	VBD	_	_	_
8	added	add	VBN	_	_	_
9	to	to	TO	_	_	_
10	a	a	DT	_	_	_
11	final	final	JJ	_	_	_
12	concentration	concentration	NN	_	_	_
13	of	of	IN	_	_	_
14	1	1	CD	_	_	_
15	%	%	NN	_	_	_
16	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	20	20	CD	_	_	_
5	minutes	minute	NNS	_	_	_
6	,	,	,	_	_	_
7	glycine	glycine	NN	_	_	_
8	was	be	VBD	_	_	_
9	added	add	VBN	_	_	_
10	to	to	TO	_	_	_
11	a	a	DT	_	_	_
12	final	final	JJ	_	_	_
13	concentration	concentration	NN	_	_	_
14	of	of	IN	_	_	_
15	0.5	0.5	CD	_	_	_
16	M	m	NN	_	_	_
17	and	and	CC	_	_	_
18	incubated	incubate	VBN	_	_	_
19	for	for	IN	_	_	_
20	5	5	CD	_	_	_
21	minutes	minute	NNS	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	NC	NC	NNP	_	_	_
7	_	_	NNP	_	_	_
8	000913.2	000913.2	CD	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	genotype	genotype	NN	_	_	_
11	:	:	:	_	_	_
12	MG1655	mg1655	NN	_	_	_
13	del	del	FW	_	_	_
14	ssrS	ssrs	FW	GEN	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	genotype	genotype	NN	_	_	_
17	:	:	:	_	_	_
18	MG1655	mg1655	NN	_	_	_
19	wild-type	wild-type	JJ	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Libraries	library	NNS	_	_	_
22	were	be	VBD	_	_	_
23	prepared	prepare	VBN	_	_	_
24	for	for	IN	_	_	_
25	sequencing	sequencing	NN	_	_	_
26	using	use	VBG	_	_	_
27	standard	standard	JJ	_	_	_
28	Illumina	Illumina	NNP	_	_	_
29	protocols	protocol	NNS	_	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
31	Raw	raw	NN	_	_	_
32	sequence	sequence	NN	_	_	_
33	data	datum	NNS	_	_	_
34	obtained	obtain	VBN	_	_	_
35	in	in	IN	_	_	_
36	the	the	DT	_	_	_
37	fastq	fastq	NN	_	_	_
38	format	format	NN	_	_	_
39	were	be	VBD	_	_	_
40	aligned	align	VBN	_	_	_
41	to	to	TO	_	_	_
42	the	the	DT	_	_	_
43	genome	genome	NN	_	_	_
44	of	of	IN	_	_	_
45	E.	e.	FW	_	_	_
46	coli	coli	FW	_	_	_
47	K12	k12	NN	_	_	_
48	MG1655	mg1655	NN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	NC	nc	NN	_	_	_
51	_	_	CD	_	_	_
52	000913.2	000913.2	CD	_	_	_
53	-RRB-	-rrb-	-RRB-	_	_	_
54	using	use	VBG	_	_	_
55	the	the	DT	_	_	_
56	Burrows-Wheeler	Burrows-Wheeler	NNP	_	_	_
57	matching	match	VBG	_	_	_
58	program	program	NN	_	_	_
59	BWA	bwa	NN	_	_	_
60	.	.	.	_	_	_

1	Reads	read	NNS	_	_	_
2	mapping	map	VBG	_	_	_
3	uniquely	uniquely	RB	_	_	_
4	to	to	TO	_	_	_
5	the	the	DT	_	_	_
6	genome	genome	NN	_	_	_
7	were	be	VBD	_	_	_
8	selected	select	VBN	_	_	_
9	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	sequence	sequence	NN	_	_	_
4	data	datum	NNS	_	_	_
5	obtained	obtain	VBN	_	_	_
6	in	in	IN	_	_	_
7	the	the	DT	_	_	_
8	fastq	fastq	NN	_	_	_
9	format	format	NN	_	_	_
10	were	be	VBD	_	_	_
11	aligned	align	VBN	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	genome	genome	NN	_	_	_
15	of	of	IN	_	_	_
16	E.	e.	FW	_	_	_
17	coli	coli	FW	_	_	_
18	K12	k12	NN	_	_	_
19	MG1655	mg1655	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	NC	nc	NN	_	_	_
22	_	_	CD	_	_	_
23	000913.2	000913.2	CD	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	using	use	VBG	_	_	_
26	the	the	DT	_	_	_
27	Burrows-Wheeler	Burrows-Wheeler	NNP	_	_	_
28	matching	match	VBG	_	_	_
29	program	program	NN	_	_	_
30	BWA	bwa	NN	_	_	_
31	.	.	.	_	_	_

1	Reads	read	NNS	_	_	_
2	mapping	map	VBG	_	_	_
3	uniquely	uniquely	RB	_	_	_
4	to	to	TO	_	_	_
5	the	the	DT	_	_	_
6	genome	genome	NN	_	_	_
7	were	be	VBD	_	_	_
8	selected	select	VBN	_	_	_
9	.	.	.	_	_	_

1	Files	file	NNS	_	_	_
2	were	be	VBD	_	_	_
3	coverted	covert	VBN	_	_	_
4	to	to	TO	_	_	_
5	.	.	.	_	_	_

1	bam	bam	NN	_	_	_
2	format	format	NN	_	_	_
3	using	use	VBG	_	_	_
4	samtools	samtool	NNS	_	_	_
5	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	MACS	macs	NN	_	_	_
3	2.1.0	2.1.0	CD	_	_	_
4	software	software	NN	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	to	to	TO	_	_	_
8	call	call	VB	_	_	_
9	peaks	peak	NNS	_	_	_
10	.	.	.	_	_	_

1	Peaks	peak	NNS	_	_	_
2	overlapping	overlap	VBG	_	_	_
3	in	in	IN	_	_	_
4	both	both	CC	_	_	_
5	replicates	replicate	VBZ	_	_	_
6	were	be	VBD	_	_	_
7	selected	select	VBN	_	_	_
8	for	for	IN	_	_	_
9	further	further	JJ	_	_	_
10	analysis	analysis	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	sequence	sequence	NN	_	_	_
4	data	datum	NNS	_	_	_
5	obtained	obtain	VBN	_	_	_
6	in	in	IN	_	_	_
7	the	the	DT	_	_	_
8	fastq	fastq	NN	_	_	_
9	format	format	NN	_	_	_
10	were	be	VBD	_	_	_
11	aligned	align	VBN	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	genome	genome	NN	_	_	_
15	of	of	IN	_	_	_
16	E.	e.	FW	_	_	_
17	coli	coli	FW	_	_	_
18	K12	k12	NN	_	_	_
19	MG1655	mg1655	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	NC	nc	NN	_	_	_
22	_	_	CD	_	_	_
23	000913.2	000913.2	CD	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	using	use	VBG	_	_	_
26	the	the	DT	_	_	_
27	Burrows-Wheeler	Burrows-Wheeler	NNP	_	_	_
28	matching	match	VBG	_	_	_
29	program	program	NN	_	_	_
30	BWA	bwa	NN	_	_	_
31	.	.	.	_	_	_

1	Reads	read	NNS	_	_	_
2	mapping	map	VBG	_	_	_
3	uniquely	uniquely	RB	_	_	_
4	to	to	TO	_	_	_
5	the	the	DT	_	_	_
6	genome	genome	NN	_	_	_
7	were	be	VBD	_	_	_
8	selected	select	VBN	_	_	_
9	.	.	.	_	_	_

1	Files	file	NNS	_	_	_
2	were	be	VBD	_	_	_
3	coverted	covert	VBN	_	_	_
4	to	to	TO	_	_	_
5	.	.	.	_	_	_

1	bam	bam	NN	_	_	_
2	format	format	NN	_	_	_
3	using	use	VBG	_	_	_
4	samtools	samtool	NNS	_	_	_
5	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	MACS	macs	NN	_	_	_
3	2.1.0	2.1.0	CD	_	_	_
4	software	software	NN	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	to	to	TO	_	_	_
8	call	call	VB	_	_	_
9	peaks	peak	NNS	_	_	_
10	.	.	.	_	_	_

1	Peaks	peak	NNS	_	_	_
2	overlapping	overlap	VBG	_	_	_
3	in	in	IN	_	_	_
4	both	both	CC	_	_	_
5	replicates	replicate	VBZ	_	_	_
6	were	be	VBD	_	_	_
7	selected	select	VBN	_	_	_
8	for	for	IN	_	_	_
9	further	further	JJ	_	_	_
10	analysis	analysis	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Reads	Reads	NNPS	_	_	_
3	were	be	VBD	_	_	_
4	trimmed	trim	VBN	_	_	_
5	for	for	IN	_	_	_
6	quality	quality	NN	_	_	_
7	using	use	VBG	_	_	_
8	Trimmomatic-0.32	trimmomatic-0.32	NN	_	_	_
9	with	with	IN	_	_	_
10	a	a	DT	_	_	_
11	cutoff	cutoff	JJ	_	_	_
12	quality	quality	NN	_	_	_
13	score	score	NN	_	_	_
14	of	of	IN	_	_	_
15	20	20	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	ssrS	ssrs	NN	GEN	_	_
18	_	_	NN	_	_	_
19	1	1	CD	_	_	_
20	_	_	NN	_	_	_
21	input	input	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	ssrS	ssrs	NN	GEN	_	_
24	_	_	NN	_	_	_
25	1	1	CD	_	_	_
26	_	_	CD	_	_	_
27	IP	IP	NNP	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	Supplementary	Supplementary	NNP	_	_	_
30	_	_	VBD	_	_	_
31	files	file	NNS	_	_	_
32	_	_	IN	_	_	_
33	format	format	NN	_	_	_
34	_	_	NN	_	_	_
35	and	and	CC	_	_	_
36	_	_	NN	_	_	_
37	content	content	NN	_	_	_
38	:	:	:	_	_	_
39	.	.	.	_	_	_

1	narrowPeak	narrowpeak	NN	_	_	_
2	files	file	NNS	_	_	_
3	output	output	NN	_	_	_
4	by	by	IN	_	_	_
5	macs2	macs2	NN	_	_	_
6	,	,	,	_	_	_
7	giving	give	VBG	_	_	_
8	peak	peak	JJ	_	_	_
9	start	start	NN	_	_	_
10	and	and	CC	_	_	_
11	end	end	NN	_	_	_
12	positions	position	NNS	_	_	_
13	,	,	,	_	_	_
14	as	as	RB	_	_	_
15	well	well	RB	_	_	_
16	as	as	IN	_	_	_
17	fold-change	fold-change	NN	_	_	_
18	,	,	,	_	_	_
19	-	-	:	_	_	_
20	log10pvalue	log10pvalue	NN	_	_	_
21	,	,	,	_	_	_
22	-	-	:	_	_	_
23	log10qvalue	log10qvalue	NN	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	relative	relative	JJ	_	_	_
27	summit	summit	NN	_	_	_
28	position	position	NN	_	_	_
29	to	to	TO	_	_	_
30	peak	peak	VB	_	_	_
31	start	start	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	Supplementary	supplementary	JJ	_	_	_
34	_	_	NN	_	_	_
35	files	file	NNS	_	_	_
36	_	_	IN	_	_	_
37	format	format	NN	_	_	_
38	_	_	NN	_	_	_
39	and	and	CC	_	_	_
40	_	_	NN	_	_	_
41	content	content	NN	_	_	_
42	:	:	:	_	_	_
43	.	.	.	_	_	_

1	narrowPeak	narrowpeak	NN	_	_	_
2	files	file	NNS	_	_	_
3	output	output	NN	_	_	_
4	by	by	IN	_	_	_
5	MACS	mac	NNS	_	_	_
6	,	,	,	_	_	_
7	giving	give	VBG	_	_	_
8	peak	peak	JJ	_	_	_
9	start	start	NN	_	_	_
10	and	and	CC	_	_	_
11	end	end	NN	_	_	_
12	positions	position	NNS	_	_	_
13	,	,	,	_	_	_
14	as	as	RB	_	_	_
15	well	well	RB	_	_	_
16	as	as	IN	_	_	_
17	fold-change	fold-change	NN	_	_	_
18	,	,	,	_	_	_
19	-	-	:	_	_	_
20	log10pvalue	log10pvalue	NN	_	_	_
21	,	,	,	_	_	_
22	-	-	:	_	_	_
23	log10qvalue	log10qvalue	NN	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	relative	relative	JJ	_	_	_
27	summit	summit	NN	_	_	_
28	position	position	NN	_	_	_
29	to	to	TO	_	_	_
30	peak	peak	VB	_	_	_
31	start	start	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	The	the	DT	_	_	_
34	MACS	macs	NN	_	_	_
35	2.1.0	2.1.0	CD	_	_	_
36	software	software	NN	_	_	_
37	was	be	VBD	_	_	_
38	used	use	VBN	_	_	_
39	to	to	TO	_	_	_
40	call	call	VB	_	_	_
41	peaks	peak	NNS	_	_	_
42	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	MACS2	macs2	NN	_	_	_
4	software	software	NN	_	_	_
5	was	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	to	to	TO	_	_	_
8	call	call	VB	_	_	_
9	peaks	peak	NNS	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	wt	wt	JJ	_	_	_
3	_	_	NN	_	_	_
4	1	1	CD	_	_	_
5	_	_	NN	_	_	_
6	input	input	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	wt	wt	JJ	_	_	_
9	_	_	NN	_	_	_
10	1	1	CD	_	_	_
11	_	_	CD	_	_	_
12	IP	IP	NNP	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	wt	wt	JJ	_	_	_
15	_	_	NN	_	_	_
16	2	2	CD	_	_	_
17	_	_	NN	_	_	_
18	input	input	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	wt	wt	JJ	_	_	_
21	_	_	NN	_	_	_
22	2	2	CD	_	_	_
23	_	_	CD	_	_	_
24	IP	IP	NNP	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	Cells	cell	NNS	_	_	_
27	were	be	VBD	_	_	_
28	grown	grow	VBN	_	_	_
29	aerobically	aerobically	RB	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	70	70	CD	_	_	_
32	%	%	NN	_	_	_
33	N2	n2	NN	_	_	_
34	,	,	,	_	_	_
35	25	25	CD	_	_	_
36	%	%	NN	_	_	_
37	O2	o2	CD	_	_	_
38	,	,	,	_	_	_
39	and	and	CC	_	_	_
40	5	5	CD	_	_	_
41	%	%	NN	_	_	_
42	CO2	co2	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	or	or	CC	_	_	_
45	anaerobically	anaerobically	RB	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	95	95	CD	_	_	_
48	%	%	NN	_	_	_
49	N2	n2	NN	_	_	_
50	and	and	CC	_	_	_
51	5	5	CD	_	_	_
52	%	%	NN	_	_	_
53	CO2	co2	NN	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	until	until	IN	_	_	_
56	mid-log	mid-log	JJ	_	_	_
57	phase	phase	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	OD600	od600	NN	_	_	_
60	of	of	IN	_	_	_
61	~	~	NN	_	_	_
62	0.3-0.35	0.3-0.35	CD	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	in	in	IN	_	_	_
65	MOPS	mop	NNS	MED	_	_
66	minimal	minimal	JJ	_	_	_
67	glucose	glucose	NN	SUPP	_	_
68	media	media	NNS	_	_	_
69	containing	contain	VBG	_	_	_
70	10	10	CD	_	_	_
71	µM	µm	NN	_	_	_
72	FeSO4	feso4	NN	_	_	_
73	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	treated	treat	VBN	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	stop	stop	NN	_	_	_
8	solution	solution	NN	_	_	_
9	of	of	IN	_	_	_
10	phenol	phenol	NN	_	_	_
11	and	and	CC	_	_	_
12	ethanol	ethanol	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Khodursky	Khodursky	NNP	_	_	_
15	et	et	FW	_	_	_
16	al	al	FW	_	_	_
17	,	,	,	_	_	_
18	Methods	method	NNS	_	_	_
19	in	in	IN	_	_	_
20	Molecular	molecular	JJ	_	_	_
21	Biology	Biology	NNP	_	_	_
22	2003	2003	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	,	,	,	_	_	_
25	spun	spin	VBD	_	_	_
26	down	down	RP	_	_	_
27	,	,	,	_	_	_
28	and	and	CC	_	_	_
29	flash	flash	NN	_	_	_
30	frozen	frozen	JJ	_	_	_
31	and	and	CC	_	_	_
32	stored	store	VBN	_	_	_
33	at	at	IN	_	_	_
34	-80	-80	CD	_	_	_
35	°C	°c	NN	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2	culture	culture	NN	_	_	_
3	condition	condition	NN	_	_	_
4	:	:	:	_	_	_
5	Aerobic	aerobic	JJ	_	_	_
6	cultures	culture	NNS	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
8	culture	culture	NN	_	_	_
9	condition	condition	NN	_	_	_
10	:	:	:	_	_	_
11	Anaerobic	anaerobic	JJ	_	_	_
12	cultures	culture	NNS	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Escherichia	escherichia	FW	Organism	_	_
15	coli	coli	FW	Organism	_	_
16	str	str	FW	_	_	_
17	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	∆	∆	CD	_	_	_
4	fur	fur	NN	GEN	_	_
5	Aerobic	aerobic	JJ	_	_	_
6	A	a	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	∆	∆	CD	_	_	_
9	fur	fur	NN	GEN	_	_
10	Aerobic	aerobic	JJ	_	_	_
11	B	b	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	∆	∆	CD	_	_	_
14	fur	fur	NN	GEN	_	_
15	Anaerobic	anaerobic	JJ	_	_	_
16	A	a	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	∆	∆	CD	_	_	_
19	fur	fur	NN	GEN	_	_
20	Anaerobic	anaerobic	JJ	_	_	_
21	B	b	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Fur-minus	fur-minus	NN	_	_	_
24	_	_	CD	_	_	_
25	cDNA	cdna	NN	_	_	_
26	_	_	CD	_	_	_
27	Aerobic	aerobic	JJ	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Fur-minus	fur-minus	NN	_	_	_
30	_	_	CD	_	_	_
31	cDNA	cdna	NN	_	_	_
32	_	_	CD	_	_	_
33	Anaerobic	anaerobic	JJ	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	Fur-minus	fur-minus	NN	_	_	_
36	_	_	CD	_	_	_
37	RyhB-minus	RyhB-minus	NNP	_	_	_
38	_	_	NNP	_	_	_
39	cDNA	cdna	NN	_	_	_
40	_	_	CD	_	_	_
41	Aerobic	aerobic	JJ	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	Fur-minus	fur-minus	NN	_	_	_
44	_	_	CD	_	_	_
45	RyhB-minus	RyhB-minus	NNP	_	_	_
46	_	_	NNP	_	_	_
47	cDNA	cdna	NN	_	_	_
48	_	_	CD	_	_	_
49	Anaerobic	anaerobic	JJ	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	∆	∆	NN	_	_	_
52	fur	fur	NN	GEN	_	_
53	∆	∆	CD	_	_	_
54	ryhB	ryhb	NN	GEN	_	_
55	Aerobic	aerobic	JJ	_	_	_
56	A	a	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	∆	∆	CD	_	_	_
59	fur	fur	NN	GEN	_	_
60	∆	∆	CD	_	_	_
61	ryhB	ryhb	NN	GEN	_	_
62	Aerobic	aerobic	JJ	_	_	_
63	B	b	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	∆	∆	CD	_	_	_
66	fur	fur	NN	GEN	_	_
67	∆	∆	CD	_	_	_
68	ryhB	ryhb	NN	GEN	_	_
69	Anaerobic	anaerobic	JJ	_	_	_
70	A	a	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	∆	∆	CD	_	_	_
73	fur	fur	NN	GEN	_	_
74	∆	∆	CD	_	_	_
75	ryhB	ryhb	NN	GEN	_	_
76	Anaerobic	anaerobic	JJ	_	_	_
77	B	b	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	genotype	genotype	NN	_	_	_
80	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
81	Raw	raw	NN	_	_	_
82	probe	probe	NN	_	_	_
83	intensities	intensity	NNS	_	_	_
84	were	be	VBD	_	_	_
85	normalized	normalize	VBN	_	_	_
86	across	across	IN	_	_	_
87	all	all	DT	_	_	_
88	samples	sample	NNS	_	_	_
89	using	use	VBG	_	_	_
90	the	the	DT	_	_	_
91	Robust	Robust	NNP	_	_	_
92	Multichip	Multichip	NNP	_	_	_
93	Average	Average	NNP	_	_	_
94	-LRB-	-lrb-	-LRB-	_	_	_
95	RMA	RMA	NNP	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	algorithm	algorithm	NN	_	_	_
98	in	in	IN	_	_	_
99	the	the	DT	_	_	_
100	NimbleScan	NimbleScan	NNP	_	_	_
101	software	software	NN	_	_	_
102	package	package	NN	_	_	_
103	-LRB-	-lrb-	-LRB-	_	_	_
104	version	version	NN	_	_	_
105	2.5	2.5	CD	_	_	_
106	-RRB-	-rrb-	-RRB-	_	_	_
107	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RMA	rma	NN	_	_	_
3	normalized	normalize	VBD	_	_	_
4	probe	probe	NN	_	_	_
5	data	datum	NNS	_	_	_
6	was	be	VBD	_	_	_
7	uploaded	upload	VBN	_	_	_
8	into	into	IN	_	_	_
9	the	the	DT	_	_	_
10	Mochiview	Mochiview	NNP	_	_	_
11	visualization	visualization	NN	_	_	_
12	software	software	NN	_	_	_
13	where	where	WRB	_	_	_
14	data	datum	NNS	_	_	_
15	cooresponding	coorespond	VBG	_	_	_
16	to	to	TO	_	_	_
17	the	the	DT	_	_	_
18	plus	plus	NN	_	_	_
19	and	and	CC	_	_	_
20	minus	minus	CC	_	_	_
21	strands	strand	NNS	_	_	_
22	were	be	VBD	_	_	_
23	subtracted	subtract	VBN	_	_	_
24	to	to	TO	_	_	_
25	get	get	VB	_	_	_
26	a	a	DT	_	_	_
27	strand-specific	strand-specific	JJ	_	_	_
28	probe	probe	NN	_	_	_
29	intesenity	intesenity	NN	_	_	_
30	per	per	IN	_	_	_
31	base	base	NN	_	_	_
32	as	as	IN	_	_	_
33	reported	report	VBN	_	_	_
34	in	in	IN	_	_	_
35	the	the	DT	_	_	_
36	processed	process	VBN	_	_	_
37	data	datum	NNS	_	_	_
38	files	file	NNS	_	_	_
39	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	∆	∆	SYM	_	_	_
3	ryhB	ryhb	NN	GEN	_	_
4	Aerobic	aerobic	JJ	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	∆	∆	CD	_	_	_
7	ryhB	ryhb	NN	GEN	_	_
8	Anaerobic	anaerobic	JJ	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	RyhB-minus_cDNA_Aerobic_WIG.txt	ryhb-minus_cdna_aerobic_wig.txt	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	RyhB-minus_cDNA_Anaerobic_WIG.txt	ryhb-minus_cdna_anaerobic_wig.txt	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Total	total	JJ	_	_	_
15	RNA	rna	NN	_	_	_
16	was	be	VBD	_	_	_
17	extracted	extract	VBN	_	_	_
18	using	use	VBG	_	_	_
19	a	a	DT	_	_	_
20	hot	hot	JJ	_	_	_
21	phenol	phenol	NN	_	_	_
22	method	method	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Khodursky	Khodursky	NNP	_	_	_
25	et	et	FW	_	_	_
26	al	al	FW	_	_	_
27	,	,	,	_	_	_
28	Methods	method	NNS	_	_	_
29	in	in	IN	_	_	_
30	Molecular	molecular	JJ	_	_	_
31	Biology	Biology	NNP	_	_	_
32	2003	2003	CD	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Wild-type	wild-type	JJ	_	_	_
3	Aerobic	Aerobic	NNP	_	_	_
4	A	A	NNP	_	_	_
5	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
6	Wild-type	wild-type	JJ	_	_	_
7	Aerobic	aerobic	JJ	_	_	_
8	B	b	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Wild-type	wild-type	JJ	_	_	_
11	Anaerobic	anaerobic	JJ	_	_	_
12	A	a	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Wild-type	wild-type	JJ	_	_	_
15	Anaerobic	anaerobic	JJ	_	_	_
16	B	b	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Wild-type	wild-type	JJ	_	_	_
19	_	_	NN	_	_	_
20	cDNA	cdna	NN	_	_	_
21	_	_	CD	_	_	_
22	Aerobic	aerobic	JJ	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	Wild-type	wild-type	JJ	_	_	_
25	_	_	NN	_	_	_
26	cDNA	cdna	NN	_	_	_
27	_	_	CD	_	_	_
28	Anaerobic	anaerobic	JJ	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Cultures	culture	NNS	_	_	_
31	grown	grow	VBN	_	_	_
32	in	in	IN	_	_	_
33	MOPS	mop	NNS	MED	_	_
34	minimal	minimal	JJ	_	_	_
35	glucose	glucose	NN	SUPP	_	_
36	media	media	NNS	_	_	_
37	containing	contain	VBG	_	_	_
38	10	10	CD	_	_	_
39	µM	µm	NN	_	_	_
40	FeSO4	feso4	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	Custom	Custom	NNP	_	_	_
43	anti-Fur	anti-fur	JJ	_	_	_
44	antibodies	antibody	NNS	_	_	_
45	were	be	VBD	_	_	_
46	purified	purify	VBN	_	_	_
47	over	over	IN	_	_	_
48	a	a	DT	_	_	_
49	His6-Fur	his6-fur	NN	_	_	_
50	bound	bind	VBD	_	_	_
51	HiTrap	HiTrap	NNP	_	_	_
52	NHS-activated	NHS-activated	NNP	_	_	_
53	HP	HP	NNP	_	_	_
54	column	column	NN	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	GE	GE	NNP	_	_	_
57	Healthcare	Healthcare	NNP	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	as	as	IN	_	_	_
60	previously	previously	RB	_	_	_
61	described	describe	VBN	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	PMID	pmid	NN	_	_	_
64	:	:	:	_	_	_
65	21478858	21478858	CD	_	_	_
66	-RRB-	-rrb-	-RRB-	_	_	_
67	.	.	.	_	_	_

1	Western	western	NN	_	_	_
2	blot	blot	NN	_	_	_
3	analyses	analysis	NNS	_	_	_
4	showed	show	VBD	_	_	_
5	that	that	IN	_	_	_
6	the	the	DT	_	_	_
7	purified	purify	VBN	_	_	_
8	antibody	antibody	NN	_	_	_
9	was	be	VBD	_	_	_
10	specific	specific	JJ	_	_	_
11	for	for	IN	_	_	_
12	Fur	Fur	NNP	TF	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	∆	∆	CD	_	_	_
4	fur	fur	NN	GEN	_	_
5	Anaerobic	anaerobic	JJ	_	_	_
6	-LSB-	-lsb-	-LRB-	_	_	_
7	IP	IP	NNP	_	_	_
8	vs	vs	CC	_	_	_
9	nput	nput	NN	_	_	_
10	-RSB-	-rsb-	-RRB-	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	genotype	genotype	NN	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Input	Input	NNP	_	_	_
15	∆	∆	NNP	_	_	_
16	fur	fur	NN	GEN	_	_
17	Anaerobic	anaerobic	JJ	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	ip	ip	NN	_	_	_
20	antibody	antibody	NN	_	_	_
21	:	:	:	_	_	_
22	affinity	affinity	NN	_	_	_
23	purified	purify	VBN	_	_	_
24	anti-Fur	anti-fur	JJ	_	_	_
25	antibody	antibody	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	IP	IP	NNP	_	_	_
28	∆	∆	NNP	_	_	_
29	fur	fur	NN	GEN	_	_
30	Anaerobic	anaerobic	JJ	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	NimbleScan	nimblescan	NN	_	_	_
33	software	software	NN	_	_	_
34	package	package	NN	_	_	_
35	,	,	,	_	_	_
36	version	version	NN	_	_	_
37	2.5	2.5	CD	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	Roche	Roche	NNP	_	_	_
40	NimbleGen	NimbleGen	NNP	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	was	be	VBD	_	_	_
43	used	use	VBN	_	_	_
44	to	to	TO	_	_	_
45	extract	extract	VB	_	_	_
46	the	the	DT	_	_	_
47	scanned	scan	VBN	_	_	_
48	data	datum	NNS	_	_	_
49	,	,	,	_	_	_
50	which	which	WDT	_	_	_
51	was	be	VBD	_	_	_
52	subsequently	subsequently	RB	_	_	_
53	qunatile	qunatile	JJ	_	_	_
54	normalized	normalize	VBN	_	_	_
55	using	use	VBG	_	_	_
56	the	the	DT	_	_	_
57	statistical	statistical	JJ	_	_	_
58	program	program	NN	_	_	_
59	R	r	NN	_	_	_
60	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	sample	sample	NN	_	_	_
3	data	datum	NNS	_	_	_
4	table	table	NN	_	_	_
5	contains	contain	VBZ	_	_	_
6	the	the	DT	_	_	_
7	log2	log2	NN	_	_	_
8	ratio	ratio	NN	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	IP	IP	NNP	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	sample	sample	NN	_	_	_
14	type	type	NN	_	_	_
15	:	:	:	_	_	_
16	input	input	NN	_	_	_
17	control	control	NN	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Sodium	sodium	NN	_	_	_
20	phosphate	phosphate	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	1	1	CD	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	Aerobic	aerobic	JJ	_	_	_
25	cultures	culture	NNS	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	Anaerobic	anaerobic	JJ	_	_	_
28	cultures	culture	NNS	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
30	Anaerobic	anaerobic	JJ	_	_	_
31	,	,	,	_	_	_
32	Iron	iron	JJ	_	_	_
33	Deficient	deficient	JJ	_	_	_
34	cultures	culture	NNS	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
36	Call	call	VB	_	_	_
37	peaks	peak	NNS	_	_	_
38	to	to	TO	_	_	_
39	and	and	CC	_	_	_
40	FDR	FDR	NNP	_	_	_
41	0.1	0.1	CD	_	_	_
42	,	,	,	_	_	_
43	MOSAiCs	MOSAiCs	NNP	_	_	_
44	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
45	Cell	cell	NN	_	_	_
46	pellets	pellet	NNS	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	from	from	IN	_	_	_
49	initial	initial	JJ	_	_	_
50	250	250	CD	_	_	_
51	mL	ml	NN	_	_	_
52	of	of	IN	_	_	_
53	culture	culture	NN	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	were	be	VBD	_	_	_
56	thawed	thaw	VBN	_	_	_
57	and	and	CC	_	_	_
58	resuspended	resuspend	VBN	_	_	_
59	in	in	IN	_	_	_
60	250	250	CD	_	_	_
61	μL	μl	NN	_	_	_
62	of	of	IN	_	_	_
63	IP	IP	NNP	_	_	_
64	buffer	buffer	NN	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	100	100	CD	_	_	_
67	mM	mm	NN	KWSUPP	_	_
68	Tris	Tris	NNP	_	_	_
69	pH	ph	NN	_	_	_
70	8	8	CD	_	_	_
71	,	,	,	_	_	_
72	300	300	CD	_	_	_
73	mM	mm	NN	KWSUPP	_	_
74	NaCl	nacl	NN	_	_	_
75	,	,	,	_	_	_
76	1	1	CD	_	_	_
77	%	%	NN	_	_	_
78	TritonX-100	tritonx-100	NN	_	_	_
79	-RRB-	-rrb-	-RRB-	_	_	_
80	and	and	CC	_	_	_
81	sonicated	sonicate	VBN	_	_	_
82	using	use	VBG	_	_	_
83	a	a	DT	_	_	_
84	microtip	microtip	NN	_	_	_
85	sonicator	sonicator	NN	_	_	_
86	set	set	VBN	_	_	_
87	at	at	IN	_	_	_
88	10	10	CD	_	_	_
89	%	%	NN	_	_	_
90	output	output	NN	_	_	_
91	for	for	IN	_	_	_
92	20	20	CD	_	_	_
93	second	second	JJ	_	_	_
94	intervals	interval	NNS	_	_	_
95	with	with	IN	_	_	_
96	periods	period	NNS	_	_	_
97	of	of	IN	_	_	_
98	cooling	cool	VBG	_	_	_
99	in	in	IN	_	_	_
100	between	between	IN	_	_	_
101	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	treated	treat	VBN	_	_	_
5	for	for	IN	_	_	_
6	one	one	CD	_	_	_
7	hour	hour	NN	_	_	_
8	at	at	IN	_	_	_
9	4	4	CD	_	_	_
10	°C	°c	NN	_	_	_
11	with	with	IN	_	_	_
12	RNase	rnase	NN	_	_	_
13	A	a	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	2	2	CD	_	_	_
16	ng	ng	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Cells	cell	NNS	_	_	_
19	were	be	VBD	_	_	_
20	grown	grow	VBN	_	_	_
21	aerobically	aerobically	RB	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	70	70	CD	_	_	_
24	%	%	NN	_	_	_
25	N2	n2	NN	_	_	_
26	,	,	,	_	_	_
27	25	25	CD	_	_	_
28	%	%	NN	_	_	_
29	O2	o2	CD	_	_	_
30	,	,	,	_	_	_
31	and	and	CC	_	_	_
32	5	5	CD	_	_	_
33	%	%	NN	_	_	_
34	CO2	co2	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	or	or	CC	_	_	_
37	anaerobically	anaerobically	RB	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	95	95	CD	_	_	_
40	%	%	NN	_	_	_
41	N2	n2	NN	_	_	_
42	and	and	CC	_	_	_
43	5	5	CD	_	_	_
44	%	%	NN	_	_	_
45	CO2	co2	NN	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	until	until	IN	_	_	_
48	mid-log	mid-log	JJ	_	_	_
49	phase	phase	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	OD600	od600	NN	_	_	_
52	of	of	IN	_	_	_
53	~	~	NN	_	_	_
54	0.3-0.35	0.3-0.35	CD	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	chip	chip	NN	_	_	_
3	antibody	antibody	NN	_	_	_
4	:	:	:	_	_	_
5	Custom	Custom	NNP	_	_	_
6	anti-Fur	anti-fur	JJ	_	_	_
7	polyclonal	polyclonal	JJ	_	_	_
8	antibody	antibody	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
10	chip	chip	NN	_	_	_
11	antibody	antibody	NN	_	_	_
12	:	:	:	_	_	_
13	none	none	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	ChIP-Seq	chip-seq	JJ	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
17	Combined	combine	VBN	_	_	_
18	input	input	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
20	Custom	Custom	NNP	_	_	_
21	anti-Fur	anti-fur	JJ	_	_	_
22	antibodies	antibody	NNS	_	_	_
23	were	be	VBD	_	_	_
24	purified	purify	VBN	_	_	_
25	over	over	IN	_	_	_
26	a	a	DT	_	_	_
27	His6-Fur	his6-fur	NN	_	_	_
28	bound	bind	VBD	_	_	_
29	HiTrap	HiTrap	NNP	_	_	_
30	NHS-activated	NHS-activated	NNP	_	_	_
31	HP	HP	NNP	_	_	_
32	column	column	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	GE	GE	NNP	_	_	_
35	Healthcare	Healthcare	NNP	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	as	as	IN	_	_	_
38	previously	previously	RB	_	_	_
39	described	describe	VBN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	PMID	pmid	NN	_	_	_
42	:	:	:	_	_	_
43	21478858	21478858	CD	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	.	.	.	_	_	_

1	Western	western	NN	_	_	_
2	blot	blot	NN	_	_	_
3	analyses	analysis	NNS	_	_	_
4	showed	show	VBD	_	_	_
5	that	that	IN	_	_	_
6	the	the	DT	_	_	_
7	purified	purify	VBN	_	_	_
8	antibody	antibody	NN	_	_	_
9	was	be	VBD	_	_	_
10	specific	specific	JJ	_	_	_
11	for	for	IN	_	_	_
12	Fur	Fur	NNP	TF	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Deconvolute	deconvolute	JJ	_	_	_
3	peaks	peak	NNS	_	_	_
4	in	in	IN	_	_	_
5	close	close	JJ	_	_	_
6	proximity	proximity	NN	_	_	_
7	,	,	,	_	_	_
8	dPeak	dpeak	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	DNA	dna	NN	_	_	_
11	samples	sample	NNS	_	_	_
12	were	be	VBD	_	_	_
13	submitted	submit	VBN	_	_	_
14	to	to	TO	_	_	_
15	the	the	DT	_	_	_
16	University	University	NNP	_	_	_
17	of	of	IN	_	_	_
18	Wisconsin-Madison	Wisconsin-Madison	NNP	_	_	_
19	DNA	DNA	NNP	_	_	_
20	Sequencing	sequencing	NN	_	_	_
21	Facility	facility	NN	_	_	_
22	for	for	IN	_	_	_
23	ChIP-seq	ChIP-seq	NNP	_	_	_
24	library	library	NN	_	_	_
25	preparation	preparation	NN	_	_	_
26	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	libraries	library	NNS	_	_	_
3	were	be	VBD	_	_	_
4	generated	generate	VBN	_	_	_
5	using	use	VBG	_	_	_
6	reagents	reagent	NNS	_	_	_
7	from	from	IN	_	_	_
8	the	the	DT	_	_	_
9	Illumina	Illumina	NNP	_	_	_
10	Paired	Paired	NNP	_	_	_
11	End	End	NNP	_	_	_
12	Sample	Sample	NNP	_	_	_
13	Preparation	Preparation	NNP	_	_	_
14	Kit	kit	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Illumina	Illumina	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	the	the	DT	_	_	_
20	Illumina	Illumina	NNP	_	_	_
21	protocol	protocol	NN	_	_	_
22	``	``	``	_	_	_
23	Preparing	prepare	VBG	_	_	_
24	Samples	sample	NNS	_	_	_
25	for	for	IN	_	_	_
26	ChIP	chip	NN	_	_	_
27	Sequencing	sequencing	NN	_	_	_
28	of	of	IN	_	_	_
29	DNA	dna	NN	_	_	_
30	''	''	''	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Illumina	Illumina	NNP	_	_	_
33	part	part	NN	_	_	_
34	#	#	#	_	_	_
35	11257047	11257047	CD	_	_	_
36	RevA	reva	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	as	as	IN	_	_	_
39	per	per	IN	_	_	_
40	the	the	DT	_	_	_
41	manufacturer	manufacturer	NN	_	_	_
42	's	's	POS	_	_	_
43	instructions	instruction	NNS	_	_	_
44	,	,	,	_	_	_
45	except	except	IN	_	_	_
46	products	product	NNS	_	_	_
47	of	of	IN	_	_	_
48	the	the	DT	_	_	_
49	ligation	ligation	NN	_	_	_
50	reaction	reaction	NN	_	_	_
51	were	be	VBD	_	_	_
52	purified	purify	VBN	_	_	_
53	by	by	IN	_	_	_
54	gel	gel	NN	_	_	_
55	electrophoresis	electrophoresis	NN	_	_	_
56	using	use	VBG	_	_	_
57	2	2	CD	_	_	_
58	%	%	NN	_	_	_
59	SizeSelect	sizeselect	NN	_	_	_
60	agarose	agarose	NN	_	_	_
61	gels	gel	NNS	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	Invitrogen	Invitrogen	NNP	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	targeting	target	VBG	_	_	_
66	50	50	CD	_	_	_
67	bp	bp	NN	_	_	_
68	fragments	fragment	NNS	_	_	_
69	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	library	library	NN	_	_	_
3	construction	construction	NN	_	_	_
4	and	and	CC	_	_	_
5	amplification	amplification	NN	_	_	_
6	,	,	,	_	_	_
7	quality	quality	NN	_	_	_
8	and	and	CC	_	_	_
9	quantity	quantity	NN	_	_	_
10	were	be	VBD	_	_	_
11	assessed	assess	VBN	_	_	_
12	using	use	VBG	_	_	_
13	an	a	DT	_	_	_
14	Agilent	agilent	JJ	_	_	_
15	DNA	dna	NN	_	_	_
16	1000	1000	CD	_	_	_
17	series	series	NN	_	_	_
18	chip	chip	NN	_	_	_
19	assay	assay	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Agilent	agilent	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	and	and	CC	_	_	_
24	QuantIT	quantit	NN	_	_	_
25	PicoGreen	picogreen	NN	_	_	_
26	dsDNA	dsdna	NN	_	_	_
27	Kit	kit	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Invitrogen	invitrogen	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	,	,	,	_	_	_
32	respectively	respectively	RB	_	_	_
33	,	,	,	_	_	_
34	and	and	CC	_	_	_
35	libraries	library	NNS	_	_	_
36	were	be	VBD	_	_	_
37	standardized	standardized	JJ	_	_	_
38	to	to	TO	_	_	_
39	10μM	10μm	NN	_	_	_
40	.	.	.	_	_	_

1	Cluster	cluster	NN	_	_	_
2	generation	generation	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	using	use	VBG	_	_	_
6	a	a	DT	_	_	_
7	cBot	cBot	NNP	_	_	_
8	Single	single	JJ	_	_	_
9	Read	Read	NNP	_	_	_
10	Cluster	Cluster	NNP	_	_	_
11	Generation	Generation	NNP	_	_	_
12	Kit	kit	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	v4	v4	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	and	and	CC	_	_	_
17	placed	place	VBN	_	_	_
18	on	on	IN	_	_	_
19	the	the	DT	_	_	_
20	Illumina	Illumina	NNP	_	_	_
21	cBot	cBot	NNP	_	_	_
22	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	aerobic	aerobic	JJ	_	_	_
3	and	and	CC	_	_	_
4	anaerobic	anaerobic	JJ	_	_	_
5	replicates	replicate	VBZ	_	_	_
6	A	a	NN	_	_	_
7	,	,	,	_	_	_
8	a	a	DT	_	_	_
9	single	single	JJ	_	_	_
10	read	read	NN	_	_	_
11	,	,	,	_	_	_
12	50	50	CD	_	_	_
13	bp	bp	NN	_	_	_
14	run	run	NN	_	_	_
15	was	be	VBD	_	_	_
16	performed	perform	VBN	_	_	_
17	,	,	,	_	_	_
18	using	use	VBG	_	_	_
19	standard	standard	JJ	_	_	_
20	SBS	SBS	NNP	_	_	_
21	kits	kit	NNS	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	v4	v4	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	and	and	CC	_	_	_
26	SCS	scs	NN	_	_	_
27	2.6	2.6	CD	_	_	_
28	on	on	IN	_	_	_
29	an	a	DT	_	_	_
30	Illumina	Illumina	NNP	_	_	_
31	Genome	Genome	NNP	_	_	_
32	Analyzer	Analyzer	NNP	_	_	_
33	IIx	IIx	NNP	_	_	_
34	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	aerobic	aerobic	JJ	_	_	_
3	and	and	CC	_	_	_
4	anaerobic	anaerobic	JJ	_	_	_
5	replicates	replicate	VBZ	_	_	_
6	B	b	NN	_	_	_
7	and	and	CC	_	_	_
8	C	c	NN	_	_	_
9	,	,	,	_	_	_
10	the	the	DT	_	_	_
11	input	input	NN	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	the	the	DT	_	_	_
15	anaerobic	anaerobic	JJ	_	_	_
16	,	,	,	_	_	_
17	iron	iron	NN	_	_	_
18	deficient	deficient	JJ	_	_	_
19	samples	sample	NNS	_	_	_
20	,	,	,	_	_	_
21	a	a	DT	_	_	_
22	single	single	JJ	_	_	_
23	read	read	NN	_	_	_
24	,	,	,	_	_	_
25	50	50	CD	_	_	_
26	bp	bp	NN	_	_	_
27	run	run	NN	_	_	_
28	was	be	VBD	_	_	_
29	performed	perform	VBN	_	_	_
30	,	,	,	_	_	_
31	using	use	VBG	_	_	_
32	standard	standard	JJ	_	_	_
33	SBS	SBS	NNP	_	_	_
34	kits	kit	NNS	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	v3	v3	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	and	and	CC	_	_	_
39	SCS	scs	NN	_	_	_
40	1.8.2	1.8.2	CD	_	_	_
41	on	on	IN	_	_	_
42	an	a	DT	_	_	_
43	Illumina	Illumina	NNP	_	_	_
44	HiSeq2000	hiseq2000	NN	_	_	_
45	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
3	Fur	Fur	NNP	TF	_	_
4	IP	IP	NNP	_	_	_
5	ChIP-Seq	ChIP-Seq	NNP	_	_	_
6	Aerobic	Aerobic	NNP	_	_	_
7	A	A	NNP	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	Fur	Fur	NNP	TF	_	_
10	IP	IP	NNP	_	_	_
11	ChIP-Seq	ChIP-Seq	NNP	_	_	_
12	Aerobic	Aerobic	NNP	_	_	_
13	B	B	NNP	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	Fur	Fur	NNP	TF	_	_
16	IP	IP	NNP	_	_	_
17	ChIP-Seq	ChIP-Seq	NNP	_	_	_
18	Aerobic	Aerobic	NNP	_	_	_
19	C	C	NNP	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	Fur	Fur	NNP	TF	_	_
22	IP	IP	NNP	_	_	_
23	ChIP-Seq	ChIP-Seq	NNP	_	_	_
24	Anaerobic	Anaerobic	NNP	_	_	_
25	A	A	NNP	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	Fur	Fur	NNP	TF	_	_
28	IP	IP	NNP	_	_	_
29	ChIP-Seq	ChIP-Seq	NNP	_	_	_
30	Anaerobic	anaerobic	JJ	_	_	_
31	B	b	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
33	Fur	Fur	NNP	TF	_	_
34	IP	IP	NNP	_	_	_
35	ChIP-Seq	ChIP-Seq	NNP	_	_	_
36	Anaerobic	Anaerobic	NNP	_	_	_
37	C	C	NNP	_	_	_
38	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
39	Fur	Fur	NNP	TF	_	_
40	IP	IP	NNP	_	_	_
41	ChIP-Seq	ChIP-Seq	NNP	_	_	_
42	Anaerobic	Anaerobic	NNP	_	_	_
43	,	,	,	_	_	_
44	Iron	Iron	NNP	_	_	_
45	Deficient	Deficient	NNP	_	_	_
46	A	A	NNP	_	_	_
47	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
48	Fur	Fur	NNP	TF	_	_
49	IP	IP	NNP	_	_	_
50	ChIP-Seq	ChIP-Seq	NNP	_	_	_
51	Anaerobic	Anaerobic	NNP	_	_	_
52	,	,	,	_	_	_
53	Iron	Iron	NNP	_	_	_
54	Deficient	deficient	JJ	_	_	_
55	B	b	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	Genome	Genome	NNP	_	_	_
58	_	_	NNP	_	_	_
59	build	build	VB	_	_	_
60	:	:	:	_	_	_
61	Escherichia	escherichia	FW	Organism	_	_
62	coli	coli	FW	Organism	_	_
63	MG1655	mg1655	NN	_	_	_
64	K-12	k-12	NN	_	_	_
65	genome	genome	NN	_	_	_
66	version	version	NN	_	_	_
67	U00096	u00096	NN	_	_	_
68	.2	.2	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	genotype	genotype	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	growth	growth	NN	_	_	_
73	medium	medium	NN	_	_	_
74	:	:	:	_	_	_
75	Combined	combine	VBN	_	_	_
76	input	input	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	growth	growth	NN	_	_	_
79	medium	medium	NN	_	_	_
80	:	:	:	_	_	_
81	MOPS	mop	NNS	MED	_	_
82	minimal	minimal	JJ	_	_	_
83	glucose	glucose	NN	SUPP	_	_
84	media	media	NNS	_	_	_
85	containing	contain	VBG	_	_	_
86	10	10	CD	_	_	_
87	µM	µm	NN	_	_	_
88	FeSO4	feso4	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	growth	growth	NN	_	_	_
91	medium	medium	NN	_	_	_
92	:	:	:	_	_	_
93	MOPS	mop	NNS	MED	_	_
94	minimal	minimal	JJ	_	_	_
95	glucose	glucose	NN	SUPP	_	_
96	media	media	NNS	_	_	_
97	containing	contain	VBG	_	_	_
98	1	1	CD	_	_	_
99	µM	µm	NN	_	_	_
100	FeSO4	feso4	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	Input	input	NN	_	_	_
103	ChIP-Seq	chip-seq	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
105	Map	map	NN	_	_	_
106	reads	read	VBZ	_	_	_
107	to	to	TO	_	_	_
108	theEscherichia	theescherichia	FW	_	_	_
109	coli	coli	FW	_	_	_
110	MG1655	mg1655	NN	_	_	_
111	K-12	k-12	NN	_	_	_
112	genome	genome	NN	_	_	_
113	,	,	,	_	_	_
114	Bowtie	bowtie	NN	_	_	_
115	2	2	CD	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
117	Reformat	reformat	VB	_	_	_
118	Illumina	Illumina	NNP	_	_	_
119	files	file	NNS	_	_	_
120	to	to	TO	_	_	_
121	Sanger	Sanger	NNP	_	_	_
122	format	format	NN	_	_	_
123	,	,	,	_	_	_
124	FASTQ	FASTQ	NNP	_	_	_
125	Groomer	Groomer	NNP	_	_	_
126	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
127	Require	require	VB	_	_	_
128	peaks	peak	NNS	_	_	_
129	to	to	TO	_	_	_
130	be	be	VB	_	_	_
131	present	present	JJ	_	_	_
132	in	in	IN	_	_	_
133	at	at	IN	_	_	_
134	least	least	JJS	_	_	_
135	2	2	CD	_	_	_
136	replicates	replicate	VBZ	_	_	_
137	and	and	CC	_	_	_
138	conform	conform	VB	_	_	_
139	to	to	TO	_	_	_
140	a	a	DT	_	_	_
141	peak	peak	JJ	_	_	_
142	shape	shape	NN	_	_	_
143	by	by	IN	_	_	_
144	visual	visual	JJ	_	_	_
145	inspection	inspection	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	Scale	Scale	NNP	_	_	_
148	data	datum	NNS	_	_	_
149	set	set	VBN	_	_	_
150	to	to	TO	_	_	_
151	20	20	CD	_	_	_
152	million	million	CD	_	_	_
153	reads	read	VBZ	_	_	_
154	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
155	Sodium	sodium	NN	_	_	_
156	phosphate	phosphate	NN	_	_	_
157	-LRB-	-lrb-	-LRB-	_	_	_
158	1	1	CD	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	Supplementary	supplementary	JJ	_	_	_
161	_	_	NN	_	_	_
162	files	file	NNS	_	_	_
163	_	_	IN	_	_	_
164	format	format	NN	_	_	_
165	_	_	NN	_	_	_
166	and	and	CC	_	_	_
167	_	_	NN	_	_	_
168	content	content	NN	_	_	_
169	:	:	:	_	_	_
170	Processed	process	VBN	_	_	_
171	data	datum	NNS	_	_	_
172	files	file	NNS	_	_	_
173	contain	contain	VBP	_	_	_
174	the	the	DT	_	_	_
175	number	number	NN	_	_	_
176	of	of	IN	_	_	_
177	reads	read	VBZ	_	_	_
178	mapped	map	VBN	_	_	_
179	to	to	TO	_	_	_
180	each	each	DT	_	_	_
181	base	base	NN	_	_	_
182	pair	pair	NN	_	_	_
183	after	after	IN	_	_	_
184	the	the	DT	_	_	_
185	total	total	JJ	_	_	_
186	number	number	NN	_	_	_
187	of	of	IN	_	_	_
188	reads	read	VBZ	_	_	_
189	were	be	VBD	_	_	_
190	scaled	scale	VBN	_	_	_
191	to	to	TO	_	_	_
192	20	20	CD	_	_	_
193	million	million	CD	_	_	_
194	reads	read	VBZ	_	_	_
195	per	per	IN	_	_	_
196	experiment	experiment	NN	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	5	5	CD	_	_	_
199	'	'	''	_	_	_
200	10	10	CD	_	_	_
201	ug	ug	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	5	5	CD	_	_	_
204	'	'	''	_	_	_
205	15	15	CD	_	_	_
206	ug	ug	NN	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	5	5	CD	_	_	_
209	'	'	''	_	_	_
210	+50	+50	CD	_	_	_
211	ug	ug	NN	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
213	Bacteria	bacterium	NNS	_	_	_
214	were	be	VBD	_	_	_
215	lyzed	lyze	VBN	_	_	_
216	with	with	IN	_	_	_
217	lyzozyme	lyzozyme	NN	_	_	_
218	and	and	CC	_	_	_
219	sonicated	sonicate	VBN	_	_	_
220	to	to	TO	_	_	_
221	shear	shear	NN	_	_	_
222	DNA	dna	NN	_	_	_
223	.	.	.	_	_	_

1	TopoIV-DNA	topoiv-dna	JJ	_	_	_
2	complexes	complex	NNS	_	_	_
3	were	be	VBD	_	_	_
4	isolated	isolate	VBN	_	_	_
5	with	with	IN	_	_	_
6	antibody	antibody	NN	_	_	_
7	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Basecalls	basecall	NNS	_	_	_
3	performed	perform	VBN	_	_	_
4	using	use	VBG	_	_	_
5	CASAVA	CASAVA	NNP	_	_	_
6	version	version	NN	_	_	_
7	1.8.2	1.8.2	CD	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
9	chip	chip	NN	_	_	_
10	antibody	antibody	NN	_	_	_
11	:	:	:	_	_	_
12	antiFlag	antiflag	NN	_	_	_
13	M2	m2	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
15	chip	chip	NN	_	_	_
16	antibody	antibody	NN	_	_	_
17	:	:	:	_	_	_
18	none	none	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	ChIP-Seq	chip-seq	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	ChIP-seq	chip-seq	NN	_	_	_
23	reads	read	VBZ	_	_	_
24	were	be	VBD	_	_	_
25	aligned	align	VBN	_	_	_
26	to	to	TO	_	_	_
27	the	the	DT	_	_	_
28	E.	e.	FW	_	_	_
29	coli	coli	FW	_	_	_
30	NC	nc	FW	_	_	_
31	_	_	SYM	_	_	_
32	000913	000913	CD	_	_	_
33	genome	genome	NN	_	_	_
34	using	use	VBG	_	_	_
35	BWA	BWA	NNP	_	_	_
36	0.6.2	0.6.2	CD	_	_	_
37	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
38	E.	E.	NNP	_	_	_
39	coli	coli	NN	_	_	_
40	MG1655	mg1655	NN	_	_	_
41	parC	parc	NN	GEN	_	_
42	:	:	:	_	_	_
43	:	:	:	_	_	_
44	flag	flag	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	E.	e.	FW	_	_	_
47	coli	coli	FW	_	_	_
48	MG1655	mg1655	NN	_	_	_
49	parE	pare	NN	GEN	_	_
50	:	:	:	_	_	_
51	:	:	:	_	_	_
52	flag	flag	NN	_	_	_
53	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
54	E.	E.	NNP	_	_	_
55	coli	coli	NNS	_	_	_
56	were	be	VBD	_	_	_
57	grown	grow	VBN	_	_	_
58	in	in	IN	_	_	_
59	LB	lb	NN	_	_	_
60	or	or	CC	_	_	_
61	minimal	minimal	JJ	_	_	_
62	medium	medium	NN	_	_	_
63	supplemented	supplement	VBN	_	_	_
64	with	with	IN	_	_	_
65	casaminoacids	casaminoacid	NNS	_	_	_
66	-LRB-	-lrb-	-LRB-	_	_	_
67	0,1	0,1	CD	_	_	_
68	%	%	NN	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	and	and	CC	_	_	_
71	succinate	succinate	NN	SUPP	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	0,1	0,1	CD	_	_	_
74	%	%	NN	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	until	until	IN	_	_	_
77	OD	od	NN	_	_	_
78	0,2-0,4	0,2-0,4	CD	_	_	_
79	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
80	Escherichia	escherichia	FW	Organism	_	_
81	coli	coli	FW	Organism	_	_
82	str	str	FW	_	_	_
83	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	For	for	IN	_	_	_
4	ChIP-seq	chip-seq	JJ	_	_	_
5	experiments	experiment	NNS	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	culture	culture	NN	_	_	_
9	were	be	VBD	_	_	_
10	fixed	fix	VBN	_	_	_
11	with	with	IN	_	_	_
12	formaldehyde	formaldehyde	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	1	1	CD	_	_	_
15	%	%	NN	_	_	_
16	final	final	JJ	_	_	_
17	concentration	concentration	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	;	;	:	_	_	_
20	for	for	IN	_	_	_
21	NorfliP	norflip	NN	_	_	_
22	experiments	experiment	NNS	_	_	_
23	TopoIV	topoiv	NN	_	_	_
24	was	be	VBD	_	_	_
25	crosslinked	crosslink	VBN	_	_	_
26	with	with	IN	_	_	_
27	Norfloxacin	norfloxacin	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	2µM	2µm	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Genome	Genome	NNP	_	_	_
33	_	_	NNP	_	_	_
34	build	build	VB	_	_	_
35	:	:	:	_	_	_
36	NC	NC	NNP	_	_	_
37	_	_	NNP	_	_	_
38	000913	000913	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	growth	growth	NN	_	_	_
41	conditions	condition	NNS	_	_	_
42	:	:	:	_	_	_
43	LB	lb	NN	_	_	_
44	growth	growth	NN	_	_	_
45	OD	od	NN	_	_	_
46	0,3	0,3	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	growth	growth	NN	_	_	_
49	conditions	condition	NNS	_	_	_
50	:	:	:	_	_	_
51	LB	lb	NN	_	_	_
52	growth	growth	NN	_	_	_
53	OD	od	NN	_	_	_
54	0,5	0,5	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	growth	growth	NN	_	_	_
57	conditions	condition	NNS	_	_	_
58	:	:	:	_	_	_
59	Minimal	minimal	JJ	_	_	_
60	Medium	medium	NN	_	_	_
61	A	a	DT	_	_	_
62	supplemented	supplement	VBN	_	_	_
63	with	with	IN	_	_	_
64	casaminoacids	casaminoacid	NNS	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	0,1	0,1	CD	_	_	_
67	%	%	NN	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	and	and	CC	_	_	_
70	succinate	succinate	NN	SUPP	_	_
71	-LRB-	-lrb-	-LRB-	_	_	_
72	0,2	0,2	CD	_	_	_
73	%	%	NN	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	,	,	,	_	_	_
76	OD	od	NN	_	_	_
77	0,2	0,2	CD	_	_	_
78	at	at	IN	_	_	_
79	40	40	CD	_	_	_
80	°C	°c	NN	_	_	_
81	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
82	Input	Input	NNP	_	_	_
83	ParC-flag	ParC-flag	NNP	_	_	_
84	1	1	CD	_	_	_
85	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
86	Input	Input	NNP	_	_	_
87	ParE-flag	ParE-flag	NNP	_	_	_
88	1	1	CD	_	_	_
89	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
90	Input	Input	NNP	_	_	_
91	ParE-flag	ParE-flag	NNP	_	_	_
92	2	2	CD	_	_	_
93	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
94	Input	Input	NNP	_	_	_
95	ParE-flag	ParE-flag	NNP	_	_	_
96	G1	g1	NN	_	_	_
97	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
98	Input	Input	NNP	_	_	_
99	ParE-flag	ParE-flag	NNP	_	_	_
100	G2	g2	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	Input	input	NN	_	_	_
103	ParE-flag	pare-flag	NN	_	_	_
104	S20min	s20min	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	Input	input	NN	_	_	_
107	ParE-flag	pare-flag	NN	_	_	_
108	S40min	s40min	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	IP	IP	NNP	_	_	_
111	ParC-flag	ParC-flag	NNP	_	_	_
112	1	1	CD	_	_	_
113	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
114	IP	IP	NNP	_	_	_
115	ParE-flag	ParE-flag	NNP	_	_	_
116	1	1	CD	_	_	_
117	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
118	IP	IP	NNP	_	_	_
119	ParE-flag	ParE-flag	NNP	_	_	_
120	2	2	CD	_	_	_
121	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
122	IP	IP	NNP	_	_	_
123	ParE-flag	ParE-flag	NNP	_	_	_
124	G1	g1	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	IP	IP	NNP	_	_	_
127	ParE-flag	ParE-flag	NNP	_	_	_
128	G2	g2	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	IP	IP	NNP	_	_	_
131	ParE-flag	ParE-flag	NNP	_	_	_
132	S20min	S20min	NNP	_	_	_
133	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
134	IP	IP	NNP	_	_	_
135	ParE-flag	ParE-flag	NNP	_	_	_
136	S40min	S40min	NNP	_	_	_
137	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
138	Libraries	Libraries	NNPS	_	_	_
139	were	be	VBD	_	_	_
140	prepared	prepared	JJ	_	_	_
141	according	accord	VBG	_	_	_
142	to	to	TO	_	_	_
143	Illumina	Illumina	NNP	_	_	_
144	's	's	POS	_	_	_
145	instructions	instruction	NNS	_	_	_
146	accompanying	accompany	VBG	_	_	_
147	the	the	DT	_	_	_
148	DNA	dna	NN	_	_	_
149	Sample	sample	NN	_	_	_
150	Kit	kit	NN	_	_	_
151	-LRB-	-lrb-	-LRB-	_	_	_
152	FC-104-5001	fc-104-5001	NN	_	_	_
153	-RRB-	-rrb-	-RRB-	_	_	_
154	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	DNA	dna	NN	_	_	_
4	was	be	VBD	_	_	_
5	end-repaired	end-repaired	JJ	_	_	_
6	using	use	VBG	_	_	_
7	a	a	DT	_	_	_
8	combination	combination	NN	_	_	_
9	of	of	IN	_	_	_
10	T4	t4	NN	_	_	_
11	DNA	dna	NN	_	_	_
12	polymerase	polymerase	NN	_	_	_
13	,	,	,	_	_	_
14	E.	e.	FW	_	_	_
15	coli	coli	FW	_	_	_
16	DNA	dna	NN	_	_	_
17	Pol	pol	NN	_	_	_
18	I	I	PRP	_	_	_
19	large	large	JJ	_	_	_
20	fragment	fragment	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Klenow	klenow	NN	_	_	_
23	polymerase	polymerase	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	and	and	CC	_	_	_
26	T4	t4	NN	_	_	_
27	polynucleotide	polynucleotide	NN	_	_	_
28	kinase	kinase	NN	_	_	_
29	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	blunt	blunt	JJ	_	_	_
3	,	,	,	_	_	_
4	phosphorylated	phosphorylated	JJ	_	_	_
5	ends	end	NNS	_	_	_
6	were	be	VBD	_	_	_
7	treated	treat	VBN	_	_	_
8	with	with	IN	_	_	_
9	Klenow	Klenow	NNP	_	_	_
10	fragment	fragment	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	32	32	CD	_	_	_
13	to	to	TO	_	_	_
14	52	52	CD	_	_	_
15	exo	exo	NN	_	_	_
16	minus	minus	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	dATP	datp	NN	_	_	_
20	to	to	TO	_	_	_
21	yield	yield	VB	_	_	_
22	a	a	DT	_	_	_
23	protruding	protrude	VBG	_	_	_
24	3	3	LS	_	_	_
25	-	-	:	_	_	_
26	`	`	``	_	_	_
27	A	a	DT	_	_	_
28	'	'	''	_	_	_
29	base	base	NN	_	_	_
30	for	for	IN	_	_	_
31	ligation	ligation	NN	_	_	_
32	of	of	IN	_	_	_
33	Illumina	Illumina	NNP	_	_	_
34	's	's	POS	_	_	_
35	adapters	adapter	NNS	_	_	_
36	which	which	WDT	_	_	_
37	have	have	VBP	_	_	_
38	a	a	DT	_	_	_
39	single	single	JJ	_	_	_
40	`	`	``	_	_	_
41	T	t	NN	_	_	_
42	'	'	''	_	_	_
43	base	base	NN	_	_	_
44	overhang	overhang	NN	_	_	_
45	at	at	IN	_	_	_
46	the	the	DT	_	_	_
47	3	3	CD	_	_	_
48	'	'	''	_	_	_
49	end	end	NN	_	_	_
50	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	adapter	adapter	NN	_	_	_
3	ligation	ligation	NN	_	_	_
4	DNA	dna	NN	_	_	_
5	was	be	VBD	_	_	_
6	PCR	pcr	NN	_	_	_
7	amplified	amplify	VBN	_	_	_
8	with	with	IN	_	_	_
9	Illumina	Illumina	NNP	_	_	_
10	primers	primer	NNS	_	_	_
11	for	for	IN	_	_	_
12	15	15	CD	_	_	_
13	cycles	cycle	NNS	_	_	_
14	and	and	CC	_	_	_
15	library	library	NN	_	_	_
16	fragments	fragment	NNS	_	_	_
17	of	of	IN	_	_	_
18	~	~	NN	_	_	_
19	250	250	CD	_	_	_
20	bp	bp	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	insert	insert	NN	_	_	_
23	plus	plus	CC	_	_	_
24	adaptor	adaptor	NN	_	_	_
25	and	and	CC	_	_	_
26	PCR	pcr	NN	_	_	_
27	primer	primer	NN	_	_	_
28	sequences	sequence	NNS	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	were	be	VBD	_	_	_
31	band	band	NN	_	_	_
32	isolated	isolate	VBN	_	_	_
33	from	from	IN	_	_	_
34	an	a	DT	_	_	_
35	agarose	agarose	NN	_	_	_
36	gel	gel	NN	_	_	_
37	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	purified	purify	VBN	_	_	_
3	DNA	dna	NN	_	_	_
4	was	be	VBD	_	_	_
5	captured	capture	VBN	_	_	_
6	on	on	IN	_	_	_
7	an	a	DT	_	_	_
8	Illumina	Illumina	NNP	_	_	_
9	flow	flow	NN	_	_	_
10	cell	cell	NN	_	_	_
11	for	for	IN	_	_	_
12	cluster	cluster	NN	_	_	_
13	generation	generation	NN	_	_	_
14	.	.	.	_	_	_

1	Libraries	library	NNS	_	_	_
2	were	be	VBD	_	_	_
3	sequenced	sequence	VBN	_	_	_
4	on	on	IN	_	_	_
5	the	the	DT	_	_	_
6	Genome	Genome	NNP	_	_	_
7	Analyzer	Analyzer	NNP	_	_	_
8	following	follow	VBG	_	_	_
9	the	the	DT	_	_	_
10	manufacturer	manufacturer	NN	_	_	_
11	's	's	POS	_	_	_
12	protocols	protocol	NNS	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	NorflIP	norflip	NN	_	_	_
3	Input	input	NN	_	_	_
4	ParC-flag	parc-flag	NN	_	_	_
5	1	1	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	NorflIP	norflip	NN	_	_	_
8	Input	input	NN	_	_	_
9	ParC-flag	parc-flag	NN	_	_	_
10	2	2	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	NorflIP	norflip	NN	_	_	_
13	Input	input	NN	_	_	_
14	ParE-flag	pare-flag	NN	_	_	_
15	1	1	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	NorflIP	norflip	NN	_	_	_
18	IP	IP	NNP	_	_	_
19	ParC-flag	ParC-flag	NNP	_	_	_
20	1	1	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	NorflIP	norflip	NN	_	_	_
23	IP	IP	NNP	_	_	_
24	ParC-flag	ParC-flag	NNP	_	_	_
25	2	2	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	NorflIP	norflip	NN	_	_	_
28	IP	IP	NNP	_	_	_
29	ParE-flag	ParE-flag	NNP	_	_	_
30	1	1	CD	_	_	_
31	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
32	Supplementary	Supplementary	NNP	_	_	_
33	_	_	VBD	_	_	_
34	files	file	NNS	_	_	_
35	_	_	IN	_	_	_
36	format	format	NN	_	_	_
37	_	_	NN	_	_	_
38	and	and	CC	_	_	_
39	_	_	NN	_	_	_
40	content	content	NN	_	_	_
41	:	:	:	_	_	_
42	Enrichement	enrichement	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	IP	IP	NNP	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	bla	bla	NN	_	_	_
47	_	_	NN	_	_	_
48	0	0	CD	_	_	_
49	min	min	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	bla	bla	NN	_	_	_
52	_	_	CD	_	_	_
53	10	10	CD	_	_	_
54	min	min	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	bla	bla	NN	_	_	_
57	_	_	CD	_	_	_
58	15	15	CD	_	_	_
59	min	min	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	bla	bla	NN	_	_	_
62	_	_	NN	_	_	_
63	1	1	CD	_	_	_
64	min	min	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	bla	bla	NN	_	_	_
67	_	_	NN	_	_	_
68	2	2	CD	_	_	_
69	min	min	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	bla	bla	NN	_	_	_
72	_	_	CD	_	_	_
73	4	4	CD	_	_	_
74	min	min	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	bla	bla	NN	_	_	_
77	_	_	CD	_	_	_
78	6	6	CD	_	_	_
79	min	min	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	bla	bla	NN	_	_	_
82	_	_	CD	_	_	_
83	8	8	CD	_	_	_
84	min	min	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	Cells	cell	NNS	_	_	_
87	were	be	VBD	_	_	_
88	collected	collect	VBN	_	_	_
89	as	as	IN	_	_	_
90	a	a	DT	_	_	_
91	function	function	NN	_	_	_
92	of	of	IN	_	_	_
93	time	time	NN	_	_	_
94	after	after	IN	_	_	_
95	rifampicin	rifampicin	NN	SUPP	_	_
96	treatment	treatment	NN	_	_	_
97	at	at	IN	_	_	_
98	the	the	DT	_	_	_
99	specified	specify	VBN	_	_	_
100	times	time	NNS	_	_	_
101	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	extracted	extract	VBN	_	_	_
4	using	use	VBG	_	_	_
5	the	the	DT	_	_	_
6	RNAsnap	rnasnap	NN	_	_	_
7	protocol	protocol	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	to	to	TO	_	_	_
6	an	a	DT	_	_	_
7	OD	od	NN	_	_	_
8	_	_	NN	_	_	_
9	600	600	CD	_	_	_
10	of	of	IN	_	_	_
11	0.4	0.4	CD	_	_	_
12	in	in	IN	_	_	_
13	Luria	Luria	NNP	_	_	_
14	Broth	Broth	NNP	_	_	_
15	Lennox	Lennox	NNP	_	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Cells	cell	NNS	_	_	_
18	were	be	VBD	_	_	_
19	treated	treat	VBN	_	_	_
20	with	with	IN	_	_	_
21	rifampicin	rifampicin	NN	SUPP	_	_
22	before	before	IN	_	_	_
23	sample	sample	NN	_	_	_
24	collection	collection	NN	_	_	_
25	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	some	some	DT	_	_	_
3	cases	case	NNS	_	_	_
4	,	,	,	_	_	_
5	kasugamycin	kasugamycin	NN	_	_	_
6	was	be	VBD	_	_	_
7	added	add	VBN	_	_	_
8	15	15	CD	_	_	_
9	minutes	minute	NNS	_	_	_
10	before	before	IN	_	_	_
11	the	the	DT	_	_	_
12	rifampicin	rifampicin	NN	SUPP	_	_
13	addition	addition	NN	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	csv	csv	NN	_	_	_
3	files	file	NNS	_	_	_
4	contain	contain	VBP	_	_	_
5	16	16	CD	_	_	_
6	columns	column	NNS	_	_	_
7	of	of	IN	_	_	_
8	the	the	DT	_	_	_
9	data	datum	NNS	_	_	_
10	,	,	,	_	_	_
11	each	each	DT	_	_	_
12	pair	pair	NN	_	_	_
13	corresponds	correspond	VBZ	_	_	_
14	to	to	TO	_	_	_
15	the	the	DT	_	_	_
16	counts	count	NNS	_	_	_
17	from	from	IN	_	_	_
18	the	the	DT	_	_	_
19	top	top	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	odd	odd	JJ	_	_	_
22	numbers	number	NNS	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	and	and	CC	_	_	_
25	bottom	bottom	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	even	even	RB	_	_	_
28	numbers	number	NNS	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	strand	strand	NN	_	_	_
31	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	first	first	JJ	_	_	_
3	pair	pair	NN	_	_	_
4	corresponds	correspond	VBZ	_	_	_
5	to	to	TO	_	_	_
6	counts	count	NNS	_	_	_
7	collected	collect	VBN	_	_	_
8	at	at	IN	_	_	_
9	0	0	CD	_	_	_
10	minutes	minute	NNS	_	_	_
11	after	after	IN	_	_	_
12	rifampicin	rifampicin	NN	SUPP	_	_
13	addition	addition	NN	_	_	_
14	.	.	.	_	_	_

1	Similarly	similarly	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	second	second	JJ	_	_	_
5	,	,	,	_	_	_
6	third	third	JJ	_	_	_
7	,	,	,	_	_	_
8	fourth	fourth	JJ	_	_	_
9	,	,	,	_	_	_
10	fifth	fifth	JJ	_	_	_
11	,	,	,	_	_	_
12	sixth	sixth	JJ	_	_	_
13	,	,	,	_	_	_
14	seventh	seventh	JJ	_	_	_
15	,	,	,	_	_	_
16	and	and	CC	_	_	_
17	eigth	eigth	NN	_	_	_
18	pairs	pair	NNS	_	_	_
19	correspond	correspond	VBP	_	_	_
20	to	to	TO	_	_	_
21	counts	count	NNS	_	_	_
22	collected	collect	VBN	_	_	_
23	at	at	IN	_	_	_
24	2	2	CD	_	_	_
25	,	,	,	_	_	_
26	4	4	CD	_	_	_
27	,	,	,	_	_	_
28	6	6	CD	_	_	_
29	,	,	,	_	_	_
30	8	8	CD	_	_	_
31	,	,	,	_	_	_
32	10	10	CD	_	_	_
33	,	,	,	_	_	_
34	15	15	CD	_	_	_
35	,	,	,	_	_	_
36	and	and	CC	_	_	_
37	20	20	CD	_	_	_
38	minutes	minute	NNS	_	_	_
39	after	after	IN	_	_	_
40	rifampicin	rifampicin	NN	SUPP	_	_
41	addition	addition	NN	_	_	_
42	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	ith	ith	NN	_	_	_
3	row	row	NN	_	_	_
4	in	in	IN	_	_	_
5	each	each	DT	_	_	_
6	column	column	NN	_	_	_
7	corresponds	correspond	VBZ	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	number	number	NN	_	_	_
11	of	of	IN	_	_	_
12	alignments	alignment	NNS	_	_	_
13	at	at	IN	_	_	_
14	the	the	DT	_	_	_
15	ith	ith	NN	_	_	_
16	base	base	NN	_	_	_
17	in	in	IN	_	_	_
18	NC	NC	NNP	_	_	_
19	_	_	SYM	_	_	_
20	000913.2	000913.2	CD	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	with	with	IN	_	_	_
6	Dnase	Dnase	NNP	_	_	_
7	I.	I.	NNP	_	_	_
8	rRNA	rrna	NN	_	_	_
9	was	be	VBD	_	_	_
10	removed	remove	VBN	_	_	_
11	with	with	IN	_	_	_
12	the	the	DT	_	_	_
13	gram-negative	gram-negative	JJ	_	_	_
14	RiboZero	RiboZero	NNP	_	_	_
15	kit	kit	NN	_	_	_
16	.	.	.	_	_	_

1	Libraries	library	NNS	_	_	_
2	were	be	VBD	_	_	_
3	prepared	prepare	VBN	_	_	_
4	with	with	IN	_	_	_
5	the	the	DT	_	_	_
6	RNAUltra	rnaultra	NN	_	_	_
7	directional	directional	JJ	_	_	_
8	kit	kit	NN	_	_	_
9	from	from	IN	_	_	_
10	New	New	NNP	_	_	_
11	England	England	NNP	_	_	_
12	Biolabs	Biolabs	NNP	_	_	_
13	for	for	IN	_	_	_
14	total	total	JJ	_	_	_
15	RNA	rna	NN	_	_	_
16	sequencing	sequencing	NN	_	_	_
17	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	signal	signal	NN	_	_	_
3	peptide	peptide	NN	_	_	_
4	fusions	fusion	NNS	_	_	_
5	,	,	,	_	_	_
6	cDNA	cdna	NN	_	_	_
7	was	be	VBD	_	_	_
8	constructed	construct	VBN	_	_	_
9	using	use	VBG	_	_	_
10	primers	primer	NNS	_	_	_
11	that	that	WDT	_	_	_
12	target	target	VBP	_	_	_
13	the	the	DT	_	_	_
14	signal-peptide-coding	signal-peptide-coding	JJ	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	Escherichia	escherichia	FW	Organism	_	_
17	coli	coli	FW	Organism	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Genome	Genome	NNP	_	_	_
20	_	_	NNP	_	_	_
21	build	build	VB	_	_	_
22	:	:	:	_	_	_
23	NC	NC	NNP	_	_	_
24	_	_	NNP	_	_	_
25	000913.2	000913.2	CD	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	genotype	genotype	NN	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	lacZ	lacz	NN	GEN	_	_
30	_	_	NN	_	_	_
31	0	0	CD	_	_	_
32	min	min	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	lacZ	lacz	NN	GEN	_	_
35	_	_	CD	_	_	_
36	10	10	CD	_	_	_
37	min	min	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	lacZ	lacz	NN	GEN	_	_
40	_	_	CD	_	_	_
41	15	15	CD	_	_	_
42	min	min	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	lacZ	lacz	NN	GEN	_	_
45	_	_	NN	_	_	_
46	1	1	CD	_	_	_
47	min	min	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	lacZ	lacz	NN	GEN	_	_
50	_	_	NN	_	_	_
51	2	2	CD	_	_	_
52	min	min	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	lacZ	lacz	NN	GEN	_	_
55	_	_	CD	_	_	_
56	4	4	CD	_	_	_
57	min	min	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	lacZ	lacz	NN	GEN	_	_
60	_	_	CD	_	_	_
61	6	6	CD	_	_	_
62	min	min	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	lacZ	lacz	NN	GEN	_	_
65	_	_	CD	_	_	_
66	8	8	CD	_	_	_
67	min	min	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	mg1655	mg1655	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	mMaple3	mmaple3	NN	_	_	_
72	_	_	NN	_	_	_
73	0	0	CD	_	_	_
74	min	min	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	mMaple3	mmaple3	NN	_	_	_
77	_	_	CD	_	_	_
78	10	10	CD	_	_	_
79	min	min	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	mMaple3	mmaple3	NN	_	_	_
82	_	_	CD	_	_	_
83	15	15	CD	_	_	_
84	min	min	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	mMaple3	mmaple3	NN	_	_	_
87	_	_	NN	_	_	_
88	1	1	CD	_	_	_
89	min	min	NN	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	mMaple3	mmaple3	NN	_	_	_
92	_	_	NN	_	_	_
93	2	2	CD	_	_	_
94	min	min	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	mMaple3	mmaple3	NN	_	_	_
97	_	_	CD	_	_	_
98	4	4	CD	_	_	_
99	min	min	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	mMaple3	mmaple3	NN	_	_	_
102	_	_	CD	_	_	_
103	6	6	CD	_	_	_
104	min	min	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	mMaple3	mmaple3	NN	_	_	_
107	_	_	CD	_	_	_
108	8	8	CD	_	_	_
109	min	min	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	MutRep1	mutrep1	NN	_	_	_
112	_	_	NN	_	_	_
113	0	0	CD	_	_	_
114	min	min	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	MutRep1	mutrep1	NN	_	_	_
117	_	_	CD	_	_	_
118	10	10	CD	_	_	_
119	min	min	NN	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	MutRep1	mutrep1	NN	_	_	_
122	_	_	CD	_	_	_
123	15	15	CD	_	_	_
124	min	min	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	MutRep1	mutrep1	NN	_	_	_
127	_	_	CD	_	_	_
128	20	20	CD	_	_	_
129	min	min	NN	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	MutRep1	mutrep1	NN	_	_	_
132	_	_	NN	_	_	_
133	2	2	CD	_	_	_
134	min	min	NN	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	MutRep1	mutrep1	NN	_	_	_
137	_	_	CD	_	_	_
138	4	4	CD	_	_	_
139	min	min	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	MutRep1	mutrep1	NN	_	_	_
142	_	_	CD	_	_	_
143	6	6	CD	_	_	_
144	min	min	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	MutRep1	mutrep1	NN	_	_	_
147	_	_	CD	_	_	_
148	8	8	CD	_	_	_
149	min	min	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	MutRep2	mutrep2	NN	_	_	_
152	_	_	NN	_	_	_
153	0	0	CD	_	_	_
154	min	min	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	MutRep2	mutrep2	NN	_	_	_
157	_	_	CD	_	_	_
158	10	10	CD	_	_	_
159	min	min	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	MutRep2	mutrep2	NN	_	_	_
162	_	_	CD	_	_	_
163	15	15	CD	_	_	_
164	min	min	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	MutRep2	mutrep2	NN	_	_	_
167	_	_	CD	_	_	_
168	20	20	CD	_	_	_
169	min	min	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	MutRep2	mutrep2	NN	_	_	_
172	_	_	NN	_	_	_
173	2	2	CD	_	_	_
174	min	min	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	MutRep2	mutrep2	NN	_	_	_
177	_	_	CD	_	_	_
178	4	4	CD	_	_	_
179	min	min	NN	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	MutRep2	mutrep2	NN	_	_	_
182	_	_	CD	_	_	_
183	6	6	CD	_	_	_
184	min	min	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	MutRep2	mutrep2	NN	_	_	_
187	_	_	CD	_	_	_
188	8	8	CD	_	_	_
189	min	min	NN	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	neo	neo	NN	_	_	_
192	_	_	NN	_	_	_
193	0	0	CD	_	_	_
194	min	min	NN	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	neo	neo	NN	_	_	_
197	_	_	CD	_	_	_
198	10	10	CD	_	_	_
199	min	min	NN	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	neo	neo	NN	_	_	_
202	_	_	CD	_	_	_
203	15	15	CD	_	_	_
204	min	min	NN	_	_	_
205	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
206	neo	neo	NN	_	_	_
207	_	_	NN	_	_	_
208	1	1	CD	_	_	_
209	min	min	NN	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	neo	neo	NN	_	_	_
212	_	_	NN	_	_	_
213	2	2	CD	_	_	_
214	min	min	NN	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	neo	neo	NN	_	_	_
217	_	_	NN	_	_	_
218	4	4	CD	_	_	_
219	min	min	NN	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	neo	neo	NN	_	_	_
222	_	_	NN	_	_	_
223	6	6	CD	_	_	_
224	min	min	NN	_	_	_
225	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
226	neo	neo	NN	_	_	_
227	_	_	NN	_	_	_
228	8	8	CD	_	_	_
229	min	min	NN	_	_	_
230	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
231	phoA	phoa	NN	GEN	_	_
232	_	_	NN	_	_	_
233	0	0	CD	_	_	_
234	min	min	NN	_	_	_
235	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
236	phoA	phoa	NN	GEN	_	_
237	_	_	CD	_	_	_
238	10	10	CD	_	_	_
239	min	min	NN	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
241	phoA	phoa	NN	GEN	_	_
242	_	_	CD	_	_	_
243	15	15	CD	_	_	_
244	min	min	NN	_	_	_
245	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
246	phoA	phoa	NN	GEN	_	_
247	_	_	NN	_	_	_
248	1	1	CD	_	_	_
249	min	min	NN	_	_	_
250	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
251	phoA	phoa	NN	GEN	_	_
252	_	_	NN	_	_	_
253	2	2	CD	_	_	_
254	min	min	NN	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	phoA	phoa	NN	GEN	_	_
257	_	_	CD	_	_	_
258	4	4	CD	_	_	_
259	min	min	NN	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	phoA	phoa	NN	GEN	_	_
262	_	_	CD	_	_	_
263	6	6	CD	_	_	_
264	min	min	NN	_	_	_
265	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
266	phoA	phoa	NN	GEN	_	_
267	_	_	CD	_	_	_
268	8	8	CD	_	_	_
269	min	min	NN	_	_	_
270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
271	RNA-Seq	rna-seq	NN	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	Sequencing	sequencing	NN	_	_	_
274	reads	read	VBZ	_	_	_
275	were	be	VBD	_	_	_
276	aligned	align	VBN	_	_	_
277	to	to	TO	_	_	_
278	the	the	DT	_	_	_
279	mg1655	mg1655	NN	_	_	_
280	genome	genome	NN	_	_	_
281	-LRB-	-lrb-	-LRB-	_	_	_
282	NC	nc	NN	_	_	_
283	_	_	CD	_	_	_
284	000913.2	000913.2	CD	_	_	_
285	-RRB-	-rrb-	-RRB-	_	_	_
286	or	or	CC	_	_	_
287	a	a	DT	_	_	_
288	list	list	NN	_	_	_
289	of	of	IN	_	_	_
290	the	the	DT	_	_	_
291	designed	design	VBN	_	_	_
292	signal	signal	NN	_	_	_
293	peptide	peptide	NN	_	_	_
294	fusions	fusion	NNS	_	_	_
295	using	use	VBG	_	_	_
296	bowtie	bowtie	NN	_	_	_
297	0.12.9	0.12.9	CD	_	_	_
298	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
299	Supplementary	supplementary	JJ	_	_	_
300	_	_	NN	_	_	_
301	files	file	NNS	_	_	_
302	_	_	IN	_	_	_
303	format	format	NN	_	_	_
304	_	_	NN	_	_	_
305	and	and	CC	_	_	_
306	_	_	NN	_	_	_
307	content	content	NN	_	_	_
308	:	:	:	_	_	_
309	sam	sam	NN	_	_	_
310	containing	contain	VBG	_	_	_
311	aligned	align	VBN	_	_	_
312	sequences	sequence	NNS	_	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
314	The	the	DT	_	_	_
315	sigPep.csv	sigpep.csv	NN	_	_	_
316	file	file	NN	_	_	_
317	contains	contain	VBZ	_	_	_
318	the	the	DT	_	_	_
319	counts	count	NNS	_	_	_
320	for	for	IN	_	_	_
321	each	each	DT	_	_	_
322	specific	specific	JJ	_	_	_
323	signal	signal	NN	_	_	_
324	peptide	peptide	NN	_	_	_
325	fusion	fusion	NN	_	_	_
326	to	to	TO	_	_	_
327	each	each	DT	_	_	_
328	specific	specific	JJ	_	_	_
329	test	test	NN	_	_	_
330	gene	gene	NN	_	_	_
331	.	.	.	_	_	_

1	Entries	entry	NNS	_	_	_
2	with	with	IN	_	_	_
3	SP	sp	NN	_	_	_
4	_	_	CD	_	_	_
5	spkA	spka	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	time	time	NN	_	_	_
8	point	point	NN	_	_	_
9	:	:	:	_	_	_
10	0	0	CD	_	_	_
11	min	min	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	time	time	NN	_	_	_
14	point	point	NN	_	_	_
15	:	:	:	_	_	_
16	10	10	CD	_	_	_
17	min	min	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	time	time	NN	_	_	_
20	point	point	NN	_	_	_
21	:	:	:	_	_	_
22	15	15	CD	_	_	_
23	min	min	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	time	time	NN	_	_	_
26	point	point	NN	_	_	_
27	:	:	:	_	_	_
28	1	1	CD	_	_	_
29	min	min	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	time	time	NN	_	_	_
32	point	point	NN	_	_	_
33	:	:	:	_	_	_
34	20	20	CD	_	_	_
35	min	min	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	time	time	NN	_	_	_
38	point	point	NN	_	_	_
39	:	:	:	_	_	_
40	2	2	CD	_	_	_
41	min	min	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	time	time	NN	_	_	_
44	point	point	NN	_	_	_
45	:	:	:	_	_	_
46	4	4	CD	_	_	_
47	min	min	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	time	time	NN	_	_	_
50	point	point	NN	_	_	_
51	:	:	:	_	_	_
52	6	6	CD	_	_	_
53	min	min	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	time	time	NN	_	_	_
56	point	point	NN	_	_	_
57	:	:	:	_	_	_
58	8	8	CD	_	_	_
59	min	min	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	treatment	treatment	NN	_	_	_
62	:	:	:	_	_	_
63	rifampicin	rifampicin	NN	SUPP	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	WTKasRep1	wtkasrep1	NN	_	_	_
66	_	_	NN	_	_	_
67	0	0	CD	_	_	_
68	min	min	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	WTKasRep1	wtkasrep1	NN	_	_	_
71	_	_	CD	_	_	_
72	15	15	CD	_	_	_
73	min	min	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	WTKasRep1	wtkasrep1	NN	_	_	_
76	_	_	CD	_	_	_
77	20	20	CD	_	_	_
78	min	min	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	WTKasRep1	wtkasrep1	NN	_	_	_
81	_	_	NN	_	_	_
82	2	2	CD	_	_	_
83	min	min	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	WTKasRep1	wtkasrep1	NN	_	_	_
86	_	_	CD	_	_	_
87	4	4	CD	_	_	_
88	min	min	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	WTKasRep1	wtkasrep1	NN	_	_	_
91	_	_	CD	_	_	_
92	6	6	CD	_	_	_
93	min	min	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	WTKasRep1	wtkasrep1	NN	_	_	_
96	_	_	CD	_	_	_
97	8	8	CD	_	_	_
98	min	min	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	WTKasRep2	wtkasrep2	NN	_	_	_
101	_	_	NN	_	_	_
102	0	0	CD	_	_	_
103	min	min	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	WTKasRep2	wtkasrep2	NN	_	_	_
106	_	_	CD	_	_	_
107	10	10	CD	_	_	_
108	min	min	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	WTKasRep2	wtkasrep2	NN	_	_	_
111	_	_	CD	_	_	_
112	15	15	CD	_	_	_
113	min	min	NN	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	WTKasRep2	wtkasrep2	NN	_	_	_
116	_	_	CD	_	_	_
117	20	20	CD	_	_	_
118	min	min	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	WTKasRep2	wtkasrep2	NN	_	_	_
121	_	_	NN	_	_	_
122	2	2	CD	_	_	_
123	min	min	NN	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	WTKasRep2	wtkasrep2	NN	_	_	_
126	_	_	CD	_	_	_
127	4	4	CD	_	_	_
128	min	min	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	WTKasRep2	wtkasrep2	NN	_	_	_
131	_	_	CD	_	_	_
132	6	6	CD	_	_	_
133	min	min	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	WTKasRep2	wtkasrep2	NN	_	_	_
136	_	_	CD	_	_	_
137	8	8	CD	_	_	_
138	min	min	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	WTRep1	wtrep1	NN	_	_	_
141	_	_	NN	_	_	_
142	0	0	CD	_	_	_
143	min	min	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	WTRep1	wtrep1	NN	_	_	_
146	_	_	CD	_	_	_
147	10	10	CD	_	_	_
148	min	min	NN	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	WTRep1	wtrep1	NN	_	_	_
151	_	_	CD	_	_	_
152	15	15	CD	_	_	_
153	min	min	NN	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	WTRep1	wtrep1	NN	_	_	_
156	_	_	CD	_	_	_
157	20	20	CD	_	_	_
158	min	min	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	WTRep1	wtrep1	NN	_	_	_
161	_	_	NN	_	_	_
162	2	2	CD	_	_	_
163	min	min	NN	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	WTRep1	wtrep1	NN	_	_	_
166	_	_	CD	_	_	_
167	4	4	CD	_	_	_
168	min	min	NN	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	WTRep1	wtrep1	NN	_	_	_
171	_	_	CD	_	_	_
172	6	6	CD	_	_	_
173	min	min	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	WTRep1	wtrep1	NN	_	_	_
176	_	_	CD	_	_	_
177	8	8	CD	_	_	_
178	min	min	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	WTRep2	wtrep2	NN	_	_	_
181	_	_	NN	_	_	_
182	0	0	CD	_	_	_
183	min	min	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	WTRep2	wtrep2	NN	_	_	_
186	_	_	CD	_	_	_
187	10	10	CD	_	_	_
188	min	min	NN	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	WTRep2	wtrep2	NN	_	_	_
191	_	_	CD	_	_	_
192	15	15	CD	_	_	_
193	min	min	NN	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	WTRep2	wtrep2	NN	_	_	_
196	_	_	CD	_	_	_
197	20	20	CD	_	_	_
198	min	min	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	WTRep2	wtrep2	NN	_	_	_
201	_	_	NN	_	_	_
202	2	2	CD	_	_	_
203	min	min	NN	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	WTRep2	wtrep2	NN	_	_	_
206	_	_	CD	_	_	_
207	4	4	CD	_	_	_
208	min	min	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	WTRep2	wtrep2	NN	_	_	_
211	_	_	CD	_	_	_
212	6	6	CD	_	_	_
213	min	min	NN	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	WTRep2	wtrep2	NN	_	_	_
216	_	_	CD	_	_	_
217	8	8	CD	_	_	_
218	min	min	NN	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	cDNA	cdna	NN	_	_	_
221	of	of	IN	_	_	_
222	EPEC	epec	NN	_	_	_
223	strain	strain	NN	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
225	CIP2G	cip2g	NN	_	_	_
226	_	_	CD	_	_	_
227	00000	00000	CD	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	CIP2G	cip2g	NN	_	_	_
230	_	_	CD	_	_	_
231	00045	00045	CD	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	CIP2G	cip2g	NN	_	_	_
234	_	_	CD	_	_	_
235	00090	00090	CD	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
237	CIP2G	cip2g	NN	_	_	_
238	_	_	CD	_	_	_
239	00135	00135	CD	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
241	CIP2G	cip2g	NN	_	_	_
242	_	_	CD	_	_	_
243	00180	00180	CD	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	CIP4G	cip4g	NN	_	_	_
246	_	_	CD	_	_	_
247	00000	00000	CD	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
249	CIP4G	cip4g	NN	_	_	_
250	_	_	CD	_	_	_
251	00045	00045	CD	_	_	_
252	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
253	CIP4G	cip4g	NN	_	_	_
254	_	_	CD	_	_	_
255	00090	00090	CD	_	_	_
256	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
257	CIP4G	cip4g	NN	_	_	_
258	_	_	CD	_	_	_
259	00135	00135	CD	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	CIP4G	cip4g	NN	_	_	_
262	_	_	CD	_	_	_
263	00180	00180	CD	_	_	_
264	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
265	CIPSG	cipsg	NN	_	_	_
266	_	_	CD	_	_	_
267	00000	00000	CD	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	CIPSG	cipsg	NN	_	_	_
270	_	_	CD	_	_	_
271	00045	00045	CD	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	CIPSG	cipsg	NN	_	_	_
274	_	_	CD	_	_	_
275	00090	00090	CD	_	_	_
276	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
277	CIPSG	cipsg	NN	_	_	_
278	_	_	CD	_	_	_
279	00135	00135	CD	_	_	_
280	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
281	CIPSG	cipsg	NN	_	_	_
282	_	_	CD	_	_	_
283	00180	00180	CD	_	_	_
284	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
285	Escherichia	escherichia	FW	Organism	_	_
286	coli	coli	FW	Organism	_	_
287	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
288	RNA	rna	NN	_	_	_
289	was	be	VBD	_	_	_
290	prepared	prepare	VBN	_	_	_
291	using	use	VBG	_	_	_
292	the	the	DT	_	_	_
293	Trizol	Trizol	NNP	_	_	_
294	Reagent	Reagent	NNP	_	_	_
295	and	and	CC	_	_	_
296	a	a	DT	_	_	_
297	RiboPure	RiboPure	NNP	_	_	_
298	kit	kit	NN	_	_	_
299	-LRB-	-lrb-	-LRB-	_	_	_
300	Invitrogen	Invitrogen	NNP	_	_	_
301	,	,	,	_	_	_
302	Carlsbad	Carlsbad	NNP	_	_	_
303	,	,	,	_	_	_
304	CA	CA	NNP	_	_	_
305	,	,	,	_	_	_
306	USA	USA	NNP	_	_	_
307	-RRB-	-rrb-	-RRB-	_	_	_
308	following	follow	VBG	_	_	_
309	the	the	DT	_	_	_
310	manufacturer	manufacturer	NN	_	_	_
311	's	's	POS	_	_	_
312	protocol	protocol	NN	_	_	_
313	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	integrity	integrity	NN	_	_	_
3	was	be	VBD	_	_	_
4	assessed	assess	VBN	_	_	_
5	using	use	VBG	_	_	_
6	an	a	DT	_	_	_
7	Agilent	Agilent	NNP	_	_	_
8	2100	2100	CD	_	_	_
9	bioanalyser	bioanalyser	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Agilent	Agilent	NNP	_	_	_
12	,	,	,	_	_	_
13	Palo	Palo	NNP	_	_	_
14	Alto	Alto	NNP	_	_	_
15	,	,	,	_	_	_
16	CA	CA	NNP	_	_	_
17	,	,	,	_	_	_
18	USA	USA	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	EPEC	epec	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
6	The	the	DT	_	_	_
7	scanned	scan	VBN	_	_	_
8	images	image	NNS	_	_	_
9	were	be	VBD	_	_	_
10	analyzed	analyze	VBN	_	_	_
11	using	use	VBG	_	_	_
12	the	the	DT	_	_	_
13	Feature	Feature	NNP	_	_	_
14	Extraction	Extraction	NNP	_	_	_
15	Software	Software	NNP	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Agilent	Agilent	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	with	with	IN	_	_	_
20	default	default	NN	_	_	_
21	parameters	parameter	NNS	_	_	_
22	to	to	TO	_	_	_
23	obtain	obtain	VB	_	_	_
24	background	background	NN	_	_	_
25	subtracted	subtract	VBN	_	_	_
26	and	and	CC	_	_	_
27	spatially	spatially	RB	_	_	_
28	detrended	detrend	VBD	_	_	_
29	Processed	processed	JJ	_	_	_
30	Signal	signal	NN	_	_	_
31	intensities	intensity	NNS	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	time	time	NN	_	_	_
3	point	point	NN	_	_	_
4	:	:	:	_	_	_
5	0	0	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	time	time	NN	_	_	_
8	point	point	NN	_	_	_
9	:	:	:	_	_	_
10	135	135	CD	_	_	_
11	min	min	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	time	time	NN	_	_	_
14	point	point	NN	_	_	_
15	:	:	:	_	_	_
16	180	180	CD	_	_	_
17	min	min	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	time	time	NN	_	_	_
20	point	point	NN	_	_	_
21	:	:	:	_	_	_
22	45	45	CD	_	_	_
23	min	min	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	time	time	NN	_	_	_
26	point	point	NN	_	_	_
27	:	:	:	_	_	_
28	90	90	CD	_	_	_
29	min	min	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	treatment	treatment	NN	_	_	_
32	:	:	:	_	_	_
33	2ug	2ug	JJ	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	treatment	treatment	NN	_	_	_
36	:	:	:	_	_	_
37	4ug	4ug	JJ	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	treatment	treatment	NN	_	_	_
40	:	:	:	_	_	_
41	saline	saline	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	5	5	CD	_	_	_
44	'	'	''	_	_	_
45	in	in	IN	_	_	_
46	minimal	minimal	JJ	_	_	_
47	medium	medium	NN	_	_	_
48	+0.2	+0.2	CD	_	_	_
49	%	%	NN	_	_	_
50	glu	glu	NN	_	_	_
51	,	,	,	_	_	_
52	25	25	CD	_	_	_
53	ug	ug	NN	_	_	_
54	total	total	JJ	_	_	_
55	RNA	rna	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	5	5	CD	_	_	_
58	'	'	''	_	_	_
59	in	in	IN	_	_	_
60	min	min	NN	_	_	_
61	med	med	VBD	_	_	_
62	+0.2	+0.2	CD	_	_	_
63	%	%	NN	_	_	_
64	glu	glu	NN	_	_	_
65	+50	+50	CD	_	_	_
66	ug	ug	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	5	5	CD	_	_	_
69	'	'	''	_	_	_
70	vs	vs	CC	_	_	_
71	0	0	CD	_	_	_
72	'	'	''	_	_	_
73	in	in	IN	_	_	_
74	minimal	minimal	JJ	_	_	_
75	medium	medium	NN	_	_	_
76	+0.2	+0.2	CD	_	_	_
77	%	%	NN	_	_	_
78	glu	glu	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	60	60	CD	_	_	_
81	'	'	''	_	_	_
82	10	10	CD	_	_	_
83	ug	ug	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	60	60	CD	_	_	_
86	'	'	''	_	_	_
87	15	15	CD	_	_	_
88	ug	ug	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	60	60	CD	_	_	_
91	'	'	''	_	_	_
92	+	+	CC	_	_	_
93	50	50	CD	_	_	_
94	ug	ug	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	60	60	CD	_	_	_
97	'	'	''	_	_	_
98	50	50	CD	_	_	_
99	ug	ug	NN	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	60	60	CD	_	_	_
102	'	'	''	_	_	_
103	+50	+50	CD	_	_	_
104	ug	ug	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	60	60	CD	_	_	_
107	'	'	''	_	_	_
108	in	in	IN	_	_	_
109	min	min	NN	_	_	_
110	+.2	+.2	CD	_	_	_
111	%	%	NN	_	_	_
112	glu	glu	NN	_	_	_
113	,	,	,	_	_	_
114	25	25	CD	_	_	_
115	ug	ug	NN	_	_	_
116	RNA	rna	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	60	60	CD	_	_	_
119	'	'	''	_	_	_
120	in	in	IN	_	_	_
121	minimal	minimal	JJ	_	_	_
122	medium	medium	NN	_	_	_
123	+0.2	+0.2	CD	_	_	_
124	%	%	NN	_	_	_
125	glu	glu	NN	_	_	_
126	,	,	,	_	_	_
127	25	25	CD	_	_	_
128	ug	ug	NN	_	_	_
129	total	total	JJ	_	_	_
130	RNA	rna	NN	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	60	60	CD	_	_	_
133	'	'	''	_	_	_
134	in	in	IN	_	_	_
135	min	min	NN	_	_	_
136	med	med	VBD	_	_	_
137	+0.2	+0.2	CD	_	_	_
138	%	%	NN	_	_	_
139	glu	glu	NN	_	_	_
140	+50	+50	CD	_	_	_
141	ug	ug	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	60	60	CD	_	_	_
144	'	'	''	_	_	_
145	vs.	vs.	CC	_	_	_
146	0	0	CD	_	_	_
147	'	'	''	_	_	_
148	,	,	,	_	_	_
149	50	50	CD	_	_	_
150	ug	ug	NN	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	60	60	CD	_	_	_
153	'	'	''	_	_	_
154	vs	vs	CC	_	_	_
155	0	0	CD	_	_	_
156	'	'	''	_	_	_
157	in	in	IN	_	_	_
158	minimal	minimal	JJ	_	_	_
159	medium	medium	NN	_	_	_
160	+0.2	+0.2	CD	_	_	_
161	%	%	NN	_	_	_
162	glu	glu	NN	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	60	60	CD	_	_	_
165	'	'	''	_	_	_
166	vs	vs	CC	_	_	_
167	0	0	CD	_	_	_
168	'	'	''	_	_	_
169	in	in	IN	_	_	_
170	minimal	minimal	JJ	_	_	_
171	medium	medium	NN	_	_	_
172	+0.2	+0.2	CD	_	_	_
173	%	%	NN	_	_	_
174	glu	glu	NN	_	_	_
175	,	,	,	_	_	_
176	II	ii	CD	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	Basecalls	basecall	NNS	_	_	_
179	performed	perform	VBN	_	_	_
180	using	use	VBG	_	_	_
181	HCS	hcs	NN	_	_	_
182	2.0.5	2.0.5	CD	_	_	_
183	and	and	CC	_	_	_
184	RTA	RTA	NNP	_	_	_
185	1.17.20	1.17.20	CD	_	_	_
186	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
187	Escherichia	escherichia	FW	Organism	_	_
188	coli	coli	FW	Organism	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	Escherichia	escherichia	FW	Organism	_	_
191	coli	coli	FW	Organism	_	_
192	_	_	FW	_	_	_
193	control	control	NN	_	_	_
194	condition	condition	NN	_	_	_
195	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
196	Escherichia	escherichia	FW	Organism	_	_
197	coli	coli	FW	Organism	_	_
198	_	_	FW	_	_	_
199	nickel	nickel	NN	_	_	_
200	condition	condition	NN	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	Gene	gene	NN	_	_	_
203	expression	expression	NN	_	_	_
204	-LRB-	-lrb-	-LRB-	_	_	_
205	based	base	VBN	_	_	_
206	on	on	IN	_	_	_
207	known	known	JJ	_	_	_
208	genes	gene	NNS	_	_	_
209	-RRB-	-rrb-	-RRB-	_	_	_
210	was	be	VBD	_	_	_
211	determined	determine	VBN	_	_	_
212	using	use	VBG	_	_	_
213	Cufflinks	Cufflinks	NNP	_	_	_
214	2.0.2	2.0.2	CD	_	_	_
215	,	,	,	_	_	_
216	only	only	RB	_	_	_
217	PF	pf	NN	_	_	_
218	reads	read	VBZ	_	_	_
219	were	be	VBD	_	_	_
220	retained	retain	VBN	_	_	_
221	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
222	Genome	Genome	NNP	_	_	_
223	_	_	NNP	_	_	_
224	build	build	VB	_	_	_
225	:	:	:	_	_	_
226	W3110	w3110	NN	_	_	_
227	-LRB-	-lrb-	-LRB-	_	_	_
228	NC	nc	NN	_	_	_
229	_	_	CD	_	_	_
230	007779	007779	CD	_	_	_
231	-RRB-	-rrb-	-RRB-	_	_	_
232	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
233	genotype	genotype	NN	_	_	_
234	:	:	:	_	_	_
235	wild	wild	JJ	_	_	_
236	type	type	NN	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	growth	growth	NN	_	_	_
239	phase	phase	NN	_	_	_
240	:	:	:	_	_	_
241	log	log	NN	_	_	_
242	phase	phase	NN	_	_	_
243	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
244	Library	Library	NNP	_	_	_
245	preparation	preparation	NN	_	_	_
246	were	be	VBD	_	_	_
247	performed	perform	VBN	_	_	_
248	with	with	IN	_	_	_
249	Epicentre	Epicentre	NNP	_	_	_
250	ScriptseqTM	ScriptseqTM	NNP	_	_	_
251	v2	v2	NN	_	_	_
252	RNA-Seq	rna-seq	NN	_	_	_
253	Library	Library	NNP	_	_	_
254	preparation	preparation	NN	_	_	_
255	kit	kit	NN	_	_	_
256	with	with	IN	_	_	_
257	50	50	CD	_	_	_
258	ng	ng	NN	_	_	_
259	of	of	IN	_	_	_
260	depleted	deplete	VBN	_	_	_
261	RNA	rna	NN	_	_	_
262	;	;	:	_	_	_
263	Strand	Strand	NNP	_	_	_
264	orientated	orientate	VBD	_	_	_
265	RNA-Seq	rna-seq	JJ	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
267	RNA-Seq	rna-seq	NN	_	_	_
268	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
269	RNA-seq	rna-seq	NN	_	_	_
270	reads	read	VBZ	_	_	_
271	were	be	VBD	_	_	_
272	aligned	align	VBN	_	_	_
273	to	to	TO	_	_	_
274	the	the	DT	_	_	_
275	W3110	w3110	NN	_	_	_
276	genome	genome	NN	_	_	_
277	using	use	VBG	_	_	_
278	CASAVA	CASAVA	NNP	_	_	_
279	1.8.2	1.8.2	CD	_	_	_
280	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
281	Rodrigue	Rodrigue	NNP	_	_	_
282	_	_	SYM	_	_	_
283	10-WT-Ni-3	10-wt-ni-3	NN	_	_	_
284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
285	Rodrigue	Rodrigue	NNP	_	_	_
286	_	_	SYM	_	_	_
287	1-WT-phiNi-1	1-wt-phini-1	NN	_	_	_
288	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
289	Rodrigue	Rodrigue	NNP	_	_	_
290	_	_	SYM	_	_	_
291	2-WT-Ni-1	2-wt-ni-1	NN	_	_	_
292	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
293	Rodrigue	Rodrigue	NNP	_	_	_
294	_	_	SYM	_	_	_
295	5-WT-Ni-2	5-wt-ni-2	NN	_	_	_
296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
297	Rodrigue	Rodrigue	NNP	_	_	_
298	_	_	SYM	_	_	_
299	6-WT-phiNi-2	6-wt-phini-2	JJ	_	_	_
300	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
301	Rodrigue	Rodrigue	NNP	_	_	_
302	_	_	SYM	_	_	_
303	9-WT-phiNi-3	9-wt-phini-3	NN	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	strain	strain	NN	_	_	_
306	:	:	:	_	_	_
307	W3110	w3110	NN	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	Supplementary	supplementary	JJ	_	_	_
310	_	_	NN	_	_	_
311	files	file	NNS	_	_	_
312	_	_	IN	_	_	_
313	format	format	NN	_	_	_
314	_	_	NN	_	_	_
315	and	and	CC	_	_	_
316	_	_	NN	_	_	_
317	content	content	NN	_	_	_
318	:	:	:	_	_	_
319	excel	excel	VB	_	_	_
320	file	file	NN	_	_	_
321	with	with	IN	_	_	_
322	coverage	coverage	NN	_	_	_
323	and	and	CC	_	_	_
324	FPKM	fpkm	NN	_	_	_
325	measurements	measurement	NNS	_	_	_
326	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
327	Total	Total	NNP	_	_	_
328	RNA	rna	NN	_	_	_
329	was	be	VBD	_	_	_
330	extracted	extract	VBN	_	_	_
331	using	use	VBG	_	_	_
332	the	the	DT	_	_	_
333	frozen	frozen	JJ	_	_	_
334	acid-phenol	acid-phenol	NN	_	_	_
335	method	method	NN	_	_	_
336	described	describe	VBN	_	_	_
337	by	by	IN	_	_	_
338	Maes	mae	NNS	_	_	_
339	and	and	CC	_	_	_
340	Messens	messen	NNS	_	_	_
341	-LRB-	-lrb-	-LRB-	_	_	_
342	Maes	mae	NNS	_	_	_
343	and	and	CC	_	_	_
344	Messens	messen	NNS	_	_	_
345	,	,	,	_	_	_
346	1992	1992	CD	_	_	_
347	-RRB-	-rrb-	-RRB-	_	_	_
348	and	and	CC	_	_	_
349	then	then	RB	_	_	_
350	treated	treat	VBN	_	_	_
351	with	with	IN	_	_	_
352	RNase-free	rnase-free	JJ	_	_	_
353	DNaseI	dnasei	NN	_	_	_
354	according	accord	VBG	_	_	_
355	to	to	TO	_	_	_
356	the	the	DT	_	_	_
357	manufacturer	manufacturer	NN	_	_	_
358	's	's	POS	_	_	_
359	recommendations	recommendation	NNS	_	_	_
360	-LRB-	-lrb-	-LRB-	_	_	_
361	Ambion	Ambion	NNP	_	_	_
362	,	,	,	_	_	_
363	USA	USA	NNP	_	_	_
364	-RRB-	-rrb-	-RRB-	_	_	_
365	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Transcriptomic	transcriptomic	JJ	_	_	_
3	analyses	analysis	NNS	_	_	_
4	were	be	VBD	_	_	_
5	carried	carry	VBN	_	_	_
6	out	out	RP	_	_	_
7	after	after	IN	_	_	_
8	growing	grow	VBG	_	_	_
9	bacteria	bacterium	NNS	_	_	_
10	in	in	IN	_	_	_
11	minimal	minimal	JJ	_	_	_
12	media	media	NNS	_	_	_
13	supplemented	supplement	VBN	_	_	_
14	with	with	IN	_	_	_
15	glucose	glucose	NN	SUPP	_	_
16	.	.	.	_	_	_

1	Several	several	JJ	_	_	_
2	Ni	ni	NN	_	_	_
3	concentrations	concentration	NNS	_	_	_
4	and	and	CC	_	_	_
5	exposure	exposure	NN	_	_	_
6	times	time	NNS	_	_	_
7	were	be	VBD	_	_	_
8	assayed	assay	VBN	_	_	_
9	.	.	.	_	_	_

1	rcnA	rcna	NN	GEN	_	_
2	gene	gene	NN	_	_	_
3	expression	expression	NN	_	_	_
4	was	be	VBD	_	_	_
5	taken	take	VBN	_	_	_
6	as	as	IN	_	_	_
7	an	a	DT	_	_	_
8	internal	internal	JJ	_	_	_
9	control	control	NN	_	_	_
10	to	to	TO	_	_	_
11	arbitrate	arbitrate	VB	_	_	_
12	between	between	IN	_	_	_
13	the	the	DT	_	_	_
14	different	different	JJ	_	_	_
15	conditions	condition	NNS	_	_	_
16	.	.	.	_	_	_

1	rcnA	rcna	NN	GEN	_	_
2	is	be	VBZ	_	_	_
3	induced	induce	VBN	_	_	_
4	by	by	IN	_	_	_
5	Ni	ni	NN	_	_	_
6	when	when	WRB	_	_	_
7	cells	cell	NNS	_	_	_
8	are	be	VBP	_	_	_
9	overloaded	overload	VBN	_	_	_
10	with	with	IN	_	_	_
11	this	this	DT	_	_	_
12	ion	ion	NN	_	_	_
13	and	and	CC	_	_	_
14	must	must	MD	_	_	_
15	detoxify	detoxify	VB	_	_	_
16	the	the	DT	_	_	_
17	cytoplasm	cytoplasm	NN	_	_	_
18	by	by	IN	_	_	_
19	extruding	extrude	VBG	_	_	_
20	excess	excess	JJ	_	_	_
21	metal	metal	NN	_	_	_
22	via	via	IN	_	_	_
23	the	the	DT	_	_	_
24	RcnAB	rcnab	NN	_	_	_
25	efflux	efflux	NN	_	_	_
26	system	system	NN	_	_	_
27	.	.	.	_	_	_

1	rcnA	rcna	NN	GEN	_	_
2	induction	induction	NN	_	_	_
3	was	be	VBD	_	_	_
4	maximised	maximise	VBN	_	_	_
5	after	after	IN	_	_	_
6	culture	culture	NN	_	_	_
7	incubation	incubation	NN	_	_	_
8	for	for	IN	_	_	_
9	10	10	CD	_	_	_
10	min	min	NN	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	longer	longer	RBR	_	_	_
14	periods	period	NNS	_	_	_
15	of	of	IN	_	_	_
16	incubation	incubation	NN	_	_	_
17	lead	lead	NN	_	_	_
18	to	to	TO	_	_	_
19	a	a	DT	_	_	_
20	decline	decline	NN	_	_	_
21	in	in	IN	_	_	_
22	rcnA	rcna	NN	GEN	_	_
23	expression	expression	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Fig	fig	NN	_	_	_
26	.	.	.	_	_	_

1	S1	s1	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	the	the	DT	_	_	_
3	RNA-Seq	rna-seq	NN	_	_	_
4	experiments	experiment	NNS	_	_	_
5	,	,	,	_	_	_
6	bacteria	bacterium	NNS	_	_	_
7	were	be	VBD	_	_	_
8	grown	grow	VBN	_	_	_
9	until	until	IN	_	_	_
10	O.D600nm	o.d600nm	NN	_	_	_
11	=	=	JJ	_	_	_
12	0.3	0.3	CD	_	_	_
13	,	,	,	_	_	_
14	were	be	VBD	_	_	_
15	treated	treat	VBN	_	_	_
16	with	with	IN	_	_	_
17	50	50	CD	_	_	_
18	µM	µm	NN	_	_	_
19	NiCl2	nicl2	NN	_	_	_
20	for	for	IN	_	_	_
21	10	10	CD	_	_	_
22	min	min	NN	_	_	_
23	and	and	CC	_	_	_
24	were	be	VBD	_	_	_
25	frozen	freeze	VBN	_	_	_
26	prior	prior	RB	_	_	_
27	to	to	TO	_	_	_
28	RNA	rna	NN	_	_	_
29	extraction	extraction	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	DicF	dicf	NN	_	_	_
3	rep1	rep1	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	DicF	dicf	NN	_	_	_
6	rep2	rep2	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	DicF	dicf	NN	_	_	_
9	rep3	rep3	NN	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	E.	E.	NNP	_	_	_
12	coli	coli	NN	_	_	_
13	cells	cell	NNS	_	_	_
14	were	be	VBD	_	_	_
15	grown	grow	VBN	_	_	_
16	in	in	IN	_	_	_
17	Luria	Luria	NNP	_	_	_
18	Broth	Broth	NNP	_	_	_
19	supplemented	supplement	VBN	_	_	_
20	with	with	IN	_	_	_
21	100ug	100ug	CD	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	E.	E.	NNP	_	_	_
24	coli	coli	NN	_	_	_
25	cells	cell	NNS	_	_	_
26	were	be	VBD	_	_	_
27	grown	grow	VBN	_	_	_
28	until	until	IN	_	_	_
29	mid-exponential	mid-exponential	JJ	_	_	_
30	phase	phase	NN	_	_	_
31	and	and	CC	_	_	_
32	treated	treat	VBN	_	_	_
33	with	with	IN	_	_	_
34	0.5	0.5	CD	_	_	_
35	mM	mm	NN	KWSUPP	_	_
36	isopropyl-β-d-thiogalactopyranoside	isopropyl-β-d-thiogalactopyranoside	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	IPTG	iptg	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	to	to	TO	_	_	_
41	induce	induce	VB	_	_	_
42	expression	expression	NN	_	_	_
43	of	of	IN	_	_	_
44	the	the	DT	_	_	_
45	empty	empty	JJ	_	_	_
46	vector	vector	NN	_	_	_
47	or	or	CC	_	_	_
48	the	the	DT	_	_	_
49	small	small	JJ	_	_	_
50	RNA	rna	NN	_	_	_
51	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Genome	Genome	NNP	_	_	_
4	_	_	NNP	_	_	_
5	build	build	VB	_	_	_
6	:	:	:	_	_	_
7	K-12	k-12	NN	_	_	_
8	subst	subst	NN	_	_	_
9	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	genome	genome	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	NC	nc	NN	_	_	_
5	_	_	CD	_	_	_
6	000913.3	000913.3	CD	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	genotype	genotype	NN	_	_	_
10	:	:	:	_	_	_
11	delta	delta	NN	_	_	_
12	dicF	dicf	NN	GEN	_	_
13	,	,	,	_	_	_
14	lacIq	laciq	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
16	Hot	hot	JJ	_	_	_
17	phenol	phenol	NN	_	_	_
18	RNA	rna	NN	_	_	_
19	extraction	extraction	NN	_	_	_
20	as	as	IN	_	_	_
21	described	describe	VBN	_	_	_
22	in	in	IN	_	_	_
23	Aiba	Aiba	NNP	_	_	_
24	,	,	,	_	_	_
25	Adhya	Adhya	NNP	_	_	_
26	and	and	CC	_	_	_
27	Crombrugge	Crombrugge	NNP	_	_	_
28	.	.	.	_	_	_

1	J.	J.	NNP	_	_	_
2	Bio	Bio	NNP	_	_	_
3	Chem	Chem	NNP	_	_	_
4	.	.	.	_	_	_

1	1981	1981	CD	_	_	_
2	,	,	,	_	_	_
3	256	256	CD	_	_	_
4	:	:	:	_	_	_
5	p11905-11910	p11905-11910	JJ	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	protocol	protocol	NN	_	_	_
8	:	:	:	_	_	_
9	small	small	JJ	_	_	_
10	RNA	rna	NN	_	_	_
11	DicF	dicf	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	protocol	protocol	NN	_	_	_
14	:	:	:	_	_	_
15	vector	vector	NN	_	_	_
16	control	control	NN	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	Ribosomal	ribosomal	JJ	_	_	_
19	RNA	rna	NN	_	_	_
20	was	be	VBD	_	_	_
21	removed	remove	VBN	_	_	_
22	from	from	IN	_	_	_
23	1	1	CD	_	_	_
24	μg	μg	NN	_	_	_
25	of	of	IN	_	_	_
26	total	total	JJ	_	_	_
27	RNA	rna	NN	_	_	_
28	using	use	VBG	_	_	_
29	Ribozero	Ribozero	NNP	_	_	_
30	rRNA	rrna	NN	_	_	_
31	Removal	removal	NN	_	_	_
32	Meta-Bacteria	Meta-Bacteria	NNP	_	_	_
33	Kit	kit	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Epicentre	Epicentre	NNP	_	_	_
36	Biotechnologies	Biotechnologies	NNPS	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	and	and	CC	_	_	_
39	the	the	DT	_	_	_
40	mRNA-enriched	mrna-enriched	JJ	_	_	_
41	fraction	fraction	NN	_	_	_
42	was	be	VBD	_	_	_
43	converted	convert	VBN	_	_	_
44	to	to	TO	_	_	_
45	indexed	index	VBN	_	_	_
46	RNA-seq	rna-seq	NN	_	_	_
47	libraries	library	NNS	_	_	_
48	with	with	IN	_	_	_
49	the	the	DT	_	_	_
50	ScriptSeq	ScriptSeq	NNP	_	_	_
51	™	™	CD	_	_	_
52	v2	v2	NN	_	_	_
53	RNA-Seq	rna-seq	NN	_	_	_
54	Library	Library	NNP	_	_	_
55	Preparation	Preparation	NNP	_	_	_
56	Kit	kit	NN	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	Epicentre	Epicentre	NNP	_	_	_
59	Biotechnologies	Biotechnologies	NNPS	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Supplementary	supplementary	JJ	_	_	_
5	_	_	NN	_	_	_
6	files	file	NNS	_	_	_
7	_	_	IN	_	_	_
8	format	format	NN	_	_	_
9	_	_	NN	_	_	_
10	and	and	CC	_	_	_
11	_	_	NN	_	_	_
12	content	content	NN	_	_	_
13	:	:	:	_	_	_
14	Excel	Excel	NNP	_	_	_
15	formatted	format	VBD	_	_	_
16	matrix	matrix	NN	_	_	_
17	table	table	NN	_	_	_
18	containing	contain	VBG	_	_	_
19	transcript	transcript	NN	_	_	_
20	coordinates	coordinate	VBZ	_	_	_
21	,	,	,	_	_	_
22	normalized	normalize	VBD	_	_	_
23	abundance	abundance	NN	_	_	_
24	estimates	estimate	NNS	_	_	_
25	across	across	IN	_	_	_
26	the	the	DT	_	_	_
27	biological	biological	JJ	_	_	_
28	replicates	replicate	VBZ	_	_	_
29	and	and	CC	_	_	_
30	fold-changes	fold-change	VBZ	_	_	_
31	in	in	IN	_	_	_
32	gene	gene	NN	_	_	_
33	expression	expression	NN	_	_	_
34	between	between	IN	_	_	_
35	cells	cell	NNS	_	_	_
36	expressing	express	VBG	_	_	_
37	Vector	Vector	NNP	_	_	_
38	and	and	CC	_	_	_
39	DicF	dicf	NN	_	_	_
40	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Supplementary	Supplementary	NNP	_	_	_
3	_	_	VBD	_	_	_
4	files	file	NNS	_	_	_
5	_	_	IN	_	_	_
6	format	format	NN	_	_	_
7	_	_	NN	_	_	_
8	and	and	CC	_	_	_
9	_	_	NN	_	_	_
10	content	content	NN	_	_	_
11	:	:	:	_	_	_
12	Processed-VectorvsDicF-operon	Processed-VectorvsDicF-operon	NNP	_	_	_
13	.	.	.	_	_	_

1	txt	txt	NN	_	_	_
2	:	:	:	_	_	_
3	.	.	.	_	_	_

1	txt	txt	NN	_	_	_
2	tab	tab	NN	_	_	_
3	delimited	delimit	VBD	_	_	_
4	file	file	NN	_	_	_
5	with	with	IN	_	_	_
6	operons	operon	NNS	_	_	_
7	expressed	express	VBN	_	_	_
8	differently	differently	RB	_	_	_
9	between	between	IN	_	_	_
10	vector	vector	NN	_	_	_
11	and	and	CC	_	_	_
12	DicF	dicf	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
14	Supplementary	supplementary	JJ	_	_	_
15	_	_	NN	_	_	_
16	files	file	NNS	_	_	_
17	_	_	IN	_	_	_
18	format	format	NN	_	_	_
19	_	_	NN	_	_	_
20	and	and	CC	_	_	_
21	_	_	NN	_	_	_
22	content	content	NN	_	_	_
23	:	:	:	_	_	_
24	Processed-VectorvsDicF-transcripts	Processed-VectorvsDicF-transcripts	NNP	_	_	_
25	.	.	.	_	_	_

1	txt	txt	NN	_	_	_
2	:	:	:	_	_	_
3	.	.	.	_	_	_

1	txt	txt	NN	_	_	_
2	raw	raw	JJ	_	_	_
3	output	output	NN	_	_	_
4	file	file	NN	_	_	_
5	from	from	IN	_	_	_
6	Rockhopper	Rockhopper	NNP	_	_	_
7	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
8	Supplementary	Supplementary	NNP	_	_	_
9	_	_	VBD	_	_	_
10	files	file	NNS	_	_	_
11	_	_	IN	_	_	_
12	format	format	NN	_	_	_
13	_	_	NN	_	_	_
14	and	and	CC	_	_	_
15	_	_	NN	_	_	_
16	content	content	NN	_	_	_
17	:	:	:	_	_	_
18	Processed-VectorvsDicF-transcripts	Processed-VectorvsDicF-transcripts	NNP	_	_	_
19	.	.	.	_	_	_

1	xlsx	xlsx	NN	_	_	_
2	:	:	:	_	_	_
3	Excel	Excel	NNP	_	_	_
4	file	file	NN	_	_	_
5	with	with	IN	_	_	_
6	transcription	transcription	NN	_	_	_
7	start	start	NN	_	_	_
8	and	and	CC	_	_	_
9	stop	stop	VB	_	_	_
10	,	,	,	_	_	_
11	expression	expression	NN	_	_	_
12	values	value	NNS	_	_	_
13	of	of	IN	_	_	_
14	all	all	DT	_	_	_
15	genes	gene	NNS	_	_	_
16	in	in	IN	_	_	_
17	the	the	DT	_	_	_
18	E.	e.	FW	_	_	_
19	coli	coli	FW	_	_	_
20	genome	genome	NN	_	_	_
21	in	in	IN	_	_	_
22	vector	vector	NN	_	_	_
23	and	and	CC	_	_	_
24	DicF	dicf	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
26	The	the	DT	_	_	_
27	program	program	NN	_	_	_
28	Rockhopper	rockhopper	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	described	describe	VBN	_	_	_
31	in	in	IN	_	_	_
32	Mc	mc	NN	_	_	_
33	Clure	clure	NN	_	_	_
34	,	,	,	_	_	_
35	et	et	FW	_	_	_
36	al.	al.	FW	_	_	_
37	.	.	.	_	_	_

1	Nucleic	nucleic	JJ	_	_	_
2	Acids	Acids	NNP	_	_	_
3	Research	Research	NNP	_	_	_
4	.	.	.	_	_	_

1	2013	2013	CD	_	_	_
2	,	,	,	_	_	_
3	41	41	CD	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	14	14	CD	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	was	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	for	for	IN	_	_	_
11	alignment	alignment	NN	_	_	_
12	,	,	,	_	_	_
13	normalization	normalization	NN	_	_	_
14	,	,	,	_	_	_
15	and	and	CC	_	_	_
16	quantification	quantification	NN	_	_	_
17	.	.	.	_	_	_

1	Genome	Genome	NNP	_	_	_
2	_	_	SYM	_	_	_
3	builg	builg	NN	_	_	_
4	:	:	:	_	_	_
5	K-12	k-12	NN	_	_	_
6	subst	subst	NN	_	_	_
7	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	genome	genome	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	NC	nc	NN	_	_	_
5	_	_	CD	_	_	_
6	000913.3	000913.3	CD	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	Total	Total	NNP	_	_	_
10	RNA	rna	NN	_	_	_
11	from	from	IN	_	_	_
12	bacterial	bacterial	JJ	_	_	_
13	culture	culture	NN	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	Vector	Vector	NNP	_	_	_
16	rep1	rep1	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Vector	Vector	NNP	_	_	_
19	rep2	rep2	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Vector	Vector	NNP	_	_	_
22	rep3	rep3	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	Bacterial	bacterial	JJ	_	_	_
25	cell	cell	NN	_	_	_
26	pellet	pellet	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Bacterial	bacterial	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	grown	grow	VBN	_	_	_
31	overnight	overnight	RB	_	_	_
32	at	at	IN	_	_	_
33	37C	37c	NN	_	_	_
34	,	,	,	_	_	_
35	given	give	VBN	_	_	_
36	1	1	CD	_	_	_
37	%	%	NN	_	_	_
38	sub-culturing	sub-culturing	JJ	_	_	_
39	till	till	IN	_	_	_
40	OD	od	NN	_	_	_
41	at	at	IN	_	_	_
42	600nm	600nm	NN	_	_	_
43	was	be	VBD	_	_	_
44	0.4	0.4	CD	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	Escherichia	escherichia	FW	Organism	_	_
47	coli	coli	FW	Organism	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	Images	image	NNS	_	_	_
50	were	be	VBD	_	_	_
51	quantified	quantify	VBN	_	_	_
52	using	use	VBG	_	_	_
53	Feature	Feature	NNP	_	_	_
54	Extraction	Extraction	NNP	_	_	_
55	Software	Software	NNP	_	_	_
56	-LRB-	-lrb-	-LRB-	_	_	_
57	Agilent	Agilent	NNP	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	.	.	.	_	_	_

1	Feature	feature	NN	_	_	_
2	extracted	extract	VBN	_	_	_
3	raw	raw	JJ	_	_	_
4	data	datum	NNS	_	_	_
5	was	be	VBD	_	_	_
6	analyzed	analyze	VBN	_	_	_
7	using	use	VBG	_	_	_
8	GeneSpring	GeneSpring	NNP	_	_	_
9	GX	GX	NNP	_	_	_
10	Version	Version	NNP	_	_	_
11	software	software	NN	_	_	_
12	from	from	IN	_	_	_
13	Agilent	Agilent	NNP	_	_	_
14	.	.	.	_	_	_

1	Normalization	normalization	NN	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	data	datum	NNS	_	_	_
5	was	be	VBD	_	_	_
6	done	do	VBN	_	_	_
7	in	in	IN	_	_	_
8	GeneSpring	GeneSpring	NNP	_	_	_
9	GX	GX	NNP	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	75th	75th	JJ	_	_	_
13	percentile	percentile	NN	_	_	_
14	shift	shift	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	MG1655	mg1655	NN	_	_	_
17	G181D	g181d	NN	_	_	_
18	NusA	nusa	NN	_	_	_
19	BR	br	NN	_	_	_
20	,	,	,	_	_	_
21	treated	treat	VBN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	MG1655	mg1655	NN	_	_	_
24	G181D	g181d	NN	_	_	_
25	NusA	nusa	NN	_	_	_
26	,	,	,	_	_	_
27	treated	treat	VBN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	MG1655	mg1655	NN	_	_	_
30	R258C	r258c	NN	_	_	_
31	NusA	nusa	NN	_	_	_
32	BR	br	NN	_	_	_
33	,	,	,	_	_	_
34	treated	treat	VBN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	MG1655	mg1655	NN	_	_	_
37	R258C	r258c	NN	_	_	_
38	NusA	nusa	NN	_	_	_
39	,	,	,	_	_	_
40	treated	treat	VBN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	MG1655	mg1655	NN	_	_	_
43	WT	WT	NNP	_	_	_
44	NusA	NusA	NNP	_	_	_
45	BR	BR	NNP	_	_	_
46	,	,	,	_	_	_
47	control	control	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	MG1655	mg1655	NN	_	_	_
50	WT	WT	NNP	_	_	_
51	NusA	NusA	NNP	_	_	_
52	,	,	,	_	_	_
53	control	control	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
55	plasmid	plasmid	NN	_	_	_
56	:	:	:	_	_	_
57	G181D	g181d	NN	_	_	_
58	NusA	nusa	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	plasmid	plasmid	NN	_	_	_
61	:	:	:	_	_	_
62	R258C	r258c	NN	_	_	_
63	NusA	nusa	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	plasmid	plasmid	NN	_	_	_
66	:	:	:	_	_	_
67	wild	wild	JJ	_	_	_
68	type	type	NN	_	_	_
69	NusA	nusa	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	strain	strain	NN	_	_	_
72	:	:	:	_	_	_
73	MG1655	mg1655	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
75	The	the	DT	_	_	_
76	RNA	rna	NN	_	_	_
77	extraction	extraction	NN	_	_	_
78	from	from	IN	_	_	_
79	the	the	DT	_	_	_
80	samples	sample	NNS	_	_	_
81	was	be	VBD	_	_	_
82	performed	perform	VBN	_	_	_
83	by	by	IN	_	_	_
84	Qiagen	Qiagen	NNP	_	_	_
85	RNeasy	RNeasy	NNP	_	_	_
86	Mini	Mini	NNP	_	_	_
87	Kit	kit	NN	_	_	_
88	with	with	IN	_	_	_
89	DNAse	dnase	NN	_	_	_
90	treatment	treatment	NN	_	_	_
91	-LRB-	-lrb-	-LRB-	_	_	_
92	Cat.No	cat.no	NN	_	_	_
93	.	.	.	_	_	_

1	74004	74004	CD	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	as	as	IN	_	_	_
4	per	per	IN	_	_	_
5	manufacturer	manufacturer	NN	_	_	_
6	's	's	POS	_	_	_
7	protocol	protocol	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Treated	treat	VBN	_	_	_
3	experimental	experimental	JJ	_	_	_
4	sets	set	NNS	_	_	_
5	transformed	transform	VBN	_	_	_
6	with	with	IN	_	_	_
7	plasmids	plasmid	NNS	_	_	_
8	containing	contain	VBG	_	_	_
9	WT	wt	JJ	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Bacterial	bacterial	JJ	_	_	_
12	cell	cell	NN	_	_	_
13	pellet	pellet	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Bacterial	bacterial	JJ	_	_	_
16	culture	culture	NN	_	_	_
17	grown	grow	VBN	_	_	_
18	overnight	overnight	RB	_	_	_
19	at	at	IN	_	_	_
20	37C	37c	NN	_	_	_
21	,	,	,	_	_	_
22	given	give	VBN	_	_	_
23	1	1	CD	_	_	_
24	%	%	NN	_	_	_
25	sub-culturing	sub-culturing	JJ	_	_	_
26	till	till	IN	_	_	_
27	OD	od	NN	_	_	_
28	at	at	IN	_	_	_
29	600nm	600nm	NN	_	_	_
30	was	be	VBD	_	_	_
31	0.4	0.4	CD	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	Escherichia	escherichia	FW	Organism	_	_
34	coli	coli	FW	Organism	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	Images	image	NNS	_	_	_
37	were	be	VBD	_	_	_
38	quantified	quantify	VBN	_	_	_
39	using	use	VBG	_	_	_
40	Feature	Feature	NNP	_	_	_
41	Extraction	Extraction	NNP	_	_	_
42	Software	Software	NNP	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	Agilent	Agilent	NNP	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	.	.	.	_	_	_

1	Feature	feature	NN	_	_	_
2	extracted	extract	VBN	_	_	_
3	raw	raw	JJ	_	_	_
4	data	datum	NNS	_	_	_
5	was	be	VBD	_	_	_
6	analyzed	analyze	VBN	_	_	_
7	using	use	VBG	_	_	_
8	GeneSpring	GeneSpring	NNP	_	_	_
9	GX	GX	NNP	_	_	_
10	Version	Version	NNP	_	_	_
11	software	software	NN	_	_	_
12	from	from	IN	_	_	_
13	Agilent	Agilent	NNP	_	_	_
14	.	.	.	_	_	_

1	Normalization	normalization	NN	_	_	_
2	of	of	IN	_	_	_
3	the	the	DT	_	_	_
4	data	datum	NNS	_	_	_
5	was	be	VBD	_	_	_
6	done	do	VBN	_	_	_
7	in	in	IN	_	_	_
8	GeneSpring	GeneSpring	NNP	_	_	_
9	GX	GX	NNP	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	75th	75th	JJ	_	_	_
13	percentile	percentile	NN	_	_	_
14	shift	shift	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	MG1655	mg1655	NN	_	_	_
17	G181D	g181d	NN	_	_	_
18	NusA	nusa	NN	_	_	_
19	BR1	br1	NN	_	_	_
20	,	,	,	_	_	_
21	treated	treat	VBN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	MG1655	mg1655	NN	_	_	_
24	G181D	g181d	NN	_	_	_
25	NusA	nusa	NN	_	_	_
26	BR2	br2	NN	_	_	_
27	,	,	,	_	_	_
28	treated	treat	VBN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	MG1655	mg1655	NN	_	_	_
31	R258C	r258c	NN	_	_	_
32	NusA	nusa	NN	_	_	_
33	BR1	br1	NN	_	_	_
34	,	,	,	_	_	_
35	treated	treat	VBN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	MG1655	mg1655	NN	_	_	_
38	R258C	r258c	NN	_	_	_
39	NusA	nusa	NN	_	_	_
40	BR2	br2	NN	_	_	_
41	,	,	,	_	_	_
42	treated	treat	VBN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	MG1655	mg1655	NN	_	_	_
45	WT	WT	NNP	_	_	_
46	NusA	NusA	NNP	_	_	_
47	BR1	br1	NN	_	_	_
48	,	,	,	_	_	_
49	control	control	NN	_	_	_
50	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
51	MG1655	MG1655	NNP	_	_	_
52	WT	WT	NNP	_	_	_
53	NusA	nusa	NN	_	_	_
54	BR2	br2	NN	_	_	_
55	,	,	,	_	_	_
56	control	control	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
58	plasmid	plasmid	NN	_	_	_
59	:	:	:	_	_	_
60	G181D	g181d	NN	_	_	_
61	NusA	nusa	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	plasmid	plasmid	NN	_	_	_
64	:	:	:	_	_	_
65	R258C	r258c	NN	_	_	_
66	NuSA	nusa	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	plasmid	plasmid	NN	_	_	_
69	:	:	:	_	_	_
70	wild	wild	JJ	_	_	_
71	type	type	NN	_	_	_
72	NusA	nusa	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	strain	strain	NN	_	_	_
75	:	:	:	_	_	_
76	MG1655	mg1655	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
78	The	the	DT	_	_	_
79	RNA	rna	NN	_	_	_
80	extraction	extraction	NN	_	_	_
81	from	from	IN	_	_	_
82	the	the	DT	_	_	_
83	samples	sample	NNS	_	_	_
84	was	be	VBD	_	_	_
85	performed	perform	VBN	_	_	_
86	by	by	IN	_	_	_
87	Qiagen	Qiagen	NNP	_	_	_
88	RNeasy	RNeasy	NNP	_	_	_
89	Mini	Mini	NNP	_	_	_
90	Kit	kit	NN	_	_	_
91	with	with	IN	_	_	_
92	DNAse	dnase	NN	_	_	_
93	treatment	treatment	NN	_	_	_
94	-LRB-	-lrb-	-LRB-	_	_	_
95	Cat.No	cat.no	NN	_	_	_
96	.	.	.	_	_	_

1	74004	74004	CD	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	as	as	IN	_	_	_
4	per	per	IN	_	_	_
5	manufacturer	manufacturer	NN	_	_	_
6	's	's	POS	_	_	_
7	protocol	protocol	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Treated	treat	VBN	_	_	_
3	experimental	experimental	JJ	_	_	_
4	sets	set	NNS	_	_	_
5	transformed	transform	VBN	_	_	_
6	with	with	IN	_	_	_
7	plasmids	plasmid	NNS	_	_	_
8	containing	contain	VBG	_	_	_
9	WT	wt	JJ	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Bacterial	bacterial	JJ	_	_	_
12	cell	cell	NN	_	_	_
13	pellet	pellet	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Bacterial	bacterial	JJ	_	_	_
16	culture	culture	NN	_	_	_
17	grown	grow	VBN	_	_	_
18	overnight	overnight	RB	_	_	_
19	at	at	IN	_	_	_
20	37C	37c	NN	_	_	_
21	,	,	,	_	_	_
22	given	give	VBN	_	_	_
23	1	1	CD	_	_	_
24	%	%	NN	_	_	_
25	sub-culturing	sub-culturing	JJ	_	_	_
26	till	till	IN	_	_	_
27	OD	od	NN	_	_	_
28	at	at	IN	_	_	_
29	600nm	600nm	NN	_	_	_
30	was	be	VBD	_	_	_
31	0.4	0.4	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
33	E.	e.	FW	_	_	_
34	coli	coli	FW	_	_	_
35	MG1655	mg1655	NN	_	_	_
36	,	,	,	_	_	_
37	BCM	BCM	NNP	_	_	_
38	treated-Replicate1	treated-replicate1	NN	_	_	_
39	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
40	E.	E.	NNP	_	_	_
41	coli	coli	NN	_	_	_
42	MG1655	mg1655	NN	_	_	_
43	,	,	,	_	_	_
44	BCM	BCM	NNP	_	_	_
45	treated-Replicate2	treated-replicate2	NN	_	_	_
46	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
47	E.	E.	NNP	_	_	_
48	coli	coli	NN	_	_	_
49	MG1655	mg1655	NN	_	_	_
50	,	,	,	_	_	_
51	Vector	Vector	NNP	_	_	_
52	control-Replicate1	control-replicate1	NN	_	_	_
53	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
54	E.	E.	NNP	_	_	_
55	coli	coli	NN	_	_	_
56	MG1655	mg1655	NN	_	_	_
57	,	,	,	_	_	_
58	Vector	Vector	NNP	_	_	_
59	control-Replicate2	control-replicate2	NN	_	_	_
60	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
61	E.	E.	NNP	_	_	_
62	coli	coli	NN	_	_	_
63	MG1655	mg1655	NN	_	_	_
64	,	,	,	_	_	_
65	WT	WT	NNP	_	_	_
66	Rho	rho	NN	_	_	_
67	treated-Replicate1	treated-replicate1	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	E.	e.	FW	_	_	_
70	coli	coli	FW	_	_	_
71	MG1655	mg1655	NN	_	_	_
72	,	,	,	_	_	_
73	WT	WT	NNP	_	_	_
74	Rho	rho	NN	_	_	_
75	treated-Replicate2	treated-replicate2	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	Escherichia	escherichia	FW	Organism	_	_
78	coli	coli	FW	Organism	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	Images	image	NNS	_	_	_
81	Analysis	analysis	NN	_	_	_
82	using	use	VBG	_	_	_
83	Agilent	Agilent	NNP	_	_	_
84	Feature	Feature	NNP	_	_	_
85	Extraction	Extraction	NNP	_	_	_
86	Software	Software	NNP	_	_	_
87	Version	Version	NNP	_	_	_
88	11.5	11.5	CD	_	_	_
89	to	to	TO	_	_	_
90	obtain	obtain	VB	_	_	_
91	raw	raw	JJ	_	_	_
92	data.Probe	data.probe	NN	_	_	_
93	intensities	intensity	NNS	_	_	_
94	generated	generate	VBN	_	_	_
95	from	from	IN	_	_	_
96	feature	feature	NN	_	_	_
97	extraction	extraction	NN	_	_	_
98	raw	raw	JJ	_	_	_
99	data	datum	NNS	_	_	_
100	were	be	VBD	_	_	_
101	split	split	VBN	_	_	_
102	based	base	VBN	_	_	_
103	on	on	IN	_	_	_
104	channel	channel	NN	_	_	_
105	type	type	NN	_	_	_
106	and	and	CC	_	_	_
107	analysis	analysis	NN	_	_	_
108	was	be	VBD	_	_	_
109	performed	perform	VBN	_	_	_
110	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
6	The	the	DT	_	_	_
7	RNA	rna	NN	_	_	_
8	extraction	extraction	NN	_	_	_
9	from	from	IN	_	_	_
10	the	the	DT	_	_	_
11	samples	sample	NNS	_	_	_
12	was	be	VBD	_	_	_
13	performed	perform	VBN	_	_	_
14	by	by	IN	_	_	_
15	Qiagen	Qiagen	NNP	_	_	_
16	RNeasy	RNeasy	NNP	_	_	_
17	Mini	Mini	NNP	_	_	_
18	Kit	kit	NN	_	_	_
19	with	with	IN	_	_	_
20	DNAse	dnase	NN	_	_	_
21	treatment	treatment	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Cat.No	cat.no	NN	_	_	_
24	.	.	.	_	_	_

1	74004	74004	CD	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	as	as	IN	_	_	_
4	per	per	IN	_	_	_
5	manufacturer	manufacturer	NN	_	_	_
6	's	's	POS	_	_	_
7	protocol	protocol	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Treated	treat	VBN	_	_	_
3	experimental	experimental	JJ	_	_	_
4	sets	set	NNS	_	_	_
5	transformed	transform	VBN	_	_	_
6	with	with	IN	_	_	_
7	plasmids	plasmid	NNS	_	_	_
8	containing	contain	VBG	_	_	_
9	BCM	BCM	NNP	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	treatment	treatment	NN	_	_	_
12	:	:	:	_	_	_
13	BCM	BCM	NNP	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	treatment	treatment	NN	_	_	_
16	:	:	:	_	_	_
17	vector	vector	NN	_	_	_
18	control	control	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	treatment	treatment	NN	_	_	_
21	:	:	:	_	_	_
22	WT	WT	NNP	_	_	_
23	Rho	rho	NN	_	_	_
24	plasmid	plasmid	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Bacterial	bacterial	JJ	_	_	_
27	cell	cell	NN	_	_	_
28	pellet	pellet	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Bacterial	bacterial	JJ	_	_	_
31	culture	culture	NN	_	_	_
32	grown	grow	VBN	_	_	_
33	overnight	overnight	RB	_	_	_
34	at	at	IN	_	_	_
35	37C	37c	NN	_	_	_
36	,	,	,	_	_	_
37	given	give	VBN	_	_	_
38	1	1	CD	_	_	_
39	%	%	NN	_	_	_
40	sub-culturing	sub-culturing	JJ	_	_	_
41	till	till	IN	_	_	_
42	OD	od	NN	_	_	_
43	at	at	IN	_	_	_
44	600nm	600nm	NN	_	_	_
45	was	be	VBD	_	_	_
46	0.4	0.4	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
48	E.	e.	FW	_	_	_
49	coli	coli	FW	_	_	_
50	MG1655	mg1655	NN	_	_	_
51	∆	∆	CD	_	_	_
52	Rac	rac	NN	_	_	_
53	G324D	g324d	NN	_	_	_
54	,	,	,	_	_	_
55	treated-Replicate1-mutant	treated-replicate1-mutant	JJ	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
57	E.	e.	FW	_	_	_
58	coli	coli	FW	_	_	_
59	MG1655	mg1655	NN	_	_	_
60	∆	∆	CD	_	_	_
61	Rac	rac	NN	_	_	_
62	G324D	g324d	NN	_	_	_
63	,	,	,	_	_	_
64	treated-Replicate2-mutant	treated-replicate2-mutant	JJ	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
66	E.	e.	FW	_	_	_
67	coli	coli	FW	_	_	_
68	MG1655	mg1655	NN	_	_	_
69	∆	∆	CD	_	_	_
70	Rac	rac	NN	_	_	_
71	N340S	n340s	NN	_	_	_
72	,	,	,	_	_	_
73	treated-Replicate1-mutant	treated-replicate1-mutant	JJ	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
75	E.	e.	FW	_	_	_
76	coli	coli	FW	_	_	_
77	MG1655	mg1655	NN	_	_	_
78	∆	∆	CD	_	_	_
79	Rac	rac	NN	_	_	_
80	N340S	n340s	NN	_	_	_
81	,	,	,	_	_	_
82	treated-Replicate2-mutant	treated-replicate2-mutant	JJ	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
84	E.	e.	FW	_	_	_
85	coli	coli	FW	_	_	_
86	MG1655	mg1655	NN	_	_	_
87	∆	∆	CD	_	_	_
88	Rac	rac	NN	_	_	_
89	WT	WT	NNP	_	_	_
90	,	,	,	_	_	_
91	control-Replicate1-Wildtype	control-replicate1-wildtype	JJ	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
93	E.	e.	FW	_	_	_
94	coli	coli	FW	_	_	_
95	MG1655	mg1655	NN	_	_	_
96	∆	∆	CD	_	_	_
97	Rac	rac	NN	_	_	_
98	WT	WT	NNP	_	_	_
99	,	,	,	_	_	_
100	control-Replicate2-Wildtype	control-replicate2-wildtype	JJ	_	_	_
101	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
102	Escherichia	escherichia	FW	Organism	_	_
103	coli	coli	FW	Organism	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	genotype	genotype	NN	_	_	_
106	:	:	:	_	_	_
107	delta-rac	delta-rac	JJ	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	Images	image	NNS	_	_	_
110	Analysis	analysis	NN	_	_	_
111	using	use	VBG	_	_	_
112	Agilent	Agilent	NNP	_	_	_
113	Feature	Feature	NNP	_	_	_
114	Extraction	Extraction	NNP	_	_	_
115	Software	Software	NNP	_	_	_
116	Version	Version	NNP	_	_	_
117	11.5	11.5	CD	_	_	_
118	to	to	TO	_	_	_
119	obtain	obtain	VB	_	_	_
120	raw	raw	JJ	_	_	_
121	data.Probe	data.probe	NN	_	_	_
122	intensities	intensity	NNS	_	_	_
123	generated	generate	VBN	_	_	_
124	from	from	IN	_	_	_
125	feature	feature	NN	_	_	_
126	extraction	extraction	NN	_	_	_
127	raw	raw	JJ	_	_	_
128	data	datum	NNS	_	_	_
129	were	be	VBD	_	_	_
130	split	split	VBN	_	_	_
131	based	base	VBN	_	_	_
132	on	on	IN	_	_	_
133	channel	channel	NN	_	_	_
134	type	type	NN	_	_	_
135	and	and	CC	_	_	_
136	analysis	analysis	NN	_	_	_
137	was	be	VBD	_	_	_
138	performed	perform	VBN	_	_	_
139	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	plasmid	plasmid	NN	_	_	_
3	:	:	:	_	_	_
4	G324D	g324d	NN	_	_	_
5	Rho	rho	NN	_	_	_
6	mutant	mutant	JJ	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	plasmid	plasmid	NN	_	_	_
9	:	:	:	_	_	_
10	N340S	n340s	NN	_	_	_
11	Rho	rho	NN	_	_	_
12	mutant	mutant	JJ	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	plasmid	plasmid	NN	_	_	_
15	:	:	:	_	_	_
16	WT	WT	NNP	_	_	_
17	Rho	rho	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	strain	strain	NN	_	_	_
20	:	:	:	_	_	_
21	MG1655	mg1655	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	The	the	DT	_	_	_
24	RNA	rna	NN	_	_	_
25	extraction	extraction	NN	_	_	_
26	from	from	IN	_	_	_
27	the	the	DT	_	_	_
28	samples	sample	NNS	_	_	_
29	was	be	VBD	_	_	_
30	performed	perform	VBN	_	_	_
31	by	by	IN	_	_	_
32	Qiagen	Qiagen	NNP	_	_	_
33	RNeasy	RNeasy	NNP	_	_	_
34	Mini	Mini	NNP	_	_	_
35	Kit	kit	NN	_	_	_
36	with	with	IN	_	_	_
37	DNAse	dnase	NN	_	_	_
38	treatment	treatment	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	Cat.No	cat.no	NN	_	_	_
41	.	.	.	_	_	_

1	74004	74004	CD	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	as	as	IN	_	_	_
4	per	per	IN	_	_	_
5	manufacturer	manufacturer	NN	_	_	_
6	's	's	POS	_	_	_
7	protocol	protocol	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Treated	treat	VBN	_	_	_
3	experimental	experimental	JJ	_	_	_
4	sets	set	NNS	_	_	_
5	transformed	transform	VBN	_	_	_
6	with	with	IN	_	_	_
7	plasmids	plasmid	NNS	_	_	_
8	containing	contain	VBG	_	_	_
9	Rho	rho	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	WT	wt	JJ	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	Adaptor	adaptor	NN	_	_	_
14	Sequences	sequence	NNS	_	_	_
15	were	be	VBD	_	_	_
16	removed	remove	VBN	_	_	_
17	using	use	VBG	_	_	_
18	fastx	fastx	NN	_	_	_
19	_	_	NN	_	_	_
20	clipper	clipper	NN	_	_	_
21	.	.	.	_	_	_

1	-LRB-	-lrb-	-LRB-	_	_	_
2	http	http	NN	_	_	_
3	:	:	:	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
5	All	all	DT	_	_	_
6	samples	sample	NNS	_	_	_
7	were	be	VBD	_	_	_
8	processed	process	VBN	_	_	_
9	following	follow	VBG	_	_	_
10	NEB	NEB	NNP	_	_	_
11	's	's	POS	_	_	_
12	protocol	protocol	NN	_	_	_
13	from	from	IN	_	_	_
14	the	the	DT	_	_	_
15	NEBNext	nebnext	NN	_	_	_
16	®	®	NN	_	_	_
17	ChIP-Seq	chip-seq	JJ	_	_	_
18	library	library	NN	_	_	_
19	preparation	preparation	NN	_	_	_
20	kit	kit	NN	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Bacterial	bacterial	JJ	_	_	_
3	Cell	cell	NN	_	_	_
4	Lysates	lysate	NNS	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Cells	cell	NNS	_	_	_
7	were	be	VBD	_	_	_
8	collected	collect	VBN	_	_	_
9	by	by	IN	_	_	_
10	centrifugation	centrifugation	NN	_	_	_
11	and	and	CC	_	_	_
12	washed	wash	VBN	_	_	_
13	three	three	CD	_	_	_
14	times	time	NNS	_	_	_
15	in	in	IN	_	_	_
16	ice-cold	ice-cold	JJ	_	_	_
17	1X	1x	NN	_	_	_
18	PBS	PBS	NNP	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	re-suspended	re-suspended	JJ	_	_	_
6	in	in	IN	_	_	_
7	250	250	CD	_	_	_
8	μl	μl	NN	_	_	_
9	ChIP	chip	NN	_	_	_
10	buffer	buffer	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	200	200	CD	_	_	_
13	mM	mm	NN	KWSUPP	_	_
14	Tris-HCl	tris-hcl	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	pH	ph	NN	_	_	_
17	8.0	8.0	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	600	600	CD	_	_	_
21	mM	mm	NN	KWSUPP	_	_
22	NaCl	nacl	NN	_	_	_
23	4	4	CD	_	_	_
24	%	%	NN	_	_	_
25	Triton	Triton	NNP	_	_	_
26	X	X	NNP	_	_	_
27	,	,	,	_	_	_
28	Complete	complete	JJ	_	_	_
29	protease	protease	NN	_	_	_
30	inhibitor	inhibitor	NN	_	_	_
31	cocktail	cocktail	NN	_	_	_
32	EDTA-free	edta-free	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	Roche	Roche	NNP	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	.	.	.	_	_	_

1	Sonication	sonication	NN	_	_	_
2	of	of	IN	_	_	_
3	crosslinked	crosslink	VBN	_	_	_
4	samples	sample	NNS	_	_	_
5	was	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	using	use	VBG	_	_	_
8	the	the	DT	_	_	_
9	Diagenode	Diagenode	NNP	_	_	_
10	Bioruptor	Bioruptor	NNP	_	_	_
11	®	®	NN	_	_	_
12	at	at	IN	_	_	_
13	30s	30s	CD	_	_	_
14	intervals	interval	NNS	_	_	_
15	for	for	IN	_	_	_
16	10	10	CD	_	_	_
17	min	min	NN	_	_	_
18	at	at	IN	_	_	_
19	high	high	JJ	_	_	_
20	amplitude	amplitude	NN	_	_	_
21	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	sonication	sonication	NN	_	_	_
3	,	,	,	_	_	_
4	350	350	CD	_	_	_
5	μl	μl	NN	_	_	_
6	of	of	IN	_	_	_
7	ChIP	chip	NN	_	_	_
8	buffer	buffer	NN	_	_	_
9	was	be	VBD	_	_	_
10	added	add	VBN	_	_	_
11	to	to	TO	_	_	_
12	each	each	DT	_	_	_
13	sample	sample	NN	_	_	_
14	,	,	,	_	_	_
15	the	the	DT	_	_	_
16	samples	sample	NNS	_	_	_
17	were	be	VBD	_	_	_
18	mixed	mix	VBN	_	_	_
19	by	by	IN	_	_	_
20	gentle	gentle	JJ	_	_	_
21	pipetting	pipetting	NN	_	_	_
22	and	and	CC	_	_	_
23	100	100	CD	_	_	_
24	μl	μl	NN	_	_	_
25	of	of	IN	_	_	_
26	each	each	DT	_	_	_
27	lysate	lysate	NN	_	_	_
28	was	be	VBD	_	_	_
29	removed	remove	VBN	_	_	_
30	and	and	CC	_	_	_
31	stored	store	VBN	_	_	_
32	as	as	IN	_	_	_
33	`	`	``	_	_	_
34	input	input	NN	_	_	_
35	'	'	''	_	_	_
36	.	.	.	_	_	_

1	Immunoprecipitation	immunoprecipitation	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	overnight	overnight	RB	_	_	_
5	at	at	IN	_	_	_
6	4	4	CD	_	_	_
7	°C	°c	NN	_	_	_
8	using	use	VBG	_	_	_
9	1	1	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Cells	cell	NNS	_	_	_
12	were	be	VBD	_	_	_
13	grown	grow	VBN	_	_	_
14	in	in	IN	_	_	_
15	LB	LB	NNP	MED	_	_
16	media	media	NNS	MED	_	_
17	supplemented	supplement	VBN	_	_	_
18	with	with	IN	_	_	_
19	0.2	0.2	CD	_	_	_
20	%	%	NN	_	_	_
21	arabinose	arabinose	NN	_	_	_
22	at	at	IN	_	_	_
23	37	37	CD	_	_	_
24	°C	°c	NN	_	_	_
25	to	to	TO	_	_	_
26	and	and	CC	_	_	_
27	OD600nm	od600nm	NN	_	_	_
28	of	of	IN	_	_	_
29	0.2-0.25	0.2-0.25	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	ChIP-Seq	chip-seq	NN	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	Data	Data	NNP	_	_	_
34	collapsed	collapse	VBD	_	_	_
35	using	use	VBG	_	_	_
36	fastx	fastx	NN	_	_	_
37	collapser	collapser	NN	_	_	_
38	to	to	TO	_	_	_
39	remove	remove	VB	_	_	_
40	identical	identical	JJ	_	_	_
41	sequencing	sequencing	NN	_	_	_
42	reads	read	VBZ	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	http	http	NN	_	_	_
45	:	:	:	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	DL4184C	dl4184c	NN	_	_	_
48	_	_	CD	_	_	_
49	ChIP-seq	ChIP-seq	NNP	_	_	_
50	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
51	DL4201C	DL4201C	NNP	_	_	_
52	_	_	SYM	_	_	_
53	ChIP-seq	ChIP-seq	NNP	_	_	_
54	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
55	DL4311C	DL4311C	NNP	_	_	_
56	_	_	SYM	_	_	_
57	ChIP-seq	ChIP-seq	NNP	_	_	_
58	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
59	DL4312C	DL4312C	NNP	_	_	_
60	_	_	SYM	_	_	_
61	ChIP-seq	ChIP-seq	NNP	_	_	_
62	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
63	Escherichia	escherichia	FW	Organism	_	_
64	coli	coli	FW	Organism	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	Genome	Genome	NNP	_	_	_
67	_	_	NNP	_	_	_
68	build	build	VB	_	_	_
69	:	:	:	_	_	_
70	Escherichia	escherichia	FW	Organism	_	_
71	coli	coli	FW	Organism	_	_
72	K12	k12	NN	_	_	_
73	MG1655	mg1655	NN	_	_	_
74	NC000913	nc000913	NN	_	_	_
75	.3	.3	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	genotype	genotype	NN	_	_	_
78	:	:	:	_	_	_
79	delta	delta	NN	_	_	_
80	_	_	SYM	_	_	_
81	recG263	recg263	NN	_	_	_
82	:	:	:	_	_	_
83	:	:	:	_	_	_
84	KanR	kanr	NN	_	_	_
85	lacZ	lacz	NN	GEN	_	_
86	:	:	:	_	_	_
87	:	:	:	_	_	_
88	χχχ	χχχ	NN	_	_	_
89	mhpR	mhpr	NN	GEN	_	_
90	:	:	:	_	_	_
91	:	:	:	_	_	_
92	χχχ	χχχ	NN	_	_	_
93	proA	proa	NN	GEN	_	_
94	:	:	:	_	_	_
95	:	:	:	_	_	_
96	ISceIcs	isceic	NNS	_	_	_
97	tsx	tsx	NN	GEN	_	_
98	:	:	:	_	_	_
99	:	:	:	_	_	_
100	ISceIcs	isceic	NNS	_	_	_
101	PBAD-sbcDC	pbad-sbcdc	NN	_	_	_
102	lacZ	lacz	NN	GEN	_	_
103	+	+	CC	_	_	_
104	cynX	cynx	NN	GEN	_	_
105	:	:	:	_	_	_
106	:	:	:	_	_	_
107	GmR	gmr	NN	_	_	_
108	lacIq	laciq	NN	_	_	_
109	lacZχ	laczχ	NN	_	_	_
110	-	-	:	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	genotype	genotype	NN	_	_	_
113	:	:	:	_	_	_
114	delta	delta	NN	_	_	_
115	_	_	SYM	_	_	_
116	recG263	recg263	NN	_	_	_
117	:	:	:	_	_	_
118	:	:	:	_	_	_
119	KanR	kanr	NN	_	_	_
120	lacZ	lacz	NN	GEN	_	_
121	:	:	:	_	_	_
122	:	:	:	_	_	_
123	χχχ	χχχ	NN	_	_	_
124	mhpR	mhpr	NN	GEN	_	_
125	:	:	:	_	_	_
126	:	:	:	_	_	_
127	χχχ	χχχ	NN	_	_	_
128	proA	proa	NN	GEN	_	_
129	:	:	:	_	_	_
130	:	:	:	_	_	_
131	ISceIcs	isceic	NNS	_	_	_
132	tsx	tsx	NN	GEN	_	_
133	:	:	:	_	_	_
134	:	:	:	_	_	_
135	ISceIcs	isceic	NNS	_	_	_
136	PBAD-sbcDC	pbad-sbcdc	NN	_	_	_
137	lacZ	lacz	NN	GEN	_	_
138	:	:	:	_	_	_
139	:	:	:	_	_	_
140	pal246	pal246	NN	_	_	_
141	cynX	cynx	NN	GEN	_	_
142	:	:	:	_	_	_
143	:	:	:	_	_	_
144	GmR	gmr	NN	_	_	_
145	lacIq	laciq	NN	_	_	_
146	lacZχ	laczχ	NN	_	_	_
147	-	-	:	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	genotype	genotype	NN	_	_	_
150	:	:	:	_	_	_
151	lacZ	lacz	NN	GEN	_	_
152	:	:	:	_	_	_
153	:	:	:	_	_	_
154	χχχ	χχχ	NN	_	_	_
155	mhpR	mhpr	NN	GEN	_	_
156	:	:	:	_	_	_
157	:	:	:	_	_	_
158	χχχ	χχχ	NN	_	_	_
159	proA	proa	NN	GEN	_	_
160	:	:	:	_	_	_
161	:	:	:	_	_	_
162	ISceIcs	isceic	NNS	_	_	_
163	tsx	tsx	NN	GEN	_	_
164	:	:	:	_	_	_
165	:	:	:	_	_	_
166	ISceIcs	isceic	NNS	_	_	_
167	PBAD-sbcDC	pbad-sbcdc	NN	_	_	_
168	lacZ	lacz	NN	GEN	_	_
169	+	+	CC	_	_	_
170	cynX	cynx	NN	GEN	_	_
171	:	:	:	_	_	_
172	:	:	:	_	_	_
173	GmR	gmr	NN	_	_	_
174	lacIq	laciq	NN	_	_	_
175	lacZχ	laczχ	NN	_	_	_
176	-	-	:	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	genotype	genotype	NN	_	_	_
179	:	:	:	_	_	_
180	lacZ	lacz	NN	GEN	_	_
181	:	:	:	_	_	_
182	:	:	:	_	_	_
183	χχχ	χχχ	NN	_	_	_
184	mhpR	mhpr	NN	GEN	_	_
185	:	:	:	_	_	_
186	:	:	:	_	_	_
187	χχχ	χχχ	NN	_	_	_
188	proA	proa	NN	GEN	_	_
189	:	:	:	_	_	_
190	:	:	:	_	_	_
191	ISceIcs	isceic	NNS	_	_	_
192	tsx	tsx	NN	GEN	_	_
193	:	:	:	_	_	_
194	:	:	:	_	_	_
195	ISceIcs	isceic	NNS	_	_	_
196	PBAD-sbcDC	pbad-sbcdc	NN	_	_	_
197	lacZ	lacz	NN	GEN	_	_
198	:	:	:	_	_	_
199	:	:	:	_	_	_
200	pal246	pal246	NN	_	_	_
201	cynX	cynx	NN	GEN	_	_
202	:	:	:	_	_	_
203	:	:	:	_	_	_
204	GmR	gmr	NN	_	_	_
205	lacIq	laciq	NN	_	_	_
206	lacZχ	laczχ	NN	_	_	_
207	-	-	:	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	Protein	protein	NN	_	_	_
210	DNA	dna	NN	_	_	_
211	interactions	interaction	NNS	_	_	_
212	were	be	VBD	_	_	_
213	crosslinked	crosslink	VBN	_	_	_
214	for	for	IN	_	_	_
215	10	10	CD	_	_	_
216	min	min	NN	_	_	_
217	at	at	IN	_	_	_
218	22.5	22.5	CD	_	_	_
219	C	c	NN	_	_	_
220	with	with	IN	_	_	_
221	1	1	CD	_	_	_
222	%	%	NN	_	_	_
223	formaldehyde	formaldehyde	NN	_	_	_
224	and	and	CC	_	_	_
225	quenched	quench	VBN	_	_	_
226	using	use	VBG	_	_	_
227	glycine	glycine	NN	_	_	_
228	to	to	TO	_	_	_
229	a	a	DT	_	_	_
230	final	final	JJ	_	_	_
231	concentration	concentration	NN	_	_	_
232	of	of	IN	_	_	_
233	0.5	0.5	CD	_	_	_
234	M	m	NN	_	_	_
235	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
236	reads	read	VBZ	_	_	_
237	were	be	VBD	_	_	_
238	mapped	map	VBN	_	_	_
239	to	to	TO	_	_	_
240	the	the	DT	_	_	_
241	E.	e.	FW	_	_	_
242	coli	coli	FW	_	_	_
243	K12	k12	NN	_	_	_
244	MG1655	mg1655	NN	_	_	_
245	-LRB-	-lrb-	-LRB-	_	_	_
246	NC000913	nc000913	NN	_	_	_
247	.3	.3	NN	_	_	_
248	-RRB-	-rrb-	-RRB-	_	_	_
249	genome	genome	NN	_	_	_
250	using	use	VBG	_	_	_
251	Novoalign	novoalign	JJ	_	_	_
252	version	version	NN	_	_	_
253	2.07	2.07	CD	_	_	_
254	-LRB-	-lrb-	-LRB-	_	_	_
255	www.novocraft.com	www.novocraft.com	NN	_	_	_
256	-RRB-	-rrb-	-RRB-	_	_	_
257	-	-	:	_	_	_
258	Example	example	NN	_	_	_
259	:	:	:	_	_	_
260	-LRB-	-lrb-	-LRB-	_	_	_
261	novoalign	novoalign	JJ	_	_	_
262	-	-	:	_	_	_
263	f	f	FW	_	_	_
264	DL4900	dl4900	FW	_	_	_
265	_	_	SYM	_	_	_
266	clip	clip	VB	_	_	_
267	_	_	SYM	_	_	_
268	clp.fasta	clp.fasta	SYM	_	_	_
269	-	-	:	_	_	_
270	d	d	NN	_	_	_
271	NC000913	nc000913	NN	_	_	_
272	.3	.3	NN	_	_	_
273	.	.	.	_	_	_

1	nix	nix	SYM	_	_	_
2	-	-	:	_	_	_
3	r	r	NN	_	_	_
4	Random	Random	NNP	_	_	_
5	>	>	JJR	_	_	_
6	DL4900.novo	dl4900.novo	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	strain	strain	NN	_	_	_
10	:	:	:	_	_	_
11	K-12	k-12	NN	_	_	_
12	MG1655	mg1655	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Supplementary	supplementary	JJ	_	_	_
15	_	_	NN	_	_	_
16	files	file	NNS	_	_	_
17	_	_	IN	_	_	_
18	format	format	NN	_	_	_
19	_	_	NN	_	_	_
20	and	and	CC	_	_	_
21	_	_	NN	_	_	_
22	content	content	NN	_	_	_
23	:	:	:	_	_	_
24	txt	txt	NN	_	_	_
25	files	file	NNS	_	_	_
26	including	include	VBG	_	_	_
27	count	count	NN	_	_	_
28	data	datum	NNS	_	_	_
29	for	for	IN	_	_	_
30	the	the	DT	_	_	_
31	whole	whole	JJ	_	_	_
32	genome	genome	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	yPileup	ypileup	NN	_	_	_
35	was	be	VBD	_	_	_
36	used	use	VBN	_	_	_
37	to	to	TO	_	_	_
38	generate	generate	VB	_	_	_
39	count	count	NN	_	_	_
40	data	datum	NNS	_	_	_
41	for	for	IN	_	_	_
42	the	the	DT	_	_	_
43	whole	whole	JJ	_	_	_
44	genome	genome	NN	_	_	_
45	-	-	:	_	_	_
46	Example	example	NN	_	_	_
47	:	:	:	_	_	_
48	pyPileup.py	pypileup.py	NN	_	_	_
49	--	--	:	_	_	_
50	file	file	NN	_	_	_
51	_	_	NN	_	_	_
52	type	type	NN	_	_	_
53	=	=	JJ	_	_	_
54	novo	novo	FW	_	_	_
55	-	-	:	_	_	_
56	f	f	LS	_	_	_
57	DL4184.novo	dl4184.novo	NN	_	_	_
58	--	--	:	_	_	_
59	tab	tab	NN	_	_	_
60	=	=	JJ	_	_	_
61	NC000913	nc000913	NN	_	_	_
62	.3	.3	NN	_	_	_
63	.	.	.	_	_	_

1	tab	tab	NN	_	_	_
2	--	--	:	_	_	_
3	chr	chr	NN	_	_	_
4	=	=	JJ	_	_	_
5	Wholechom.txt	wholechom.txt	NN	_	_	_
6	--	--	:	_	_	_
7	ignorestrand	ignorestrand	JJ	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	A	a	DT	_	_	_
10	minimal	minimal	JJ	_	_	_
11	growth	growth	NN	_	_	_
12	medium	medium	NN	_	_	_
13	as	as	IN	_	_	_
14	described	describe	VBN	_	_	_
15	in	in	IN	_	_	_
16	the	the	DT	_	_	_
17	study	study	NN	_	_	_
18	by	by	IN	_	_	_
19	Ihssen	Ihssen	NNP	_	_	_
20	and	and	CC	_	_	_
21	Egli	Egli	NNP	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	2004	2004	CD	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	was	be	VBD	_	_	_
26	used	use	VBN	_	_	_
27	for	for	IN	_	_	_
28	all	all	DT	_	_	_
29	experiments	experiment	NNS	_	_	_
30	.	.	.	_	_	_

1	Bacterial	bacterial	JJ	_	_	_
2	stock	stock	NN	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	streaked	streak	VBN	_	_	_
6	onto	onto	IN	_	_	_
7	agar	agar	NN	_	_	_
8	plates	plate	NNS	_	_	_
9	and	and	CC	_	_	_
10	incubated	incubate	VBN	_	_	_
11	overnight	overnight	JJ	_	_	_
12	.	.	.	_	_	_

1	One	one	CD	_	_	_
2	colony	colony	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	transferred	transfer	VBN	_	_	_
6	into	into	IN	_	_	_
7	20	20	CD	_	_	_
8	ml	ml	NN	_	_	_
9	minimal	minimal	JJ	_	_	_
10	medium	medium	NN	_	_	_
11	,	,	,	_	_	_
12	grown	grow	VBN	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	250	250	CD	_	_	_
18	r.p.m.	r.p.m.	NNS	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	over	over	IN	_	_	_
21	night	night	NN	_	_	_
22	culture	culture	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	ONC	onc	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	and	and	CC	_	_	_
27	served	serve	VBD	_	_	_
28	as	as	IN	_	_	_
29	the	the	DT	_	_	_
30	inoculum	inoculum	NN	_	_	_
31	for	for	IN	_	_	_
32	experiments	experiment	NNS	_	_	_
33	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	continuous	continuous	JJ	_	_	_
3	culture	culture	NN	_	_	_
4	experiments	experiment	NNS	_	_	_
5	we	we	PRP	_	_	_
6	designed	design	VBD	_	_	_
7	and	and	CC	_	_	_
8	constructed	construct	VBD	_	_	_
9	500	500	CD	_	_	_
10	ml	ml	NN	_	_	_
11	bioreactors	bioreactor	NNS	_	_	_
12	according	accord	VBG	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	study	study	NN	_	_	_
16	by	by	IN	_	_	_
17	Huwiler	Huwiler	NNP	_	_	_
18	et	et	FW	_	_	_
19	al.	al.	FW	_	_	_
20	,	,	,	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	2012	2012	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	that	that	WDT	_	_	_
25	were	be	VBD	_	_	_
26	half-filled	half-filled	JJ	_	_	_
27	with	with	IN	_	_	_
28	medium	medium	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	0.5	0.5	CD	_	_	_
31	g	g	NN	_	_	_
32	glucose	glucose	NN	SUPP	_	_
33	per	per	IN	_	_	_
34	l	l	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	and	and	CC	_	_	_
37	incubated	incubate	VBN	_	_	_
38	at	at	IN	_	_	_
39	37	37	CD	_	_	_
40	°C	°c	NN	_	_	_
41	in	in	IN	_	_	_
42	a	a	DT	_	_	_
43	temperature	temperature	NN	_	_	_
44	controlled	controlled	JJ	_	_	_
45	water	water	NN	_	_	_
46	bath	bath	NN	_	_	_
47	.	.	.	_	_	_

1	Before	before	IN	_	_	_
2	continuous	continuous	JJ	_	_	_
3	cultivation	cultivation	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	dilution	dilution	NN	_	_	_
6	rate	rate	NN	_	_	_
7	=	=	JJ	_	_	_
8	0.25	0.25	CD	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	,	,	,	_	_	_
11	1	1	CD	_	_	_
12	--	--	:	_	_	_
13	2	2	CD	_	_	_
14	ml	ml	NN	_	_	_
15	of	of	IN	_	_	_
16	the	the	DT	_	_	_
17	ONC	onc	NN	_	_	_
18	was	be	VBD	_	_	_
19	transferred	transfer	VBN	_	_	_
20	and	and	CC	_	_	_
21	grown	grow	VBN	_	_	_
22	in	in	IN	_	_	_
23	batch-mode	batch-mode	NN	_	_	_
24	until	until	IN	_	_	_
25	reactors	reactor	NNS	_	_	_
26	became	become	VBD	_	_	_
27	visibly	visibly	RB	_	_	_
28	turbid	turbid	JJ	_	_	_
29	.	.	.	_	_	_

1	Subsequently	subsequently	RB	_	_	_
2	,	,	,	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	to	to	TO	_	_	_
7	steady-state	steady-state	JJ	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	defined	define	VBN	_	_	_
10	as	as	IN	_	_	_
11	constant	constant	JJ	_	_	_
12	optical	optical	JJ	_	_	_
13	density	density	NN	_	_	_
14	over	over	IN	_	_	_
15	time	time	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	and	and	CC	_	_	_
18	harvested	harvest	VBN	_	_	_
19	for	for	IN	_	_	_
20	experimentation	experimentation	NN	_	_	_
21	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	starvation	starvation	NN	_	_	_
3	experiments	experiment	NNS	_	_	_
4	the	the	DT	_	_	_
5	medium	medium	NN	_	_	_
6	flow	flow	NN	_	_	_
7	was	be	VBD	_	_	_
8	stopped	stop	VBN	_	_	_
9	during	during	IN	_	_	_
10	steady-state	steady-state	JJ	_	_	_
11	and	and	CC	_	_	_
12	bacteria	bacterium	NNS	_	_	_
13	were	be	VBD	_	_	_
14	collected	collect	VBN	_	_	_
15	after	after	IN	_	_	_
16	4	4	CD	_	_	_
17	h.	h.	NN	_	_	_
18	To	to	TO	_	_	_
19	avoid	avoid	VB	_	_	_
20	gene-expression	gene-expression	NN	_	_	_
21	signatures	signature	NNS	_	_	_
22	of	of	IN	_	_	_
23	stationary	stationary	JJ	_	_	_
24	cells	cell	NNS	_	_	_
25	from	from	IN	_	_	_
26	the	the	DT	_	_	_
27	ONC	ONC	NNP	_	_	_
28	,	,	,	_	_	_
29	batch	batch	NN	_	_	_
30	cultures	culture	NNS	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	1000	1000	CD	_	_	_
33	ml	ml	NN	_	_	_
34	Erlenmeyer	erlenmeyer	NN	_	_	_
35	flasks	flask	NNS	_	_	_
36	containing	contain	VBG	_	_	_
37	100	100	CD	_	_	_
38	ml	ml	NN	_	_	_
39	of	of	IN	_	_	_
40	pre-warmed	pre-warmed	JJ	_	_	_
41	medium	medium	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	1	1	CD	_	_	_
44	g	g	NN	_	_	_
45	glucose	glucose	NN	SUPP	_	_
46	per	per	IN	_	_	_
47	l	l	NN	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	;	;	:	_	_	_
50	37	37	CD	_	_	_
51	°C	°c	NN	_	_	_
52	;	;	:	_	_	_
53	250	250	CD	_	_	_
54	r.p.m.	r.p.m.	NNS	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	were	be	VBD	_	_	_
58	inoculated	inoculate	VBN	_	_	_
59	with	with	IN	_	_	_
60	5	5	CD	_	_	_
61	ml	ml	NN	_	_	_
62	of	of	IN	_	_	_
63	an	a	DT	_	_	_
64	exponentially	exponentially	RB	_	_	_
65	growing	grow	VBG	_	_	_
66	pre-culture	pre-culture	JJ	_	_	_
67	that	that	IN	_	_	_
68	derived	derive	VBN	_	_	_
69	from	from	IN	_	_	_
70	the	the	DT	_	_	_
71	ONC	ONC	NNP	_	_	_
72	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Differential	differential	JJ	_	_	_
3	expression	expression	NN	_	_	_
4	analysis	analysis	NN	_	_	_
5	with	with	IN	_	_	_
6	DESeq	deseq	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Anders	Anders	NNP	_	_	_
9	and	and	CC	_	_	_
10	Huber	Huber	NNP	_	_	_
11	2010	2010	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	with	with	IN	_	_	_
14	the	the	DT	_	_	_
15	default	default	NN	_	_	_
16	setting	set	VBG	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	Escherichia	escherichia	FW	Organism	_	_
19	coli	coli	FW	Organism	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Genome	Genome	NNP	_	_	_
22	_	_	NNP	_	_	_
23	build	build	VB	_	_	_
24	:	:	:	_	_	_
25	NC	NC	NNP	_	_	_
26	_	_	NNP	_	_	_
27	011741	011741	CD	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	E.coli	e.coli	NN	_	_	_
30	strain	strain	NN	_	_	_
31	IAI1	iai1	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	,	,	,	_	_	_
34	NC	nc	NN	_	_	_
35	_	_	SYM	_	_	_
36	000913.2	000913.2	CD	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	E.coli	e.coli	NN	_	_	_
39	strain	strain	NN	_	_	_
40	MG1655	mg1655	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	,	,	,	_	_	_
43	TW09308	tw09308	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	E.coli	e.coli	NN	_	_	_
46	strain	strain	NN	_	_	_
47	TW09308	tw09308	NN	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	,	,	,	_	_	_
50	and	and	CC	_	_	_
51	TW11588	tw11588	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	E.coli	e.coli	NN	_	_	_
54	strain	strain	NN	_	_	_
55	TW11588	tw11588	NN	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	growth	growth	NN	_	_	_
59	protocol	protocol	NN	_	_	_
60	:	:	:	_	_	_
61	Bacteria	bacterium	NNS	_	_	_
62	liquid	liquid	JJ	_	_	_
63	culture	culture	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	Harvested	harvest	VBN	_	_	_
66	cells	cell	NNS	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	4	4	CD	_	_	_
69	×	×	NN	_	_	_
70	6	6	CD	_	_	_
71	ml	ml	NN	_	_	_
72	-RRB-	-rrb-	-RRB-	_	_	_
73	were	be	VBD	_	_	_
74	immediately	immediately	RB	_	_	_
75	combined	combine	VBN	_	_	_
76	with	with	IN	_	_	_
77	6	6	CD	_	_	_
78	ml	ml	NN	_	_	_
79	RNAlater	rnalater	NN	_	_	_
80	-LRB-	-lrb-	-LRB-	_	_	_
81	Life	Life	NNP	_	_	_
82	Technologies	Technologies	NNPS	_	_	_
83	,	,	,	_	_	_
84	Grand	Grand	NNP	_	_	_
85	Island	Island	NNP	_	_	_
86	,	,	,	_	_	_
87	NY	NY	NNP	_	_	_
88	,	,	,	_	_	_
89	USA	USA	NNP	_	_	_
90	-RRB-	-rrb-	-RRB-	_	_	_
91	,	,	,	_	_	_
92	centrifuged	centrifuge	VBN	_	_	_
93	for	for	IN	_	_	_
94	15	15	CD	_	_	_
95	min	min	NN	_	_	_
96	at	at	IN	_	_	_
97	12000	12000	CD	_	_	_
98	r.p.m.	r.p.m.	NN	_	_	_
99	,	,	,	_	_	_
100	washed	wash	VBN	_	_	_
101	with	with	IN	_	_	_
102	1	1	CD	_	_	_
103	ml	ml	NN	_	_	_
104	RNAlater	rnalater	NN	_	_	_
105	-LRB-	-lrb-	-LRB-	_	_	_
106	3	3	CD	_	_	_
107	min	min	NN	_	_	_
108	at	at	IN	_	_	_
109	15000	15000	CD	_	_	_
110	r.p.m.	r.p.m.	NN	_	_	_
111	-RRB-	-rrb-	-RRB-	_	_	_
112	,	,	,	_	_	_
113	re-suspended	re-suspended	JJ	_	_	_
114	in	in	IN	_	_	_
115	0.5	0.5	CD	_	_	_
116	ml	ml	NN	_	_	_
117	RNAlater	rnalater	NN	_	_	_
118	and	and	CC	_	_	_
119	stored	store	VBD	_	_	_
120	at	at	IN	_	_	_
121	−	−	CD	_	_	_
122	20	20	CD	_	_	_
123	°C	°c	NN	_	_	_
124	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	RNA	rna	NN	_	_	_
3	extraction	extraction	NN	_	_	_
4	the	the	DT	_	_	_
5	RiboPure-Bacteria	RiboPure-Bacteria	NNP	_	_	_
6	Kit	kit	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Life	Life	NNP	_	_	_
9	Technologies	Technologies	NNPS	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	was	be	VBD	_	_	_
12	used	use	VBN	_	_	_
13	according	accord	VBG	_	_	_
14	to	to	TO	_	_	_
15	the	the	DT	_	_	_
16	manufacturer	manufacturer	NN	_	_	_
17	's	's	POS	_	_	_
18	instructions	instruction	NNS	_	_	_
19	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	achieve	achieve	VB	_	_	_
3	high	high	JJ	_	_	_
4	RNA	rna	NN	_	_	_
5	yields	yield	NNS	_	_	_
6	several	several	JJ	_	_	_
7	reactions	reaction	NNS	_	_	_
8	for	for	IN	_	_	_
9	each	each	DT	_	_	_
10	sample	sample	NN	_	_	_
11	were	be	VBD	_	_	_
12	done	do	VBN	_	_	_
13	in	in	IN	_	_	_
14	parallel	parallel	NN	_	_	_
15	and	and	CC	_	_	_
16	pooled	pool	VBD	_	_	_
17	at	at	IN	_	_	_
18	the	the	DT	_	_	_
19	end	end	NN	_	_	_
20	of	of	IN	_	_	_
21	the	the	DT	_	_	_
22	procedure	procedure	NN	_	_	_
23	.	.	.	_	_	_

1	An	a	DT	_	_	_
2	additional	additional	JJ	_	_	_
3	DNase	dnase	NN	_	_	_
4	treatment	treatment	NN	_	_	_
5	step	step	NN	_	_	_
6	with	with	IN	_	_	_
7	TURBO	TURBO	NNP	_	_	_
8	DNase	dnase	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Life	Life	NNP	_	_	_
11	Technologies	Technologies	NNPS	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	was	be	VBD	_	_	_
14	included	include	VBN	_	_	_
15	to	to	TO	_	_	_
16	assure	assure	VB	_	_	_
17	no	no	DT	_	_	_
18	genomic	genomic	JJ	_	_	_
19	DNA	dna	NN	_	_	_
20	contamination	contamination	NN	_	_	_
21	.	.	.	_	_	_

1	Messenger	messenger	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	enriched	enrich	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	RiboMinus	RiboMinus	NNP	_	_	_
8	Bacteria	bacterium	NNS	_	_	_
9	Kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Life	Life	NNP	_	_	_
12	Technologies	Technologies	NNPS	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	according	accord	VBG	_	_	_
15	to	to	TO	_	_	_
16	the	the	DT	_	_	_
17	manufacturer	manufacturer	NN	_	_	_
18	's	's	POS	_	_	_
19	instructions	instruction	NNS	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	IAI1	iai1	NN	_	_	_
3	batch	batch	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	IAI1	iai1	NN	_	_	_
6	chemostat	chemostat	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	IAI1	iai1	NN	_	_	_
9	starvation	starvation	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	IAI1	iai1	NN	_	_	_
12	transcriptome	transcriptome	NN	_	_	_
13	from	from	IN	_	_	_
14	batch	batch	NN	_	_	_
15	growth	growth	NN	_	_	_
16	_	_	NN	_	_	_
17	1	1	CD	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	IAI1	iai1	NN	_	_	_
20	transcriptome	transcriptome	NN	_	_	_
21	from	from	IN	_	_	_
22	batch	batch	NN	_	_	_
23	growth	growth	NN	_	_	_
24	_	_	NN	_	_	_
25	2	2	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	IAI1	iai1	NN	_	_	_
28	transcriptome	transcriptome	NN	_	_	_
29	from	from	IN	_	_	_
30	chemostat	chemostat	NN	_	_	_
31	growth	growth	NN	_	_	_
32	_	_	NN	_	_	_
33	1	1	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	IAI1	iai1	NN	_	_	_
36	transcriptome	transcriptome	NN	_	_	_
37	from	from	IN	_	_	_
38	chemostat	chemostat	NN	_	_	_
39	growth	growth	NN	_	_	_
40	_	_	NN	_	_	_
41	2	2	CD	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	IAI1	iai1	NN	_	_	_
44	transcriptome	transcriptome	NN	_	_	_
45	from	from	IN	_	_	_
46	starvation	starvation	NN	_	_	_
47	growth	growth	NN	_	_	_
48	_	_	NN	_	_	_
49	1	1	CD	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	IAI1	iai1	NN	_	_	_
52	transcriptome	transcriptome	NN	_	_	_
53	from	from	IN	_	_	_
54	starvation	starvation	NN	_	_	_
55	growth	growth	NN	_	_	_
56	_	_	NN	_	_	_
57	2	2	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
59	Map	map	NN	_	_	_
60	RNA-Seq	rna-seq	NN	_	_	_
61	reads	read	VBZ	_	_	_
62	to	to	TO	_	_	_
63	reference	reference	VB	_	_	_
64	genomes	genome	NNS	_	_	_
65	using	use	VBG	_	_	_
66	Bowtie	Bowtie	NNP	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	Langmead	Langmead	NNP	_	_	_
69	et	et	FW	_	_	_
70	al.	al.	FW	_	_	_
71	,	,	,	_	_	_
72	2009	2009	CD	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	with	with	IN	_	_	_
75	alignment	alignment	NN	_	_	_
76	parameters	parameter	NNS	_	_	_
77	-LRB-	-lrb-	-LRB-	_	_	_
78	-	-	:	_	_	_
79	n	n	NN	_	_	_
80	2-e	2-e	JJ	_	_	_
81	70-l	70-l	JJ	_	_	_
82	28	28	CD	_	_	_
83	--	--	:	_	_	_
84	best	best	JJS	_	_	_
85	-RRB-	-rrb-	-RRB-	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	MG1655	mg1655	NN	_	_	_
88	batch	batch	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	MG1655	mg1655	NN	_	_	_
91	chemostat	chemostat	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	MG1655	mg1655	NN	_	_	_
94	starvation	starvation	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	MG1655	mg1655	NN	_	_	_
97	transcriptome	transcriptome	NN	_	_	_
98	from	from	IN	_	_	_
99	batch	batch	NN	_	_	_
100	growth	growth	NN	_	_	_
101	_	_	NN	_	_	_
102	1	1	CD	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	MG1655	mg1655	NN	_	_	_
105	transcriptome	transcriptome	NN	_	_	_
106	from	from	IN	_	_	_
107	batch	batch	NN	_	_	_
108	growth	growth	NN	_	_	_
109	_	_	NN	_	_	_
110	2	2	CD	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	MG1655	mg1655	NN	_	_	_
113	transcriptome	transcriptome	NN	_	_	_
114	from	from	IN	_	_	_
115	chemostat	chemostat	NN	_	_	_
116	growth	growth	NN	_	_	_
117	_	_	NN	_	_	_
118	1	1	CD	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	MG1655	mg1655	NN	_	_	_
121	transcriptome	transcriptome	NN	_	_	_
122	from	from	IN	_	_	_
123	chemostat	chemostat	NN	_	_	_
124	growth	growth	NN	_	_	_
125	_	_	NN	_	_	_
126	2	2	CD	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	MG1655	mg1655	NN	_	_	_
129	transcriptome	transcriptome	NN	_	_	_
130	from	from	IN	_	_	_
131	starvation	starvation	NN	_	_	_
132	growth	growth	NN	_	_	_
133	_	_	NN	_	_	_
134	1	1	CD	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	MG1655	mg1655	NN	_	_	_
137	transcriptome	transcriptome	NN	_	_	_
138	from	from	IN	_	_	_
139	starvation	starvation	NN	_	_	_
140	growth	growth	NN	_	_	_
141	_	_	NN	_	_	_
142	2	2	CD	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
144	Quality	quality	JJ	_	_	_
145	trimming	trim	VBG	_	_	_
146	of	of	IN	_	_	_
147	3	3	CD	_	_	_
148	'	'	''	_	_	_
149	end	end	NN	_	_	_
150	at	at	IN	_	_	_
151	Read	Read	NNP	_	_	_
152	Segment	Segment	NNP	_	_	_
153	Quality	Quality	NNP	_	_	_
154	Control	Control	NNP	_	_	_
155	Indicator	Indicator	NNP	_	_	_
156	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Remove	remove	VBP	_	_	_
3	non-protein	non-protein	JJ	_	_	_
4	coding	code	VBG	_	_	_
5	counts	count	NNS	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
7	RNA	rna	NN	_	_	_
8	quality	quality	NN	_	_	_
9	was	be	VBD	_	_	_
10	confirmed	confirm	VBN	_	_	_
11	with	with	IN	_	_	_
12	the	the	DT	_	_	_
13	Bioanalyzer	Bioanalyzer	NNP	_	_	_
14	system	system	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Agilent	Agilent	NNP	_	_	_
17	Technologies	Technologies	NNPS	_	_	_
18	,	,	,	_	_	_
19	Santa	Santa	NNP	_	_	_
20	Clara	Clara	NNP	_	_	_
21	,	,	,	_	_	_
22	CA	CA	NNP	_	_	_
23	,	,	,	_	_	_
24	USA	USA	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	and	and	CC	_	_	_
27	sequencing	sequencing	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	50	50	CD	_	_	_
30	cycles	cycle	NNS	_	_	_
31	,	,	,	_	_	_
32	pooling	pool	VBG	_	_	_
33	eight	eight	CD	_	_	_
34	bar-coded	bar-coded	JJ	_	_	_
35	samples	sample	NNS	_	_	_
36	per	per	IN	_	_	_
37	lane	lane	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	was	be	VBD	_	_	_
40	performed	perform	VBN	_	_	_
41	on	on	IN	_	_	_
42	the	the	DT	_	_	_
43	Illumina	Illumina	NNP	_	_	_
44	HiSeq	HiSeq	NNP	_	_	_
45	platform	platform	NN	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	Illumina	Illumina	NNP	_	_	_
48	,	,	,	_	_	_
49	San	San	NNP	_	_	_
50	Diego	Diego	NNP	_	_	_
51	,	,	,	_	_	_
52	CA	CA	NNP	_	_	_
53	,	,	,	_	_	_
54	USA	USA	NNP	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	at	at	IN	_	_	_
57	the	the	DT	_	_	_
58	Research	Research	NNP	_	_	_
59	Technology	Technology	NNP	_	_	_
60	Support	support	NN	_	_	_
61	Facility	facility	NN	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	RTSF	rtsf	NN	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	at	at	IN	_	_	_
66	Michigan	Michigan	NNP	_	_	_
67	State	State	NNP	_	_	_
68	University	University	NNP	_	_	_
69	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	strain	strain	NN	_	_	_
5	:	:	:	_	_	_
6	IAI1	iai1	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	strain	strain	NN	_	_	_
9	:	:	:	_	_	_
10	K12	k12	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	MG1655	mg1655	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	strain	strain	NN	_	_	_
16	:	:	:	_	_	_
17	TW09308	tw09308	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	strain	strain	NN	_	_	_
20	:	:	:	_	_	_
21	TW11588	tw11588	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Summarize	summarize	VB	_	_	_
24	the	the	DT	_	_	_
25	read	read	NN	_	_	_
26	count	count	NN	_	_	_
27	to	to	TO	_	_	_
28	each	each	DT	_	_	_
29	annotated	annotated	JJ	_	_	_
30	gene	gene	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Supplementary	supplementary	JJ	_	_	_
33	_	_	NN	_	_	_
34	files	file	NNS	_	_	_
35	_	_	IN	_	_	_
36	format	format	NN	_	_	_
37	_	_	NN	_	_	_
38	and	and	CC	_	_	_
39	_	_	NN	_	_	_
40	content	content	NN	_	_	_
41	:	:	:	_	_	_
42	All	all	DT	_	_	_
43	in	in	IN	_	_	_
44	tab-delimited	tab-delimited	JJ	_	_	_
45	ASCII	ASCII	NNP	_	_	_
46	format	format	NN	_	_	_
47	.	.	.	_	_	_

1	raw_count.txt	raw_count.txt	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	pre-normalized	pre-normalized	JJ	_	_	_
4	read	read	NN	_	_	_
5	count	count	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	,	,	,	_	_	_
8	normalized_count.txt	normalized_count.txt	NN	_	_	_
9	,	,	,	_	_	_
10	panGeneMap.txt	pangenemap.txt	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	geneID	geneid	NN	_	_	_
13	map	map	NN	GEN	_	_
14	between	between	IN	_	_	_
15	the	the	DT	_	_	_
16	strains	strain	NNS	_	_	_
17	and	and	CC	_	_	_
18	pangene	pangene	NN	_	_	_
19	ID	id	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	,	,	,	_	_	_
22	Gene_annotations.txt	gene_annotations.txt	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	annotation	annotation	NN	_	_	_
25	of	of	IN	_	_	_
26	genes	gene	NNS	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	treatment	treatment	NN	_	_	_
30	:	:	:	_	_	_
31	batch	batch	NN	_	_	_
32	growth	growth	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	treatment	treatment	NN	_	_	_
35	:	:	:	_	_	_
36	chemostat	chemostat	NN	_	_	_
37	growth	growth	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	treatment	treatment	NN	_	_	_
40	:	:	:	_	_	_
41	starvation	starvation	NN	_	_	_
42	growth	growth	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	TW09308	tw09308	NN	_	_	_
45	batch	batch	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	TW09308	tw09308	NN	_	_	_
48	chemostat	chemostat	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	TW09308	tw09308	NN	_	_	_
51	starvation	starvation	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	TW09308	tw09308	NN	_	_	_
54	transcriptome	transcriptome	NN	_	_	_
55	from	from	IN	_	_	_
56	batch	batch	NN	_	_	_
57	growth	growth	NN	_	_	_
58	_	_	NN	_	_	_
59	1	1	CD	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	TW09308	tw09308	NN	_	_	_
62	transcriptome	transcriptome	NN	_	_	_
63	from	from	IN	_	_	_
64	batch	batch	NN	_	_	_
65	growth	growth	NN	_	_	_
66	_	_	NN	_	_	_
67	2	2	CD	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	TW09308	tw09308	NN	_	_	_
70	transcriptome	transcriptome	NN	_	_	_
71	from	from	IN	_	_	_
72	chemostat	chemostat	NN	_	_	_
73	growth	growth	NN	_	_	_
74	_	_	NN	_	_	_
75	1	1	CD	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	TW09308	tw09308	NN	_	_	_
78	transcriptome	transcriptome	NN	_	_	_
79	from	from	IN	_	_	_
80	chemostat	chemostat	NN	_	_	_
81	growth	growth	NN	_	_	_
82	_	_	NN	_	_	_
83	2	2	CD	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	TW09308	tw09308	NN	_	_	_
86	transcriptome	transcriptome	NN	_	_	_
87	from	from	IN	_	_	_
88	starvation	starvation	NN	_	_	_
89	growth	growth	NN	_	_	_
90	_	_	NN	_	_	_
91	1	1	CD	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	TW09308	tw09308	NN	_	_	_
94	transcriptome	transcriptome	NN	_	_	_
95	from	from	IN	_	_	_
96	starvation	starvation	NN	_	_	_
97	growth	growth	NN	_	_	_
98	_	_	NN	_	_	_
99	2	2	CD	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	TW11588	tw11588	NN	_	_	_
102	batch	batch	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	TW11588	tw11588	NN	_	_	_
105	chemostat	chemostat	NN	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	TW11588	tw11588	NN	_	_	_
108	starvation	starvation	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	TW11588	tw11588	NN	_	_	_
111	transcriptome	transcriptome	NN	_	_	_
112	from	from	IN	_	_	_
113	batch	batch	NN	_	_	_
114	growth	growth	NN	_	_	_
115	_	_	NN	_	_	_
116	1	1	CD	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	TW11588	tw11588	NN	_	_	_
119	transcriptome	transcriptome	NN	_	_	_
120	from	from	IN	_	_	_
121	batch	batch	NN	_	_	_
122	growth	growth	NN	_	_	_
123	_	_	NN	_	_	_
124	2	2	CD	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	TW11588	tw11588	NN	_	_	_
127	transcriptome	transcriptome	NN	_	_	_
128	from	from	IN	_	_	_
129	chemostat	chemostat	NN	_	_	_
130	growth	growth	NN	_	_	_
131	_	_	NN	_	_	_
132	1	1	CD	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	TW11588	tw11588	NN	_	_	_
135	transcriptome	transcriptome	NN	_	_	_
136	from	from	IN	_	_	_
137	chemostat	chemostat	NN	_	_	_
138	growth	growth	NN	_	_	_
139	_	_	NN	_	_	_
140	2	2	CD	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	TW11588	tw11588	NN	_	_	_
143	transcriptome	transcriptome	NN	_	_	_
144	from	from	IN	_	_	_
145	starvation	starvation	NN	_	_	_
146	growth	growth	NN	_	_	_
147	_	_	NN	_	_	_
148	1	1	CD	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	TW11588	tw11588	NN	_	_	_
151	transcriptome	transcriptome	NN	_	_	_
152	from	from	IN	_	_	_
153	starvation	starvation	NN	_	_	_
154	growth	growth	NN	_	_	_
155	_	_	NN	_	_	_
156	2	2	CD	_	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
158	All	all	DT	_	_	_
159	cultures	culture	NNS	_	_	_
160	were	be	VBD	_	_	_
161	based	base	VBN	_	_	_
162	on	on	IN	_	_	_
163	MOPS	mop	NNS	MED	_	_
164	media	media	NNS	_	_	_
165	with	with	IN	_	_	_
166	0.2	0.2	CD	_	_	_
167	%	%	NN	_	_	_
168	glucose	glucose	NN	SUPP	_	_
169	-LRB-	-lrb-	-LRB-	_	_	_
170	Teknova	teknova	NN	_	_	_
171	-RRB-	-rrb-	-RRB-	_	_	_
172	,	,	,	_	_	_
173	with	with	IN	_	_	_
174	full	full	JJ	_	_	_
175	supplement	supplement	NN	_	_	_
176	-LRB-	-lrb-	-LRB-	_	_	_
177	Neidhardt	Neidhardt	NNP	_	_	_
178	et	et	FW	_	_	_
179	al.	al.	FW	_	_	_
180	,	,	,	_	_	_
181	1974	1974	CD	_	_	_
182	-RRB-	-rrb-	-RRB-	_	_	_
183	minus	minus	CC	_	_	_
184	methionine	methionine	NN	SUPP	_	_
185	.	.	.	_	_	_

1	An	a	DT	_	_	_
2	overnight	overnight	JJ	_	_	_
3	liquid	liquid	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	diluted	dilute	VBN	_	_	_
7	400-fold	400-fold	JJ	_	_	_
8	into	into	IN	_	_	_
9	200	200	CD	_	_	_
10	ml	ml	NN	_	_	_
11	fresh	fresh	JJ	_	_	_
12	media	media	NNS	_	_	_
13	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	kept	keep	VBN	_	_	_
5	in	in	IN	_	_	_
6	a	a	DT	_	_	_
7	1	1	CD	_	_	_
8	liter	liter	NN	_	_	_
9	flask	flask	NN	_	_	_
10	at	at	IN	_	_	_
11	37	37	CD	_	_	_
12	°C	°c	NN	_	_	_
13	with	with	IN	_	_	_
14	aeration	aeration	NN	_	_	_
15	until	until	IN	_	_	_
16	OD420	od420	NN	_	_	_
17	reached	reach	VBD	_	_	_
18	0.4	0.4	CD	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	bacteria	bacterium	NNS	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Basecalls	basecall	NNS	_	_	_
5	performed	perform	VBN	_	_	_
6	using	use	VBG	_	_	_
7	Casava	Casava	NNP	_	_	_
8	versions	version	NNS	_	_	_
9	1.6	1.6	CD	_	_	_
10	or	or	CC	_	_	_
11	1.7	1.7	CD	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Bowtie	Bowtie	NNP	_	_	_
3	alignments	alignment	NNS	_	_	_
4	against	against	IN	_	_	_
5	the	the	DT	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	genome	genome	NN	_	_	_
9	were	be	VBD	_	_	_
10	converted	convert	VBN	_	_	_
11	to	to	TO	_	_	_
12	wiggle	wiggle	VB	_	_	_
13	files	file	NNS	_	_	_
14	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	ribosome	ribosome	NN	_	_	_
3	footprints	footprint	NNS	_	_	_
4	and	and	CC	_	_	_
5	mRNA-seq	mrna-seq	NN	_	_	_
6	,	,	,	_	_	_
7	the	the	DT	_	_	_
8	position	position	NN	_	_	_
9	of	of	IN	_	_	_
10	each	each	DT	_	_	_
11	alignment	alignment	NN	_	_	_
12	is	be	VBZ	_	_	_
13	distributed	distribute	VBN	_	_	_
14	into	into	IN	_	_	_
15	several	several	JJ	_	_	_
16	nucleotides	nucleotide	NNS	_	_	_
17	in	in	IN	_	_	_
18	the	the	DT	_	_	_
19	center	center	NN	_	_	_
20	of	of	IN	_	_	_
21	each	each	DT	_	_	_
22	read	read	NN	_	_	_
23	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	read	read	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	center	center	NN	_	_	_
7	residues	residue	NNS	_	_	_
8	that	that	WDT	_	_	_
9	are	be	VBP	_	_	_
10	at	at	IN	_	_	_
11	least	least	JJS	_	_	_
12	10	10	CD	_	_	_
13	nucleotides	nucleotide	NNS	_	_	_
14	away	away	RB	_	_	_
15	from	from	IN	_	_	_
16	either	either	CC	_	_	_
17	ends	end	NNS	_	_	_
18	were	be	VBD	_	_	_
19	given	give	VBN	_	_	_
20	the	the	DT	_	_	_
21	same	same	JJ	_	_	_
22	score	score	NN	_	_	_
23	,	,	,	_	_	_
24	which	which	WDT	_	_	_
25	is	be	VBZ	_	_	_
26	weighted	weight	VBN	_	_	_
27	by	by	IN	_	_	_
28	the	the	DT	_	_	_
29	length	length	NN	_	_	_
30	of	of	IN	_	_	_
31	the	the	DT	_	_	_
32	fragment	fragment	NN	_	_	_
33	-LSB-	-lsb-	-LRB-	_	_	_
34	Oh	oh	UH	_	_	_
35	et	et	FW	_	_	_
36	al	al	FW	_	_	_
37	,	,	,	_	_	_
38	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	147	147	CD	_	_	_
3	,	,	,	_	_	_
4	1295	1295	CD	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	2011	2011	CD	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	-RSB-	-rsb-	-RRB-	_	_	_
9	.	.	.	_	_	_

1	Scores	score	NNS	_	_	_
2	therefore	therefore	RB	_	_	_
3	represent	represent	VBP	_	_	_
4	the	the	DT	_	_	_
5	number	number	NN	_	_	_
6	of	of	IN	_	_	_
7	read	read	VBN	_	_	_
8	alignments	alignment	NNS	_	_	_
9	attributed	attribute	VBD	_	_	_
10	to	to	TO	_	_	_
11	each	each	DT	_	_	_
12	genomic	genomic	JJ	_	_	_
13	position	position	NN	_	_	_
14	under	under	IN	_	_	_
15	each	each	DT	_	_	_
16	scoring	score	VBG	_	_	_
17	scheme	scheme	NN	_	_	_
18	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	DMS-seq	dms-seq	NN	_	_	_
3	,	,	,	_	_	_
4	the	the	DT	_	_	_
5	position	position	NN	_	_	_
6	of	of	IN	_	_	_
7	each	each	DT	_	_	_
8	alignment	alignment	NN	_	_	_
9	was	be	VBD	_	_	_
10	the	the	DT	_	_	_
11	position	position	NN	_	_	_
12	immediately	immediately	RB	_	_	_
13	5	5	CD	_	_	_
14	'	'	''	_	_	_
15	of	of	IN	_	_	_
16	the	the	DT	_	_	_
17	5	5	CD	_	_	_
18	'	'	''	_	_	_
19	end	end	NN	_	_	_
20	of	of	IN	_	_	_
21	the	the	DT	_	_	_
22	read	read	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Extraction	extraction	NN	_	_	_
6	was	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	as	as	IN	_	_	_
9	described	describe	VBN	_	_	_
10	previously	previously	RB	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Li	Li	NNP	_	_	_
13	et	et	FW	_	_	_
14	al.	al.	FW	_	_	_
15	,	,	,	_	_	_
16	2012	2012	CD	_	_	_
17	;	;	:	_	_	_
18	Oh	oh	UH	_	_	_
19	et	et	FW	_	_	_
20	al.	al.	FW	_	_	_
21	,	,	,	_	_	_
22	2011	2011	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	ribosome	ribosome	NN	_	_	_
3	profiling	profiling	NN	_	_	_
4	,	,	,	_	_	_
5	200	200	CD	_	_	_
6	mL	ml	NN	_	_	_
7	of	of	IN	_	_	_
8	cell	cell	NN	_	_	_
9	culture	culture	NN	_	_	_
10	were	be	VBD	_	_	_
11	filtered	filter	VBN	_	_	_
12	rapidly	rapidly	RB	_	_	_
13	and	and	CC	_	_	_
14	the	the	DT	_	_	_
15	resulting	result	VBG	_	_	_
16	cell	cell	NN	_	_	_
17	pellet	pellet	NN	_	_	_
18	was	be	VBD	_	_	_
19	flash-frozen	flash-frozen	JJ	_	_	_
20	in	in	IN	_	_	_
21	liquid	liquid	JJ	_	_	_
22	nitrogen	nitrogen	NN	_	_	_
23	and	and	CC	_	_	_
24	combined	combine	VBN	_	_	_
25	with	with	IN	_	_	_
26	650	650	CD	_	_	_
27	µL	µl	NN	_	_	_
28	of	of	IN	_	_	_
29	frozen	frozen	JJ	_	_	_
30	lysis	lysis	NN	_	_	_
31	buffer	buffer	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	10	10	CD	_	_	_
34	mM	mm	NN	KWSUPP	_	_
35	MgCl2	mgcl2	NN	_	_	_
36	,	,	,	_	_	_
37	100mM	100mm	NN	_	_	_
38	NH4Cl	nh4cl	NN	_	_	_
39	,	,	,	_	_	_
40	20mM	20mm	NN	_	_	_
41	Tris-HCl	tris-hcl	NN	_	_	_
42	pH	ph	NN	_	_	_
43	8.0	8.0	CD	_	_	_
44	,	,	,	_	_	_
45	0.1	0.1	CD	_	_	_
46	%	%	NN	_	_	_
47	Nonidet	nonidet	JJ	_	_	_
48	P40	p40	NN	_	_	_
49	,	,	,	_	_	_
50	0.4	0.4	CD	_	_	_
51	%	%	NN	_	_	_
52	Triton	Triton	NNP	_	_	_
53	X-100	x-100	NN	_	_	_
54	,	,	,	_	_	_
55	100	100	CD	_	_	_
56	U	U	NNP	_	_	_
57	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
58	For	for	IN	_	_	_
59	in	in	FW	_	_	_
60	vivo	vivo	FW	_	_	_
61	DMS	dms	FW	_	_	_
62	modification	modification	NN	_	_	_
63	,	,	,	_	_	_
64	15	15	CD	_	_	_
65	mL	ml	NN	_	_	_
66	of	of	IN	_	_	_
67	exponentially	exponentially	RB	_	_	_
68	growing	grow	VBG	_	_	_
69	E.	e.	FW	_	_	_
70	coli	coli	FW	_	_	_
71	were	be	VBD	_	_	_
72	incubated	incubate	VBN	_	_	_
73	with	with	IN	_	_	_
74	750	750	CD	_	_	_
75	µL	µl	NN	_	_	_
76	DMS	dms	NN	_	_	_
77	for	for	IN	_	_	_
78	2	2	CD	_	_	_
79	min	min	NN	_	_	_
80	at	at	IN	_	_	_
81	37	37	CD	_	_	_
82	°C	°c	NN	_	_	_
83	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	kasugamycin	kasugamycin	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	ksg	ksg	NN	_	_	_
5	-RRB-	-rrb-	-RRB-	_	_	_
6	experiments	experiment	NNS	_	_	_
7	,	,	,	_	_	_
8	ksg	ksg	NN	_	_	_
9	was	be	VBD	_	_	_
10	added	add	VBN	_	_	_
11	to	to	TO	_	_	_
12	a	a	DT	_	_	_
13	final	final	JJ	_	_	_
14	concentration	concentration	NN	_	_	_
15	of	of	IN	_	_	_
16	10	10	CD	_	_	_
17	mg	mg	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Genome	Genome	NNP	_	_	_
20	_	_	NNP	_	_	_
21	build	build	VB	_	_	_
22	:	:	:	_	_	_
23	NC000913	nc000913	NN	_	_	_
24	.2	.2	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	mRNA-seq	mrna-seq	NN	_	_	_
27	37	37	CD	_	_	_
28	°C	°c	NN	_	_	_
29	in	in	IN	_	_	_
30	WT	wt	JJ	_	_	_
31	with	with	IN	_	_	_
32	control	control	NN	_	_	_
33	plasmid	plasmid	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	mRNA-seq	mrna-seq	NN	_	_	_
36	37	37	CD	_	_	_
37	°C	°c	NN	_	_	_
38	in	in	IN	_	_	_
39	WT	wt	JJ	_	_	_
40	with	with	IN	_	_	_
41	plasmid	plasmid	NN	_	_	_
42	expressing	express	VBG	_	_	_
43	mini-ORF	mini-orf	NN	_	_	_
44	CUA	cua	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	mRNA-seq	mrna-seq	NN	_	_	_
47	37	37	CD	_	_	_
48	°C	°c	NN	_	_	_
49	in	in	IN	_	_	_
50	WT	wt	JJ	_	_	_
51	with	with	IN	_	_	_
52	plasmid	plasmid	NN	_	_	_
53	expressing	express	VBG	_	_	_
54	mini-ORF	mini-orf	NN	_	_	_
55	CUG	cug	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	RNA-Seq	rna-seq	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	Sequenced	sequence	VBN	_	_	_
60	reads	read	VBZ	_	_	_
61	were	be	VBD	_	_	_
62	trimmed	trim	VBN	_	_	_
63	for	for	IN	_	_	_
64	adaptor	adaptor	NN	_	_	_
65	sequence	sequence	NN	_	_	_
66	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	-LSB-	-lsb-	-LRB-	_	_	_
6	p-CTRL	p-ctrl	NN	_	_	_
7	-RSB-	-rsb-	-RRB-	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	strain	strain	NN	_	_	_
10	:	:	:	_	_	_
11	MG1655	mg1655	NN	_	_	_
12	-LSB-	-lsb-	-LRB-	_	_	_
13	p-CUA	p-cua	NN	_	_	_
14	-RSB-	-rsb-	-RRB-	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	strain	strain	NN	_	_	_
17	:	:	:	_	_	_
18	MG1655	mg1655	NN	_	_	_
19	-LSB-	-lsb-	-LRB-	_	_	_
20	p-CUG	p-cug	NN	_	_	_
21	-RSB-	-rsb-	-RRB-	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Supplementary	supplementary	JJ	_	_	_
24	_	_	NN	_	_	_
25	files	file	NNS	_	_	_
26	_	_	IN	_	_	_
27	format	format	NN	_	_	_
28	_	_	NN	_	_	_
29	and	and	CC	_	_	_
30	_	_	NN	_	_	_
31	content	content	NN	_	_	_
32	:	:	:	_	_	_
33	Wiggle	Wiggle	NNP	_	_	_
34	files	file	VBZ	_	_	_
35	with	with	IN	_	_	_
36	two	two	CD	_	_	_
37	columns	column	NNS	_	_	_
38	:	:	:	_	_	_
39	first	first	JJ	_	_	_
40	column	column	NN	_	_	_
41	containing	contain	VBG	_	_	_
42	chromosome	chromosome	NN	_	_	_
43	positions	position	NNS	_	_	_
44	and	and	CC	_	_	_
45	second	second	JJ	_	_	_
46	column	column	NN	_	_	_
47	containing	contain	VBG	_	_	_
48	the	the	DT	_	_	_
49	number	number	NN	_	_	_
50	of	of	IN	_	_	_
51	reads	read	VBZ	_	_	_
52	mapped	map	VBN	_	_	_
53	to	to	TO	_	_	_
54	the	the	DT	_	_	_
55	position	position	NN	_	_	_
56	-LRB-	-lrb-	-LRB-	_	_	_
57	see	see	VB	_	_	_
58	publication	publication	NN	_	_	_
59	for	for	IN	_	_	_
60	details	detail	NNS	_	_	_
61	-RRB-	-rrb-	-RRB-	_	_	_
62	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	remaining	remain	VBG	_	_	_
4	reads	read	VBZ	_	_	_
5	were	be	VBD	_	_	_
6	aligned	align	VBN	_	_	_
7	using	use	VBG	_	_	_
8	Bowtie	Bowtie	NNP	_	_	_
9	v0	v0	NN	_	_	_
10	.12.7	.12.7	CD	_	_	_
11	against	against	IN	_	_	_
12	E.	e.	FW	_	_	_
13	coli	coli	FW	_	_	_
14	MG1655	mg1655	NN	_	_	_
15	genome	genome	NN	_	_	_
16	using	use	VBG	_	_	_
17	parameters	parameter	NNS	_	_	_
18	-	-	:	_	_	_
19	v1	v1	SYM	_	_	_
20	-	-	:	_	_	_
21	m2	m2	SYM	_	_	_
22	-	-	:	_	_	_
23	k1	k1	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	ribosome	ribosome	NN	_	_	_
4	footprints	footprint	NNS	_	_	_
5	and	and	CC	_	_	_
6	fragmented	fragmented	JJ	_	_	_
7	mRNA	mrna	NN	_	_	_
8	were	be	VBD	_	_	_
9	ligated	ligate	VBN	_	_	_
10	to	to	TO	_	_	_
11	miRNA	miRNA	NNP	_	_	_
12	cloning	clone	VBG	_	_	_
13	linker-1	linker-1	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	IDT	idt	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	using	use	VBG	_	_	_
18	truncated	truncate	VBN	_	_	_
19	T4	t4	NN	_	_	_
20	RNA	rna	NN	_	_	_
21	ligase	ligase	NN	_	_	_
22	2	2	CD	_	_	_
23	K227Q	k227q	NN	_	_	_
24	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	ligated	ligate	VBN	_	_	_
3	RNA	rna	NN	_	_	_
4	fragments	fragment	NNS	_	_	_
5	were	be	VBD	_	_	_
6	reverse	reverse	JJ	_	_	_
7	transribed	transribe	VBN	_	_	_
8	using	use	VBG	_	_	_
9	the	the	DT	_	_	_
10	primer	primer	NN	_	_	_
11	5Phos	5phos	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	treatment	treatment	NN	_	_	_
14	:	:	:	_	_	_
15	1mM	1mm	NN	_	_	_
16	IPTG	iptg	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Trimmed	trim	VBD	_	_	_
19	reads	read	VBZ	_	_	_
20	were	be	VBD	_	_	_
21	sequentially	sequentially	RB	_	_	_
22	aligned	align	VBN	_	_	_
23	using	use	VBG	_	_	_
24	Bowtie	Bowtie	NNP	_	_	_
25	v0	v0	NN	_	_	_
26	.12.7	.12.7	CD	_	_	_
27	to	to	TO	_	_	_
28	E.	e.	FW	_	_	_
29	coli	coli	FW	_	_	_
30	rRNA	rrna	NN	_	_	_
31	and	and	CC	_	_	_
32	noncoding	noncoding	JJ	_	_	_
33	RNA	rna	NN	_	_	_
34	allowing	allow	VBG	_	_	_
35	one	one	CD	_	_	_
36	mismatch	mismatch	NN	_	_	_
37	.	.	.	_	_	_

1	Reads	read	VBZ	_	_	_
2	aligning	align	VBG	_	_	_
3	to	to	TO	_	_	_
4	any	any	DT	_	_	_
5	of	of	IN	_	_	_
6	these	these	DT	_	_	_
7	indices	index	NNS	_	_	_
8	were	be	VBD	_	_	_
9	discarded	discard	VBN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	5	5	CD	_	_	_
3	'	'	''	_	_	_
4	linker	linker	NN	_	_	_
5	and	and	CC	_	_	_
6	poly	poly	NN	_	_	_
7	A-tail	a-tail	NN	_	_	_
8	removal	removal	NN	_	_	_
9	using	use	VBG	_	_	_
10	READemption	reademption	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	5	5	CD	_	_	_
13	ml	ml	NN	_	_	_
14	of	of	IN	_	_	_
15	cell	cell	NN	_	_	_
16	suspension	suspension	NN	_	_	_
17	were	be	VBD	_	_	_
18	added	add	VBN	_	_	_
19	to	to	TO	_	_	_
20	0.625	0.625	CD	_	_	_
21	ml	ml	NN	_	_	_
22	of	of	IN	_	_	_
23	pre-chilled	pre-chilled	JJ	_	_	_
24	stop	stop	NN	_	_	_
25	solution	solution	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	5	5	CD	_	_	_
28	%	%	NN	_	_	_
29	phenol	phenol	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
31	An	a	DT	_	_	_
32	overnight	overnight	JJ	_	_	_
33	culture	culture	NN	_	_	_
34	of	of	IN	_	_	_
35	E.	e.	FW	_	_	_
36	coli	coli	FW	_	_	_
37	O104	o104	NN	_	_	_
38	:	:	:	_	_	_
39	H4	h4	NN	_	_	_
40	strain	strain	NN	_	_	_
41	LB226692	lb226692	NN	_	_	_
42	was	be	VBD	_	_	_
43	diluted	dilute	VBN	_	_	_
44	1:10,000	1:10,000	CD	_	_	_
45	in	in	IN	_	_	_
46	pre-warmed	pre-warmed	JJ	_	_	_
47	LB	lb	NN	MED	_	_
48	medium	medium	NN	MED	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	10	10	CD	_	_	_
51	g	g	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	cDNA	cdna	NN	_	_	_
54	libraries	library	NNS	_	_	_
55	for	for	IN	_	_	_
56	the	the	DT	_	_	_
57	Illumina	Illumina	NNP	_	_	_
58	sequencing	sequencing	NN	_	_	_
59	platform	platform	NN	_	_	_
60	were	be	VBD	_	_	_
61	constructed	construct	VBN	_	_	_
62	by	by	IN	_	_	_
63	vertis	vertis	NN	_	_	_
64	Biotechnology	Biotechnology	NNP	_	_	_
65	AG	AG	NNP	_	_	_
66	,	,	,	_	_	_
67	Germany	Germany	NNP	_	_	_
68	,	,	,	_	_	_
69	as	as	IN	_	_	_
70	described	describe	VBN	_	_	_
71	previously	previously	RB	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	Berezikov	Berezikov	NNP	_	_	_
74	et	et	FW	_	_	_
75	al.	al.	FW	_	_	_
76	,2006	,2006	CD	_	_	_
77	-RRB-	-rrb-	-RRB-	_	_	_
78	,	,	,	_	_	_
79	without	without	IN	_	_	_
80	the	the	DT	_	_	_
81	RNA	rna	NN	_	_	_
82	size-fractionation	size-fractionation	NN	_	_	_
83	step	step	NN	_	_	_
84	prior	prior	RB	_	_	_
85	to	to	TO	_	_	_
86	cDNA	cdna	NN	_	_	_
87	synthesis	synthesis	NN	_	_	_
88	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	RNA	rna	NN	_	_	_
4	samples	sample	NNS	_	_	_
5	were	be	VBD	_	_	_
6	polyA-tailed	polya-tailed	JJ	_	_	_
7	using	use	VBG	_	_	_
8	polyA	polya	NN	_	_	_
9	polymerase	polymerase	NN	_	_	_
10	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	5	5	CD	_	_	_
5	'	'	''	_	_	_
6	-	-	:	_	_	_
7	PPP	ppp	NN	_	_	_
8	termini	terminus	NNS	_	_	_
9	were	be	VBD	_	_	_
10	converted	convert	VBN	_	_	_
11	to	to	TO	_	_	_
12	5	5	CD	_	_	_
13	'	'	''	_	_	_
14	-	-	:	_	_	_
15	P	p	NN	_	_	_
16	using	use	VBG	_	_	_
17	tobacco	tobacco	NN	_	_	_
18	acid	acid	NN	_	_	_
19	pyrophosphatase	pyrophosphatase	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	TAP	tap	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	to	to	TO	_	_	_
24	allow	allow	VB	_	_	_
25	for	for	IN	_	_	_
26	the	the	DT	_	_	_
27	ligation	ligation	NN	_	_	_
28	of	of	IN	_	_	_
29	the	the	DT	_	_	_
30	5	5	CD	_	_	_
31	'	'	''	_	_	_
32	end	end	NN	_	_	_
33	RNA	rna	NN	_	_	_
34	adapter	adapter	NN	_	_	_
35	.	.	.	_	_	_

1	First-strand	first-strand	JJ	_	_	_
2	cDNA	cdna	NN	_	_	_
3	was	be	VBD	_	_	_
4	synthesized	synthesize	VBN	_	_	_
5	by	by	IN	_	_	_
6	an	a	DT	_	_	_
7	oligo	oligo	JJ	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	dT	dt	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	-	-	:	_	_	_
12	adapter	adapter	NN	_	_	_
13	primer	primer	NN	_	_	_
14	and	and	CC	_	_	_
15	the	the	DT	_	_	_
16	M-MLV	m-mlv	NN	_	_	_
17	reverse	reverse	JJ	_	_	_
18	transcriptase	transcriptase	NN	_	_	_
19	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	a	a	DT	_	_	_
3	PCR-based	pcr-based	JJ	_	_	_
4	amplification	amplification	NN	_	_	_
5	step	step	NN	_	_	_
6	using	use	VBG	_	_	_
7	a	a	DT	_	_	_
8	high	high	JJ	_	_	_
9	fidelity	fidelity	NN	_	_	_
10	DNA	dna	NN	_	_	_
11	polymerase	polymerase	NN	_	_	_
12	the	the	DT	_	_	_
13	cDNA	cdna	NN	_	_	_
14	concentration	concentration	NN	_	_	_
15	was	be	VBD	_	_	_
16	increased	increase	VBN	_	_	_
17	to	to	TO	_	_	_
18	20-30	20-30	CD	_	_	_
19	ng	ng	NN	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	Escherichia	escherichia	FW	Organism	_	_
22	coli	coli	FW	Organism	_	_
23	O104	o104	NN	_	_	_
24	:	:	:	_	_	_
25	H4	h4	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	exponentially	exponentially	RB	_	_	_
28	growing	grow	VBG	_	_	_
29	cells	cell	NNS	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
31	FastQ	fastq	JJ	_	_	_
32	quality	quality	NN	_	_	_
33	trimming	trim	VBG	_	_	_
34	using	use	VBG	_	_	_
35	FastX	fastx	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	version	version	NN	_	_	_
38	0.0.13	0.0.13	CD	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	and	and	CC	_	_	_
41	a	a	DT	_	_	_
42	cut-off	cut-off	JJ	_	_	_
43	value	value	NN	_	_	_
44	of	of	IN	_	_	_
45	20	20	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	Fastq	fastq	NN	_	_	_
48	to	to	TO	_	_	_
49	fasta	fasta	NN	_	_	_
50	conversion	conversion	NN	_	_	_
51	using	use	VBG	_	_	_
52	FastX	fastx	NN	_	_	_
53	FastX	fastx	NN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	version	version	NN	_	_	_
56	0.0.13	0.0.13	CD	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	generation	generation	NN	_	_	_
60	of	of	IN	_	_	_
61	coverage	coverage	NN	_	_	_
62	graphs	graph	NNS	_	_	_
63	representing	represent	VBG	_	_	_
64	the	the	DT	_	_	_
65	number	number	NN	_	_	_
66	of	of	IN	_	_	_
67	pAA	paa	NN	_	_	_
68	plasmid-associated	plasmid-associated	JJ	_	_	_
69	mapped	map	VBN	_	_	_
70	reads	read	VBZ	_	_	_
71	per	per	IN	_	_	_
72	nucleotide	nucleotide	NN	_	_	_
73	using	use	VBG	_	_	_
74	READemption	reademption	NN	_	_	_
75	0.3.7	0.3.7	CD	_	_	_
76	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
77	Genome	Genome	NNP	_	_	_
78	_	_	NNP	_	_	_
79	build	build	VB	_	_	_
80	:	:	:	_	_	_
81	NC	NC	NNP	_	_	_
82	_	_	NNP	_	_	_
83	018658.1	018658.1	CD	_	_	_
84	,	,	,	_	_	_
85	NC	NC	NNP	_	_	_
86	_	_	NNP	_	_	_
87	018659.1	018659.1	CD	_	_	_
88	,	,	,	_	_	_
89	NC	NC	NNP	_	_	_
90	_	_	NNP	_	_	_
91	018660.1	018660.1	CD	_	_	_
92	,	,	,	_	_	_
93	NC	NC	NNP	_	_	_
94	_	_	SYM	_	_	_
95	018666.1	018666.1	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	mapping	mapping	NN	_	_	_
98	of	of	IN	_	_	_
99	non-rRNA	non-rrna	JJ	_	_	_
100	and	and	CC	_	_	_
101	tRNA	trna	NN	_	_	_
102	reads	read	VBZ	_	_	_
103	to	to	TO	_	_	_
104	E.	e.	FW	_	_	_
105	coli	coli	FW	_	_	_
106	O104	o104	NN	_	_	_
107	:	:	:	_	_	_
108	H4	h4	NN	_	_	_
109	chromosome	chromosome	NN	_	_	_
110	and	and	CC	_	_	_
111	plasmids	plasmid	NNS	_	_	_
112	using	use	VBG	_	_	_
113	READemption	reademption	NN	_	_	_
114	0.3.7	0.3.7	CD	_	_	_
115	and	and	CC	_	_	_
116	segemehl	segemehl	NN	_	_	_
117	0.2.0	0.2.0	CD	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	mapping	mapping	NN	_	_	_
120	of	of	IN	_	_	_
121	reads	read	VBZ	_	_	_
122	to	to	TO	_	_	_
123	E.	e.	FW	_	_	_
124	coli	coli	FW	_	_	_
125	O104	o104	NN	_	_	_
126	:	:	:	_	_	_
127	H4	h4	NN	_	_	_
128	rRNAs	rrna	NNS	_	_	_
129	and	and	CC	_	_	_
130	tRNAs	trna	NNS	_	_	_
131	using	use	VBG	_	_	_
132	READemption	reademption	NN	_	_	_
133	0.3.7	0.3.7	CD	_	_	_
134	and	and	CC	_	_	_
135	segemehl	segemehl	NN	_	_	_
136	0.2.0	0.2.0	CD	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	normalization	normalization	NN	_	_	_
139	of	of	IN	_	_	_
140	graphs	graph	NNS	_	_	_
141	to	to	TO	_	_	_
142	the	the	DT	_	_	_
143	total	total	JJ	_	_	_
144	number	number	NN	_	_	_
145	of	of	IN	_	_	_
146	mapped	map	VBN	_	_	_
147	reads	read	VBZ	_	_	_
148	per	per	IN	_	_	_
149	library	library	NN	_	_	_
150	using	use	VBG	_	_	_
151	READemption	reademption	NN	_	_	_
152	0.3.7	0.3.7	CD	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	origin	origin	NN	_	_	_
155	of	of	IN	_	_	_
156	isolation	isolation	NN	_	_	_
157	:	:	:	_	_	_
158	patient	patient	NN	_	_	_
159	with	with	IN	_	_	_
160	hemolytic	hemolytic	JJ	_	_	_
161	uremic	uremic	JJ	_	_	_
162	syndrome	syndrome	NN	_	_	_
163	-LRB-	-lrb-	-LRB-	_	_	_
164	HUS	hus	NN	_	_	_
165	-RRB-	-rrb-	-RRB-	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	outbreak	outbreak	NN	_	_	_
168	:	:	:	_	_	_
169	2011	2011	CD	_	_	_
170	outbreak	outbreak	NN	_	_	_
171	centered	center	VBN	_	_	_
172	in	in	IN	_	_	_
173	Northern	Northern	NNP	_	_	_
174	Germany	Germany	NNP	_	_	_
175	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
176	RNA-Seq	rna-seq	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	strain	strain	NN	_	_	_
179	:	:	:	_	_	_
180	clinical	clinical	JJ	_	_	_
181	isolate	isolate	JJ	_	_	_
182	LB226692	lb226692	NN	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	Supplementary	supplementary	JJ	_	_	_
185	_	_	NN	_	_	_
186	files	file	NNS	_	_	_
187	_	_	IN	_	_	_
188	format	format	NN	_	_	_
189	_	_	NN	_	_	_
190	and	and	CC	_	_	_
191	_	_	NN	_	_	_
192	content	content	NN	_	_	_
193	:	:	:	_	_	_
194	wig	wig	NN	_	_	_
195	files	file	NNS	_	_	_
196	representing	represent	VBG	_	_	_
197	the	the	DT	_	_	_
198	normalized	normalize	VBN	_	_	_
199	number	number	NN	_	_	_
200	of	of	IN	_	_	_
201	pAA-associated	paa-associated	JJ	_	_	_
202	mapped	map	VBN	_	_	_
203	reads	read	VBZ	_	_	_
204	per	per	IN	_	_	_
205	nucleotide	nucleotide	NN	_	_	_
206	.	.	.	_	_	_

1	Files	file	NNS	_	_	_
2	contain	contain	VBP	_	_	_
3	wiggle-formatted	wiggle-formatted	JJ	_	_	_
4	files	file	NNS	_	_	_
5	data	datum	NNS	_	_	_
6	for	for	IN	_	_	_
7	accessions	accession	NNS	_	_	_
8	NC	NC	NNP	_	_	_
9	_	_	SYM	_	_	_
10	018658.1	018658.1	CD	_	_	_
11	,	,	,	_	_	_
12	NC	NC	NNP	_	_	_
13	_	_	NNP	_	_	_
14	018659.1	018659.1	CD	_	_	_
15	,	,	,	_	_	_
16	NC	NC	NNP	_	_	_
17	_	_	NNP	_	_	_
18	018660.1	018660.1	CD	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	NC	NC	NNP	_	_	_
22	_	_	SYM	_	_	_
23	018666.1	018666.1	CD	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	TEX	TEX	NNP	_	_	_
3	-	-	:	_	_	_
4	_	_	SYM	_	_	_
5	E.	e.	FW	_	_	_
6	coli	coli	FW	_	_	_
7	O104	o104	NN	_	_	_
8	:	:	:	_	_	_
9	H4	h4	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	TEX	tex	NN	_	_	_
12	+	+	CC	_	_	_
13	_	_	SYM	_	_	_
14	E.	e.	FW	_	_	_
15	coli	coli	FW	_	_	_
16	O104	o104	NN	_	_	_
17	:	:	:	_	_	_
18	H4	h4	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Total	total	JJ	_	_	_
21	RNA	rna	NN	_	_	_
22	was	be	VBD	_	_	_
23	extracted	extract	VBN	_	_	_
24	using	use	VBG	_	_	_
25	the	the	DT	_	_	_
26	Trizol	Trizol	NNP	_	_	_
27	reagent	reagent	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Thermo	Thermo	NNP	_	_	_
30	Fisher	Fisher	NNP	_	_	_
31	Scientific	Scientific	NNP	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	and	and	CC	_	_	_
34	the	the	DT	_	_	_
35	concentration	concentration	NN	_	_	_
36	and	and	CC	_	_	_
37	purity	purity	NN	_	_	_
38	of	of	IN	_	_	_
39	the	the	DT	_	_	_
40	samples	sample	NNS	_	_	_
41	were	be	VBD	_	_	_
42	determined	determine	VBN	_	_	_
43	using	use	VBG	_	_	_
44	Nano	Nano	NNP	_	_	_
45	Drop	Drop	NNP	_	_	_
46	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	integrity	integrity	NN	_	_	_
3	was	be	VBD	_	_	_
4	monitored	monitor	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	R6K	r6k	NN	_	_	_
8	ScreenTape	screentape	NN	_	_	_
9	system	system	NN	_	_	_
10	on	on	IN	_	_	_
11	the	the	DT	_	_	_
12	Agilent	Agilent	NNP	_	_	_
13	2200	2200	CD	_	_	_
14	TapeStation	TapeStation	NNP	_	_	_
15	.	.	.	_	_	_

1	gDNA	gdna	NN	_	_	_
2	was	be	VBD	_	_	_
3	removed	remove	VBN	_	_	_
4	by	by	IN	_	_	_
5	Turbo	Turbo	NNP	_	_	_
6	DNase	dnase	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Thermo	Thermo	NNP	_	_	_
9	Fisher	Fisher	NNP	_	_	_
10	Scientific	Scientific	NNP	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	in	in	IN	_	_	_
13	the	the	DT	_	_	_
14	presence	presence	NN	_	_	_
15	of	of	IN	_	_	_
16	1U	1u	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Cells	cell	NNS	_	_	_
19	were	be	VBD	_	_	_
20	harvested	harvest	VBN	_	_	_
21	from	from	IN	_	_	_
22	aerobic	aerobic	JJ	_	_	_
23	and	and	CC	_	_	_
24	anaerobic	anaerobic	JJ	_	_	_
25	cultures	culture	NNS	_	_	_
26	of	of	IN	_	_	_
27	seven	seven	CD	_	_	_
28	E.	e.	FW	_	_	_
29	coli	coli	FW	_	_	_
30	strains	strain	NNS	_	_	_
31	grown	grow	VBN	_	_	_
32	to	to	TO	_	_	_
33	an	a	DT	_	_	_
34	OD600	od600	NN	_	_	_
35	of	of	IN	_	_	_
36	0.6	0.6	CD	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	exponential	exponential	JJ	GrowthPhase	_	_
39	phase	phase	NN	GrowthPhase	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	divided	divide	VBN	_	_	_
4	into	into	IN	_	_	_
5	10	10	CD	_	_	_
6	ml	ml	NN	_	_	_
7	aliquots	aliquot	NNS	_	_	_
8	and	and	CC	_	_	_
9	were	be	VBD	_	_	_
10	immediately	immediately	RB	_	_	_
11	mixed	mix	VBN	_	_	_
12	with	with	IN	_	_	_
13	0.2	0.2	CD	_	_	_
14	volumes	volume	NNS	_	_	_
15	of	of	IN	_	_	_
16	ice-cold	ice-cold	JJ	_	_	_
17	STOP	stop	NN	_	_	_
18	solution	solution	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	95	95	CD	_	_	_
21	%	%	NN	_	_	_
22	ethanol	ethanol	NN	_	_	_
23	,	,	,	_	_	_
24	5	5	CD	_	_	_
25	%	%	NN	_	_	_
26	phenol	phenol	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	pH	ph	NN	_	_	_
29	4.7	4.7	CD	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	20	20	CD	_	_	_
3	min	min	NN	_	_	_
4	incubation	incubation	NN	_	_	_
5	on	on	IN	_	_	_
6	ice	ice	NN	_	_	_
7	,	,	,	_	_	_
8	samples	sample	NNS	_	_	_
9	were	be	VBD	_	_	_
10	spun	spin	VBN	_	_	_
11	down	down	RP	_	_	_
12	for	for	IN	_	_	_
13	10	10	CD	_	_	_
14	min	min	NN	_	_	_
15	at	at	IN	_	_	_
16	4	4	CD	_	_	_
17	˚C	˚c	NN	_	_	_
18	and	and	CC	_	_	_
19	7000	7000	CD	_	_	_
20	x	x	CC	_	_	_
21	g	g	NN	_	_	_
22	in	in	IN	_	_	_
23	a	a	DT	_	_	_
24	centrifuge	centrifuge	NN	_	_	_
25	.	.	.	_	_	_

1	Pellets	pellet	NNS	_	_	_
2	from	from	IN	_	_	_
3	one	one	CD	_	_	_
4	aliquot	aliquot	NN	_	_	_
5	were	be	VBD	_	_	_
6	gently	gently	RB	_	_	_
7	resuspended	resuspend	VBN	_	_	_
8	in	in	IN	_	_	_
9	RNAProtect	rnaprotect	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	QIAGEN	QIAGEN	NNP	_	_	_
12	,	,	,	_	_	_
13	Germany	Germany	NNP	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	to	to	TO	_	_	_
16	further	further	JJ	_	_	_
17	stabilize	stabilize	VB	_	_	_
18	the	the	DT	_	_	_
19	RNA	rna	NN	_	_	_
20	.	.	.	_	_	_

1	Remaining	remain	VBG	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	mixed	mix	VBN	_	_	_
5	with	with	IN	_	_	_
6	RNAlater	rnalater	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	QIAGEN	QIAGEN	NNP	_	_	_
9	,	,	,	_	_	_
10	Germany	Germany	NNP	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	and	and	CC	_	_	_
13	placed	place	VBN	_	_	_
14	at	at	IN	_	_	_
15	-80	-80	CD	_	_	_
16	˚C	˚c	NN	_	_	_
17	for	for	IN	_	_	_
18	archival	archival	JJ	_	_	_
19	storage	storage	NN	_	_	_
20	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	using	use	VBG	_	_	_
6	RNeasy	RNeasy	NNP	_	_	_
7	Mini	Mini	NNP	_	_	_
8	kit	kit	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	QIAGEN	QIAGEN	NNP	_	_	_
11	,	,	,	_	_	_
12	Germany	Germany	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	and	and	CC	_	_	_
15	on	on	IN	_	_	_
16	column	column	NN	_	_	_
17	DNase	dnase	NN	_	_	_
18	treatment	treatment	NN	_	_	_
19	following	follow	VBG	_	_	_
20	the	the	DT	_	_	_
21	manufacturers	manufacturer	NNS	_	_	_
22	'	'	POS	_	_	_
23	instructions	instruction	NNS	_	_	_
24	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	23S	23s	NN	_	_	_
3	and	and	CC	_	_	_
4	16S	16s	NN	_	_	_
5	rRNAs	rrna	NNS	_	_	_
6	were	be	VBD	_	_	_
7	removed	remove	VBN	_	_	_
8	by	by	IN	_	_	_
9	subtractive	subtractive	JJ	_	_	_
10	hybridization	hybridization	NN	_	_	_
11	using	use	VBG	_	_	_
12	the	the	DT	_	_	_
13	MICROBExpress	microbexpress	NN	_	_	_
14	kit	kit	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Ambion	Ambion	NNP	_	_	_
17	,	,	,	_	_	_
18	USA	USA	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	with	with	IN	_	_	_
21	modifications	modification	NNS	_	_	_
22	.	.	.	_	_	_

1	Compared	compare	VBN	_	_	_
2	with	with	IN	_	_	_
3	the	the	DT	_	_	_
4	standard	standard	JJ	_	_	_
5	protocol	protocol	NN	_	_	_
6	,	,	,	_	_	_
7	50	50	CD	_	_	_
8	%	%	NN	_	_	_
9	more	more	JJR	_	_	_
10	capture	capture	NN	_	_	_
11	oligonucleotides	oligonucleotide	NNS	_	_	_
12	and	and	CC	_	_	_
13	magnetic	magnetic	JJ	_	_	_
14	beads	bead	NNS	_	_	_
15	were	be	VBD	_	_	_
16	used	use	VBN	_	_	_
17	.	.	.	_	_	_

1	5S	5s	NN	_	_	_
2	rRNAs	rrna	NNS	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	120	120	CD	_	_	_
5	nt	nt	NNS	_	_	_
6	in	in	IN	_	_	_
7	length	length	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	were	be	VBD	_	_	_
10	removed	remove	VBN	_	_	_
11	during	during	IN	_	_	_
12	the	the	DT	_	_	_
13	total	total	JJ	_	_	_
14	RNA	rna	NN	_	_	_
15	extraction	extraction	NN	_	_	_
16	on	on	IN	_	_	_
17	column	column	NN	_	_	_
18	.	.	.	_	_	_

1	Specifically	specifically	RB	_	_	_
2	,	,	,	_	_	_
3	ribosomal	ribosomal	JJ	_	_	_
4	depletion	depletion	NN	_	_	_
5	on	on	IN	_	_	_
6	total	total	JJ	_	_	_
7	RNA	rna	NN	_	_	_
8	isolated	isolate	VBN	_	_	_
9	from	from	IN	_	_	_
10	the	the	DT	_	_	_
11	E.	e.	FW	_	_	_
12	coli	coli	FW	_	_	_
13	BL21	bl21	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	DE3	de3	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	was	be	VBD	_	_	_
18	performed	perform	VBN	_	_	_
19	using	use	VBG	_	_	_
20	RiboZero	RiboZero	NNP	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Gram	Gram	NNP	_	_	_
23	Negative	negative	JJ	_	_	_
24	Bacteria	bacterium	NNS	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	kit	kit	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Epicenter	epicenter	NN	_	_	_
29	,	,	,	_	_	_
30	USA	USA	NNP	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	stored	store	VBN	_	_	_
5	at	at	IN	_	_	_
6	-80	-80	CD	_	_	_
7	°C	°c	NN	_	_	_
8	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Crooks	Crooks	NNPS	_	_	_
3	_	_	SYM	_	_	_
4	aero	aero	FW	_	_	_
5	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
6	Crooks	Crooks	NNPS	_	_	_
7	_	_	SYM	_	_	_
8	anaero	anaero	FW	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
10	Escherichia	escherichia	FW	Organism	_	_
11	coli	coli	FW	Organism	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	Escherichia	escherichia	FW	Organism	_	_
14	coli	coli	FW	Organism	_	_
15	strains	strain	NNS	_	_	_
16	E.coli	e.coli	JJ	_	_	_
17	C	c	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	DSMZ	dsmz	NN	_	_	_
20	4860	4860	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	,	,	,	_	_	_
23	E.	e.	FW	_	_	_
24	coli	coli	FW	_	_	_
25	Crooks	crook	NNS	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	DSMZ	dsmz	NN	_	_	_
28	1576	1576	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	,	,	,	_	_	_
31	E.	e.	FW	_	_	_
32	coli	coli	FW	_	_	_
33	DH5α	dh5α	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	DSMZ	dsmz	NN	_	_	_
36	6897	6897	CD	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	E.	e.	FW	_	_	_
39	coli	coli	FW	_	_	_
40	W	w	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	DSMZ	dsmz	NN	_	_	_
43	1116	1116	CD	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	,	,	,	_	_	_
46	E.	e.	FW	_	_	_
47	coli	coli	FW	_	_	_
48	W3110	w3110	NN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	DSMZ	dsmz	NN	_	_	_
51	5911	5911	CD	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	were	be	VBD	_	_	_
54	obtained	obtain	VBN	_	_	_
55	from	from	IN	_	_	_
56	DSMZ-German	DSMZ-German	NNP	_	_	_
57	Collection	Collection	NNP	_	_	_
58	of	of	IN	_	_	_
59	Microorganism	Microorganism	NNP	_	_	_
60	and	and	CC	_	_	_
61	Cell	cell	NN	_	_	_
62	Cultures	culture	NNS	_	_	_
63	;	;	:	_	_	_
64	E.	e.	FW	_	_	_
65	coli	coli	FW	_	_	_
66	BL21	bl21	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	DE3	de3	NN	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	was	be	VBD	_	_	_
71	purchased	purchase	VBN	_	_	_
72	as	as	IN	_	_	_
73	competent	competent	JJ	_	_	_
74	cells	cell	NNS	_	_	_
75	from	from	IN	_	_	_
76	Agilent	Agilent	NNP	_	_	_
77	-LRB-	-lrb-	-LRB-	_	_	_
78	Agilent	Agilent	NNP	_	_	_
79	Technologies	Technologies	NNPS	_	_	_
80	Inc.	Inc.	NNP	_	_	_
81	,	,	,	_	_	_
82	USA	USA	NNP	_	_	_
83	-RRB-	-rrb-	-RRB-	_	_	_
84	,	,	,	_	_	_
85	E.	e.	FW	_	_	_
86	coli	coli	FW	_	_	_
87	K-12	k-12	NN	_	_	_
88	MG1655	mg1655	NN	_	_	_
89	-LRB-	-lrb-	-LRB-	_	_	_
90	ATCC	atcc	NN	_	_	_
91	700926	700926	CD	_	_	_
92	-RRB-	-rrb-	-RRB-	_	_	_
93	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	strains	strain	NNS	_	_	_
3	were	be	VBD	_	_	_
4	cultured	culture	VBN	_	_	_
5	in	in	IN	_	_	_
6	M9	m9	NN	MED	_	_
7	minimal	minimal	JJ	MED	_	_
8	medium	medium	NN	MED	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	1	1	CD	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	containing	contain	VBG	_	_	_
13	Na2HPO4	na2hpo4	NN	_	_	_
14	x	x	NN	_	_	_
15	7H2O	7h2o	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	6.8	6.8	CD	_	_	_
18	g	g	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	,	,	,	_	_	_
21	KH2PO4	kh2po4	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	3	3	CD	_	_	_
24	g	g	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	,	,	,	_	_	_
27	NaCl	nacl	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	0.5	0.5	CD	_	_	_
30	g	g	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	,	,	,	_	_	_
33	NH4Cl	nh4cl	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	1	1	CD	_	_	_
36	g	g	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	,	,	,	_	_	_
39	MgSO4	mgso4	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	2	2	CD	_	_	_
42	mmol	mmol	NN	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	,	,	,	_	_	_
45	CaCl2	cacl2	NN	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	0.1	0.1	CD	_	_	_
48	mmol	mmol	NN	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	,	,	,	_	_	_
51	trace	trace	NN	_	_	_
52	elements	element	NNS	_	_	_
53	,	,	,	_	_	_
54	Wolf	Wolf	NNP	_	_	_
55	's	's	POS	_	_	_
56	vitamin	vitamin	NN	_	_	_
57	solution	solution	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	2	2	CD	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	and	and	CC	_	_	_
62	glucose	glucose	NN	SUPP	_	_
63	-LRB-	-lrb-	-LRB-	_	_	_
64	2	2	CD	_	_	_
65	g	g	NN	_	_	_
66	L-1	l-1	NN	_	_	_
67	-RRB-	-rrb-	-RRB-	_	_	_
68	.	.	.	_	_	_

1	Anoxic	anoxic	JJ	_	_	_
2	M9	m9	NN	MED	_	_
3	minimal	minimal	JJ	MED	_	_
4	media	media	NNS	MED	_	_
5	with	with	IN	_	_	_
6	glucose	glucose	NN	SUPP	_	_
7	was	be	VBD	_	_	_
8	obtained	obtain	VBN	_	_	_
9	by	by	IN	_	_	_
10	flushing	flush	VBG	_	_	_
11	solution	solution	NN	_	_	_
12	with	with	IN	_	_	_
13	oxygen	oxygen	NN	_	_	_
14	free	free	JJ	_	_	_
15	nitrogen	nitrogen	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	95	95	CD	_	_	_
18	%	%	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	Overnight	overnight	JJ	_	_	_
2	cultures	culture	NNS	_	_	_
3	from	from	IN	_	_	_
4	single	single	JJ	_	_	_
5	colonies	colony	NNS	_	_	_
6	of	of	IN	_	_	_
7	each	each	DT	_	_	_
8	of	of	IN	_	_	_
9	seven	seven	CD	_	_	_
10	E.	e.	FW	_	_	_
11	coli	coli	FW	_	_	_
12	strains	strain	NNS	_	_	_
13	were	be	VBD	_	_	_
14	diluted	dilute	VBN	_	_	_
15	to	to	TO	_	_	_
16	a	a	DT	_	_	_
17	starting	start	VBG	_	_	_
18	optical	optical	JJ	_	_	_
19	density	density	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	OD600	od600	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	of	of	IN	_	_	_
24	0.01	0.01	CD	_	_	_
25	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	grown	grow	VBN	_	_	_
4	in	in	IN	_	_	_
5	250	250	CD	_	_	_
6	ml	ml	NN	_	_	_
7	flasks	flask	NNS	_	_	_
8	or	or	CC	_	_	_
9	300	300	CD	_	_	_
10	ml	ml	NN	_	_	_
11	oxygen-free	oxygen-free	JJ	_	_	_
12	sealed	sealed	JJ	_	_	_
13	bottles	bottle	NNS	_	_	_
14	containing	contain	VBG	_	_	_
15	50	50	CD	_	_	_
16	ml	ml	NN	_	_	_
17	glucose-M9	glucose-m9	NN	_	_	_
18	minimal	minimal	JJ	_	_	_
19	media	media	NNS	_	_	_
20	in	in	IN	_	_	_
21	a	a	DT	_	_	_
22	shaking	shake	VBG	_	_	_
23	incubator	incubator	NN	_	_	_
24	at	at	IN	_	_	_
25	37	37	CD	_	_	_
26	°C	°c	NN	_	_	_
27	and	and	CC	_	_	_
28	250	250	CD	_	_	_
29	rpm	rpm	NN	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Gene	Gene	NNP	_	_	_
3	expression	expression	NN	_	_	_
4	data	datum	NNS	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	3	3	CD	_	_	_
7	biological	biological	JJ	_	_	_
8	replicates	replicate	VBZ	_	_	_
9	per	per	IN	_	_	_
10	strain	strain	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	were	be	VBD	_	_	_
13	analyzed	analyze	VBN	_	_	_
14	in	in	IN	_	_	_
15	the	the	DT	_	_	_
16	statistical	statistical	JJ	_	_	_
17	software	software	NN	_	_	_
18	program	program	NN	_	_	_
19	R	r	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	www.r-project.org	www.r-project.org	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	using	use	VBG	_	_	_
24	the	the	DT	_	_	_
25	EdgeR	edger	NN	_	_	_
26	package	package	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	3	3	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	Data	datum	NNS	_	_	_
2	were	be	VBD	_	_	_
3	normalized	normalize	VBN	_	_	_
4	using	use	VBG	_	_	_
5	the	the	DT	_	_	_
6	CQN	cqn	NN	_	_	_
7	package	package	NN	_	_	_
8	,	,	,	_	_	_
9	which	which	WDT	_	_	_
10	accounts	account	VBZ	_	_	_
11	for	for	IN	_	_	_
12	both	both	DT	_	_	_
13	gene	gene	NN	_	_	_
14	length	length	NN	_	_	_
15	and	and	CC	_	_	_
16	GC	gc	NN	_	_	_
17	content	content	JJ	_	_	_
18	effects	effect	NNS	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	4	4	LS	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	.	.	.	_	_	_

1	Differentially	differentially	RB	_	_	_
2	expressed	express	VBN	_	_	_
3	genes	gene	NNS	_	_	_
4	were	be	VBD	_	_	_
5	determined	determine	VBN	_	_	_
6	by	by	IN	_	_	_
7	comparing	compare	VBG	_	_	_
8	expression	expression	NN	_	_	_
9	values	value	NNS	_	_	_
10	under	under	IN	_	_	_
11	anaerobic	anaerobic	JJ	_	_	_
12	and	and	CC	_	_	_
13	aerobic	aerobic	JJ	_	_	_
14	conditions	condition	NNS	_	_	_
15	.	.	.	_	_	_

1	Those	those	DT	_	_	_
2	genes	gene	NNS	_	_	_
3	with	with	IN	_	_	_
4	adjusted	adjusted	JJ	_	_	_
5	P	p	NN	_	_	_
6	values	value	NNS	_	_	_
7	less	less	JJR	_	_	_
8	than	than	IN	_	_	_
9	0.01	0.01	CD	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	i.e.	i.e.	FW	_	_	_
12	,	,	,	_	_	_
13	false	false	JJ	_	_	_
14	discovery	discovery	NN	_	_	_
15	rate	rate	NN	_	_	_
16	less	less	JJR	_	_	_
17	than	than	IN	_	_	_
18	1	1	CD	_	_	_
19	%	%	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	were	be	VBD	_	_	_
22	identified	identify	VBN	_	_	_
23	as	as	IN	_	_	_
24	significantly	significantly	RB	_	_	_
25	differentially	differentially	RB	_	_	_
26	expressed	express	VBN	_	_	_
27	genes	gene	NNS	_	_	_
28	.	.	.	_	_	_

1	Finally	finally	RB	_	_	_
2	,	,	,	_	_	_
3	gene	gene	NN	_	_	_
4	annotations	annotation	NNS	_	_	_
5	were	be	VBD	_	_	_
6	automatically	automatically	RB	_	_	_
7	made	make	VBN	_	_	_
8	using	use	VBG	_	_	_
9	the	the	DT	_	_	_
10	biomaRt	biomart	NN	_	_	_
11	package	package	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	5	5	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	together	together	RB	_	_	_
16	with	with	IN	_	_	_
17	the	the	DT	_	_	_
18	annotation	annotation	NN	_	_	_
19	files	file	VBZ	_	_	_
20	available	available	JJ	_	_	_
21	at	at	IN	_	_	_
22	the	the	DT	_	_	_
23	Ensembl	ensembl	NN	_	_	_
24	database	database	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	www.ensembl.org	www.ensembl.org	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	and	and	CC	_	_	_
29	gene	gene	NN	_	_	_
30	set	set	NN	_	_	_
31	enrichment	enrichment	NN	_	_	_
32	analysis	analysis	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	GSEA	gsea	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	was	be	VBD	_	_	_
37	performed	perform	VBN	_	_	_
38	using	use	VBG	_	_	_
39	the	the	DT	_	_	_
40	piano	piano	NN	_	_	_
41	package	package	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	6	6	CD	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	R	r	NN	_	_	_
3	packages	package	NNS	_	_	_
4	used	use	VBN	_	_	_
5	in	in	IN	_	_	_
6	this	this	DT	_	_	_
7	study	study	NN	_	_	_
8	are	be	VBP	_	_	_
9	available	available	JJ	_	_	_
10	in	in	IN	_	_	_
11	Bioconductor	Bioconductor	NNP	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	www.bioconductor.org	www.bioconductor.org	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	strain	strain	NN	_	_	_
5	:	:	:	_	_	_
6	Crooks	crook	NNS	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
8	Supplementary	supplementary	JJ	_	_	_
9	_	_	NN	_	_	_
10	files	file	NNS	_	_	_
11	_	_	IN	_	_	_
12	format	format	NN	_	_	_
13	_	_	NN	_	_	_
14	and	and	CC	_	_	_
15	_	_	NN	_	_	_
16	content	content	NN	_	_	_
17	:	:	:	_	_	_
18	tab-delimited	tab-delimited	JJ	_	_	_
19	text	text	NN	_	_	_
20	files	file	NNS	_	_	_
21	include	include	VBP	_	_	_
22	gene	gene	NN	_	_	_
23	expresion	expresion	NN	_	_	_
24	values	value	NNS	_	_	_
25	for	for	IN	_	_	_
26	each	each	DT	_	_	_
27	Sample	Sample	NNP	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	The	The	NNP	_	_	_
30	sequencing	sequencing	NN	_	_	_
31	libraries	library	NNS	_	_	_
32	were	be	VBD	_	_	_
33	constructed	construct	VBN	_	_	_
34	using	use	VBG	_	_	_
35	the	the	DT	_	_	_
36	TruSeq	TruSeq	NNP	_	_	_
37	RNA	rna	NN	_	_	_
38	Sample	sample	NN	_	_	_
39	Preparation	preparation	NN	_	_	_
40	kit	kit	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	Illumina	Illumina	NNP	_	_	_
43	Inc.	Inc.	NNP	_	_	_
44	,	,	,	_	_	_
45	USA	USA	NNP	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	library	library	NN	_	_	_
3	was	be	VBD	_	_	_
4	prepared	prepare	VBN	_	_	_
5	with	with	IN	_	_	_
6	RNA	rna	NN	_	_	_
7	isolated	isolate	VBN	_	_	_
8	from	from	IN	_	_	_
9	seven	seven	CD	_	_	_
10	E.	e.	FW	_	_	_
11	coli	coli	FW	_	_	_
12	cultures	culture	NNS	_	_	_
13	grown	grow	VBN	_	_	_
14	in	in	IN	_	_	_
15	triplicate	triplicate	NN	_	_	_
16	to	to	TO	_	_	_
17	an	a	DT	_	_	_
18	exponential	exponential	JJ	GrowthPhase	_	_
19	phase	phase	NN	GrowthPhase	_	_
20	under	under	IN	_	_	_
21	aerobic	aerobic	JJ	_	_	_
22	and	and	CC	_	_	_
23	anaerobic	anaerobic	JJ	_	_	_
24	conditions	condition	NNS	_	_	_
25	.	.	.	_	_	_

1	RT-PCR	rt-pcr	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	with	with	IN	_	_	_
5	SuperScript	SuperScript	NNP	_	_	_
6	®	®	NNP	_	_	_
7	II	II	NNP	_	_	_
8	One-step	one-step	JJ	_	_	_
9	RT-PCR	rt-pcr	NN	_	_	_
10	reagents	reagent	NNS	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Invitrogen	Invitrogen	NNP	_	_	_
13	,	,	,	_	_	_
14	USA	USA	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	libraries	library	NNS	_	_	_
3	were	be	VBD	_	_	_
4	sequenced	sequence	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	Illumina	Illumina	NNP	_	_	_
8	HiSeq2000	hiseq2000	NN	_	_	_
9	platform	platform	NN	_	_	_
10	with	with	IN	_	_	_
11	a	a	DT	_	_	_
12	paired-end	paired-end	NN	_	_	_
13	protocol	protocol	NN	_	_	_
14	and	and	CC	_	_	_
15	read	read	VB	_	_	_
16	lengths	length	NNS	_	_	_
17	of	of	IN	_	_	_
18	50	50	CD	_	_	_
19	nt	nt	NNS	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	final	final	JJ	_	_	_
3	concentration	concentration	NN	_	_	_
4	of	of	IN	_	_	_
5	DNA	dna	NN	_	_	_
6	and	and	CC	_	_	_
7	RNA	rna	NN	_	_	_
8	was	be	VBD	_	_	_
9	measured	measure	VBN	_	_	_
10	using	use	VBG	_	_	_
11	a	a	DT	_	_	_
12	Qubit	Qubit	NNP	_	_	_
13	2.0	2.0	CD	_	_	_
14	Fluorometer	Fluorometer	NNP	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Invitrogen	Invitrogen	NNP	_	_	_
17	,	,	,	_	_	_
18	USA	USA	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	integrity	integrity	NN	_	_	_
3	of	of	IN	_	_	_
4	total	total	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	,	,	,	_	_	_
7	DNA	dna	NN	_	_	_
8	contamination	contamination	NN	_	_	_
9	,	,	,	_	_	_
10	removal	removal	NN	_	_	_
11	of	of	IN	_	_	_
12	rRNAs	rrna	NNS	_	_	_
13	and	and	CC	_	_	_
14	cDNA	cdna	NN	_	_	_
15	library	library	NN	_	_	_
16	validation	validation	NN	_	_	_
17	were	be	VBD	_	_	_
18	assessed	assess	VBN	_	_	_
19	with	with	IN	_	_	_
20	Agilent	Agilent	NNP	_	_	_
21	2100	2100	CD	_	_	_
22	Bioanalyzer	Bioanalyzer	NNP	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Agilent	Agilent	NNP	_	_	_
25	Technologies	Technologies	NNPS	_	_	_
26	,	,	,	_	_	_
27	USA	USA	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2	carbon	carbon	NN	_	_	_
3	source	source	NN	_	_	_
4	:	:	:	_	_	_
5	glycerol	glycerol	NN	SUPP	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	carbon	carbon	NN	_	_	_
8	source	source	NN	_	_	_
9	:	:	:	_	_	_
10	glycerol	glycerol	NN	SUPP	_	_
11	+	+	CC	_	_	_
12	propionate	propionate	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Cells	cell	NNS	_	_	_
15	were	be	VBD	_	_	_
16	grown	grow	VBN	_	_	_
17	at	at	IN	_	_	_
18	37	37	CD	_	_	_
19	°C	°c	NN	_	_	_
20	in	in	IN	_	_	_
21	M4	m4	NN	_	_	_
22	minimal	minimal	JJ	_	_	_
23	medium	medium	NN	_	_	_
24	under	under	IN	_	_	_
25	oxic	oxic	JJ	_	_	_
26	and	and	CC	_	_	_
27	anoxic	anoxic	JJ	_	_	_
28	conditions	condition	NNS	_	_	_
29	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	minimal	minimal	JJ	_	_	_
3	medium	medium	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	1.27	1.27	CD	_	_	_
6	mM	mm	NN	KWSUPP	_	_
7	K2HPO4	k2hpo4	NN	_	_	_
8	,	,	,	_	_	_
9	0.73	0.73	CD	_	_	_
10	mM	mm	NN	KWSUPP	_	_
11	KH2PO4	kh2po4	NN	_	_	_
12	,	,	,	_	_	_
13	5	5	CD	_	_	_
14	mM	mm	NN	KWSUPP	_	_
15	sodium	sodium	NN	_	_	_
16	HEPES	hepes	NN	_	_	_
17	,	,	,	_	_	_
18	150	150	CD	_	_	_
19	mM	mm	NN	KWSUPP	_	_
20	NaCl	nacl	NN	_	_	_
21	,	,	,	_	_	_
22	9	9	CD	_	_	_
23	mM	mm	NN	KWSUPP	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	NH4	nh4	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	2SO4	2so4	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	was	be	VBD	_	_	_
30	supplemented	supplement	VBN	_	_	_
31	with	with	IN	_	_	_
32	0.1	0.1	CD	_	_	_
33	g	g	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	Cluster	cluster	NN	_	_	_
36	detection	detection	NN	_	_	_
37	and	and	CC	_	_	_
38	base	base	NN	_	_	_
39	calling	calling	NN	_	_	_
40	were	be	VBD	_	_	_
41	performed	perform	VBN	_	_	_
42	using	use	VBG	_	_	_
43	RTA	RTA	NNP	_	_	_
44	v1	v1	NN	_	_	_
45	.13	.13	CD	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	Illumina	Illumina	NNP	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	,	,	,	_	_	_
50	and	and	CC	_	_	_
51	the	the	DT	_	_	_
52	quality	quality	NN	_	_	_
53	of	of	IN	_	_	_
54	the	the	DT	_	_	_
55	reads	read	VBZ	_	_	_
56	was	be	VBD	_	_	_
57	assessed	assess	VBN	_	_	_
58	with	with	IN	_	_	_
59	CASAVA	casava	NN	_	_	_
60	v1	v1	NN	_	_	_
61	.8.1	.8.1	CD	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	Illumina	Illumina	NNP	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	delta-rnr	delta-rnr	NN	_	_	_
3	mutant	mutant	JJ	_	_	_
4	_	_	NN	_	_	_
5	anoxic	anoxic	JJ	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	NO3	no3	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	_	_	SYM	_	_	_
10	glycerol	glycerol	NN	SUPP	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	delta-rnr	delta-rnr	JJ	_	_	_
13	mutant	mutant	JJ	_	_	_
14	_	_	NN	_	_	_
15	anoxic	anoxic	JJ	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	NO3	no3	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	_	_	SYM	_	_	_
20	glycerol	glycerol	NN	SUPP	_	_
21	+	+	CC	_	_	_
22	propionate	propionate	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	delta-rnr	delta-rnr	JJ	_	_	_
25	mutant	mutant	JJ	_	_	_
26	_	_	NN	_	_	_
27	oxic	oxic	JJ	_	_	_
28	_	_	NN	_	_	_
29	glycerol	glycerol	NN	SUPP	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	delta-rnr	delta-rnr	JJ	_	_	_
32	mutant	mutant	JJ	_	_	_
33	_	_	NN	_	_	_
34	oxic	oxic	JJ	_	_	_
35	_	_	NN	_	_	_
36	glycerol	glycerol	NN	SUPP	_	_
37	+	+	CC	_	_	_
38	propionate	propionate	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	d	d	NN	_	_	_
41	_	_	CD	_	_	_
42	rnr	rnr	NN	GEN	_	_
43	NO3	no3	NN	_	_	_
44	1	1	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	d	d	NN	_	_	_
47	_	_	CD	_	_	_
48	rnr	rnr	NN	GEN	_	_
49	NO3	no3	NN	_	_	_
50	2	2	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	d	d	NN	_	_	_
53	_	_	CD	_	_	_
54	rnr	rnr	NN	GEN	_	_
55	NO3	no3	NN	_	_	_
56	w	w	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	d	d	NN	_	_	_
59	_	_	CD	_	_	_
60	rnr	rnr	NN	GEN	_	_
61	O2	o2	CD	_	_	_
62	1	1	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	d	d	NN	_	_	_
65	_	_	CD	_	_	_
66	rnr	rnr	NN	GEN	_	_
67	O2	o2	CD	_	_	_
68	2	2	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	d	d	NN	_	_	_
71	_	_	CD	_	_	_
72	rnr	rnr	NN	GEN	_	_
73	O2	o2	CD	_	_	_
74	w	w	NN	_	_	_
75	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
76	Escherichia	escherichia	FW	Organism	_	_
77	coli	coli	FW	Organism	_	_
78	K-12	k-12	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	Gene	gene	NN	_	_	_
81	expression	expression	NN	_	_	_
82	was	be	VBD	_	_	_
83	calculated	calculate	VBN	_	_	_
84	as	as	IN	_	_	_
85	reads	read	VBZ	_	_	_
86	per	per	IN	_	_	_
87	gene	gene	NN	_	_	_
88	by	by	IN	_	_	_
89	determining	determine	VBG	_	_	_
90	the	the	DT	_	_	_
91	number	number	NN	_	_	_
92	of	of	IN	_	_	_
93	reads	read	VBZ	_	_	_
94	that	that	IN	_	_	_
95	overlapped	overlap	VBD	_	_	_
96	with	with	IN	_	_	_
97	the	the	DT	_	_	_
98	annotated	annotated	JJ	_	_	_
99	gene	gene	NN	_	_	_
100	loci	locus	NNS	_	_	_
101	using	use	VBG	_	_	_
102	HTSeq	htseq	NN	_	_	_
103	-LRB-	-lrb-	-LRB-	_	_	_
104	Anders	Anders	NNP	_	_	_
105	et	et	FW	_	_	_
106	al.	al.	FW	_	_	_
107	,	,	,	_	_	_
108	2015	2015	CD	_	_	_
109	,	,	,	_	_	_
110	doi	doi	FW	_	_	_
111	:	:	:	_	_	_
112	10.1093	10.1093	CD	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	Genome	Genome	NNP	_	_	_
115	_	_	NNP	_	_	_
116	build	build	VB	_	_	_
117	:	:	:	_	_	_
118	NC	NC	NNP	_	_	_
119	_	_	SYM	_	_	_
120	000913.3	000913.3	CD	_	_	_
121	E.	e.	FW	_	_	_
122	coli	coli	FW	_	_	_
123	K12	k12	NN	_	_	_
124	substr	substr	NN	_	_	_
125	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	genotype	genotype	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	molecule	molecule	NN	_	_	_
6	subtype	subtype	NN	_	_	_
7	:	:	:	_	_	_
8	total	total	JJ	_	_	_
9	RNA	rna	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	ribosome-depleted	ribosome-depleted	JJ	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
14	No	no	DT	_	_	_
15	further	further	JJ	_	_	_
16	treatment	treatment	NN	_	_	_
17	was	be	VBD	_	_	_
18	applied	apply	VBN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	oxic	oxic	JJ	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	RNA-Seq	rna-seq	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Strand-specific	strand-specific	JJ	_	_	_
7	cDNA	cdna	NN	_	_	_
8	libraries	library	NNS	_	_	_
9	were	be	VBD	_	_	_
10	prepared	prepare	VBN	_	_	_
11	from	from	IN	_	_	_
12	50	50	CD	_	_	_
13	ng	ng	NN	_	_	_
14	of	of	IN	_	_	_
15	rRNA-depleted	rrna-depleted	JJ	_	_	_
16	samples	sample	NNS	_	_	_
17	following	follow	VBG	_	_	_
18	the	the	DT	_	_	_
19	TruSeq	TruSeq	NNP	_	_	_
20	RNA	rna	NN	_	_	_
21	protocol	protocol	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Illumina	Illumina	NNP	_	_	_
24	,	,	,	_	_	_
25	San	San	NNP	_	_	_
26	Diego	Diego	NNP	_	_	_
27	,	,	,	_	_	_
28	CA	CA	NNP	_	_	_
29	,	,	,	_	_	_
30	USA	USA	NNP	_	_	_
31	,	,	,	_	_	_
32	without	without	IN	_	_	_
33	purification	purification	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	with	with	IN	_	_	_
36	modification	modification	NN	_	_	_
37	of	of	IN	_	_	_
38	the	the	DT	_	_	_
39	2nd	2nd	JJ	_	_	_
40	strand	strand	NN	_	_	_
41	cDNA	cdna	NN	_	_	_
42	synthesis	synthesis	NN	_	_	_
43	as	as	IN	_	_	_
44	previously	previously	RB	_	_	_
45	described	describe	VBN	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	Parkhomchuk	Parkhomchuk	NNP	_	_	_
48	et	et	FW	_	_	_
49	al.	al.	FW	_	_	_
50	2009	2009	CD	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	libraries	library	NNS	_	_	_
3	were	be	VBD	_	_	_
4	prepared	prepare	VBN	_	_	_
5	using	use	VBG	_	_	_
6	multiplex	multiplex	JJ	_	_	_
7	primers	primer	NNS	_	_	_
8	to	to	TO	_	_	_
9	allow	allow	VB	_	_	_
10	simultaneous	simultaneous	JJ	_	_	_
11	sequencing	sequencing	NN	_	_	_
12	in	in	IN	_	_	_
13	a	a	DT	_	_	_
14	single	single	JJ	_	_	_
15	lane	lane	NN	_	_	_
16	.	.	.	_	_	_

1	Sequencing	sequencing	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	on	on	IN	_	_	_
5	a	a	DT	_	_	_
6	HiSeq1500	hiseq1500	NN	_	_	_
7	using	use	VBG	_	_	_
8	SBS	SBS	NNP	_	_	_
9	v3	v3	NN	_	_	_
10	kits	kit	NNS	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Illumina	Illumina	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	to	to	TO	_	_	_
15	generate	generate	VB	_	_	_
16	paired-end	paired-end	NN	_	_	_
17	reads	read	VBZ	_	_	_
18	of	of	IN	_	_	_
19	2	2	CD	_	_	_
20	x	x	CC	_	_	_
21	50	50	CD	_	_	_
22	nucleotides	nucleotide	NNS	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Supplementary	Supplementary	NNP	_	_	_
3	_	_	VBD	_	_	_
4	files	file	NNS	_	_	_
5	_	_	IN	_	_	_
6	format	format	NN	_	_	_
7	_	_	NN	_	_	_
8	and	and	CC	_	_	_
9	_	_	NN	_	_	_
10	content	content	NN	_	_	_
11	:	:	:	_	_	_
12	RPG	rpg	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	reads	read	VBZ	_	_	_
15	per	per	IN	_	_	_
16	gene	gene	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	files	file	NNS	_	_	_
19	were	be	VBD	_	_	_
20	created	create	VBN	_	_	_
21	using	use	VBG	_	_	_
22	HTSeq	htseq	NN	_	_	_
23	,	,	,	_	_	_
24	mapping	map	VBG	_	_	_
25	raw	raw	JJ	_	_	_
26	reads	read	VBZ	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	fastq	fastq	NN	_	_	_
29	format	format	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	against	against	IN	_	_	_
32	the	the	DT	_	_	_
33	E.	e.	FW	_	_	_
34	coli	coli	FW	_	_	_
35	K12	k12	NN	_	_	_
36	genome	genome	NN	_	_	_
37	and	and	CC	_	_	_
38	using	use	VBG	_	_	_
39	a	a	DT	_	_	_
40	GFF	gff	NN	_	_	_
41	file	file	NN	_	_	_
42	derived	derive	VBN	_	_	_
43	from	from	IN	_	_	_
44	the	the	DT	_	_	_
45	annotation	annotation	NN	_	_	_
46	of	of	IN	_	_	_
47	NC	NC	NNP	_	_	_
48	_	_	SYM	_	_	_
49	000913.3	000913.3	CD	_	_	_
50	available	available	JJ	_	_	_
51	from	from	IN	_	_	_
52	NCBI	NCBI	NNP	_	_	_
53	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	sequence	sequence	NN	_	_	_
4	data	datum	NNS	_	_	_
5	were	be	VBD	_	_	_
6	mapped	map	VBN	_	_	_
7	against	against	IN	_	_	_
8	the	the	DT	_	_	_
9	genome	genome	NN	_	_	_
10	sequence	sequence	NN	_	_	_
11	of	of	IN	_	_	_
12	E.	e.	FW	_	_	_
13	coli	coli	FW	_	_	_
14	K12	k12	NN	_	_	_
15	substr	substr	NN	_	_	_
16	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	NCBI	ncbi	NN	_	_	_
4	accession	accession	NN	_	_	_
5	number	number	NN	_	_	_
6	NC	nc	NN	_	_	_
7	_	_	CD	_	_	_
8	000913.3	000913.3	CD	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	using	use	VBG	_	_	_
11	Bowtie2	bowtie2	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Langmead	langmead	NN	_	_	_
14	and	and	CC	_	_	_
15	Salzberg	Salzberg	NNP	_	_	_
16	,	,	,	_	_	_
17	2012	2012	CD	_	_	_
18	,	,	,	_	_	_
19	doi	doi	FW	_	_	_
20	:	:	:	_	_	_
21	10.1038	10.1038	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	Total	total	JJ	_	_	_
24	RNA	rna	NN	_	_	_
25	was	be	VBD	_	_	_
26	isolated	isolate	VBN	_	_	_
27	with	with	IN	_	_	_
28	the	the	DT	_	_	_
29	RNeasy	RNeasy	NNP	_	_	_
30	Protect	Protect	NNP	_	_	_
31	Bacteria	bacterium	NNS	_	_	_
32	Mini	Mini	NNP	_	_	_
33	Kit	kit	NN	_	_	_
34	from	from	IN	_	_	_
35	Qiagen	Qiagen	NNP	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	Hilden	Hilden	NNP	_	_	_
38	,	,	,	_	_	_
39	Germany	Germany	NNP	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	isolated	isolate	VBN	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	further	further	JJ	_	_	_
6	purified	purify	VBN	_	_	_
7	from	from	IN	_	_	_
8	genomic	genomic	JJ	_	_	_
9	DNA	dna	NN	_	_	_
10	contaminations	contamination	NNS	_	_	_
11	using	use	VBG	_	_	_
12	Ambion	Ambion	NNP	_	_	_
13	DNase	dnase	NN	_	_	_
14	I	i	CD	_	_	_
15	treatment	treatment	NN	_	_	_
16	following	follow	VBG	_	_	_
17	the	the	DT	_	_	_
18	manufacturer	manufacturer	NN	_	_	_
19	's	's	POS	_	_	_
20	instructions	instruction	NNS	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	DNA-free	dna-free	NN	_	_	_
23	,	,	,	_	_	_
24	Ambion	Ambion	NNP	_	_	_
25	by	by	IN	_	_	_
26	Life	Life	NNP	_	_	_
27	Technologies	Technologies	NNPS	_	_	_
28	,	,	,	_	_	_
29	Darmstadt	Darmstadt	NNP	_	_	_
30	,	,	,	_	_	_
31	Germany	Germany	NNP	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	further	further	JJ	_	_	_
5	subjected	subject	VBN	_	_	_
6	to	to	TO	_	_	_
7	an	a	DT	_	_	_
8	mRNA	mrna	NN	_	_	_
9	enrichment	enrichment	NN	_	_	_
10	step	step	NN	_	_	_
11	using	use	VBG	_	_	_
12	the	the	DT	_	_	_
13	MICROBExpress	MICROBExpress	NNP	_	_	_
14	Kit	kit	NN	_	_	_
15	from	from	IN	_	_	_
16	Ambion	Ambion	NNP	_	_	_
17	according	accord	VBG	_	_	_
18	to	to	TO	_	_	_
19	the	the	DT	_	_	_
20	manufacturer	manufacturer	NN	_	_	_
21	`	`	``	_	_	_
22	s	be	VBZ	_	_	_
23	instructions	instruction	NNS	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Life	Life	NNP	_	_	_
26	Technologies	Technologies	NNPS	_	_	_
27	,	,	,	_	_	_
28	Darmstadt	Darmstadt	NNP	_	_	_
29	,	,	,	_	_	_
30	Germany	Germany	NNP	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	wild	wild	JJ	_	_	_
3	type	type	NN	_	_	_
4	_	_	CD	_	_	_
5	anoxic	anoxic	JJ	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	NO3	no3	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	_	_	SYM	_	_	_
10	glycerol	glycerol	NN	SUPP	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	wild	wild	JJ	_	_	_
13	type	type	NN	_	_	_
14	_	_	CD	_	_	_
15	anoxic	anoxic	JJ	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	NO3	no3	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	_	_	SYM	_	_	_
20	glycerol	glycerol	NN	SUPP	_	_
21	+	+	CC	_	_	_
22	propionate	propionate	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	wild	wild	JJ	_	_	_
25	type	type	NN	_	_	_
26	_	_	CD	_	_	_
27	oxic	oxic	JJ	_	_	_
28	_	_	NN	_	_	_
29	glycerol	glycerol	NN	SUPP	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	wild	wild	JJ	_	_	_
32	type	type	NN	_	_	_
33	_	_	CD	_	_	_
34	oxic	oxic	JJ	_	_	_
35	_	_	NN	_	_	_
36	glycerol	glycerol	NN	SUPP	_	_
37	+	+	CC	_	_	_
38	propionate	propionate	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	WT	wt	JJ	_	_	_
41	NO3	no3	NN	_	_	_
42	1	1	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	WT	wt	JJ	_	_	_
45	NO3	no3	NN	_	_	_
46	2	2	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	WT	wt	JJ	_	_	_
49	NO3	no3	NN	_	_	_
50	w	w	NN	_	_	_
51	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
52	WT	WT	NNP	_	_	_
53	O2	o2	CD	_	_	_
54	1	1	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	WT	wt	NN	_	_	_
57	O2	o2	CD	_	_	_
58	2	2	CD	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	WT	wt	NN	_	_	_
61	O2	o2	CD	_	_	_
62	w	w	NN	_	_	_
63	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
64	Control	Control	NNP	_	_	_
65	,	,	,	_	_	_
66	0.8	0.8	CD	_	_	_
67	%	%	NN	_	_	_
68	butanol	butanol	NN	_	_	_
69	,1.5	,1.5	CD	_	_	_
70	h	h	NN	_	_	_
71	,	,	,	_	_	_
72	replicate	replicate	VB	_	_	_
73	1	1	CD	_	_	_
74	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
75	Control	Control	NNP	_	_	_
76	,	,	,	_	_	_
77	0.8	0.8	CD	_	_	_
78	%	%	NN	_	_	_
79	butanol	butanol	NN	_	_	_
80	,1.5	,1.5	CD	_	_	_
81	h	h	NN	_	_	_
82	,	,	,	_	_	_
83	replicate	replicate	VB	_	_	_
84	2	2	CD	_	_	_
85	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
86	Control	Control	NNP	_	_	_
87	,	,	,	_	_	_
88	0.8	0.8	CD	_	_	_
89	%	%	NN	_	_	_
90	butanol	butanol	NN	_	_	_
91	,1.5	,1.5	CD	_	_	_
92	h	h	NN	_	_	_
93	,	,	,	_	_	_
94	replicate	replicate	VB	_	_	_
95	3	3	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	Control109	control109	NN	_	_	_
98	_	_	CD	_	_	_
99	0.8	0.8	CD	_	_	_
100	%	%	NN	_	_	_
101	Bu	bu	NN	_	_	_
102	_	_	CD	_	_	_
103	1.5	1.5	CD	_	_	_
104	h	h	NN	_	_	_
105	_	_	CD	_	_	_
106	rep1	rep1	NN	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	Control109	control109	NN	_	_	_
109	_	_	CD	_	_	_
110	0.8	0.8	CD	_	_	_
111	%	%	NN	_	_	_
112	Bu	bu	NN	_	_	_
113	_	_	CD	_	_	_
114	1.5	1.5	CD	_	_	_
115	h	h	NN	_	_	_
116	_	_	CD	_	_	_
117	rep2	rep2	NN	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	Control109	control109	NN	_	_	_
120	_	_	CD	_	_	_
121	0.8	0.8	CD	_	_	_
122	%	%	NN	_	_	_
123	Bu	bu	NN	_	_	_
124	_	_	CD	_	_	_
125	1.5	1.5	CD	_	_	_
126	h	h	NN	_	_	_
127	_	_	CD	_	_	_
128	rep3	rep3	NN	_	_	_
129	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
130	Data	Data	NNP	_	_	_
131	was	be	VBD	_	_	_
132	extracted	extract	VBN	_	_	_
133	with	with	IN	_	_	_
134	Agilent	Agilent	NNP	_	_	_
135	Feature	Feature	NNP	_	_	_
136	Extraction	Extraction	NNP	_	_	_
137	software	software	NN	_	_	_
138	10.7	10.7	CD	_	_	_
139	-LRB-	-lrb-	-LRB-	_	_	_
140	Agilent	Agilent	NNP	_	_	_
141	-RRB-	-rrb-	-RRB-	_	_	_
142	using	use	VBG	_	_	_
143	default	default	NN	_	_	_
144	parameters	parameter	NNS	_	_	_
145	-LRB-	-lrb-	-LRB-	_	_	_
146	protocol	protocol	NN	_	_	_
147	GE1-v1	ge1-v1	NN	_	_	_
148	_	_	CD	_	_	_
149	91	91	CD	_	_	_
150	-RRB-	-rrb-	-RRB-	_	_	_
151	to	to	TO	_	_	_
152	obtain	obtain	VB	_	_	_
153	background	background	NN	_	_	_
154	subtracted	subtract	VBN	_	_	_
155	and	and	CC	_	_	_
156	spatially	spatially	RB	_	_	_
157	detrended	detrend	VBD	_	_	_
158	Processed	processed	JJ	_	_	_
159	Signal	signal	NN	_	_	_
160	intensities	intensity	NNS	_	_	_
161	.	.	.	_	_	_

1	Features	feature	NNS	_	_	_
2	flagged	flag	VBD	_	_	_
3	in	in	IN	_	_	_
4	Feature	Feature	NNP	_	_	_
5	Extraction	Extraction	NNP	_	_	_
6	as	as	IN	_	_	_
7	Feature	Feature	NNP	_	_	_
8	Non-uniform	non-uniform	JJ	_	_	_
9	outliers	outlier	NNS	_	_	_
10	were	be	VBD	_	_	_
11	excluded	exclude	VBN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	strains	strain	NNS	_	_	_
5	harboring	harbor	VBG	_	_	_
6	σ70	σ70	NN	_	_	_
7	mutant	mutant	JJ	_	_	_
8	B8	b8	NN	_	_	_
9	and	and	CC	_	_	_
10	WT	wt	NN	_	_	_
11	were	be	VBD	_	_	_
12	cultured	culture	VBN	_	_	_
13	overnight	overnight	JJ	_	_	_
14	and	and	CC	_	_	_
15	inoculated	inoculate	VBN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	1	1	CD	_	_	_
18	%	%	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	into	into	IN	_	_	_
21	fresh	fresh	JJ	_	_	_
22	medium	medium	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	genotype	genotype	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Mutant	mutant	JJ	_	_	_
8	B8	b8	NN	_	_	_
9	_	_	NN	_	_	_
10	0.8	0.8	CD	_	_	_
11	%	%	NN	_	_	_
12	Bu	bu	NN	_	_	_
13	_	_	CD	_	_	_
14	1.5	1.5	CD	_	_	_
15	h	h	NN	_	_	_
16	_	_	CD	_	_	_
17	rep1	rep1	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
19	Mutant	mutant	JJ	_	_	_
20	B8	b8	NN	_	_	_
21	_	_	NN	_	_	_
22	0.8	0.8	CD	_	_	_
23	%	%	NN	_	_	_
24	Bu	bu	NN	_	_	_
25	_	_	CD	_	_	_
26	1.5	1.5	CD	_	_	_
27	h	h	NN	_	_	_
28	_	_	CD	_	_	_
29	rep2	rep2	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
31	Mutant	mutant	JJ	_	_	_
32	B8	b8	NN	_	_	_
33	_	_	NN	_	_	_
34	0.8	0.8	CD	_	_	_
35	%	%	NN	_	_	_
36	Bu	bu	NN	_	_	_
37	_	_	CD	_	_	_
38	1.5	1.5	CD	_	_	_
39	h	h	NN	_	_	_
40	_	_	CD	_	_	_
41	rep3	rep3	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
43	Mutant	mutant	JJ	_	_	_
44	B8	b8	NN	_	_	_
45	,	,	,	_	_	_
46	0.8	0.8	CD	_	_	_
47	%	%	NN	_	_	_
48	butanol	butanol	NN	_	_	_
49	,1.5	,1.5	CD	_	_	_
50	h	h	NN	_	_	_
51	,	,	,	_	_	_
52	replicate	replicate	VB	_	_	_
53	1	1	CD	_	_	_
54	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
55	Mutant	mutant	JJ	_	_	_
56	B8	b8	NN	_	_	_
57	,	,	,	_	_	_
58	0.8	0.8	CD	_	_	_
59	%	%	NN	_	_	_
60	butanol	butanol	NN	_	_	_
61	,1.5	,1.5	CD	_	_	_
62	h	h	NN	_	_	_
63	,	,	,	_	_	_
64	replicate	replicate	VB	_	_	_
65	2	2	CD	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
67	Mutant	mutant	JJ	_	_	_
68	B8	b8	NN	_	_	_
69	,	,	,	_	_	_
70	0.8	0.8	CD	_	_	_
71	%	%	NN	_	_	_
72	butanol	butanol	NN	_	_	_
73	,1.5	,1.5	CD	_	_	_
74	h	h	NN	_	_	_
75	,	,	,	_	_	_
76	replicate	replicate	VB	_	_	_
77	3	3	CD	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	n-Butanol	n-butanol	NN	_	_	_
80	-LRB-	-lrb-	-LRB-	_	_	_
81	0.8	0.8	CD	_	_	_
82	%	%	NN	_	_	_
83	,	,	,	_	_	_
84	v	v	LS	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
86	phenotype	phenotype	NN	_	_	_
87	:	:	:	_	_	_
88	0.6	0.6	CD	_	_	_
89	%	%	NN	_	_	_
90	n-butanol	n-butanol	NN	_	_	_
91	tolerance	tolerance	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	phenotype	phenotype	NN	_	_	_
94	:	:	:	_	_	_
95	2	2	CD	_	_	_
96	%	%	NN	_	_	_
97	n-butanol	n-butanol	NN	_	_	_
98	tolerance	tolerance	NN	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	strain	strain	NN	_	_	_
101	:	:	:	_	_	_
102	JM109	jm109	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	Total	total	JJ	_	_	_
105	RNA	rna	NN	_	_	_
106	was	be	VBD	_	_	_
107	extracted	extract	VBN	_	_	_
108	using	use	VBG	_	_	_
109	Qiagen	Qiagen	NNP	_	_	_
110	RNeasy	RNeasy	NNP	_	_	_
111	kit	kit	NN	_	_	_
112	-LRB-	-lrb-	-LRB-	_	_	_
113	Hilden	hilden	NN	_	_	_
114	,	,	,	_	_	_
115	Germany	Germany	NNP	_	_	_
116	-RRB-	-rrb-	-RRB-	_	_	_
117	following	follow	VBG	_	_	_
118	manufacturer	manufacturer	NN	_	_	_
119	's	's	POS	_	_	_
120	instructions	instruction	NNS	_	_	_
121	and	and	CC	_	_	_
122	checked	check	VBD	_	_	_
123	for	for	IN	_	_	_
124	a	a	DT	_	_	_
125	RIN	rin	NN	_	_	_
126	number	number	NN	_	_	_
127	to	to	TO	_	_	_
128	inspect	inspect	VB	_	_	_
129	RNA	rna	NN	_	_	_
130	integration	integration	NN	_	_	_
131	by	by	IN	_	_	_
132	an	a	DT	_	_	_
133	Agilent	Agilent	NNP	_	_	_
134	Bioanalyzer	Bioanalyzer	NNP	_	_	_
135	2100	2100	CD	_	_	_
136	-LRB-	-lrb-	-LRB-	_	_	_
137	Agilent	agilent	JJ	_	_	_
138	technologies	technology	NNS	_	_	_
139	,	,	,	_	_	_
140	Santa	Santa	NNP	_	_	_
141	Clara	Clara	NNP	_	_	_
142	,	,	,	_	_	_
143	CA	CA	NNP	_	_	_
144	,	,	,	_	_	_
145	US	US	NNP	_	_	_
146	-RRB-	-rrb-	-RRB-	_	_	_
147	.	.	.	_	_	_

1	Qualified	qualify	VBN	_	_	_
2	total	total	JJ	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	further	further	JJ	_	_	_
6	purified	purify	VBN	_	_	_
7	by	by	IN	_	_	_
8	RNeasy	rneasy	NN	_	_	_
9	mini	minus	NNS	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	QIAGEN	QIAGEN	NNP	_	_	_
13	,	,	,	_	_	_
14	GmBH	GmBH	NNP	_	_	_
15	,	,	,	_	_	_
16	Germany	Germany	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	RNase‐Free	rnase‐free	NN	_	_	_
20	DNase	dnase	NN	_	_	_
21	Set	set	VB	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	QIAGEN	QIAGEN	NNP	_	_	_
24	,	,	,	_	_	_
25	GmBH	GmBH	NNP	_	_	_
26	,	,	,	_	_	_
27	Germany	Germany	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	to	to	TO	_	_	_
6	the	the	DT	_	_	_
7	stationary	stationary	JJ	GrowthPhase	_	_
8	phase	phase	NN	GrowthPhase	_	_
9	at	at	IN	_	_	_
10	37ºC	37ºc	NN	_	_	_
11	in	in	IN	_	_	_
12	Luria-Bertani	luria-bertani	JJ	_	_	_
13	medium	medium	NN	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Enteroheamorragic	enteroheamorragic	JJ	_	_	_
3	E.	e.	FW	_	_	_
4	coli	coli	FW	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Escherichia	escherichia	FW	Organism	_	_
7	coli	coli	FW	Organism	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
9	Genomic	genomic	JJ	_	_	_
10	DNA	dna	NN	_	_	_
11	from	from	IN	_	_	_
12	O111	o111	NN	_	_	_
13	strain	strain	NN	_	_	_
14	10828	10828	CD	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	Genomic	genomic	JJ	_	_	_
17	DNA	dna	NN	_	_	_
18	from	from	IN	_	_	_
19	O111	o111	NN	_	_	_
20	strain	strain	NN	_	_	_
21	11109	11109	CD	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	Genomic	genomic	JJ	_	_	_
24	DNA	dna	NN	_	_	_
25	from	from	IN	_	_	_
26	O111	o111	NN	_	_	_
27	strain	strain	NN	_	_	_
28	11117	11117	CD	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	Genomic	genomic	JJ	_	_	_
31	DNA	dna	NN	_	_	_
32	from	from	IN	_	_	_
33	O111	o111	NN	_	_	_
34	strain	strain	NN	_	_	_
35	11128	11128	CD	_	_	_
36	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
37	Genomic	genomic	JJ	_	_	_
38	DNA	dna	NN	_	_	_
39	from	from	IN	_	_	_
40	O111	o111	NN	_	_	_
41	strain	strain	NN	_	_	_
42	11619	11619	CD	_	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	Genomic	genomic	JJ	_	_	_
45	DNA	dna	NN	_	_	_
46	from	from	IN	_	_	_
47	O111	o111	NN	_	_	_
48	strain	strain	NN	_	_	_
49	11711	11711	CD	_	_	_
50	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
51	Genomic	genomic	JJ	_	_	_
52	DNA	dna	NN	_	_	_
53	from	from	IN	_	_	_
54	O111	o111	NN	_	_	_
55	strain	strain	NN	_	_	_
56	11788	11788	CD	_	_	_
57	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
58	Genomic	genomic	JJ	_	_	_
59	DNA	dna	NN	_	_	_
60	from	from	IN	_	_	_
61	O111	o111	NN	_	_	_
62	strain	strain	NN	_	_	_
63	11845	11845	CD	_	_	_
64	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
65	Genomic	genomic	JJ	_	_	_
66	DNA	dna	NN	_	_	_
67	from	from	IN	_	_	_
68	O111	o111	NN	_	_	_
69	strain	strain	NN	_	_	_
70	12009	12009	CD	_	_	_
71	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
72	Genomic	genomic	JJ	_	_	_
73	DNA	dna	NN	_	_	_
74	from	from	IN	_	_	_
75	O111	o111	NN	_	_	_
76	strain	strain	NN	_	_	_
77	13369	13369	CD	_	_	_
78	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
79	Genomic	genomic	JJ	_	_	_
80	DNA	dna	NN	_	_	_
81	from	from	IN	_	_	_
82	O111	o111	NN	_	_	_
83	strain	strain	NN	_	_	_
84	ED71	ed71	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
86	Genomic	genomic	JJ	_	_	_
87	DNA	dna	NN	_	_	_
88	from	from	IN	_	_	_
89	O111	o111	NN	_	_	_
90	strain	strain	NN	_	_	_
91	PMK5	pmk5	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
93	Genomic	genomic	JJ	_	_	_
94	DNA	dna	NN	_	_	_
95	from	from	IN	_	_	_
96	O157	o157	NN	_	_	_
97	strain	strain	NN	_	_	_
98	980551	980551	CD	_	_	_
99	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
100	Genomic	genomic	JJ	_	_	_
101	DNA	dna	NN	_	_	_
102	from	from	IN	_	_	_
103	O157	o157	NN	_	_	_
104	strain	strain	NN	_	_	_
105	980706	980706	CD	_	_	_
106	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
107	Genomic	genomic	JJ	_	_	_
108	DNA	dna	NN	_	_	_
109	from	from	IN	_	_	_
110	O157	o157	NN	_	_	_
111	strain	strain	NN	_	_	_
112	980938	980938	CD	_	_	_
113	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
114	Genomic	genomic	JJ	_	_	_
115	DNA	dna	NN	_	_	_
116	from	from	IN	_	_	_
117	O157	o157	NN	_	_	_
118	strain	strain	NN	_	_	_
119	981456	981456	CD	_	_	_
120	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
121	Genomic	genomic	JJ	_	_	_
122	DNA	dna	NN	_	_	_
123	from	from	IN	_	_	_
124	O157	o157	NN	_	_	_
125	strain	strain	NN	_	_	_
126	981795	981795	CD	_	_	_
127	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
128	Genomic	genomic	JJ	_	_	_
129	DNA	dna	NN	_	_	_
130	from	from	IN	_	_	_
131	O157	o157	NN	_	_	_
132	strain	strain	NN	_	_	_
133	982243	982243	CD	_	_	_
134	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
135	Genomic	genomic	JJ	_	_	_
136	DNA	dna	NN	_	_	_
137	from	from	IN	_	_	_
138	O157	o157	NN	_	_	_
139	strain	strain	NN	_	_	_
140	990281	990281	CD	_	_	_
141	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
142	Genomic	genomic	JJ	_	_	_
143	DNA	dna	NN	_	_	_
144	from	from	IN	_	_	_
145	O157	o157	NN	_	_	_
146	strain	strain	NN	_	_	_
147	990570	990570	CD	_	_	_
148	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
149	Genomic	genomic	JJ	_	_	_
150	DNA	dna	NN	_	_	_
151	from	from	IN	_	_	_
152	O26	o26	NN	_	_	_
153	strain	strain	NN	_	_	_
154	11044	11044	CD	_	_	_
155	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
156	Genomic	genomic	JJ	_	_	_
157	DNA	dna	NN	_	_	_
158	from	from	IN	_	_	_
159	O26	o26	NN	_	_	_
160	strain	strain	NN	_	_	_
161	11368	11368	CD	_	_	_
162	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
163	Genomic	genomic	JJ	_	_	_
164	DNA	dna	NN	_	_	_
165	from	from	IN	_	_	_
166	O26	o26	NN	_	_	_
167	strain	strain	NN	_	_	_
168	11656	11656	CD	_	_	_
169	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
170	Genomic	genomic	JJ	_	_	_
171	DNA	dna	NN	_	_	_
172	from	from	IN	_	_	_
173	O26	o26	NN	_	_	_
174	strain	strain	NN	_	_	_
175	12719	12719	CD	_	_	_
176	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
177	Genomic	genomic	JJ	_	_	_
178	DNA	dna	NN	_	_	_
179	from	from	IN	_	_	_
180	O26	o26	NN	_	_	_
181	strain	strain	NN	_	_	_
182	12929	12929	CD	_	_	_
183	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
184	Genomic	genomic	JJ	_	_	_
185	DNA	dna	NN	_	_	_
186	from	from	IN	_	_	_
187	O26	o26	NN	_	_	_
188	strain	strain	NN	_	_	_
189	13065	13065	CD	_	_	_
190	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
191	Genomic	genomic	JJ	_	_	_
192	DNA	dna	NN	_	_	_
193	from	from	IN	_	_	_
194	O26	o26	NN	_	_	_
195	strain	strain	NN	_	_	_
196	13247	13247	CD	_	_	_
197	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
198	Genomic	genomic	JJ	_	_	_
199	DNA	dna	NN	_	_	_
200	from	from	IN	_	_	_
201	O26	o26	NN	_	_	_
202	strain	strain	NN	_	_	_
203	ED411	ed411	NN	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
205	Genomic	genomic	JJ	_	_	_
206	DNA	dna	NN	_	_	_
207	was	be	VBD	_	_	_
208	purified	purify	VBN	_	_	_
209	using	use	VBG	_	_	_
210	the	the	DT	_	_	_
211	Genomic-tip	genomic-tip	NN	_	_	_
212	100	100	CD	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	O103	o103	NN	_	_	_
215	no.	no.	NN	_	_	_
216	1	1	CD	_	_	_
217	-LRB-	-lrb-	-LRB-	_	_	_
218	strain	strain	NN	_	_	_
219	10828	10828	CD	_	_	_
220	-RRB-	-rrb-	-RRB-	_	_	_
221	replicate	replicate	VBP	_	_	_
222	1	1	CD	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	O103	o103	NN	_	_	_
225	no.	no.	NN	_	_	_
226	1	1	CD	_	_	_
227	-LRB-	-lrb-	-LRB-	_	_	_
228	strain	strain	NN	_	_	_
229	10828	10828	CD	_	_	_
230	-RRB-	-rrb-	-RRB-	_	_	_
231	replicate	replicate	VBP	_	_	_
232	2	2	CD	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
234	O103	o103	NN	_	_	_
235	no.	no.	NN	_	_	_
236	2	2	CD	_	_	_
237	-LRB-	-lrb-	-LRB-	_	_	_
238	strain	strain	NN	_	_	_
239	11117	11117	CD	_	_	_
240	-RRB-	-rrb-	-RRB-	_	_	_
241	replicate	replicate	VBP	_	_	_
242	1	1	CD	_	_	_
243	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
244	O103	o103	NN	_	_	_
245	no.	no.	NN	_	_	_
246	2	2	CD	_	_	_
247	-LRB-	-lrb-	-LRB-	_	_	_
248	strain	strain	NN	_	_	_
249	11117	11117	CD	_	_	_
250	-RRB-	-rrb-	-RRB-	_	_	_
251	replicate	replicate	VBP	_	_	_
252	2	2	CD	_	_	_
253	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
254	O103	o103	NN	_	_	_
255	no.	no.	NN	_	_	_
256	3	3	CD	_	_	_
257	-LRB-	-lrb-	-LRB-	_	_	_
258	strain	strain	NN	_	_	_
259	11711	11711	CD	_	_	_
260	-RRB-	-rrb-	-RRB-	_	_	_
261	replicate	replicate	VBP	_	_	_
262	1	1	CD	_	_	_
263	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
264	O103	o103	NN	_	_	_
265	no.	no.	NN	_	_	_
266	3	3	CD	_	_	_
267	-LRB-	-lrb-	-LRB-	_	_	_
268	strain	strain	NN	_	_	_
269	11711	11711	CD	_	_	_
270	-RRB-	-rrb-	-RRB-	_	_	_
271	replicate	replicate	VBP	_	_	_
272	2	2	CD	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
274	O103	o103	NN	_	_	_
275	no.	no.	NN	_	_	_
276	4	4	CD	_	_	_
277	-LRB-	-lrb-	-LRB-	_	_	_
278	strain	strain	NN	_	_	_
279	11845	11845	CD	_	_	_
280	-RRB-	-rrb-	-RRB-	_	_	_
281	replicate	replicate	VBP	_	_	_
282	1	1	CD	_	_	_
283	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
284	O103	o103	NN	_	_	_
285	no.	no.	NN	_	_	_
286	4	4	CD	_	_	_
287	-LRB-	-lrb-	-LRB-	_	_	_
288	strain	strain	NN	_	_	_
289	11845	11845	CD	_	_	_
290	-RRB-	-rrb-	-RRB-	_	_	_
291	replicate	replicate	VBP	_	_	_
292	2	2	CD	_	_	_
293	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
294	O103	o103	NN	_	_	_
295	no.	no.	NN	_	_	_
296	5	5	CD	_	_	_
297	-LRB-	-lrb-	-LRB-	_	_	_
298	strain	strain	NN	_	_	_
299	12009	12009	CD	_	_	_
300	-RRB-	-rrb-	-RRB-	_	_	_
301	replicate	replicate	VBP	_	_	_
302	1	1	CD	_	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
304	O103	o103	NN	_	_	_
305	no.	no.	NN	_	_	_
306	5	5	CD	_	_	_
307	-LRB-	-lrb-	-LRB-	_	_	_
308	strain	strain	NN	_	_	_
309	12009	12009	CD	_	_	_
310	-RRB-	-rrb-	-RRB-	_	_	_
311	replicate	replicate	VBP	_	_	_
312	2	2	CD	_	_	_
313	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
314	O103	o103	NN	_	_	_
315	no.	no.	NN	_	_	_
316	6	6	CD	_	_	_
317	-LRB-	-lrb-	-LRB-	_	_	_
318	strain	strain	NN	_	_	_
319	PMK5	pmk5	NN	_	_	_
320	-RRB-	-rrb-	-RRB-	_	_	_
321	replicate	replicate	VBP	_	_	_
322	1	1	CD	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	O103	o103	NN	_	_	_
325	no.	no.	NN	_	_	_
326	6	6	CD	_	_	_
327	-LRB-	-lrb-	-LRB-	_	_	_
328	strain	strain	NN	_	_	_
329	PMK5	pmk5	NN	_	_	_
330	-RRB-	-rrb-	-RRB-	_	_	_
331	replicate	replicate	VBP	_	_	_
332	2	2	CD	_	_	_
333	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
334	O111	o111	NN	_	_	_
335	no.	no.	NN	_	_	_
336	1	1	CD	_	_	_
337	-LRB-	-lrb-	-LRB-	_	_	_
338	strain	strain	NN	_	_	_
339	11109	11109	CD	_	_	_
340	-RRB-	-rrb-	-RRB-	_	_	_
341	replicate	replicate	VBP	_	_	_
342	1	1	CD	_	_	_
343	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
344	O111	o111	NN	_	_	_
345	no.	no.	NN	_	_	_
346	1	1	CD	_	_	_
347	-LRB-	-lrb-	-LRB-	_	_	_
348	strain	strain	NN	_	_	_
349	11109	11109	CD	_	_	_
350	-RRB-	-rrb-	-RRB-	_	_	_
351	replicate	replicate	VBP	_	_	_
352	2	2	CD	_	_	_
353	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
354	O111	o111	NN	_	_	_
355	no.	no.	NN	_	_	_
356	2	2	CD	_	_	_
357	-LRB-	-lrb-	-LRB-	_	_	_
358	strain	strain	NN	_	_	_
359	11128	11128	CD	_	_	_
360	-RRB-	-rrb-	-RRB-	_	_	_
361	replicate	replicate	VBP	_	_	_
362	1	1	CD	_	_	_
363	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
364	O111	o111	NN	_	_	_
365	no.	no.	NN	_	_	_
366	2	2	CD	_	_	_
367	-LRB-	-lrb-	-LRB-	_	_	_
368	strain	strain	NN	_	_	_
369	11128	11128	CD	_	_	_
370	-RRB-	-rrb-	-RRB-	_	_	_
371	replicate	replicate	VBP	_	_	_
372	2	2	CD	_	_	_
373	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
374	O111	o111	NN	_	_	_
375	no.	no.	NN	_	_	_
376	3	3	CD	_	_	_
377	-LRB-	-lrb-	-LRB-	_	_	_
378	strain	strain	NN	_	_	_
379	11619	11619	CD	_	_	_
380	-RRB-	-rrb-	-RRB-	_	_	_
381	replicate	replicate	VBP	_	_	_
382	1	1	CD	_	_	_
383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
384	O111	o111	NN	_	_	_
385	no.	no.	NN	_	_	_
386	3	3	CD	_	_	_
387	-LRB-	-lrb-	-LRB-	_	_	_
388	strain	strain	NN	_	_	_
389	11619	11619	CD	_	_	_
390	-RRB-	-rrb-	-RRB-	_	_	_
391	replicate	replicate	VBP	_	_	_
392	2	2	CD	_	_	_
393	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
394	O111	o111	NN	_	_	_
395	no.	no.	RB	_	_	_
396	4	4	CD	_	_	_
397	-LRB-	-lrb-	-LRB-	_	_	_
398	strain	strain	NN	_	_	_
399	11788	11788	CD	_	_	_
400	-RRB-	-rrb-	-RRB-	_	_	_
401	replicate	replicate	VBP	_	_	_
402	1	1	CD	_	_	_
403	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
404	O111	o111	NN	_	_	_
405	no.	no.	NN	_	_	_
406	4	4	CD	_	_	_
407	-LRB-	-lrb-	-LRB-	_	_	_
408	strain	strain	NN	_	_	_
409	11788	11788	CD	_	_	_
410	-RRB-	-rrb-	-RRB-	_	_	_
411	replicate	replicate	VBP	_	_	_
412	2	2	CD	_	_	_
413	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
414	O111	o111	NN	_	_	_
415	no.	no.	NN	_	_	_
416	5	5	CD	_	_	_
417	-LRB-	-lrb-	-LRB-	_	_	_
418	strain	strain	NN	_	_	_
419	13369	13369	CD	_	_	_
420	-RRB-	-rrb-	-RRB-	_	_	_
421	replicate	replicate	VBP	_	_	_
422	1	1	CD	_	_	_
423	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
424	O111	o111	NN	_	_	_
425	no.	no.	NN	_	_	_
426	5	5	CD	_	_	_
427	-LRB-	-lrb-	-LRB-	_	_	_
428	strain	strain	NN	_	_	_
429	13369	13369	CD	_	_	_
430	-RRB-	-rrb-	-RRB-	_	_	_
431	replicate	replicate	VBP	_	_	_
432	2	2	CD	_	_	_
433	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
434	O111	o111	NN	_	_	_
435	no.	no.	NN	_	_	_
436	6	6	CD	_	_	_
437	-LRB-	-lrb-	-LRB-	_	_	_
438	strain	strain	NN	_	_	_
439	ED71	ed71	NN	_	_	_
440	-RRB-	-rrb-	-RRB-	_	_	_
441	replicate	replicate	VBP	_	_	_
442	1	1	CD	_	_	_
443	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
444	O111	o111	NN	_	_	_
445	no.	no.	NN	_	_	_
446	6	6	CD	_	_	_
447	-LRB-	-lrb-	-LRB-	_	_	_
448	strain	strain	NN	_	_	_
449	ED71	ed71	NN	_	_	_
450	-RRB-	-rrb-	-RRB-	_	_	_
451	replicate	replicate	VBP	_	_	_
452	2	2	CD	_	_	_
453	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
454	O157	o157	NN	_	_	_
455	no.	no.	NN	_	_	_
456	2	2	CD	_	_	_
457	-LRB-	-lrb-	-LRB-	_	_	_
458	strain	strain	NN	_	_	_
459	980938	980938	CD	_	_	_
460	-RRB-	-rrb-	-RRB-	_	_	_
461	replicate	replicate	VBP	_	_	_
462	1	1	CD	_	_	_
463	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
464	O157	o157	NN	_	_	_
465	no.	no.	NN	_	_	_
466	2	2	CD	_	_	_
467	-LRB-	-lrb-	-LRB-	_	_	_
468	strain	strain	NN	_	_	_
469	980938	980938	CD	_	_	_
470	-RRB-	-rrb-	-RRB-	_	_	_
471	replicate	replicate	VBP	_	_	_
472	2	2	CD	_	_	_
473	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
474	O157	o157	NN	_	_	_
475	no.	no.	NN	_	_	_
476	3	3	CD	_	_	_
477	-LRB-	-lrb-	-LRB-	_	_	_
478	strain	strain	NN	_	_	_
479	980706	980706	CD	_	_	_
480	-RRB-	-rrb-	-RRB-	_	_	_
481	replicate	replicate	VBP	_	_	_
482	1	1	CD	_	_	_
483	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
484	O157	o157	NN	_	_	_
485	no.	no.	NN	_	_	_
486	3	3	CD	_	_	_
487	-LRB-	-lrb-	-LRB-	_	_	_
488	strain	strain	NN	_	_	_
489	980706	980706	CD	_	_	_
490	-RRB-	-rrb-	-RRB-	_	_	_
491	replicate	replicate	VBP	_	_	_
492	2	2	CD	_	_	_
493	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
494	O157	o157	NN	_	_	_
495	no.	no.	NN	_	_	_
496	4	4	CD	_	_	_
497	-LRB-	-lrb-	-LRB-	_	_	_
498	strain	strain	NN	_	_	_
499	990281	990281	CD	_	_	_
500	-RRB-	-rrb-	-RRB-	_	_	_
501	replicate	replicate	VBP	_	_	_
502	1	1	CD	_	_	_
503	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
504	O157	o157	NN	_	_	_
505	no.	no.	NN	_	_	_
506	4	4	CD	_	_	_
507	-LRB-	-lrb-	-LRB-	_	_	_
508	strain	strain	NN	_	_	_
509	990281	990281	CD	_	_	_
510	-RRB-	-rrb-	-RRB-	_	_	_
511	replicate	replicate	VBP	_	_	_
512	2	2	CD	_	_	_
513	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
514	O157	o157	NN	_	_	_
515	no.	no.	NN	_	_	_
516	5	5	CD	_	_	_
517	-LRB-	-lrb-	-LRB-	_	_	_
518	strain	strain	NN	_	_	_
519	980551	980551	CD	_	_	_
520	-RRB-	-rrb-	-RRB-	_	_	_
521	replicate	replicate	VBP	_	_	_
522	1	1	CD	_	_	_
523	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
524	O157	o157	NN	_	_	_
525	no.	no.	NN	_	_	_
526	5	5	CD	_	_	_
527	-LRB-	-lrb-	-LRB-	_	_	_
528	strain	strain	NN	_	_	_
529	980551	980551	CD	_	_	_
530	-RRB-	-rrb-	-RRB-	_	_	_
531	replicate	replicate	VBP	_	_	_
532	2	2	CD	_	_	_
533	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
534	O157	o157	NN	_	_	_
535	no.	no.	NN	_	_	_
536	6	6	CD	_	_	_
537	-LRB-	-lrb-	-LRB-	_	_	_
538	strain	strain	NN	_	_	_
539	990570	990570	CD	_	_	_
540	-RRB-	-rrb-	-RRB-	_	_	_
541	replicate	replicate	VBP	_	_	_
542	1	1	CD	_	_	_
543	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
544	O157	o157	NN	_	_	_
545	no.	no.	NN	_	_	_
546	6	6	CD	_	_	_
547	-LRB-	-lrb-	-LRB-	_	_	_
548	strain	strain	NN	_	_	_
549	990570	990570	CD	_	_	_
550	-RRB-	-rrb-	-RRB-	_	_	_
551	replicate	replicate	VBP	_	_	_
552	2	2	CD	_	_	_
553	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
554	O157	o157	NN	_	_	_
555	no.	no.	NN	_	_	_
556	7	7	CD	_	_	_
557	-LRB-	-lrb-	-LRB-	_	_	_
558	strain	strain	NN	_	_	_
559	981456	981456	CD	_	_	_
560	-RRB-	-rrb-	-RRB-	_	_	_
561	replicate	replicate	VBP	_	_	_
562	1	1	CD	_	_	_
563	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
564	O157	o157	NN	_	_	_
565	no.	no.	NN	_	_	_
566	7	7	CD	_	_	_
567	-LRB-	-lrb-	-LRB-	_	_	_
568	strain	strain	NN	_	_	_
569	981456	981456	CD	_	_	_
570	-RRB-	-rrb-	-RRB-	_	_	_
571	replicate	replicate	VBP	_	_	_
572	2	2	CD	_	_	_
573	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
574	O157	o157	NN	_	_	_
575	no.	no.	NN	_	_	_
576	8	8	CD	_	_	_
577	-LRB-	-lrb-	-LRB-	_	_	_
578	strain	strain	NN	_	_	_
579	982243	982243	CD	_	_	_
580	-RRB-	-rrb-	-RRB-	_	_	_
581	replicate	replicate	VBP	_	_	_
582	1	1	CD	_	_	_
583	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
584	O157	o157	NN	_	_	_
585	no.	no.	NN	_	_	_
586	8	8	CD	_	_	_
587	-LRB-	-lrb-	-LRB-	_	_	_
588	strain	strain	NN	_	_	_
589	982243	982243	CD	_	_	_
590	-RRB-	-rrb-	-RRB-	_	_	_
591	replicate	replicate	VBP	_	_	_
592	2	2	CD	_	_	_
593	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
594	O157	o157	NN	_	_	_
595	no.	no.	NN	_	_	_
596	9	9	CD	_	_	_
597	-LRB-	-lrb-	-LRB-	_	_	_
598	strain	strain	NN	_	_	_
599	981795	981795	CD	_	_	_
600	-RRB-	-rrb-	-RRB-	_	_	_
601	replicate	replicate	VBP	_	_	_
602	1	1	CD	_	_	_
603	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
604	O157	o157	NN	_	_	_
605	no.	no.	NN	_	_	_
606	9	9	CD	_	_	_
607	-LRB-	-lrb-	-LRB-	_	_	_
608	strain	strain	NN	_	_	_
609	981795	981795	CD	_	_	_
610	-RRB-	-rrb-	-RRB-	_	_	_
611	replicate	replicate	VBP	_	_	_
612	2	2	CD	_	_	_
613	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
614	O157	o157	NN	_	_	_
615	strain	strain	NN	_	_	_
616	Sakai	Sakai	NNP	_	_	_
617	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
618	O26	o26	NN	_	_	_
619	no.	no.	NN	_	_	_
620	1	1	CD	_	_	_
621	-LRB-	-lrb-	-LRB-	_	_	_
622	strain	strain	NN	_	_	_
623	11044	11044	CD	_	_	_
624	-RRB-	-rrb-	-RRB-	_	_	_
625	replicate	replicate	VBP	_	_	_
626	1	1	CD	_	_	_
627	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
628	O26	o26	NN	_	_	_
629	no.	no.	NN	_	_	_
630	1	1	CD	_	_	_
631	-LRB-	-lrb-	-LRB-	_	_	_
632	strain	strain	NN	_	_	_
633	11044	11044	CD	_	_	_
634	-RRB-	-rrb-	-RRB-	_	_	_
635	replicate	replicate	VBP	_	_	_
636	2	2	CD	_	_	_
637	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
638	O26	o26	NN	_	_	_
639	no.	no.	NN	_	_	_
640	2	2	CD	_	_	_
641	-LRB-	-lrb-	-LRB-	_	_	_
642	strain	strain	NN	_	_	_
643	11368	11368	CD	_	_	_
644	-RRB-	-rrb-	-RRB-	_	_	_
645	replicate	replicate	VBP	_	_	_
646	1	1	CD	_	_	_
647	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
648	O26	o26	NN	_	_	_
649	no.	no.	NN	_	_	_
650	2	2	CD	_	_	_
651	-LRB-	-lrb-	-LRB-	_	_	_
652	strain	strain	NN	_	_	_
653	11368	11368	CD	_	_	_
654	-RRB-	-rrb-	-RRB-	_	_	_
655	replicate	replicate	VBP	_	_	_
656	2	2	CD	_	_	_
657	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
658	O26	o26	NN	_	_	_
659	no.	no.	NN	_	_	_
660	3	3	CD	_	_	_
661	-LRB-	-lrb-	-LRB-	_	_	_
662	strain	strain	NN	_	_	_
663	11656	11656	CD	_	_	_
664	-RRB-	-rrb-	-RRB-	_	_	_
665	replicate	replicate	VBP	_	_	_
666	1	1	CD	_	_	_
667	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
668	O26	o26	NN	_	_	_
669	no.	no.	NN	_	_	_
670	3	3	CD	_	_	_
671	-LRB-	-lrb-	-LRB-	_	_	_
672	strain	strain	NN	_	_	_
673	11656	11656	CD	_	_	_
674	-RRB-	-rrb-	-RRB-	_	_	_
675	replicate	replicate	VBP	_	_	_
676	2	2	CD	_	_	_
677	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
678	O26	o26	NN	_	_	_
679	no.	no.	NN	_	_	_
680	4	4	CD	_	_	_
681	-LRB-	-lrb-	-LRB-	_	_	_
682	strain	strain	NN	_	_	_
683	12719	12719	CD	_	_	_
684	-RRB-	-rrb-	-RRB-	_	_	_
685	replicate	replicate	VBP	_	_	_
686	1	1	CD	_	_	_
687	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
688	O26	o26	NN	_	_	_
689	no.	no.	NN	_	_	_
690	4	4	CD	_	_	_
691	-LRB-	-lrb-	-LRB-	_	_	_
692	strain	strain	NN	_	_	_
693	12719	12719	CD	_	_	_
694	-RRB-	-rrb-	-RRB-	_	_	_
695	replicate	replicate	VBP	_	_	_
696	2	2	CD	_	_	_
697	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
698	O26	o26	NN	_	_	_
699	no.	no.	NN	_	_	_
700	5	5	CD	_	_	_
701	-LRB-	-lrb-	-LRB-	_	_	_
702	strain	strain	NN	_	_	_
703	12929	12929	CD	_	_	_
704	-RRB-	-rrb-	-RRB-	_	_	_
705	replicate	replicate	VBP	_	_	_
706	1	1	CD	_	_	_
707	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
708	O26	o26	NN	_	_	_
709	no.	no.	NN	_	_	_
710	5	5	CD	_	_	_
711	-LRB-	-lrb-	-LRB-	_	_	_
712	strain	strain	NN	_	_	_
713	12929	12929	CD	_	_	_
714	-RRB-	-rrb-	-RRB-	_	_	_
715	replicate	replicate	VBP	_	_	_
716	2	2	CD	_	_	_
717	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
718	O26	o26	NN	_	_	_
719	no.	no.	NN	_	_	_
720	6	6	CD	_	_	_
721	-LRB-	-lrb-	-LRB-	_	_	_
722	strain	strain	NN	_	_	_
723	13065	13065	CD	_	_	_
724	-RRB-	-rrb-	-RRB-	_	_	_
725	replicate	replicate	VBP	_	_	_
726	1	1	CD	_	_	_
727	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
728	O26	o26	NN	_	_	_
729	no.	no.	NN	_	_	_
730	6	6	CD	_	_	_
731	-LRB-	-lrb-	-LRB-	_	_	_
732	strain	strain	NN	_	_	_
733	13065	13065	CD	_	_	_
734	-RRB-	-rrb-	-RRB-	_	_	_
735	replicate	replicate	VBP	_	_	_
736	2	2	CD	_	_	_
737	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
738	O26	o26	NN	_	_	_
739	no.	no.	NN	_	_	_
740	7	7	CD	_	_	_
741	-LRB-	-lrb-	-LRB-	_	_	_
742	strain	strain	NN	_	_	_
743	13247	13247	CD	_	_	_
744	-RRB-	-rrb-	-RRB-	_	_	_
745	replicate	replicate	VBP	_	_	_
746	1	1	CD	_	_	_
747	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
748	O26	o26	NN	_	_	_
749	no.	no.	NN	_	_	_
750	7	7	CD	_	_	_
751	-LRB-	-lrb-	-LRB-	_	_	_
752	strain	strain	NN	_	_	_
753	13247	13247	CD	_	_	_
754	-RRB-	-rrb-	-RRB-	_	_	_
755	replicate	replicate	VBP	_	_	_
756	2	2	CD	_	_	_
757	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
758	O26	o26	NN	_	_	_
759	no.	no.	NN	_	_	_
760	8	8	CD	_	_	_
761	-LRB-	-lrb-	-LRB-	_	_	_
762	strain	strain	NN	_	_	_
763	ED411	ed411	NN	_	_	_
764	-RRB-	-rrb-	-RRB-	_	_	_
765	replicate	replicate	VBP	_	_	_
766	1	1	CD	_	_	_
767	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
768	O26	o26	NN	_	_	_
769	no.	no.	NN	_	_	_
770	8	8	CD	_	_	_
771	-LRB-	-lrb-	-LRB-	_	_	_
772	strain	strain	NN	_	_	_
773	ED411	ed411	NN	_	_	_
774	-RRB-	-rrb-	-RRB-	_	_	_
775	replicate	replicate	VBP	_	_	_
776	2	2	CD	_	_	_
777	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
778	Spots	spot	NNS	_	_	_
779	with	with	IN	_	_	_
780	reference	reference	NN	_	_	_
781	signal	signal	NN	_	_	_
782	intensities	intensity	NNS	_	_	_
783	lower	lower	JJR	_	_	_
784	than	than	IN	_	_	_
785	the	the	DT	_	_	_
786	local	local	JJ	_	_	_
787	background	background	NN	_	_	_
788	-LRB-	-lrb-	-LRB-	_	_	_
789	LBG	lbg	NN	_	_	_
790	-RRB-	-rrb-	-RRB-	_	_	_
791	plus	plus	CC	_	_	_
792	5	5	CD	_	_	_
793	standard	standard	JJ	_	_	_
794	deviations	deviation	NNS	_	_	_
795	or	or	CC	_	_	_
796	with	with	IN	_	_	_
797	some	some	DT	_	_	_
798	spotting	spot	VBG	_	_	_
799	abnormalities	abnormality	NNS	_	_	_
800	were	be	VBD	_	_	_
801	removed	remove	VBN	_	_	_
802	from	from	IN	_	_	_
803	analysis	analysis	NN	_	_	_
804	.	.	.	_	_	_

1	Signal	signal	NN	_	_	_
2	intensities	intensity	NNS	_	_	_
3	of	of	IN	_	_	_
4	other	other	JJ	_	_	_
5	spots	spot	NNS	_	_	_
6	were	be	VBD	_	_	_
7	corrected	correct	VBN	_	_	_
8	by	by	IN	_	_	_
9	subtracting	subtract	VBG	_	_	_
10	the	the	DT	_	_	_
11	LBG	LBG	NNP	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	172mM	172mm	NN	_	_	_
3	SCFA	scfa	NN	_	_	_
4	replicate	replicate	VBP	_	_	_
5	1	1	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	172mM	172mm	NN	_	_	_
8	SCFA	scfa	NN	_	_	_
9	replicate	replicate	VBP	_	_	_
10	2	2	CD	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
12	30mM	30mm	NN	_	_	_
13	SCFA	scfa	NN	_	_	_
14	replicate	replicate	VBP	_	_	_
15	1	1	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	30mM	30mm	NN	_	_	_
18	SCFA	scfa	NN	_	_	_
19	replicate	replicate	VBP	_	_	_
20	2	2	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
22	30mM	30mm	NN	_	_	_
23	SCFA	scfa	NN	_	_	_
24	replicate	replicate	VBP	_	_	_
25	3	3	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	30mM	30mm	NN	_	_	_
28	SCFA	scfa	NN	_	_	_
29	replicate	replicate	VB	_	_	_
30	4	4	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
32	e.	e.	FW	_	_	_
33	coli	coli	FW	_	_	_
34	subset	subset	NN	_	_	_
35	:	:	:	_	_	_
36	enterohemorrhagic	enterohemorrhagic	JJ	_	_	_
37	E.coli	e.coli	JJ	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	enterohemorrhagic	enterohemorrhagic	JJ	_	_	_
40	E.	e.	FW	_	_	_
41	coli	coli	FW	_	_	_
42	_	_	SYM	_	_	_
43	172mM	172mm	NN	_	_	_
44	short	short	JJ	_	_	_
45	chain	chain	NN	_	_	_
46	fatty	fatty	JJ	_	_	_
47	acid	acid	NN	_	_	_
48	mix	mix	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	enterohemorrhagic	enterohemorrhagic	JJ	_	_	_
51	E.	e.	FW	_	_	_
52	coli	coli	FW	_	_	_
53	_	_	SYM	_	_	_
54	30mM	30mM	NNP	_	_	_
55	short	short	JJ	_	_	_
56	chain	chain	NN	_	_	_
57	fatty	fatty	JJ	_	_	_
58	acid	acid	NN	_	_	_
59	mix	mix	NN	_	_	_
60	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
61	Escherichia	escherichia	FW	Organism	_	_
62	coli	coli	FW	Organism	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	Images	image	NNS	_	_	_
65	were	be	VBD	_	_	_
66	quantified	quantify	VBN	_	_	_
67	and	and	CC	_	_	_
68	normalized	normalize	VBN	_	_	_
69	using	use	VBG	_	_	_
70	extraction	extraction	NN	_	_	_
71	protocol	protocol	NN	_	_	_
72	GE2	ge2	NN	_	_	_
73	_	_	NN	_	_	_
74	107	107	CD	_	_	_
75	_	_	SYM	_	_	_
76	Sept09	sept09	NN	_	_	_
77	and	and	CC	_	_	_
78	Agilent	Agilent	NNP	_	_	_
79	Feature	Feature	NNP	_	_	_
80	Extraction	Extraction	NNP	_	_	_
81	Software	Software	NNP	_	_	_
82	-LRB-	-lrb-	-LRB-	_	_	_
83	version	version	NN	_	_	_
84	10.7.3.1	10.7.3.1	CD	_	_	_
85	-RRB-	-rrb-	-RRB-	_	_	_
86	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	N172-1	n172-1	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	N172-2	n172-2	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	N30-1	n30-1	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	N30-2	n30-2	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	N30-3	n30-3	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	N30-4	n30-4	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	overnight	overnight	JJ	_	_	_
15	bacterial	bacterial	JJ	_	_	_
16	culture	culture	NN	_	_	_
17	in	in	IN	_	_	_
18	Luria	Luria	NNP	_	_	_
19	Broth	Broth	NNP	_	_	_
20	at	at	IN	_	_	_
21	37C	37c	NN	_	_	_
22	with	with	IN	_	_	_
23	shaking	shake	VBG	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	overnight	overnight	JJ	_	_	_
26	culture	culture	NN	_	_	_
27	subcultured	subculture	VBN	_	_	_
28	in	in	IN	_	_	_
29	either	either	DT	_	_	_
30	of	of	IN	_	_	_
31	the	the	DT	_	_	_
32	SCFA	scfa	NN	_	_	_
33	mixes	mix	VBZ	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	or	or	CC	_	_	_
36	the	the	DT	_	_	_
37	sodium	sodium	NN	SUPP	_	_
38	chloride	chloride	NN	SUPP	_	_
39	controls	control	NNS	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	at	at	IN	_	_	_
42	37C	37c	NN	_	_	_
43	,	,	,	_	_	_
44	static	static	JJ	_	_	_
45	with	with	IN	_	_	_
46	5	5	CD	_	_	_
47	%	%	NN	_	_	_
48	CO2	co2	NN	_	_	_
49	to	to	TO	_	_	_
50	OD600	od600	NN	_	_	_
51	of	of	IN	_	_	_
52	1	1	CD	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	total	total	JJ	_	_	_
55	RNA	rna	NN	_	_	_
56	extracted	extract	VBN	_	_	_
57	using	use	VBG	_	_	_
58	Trizol	Trizol	NNP	_	_	_
59	Extraction	Extraction	NNP	_	_	_
60	Protocol	Protocol	NNP	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	treated	treat	VBN	_	_	_
63	with	with	IN	_	_	_
64	:	:	:	_	_	_
65	172mM	172mm	NN	_	_	_
66	NaCl	nacl	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	treated	treat	VBN	_	_	_
69	with	with	IN	_	_	_
70	:	:	:	_	_	_
71	172mM	172mm	NN	_	_	_
72	short	short	JJ	_	_	_
73	chain	chain	NN	_	_	_
74	fatty	fatty	JJ	_	_	_
75	acid	acid	NN	_	_	_
76	mix	mix	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	treated	treat	VBN	_	_	_
79	with	with	IN	_	_	_
80	:	:	:	_	_	_
81	30mM	30mm	NN	_	_	_
82	NaCl	nacl	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	treated	treat	VBN	_	_	_
85	with	with	IN	_	_	_
86	:	:	:	_	_	_
87	30mM	30mm	NN	_	_	_
88	short	short	JJ	_	_	_
89	chain	chain	NN	_	_	_
90	fatty	fatty	JJ	_	_	_
91	acid	acid	NN	_	_	_
92	mix	mix	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	Caulobacter	caulobacter	NN	_	_	_
95	crescentus	crescentus	NN	_	_	_
96	and	and	CC	_	_	_
97	derivatives	derivative	NNS	_	_	_
98	were	be	VBD	_	_	_
99	grown	grow	VBN	_	_	_
100	at	at	IN	_	_	_
101	30	30	CD	_	_	_
102	°C	°c	NN	_	_	_
103	in	in	IN	_	_	_
104	PYE	pye	NN	_	_	_
105	-LRB-	-lrb-	-LRB-	_	_	_
106	Peptone	peptone	NN	_	_	_
107	yeast	yeast	NN	SUPP	_	_
108	extract	extract	NN	SUPP	_	_
109	-RRB-	-rrb-	-RRB-	_	_	_
110	or	or	CC	_	_	_
111	LB	lb	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	DNA	dna	NN	_	_	_
114	libraries	library	NNS	_	_	_
115	were	be	VBD	_	_	_
116	prepared	prepare	VBN	_	_	_
117	for	for	IN	_	_	_
118	sequencing	sequencing	NN	_	_	_
119	using	use	VBG	_	_	_
120	standard	standard	JJ	_	_	_
121	Illumina	Illumina	NNP	_	_	_
122	protocols	protocol	NNS	_	_	_
123	by	by	IN	_	_	_
124	FASTERIS	FASTERIS	NNP	_	_	_
125	SA	SA	NNP	_	_	_
126	,	,	,	_	_	_
127	Switzerland	Switzerland	NNP	_	_	_
128	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
129	Escherichia	escherichia	FW	Organism	_	_
130	coli	coli	FW	Organism	_	_
131	MG1655	mg1655	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	Escherichia	escherichia	FW	Organism	_	_
134	coli	coli	FW	Organism	_	_
135	str	str	FW	_	_	_
136	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	For	for	IN	_	_	_
4	REC-Seq	rec-seq	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	restriction	restriction	NN	_	_	_
7	enzyme	enzyme	NN	_	_	_
8	cleavage	cleavage	NN	_	_	_
9	--	--	:	_	_	_
10	sequencing	sequencing	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	1	1	CD	_	_	_
13	ug	ug	NN	_	_	_
14	of	of	IN	_	_	_
15	genomic	genomic	JJ	_	_	_
16	DNA	dna	NN	_	_	_
17	from	from	IN	_	_	_
18	C.	c.	FW	_	_	_
19	crescentus	crescentus	FW	_	_	_
20	NA1000	na1000	NN	_	_	_
21	and	and	CC	_	_	_
22	S.	S.	NNP	_	_	_
23	meliloti	melilotus	NNS	_	_	_
24	Rm2011	rm2011	NN	_	_	_
25	was	be	VBD	_	_	_
26	cleaved	cleave	VBN	_	_	_
27	with	with	IN	_	_	_
28	HinfI	hinfi	NN	_	_	_
29	,	,	,	_	_	_
30	a	a	DT	_	_	_
31	blocked	block	VBN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	5	5	CD	_	_	_
34	'	'	''	_	_	_
35	biotinylated	biotinylate	VBN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	specific	specific	JJ	_	_	_
38	adaptor	adaptor	NN	_	_	_
39	was	be	VBD	_	_	_
40	ligated	ligate	VBN	_	_	_
41	to	to	TO	_	_	_
42	the	the	DT	_	_	_
43	ends	end	NNS	_	_	_
44	and	and	CC	_	_	_
45	the	the	DT	_	_	_
46	ligated	ligate	VBN	_	_	_
47	fragments	fragment	NNS	_	_	_
48	were	be	VBD	_	_	_
49	then	then	RB	_	_	_
50	sheared	shear	VBN	_	_	_
51	to	to	TO	_	_	_
52	an	a	DT	_	_	_
53	average	average	JJ	_	_	_
54	size	size	NN	_	_	_
55	of	of	IN	_	_	_
56	150-400	150-400	CD	_	_	_
57	bp	bp	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	Fasteris	fasteris	NN	_	_	_
60	SA	SA	NNP	_	_	_
61	,	,	,	_	_	_
62	Geneva	Geneva	NNP	_	_	_
63	,	,	,	_	_	_
64	CH	ch	NN	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	.	.	.	_	_	_

1	Illumina	Illumina	NNP	_	_	_
2	adaptors	adaptor	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	ligated	ligate	VBN	_	_	_
6	to	to	TO	_	_	_
7	the	the	DT	_	_	_
8	sheared	sheared	JJ	_	_	_
9	ends	end	NNS	_	_	_
10	followed	follow	VBN	_	_	_
11	by	by	IN	_	_	_
12	deep-sequencing	deep-sequencing	NN	_	_	_
13	using	use	VBG	_	_	_
14	a	a	DT	_	_	_
15	Hi-Seq	hi-seq	JJ	_	_	_
16	Illumina	Illumina	NNP	_	_	_
17	sequencer	sequencer	NN	_	_	_
18	,	,	,	_	_	_
19	and	and	CC	_	_	_
20	the	the	DT	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	50	50	CD	_	_	_
23	bp	bp	NN	_	_	_
24	single	single	JJ	_	_	_
25	end	end	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	reads	read	VBZ	_	_	_
28	were	be	VBD	_	_	_
29	quality	quality	NN	_	_	_
30	controlled	control	VBN	_	_	_
31	with	with	IN	_	_	_
32	FastQC	fastqc	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	http	http	NN	_	_	_
35	:	:	:	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	genome	genome	NN	_	_	_
38	build	build	VB	_	_	_
39	:	:	:	_	_	_
40	NC	NC	NNP	_	_	_
41	_	_	NNP	_	_	_
42	000913.3	000913.3	CD	_	_	_
43	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
44	genotype	genotype	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	GHA507	gha507	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	Library	Library	NNP	_	_	_
49	strategy	strategy	NN	_	_	_
50	:	:	:	_	_	_
51	REC-Seq	rec-seq	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
53	OTHER	other	JJ	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	strain	strain	NN	_	_	_
56	:	:	:	_	_	_
57	K12	k12	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	Supplementary	supplementary	JJ	_	_	_
60	_	_	NN	_	_	_
61	files	file	NNS	_	_	_
62	_	_	IN	_	_	_
63	format	format	NN	_	_	_
64	_	_	NN	_	_	_
65	and	and	CC	_	_	_
66	_	_	NN	_	_	_
67	content	content	NN	_	_	_
68	:	:	:	_	_	_
69	tab	tab	NN	_	_	_
70	delimited	delimit	VBD	_	_	_
71	text	text	NN	_	_	_
72	files	file	NNS	_	_	_
73	,	,	,	_	_	_
74	with	with	IN	_	_	_
75	feature	feature	NN	_	_	_
76	annotation	annotation	NN	_	_	_
77	,	,	,	_	_	_
78	REC	rec	NN	_	_	_
79	_	_	CD	_	_	_
80	seq	seq	NN	_	_	_
81	score	score	NN	_	_	_
82	,	,	,	_	_	_
83	gene	gene	NN	_	_	_
84	name	name	NN	_	_	_
85	and	and	CC	_	_	_
86	description	description	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	To	to	TO	_	_	_
89	remove	remove	VB	_	_	_
90	contaminating	contaminate	VBG	_	_	_
91	sequences	sequence	NNS	_	_	_
92	,	,	,	_	_	_
93	the	the	DT	_	_	_
94	reads	read	VBZ	_	_	_
95	were	be	VBD	_	_	_
96	split	split	VBN	_	_	_
97	according	accord	VBG	_	_	_
98	to	to	TO	_	_	_
99	the	the	DT	_	_	_
100	HinfI	hinfi	NN	_	_	_
101	consensus	consensus	NN	_	_	_
102	motif	motif	NN	_	_	_
103	-LRB-	-lrb-	-LRB-	_	_	_
104	5	5	CD	_	_	_
105	'	'	''	_	_	_
106	-	-	:	_	_	_
107	G	g	NN	_	_	_
108	^	^	SYM	_	_	_
109	ANTC-3	antc-3	NN	_	_	_
110	'	'	''	_	_	_
111	-RRB-	-rrb-	-RRB-	_	_	_
112	considered	consider	VBN	_	_	_
113	as	as	IN	_	_	_
114	a	a	DT	_	_	_
115	barcode	barcode	NN	_	_	_
116	sequence	sequence	NN	_	_	_
117	using	use	VBG	_	_	_
118	fastx	fastx	NN	_	_	_
119	_	_	NN	_	_	_
120	toolkit	toolkit	NN	_	_	_
121	-LRB-	-lrb-	-LRB-	_	_	_
122	http	http	NN	_	_	_
123	:	:	:	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	cy	cy	NN	_	_	_
126	_	_	CD	_	_	_
127	a4	a4	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	cy	cy	NN	_	_	_
130	_	_	CD	_	_	_
131	b4	b4	NN	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	cyc1	cyc1	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	cyc2	cyc2	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	cyc3	cyc3	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	cyc4	cyc4	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	cyd1	cyd1	NN	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	cyd2	cyd2	NN	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	cyd3	cyd3	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	cyd4	cyd4	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	dnaC	dnac	NN	GEN	_	_
150	genomic	genomic	JJ	_	_	_
151	DNA	dna	NN	_	_	_
152	,	,	,	_	_	_
153	Sau3A	sau3a	NN	_	_	_
154	,	,	,	_	_	_
155	2	2	CD	_	_	_
156	ug	ug	NN	_	_	_
157	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
158	Escherichia	escherichia	FW	Organism	_	_
159	coli	coli	FW	Organism	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	reference	reference	NN	_	_	_
162	0	0	CD	_	_	_
163	'	'	''	_	_	_
164	,	,	,	_	_	_
165	min	min	NN	_	_	_
166	+.2	+.2	CD	_	_	_
167	%	%	NN	_	_	_
168	glu	glu	NN	_	_	_
169	,	,	,	_	_	_
170	25	25	CD	_	_	_
171	ug	ug	NN	_	_	_
172	RNA	rna	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	tnaA2trpA46PR9	tnaa2trpa46pr9	NN	_	_	_
175	vs.	vs.	CC	_	_	_
176	tnaA2	tnaa2	NN	_	_	_
177	,	,	,	_	_	_
178	W3110	w3110	NN	_	_	_
179	min	min	NN	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	tnaA2trpA46PR9	tnaa2trpa46pr9	NN	_	_	_
182	,	,	,	_	_	_
183	W3110	w3110	NN	_	_	_
184	min	min	NN	_	_	_
185	,	,	,	_	_	_
186	30	30	CD	_	_	_
187	ug	ug	NN	_	_	_
188	total	total	JJ	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	tnaA2trpR2	tnaa2trpr2	NN	_	_	_
191	vs.	vs.	CC	_	_	_
192	tnaA2	tnaa2	NN	_	_	_
193	,	,	,	_	_	_
194	W3110	w3110	NN	_	_	_
195	min	min	NN	_	_	_
196	+	+	CC	_	_	_
197	Trp	trp	NN	_	_	_
198	50ug	50ug	JJ	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	tnaA2trpR2	tnaa2trpr2	NN	_	_	_
201	,	,	,	_	_	_
202	W3110	w3110	NN	_	_	_
203	min	min	NN	_	_	_
204	+	+	CC	_	_	_
205	Trp	trp	NN	_	_	_
206	50ug	50ug	JJ	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	tnaA2	tnaa2	NN	_	_	_
209	,	,	,	_	_	_
210	W3110	w3110	NN	_	_	_
211	min	min	NN	_	_	_
212	,30	,30	CD	_	_	_
213	ug	ug	NN	_	_	_
214	total	total	JJ	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	tnaA2	tnaa2	NN	_	_	_
217	,	,	,	_	_	_
218	W3110	w3110	NN	_	_	_
219	minimal	minimal	JJ	_	_	_
220	+	+	CC	_	_	_
221	Trp	trp	NN	_	_	_
222	50ug	50ug	JJ	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	tnaA2	tnaa2	NN	_	_	_
225	,	,	,	_	_	_
226	W3110	w3110	NN	_	_	_
227	min	min	NN	_	_	_
228	+	+	CC	_	_	_
229	Trp	trp	NN	_	_	_
230	50ug	50ug	JJ	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	trpEA2trpR2	trpea2trpr2	NN	_	_	_
233	vs.	vs.	CC	_	_	_
234	trpEA2	trpea2	NN	_	_	_
235	,	,	,	_	_	_
236	W3110	w3110	NN	_	_	_
237	min	min	NN	_	_	_
238	+	+	CC	_	_	_
239	Trp	trp	NN	_	_	_
240	50ug	50ug	JJ	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	trpEA2trpR2	trpea2trpr2	NN	_	_	_
243	,	,	,	_	_	_
244	W3110	w3110	NN	_	_	_
245	min	min	NN	_	_	_
246	+	+	CC	_	_	_
247	Trp	trp	NN	_	_	_
248	50ug	50ug	JJ	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	trpEA2	trpea2	NN	_	_	_
251	,	,	,	_	_	_
252	W3110	w3110	NN	_	_	_
253	min	min	NN	_	_	_
254	+	+	CC	_	_	_
255	Trp	trp	NN	_	_	_
256	50ug	50ug	JJ	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	trpR2	trpr2	NN	_	_	_
259	+50	+50	CD	_	_	_
260	ug	ug	NN	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
262	trpR2tnaA2	trpr2tnaa2	NN	_	_	_
263	,	,	,	_	_	_
264	W3110	w3110	NN	_	_	_
265	minimal	minimal	JJ	_	_	_
266	+	+	CC	_	_	_
267	Trp	trp	NN	_	_	_
268	50ug	50ug	JJ	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	trpR2tnaA2	trpr2tnaa2	NN	_	_	_
271	,	,	,	_	_	_
272	W3110	w3110	NN	_	_	_
273	min	min	NN	_	_	_
274	+	+	CC	_	_	_
275	Trp	trp	NN	_	_	_
276	50ug	50ug	JJ	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	trpR2	trpr2	NN	_	_	_
279	+	+	CC	_	_	_
280	trp	trp	NN	_	_	_
281	vs.	vs.	NN	_	_	_
282	-	-	:	_	_	_
283	trp	trp	NN	_	_	_
284	,	,	,	_	_	_
285	min	min	NN	_	_	_
286	+.2	+.2	CD	_	_	_
287	%	%	NN	_	_	_
288	glucose	glucose	NN	SUPP	_	_
289	,	,	,	_	_	_
290	W3110	w3110	NN	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	trpR2	trpr2	NN	_	_	_
293	vs.	vs.	CC	_	_	_
294	wt	wt	JJ	_	_	_
295	,	,	,	_	_	_
296	min	min	NN	_	_	_
297	+.2	+.2	CD	_	_	_
298	%	%	NN	_	_	_
299	glucose	glucose	NN	SUPP	_	_
300	,	,	,	_	_	_
301	W3110	w3110	NN	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
303	W3110	w3110	NN	_	_	_
304	trpR2	trpr2	NN	_	_	_
305	,	,	,	_	_	_
306	min	min	NN	_	_	_
307	+.2	+.2	CD	_	_	_
308	%	%	NN	_	_	_
309	glucose	glucose	NN	SUPP	_	_
310	,	,	,	_	_	_
311	30	30	CD	_	_	_
312	ug	ug	NN	_	_	_
313	RNA	rna	NN	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	W3110	w3110	NN	_	_	_
316	trpR2	trpr2	NN	_	_	_
317	-	-	:	_	_	_
318	trp	trp	NN	_	_	_
319	,	,	,	_	_	_
320	30	30	CD	_	_	_
321	ug	ug	NN	_	_	_
322	total	total	JJ	_	_	_
323	RNA	rna	NN	_	_	_
324	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
325	W3110	w3110	NN	_	_	_
326	trpR2	trpr2	NN	_	_	_
327	+	+	CC	_	_	_
328	trp	trp	NN	_	_	_
329	,	,	,	_	_	_
330	30	30	CD	_	_	_
331	ug	ug	NN	_	_	_
332	total	total	JJ	_	_	_
333	RNA	rna	NN	_	_	_
334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
335	W3110	w3110	NN	_	_	_
336	wt	wt	JJ	_	_	_
337	,	,	,	_	_	_
338	min	min	NN	_	_	_
339	+.2	+.2	CD	_	_	_
340	%	%	NN	_	_	_
341	glucose	glucose	NN	SUPP	_	_
342	,	,	,	_	_	_
343	30	30	CD	_	_	_
344	ug	ug	NN	_	_	_
345	RNA	rna	NN	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	W3110	w3110	NN	_	_	_
348	wt-trp	wt-trp	NN	_	_	_
349	,	,	,	_	_	_
350	30	30	CD	_	_	_
351	ug	ug	NN	_	_	_
352	total	total	JJ	_	_	_
353	RNA	rna	NN	_	_	_
354	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
355	W3110	w3110	NN	_	_	_
356	wt	wt	JJ	_	_	_
357	+	+	CC	_	_	_
358	trp	trp	NN	_	_	_
359	,	,	,	_	_	_
360	30	30	CD	_	_	_
361	ug	ug	NN	_	_	_
362	total	total	JJ	_	_	_
363	RNA	rna	NN	_	_	_
364	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
365	wt	wt	JJ	_	_	_
366	+50	+50	CD	_	_	_
367	ug	ug	NN	_	_	_
368	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
369	wt	wt	JJ	_	_	_
370	+	+	CC	_	_	_
371	trp	trp	NN	_	_	_
372	vs.	vs.	NN	_	_	_
373	-	-	:	_	_	_
374	trp	trp	NN	_	_	_
375	,	,	,	_	_	_
376	min	min	NN	_	_	_
377	+.2	+.2	CD	_	_	_
378	%	%	NN	_	_	_
379	glucose	glucose	NN	SUPP	_	_
380	,	,	,	_	_	_
381	W3110	w3110	NN	_	_	_
382	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
383	At	at	IN	_	_	_
384	each	each	DT	_	_	_
385	time	time	NN	_	_	_
386	point	point	NN	_	_	_
387	,	,	,	_	_	_
388	15	15	CD	_	_	_
389	ml	ml	NN	_	_	_
390	of	of	IN	_	_	_
391	each	each	DT	_	_	_
392	culture	culture	NN	_	_	_
393	was	be	VBD	_	_	_
394	mixed	mix	VBN	_	_	_
395	with	with	IN	_	_	_
396	30	30	CD	_	_	_
397	ml	ml	NN	_	_	_
398	of	of	IN	_	_	_
399	RNAprotect	rnaprotect	NN	_	_	_
400	Bacteria	bacterium	NNS	_	_	_
401	Reagent	reagent	NN	_	_	_
402	-LRB-	-lrb-	-LRB-	_	_	_
403	Qiagen	qiagen	NN	_	_	_
404	-RRB-	-rrb-	-RRB-	_	_	_
405	,	,	,	_	_	_
406	vortexed	vortex	VBN	_	_	_
407	for	for	IN	_	_	_
408	5s	5	NNS	_	_	_
409	,	,	,	_	_	_
410	incubated	incubate	VBN	_	_	_
411	for	for	IN	_	_	_
412	5	5	CD	_	_	_
413	min	min	NN	_	_	_
414	at	at	IN	_	_	_
415	room	room	NN	_	_	_
416	temperature	temperature	NN	_	_	_
417	,	,	,	_	_	_
418	and	and	CC	_	_	_
419	centrifuged	centrifuge	VBN	_	_	_
420	for	for	IN	_	_	_
421	10	10	CD	_	_	_
422	min	min	NN	_	_	_
423	at	at	IN	_	_	_
424	5000g	5000g	CD	_	_	_
425	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	pellet	pellet	NN	_	_	_
3	was	be	VBD	_	_	_
4	processed	process	VBN	_	_	_
5	using	use	VBG	_	_	_
6	a	a	DT	_	_	_
7	Qiagen	Qiagen	NNP	_	_	_
8	RNeasy	RNeasy	NNP	_	_	_
9	Midi	Midi	NNP	_	_	_
10	kit	kit	NN	_	_	_
11	with	with	IN	_	_	_
12	on-column	on-column	JJ	_	_	_
13	DNase	dnase	NN	_	_	_
14	digestion	digestion	NN	_	_	_
15	using	use	VBG	_	_	_
16	Qiagen	Qiagen	NNP	_	_	_
17	DNase	dnase	NN	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	final	final	JJ	_	_	_
3	elution	elution	NN	_	_	_
4	of	of	IN	_	_	_
5	RNA	rna	NN	_	_	_
6	from	from	IN	_	_	_
7	the	the	DT	_	_	_
8	column	column	NN	_	_	_
9	was	be	VBD	_	_	_
10	with	with	IN	_	_	_
11	160	160	CD	_	_	_
12	μl	μl	NN	_	_	_
13	RNase-free	rnase-free	NN	_	_	_
14	water	water	NN	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	At	at	IN	_	_	_
3	OD630nm	od630nm	NN	_	_	_
4	=	=	JJ	_	_	_
5	0.1	0.1	CD	_	_	_
6	,	,	,	_	_	_
7	the	the	DT	_	_	_
8	cultures	culture	NNS	_	_	_
9	were	be	VBD	_	_	_
10	filtered	filter	VBN	_	_	_
11	through	through	IN	_	_	_
12	47-mm	47-mm	JJ	_	_	_
13	diameter	diameter	NN	_	_	_
14	polycarbonate	polycarbonate	JJ	_	_	_
15	membrane	membrane	NN	_	_	_
16	filter	filter	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	0.4	0.4	CD	_	_	_
19	µm	µm	NN	_	_	_
20	pore	pore	NN	_	_	_
21	size	size	NN	_	_	_
22	;	;	:	_	_	_
23	Millipore	Millipore	NNP	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	,	,	,	_	_	_
26	washed	wash	VBN	_	_	_
27	with	with	IN	_	_	_
28	the	the	DT	_	_	_
29	same	same	JJ	_	_	_
30	medium	medium	NN	_	_	_
31	without	without	IN	_	_	_
32	hypoxanthine	hypoxanthine	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	Hx	hx	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	,	,	,	_	_	_
37	and	and	CC	_	_	_
38	then	then	RB	_	_	_
39	resuspended	resuspend	VBD	_	_	_
40	at	at	IN	_	_	_
41	the	the	DT	_	_	_
42	same	same	JJ	_	_	_
43	cell	cell	NN	_	_	_
44	density	density	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	OD630	od630	NN	_	_	_
47	=	=	JJ	_	_	_
48	0.1	0.1	CD	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	in	in	IN	_	_	_
51	the	the	DT	_	_	_
52	medium	medium	NN	_	_	_
53	without	without	IN	_	_	_
54	Hx	hx	NN	_	_	_
55	,	,	,	_	_	_
56	and	and	CC	_	_	_
57	growth	growth	NN	_	_	_
58	was	be	VBD	_	_	_
59	continued	continue	VBN	_	_	_
60	as	as	IN	_	_	_
61	before	before	RB	_	_	_
62	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	OD630	od630	NN	_	_	_
3	was	be	VBD	_	_	_
4	followed	follow	VBN	_	_	_
5	closely	closely	RB	_	_	_
6	during	during	IN	_	_	_
7	the	the	DT	_	_	_
8	next	next	JJ	_	_	_
9	two	two	CD	_	_	_
10	hours	hour	NNS	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	cells	cell	NNS	_	_	_
15	were	be	VBD	_	_	_
16	periodically	periodically	RB	_	_	_
17	diluted	dilute	VBN	_	_	_
18	with	with	IN	_	_	_
19	fresh	fresh	JJ	_	_	_
20	,	,	,	_	_	_
21	pre-warmed	pre-warmed	JJ	_	_	_
22	medium	medium	NN	_	_	_
23	without	without	IN	_	_	_
24	Hx	hx	NN	_	_	_
25	to	to	TO	_	_	_
26	keep	keep	VB	_	_	_
27	OD	od	NN	_	_	_
28	between	between	IN	_	_	_
29	values	value	NNS	_	_	_
30	0.1	0.1	CD	_	_	_
31	and	and	CC	_	_	_
32	0.3	0.3	CD	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	low-dilution	low-dilution	JJ	_	_	_
35	protocol	protocol	NN	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	taken	take	VBN	_	_	_
4	for	for	IN	_	_	_
5	microarray	microarray	NN	_	_	_
6	analysis	analysis	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	see	see	VB	_	_	_
9	below	below	IN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	at	at	IN	_	_	_
12	0	0	CD	_	_	_
13	,	,	,	_	_	_
14	15	15	CD	_	_	_
15	,	,	,	_	_	_
16	30	30	CD	_	_	_
17	,	,	,	_	_	_
18	45	45	CD	_	_	_
19	,	,	,	_	_	_
20	60	60	CD	_	_	_
21	and	and	CC	_	_	_
22	120	120	CD	_	_	_
23	minutes	minute	NNS	_	_	_
24	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	a	a	DT	_	_	_
3	parallel	parallel	JJ	_	_	_
4	procedure	procedure	NN	_	_	_
5	,	,	,	_	_	_
6	the	the	DT	_	_	_
7	optA1	opta1	NN	_	_	_
8	gpt	gpt	NN	GEN	_	_
9	double	double	JJ	_	_	_
10	mutant	mutant	NN	_	_	_
11	was	be	VBD	_	_	_
12	also	also	RB	_	_	_
13	followed	follow	VBN	_	_	_
14	in	in	IN	_	_	_
15	a	a	DT	_	_	_
16	near-identical	near-identical	JJ	_	_	_
17	manner	manner	NN	_	_	_
18	using	use	VBG	_	_	_
19	a	a	DT	_	_	_
20	more	more	RBR	_	_	_
21	highly	highly	RB	_	_	_
22	diluted	dilute	VBN	_	_	_
23	culture	culture	NN	_	_	_
24	over	over	IN	_	_	_
25	a	a	DT	_	_	_
26	six-hour	six-hour	JJ	_	_	_
27	incubation	incubation	NN	_	_	_
28	period	period	NN	_	_	_
29	in	in	IN	_	_	_
30	the	the	DT	_	_	_
31	absence	absence	NN	_	_	_
32	of	of	IN	_	_	_
33	hypoxanthine	hypoxanthine	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	high-dilution	high-dilution	JJ	_	_	_
36	protocol	protocol	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	effectiveness	effectiveness	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	latter	latter	JJ	_	_	_
6	treatment	treatment	NN	_	_	_
7	was	be	VBD	_	_	_
8	followed	follow	VBN	_	_	_
9	microscopically	microscopically	RB	_	_	_
10	by	by	IN	_	_	_
11	observing	observe	VBG	_	_	_
12	the	the	DT	_	_	_
13	extensive	extensive	JJ	_	_	_
14	cellular	cellular	JJ	_	_	_
15	filamentation	filamentation	NN	_	_	_
16	associated	associate	VBN	_	_	_
17	with	with	IN	_	_	_
18	dGTP	dgtp	NN	_	_	_
19	starvation	starvation	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	control	control	NN	_	_	_
3	strain	strain	NN	_	_	_
4	w	w	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	control	control	NN	_	_	_
7	strain	strain	NN	_	_	_
8	with	with	IN	_	_	_
9	hypoxanthine	hypoxanthine	NN	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Data	Data	NNP	_	_	_
12	was	be	VBD	_	_	_
13	obtained	obtain	VBN	_	_	_
14	using	use	VBG	_	_	_
15	the	the	DT	_	_	_
16	GeneChip	GeneChip	NNP	_	_	_
17	®	®	NNP	_	_	_
18	Command	command	NN	_	_	_
19	Console	console	NN	_	_	_
20	and	and	CC	_	_	_
21	Expression	expression	NN	_	_	_
22	Console	Console	NNP	_	_	_
23	Software	Software	NNP	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	AGCC	AGCC	NNP	_	_	_
26	;	;	:	_	_	_
27	Version	Version	NNP	_	_	_
28	3.2	3.2	CD	_	_	_
29	and	and	CC	_	_	_
30	Expression	expression	NN	_	_	_
31	Console	console	NN	_	_	_
32	;	;	:	_	_	_
33	Version	Version	NNP	_	_	_
34	1.2	1.2	CD	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	using	use	VBG	_	_	_
37	the	the	DT	_	_	_
38	MAS5	mas5	NN	_	_	_
39	algorithm	algorithm	NN	_	_	_
40	to	to	TO	_	_	_
41	generate	generate	VB	_	_	_
42	.	.	.	_	_	_

1	CHP	chp	NN	_	_	_
2	files	file	NNS	_	_	_
3	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	gpt	gpt	NN	GEN	_	_
4	_	_	NN	_	_	_
5	0	0	CD	_	_	_
6	_	_	NN	_	_	_
7	Hx	hx	NN	_	_	_
8	Rep1	rep1	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	gpt	gpt	NN	GEN	_	_
11	_	_	NN	_	_	_
12	0	0	CD	_	_	_
13	_	_	SYM	_	_	_
14	Hx	hx	FW	_	_	_
15	Rep2	rep2	JJ	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	gpt	gpt	NN	GEN	_	_
18	_	_	NN	_	_	_
19	0	0	CD	_	_	_
20	_	_	SYM	_	_	_
21	Hx	hx	FW	_	_	_
22	Rep3	rep3	JJ	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	gpt	gpt	NN	GEN	_	_
25	_	_	NN	_	_	_
26	120	120	CD	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Low	low	JJ	_	_	_
29	Dilution	dilution	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	Rep1	rep1	JJ	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	gpt	gpt	NN	GEN	_	_
34	_	_	NN	_	_	_
35	120	120	CD	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	Low	low	JJ	_	_	_
38	Dilution	dilution	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	Rep2	rep2	JJ	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	gpt	gpt	NN	GEN	_	_
43	_	_	NN	_	_	_
44	120	120	CD	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	Low	low	JJ	_	_	_
47	Dilution	dilution	NN	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	Rep3	rep3	JJ	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	gpt	gpt	NN	GEN	_	_
52	_	_	CD	_	_	_
53	15	15	CD	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	Low	low	JJ	_	_	_
56	Dilution	dilution	NN	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	Rep1	rep1	JJ	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	gpt	gpt	NN	GEN	_	_
61	_	_	CD	_	_	_
62	15	15	CD	_	_	_
63	-LRB-	-lrb-	-LRB-	_	_	_
64	Low	low	JJ	_	_	_
65	Dilution	dilution	NN	_	_	_
66	-RRB-	-rrb-	-RRB-	_	_	_
67	Rep2	rep2	JJ	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	gpt	gpt	NN	GEN	_	_
70	_	_	CD	_	_	_
71	15	15	CD	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	Low	low	JJ	_	_	_
74	Dilution	dilution	NN	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	Rep3	rep3	JJ	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	gpt	gpt	NN	GEN	_	_
79	_	_	CD	_	_	_
80	30	30	CD	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	Low	low	JJ	_	_	_
83	Dilution	dilution	NN	_	_	_
84	-RRB-	-rrb-	-RRB-	_	_	_
85	Rep1	rep1	JJ	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	gpt	gpt	NN	GEN	_	_
88	_	_	CD	_	_	_
89	30	30	CD	_	_	_
90	-LRB-	-lrb-	-LRB-	_	_	_
91	Low	low	JJ	_	_	_
92	Dilution	dilution	NN	_	_	_
93	-RRB-	-rrb-	-RRB-	_	_	_
94	Rep2	rep2	JJ	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	gpt	gpt	NN	GEN	_	_
97	_	_	CD	_	_	_
98	30	30	CD	_	_	_
99	-LRB-	-lrb-	-LRB-	_	_	_
100	Low	low	JJ	_	_	_
101	Dilution	dilution	NN	_	_	_
102	-RRB-	-rrb-	-RRB-	_	_	_
103	Rep3	rep3	JJ	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	gpt	gpt	NN	GEN	_	_
106	_	_	CD	_	_	_
107	45	45	CD	_	_	_
108	-LRB-	-lrb-	-LRB-	_	_	_
109	Low	low	JJ	_	_	_
110	Dilution	dilution	NN	_	_	_
111	-RRB-	-rrb-	-RRB-	_	_	_
112	Rep1	rep1	JJ	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	gpt	gpt	NN	GEN	_	_
115	_	_	CD	_	_	_
116	45	45	CD	_	_	_
117	-LRB-	-lrb-	-LRB-	_	_	_
118	Low	low	JJ	_	_	_
119	Dilution	dilution	NN	_	_	_
120	-RRB-	-rrb-	-RRB-	_	_	_
121	Rep2	rep2	JJ	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	gpt	gpt	NN	GEN	_	_
124	_	_	CD	_	_	_
125	45	45	CD	_	_	_
126	-LRB-	-lrb-	-LRB-	_	_	_
127	Low	low	JJ	_	_	_
128	Dilution	dilution	NN	_	_	_
129	-RRB-	-rrb-	-RRB-	_	_	_
130	Rep3	rep3	JJ	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	gpt	gpt	NN	GEN	_	_
133	_	_	CD	_	_	_
134	60	60	CD	_	_	_
135	-LRB-	-lrb-	-LRB-	_	_	_
136	Low	low	JJ	_	_	_
137	Dilution	dilution	NN	_	_	_
138	-RRB-	-rrb-	-RRB-	_	_	_
139	Rep1	rep1	JJ	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	gpt	gpt	NN	GEN	_	_
142	_	_	CD	_	_	_
143	60	60	CD	_	_	_
144	-LRB-	-lrb-	-LRB-	_	_	_
145	Low	low	JJ	_	_	_
146	Dilution	dilution	NN	_	_	_
147	-RRB-	-rrb-	-RRB-	_	_	_
148	Rep2	rep2	JJ	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	gpt	gpt	NN	GEN	_	_
151	_	_	CD	_	_	_
152	60	60	CD	_	_	_
153	-LRB-	-lrb-	-LRB-	_	_	_
154	Low	low	JJ	_	_	_
155	Dilution	dilution	NN	_	_	_
156	-RRB-	-rrb-	-RRB-	_	_	_
157	Rep3	rep3	JJ	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	gpt	gpt	NN	GEN	_	_
160	strain	strain	NN	_	_	_
161	w	w	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	gpt	gpt	NN	GEN	_	_
164	strain	strain	NN	_	_	_
165	with	with	IN	_	_	_
166	hypoxanthine	hypoxanthine	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	optA1	opta1	NN	_	_	_
169	_	_	NN	_	_	_
170	0	0	CD	_	_	_
171	_	_	NN	_	_	_
172	Hx	hx	NN	_	_	_
173	Rep1	rep1	NN	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	optA1	opta1	NN	_	_	_
176	_	_	NN	_	_	_
177	0	0	CD	_	_	_
178	_	_	SYM	_	_	_
179	Hx	hx	FW	_	_	_
180	Rep2	rep2	JJ	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	optA1	opta1	NN	_	_	_
183	_	_	NN	_	_	_
184	0	0	CD	_	_	_
185	_	_	SYM	_	_	_
186	Hx	hx	FW	_	_	_
187	Rep3	rep3	JJ	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	optA1	opta1	NN	_	_	_
190	_	_	NN	_	_	_
191	120	120	CD	_	_	_
192	-LRB-	-lrb-	-LRB-	_	_	_
193	Low	low	JJ	_	_	_
194	Dilution	dilution	NN	_	_	_
195	-RRB-	-rrb-	-RRB-	_	_	_
196	Rep1	rep1	JJ	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	optA1	opta1	NN	_	_	_
199	_	_	NN	_	_	_
200	120	120	CD	_	_	_
201	-LRB-	-lrb-	-LRB-	_	_	_
202	Low	low	JJ	_	_	_
203	Dilution	dilution	NN	_	_	_
204	-RRB-	-rrb-	-RRB-	_	_	_
205	Rep2	rep2	JJ	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	optA1	opta1	NN	_	_	_
208	_	_	NN	_	_	_
209	120	120	CD	_	_	_
210	-LRB-	-lrb-	-LRB-	_	_	_
211	Low	low	JJ	_	_	_
212	Dilution	dilution	NN	_	_	_
213	-RRB-	-rrb-	-RRB-	_	_	_
214	Rep3	rep3	JJ	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	optA1	opta1	NN	_	_	_
217	_	_	CD	_	_	_
218	15	15	CD	_	_	_
219	-LRB-	-lrb-	-LRB-	_	_	_
220	Low	low	JJ	_	_	_
221	Dilution	dilution	NN	_	_	_
222	-RRB-	-rrb-	-RRB-	_	_	_
223	Rep1	rep1	JJ	_	_	_
224	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
225	optA1	opta1	NN	_	_	_
226	_	_	CD	_	_	_
227	15	15	CD	_	_	_
228	-LRB-	-lrb-	-LRB-	_	_	_
229	Low	low	JJ	_	_	_
230	Dilution	dilution	NN	_	_	_
231	-RRB-	-rrb-	-RRB-	_	_	_
232	Rep2	rep2	JJ	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	optA1	opta1	NN	_	_	_
235	_	_	CD	_	_	_
236	15	15	CD	_	_	_
237	-LRB-	-lrb-	-LRB-	_	_	_
238	Low	low	JJ	_	_	_
239	Dilution	dilution	NN	_	_	_
240	-RRB-	-rrb-	-RRB-	_	_	_
241	Rep3	rep3	JJ	_	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
243	optA1	opta1	NN	_	_	_
244	_	_	CD	_	_	_
245	30	30	CD	_	_	_
246	-LRB-	-lrb-	-LRB-	_	_	_
247	Low	low	JJ	_	_	_
248	Dilution	dilution	NN	_	_	_
249	-RRB-	-rrb-	-RRB-	_	_	_
250	Rep1	rep1	JJ	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	optA1	opta1	NN	_	_	_
253	_	_	CD	_	_	_
254	30	30	CD	_	_	_
255	-LRB-	-lrb-	-LRB-	_	_	_
256	Low	low	JJ	_	_	_
257	Dilution	dilution	NN	_	_	_
258	-RRB-	-rrb-	-RRB-	_	_	_
259	Rep2	rep2	JJ	_	_	_
260	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
261	optA1	opta1	NN	_	_	_
262	_	_	CD	_	_	_
263	30	30	CD	_	_	_
264	-LRB-	-lrb-	-LRB-	_	_	_
265	Low	low	JJ	_	_	_
266	Dilution	dilution	NN	_	_	_
267	-RRB-	-rrb-	-RRB-	_	_	_
268	Rep3	rep3	JJ	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	optA1	opta1	NN	_	_	_
271	_	_	CD	_	_	_
272	45	45	CD	_	_	_
273	-LRB-	-lrb-	-LRB-	_	_	_
274	Low	low	JJ	_	_	_
275	Dilution	dilution	NN	_	_	_
276	-RRB-	-rrb-	-RRB-	_	_	_
277	Rep1	rep1	JJ	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
279	optA1	opta1	NN	_	_	_
280	_	_	CD	_	_	_
281	45	45	CD	_	_	_
282	-LRB-	-lrb-	-LRB-	_	_	_
283	Low	low	JJ	_	_	_
284	Dilution	dilution	NN	_	_	_
285	-RRB-	-rrb-	-RRB-	_	_	_
286	Rep2	rep2	JJ	_	_	_
287	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
288	optA1	opta1	NN	_	_	_
289	_	_	CD	_	_	_
290	45	45	CD	_	_	_
291	-LRB-	-lrb-	-LRB-	_	_	_
292	Low	low	JJ	_	_	_
293	Dilution	dilution	NN	_	_	_
294	-RRB-	-rrb-	-RRB-	_	_	_
295	Rep3	rep3	JJ	_	_	_
296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
297	optA1	opta1	NN	_	_	_
298	_	_	CD	_	_	_
299	60	60	CD	_	_	_
300	-LRB-	-lrb-	-LRB-	_	_	_
301	Low	low	JJ	_	_	_
302	Dilution	dilution	NN	_	_	_
303	-RRB-	-rrb-	-RRB-	_	_	_
304	Rep1	rep1	JJ	_	_	_
305	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
306	optA1	opta1	NN	_	_	_
307	_	_	CD	_	_	_
308	60	60	CD	_	_	_
309	-LRB-	-lrb-	-LRB-	_	_	_
310	Low	low	JJ	_	_	_
311	Dilution	dilution	NN	_	_	_
312	-RRB-	-rrb-	-RRB-	_	_	_
313	Rep2	rep2	JJ	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	optA1	opta1	NN	_	_	_
316	_	_	CD	_	_	_
317	60	60	CD	_	_	_
318	-LRB-	-lrb-	-LRB-	_	_	_
319	Low	low	JJ	_	_	_
320	Dilution	dilution	NN	_	_	_
321	-RRB-	-rrb-	-RRB-	_	_	_
322	Rep3	rep3	JJ	_	_	_
323	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
324	optA1	opta1	NN	_	_	_
325	_	_	CD	_	_	_
326	gpt	gpt	NN	GEN	_	_
327	_	_	NN	_	_	_
328	0	0	CD	_	_	_
329	_	_	NN	_	_	_
330	Hx	hx	NN	_	_	_
331	Rep1	rep1	NN	_	_	_
332	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
333	optA1	opta1	NN	_	_	_
334	_	_	CD	_	_	_
335	gpt	gpt	NN	GEN	_	_
336	_	_	NN	_	_	_
337	0	0	CD	_	_	_
338	_	_	SYM	_	_	_
339	Hx	hx	FW	_	_	_
340	Rep2	rep2	JJ	_	_	_
341	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
342	optA1	opta1	NN	_	_	_
343	_	_	CD	_	_	_
344	gpt	gpt	NN	GEN	_	_
345	_	_	NN	_	_	_
346	0	0	CD	_	_	_
347	_	_	SYM	_	_	_
348	Hx	hx	FW	_	_	_
349	Rep3	rep3	JJ	_	_	_
350	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
351	optA1	opta1	NN	_	_	_
352	_	_	CD	_	_	_
353	gpt	gpt	NN	GEN	_	_
354	_	_	NN	_	_	_
355	120	120	CD	_	_	_
356	-LRB-	-lrb-	-LRB-	_	_	_
357	High	high	JJ	_	_	_
358	Dilution	dilution	NN	_	_	_
359	-RRB-	-rrb-	-RRB-	_	_	_
360	Rep1	rep1	JJ	_	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
362	optA1	opta1	NN	_	_	_
363	_	_	CD	_	_	_
364	gpt	gpt	NN	GEN	_	_
365	_	_	NN	_	_	_
366	120	120	CD	_	_	_
367	-LRB-	-lrb-	-LRB-	_	_	_
368	High	high	JJ	_	_	_
369	Dilution	dilution	NN	_	_	_
370	-RRB-	-rrb-	-RRB-	_	_	_
371	Rep2	rep2	JJ	_	_	_
372	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
373	optA1	opta1	NN	_	_	_
374	_	_	CD	_	_	_
375	gpt	gpt	NN	GEN	_	_
376	_	_	NN	_	_	_
377	120	120	CD	_	_	_
378	-LRB-	-lrb-	-LRB-	_	_	_
379	High	high	JJ	_	_	_
380	Dilution	dilution	NN	_	_	_
381	-RRB-	-rrb-	-RRB-	_	_	_
382	Rep3	rep3	JJ	_	_	_
383	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
384	optA1	opta1	NN	_	_	_
385	_	_	CD	_	_	_
386	gpt	gpt	NN	GEN	_	_
387	_	_	NN	_	_	_
388	120	120	CD	_	_	_
389	-LRB-	-lrb-	-LRB-	_	_	_
390	Low	low	JJ	_	_	_
391	Dilution	dilution	NN	_	_	_
392	-RRB-	-rrb-	-RRB-	_	_	_
393	Rep1	rep1	JJ	_	_	_
394	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
395	optA1	opta1	NN	_	_	_
396	_	_	CD	_	_	_
397	gpt	gpt	NN	GEN	_	_
398	_	_	NN	_	_	_
399	120	120	CD	_	_	_
400	-LRB-	-lrb-	-LRB-	_	_	_
401	Low	low	JJ	_	_	_
402	Dilution	dilution	NN	_	_	_
403	-RRB-	-rrb-	-RRB-	_	_	_
404	Rep2	rep2	JJ	_	_	_
405	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
406	optA1	opta1	NN	_	_	_
407	_	_	CD	_	_	_
408	gpt	gpt	NN	GEN	_	_
409	_	_	NN	_	_	_
410	120	120	CD	_	_	_
411	-LRB-	-lrb-	-LRB-	_	_	_
412	Low	low	JJ	_	_	_
413	Dilution	dilution	NN	_	_	_
414	-RRB-	-rrb-	-RRB-	_	_	_
415	Rep3	rep3	JJ	_	_	_
416	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
417	optA1	opta1	NN	_	_	_
418	_	_	SYM	_	_	_
419	gpt	gpt	FW	GEN	_	_
420	_	_	FW	_	_	_
421	15	15	CD	_	_	_
422	-LRB-	-lrb-	-LRB-	_	_	_
423	Low	low	JJ	_	_	_
424	Dilution	dilution	NN	_	_	_
425	-RRB-	-rrb-	-RRB-	_	_	_
426	Rep1	rep1	JJ	_	_	_
427	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
428	optA1	opta1	NN	_	_	_
429	_	_	SYM	_	_	_
430	gpt	gpt	FW	GEN	_	_
431	_	_	FW	_	_	_
432	15	15	CD	_	_	_
433	-LRB-	-lrb-	-LRB-	_	_	_
434	Low	low	JJ	_	_	_
435	Dilution	dilution	NN	_	_	_
436	-RRB-	-rrb-	-RRB-	_	_	_
437	Rep2	rep2	JJ	_	_	_
438	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
439	optA1	opta1	NN	_	_	_
440	_	_	SYM	_	_	_
441	gpt	gpt	FW	GEN	_	_
442	_	_	FW	_	_	_
443	15	15	CD	_	_	_
444	-LRB-	-lrb-	-LRB-	_	_	_
445	Low	low	JJ	_	_	_
446	Dilution	dilution	NN	_	_	_
447	-RRB-	-rrb-	-RRB-	_	_	_
448	Rep3	rep3	JJ	_	_	_
449	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
450	optA1	opta1	NN	_	_	_
451	_	_	CD	_	_	_
452	gpt	gpt	NN	GEN	_	_
453	_	_	NN	_	_	_
454	180	180	CD	_	_	_
455	-LRB-	-lrb-	-LRB-	_	_	_
456	High	high	JJ	_	_	_
457	Dilution	dilution	NN	_	_	_
458	-RRB-	-rrb-	-RRB-	_	_	_
459	Rep1	rep1	JJ	_	_	_
460	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
461	optA1	opta1	NN	_	_	_
462	_	_	CD	_	_	_
463	gpt	gpt	NN	GEN	_	_
464	_	_	NN	_	_	_
465	180	180	CD	_	_	_
466	-LRB-	-lrb-	-LRB-	_	_	_
467	High	high	JJ	_	_	_
468	Dilution	dilution	NN	_	_	_
469	-RRB-	-rrb-	-RRB-	_	_	_
470	Rep2	rep2	JJ	_	_	_
471	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
472	optA1	opta1	NN	_	_	_
473	_	_	CD	_	_	_
474	gpt	gpt	NN	GEN	_	_
475	_	_	NN	_	_	_
476	180	180	CD	_	_	_
477	-LRB-	-lrb-	-LRB-	_	_	_
478	High	high	JJ	_	_	_
479	Dilution	dilution	NN	_	_	_
480	-RRB-	-rrb-	-RRB-	_	_	_
481	Rep3	rep3	JJ	_	_	_
482	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
483	optA1	opta1	NN	_	_	_
484	_	_	CD	_	_	_
485	gpt	gpt	NN	GEN	_	_
486	_	_	NN	_	_	_
487	240	240	CD	_	_	_
488	-LRB-	-lrb-	-LRB-	_	_	_
489	High	high	JJ	_	_	_
490	Dilution	dilution	NN	_	_	_
491	-RRB-	-rrb-	-RRB-	_	_	_
492	Rep1	rep1	JJ	_	_	_
493	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
494	optA1	opta1	NN	_	_	_
495	_	_	CD	_	_	_
496	gpt	gpt	NN	GEN	_	_
497	_	_	NN	_	_	_
498	240	240	CD	_	_	_
499	-LRB-	-lrb-	-LRB-	_	_	_
500	High	high	JJ	_	_	_
501	Dilution	dilution	NN	_	_	_
502	-RRB-	-rrb-	-RRB-	_	_	_
503	Rep2	rep2	JJ	_	_	_
504	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
505	optA1	opta1	NN	_	_	_
506	_	_	CD	_	_	_
507	gpt	gpt	NN	GEN	_	_
508	_	_	NN	_	_	_
509	240	240	CD	_	_	_
510	-LRB-	-lrb-	-LRB-	_	_	_
511	High	high	JJ	_	_	_
512	Dilution	dilution	NN	_	_	_
513	-RRB-	-rrb-	-RRB-	_	_	_
514	Rep3	rep3	JJ	_	_	_
515	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
516	optA1	opta1	NN	_	_	_
517	_	_	CD	_	_	_
518	gpt	gpt	NN	GEN	_	_
519	_	_	NN	_	_	_
520	300	300	CD	_	_	_
521	-LRB-	-lrb-	-LRB-	_	_	_
522	High	high	JJ	_	_	_
523	Dilution	dilution	NN	_	_	_
524	-RRB-	-rrb-	-RRB-	_	_	_
525	Rep1	rep1	JJ	_	_	_
526	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
527	optA1	opta1	NN	_	_	_
528	_	_	CD	_	_	_
529	gpt	gpt	NN	GEN	_	_
530	_	_	NN	_	_	_
531	300	300	CD	_	_	_
532	-LRB-	-lrb-	-LRB-	_	_	_
533	High	high	JJ	_	_	_
534	Dilution	dilution	NN	_	_	_
535	-RRB-	-rrb-	-RRB-	_	_	_
536	Rep2	rep2	JJ	_	_	_
537	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
538	optA1	opta1	NN	_	_	_
539	_	_	CD	_	_	_
540	gpt	gpt	NN	GEN	_	_
541	_	_	NN	_	_	_
542	300	300	CD	_	_	_
543	-LRB-	-lrb-	-LRB-	_	_	_
544	High	high	JJ	_	_	_
545	Dilution	dilution	NN	_	_	_
546	-RRB-	-rrb-	-RRB-	_	_	_
547	Rep3	rep3	JJ	_	_	_
548	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
549	optA1	opta1	NN	_	_	_
550	_	_	SYM	_	_	_
551	gpt	gpt	FW	GEN	_	_
552	_	_	FW	_	_	_
553	30	30	CD	_	_	_
554	-LRB-	-lrb-	-LRB-	_	_	_
555	Low	low	JJ	_	_	_
556	Dilution	dilution	NN	_	_	_
557	-RRB-	-rrb-	-RRB-	_	_	_
558	Rep1	rep1	JJ	_	_	_
559	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
560	optA1	opta1	NN	_	_	_
561	_	_	SYM	_	_	_
562	gpt	gpt	FW	GEN	_	_
563	_	_	FW	_	_	_
564	30	30	CD	_	_	_
565	-LRB-	-lrb-	-LRB-	_	_	_
566	Low	low	JJ	_	_	_
567	Dilution	dilution	NN	_	_	_
568	-RRB-	-rrb-	-RRB-	_	_	_
569	Rep2	rep2	JJ	_	_	_
570	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
571	optA1	opta1	NN	_	_	_
572	_	_	SYM	_	_	_
573	gpt	gpt	FW	GEN	_	_
574	_	_	FW	_	_	_
575	30	30	CD	_	_	_
576	-LRB-	-lrb-	-LRB-	_	_	_
577	Low	low	JJ	_	_	_
578	Dilution	dilution	NN	_	_	_
579	-RRB-	-rrb-	-RRB-	_	_	_
580	Rep3	rep3	JJ	_	_	_
581	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
582	optA1	opta1	NN	_	_	_
583	_	_	CD	_	_	_
584	gpt	gpt	NN	GEN	_	_
585	_	_	NN	_	_	_
586	360	360	CD	_	_	_
587	-LRB-	-lrb-	-LRB-	_	_	_
588	High	high	JJ	_	_	_
589	Dilution	dilution	NN	_	_	_
590	-RRB-	-rrb-	-RRB-	_	_	_
591	Rep1	rep1	JJ	_	_	_
592	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
593	optA1	opta1	NN	_	_	_
594	_	_	CD	_	_	_
595	gpt	gpt	NN	GEN	_	_
596	_	_	NN	_	_	_
597	360	360	CD	_	_	_
598	-LRB-	-lrb-	-LRB-	_	_	_
599	High	high	JJ	_	_	_
600	Dilution	dilution	NN	_	_	_
601	-RRB-	-rrb-	-RRB-	_	_	_
602	Rep2	rep2	JJ	_	_	_
603	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
604	optA1	opta1	NN	_	_	_
605	_	_	CD	_	_	_
606	gpt	gpt	NN	GEN	_	_
607	_	_	NN	_	_	_
608	360	360	CD	_	_	_
609	-LRB-	-lrb-	-LRB-	_	_	_
610	High	high	JJ	_	_	_
611	Dilution	dilution	NN	_	_	_
612	-RRB-	-rrb-	-RRB-	_	_	_
613	Rep3	rep3	JJ	_	_	_
614	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
615	optA1	opta1	NN	_	_	_
616	_	_	CD	_	_	_
617	gpt	gpt	NN	GEN	_	_
618	_	_	NN	_	_	_
619	360	360	CD	_	_	_
620	-LRB-	-lrb-	-LRB-	_	_	_
621	Low	low	JJ	_	_	_
622	Dilution	dilution	NN	_	_	_
623	-RRB-	-rrb-	-RRB-	_	_	_
624	Rep1	rep1	JJ	_	_	_
625	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
626	optA1	opta1	NN	_	_	_
627	_	_	CD	_	_	_
628	gpt	gpt	NN	GEN	_	_
629	_	_	NN	_	_	_
630	360	360	CD	_	_	_
631	-LRB-	-lrb-	-LRB-	_	_	_
632	Low	low	JJ	_	_	_
633	Dilution	dilution	NN	_	_	_
634	-RRB-	-rrb-	-RRB-	_	_	_
635	Rep2	rep2	JJ	_	_	_
636	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
637	optA1	opta1	NN	_	_	_
638	_	_	CD	_	_	_
639	gpt	gpt	NN	GEN	_	_
640	_	_	NN	_	_	_
641	360	360	CD	_	_	_
642	-LRB-	-lrb-	-LRB-	_	_	_
643	Low	low	JJ	_	_	_
644	Dilution	dilution	NN	_	_	_
645	-RRB-	-rrb-	-RRB-	_	_	_
646	Rep3	rep3	JJ	_	_	_
647	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
648	optA1	opta1	NN	_	_	_
649	_	_	SYM	_	_	_
650	gpt	gpt	FW	GEN	_	_
651	_	_	FW	_	_	_
652	45	45	CD	_	_	_
653	-LRB-	-lrb-	-LRB-	_	_	_
654	Low	low	JJ	_	_	_
655	Dilution	dilution	NN	_	_	_
656	-RRB-	-rrb-	-RRB-	_	_	_
657	Rep1	rep1	JJ	_	_	_
658	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
659	optA1	opta1	NN	_	_	_
660	_	_	SYM	_	_	_
661	gpt	gpt	FW	GEN	_	_
662	_	_	FW	_	_	_
663	45	45	CD	_	_	_
664	-LRB-	-lrb-	-LRB-	_	_	_
665	Low	low	JJ	_	_	_
666	Dilution	dilution	NN	_	_	_
667	-RRB-	-rrb-	-RRB-	_	_	_
668	Rep2	rep2	JJ	_	_	_
669	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
670	optA1	opta1	NN	_	_	_
671	_	_	SYM	_	_	_
672	gpt	gpt	FW	GEN	_	_
673	_	_	FW	_	_	_
674	45	45	CD	_	_	_
675	-LRB-	-lrb-	-LRB-	_	_	_
676	Low	low	JJ	_	_	_
677	Dilution	dilution	NN	_	_	_
678	-RRB-	-rrb-	-RRB-	_	_	_
679	Rep3	rep3	JJ	_	_	_
680	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
681	optA1	opta1	NN	_	_	_
682	_	_	SYM	_	_	_
683	gpt	gpt	FW	GEN	_	_
684	_	_	FW	_	_	_
685	60	60	CD	_	_	_
686	-LRB-	-lrb-	-LRB-	_	_	_
687	Low	low	JJ	_	_	_
688	Dilution	dilution	NN	_	_	_
689	-RRB-	-rrb-	-RRB-	_	_	_
690	Rep1	rep1	JJ	_	_	_
691	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
692	optA1	opta1	NN	_	_	_
693	_	_	SYM	_	_	_
694	gpt	gpt	FW	GEN	_	_
695	_	_	FW	_	_	_
696	60	60	CD	_	_	_
697	-LRB-	-lrb-	-LRB-	_	_	_
698	Low	low	JJ	_	_	_
699	Dilution	dilution	NN	_	_	_
700	-RRB-	-rrb-	-RRB-	_	_	_
701	Rep2	rep2	JJ	_	_	_
702	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
703	optA1	opta1	NN	_	_	_
704	_	_	SYM	_	_	_
705	gpt	gpt	FW	GEN	_	_
706	_	_	FW	_	_	_
707	60	60	CD	_	_	_
708	-LRB-	-lrb-	-LRB-	_	_	_
709	Low	low	JJ	_	_	_
710	Dilution	dilution	NN	_	_	_
711	-RRB-	-rrb-	-RRB-	_	_	_
712	Rep3	rep3	JJ	_	_	_
713	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
714	optA1	opta1	NN	_	_	_
715	gpt	gpt	NN	GEN	_	_
716	strain	strain	NN	_	_	_
717	w	w	NN	_	_	_
718	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
719	optA1	opta1	NN	_	_	_
720	gpt	gpt	NN	GEN	_	_
721	strain	strain	NN	_	_	_
722	with	with	IN	_	_	_
723	hypoxanthine	hypoxanthine	NN	_	_	_
724	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
725	optA1	opta1	NN	_	_	_
726	strain	strain	NN	_	_	_
727	w	w	NN	_	_	_
728	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
729	optA1	opta1	NN	_	_	_
730	strain	strain	NN	_	_	_
731	with	with	IN	_	_	_
732	hypoxanthine	hypoxanthine	NN	_	_	_
733	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
734	strain	strain	NN	_	_	_
735	:	:	:	_	_	_
736	MG1655	mg1655	NN	_	_	_
737	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
738	The	the	DT	_	_	_
739	strains	strain	NNS	_	_	_
740	were	be	VBD	_	_	_
741	grown	grow	VBN	_	_	_
742	exponentially	exponentially	RB	_	_	_
743	-LRB-	-lrb-	-LRB-	_	_	_
744	after	after	IN	_	_	_
745	initiation	initiation	NN	_	_	_
746	by	by	IN	_	_	_
747	a	a	DT	_	_	_
748	1,000-fold	1,000-fold	JJ	_	_	_
749	dilution	dilution	NN	_	_	_
750	from	from	IN	_	_	_
751	overnight	overnight	JJ	_	_	_
752	cultures	culture	NNS	_	_	_
753	-RRB-	-rrb-	-RRB-	_	_	_
754	for	for	IN	_	_	_
755	~	~	NN	_	_	_
756	5	5	CD	_	_	_
757	generations	generation	NNS	_	_	_
758	at	at	IN	_	_	_
759	37	37	CD	_	_	_
760	°C	°c	NN	_	_	_
761	in	in	IN	_	_	_
762	Vogel-Bonner	Vogel-Bonner	NNP	_	_	_
763	-LRB-	-lrb-	-LRB-	_	_	_
764	VB	VB	NNP	_	_	_
765	-RRB-	-rrb-	-RRB-	_	_	_
766	minimal	minimal	JJ	_	_	_
767	medium	medium	NN	_	_	_
768	supplemented	supplement	VBN	_	_	_
769	with	with	IN	_	_	_
770	glucose	glucose	NN	SUPP	_	_
771	-LRB-	-lrb-	-LRB-	_	_	_
772	0.4	0.4	CD	_	_	_
773	%	%	NN	_	_	_
774	-RRB-	-rrb-	-RRB-	_	_	_
775	,	,	,	_	_	_
776	pantothenic	pantothenic	JJ	_	_	_
777	acid	acid	NN	_	_	_
778	-LRB-	-lrb-	-LRB-	_	_	_
779	5	5	CD	_	_	_
780	µg	µg	NN	_	_	_
781	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
782	WT	wt	JJ	_	_	_
783	_	_	NN	_	_	_
784	0	0	CD	_	_	_
785	_	_	NN	_	_	_
786	Hx	hx	NN	_	_	_
787	Rep1	rep1	NN	_	_	_
788	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
789	WT	wt	JJ	_	_	_
790	_	_	NN	_	_	_
791	0	0	CD	_	_	_
792	_	_	SYM	_	_	_
793	Hx	hx	FW	_	_	_
794	Rep2	rep2	JJ	_	_	_
795	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
796	WT	wt	JJ	_	_	_
797	_	_	NN	_	_	_
798	0	0	CD	_	_	_
799	_	_	SYM	_	_	_
800	Hx	hx	FW	_	_	_
801	Rep3	rep3	JJ	_	_	_
802	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
803	WT	wt	JJ	_	_	_
804	_	_	NN	_	_	_
805	120	120	CD	_	_	_
806	-LRB-	-lrb-	-LRB-	_	_	_
807	Low	low	JJ	_	_	_
808	Dilution	dilution	NN	_	_	_
809	-RRB-	-rrb-	-RRB-	_	_	_
810	Rep1	rep1	JJ	_	_	_
811	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
812	WT	wt	JJ	_	_	_
813	_	_	NN	_	_	_
814	120	120	CD	_	_	_
815	-LRB-	-lrb-	-LRB-	_	_	_
816	Low	low	JJ	_	_	_
817	Dilution	dilution	NN	_	_	_
818	-RRB-	-rrb-	-RRB-	_	_	_
819	Rep2	rep2	JJ	_	_	_
820	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
821	WT	wt	JJ	_	_	_
822	_	_	NN	_	_	_
823	120	120	CD	_	_	_
824	-LRB-	-lrb-	-LRB-	_	_	_
825	Low	low	JJ	_	_	_
826	Dilution	dilution	NN	_	_	_
827	-RRB-	-rrb-	-RRB-	_	_	_
828	Rep3	rep3	JJ	_	_	_
829	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
830	WT	wt	JJ	_	_	_
831	_	_	NN	_	_	_
832	15	15	CD	_	_	_
833	-LRB-	-lrb-	-LRB-	_	_	_
834	Low	low	JJ	_	_	_
835	Dilution	dilution	NN	_	_	_
836	-RRB-	-rrb-	-RRB-	_	_	_
837	Rep1	rep1	JJ	_	_	_
838	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
839	WT	wt	JJ	_	_	_
840	_	_	NN	_	_	_
841	15	15	CD	_	_	_
842	-LRB-	-lrb-	-LRB-	_	_	_
843	Low	low	JJ	_	_	_
844	Dilution	dilution	NN	_	_	_
845	-RRB-	-rrb-	-RRB-	_	_	_
846	Rep2	rep2	JJ	_	_	_
847	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
848	WT	wt	JJ	_	_	_
849	_	_	NN	_	_	_
850	15	15	CD	_	_	_
851	-LRB-	-lrb-	-LRB-	_	_	_
852	Low	low	JJ	_	_	_
853	Dilution	dilution	NN	_	_	_
854	-RRB-	-rrb-	-RRB-	_	_	_
855	Rep3	rep3	JJ	_	_	_
856	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
857	WT	wt	JJ	_	_	_
858	_	_	NN	_	_	_
859	30	30	CD	_	_	_
860	-LRB-	-lrb-	-LRB-	_	_	_
861	Low	low	JJ	_	_	_
862	Dilution	dilution	NN	_	_	_
863	-RRB-	-rrb-	-RRB-	_	_	_
864	Rep1	rep1	JJ	_	_	_
865	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
866	WT	wt	JJ	_	_	_
867	_	_	NN	_	_	_
868	30	30	CD	_	_	_
869	-LRB-	-lrb-	-LRB-	_	_	_
870	Low	low	JJ	_	_	_
871	Dilution	dilution	NN	_	_	_
872	-RRB-	-rrb-	-RRB-	_	_	_
873	Rep2	rep2	JJ	_	_	_
874	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
875	WT	wt	JJ	_	_	_
876	_	_	NN	_	_	_
877	30	30	CD	_	_	_
878	-LRB-	-lrb-	-LRB-	_	_	_
879	Low	low	JJ	_	_	_
880	Dilution	dilution	NN	_	_	_
881	-RRB-	-rrb-	-RRB-	_	_	_
882	Rep3	rep3	JJ	_	_	_
883	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
884	WT	wt	JJ	_	_	_
885	_	_	NN	_	_	_
886	45	45	CD	_	_	_
887	-LRB-	-lrb-	-LRB-	_	_	_
888	Low	low	JJ	_	_	_
889	Dilution	dilution	NN	_	_	_
890	-RRB-	-rrb-	-RRB-	_	_	_
891	Rep1	rep1	JJ	_	_	_
892	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
893	WT	wt	JJ	_	_	_
894	_	_	NN	_	_	_
895	45	45	CD	_	_	_
896	-LRB-	-lrb-	-LRB-	_	_	_
897	Low	low	JJ	_	_	_
898	Dilution	dilution	NN	_	_	_
899	-RRB-	-rrb-	-RRB-	_	_	_
900	Rep2	rep2	JJ	_	_	_
901	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
902	WT	wt	JJ	_	_	_
903	_	_	NN	_	_	_
904	45	45	CD	_	_	_
905	-LRB-	-lrb-	-LRB-	_	_	_
906	Low	low	JJ	_	_	_
907	Dilution	dilution	NN	_	_	_
908	-RRB-	-rrb-	-RRB-	_	_	_
909	Rep3	rep3	JJ	_	_	_
910	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
911	WT	wt	JJ	_	_	_
912	_	_	NN	_	_	_
913	60	60	CD	_	_	_
914	-LRB-	-lrb-	-LRB-	_	_	_
915	Low	low	JJ	_	_	_
916	Dilution	dilution	NN	_	_	_
917	-RRB-	-rrb-	-RRB-	_	_	_
918	Rep1	rep1	JJ	_	_	_
919	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
920	WT	wt	JJ	_	_	_
921	_	_	NN	_	_	_
922	60	60	CD	_	_	_
923	-LRB-	-lrb-	-LRB-	_	_	_
924	Low	low	JJ	_	_	_
925	Dilution	dilution	NN	_	_	_
926	-RRB-	-rrb-	-RRB-	_	_	_
927	Rep2	rep2	JJ	_	_	_
928	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
929	WT	wt	JJ	_	_	_
930	_	_	NN	_	_	_
931	60	60	CD	_	_	_
932	-LRB-	-lrb-	-LRB-	_	_	_
933	Low	low	JJ	_	_	_
934	Dilution	dilution	NN	_	_	_
935	-RRB-	-rrb-	-RRB-	_	_	_
936	Rep3	rep3	JJ	_	_	_
937	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
938	Alignment	alignment	NN	_	_	_
939	to	to	TO	_	_	_
940	the	the	DT	_	_	_
941	E.	e.	FW	_	_	_
942	coli	coli	FW	_	_	_
943	K12	k12	NN	_	_	_
944	MG1655	mg1655	NN	_	_	_
945	genome	genome	NN	_	_	_
946	sequence	sequence	NN	_	_	_
947	was	be	VBD	_	_	_
948	performed	perform	VBN	_	_	_
949	using	use	VBG	_	_	_
950	TMAP	tmap	NN	_	_	_
951	map4	map4	NN	_	_	_
952	algorithm	algorithm	NN	_	_	_
953	with	with	IN	_	_	_
954	5	5	CD	_	_	_
955	'	'	''	_	_	_
956	and	and	CC	_	_	_
957	3	3	CD	_	_	_
958	'	'	''	_	_	_
959	soft-clipping	soft-clipping	JJ	_	_	_
960	and	and	CC	_	_	_
961	a	a	DT	_	_	_
962	minimum	minimum	JJ	_	_	_
963	seed	seed	NN	_	_	_
964	length	length	NN	_	_	_
965	of	of	IN	_	_	_
966	20	20	CD	_	_	_
967	nt	nt	NNS	_	_	_
968	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
969	Basecalling	basecalling	NN	_	_	_
970	was	be	VBD	_	_	_
971	performed	perform	VBN	_	_	_
972	by	by	IN	_	_	_
973	Torrent	Torrent	NNP	_	_	_
974	Suite	Suite	NNP	_	_	_
975	version	version	NN	_	_	_
976	5	5	CD	_	_	_
977	software	software	NN	_	_	_
978	using	use	VBG	_	_	_
979	the	the	DT	_	_	_
980	default	default	NN	_	_	_
981	settings	setting	NNS	_	_	_
982	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Briefly	briefly	RB	_	_	_
3	,	,	,	_	_	_
4	hot	hot	JJ	_	_	_
5	phenol-chloroform	phenol-chloroform	JJ	_	_	_
6	extraction	extraction	NN	_	_	_
7	was	be	VBD	_	_	_
8	done	do	VBN	_	_	_
9	by	by	IN	_	_	_
10	mixing	mix	VBG	_	_	_
11	the	the	DT	_	_	_
12	cell	cell	NN	_	_	_
13	culture	culture	NN	_	_	_
14	in	in	IN	_	_	_
15	1/2	1/2	CD	_	_	_
16	volume	volume	NN	_	_	_
17	of	of	IN	_	_	_
18	99	99	CD	_	_	_
19	°C	°c	NN	_	_	_
20	lysis	lysis	NN	_	_	_
21	solution	solution	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	2	2	CD	_	_	_
24	%	%	NN	_	_	_
25	SDS	sds	NN	_	_	_
26	,	,	,	_	_	_
27	16	16	CD	_	_	_
28	mM	mm	NN	KWSUPP	_	_
29	EDTA	edta	NN	_	_	_
30	,	,	,	_	_	_
31	200	200	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	NaCl	nacl	NN	_	_	_
34	made	make	VBN	_	_	_
35	in	in	IN	_	_	_
36	RNAse-free	rnase-free	JJ	_	_	_
37	H2O	h2o	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	for	for	IN	_	_	_
40	10	10	CD	_	_	_
41	min	min	NN	_	_	_
42	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	suspension	suspension	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	twice	twice	RB	_	_	_
6	with	with	IN	_	_	_
7	1	1	CD	_	_	_
8	volume	volume	NN	_	_	_
9	of	of	IN	_	_	_
10	65	65	CD	_	_	_
11	°C	°c	NN	_	_	_
12	acid	acid	NN	_	_	_
13	phenol	phenol	NN	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	Clindamycin	Clindamycin	NNP	_	_	_
16	_	_	NNP	_	_	_
17	replicate	replicate	VB	_	_	_
18	_	_	SYM	_	_	_
19	1	1	CD	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Clindamycin	clindamycin	NN	_	_	_
22	_	_	NN	_	_	_
23	replicate	replicate	VBP	_	_	_
24	_	_	NN	_	_	_
25	2	2	CD	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	Clindamycin	Clindamycin	NNP	_	_	_
28	_	_	NNP	_	_	_
29	replicate	replicate	VB	_	_	_
30	_	_	SYM	_	_	_
31	3	3	CD	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	E.	e.	FW	_	_	_
34	coli	coli	FW	_	_	_
35	strain	strain	NN	_	_	_
36	K12	k12	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	E.	e.	FW	_	_	_
39	coli	coli	FW	_	_	_
40	strain	strain	NN	_	_	_
41	NM580	nm580	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	genotype	genotype	NN	_	_	_
44	MG1655	mg1655	NN	_	_	_
45	ermBL-ermB	ermbl-ermb	NN	_	_	_
46	'	'	''	_	_	_
47	:	:	:	_	_	_
48	:	:	:	_	_	_
49	LacZ	lacz	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	cells	cell	NNS	_	_	_
52	were	be	VBD	_	_	_
53	grown	grow	VBN	_	_	_
54	in	in	IN	_	_	_
55	LB	lb	NN	MED	_	_
56	broth	broth	NN	MED	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	37	37	CD	_	_	_
59	°C	°c	NN	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	until	until	IN	_	_	_
62	OD600	od600	NN	_	_	_
63	of	of	IN	_	_	_
64	~	~	NN	_	_	_
65	0.3	0.3	CD	_	_	_
66	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Erythromycin	Erythromycin	NNP	_	_	_
3	_	_	NNP	_	_	_
4	replicate	replicate	VB	_	_	_
5	_	_	SYM	_	_	_
6	1	1	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Erythromycin	erythromycin	NN	_	_	_
9	_	_	NN	_	_	_
10	replicate	replicate	VBP	_	_	_
11	_	_	NN	_	_	_
12	2	2	CD	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Erythromycin	Erythromycin	NNP	_	_	_
15	_	_	NNP	_	_	_
16	replicate	replicate	VB	_	_	_
17	_	_	SYM	_	_	_
18	3	3	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Escherichia	escherichia	FW	Organism	_	_
21	coli	coli	FW	Organism	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Genome	Genome	NNP	_	_	_
24	_	_	NNP	_	_	_
25	build	build	VB	_	_	_
26	:	:	:	_	_	_
27	Escherichia	escherichia	FW	Organism	_	_
28	coli	coli	FW	Organism	_	_
29	str	str	FW	_	_	_
30	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	,	,	,	_	_	_
3	NCBI	NCBI	NNP	_	_	_
4	Reference	Reference	NNP	_	_	_
5	Sequence	sequence	NN	_	_	_
6	:	:	:	_	_	_
7	NC	NC	NNP	_	_	_
8	_	_	NNP	_	_	_
9	000913.3	000913.3	CD	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Ion	Ion	NNP	_	_	_
12	Xpress	Xpress	NNP	_	_	_
13	barcoded	barcode	VBD	_	_	_
14	libraries	library	NNS	_	_	_
15	were	be	VBD	_	_	_
16	constructed	construct	VBN	_	_	_
17	using	use	VBG	_	_	_
18	the	the	DT	_	_	_
19	Ribo-Zero	Ribo-Zero	NNP	_	_	_
20	Magnatic	Magnatic	NNP	_	_	_
21	Kit	kit	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Gram-negative	gram-negative	JJ	_	_	_
24	bacteria	bacterium	NNS	_	_	_
25	,	,	,	_	_	_
26	Epicentre	Epicentre	NNP	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	and	and	CC	_	_	_
29	IonXpress	ionxpress	NN	_	_	_
30	RNA-seq	rna-seq	NN	_	_	_
31	v2	v2	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	Life	Life	NNP	_	_	_
34	Technologies	Technologies	NNPS	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	kits	kit	NNS	_	_	_
37	according	accord	VBG	_	_	_
38	to	to	TO	_	_	_
39	the	the	DT	_	_	_
40	manufacturer	manufacturer	NN	_	_	_
41	's	's	POS	_	_	_
42	directions	direction	NNS	_	_	_
43	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Supplementary	supplementary	JJ	_	_	_
5	_	_	NN	_	_	_
6	files	file	NNS	_	_	_
7	_	_	IN	_	_	_
8	format	format	NN	_	_	_
9	_	_	NN	_	_	_
10	and	and	CC	_	_	_
11	_	_	NN	_	_	_
12	content	content	NN	_	_	_
13	:	:	:	_	_	_
14	Microsoft	Microsoft	NNP	_	_	_
15	Excel	Excel	NNP	_	_	_
16	File	file	VB	_	_	_
17	with	with	IN	_	_	_
18	normalized	normalize	VBN	_	_	_
19	sequencing	sequencing	NN	_	_	_
20	coverage	coverage	NN	_	_	_
21	of	of	IN	_	_	_
22	all	all	DT	_	_	_
23	annotated	annotated	JJ	_	_	_
24	genes	gene	NNS	_	_	_
25	and	and	CC	_	_	_
26	statistical	statistical	JJ	_	_	_
27	comparison	comparison	NN	_	_	_
28	of	of	IN	_	_	_
29	expression	expression	NN	_	_	_
30	in	in	IN	_	_	_
31	antibiotic	antibiotic	JJ	_	_	_
32	treated	treat	VBN	_	_	_
33	to	to	TO	_	_	_
34	untreated	untreated	JJ	_	_	_
35	cells	cell	NNS	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	untreated	untreated	JJ	_	_	_
6	,	,	,	_	_	_
7	or	or	CC	_	_	_
8	treated	treat	VBN	_	_	_
9	with	with	IN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	100µg	100µg	JJ	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
13	The	the	DT	_	_	_
14	total	total	JJ	_	_	_
15	sequencing	sequencing	NN	_	_	_
16	base	base	NN	_	_	_
17	pair	pair	NN	_	_	_
18	coverage	coverage	NN	_	_	_
19	for	for	IN	_	_	_
20	all	all	DT	_	_	_
21	annotated	annotated	JJ	_	_	_
22	genes	gene	NNS	_	_	_
23	was	be	VBD	_	_	_
24	summed	sum	VBN	_	_	_
25	for	for	IN	_	_	_
26	each	each	DT	_	_	_
27	sample	sample	NN	_	_	_
28	and	and	CC	_	_	_
29	normalized	normalize	VBD	_	_	_
30	to	to	TO	_	_	_
31	total	total	JJ	_	_	_
32	coverage	coverage	NN	_	_	_
33	using	use	VBG	_	_	_
34	bedtools	bedtool	NNS	_	_	_
35	and	and	CC	_	_	_
36	custom	custom	NN	_	_	_
37	R	r	NN	_	_	_
38	scripts	script	NNS	_	_	_
39	as	as	IN	_	_	_
40	described	describe	VBN	_	_	_
41	in	in	IN	_	_	_
42	Wu	Wu	NNP	_	_	_
43	et	et	FW	_	_	_
44	al.	al.	FW	_	_	_
45	2015	2015	CD	_	_	_
46	PLoS	PLoS	NNP	_	_	_
47	Genetics	Genetics	NNP	_	_	_
48	Nov	Nov	NNP	_	_	_
49	6	6	CD	_	_	_
50	;	;	:	_	_	_
51	11	11	CD	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	11	11	CD	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	:	:	:	_	_	_
56	e1005655	e1005655	NN	_	_	_
57	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	clindamycin	clindamycin	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	treatment	treatment	NN	_	_	_
7	:	:	:	_	_	_
8	erythromycin	erythromycin	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	treatment	treatment	NN	_	_	_
11	:	:	:	_	_	_
12	untreated	untreated	JJ	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Untreated	untreated	JJ	_	_	_
15	_	_	NN	_	_	_
16	replicate	replicate	VB	_	_	_
17	_	_	SYM	_	_	_
18	1	1	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Untreated	untreated	JJ	_	_	_
21	_	_	NN	_	_	_
22	replicate	replicate	VBP	_	_	_
23	_	_	NN	_	_	_
24	2	2	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
26	Untreated	untreated	JJ	_	_	_
27	_	_	NN	_	_	_
28	replicate	replicate	VB	_	_	_
29	_	_	SYM	_	_	_
30	3	3	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	Aerobic	aerobic	JJ	_	_	_
33	1	1	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	Aerobic	aerobic	JJ	_	_	_
36	2	2	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
38	Aerobic	aerobic	JJ	_	_	_
39	3	3	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	Aerobic	aerobic	JJ	_	_	_
42	and	and	CC	_	_	_
43	anaerobic	anaerobic	JJ	_	_	_
44	cultures	culture	NNS	_	_	_
45	were	be	VBD	_	_	_
46	grown	grow	VBN	_	_	_
47	in	in	IN	_	_	_
48	600	600	CD	_	_	_
49	mL	ml	NN	_	_	_
50	aliquots	aliquot	NNS	_	_	_
51	of	of	IN	_	_	_
52	DM25	dm25	NN	_	_	_
53	and	and	CC	_	_	_
54	incubated	incubate	VBN	_	_	_
55	at	at	IN	_	_	_
56	37	37	CD	_	_	_
57	°C	°c	NN	_	_	_
58	with	with	IN	_	_	_
59	an	a	DT	_	_	_
60	orbital	orbital	JJ	_	_	_
61	shaking	shake	VBG	_	_	_
62	of	of	IN	_	_	_
63	150	150	CD	_	_	_
64	RPM	rpm	NN	_	_	_
65	and	and	CC	_	_	_
66	inoculated	inoculate	VBN	_	_	_
67	with	with	IN	_	_	_
68	1	1	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	Anaerobic	anaerobic	JJ	_	_	_
71	1	1	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	Anaerobic	anaerobic	JJ	_	_	_
74	3	3	CD	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	Bowtie	bowtie	NN	_	_	_
77	2	2	CD	_	_	_
78	-LRB-	-lrb-	-LRB-	_	_	_
79	Langmead	langmead	NN	_	_	_
80	B	b	NN	_	_	_
81	&	&	CC	_	_	_
82	Salzberg	Salzberg	NNP	_	_	_
83	SL	SL	NNP	_	_	_
84	,	,	,	_	_	_
85	2012	2012	CD	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	was	be	VBD	_	_	_
88	used	use	VBN	_	_	_
89	with	with	IN	_	_	_
90	default	default	NN	_	_	_
91	parameters	parameter	NNS	_	_	_
92	,	,	,	_	_	_
93	to	to	TO	_	_	_
94	remove	remove	VB	_	_	_
95	any	any	DT	_	_	_
96	sequence	sequence	NN	_	_	_
97	reads	read	VBZ	_	_	_
98	aligning	align	VBG	_	_	_
99	to	to	TO	_	_	_
100	ribosomal	ribosomal	JJ	_	_	_
101	RNA	rna	NN	_	_	_
102	,	,	,	_	_	_
103	transfer	transfer	NN	_	_	_
104	RNA	rna	NN	_	_	_
105	and	and	CC	_	_	_
106	non-coding	non-coding	JJ	_	_	_
107	RNA	rna	NN	_	_	_
108	sequences	sequence	NNS	_	_	_
109	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Cultured	culture	VBN	_	_	_
3	cells	cell	NNS	_	_	_
4	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
5	Differential	differential	JJ	_	_	_
6	expression	expression	NN	_	_	_
7	between	between	IN	_	_	_
8	aerobic	aerobic	JJ	_	_	_
9	and	and	CC	_	_	_
10	anaerobic	anaerobic	JJ	_	_	_
11	environments	environment	NNS	_	_	_
12	was	be	VBD	_	_	_
13	identified	identify	VBN	_	_	_
14	by	by	IN	_	_	_
15	using	use	VBG	_	_	_
16	DESeq2	deseq2	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Love	love	NN	_	_	_
19	M	m	NN	_	_	_
20	,	,	,	_	_	_
21	Huber	Huber	NNP	_	_	_
22	W	W	NNP	_	_	_
23	and	and	CC	_	_	_
24	Anders	Anders	NNP	_	_	_
25	S	s	NN	_	_	_
26	,	,	,	_	_	_
27	2014	2014	CD	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
30	Escherichia	escherichia	FW	Organism	_	_
31	coli	coli	FW	Organism	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	Genome	Genome	NNP	_	_	_
34	_	_	NNP	_	_	_
35	build	build	VB	_	_	_
36	:	:	:	_	_	_
37	Escherichia	escherichia	FW	Organism	_	_
38	coli	coli	FW	Organism	_	_
39	B	b	NN	_	_	_
40	str	str	NN	_	_	_
41	.	.	.	_	_	_

1	REL606	rel606	NN	_	_	_
2	;	;	:	_	_	_
3	NC	NC	NNP	_	_	_
4	_	_	NNP	_	_	_
5	012967.1	012967.1	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	growth	growth	NN	_	_	_
8	environment	environment	NN	_	_	_
9	:	:	:	_	_	_
10	Aerobic	aerobic	JJ	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	growth	growth	NN	_	_	_
13	environment	environment	NN	_	_	_
14	:	:	:	_	_	_
15	Anaerobic	anaerobic	JJ	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	growth	growth	NN	_	_	_
18	phase	phase	NN	_	_	_
19	:	:	:	_	_	_
20	Stationary	stationary	JJ	_	_	_
21	phase	phase	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	RNA	rna	NN	_	_	_
24	libraries	library	NNS	_	_	_
25	were	be	VBD	_	_	_
26	prepared	prepare	VBN	_	_	_
27	for	for	IN	_	_	_
28	sequencing	sequencing	NN	_	_	_
29	using	use	VBG	_	_	_
30	standard	standard	JJ	_	_	_
31	Illumina	Illumina	NNP	_	_	_
32	protocols	protocol	NNS	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
34	RNA-Seq	rna-seq	JJ	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	RNA-Seq	rna-seq	NN	_	_	_
37	reads	read	VBZ	_	_	_
38	were	be	VBD	_	_	_
39	mapped	map	VBN	_	_	_
40	to	to	TO	_	_	_
41	the	the	DT	_	_	_
42	reference	reference	NN	_	_	_
43	genome	genome	NN	_	_	_
44	using	use	VBG	_	_	_
45	EDGE-Pro	edge-pro	NN	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	Magoc	magoc	NN	_	_	_
48	T	t	NN	_	_	_
49	,	,	,	_	_	_
50	Wood	Wood	NNP	_	_	_
51	D	D	NNP	_	_	_
52	and	and	CC	_	_	_
53	Salzberg	Salzberg	NNP	_	_	_
54	SL	SL	NNP	_	_	_
55	,	,	,	_	_	_
56	2013	2013	CD	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	-RRB-	-rrb-	-RRB-	_	_	_
59	with	with	IN	_	_	_
60	default	default	NN	_	_	_
61	parameters	parameter	NNS	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
63	RNA	rna	NN	_	_	_
64	was	be	VBD	_	_	_
65	extracted	extract	VBN	_	_	_
66	from	from	IN	_	_	_
67	harvested	harvest	VBN	_	_	_
68	cultures	culture	NNS	_	_	_
69	using	use	VBG	_	_	_
70	a	a	DT	_	_	_
71	hot	hot	JJ	_	_	_
72	lysis	lysis	NN	_	_	_
73	buffer	buffer	NN	_	_	_
74	and	and	CC	_	_	_
75	acid	acid	NN	_	_	_
76	phenol-based	phenol-based	JJ	_	_	_
77	extraction	extraction	NN	_	_	_
78	method	method	NN	_	_	_
79	and	and	CC	_	_	_
80	isopropanol	isopropanol	NN	_	_	_
81	precipitation	precipitation	NN	_	_	_
82	.	.	.	_	_	_

1	Following	follow	VBG	_	_	_
2	RNA	rna	NN	_	_	_
3	extraction	extraction	NN	_	_	_
4	,	,	,	_	_	_
5	Turbo	Turbo	NNP	_	_	_
6	DNase	dnase	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Ambion	Ambion	NNP	_	_	_
9	,	,	,	_	_	_
10	USA	USA	NNP	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	was	be	VBD	_	_	_
13	used	use	VBN	_	_	_
14	to	to	TO	_	_	_
15	treat	treat	VB	_	_	_
16	the	the	DT	_	_	_
17	samples	sample	NNS	_	_	_
18	as	as	IN	_	_	_
19	per	per	IN	_	_	_
20	manufacturer	manufacturer	NN	_	_	_
21	's	's	POS	_	_	_
22	instructions	instruction	NNS	_	_	_
23	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	sample	sample	NN	_	_	_
3	was	be	VBD	_	_	_
4	split	split	VBN	_	_	_
5	into	into	IN	_	_	_
6	five	five	CD	_	_	_
7	20	20	CD	_	_	_
8	μL	μl	NN	_	_	_
9	aliquots	aliquot	NNS	_	_	_
10	and	and	CC	_	_	_
11	two	two	CD	_	_	_
12	rounds	round	NNS	_	_	_
13	of	of	IN	_	_	_
14	DNase	dnase	NN	_	_	_
15	treatment	treatment	NN	_	_	_
16	were	be	VBD	_	_	_
17	performed	perform	VBN	_	_	_
18	on	on	IN	_	_	_
19	each	each	DT	_	_	_
20	aliquot	aliquot	NN	_	_	_
21	.	.	.	_	_	_

1	Following	follow	VBG	_	_	_
2	DNase	dnase	NN	_	_	_
3	treatment	treatment	NN	_	_	_
4	,	,	,	_	_	_
5	RNA	rna	NN	_	_	_
6	samples	sample	NNS	_	_	_
7	were	be	VBD	_	_	_
8	purified	purify	VBN	_	_	_
9	using	use	VBG	_	_	_
10	the	the	DT	_	_	_
11	RNeasy	RNeasy	NNP	_	_	_
12	Mini	Mini	NNP	_	_	_
13	kit	kit	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Qiagen	Qiagen	NNP	_	_	_
16	,	,	,	_	_	_
17	Germany	Germany	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	as	as	IN	_	_	_
20	per	per	IN	_	_	_
21	the	the	DT	_	_	_
22	manufacturer	manufacturer	NN	_	_	_
23	's	's	POS	_	_	_
24	instructions	instruction	NNS	_	_	_
25	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	each	each	DT	_	_	_
3	sample	sample	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	DNase-treated	dnase-treated	JJ	_	_	_
7	aliquots	aliquot	NNS	_	_	_
8	were	be	VBD	_	_	_
9	pooled	pool	VBN	_	_	_
10	together	together	RB	_	_	_
11	before	before	IN	_	_	_
12	purification	purification	NN	_	_	_
13	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	quality	quality	NN	_	_	_
3	was	be	VBD	_	_	_
4	measured	measure	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	Agilent	Agilent	NNP	_	_	_
8	2100	2100	CD	_	_	_
9	Bioanalyzer	Bioanalyzer	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Agilent	Agilent	NNP	_	_	_
12	Technologies	Technologies	NNPS	_	_	_
13	,	,	,	_	_	_
14	USA	USA	NNP	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	with	with	IN	_	_	_
17	the	the	DT	_	_	_
18	RNA	rna	NN	_	_	_
19	6000	6000	CD	_	_	_
20	Nano	Nano	NNP	_	_	_
21	Chip	Chip	NNP	_	_	_
22	kit	kit	NN	_	_	_
23	according	accord	VBG	_	_	_
24	to	to	TO	_	_	_
25	the	the	DT	_	_	_
26	manufacturer	manufacturer	NN	_	_	_
27	's	's	POS	_	_	_
28	instructions	instruction	NNS	_	_	_
29	while	while	IN	_	_	_
30	RNA	rna	NN	_	_	_
31	was	be	VBD	_	_	_
32	quantified	quantify	VBN	_	_	_
33	using	use	VBG	_	_	_
34	the	the	DT	_	_	_
35	Quant-iT	quant-it	JJ	_	_	_
36	RNA	rna	NN	_	_	_
37	Assay	assay	NN	_	_	_
38	kit	kit	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	Life	Life	NNP	_	_	_
41	Technologies	Technologies	NNPS	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	and	and	CC	_	_	_
44	measured	measure	VBN	_	_	_
45	on	on	IN	_	_	_
46	a	a	DT	_	_	_
47	Qubit	Qubit	NNP	_	_	_
48	®	®	NNP	_	_	_
49	2.0	2.0	CD	_	_	_
50	fluorometer	fluorometer	NN	_	_	_
51	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	sequenced	sequence	VBN	_	_	_
4	on	on	IN	_	_	_
5	the	the	DT	_	_	_
6	Illumina	Illumina	NNP	_	_	_
7	HiSeq	HiSeq	NNP	_	_	_
8	2000	2000	CD	_	_	_
9	platform	platform	NN	_	_	_
10	at	at	IN	_	_	_
11	BGI	BGI	NNP	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Shenzen	Shenzen	NNP	_	_	_
14	,	,	,	_	_	_
15	China	China	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Sequence	sequence	NN	_	_	_
3	data	datum	NNS	_	_	_
4	from	from	IN	_	_	_
5	BGI	BGI	NNP	_	_	_
6	had	have	VBD	_	_	_
7	been	be	VBN	_	_	_
8	filtered	filter	VBN	_	_	_
9	to	to	TO	_	_	_
10	remove	remove	VB	_	_	_
11	reads	read	VBZ	_	_	_
12	containing	contain	VBG	_	_	_
13	≥	≥	SYM	_	_	_
14	10	10	CD	_	_	_
15	%	%	NN	_	_	_
16	unreadable	unreadable	JJ	_	_	_
17	bases	basis	NNS	_	_	_
18	,	,	,	_	_	_
19	≥	≥	SYM	_	_	_
20	20	20	CD	_	_	_
21	%	%	NN	_	_	_
22	low	low	JJ	_	_	_
23	quality	quality	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	≤	≤	CD	_	_	_
26	Q20	q20	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	bases	basis	NNS	_	_	_
29	,	,	,	_	_	_
30	adapter	adapter	NN	_	_	_
31	contamination	contamination	NN	_	_	_
32	or	or	CC	_	_	_
33	duplicate	duplicate	VB	_	_	_
34	read-pairs	read-pairs	JJ	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	strain	strain	NN	_	_	_
37	:	:	:	_	_	_
38	REL4536	rel4536	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Supplementary	supplementary	JJ	_	_	_
41	_	_	NN	_	_	_
42	files	file	NNS	_	_	_
43	_	_	IN	_	_	_
44	format	format	NN	_	_	_
45	_	_	NN	_	_	_
46	and	and	CC	_	_	_
47	_	_	NN	_	_	_
48	content	content	NN	_	_	_
49	:	:	:	_	_	_
50	Tab-delimited	tab-delimited	JJ	_	_	_
51	text	text	NN	_	_	_
52	files	file	NNS	_	_	_
53	include	include	VBP	_	_	_
54	RPKM	rpkm	NN	_	_	_
55	values	value	NNS	_	_	_
56	for	for	IN	_	_	_
57	each	each	DT	_	_	_
58	sample	sample	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	The	the	DT	_	_	_
61	quality	quality	NN	_	_	_
62	of	of	IN	_	_	_
63	reads	read	VBZ	_	_	_
64	was	be	VBD	_	_	_
65	assessed	assess	VBN	_	_	_
66	by	by	IN	_	_	_
67	using	use	VBG	_	_	_
68	FastQC	fastqc	NN	_	_	_
69	-LRB-	-lrb-	-LRB-	_	_	_
70	Andrews	Andrews	NNP	_	_	_
71	S	s	NN	_	_	_
72	,	,	,	_	_	_
73	2010	2010	CD	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	and	and	CC	_	_	_
76	any	any	DT	_	_	_
77	reads	read	VBZ	_	_	_
78	with	with	IN	_	_	_
79	a	a	DT	_	_	_
80	quality	quality	NN	_	_	_
81	score	score	NN	_	_	_
82	≤	≤	CD	_	_	_
83	Q28	q28	NN	_	_	_
84	were	be	VBD	_	_	_
85	trimmed	trim	VBN	_	_	_
86	using	use	VBG	_	_	_
87	Trim	Trim	NNP	_	_	_
88	Galore	Galore	NNP	_	_	_
89	!	!	.	_	_	_

1	-LRB-	-lrb-	-LRB-	_	_	_
2	Krueger	krueger	NN	_	_	_
3	F	f	NN	_	_	_
4	,	,	,	_	_	_
5	2013	2013	CD	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	DMSO	dmso	NN	_	_	_
3	_	_	VBD	_	_	_
4	0	0	CD	_	_	_
5	min	min	NN	_	_	_
6	_	_	CD	_	_	_
7	rep1	rep1	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
9	DMSO	dmso	NN	_	_	_
10	_	_	VBD	_	_	_
11	0	0	CD	_	_	_
12	min	min	NN	_	_	_
13	_	_	CD	_	_	_
14	rep2	rep2	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
16	DMSO	dmso	NN	_	_	_
17	_	_	VBD	_	_	_
18	0	0	CD	_	_	_
19	min	min	NN	_	_	_
20	_	_	CD	_	_	_
21	rep3	rep3	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	DMSO	dmso	NN	_	_	_
24	_	_	SYM	_	_	_
25	60	60	CD	_	_	_
26	min	min	NN	_	_	_
27	_	_	CD	_	_	_
28	rep1	rep1	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
30	DMSO	dmso	NN	_	_	_
31	_	_	SYM	_	_	_
32	60	60	CD	_	_	_
33	min	min	NN	_	_	_
34	_	_	CD	_	_	_
35	rep2	rep2	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
37	DMSO	dmso	NN	_	_	_
38	_	_	SYM	_	_	_
39	60	60	CD	_	_	_
40	min	min	NN	_	_	_
41	_	_	CD	_	_	_
42	rep3	rep3	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
44	DMSO	dmso	NN	_	_	_
45	_	_	SYM	_	_	_
46	60	60	CD	_	_	_
47	min	min	NN	_	_	_
48	_	_	CD	_	_	_
49	rep4	rep4	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
51	DMSO	dmso	NN	_	_	_
52	treatment	treatment	NN	_	_	_
53	,	,	,	_	_	_
54	0	0	CD	_	_	_
55	min	min	NN	_	_	_
56	,	,	,	_	_	_
57	replicate	replicate	VB	_	_	_
58	1	1	CD	_	_	_
59	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
60	DMSO	dmso	NN	_	_	_
61	treatment	treatment	NN	_	_	_
62	,	,	,	_	_	_
63	0	0	CD	_	_	_
64	min	min	NN	_	_	_
65	,	,	,	_	_	_
66	replicate	replicate	VB	_	_	_
67	2	2	CD	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
69	DMSO	dmso	NN	_	_	_
70	treatment	treatment	NN	_	_	_
71	,	,	,	_	_	_
72	0	0	CD	_	_	_
73	min	min	NN	_	_	_
74	,	,	,	_	_	_
75	replicate	replicate	VB	_	_	_
76	3	3	CD	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
78	DMSO	dmso	NN	_	_	_
79	treatment	treatment	NN	_	_	_
80	,	,	,	_	_	_
81	60	60	CD	_	_	_
82	min	min	NN	_	_	_
83	,	,	,	_	_	_
84	replicate	replicate	VB	_	_	_
85	1	1	CD	_	_	_
86	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
87	DMSO	dmso	NN	_	_	_
88	treatment	treatment	NN	_	_	_
89	,	,	,	_	_	_
90	60	60	CD	_	_	_
91	min	min	NN	_	_	_
92	,	,	,	_	_	_
93	replicate	replicate	VB	_	_	_
94	2	2	CD	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
96	DMSO	dmso	NN	_	_	_
97	treatment	treatment	NN	_	_	_
98	,	,	,	_	_	_
99	60	60	CD	_	_	_
100	min	min	NN	_	_	_
101	,	,	,	_	_	_
102	replicate	replicate	VB	_	_	_
103	3	3	CD	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
105	DMSO	dmso	NN	_	_	_
106	treatment	treatment	NN	_	_	_
107	,	,	,	_	_	_
108	60	60	CD	_	_	_
109	min	min	NN	_	_	_
110	,	,	,	_	_	_
111	replicate	replicate	VB	_	_	_
112	4	4	CD	_	_	_
113	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
114	Escherichia	escherichia	FW	Organism	_	_
115	coli	coli	FW	Organism	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	Raw	raw	NN	_	_	_
118	Microarray	Microarray	NNP	_	_	_
119	data	datum	NNS	_	_	_
120	evaluation	evaluation	NN	_	_	_
121	including	include	VBG	_	_	_
122	preprocessing	preprocessing	NN	_	_	_
123	,	,	,	_	_	_
124	normalization	normalization	NN	_	_	_
125	,	,	,	_	_	_
126	grouping	group	VBG	_	_	_
127	the	the	DT	_	_	_
128	differentially	differentially	RB	_	_	_
129	expressed	express	VBN	_	_	_
130	genes	gene	NNS	_	_	_
131	and	and	CC	_	_	_
132	statistical	statistical	JJ	_	_	_
133	analyses	analysis	NNS	_	_	_
134	with	with	IN	_	_	_
135	Moderated	moderate	VBN	_	_	_
136	T-test	t-test	NN	_	_	_
137	and	and	CC	_	_	_
138	Bonferroni	Bonferroni	NNP	_	_	_
139	FWER	FWER	NNP	_	_	_
140	was	be	VBD	_	_	_
141	carried	carry	VBN	_	_	_
142	out	out	RP	_	_	_
143	with	with	IN	_	_	_
144	GeneSpring	genespring	NN	_	_	_
145	13.0	13.0	CD	_	_	_
146	Software	Software	NNP	_	_	_
147	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Roemerine	roemerine	NN	_	_	_
3	_	_	NN	_	_	_
4	0	0	CD	_	_	_
5	min	min	NN	_	_	_
6	_	_	CD	_	_	_
7	rep1	rep1	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Roemerine	roemerine	JJ	_	_	_
10	_	_	NN	_	_	_
11	0	0	CD	_	_	_
12	min	min	NN	_	_	_
13	_	_	CD	_	_	_
14	rep2	rep2	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Roemerine	roemerine	JJ	_	_	_
17	_	_	NN	_	_	_
18	0	0	CD	_	_	_
19	min	min	NN	_	_	_
20	_	_	CD	_	_	_
21	rep3	rep3	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Roemerine	roemerine	JJ	_	_	_
24	_	_	NN	_	_	_
25	60	60	CD	_	_	_
26	min	min	NN	_	_	_
27	_	_	CD	_	_	_
28	rep1	rep1	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Roemerine	roemerine	JJ	_	_	_
31	_	_	NN	_	_	_
32	60	60	CD	_	_	_
33	min	min	NN	_	_	_
34	_	_	CD	_	_	_
35	rep2	rep2	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Roemerine	roemerine	JJ	_	_	_
38	_	_	NN	_	_	_
39	60	60	CD	_	_	_
40	min	min	NN	_	_	_
41	_	_	CD	_	_	_
42	rep3	rep3	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	-	-	:	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	-	-	:	_	_	_
48	Roemerine	roemerine	NN	_	_	_
49	treatment	treatment	NN	_	_	_
50	,	,	,	_	_	_
51	0	0	CD	_	_	_
52	min	min	NN	_	_	_
53	,	,	,	_	_	_
54	replicate	replicate	VB	_	_	_
55	1	1	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	-	-	:	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	-	-	:	_	_	_
61	Roemerine	roemerine	NN	_	_	_
62	treatment	treatment	NN	_	_	_
63	,	,	,	_	_	_
64	0	0	CD	_	_	_
65	min	min	NN	_	_	_
66	,	,	,	_	_	_
67	replicate	replicate	VB	_	_	_
68	2	2	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
70	-LRB-	-lrb-	-LRB-	_	_	_
71	-	-	:	_	_	_
72	-RRB-	-rrb-	-RRB-	_	_	_
73	-	-	:	_	_	_
74	Roemerine	roemerine	NN	_	_	_
75	treatment	treatment	NN	_	_	_
76	,	,	,	_	_	_
77	0	0	CD	_	_	_
78	min	min	NN	_	_	_
79	,	,	,	_	_	_
80	replicate	replicate	VB	_	_	_
81	3	3	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	-LRB-	-lrb-	-LRB-	_	_	_
84	-	-	:	_	_	_
85	-RRB-	-rrb-	-RRB-	_	_	_
86	-	-	:	_	_	_
87	Roemerine	roemerine	NN	_	_	_
88	treatment	treatment	NN	_	_	_
89	,	,	,	_	_	_
90	60	60	CD	_	_	_
91	min	min	NN	_	_	_
92	,	,	,	_	_	_
93	replicate	replicate	VB	_	_	_
94	1	1	CD	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	-LRB-	-lrb-	-LRB-	_	_	_
97	-	-	:	_	_	_
98	-RRB-	-rrb-	-RRB-	_	_	_
99	-	-	:	_	_	_
100	Roemerine	roemerine	NN	_	_	_
101	treatment	treatment	NN	_	_	_
102	,	,	,	_	_	_
103	60	60	CD	_	_	_
104	min	min	NN	_	_	_
105	,	,	,	_	_	_
106	replicate	replicate	VB	_	_	_
107	2	2	CD	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
109	-LRB-	-lrb-	-LRB-	_	_	_
110	-	-	:	_	_	_
111	-RRB-	-rrb-	-RRB-	_	_	_
112	-	-	:	_	_	_
113	Roemerine	roemerine	NN	_	_	_
114	treatment	treatment	NN	_	_	_
115	,	,	,	_	_	_
116	60	60	CD	_	_	_
117	min	min	NN	_	_	_
118	,	,	,	_	_	_
119	replicate	replicate	VB	_	_	_
120	3	3	CD	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	strain	strain	NN	_	_	_
123	:	:	:	_	_	_
124	TB1	tb1	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
126	The	the	DT	_	_	_
127	pre-culture	pre-culture	JJ	_	_	_
128	was	be	VBD	_	_	_
129	the	the	DT	_	_	_
130	overnight	overnight	JJ	_	_	_
131	propagated	propagate	VBN	_	_	_
132	cells	cell	NNS	_	_	_
133	in	in	IN	_	_	_
134	5	5	CD	_	_	_
135	ml	ml	NN	_	_	_
136	of	of	IN	_	_	_
137	LB	lb	NN	MED	_	_
138	medium	medium	NN	MED	_	_
139	at	at	IN	_	_	_
140	37ºC	37ºc	NN	_	_	_
141	and	and	CC	_	_	_
142	180	180	CD	_	_	_
143	rpm	rpm	NN	_	_	_
144	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	main	main	JJ	_	_	_
3	bacterial	bacterial	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	prepared	prepare	VBN	_	_	_
7	by	by	IN	_	_	_
8	1	1	CD	_	_	_
9	%	%	NN	_	_	_
10	inoculation	inoculation	NN	_	_	_
11	from	from	IN	_	_	_
12	pre-culture	pre-culture	JJ	_	_	_
13	when	when	WRB	_	_	_
14	optical	optical	JJ	_	_	_
15	densities	density	NNS	_	_	_
16	at	at	IN	_	_	_
17	600	600	CD	_	_	_
18	nm	nm	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	i.e.	i.e.	FW	_	_	_
21	,	,	,	_	_	_
22	OD600	od600	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	reached	reach	VBD	_	_	_
25	0.7	0.7	CD	_	_	_
26	.	.	.	_	_	_

1	Growth	growth	NN	_	_	_
2	was	be	VBD	_	_	_
3	achieved	achieve	VBN	_	_	_
4	in	in	IN	_	_	_
5	50	50	CD	_	_	_
6	ml	ml	NN	_	_	_
7	of	of	IN	_	_	_
8	LB	lb	NN	MED	_	_
9	medium	medium	NN	MED	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	extraction	extraction	NN	_	_	_
5	was	be	VBD	_	_	_
6	carried	carry	VBN	_	_	_
7	out	out	RP	_	_	_
8	based	base	VBN	_	_	_
9	on	on	IN	_	_	_
10	the	the	DT	_	_	_
11	protocols	protocol	NNS	_	_	_
12	given	give	VBN	_	_	_
13	in	in	IN	_	_	_
14	the	the	DT	_	_	_
15	manual	manual	NN	_	_	_
16	of	of	IN	_	_	_
17	QIAGEN	QIAGEN	NNP	_	_	_
18	-	-	:	_	_	_
19	RNAprotect	rnaprotect	NN	_	_	_
20	Bacteria	bacterium	NNS	_	_	_
21	Reagent	Reagent	NNP	_	_	_
22	Handbook	Handbook	NNP	_	_	_
23	,	,	,	_	_	_
24	QIAGEN	QIAGEN	NNP	_	_	_
25	-	-	:	_	_	_
26	RNeasy	RNeasy	NNP	_	_	_
27	Mini	Mini	NNP	_	_	_
28	Kit	kit	NN	_	_	_
29	and	and	CC	_	_	_
30	QIAGEN	QIAGEN	NNP	_	_	_
31	-	-	:	_	_	_
32	RNase-free	rnase-free	JJ	_	_	_
33	DNase	dnase	NN	_	_	_
34	set	set	NN	_	_	_
35	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	concentration	concentration	NN	_	_	_
3	of	of	IN	_	_	_
4	each	each	DT	_	_	_
5	RNA	rna	NN	_	_	_
6	sample	sample	NN	_	_	_
7	was	be	VBD	_	_	_
8	measured	measure	VBN	_	_	_
9	by	by	IN	_	_	_
10	Qubit	Qubit	NNP	_	_	_
11	®	®	NNP	_	_	_
12	RNA	rna	NN	_	_	_
13	BR	br	NN	_	_	_
14	Assay	assay	NN	_	_	_
15	Kit	kit	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Invitrogen	invitrogen	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	When	when	WRB	_	_	_
3	OD600	od600	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	culture	culture	NN	_	_	_
7	reached	reach	VBD	_	_	_
8	0.54	0.54	CD	_	_	_
9	±	±	SYM	_	_	_
10	0.06	0.06	CD	_	_	_
11	,	,	,	_	_	_
12	cells	cell	NNS	_	_	_
13	were	be	VBD	_	_	_
14	treated	treat	VBN	_	_	_
15	with	with	IN	_	_	_
16	100	100	CD	_	_	_
17	µg	µg	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	0	0	CD	_	_	_
20	min	min	NN	_	_	_
21	Nov0	nov0	NN	_	_	_
22	ug	ug	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	0	0	CD	_	_	_
25	min	min	NN	_	_	_
26	Nov500	nov500	NN	_	_	_
27	ug	ug	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	1005	1005	CD	_	_	_
30	fork-blocking	fork-blocking	NN	_	_	_
31	strain	strain	NN	_	_	_
32	induced	induce	VBD	_	_	_
33	for	for	IN	_	_	_
34	Tus	Tus	NNP	_	_	_
35	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
36	1005	1005	CD	_	_	_
37	fork-blocking	fork-blocking	JJ	_	_	_
38	strain	strain	NN	_	_	_
39	induced	induce	VBN	_	_	_
40	for	for	IN	_	_	_
41	Tus	Tus	NNP	_	_	_
42	:	:	:	_	_	_
43	fork5	fork5	CD	_	_	_
44	_	_	NN	_	_	_
45	2	2	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
47	1005	1005	CD	_	_	_
48	fork-blocking	fork-blocking	JJ	_	_	_
49	strain	strain	NN	_	_	_
50	induced	induce	VBN	_	_	_
51	for	for	IN	_	_	_
52	Tus	Tus	NNP	_	_	_
53	:	:	:	_	_	_
54	fork5	fork5	CD	_	_	_
55	_	_	SYM	_	_	_
56	3	3	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	1005	1005	CD	_	_	_
59	,	,	,	_	_	_
60	LB	lb	NN	_	_	_
61	+	+	CC	_	_	_
62	0.2	0.2	CD	_	_	_
63	%	%	NN	_	_	_
64	glucose	glucose	NN	SUPP	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	tus	tus	NN	GEN	_	_
67	repressed	repress	VBN	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
70	1005	1005	CD	_	_	_
71	,	,	,	_	_	_
72	LB	lb	NN	_	_	_
73	+	+	CC	_	_	_
74	0.4	0.4	CD	_	_	_
75	%	%	NN	_	_	_
76	arabinose	arabinose	NN	_	_	_
77	,	,	,	_	_	_
78	2.5	2.5	CD	_	_	_
79	hr	hr	NN	_	_	_
80	-LRB-	-lrb-	-LRB-	_	_	_
81	tus	tus	NN	GEN	_	_
82	induced	induce	VBN	_	_	_
83	-RRB-	-rrb-	-RRB-	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
85	1005	1005	CD	_	_	_
86	,	,	,	_	_	_
87	LB	lb	NN	_	_	_
88	+	+	CC	_	_	_
89	0.4	0.4	CD	_	_	_
90	%	%	NN	_	_	_
91	arabinose	arabinose	NN	_	_	_
92	,	,	,	_	_	_
93	3.5	3.5	CD	_	_	_
94	hr	hr	NN	_	_	_
95	-LRB-	-lrb-	-LRB-	_	_	_
96	tus	tus	NN	GEN	_	_
97	induced	induce	VBN	_	_	_
98	-RRB-	-rrb-	-RRB-	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
100	1005	1005	CD	_	_	_
101	,	,	,	_	_	_
102	LB	lb	NN	_	_	_
103	+	+	CC	_	_	_
104	0.4	0.4	CD	_	_	_
105	%	%	NN	_	_	_
106	arabinose	arabinose	NN	_	_	_
107	,	,	,	_	_	_
108	90	90	CD	_	_	_
109	'	'	''	_	_	_
110	-LRB-	-lrb-	-LRB-	_	_	_
111	tus	tus	FW	GEN	_	_
112	induced	induce	VBN	_	_	_
113	-RRB-	-rrb-	-RRB-	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	BAM	bam	NN	_	_	_
116	files	file	NNS	_	_	_
117	of	of	IN	_	_	_
118	the	the	DT	_	_	_
119	resulting	result	VBG	_	_	_
120	assembly	assembly	NN	_	_	_
121	data	datum	NNS	_	_	_
122	were	be	VBD	_	_	_
123	exported	export	VBN	_	_	_
124	to	to	TO	_	_	_
125	JMP	JMP	NNP	_	_	_
126	Genomics	Genomics	NNP	_	_	_
127	-LRB-	-lrb-	-LRB-	_	_	_
128	SAS	SAS	NNP	_	_	_
129	-RRB-	-rrb-	-RRB-	_	_	_
130	.	.	.	_	_	_

1	TMM	TMM	NNP	_	_	_
2	normalization	normalization	NN	_	_	_
3	and	and	CC	_	_	_
4	ANOVA	anova	NN	_	_	_
5	analysis	analysis	NN	_	_	_
6	of	of	IN	_	_	_
7	the	the	DT	_	_	_
8	read	read	NN	_	_	_
9	samples	sample	NNS	_	_	_
10	were	be	VBD	_	_	_
11	conducted	conduct	VBN	_	_	_
12	in	in	IN	_	_	_
13	JMP	JMP	NNP	_	_	_
14	Genomics	Genomics	NNPS	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	Cell	cell	NN	_	_	_
17	pellets	pellet	NNS	_	_	_
18	were	be	VBD	_	_	_
19	lysed	lyse	VBN	_	_	_
20	and	and	CC	_	_	_
21	RNA	rna	NN	_	_	_
22	collected	collect	VBN	_	_	_
23	using	use	VBG	_	_	_
24	Qiagen	Qiagen	NNP	_	_	_
25	's	's	POS	_	_	_
26	RNeasy	RNeasy	NNP	_	_	_
27	Plus	Plus	NNP	_	_	_
28	Mini	Mini	NNP	_	_	_
29	Kit	kit	NN	_	_	_
30	with	with	IN	_	_	_
31	Qiagen	Qiagen	NNP	_	_	_
32	Bacteria	bacterium	NNS	_	_	_
33	Protect	protect	VB	_	_	_
34	RNA	rna	NN	_	_	_
35	kit	kit	NN	_	_	_
36	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	treated	treat	VBN	_	_	_
6	with	with	IN	_	_	_
7	DNase	dnase	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	New	New	NNP	_	_	_
10	England	England	NNP	_	_	_
11	Biolabs	Biolabs	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	for	for	IN	_	_	_
14	30	30	CD	_	_	_
15	min	min	NN	_	_	_
16	at	at	IN	_	_	_
17	37	37	CD	_	_	_
18	°C	°c	NN	_	_	_
19	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	to	to	TO	_	_	_
6	approximately	approximately	RB	_	_	_
7	mid-log	mid-log	JJ	_	_	_
8	phase	phase	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	OD560	od560	NN	_	_	_
11	=	=	JJ	_	_	_
12	approximately	approximately	RB	_	_	_
13	0.5	0.5	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	in	in	IN	_	_	_
16	LB	lb	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	genotype	genotype	NN	_	_	_
6	:	:	:	_	_	_
7	mfd	mfd	SYM	GEN	_	_
8	-	-	:	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	genotype	genotype	NN	_	_	_
11	:	:	:	_	_	_
12	Mfd	mfd	NN	_	_	_
13	+	+	CC	_	_	_
14	+	+	CC	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	genotype	genotype	NN	_	_	_
17	:	:	:	_	_	_
18	Wildtype	wildtype	JJ	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	genotype	genotype	NN	_	_	_
21	:	:	:	_	_	_
22	Wildtype	wildtype	NN	_	_	_
23	with	with	IN	_	_	_
24	vector	vector	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	mfd	mfd	NN	GEN	_	_
27	_	_	NN	_	_	_
28	1	1	CD	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	MFD	mfd	NN	_	_	_
31	+	+	CC	_	_	_
32	+	+	CC	_	_	_
33	_	_	SYM	_	_	_
34	1	1	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	mfd	mfd	NN	GEN	_	_
37	_	_	NN	_	_	_
38	2	2	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	MFD	mfd	NN	_	_	_
41	+	+	CC	_	_	_
42	+	+	CC	_	_	_
43	_	_	SYM	_	_	_
44	2	2	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	mfd	mfd	NN	GEN	_	_
47	_	_	NN	_	_	_
48	3	3	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	MG1655	mg1655	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	MG1655	mg1655	NN	_	_	_
53	_	_	NN	_	_	_
54	1	1	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	MG1655	mg1655	NN	_	_	_
57	_	_	NN	_	_	_
58	2	2	CD	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	MG1655	mg1655	NN	_	_	_
61	_	_	CD	_	_	_
62	3	3	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	MG1655	mg1655	NN	_	_	_
65	pCA24N	pca24n	NN	_	_	_
66	and	and	CC	_	_	_
67	MG1655	mg1655	NN	_	_	_
68	pCA24N-Mfd	pca24n-mfd	NN	_	_	_
69	cells	cell	NNS	_	_	_
70	were	be	VBD	_	_	_
71	grown	grow	VBN	_	_	_
72	to	to	TO	_	_	_
73	an	a	DT	_	_	_
74	OD560	od560	NN	_	_	_
75	of	of	IN	_	_	_
76	approximately	approximately	RB	_	_	_
77	0.25	0.25	CD	_	_	_
78	and	and	CC	_	_	_
79	treated	treat	VBN	_	_	_
80	with	with	IN	_	_	_
81	100	100	CD	_	_	_
82	μM	μm	NN	_	_	_
83	IPTG	iptg	NN	_	_	_
84	for	for	IN	_	_	_
85	1	1	CD	_	_	_
86	hour	hour	NN	_	_	_
87	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	MG1655	mg1655	NN	_	_	_
3	_	_	NN	_	_	_
4	vector	vector	NN	_	_	_
5	_	_	NN	_	_	_
6	1	1	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	MG1655	mg1655	NN	_	_	_
9	_	_	NN	_	_	_
10	vector	vector	NN	_	_	_
11	_	_	NN	_	_	_
12	2	2	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
14	Read	read	VBP	_	_	_
15	coverage	coverage	NN	_	_	_
16	maps	map	NNS	_	_	_
17	and	and	CC	_	_	_
18	RPKM	RPKM	NNP	_	_	_
19	data	datum	NNS	_	_	_
20	was	be	VBD	_	_	_
21	subsequently	subsequently	RB	_	_	_
22	generated	generate	VBN	_	_	_
23	by	by	IN	_	_	_
24	Geneious	Geneious	NNP	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	prepared	prepare	VBN	_	_	_
6	for	for	IN	_	_	_
7	sequencing	sequencing	NN	_	_	_
8	using	use	VBG	_	_	_
9	standard	standard	JJ	_	_	_
10	Illumina	Illumina	NNP	_	_	_
11	protocols	protocol	NNS	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	RNA-Seq	RNA-Seq	NNP	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	Sequencing	sequencing	NN	_	_	_
16	reads	read	VBZ	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	approximately	approximately	RB	_	_	_
19	13	13	CD	_	_	_
20	to	to	TO	_	_	_
21	25	25	CD	_	_	_
22	million	million	CD	_	_	_
23	per	per	IN	_	_	_
24	sample	sample	NN	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	were	be	VBD	_	_	_
27	imported	import	VBN	_	_	_
28	into	into	IN	_	_	_
29	Geneious	geneious	JJ	_	_	_
30	Pro	pro	FW	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Biomatters	biomatter	NNS	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	and	and	CC	_	_	_
35	assembled	assemble	VBN	_	_	_
36	to	to	TO	_	_	_
37	the	the	DT	_	_	_
38	reference	reference	NN	_	_	_
39	chromosome	chromosome	NN	_	_	_
40	MG1655	mg1655	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	GenBank	genbank	NN	_	_	_
43	Accession	Accession	NNP	_	_	_
44	Number	number	NN	_	_	_
45	000913.2	000913.2	CD	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	assembly	assembly	NN	_	_	_
3	process	process	NN	_	_	_
4	was	be	VBD	_	_	_
5	set	set	VBN	_	_	_
6	to	to	TO	_	_	_
7	medium	medium	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	bacteria	bacterium	NNS	_	_	_
10	grown	grow	VBN	_	_	_
11	in	in	IN	_	_	_
12	LB	lb	NN	_	_	_
13	in	in	FW	_	_	_
14	vitro	vitro	FW	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	bacteria	bacterium	NNS	_	_	_
17	harvested	harvest	VBN	_	_	_
18	from	from	IN	_	_	_
19	blood	blood	NN	_	_	_
20	of	of	IN	_	_	_
21	chickens	chicken	NNS	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	condition	condition	NN	_	_	_
24	:	:	:	_	_	_
25	in	in	FW	_	_	_
26	vitro	vitro	FW	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	condition	condition	NN	_	_	_
29	:	:	:	_	_	_
30	in	in	FW	_	_	_
31	vivo	vivo	FW	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	E058	e058	NN	_	_	_
34	in	in	FW	_	_	_
35	vitro	vitro	FW	_	_	_
36	,	,	,	_	_	_
37	biological	biological	JJ	_	_	_
38	rep1	rep1	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	E058	e058	NN	_	_	_
41	in	in	FW	_	_	_
42	vitro	vitro	FW	_	_	_
43	,	,	,	_	_	_
44	biological	biological	JJ	_	_	_
45	rep2	rep2	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	E058	e058	NN	_	_	_
48	in	in	FW	_	_	_
49	vivo	vivo	FW	_	_	_
50	,	,	,	_	_	_
51	biological	biological	JJ	_	_	_
52	rep1	rep1	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	E058	e058	NN	_	_	_
55	in	in	FW	_	_	_
56	vivo	vivo	FW	_	_	_
57	,	,	,	_	_	_
58	biological	biological	JJ	_	_	_
59	rep2	rep2	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	E058	e058	NN	_	_	_
62	in	in	FW	_	_	_
63	vivo	vivo	FW	_	_	_
64	,	,	,	_	_	_
65	biological	biological	JJ	_	_	_
66	rep3	rep3	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	Escherichia	escherichia	FW	Organism	_	_
69	coli	coli	FW	Organism	_	_
70	APEC	apec	NN	_	_	_
71	O2	o2	CD	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	strain	strain	NN	_	_	_
74	:	:	:	_	_	_
75	O2	o2	CD	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
77	The	the	DT	_	_	_
78	data	datum	NNS	_	_	_
79	were	be	VBD	_	_	_
80	analyzed	analyze	VBN	_	_	_
81	with	with	IN	_	_	_
82	Microarray	Microarray	NNP	_	_	_
83	Suite	Suite	NNP	_	_	_
84	version	version	NN	_	_	_
85	5.0	5.0	CD	_	_	_
86	-LRB-	-lrb-	-LRB-	_	_	_
87	MAS	mas	NN	_	_	_
88	5.0	5.0	CD	_	_	_
89	-RRB-	-rrb-	-RRB-	_	_	_
90	using	use	VBG	_	_	_
91	Affymetrix	Affymetrix	NNP	_	_	_
92	default	default	NN	_	_	_
93	analysis	analysis	NN	_	_	_
94	settings	setting	NNS	_	_	_
95	and	and	CC	_	_	_
96	global	global	JJ	_	_	_
97	scaling	scaling	NN	_	_	_
98	as	as	IN	_	_	_
99	normalization	normalization	NN	_	_	_
100	method	method	NN	_	_	_
101	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	trimmed	trim	VBN	_	_	_
3	mean	mean	NN	_	_	_
4	target	target	NN	_	_	_
5	intensity	intensity	NN	_	_	_
6	of	of	IN	_	_	_
7	each	each	DT	_	_	_
8	array	array	NN	_	_	_
9	was	be	VBD	_	_	_
10	arbitrarily	arbitrarily	RB	_	_	_
11	set	set	VBN	_	_	_
12	to	to	TO	_	_	_
13	100	100	CD	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	in	in	FW	_	_	_
4	vitro	vitro	FW	_	_	_
5	bacterial	bacterial	JJ	_	_	_
6	samples	sample	NNS	_	_	_
7	were	be	VBD	_	_	_
8	harvested	harvest	VBN	_	_	_
9	by	by	IN	_	_	_
10	centrifugation	centrifugation	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	5000	5000	CD	_	_	_
13	×	×	CD	_	_	_
14	g	g	NN	_	_	_
15	,	,	,	_	_	_
16	10	10	CD	_	_	_
17	min	min	NN	_	_	_
18	,	,	,	_	_	_
19	4	4	CD	_	_	_
20	°C	°c	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	and	and	CC	_	_	_
23	the	the	DT	_	_	_
24	pellet	pellet	NN	_	_	_
25	was	be	VBD	_	_	_
26	frozen	freeze	VBN	_	_	_
27	at	at	IN	_	_	_
28	−	−	CD	_	_	_
29	70	70	CD	_	_	_
30	°C	°c	NN	_	_	_
31	until	until	IN	_	_	_
32	RNA	rna	NN	_	_	_
33	extraction	extraction	NN	_	_	_
34	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	in	in	FW	_	_	_
3	vivo	vivo	FW	_	_	_
4	bacterial	bacterial	JJ	_	_	_
5	samples	sample	NNS	_	_	_
6	were	be	VBD	_	_	_
7	harvested	harvest	VBN	_	_	_
8	with	with	IN	_	_	_
9	two-step	two-step	JJ	_	_	_
10	centrifugation	centrifugation	NN	_	_	_
11	.	.	.	_	_	_

1	We	we	PRP	_	_	_
2	first	first	RB	_	_	_
3	centrifuged	centrifuge	VBD	_	_	_
4	the	the	DT	_	_	_
5	collected	collect	VBN	_	_	_
6	anticoagulated	anticoagulated	JJ	_	_	_
7	blood	blood	NN	_	_	_
8	samples	sample	NNS	_	_	_
9	at	at	IN	_	_	_
10	low	low	JJ	_	_	_
11	speed	speed	NN	_	_	_
12	to	to	TO	_	_	_
13	remove	remove	VB	_	_	_
14	the	the	DT	_	_	_
15	abundant	abundant	JJ	_	_	_
16	red	red	JJ	_	_	_
17	and	and	CC	_	_	_
18	white	white	JJ	_	_	_
19	blood	blood	NN	_	_	_
20	cells	cell	NNS	_	_	_
21	and	and	CC	_	_	_
22	collected	collect	VBN	_	_	_
23	the	the	DT	_	_	_
24	upper	upper	JJ	_	_	_
25	serum	serum	NN	_	_	_
26	layer	layer	NN	_	_	_
27	.	.	.	_	_	_

1	We	we	PRP	_	_	_
2	then	then	RB	_	_	_
3	used	use	VBD	_	_	_
4	high-speed	high-speed	JJ	_	_	_
5	centrifugation	centrifugation	NN	_	_	_
6	to	to	TO	_	_	_
7	precipitate	precipitate	VB	_	_	_
8	the	the	DT	_	_	_
9	bacteria	bacterium	NNS	_	_	_
10	from	from	IN	_	_	_
11	the	the	DT	_	_	_
12	serum	serum	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	To	to	TO	_	_	_
3	prepare	prepare	VB	_	_	_
4	the	the	DT	_	_	_
5	in	in	FW	_	_	_
6	vitro	vitro	FW	_	_	_
7	samples	sample	NNS	_	_	_
8	,	,	,	_	_	_
9	APEC	APEC	NNP	_	_	_
10	strain	strain	NN	_	_	_
11	E058	e058	NN	_	_	_
12	was	be	VBD	_	_	_
13	grown	grow	VBN	_	_	_
14	statically	statically	RB	_	_	_
15	at	at	IN	_	_	_
16	37	37	CD	_	_	_
17	°C	°c	NN	_	_	_
18	in	in	IN	_	_	_
19	10	10	CD	_	_	_
20	mL	ml	NN	_	_	_
21	of	of	IN	_	_	_
22	LB	lb	NN	MED	_	_
23	broth	broth	NN	MED	_	_
24	until	until	IN	_	_	_
25	the	the	DT	_	_	_
26	absorbance	absorbance	NN	_	_	_
27	at	at	IN	_	_	_
28	600	600	CD	_	_	_
29	nm	nm	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	A600	a600	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	reached	reach	VBD	_	_	_
34	0.4	0.4	CD	_	_	_
35	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	prepare	prepare	VB	_	_	_
3	the	the	DT	_	_	_
4	in	in	FW	_	_	_
5	vivo	vivo	FW	_	_	_
6	samples	sample	NNS	_	_	_
7	,	,	,	_	_	_
8	the	the	DT	_	_	_
9	bacteria	bacterium	NNS	_	_	_
10	was	be	VBD	_	_	_
11	harvested	harvest	VBN	_	_	_
12	from	from	IN	_	_	_
13	cardiac	cardiac	JJ	_	_	_
14	blood	blood	NN	_	_	_
15	in	in	IN	_	_	_
16	1-day-old	1-day-old	JJ	_	_	_
17	chickens	chicken	NNS	_	_	_
18	at	at	IN	_	_	_
19	5	5	CD	_	_	_
20	hours	hour	NNS	_	_	_
21	post	post	NN	_	_	_
22	infection	infection	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	from	from	IN	_	_	_
5	both	both	CC	_	_	_
6	the	the	DT	_	_	_
7	in	in	FW	_	_	_
8	vitro	vitro	FW	_	_	_
9	and	and	CC	_	_	_
10	in	in	FW	_	_	_
11	vivo	vivo	FW	_	_	_
12	samples	sample	NNS	_	_	_
13	of	of	IN	_	_	_
14	APEC	APEC	NNP	_	_	_
15	E058	e058	NN	_	_	_
16	was	be	VBD	_	_	_
17	extracted	extract	VBN	_	_	_
18	with	with	IN	_	_	_
19	the	the	DT	_	_	_
20	RNAiso	rnaiso	NN	_	_	_
21	Plus	plus	NN	_	_	_
22	kit	kit	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Takara	Takara	NNP	_	_	_
25	,	,	,	_	_	_
26	Dalian	Dalian	NNP	_	_	_
27	,	,	,	_	_	_
28	China	China	NNP	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	and	and	CC	_	_	_
31	further	further	JJ	_	_	_
32	purified	purify	VBN	_	_	_
33	with	with	IN	_	_	_
34	NucleoSpin	nucleospin	NN	_	_	_
35	RNA	rna	NN	_	_	_
36	Clean-up	clean-up	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Macherey-Nagel	Macherey-Nagel	NNP	_	_	_
39	,	,	,	_	_	_
40	Germany	Germany	NNP	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	,	,	,	_	_	_
43	according	accord	VBG	_	_	_
44	to	to	TO	_	_	_
45	the	the	DT	_	_	_
46	manufacturers	manufacturer	NNS	_	_	_
47	'	'	POS	_	_	_
48	instructions	instruction	NNS	_	_	_
49	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	1	1	CD	_	_	_
3	min	min	NN	_	_	_
4	Nov0	nov0	NN	_	_	_
5	ug	ug	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	1	1	CD	_	_	_
8	min	min	NN	_	_	_
9	Nov500	nov500	NN	_	_	_
10	ug	ug	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	20	20	CD	_	_	_
13	min	min	NN	_	_	_
14	Nov0	nov0	NN	_	_	_
15	ug	ug	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	20	20	CD	_	_	_
18	min	min	NN	_	_	_
19	Nov500	nov500	NN	_	_	_
20	ug	ug	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	20	20	CD	_	_	_
23	min	min	NN	_	_	_
24	Nov50	nov50	NN	_	_	_
25	ug	ug	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	1.1	1.1	CD	_	_	_
28	A	a	DT	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	1.1	1.1	CD	_	_	_
31	A	a	DT	_	_	_
32	_	_	NN	_	_	_
33	Earth	Earth	NNP	_	_	_
34	_	_	SYM	_	_	_
35	25	25	CD	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	1.2	1.2	CD	_	_	_
38	A	a	DT	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	1.2	1.2	CD	_	_	_
41	A	a	DT	_	_	_
42	_	_	NN	_	_	_
43	Space	space	NN	_	_	_
44	_	_	CD	_	_	_
45	25	25	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	1.3	1.3	CD	_	_	_
48	A	a	DT	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	1.3	1.3	CD	_	_	_
51	A	a	DT	_	_	_
52	_	_	NN	_	_	_
53	Earth	Earth	NNP	_	_	_
54	_	_	SYM	_	_	_
55	25	25	CD	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	1.4	1.4	CD	_	_	_
58	A	a	DT	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	1.4	1.4	CD	_	_	_
61	A	a	DT	_	_	_
62	_	_	NN	_	_	_
63	Space	space	NN	_	_	_
64	_	_	CD	_	_	_
65	25	25	CD	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	1.5	1.5	CD	_	_	_
68	A	a	DT	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	1.5	1.5	CD	_	_	_
71	A	a	DT	_	_	_
72	_	_	NN	_	_	_
73	Earth	Earth	NNP	_	_	_
74	_	_	SYM	_	_	_
75	50	50	CD	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
77	1.6	1.6	CD	_	_	_
78	A	a	DT	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	1.6	1.6	CD	_	_	_
81	A	a	DT	_	_	_
82	_	_	NN	_	_	_
83	Space	space	NN	_	_	_
84	_	_	CD	_	_	_
85	50	50	CD	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
87	17.1	17.1	CD	_	_	_
88	A	a	DT	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	17.1	17.1	CD	_	_	_
91	A	a	DT	_	_	_
92	_	_	NN	_	_	_
93	Space	space	NN	_	_	_
94	_	_	CD	_	_	_
95	25	25	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	17.2	17.2	CD	_	_	_
98	A	a	DT	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	17.2	17.2	CD	_	_	_
101	A	a	DT	_	_	_
102	_	_	NN	_	_	_
103	Earth	Earth	NNP	_	_	_
104	_	_	SYM	_	_	_
105	25	25	CD	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	17.3	17.3	CD	_	_	_
108	A	a	DT	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	17.3	17.3	CD	_	_	_
111	A	a	DT	_	_	_
112	_	_	NN	_	_	_
113	Space	space	NN	_	_	_
114	_	_	CD	_	_	_
115	25	25	CD	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	17.4	17.4	CD	_	_	_
118	A	a	DT	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	17.4	17.4	CD	_	_	_
121	A	a	DT	_	_	_
122	_	_	NN	_	_	_
123	Earth	Earth	NNP	_	_	_
124	_	_	SYM	_	_	_
125	25	25	CD	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	17.5	17.5	CD	_	_	_
128	A	a	DT	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	17.5	17.5	CD	_	_	_
131	A	a	DT	_	_	_
132	_	_	NN	_	_	_
133	Space	space	NN	_	_	_
134	_	_	CD	_	_	_
135	50	50	CD	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	17.6	17.6	CD	_	_	_
138	A	a	DT	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	17.6	17.6	CD	_	_	_
141	A	a	DT	_	_	_
142	_	_	NN	_	_	_
143	Space	space	NN	_	_	_
144	_	_	CD	_	_	_
145	50	50	CD	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
147	17.8	17.8	CD	_	_	_
148	A	a	DT	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	17.8	17.8	CD	_	_	_
151	A	a	DT	_	_	_
152	_	_	NN	_	_	_
153	Earth	Earth	NNP	_	_	_
154	_	_	SYM	_	_	_
155	50	50	CD	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
157	1.7	1.7	CD	_	_	_
158	A	a	DT	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	1.7	1.7	CD	_	_	_
161	A	a	DT	_	_	_
162	_	_	NN	_	_	_
163	Earth	Earth	NNP	_	_	_
164	_	_	SYM	_	_	_
165	50	50	CD	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
167	18.2	18.2	CD	_	_	_
168	A	a	DT	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	18.2	18.2	CD	_	_	_
171	A	a	DT	_	_	_
172	_	_	NN	_	_	_
173	Earth	Earth	NNP	_	_	_
174	_	_	SYM	_	_	_
175	75	75	CD	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	18.3	18.3	CD	_	_	_
178	A	a	DT	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	18.3	18.3	CD	_	_	_
181	A	a	DT	_	_	_
182	_	_	NN	_	_	_
183	Space	space	NN	_	_	_
184	_	_	CD	_	_	_
185	75	75	CD	_	_	_
186	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
187	18.4	18.4	CD	_	_	_
188	A	a	DT	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	18.4	18.4	CD	_	_	_
191	A	a	DT	_	_	_
192	_	_	NN	_	_	_
193	Earth	Earth	NNP	_	_	_
194	_	_	SYM	_	_	_
195	75	75	CD	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	2.1	2.1	CD	_	_	_
198	A	a	DT	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	2.1	2.1	CD	_	_	_
201	A	a	DT	_	_	_
202	_	_	NN	_	_	_
203	Earth	Earth	NNP	_	_	_
204	_	_	SYM	_	_	_
205	75	75	CD	_	_	_
206	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
207	2.3	2.3	CD	_	_	_
208	A	a	DT	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	2.3	2.3	CD	_	_	_
211	A	a	DT	_	_	_
212	_	_	NN	_	_	_
213	Earth	Earth	NNP	_	_	_
214	_	_	SYM	_	_	_
215	75	75	CD	_	_	_
216	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
217	2.4	2.4	CD	_	_	_
218	A	a	DT	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	2.4	2.4	CD	_	_	_
221	A	a	DT	_	_	_
222	_	_	NN	_	_	_
223	Space	space	NN	_	_	_
224	_	_	CD	_	_	_
225	75	75	CD	_	_	_
226	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
227	Escherichia	escherichia	FW	Organism	_	_
228	coli	coli	FW	Organism	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
230	Four	four	CD	_	_	_
231	ml	ml	NN	_	_	_
232	of	of	IN	_	_	_
233	the	the	DT	_	_	_
234	bacterial	bacterial	JJ	_	_	_
235	suspension	suspension	NN	_	_	_
236	in	in	IN	_	_	_
237	RNALater	rnalater	NN	_	_	_
238	II	ii	CD	_	_	_
239	and	and	CC	_	_	_
240	Medium	medium	NN	_	_	_
241	E	e	NN	_	_	_
242	growth	growth	NN	_	_	_
243	medium	medium	NN	_	_	_
244	were	be	VBD	_	_	_
245	spun	spin	VBN	_	_	_
246	down	down	RP	_	_	_
247	at	at	IN	_	_	_
248	200g	200g	NN	_	_	_
249	for	for	IN	_	_	_
250	5	5	CD	_	_	_
251	min	min	NN	_	_	_
252	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	supernatant	supernatant	NN	_	_	_
3	was	be	VBD	_	_	_
4	discarded	discard	VBN	_	_	_
5	and	and	CC	_	_	_
6	the	the	DT	_	_	_
7	pellet	pellet	NN	_	_	_
8	were	be	VBD	_	_	_
9	resuspended	resuspend	VBN	_	_	_
10	in	in	IN	_	_	_
11	200ul	200ul	JJ	_	_	_
12	PBS	PBS	NNP	_	_	_
13	and	and	CC	_	_	_
14	mixed	mix	VBN	_	_	_
15	by	by	IN	_	_	_
16	pipetting	pipetting	NN	_	_	_
17	.	.	.	_	_	_

1	100ul	100ul	NN	_	_	_
2	aliquots	aliquot	NNS	_	_	_
3	were	be	VBD	_	_	_
4	taken	take	VBN	_	_	_
5	out	out	RP	_	_	_
6	for	for	IN	_	_	_
7	DNA	dna	NN	_	_	_
8	and	and	CC	_	_	_
9	RNA	rna	NN	_	_	_
10	extraction	extraction	NN	_	_	_
11	from	from	IN	_	_	_
12	the	the	DT	_	_	_
13	same	same	JJ	_	_	_
14	sample	sample	NN	_	_	_
15	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	extraction	extraction	NN	_	_	_
3	was	be	VBD	_	_	_
4	done	do	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Qiagen	Qiagen	NNP	_	_	_
7	RNeasy	RNeasy	NNP	_	_	_
8	mini	minus	NNS	_	_	_
9	kit	kit	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Qiagen	Qiagen	NNP	_	_	_
12	,	,	,	_	_	_
13	Hilden	Hilden	NNP	_	_	_
14	,	,	,	_	_	_
15	Germany	Germany	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	with	with	IN	_	_	_
18	on-column	on-column	JJ	_	_	_
19	DNase	dnase	NN	_	_	_
20	digestion	digestion	NN	_	_	_
21	.	.	.	_	_	_

1	Final	final	JJ	_	_	_
2	elution	elution	NN	_	_	_
3	was	be	VBD	_	_	_
4	made	make	VBN	_	_	_
5	in	in	IN	_	_	_
6	30	30	CD	_	_	_
7	μL	μl	NN	_	_	_
8	dH2O	dh2o	NN	_	_	_
9	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	concentration	concentration	NN	_	_	_
3	and	and	CC	_	_	_
4	integrity	integrity	NN	_	_	_
5	of	of	IN	_	_	_
6	the	the	DT	_	_	_
7	total	total	JJ	_	_	_
8	RNA	rna	NN	_	_	_
9	was	be	VBD	_	_	_
10	estimated	estimate	VBN	_	_	_
11	by	by	IN	_	_	_
12	Quant-iT	quant-it	NN	_	_	_
13	™	™	CD	_	_	_
14	RiboGreen	RiboGreen	NNP	_	_	_
15	®	®	CD	_	_	_
16	RNA	rna	NN	_	_	_
17	Assay	assay	NN	_	_	_
18	Kit	kit	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	ThermoFisher	ThermoFisher	NNP	_	_	_
21	Scientific	Scientific	NNP	_	_	_
22	,	,	,	_	_	_
23	Waltham	Waltham	NNP	_	_	_
24	,	,	,	_	_	_
25	MA	MA	NNP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	,	,	,	_	_	_
28	and	and	CC	_	_	_
29	Agilent	Agilent	NNP	_	_	_
30	2100	2100	CD	_	_	_
31	Bioanalyzer	Bioanalyzer	NNP	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	Applied	Applied	NNP	_	_	_
34	Biosystems	Biosystems	NNP	_	_	_
35	,	,	,	_	_	_
36	Carlsbad	Carlsbad	NNP	_	_	_
37	,	,	,	_	_	_
38	CA	CA	NNP	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	,	,	,	_	_	_
41	respectively	respectively	RB	_	_	_
42	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	Escherichia	escherichia	FW	Organism	_	_
7	coli	coli	FW	Organism	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	DH10B	dh10b	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	gentamycin	gentamycin	NN	_	_	_
13	concentration	concentration	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	ug	ug	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	location	location	NN	_	_	_
18	:	:	:	_	_	_
19	Earth	Earth	NNP	_	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	location	location	NN	_	_	_
22	:	:	:	_	_	_
23	Space	Space	NNP	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	Nineteen	nineteen	CD	_	_	_
26	hours	hour	NNS	_	_	_
27	after	after	IN	_	_	_
28	experiment	experiment	NN	_	_	_
29	start	start	NN	_	_	_
30	,	,	,	_	_	_
31	antibiotic	antibiotic	JJ	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	Gentamicin	gentamicin	NN	_	_	_
34	Sulfate	sulfate	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	MP	mp	NN	_	_	_
37	Biomedical	biomedical	NN	_	_	_
38	,	,	,	_	_	_
39	Cat	Cat	NNP	_	_	_
40	No.	No.	NNP	_	_	_
41	1676045	1676045	CD	_	_	_
42	,	,	,	_	_	_
43	Santa	Santa	NNP	_	_	_
44	Ana	Ana	NNP	_	_	_
45	,	,	,	_	_	_
46	CA	CA	NNP	_	_	_
47	,	,	,	_	_	_
48	USA	USA	NNP	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	was	be	VBD	_	_	_
52	introducing	introduce	VBG	_	_	_
53	into	into	IN	_	_	_
54	the	the	DT	_	_	_
55	cultures	culture	NNS	_	_	_
56	.	.	.	_	_	_

1	Antibiotic	antibiotic	JJ	_	_	_
2	concentration	concentration	NN	_	_	_
3	varied	vary	VBD	_	_	_
4	from	from	IN	_	_	_
5	one	one	CD	_	_	_
6	sample	sample	NN	_	_	_
7	to	to	TO	_	_	_
8	the	the	DT	_	_	_
9	next	next	JJ	_	_	_
10	from	from	IN	_	_	_
11	0	0	CD	_	_	_
12	to	to	TO	_	_	_
13	150	150	CD	_	_	_
14	ug	ug	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Post-processing	post-processing	NN	_	_	_
17	of	of	IN	_	_	_
18	the	the	DT	_	_	_
19	sequencing	sequencing	NN	_	_	_
20	reads	read	VBZ	_	_	_
21	from	from	IN	_	_	_
22	RNA-seq	rna-seq	NN	_	_	_
23	experiments	experiment	NNS	_	_	_
24	for	for	IN	_	_	_
25	each	each	DT	_	_	_
26	sample	sample	NN	_	_	_
27	was	be	VBD	_	_	_
28	performed	perform	VBN	_	_	_
29	using	use	VBG	_	_	_
30	HudsonAlpha	HudsonAlpha	NNP	_	_	_
31	's	's	POS	_	_	_
32	unique	unique	JJ	_	_	_
33	in-house	in-house	JJ	_	_	_
34	RNA-seq	rna-seq	NN	_	_	_
35	data	data	NN	_	_	_
36	analysis	analysis	NN	_	_	_
37	pipeline	pipeline	NN	_	_	_
38	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	quality	quality	NN	_	_	_
4	control	control	NN	_	_	_
5	checks	check	NNS	_	_	_
6	on	on	IN	_	_	_
7	raw	raw	JJ	_	_	_
8	sequence	sequence	NN	_	_	_
9	data	datum	NNS	_	_	_
10	for	for	IN	_	_	_
11	each	each	DT	_	_	_
12	sample	sample	NN	_	_	_
13	were	be	VBD	_	_	_
14	performed	perform	VBN	_	_	_
15	using	use	VBG	_	_	_
16	FastQC	fastqc	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Babraham	babraham	NN	_	_	_
19	Bioinformatics	bioinformatic	NNS	_	_	_
20	,	,	,	_	_	_
21	Cambridge	Cambridge	NNP	_	_	_
22	,	,	,	_	_	_
23	UK	UK	NNP	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	.	.	.	_	_	_

1	Data-analysis	data-analysis	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	using	use	VBG	_	_	_
5	the	the	DT	_	_	_
6	CLC	clc	NN	_	_	_
7	Genomics	genomic	NNS	_	_	_
8	Workbench	Workbench	NNP	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Version	Version	NNP	_	_	_
11	7.5.1	7.5.1	CD	_	_	_
12	,	,	,	_	_	_
13	CLC	clc	NN	_	_	_
14	Bio	bio	NN	_	_	_
15	,	,	,	_	_	_
16	Aarhus	Aarhus	NNP	_	_	_
17	,	,	,	_	_	_
18	Denmark	Denmark	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	reference	reference	NN	_	_	_
3	genome	genome	NN	_	_	_
4	Escherichia	escherichia	FW	Organism	_	_
5	coli	coli	FW	Organism	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	DH10B	dh10b	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	sequence	sequence	NN	_	_	_
10	was	be	VBD	_	_	_
11	downloaded	download	VBN	_	_	_
12	from	from	IN	_	_	_
13	the	the	DT	_	_	_
14	UCSC	UCSC	NNP	_	_	_
15	genome	genome	NN	_	_	_
16	browser	browser	NN	_	_	_
17	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	read	read	VBN	_	_	_
3	mapping	mapping	NN	_	_	_
4	,	,	,	_	_	_
5	the	the	DT	_	_	_
6	following	follow	VBG	_	_	_
7	parameters	parameter	NNS	_	_	_
8	were	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	:	:	:	_	_	_
11	mismatch	mismatch	NN	_	_	_
12	cost	cost	NN	_	_	_
13	=	=	JJ	_	_	_
14	2	2	CD	_	_	_
15	,	,	,	_	_	_
16	insertion	insertion	NN	_	_	_
17	and	and	CC	_	_	_
18	deletion	deletion	NN	_	_	_
19	cost	cost	NN	_	_	_
20	=	=	JJ	_	_	_
21	3	3	CD	_	_	_
22	,	,	,	_	_	_
23	length	length	NN	_	_	_
24	fraction	fraction	NN	_	_	_
25	:	:	:	_	_	_
26	0.8	0.8	CD	_	_	_
27	,	,	,	_	_	_
28	similarity	similarity	NN	_	_	_
29	fraction	fraction	NN	_	_	_
30	=	=	JJ	_	_	_
31	0.8	0.8	CD	_	_	_
32	,	,	,	_	_	_
33	global	global	JJ	_	_	_
34	alignment	alignment	NN	_	_	_
35	=	=	JJ	_	_	_
36	no	no	DT	_	_	_
37	,	,	,	_	_	_
38	auto-detect	auto-detect	JJ	_	_	_
39	paired	paired	JJ	_	_	_
40	distances	distance	NNS	_	_	_
41	=	=	JJ	_	_	_
42	yes	yes	UH	_	_	_
43	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	grouped	group	VBN	_	_	_
4	and	and	CC	_	_	_
5	differential	differential	JJ	_	_	_
6	expression	expression	NN	_	_	_
7	of	of	IN	_	_	_
8	genes	gene	NNS	_	_	_
9	was	be	VBD	_	_	_
10	calculated	calculate	VBN	_	_	_
11	on	on	IN	_	_	_
12	the	the	DT	_	_	_
13	basis	basis	NN	_	_	_
14	of	of	IN	_	_	_
15	fold	fold	JJ	_	_	_
16	changes	change	NNS	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	using	use	VBG	_	_	_
19	the	the	DT	_	_	_
20	default	default	NN	_	_	_
21	cut-off	cut-off	JJ	_	_	_
22	≥	≥	NN	_	_	_
23	±	±	NN	_	_	_
24	2.0	2.0	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	observed	observe	VBN	_	_	_
27	in	in	IN	_	_	_
28	comparisons	comparison	NNS	_	_	_
29	between	between	IN	_	_	_
30	defined	define	VBN	_	_	_
31	conditions	condition	NNS	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Ribosomal	ribosomal	JJ	_	_	_
3	RNA	rna	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	rRNA	rrna	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	was	be	VBD	_	_	_
8	removed	remove	VBN	_	_	_
9	using	use	VBG	_	_	_
10	Ribo-Zero	Ribo-Zero	NNP	_	_	_
11	™	™	NNP	_	_	_
12	Gold	Gold	NNP	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Yeast	yeast	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	kit	kit	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Epicenter	epicenter	NN	_	_	_
19	,	,	,	_	_	_
20	Madison	Madison	NNP	_	_	_
21	,	,	,	_	_	_
22	WI	WI	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	using	use	VBG	_	_	_
25	manufacturer	manufacturer	NN	_	_	_
26	's	's	POS	_	_	_
27	recommended	recommend	VBN	_	_	_
28	protocol	protocol	NN	_	_	_
29	.	.	.	_	_	_

1	Immediately	immediately	RB	_	_	_
2	after	after	IN	_	_	_
3	the	the	DT	_	_	_
4	rRNA	rrna	NN	_	_	_
5	removal	removal	NN	_	_	_
6	the	the	DT	_	_	_
7	RNA	rna	NN	_	_	_
8	was	be	VBD	_	_	_
9	fragmented	fragmented	JJ	_	_	_
10	and	and	CC	_	_	_
11	primed	prime	VBN	_	_	_
12	for	for	IN	_	_	_
13	the	the	DT	_	_	_
14	first	first	JJ	_	_	_
15	strand	strand	NN	_	_	_
16	synthesis	synthesis	NN	_	_	_
17	using	use	VBG	_	_	_
18	the	the	DT	_	_	_
19	NEBnext	NEBnext	NNP	_	_	_
20	First	First	NNP	_	_	_
21	Strand	Strand	NNP	_	_	_
22	synthesis	synthesis	NN	_	_	_
23	module	module	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	New	New	NNP	_	_	_
26	England	England	NNP	_	_	_
27	BioLabs	BioLabs	NNP	_	_	_
28	Inc.	Inc.	NNP	_	_	_
29	,	,	,	_	_	_
30	Ipswich	Ipswich	NNP	_	_	_
31	,	,	,	_	_	_
32	MA	MA	NNP	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	Directional	directional	JJ	_	_	_
2	second	second	JJ	_	_	_
3	strand	strand	NN	_	_	_
4	synthesis	synthesis	NN	_	_	_
5	was	be	VBD	_	_	_
6	performed	perform	VBN	_	_	_
7	using	use	VBG	_	_	_
8	NEBNExt	NEBNExt	NNP	_	_	_
9	Ultra	Ultra	NNP	_	_	_
10	Directional	Directional	NNP	_	_	_
11	second	second	JJ	_	_	_
12	strand	strand	NN	_	_	_
13	synthesis	synthesis	NN	_	_	_
14	kit	kit	NN	_	_	_
15	.	.	.	_	_	_

1	Following	follow	VBG	_	_	_
2	this	this	DT	_	_	_
3	the	the	DT	_	_	_
4	samples	sample	NNS	_	_	_
5	were	be	VBD	_	_	_
6	taken	take	VBN	_	_	_
7	into	into	IN	_	_	_
8	standard	standard	JJ	_	_	_
9	library	library	NN	_	_	_
10	preparation	preparation	NN	_	_	_
11	protocol	protocol	NN	_	_	_
12	using	use	VBG	_	_	_
13	NEBNext	nebnext	NN	_	_	_
14	®	®	NN	_	_	_
15	DNA	dna	NN	_	_	_
16	Library	Library	NNP	_	_	_
17	Prep	Prep	NNP	_	_	_
18	Master	Master	NNP	_	_	_
19	Mix	Mix	NNP	_	_	_
20	Set	set	VB	_	_	_
21	for	for	IN	_	_	_
22	Illumina	Illumina	NNP	_	_	_
23	®	®	SYM	_	_	_
24	with	with	IN	_	_	_
25	slight	slight	JJ	_	_	_
26	modifications	modification	NNS	_	_	_
27	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	end-repair	end-repair	NN	_	_	_
4	was	be	VBD	_	_	_
5	done	do	VBN	_	_	_
6	followed	follow	VBN	_	_	_
7	by	by	IN	_	_	_
8	polyA	polya	NN	_	_	_
9	addition	addition	NN	_	_	_
10	and	and	CC	_	_	_
11	adapter	adapter	NN	_	_	_
12	ligation	ligation	NN	_	_	_
13	.	.	.	_	_	_

1	Post-ligated	post-ligated	JJ	_	_	_
2	materials	material	NNS	_	_	_
3	were	be	VBD	_	_	_
4	individually	individually	RB	_	_	_
5	barcoded	barcode	VBN	_	_	_
6	with	with	IN	_	_	_
7	primers	primer	NNS	_	_	_
8	and	and	CC	_	_	_
9	amplified	amplify	VBN	_	_	_
10	through	through	IN	_	_	_
11	12	12	CD	_	_	_
12	cycles	cycle	NNS	_	_	_
13	of	of	IN	_	_	_
14	PCR	pcr	NN	_	_	_
15	.	.	.	_	_	_

1	Final	final	JJ	_	_	_
2	library	library	NN	_	_	_
3	quantity	quantity	NN	_	_	_
4	was	be	VBD	_	_	_
5	assessed	assess	VBN	_	_	_
6	by	by	IN	_	_	_
7	Quant-iT	quant-it	NN	_	_	_
8	™	™	CD	_	_	_
9	PicoGreen	PicoGreen	NNP	_	_	_
10	®	®	CD	_	_	_
11	dsDNA	dsDNA	NNP	_	_	_
12	Assay	assay	NN	_	_	_
13	Kit	kit	NN	_	_	_
14	and	and	CC	_	_	_
15	the	the	DT	_	_	_
16	library	library	NN	_	_	_
17	quality	quality	NN	_	_	_
18	was	be	VBD	_	_	_
19	estimated	estimate	VBN	_	_	_
20	on	on	IN	_	_	_
21	LabChip	LabChip	NNP	_	_	_
22	®	®	NNP	_	_	_
23	GX	GX	NNP	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Caliper	Caliper	NNP	_	_	_
26	,	,	,	_	_	_
27	PerkinElmer	PerkinElmer	NNP	_	_	_
28	,	,	,	_	_	_
29	Waltham	Waltham	NNP	_	_	_
30	,	,	,	_	_	_
31	MA	MA	NNP	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Accurate	accurate	JJ	_	_	_
2	quantification	quantification	NN	_	_	_
3	of	of	IN	_	_	_
4	the	the	DT	_	_	_
5	final	final	JJ	_	_	_
6	libraries	library	NNS	_	_	_
7	for	for	IN	_	_	_
8	sequencing	sequencing	NN	_	_	_
9	applications	application	NNS	_	_	_
10	was	be	VBD	_	_	_
11	determined	determine	VBN	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	qPCR-based	qpcr-based	JJ	_	_	_
15	KAPA	KAPA	NNP	_	_	_
16	Biosystems	Biosystems	NNP	_	_	_
17	Library	Library	NNP	_	_	_
18	Quantification	Quantification	NNP	_	_	_
19	kit	kit	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Kapa	Kapa	NNP	_	_	_
22	Biosystems	Biosystems	NNP	_	_	_
23	,	,	,	_	_	_
24	Inc.	Inc.	NNP	_	_	_
25	,	,	,	_	_	_
26	Woburn	Woburn	NNP	_	_	_
27	,	,	,	_	_	_
28	MA	MA	NNP	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	library	library	NN	_	_	_
3	was	be	VBD	_	_	_
4	diluted	dilute	VBN	_	_	_
5	to	to	TO	_	_	_
6	a	a	DT	_	_	_
7	final	final	JJ	_	_	_
8	concentration	concentration	NN	_	_	_
9	of	of	IN	_	_	_
10	12.5	12.5	CD	_	_	_
11	nM	nm	NN	_	_	_
12	and	and	CC	_	_	_
13	pooled	pooled	JJ	_	_	_
14	equimolar	equimolar	JJ	_	_	_
15	prior	prior	JJ	_	_	_
16	to	to	TO	_	_	_
17	clustering	clustering	NN	_	_	_
18	.	.	.	_	_	_

1	Paired-End	paired-end	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	PE	pe	NN	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	sequencing	sequencing	NN	_	_	_
6	was	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	on	on	IN	_	_	_
9	an	a	DT	_	_	_
10	Illumina	Illumina	NNP	_	_	_
11	HiSeq2500	hiseq2500	NN	_	_	_
12	sequencer	sequencer	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Illumina	Illumina	NNP	_	_	_
15	,	,	,	_	_	_
16	Inc.	Inc.	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Samples	sample	NNS	_	_	_
5	were	be	VBD	_	_	_
6	sent	send	VBN	_	_	_
7	to	to	TO	_	_	_
8	the	the	DT	_	_	_
9	International	International	NNP	_	_	_
10	Space	Space	NNP	_	_	_
11	Station	Station	NNP	_	_	_
12	at	at	IN	_	_	_
13	4C	4c	NN	_	_	_
14	in	in	IN	_	_	_
15	FPAs	fpa	NNS	_	_	_
16	,	,	,	_	_	_
17	as	as	IN	_	_	_
18	described	describe	VBN	_	_	_
19	above	above	IN	_	_	_
20	.	.	.	_	_	_

1	Temperature	temperature	NN	_	_	_
2	was	be	VBD	_	_	_
3	increased	increase	VBN	_	_	_
4	to	to	TO	_	_	_
5	37C	37c	NN	_	_	_
6	and	and	CC	_	_	_
7	23	23	CD	_	_	_
8	hours	hour	NNS	_	_	_
9	later	later	RB	_	_	_
10	,	,	,	_	_	_
11	the	the	DT	_	_	_
12	experiment	experiment	NN	_	_	_
13	was	be	VBD	_	_	_
14	started	start	VBN	_	_	_
15	by	by	IN	_	_	_
16	introducing	introduce	VBG	_	_	_
17	the	the	DT	_	_	_
18	inoculum	inoculum	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	E.	e.	FW	_	_	_
21	coli	coli	FW	_	_	_
22	ATCC	atcc	NN	_	_	_
23	4157	4157	CD	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	into	into	IN	_	_	_
26	the	the	DT	_	_	_
27	growth	growth	NN	_	_	_
28	medium	medium	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Medium	medium	NN	_	_	_
31	E	e	NN	_	_	_
32	as	as	IN	_	_	_
33	described	describe	VBN	_	_	_
34	in	in	IN	_	_	_
35	Vogel	Vogel	NNP	_	_	_
36	&	&	CC	_	_	_
37	Bonner	Bonner	NNP	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	1956	1956	CD	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	supplemented	supplement	VBN	_	_	_
42	with	with	IN	_	_	_
43	5	5	CD	_	_	_
44	g	g	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	strain	strain	NN	_	_	_
47	:	:	:	_	_	_
48	ATCC	atcc	NN	_	_	_
49	4157	4157	CD	_	_	_
50	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
51	Supplementary	Supplementary	NNP	_	_	_
52	_	_	VBD	_	_	_
53	files	file	NNS	_	_	_
54	_	_	IN	_	_	_
55	format	format	NN	_	_	_
56	_	_	NN	_	_	_
57	and	and	CC	_	_	_
58	_	_	NN	_	_	_
59	content	content	NN	_	_	_
60	:	:	:	_	_	_
61	excel	excel	VB	_	_	_
62	file	file	NN	_	_	_
63	include	include	VBP	_	_	_
64	RPKM	rpkm	NN	_	_	_
65	values	value	NNS	_	_	_
66	for	for	IN	_	_	_
67	each	each	DT	_	_	_
68	Sample	Sample	NNP	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	2	2	CD	_	_	_
71	min	min	NN	_	_	_
72	Nov10	nov10	NN	_	_	_
73	ug	ug	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	2	2	CD	_	_	_
76	min	min	NN	_	_	_
77	Nov2	nov2	NN	_	_	_
78	ug	ug	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	2	2	CD	_	_	_
81	min	min	NN	_	_	_
82	Nov5	nov5	NN	_	_	_
83	ug	ug	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	15	15	CD	_	_	_
86	min	min	NN	_	_	_
87	after	after	IN	_	_	_
88	turning	turn	VBG	_	_	_
89	off	off	RP	_	_	_
90	oxygen	oxygen	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
92	2003	2003	CD	_	_	_
93	,	,	,	_	_	_
94	PNAS	PNAS	NNP	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	minimize	minimize	VB	_	_	_
3	the	the	DT	_	_	_
4	effect	effect	NN	_	_	_
5	of	of	IN	_	_	_
6	such	such	JJ	_	_	_
7	contributions	contribution	NNS	_	_	_
8	,	,	,	_	_	_
9	microarray	microarray	NN	_	_	_
10	data	datum	NNS	_	_	_
11	were	be	VBD	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	25	25	CD	_	_	_
14	min	min	NN	_	_	_
15	after	after	IN	_	_	_
16	turning	turn	VBG	_	_	_
17	off	off	RP	_	_	_
18	oxygen	oxygen	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	2	2	CD	_	_	_
21	min	min	NN	_	_	_
22	after	after	IN	_	_	_
23	turning	turn	VBG	_	_	_
24	off	off	RP	_	_	_
25	oxygen	oxygen	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	55	55	CD	_	_	_
28	min	min	NN	_	_	_
29	after	after	IN	_	_	_
30	turning	turn	VBG	_	_	_
31	off	off	RP	_	_	_
32	oxygen	oxygen	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
34	5	5	CD	_	_	_
35	min	min	NN	_	_	_
36	after	after	IN	_	_	_
37	turning	turn	VBG	_	_	_
38	off	off	RP	_	_	_
39	oxygen	oxygen	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
41	5	5	CD	_	_	_
42	min	min	NN	_	_	_
43	after	after	IN	_	_	_
44	turning	turn	VBG	_	_	_
45	off	off	RP	_	_	_
46	oxygen	oxygen	NN	_	_	_
47	first	first	RB	_	_	_
48	replicate	replicate	VB	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	B	b	NN	_	_	_
52	-RRB-	-rrb-	-RRB-	_	_	_
53	,	,	,	_	_	_
54	column	column	NN	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	X	x	NN	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	,	,	,	_	_	_
59	and	and	CC	_	_	_
60	row	row	NN	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	Y	y	NN	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	number	number	NN	_	_	_
65	,	,	,	_	_	_
66	red	red	JJ	_	_	_
67	foreground	foreground	NN	_	_	_
68	-LRB-	-lrb-	-LRB-	_	_	_
69	f	f	FW	_	_	_
70	_	_	FW	_	_	_
71	r	r	NN	_	_	_
72	-RRB-	-rrb-	-RRB-	_	_	_
73	and	and	CC	_	_	_
74	background	background	NN	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	b	b	NN	_	_	_
77	_	_	CD	_	_	_
78	r	r	NN	_	_	_
79	-RRB-	-rrb-	-RRB-	_	_	_
80	,	,	,	_	_	_
81	green	green	JJ	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	completely	completely	RB	_	_	_
84	aerobic	aerobic	JJ	_	_	_
85	conditions	condition	NNS	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
87	corresponding	correspond	VBG	_	_	_
88	to	to	TO	_	_	_
89	the	the	DT	_	_	_
90	same	same	JJ	_	_	_
91	tip	tip	NN	_	_	_
92	.	.	.	_	_	_

1	Finally	finally	RB	_	_	_
2	,	,	,	_	_	_
3	all	all	PDT	_	_	_
4	the	the	DT	_	_	_
5	log	log	NN	_	_	_
6	ratios	ratio	NNS	_	_	_
7	of	of	IN	_	_	_
8	the	the	DT	_	_	_
9	same	same	JJ	_	_	_
10	gene	gene	NN	_	_	_
11	from	from	IN	_	_	_
12	each	each	DT	_	_	_
13	slide	slide	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	E	e	NN	_	_	_
16	coli	coli	NN	_	_	_
17	,	,	,	_	_	_
18	0	0	CD	_	_	_
19	min	min	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	E	e	NN	_	_	_
22	coli	coli	NN	_	_	_
23	,	,	,	_	_	_
24	15	15	CD	_	_	_
25	min	min	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	E	e	NN	_	_	_
28	coli	coli	NN	_	_	_
29	,	,	,	_	_	_
30	25	25	CD	_	_	_
31	min	min	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	E	e	NN	_	_	_
34	coli	coli	NN	_	_	_
35	,	,	,	_	_	_
36	25	25	CD	_	_	_
37	min	min	NN	_	_	_
38	after	after	IN	_	_	_
39	turning	turn	VBG	_	_	_
40	off	off	RP	_	_	_
41	oxygen	oxygen	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
43	Ecoli	ecolus	NNS	_	_	_
44	,	,	,	_	_	_
45	2	2	CD	_	_	_
46	min	min	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	E	e	NN	_	_	_
49	coli	coli	NN	_	_	_
50	,	,	,	_	_	_
51	2	2	CD	_	_	_
52	min	min	NN	_	_	_
53	after	after	IN	_	_	_
54	turning	turn	VBG	_	_	_
55	off	off	RP	_	_	_
56	oxygen	oxygen	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
58	E	e	NN	_	_	_
59	coli	coli	NN	_	_	_
60	,	,	,	_	_	_
61	35	35	CD	_	_	_
62	min	min	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	E	e	NN	_	_	_
65	coli	coli	NN	_	_	_
66	,	,	,	_	_	_
67	35	35	CD	_	_	_
68	min	min	NN	_	_	_
69	after	after	IN	_	_	_
70	turning	turn	VBG	_	_	_
71	off	off	RP	_	_	_
72	oxygen	oxygen	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
74	E	e	NN	_	_	_
75	coli	coli	NN	_	_	_
76	,	,	,	_	_	_
77	45	45	CD	_	_	_
78	min	min	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	E	e	NN	_	_	_
81	coli	coli	NN	_	_	_
82	,	,	,	_	_	_
83	45	45	CD	_	_	_
84	min	min	NN	_	_	_
85	after	after	IN	_	_	_
86	turning	turn	VBG	_	_	_
87	off	off	RP	_	_	_
88	oxygen	oxygen	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
90	E	e	NN	_	_	_
91	coli	coli	NN	_	_	_
92	,	,	,	_	_	_
93	55	55	CD	_	_	_
94	min	min	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	E	e	NN	_	_	_
97	coli	coli	NN	_	_	_
98	,	,	,	_	_	_
99	5	5	CD	_	_	_
100	min	min	NN	_	_	_
101	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
102	Ecoli	Ecoli	NNP	_	_	_
103	,	,	,	_	_	_
104	5	5	CD	_	_	_
105	min	min	NN	_	_	_
106	after	after	IN	_	_	_
107	turning	turn	VBG	_	_	_
108	off	off	RP	_	_	_
109	oxygen	oxygen	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
111	E	e	NN	_	_	_
112	coli	coli	NN	_	_	_
113	,	,	,	_	_	_
114	5	5	CD	_	_	_
115	min	min	NN	_	_	_
116	after	after	IN	_	_	_
117	turning	turn	VBG	_	_	_
118	off	off	RP	_	_	_
119	oxygen	oxygen	NN	_	_	_
120	first	first	RB	_	_	_
121	replicate	replicate	VB	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	ecoli	ecolus	NNS	_	_	_
124	_	_	VBP	_	_	_
125	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
126	_	_	NN	_	_	_
127	0	0	CD	_	_	_
128	min	min	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	ecoli	ecolus	NNS	_	_	_
131	_	_	VBP	_	_	_
132	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
133	_	_	NN	_	_	_
134	15	15	CD	_	_	_
135	min	min	NN	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	ecoli	ecolus	NNS	_	_	_
138	_	_	VBP	_	_	_
139	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
140	_	_	NN	_	_	_
141	25	25	CD	_	_	_
142	min	min	NN	_	_	_
143	_	_	CD	_	_	_
144	rep1	rep1	NN	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	ecoli	ecolus	NNS	_	_	_
147	_	_	VBP	_	_	_
148	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
149	_	_	NN	_	_	_
150	25	25	CD	_	_	_
151	min	min	NN	_	_	_
152	_	_	CD	_	_	_
153	rep2	rep2	NN	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	ecoli	ecolus	NNS	_	_	_
156	_	_	VBP	_	_	_
157	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
158	_	_	NN	_	_	_
159	2	2	CD	_	_	_
160	min	min	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	ecoli	ecolus	NNS	_	_	_
163	_	_	VBP	_	_	_
164	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
165	_	_	NN	_	_	_
166	35	35	CD	_	_	_
167	min	min	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	ecoli	ecolus	NNS	_	_	_
170	_	_	VBP	_	_	_
171	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
172	_	_	NN	_	_	_
173	45	45	CD	_	_	_
174	min	min	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	ecoli	ecolus	NNS	_	_	_
177	_	_	VBP	_	_	_
178	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
179	_	_	NN	_	_	_
180	55	55	CD	_	_	_
181	min	min	NN	_	_	_
182	_	_	CD	_	_	_
183	rep1	rep1	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	ecoli	ecolus	NNS	_	_	_
186	_	_	VBP	_	_	_
187	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
188	_	_	NN	_	_	_
189	55	55	CD	_	_	_
190	min	min	NN	_	_	_
191	_	_	CD	_	_	_
192	rep2	rep2	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	ecoli	ecolus	NNS	_	_	_
195	_	_	VBP	_	_	_
196	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
197	_	_	NN	_	_	_
198	5	5	CD	_	_	_
199	min	min	NN	_	_	_
200	_	_	SYM	_	_	_
201	Rep1	rep1	JJ	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	ecoli	ecolus	NNS	_	_	_
204	_	_	VBP	_	_	_
205	aerobicanaerobic	aerobicanaerobic	JJ	_	_	_
206	_	_	NN	_	_	_
207	5	5	CD	_	_	_
208	min	min	NN	_	_	_
209	_	_	CD	_	_	_
210	rep2	rep2	NN	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	Ecoli	ecolus	NNS	_	_	_
213	,	,	,	_	_	_
214	completely	completely	RB	_	_	_
215	aerobic	aerobic	JJ	_	_	_
216	conditions	condition	NNS	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
218	E	e	NN	_	_	_
219	coli	coli	NN	_	_	_
220	,	,	,	_	_	_
221	immediately	immediately	RB	_	_	_
222	after	after	IN	_	_	_
223	turning	turn	VBG	_	_	_
224	off	off	RP	_	_	_
225	oxygen	oxygen	NN	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
227	Epicentre	Epicentre	NNP	_	_	_
228	MasterPure	MasterPure	NNP	_	_	_
229	RNA	rna	NN	_	_	_
230	isolation	isolation	NN	_	_	_
231	Kit	kit	NN	_	_	_
232	,	,	,	_	_	_
233	Madison	Madison	NNP	_	_	_
234	,	,	,	_	_	_
235	WI	WI	NNP	_	_	_
236	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
237	Escherichia	escherichia	FW	Organism	_	_
238	coli	coli	FW	Organism	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	fluorescent	fluorescent	JJ	_	_	_
241	labeling	labeling	NN	_	_	_
242	and	and	CC	_	_	_
243	hybridization	hybridization	NN	_	_	_
244	and	and	CC	_	_	_
245	scanning	scanning	NN	_	_	_
246	of	of	IN	_	_	_
247	the	the	DT	_	_	_
248	microarray	microarray	NN	_	_	_
249	images	image	NNS	_	_	_
250	-LRB-	-lrb-	-LRB-	_	_	_
251	Balazsi	balazsus	NNS	_	_	_
252	et	et	FW	_	_	_
253	al.	al.	FW	_	_	_
254	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	foreground	foreground	NN	_	_	_
3	and	and	CC	_	_	_
4	background	background	NN	_	_	_
5	,	,	,	_	_	_
6	and	and	CC	_	_	_
7	the	the	DT	_	_	_
8	median	median	JJ	_	_	_
9	Cy3	cy3	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	green	green	JJ	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	foreground	foreground	NN	_	_	_
14	and	and	CC	_	_	_
15	background	background	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	foreground	foreground	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	f	f	FW	_	_	_
20	_	_	FW	_	_	_
21	g	g	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	and	and	CC	_	_	_
24	background	background	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	b	b	NN	_	_	_
27	_	_	CD	_	_	_
28	g	g	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	intensity	intensity	NN	_	_	_
31	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	position	position	NN	_	_	_
3	of	of	IN	_	_	_
4	each	each	DT	_	_	_
5	probe	probe	NN	_	_	_
6	within	within	IN	_	_	_
7	a	a	DT	_	_	_
8	block	block	NN	_	_	_
9	,	,	,	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	further	further	JJ	_	_	_
12	analysis	analysis	NN	_	_	_
13	if	if	IN	_	_	_
14	the	the	DT	_	_	_
15	foreground	foreground	NN	_	_	_
16	intensity	intensity	NN	_	_	_
17	of	of	IN	_	_	_
18	less	less	JJR	_	_	_
19	than	than	IN	_	_	_
20	50	50	CD	_	_	_
21	%	%	NN	_	_	_
22	of	of	IN	_	_	_
23	the	the	DT	_	_	_
24	pixels	pixel	NNS	_	_	_
25	within	within	IN	_	_	_
26	the	the	DT	_	_	_
27	spot	spot	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Immediately	immediately	RB	_	_	_
30	after	after	IN	_	_	_
31	turning	turn	VBG	_	_	_
32	off	off	RP	_	_	_
33	oxygen	oxygen	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
35	infinity	infinity	NN	_	_	_
36	.	.	.	_	_	_

1	These	these	DT	_	_	_
2	values	value	NNS	_	_	_
3	were	be	VBD	_	_	_
4	eliminated	eliminate	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	find	find	VB	_	_	_
8	,	,	,	_	_	_
9	imag	imag	NN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	isfinite	isfinite	NN	_	_	_
13	functions	function	NNS	_	_	_
14	in	in	IN	_	_	_
15	Matlab	Matlab	NNP	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	in	in	IN	_	_	_
3	Microsoft	Microsoft	NNP	_	_	_
4	Excel	Excel	NNP	_	_	_
5	,	,	,	_	_	_
6	containing	contain	VBG	_	_	_
7	the	the	DT	_	_	_
8	following	follow	VBG	_	_	_
9	information	information	NN	_	_	_
10	for	for	IN	_	_	_
11	each	each	DT	_	_	_
12	of	of	IN	_	_	_
13	the	the	DT	_	_	_
14	14,352	14,352	CD	_	_	_
15	entries	entry	NNS	_	_	_
16	:	:	:	_	_	_
17	block	block	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	intensities	intensity	NNS	_	_	_
20	,	,	,	_	_	_
21	respectively	respectively	RB	_	_	_
22	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	some	some	DT	_	_	_
3	cases	case	NNS	_	_	_
4	,	,	,	_	_	_
5	when	when	WRB	_	_	_
6	the	the	DT	_	_	_
7	intensity	intensity	NN	_	_	_
8	of	of	IN	_	_	_
9	the	the	DT	_	_	_
10	background	background	NN	_	_	_
11	was	be	VBD	_	_	_
12	higher	higher	JJR	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Next	Next	NNP	_	_	_
15	,	,	,	_	_	_
16	data	datum	NNS	_	_	_
17	were	be	VBD	_	_	_
18	normalized	normalize	VBN	_	_	_
19	,	,	,	_	_	_
20	by	by	IN	_	_	_
21	averaging	average	VBG	_	_	_
22	the	the	DT	_	_	_
23	log	log	NN	_	_	_
24	ratios	ratio	NNS	_	_	_
25	resulting	result	VBG	_	_	_
26	from	from	IN	_	_	_
27	all	all	DT	_	_	_
28	spots	spot	NNS	_	_	_
29	printed	print	VBN	_	_	_
30	by	by	IN	_	_	_
31	a	a	DT	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	normalized	normalize	VBD	_	_	_
34	as	as	IN	_	_	_
35	described	describe	VBN	_	_	_
36	before	before	IN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Tong	Tong	NNP	_	_	_
39	et	et	FW	_	_	_
40	al.	al.	FW	_	_	_
41	2004	2004	CD	_	_	_
42	BBRC	BBRC	NNP	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	spots	spot	NNS	_	_	_
4	were	be	VBD	_	_	_
5	excluded	exclude	VBN	_	_	_
6	from	from	IN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	of	of	IN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	F	f	NN	_	_	_
11	_	_	CD	_	_	_
12	r-B	r-b	NN	_	_	_
13	_	_	NN	_	_	_
14	r	r	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	originate	originate	VB	_	_	_
18	during	during	IN	_	_	_
19	array	array	NN	_	_	_
20	printing	printing	NN	_	_	_
21	,	,	,	_	_	_
22	as	as	RB	_	_	_
23	well	well	RB	_	_	_
24	as	as	IN	_	_	_
25	during	during	IN	_	_	_
26	the	the	DT	_	_	_
27	collection	collection	NN	_	_	_
28	and	and	CC	_	_	_
29	processing	processing	NN	_	_	_
30	of	of	IN	_	_	_
31	samples	sample	NNS	_	_	_
32	,	,	,	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	P	p	NN	_	_	_
35	is	be	VBZ	_	_	_
36	defined	define	VBN	_	_	_
37	by	by	IN	_	_	_
38	the	the	DT	_	_	_
39	pair	pair	NN	_	_	_
40	of	of	IN	_	_	_
41	integers	integer	NNS	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	X	x	NN	_	_	_
44	,	,	,	_	_	_
45	Y	y	NN	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	.	.	.	_	_	_

1	Log	log	VB	_	_	_
2	ratios	ratio	NNS	_	_	_
3	were	be	VBD	_	_	_
4	defined	define	VBN	_	_	_
5	as	as	IN	_	_	_
6	the	the	DT	_	_	_
7	base	base	NN	_	_	_
8	10	10	CD	_	_	_
9	logarithm	logarithm	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	print	print	NN	_	_	_
12	tip	tip	NN	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	subtracting	subtract	VBG	_	_	_
16	the	the	DT	_	_	_
17	resulting	result	VBG	_	_	_
18	average	average	NN	_	_	_
19	from	from	IN	_	_	_
20	all	all	DT	_	_	_
21	the	the	DT	_	_	_
22	individual	individual	JJ	_	_	_
23	log	log	NN	_	_	_
24	ratios	ratio	NNS	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	than	than	IN	_	_	_
27	or	or	CC	_	_	_
28	equal	equal	JJ	_	_	_
29	to	to	TO	_	_	_
30	the	the	DT	_	_	_
31	intensity	intensity	NN	_	_	_
32	of	of	IN	_	_	_
33	the	the	DT	_	_	_
34	foreground	foreground	NN	_	_	_
35	,	,	,	_	_	_
36	the	the	DT	_	_	_
37	resulting	result	VBG	_	_	_
38	log	log	NN	_	_	_
39	ratios	ratio	NNS	_	_	_
40	became	become	VBD	_	_	_
41	complex	complex	NN	_	_	_
42	or	or	CC	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Two	two	CD	_	_	_
45	color	color	NN	_	_	_
46	cDNA	cdna	NN	_	_	_
47	microarray	microarray	NN	_	_	_
48	data	datum	NNS	_	_	_
49	are	be	VBP	_	_	_
50	never	never	RB	_	_	_
51	devoid	devoid	JJ	_	_	_
52	of	of	IN	_	_	_
53	spurious	spurious	JJ	_	_	_
54	technical	technical	JJ	_	_	_
55	contributions	contribution	NNS	_	_	_
56	that	that	WDT	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
58	Two	two	CD	_	_	_
59	color	color	NN	_	_	_
60	cDNA	cdna	NN	_	_	_
61	microarray	microarray	NN	_	_	_
62	data	datum	NNS	_	_	_
63	are	be	VBP	_	_	_
64	never	never	RB	_	_	_
65	devoid	devoid	JJ	_	_	_
66	of	of	IN	_	_	_
67	spurious	spurious	JJ	_	_	_
68	technical	technical	JJ	_	_	_
69	contributions	contribution	NNS	_	_	_
70	that	that	WDT	_	_	_
71	originate	originate	VBP	_	_	_
72	during	during	IN	_	_	_
73	array	array	NN	_	_	_
74	printing	printing	NN	_	_	_
75	,	,	,	_	_	_
76	as	as	RB	_	_	_
77	well	well	RB	_	_	_
78	as	as	IN	_	_	_
79	during	during	IN	_	_	_
80	the	the	DT	_	_	_
81	collection	collection	NN	_	_	_
82	and	and	CC	_	_	_
83	processing	processing	NN	_	_	_
84	of	of	IN	_	_	_
85	samples	sample	NNS	_	_	_
86	,	,	,	_	_	_
87	fluorescent	fluorescent	JJ	_	_	_
88	labeling	labeling	NN	_	_	_
89	and	and	CC	_	_	_
90	hybridization	hybridization	NN	_	_	_
91	and	and	CC	_	_	_
92	scanning	scanning	NN	_	_	_
93	of	of	IN	_	_	_
94	the	the	DT	_	_	_
95	microarray	microarray	NN	_	_	_
96	images	image	NNS	_	_	_
97	-LRB-	-lrb-	-LRB-	_	_	_
98	Balazsi	balazsus	NNS	_	_	_
99	et	et	FW	_	_	_
100	al.	al.	FW	_	_	_
101	2003	2003	CD	_	_	_
102	,	,	,	_	_	_
103	PNAS	PNAS	NNP	_	_	_
104	-RRB-	-rrb-	-RRB-	_	_	_
105	.	.	.	_	_	_

1	To	to	TO	_	_	_
2	minimize	minimize	VB	_	_	_
3	the	the	DT	_	_	_
4	effect	effect	NN	_	_	_
5	of	of	IN	_	_	_
6	such	such	JJ	_	_	_
7	contributions	contribution	NNS	_	_	_
8	,	,	,	_	_	_
9	microarray	microarray	NN	_	_	_
10	data	datum	NNS	_	_	_
11	were	be	VBD	_	_	_
12	normalized	normalize	VBN	_	_	_
13	as	as	IN	_	_	_
14	described	describe	VBN	_	_	_
15	before	before	IN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Tong	Tong	NNP	_	_	_
18	et	et	FW	_	_	_
19	al.	al.	FW	_	_	_
20	2004	2004	CD	_	_	_
21	BBRC	BBRC	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	spots	spot	NNS	_	_	_
4	were	be	VBD	_	_	_
5	excluded	exclude	VBN	_	_	_
6	from	from	IN	_	_	_
7	further	further	JJ	_	_	_
8	analysis	analysis	NN	_	_	_
9	if	if	IN	_	_	_
10	the	the	DT	_	_	_
11	foreground	foreground	NN	_	_	_
12	intensity	intensity	NN	_	_	_
13	of	of	IN	_	_	_
14	less	less	JJR	_	_	_
15	than	than	IN	_	_	_
16	50	50	CD	_	_	_
17	%	%	NN	_	_	_
18	of	of	IN	_	_	_
19	the	the	DT	_	_	_
20	pixels	pixel	NNS	_	_	_
21	within	within	IN	_	_	_
22	the	the	DT	_	_	_
23	spot	spot	NN	_	_	_
24	were	be	VBD	_	_	_
25	above	above	IN	_	_	_
26	2	2	CD	_	_	_
27	standard	standard	JJ	_	_	_
28	deviations	deviation	NNS	_	_	_
29	of	of	IN	_	_	_
30	the	the	DT	_	_	_
31	background	background	NN	_	_	_
32	.	.	.	_	_	_

1	We	we	PRP	_	_	_
2	generated	generate	VBD	_	_	_
3	expression	expression	NN	_	_	_
4	data	datum	NNS	_	_	_
5	tables	table	NNS	_	_	_
6	in	in	IN	_	_	_
7	Microsoft	Microsoft	NNP	_	_	_
8	Excel	Excel	NNP	_	_	_
9	,	,	,	_	_	_
10	containing	contain	VBG	_	_	_
11	the	the	DT	_	_	_
12	following	follow	VBG	_	_	_
13	information	information	NN	_	_	_
14	for	for	IN	_	_	_
15	each	each	DT	_	_	_
16	of	of	IN	_	_	_
17	the	the	DT	_	_	_
18	14,352	14,352	CD	_	_	_
19	entries	entry	NNS	_	_	_
20	:	:	:	_	_	_
21	block	block	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	B	b	NN	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	,	,	,	_	_	_
26	column	column	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	X	x	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	,	,	,	_	_	_
31	and	and	CC	_	_	_
32	row	row	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	Y	y	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	number	number	NN	_	_	_
37	,	,	,	_	_	_
38	red	red	JJ	_	_	_
39	foreground	foreground	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	f	f	FW	_	_	_
42	_	_	FW	_	_	_
43	r	r	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	and	and	CC	_	_	_
46	background	background	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	b	b	NN	_	_	_
49	_	_	CD	_	_	_
50	r	r	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	,	,	,	_	_	_
53	green	green	JJ	_	_	_
54	foreground	foreground	NN	_	_	_
55	-LRB-	-lrb-	-LRB-	_	_	_
56	f	f	FW	_	_	_
57	_	_	FW	_	_	_
58	g	g	NN	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	and	and	CC	_	_	_
61	background	background	NN	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	b	b	NN	_	_	_
64	_	_	CD	_	_	_
65	g	g	NN	_	_	_
66	-RRB-	-rrb-	-RRB-	_	_	_
67	intensity	intensity	NN	_	_	_
68	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	position	position	NN	_	_	_
3	of	of	IN	_	_	_
4	each	each	DT	_	_	_
5	probe	probe	NN	_	_	_
6	within	within	IN	_	_	_
7	a	a	DT	_	_	_
8	block	block	NN	_	_	_
9	,	,	,	_	_	_
10	P	p	NN	_	_	_
11	is	be	VBZ	_	_	_
12	defined	define	VBN	_	_	_
13	by	by	IN	_	_	_
14	the	the	DT	_	_	_
15	pair	pair	NN	_	_	_
16	of	of	IN	_	_	_
17	integers	integer	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	X	x	NN	_	_	_
20	,	,	,	_	_	_
21	Y	y	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

1	Log	log	VB	_	_	_
2	ratios	ratio	NNS	_	_	_
3	were	be	VBD	_	_	_
4	defined	define	VBN	_	_	_
5	as	as	IN	_	_	_
6	the	the	DT	_	_	_
7	base	base	NN	_	_	_
8	10	10	CD	_	_	_
9	logarithm	logarithm	NN	_	_	_
10	of	of	IN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	F	f	NN	_	_	_
13	_	_	CD	_	_	_
14	r-B	r-b	NN	_	_	_
15	_	_	NN	_	_	_
16	r	r	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	were	be	VBD	_	_	_
20	above	above	IN	_	_	_
21	2	2	CD	_	_	_
22	standard	standard	JJ	_	_	_
23	deviations	deviation	NNS	_	_	_
24	of	of	IN	_	_	_
25	the	the	DT	_	_	_
26	background	background	NN	_	_	_
27	.	.	.	_	_	_

1	We	we	PRP	_	_	_
2	generated	generate	VBD	_	_	_
3	expression	expression	NN	_	_	_
4	data	datum	NNS	_	_	_
5	tables	table	NNS	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
7	were	be	VBD	_	_	_
8	averaged	average	VBN	_	_	_
9	and	and	CC	_	_	_
10	listed	list	VBN	_	_	_
11	in	in	IN	_	_	_
12	a	a	DT	_	_	_
13	new	new	JJ	_	_	_
14	file	file	NN	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	40	40	CD	_	_	_
3	min	min	NN	_	_	_
4	Nov10	nov10	NN	_	_	_
5	ug	ug	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	40	40	CD	_	_	_
8	min	min	NN	_	_	_
9	Nov2	nov2	NN	_	_	_
10	ug	ug	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	40	40	CD	_	_	_
13	min	min	NN	_	_	_
14	Nov5	nov5	NN	_	_	_
15	ug	ug	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	CAR005	car005	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	CAR005	car005	NN	_	_	_
20	strain	strain	NN	_	_	_
21	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
22	Detailed	detailed	JJ	_	_	_
23	parameters	parameter	NNS	_	_	_
24	for	for	IN	_	_	_
25	reads	read	VBZ	_	_	_
26	mapping	mapping	NN	_	_	_
27	:	:	:	_	_	_
28	bowtie2	bowtie2	NN	_	_	_
29	-	-	:	_	_	_
30	x	x	CC	_	_	_
31	ATCC8739	atcc8739	NN	_	_	_
32	-1	-1	CD	_	_	_
33	X	x	NN	_	_	_
34	_	_	NN	_	_	_
35	1	1	CD	_	_	_
36	.	.	.	_	_	_

1	fq	fq	NN	_	_	_
2	-2	-2	CD	_	_	_
3	X	x	NN	_	_	_
4	_	_	NN	_	_	_
5	2	2	CD	_	_	_
6	.	.	.	_	_	_

1	fq	fq	NN	_	_	_
2	--	--	:	_	_	_
3	no-mixed	no-mixed	JJ	_	_	_
4	-	-	:	_	_	_
5	p	p	NN	_	_	_
6	2	2	CD	_	_	_
7	-	-	:	_	_	_
8	S	s	NN	_	_	_
9	X.sam	x.sam	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	Escherichia	escherichia	FW	Organism	_	_
12	coli	coli	FW	Organism	_	_
13	ATCC	atcc	NN	_	_	_
14	8739	8739	CD	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	G4H14	g4h14	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	G4H14	g4h14	NN	_	_	_
19	strain	strain	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Genome	Genome	NNP	_	_	_
22	_	_	NNP	_	_	_
23	build	build	VB	_	_	_
24	:	:	:	_	_	_
25	ASM1938v1	asm1938v1	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	Illumina	Illumina	NNP	_	_	_
28	Casava1	Casava1	NNP	_	_	_
29	.7	.7	CD	_	_	_
30	software	software	NN	_	_	_
31	used	use	VBN	_	_	_
32	for	for	IN	_	_	_
33	basecalling	basecalling	NN	_	_	_
34	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	IspG1	ispg1	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	IspG1	ispg1	NN	_	_	_
5	strain	strain	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Reads	read	VBZ	_	_	_
8	Per	per	IN	_	_	_
9	Kilobase	kilobase	NN	_	_	_
10	of	of	IN	_	_	_
11	exon	exon	NN	_	_	_
12	per	per	IN	_	_	_
13	Megabase	megabase	NN	_	_	_
14	of	of	IN	_	_	_
15	library	library	NN	_	_	_
16	size	size	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	RPKM	rpkm	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	were	be	VBD	_	_	_
21	calculated	calculate	VBN	_	_	_
22	using	use	VBG	_	_	_
23	a	a	DT	_	_	_
24	protocol	protocol	NN	_	_	_
25	from	from	IN	_	_	_
26	Chepelev	Chepelev	NNP	_	_	_
27	et	et	FW	_	_	_
28	al.	al.	FW	_	_	_
29	,	,	,	_	_	_
30	Nucleic	Nucleic	NNP	_	_	_
31	Acids	Acids	NNP	_	_	_
32	Research	Research	NNP	_	_	_
33	,	,	,	_	_	_
34	2009	2009	CD	_	_	_
35	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	prepared	prepare	VBN	_	_	_
6	for	for	IN	_	_	_
7	sequencing	sequencing	NN	_	_	_
8	using	use	VBG	_	_	_
9	standard	standard	JJ	_	_	_
10	Illumina	Illumina	NNP	_	_	_
11	protocols	protocol	NNS	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
13	RNA-Seq	rna-seq	JJ	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Sequenced	sequence	VBN	_	_	_
16	reads	read	VBZ	_	_	_
17	were	be	VBD	_	_	_
18	trimmed	trim	VBN	_	_	_
19	for	for	IN	_	_	_
20	adaptor	adaptor	NN	_	_	_
21	sequence	sequence	NN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	masked	mask	VBN	_	_	_
25	for	for	IN	_	_	_
26	low-complexity	low-complexity	NN	_	_	_
27	or	or	CC	_	_	_
28	low-quality	low-quality	JJ	_	_	_
29	sequence	sequence	NN	_	_	_
30	,	,	,	_	_	_
31	then	then	RB	_	_	_
32	mapped	map	VBD	_	_	_
33	to	to	TO	_	_	_
34	Escherichia	escherichia	FW	Organism	_	_
35	coli	coli	FW	Organism	_	_
36	ATCC8739	atcc8739	NN	_	_	_
37	genome	genome	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	GenBank	genbank	NN	_	_	_
40	CP000946	cp000946	NN	_	_	_
41	.1	.1	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	using	use	VBG	_	_	_
44	Bowtie	Bowtie	NNP	_	_	_
45	2	2	CD	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	version	version	NN	_	_	_
48	2.2.5	2.2.5	CD	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
51	Single	single	JJ	_	_	_
52	colonies	colony	NNS	_	_	_
53	were	be	VBD	_	_	_
54	inoculated	inoculate	VBN	_	_	_
55	into	into	IN	_	_	_
56	15x100	15x100	CD	_	_	_
57	mm	mm	NN	_	_	_
58	tubes	tube	NNS	_	_	_
59	containing	contain	VBG	_	_	_
60	4	4	CD	_	_	_
61	ml	ml	NN	_	_	_
62	LB	lb	NN	_	_	_
63	,	,	,	_	_	_
64	and	and	CC	_	_	_
65	grown	grow	VBN	_	_	_
66	at	at	IN	_	_	_
67	30ºC	30ºc	NN	_	_	_
68	and	and	CC	_	_	_
69	250	250	CD	_	_	_
70	rpm	rpm	NN	_	_	_
71	overnight	overnight	JJ	_	_	_
72	.	.	.	_	_	_

1	100	100	CD	_	_	_
2	μl	μl	NN	_	_	_
3	seed	seed	NN	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	inoculated	inoculate	VBN	_	_	_
7	into	into	IN	_	_	_
8	a	a	DT	_	_	_
9	100	100	CD	_	_	_
10	ml	ml	NN	_	_	_
11	flask	flask	NN	_	_	_
12	containing	contain	VBG	_	_	_
13	10	10	CD	_	_	_
14	ml	ml	NN	_	_	_
15	LB	lb	NN	MED	_	_
16	medium	medium	NN	MED	_	_
17	,	,	,	_	_	_
18	and	and	CC	_	_	_
19	grown	grow	VBN	_	_	_
20	at	at	IN	_	_	_
21	30ºC	30ºc	NN	_	_	_
22	and	and	CC	_	_	_
23	250	250	CD	_	_	_
24	rpm	rpm	NN	_	_	_
25	for	for	IN	_	_	_
26	5	5	CD	_	_	_
27	h.	h.	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	strain	strain	NN	_	_	_
30	:	:	:	_	_	_
31	CAR005	car005	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	strain	strain	NN	_	_	_
34	:	:	:	_	_	_
35	G4H14	g4h14	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	strain	strain	NN	_	_	_
38	:	:	:	_	_	_
39	IspG1	ispg1	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	Supplementary	supplementary	JJ	_	_	_
42	_	_	NN	_	_	_
43	files	file	NNS	_	_	_
44	_	_	IN	_	_	_
45	format	format	NN	_	_	_
46	_	_	NN	_	_	_
47	and	and	CC	_	_	_
48	_	_	NN	_	_	_
49	content	content	NN	_	_	_
50	:	:	:	_	_	_
51	-LSB-	-lsb-	-LRB-	_	_	_
52	.	.	.	_	_	_

1	txt	txt	NN	_	_	_
2	-RSB-	-rsb-	-RRB-	_	_	_
3	tab-delimited	tab-delimited	JJ	_	_	_
4	text	text	NN	_	_	_
5	file	file	NN	_	_	_
6	includes	include	VBZ	_	_	_
7	RPKM	rpkm	NN	_	_	_
8	values	value	NNS	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	Total	Total	NNP	_	_	_
11	RNA	rna	NN	_	_	_
12	was	be	VBD	_	_	_
13	isolated	isolate	VBN	_	_	_
14	by	by	IN	_	_	_
15	the	the	DT	_	_	_
16	Trizol-Phenol-Chloroform	trizol-phenol-chloroform	NN	_	_	_
17	method	method	NN	_	_	_
18	.	.	.	_	_	_

1	An	a	DT	_	_	_
2	additional	additional	JJ	_	_	_
3	clean-up	clean-up	JJ	_	_	_
4	including	include	VBG	_	_	_
5	the	the	DT	_	_	_
6	on-column	on-column	JJ	_	_	_
7	DNase	dnase	NN	_	_	_
8	I	i	CD	_	_	_
9	treatment	treatment	NN	_	_	_
10	was	be	VBD	_	_	_
11	performed	perform	VBN	_	_	_
12	by	by	IN	_	_	_
13	using	use	VBG	_	_	_
14	the	the	DT	_	_	_
15	RNeasy	rneasy	NN	_	_	_
16	mini	minus	NNS	_	_	_
17	kit	kit	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Qiagen	qiagen	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Detailed	detailed	JJ	_	_	_
3	parameters	parameter	NNS	_	_	_
4	for	for	IN	_	_	_
5	reads	read	VBZ	_	_	_
6	mapping	mapping	NN	_	_	_
7	:	:	:	_	_	_
8	bowtie2	bowtie2	NN	_	_	_
9	-	-	:	_	_	_
10	x	x	CC	_	_	_
11	ATCC8739	atcc8739	NN	_	_	_
12	-1	-1	CD	_	_	_
13	X	x	NN	_	_	_
14	_	_	NN	_	_	_
15	1	1	CD	_	_	_
16	.	.	.	_	_	_

1	fq	fq	NN	_	_	_
2	-2	-2	CD	_	_	_
3	X	x	NN	_	_	_
4	_	_	NN	_	_	_
5	2	2	CD	_	_	_
6	.	.	.	_	_	_

1	fq	fq	NN	_	_	_
2	--	--	:	_	_	_
3	no-mixed	no-mixed	JJ	_	_	_
4	-	-	:	_	_	_
5	p	p	NN	_	_	_
6	2	2	CD	_	_	_
7	-	-	:	_	_	_
8	S	s	NN	_	_	_
9	X.sam	x.sam	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	E.coli	e.coli	NN	_	_	_
12	cells	cell	NNS	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Escherichia	escherichia	FW	Organism	_	_
15	coli	coli	FW	Organism	_	_
16	ATCC	atcc	NN	_	_	_
17	8739	8739	CD	_	_	_
18	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
19	Genome	Genome	NNP	_	_	_
20	_	_	NNP	_	_	_
21	build	build	VB	_	_	_
22	:	:	:	_	_	_
23	ATCC8739	atcc8739	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	growth	growth	NN	_	_	_
26	condition	condition	NN	_	_	_
27	:	:	:	_	_	_
28	normal	normal	JJ	_	_	_
29	condtion	condtion	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	5	5	CD	_	_	_
32	%	%	NN	_	_	_
33	w	w	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	growth	growth	NN	_	_	_
36	condition	condition	NN	_	_	_
37	:	:	:	_	_	_
38	osmotic	osmotic	JJ	_	_	_
39	stress	stress	NN	_	_	_
40	condtion	condtion	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	12	12	CD	_	_	_
43	%	%	NN	_	_	_
44	w	w	NN	_	_	_
45	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
46	Illumina	Illumina	NNP	_	_	_
47	Casava1	casava1	NN	_	_	_
48	.7	.7	CD	_	_	_
49	software	software	NN	_	_	_
50	used	use	VBN	_	_	_
51	for	for	IN	_	_	_
52	basecalling	basecalling	NN	_	_	_
53	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	NZ502	nz502	NN	_	_	_
3	_	_	CD	_	_	_
4	12	12	CD	_	_	_
5	%	%	NN	_	_	_
6	Glu	glu	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	NZ502	nz502	NN	_	_	_
9	_	_	CD	_	_	_
10	5	5	CD	_	_	_
11	%	%	NN	_	_	_
12	Glu	Glu	NNP	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Reads	read	VBZ	_	_	_
15	Per	per	IN	_	_	_
16	Kilobase	kilobase	NN	_	_	_
17	of	of	IN	_	_	_
18	exon	exon	NN	_	_	_
19	per	per	IN	_	_	_
20	Megabase	megabase	NN	_	_	_
21	of	of	IN	_	_	_
22	library	library	NN	_	_	_
23	size	size	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	RPKM	rpkm	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	were	be	VBD	_	_	_
28	calculated	calculate	VBN	_	_	_
29	using	use	VBG	_	_	_
30	a	a	DT	_	_	_
31	protocol	protocol	NN	_	_	_
32	from	from	IN	_	_	_
33	Chepelev	Chepelev	NNP	_	_	_
34	et	et	FW	_	_	_
35	al.	al.	FW	_	_	_
36	,	,	,	_	_	_
37	Nucleic	Nucleic	NNP	_	_	_
38	Acids	Acids	NNP	_	_	_
39	Research	Research	NNP	_	_	_
40	,	,	,	_	_	_
41	2009	2009	CD	_	_	_
42	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	prepared	prepare	VBN	_	_	_
6	for	for	IN	_	_	_
7	sequencing	sequencing	NN	_	_	_
8	using	use	VBG	_	_	_
9	standard	standard	JJ	_	_	_
10	Illumina	Illumina	NNP	_	_	_
11	protocols	protocol	NNS	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
13	RNA-Seq	rna-seq	JJ	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	Sequenced	sequence	VBN	_	_	_
16	reads	read	VBZ	_	_	_
17	were	be	VBD	_	_	_
18	trimmed	trim	VBN	_	_	_
19	for	for	IN	_	_	_
20	adaptor	adaptor	NN	_	_	_
21	sequence	sequence	NN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	masked	mask	VBN	_	_	_
25	for	for	IN	_	_	_
26	low-complexity	low-complexity	NN	_	_	_
27	or	or	CC	_	_	_
28	low-quality	low-quality	JJ	_	_	_
29	sequence	sequence	NN	_	_	_
30	,	,	,	_	_	_
31	then	then	RB	_	_	_
32	mapped	map	VBD	_	_	_
33	to	to	TO	_	_	_
34	Escherichia	escherichia	FW	Organism	_	_
35	coli	coli	FW	Organism	_	_
36	ATCC8739	atcc8739	NN	_	_	_
37	genome	genome	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	GenBank	genbank	NN	_	_	_
40	CP000946	cp000946	NN	_	_	_
41	.1	.1	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	using	use	VBG	_	_	_
44	Bowtie	Bowtie	NNP	_	_	_
45	2	2	CD	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	version	version	NN	_	_	_
48	2.2.5	2.2.5	CD	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	strain	strain	NN	_	_	_
52	:	:	:	_	_	_
53	NZ-502	nz-502	NN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	RpoB	rpob	NN	_	_	_
56	mutant	mutant	NN	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	strain	strain	NN	_	_	_
60	:	:	:	_	_	_
61	Suc-T110	suc-t110	NN	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	parental	parental	JJ	_	_	_
64	strain	strain	NN	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	SucT110	suct110	NN	_	_	_
68	_	_	CD	_	_	_
69	12	12	CD	_	_	_
70	%	%	NN	_	_	_
71	Glu	glu	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	SucT110	suct110	NN	_	_	_
74	_	_	CD	_	_	_
75	5	5	CD	_	_	_
76	%	%	NN	_	_	_
77	Glu	Glu	NNP	_	_	_
78	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
79	Supplementary	Supplementary	NNP	_	_	_
80	_	_	VBD	_	_	_
81	files	file	NNS	_	_	_
82	_	_	IN	_	_	_
83	format	format	NN	_	_	_
84	_	_	NN	_	_	_
85	and	and	CC	_	_	_
86	_	_	NN	_	_	_
87	content	content	NN	_	_	_
88	:	:	:	_	_	_
89	tab-delimited	tab-delimited	JJ	_	_	_
90	text	text	NN	_	_	_
91	files	file	NNS	_	_	_
92	include	include	VBP	_	_	_
93	RPKM	rpkm	NN	_	_	_
94	values	value	NNS	_	_	_
95	for	for	IN	_	_	_
96	each	each	DT	_	_	_
97	Sample	Sample	NNP	_	_	_
98	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	isolated	isolate	VBN	_	_	_
6	by	by	IN	_	_	_
7	the	the	DT	_	_	_
8	Trizol-Phenol-Chloroform	trizol-phenol-chloroform	NN	_	_	_
9	method	method	NN	_	_	_
10	.	.	.	_	_	_

1	An	a	DT	_	_	_
2	additional	additional	JJ	_	_	_
3	clean-up	clean-up	JJ	_	_	_
4	including	include	VBG	_	_	_
5	the	the	DT	_	_	_
6	on-column	on-column	JJ	_	_	_
7	DNase	dnase	NN	_	_	_
8	I	i	CD	_	_	_
9	treatment	treatment	NN	_	_	_
10	was	be	VBD	_	_	_
11	performed	perform	VBN	_	_	_
12	by	by	IN	_	_	_
13	using	use	VBG	_	_	_
14	the	the	DT	_	_	_
15	RNeasy	rneasy	NN	_	_	_
16	mini	minus	NNS	_	_	_
17	kit	kit	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Qiagen	qiagen	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	ChIP-Seq	chip-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Escherichia	escherichia	FW	Organism	_	_
5	coli	coli	FW	Organism	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Genome	Genome	NNP	_	_	_
8	_	_	NNP	_	_	_
9	build	build	VB	_	_	_
10	:	:	:	_	_	_
11	K12	k12	SYM	_	_	_
12	-	-	:	_	_	_
13	MG1655	mg1655	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	growth	growth	NN	_	_	_
16	condition	condition	NN	_	_	_
17	:	:	:	_	_	_
18	Exponential	Exponential	NNP	_	_	_
19	+	+	CC	_	_	_
20	O2	o2	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	growth	growth	NN	_	_	_
23	condition	condition	NN	_	_	_
24	:	:	:	_	_	_
25	Static	static	JJ	_	_	_
26	+	+	CC	_	_	_
27	O2	o2	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
29	library	library	NN	_	_	_
30	strategy	strategy	NN	_	_	_
31	:	:	:	_	_	_
32	ChIP-exo	ChIP-exo	NNP	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	replicate	replicate	VB	_	_	_
35	:	:	:	_	_	_
36	1	1	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	replicate	replicate	VB	_	_	_
39	:	:	:	_	_	_
40	2	2	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	Samples	sample	NNS	_	_	_
43	931	931	CD	_	_	_
44	,	,	,	_	_	_
45	933	933	CD	_	_	_
46	,	,	,	_	_	_
47	935	935	CD	_	_	_
48	and	and	CC	_	_	_
49	937	937	CD	_	_	_
50	were	be	VBD	_	_	_
51	aligned	align	VBN	_	_	_
52	with	with	IN	_	_	_
53	bowtie	bowtie	NN	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	V	v	NN	_	_	_
56	1.1.2	1.1.2	CD	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	with	with	IN	_	_	_
59	parameters	parameter	NNS	_	_	_
60	--	--	:	_	_	_
61	wrapper	wrapper	NN	_	_	_
62	basic-0	basic-0	NN	_	_	_
63	-	-	:	_	_	_
64	q	q	SYM	_	_	_
65	-	-	:	_	_	_
66	m	m	NN	_	_	_
67	1	1	CD	_	_	_
68	-	-	:	_	_	_
69	l	l	NN	_	_	_
70	55	55	CD	_	_	_
71	-	-	:	_	_	_
72	k	k	NN	_	_	_
73	1	1	CD	_	_	_
74	-5	-5	CD	_	_	_
75	3	3	CD	_	_	_
76	-3	-3	CD	_	_	_
77	40	40	CD	_	_	_
78	--	--	:	_	_	_
79	best	best	JJS	_	_	_
80	-	-	:	_	_	_
81	S	s	NN	_	_	_
82	-	-	:	_	_	_
83	p	p	NN	_	_	_
84	24	24	CD	_	_	_
85	,	,	,	_	_	_
86	and	and	CC	_	_	_
87	samples	sample	NNS	_	_	_
88	1311	1311	CD	_	_	_
89	,	,	,	_	_	_
90	1314	1314	CD	_	_	_
91	,	,	,	_	_	_
92	1317	1317	CD	_	_	_
93	and	and	CC	_	_	_
94	1320	1320	CD	_	_	_
95	were	be	VBD	_	_	_
96	aligned	align	VBN	_	_	_
97	with	with	IN	_	_	_
98	bowtie	bowtie	NN	_	_	_
99	-LRB-	-lrb-	-LRB-	_	_	_
100	V	v	NN	_	_	_
101	1.1.2	1.1.2	CD	_	_	_
102	-RRB-	-rrb-	-RRB-	_	_	_
103	with	with	IN	_	_	_
104	paramters	paramter	NNS	_	_	_
105	--	--	:	_	_	_
106	wrapper	wrapper	NN	_	_	_
107	basic-0	basic-0	NN	_	_	_
108	-	-	:	_	_	_
109	q	q	SYM	_	_	_
110	-	-	:	_	_	_
111	m	m	NN	_	_	_
112	1	1	CD	_	_	_
113	-	-	:	_	_	_
114	v	v	LS	_	_	_
115	2	2	CD	_	_	_
116	--	--	:	_	_	_
117	best	best	JJS	_	_	_
118	-	-	:	_	_	_
119	p	p	NN	_	_	_
120	24	24	CD	_	_	_
121	-	-	:	_	_	_
122	S	s	NN	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	Sig70	sig70	NN	_	_	_
125	in	in	IN	_	_	_
126	E.	e.	FW	_	_	_
127	coli	coli	FW	_	_	_
128	_	_	SYM	_	_	_
129	exponential	exponential	JJ	_	_	_
130	aerobic	aerobic	JJ	_	_	_
131	growth	growth	NN	_	_	_
132	_	_	IN	_	_	_
133	no	no	DT	_	_	_
134	rifampicin	rifampicin	NN	SUPP	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	Sig70	sig70	NN	_	_	_
137	in	in	IN	_	_	_
138	E.	e.	FW	_	_	_
139	coli	coli	FW	_	_	_
140	,	,	,	_	_	_
141	exponential	exponential	JJ	_	_	_
142	aerobic	aerobic	JJ	_	_	_
143	growth	growth	NN	_	_	_
144	,	,	,	_	_	_
145	no	no	DT	_	_	_
146	rifampicin	rifampicin	NN	SUPP	_	_
147	applied	apply	VBD	_	_	_
148	replicate	replicate	VB	_	_	_
149	1	1	CD	_	_	_
150	-LRB-	-lrb-	-LRB-	_	_	_
151	run	run	NN	_	_	_
152	299	299	CD	_	_	_
153	-RRB-	-rrb-	-RRB-	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	Sig70	sig70	NN	_	_	_
156	in	in	IN	_	_	_
157	E.	e.	FW	_	_	_
158	coli	coli	FW	_	_	_
159	,	,	,	_	_	_
160	exponential	exponential	JJ	_	_	_
161	aerobic	aerobic	JJ	_	_	_
162	growth	growth	NN	_	_	_
163	,	,	,	_	_	_
164	no	no	DT	_	_	_
165	rifampicin	rifampicin	NN	SUPP	_	_
166	applied	apply	VBD	_	_	_
167	replicate	replicate	VB	_	_	_
168	1	1	CD	_	_	_
169	-LRB-	-lrb-	-LRB-	_	_	_
170	run	run	NN	_	_	_
171	423	423	CD	_	_	_
172	-RRB-	-rrb-	-RRB-	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	Sig70	sig70	NN	_	_	_
175	in	in	IN	_	_	_
176	E.	e.	FW	_	_	_
177	coli	coli	FW	_	_	_
178	,	,	,	_	_	_
179	exponential	exponential	JJ	_	_	_
180	aerobic	aerobic	JJ	_	_	_
181	growth	growth	NN	_	_	_
182	,	,	,	_	_	_
183	no	no	DT	_	_	_
184	rifampicin	rifampicin	NN	SUPP	_	_
185	applied	apply	VBD	_	_	_
186	replicate	replicate	VB	_	_	_
187	2	2	CD	_	_	_
188	-LRB-	-lrb-	-LRB-	_	_	_
189	run	run	NN	_	_	_
190	299	299	CD	_	_	_
191	-RRB-	-rrb-	-RRB-	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	Sig70	sig70	NN	_	_	_
194	in	in	IN	_	_	_
195	E.	e.	FW	_	_	_
196	coli	coli	FW	_	_	_
197	,	,	,	_	_	_
198	exponential	exponential	JJ	_	_	_
199	aerobic	aerobic	JJ	_	_	_
200	growth	growth	NN	_	_	_
201	,	,	,	_	_	_
202	no	no	DT	_	_	_
203	rifampicin	rifampicin	NN	SUPP	_	_
204	applied	apply	VBD	_	_	_
205	replicate	replicate	VB	_	_	_
206	2	2	CD	_	_	_
207	-LRB-	-lrb-	-LRB-	_	_	_
208	run	run	NN	_	_	_
209	423	423	CD	_	_	_
210	-RRB-	-rrb-	-RRB-	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	Sig70	sig70	NN	_	_	_
213	in	in	IN	_	_	_
214	E.	e.	FW	_	_	_
215	coli	coli	FW	_	_	_
216	_	_	SYM	_	_	_
217	exponential	exponential	JJ	_	_	_
218	aerobic	aerobic	JJ	_	_	_
219	growth	growth	NN	_	_	_
220	_	_	NN	_	_	_
221	rifampicin	rifampicin	NN	SUPP	_	_
222	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
223	Sig70	sig70	NN	_	_	_
224	in	in	IN	_	_	_
225	E.	e.	FW	_	_	_
226	coli	coli	FW	_	_	_
227	,	,	,	_	_	_
228	exponential	exponential	JJ	_	_	_
229	aerobic	aerobic	JJ	_	_	_
230	growth	growth	NN	_	_	_
231	,	,	,	_	_	_
232	rifampicin	rifampicin	NN	SUPP	_	_
233	applied	apply	VBD	_	_	_
234	for	for	IN	_	_	_
235	20	20	CD	_	_	_
236	minutes	minute	NNS	_	_	_
237	,	,	,	_	_	_
238	replicate	replicate	VBP	_	_	_
239	1	1	CD	_	_	_
240	-LRB-	-lrb-	-LRB-	_	_	_
241	run	run	NN	_	_	_
242	423	423	CD	_	_	_
243	-RRB-	-rrb-	-RRB-	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	Sig70	sig70	NN	_	_	_
246	in	in	IN	_	_	_
247	E.	e.	FW	_	_	_
248	coli	coli	FW	_	_	_
249	,	,	,	_	_	_
250	exponential	exponential	JJ	_	_	_
251	aerobic	aerobic	JJ	_	_	_
252	growth	growth	NN	_	_	_
253	,	,	,	_	_	_
254	rifampicin	rifampicin	NN	SUPP	_	_
255	applied	apply	VBD	_	_	_
256	for	for	IN	_	_	_
257	20	20	CD	_	_	_
258	minutes	minute	NNS	_	_	_
259	,	,	,	_	_	_
260	replicate	replicate	VBP	_	_	_
261	2	2	CD	_	_	_
262	-LRB-	-lrb-	-LRB-	_	_	_
263	run	run	NN	_	_	_
264	423	423	CD	_	_	_
265	-RRB-	-rrb-	-RRB-	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
267	Sig70	sig70	NN	_	_	_
268	in	in	IN	_	_	_
269	E.	e.	FW	_	_	_
270	coli	coli	FW	_	_	_
271	_	_	SYM	_	_	_
272	static	static	JJ	_	_	_
273	aerobic	aerobic	JJ	_	_	_
274	growth	growth	NN	_	_	_
275	_	_	IN	_	_	_
276	no	no	DT	_	_	_
277	rifampicin	rifampicin	NN	SUPP	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
279	Sig70	sig70	NN	_	_	_
280	in	in	IN	_	_	_
281	E.	e.	FW	_	_	_
282	coli	coli	FW	_	_	_
283	,	,	,	_	_	_
284	static	static	JJ	_	_	_
285	aerobic	aerobic	JJ	_	_	_
286	growth	growth	NN	_	_	_
287	,	,	,	_	_	_
288	no	no	DT	_	_	_
289	rifampicin	rifampicin	NN	SUPP	_	_
290	applied	apply	VBD	_	_	_
291	replicate	replicate	VB	_	_	_
292	1	1	CD	_	_	_
293	-LRB-	-lrb-	-LRB-	_	_	_
294	run	run	NN	_	_	_
295	299	299	CD	_	_	_
296	-RRB-	-rrb-	-RRB-	_	_	_
297	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
298	Sig70	sig70	NN	_	_	_
299	in	in	IN	_	_	_
300	E.	e.	FW	_	_	_
301	coli	coli	FW	_	_	_
302	,	,	,	_	_	_
303	static	static	JJ	_	_	_
304	aerobic	aerobic	JJ	_	_	_
305	growth	growth	NN	_	_	_
306	,	,	,	_	_	_
307	no	no	DT	_	_	_
308	rifampicin	rifampicin	NN	SUPP	_	_
309	applied	apply	VBD	_	_	_
310	replicate	replicate	VB	_	_	_
311	2	2	CD	_	_	_
312	-LRB-	-lrb-	-LRB-	_	_	_
313	run	run	NN	_	_	_
314	299	299	CD	_	_	_
315	-RRB-	-rrb-	-RRB-	_	_	_
316	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
317	Supplementary	Supplementary	NNP	_	_	_
318	_	_	VBD	_	_	_
319	files	file	NNS	_	_	_
320	_	_	IN	_	_	_
321	format	format	NN	_	_	_
322	_	_	NN	_	_	_
323	and	and	CC	_	_	_
324	_	_	NN	_	_	_
325	content	content	NN	_	_	_
326	:	:	:	_	_	_
327	Each	each	DT	_	_	_
328	wig	wig	NN	_	_	_
329	file	file	NN	_	_	_
330	contains	contain	VBZ	_	_	_
331	the	the	DT	_	_	_
332	alignd	alignd	NN	_	_	_
333	reads	read	VBZ	_	_	_
334	of	of	IN	_	_	_
335	each	each	DT	_	_	_
336	ChIP-exo	ChIP-exo	NNP	_	_	_
337	sample	sample	NN	_	_	_
338	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	ChIP-exo	chip-exo	JJ	_	_	_
4	experiments	experiment	NNS	_	_	_
5	were	be	VBD	_	_	_
6	generated	generate	VBN	_	_	_
7	by	by	IN	_	_	_
8	following	follow	VBG	_	_	_
9	the	the	DT	_	_	_
10	steps	step	NNS	_	_	_
11	presented	present	VBN	_	_	_
12	by	by	IN	_	_	_
13	Rhee	Rhee	NNP	_	_	_
14	and	and	CC	_	_	_
15	Pugh	Pugh	NNP	_	_	_
16	,	,	,	_	_	_
17	2011	2011	CD	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	samples	sample	NNS	_	_	_
4	were	be	VBD	_	_	_
5	sonicated	sonicate	VBN	_	_	_
6	for	for	IN	_	_	_
7	a	a	DT	_	_	_
8	total	total	NN	_	_	_
9	of	of	IN	_	_	_
10	16	16	CD	_	_	_
11	minutes	minute	NNS	_	_	_
12	and	and	CC	_	_	_
13	50	50	CD	_	_	_
14	uL	ul	NN	_	_	_
15	protein	protein	NN	_	_	_
16	A	a	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	treated	treat	VBN	_	_	_
19	with	with	IN	_	_	_
20	:	:	:	_	_	_
21	none	none	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	treated	treat	VBN	_	_	_
24	with	with	IN	_	_	_
25	:	:	:	_	_	_
26	Rifampicin	Rifampicin	NNP	_	_	_
27	for	for	IN	_	_	_
28	20	20	CD	_	_	_
29	minutes	minute	NNS	_	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
31	E.	e.	FW	_	_	_
32	coli	coli	FW	_	_	_
33	W3110	w3110	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	E.	e.	FW	_	_	_
36	coli	coli	FW	_	_	_
37	W3110	w3110	NN	_	_	_
38	expressing	express	VBG	_	_	_
39	PCK	pck	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
41	E.	e.	FW	_	_	_
42	coli	coli	FW	_	_	_
43	W3110	w3110	NN	_	_	_
44	expressing	express	VBG	_	_	_
45	ppc	ppc	NN	GEN	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
47	E.	e.	FW	_	_	_
48	coli	coli	FW	_	_	_
49	W3110	w3110	NN	_	_	_
50	expressing	express	VBG	_	_	_
51	ppc	ppc	NN	GEN	_	_
52	at	at	IN	_	_	_
53	LB-GlC	lb-glc	JJ	_	_	_
54	medium	medium	NN	_	_	_
55	,	,	,	_	_	_
56	D	d	NN	_	_	_
57	=	=	JJ	_	_	_
58	0.1	0.1	CD	_	_	_
59	h-1	h-1	NN	_	_	_
60	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
61	E.	E.	NNP	_	_	_
62	coli	coli	NN	_	_	_
63	W3110	w3110	NN	_	_	_
64	grown	grow	VBN	_	_	_
65	at	at	IN	_	_	_
66	glucose-minimal	glucose-minimal	JJ	_	_	_
67	medium	medium	NN	_	_	_
68	-LRB-	-lrb-	-LRB-	_	_	_
69	IPTG	iptg	NN	_	_	_
70	induction	induction	NN	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	in	in	IN	_	_	_
73	early	early	JJ	_	_	_
74	log	log	NN	_	_	_
75	phase	phase	NN	_	_	_
76	-LRB-	-lrb-	-LRB-	_	_	_
77	u	u	NN	_	_	_
78	=	=	JJ	_	_	_
79	0.25	0.25	CD	_	_	_
80	h-1	h-1	NN	_	_	_
81	-RRB-	-rrb-	-RRB-	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	E.	e.	FW	_	_	_
84	coli	coli	FW	_	_	_
85	W3110	w3110	NN	_	_	_
86	grown	grow	VBN	_	_	_
87	at	at	IN	_	_	_
88	LB-glucose	lb-glucose	JJ	_	_	_
89	medium	medium	NN	_	_	_
90	-LRB-	-lrb-	-LRB-	_	_	_
91	IPTG	iptg	NN	_	_	_
92	induction	induction	NN	_	_	_
93	-RRB-	-rrb-	-RRB-	_	_	_
94	in	in	IN	_	_	_
95	chemostat	chemostat	NN	_	_	_
96	-LRB-	-lrb-	-LRB-	_	_	_
97	D	d	NN	_	_	_
98	=	=	JJ	_	_	_
99	0.1	0.1	CD	_	_	_
100	h-1	h-1	NN	_	_	_
101	-RRB-	-rrb-	-RRB-	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	E.	e.	FW	_	_	_
104	coli	coli	FW	_	_	_
105	W3110	w3110	NN	_	_	_
106	-LRB-	-lrb-	-LRB-	_	_	_
107	KCTC	kctc	NN	_	_	_
108	2223	2223	CD	_	_	_
109	-RRB-	-rrb-	-RRB-	_	_	_
110	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
111	E.	e.	FW	_	_	_
112	coli	coli	FW	_	_	_
113	W3110	w3110	NN	_	_	_
114	-LRB-	-lrb-	-LRB-	_	_	_
115	KCTC	kctc	NN	_	_	_
116	2223	2223	CD	_	_	_
117	-RRB-	-rrb-	-RRB-	_	_	_
118	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
119	E.	e.	FW	_	_	_
120	coli	coli	FW	_	_	_
121	W3110	w3110	NN	_	_	_
122	-LRB-	-lrb-	-LRB-	_	_	_
123	KCTC	kctc	NN	_	_	_
124	2223	2223	CD	_	_	_
125	-RRB-	-rrb-	-RRB-	_	_	_
126	at	at	IN	_	_	_
127	LB-GlC	lb-glc	JJ	_	_	_
128	medium	medium	NN	_	_	_
129	,	,	,	_	_	_
130	D	d	NN	_	_	_
131	=	=	JJ	_	_	_
132	0.1	0.1	CD	_	_	_
133	h-1	h-1	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
135	E.	e.	FW	_	_	_
136	coli	coli	FW	_	_	_
137	W3110	w3110	NN	_	_	_
138	with	with	IN	_	_	_
139	glucose-minimal	glucose-minimal	JJ	_	_	_
140	medium	medium	NN	_	_	_
141	-LRB-	-lrb-	-LRB-	_	_	_
142	IPTG	iptg	NN	_	_	_
143	induced	induce	VBN	_	_	_
144	-RRB-	-rrb-	-RRB-	_	_	_
145	at	at	IN	_	_	_
146	early	early	JJ	_	_	_
147	log	log	NN	_	_	_
148	phase	phase	NN	_	_	_
149	-LRB-	-lrb-	-LRB-	_	_	_
150	u	u	NN	_	_	_
151	=	=	JJ	_	_	_
152	0.25	0.25	CD	_	_	_
153	-RRB-	-rrb-	-RRB-	_	_	_
154	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
155	Escherichia	escherichia	FW	Organism	_	_
156	coli	coli	FW	Organism	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	PCK	pck	NN	_	_	_
159	_	_	CD	_	_	_
160	glucose-minimal	glucose-minimal	JJ	_	_	_
161	medium	medium	NN	_	_	_
162	_	_	NN	_	_	_
163	early	early	JJ	_	_	_
164	log	log	NN	_	_	_
165	phase	phase	NN	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	PCK	pck	NN	_	_	_
168	_	_	CD	_	_	_
169	LB-GlC	lb-glc	JJ	_	_	_
170	medium	medium	NN	_	_	_
171	_	_	NN	_	_	_
172	D	d	NN	_	_	_
173	=	=	JJ	_	_	_
174	0.1	0.1	CD	_	_	_
175	h-1	h-1	NN	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
177	PPC	PPC	NNP	_	_	_
178	_	_	SYM	_	_	_
179	glucose-minimal	glucose-minimal	JJ	_	_	_
180	medium	medium	NN	_	_	_
181	_	_	NN	_	_	_
182	early	early	JJ	_	_	_
183	log	log	NN	_	_	_
184	phase	phase	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	PPC	PPC	NNP	_	_	_
187	_	_	SYM	_	_	_
188	LB-GlC	lb-glc	JJ	_	_	_
189	medium	medium	NN	_	_	_
190	_	_	NN	_	_	_
191	D	d	NN	_	_	_
192	=	=	JJ	_	_	_
193	0.1	0.1	CD	_	_	_
194	h-1	h-1	NN	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	Scanned	scan	VBD	_	_	_
197	images	image	NNS	_	_	_
198	were	be	VBD	_	_	_
199	analyzed	analyze	VBN	_	_	_
200	with	with	IN	_	_	_
201	GenePix	GenePix	NNP	_	_	_
202	Pro	pro	FW	_	_	_
203	3.0	3.0	CD	_	_	_
204	software	software	NN	_	_	_
205	-LRB-	-lrb-	-LRB-	_	_	_
206	Axon	Axon	NNP	_	_	_
207	Instruments	Instruments	NNP	_	_	_
208	,	,	,	_	_	_
209	Union	Union	NNP	_	_	_
210	City	City	NNP	_	_	_
211	,	,	,	_	_	_
212	CA	CA	NNP	_	_	_
213	-RRB-	-rrb-	-RRB-	_	_	_
214	to	to	TO	_	_	_
215	obtain	obtain	VB	_	_	_
216	gene	gene	NN	_	_	_
217	expression	expression	NN	_	_	_
218	ratios	ratio	NNS	_	_	_
219	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Scanned	scan	VBD	_	_	_
3	images	image	NNS	_	_	_
4	were	be	VBD	_	_	_
5	analyzed	analyze	VBN	_	_	_
6	with	with	IN	_	_	_
7	GenePix	GenePix	NNP	_	_	_
8	Pro	pro	FW	_	_	_
9	3.0	3.0	CD	_	_	_
10	software	software	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Axon	Axon	NNP	_	_	_
13	Instruments	Instruments	NNP	_	_	_
14	,	,	,	_	_	_
15	Union	Union	NNP	_	_	_
16	City	City	NNP	_	_	_
17	,	,	,	_	_	_
18	CA	CA	NNP	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	to	to	TO	_	_	_
21	obtain	obtain	VB	_	_	_
22	gene	gene	NN	_	_	_
23	expression	expression	NN	_	_	_
24	ratios	ratio	NNS	_	_	_
25	.	.	.	_	_	_

1	Logged	log	VBN	_	_	_
2	gene	gene	NN	_	_	_
3	expression	expression	NN	_	_	_
4	ratios	ratio	NNS	_	_	_
5	were	be	VBD	_	_	_
6	normalized	normalize	VBN	_	_	_
7	by	by	IN	_	_	_
8	LOWESS	lowess	NN	_	_	_
9	regression	regression	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Yang	Yang	NNP	_	_	_
12	et	et	FW	_	_	_
13	al.	al.	FW	_	_	_
14	,	,	,	_	_	_
15	2002	2002	CD	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	using	use	VBG	_	_	_
18	the	the	DT	_	_	_
19	GeneSpring	GeneSpring	NNP	_	_	_
20	GX	GX	NNP	_	_	_
21	7.3	7.3	CD	_	_	_
22	software	software	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Agilent	Agilent	NNP	_	_	_
25	Technologies	Technologies	NNPS	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	medium	medium	NN	_	_	_
4	for	for	IN	_	_	_
5	batch	batch	NN	_	_	_
6	culture	culture	NN	_	_	_
7	was	be	VBD	_	_	_
8	consisted	consist	VBN	_	_	_
9	of	of	IN	_	_	_
10	11.3	11.3	CD	_	_	_
11	g	g	NN	_	_	_
12	M9	m9	NN	_	_	_
13	medium	medium	NN	_	_	_
14	,	,	,	_	_	_
15	0.2	0.2	CD	_	_	_
16	g	g	NN	_	_	_
17	MgSO4	mgso4	NN	_	_	_
18	•	•	SYM	_	_	_
19	7H2O	7H2O	NNP	_	_	_
20	,	,	,	_	_	_
21	0.1	0.1	CD	_	_	_
22	g	g	NN	_	_	_
23	CaCl2	cacl2	NN	_	_	_
24	,	,	,	_	_	_
25	1	1	CD	_	_	_
26	mg	mg	NN	_	_	_
27	thiamine	thiamine	NN	SUPP	_	_
28	,	,	,	_	_	_
29	10	10	CD	_	_	_
30	g	g	NN	_	_	_
31	NaHCO3	nahco3	NN	_	_	_
32	and	and	CC	_	_	_
33	9	9	CD	_	_	_
34	g	g	NN	_	_	_
35	glucose	glucose	NN	SUPP	_	_
36	,	,	,	_	_	_
37	50	50	CD	_	_	_
38	mg	mg	NN	_	_	_
39	ampicillin	ampicillin	NN	_	_	_
40	and	and	CC	_	_	_
41	0.1	0.1	CD	_	_	_
42	mmole	mmole	NN	_	_	_
43	IPTG	iptg	NN	_	_	_
44	per	per	IN	_	_	_
45	liter	liter	NN	_	_	_
46	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	medium	medium	NN	_	_	_
4	for	for	IN	_	_	_
5	continuous	continuous	JJ	_	_	_
6	culture	culture	NN	_	_	_
7	contained	contain	VBD	_	_	_
8	20	20	CD	_	_	_
9	g	g	NN	_	_	_
10	LB	lb	NN	_	_	_
11	,	,	,	_	_	_
12	9	9	CD	_	_	_
13	g	g	NN	_	_	_
14	glucose	glucose	NN	SUPP	_	_
15	,	,	,	_	_	_
16	10	10	CD	_	_	_
17	g	g	NN	_	_	_
18	NaHCO3	nahco3	NN	_	_	_
19	,	,	,	_	_	_
20	50	50	CD	_	_	_
21	mg	mg	NN	_	_	_
22	ampicillin	ampicillin	NN	_	_	_
23	per	per	IN	_	_	_
24	liter	liter	NN	_	_	_
25	and	and	CC	_	_	_
26	isopropyl	isopropyl	NN	_	_	_
27	-	-	:	_	_	_
28	-	-	:	_	_	_
29	D-thiogalactopyranoside	d-thiogalactopyranoside	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	IPTG	iptg	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	was	be	VBD	_	_	_
34	supplemented	supplement	VBN	_	_	_
35	to	to	TO	_	_	_
36	be	be	VB	_	_	_
37	0.1	0.1	CD	_	_	_
38	mM	mm	NN	KWSUPP	_	_
39	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	initial	initial	JJ	_	_	_
3	pH	ph	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	medium	medium	NN	_	_	_
7	was	be	VBD	_	_	_
8	set	set	VBN	_	_	_
9	to	to	TO	_	_	_
10	be	be	VB	_	_	_
11	pH	ph	NN	_	_	_
12	7.3	7.3	CD	_	_	_
13	by	by	IN	_	_	_
14	adding	add	VBG	_	_	_
15	1	1	CD	_	_	_
16	N	n	NN	_	_	_
17	HCl	hcl	NN	_	_	_
18	solution	solution	NN	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	inoculation	inoculation	NN	_	_	_
3	culture	culture	NN	_	_	_
4	was	be	VBD	_	_	_
5	transferred	transfer	VBN	_	_	_
6	into	into	IN	_	_	_
7	a	a	DT	_	_	_
8	250	250	CD	_	_	_
9	mL-fermentor	ml-fermentor	NN	_	_	_
10	containing	contain	VBG	_	_	_
11	100	100	CD	_	_	_
12	mL	ml	NN	_	_	_
13	medium	medium	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Small	small	JJ	_	_	_
16	scale	scale	NN	_	_	_
17	multi-chemostat	multi-chemostat	JJ	_	_	_
18	fermentor	fermentor	NN	_	_	_
19	;	;	:	_	_	_
20	Biotron	Biotron	NNP	_	_	_
21	Inc.	Inc.	NNP	_	_	_
22	,	,	,	_	_	_
23	Bucheon	Bucheon	NNP	_	_	_
24	,	,	,	_	_	_
25	Korea	Korea	NNP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	culture	culture	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	at	at	IN	_	_	_
6	37	37	CD	_	_	_
7	C	c	NN	_	_	_
8	,	,	,	_	_	_
9	350	350	CD	_	_	_
10	rpm	rpm	NN	_	_	_
11	with	with	IN	_	_	_
12	flushing	flushing	NN	_	_	_
13	CO2	co2	NN	_	_	_
14	gas	gas	NN	_	_	_
15	at	at	IN	_	_	_
16	20	20	CD	_	_	_
17	mL	ml	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Transcriptome	transcriptome	NN	_	_	_
20	of	of	IN	_	_	_
21	cells	cell	NNS	_	_	_
22	was	be	VBD	_	_	_
23	prepared	prepare	VBN	_	_	_
24	using	use	VBG	_	_	_
25	a	a	DT	_	_	_
26	RNA	rna	NN	_	_	_
27	extraction	extraction	NN	_	_	_
28	kit	kit	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	RNeasy	rneasy	NN	_	_	_
31	mini	minus	NNS	_	_	_
32	kit	kit	NN	_	_	_
33	;	;	:	_	_	_
34	Qiagen	Qiagen	NNP	_	_	_
35	,	,	,	_	_	_
36	Hilden	Hilden	NNP	_	_	_
37	,	,	,	_	_	_
38	Germany	Germany	NNP	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	W3110	w3110	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	KCTC	kctc	NN	_	_	_
44	2223	2223	CD	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	W3110	w3110	NN	_	_	_
48	overexpressing	overexpress	VBG	_	_	_
49	pck	pck	NN	GEN	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	BnTR1	bntr1	NN	_	_	_
52	,	,	,	_	_	_
53	37	37	CD	_	_	_
54	°C	°c	NN	_	_	_
55	,	,	,	_	_	_
56	replicate	replicate	VB	_	_	_
57	1	1	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	BnTR1	bntr1	NN	_	_	_
60	,	,	,	_	_	_
61	37	37	CD	_	_	_
62	°C	°c	NN	_	_	_
63	,	,	,	_	_	_
64	replicate	replicate	VB	_	_	_
65	2	2	CD	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
67	BnTR1	bntr1	NN	_	_	_
68	,	,	,	_	_	_
69	37	37	CD	_	_	_
70	°C	°c	NN	_	_	_
71	,	,	,	_	_	_
72	replicate	replicate	VB	_	_	_
73	3	3	CD	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	BnTR1	bntr1	NN	_	_	_
76	_	_	NN	_	_	_
77	37	37	CD	_	_	_
78	_	_	CD	_	_	_
79	rep1	rep1	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	BnTR1	bntr1	NN	_	_	_
82	_	_	NN	_	_	_
83	37	37	CD	_	_	_
84	_	_	CD	_	_	_
85	rep2	rep2	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	BnTR1	bntr1	NN	_	_	_
88	_	_	NN	_	_	_
89	37	37	CD	_	_	_
90	_	_	CD	_	_	_
91	rep3	rep3	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	BnTR1	bntr1	NN	_	_	_
94	,	,	,	_	_	_
95	42	42	CD	_	_	_
96	°C	°c	NN	_	_	_
97	,	,	,	_	_	_
98	replicate	replicate	VB	_	_	_
99	1	1	CD	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	BnTR1	bntr1	NN	_	_	_
102	,	,	,	_	_	_
103	42	42	CD	_	_	_
104	°C	°c	NN	_	_	_
105	,	,	,	_	_	_
106	replicate	replicate	VB	_	_	_
107	2	2	CD	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
109	BnTR1	bntr1	NN	_	_	_
110	,	,	,	_	_	_
111	42	42	CD	_	_	_
112	°C	°c	NN	_	_	_
113	,	,	,	_	_	_
114	replicate	replicate	VB	_	_	_
115	3	3	CD	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	BnTR1	bntr1	NN	_	_	_
118	_	_	CD	_	_	_
119	42	42	CD	_	_	_
120	_	_	NN	_	_	_
121	rep1	rep1	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	BnTR1	bntr1	NN	_	_	_
124	_	_	CD	_	_	_
125	42	42	CD	_	_	_
126	_	_	NN	_	_	_
127	rep2	rep2	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	BnTR1	bntr1	NN	_	_	_
130	_	_	CD	_	_	_
131	42	42	CD	_	_	_
132	_	_	SYM	_	_	_
133	rep3	rep3	CD	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
135	Collected	collect	VBN	_	_	_
136	cells	cell	NNS	_	_	_
137	were	be	VBD	_	_	_
138	lysed	lyse	VBN	_	_	_
139	using	use	VBG	_	_	_
140	Trizol	Trizol	NNP	_	_	_
141	-LRB-	-lrb-	-LRB-	_	_	_
142	Invitrogen	Invitrogen	NNP	_	_	_
143	-RRB-	-rrb-	-RRB-	_	_	_
144	,	,	,	_	_	_
145	and	and	CC	_	_	_
146	total	total	JJ	_	_	_
147	RNA	rna	NN	_	_	_
148	was	be	VBD	_	_	_
149	isolated	isolate	VBN	_	_	_
150	using	use	VBG	_	_	_
151	phenol-chloroform	phenol-chloroform	JJ	_	_	_
152	and	and	CC	_	_	_
153	precipitated	precipitated	JJ	_	_	_
154	with	with	IN	_	_	_
155	ice	ice	NN	_	_	_
156	cold	cold	JJ	_	_	_
157	isopropanol	isopropanol	NN	_	_	_
158	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	the	the	DT	_	_	_
3	precipitations	precipitation	NNS	_	_	_
4	were	be	VBD	_	_	_
5	further	further	JJ	_	_	_
6	washed	wash	VBN	_	_	_
7	with	with	IN	_	_	_
8	70	70	CD	_	_	_
9	%	%	NN	_	_	_
10	ethanol	ethanol	NN	_	_	_
11	and	and	CC	_	_	_
12	dissolved	dissolve	VBN	_	_	_
13	in	in	IN	_	_	_
14	RNase-free	rnase-free	JJ	_	_	_
15	water	water	NN	_	_	_
16	.	.	.	_	_	_

1	Genomic	genomic	JJ	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	using	use	VBG	_	_	_
6	RNase-free	rnase-free	JJ	_	_	_
7	DNase	dnase	NN	_	_	_
8	I.	i.	NN	_	_	_
9	RNA	rna	NN	_	_	_
10	samples	sample	NNS	_	_	_
11	were	be	VBD	_	_	_
12	further	further	JJ	_	_	_
13	purified	purify	VBN	_	_	_
14	using	use	VBG	_	_	_
15	RNeasy	RNeasy	NNP	_	_	_
16	Mini	Mini	NNP	_	_	_
17	Kits	Kits	NNP	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	Qiagen	Qiagen	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	concentration	concentration	NN	_	_	_
3	and	and	CC	_	_	_
4	quality	quality	NN	_	_	_
5	were	be	VBD	_	_	_
6	determined	determine	VBN	_	_	_
7	using	use	VBG	_	_	_
8	A	a	DT	_	_	_
9	Nanodrop	nanodrop	JJ	_	_	_
10	ND	nd	NN	_	_	_
11	1000	1000	CD	_	_	_
12	spectrophotometer	spectrophotometer	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Thermo	Thermo	NNP	_	_	_
15	Fisher	Fisher	NNP	_	_	_
16	Scientific	Scientific	NNP	_	_	_
17	,	,	,	_	_	_
18	Pittsburgh	Pittsburgh	NNP	_	_	_
19	,	,	,	_	_	_
20	PA	pa	NN	_	_	_
21	,	,	,	_	_	_
22	USA	USA	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	and	and	CC	_	_	_
25	agarose	agarose	NN	_	_	_
26	gel	gel	NN	_	_	_
27	electrophoresis	electrophoresis	NN	_	_	_
28	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	isolated	isolate	VBN	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	stored	store	VBN	_	_	_
6	at	at	IN	_	_	_
7	−	−	CD	_	_	_
8	80	80	CD	_	_	_
9	°C	°c	NN	_	_	_
10	before	before	IN	_	_	_
11	use	use	NN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2	culture	culture	NN	_	_	_
3	temperature	temperature	NN	_	_	_
4	:	:	:	_	_	_
5	37	37	CD	_	_	_
6	°C	°c	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	culture	culture	NN	_	_	_
9	temperature	temperature	NN	_	_	_
10	:	:	:	_	_	_
11	42	42	CD	_	_	_
12	°C	°c	NN	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	E.	E.	NNP	_	_	_
15	coli	coli	NN	_	_	_
16	cells	cell	NNS	_	_	_
17	with	with	IN	_	_	_
18	or	or	CC	_	_	_
19	without	without	IN	_	_	_
20	BnTR1	bntr1	NN	_	_	_
21	were	be	VBD	_	_	_
22	transferred	transfer	VBN	_	_	_
23	and	and	CC	_	_	_
24	incubated	incubate	VBN	_	_	_
25	at	at	IN	_	_	_
26	37	37	CD	_	_	_
27	°C	°c	NN	_	_	_
28	and	and	CC	_	_	_
29	42	42	CD	_	_	_
30	°C	°c	NN	_	_	_
31	for	for	IN	_	_	_
32	1	1	CD	_	_	_
33	hour	hour	NN	_	_	_
34	,	,	,	_	_	_
35	respectively	respectively	RB	_	_	_
36	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
37	E.	E.	NNP	_	_	_
38	coli	coli	NN	_	_	_
39	Rosetta	rosetta	NN	_	_	_
40	cells	cell	NNS	_	_	_
41	transformed	transform	VBN	_	_	_
42	with	with	IN	_	_	_
43	pET-28a	pet-28a	NN	_	_	_
44	or	or	CC	_	_	_
45	pET-28a-BnTR1	pet-28a-bntr1	NN	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	OD600nm	od600nm	NN	_	_	_
48	=	=	JJ	_	_	_
49	0.6	0.6	CD	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	were	be	VBD	_	_	_
52	induced	induce	VBN	_	_	_
53	with	with	IN	_	_	_
54	0.1	0.1	CD	_	_	_
55	mM	mm	NN	KWSUPP	_	_
56	IPTG	iptg	NN	_	_	_
57	at	at	IN	_	_	_
58	37	37	CD	_	_	_
59	°C	°c	NN	_	_	_
60	for	for	IN	_	_	_
61	1	1	CD	_	_	_
62	hour	hour	NN	_	_	_
63	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Emplty	Emplty	NNP	_	_	_
3	Vector	Vector	NNP	_	_	_
4	,	,	,	_	_	_
5	37	37	CD	_	_	_
6	°C	°c	NN	_	_	_
7	,	,	,	_	_	_
8	replicate	replicate	VB	_	_	_
9	1	1	CD	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Emplty	Emplty	NNP	_	_	_
12	Vector	Vector	NNP	_	_	_
13	,	,	,	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	,	,	,	_	_	_
17	replicate	replicate	VB	_	_	_
18	2	2	CD	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	Emplty	Emplty	NNP	_	_	_
21	Vector	Vector	NNP	_	_	_
22	,	,	,	_	_	_
23	37	37	CD	_	_	_
24	°C	°c	NN	_	_	_
25	,	,	,	_	_	_
26	replicate	replicate	VB	_	_	_
27	3	3	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	Emplty	Emplty	NNP	_	_	_
30	Vector	Vector	NNP	_	_	_
31	,	,	,	_	_	_
32	42	42	CD	_	_	_
33	°C	°c	NN	_	_	_
34	,	,	,	_	_	_
35	replicate	replicate	VB	_	_	_
36	1	1	CD	_	_	_
37	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
38	Emplty	Emplty	NNP	_	_	_
39	Vector	Vector	NNP	_	_	_
40	,	,	,	_	_	_
41	42	42	CD	_	_	_
42	°C	°c	NN	_	_	_
43	,	,	,	_	_	_
44	replicate	replicate	VB	_	_	_
45	2	2	CD	_	_	_
46	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
47	Emplty	Emplty	NNP	_	_	_
48	Vector	Vector	NNP	_	_	_
49	,	,	,	_	_	_
50	42	42	CD	_	_	_
51	°C	°c	NN	_	_	_
52	,	,	,	_	_	_
53	replicate	replicate	VB	_	_	_
54	3	3	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	EmptyVector	EmptyVector	NNP	_	_	_
57	_	_	SYM	_	_	_
58	37	37	CD	_	_	_
59	_	_	CD	_	_	_
60	rep1	rep1	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	EmptyVector	EmptyVector	NNP	_	_	_
63	_	_	SYM	_	_	_
64	37	37	CD	_	_	_
65	_	_	CD	_	_	_
66	rep2	rep2	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	EmptyVector	EmptyVector	NNP	_	_	_
69	_	_	SYM	_	_	_
70	37	37	CD	_	_	_
71	_	_	CD	_	_	_
72	rep3	rep3	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	EmptyVector	EmptyVector	NNP	_	_	_
75	_	_	SYM	_	_	_
76	42	42	CD	_	_	_
77	_	_	CD	_	_	_
78	rep1	rep1	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	EmptyVector	EmptyVector	NNP	_	_	_
81	_	_	SYM	_	_	_
82	42	42	CD	_	_	_
83	_	_	CD	_	_	_
84	rep2	rep2	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	EmptyVector	EmptyVector	NNP	_	_	_
87	_	_	SYM	_	_	_
88	42	42	CD	_	_	_
89	_	_	SYM	_	_	_
90	rep3	rep3	CD	_	_	_
91	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
92	Escherichia	escherichia	FW	Organism	_	_
93	coli	coli	FW	Organism	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	Raw	raw	NN	_	_	_
96	data	datum	NNS	_	_	_
97	were	be	VBD	_	_	_
98	normalized	normalize	VBN	_	_	_
99	-LRB-	-lrb-	-LRB-	_	_	_
100	quantile	quantile	JJ	_	_	_
101	method	method	NN	_	_	_
102	-RRB-	-rrb-	-RRB-	_	_	_
103	,	,	,	_	_	_
104	merged	merged	JJ	_	_	_
105	and	and	CC	_	_	_
106	filtered	filter	VBN	_	_	_
107	by	by	IN	_	_	_
108	Feature	Feature	NNP	_	_	_
109	Extraction	Extraction	NNP	_	_	_
110	Software	Software	NNP	_	_	_
111	-LRB-	-lrb-	-LRB-	_	_	_
112	Agilent	Agilent	NNP	_	_	_
113	Technologies	Technologies	NNPS	_	_	_
114	Inc.	Inc.	NNP	_	_	_
115	-RRB-	-rrb-	-RRB-	_	_	_
116	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	the	the	DT	_	_	_
3	sibiling	sibiling	NN	_	_	_
4	probes	probe	NNS	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	multiple	multiple	JJ	_	_	_
7	probes	probe	NNS	_	_	_
8	to	to	TO	_	_	_
9	one	one	CD	_	_	_
10	gene	gene	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	,	,	,	_	_	_
13	we	we	PRP	_	_	_
14	used	use	VBD	_	_	_
15	the	the	DT	_	_	_
16	median	median	JJ	_	_	_
17	indensity	indensity	NN	_	_	_
18	for	for	IN	_	_	_
19	representation	representation	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	vector	vector	NN	_	_	_
3	:	:	:	_	_	_
4	pET-28a	pet-28a	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	vector	vector	NN	_	_	_
7	:	:	:	_	_	_
8	pET-28a-BnTR1	pet-28a-bntr1	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	base	base	NN	_	_	_
11	calls	call	VBZ	_	_	_
12	with	with	IN	_	_	_
13	quality	quality	NN	_	_	_
14	metrics	metric	NNS	_	_	_
15	were	be	VBD	_	_	_
16	generated	generate	VBN	_	_	_
17	using	use	VBG	_	_	_
18	the	the	DT	_	_	_
19	HiSeq	HiSeq	NNP	_	_	_
20	2500	2500	CD	_	_	_
21	Control	Control	NNP	_	_	_
22	software	software	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	cells	cell	NNS	_	_	_
25	were	be	VBD	_	_	_
26	grown	grow	VBN	_	_	_
27	in	in	IN	_	_	_
28	M9	m9	NN	_	_	_
29	glucose	glucose	NN	SUPP	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	0.4	0.4	CD	_	_	_
32	%	%	NN	_	_	_
33	w	w	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	∆	∆	CD	_	_	_
36	dapF	dapf	NN	GEN	_	_
37	parent	parent	NN	_	_	_
38	Sample	sample	NN	_	_	_
39	28	28	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	∆	∆	CD	_	_	_
42	dapF	dapf	NN	GEN	_	_
43	parent	parent	NN	_	_	_
44	Sample	sample	NN	_	_	_
45	47	47	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	∆	∆	CD	_	_	_
48	dapF	dapf	NN	GEN	_	_
49	parent	parent	NN	_	_	_
50	Sample	Sample	NNP	_	_	_
51	9	9	CD	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	dapF	dapf	NN	GEN	_	_
54	suppressor	suppressor	NN	_	_	_
55	1-1	1-1	CD	_	_	_
56	Sample	sample	NN	_	_	_
57	10	10	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	dapF	dapf	NN	GEN	_	_
60	suppressor	suppressor	NN	_	_	_
61	1-1	1-1	CD	_	_	_
62	Sample	sample	NN	_	_	_
63	29	29	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	dapF	dapf	NN	GEN	_	_
66	suppressor	suppressor	NN	_	_	_
67	1-1	1-1	CD	_	_	_
68	Sample	sample	NN	_	_	_
69	48	48	CD	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	dapF	dapf	NN	GEN	_	_
72	suppressor	suppressor	NN	_	_	_
73	3-1	3-1	CD	_	_	_
74	Sample	Sample	NNP	_	_	_
75	11	11	CD	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	dapF	dapf	NN	GEN	_	_
78	suppressor	suppressor	NN	_	_	_
79	3-1	3-1	CD	_	_	_
80	Sample	Sample	NNP	_	_	_
81	30	30	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	dapF	dapf	NN	GEN	_	_
84	suppressor	suppressor	NN	_	_	_
85	3-1	3-1	CD	_	_	_
86	Sample	sample	NN	_	_	_
87	49	49	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	∆	∆	CD	_	_	_
90	dgk	dgk	NN	_	_	_
91	parent	parent	NN	_	_	_
92	Sample	sample	NN	_	_	_
93	16	16	CD	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	∆	∆	CD	_	_	_
96	dgk	dgk	NN	_	_	_
97	parent	parent	NN	_	_	_
98	Sample	sample	NN	_	_	_
99	35	35	CD	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	∆	∆	CD	_	_	_
102	dgk	dgk	NN	_	_	_
103	parent	parent	NN	_	_	_
104	Sample	sample	NN	_	_	_
105	54	54	CD	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	dgk	dgk	NN	_	_	_
108	suppressor	suppressor	NN	_	_	_
109	1-1	1-1	CD	_	_	_
110	Sample	sample	NN	_	_	_
111	17	17	CD	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	dgk	dgk	NN	_	_	_
114	suppressor	suppressor	NN	_	_	_
115	1-1	1-1	CD	_	_	_
116	Sample	sample	NN	_	_	_
117	36	36	CD	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	dgk	dgk	NN	_	_	_
120	suppressor	suppressor	NN	_	_	_
121	1-1	1-1	CD	_	_	_
122	Sample	sample	NN	_	_	_
123	55	55	CD	_	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
125	dgk	dgk	NN	_	_	_
126	suppressor	suppressor	NN	_	_	_
127	2-1	2-1	CD	_	_	_
128	Sample	sample	NN	_	_	_
129	18	18	CD	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	dgk	dgk	NN	_	_	_
132	suppressor	suppressor	NN	_	_	_
133	2-1	2-1	CD	_	_	_
134	Sample	sample	NN	_	_	_
135	37	37	CD	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	dgk	dgk	NN	_	_	_
138	suppressor	suppressor	NN	_	_	_
139	2-1	2-1	CD	_	_	_
140	Sample	sample	NN	_	_	_
141	56	56	CD	_	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	dgk	dgk	NN	_	_	_
144	suppressor	suppressor	NN	_	_	_
145	3-1	3-1	CD	_	_	_
146	Sample	sample	NN	_	_	_
147	19	19	CD	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	dgk	dgk	NN	_	_	_
150	suppressor	suppressor	NN	_	_	_
151	3-1	3-1	CD	_	_	_
152	Sample	sample	NN	_	_	_
153	38	38	CD	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	dgk	dgk	NN	_	_	_
156	suppressor	suppressor	NN	_	_	_
157	3-1	3-1	CD	_	_	_
158	Sample	sample	NN	_	_	_
159	57	57	CD	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	∆	∆	CD	_	_	_
162	entC	entc	NN	GEN	_	_
163	parent	parent	NN	_	_	_
164	Sample	sample	NN	_	_	_
165	12	12	CD	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	∆	∆	CD	_	_	_
168	entC	entc	NN	GEN	_	_
169	parent	parent	NN	_	_	_
170	Sample	Sample	NNP	_	_	_
171	31	31	CD	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
173	∆	∆	CD	_	_	_
174	entC	entc	NN	GEN	_	_
175	parent	parent	NN	_	_	_
176	Sample	sample	NN	_	_	_
177	50	50	CD	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	entC	entc	NN	GEN	_	_
180	suppressor	suppressor	NN	_	_	_
181	1-1	1-1	CD	_	_	_
182	Sample	Sample	NNP	_	_	_
183	13	13	CD	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	entC	entc	NN	GEN	_	_
186	suppressor	suppressor	NN	_	_	_
187	1-1	1-1	CD	_	_	_
188	Sample	sample	NN	_	_	_
189	32	32	CD	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
191	entC	entc	NN	GEN	_	_
192	suppressor	suppressor	NN	_	_	_
193	1-1	1-1	CD	_	_	_
194	Sample	sample	NN	_	_	_
195	51	51	CD	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	entC	entc	NN	GEN	_	_
198	suppressor	suppressor	NN	_	_	_
199	2-1	2-1	CD	_	_	_
200	Sample	sample	NN	_	_	_
201	14	14	CD	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	entC	entc	NN	GEN	_	_
204	suppressor	suppressor	NN	_	_	_
205	2-1	2-1	CD	_	_	_
206	Sample	sample	NN	_	_	_
207	33	33	CD	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	entC	entc	NN	GEN	_	_
210	suppressor	suppressor	NN	_	_	_
211	2-1	2-1	CD	_	_	_
212	Sample	sample	NN	_	_	_
213	52	52	CD	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	entC	entc	NN	GEN	_	_
216	suppressor	suppressor	NN	_	_	_
217	3-1	3-1	CD	_	_	_
218	Sample	Sample	NNP	_	_	_
219	15	15	CD	_	_	_
220	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
221	entC	entc	NN	GEN	_	_
222	suppressor	suppressor	NN	_	_	_
223	3-1	3-1	CD	_	_	_
224	Sample	sample	NN	_	_	_
225	34	34	CD	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	entC	entc	NN	GEN	_	_
228	suppressor	suppressor	NN	_	_	_
229	3-1	3-1	CD	_	_	_
230	Sample	Sample	NNP	_	_	_
231	53	53	CD	_	_	_
232	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
233	Escherichia	escherichia	FW	Organism	_	_
234	coli	coli	FW	Organism	_	_
235	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
236	Escherichia	escherichia	FW	Organism	_	_
237	coli	coli	FW	Organism	_	_
238	cell	cell	NN	_	_	_
239	lysate	lysate	NN	_	_	_
240	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
241	Genome	Genome	NNP	_	_	_
242	_	_	NNP	_	_	_
243	build	build	VB	_	_	_
244	:	:	:	_	_	_
245	E.	e.	FW	_	_	_
246	coli	coli	FW	_	_	_
247	strain	strain	NN	_	_	_
248	BW25113	bw25113	NN	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	library	library	NN	_	_	_
251	construction	construction	NN	_	_	_
252	followed	follow	VBD	_	_	_
253	Illumina	Illumina	NNP	_	_	_
254	manufacturer	manufacturer	NN	_	_	_
255	protocol	protocol	NN	_	_	_
256	for	for	IN	_	_	_
257	bacteria	bacterium	NNS	_	_	_
258	using	use	VBG	_	_	_
259	the	the	DT	_	_	_
260	Nextera	Nextera	NNP	_	_	_
261	XT	XT	NNP	_	_	_
262	DNA	DNA	NNP	_	_	_
263	Library	Library	NNP	_	_	_
264	Preparation	Preparation	NNP	_	_	_
265	Kit	kit	NN	_	_	_
266	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
267	∆	∆	CD	_	_	_
268	ppk	ppk	NN	GEN	_	_
269	parent	parent	NN	_	_	_
270	Sample	sample	NN	_	_	_
271	24	24	CD	_	_	_
272	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
273	∆	∆	CD	_	_	_
274	ppk	ppk	NN	GEN	_	_
275	parent	parent	NN	_	_	_
276	Sample	sample	NN	_	_	_
277	43	43	CD	_	_	_
278	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
279	∆	∆	CD	_	_	_
280	ppk	ppk	NN	GEN	_	_
281	parent	parent	NN	_	_	_
282	Sample	sample	NN	_	_	_
283	5	5	CD	_	_	_
284	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
285	ppk	ppk	NN	GEN	_	_
286	suppressor	suppressor	NN	_	_	_
287	1-1	1-1	CD	_	_	_
288	Sample	sample	NN	_	_	_
289	25	25	CD	_	_	_
290	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
291	ppk	ppk	NN	GEN	_	_
292	suppressor	suppressor	NN	_	_	_
293	1-1	1-1	CD	_	_	_
294	Sample	sample	NN	_	_	_
295	44	44	CD	_	_	_
296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
297	ppk	ppk	NN	GEN	_	_
298	suppressor	suppressor	NN	_	_	_
299	1-1	1-1	CD	_	_	_
300	Sample	sample	NN	_	_	_
301	6	6	CD	_	_	_
302	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
303	ppk	ppk	NN	GEN	_	_
304	suppressor	suppressor	NN	_	_	_
305	2-1	2-1	CD	_	_	_
306	Sample	sample	NN	_	_	_
307	26	26	CD	_	_	_
308	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
309	ppk	ppk	NN	GEN	_	_
310	suppressor	suppressor	NN	_	_	_
311	2-1	2-1	CD	_	_	_
312	Sample	sample	NN	_	_	_
313	45	45	CD	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	ppk	ppk	NN	GEN	_	_
316	suppressor	suppressor	NN	_	_	_
317	2-1	2-1	CD	_	_	_
318	Sample	sample	NN	_	_	_
319	7	7	CD	_	_	_
320	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
321	ppk	ppk	NN	GEN	_	_
322	suppressor	suppressor	NN	_	_	_
323	3-1	3-1	CD	_	_	_
324	Sample	sample	NN	_	_	_
325	27	27	CD	_	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	ppk	ppk	NN	GEN	_	_
328	suppressor	suppressor	NN	_	_	_
329	3-1	3-1	CD	_	_	_
330	Sample	sample	NN	_	_	_
331	46	46	CD	_	_	_
332	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
333	ppk	ppk	NN	GEN	_	_
334	suppressor	suppressor	NN	_	_	_
335	3-1	3-1	CD	_	_	_
336	Sample	sample	NN	_	_	_
337	8	8	CD	_	_	_
338	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
339	RNA-Seq	rna-seq	NN	_	_	_
340	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
341	RNA	rna	NN	_	_	_
342	was	be	VBD	_	_	_
343	isolated	isolate	VBN	_	_	_
344	using	use	VBG	_	_	_
345	standard	standard	JJ	_	_	_
346	Trizol	trizol	NN	_	_	_
347	lysis	lysis	NN	_	_	_
348	and	and	CC	_	_	_
349	aqueous	aqueous	JJ	_	_	_
350	extraction	extraction	NN	_	_	_
351	,	,	,	_	_	_
352	followed	follow	VBN	_	_	_
353	by	by	IN	_	_	_
354	further	further	JJ	_	_	_
355	purification	purification	NN	_	_	_
356	using	use	VBG	_	_	_
357	a	a	DT	_	_	_
358	Qiagen	Qiagen	NNP	_	_	_
359	RNAeasy	RNAeasy	NNP	_	_	_
360	kit	kit	NN	_	_	_
361	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	sequences	sequence	NNS	_	_	_
3	were	be	VBD	_	_	_
4	aligned	align	VBN	_	_	_
5	to	to	TO	_	_	_
6	the	the	DT	_	_	_
7	parent	parent	NN	_	_	_
8	E.	e.	FW	_	_	_
9	coli	coli	FW	_	_	_
10	strain	strain	NN	_	_	_
11	genome	genome	NN	_	_	_
12	template	template	NN	_	_	_
13	and	and	CC	_	_	_
14	transcript	transcript	NN	_	_	_
15	levels	level	NNS	_	_	_
16	were	be	VBD	_	_	_
17	quantified	quantify	VBN	_	_	_
18	for	for	IN	_	_	_
19	triplicate	triplicate	NN	_	_	_
20	groups	group	NNS	_	_	_
21	of	of	IN	_	_	_
22	each	each	DT	_	_	_
23	primary	primary	JJ	_	_	_
24	deletion	deletion	NN	_	_	_
25	strain	strain	NN	_	_	_
26	and	and	CC	_	_	_
27	synthetic	synthetic	JJ	_	_	_
28	rescue	rescue	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	i.e.	i.e.	FW	_	_	_
31	sup	sup	FW	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	strain	strain	NN	_	_	_
34	using	use	VBG	_	_	_
35	Rockhopper	Rockhopper	NNP	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	version	version	NN	_	_	_
38	2.0.3	2.0.3	CD	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	strain	strain	NN	_	_	_
42	:	:	:	_	_	_
43	BW25113	bw25113	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	transcript	transcript	NN	_	_	_
46	abundance	abundance	NN	_	_	_
47	was	be	VBD	_	_	_
48	quantified	quantify	VBN	_	_	_
49	using	use	VBG	_	_	_
50	rockhopper	rockhopper	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	WT	wt	SYM	_	_	_
53	-	-	:	_	_	_
54	Keio	Keio	NNP	_	_	_
55	Sample	Sample	NNP	_	_	_
56	1	1	CD	_	_	_
57	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
58	WT	wt	SYM	_	_	_
59	-	-	:	_	_	_
60	Keio	Keio	NNP	_	_	_
61	Sample	Sample	NNP	_	_	_
62	20	20	CD	_	_	_
63	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
64	WT	wt	SYM	_	_	_
65	-	-	:	_	_	_
66	Keio	Keio	NNP	_	_	_
67	Sample	Sample	NNP	_	_	_
68	39	39	CD	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	∆	∆	CD	_	_	_
71	zwf	zwf	NN	GEN	_	_
72	parent	parent	NN	_	_	_
73	Sample	sample	NN	_	_	_
74	2	2	CD	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	∆	∆	CD	_	_	_
77	zwf	zwf	NN	GEN	_	_
78	parent	parent	NN	_	_	_
79	Sample	sample	NN	_	_	_
80	21	21	CD	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	∆	∆	CD	_	_	_
83	zwf	zwf	NN	GEN	_	_
84	parent	parent	NN	_	_	_
85	Sample	Sample	NNP	_	_	_
86	40	40	CD	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	zwf	zwf	NN	GEN	_	_
89	suppressor	suppressor	NN	_	_	_
90	1-1	1-1	CD	_	_	_
91	Sample	sample	NN	_	_	_
92	22	22	CD	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	zwf	zwf	NN	GEN	_	_
95	suppressor	suppressor	NN	_	_	_
96	1-1	1-1	CD	_	_	_
97	Sample	sample	NN	_	_	_
98	3	3	CD	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
100	zwf	zwf	NN	GEN	_	_
101	suppressor	suppressor	NN	_	_	_
102	1-1	1-1	CD	_	_	_
103	Sample	sample	NN	_	_	_
104	41	41	CD	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	zwf	zwf	NN	GEN	_	_
107	suppressor	suppressor	NN	_	_	_
108	1-2	1-2	CD	_	_	_
109	Sample	sample	NN	_	_	_
110	23	23	CD	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	zwf	zwf	NN	GEN	_	_
113	suppressor	suppressor	NN	_	_	_
114	1-2	1-2	CD	_	_	_
115	Sample	sample	NN	_	_	_
116	4	4	CD	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	zwf	zwf	NN	GEN	_	_
119	suppressor	suppressor	NN	_	_	_
120	1-2	1-2	CD	_	_	_
121	Sample	sample	NN	_	_	_
122	42	42	CD	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	conducted	conduct	VBN	_	_	_
125	by	by	IN	_	_	_
126	CeGaT	cegat	NN	_	_	_
127	-LRB-	-lrb-	-LRB-	_	_	_
128	Tübingen	tübingen	NN	_	_	_
129	,	,	,	_	_	_
130	Germany	Germany	NNP	_	_	_
131	-RRB-	-rrb-	-RRB-	_	_	_
132	according	accord	VBG	_	_	_
133	to	to	TO	_	_	_
134	SOLiD	solid	JJ	_	_	_
135	standard	standard	JJ	_	_	_
136	protocols	protocol	NNS	_	_	_
137	for	for	IN	_	_	_
138	RNA-seq	rna-seq	JJ	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	conversion	conversion	NN	_	_	_
141	:	:	:	_	_	_
142	Convert	convert	VB	_	_	_
143	SOLiD	solid	JJ	_	_	_
144	output	output	NN	_	_	_
145	to	to	TO	_	_	_
146	fastq	fastq	NN	_	_	_
147	-LRB-	-lrb-	-LRB-	_	_	_
148	Galaxy	galaxy	NN	_	_	_
149	Version	version	NN	_	_	_
150	1.0.0	1.0.0	CD	_	_	_
151	-RRB-	-rrb-	-RRB-	_	_	_
152	;	;	:	_	_	_
153	default	default	NN	_	_	_
154	parameters	parameter	NNS	_	_	_
155	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	counting	counting	NN	_	_	_
3	:	:	:	_	_	_
4	countOverlaps	countoverlap	NNS	_	_	_
5	of	of	IN	_	_	_
6	Iranges	irange	NNS	_	_	_
7	;	;	:	_	_	_
8	default	default	NN	_	_	_
9	parameters	parameter	NNS	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
11	culture	culture	NN	_	_	_
12	:	:	:	_	_	_
13	18	18	CD	_	_	_
14	h	h	NN	_	_	_
15	at	at	IN	_	_	_
16	37	37	CD	_	_	_
17	°C	°c	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	differential	differential	JJ	_	_	_
20	expression	expression	NN	_	_	_
21	:	:	:	_	_	_
22	Bioconductor	Bioconductor	NNP	_	_	_
23	package	package	NN	_	_	_
24	edgeR	edger	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	version	version	NN	_	_	_
27	3.2.3	3.2.3	CD	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	;	;	:	_	_	_
30	default	default	NN	_	_	_
31	parameters	parameter	NNS	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
33	EHEC	ehec	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	EHEC	ehec	NN	_	_	_
36	either	either	CC	_	_	_
37	grown	grow	VBN	_	_	_
38	on	on	IN	_	_	_
39	plain	plain	JJ	_	_	_
40	LB	lb	NN	_	_	_
41	plates	plate	NNS	_	_	_
42	or	or	CC	_	_	_
43	LB	lb	NN	_	_	_
44	plates	plate	NNS	_	_	_
45	containing	contain	VBG	_	_	_
46	Symbioflor	symbioflor	NN	_	_	_
47	within	within	IN	_	_	_
48	the	the	DT	_	_	_
49	agar	agar	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	EHEC	ehec	NN	_	_	_
52	plus	plus	CC	_	_	_
53	Symbioflor	Symbioflor	NNP	_	_	_
54	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
55	Escherichia	escherichia	FW	Organism	_	_
56	coli	coli	FW	Organism	_	_
57	O157	o157	NN	_	_	_
58	:	:	:	_	_	_
59	H7	h7	NN	_	_	_
60	str	str	NN	_	_	_
61	.	.	.	_	_	_

1	EDL933	edl933	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Genome	Genome	NNP	_	_	_
4	_	_	NNP	_	_	_
5	build	build	VB	_	_	_
6	:	:	:	_	_	_
7	NC	NC	NNP	_	_	_
8	_	_	NNP	_	_	_
9	002655	002655	CD	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	LB	LB	NNP	_	_	_
12	agar	agar	NN	_	_	_
13	plates	plate	NNS	_	_	_
14	,	,	,	_	_	_
15	37	37	CD	_	_	_
16	°C	°c	NN	_	_	_
17	for	for	IN	_	_	_
18	18	18	CD	_	_	_
19	h	h	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	mapping	mapping	NN	_	_	_
22	:	:	:	_	_	_
23	bowtie	bowtie	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Galaxy	galaxy	NN	_	_	_
26	Version	version	NN	_	_	_
27	1.1.2	1.1.2	CD	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	;	;	:	_	_	_
30	28	28	CD	_	_	_
31	nt	nt	NNS	_	_	_
32	seed	seed	NN	_	_	_
33	length	length	NN	_	_	_
34	,	,	,	_	_	_
35	maximal	maximal	JJ	_	_	_
36	two	two	CD	_	_	_
37	mismatches	mismatch	NNS	_	_	_
38	in	in	IN	_	_	_
39	the	the	DT	_	_	_
40	seed	seed	NN	_	_	_
41	,	,	,	_	_	_
42	a	a	DT	_	_	_
43	maximal	maximal	JJ	_	_	_
44	threshold	threshold	NN	_	_	_
45	of	of	IN	_	_	_
46	70	70	CD	_	_	_
47	for	for	IN	_	_	_
48	the	the	DT	_	_	_
49	sum	sum	NN	_	_	_
50	of	of	IN	_	_	_
51	the	the	DT	_	_	_
52	quality	quality	NN	_	_	_
53	values	value	NNS	_	_	_
54	at	at	IN	_	_	_
55	mismatched	mismatched	JJ	_	_	_
56	positions	position	NNS	_	_	_
57	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
2	medium	medium	NN	_	_	_
3	:	:	:	_	_	_
4	LB	lb	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	normalizing	normalizing	NN	_	_	_
7	:	:	:	_	_	_
8	convert	convert	VB	_	_	_
9	counts	count	NNS	_	_	_
10	in	in	IN	_	_	_
11	RPKM	rpkm	NN	_	_	_
12	using	use	VBG	_	_	_
13	Excel	Excel	NNP	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	plus	plus	CC	_	_	_
16	Symbioflor	Symbioflor	NNP	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	RNA-Seq	rna-seq	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	scraping	scrape	VBG	_	_	_
21	bacteria	bacterium	NNS	_	_	_
22	,	,	,	_	_	_
23	opening	open	VBG	_	_	_
24	with	with	IN	_	_	_
25	bead	bead	NN	_	_	_
26	beating	beating	NN	_	_	_
27	,	,	,	_	_	_
28	Trizol-based	trizol-based	JJ	_	_	_
29	RNA	rna	NN	_	_	_
30	isolation	isolation	NN	_	_	_
31	,	,	,	_	_	_
32	rRNA	rrna	NN	_	_	_
33	depletion	depletion	NN	_	_	_
34	with	with	IN	_	_	_
35	RiboZero	RiboZero	NNP	_	_	_
36	,	,	,	_	_	_
37	DNA	DNA	NNP	_	_	_
38	digest	digest	VB	_	_	_
39	,	,	,	_	_	_
40	SoLiD	solid	JJ	_	_	_
41	seq	seq	NN	_	_	_
42	by	by	IN	_	_	_
43	CeGaT	cegat	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	Tübingen	tübingen	NN	_	_	_
46	,	,	,	_	_	_
47	Germany	Germany	NNP	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	Supplementary	Supplementary	NNP	_	_	_
51	_	_	VBD	_	_	_
52	files	file	NNS	_	_	_
53	_	_	IN	_	_	_
54	format	format	NN	_	_	_
55	_	_	NN	_	_	_
56	and	and	CC	_	_	_
57	_	_	NN	_	_	_
58	content	content	NN	_	_	_
59	:	:	:	_	_	_
60	xlsx	xlsx	NN	_	_	_
61	:	:	:	_	_	_
62	logFC	logfc	NN	_	_	_
63	and	and	CC	_	_	_
64	p-value	p-value	JJ	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	symbioflor	symbioflor	NN	_	_	_
67	status	status	NN	_	_	_
68	:	:	:	_	_	_
69	without	without	IN	_	_	_
70	Symbioflor	Symbioflor	NNP	_	_	_
71	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
72	symbioflor	symbioflor	NN	_	_	_
73	status	status	NN	_	_	_
74	:	:	:	_	_	_
75	with	with	IN	_	_	_
76	Symbioflor	Symbioflor	NNP	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
78	without	without	IN	_	_	_
79	Symbioflor	Symbioflor	NNP	_	_	_
80	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
81	Co-hybridization	co-hybridization	NN	_	_	_
82	of	of	IN	_	_	_
83	E.	e.	FW	_	_	_
84	coli	coli	FW	_	_	_
85	G	g	NN	_	_	_
86	1	1	CD	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	Co-hybridization	co-hybridization	NN	_	_	_
89	of	of	IN	_	_	_
90	E.	e.	FW	_	_	_
91	coli	coli	FW	_	_	_
92	G	g	NN	_	_	_
93	3	3	CD	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	Co-hybridization	co-hybridization	NN	_	_	_
96	of	of	IN	_	_	_
97	E.	e.	FW	_	_	_
98	coli	coli	FW	_	_	_
99	G	g	NN	_	_	_
100	4	4	CD	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	Co-hybridization	co-hybridization	NN	_	_	_
103	of	of	IN	_	_	_
104	E.	e.	FW	_	_	_
105	coli	coli	FW	_	_	_
106	G5	g5	NN	_	_	_
107	isolate	isolate	NN	_	_	_
108	with	with	IN	_	_	_
109	E.	e.	FW	_	_	_
110	coli	coli	FW	_	_	_
111	K-12	k-12	NN	_	_	_
112	MG1655	mg1655	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	Co-hybridization	co-hybridization	NN	_	_	_
115	of	of	IN	_	_	_
116	E.	e.	FW	_	_	_
117	coli	coli	FW	_	_	_
118	G5	g5	NN	_	_	_
119	isolate	isolate	NN	_	_	_
120	with	with	IN	_	_	_
121	E.	e.	FW	_	_	_
122	coli	coli	FW	_	_	_
123	O157	o157	NN	_	_	_
124	:	:	:	_	_	_
125	H7	h7	NN	_	_	_
126	EDL933	edl933	NN	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	Co-hybridization	co-hybridization	NN	_	_	_
129	of	of	IN	_	_	_
130	E.	e.	FW	_	_	_
131	coli	coli	FW	_	_	_
132	isolate	isolate	NN	_	_	_
133	G	g	NN	_	_	_
134	3	3	CD	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	Co-hybridization	co-hybridization	NN	_	_	_
137	of	of	IN	_	_	_
138	E.	e.	FW	_	_	_
139	coli	coli	FW	_	_	_
140	isolate	isolate	NN	_	_	_
141	G	g	NN	_	_	_
142	4	4	CD	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	Co-hybridization	co-hybridization	NN	_	_	_
145	of	of	IN	_	_	_
146	E.	e.	FW	_	_	_
147	coli	coli	FW	_	_	_
148	O157	o157	NN	_	_	_
149	:	:	:	_	_	_
150	H7	h7	NN	_	_	_
151	EDL933	edl933	NN	_	_	_
152	with	with	IN	_	_	_
153	E.	e.	FW	_	_	_
154	coli	coli	FW	_	_	_
155	K-12	k-12	NN	_	_	_
156	M1655	m1655	NN	_	_	_
157	#	#	#	_	_	_
158	1	1	CD	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	Co-hybridization	co-hybridization	NN	_	_	_
161	of	of	IN	_	_	_
162	E.	e.	FW	_	_	_
163	coli	coli	FW	_	_	_
164	O157	o157	NN	_	_	_
165	:	:	:	_	_	_
166	H7	h7	NN	_	_	_
167	EDL933	edl933	NN	_	_	_
168	with	with	IN	_	_	_
169	E.	e.	FW	_	_	_
170	coli	coli	FW	_	_	_
171	K-12	k-12	NN	_	_	_
172	M1655	m1655	NN	_	_	_
173	#	#	#	_	_	_
174	2	2	CD	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	control	control	NN	_	_	_
177	strain	strain	NN	_	_	_
178	K-12	k-12	NN	_	_	_
179	MG1655	mg1655	NN	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	control	control	NN	_	_	_
182	strain	strain	NN	_	_	_
183	O157	o157	NN	_	_	_
184	:	:	:	_	_	_
185	H7	h7	NN	_	_	_
186	EDL933	edl933	NN	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	E.	e.	FW	_	_	_
189	coli	coli	FW	_	_	_
190	G	g	NN	_	_	_
191	1	1	CD	_	_	_
192	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
193	E.	E.	NNP	_	_	_
194	coli	coli	NN	_	_	_
195	G4	g4	NN	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	E.	e.	FW	_	_	_
198	coli	coli	FW	_	_	_
199	G5	g5	NN	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	E.	e.	FW	_	_	_
202	coli	coli	FW	_	_	_
203	isolate	isolate	NN	_	_	_
204	G	g	NN	_	_	_
205	1	1	CD	_	_	_
206	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
207	E.	E.	NNP	_	_	_
208	coli	coli	NN	_	_	_
209	isolate	isolate	NN	_	_	_
210	G3	g3	NN	_	_	_
211	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
212	E.	E.	NNP	_	_	_
213	coli	coli	NN	_	_	_
214	isolate	isolate	NN	_	_	_
215	G	g	NN	_	_	_
216	3	3	CD	_	_	_
217	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
218	E.	E.	NNP	_	_	_
219	coli	coli	NN	_	_	_
220	isolate	isolate	NN	_	_	_
221	G4	g4	NN	_	_	_
222	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
223	E.	E.	NNP	_	_	_
224	coli	coli	NN	_	_	_
225	isolate	isolate	NN	_	_	_
226	G5	g5	NN	_	_	_
227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
228	E.	e.	FW	_	_	_
229	coli	coli	FW	_	_	_
230	K-12	k-12	NN	_	_	_
231	MG1655	mg1655	NN	_	_	_
232	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
233	E.	e.	FW	_	_	_
234	coli	coli	FW	_	_	_
235	O157	o157	NN	_	_	_
236	:	:	:	_	_	_
237	H7	h7	NN	_	_	_
238	EDL933	edl933	NN	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	Escherichia	escherichia	FW	Organism	_	_
241	coli	coli	FW	Organism	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
243	Genomic	genomic	JJ	_	_	_
244	DNA	dna	NN	_	_	_
245	isolation	isolation	NN	_	_	_
246	according	accord	VBG	_	_	_
247	to	to	TO	_	_	_
248	Grimberg	Grimberg	NNP	_	_	_
249	et	et	FW	_	_	_
250	al.	al.	FW	_	_	_
251	.	.	.	_	_	_

1	Nucleic	nucleic	JJ	_	_	_
2	acids	acid	NNS	_	_	_
3	research	research	NN	_	_	_
4	1989	1989	CD	_	_	_
5	,	,	,	_	_	_
6	17	17	CD	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	21	21	CD	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	:	:	:	_	_	_
11	8893	8893	CD	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	Isolate	isolate	VB	_	_	_
14	G	g	NN	_	_	_
15	1	1	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	Isolate	isolate	VB	_	_	_
18	G	g	NN	_	_	_
19	3	3	CD	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Isolate	isolate	VB	_	_	_
22	G	g	NN	_	_	_
23	4	4	CD	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	Isolate	isolate	VB	_	_	_
26	G5	g5	NN	_	_	_
27	of	of	IN	_	_	_
28	Symbioflor2	symbioflor2	NN	_	_	_
29	probiotic	probiotic	JJ	_	_	_
30	product	product	NN	_	_	_
31	from	from	IN	_	_	_
32	Symbiopharm	Symbiopharm	NNP	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	log2	log2	NN	_	_	_
35	ratio	ratio	NN	_	_	_
36	of	of	IN	_	_	_
37	isolate	isolate	JJ	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	overnight	overnight	JJ	_	_	_
40	in	in	IN	_	_	_
41	Luria-Bertani	Luria-Bertani	NNP	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	LB	LB	NNP	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	broth	broth	NN	_	_	_
46	with	with	IN	_	_	_
47	continuous	continuous	JJ	_	_	_
48	agitation	agitation	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	overnight	overnight	JJ	_	_	_
51	in	in	IN	_	_	_
52	Lurie-Bertani	Lurie-Bertani	NNP	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	LB	LB	NNP	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	broth	broth	NN	_	_	_
57	with	with	IN	_	_	_
58	continuous	continuous	JJ	_	_	_
59	agitation	agitation	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	Agilent	Agilent	NNP	_	_	_
62	Feature	Feature	NNP	_	_	_
63	Extraction	Extraction	NNP	_	_	_
64	Software	Software	NNP	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	v	v	LS	_	_	_
67	8.5.1.1	8.5.1.1	CD	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	was	be	VBD	_	_	_
70	used	use	VBN	_	_	_
71	for	for	IN	_	_	_
72	background	background	NN	_	_	_
73	subtraction	subtraction	NN	_	_	_
74	and	and	CC	_	_	_
75	LOWESS	lowess	NN	_	_	_
76	normalization	normalization	NN	_	_	_
77	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Biological	Biological	NNP	_	_	_
3	replicates	replicate	VBZ	_	_	_
4	per	per	IN	_	_	_
5	genotype	genotype	NN	_	_	_
6	were	be	VBD	_	_	_
7	incubated	incubate	VBN	_	_	_
8	at	at	IN	_	_	_
9	1	1	CD	_	_	_
10	mg	mg	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	E.	e.	FW	_	_	_
13	coli	coli	FW	_	_	_
14	ATCC	atcc	NN	_	_	_
15	25922	25922	CD	_	_	_
16	marR	marr	NN	GEN	_	_
17	deletion	deletion	NN	_	_	_
18	+	+	CC	_	_	_
19	QnrS	qnrs	NN	_	_	_
20	replicate	replicate	VBP	_	_	_
21	1	1	CD	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	E.	E.	NNP	_	_	_
24	coli	coli	NN	_	_	_
25	ATCC	atcc	NN	_	_	_
26	25922	25922	CD	_	_	_
27	marR	marr	NN	GEN	_	_
28	deletion	deletion	NN	_	_	_
29	+	+	CC	_	_	_
30	QnrS	qnrs	NN	_	_	_
31	replicate	replicate	VBP	_	_	_
32	2	2	CD	_	_	_
33	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
34	E.	E.	NNP	_	_	_
35	coli	coli	NN	_	_	_
36	ATCC	atcc	NN	_	_	_
37	25922	25922	CD	_	_	_
38	QnrS	qnrs	NN	_	_	_
39	replicate	replicate	VBP	_	_	_
40	1	1	CD	_	_	_
41	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
42	E.	E.	NNP	_	_	_
43	coli	coli	NN	_	_	_
44	ATCC	atcc	NN	_	_	_
45	25922	25922	CD	_	_	_
46	QnrS	qnrs	NN	_	_	_
47	replicate	replicate	VBP	_	_	_
48	2	2	CD	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	E.	E.	NNP	_	_	_
51	coli	coli	NN	_	_	_
52	ATCC	atcc	NN	_	_	_
53	25922	25922	CD	_	_	_
54	Ser83Leu	ser83leu	NN	_	_	_
55	+	+	CC	_	_	_
56	QnrS	qnrs	NN	_	_	_
57	replicate	replicate	VBP	_	_	_
58	1	1	CD	_	_	_
59	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
60	E.	E.	NNP	_	_	_
61	coli	coli	NN	_	_	_
62	ATCC	atcc	NN	_	_	_
63	25922	25922	CD	_	_	_
64	Ser83Leu	ser83leu	NN	_	_	_
65	+	+	CC	_	_	_
66	QnrS	qnrs	NN	_	_	_
67	replicate	replicate	VBP	_	_	_
68	2	2	CD	_	_	_
69	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
70	E.	E.	NNP	_	_	_
71	coli	coli	NN	_	_	_
72	ATCC	atcc	NN	_	_	_
73	25922	25922	CD	_	_	_
74	-LRB-	-lrb-	-LRB-	_	_	_
75	wild-type	wild-type	JJ	_	_	_
76	-RRB-	-rrb-	-RRB-	_	_	_
77	and	and	CC	_	_	_
78	EC14	ec14	NN	_	_	_
79	,	,	,	_	_	_
80	EC19	ec19	NN	_	_	_
81	,	,	,	_	_	_
82	EC24	ec24	NN	_	_	_
83	-LRB-	-lrb-	-LRB-	_	_	_
84	LLQR	llqr	NN	_	_	_
85	-RRB-	-rrb-	-RRB-	_	_	_
86	isogenic	isogenic	JJ	_	_	_
87	strains	strain	NNS	_	_	_
88	were	be	VBD	_	_	_
89	tested	test	VBN	_	_	_
90	to	to	TO	_	_	_
91	evaluate	evaluate	VB	_	_	_
92	the	the	DT	_	_	_
93	global	global	JJ	_	_	_
94	response	response	NN	_	_	_
95	to	to	TO	_	_	_
96	relevant	relevant	JJ	_	_	_
97	fix	fix	NN	_	_	_
98	concentration	concentration	NN	_	_	_
99	of	of	IN	_	_	_
100	ciprofloxacin	ciprofloxacin	NN	_	_	_
101	-LRB-	-lrb-	-LRB-	_	_	_
102	1	1	CD	_	_	_
103	mg	mg	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	Escherichia	escherichia	FW	Organism	_	_
106	coli	coli	FW	Organism	_	_
107	ATCC	atcc	NN	_	_	_
108	25922	25922	CD	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
110	Exponential	exponential	JJ	_	_	_
111	cells	cell	NNS	_	_	_
112	-LRB-	-lrb-	-LRB-	_	_	_
113	DO600	do600	NN	_	_	_
114	=	=	JJ	_	_	_
115	0,4	0,4	CD	_	_	_
116	-RRB-	-rrb-	-RRB-	_	_	_
117	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
118	genotype	genotype	NN	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	RNA	rna	NN	_	_	_
121	extraction	extraction	NN	_	_	_
122	was	be	VBD	_	_	_
123	performed	perform	VBN	_	_	_
124	using	use	VBG	_	_	_
125	the	the	DT	_	_	_
126	RNeasy	RNeasy	NNP	_	_	_
127	Mini	Mini	NNP	_	_	_
128	Kit	kit	NN	_	_	_
129	-LRB-	-lrb-	-LRB-	_	_	_
130	Qiagen	Qiagen	NNP	_	_	_
131	,	,	,	_	_	_
132	Hilden	Hilden	NNP	_	_	_
133	,	,	,	_	_	_
134	Germany	Germany	NNP	_	_	_
135	-RRB-	-rrb-	-RRB-	_	_	_
136	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	substrain	substrain	NN	_	_	_
3	:	:	:	_	_	_
4	ATCC	atcc	NN	_	_	_
5	25922	25922	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	substrain	substrain	NN	_	_	_
8	:	:	:	_	_	_
9	EC14	ec14	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	substrain	substrain	NN	_	_	_
12	:	:	:	_	_	_
13	EC19	ec19	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	substrain	substrain	NN	_	_	_
16	:	:	:	_	_	_
17	EC24	ec24	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Wild-type	wild-type	JJ	_	_	_
20	E.	e.	FW	_	_	_
21	coli	coli	FW	_	_	_
22	ATCC	atcc	NN	_	_	_
23	25922	25922	CD	_	_	_
24	replicate	replicate	VBP	_	_	_
25	1	1	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	Wild-type	wild-type	JJ	_	_	_
28	E.	e.	FW	_	_	_
29	coli	coli	FW	_	_	_
30	ATCC	atcc	NN	_	_	_
31	25922	25922	CD	_	_	_
32	replicate	replicate	VBP	_	_	_
33	2	2	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
35	Bacterial	bacterial	JJ	_	_	_
36	RNA	rna	NN	_	_	_
37	was	be	VBD	_	_	_
38	purified	purify	VBN	_	_	_
39	with	with	IN	_	_	_
40	Qiagen	Qiagen	NNP	_	_	_
41	RNeasy	RNeasy	NNP	_	_	_
42	mini	minus	NNS	_	_	_
43	kit	kit	NN	_	_	_
44	,	,	,	_	_	_
45	and	and	CC	_	_	_
46	the	the	DT	_	_	_
47	samples	sample	NNS	_	_	_
48	with	with	IN	_	_	_
49	RNA	rna	NN	_	_	_
50	Integrity	integrity	NN	_	_	_
51	Number	number	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	RIN	rin	NN	_	_	_
54	-RRB-	-rrb-	-RRB-	_	_	_
55	>	>	JJR	_	_	_
56	9	9	CD	_	_	_
57	were	be	VBD	_	_	_
58	used	use	VBN	_	_	_
59	for	for	IN	_	_	_
60	labeling	label	VBG	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	culture	culture	NN	_	_	_
63	media	media	NNS	_	_	_
64	:	:	:	_	_	_
65	LB	lb	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	culture	culture	NN	_	_	_
68	media	media	NNS	_	_	_
69	:	:	:	_	_	_
70	LB	lb	NN	_	_	_
71	with	with	IN	_	_	_
72	2.5	2.5	CD	_	_	_
73	mM	mm	NN	KWSUPP	_	_
74	Fumaric	fumaric	JJ	_	_	_
75	acid	acid	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	EDL933	edl933	NN	_	_	_
78	_	_	CD	_	_	_
79	LB	lb	NN	_	_	_
80	_	_	NN	_	_	_
81	I	I	PRP	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBP	_	_	_
83	EDL933	edl933	NN	_	_	_
84	_	_	CD	_	_	_
85	LB	lb	NN	_	_	_
86	_	_	NN	_	_	_
87	II	ii	CD	_	_	_
88	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
89	Escherichia	escherichia	FW	Organism	_	_
90	coli	coli	FW	Organism	_	_
91	O157	o157	NN	_	_	_
92	:	:	:	_	_	_
93	H7	h7	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	GeneSpring	genespr	VBG	_	_	_
96	GX	GX	NNP	_	_	_
97	v.	v.	CC	_	_	_
98	13.1	13.1	CD	_	_	_
99	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
100	genotype	genotype	NN	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	O157	o157	NN	_	_	_
103	:	:	:	_	_	_
104	H7	h7	NN	_	_	_
105	EDL933	edl933	NN	_	_	_
106	in	in	IN	_	_	_
107	LB	LB	NNP	_	_	_
108	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
109	O157	o157	NN	_	_	_
110	:	:	:	_	_	_
111	H7	h7	NN	_	_	_
112	EDL933	edl933	NN	_	_	_
113	sdhA	sdha	NN	GEN	_	_
114	in	in	IN	_	_	_
115	LB	LB	NNP	_	_	_
116	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
117	O157	o157	NN	_	_	_
118	:	:	:	_	_	_
119	H7	h7	NN	_	_	_
120	EDL933	edl933	NN	_	_	_
121	sdhA	sdha	NN	GEN	_	_
122	in	in	IN	_	_	_
123	LB	lb	NN	_	_	_
124	with	with	IN	_	_	_
125	FA	fa	NN	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	sdhA	sdha	NN	GEN	_	_
128	_	_	CD	_	_	_
129	FA	FA	NNP	_	_	_
130	_	_	SYM	_	_	_
131	I	I	PRP	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBP	_	_	_
133	sdhA	sdha	NN	GEN	_	_
134	_	_	CD	_	_	_
135	FA	FA	NNP	_	_	_
136	_	_	NNP	_	_	_
137	II	II	NNP	_	_	_
138	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
139	sdhA	sdhA	NNP	GEN	_	_
140	_	_	NNP	_	_	_
141	FA	FA	NNP	_	_	_
142	_	_	VBD	_	_	_
143	III	iii	CD	_	_	_
144	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
145	sdhA	sdha	NN	GEN	_	_
146	_	_	CD	_	_	_
147	LB	lb	NN	_	_	_
148	_	_	NN	_	_	_
149	I	I	PRP	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBP	_	_	_
151	sdhA	sdha	NN	GEN	_	_
152	_	_	CD	_	_	_
153	LB	lb	NN	_	_	_
154	_	_	NN	_	_	_
155	II	ii	CD	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
157	sdhA	sdha	NN	GEN	_	_
158	_	_	CD	_	_	_
159	LB	lb	NN	_	_	_
160	_	_	NN	_	_	_
161	III	iii	CD	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	strain	strain	NN	_	_	_
164	background	background	NN	_	_	_
165	:	:	:	_	_	_
166	EDL933	edl933	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
168	The	the	DT	_	_	_
169	overnight	overnight	JJ	_	_	_
170	cultures	culture	NNS	_	_	_
171	of	of	IN	_	_	_
172	bacteria	bacterium	NNS	_	_	_
173	in	in	IN	_	_	_
174	LB	lb	NN	MED	_	_
175	broth	broth	NN	MED	_	_
176	were	be	VBD	_	_	_
177	refreshed	refresh	VBN	_	_	_
178	with	with	IN	_	_	_
179	the	the	DT	_	_	_
180	ratio	ratio	NN	_	_	_
181	of	of	IN	_	_	_
182	1:100	1:100	CD	_	_	_
183	into	into	IN	_	_	_
184	fresh	fresh	JJ	_	_	_
185	LB	lb	NN	MED	_	_
186	broth	broth	NN	MED	_	_
187	,	,	,	_	_	_
188	and	and	CC	_	_	_
189	incubated	incubate	VBN	_	_	_
190	at	at	IN	_	_	_
191	30	30	CD	_	_	_
192	℃	℃	NN	_	_	_
193	with	with	IN	_	_	_
194	continuous	continuous	JJ	_	_	_
195	shaking	shake	VBG	_	_	_
196	until	until	IN	_	_	_
197	the	the	DT	_	_	_
198	absorbance	absorbance	NN	_	_	_
199	at	at	IN	_	_	_
200	590	590	CD	_	_	_
201	nm	nm	NN	_	_	_
202	reached	reach	VBD	_	_	_
203	0.5	0.5	CD	_	_	_
204	to	to	TO	_	_	_
205	0.6	0.6	CD	_	_	_
206	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	values	value	NNS	_	_	_
4	below	below	IN	_	_	_
5	0.01	0.01	CD	_	_	_
6	were	be	VBD	_	_	_
7	set	set	VBN	_	_	_
8	to	to	TO	_	_	_
9	0.01	0.01	CD	_	_	_
10	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	log2	log2	NN	_	_	_
3	ratio	ratio	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	intensity	intensity	NN	_	_	_
7	of	of	IN	_	_	_
8	signal	signal	NN	_	_	_
9	channel	channel	NN	_	_	_
10	to	to	TO	_	_	_
11	that	that	DT	_	_	_
12	of	of	IN	_	_	_
13	control	control	NN	_	_	_
14	channel	channel	NN	_	_	_
15	was	be	VBD	_	_	_
16	calculated	calculate	VBN	_	_	_
17	and	and	CC	_	_	_
18	was	be	VBD	_	_	_
19	then	then	RB	_	_	_
20	normalized	normalize	VBN	_	_	_
21	to	to	TO	_	_	_
22	each	each	DT	_	_	_
23	slide	slide	NN	_	_	_
24	's	's	POS	_	_	_
25	median	median	JJ	_	_	_
26	intensity	intensity	NN	_	_	_
27	ratio	ratio	NN	_	_	_
28	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	default	default	NN	_	_	_
3	interpretation	interpretation	NN	_	_	_
4	mode	mode	NN	_	_	_
5	was	be	VBD	_	_	_
6	set	set	VBN	_	_	_
7	to	to	TO	_	_	_
8	`	`	``	_	_	_
9	log	log	NN	_	_	_
10	of	of	IN	_	_	_
11	ratio	ratio	NN	_	_	_
12	'	'	''	_	_	_
13	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	time	time	NN	_	_	_
3	point	point	NN	_	_	_
4	was	be	VBD	_	_	_
5	then	then	RB	_	_	_
6	tested	test	VBN	_	_	_
7	separately	separately	RB	_	_	_
8	for	for	IN	_	_	_
9	statistical	statistical	JJ	_	_	_
10	differences	difference	NNS	_	_	_
11	using	use	VBG	_	_	_
12	ANOVA	ANOVA	NNP	_	_	_
13	at	at	IN	_	_	_
14	5	5	CD	_	_	_
15	%	%	NN	_	_	_
16	confidence	confidence	NN	_	_	_
17	level	level	NN	_	_	_
18	,	,	,	_	_	_
19	in	in	IN	_	_	_
20	conjunction	conjunction	NN	_	_	_
21	with	with	IN	_	_	_
22	Benjamini-Hochberg	Benjamini-Hochberg	NNP	_	_	_
23	multiple	multiple	JJ	_	_	_
24	testing	testing	NN	_	_	_
25	correction	correction	NN	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	with	with	IN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	10J	10j	NN	_	_	_
5	.0	.0	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	11K	11k	CD	_	_	_
8	.60	.60	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	12L	12l	NN	_	_	_
11	.120	.120	CD	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	200	200	CD	_	_	_
14	bp	bp	NN	_	_	_
15	insert	insert	NN	_	_	_
16	,	,	,	_	_	_
17	rRNA	rrna	NN	_	_	_
18	depletion	depletion	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	7G	7g	NN	_	_	_
21	.0	.0	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	biological	biological	JJ	_	_	_
24	replicate	replicate	VB	_	_	_
25	:	:	:	_	_	_
26	Replicate	replicate	VB	_	_	_
27	1	1	CD	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	biological	biological	JJ	_	_	_
30	replicate	replicate	VB	_	_	_
31	:	:	:	_	_	_
32	t	t	NN	_	_	_
33	=	=	JJ	_	_	_
34	0	0	CD	_	_	_
35	Replicate	replicate	NN	_	_	_
36	1	1	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	biological	biological	JJ	_	_	_
39	replicate	replicate	VB	_	_	_
40	:	:	:	_	_	_
41	t	t	NN	_	_	_
42	=	=	JJ	_	_	_
43	0	0	CD	_	_	_
44	replicate	replicate	VBP	_	_	_
45	2	2	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
47	Dividing	divide	VBG	_	_	_
48	t	t	NN	_	_	_
49	=	=	JJ	_	_	_
50	2	2	CD	_	_	_
51	hours	hour	NNS	_	_	_
52	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
53	E.	E.	NNP	_	_	_
54	coli	coli	NNS	_	_	_
55	were	be	VBD	_	_	_
56	sampled	sample	VBN	_	_	_
57	at	at	IN	_	_	_
58	times	time	NNS	_	_	_
59	=	=	JJ	_	_	_
60	0	0	CD	_	_	_
61	,	,	,	_	_	_
62	1	1	CD	_	_	_
63	hour	hour	NN	_	_	_
64	,	,	,	_	_	_
65	and	and	CC	_	_	_
66	2	2	CD	_	_	_
67	hours	hour	NNS	_	_	_
68	following	follow	VBG	_	_	_
69	release	release	NN	_	_	_
70	from	from	IN	_	_	_
71	stationary	stationary	JJ	GrowthPhase	_	_
72	phase	phase	NN	GrowthPhase	_	_
73	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Genome	Genome	NNP	_	_	_
6	_	_	NNP	_	_	_
7	build	build	VB	_	_	_
8	:	:	:	_	_	_
9	Escherichia	escherichia	FW	Organism	_	_
10	coli	coli	FW	Organism	_	_
11	MG1655	mg1655	NN	_	_	_
12	reference	reference	NN	_	_	_
13	genome	genome	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	NC	nc	NN	_	_	_
16	_	_	CD	_	_	_
17	00091313-Feb-2011	00091313-feb-2011	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Growing	grow	VBG	_	_	_
20	t	t	NN	_	_	_
21	=	=	JJ	_	_	_
22	1	1	CD	_	_	_
23	hour	hour	NN	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	RNA-Seq	rna-seq	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	RNA	rna	NN	_	_	_
28	sequences	sequence	NNS	_	_	_
29	were	be	VBD	_	_	_
30	quality	quality	JJ	_	_	_
31	assessed	assess	VBN	_	_	_
32	and	and	CC	_	_	_
33	trimmed	trim	VBN	_	_	_
34	using	use	VBG	_	_	_
35	FastQC	fastqc	NN	_	_	_
36	version	version	NN	_	_	_
37	0.10.1	0.10.1	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	www.bioinformatics.babraham.ac.uk	www.bioinformatics.babraham.ac.uk	JJ	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	RNA	rna	NN	_	_	_
42	was	be	VBD	_	_	_
43	extracted	extract	VBN	_	_	_
44	from	from	IN	_	_	_
45	two	two	CD	_	_	_
46	biological	biological	JJ	_	_	_
47	replicates	replicate	VBZ	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	30	30	CD	_	_	_
50	mL	ml	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	of	of	IN	_	_	_
53	each	each	DT	_	_	_
54	bacterial	bacterial	JJ	_	_	_
55	culture	culture	NN	_	_	_
56	isolated	isolate	VBN	_	_	_
57	at	at	IN	_	_	_
58	each	each	DT	_	_	_
59	time	time	NN	_	_	_
60	point	point	NN	_	_	_
61	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	30	30	CD	_	_	_
3	mL	ml	NN	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	aliquoted	aliquote	VBN	_	_	_
7	into	into	IN	_	_	_
8	three	three	CD	_	_	_
9	15	15	CD	_	_	_
10	mL	ml	NN	_	_	_
11	tubes	tube	NNS	_	_	_
12	containing	contain	VBG	_	_	_
13	5	5	CD	_	_	_
14	mL	ml	NN	_	_	_
15	of	of	IN	_	_	_
16	ice-cold	ice-cold	JJ	_	_	_
17	EtOH	etoh	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	RNA	rna	NN	_	_	_
20	was	be	VBD	_	_	_
21	pelleted	pelleted	JJ	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	14,000	14,000	CD	_	_	_
24	rpm	rpm	NN	_	_	_
25	,	,	,	_	_	_
26	5	5	CD	_	_	_
27	min	min	NN	_	_	_
28	,	,	,	_	_	_
29	4	4	CD	_	_	_
30	°C	°c	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	and	and	CC	_	_	_
33	air	air	NN	_	_	_
34	dried	dry	VBD	_	_	_
35	before	before	IN	_	_	_
36	suspension	suspension	NN	_	_	_
37	in	in	IN	_	_	_
38	80	80	CD	_	_	_
39	µL	µl	NN	_	_	_
40	RNAse	rnase	NN	_	_	_
41	free	free	JJ	_	_	_
42	water	water	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	Invitrogen	invitrogen	NN	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	and	and	CC	_	_	_
47	treatment	treatment	NN	_	_	_
48	with	with	IN	_	_	_
49	TURBO	TURBO	NNP	_	_	_
50	DNAse	dnase	NN	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	Ambion	ambion	NN	_	_	_
53	-RRB-	-rrb-	-RRB-	_	_	_
54	according	accord	VBG	_	_	_
55	to	to	TO	_	_	_
56	the	the	DT	_	_	_
57	manufacturer	manufacturer	NN	_	_	_
58	's	's	POS	_	_	_
59	instructions	instruction	NNS	_	_	_
60	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	0.1	0.1	CD	_	_	_
4	V	v	NN	_	_	_
5	of	of	IN	_	_	_
6	10	10	CD	_	_	_
7	X	x	NN	_	_	_
8	Turbo	Turbo	NNP	_	_	_
9	DNAse	dnase	NN	_	_	_
10	buffer	buffer	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Ambion	ambion	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	was	be	VBD	_	_	_
15	added	add	VBN	_	_	_
16	to	to	TO	_	_	_
17	the	the	DT	_	_	_
18	RNA	rna	NN	_	_	_
19	solution	solution	NN	_	_	_
20	.	.	.	_	_	_

1	1	1	CD	_	_	_
2	µL	µl	NN	_	_	_
3	of	of	IN	_	_	_
4	TURBO	TURBO	NNP	_	_	_
5	DNAse	dnase	NN	_	_	_
6	was	be	VBD	_	_	_
7	added	add	VBN	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	solution	solution	NN	_	_	_
11	,	,	,	_	_	_
12	which	which	WDT	_	_	_
13	was	be	VBD	_	_	_
14	then	then	RB	_	_	_
15	incubated	incubate	VBN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	30	30	CD	_	_	_
18	min	min	NN	_	_	_
19	,	,	,	_	_	_
20	37	37	CD	_	_	_
21	°C	°c	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

1	Following	follow	VBG	_	_	_
2	incubation	incubation	NN	_	_	_
3	,	,	,	_	_	_
4	0.1	0.1	CD	_	_	_
5	V	v	NN	_	_	_
6	of	of	IN	_	_	_
7	DNase	dnase	NN	_	_	_
8	Inactivation	inactivation	NN	_	_	_
9	Reagent	reagent	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Ambion	ambion	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	was	be	VBD	_	_	_
14	added	add	VBN	_	_	_
15	and	and	CC	_	_	_
16	then	then	RB	_	_	_
17	incubated	incubate	VBN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	5	5	CD	_	_	_
20	min	min	NN	_	_	_
21	,	,	,	_	_	_
22	RT	rt	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	with	with	IN	_	_	_
25	occasional	occasional	JJ	_	_	_
26	mixing	mix	VBG	_	_	_
27	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	isolated	isolate	VBN	_	_	_
4	and	and	CC	_	_	_
5	transferred	transfer	VBN	_	_	_
6	into	into	IN	_	_	_
7	a	a	DT	_	_	_
8	fresh	fresh	JJ	_	_	_
9	microfuge	microfuge	NN	_	_	_
10	tube	tube	NN	_	_	_
11	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	quality	quality	NN	_	_	_
3	tested	test	VBN	_	_	_
4	using	use	VBG	_	_	_
5	the	the	DT	_	_	_
6	the	the	DT	_	_	_
7	Agilent	Agilent	NNP	_	_	_
8	RNA	rna	NN	_	_	_
9	6000	6000	CD	_	_	_
10	Nano	Nano	NNP	_	_	_
11	Kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Agilent	Agilent	NNP	_	_	_
14	Technologies	Technologies	NNPS	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	and	and	CC	_	_	_
17	quality	quality	NN	_	_	_
18	analysed	analyse	VBN	_	_	_
19	using	use	VBG	_	_	_
20	the	the	DT	_	_	_
21	Agilent	Agilent	NNP	_	_	_
22	2100	2100	CD	_	_	_
23	Bioanalyzer	Bioanalyzer	NNP	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Agilent	Agilent	NNP	_	_	_
26	Technologies	Technologies	NNPS	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Stationary	stationary	JJ	_	_	_
3	phase	phase	NN	_	_	_
4	t	t	NN	_	_	_
5	=	=	JJ	_	_	_
6	0	0	CD	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Synchronization	synchronization	NN	_	_	_
9	was	be	VBD	_	_	_
10	achieved	achieve	VBN	_	_	_
11	by	by	IN	_	_	_
12	passaging	passaging	NN	_	_	_
13	cells	cell	NNS	_	_	_
14	through	through	IN	_	_	_
15	one	one	CD	_	_	_
16	or	or	CC	_	_	_
17	two	two	CD	_	_	_
18	rounds	round	NNS	_	_	_
19	of	of	IN	_	_	_
20	stationary	stationary	JJ	GrowthPhase	_	_
21	phase	phase	NN	GrowthPhase	_	_
22	according	accord	VBG	_	_	_
23	to	to	TO	_	_	_
24	Cutler	Cutler	NNP	_	_	_
25	and	and	CC	_	_	_
26	Evans	Evans	NNP	_	_	_
27	1966	1966	CD	_	_	_
28	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	:	:	:	_	_	_
3	Individual	individual	JJ	_	_	_
4	colonies	colony	NNS	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	LB	lb	NN	_	_	_
7	plate	plate	NN	_	_	_
8	,	,	,	_	_	_
9	37	37	CD	_	_	_
10	°C	°c	NN	_	_	_
11	,	,	,	_	_	_
12	24	24	CD	_	_	_
13	h	h	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	were	be	VBD	_	_	_
16	inoculated	inoculate	VBN	_	_	_
17	into	into	IN	_	_	_
18	M9	m9	NN	_	_	_
19	media	media	NNS	_	_	_
20	and	and	CC	_	_	_
21	grown	grow	VBN	_	_	_
22	O	o	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
24	time	time	NN	_	_	_
25	post	post	NN	_	_	_
26	release	release	NN	_	_	_
27	:	:	:	_	_	_
28	E.	e.	FW	_	_	_
29	coli	coli	FW	_	_	_
30	cells	cell	NNS	_	_	_
31	1	1	CD	_	_	_
32	hour	hour	NN	_	_	_
33	following	follow	VBG	_	_	_
34	release	release	NN	_	_	_
35	from	from	IN	_	_	_
36	Stationary	stationary	JJ	_	_	_
37	phase	phase	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	t	t	NN	_	_	_
40	=	=	JJ	_	_	_
41	1	1	CD	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	time	time	NN	_	_	_
45	post	post	NN	_	_	_
46	release	release	NN	_	_	_
47	:	:	:	_	_	_
48	E.	e.	FW	_	_	_
49	coli	coli	FW	_	_	_
50	cells	cell	NNS	_	_	_
51	2	2	CD	_	_	_
52	hour2	hour2	NN	_	_	_
53	following	follow	VBG	_	_	_
54	release	release	NN	_	_	_
55	from	from	IN	_	_	_
56	Stationary	stationary	JJ	_	_	_
57	phase	phase	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	t	t	NN	_	_	_
60	=	=	JJ	_	_	_
61	2	2	CD	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	time	time	NN	_	_	_
65	post	post	NN	_	_	_
66	release	release	NN	_	_	_
67	:	:	:	_	_	_
68	E.	e.	FW	_	_	_
69	coli	coli	FW	_	_	_
70	cells	cell	NNS	_	_	_
71	immediately	immediately	RB	_	_	_
72	following	follow	VBG	_	_	_
73	release	release	NN	_	_	_
74	from	from	IN	_	_	_
75	Stationary	stationary	JJ	_	_	_
76	phase	phase	NN	_	_	_
77	t	t	NN	_	_	_
78	=	=	JJ	_	_	_
79	0	0	CD	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	BW25113	bw25113	NN	_	_	_
82	hha	hha	NN	GEN	_	_
83	deletion	deletion	NN	_	_	_
84	mutant	mutant	JJ	_	_	_
85	LB	lb	NN	_	_	_
86	4	4	CD	_	_	_
87	hr	hr	NN	_	_	_
88	biofilm	biofilm	NN	_	_	_
89	cells	cell	NNS	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
91	BW25113	bw25113	NN	_	_	_
92	hha	hha	NN	GEN	_	_
93	mutant	mutant	JJ	_	_	_
94	LB	lb	NN	_	_	_
95	glu	glu	NN	_	_	_
96	15	15	CD	_	_	_
97	hr	hr	NN	_	_	_
98	biofilm	biofilm	NN	_	_	_
99	cells	cell	NNS	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
101	BW25113	bw25113	NN	_	_	_
102	hha	hha	NN	GEN	_	_
103	mutant	mutant	JJ	_	_	_
104	LB	lb	NN	_	_	_
105	glu	glu	NN	_	_	_
106	24	24	CD	_	_	_
107	hr	hr	NN	_	_	_
108	biofilm	biofilm	NN	_	_	_
109	cells	cell	NNS	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
111	BW25113	bw25113	NN	_	_	_
112	hha	hha	NN	GEN	_	_
113	mutant	mutant	JJ	_	_	_
114	LB	lb	NN	_	_	_
115	glu	glu	NN	_	_	_
116	4	4	CD	_	_	_
117	hr	hr	NN	_	_	_
118	biofilm	biofilm	NN	_	_	_
119	cells	cell	NNS	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
121	BW25113	bw25113	NN	_	_	_
122	w	w	NN	_	_	_
123	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
124	Channel	Channel	NNP	_	_	_
125	1	1	CD	_	_	_
126	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
127	Escherichia	escherichia	FW	Organism	_	_
128	coli	coli	FW	Organism	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
130	MAS	mas	FW	_	_	_
131	5.0	5.0	CD	_	_	_
132	Expression	expression	NN	_	_	_
133	Analysis	analysis	NN	_	_	_
134	Default	Default	NNP	_	_	_
135	Setting	set	VBG	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	RNA	rna	NN	_	_	_
138	extracted	extract	VBN	_	_	_
139	from	from	IN	_	_	_
140	biofilm	biofilm	NN	_	_	_
141	cells	cell	NNS	_	_	_
142	of	of	IN	_	_	_
143	E.	e.	FW	_	_	_
144	coli	coli	FW	_	_	_
145	K-12	k-12	NN	_	_	_
146	hha	hha	NN	GEN	_	_
147	mutant	mutant	NN	_	_	_
148	after	after	IN	_	_	_
149	15	15	CD	_	_	_
150	hours	hour	NNS	_	_	_
151	of	of	IN	_	_	_
152	growth	growth	NN	_	_	_
153	at	at	IN	_	_	_
154	37C	37c	NN	_	_	_
155	in	in	IN	_	_	_
156	LB	LB	NNP	_	_	_
157	glu	glu	NN	_	_	_
158	with	with	IN	_	_	_
159	glasswool	glasswool	NN	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	RNA	rna	NN	_	_	_
162	extracted	extract	VBN	_	_	_
163	from	from	IN	_	_	_
164	biofilm	biofilm	NN	_	_	_
165	cells	cell	NNS	_	_	_
166	of	of	IN	_	_	_
167	E.	e.	FW	_	_	_
168	coli	coli	FW	_	_	_
169	K-12	k-12	NN	_	_	_
170	hha	hha	NN	GEN	_	_
171	mutant	mutant	NN	_	_	_
172	after	after	IN	_	_	_
173	24	24	CD	_	_	_
174	hours	hour	NNS	_	_	_
175	of	of	IN	_	_	_
176	growth	growth	NN	_	_	_
177	at	at	IN	_	_	_
178	37C	37c	NN	_	_	_
179	in	in	IN	_	_	_
180	LB	LB	NNP	_	_	_
181	glu	glu	NN	_	_	_
182	with	with	IN	_	_	_
183	glasswool	glasswool	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	RNA	rna	NN	_	_	_
186	extracted	extract	VBN	_	_	_
187	from	from	IN	_	_	_
188	biofilm	biofilm	NN	_	_	_
189	cells	cell	NNS	_	_	_
190	of	of	IN	_	_	_
191	E.	e.	FW	_	_	_
192	coli	coli	FW	_	_	_
193	K-12	k-12	NN	_	_	_
194	hha	hha	NN	GEN	_	_
195	mutant	mutant	NN	_	_	_
196	after	after	IN	_	_	_
197	4	4	CD	_	_	_
198	hours	hour	NNS	_	_	_
199	of	of	IN	_	_	_
200	growth	growth	NN	_	_	_
201	at	at	IN	_	_	_
202	37C	37c	NN	_	_	_
203	in	in	IN	_	_	_
204	LB	LB	NNP	_	_	_
205	glu	glu	NN	_	_	_
206	with	with	IN	_	_	_
207	glasswool	glasswool	NN	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	RNA	rna	NN	_	_	_
210	extracted	extract	VBN	_	_	_
211	from	from	IN	_	_	_
212	biofilm	biofilm	NN	_	_	_
213	cells	cell	NNS	_	_	_
214	of	of	IN	_	_	_
215	E.	e.	FW	_	_	_
216	coli	coli	FW	_	_	_
217	K-12	k-12	NN	_	_	_
218	hha	hha	NN	GEN	_	_
219	mutant	mutant	NN	_	_	_
220	after	after	IN	_	_	_
221	4	4	CD	_	_	_
222	hours	hour	NNS	_	_	_
223	of	of	IN	_	_	_
224	growth	growth	NN	_	_	_
225	at	at	IN	_	_	_
226	37C	37c	NN	_	_	_
227	in	in	IN	_	_	_
228	LB	lb	NN	_	_	_
229	with	with	IN	_	_	_
230	glasswool	glasswool	NN	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	RNA	rna	NN	_	_	_
233	extracted	extract	VBN	_	_	_
234	from	from	IN	_	_	_
235	biofilm	biofilm	NN	_	_	_
236	cells	cell	NNS	_	_	_
237	of	of	IN	_	_	_
238	E.	e.	FW	_	_	_
239	coli	coli	FW	_	_	_
240	K-12	k-12	NN	_	_	_
241	wild	wild	JJ	_	_	_
242	type	type	NN	_	_	_
243	after	after	IN	_	_	_
244	15	15	CD	_	_	_
245	hours	hour	NNS	_	_	_
246	of	of	IN	_	_	_
247	growth	growth	NN	_	_	_
248	at	at	IN	_	_	_
249	37C	37c	NN	_	_	_
250	in	in	IN	_	_	_
251	LB	LB	NNP	_	_	_
252	glu	glu	NN	_	_	_
253	with	with	IN	_	_	_
254	glasswool	glasswool	NN	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	RNA	rna	NN	_	_	_
257	extracted	extract	VBN	_	_	_
258	from	from	IN	_	_	_
259	biofilm	biofilm	NN	_	_	_
260	cells	cell	NNS	_	_	_
261	of	of	IN	_	_	_
262	E.	e.	FW	_	_	_
263	coli	coli	FW	_	_	_
264	K-12	k-12	NN	_	_	_
265	wild	wild	JJ	_	_	_
266	type	type	NN	_	_	_
267	after	after	IN	_	_	_
268	24	24	CD	_	_	_
269	hours	hour	NNS	_	_	_
270	of	of	IN	_	_	_
271	growth	growth	NN	_	_	_
272	at	at	IN	_	_	_
273	37C	37c	NN	_	_	_
274	in	in	IN	_	_	_
275	LB	LB	NNP	_	_	_
276	glu	glu	NN	_	_	_
277	with	with	IN	_	_	_
278	glasswool	glasswool	NN	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	RNA	rna	NN	_	_	_
281	extracted	extract	VBN	_	_	_
282	from	from	IN	_	_	_
283	biofilm	biofilm	NN	_	_	_
284	cells	cell	NNS	_	_	_
285	of	of	IN	_	_	_
286	E.	e.	FW	_	_	_
287	coli	coli	FW	_	_	_
288	K-12	k-12	NN	_	_	_
289	wild	wild	JJ	_	_	_
290	type	type	NN	_	_	_
291	after	after	IN	_	_	_
292	4	4	CD	_	_	_
293	hours	hour	NNS	_	_	_
294	of	of	IN	_	_	_
295	growth	growth	NN	_	_	_
296	at	at	IN	_	_	_
297	37C	37c	NN	_	_	_
298	in	in	IN	_	_	_
299	LB	LB	NNP	_	_	_
300	glu	glu	NN	_	_	_
301	with	with	IN	_	_	_
302	glasswool	glasswool	NN	_	_	_
303	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	extracted	extract	VBN	_	_	_
4	from	from	IN	_	_	_
5	biofilm	biofilm	NN	_	_	_
6	cells	cell	NNS	_	_	_
7	of	of	IN	_	_	_
8	E.	e.	FW	_	_	_
9	coli	coli	FW	_	_	_
10	K-12	k-12	NN	_	_	_
11	wild	wild	JJ	_	_	_
12	type	type	NN	_	_	_
13	after	after	IN	_	_	_
14	4	4	CD	_	_	_
15	hours	hour	NNS	_	_	_
16	of	of	IN	_	_	_
17	growth	growth	NN	_	_	_
18	at	at	IN	_	_	_
19	37C	37c	NN	_	_	_
20	in	in	IN	_	_	_
21	LB	lb	NN	_	_	_
22	with	with	IN	_	_	_
23	glasswool	glasswool	NN	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	overnight	overnight	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	2.5	2.5	CD	_	_	_
7	ml	ml	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	was	be	VBD	_	_	_
10	used	use	VBN	_	_	_
11	to	to	TO	_	_	_
12	inoculate	inoculate	VB	_	_	_
13	250	250	CD	_	_	_
14	ml	ml	NN	_	_	_
15	of	of	IN	_	_	_
16	fresh	fresh	JJ	_	_	_
17	LB	lb	NN	_	_	_
18	glu	glu	NN	_	_	_
19	medium	medium	NN	_	_	_
20	with	with	IN	_	_	_
21	10	10	CD	_	_	_
22	g	g	NN	_	_	_
23	of	of	IN	_	_	_
24	submerged	submerged	JJ	_	_	_
25	glass	glass	NN	_	_	_
26	wool	wool	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Corning	Corning	NNP	_	_	_
29	Glass	Glass	NNP	_	_	_
30	Works	Works	NNP	_	_	_
31	,	,	,	_	_	_
32	Corning	Corning	NNP	_	_	_
33	,	,	,	_	_	_
34	NY	NY	NNP	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	for	for	IN	_	_	_
37	forming	form	VBG	_	_	_
38	biofilm	biofilm	NN	_	_	_
39	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	15	15	CD	_	_	_
5	h	h	NN	_	_	_
6	at	at	IN	_	_	_
7	37	37	CD	_	_	_
8	°C	°c	NN	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	250	250	CD	_	_	_
13	rpm	rpm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	the	the	DT	_	_	_
17	glass	glass	NN	_	_	_
18	wool	wool	NN	_	_	_
19	was	be	VBD	_	_	_
20	carefully	carefully	RB	_	_	_
21	and	and	CC	_	_	_
22	quickly	quickly	RB	_	_	_
23	removed	remove	VBD	_	_	_
24	and	and	CC	_	_	_
25	rinsed	rinse	VBD	_	_	_
26	with	with	IN	_	_	_
27	100	100	CD	_	_	_
28	ml	ml	NN	_	_	_
29	of	of	IN	_	_	_
30	sterile	sterile	JJ	_	_	_
31	0.85	0.85	CD	_	_	_
32	%	%	NN	_	_	_
33	NaCl	nacl	NN	_	_	_
34	solution	solution	NN	_	_	_
35	at	at	IN	_	_	_
36	0	0	CD	_	_	_
37	°C	°c	NN	_	_	_
38	.	.	.	_	_	_

1	Biofilm	biofilm	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	sonicating	sonicate	VBG	_	_	_
7	the	the	DT	_	_	_
8	glass	glass	NN	_	_	_
9	wool	wool	NN	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	sterile	sterile	JJ	_	_	_
15	0.85	0.85	CD	_	_	_
16	%	%	NN	_	_	_
17	NaCl	nacl	NN	_	_	_
18	solution	solution	NN	_	_	_
19	at	at	IN	_	_	_
20	0	0	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	The	the	DT	_	_	_
28	overnight	overnight	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	2.5	2.5	CD	_	_	_
32	ml	ml	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	was	be	VBD	_	_	_
35	used	use	VBN	_	_	_
36	to	to	TO	_	_	_
37	inoculate	inoculate	VB	_	_	_
38	250	250	CD	_	_	_
39	ml	ml	NN	_	_	_
40	of	of	IN	_	_	_
41	fresh	fresh	JJ	_	_	_
42	LB	lb	NN	_	_	_
43	glu	glu	NN	_	_	_
44	medium	medium	NN	_	_	_
45	with	with	IN	_	_	_
46	10	10	CD	_	_	_
47	g	g	NN	_	_	_
48	of	of	IN	_	_	_
49	submerged	submerged	JJ	_	_	_
50	glass	glass	NN	_	_	_
51	wool	wool	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	Corning	Corning	NNP	_	_	_
54	Glass	Glass	NNP	_	_	_
55	Works	Works	NNP	_	_	_
56	,	,	,	_	_	_
57	Corning	Corning	NNP	_	_	_
58	,	,	,	_	_	_
59	NY	NY	NNP	_	_	_
60	-RRB-	-rrb-	-RRB-	_	_	_
61	for	for	IN	_	_	_
62	forming	form	VBG	_	_	_
63	biofilm	biofilm	NN	_	_	_
64	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	15	15	CD	_	_	_
5	h	h	NN	_	_	_
6	at	at	IN	_	_	_
7	37	37	CD	_	_	_
8	°C	°c	NN	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	250	250	CD	_	_	_
13	rpm	rpm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	the	the	DT	_	_	_
17	glass	glass	NN	_	_	_
18	wool	wool	NN	_	_	_
19	was	be	VBD	_	_	_
20	carefully	carefully	RB	_	_	_
21	and	and	CC	_	_	_
22	quickly	quickly	RB	_	_	_
23	removed	remove	VBD	_	_	_
24	and	and	CC	_	_	_
25	rinsed	rinse	VBD	_	_	_
26	with	with	IN	_	_	_
27	100	100	CD	_	_	_
28	ml	ml	NN	_	_	_
29	of	of	IN	_	_	_
30	sterile	sterile	JJ	_	_	_
31	0.85	0.85	CD	_	_	_
32	%	%	NN	_	_	_
33	NaCl	nacl	NN	_	_	_
34	solution	solution	NN	_	_	_
35	at	at	IN	_	_	_
36	0	0	CD	_	_	_
37	°C	°c	NN	_	_	_
38	.	.	.	_	_	_

1	Biofilm	biofilm	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	sonicating	sonicate	VBG	_	_	_
7	the	the	DT	_	_	_
8	glass	glass	NN	_	_	_
9	wool	wool	NN	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	sterile	sterile	JJ	_	_	_
15	0.85	0.85	CD	_	_	_
16	%	%	NN	_	_	_
17	NaCl	nacl	NN	_	_	_
18	solution	solution	NN	_	_	_
19	at	at	IN	_	_	_
20	0	0	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	``	``	``	_	_	_
3	The	the	DT	_	_	_
4	overnight	overnight	JJ	_	_	_
5	culture	culture	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	2.5	2.5	CD	_	_	_
8	ml	ml	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	was	be	VBD	_	_	_
11	used	use	VBN	_	_	_
12	to	to	TO	_	_	_
13	inoculate	inoculate	VB	_	_	_
14	250	250	CD	_	_	_
15	ml	ml	NN	_	_	_
16	of	of	IN	_	_	_
17	fresh	fresh	JJ	_	_	_
18	LB	lb	NN	MED	_	_
19	medium	medium	NN	MED	_	_
20	with	with	IN	_	_	_
21	10	10	CD	_	_	_
22	g	g	NN	_	_	_
23	of	of	IN	_	_	_
24	submerged	submerged	JJ	_	_	_
25	glass	glass	NN	_	_	_
26	wool	wool	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Corning	Corning	NNP	_	_	_
29	Glass	Glass	NNP	_	_	_
30	Works	Works	NNP	_	_	_
31	,	,	,	_	_	_
32	Corning	Corning	NNP	_	_	_
33	,	,	,	_	_	_
34	NY	NY	NNP	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	for	for	IN	_	_	_
37	forming	form	VBG	_	_	_
38	biofilm	biofilm	NN	_	_	_
39	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	15	15	CD	_	_	_
5	h	h	NN	_	_	_
6	at	at	IN	_	_	_
7	37	37	CD	_	_	_
8	°C	°c	NN	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	250	250	CD	_	_	_
13	rpm	rpm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	the	the	DT	_	_	_
17	glass	glass	NN	_	_	_
18	wool	wool	NN	_	_	_
19	was	be	VBD	_	_	_
20	carefully	carefully	RB	_	_	_
21	and	and	CC	_	_	_
22	quickly	quickly	RB	_	_	_
23	removed	remove	VBD	_	_	_
24	and	and	CC	_	_	_
25	rinsed	rinse	VBD	_	_	_
26	with	with	IN	_	_	_
27	100	100	CD	_	_	_
28	ml	ml	NN	_	_	_
29	of	of	IN	_	_	_
30	sterile	sterile	JJ	_	_	_
31	0.85	0.85	CD	_	_	_
32	%	%	NN	_	_	_
33	NaCl	nacl	NN	_	_	_
34	solution	solution	NN	_	_	_
35	at	at	IN	_	_	_
36	0	0	CD	_	_	_
37	°C	°c	NN	_	_	_
38	.	.	.	_	_	_

1	Biofilm	biofilm	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	sonicating	sonicate	VBG	_	_	_
7	the	the	DT	_	_	_
8	glass	glass	NN	_	_	_
9	wool	wool	NN	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	sterile	sterile	JJ	_	_	_
15	0.85	0.85	CD	_	_	_
16	%	%	NN	_	_	_
17	NaCl	nacl	NN	_	_	_
18	solution	solution	NN	_	_	_
19	at	at	IN	_	_	_
20	0	0	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	overnight	overnight	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	2.5	2.5	CD	_	_	_
7	ml	ml	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	was	be	VBD	_	_	_
10	used	use	VBN	_	_	_
11	to	to	TO	_	_	_
12	inoculate	inoculate	VB	_	_	_
13	250	250	CD	_	_	_
14	ml	ml	NN	_	_	_
15	of	of	IN	_	_	_
16	fresh	fresh	JJ	_	_	_
17	LB	lb	NN	MED	_	_
18	medium	medium	NN	MED	_	_
19	with	with	IN	_	_	_
20	10	10	CD	_	_	_
21	g	g	NN	_	_	_
22	of	of	IN	_	_	_
23	submerged	submerged	JJ	_	_	_
24	glass	glass	NN	_	_	_
25	wool	wool	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Corning	Corning	NNP	_	_	_
28	Glass	Glass	NNP	_	_	_
29	Works	Works	NNP	_	_	_
30	,	,	,	_	_	_
31	Corning	Corning	NNP	_	_	_
32	,	,	,	_	_	_
33	NY	NY	NNP	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	for	for	IN	_	_	_
36	forming	form	VBG	_	_	_
37	biofilm	biofilm	NN	_	_	_
38	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	15	15	CD	_	_	_
5	h	h	NN	_	_	_
6	at	at	IN	_	_	_
7	37	37	CD	_	_	_
8	°C	°c	NN	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	250	250	CD	_	_	_
13	rpm	rpm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	the	the	DT	_	_	_
17	glass	glass	NN	_	_	_
18	wool	wool	NN	_	_	_
19	was	be	VBD	_	_	_
20	carefully	carefully	RB	_	_	_
21	and	and	CC	_	_	_
22	quickly	quickly	RB	_	_	_
23	removed	remove	VBD	_	_	_
24	and	and	CC	_	_	_
25	rinsed	rinse	VBD	_	_	_
26	with	with	IN	_	_	_
27	100	100	CD	_	_	_
28	ml	ml	NN	_	_	_
29	of	of	IN	_	_	_
30	sterile	sterile	JJ	_	_	_
31	0.85	0.85	CD	_	_	_
32	%	%	NN	_	_	_
33	NaCl	nacl	NN	_	_	_
34	solution	solution	NN	_	_	_
35	at	at	IN	_	_	_
36	0	0	CD	_	_	_
37	°C	°c	NN	_	_	_
38	.	.	.	_	_	_

1	Biofilm	biofilm	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	sonicating	sonicate	VBG	_	_	_
7	the	the	DT	_	_	_
8	glass	glass	NN	_	_	_
9	wool	wool	NN	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	sterile	sterile	JJ	_	_	_
15	0.85	0.85	CD	_	_	_
16	%	%	NN	_	_	_
17	NaCl	nacl	NN	_	_	_
18	solution	solution	NN	_	_	_
19	at	at	IN	_	_	_
20	0	0	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	75th	75th	JJ	_	_	_
28	percentile	percentile	NN	_	_	_
29	shift	shift	NN	_	_	_
30	normalisation	normalisation	NN	_	_	_
31	and	and	CC	_	_	_
32	baseline	baseline	NN	_	_	_
33	adjusted	adjusted	JJ	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	agent	agent	NN	_	_	_
36	:	:	:	_	_	_
37	1x	1x	NN	_	_	_
38	CORM2	corm2	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	agent	agent	NN	_	_	_
41	:	:	:	_	_	_
42	1x	1x	NN	_	_	_
43	vehicle	vehicle	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	agent	agent	NN	_	_	_
46	:	:	:	_	_	_
47	20x	20x	CD	_	_	_
48	CORM2	corm2	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	agent	agent	NN	_	_	_
51	:	:	:	_	_	_
52	20x	20x	CD	_	_	_
53	vehicle	vehicle	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	Cultures	culture	NNS	_	_	_
56	were	be	VBD	_	_	_
57	maintained	maintain	VBN	_	_	_
58	on	on	IN	_	_	_
59	tryptic	tryptic	JJ	_	_	_
60	soy	soy	NN	_	_	_
61	agar	agar	NN	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	TSA	tsa	NN	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	-LRB-	-lrb-	-LRB-	_	_	_
66	Becton	Becton	NNP	_	_	_
67	Dickinson	Dickinson	NNP	_	_	_
68	,	,	,	_	_	_
69	Le	Le	NNP	_	_	_
70	Pont	Pont	NNP	_	_	_
71	Claix	Claix	NNP	_	_	_
72	,	,	,	_	_	_
73	France	France	NNP	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	.	.	.	_	_	_

1	Overnight	overnight	JJ	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	Difco	Difco	NNP	_	_	_
7	Luria-Bertani	Luria-Bertani	NNP	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	LB	LB	NNP	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	broth	broth	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Lennox	lennox	NN	_	_	_
14	;	;	:	_	_	_
15	Franklin	Franklin	NNP	_	_	_
16	Lakes	Lakes	NNP	_	_	_
17	,	,	,	_	_	_
18	NJ	NJ	NNP	_	_	_
19	,	,	,	_	_	_
20	USA	USA	NNP	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	at	at	IN	_	_	_
23	37	37	CD	_	_	_
24	°C	°c	NN	_	_	_
25	aerobically	aerobically	RB	_	_	_
26	on	on	IN	_	_	_
27	a	a	DT	_	_	_
28	shaker	shaker	NN	_	_	_
29	at	at	IN	_	_	_
30	200	200	CD	_	_	_
31	rpm	rpm	NN	_	_	_
32	.	.	.	_	_	_

1	Bacteria	bacterium	NNS	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	picked	pick	VBN	_	_	_
4	from	from	IN	_	_	_
5	5-10	5-10	CD	_	_	_
6	colonies	colony	NNS	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	were	be	VBD	_	_	_
9	suspended	suspend	VBN	_	_	_
10	in	in	IN	_	_	_
11	1	1	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	PBS	PBS	NNP	_	_	_
15	,	,	,	_	_	_
16	yielding	yield	VBG	_	_	_
17	a	a	DT	_	_	_
18	suspension	suspension	NN	_	_	_
19	corresponding	correspond	VBG	_	_	_
20	to	to	TO	_	_	_
21	the	the	DT	_	_	_
22	turbidity	turbidity	NN	_	_	_
23	of	of	IN	_	_	_
24	McFarland	McFarland	NNP	_	_	_
25	0.5	0.5	CD	_	_	_
26	,	,	,	_	_	_
27	and	and	CC	_	_	_
28	diluted	dilute	VBN	_	_	_
29	1:100	1:100	CD	_	_	_
30	in	in	IN	_	_	_
31	minimal	minimal	JJ	_	_	_
32	salt	salt	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	MS	ms	NN	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	-	-	:	_	_	_
37	medium	medium	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	~	~	NN	_	_	_
40	106	106	CD	_	_	_
41	CFU	CFU	NNP	_	_	_
42	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
43	E.coli-1x	e.coli-1x	NN	_	_	_
44	CORM2-rep1	corm2-rep1	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	E.coli-1x	e.coli-1x	NN	_	_	_
47	CORM2-rep2	corm2-rep2	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	E.coli-1x	e.coli-1x	NN	_	_	_
50	CORM2-rep3	corm2-rep3	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	E.coli-1x	e.coli-1x	NN	_	_	_
53	CORM2-rep4	corm2-rep4	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	E.coli-1x	e.coli-1x	NN	_	_	_
56	vehicle-rep1	vehicle-rep1	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	E.coli-1x	e.coli-1x	NN	_	_	_
59	vehicle-rep2	vehicle-rep2	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	E.coli-1x	e.coli-1x	NN	_	_	_
62	vehicle-rep3	vehicle-rep3	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	E.coli-1x	e.coli-1x	NN	_	_	_
65	vehicle-rep4	vehicle-rep4	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	E.coli-20x	e.coli-20x	NN	_	_	_
68	CORM2-rep1	corm2-rep1	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	E.coli-20x	e.coli-20x	NN	_	_	_
71	CORM2-rep2	corm2-rep2	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	E.coli-20x	e.coli-20x	NN	_	_	_
74	CORM2-rep3	corm2-rep3	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	E.coli-20x	e.coli-20x	NN	_	_	_
77	CORM2-rep4	corm2-rep4	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	E.coli-20x	e.coli-20x	NN	_	_	_
80	vehicle-rep1	vehicle-rep1	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	E.coli-20x	e.coli-20x	NN	_	_	_
83	vehicle-rep2	vehicle-rep2	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	E.coli-20x	e.coli-20x	NN	_	_	_
86	vehicle-rep3	vehicle-rep3	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	E.coli-20x	e.coli-20x	NN	_	_	_
89	vehicle-rep4	vehicle-rep4	NN	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	Escherichia	escherichia	FW	Organism	_	_
92	coli	coli	FW	Organism	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	Overnight	overnight	JJ	_	_	_
95	cultures	culture	NNS	_	_	_
96	of	of	IN	_	_	_
97	ESBL7	esbl7	NN	_	_	_
98	from	from	IN	_	_	_
99	the	the	DT	_	_	_
100	original	original	JJ	_	_	_
101	isolate	isolate	NN	_	_	_
102	,	,	,	_	_	_
103	or	or	CC	_	_	_
104	isolates	isolate	NNS	_	_	_
105	pre-exposed	pre-expose	VBN	_	_	_
106	20	20	CD	_	_	_
107	times	time	NNS	_	_	_
108	to	to	TO	_	_	_
109	CORM-2	corm-2	NN	_	_	_
110	or	or	CC	_	_	_
111	vehicle	vehicle	NN	_	_	_
112	,	,	,	_	_	_
113	were	be	VBD	_	_	_
114	used	use	VBN	_	_	_
115	to	to	TO	_	_	_
116	inoculate	inoculate	VB	_	_	_
117	MS-medium	ms-medium	NN	_	_	_
118	,	,	,	_	_	_
119	-LRB-	-lrb-	-LRB-	_	_	_
120	OD620	od620	NN	_	_	_
121	-RRB-	-rrb-	-RRB-	_	_	_
122	of	of	IN	_	_	_
123	0.1	0.1	CD	_	_	_
124	,	,	,	_	_	_
125	followed	follow	VBN	_	_	_
126	by	by	IN	_	_	_
127	exposure	exposure	NN	_	_	_
128	to	to	TO	_	_	_
129	CORM-2	corm-2	NN	_	_	_
130	-LRB-	-lrb-	-LRB-	_	_	_
131	250	250	CD	_	_	_
132	µM	µm	NN	_	_	_
133	-RRB-	-rrb-	-RRB-	_	_	_
134	or	or	CC	_	_	_
135	vehicle	vehicle	NN	_	_	_
136	for	for	IN	_	_	_
137	30	30	CD	_	_	_
138	min	min	NN	_	_	_
139	at	at	IN	_	_	_
140	37	37	CD	_	_	_
141	°C	°c	NN	_	_	_
142	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	isolation	isolation	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	using	use	VBG	_	_	_
7	an	a	DT	_	_	_
8	RNeasy	rneasy	NN	_	_	_
9	mini	minus	NNS	_	_	_
10	kit	kit	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	Qiagen	NNP	_	_	_
13	Technologies	Technologies	NNPS	_	_	_
14	,	,	,	_	_	_
15	Hilden	Hilden	NNP	_	_	_
16	,	,	,	_	_	_
17	Germany	Germany	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	according	accord	VBG	_	_	_
21	to	to	TO	_	_	_
22	the	the	DT	_	_	_
23	manufacturer	manufacturer	NN	_	_	_
24	's	's	POS	_	_	_
25	protocol	protocol	NN	_	_	_
26	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	decontamination	decontamination	NN	_	_	_
3	treatment	treatment	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	using	use	VBG	_	_	_
7	Turbo	Turbo	NNP	_	_	_
8	DNase	dnase	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Qiagen	qiagen	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	quantity	quantity	NN	_	_	_
15	and	and	CC	_	_	_
16	purity	purity	NN	_	_	_
17	of	of	IN	_	_	_
18	the	the	DT	_	_	_
19	purified	purify	VBN	_	_	_
20	RNA	rna	NN	_	_	_
21	samples	sample	NNS	_	_	_
22	were	be	VBD	_	_	_
23	determined	determine	VBN	_	_	_
24	using	use	VBG	_	_	_
25	a	a	DT	_	_	_
26	spectrophotometer	spectrophotometer	NN	_	_	_
27	Nanodrop-1000	nanodrop-1000	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Nanodrop	Nanodrop	NNP	_	_	_
30	Technologies	Technologies	NNPS	_	_	_
31	Inc.	Inc.	NNP	_	_	_
32	,	,	,	_	_	_
33	Wilmington	Wilmington	NNP	_	_	_
34	,	,	,	_	_	_
35	DE	de	NN	_	_	_
36	,	,	,	_	_	_
37	USA	USA	NNP	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	by	by	IN	_	_	_
40	measuring	measure	VBG	_	_	_
41	the	the	DT	_	_	_
42	absorbance	absorbance	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	A260	a260	NN	_	_	_
45	,	,	,	_	_	_
46	230	230	CD	_	_	_
47	,	,	,	_	_	_
48	280	280	CD	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	and	and	CC	_	_	_
51	calculating	calculate	VBG	_	_	_
52	absorbance	absorbance	NN	_	_	_
53	ratios	ratio	NNS	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	A260	a260	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	0	0	CD	_	_	_
58	%	%	NN	_	_	_
59	rep1	rep1	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	0	0	CD	_	_	_
62	%	%	NN	_	_	_
63	rep2	rep2	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	100	100	CD	_	_	_
66	%	%	NN	_	_	_
67	rep1	rep1	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	100	100	CD	_	_	_
70	%	%	NN	_	_	_
71	rep2	rep2	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	26	26	CD	_	_	_
74	%	%	NN	_	_	_
75	rep1	rep1	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	26	26	CD	_	_	_
78	%	%	NN	_	_	_
79	rep2	rep2	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	Base	base	NN	_	_	_
82	calls	call	VBZ	_	_	_
83	performed	perform	VBN	_	_	_
84	with	with	IN	_	_	_
85	RTA	rta	NN	_	_	_
86	v1	v1	NN	_	_	_
87	.18.5	.18.5	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	Cells	cell	NNS	_	_	_
90	were	be	VBD	_	_	_
91	inoculated	inoculate	VBN	_	_	_
92	from	from	IN	_	_	_
93	frozen	frozen	JJ	_	_	_
94	cultures	culture	NNS	_	_	_
95	into	into	IN	_	_	_
96	5	5	CD	_	_	_
97	mL	ml	NN	_	_	_
98	of	of	IN	_	_	_
99	LB	lb	NN	_	_	_
100	,	,	,	_	_	_
101	and	and	CC	_	_	_
102	grown	grow	VBN	_	_	_
103	.	.	.	_	_	_

1	5	5	CD	_	_	_
2	µL	µl	NN	_	_	_
3	of	of	IN	_	_	_
4	this	this	DT	_	_	_
5	overnight	overnight	JJ	_	_	_
6	culture	culture	NN	_	_	_
7	was	be	VBD	_	_	_
8	diluted	dilute	VBN	_	_	_
9	into	into	IN	_	_	_
10	5	5	CD	_	_	_
11	mL	ml	NN	_	_	_
12	of	of	IN	_	_	_
13	LB	lb	NN	_	_	_
14	with	with	IN	_	_	_
15	the	the	DT	_	_	_
16	appropriate	appropriate	JJ	_	_	_
17	concentration	concentration	NN	_	_	_
18	of	of	IN	_	_	_
19	arabinose	arabinose	NN	_	_	_
20	,	,	,	_	_	_
21	and	and	CC	_	_	_
22	grown	grow	VBN	_	_	_
23	for	for	IN	_	_	_
24	20h	20h	NN	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	culture	culture	NN	_	_	_
5	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
6	Escherichia	escherichia	FW	Organism	_	_
7	coli	coli	FW	Organism	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Reads	read	NNS	_	_	_
10	were	be	VBD	_	_	_
11	mapped	map	VBN	_	_	_
12	using	use	VBG	_	_	_
13	BWA	BWA	NNP	_	_	_
14	0.7.5	0.7.5	CD	_	_	_
15	a	a	DT	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	RNA	rna	NN	_	_	_
18	libraries	library	NNS	_	_	_
19	were	be	VBD	_	_	_
20	prepared	prepare	VBN	_	_	_
21	for	for	IN	_	_	_
22	sequencing	sequencing	NN	_	_	_
23	using	use	VBG	_	_	_
24	standard	standard	JJ	_	_	_
25	Illumina	Illumina	NNP	_	_	_
26	protocols	protocol	NNS	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
28	RNA-Seq	rna-seq	JJ	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	RNA	rna	NN	_	_	_
31	was	be	VBD	_	_	_
32	purified	purify	VBN	_	_	_
33	from	from	IN	_	_	_
34	200	200	CD	_	_	_
35	µL	µl	NN	_	_	_
36	of	of	IN	_	_	_
37	overnight	overnight	JJ	_	_	_
38	culture	culture	NN	_	_	_
39	by	by	IN	_	_	_
40	pelleting	pelleting	NN	_	_	_
41	and	and	CC	_	_	_
42	resuspeding	resuspeding	NN	_	_	_
43	in	in	IN	_	_	_
44	500	500	CD	_	_	_
45	µL	µl	NN	_	_	_
46	of	of	IN	_	_	_
47	Trizol	trizol	NN	_	_	_
48	at	at	IN	_	_	_
49	65	65	CD	_	_	_
50	°C	°c	NN	_	_	_
51	,	,	,	_	_	_
52	followed	follow	VBN	_	_	_
53	by	by	IN	_	_	_
54	purification	purification	NN	_	_	_
55	on	on	IN	_	_	_
56	a	a	DT	_	_	_
57	column	column	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	Direct-Zol	Direct-Zol	NNP	_	_	_
60	,	,	,	_	_	_
61	Zymo	Zymo	NNP	_	_	_
62	Research	Research	NNP	_	_	_
63	-RRB-	-rrb-	-RRB-	_	_	_
64	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	received	receive	VBD	_	_	_
3	two	two	CD	_	_	_
4	30-minute	30-minute	JJ	_	_	_
5	DNase	dnase	NN	_	_	_
6	treatments	treatment	NNS	_	_	_
7	using	use	VBG	_	_	_
8	TURBO	TURBO	NNP	_	_	_
9	DNA-free	dna-free	JJ	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Ambion	Ambion	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	following	follow	VBG	_	_	_
14	the	the	DT	_	_	_
15	manufacturers	manufacturer	NNS	_	_	_
16	instructions	instruction	NNS	_	_	_
17	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	purified	purify	VBN	_	_	_
6	on	on	IN	_	_	_
7	a	a	DT	_	_	_
8	column	column	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	RNA	rna	NN	_	_	_
11	Clean	Clean	NNP	_	_	_
12	&	&	CC	_	_	_
13	Concentrator	Concentrator	NNP	_	_	_
14	,	,	,	_	_	_
15	Zymo	Zymo	NNP	_	_	_
16	Research	Research	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

1	Three	three	CD	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	prepped	prep	VBN	_	_	_
5	from	from	IN	_	_	_
6	each	each	DT	_	_	_
7	culture	culture	NN	_	_	_
8	and	and	CC	_	_	_
9	pooled	pool	VBD	_	_	_
10	to	to	TO	_	_	_
11	generate	generate	VB	_	_	_
12	sufficient	sufficient	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	rpos	rpo	NNS	_	_	_
3	level	level	NN	_	_	_
4	:	:	:	_	_	_
5	0	0	CD	_	_	_
6	%	%	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	rpos	rpo	NNS	_	_	_
9	level	level	NN	_	_	_
10	:	:	:	_	_	_
11	100	100	CD	_	_	_
12	%	%	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	rpos	rpo	NNS	_	_	_
15	level	level	NN	_	_	_
16	:	:	:	_	_	_
17	26	26	CD	_	_	_
18	%	%	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	strain	strain	NN	_	_	_
21	:	:	:	_	_	_
22	BW27786	bw27786	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	K-12	k-12	NN	_	_	_
25	derivative	derivative	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	strain	strain	NN	_	_	_
29	:	:	:	_	_	_
30	DMS2545	dms2545	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	K-12	k-12	NN	_	_	_
33	derivative	derivative	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	strain	strain	NN	_	_	_
37	:	:	:	_	_	_
38	DMS2564	dms2564	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	K-12	k-12	NN	_	_	_
41	derivative	derivative	NN	_	_	_
42	-RRB-	-rrb-	-RRB-	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Supplementary	supplementary	JJ	_	_	_
45	_	_	NN	_	_	_
46	files	file	NNS	_	_	_
47	_	_	IN	_	_	_
48	format	format	NN	_	_	_
49	_	_	NN	_	_	_
50	and	and	CC	_	_	_
51	_	_	NN	_	_	_
52	content	content	NN	_	_	_
53	:	:	:	_	_	_
54	A	a	DT	_	_	_
55	tab	tab	NN	_	_	_
56	deliminited	deliminit	VBN	_	_	_
57	file	file	NN	_	_	_
58	with	with	IN	_	_	_
59	counts	count	NNS	_	_	_
60	for	for	IN	_	_	_
61	each	each	DT	_	_	_
62	gene	gene	NN	_	_	_
63	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	the	the	DT	_	_	_
3	first	first	JJ	_	_	_
4	ten	ten	CD	_	_	_
5	base	base	NN	_	_	_
6	pairs	pair	NNS	_	_	_
7	of	of	IN	_	_	_
8	each	each	DT	_	_	_
9	read	read	NN	_	_	_
10	were	be	VBD	_	_	_
11	trimmed	trim	VBN	_	_	_
12	using	use	VBG	_	_	_
13	FASTXToolkit	fastxtoolkit	NN	_	_	_
14	0.0.13	0.0.13	CD	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	number	number	NN	_	_	_
4	read	read	VBD	_	_	_
5	pairs	pair	NNS	_	_	_
6	mapped	map	VBN	_	_	_
7	to	to	TO	_	_	_
8	each	each	DT	_	_	_
9	gene	gene	NN	_	_	_
10	was	be	VBD	_	_	_
11	counted	count	VBN	_	_	_
12	with	with	IN	_	_	_
13	HTSeq	htseq	NN	_	_	_
14	0.6.1	0.6.1	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	7	7	CD	_	_	_
17	min	min	NN	_	_	_
18	Nov0	nov0	NN	_	_	_
19	ug	ug	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	7	7	CD	_	_	_
22	min	min	NN	_	_	_
23	Nov500	nov500	NN	_	_	_
24	ug	ug	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	80	80	CD	_	_	_
27	min	min	NN	_	_	_
28	Nov10	nov10	NN	_	_	_
29	ug	ug	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	80	80	CD	_	_	_
32	min	min	NN	_	_	_
33	Nov5	nov5	NN	_	_	_
34	ug	ug	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	A	a	NN	_	_	_
37	Linker-1	linker-1	NN	_	_	_
38	adapter	adapter	NN	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	IDT	idt	NN	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	was	be	VBD	_	_	_
43	ligated	ligate	VBN	_	_	_
44	onto	onto	IN	_	_	_
45	the	the	DT	_	_	_
46	3	3	CD	_	_	_
47	'	'	''	_	_	_
48	end	end	NN	_	_	_
49	of	of	IN	_	_	_
50	size	size	NN	_	_	_
51	selected	select	VBN	_	_	_
52	RNA	rna	NN	_	_	_
53	fragments	fragment	NNS	_	_	_
54	,	,	,	_	_	_
55	either	either	CC	_	_	_
56	ribosome	ribosome	NN	_	_	_
57	footprints	footprint	NNS	_	_	_
58	or	or	CC	_	_	_
59	fragmented	fragmented	JJ	_	_	_
60	total	total	JJ	_	_	_
61	RNA	rna	NN	_	_	_
62	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	cDNA	cdna	NN	_	_	_
3	library	library	NN	_	_	_
4	was	be	VBD	_	_	_
5	created	create	VBN	_	_	_
6	using	use	VBG	_	_	_
7	Superscript	Superscript	NNP	_	_	_
8	III	III	NNP	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	ThermoFisher	ThermoFisher	NNP	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	gel	gel	NN	_	_	_
3	purification	purification	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	cDNA	cdna	NN	_	_	_
7	library	library	NN	_	_	_
8	all	all	DT	_	_	_
9	ssDNA	ssdna	NN	_	_	_
10	fragments	fragment	NNS	_	_	_
11	were	be	VBD	_	_	_
12	circularized	circularize	VBN	_	_	_
13	using	use	VBG	_	_	_
14	CircLigase	CircLigase	NNP	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Epicentre	Epicentre	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

1	For	for	IN	_	_	_
2	ribosome	ribosome	NN	_	_	_
3	profiling	profiling	NN	_	_	_
4	samples	sample	NNS	_	_	_
5	rRNA	rrna	NN	_	_	_
6	containing	contain	VBG	_	_	_
7	circles	circle	NNS	_	_	_
8	were	be	VBD	_	_	_
9	depleted	deplete	VBN	_	_	_
10	using	use	VBG	_	_	_
11	oligo-biotin	oligo-biotin	JJ	_	_	_
12	and	and	CC	_	_	_
13	streptavidin	streptavidin	JJ	_	_	_
14	coupled	couple	VBN	_	_	_
15	Dynabeads	dynabead	NNS	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	ThermoFisher	thermofisher	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	subtraction	subtraction	NN	_	_	_
20	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	PCR	pcr	NN	_	_	_
3	amplification	amplification	NN	_	_	_
4	off	off	IN	_	_	_
5	the	the	DT	_	_	_
6	circles	circle	NNS	_	_	_
7	using	use	VBG	_	_	_
8	HF	hf	NN	_	_	_
9	Phusion	phusion	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	NEB	neb	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	completed	complete	VBD	_	_	_
14	the	the	DT	_	_	_
15	libraries	library	NNS	_	_	_
16	by	by	IN	_	_	_
17	adding	add	VBG	_	_	_
18	Illumina	Illumina	NNP	_	_	_
19	Tru-Seq	Tru-Seq	NNP	_	_	_
20	adapters	adapter	NNS	_	_	_
21	and	and	CC	_	_	_
22	a	a	DT	_	_	_
23	unique	unique	JJ	_	_	_
24	index	index	NN	_	_	_
25	for	for	IN	_	_	_
26	each	each	DT	_	_	_
27	sample	sample	NN	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	All	All	NNP	_	_	_
3	strains	strain	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	shaking	shake	VBG	_	_	_
7	at	at	IN	_	_	_
8	37	37	CD	_	_	_
9	°C	°c	NN	_	_	_
10	in	in	IN	_	_	_
11	200mL	200ml	NN	_	_	_
12	cultures	culture	NNS	_	_	_
13	of	of	IN	_	_	_
14	MOPS	mop	NNS	MED	_	_
15	complete-glucose	complete-glucose	JJ	_	_	_
16	liquid	liquid	JJ	_	_	_
17	media	media	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	unless	unless	IN	_	_	_
20	otherwise	otherwise	RB	_	_	_
21	annotated	annotated	JJ	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	in	in	IN	_	_	_
24	1L	1l	NN	_	_	_
25	flasks	flask	NNS	_	_	_
26	and	and	CC	_	_	_
27	cells	cell	NNS	_	_	_
28	were	be	VBD	_	_	_
29	harvested	harvest	VBN	_	_	_
30	at	at	IN	_	_	_
31	OD	od	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	420nm	420nm	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	between	between	IN	_	_	_
36	0.4	0.4	CD	_	_	_
37	-	-	:	_	_	_
38	0.6	0.6	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
40	Cells	cell	NNS	_	_	_
41	from	from	IN	_	_	_
42	each	each	DT	_	_	_
43	strain	strain	NN	_	_	_
44	were	be	VBD	_	_	_
45	rapidly	rapidly	RB	_	_	_
46	harvested	harvest	VBN	_	_	_
47	by	by	IN	_	_	_
48	filtration	filtration	NN	_	_	_
49	and	and	CC	_	_	_
50	lysate	lysate	NN	_	_	_
51	was	be	VBD	_	_	_
52	produced	produce	VBN	_	_	_
53	by	by	IN	_	_	_
54	pulverization	pulverization	NN	_	_	_
55	of	of	IN	_	_	_
56	liquid	liquid	JJ	_	_	_
57	nitrogen	nitrogen	NN	_	_	_
58	cooled	cool	VBN	_	_	_
59	samples	sample	NNS	_	_	_
60	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Genome	Genome	NNP	_	_	_
6	_	_	NNP	_	_	_
7	build	build	VB	_	_	_
8	:	:	:	_	_	_
9	NC	NC	NNP	_	_	_
10	_	_	NNP	_	_	_
11	000913	000913	CD	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	OTHER	OTHER	NNP	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	Reads	Reads	NNPS	_	_	_
16	were	be	VBD	_	_	_
17	aligned	align	VBN	_	_	_
18	to	to	TO	_	_	_
19	E.coli	e.coli	VB	_	_	_
20	rRNA	rrna	NN	_	_	_
21	and	and	CC	_	_	_
22	tRNA	trna	NN	_	_	_
23	using	use	VBG	_	_	_
24	Bowtie	Bowtie	NNP	_	_	_
25	v.	v.	CC	_	_	_
26	0.12.0	0.12.0	CD	_	_	_
27	allowing	allow	VBG	_	_	_
28	for	for	IN	_	_	_
29	one	one	CD	_	_	_
30	mismatch	mismatch	NN	_	_	_
31	and	and	CC	_	_	_
32	reads	read	VBZ	_	_	_
33	aligning	align	VBG	_	_	_
34	to	to	TO	_	_	_
35	more	more	JJR	_	_	_
36	than	than	IN	_	_	_
37	one	one	CD	_	_	_
38	position	position	NN	_	_	_
39	in	in	IN	_	_	_
40	the	the	DT	_	_	_
41	genome	genome	NN	_	_	_
42	were	be	VBD	_	_	_
43	randomly	randomly	RB	_	_	_
44	assigned	assign	VBN	_	_	_
45	to	to	TO	_	_	_
46	one	one	CD	_	_	_
47	of	of	IN	_	_	_
48	those	those	DT	_	_	_
49	positions	position	NNS	_	_	_
50	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
51	Remaining	remain	VBG	_	_	_
52	linker-1	linker-1	NN	_	_	_
53	reads	read	VBZ	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	CTGTAGGCACCATCAAT	ctgtaggcaccatcaat	NN	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	were	be	VBD	_	_	_
58	removed	remove	VBN	_	_	_
59	from	from	IN	_	_	_
60	fastq	fastq	NN	_	_	_
61	files	file	NNS	_	_	_
62	using	use	VBG	_	_	_
63	fastx	fastx	NN	_	_	_
64	_	_	NN	_	_	_
65	clipper	clipper	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	RF2	rf2	NN	_	_	_
68	*	*	SYM	_	_	_
69	_	_	SYM	_	_	_
70	exp1	exp1	NN	_	_	_
71	_	_	NN	_	_	_
72	mRNA	mrna	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	RF2	rf2	NN	_	_	_
75	*	*	SYM	_	_	_
76	_	_	SYM	_	_	_
77	exp1	exp1	FW	_	_	_
78	_	_	FW	_	_	_
79	ribosome	ribosome	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	RF2	rf2	NN	_	_	_
82	*	*	SYM	_	_	_
83	_	_	SYM	_	_	_
84	exp3	exp3	FW	_	_	_
85	_	_	FW	_	_	_
86	mRNA	mrna	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	RF2	rf2	NN	_	_	_
89	*	*	SYM	_	_	_
90	_	_	SYM	_	_	_
91	exp3	exp3	FW	_	_	_
92	_	_	FW	_	_	_
93	ribosome	ribosome	NN	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	RF2	rf2	NN	_	_	_
96	*	*	SYM	_	_	_
97	∆	∆	SYM	_	_	_
98	RF3	rf3	NN	_	_	_
99	_	_	SYM	_	_	_
100	exp2	exp2	FW	_	_	_
101	_	_	FW	_	_	_
102	repA	repa	NN	_	_	_
103	_	_	NN	_	_	_
104	mRNA	mrna	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	RF2	rf2	NN	_	_	_
107	*	*	SYM	_	_	_
108	∆	∆	SYM	_	_	_
109	RF3	rf3	NN	_	_	_
110	_	_	SYM	_	_	_
111	exp2	exp2	FW	_	_	_
112	_	_	FW	_	_	_
113	repA	repa	NN	_	_	_
114	_	_	NN	_	_	_
115	ribosome	ribosome	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	RF2	rf2	NN	_	_	_
118	*	*	SYM	_	_	_
119	∆	∆	SYM	_	_	_
120	RF3	rf3	NN	_	_	_
121	_	_	CD	_	_	_
122	exp2	exp2	NN	_	_	_
123	_	_	CD	_	_	_
124	repB	repb	NN	_	_	_
125	_	_	NN	_	_	_
126	mRNA	mrna	NN	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	RF2	rf2	NN	_	_	_
129	*	*	SYM	_	_	_
130	∆	∆	SYM	_	_	_
131	RF3	rf3	NN	_	_	_
132	_	_	CD	_	_	_
133	exp2	exp2	NN	_	_	_
134	_	_	CD	_	_	_
135	repB	repb	NN	_	_	_
136	_	_	NN	_	_	_
137	ribosome	ribosome	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	RF2	rf2	NN	_	_	_
140	*	*	SYM	_	_	_
141	∆	∆	SYM	_	_	_
142	RF3	rf3	NN	_	_	_
143	_	_	CD	_	_	_
144	exp3	exp3	NN	_	_	_
145	_	_	NN	_	_	_
146	mRNA	mrna	NN	_	_	_
147	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
148	RF2	rf2	NN	_	_	_
149	*	*	SYM	_	_	_
150	∆	∆	SYM	_	_	_
151	RF3	rf3	NN	_	_	_
152	_	_	CD	_	_	_
153	exp3	exp3	NN	_	_	_
154	_	_	NN	_	_	_
155	ribosome	ribosome	NN	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
157	RF2	rf2	NN	_	_	_
158	*	*	SYM	_	_	_
159	∆	∆	SYM	_	_	_
160	RF3	rf3	NN	_	_	_
161	_	_	SYM	_	_	_
162	exp4	exp4	FW	_	_	_
163	_	_	FW	_	_	_
164	repA	repa	NN	_	_	_
165	_	_	NN	_	_	_
166	mRNA	mrna	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	RF2	rf2	NN	_	_	_
169	*	*	SYM	_	_	_
170	∆	∆	SYM	_	_	_
171	RF3	rf3	NN	_	_	_
172	_	_	SYM	_	_	_
173	exp4	exp4	FW	_	_	_
174	_	_	FW	_	_	_
175	repA	repa	NN	_	_	_
176	_	_	NN	_	_	_
177	ribosome	ribosome	NN	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	RF2	rf2	NN	_	_	_
180	*	*	SYM	_	_	_
181	∆	∆	SYM	_	_	_
182	RF3	rf3	NN	_	_	_
183	_	_	CD	_	_	_
184	exp4	exp4	NN	_	_	_
185	_	_	CD	_	_	_
186	repB	repb	NN	_	_	_
187	_	_	NN	_	_	_
188	mRNA	mrna	NN	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	RF2	rf2	NN	_	_	_
191	*	*	SYM	_	_	_
192	∆	∆	SYM	_	_	_
193	RF3	rf3	NN	_	_	_
194	_	_	CD	_	_	_
195	exp4	exp4	NN	_	_	_
196	_	_	CD	_	_	_
197	repB	repb	NN	_	_	_
198	_	_	NN	_	_	_
199	ribosome	ribosome	NN	_	_	_
200	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
201	∆	∆	CD	_	_	_
202	RF3	rf3	NN	_	_	_
203	_	_	CD	_	_	_
204	exp1	exp1	NN	_	_	_
205	_	_	NN	_	_	_
206	mRNA	mrna	NN	_	_	_
207	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
208	∆	∆	CD	_	_	_
209	RF3	rf3	NN	_	_	_
210	_	_	CD	_	_	_
211	exp1	exp1	NN	_	_	_
212	_	_	NN	_	_	_
213	ribosome	ribosome	NN	_	_	_
214	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
215	∆	∆	CD	_	_	_
216	RF3	rf3	NN	_	_	_
217	_	_	CD	_	_	_
218	exp3	exp3	NN	_	_	_
219	_	_	NN	_	_	_
220	mRNA	mrna	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	∆	∆	CD	_	_	_
223	RF3	rf3	NN	_	_	_
224	_	_	CD	_	_	_
225	exp3	exp3	NN	_	_	_
226	_	_	NN	_	_	_
227	ribosome	ribosome	NN	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	∆	∆	CD	_	_	_
230	RF3	rf3	NN	_	_	_
231	_	_	NN	_	_	_
232	minimal	minimal	JJ	_	_	_
233	_	_	NN	_	_	_
234	mRNA	mrna	NN	_	_	_
235	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
236	∆	∆	CD	_	_	_
237	RF3	rf3	NN	_	_	_
238	_	_	NN	_	_	_
239	minimal	minimal	JJ	_	_	_
240	_	_	NN	_	_	_
241	ribosome	ribosome	NN	_	_	_
242	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
243	RNA-Seq	rna-seq	NN	_	_	_
244	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
245	strain	strain	NN	_	_	_
246	:	:	:	_	_	_
247	K12	k12	NN	_	_	_
248	MG1655	mg1655	NN	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	strain	strain	NN	_	_	_
251	:	:	:	_	_	_
252	K12	k12	NN	_	_	_
253	MG1655	mg1655	NN	_	_	_
254	deltaprfC	deltaprfc	NN	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	strain	strain	NN	_	_	_
257	:	:	:	_	_	_
258	K12	k12	NN	_	_	_
259	MG1655	mg1655	NN	_	_	_
260	prfB-Bstrain	prfb-bstrain	JJ	_	_	_
261	allele	allele	NN	_	_	_
262	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
263	strain	strain	NN	_	_	_
264	:	:	:	_	_	_
265	K12	k12	NN	_	_	_
266	MG1655	mg1655	NN	_	_	_
267	prfB-Bstrain	prfb-bstrain	JJ	_	_	_
268	allele	allele	NN	_	_	_
269	deltaprfC	deltaprfc	NN	_	_	_
270	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
271	Supplementary	supplementary	JJ	_	_	_
272	_	_	NN	_	_	_
273	files	file	NNS	_	_	_
274	_	_	IN	_	_	_
275	format	format	NN	_	_	_
276	_	_	NN	_	_	_
277	and	and	CC	_	_	_
278	_	_	NN	_	_	_
279	content	content	NN	_	_	_
280	:	:	:	_	_	_
281	Bedgraph	Bedgraph	NNP	_	_	_
282	wiggle	wiggle	NN	_	_	_
283	files	file	NNS	_	_	_
284	were	be	VBD	_	_	_
285	created	create	VBN	_	_	_
286	for	for	IN	_	_	_
287	each	each	DT	_	_	_
288	sample	sample	NN	_	_	_
289	and	and	CC	_	_	_
290	replicate	replicate	VB	_	_	_
291	for	for	IN	_	_	_
292	all	all	DT	_	_	_
293	reads	read	VBZ	_	_	_
294	aligned	align	VBN	_	_	_
295	to	to	TO	_	_	_
296	the	the	DT	_	_	_
297	genome	genome	NN	_	_	_
298	after	after	IN	_	_	_
299	computational	computational	JJ	_	_	_
300	rRNA	rrna	NN	_	_	_
301	and	and	CC	_	_	_
302	tRNA	trna	NN	_	_	_
303	subtraction	subtraction	NN	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	The	the	DT	_	_	_
306	aligned	align	VBN	_	_	_
307	reads	read	VBZ	_	_	_
308	were	be	VBD	_	_	_
309	converted	convert	VBN	_	_	_
310	to	to	TO	_	_	_
311	BAM	BAM	NNP	_	_	_
312	files	file	NNS	_	_	_
313	and	and	CC	_	_	_
314	sorted	sort	VBN	_	_	_
315	and	and	CC	_	_	_
316	indexed	index	VBN	_	_	_
317	using	use	VBG	_	_	_
318	SAMtools	samtool	NNS	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
320	The	the	DT	_	_	_
321	remaining	remain	VBG	_	_	_
322	reads	read	VBZ	_	_	_
323	were	be	VBD	_	_	_
324	aligned	align	VBN	_	_	_
325	to	to	TO	_	_	_
326	genome	genome	NN	_	_	_
327	using	use	VBG	_	_	_
328	Bowtie	Bowtie	NNP	_	_	_
329	v.	v.	CC	_	_	_
330	0.12.0	0.12.0	CD	_	_	_
331	allowing	allow	VBG	_	_	_
332	for	for	IN	_	_	_
333	one	one	CD	_	_	_
334	mismatch	mismatch	NN	_	_	_
335	and	and	CC	_	_	_
336	reads	read	VBZ	_	_	_
337	aligning	align	VBG	_	_	_
338	in	in	IN	_	_	_
339	more	more	JJR	_	_	_
340	than	than	IN	_	_	_
341	one	one	CD	_	_	_
342	position	position	NN	_	_	_
343	in	in	IN	_	_	_
344	the	the	DT	_	_	_
345	genome	genome	NN	_	_	_
346	were	be	VBD	_	_	_
347	discarded	discard	VBN	_	_	_
348	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
349	whole	whole	JJ	_	_	_
350	cell	cell	NN	_	_	_
351	lysate	lysate	NN	_	_	_
352	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
353	Whole	whole	JJ	_	_	_
354	cell	cell	NN	_	_	_
355	lysates	lysate	NNS	_	_	_
356	were	be	VBD	_	_	_
357	clarified	clarify	VBN	_	_	_
358	by	by	IN	_	_	_
359	brief	brief	JJ	_	_	_
360	centrifugation	centrifugation	NN	_	_	_
361	.	.	.	_	_	_

1	Ribosome	ribosome	NN	_	_	_
2	footprints	footprint	NNS	_	_	_
3	were	be	VBD	_	_	_
4	created	create	VBN	_	_	_
5	using	use	VBG	_	_	_
6	Mnase	Mnase	NNP	_	_	_
7	digestion	digestion	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	45	45	CD	_	_	_
10	enzyme	enzyme	NN	_	_	_
11	units	unit	NNS	_	_	_
12	per	per	IN	_	_	_
13	absorbance	absorbance	NN	_	_	_
14	unit	unit	NN	_	_	_
15	of	of	IN	_	_	_
16	lysate	lysate	NN	_	_	_
17	at	at	IN	_	_	_
18	260nm	260nm	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	.	.	.	_	_	_

1	Using	use	VBG	_	_	_
2	sucrose	sucrose	NN	_	_	_
3	gradients	gradient	NNS	_	_	_
4	the	the	DT	_	_	_
5	monosome	monosome	JJ	_	_	_
6	fraction	fraction	NN	_	_	_
7	of	of	IN	_	_	_
8	lysate	lysate	NN	_	_	_
9	was	be	VBD	_	_	_
10	isolated	isolate	VBN	_	_	_
11	and	and	CC	_	_	_
12	footprints	footprint	NNS	_	_	_
13	were	be	VBD	_	_	_
14	size	size	NN	_	_	_
15	selected	select	VBN	_	_	_
16	and	and	CC	_	_	_
17	converted	convert	VBN	_	_	_
18	to	to	TO	_	_	_
19	a	a	DT	_	_	_
20	cDNA	cdna	NN	_	_	_
21	library	library	NN	_	_	_
22	.	.	.	_	_	_

1	Total	total	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	extracted	extract	VBN	_	_	_
5	from	from	IN	_	_	_
6	purified	purify	VBN	_	_	_
7	lysate	lysate	NN	_	_	_
8	for	for	IN	_	_	_
9	a	a	DT	_	_	_
10	simultaneous	simultaneous	JJ	_	_	_
11	RNA-seq	rna-seq	NN	_	_	_
12	library	library	NN	_	_	_
13	production	production	NN	_	_	_
14	for	for	IN	_	_	_
15	total	total	JJ	_	_	_
16	RNA	rna	NN	_	_	_
17	samples	sample	NNS	_	_	_
18	.	.	.	_	_	_

1	Small	small	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	and	and	CC	_	_	_
4	ribosomal	ribosomal	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	subtraction	subtraction	NN	_	_	_
7	was	be	VBD	_	_	_
8	performed	perform	VBN	_	_	_
9	in	in	IN	_	_	_
10	total	total	JJ	_	_	_
11	RNA	rna	NN	_	_	_
12	samples	sample	NNS	_	_	_
13	using	use	VBG	_	_	_
14	MEGAClear	megaclear	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	ThermoFisher	thermofisher	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	and	and	CC	_	_	_
19	MicrobExpress	microbexpress	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	ThermoFisher	thermofisher	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	kits	kit	NNS	_	_	_
24	.	.	.	_	_	_

1	Subtracted	subtract	VBN	_	_	_
2	total	total	JJ	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	then	then	RB	_	_	_
6	subjected	subject	VBN	_	_	_
7	to	to	TO	_	_	_
8	alkaline	alkaline	NN	_	_	_
9	fragmentation	fragmentation	NN	_	_	_
10	prior	prior	RB	_	_	_
11	to	to	TO	_	_	_
12	library	library	NN	_	_	_
13	preparation	preparation	NN	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Wiggle	Wiggle	NNP	_	_	_
3	files	file	NNS	_	_	_
4	were	be	VBD	_	_	_
5	created	create	VBN	_	_	_
6	by	by	IN	_	_	_
7	center	center	NN	_	_	_
8	mapping	map	VBG	_	_	_
9	the	the	DT	_	_	_
10	reads	read	VBZ	_	_	_
11	between	between	IN	_	_	_
12	20-40bps	20-40bp	NNS	_	_	_
13	.	.	.	_	_	_

1	Using	use	VBG	_	_	_
2	a	a	DT	_	_	_
3	10bp	10bp	JJ	_	_	_
4	trim	trim	JJ	_	_	_
5	on	on	IN	_	_	_
6	either	either	DT	_	_	_
7	side	side	NN	_	_	_
8	of	of	IN	_	_	_
9	the	the	DT	_	_	_
10	read	read	NN	_	_	_
11	then	then	RB	_	_	_
12	mapping	map	VBG	_	_	_
13	the	the	DT	_	_	_
14	read	read	NN	_	_	_
15	across	across	IN	_	_	_
16	the	the	DT	_	_	_
17	remaining	remain	VBG	_	_	_
18	location	location	NN	_	_	_
19	using	use	VBG	_	_	_
20	Plastid	Plastid	NNP	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	WT	wt	VBD	_	_	_
3	_	_	CD	_	_	_
4	exp1	exp1	NN	_	_	_
5	_	_	NN	_	_	_
6	mRNA	mrna	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	WT	wt	JJ	_	_	_
9	_	_	NN	_	_	_
10	exp1	exp1	NN	_	_	_
11	_	_	NN	_	_	_
12	ribosome	ribosome	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	WT	wt	JJ	_	_	_
15	_	_	NN	_	_	_
16	exp2	exp2	NN	_	_	_
17	_	_	NN	_	_	_
18	mRNA	mrna	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	WT	wt	JJ	_	_	_
21	_	_	NN	_	_	_
22	exp2	exp2	NN	_	_	_
23	_	_	NN	_	_	_
24	ribosome	ribosome	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	WT	wt	JJ	_	_	_
27	_	_	NN	_	_	_
28	exp3	exp3	NN	_	_	_
29	_	_	NN	_	_	_
30	mRNA	mrna	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	WT	wt	JJ	_	_	_
33	_	_	NN	_	_	_
34	exp3	exp3	NN	_	_	_
35	_	_	NN	_	_	_
36	ribosome	ribosome	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	WT	wt	JJ	_	_	_
39	_	_	NN	_	_	_
40	exp4	exp4	NN	_	_	_
41	_	_	NN	_	_	_
42	mRNA	mrna	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	WT	wt	JJ	_	_	_
45	_	_	NN	_	_	_
46	exp4	exp4	NN	_	_	_
47	_	_	NN	_	_	_
48	ribosome	ribosome	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	WT	wt	JJ	_	_	_
51	_	_	NN	_	_	_
52	minimal	minimal	JJ	_	_	_
53	_	_	NN	_	_	_
54	mRNA	mrna	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	WT	wt	JJ	_	_	_
57	_	_	NN	_	_	_
58	minimal	minimal	JJ	_	_	_
59	_	_	NN	_	_	_
60	ribosome	ribosome	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	Culture	culture	NN	_	_	_
63	grown	grow	VBN	_	_	_
64	in	in	IN	_	_	_
65	14	14	CD	_	_	_
66	ml	ml	NN	_	_	_
67	tube	tube	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	Culture	culture	NN	_	_	_
70	grown	grow	VBN	_	_	_
71	in	in	IN	_	_	_
72	250	250	CD	_	_	_
73	ml	ml	NN	_	_	_
74	Erlenmeyer	erlenmeyer	NN	_	_	_
75	flask	flask	NN	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	Cultures	culture	NNS	_	_	_
78	were	be	VBD	_	_	_
79	spun	spin	VBN	_	_	_
80	down	down	RP	_	_	_
81	at	at	IN	_	_	_
82	4	4	CD	_	_	_
83	°C	°c	NN	_	_	_
84	,	,	,	_	_	_
85	15,000	15,000	CD	_	_	_
86	×	×	CD	_	_	_
87	g	g	NN	_	_	_
88	for	for	IN	_	_	_
89	3	3	CD	_	_	_
90	minutes	minute	NNS	_	_	_
91	.	.	.	_	_	_

1	Supernatants	supernatant	NNS	_	_	_
2	were	be	VBD	_	_	_
3	discarded	discard	VBN	_	_	_
4	after	after	IN	_	_	_
5	centrifugation	centrifugation	NN	_	_	_
6	and	and	CC	_	_	_
7	cell	cell	NN	_	_	_
8	pellets	pellet	NNS	_	_	_
9	were	be	VBD	_	_	_
10	flash	flash	NN	_	_	_
11	frozen	freeze	VBN	_	_	_
12	in	in	IN	_	_	_
13	liquid	liquid	JJ	_	_	_
14	nitrogen	nitrogen	NN	_	_	_
15	for	for	IN	_	_	_
16	storage	storage	NN	_	_	_
17	at	at	IN	_	_	_
18	-80	-80	CD	_	_	_
19	°C	°c	NN	_	_	_
20	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	lysed	lyse	VBN	_	_	_
4	with	with	IN	_	_	_
5	1	1	CD	_	_	_
6	mg	mg	NN	_	_	_
7	of	of	IN	_	_	_
8	lysozme	lysozme	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Sigma	Sigma	NNP	_	_	_
11	Aldrich	Aldrich	NNP	_	_	_
12	L6871	L6871	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	in	in	IN	_	_	_
15	10	10	CD	_	_	_
16	mM	mm	NN	KWSUPP	_	_
17	Tris-HCl	tris-hcl	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	pH	ph	NN	_	_	_
20	8.0	8.0	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	USB	usb	JJ	_	_	_
24	75825	75825	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	supplemented	supplement	VBN	_	_	_
27	with	with	IN	_	_	_
28	0.1	0.1	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	EDTA	edta	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	USB	usb	JJ	_	_	_
33	15694	15694	CD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	extracted	extract	VBN	_	_	_
4	with	with	IN	_	_	_
5	PureLink	purelink	NN	_	_	_
6	RNA	rna	NN	_	_	_
7	Mini	Mini	NNP	_	_	_
8	Kit	kit	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Life	Life	NNP	_	_	_
11	Technologies	Technologies	NNPS	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	further	further	JJ	_	_	_
15	purified	purify	VBN	_	_	_
16	and	and	CC	_	_	_
17	concentrated	concentrate	VBN	_	_	_
18	with	with	IN	_	_	_
19	RNA	rna	NN	_	_	_
20	Clean	Clean	NNP	_	_	_
21	&	&	CC	_	_	_
22	Concentrator-5	Concentrator-5	NNP	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Zymo	Zymo	NNP	_	_	_
25	Research	Research	NNP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	to	to	TO	_	_	_
28	assure	assure	VB	_	_	_
29	sample	sample	NN	_	_	_
30	quality	quality	NN	_	_	_
31	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	purified	purify	VBN	_	_	_
3	RNA	rna	NN	_	_	_
4	samples	sample	NNS	_	_	_
5	were	be	VBD	_	_	_
6	analyzed	analyze	VBN	_	_	_
7	using	use	VBG	_	_	_
8	a	a	DT	_	_	_
9	Bioanalyzer	Bioanalyzer	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Agilent	Agilent	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	Ribo-Zero	Ribo-Zero	NNP	_	_	_
15	rRNA	rrna	NN	_	_	_
16	Removal	removal	NN	_	_	_
17	Kit	kit	NN	_	_	_
18	for	for	IN	_	_	_
19	bacteria	bacterium	NNS	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Illumina	Illumina	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	was	be	VBD	_	_	_
24	used	use	VBN	_	_	_
25	to	to	TO	_	_	_
26	deplete	deplete	VB	_	_	_
27	rRNA	rrna	NN	_	_	_
28	from	from	IN	_	_	_
29	the	the	DT	_	_	_
30	samples	sample	NNS	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Flask	flask	NN	_	_	_
6	state	state	NN	_	_	_
7	1	1	CD	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	IPTG	iptg	SYM	_	_	_
10	-	-	:	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Flask	flask	NN	_	_	_
13	state	state	NN	_	_	_
14	2	2	CD	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	IPTG	iptg	NN	_	_	_
17	+	+	CC	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Flask	flask	NN	_	_	_
20	state	state	NN	_	_	_
21	3	3	CD	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	IPTG	iptg	SYM	_	_	_
24	-	-	:	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Flask	flask	NN	_	_	_
27	state	state	NN	_	_	_
28	4	4	CD	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	IPTG	iptg	NN	_	_	_
31	+	+	CC	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	Flask	flask	NN	_	_	_
34	state	state	NN	_	_	_
35	5	5	CD	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	IPTG	iptg	SYM	_	_	_
38	-	-	:	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Flask	flask	NN	_	_	_
41	state	state	NN	_	_	_
42	6	6	CD	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	IPTG	iptg	NN	_	_	_
45	+	+	CC	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	Flask	flask	NN	_	_	_
48	state	state	NN	_	_	_
49	7	7	CD	_	_	_
50	-LRB-	-lrb-	-LRB-	_	_	_
51	IPTG	iptg	SYM	_	_	_
52	-	-	:	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Flask	flask	NN	_	_	_
55	state	state	NN	_	_	_
56	8	8	CD	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	IPTG	iptg	NN	_	_	_
59	+	+	CC	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	Genome	Genome	NNP	_	_	_
62	_	_	NNP	_	_	_
63	build	build	VB	_	_	_
64	:	:	:	_	_	_
65	NC	NC	NNP	_	_	_
66	_	_	NNP	_	_	_
67	010473.1	010473.1	CD	_	_	_
68	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
69	Individual	Individual	NNP	_	_	_
70	colonies	colony	NNS	_	_	_
71	were	be	VBD	_	_	_
72	inoculated	inoculate	VBN	_	_	_
73	into	into	IN	_	_	_
74	MOPS	MOPS	NNP	MED	_	_
75	EZ	EZ	NNP	_	_	_
76	Rich	Rich	NNP	_	_	_
77	Defined	Defined	NNP	_	_	_
78	Medium	medium	NN	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	Teknova	teknova	NN	_	_	_
81	,	,	,	_	_	_
82	CA	CA	NNP	_	_	_
83	,	,	,	_	_	_
84	M2105	m2105	NN	_	_	_
85	-RRB-	-rrb-	-RRB-	_	_	_
86	with	with	IN	_	_	_
87	0.2	0.2	CD	_	_	_
88	%	%	NN	_	_	_
89	glycerol	glycerol	NN	SUPP	_	_
90	carbon	carbon	NN	_	_	_
91	source	source	NN	_	_	_
92	and	and	CC	_	_	_
93	50	50	CD	_	_	_
94	μg	μg	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	Normalized	normalize	VBN	_	_	_
97	FPKM	fpkm	NN	_	_	_
98	values	value	NNS	_	_	_
99	were	be	VBD	_	_	_
100	generated	generate	VBN	_	_	_
101	from	from	IN	_	_	_
102	the	the	DT	_	_	_
103	raw	raw	JJ	_	_	_
104	gene	gene	NN	_	_	_
105	counts	count	NNS	_	_	_
106	by	by	IN	_	_	_
107	custom	custom	NN	_	_	_
108	scripts	script	NNS	_	_	_
109	that	that	WDT	_	_	_
110	calculated	calculate	VBD	_	_	_
111	and	and	CC	_	_	_
112	applied	apply	VBD	_	_	_
113	a	a	DT	_	_	_
114	trimmed	trimmed	RBR	_	_	_
115	mean	mean	VB	_	_	_
116	of	of	IN	_	_	_
117	M-values	m-value	NNS	_	_	_
118	-LRB-	-lrb-	-LRB-	_	_	_
119	TMM	tmm	NN	_	_	_
120	-RRB-	-rrb-	-RRB-	_	_	_
121	factor	factor	NN	_	_	_
122	using	use	VBG	_	_	_
123	edgeR	edger	NN	_	_	_
124	version	version	NN	_	_	_
125	3.8.6	3.8.6	CD	_	_	_
126	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Read	Read	NNP	_	_	_
3	counts	count	VBZ	_	_	_
4	for	for	IN	_	_	_
5	each	each	DT	_	_	_
6	host	host	NN	_	_	_
7	and	and	CC	_	_	_
8	circuit	circuit	NN	_	_	_
9	gene	gene	NN	_	_	_
10	was	be	VBD	_	_	_
11	carried	carry	VBN	_	_	_
12	out	out	RP	_	_	_
13	using	use	VBG	_	_	_
14	the	the	DT	_	_	_
15	htseq-count	htseq-count	JJ	_	_	_
16	command	command	NN	_	_	_
17	of	of	IN	_	_	_
18	the	the	DT	_	_	_
19	HTSeq	htseq	NN	_	_	_
20	toolkit	toolkit	NN	_	_	_
21	with	with	IN	_	_	_
22	user-defined	user-defined	JJ	_	_	_
23	GFF	gff	NN	_	_	_
24	annotations	annotation	NNS	_	_	_
25	of	of	IN	_	_	_
26	the	the	DT	_	_	_
27	reference	reference	NN	_	_	_
28	sequences	sequence	NNS	_	_	_
29	and	and	CC	_	_	_
30	the	the	DT	_	_	_
31	options	option	NNS	_	_	_
32	'	'	POS	_	_	_
33	-	-	:	_	_	_
34	s	s	NNS	_	_	_
35	reverse	reverse	JJ	_	_	_
36	-	-	:	_	_	_
37	a	a	DT	_	_	_
38	10	10	CD	_	_	_
39	-	-	:	_	_	_
40	m	m	NN	_	_	_
41	union	union	NN	_	_	_
42	'	'	''	_	_	_
43	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Reads	read	VBZ	_	_	_
3	mapped	map	VBN	_	_	_
4	to	to	TO	_	_	_
5	reference	reference	NN	_	_	_
6	using	use	VBG	_	_	_
7	BWA	bwa	NN	_	_	_
8	versiopn	versiopn	NN	_	_	_
9	0.7.4	0.7.4	CD	_	_	_
10	with	with	IN	_	_	_
11	default	default	NN	_	_	_
12	settings	setting	NNS	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBP	_	_	_
14	RNA-Seq	rna-seq	JJ	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	strain	strain	NN	_	_	_
17	:	:	:	_	_	_
18	NEB	NEB	NNP	_	_	_
19	10-beta	10-beta	JJ	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Strand	strand	NN	_	_	_
22	specific	specific	JJ	_	_	_
23	RNAtag-seq	rnatag-seq	NN	_	_	_
24	libraries	library	NNS	_	_	_
25	were	be	VBD	_	_	_
26	created	create	VBN	_	_	_
27	by	by	IN	_	_	_
28	the	the	DT	_	_	_
29	Broad	Broad	NNP	_	_	_
30	Technology	Technology	NNP	_	_	_
31	Labs	Labs	NNPS	_	_	_
32	specialized	specialized	JJ	_	_	_
33	service	service	NN	_	_	_
34	facility	facility	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	SSF	ssf	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	using	use	VBG	_	_	_
39	the	the	DT	_	_	_
40	standard	standard	JJ	_	_	_
41	protocol	protocol	NN	_	_	_
42	described	describe	VBN	_	_	_
43	in	in	IN	_	_	_
44	Shishkin	Shishkin	NNP	_	_	_
45	et	et	FW	_	_	_
46	al.	al.	FW	_	_	_
47	.	.	.	_	_	_

1	Nature	Nature	NNP	_	_	_
2	Methods	method	NNS	_	_	_
3	2016	2016	CD	_	_	_
4	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Supplementary	Supplementary	NNP	_	_	_
3	_	_	VBD	_	_	_
4	files	file	NNS	_	_	_
5	_	_	IN	_	_	_
6	format	format	NN	_	_	_
7	_	_	NN	_	_	_
8	and	and	CC	_	_	_
9	_	_	NN	_	_	_
10	content	content	NN	_	_	_
11	:	:	:	_	_	_
12	CSV	CSV	NNP	_	_	_
13	files	file	NNS	_	_	_
14	of	of	IN	_	_	_
15	raw	raw	JJ	_	_	_
16	read	read	NN	_	_	_
17	counts	count	NNS	_	_	_
18	and	and	CC	_	_	_
19	normalized	normalize	VBN	_	_	_
20	gene	gene	NN	_	_	_
21	expression	expression	NN	_	_	_
22	in	in	IN	_	_	_
23	FPKM	FPKM	NNP	_	_	_
24	units	unit	NNS	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Tube	Tube	NNP	_	_	_
3	state	state	NN	_	_	_
4	1	1	CD	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	IPTG	iptg	SYM	_	_	_
7	-	-	:	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Tube	Tube	NNP	_	_	_
10	state	state	NN	_	_	_
11	2	2	CD	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	IPTG	iptg	NN	_	_	_
14	+	+	CC	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Tube	Tube	NNP	_	_	_
17	state	state	NN	_	_	_
18	3	3	CD	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	IPTG	iptg	SYM	_	_	_
21	-	-	:	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	Tube	Tube	NNP	_	_	_
24	state	state	NN	_	_	_
25	4	4	CD	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	IPTG	iptg	NN	_	_	_
28	+	+	CC	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Tube	Tube	NNP	_	_	_
31	state	state	NN	_	_	_
32	5	5	CD	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	IPTG	iptg	SYM	_	_	_
35	-	-	:	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	Tube	Tube	NNP	_	_	_
38	state	state	NN	_	_	_
39	6	6	CD	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	IPTG	iptg	NN	_	_	_
42	+	+	CC	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Tube	Tube	NNP	_	_	_
45	state	state	NN	_	_	_
46	7	7	CD	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	IPTG	iptg	SYM	_	_	_
49	-	-	:	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	Tube	Tube	NNP	_	_	_
52	state	state	NN	_	_	_
53	8	8	CD	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	IPTG	iptg	NN	_	_	_
56	+	+	CC	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
58	Cells	cell	NNS	_	_	_
59	were	be	VBD	_	_	_
60	grown	grow	VBN	_	_	_
61	to	to	TO	_	_	_
62	the	the	DT	_	_	_
63	stationary	stationary	JJ	GrowthPhase	_	_
64	phase	phase	NN	GrowthPhase	_	_
65	at	at	IN	_	_	_
66	37ºC	37ºc	NN	_	_	_
67	in	in	IN	_	_	_
68	Luria-Bertani	luria-bertani	JJ	_	_	_
69	medium	medium	NN	_	_	_
70	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Enteroheamorragic	enteroheamorragic	JJ	_	_	_
3	E.	e.	FW	_	_	_
4	coli	coli	FW	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Enteropathogenic	enteropathogenic	JJ	_	_	_
7	E.	e.	FW	_	_	_
8	coli	coli	FW	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Escherichia	escherichia	FW	Organism	_	_
11	coli	coli	FW	Organism	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
13	Genomic	genomic	JJ	_	_	_
14	DNA	dna	NN	_	_	_
15	from	from	IN	_	_	_
16	O55	o55	NN	_	_	_
17	:	:	:	_	_	_
18	H6	h6	NN	_	_	_
19	strain	strain	NN	_	_	_
20	ICC219	icc219	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
22	Genomic	genomic	JJ	_	_	_
23	DNA	dna	NN	_	_	_
24	from	from	IN	_	_	_
25	O55	o55	NN	_	_	_
26	:	:	:	_	_	_
27	H6	h6	NN	_	_	_
28	strain	strain	NN	_	_	_
29	ICC221	icc221	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
31	Genomic	genomic	JJ	_	_	_
32	DNA	dna	NN	_	_	_
33	from	from	IN	_	_	_
34	O55	o55	NN	_	_	_
35	:	:	:	_	_	_
36	H6	h6	NN	_	_	_
37	strain	strain	NN	_	_	_
38	ICC222	icc222	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
40	Genomic	genomic	JJ	_	_	_
41	DNA	dna	NN	_	_	_
42	from	from	IN	_	_	_
43	O55	o55	NN	_	_	_
44	:	:	:	_	_	_
45	H7	h7	NN	_	_	_
46	strain	strain	NN	_	_	_
47	st58	st58	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
49	Genomic	genomic	JJ	_	_	_
50	DNA	dna	NN	_	_	_
51	from	from	IN	_	_	_
52	O55	o55	NN	_	_	_
53	:	:	:	_	_	_
54	H7	h7	NN	_	_	_
55	strain	strain	NN	_	_	_
56	st957	st957	NN	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
58	Genomic	genomic	JJ	_	_	_
59	DNA	dna	NN	_	_	_
60	from	from	IN	_	_	_
61	O55	o55	NN	_	_	_
62	:	:	:	_	_	_
63	H7	h7	NN	_	_	_
64	strain	strain	NN	_	_	_
65	TB182A	tb182a	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
67	Genomic	genomic	JJ	_	_	_
68	DNA	dna	NN	_	_	_
69	from	from	IN	_	_	_
70	O55	o55	NN	_	_	_
71	:	:	:	_	_	_
72	H7	h7	NN	_	_	_
73	strain	strain	NN	_	_	_
74	WC211	wc211	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
76	Genomic	genomic	JJ	_	_	_
77	DNA	dna	NN	_	_	_
78	from	from	IN	_	_	_
79	O55	o55	NN	_	_	_
80	:	:	:	_	_	_
81	H7	h7	NN	_	_	_
82	strain	strain	NN	_	_	_
83	WC416	wc416	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
85	Genomic	genomic	JJ	_	_	_
86	DNA	dna	NN	_	_	_
87	was	be	VBD	_	_	_
88	purified	purify	VBN	_	_	_
89	using	use	VBG	_	_	_
90	the	the	DT	_	_	_
91	Genomic-tip	genomic-tip	NN	_	_	_
92	100	100	CD	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	O157	o157	NN	_	_	_
95	strain	strain	NN	_	_	_
96	Sakai	Sakai	NNP	_	_	_
97	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
98	O55	O55	NNP	_	_	_
99	:	:	:	_	_	_
100	H6	h6	NN	_	_	_
101	ICC219	icc219	NN	_	_	_
102	replicate	replicate	VBP	_	_	_
103	1	1	CD	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	O55	o55	NN	_	_	_
106	:	:	:	_	_	_
107	H6	h6	NN	_	_	_
108	ICC219	icc219	NN	_	_	_
109	replicate	replicate	VBP	_	_	_
110	2	2	CD	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
112	O55	o55	NN	_	_	_
113	:	:	:	_	_	_
114	H6	h6	NN	_	_	_
115	ICC221	icc221	NN	_	_	_
116	replicate	replicate	VBP	_	_	_
117	1	1	CD	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	O55	o55	NN	_	_	_
120	:	:	:	_	_	_
121	H6	h6	NN	_	_	_
122	ICC221	icc221	NN	_	_	_
123	replicate	replicate	VBP	_	_	_
124	2	2	CD	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
126	O55	o55	NN	_	_	_
127	:	:	:	_	_	_
128	H6	h6	NN	_	_	_
129	ICC222	icc222	NN	_	_	_
130	replicate	replicate	VBP	_	_	_
131	1	1	CD	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	O55	o55	NN	_	_	_
134	:	:	:	_	_	_
135	H6	h6	NN	_	_	_
136	ICC222	icc222	NN	_	_	_
137	replicate	replicate	VBP	_	_	_
138	2	2	CD	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
140	O55	o55	NN	_	_	_
141	:	:	:	_	_	_
142	H7	h7	NN	_	_	_
143	st58	st58	NN	_	_	_
144	replicate	replicate	VBP	_	_	_
145	1	1	CD	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	O55	o55	NN	_	_	_
148	:	:	:	_	_	_
149	H7	h7	NN	_	_	_
150	st58	st58	NN	_	_	_
151	replicate	replicate	VBP	_	_	_
152	2	2	CD	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
154	O55	o55	NN	_	_	_
155	:	:	:	_	_	_
156	H7	h7	NN	_	_	_
157	st957	st957	NN	_	_	_
158	replicate	replicate	VBP	_	_	_
159	1	1	CD	_	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	O55	o55	NN	_	_	_
162	:	:	:	_	_	_
163	H7	h7	NN	_	_	_
164	st957	st957	NN	_	_	_
165	replicate	replicate	VBP	_	_	_
166	2	2	CD	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
168	O55	o55	NN	_	_	_
169	:	:	:	_	_	_
170	H7	h7	NN	_	_	_
171	TB182A	tb182a	NN	_	_	_
172	replicate	replicate	VBP	_	_	_
173	1	1	CD	_	_	_
174	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
175	O55	o55	NN	_	_	_
176	:	:	:	_	_	_
177	H7	h7	NN	_	_	_
178	TB182A	tb182a	NN	_	_	_
179	replicate	replicate	VBP	_	_	_
180	2	2	CD	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
182	O55	o55	NN	_	_	_
183	:	:	:	_	_	_
184	H7	h7	NN	_	_	_
185	WC211	wc211	NN	_	_	_
186	replicate	replicate	VBP	_	_	_
187	1	1	CD	_	_	_
188	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
189	O55	o55	NN	_	_	_
190	:	:	:	_	_	_
191	H7	h7	NN	_	_	_
192	WC211	wc211	NN	_	_	_
193	replicate	replicate	VBP	_	_	_
194	2	2	CD	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
196	O55	o55	NN	_	_	_
197	:	:	:	_	_	_
198	H7	h7	NN	_	_	_
199	WC416	wc416	NN	_	_	_
200	replicate	replicate	VBP	_	_	_
201	1	1	CD	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	O55	o55	NN	_	_	_
204	:	:	:	_	_	_
205	H7	h7	NN	_	_	_
206	WC416	wc416	NN	_	_	_
207	replicate	replicate	VBP	_	_	_
208	2	2	CD	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
210	Spots	spot	NNS	_	_	_
211	with	with	IN	_	_	_
212	reference	reference	NN	_	_	_
213	signal	signal	NN	_	_	_
214	intensities	intensity	NNS	_	_	_
215	lower	lower	JJR	_	_	_
216	than	than	IN	_	_	_
217	the	the	DT	_	_	_
218	local	local	JJ	_	_	_
219	background	background	NN	_	_	_
220	-LRB-	-lrb-	-LRB-	_	_	_
221	LBG	lbg	NN	_	_	_
222	-RRB-	-rrb-	-RRB-	_	_	_
223	plus	plus	CC	_	_	_
224	5	5	CD	_	_	_
225	standard	standard	JJ	_	_	_
226	deviations	deviation	NNS	_	_	_
227	or	or	CC	_	_	_
228	with	with	IN	_	_	_
229	some	some	DT	_	_	_
230	spotting	spot	VBG	_	_	_
231	abnormalities	abnormality	NNS	_	_	_
232	were	be	VBD	_	_	_
233	removed	remove	VBN	_	_	_
234	from	from	IN	_	_	_
235	analysis	analysis	NN	_	_	_
236	.	.	.	_	_	_

1	Signal	signal	NN	_	_	_
2	intensities	intensity	NNS	_	_	_
3	of	of	IN	_	_	_
4	other	other	JJ	_	_	_
5	spots	spot	NNS	_	_	_
6	were	be	VBD	_	_	_
7	corrected	correct	VBN	_	_	_
8	by	by	IN	_	_	_
9	subtracting	subtract	VBG	_	_	_
10	the	the	DT	_	_	_
11	LBG	LBG	NNP	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	A	a	NN	_	_	_
3	total	total	NN	_	_	_
4	of	of	IN	_	_	_
5	two	two	CD	_	_	_
6	samples	sample	NNS	_	_	_
7	were	be	VBD	_	_	_
8	analyzed	analyze	VBN	_	_	_
9	.	.	.	_	_	_

1	ompR-8myc	ompr-8myc	NN	_	_	_
2	tagged	tag	VBD	_	_	_
3	cells	cell	NNS	_	_	_
4	were	be	VBD	_	_	_
5	cultured	culture	VBN	_	_	_
6	in	in	IN	_	_	_
7	M9	m9	NN	MED	_	_
8	minimal	minimal	JJ	MED	_	_
9	media	media	NNS	MED	_	_
10	with	with	IN	_	_	_
11	0.2	0.2	CD	_	_	_
12	%	%	NN	_	_	_
13	glucose	glucose	NN	SUPP	_	_
14	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	treated	treat	VBN	_	_	_
5	with	with	IN	_	_	_
6	0.3	0.3	CD	_	_	_
7	M	m	NN	_	_	_
8	of	of	IN	_	_	_
9	NaCl	nacl	NN	_	_	_
10	at	at	IN	_	_	_
11	mid-log	mid-log	JJ	_	_	_
12	pahse	pahse	NN	_	_	_
13	for	for	IN	_	_	_
14	30	30	CD	_	_	_
15	min	min	NN	_	_	_
16	with	with	IN	_	_	_
17	agitation	agitation	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	chip	chip	NN	_	_	_
3	antibody	antibody	NN	_	_	_
4	:	:	:	_	_	_
5	anti-myc	anti-myc	JJ	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	Santa	Santa	NNP	_	_	_
8	Cruz	Cruz	NNP	_	_	_
9	Biotech	Biotech	NNP	_	_	_
10	,	,	,	_	_	_
11	sc-28207	sc-28207	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	ChIP-exo	chip-exo	NN	_	_	_
15	reads	read	VBZ	_	_	_
16	were	be	VBD	_	_	_
17	aligned	align	VBN	_	_	_
18	to	to	TO	_	_	_
19	the	the	DT	_	_	_
20	ASM584v2	asm584v2	NN	_	_	_
21	genome	genome	NN	_	_	_
22	reference	reference	NN	_	_	_
23	sequence	sequence	NN	_	_	_
24	using	use	VBG	_	_	_
25	using	use	VBG	_	_	_
26	bowtie	bowtie	NN	_	_	_
27	v1	v1	NN	_	_	_
28	.0.0	.0.0	CD	_	_	_
29	with	with	IN	_	_	_
30	parameters	parameter	NNS	_	_	_
31	-	-	:	_	_	_
32	S	s	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
34	ChIP-Seq	chip-seq	JJ	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	ChIP-seq	chip-seq	NN	_	_	_
37	libraries	library	NNS	_	_	_
38	were	be	VBD	_	_	_
39	prepared	prepare	VBN	_	_	_
40	for	for	IN	_	_	_
41	sequencing	sequencing	NN	_	_	_
42	using	use	VBG	_	_	_
43	standard	standard	JJ	_	_	_
44	Illumina	Illumina	NNP	_	_	_
45	protocols	protocol	NNS	_	_	_
46	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
47	Crosslinked	crosslink	VBN	_	_	_
48	cells	cell	NNS	_	_	_
49	were	be	VBD	_	_	_
50	then	then	RB	_	_	_
51	resuspended	resuspend	VBN	_	_	_
52	in	in	IN	_	_	_
53	500	500	CD	_	_	_
54	ul	ul	NN	_	_	_
55	of	of	IN	_	_	_
56	lysis	lysis	NN	_	_	_
57	buffer	buffer	NN	_	_	_
58	-LRB-	-lrb-	-LRB-	_	_	_
59	10	10	CD	_	_	_
60	mM	mm	NN	KWSUPP	_	_
61	Tris-HCl	tris-hcl	NN	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	pH	ph	NN	_	_	_
64	7.5	7.5	CD	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	,	,	,	_	_	_
67	100	100	CD	_	_	_
68	mM	mm	NN	KWSUPP	_	_
69	NaCl	nacl	NN	_	_	_
70	and	and	CC	_	_	_
71	1	1	CD	_	_	_
72	mM	mm	NN	KWSUPP	_	_
73	EDTA	edta	NN	_	_	_
74	-RRB-	-rrb-	-RRB-	_	_	_
75	with	with	IN	_	_	_
76	40	40	CD	_	_	_
77	ul	ul	NN	_	_	_
78	of	of	IN	_	_	_
79	protease	protease	NN	_	_	_
80	inhibitor	inhibitor	NN	_	_	_
81	cocktail	cocktail	NN	_	_	_
82	-LRB-	-lrb-	-LRB-	_	_	_
83	50	50	CD	_	_	_
84	mg	mg	NN	_	_	_
85	in	in	IN	_	_	_
86	0.25	0.25	CD	_	_	_
87	ml	ml	NN	_	_	_
88	of	of	IN	_	_	_
89	DMSO	dmso	NN	_	_	_
90	and	and	CC	_	_	_
91	0.75	0.75	CD	_	_	_
92	ml	ml	NN	_	_	_
93	of	of	IN	_	_	_
94	TDW	tdw	NN	_	_	_
95	-RRB-	-rrb-	-RRB-	_	_	_
96	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	lyzed	lyze	VBN	_	_	_
4	with	with	IN	_	_	_
5	1	1	CD	_	_	_
6	ul	ul	NN	_	_	_
7	of	of	IN	_	_	_
8	lysozyme	lysozyme	NN	_	_	_
9	for	for	IN	_	_	_
10	30	30	CD	_	_	_
11	min	min	NN	_	_	_
12	at	at	IN	_	_	_
13	37oC	37oc	NN	_	_	_
14	on	on	IN	_	_	_
15	a	a	DT	_	_	_
16	rocker	rocker	NN	_	_	_
17	.	.	.	_	_	_

1	0.55	0.55	CD	_	_	_
2	ml	ml	NN	_	_	_
3	of	of	IN	_	_	_
4	2X	2x	NN	_	_	_
5	IP	IP	NNP	_	_	_
6	buffer	buffer	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	100	100	CD	_	_	_
9	mM	mm	NN	KWSUPP	_	_
10	Tris-HCl	tris-hcl	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	pH	ph	NN	_	_	_
13	7.5	7.5	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	200	200	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	NaCl	nacl	NN	_	_	_
19	,	,	,	_	_	_
20	2	2	CD	_	_	_
21	%	%	NN	_	_	_
22	Triton	Triton	NNP	_	_	_
23	X-100	x-100	NN	_	_	_
24	and	and	CC	_	_	_
25	1	1	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	EDTA	edta	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	were	be	VBD	_	_	_
30	added	add	VBN	_	_	_
31	to	to	TO	_	_	_
32	the	the	DT	_	_	_
33	sample	sample	NN	_	_	_
34	,	,	,	_	_	_
35	and	and	CC	_	_	_
36	then	then	RB	_	_	_
37	was	be	VBD	_	_	_
38	sonicated	sonicate	VBN	_	_	_
39	to	to	TO	_	_	_
40	fragmentize	fragmentize	VB	_	_	_
41	genomic	genomic	JJ	_	_	_
42	DNA	dna	NN	_	_	_
43	.	.	.	_	_	_

1	0.3	0.3	CD	_	_	_
2	ml	ml	NN	_	_	_
3	of	of	IN	_	_	_
4	Wash	Wash	NNP	_	_	_
5	buffer	buffer	NN	_	_	_
6	I	i	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	50	50	CD	_	_	_
9	mM	mm	NN	KWSUPP	_	_
10	Tris-HCl	tris-hcl	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	pH	ph	NN	_	_	_
13	7.5	7.5	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	140	140	CD	_	_	_
17	mM	mm	NN	KWSUPP	_	_
18	NaCl	nacl	NN	_	_	_
19	,	,	,	_	_	_
20	1	1	CD	_	_	_
21	%	%	NN	_	_	_
22	Triton	Triton	NNP	_	_	_
23	X-100	x-100	NN	_	_	_
24	and	and	CC	_	_	_
25	1mM	1mm	NN	_	_	_
26	EDTA	edta	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	was	be	VBD	_	_	_
29	added	add	VBN	_	_	_
30	to	to	TO	_	_	_
31	make	make	VB	_	_	_
32	the	the	DT	_	_	_
33	volume	volume	NN	_	_	_
34	up	up	IN	_	_	_
35	to	to	TO	_	_	_
36	1.4	1.4	CD	_	_	_
37	ml	ml	NN	_	_	_
38	.	.	.	_	_	_

1	Only	only	RB	_	_	_
2	0.7	0.7	CD	_	_	_
3	ml	ml	NN	_	_	_
4	was	be	VBD	_	_	_
5	taken	take	VBN	_	_	_
6	and	and	CC	_	_	_
7	transfered	transfer	VBN	_	_	_
8	to	to	TO	_	_	_
9	a	a	DT	_	_	_
10	new	new	JJ	_	_	_
11	tube	tube	NN	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	15	15	CD	_	_	_
15	ul	ul	NN	_	_	_
16	of	of	IN	_	_	_
17	Anti-c-myc	anti-c-myc	JJ	_	_	_
18	mouse	mouse	NN	_	_	_
19	antibody	antibody	NN	_	_	_
20	was	be	VBD	_	_	_
21	added	add	VBN	_	_	_
22	,	,	,	_	_	_
23	and	and	CC	_	_	_
24	the	the	DT	_	_	_
25	sample	sample	NN	_	_	_
26	was	be	VBD	_	_	_
27	incubated	incubate	VBN	_	_	_
28	overnight	overnight	RB	_	_	_
29	at	at	IN	_	_	_
30	4	4	CD	_	_	_
31	oC	oc	NN	_	_	_
32	to	to	TO	_	_	_
33	make	make	VB	_	_	_
34	Antibody-TF	antibody-tf	NN	_	_	_
35	complex	complex	NN	_	_	_
36	.	.	.	_	_	_

1	50	50	CD	_	_	_
2	ul	ul	NN	_	_	_
3	of	of	IN	_	_	_
4	Dynabeads	Dynabeads	NNP	_	_	_
5	Pan	Pan	NNP	_	_	_
6	mouse	mouse	NN	_	_	_
7	IgG	igg	NN	_	_	_
8	were	be	VBD	_	_	_
9	washed	wash	VBN	_	_	_
10	3	3	CD	_	_	_
11	times	time	NNS	_	_	_
12	with	with	IN	_	_	_
13	bead	bead	NN	_	_	_
14	washing	wash	VBG	_	_	_
15	solution	solution	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	250	250	CD	_	_	_
18	mg	mg	NN	_	_	_
19	BSA	bsa	NN	_	_	_
20	in	in	IN	_	_	_
21	50	50	CD	_	_	_
22	ml	ml	NN	_	_	_
23	of	of	IN	_	_	_
24	PBS	PBS	NNP	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	,	,	,	_	_	_
27	and	and	CC	_	_	_
28	were	be	VBD	_	_	_
29	added	add	VBN	_	_	_
30	to	to	TO	_	_	_
31	the	the	DT	_	_	_
32	sample	sample	NN	_	_	_
33	.	.	.	_	_	_

1	Cell	cell	NN	_	_	_
2	lysate	lysate	NN	_	_	_
3	with	with	IN	_	_	_
4	beads	bead	NNS	_	_	_
5	were	be	VBD	_	_	_
6	incubated	incubate	VBN	_	_	_
7	for	for	IN	_	_	_
8	6	6	CD	_	_	_
9	hours	hour	NNS	_	_	_
10	or	or	CC	_	_	_
11	overnight	overnight	JJ	_	_	_
12	at	at	IN	_	_	_
13	4oC	4oc	NN	_	_	_
14	to	to	TO	_	_	_
15	make	make	VB	_	_	_
16	Dynabead-antibody-TF	dynabead-antibody-tf	NN	_	_	_
17	complex	complex	NN	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	beads	bead	NNS	_	_	_
3	were	be	VBD	_	_	_
4	pulled	pull	VBN	_	_	_
5	down	down	RP	_	_	_
6	on	on	IN	_	_	_
7	a	a	DT	_	_	_
8	magnet	magnet	NN	_	_	_
9	stand	stand	NN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	washed	wash	VBN	_	_	_
13	2	2	CD	_	_	_
14	times	time	NNS	_	_	_
15	with	with	IN	_	_	_
16	wash	wash	NN	_	_	_
17	buffer	buffer	NN	_	_	_
18	I	i	NN	_	_	_
19	and	and	CC	_	_	_
20	with	with	IN	_	_	_
21	wash	wash	NN	_	_	_
22	buffer	buffer	NN	_	_	_
23	II	ii	CD	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	50	50	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	Tris-HCl	tris-hcl	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	pH	ph	NN	_	_	_
30	7.5	7.5	CD	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	,	,	,	_	_	_
33	500	500	CD	_	_	_
34	mM	mm	NN	KWSUPP	_	_
35	NaCl	nacl	NN	_	_	_
36	,	,	,	_	_	_
37	1	1	CD	_	_	_
38	%	%	NN	_	_	_
39	Triton	Triton	NNP	_	_	_
40	X-100	x-100	NN	_	_	_
41	and	and	CC	_	_	_
42	1mM	1mm	NN	_	_	_
43	EDTA	edta	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	,	,	,	_	_	_
46	wash	wash	NN	_	_	_
47	buffer	buffer	NN	_	_	_
48	III	iii	CD	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	10	10	CD	_	_	_
51	mM	mm	NN	KWSUPP	_	_
52	Tris-HCl	tris-hcl	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	pH	ph	NN	_	_	_
55	8.0	8.0	CD	_	_	_
56	-RRB-	-rrb-	-RRB-	_	_	_
57	,	,	,	_	_	_
58	250	250	CD	_	_	_
59	mM	mm	NN	KWSUPP	_	_
60	LiCl	licl	NN	_	_	_
61	,	,	,	_	_	_
62	1	1	CD	_	_	_
63	%	%	NN	_	_	_
64	Triton	Triton	NNP	_	_	_
65	X-100	x-100	NN	_	_	_
66	and	and	CC	_	_	_
67	1mM	1mm	NN	_	_	_
68	EDTA	edta	NN	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	,	,	,	_	_	_
71	and	and	CC	_	_	_
72	wash	wash	NN	_	_	_
73	buffer	buffer	NN	_	_	_
74	IV	iv	CD	_	_	_
75	-LRB-	-lrb-	-LRB-	_	_	_
76	10	10	CD	_	_	_
77	mM	mm	NN	KWSUPP	_	_
78	Tris-HCl	tris-hcl	NN	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	pH	ph	NN	_	_	_
81	8.0	8.0	CD	_	_	_
82	-RRB-	-rrb-	-RRB-	_	_	_
83	,	,	,	_	_	_
84	1mM	1mm	NN	_	_	_
85	EDTA	edta	NN	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	bead-bound	bead-bound	JJ	_	_	_
3	TF-DNA	tf-dna	NN	_	_	_
4	complex	complex	NN	_	_	_
5	was	be	VBD	_	_	_
6	then	then	RB	_	_	_
7	end-repaired	end-repaired	JJ	_	_	_
8	,	,	,	_	_	_
9	dA-tailed	da-tailed	JJ	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	ligated	ligate	VBN	_	_	_
13	to	to	TO	_	_	_
14	the	the	DT	_	_	_
15	first	first	JJ	_	_	_
16	adapter	adapter	NN	_	_	_
17	.	.	.	_	_	_

1	Adapter-ligated	adapter-ligated	JJ	_	_	_
2	sample	sample	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	treated	treat	VBN	_	_	_
6	with	with	IN	_	_	_
7	nick-repair	nick-repair	JJ	_	_	_
8	reagent	reagent	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	was	be	VBD	_	_	_
12	treated	treat	VBN	_	_	_
13	with	with	IN	_	_	_
14	lambda	lambda	NN	_	_	_
15	exonuclease	exonuclease	NN	_	_	_
16	and	and	CC	_	_	_
17	RecJ	recj	NN	_	_	_
18	exonuclease	exonuclease	NN	_	_	_
19	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	eluted	elute	VBN	_	_	_
5	away	away	RB	_	_	_
6	from	from	IN	_	_	_
7	Dynabeads	Dynabeads	NNPS	_	_	_
8	by	by	IN	_	_	_
9	incubating	incubate	VBG	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	ul	ul	NN	_	_	_
13	of	of	IN	_	_	_
14	elution	elution	NN	_	_	_
15	buffer	buffer	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	50	50	CD	_	_	_
18	mM	mm	NN	KWSUPP	_	_
19	Tris-HCl	tris-hcl	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	pH	ph	NN	_	_	_
22	8.0	8.0	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	,	,	,	_	_	_
25	1	1	CD	_	_	_
26	%	%	NN	_	_	_
27	SDS	sds	NN	_	_	_
28	and	and	CC	_	_	_
29	1	1	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	EDTA	edta	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	at	at	IN	_	_	_
34	65oC	65oc	NN	_	_	_
35	overnight	overnight	JJ	_	_	_
36	.	.	.	_	_	_

1	Protein	protein	NN	_	_	_
2	was	be	VBD	_	_	_
3	removed	remove	VBN	_	_	_
4	by	by	IN	_	_	_
5	treating	treat	VBG	_	_	_
6	4	4	CD	_	_	_
7	ul	ul	NN	_	_	_
8	of	of	IN	_	_	_
9	protease	protease	NN	_	_	_
10	K	k	NN	_	_	_
11	and	and	CC	_	_	_
12	being	be	VBG	_	_	_
13	incubated	incubate	VBN	_	_	_
14	at	at	IN	_	_	_
15	55	55	CD	_	_	_
16	oC	oc	NN	_	_	_
17	for	for	IN	_	_	_
18	2	2	CD	_	_	_
19	hours	hour	NNS	_	_	_
20	,	,	,	_	_	_
21	and	and	CC	_	_	_
22	by	by	IN	_	_	_
23	Phenol-Chloroform-IAA	phenol-chloroform-iaa	NN	_	_	_
24	extraction	extraction	NN	_	_	_
25	.	.	.	_	_	_

1	Purified	purify	VBN	_	_	_
2	DNA	dna	NN	_	_	_
3	was	be	VBD	_	_	_
4	used	use	VBN	_	_	_
5	to	to	TO	_	_	_
6	bulid	bulid	VB	_	_	_
7	the	the	DT	_	_	_
8	second	second	JJ	_	_	_
9	strand	strand	NN	_	_	_
10	synthesis	synthesis	NN	_	_	_
11	,	,	,	_	_	_
12	followed	follow	VBN	_	_	_
13	by	by	IN	_	_	_
14	another	another	DT	_	_	_
15	dA-tailing	da-tailing	NN	_	_	_
16	,	,	,	_	_	_
17	second	second	JJ	_	_	_
18	strand	strand	NN	_	_	_
19	ligation	ligation	NN	_	_	_
20	,	,	,	_	_	_
21	and	and	CC	_	_	_
22	3	3	CD	_	_	_
23	'	'	''	_	_	_
24	overhang	overhang	NN	_	_	_
25	removal	removal	NN	_	_	_
26	stpes	stpe	NNS	_	_	_
27	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	the	the	DT	_	_	_
3	sequencing	sequencing	NN	_	_	_
4	library	library	NN	_	_	_
5	was	be	VBD	_	_	_
6	amplified	amplify	VBN	_	_	_
7	with	with	IN	_	_	_
8	PCR	pcr	NN	_	_	_
9	enrichment	enrichment	NN	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	cells	cell	NNS	_	_	_
5	were	be	VBD	_	_	_
6	crosslinked	crosslink	VBN	_	_	_
7	in	in	IN	_	_	_
8	1	1	CD	_	_	_
9	%	%	NN	_	_	_
10	formaldehyde	formaldehyde	NN	_	_	_
11	for	for	IN	_	_	_
12	25	25	CD	_	_	_
13	minutes	minute	NNS	_	_	_
14	at	at	IN	_	_	_
15	RT	rt	NN	_	_	_
16	on	on	IN	_	_	_
17	a	a	DT	_	_	_
18	rocker	rocker	NN	_	_	_
19	,	,	,	_	_	_
20	then	then	RB	_	_	_
21	washed	wash	VBN	_	_	_
22	3	3	CD	_	_	_
23	times	time	NNS	_	_	_
24	with	with	IN	_	_	_
25	50	50	CD	_	_	_
26	ml	ml	NN	_	_	_
27	of	of	IN	_	_	_
28	ice-cold	ice-cold	JJ	_	_	_
29	TBS	tbs	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Tris	tris	NN	_	_	_
32	buffered	buffer	VBN	_	_	_
33	saline	saline	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	each	each	DT	_	_	_
36	time	time	NN	_	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	For	for	IN	_	_	_
4	each	each	DT	_	_	_
5	peak	peak	NN	_	_	_
6	detected	detect	VBN	_	_	_
7	with	with	IN	_	_	_
8	MACE	MACE	NNP	_	_	_
9	,	,	,	_	_	_
10	binding	bind	VBG	_	_	_
11	intensity	intensity	NN	_	_	_
12	was	be	VBD	_	_	_
13	calculated	calculate	VBN	_	_	_
14	by	by	IN	_	_	_
15	averaging	average	VBG	_	_	_
16	read	read	VBN	_	_	_
17	counts	count	NNS	_	_	_
18	from	from	IN	_	_	_
19	two	two	CD	_	_	_
20	biological	biological	JJ	_	_	_
21	replicates	replicate	VBZ	_	_	_
22	and	and	CC	_	_	_
23	dividing	divide	VBG	_	_	_
24	by	by	IN	_	_	_
25	background	background	NN	_	_	_
26	intensity	intensity	NN	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	ASM584v2	asm584v2	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	genotype	genotype	NN	_	_	_
9	:	:	:	_	_	_
10	ompR-8myc	ompr-8myc	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	MACE	mace	VBP	_	_	_
13	software	software	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	https	http	NNS	_	_	_
16	:	:	:	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
18	OmpR	ompr	NN	TF	_	_
19	NaCl	nacl	NN	_	_	_
20	1	1	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	OmpR	ompr	NN	TF	_	_
23	NaCl	nacl	NN	_	_	_
24	2	2	CD	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	Read	Read	NNP	_	_	_
27	count	count	NN	_	_	_
28	was	be	VBD	_	_	_
29	calculated	calculate	VBN	_	_	_
30	for	for	IN	_	_	_
31	each	each	DT	_	_	_
32	genomic	genomic	JJ	_	_	_
33	position	position	NN	_	_	_
34	from	from	IN	_	_	_
35	sequence	sequence	NN	_	_	_
36	alignment	alignment	NN	_	_	_
37	,	,	,	_	_	_
38	and	and	CC	_	_	_
39	95	95	CD	_	_	_
40	%	%	NN	_	_	_
41	strongest	strongest	JJS	_	_	_
42	intensity	intensity	NN	_	_	_
43	was	be	VBD	_	_	_
44	used	use	VBN	_	_	_
45	as	as	IN	_	_	_
46	background	background	NN	_	_	_
47	intensity	intensity	NN	_	_	_
48	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	K-12	k-12	NN	_	_	_
5	MG1655	mg1655	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	Supplementary	supplementary	JJ	_	_	_
8	_	_	NN	_	_	_
9	files	file	NNS	_	_	_
10	_	_	IN	_	_	_
11	format	format	NN	_	_	_
12	_	_	NN	_	_	_
13	and	and	CC	_	_	_
14	_	_	NN	_	_	_
15	content	content	NN	_	_	_
16	:	:	:	_	_	_
17	Tab-delimited	tab-delimited	JJ	_	_	_
18	text	text	NN	_	_	_
19	files	file	NNS	_	_	_
20	in	in	IN	_	_	_
21	gff	gff	NN	_	_	_
22	format	format	NN	_	_	_
23	which	which	WDT	_	_	_
24	has	have	VBZ	_	_	_
25	8	8	CD	_	_	_
26	columns	column	NNS	_	_	_
27	:	:	:	_	_	_
28	sequence	sequence	NN	_	_	_
29	id	id	NN	_	_	_
30	,	,	,	_	_	_
31	source	source	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	empty	empty	JJ	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	,	,	,	_	_	_
36	feature	feature	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	+	+	CC	_	_	_
39	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
40	E.	E.	NNP	_	_	_
41	coli	coli	NN	_	_	_
42	K-12	k-12	NN	_	_	_
43	MG1655	mg1655	NN	_	_	_
44	WT	wt	NN	_	_	_
45	and	and	CC	_	_	_
46	ΔompR	δompr	NN	_	_	_
47	were	be	VBD	_	_	_
48	grown	grow	VBN	_	_	_
49	to	to	TO	_	_	_
50	mid-log	mid-log	JJ	_	_	_
51	phase	phase	NN	_	_	_
52	aerobically	aerobically	RB	_	_	_
53	at	at	IN	_	_	_
54	37	37	CD	_	_	_
55	°C	°c	NN	_	_	_
56	in	in	IN	_	_	_
57	M9	m9	NN	MED	_	_
58	minimal	minimal	JJ	MED	_	_
59	media	media	NNS	MED	_	_
60	supplemented	supplement	VBN	_	_	_
61	with	with	IN	_	_	_
62	0.2	0.2	CD	_	_	_
63	%	%	NN	_	_	_
64	glucose	glucose	NN	SUPP	_	_
65	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	treated	treat	VBN	_	_	_
5	with	with	IN	_	_	_
6	0.3	0.3	CD	_	_	_
7	M	m	NN	_	_	_
8	of	of	IN	_	_	_
9	NaCl	nacl	NN	_	_	_
10	at	at	IN	_	_	_
11	mid-log	mid-log	JJ	_	_	_
12	pahse	pahse	NN	_	_	_
13	for	for	IN	_	_	_
14	30	30	CD	_	_	_
15	min	min	NN	_	_	_
16	with	with	IN	_	_	_
17	agitation	agitation	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Fragments	fragment	NNS	_	_	_
4	Per	per	IN	_	_	_
5	Kilobase	kilobase	NN	_	_	_
6	of	of	IN	_	_	_
7	exon	exon	NN	_	_	_
8	per	per	IN	_	_	_
9	Megabase	megabase	NN	_	_	_
10	of	of	IN	_	_	_
11	library	library	NN	_	_	_
12	size	size	NN	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	FPKM	fpkm	NN	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	were	be	VBD	_	_	_
17	calculated	calculate	VBN	_	_	_
18	using	use	VBG	_	_	_
19	cufflinks	cufflink	NNS	_	_	_
20	v.	v.	CC	_	_	_
21	1.3.0	1.3.0	CD	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	Genome	Genome	NNP	_	_	_
24	_	_	NNP	_	_	_
25	build	build	VB	_	_	_
26	:	:	:	_	_	_
27	NC	NC	NNP	_	_	_
28	_	_	NNP	_	_	_
29	000913	000913	CD	_	_	_
30	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
31	genotype	genotype	NN	_	_	_
32	:	:	:	_	_	_
33	ompR	ompr	NN	GEN	_	_
34	deletion	deletion	NN	_	_	_
35	mutant	mutant	JJ	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	genotype	genotype	NN	_	_	_
38	:	:	:	_	_	_
39	WT	wt	JJ	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	RNA	rna	NN	_	_	_
42	libraries	library	NNS	_	_	_
43	were	be	VBD	_	_	_
44	prepared	prepare	VBN	_	_	_
45	for	for	IN	_	_	_
46	sequencing	sequencing	NN	_	_	_
47	using	use	VBG	_	_	_
48	standard	standard	JJ	_	_	_
49	Illumina	Illumina	NNP	_	_	_
50	protocols	protocol	NNS	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
52	RNA-Seq	rna-seq	JJ	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Sequenced	sequence	VBN	_	_	_
55	reads	read	VBZ	_	_	_
56	were	be	VBD	_	_	_
57	mapped	map	VBN	_	_	_
58	onto	onto	IN	_	_	_
59	NC	nc	NN	_	_	_
60	_	_	CD	_	_	_
61	000913	000913	CD	_	_	_
62	reference	reference	NN	_	_	_
63	genome	genome	NN	_	_	_
64	sequence	sequence	NN	_	_	_
65	using	use	VBG	_	_	_
66	bowtie	bowtie	NN	_	_	_
67	v1	v1	NN	_	_	_
68	.0.0	.0.0	CD	_	_	_
69	with	with	IN	_	_	_
70	parameters	parameter	NNS	_	_	_
71	-	-	:	_	_	_
72	X	x	NN	_	_	_
73	1000	1000	CD	_	_	_
74	-	-	:	_	_	_
75	n	n	NN	_	_	_
76	2	2	CD	_	_	_
77	-3	-3	CD	_	_	_
78	3	3	LS	_	_	_
79	-	-	:	_	_	_
80	S	s	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	strain	strain	NN	_	_	_
83	:	:	:	_	_	_
84	K-12	k-12	NN	_	_	_
85	MG1655	mg1655	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	Supplementary	supplementary	JJ	_	_	_
88	_	_	NN	_	_	_
89	files	file	NNS	_	_	_
90	_	_	IN	_	_	_
91	format	format	NN	_	_	_
92	_	_	NN	_	_	_
93	and	and	CC	_	_	_
94	_	_	NN	_	_	_
95	content	content	NN	_	_	_
96	:	:	:	_	_	_
97	comma-delimited	comma-delimited	JJ	_	_	_
98	text	text	NN	_	_	_
99	files	file	NNS	_	_	_
100	include	include	VBP	_	_	_
101	FPKM	fpkm	NN	_	_	_
102	values	value	NNS	_	_	_
103	for	for	IN	_	_	_
104	each	each	DT	_	_	_
105	Sample	Sample	NNP	_	_	_
106	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cell	cell	NN	_	_	_
4	culture	culture	NN	_	_	_
5	was	be	VBD	_	_	_
6	treated	treat	VBN	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	RNAprotect	rnaprotect	NN	_	_	_
10	reagent	reagent	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	qiagen	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	isolated	isolate	VBN	_	_	_
5	from	from	IN	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Total	total	JJ	_	_	_
10	RNA	rna	NN	_	_	_
11	was	be	VBD	_	_	_
12	extracted	extract	VBN	_	_	_
13	using	use	VBG	_	_	_
14	the	the	DT	_	_	_
15	RNeasy	RNeasy	NNP	_	_	_
16	Plus	Plus	NNP	_	_	_
17	Mini	Mini	NNP	_	_	_
18	kit	kit	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	Qiagen	Qiagen	NNP	_	_	_
21	Inc.	Inc.	NNP	_	_	_
22	,	,	,	_	_	_
23	Valencia	Valencia	NNP	_	_	_
24	,	,	,	_	_	_
25	CA	CA	NNP	_	_	_
26	,	,	,	_	_	_
27	USA	USA	NNP	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	and	and	CC	_	_	_
30	genomic	genomic	JJ	_	_	_
31	DNA	dna	NN	_	_	_
32	was	be	VBD	_	_	_
33	removed	remove	VBN	_	_	_
34	by	by	IN	_	_	_
35	gDNA	gdna	NN	_	_	_
36	Eliminator	eliminator	NN	_	_	_
37	spin	spin	NN	_	_	_
38	column	column	NN	_	_	_
39	in	in	IN	_	_	_
40	the	the	DT	_	_	_
41	RNeasy	RNeasy	NNP	_	_	_
42	Plus	Plus	NNP	_	_	_
43	Mini	Mini	NNP	_	_	_
44	Kit	kit	NN	_	_	_
45	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	quality	quality	NN	_	_	_
3	and	and	CC	_	_	_
4	concentration	concentration	NN	_	_	_
5	was	be	VBD	_	_	_
6	determined	determine	VBN	_	_	_
7	by	by	IN	_	_	_
8	analysis	analysis	NN	_	_	_
9	with	with	IN	_	_	_
10	a	a	DT	_	_	_
11	NanoDrop	NanoDrop	NNP	_	_	_
12	1000	1000	CD	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Thermo	Thermo	NNP	_	_	_
15	Scientific	Scientific	NNP	_	_	_
16	Inc.	Inc.	NNP	_	_	_
17	,	,	,	_	_	_
18	Wilmington	Wilmington	NNP	_	_	_
19	,	,	,	_	_	_
20	DE	de	NN	_	_	_
21	,	,	,	_	_	_
22	USA	USA	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	WT	WT	NNP	_	_	_
3	NaCl	nacl	NN	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	WT	wt	JJ	_	_	_
7	NaCl	nacl	NN	_	_	_
8	2	2	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	ΔompR	δompr	NN	_	_	_
11	NaCl	nacl	NN	_	_	_
12	1	1	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	ΔompR	δompr	NN	_	_	_
15	NaCl	nacl	NN	_	_	_
16	2	2	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	0	0	CD	_	_	_
19	min	min	NN	_	_	_
20	minus	minus	CC	_	_	_
21	ciprofloxacin	ciprofloxacin	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	0	0	CD	_	_	_
24	min	min	NN	_	_	_
25	plus	plus	CC	_	_	_
26	ciprofloxacin	ciprofloxacin	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	30	30	CD	_	_	_
29	min	min	NN	_	_	_
30	minus	minus	CC	_	_	_
31	ciprofloxacin	ciprofloxacin	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	30	30	CD	_	_	_
34	min	min	NN	_	_	_
35	plus	plus	CC	_	_	_
36	ciprofloxacin	ciprofloxacin	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	90	90	CD	_	_	_
39	min	min	NN	_	_	_
40	minus	minus	CC	_	_	_
41	ciprofloxacin	ciprofloxacin	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	90	90	CD	_	_	_
44	min	min	NN	_	_	_
45	plus	plus	CC	_	_	_
46	ciprofloxacin	ciprofloxacin	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	All	all	DT	_	_	_
49	data	datum	NNS	_	_	_
50	was	be	VBD	_	_	_
51	processed	process	VBN	_	_	_
52	using	use	VBG	_	_	_
53	Rockhopper	Rockhopper	NNP	_	_	_
54	Ver	Ver	NNP	_	_	_
55	.2.03	.2.03	CD	_	_	_
56	.	.	.	_	_	_

1	Rockhopper	Rockhopper	NNP	_	_	_
2	is	be	VBZ	_	_	_
3	an	a	DT	_	_	_
4	utomatic	utomatic	JJ	_	_	_
5	\	\	NN	_	_	_
6	bacterial	bacterial	JJ	_	_	_
7	RNA-seq	rna-seq	NN	_	_	_
8	analysis	analysis	NN	_	_	_
9	tool	tool	NN	_	_	_
10	;	;	:	_	_	_
11	for	for	IN	_	_	_
12	additional	additional	JJ	_	_	_
13	information	information	NN	_	_	_
14	see	see	VB	_	_	_
15	:	:	:	_	_	_
16	McClure	McClure	NNP	_	_	_
17	,	,	,	_	_	_
18	R.	R.	NNP	_	_	_
19	,	,	,	_	_	_
20	et	et	FW	_	_	_
21	al.	al.	FW	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	2013	2013	CD	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	.	.	.	_	_	_

1	\	\	SYM	_	_	_
2	Computational	computational	JJ	_	_	_
3	analysis	analysis	NN	_	_	_
4	of	of	IN	_	_	_
5	bacterial	bacterial	JJ	_	_	_
6	RNA-Seq	rna-seq	NN	_	_	_
7	data	datum	NNS	_	_	_
8	.	.	.	_	_	_

1	\	\	SYM	_	_	_
2	Nucleic	Nucleic	NNP	_	_	_
3	Acids	Acids	NNP	_	_	_
4	Res	Res	NNP	_	_	_
5	41	41	CD	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	14	14	CD	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	:	:	:	_	_	_
10	e140	e140	NN	_	_	_
11	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	default	default	NN	_	_	_
3	general	general	JJ	_	_	_
4	parameters	parameter	NNS	_	_	_
5	were	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	erbose	erbose	JJ	_	_	_
10	output	output	NN	_	_	_
11	\	\	CD	_	_	_
12	tab	tab	NN	_	_	_
13	ticked	tick	VBN	_	_	_
14	and	and	CC	_	_	_
15	the	the	DT	_	_	_
16	\	\	JJ	_	_	_
17	orientation	orientation	NN	_	_	_
18	of	of	IN	_	_	_
19	mate-pair	mate-pair	JJ	_	_	_
20	reads	read	VBZ	_	_	_
21	\	\	RB	_	_	_
22	changed	change	VBN	_	_	_
23	to	to	TO	_	_	_
24	f	f	FW	_	_	_
25	\	\	FW	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Clinical	clinical	JJ	_	_	_
3	isolate	isolate	NN	_	_	_
4	,	,	,	_	_	_
5	minus	minus	CC	_	_	_
6	ciprofloxacin	ciprofloxacin	NN	_	_	_
7	,	,	,	_	_	_
8	0	0	CD	_	_	_
9	min	min	NN	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	Clinical	clinical	JJ	_	_	_
12	isolate	isolate	NN	_	_	_
13	,	,	,	_	_	_
14	minus	minus	CC	_	_	_
15	ciprofloxacin	ciprofloxacin	NN	_	_	_
16	,	,	,	_	_	_
17	30	30	CD	_	_	_
18	min	min	NN	_	_	_
19	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
20	Clinical	clinical	JJ	_	_	_
21	isolate	isolate	NN	_	_	_
22	,	,	,	_	_	_
23	minus	minus	CC	_	_	_
24	ciprofloxacin	ciprofloxacin	NN	_	_	_
25	,	,	,	_	_	_
26	90	90	CD	_	_	_
27	min	min	NN	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	Clinical	clinical	JJ	_	_	_
30	isolate	isolate	NN	_	_	_
31	,	,	,	_	_	_
32	plus	plus	CC	_	_	_
33	ciprofloxacin	ciprofloxacin	NN	_	_	_
34	,	,	,	_	_	_
35	0	0	CD	_	_	_
36	min	min	NN	_	_	_
37	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
38	Clinical	clinical	JJ	_	_	_
39	isolate	isolate	NN	_	_	_
40	,	,	,	_	_	_
41	plus	plus	CC	_	_	_
42	ciprofloxacin	ciprofloxacin	NN	_	_	_
43	,	,	,	_	_	_
44	30	30	CD	_	_	_
45	min	min	NN	_	_	_
46	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
47	Clinical	clinical	JJ	_	_	_
48	isolate	isolate	NN	_	_	_
49	,	,	,	_	_	_
50	plus	plus	CC	_	_	_
51	ciprofloxacin	ciprofloxacin	NN	_	_	_
52	,	,	,	_	_	_
53	90	90	CD	_	_	_
54	min	min	NN	_	_	_
55	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
56	E.	E.	NNP	_	_	_
57	coli	coli	NN	_	_	_
58	ST131	st131	NN	_	_	_
59	UR40	ur40	NN	_	_	_
60	was	be	VBD	_	_	_
61	treated	treat	VBN	_	_	_
62	with	with	IN	_	_	_
63	ciprofloxacin	ciprofloxacin	NN	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	2µg	2µg	JJ	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	Escherichia	escherichia	FW	Organism	_	_
68	coli	coli	FW	Organism	_	_
69	O25b	o25b	NN	_	_	_
70	:	:	:	_	_	_
71	H4-ST131	h4-st131	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	Extraction	extraction	NN	_	_	_
74	followed	follow	VBN	_	_	_
75	by	by	IN	_	_	_
76	DNase	dnase	NN	_	_	_
77	treatment	treatment	NN	_	_	_
78	with	with	IN	_	_	_
79	TURBO	TURBO	NNP	_	_	_
80	DNA-free	dna-free	JJ	_	_	_
81	kit	kit	NN	_	_	_
82	from	from	IN	_	_	_
83	Ambion	Ambion	NNP	_	_	_
84	.	.	.	_	_	_

1	rRNA	rrna	NN	_	_	_
2	depleted	deplete	VBN	_	_	_
3	using	use	VBG	_	_	_
4	an	a	DT	_	_	_
5	Illumina	Illumina	NNP	_	_	_
6	Ribo-zero	ribo-zero	NN	_	_	_
7	rRNA	rrna	NN	_	_	_
8	removal	removal	NN	_	_	_
9	kit	kit	NN	_	_	_
10	.	.	.	_	_	_

1	Followed	follow	VBN	_	_	_
2	by	by	IN	_	_	_
3	RNA-seq	rna-seq	JJ	_	_	_
4	library	library	NN	_	_	_
5	prep	prep	NN	_	_	_
6	using	use	VBG	_	_	_
7	an	a	DT	_	_	_
8	Illumina	Illumina	NNP	_	_	_
9	TruSeq	TruSeq	NNP	_	_	_
10	Stranded	Stranded	NNP	_	_	_
11	mRNA	mrna	NN	_	_	_
12	Library	Library	NNP	_	_	_
13	Prep	Prep	NNP	_	_	_
14	Kit	kit	NN	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	NC	NC	NNP	_	_	_
7	_	_	NNP	_	_	_
8	017644.1	017644.1	CD	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Escherichia	escherichia	FW	Organism	_	_
11	coli	coli	FW	Organism	_	_
12	NA114	na114	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	isolate	isolate	NN	_	_	_
16	:	:	:	_	_	_
17	UR40	ur40	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	RNA-Seq	rna-seq	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Supplementary	supplementary	JJ	_	_	_
22	_	_	NN	_	_	_
23	files	file	NNS	_	_	_
24	_	_	IN	_	_	_
25	format	format	NN	_	_	_
26	_	_	NN	_	_	_
27	and	and	CC	_	_	_
28	_	_	NN	_	_	_
29	content	content	NN	_	_	_
30	:	:	:	_	_	_
31	*	*	SYM	_	_	_
32	txt	txt	NN	_	_	_
33	,	,	,	_	_	_
34	*	*	SYM	_	_	_
35	xml	xml	NN	_	_	_
36	:	:	:	_	_	_
37	These	these	DT	_	_	_
38	files	file	NNS	_	_	_
39	contain	contain	VBP	_	_	_
40	the	the	DT	_	_	_
41	raw	raw	JJ	_	_	_
42	counts	count	NNS	_	_	_
43	,	,	,	_	_	_
44	normalized	normalize	VBD	_	_	_
45	counts	count	NNS	_	_	_
46	,	,	,	_	_	_
47	RPKM	rpkm	NN	_	_	_
48	values	value	NNS	_	_	_
49	,	,	,	_	_	_
50	expression	expression	NN	_	_	_
51	values	value	NNS	_	_	_
52	,	,	,	_	_	_
53	P-values	p-value	NNS	_	_	_
54	and	and	CC	_	_	_
55	Q-values	q-value	NNS	_	_	_
56	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	file	file	NN	_	_	_
3	contains	contain	VBZ	_	_	_
4	the	the	DT	_	_	_
5	values	value	NNS	_	_	_
6	for	for	IN	_	_	_
7	both	both	DT	_	_	_
8	samples	sample	NNS	_	_	_
9	at	at	IN	_	_	_
10	the	the	DT	_	_	_
11	indicated	indicate	VBN	_	_	_
12	timepoint	timepoint	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	cultures	culture	NNS	_	_	_
4	were	be	VBD	_	_	_
5	balanced	balanced	JJ	_	_	_
6	and	and	CC	_	_	_
7	grown	grow	VBN	_	_	_
8	in	in	IN	_	_	_
9	CAMHB	CAMHB	NNP	_	_	_
10	media	media	NNS	_	_	_
11	at	at	IN	_	_	_
12	37	37	CD	_	_	_
13	degrees	degree	NNS	_	_	_
14	Celsius	Celsius	NNP	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	time	time	NN	_	_	_
3	point	point	NN	_	_	_
4	:	:	:	_	_	_
5	0	0	CD	_	_	_
6	min	min	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	time	time	NN	_	_	_
9	point	point	NN	_	_	_
10	:	:	:	_	_	_
11	30	30	CD	_	_	_
12	min	min	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	time	time	NN	_	_	_
15	point	point	NN	_	_	_
16	:	:	:	_	_	_
17	90	90	CD	_	_	_
18	min	min	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	Total	total	JJ	_	_	_
21	RNA	rna	NN	_	_	_
22	was	be	VBD	_	_	_
23	extracted	extract	VBN	_	_	_
24	using	use	VBG	_	_	_
25	a	a	DT	_	_	_
26	Thermo	Thermo	NNP	_	_	_
27	Scientific	Scientific	NNP	_	_	_
28	GeneJET	GeneJET	NNP	_	_	_
29	RNA	rna	NN	_	_	_
30	isolation	isolation	NN	_	_	_
31	kit	kit	NN	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	ciprofloxacin	ciprofloxacin	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	treatment	treatment	NN	_	_	_
7	:	:	:	_	_	_
8	none	none	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	Ancestral	ancestral	JJ	_	_	_
11	E.	e.	FW	_	_	_
12	coli	coli	FW	_	_	_
13	B	b	NN	_	_	_
14	REL606	rel606	NN	_	_	_
15	strain	strain	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	A	a	NN	_	_	_
18	pool	pool	NN	_	_	_
19	of	of	IN	_	_	_
20	3	3	CD	_	_	_
21	E.	e.	FW	_	_	_
22	coli	coli	FW	_	_	_
23	clones	clone	NNS	_	_	_
24	forming	form	VBG	_	_	_
25	large	large	JJ	_	_	_
26	colonies	colony	NNS	_	_	_
27	when	when	WRB	_	_	_
28	plated	plate	VBN	_	_	_
29	on	on	IN	_	_	_
30	TTagar	ttagar	NN	_	_	_
31	and	and	CC	_	_	_
32	derived	derive	VBN	_	_	_
33	from	from	IN	_	_	_
34	E.	e.	FW	_	_	_
35	coli	coli	FW	_	_	_
36	B	b	NN	_	_	_
37	REL606	rel606	NN	_	_	_
38	after	after	IN	_	_	_
39	150	150	CD	_	_	_
40	days	day	NNS	_	_	_
41	of	of	IN	_	_	_
42	seasonal	seasonal	JJ	_	_	_
43	evolution	evolution	NN	_	_	_
44	experiment	experiment	NN	_	_	_
45	in	in	IN	_	_	_
46	18	18	CD	_	_	_
47	mm	mm	NN	_	_	_
48	test	test	NN	_	_	_
49	tubes	tube	NNS	_	_	_
50	in	in	IN	_	_	_
51	DMga	dmga	JJ	_	_	_
52	medium	medium	NN	_	_	_
53	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	A	a	NN	_	_	_
3	pool	pool	NN	_	_	_
4	of	of	IN	_	_	_
5	3	3	CD	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	clones	clone	NNS	_	_	_
9	forming	form	VBG	_	_	_
10	small	small	JJ	_	_	_
11	colonies	colony	NNS	_	_	_
12	when	when	WRB	_	_	_
13	plated	plate	VBN	_	_	_
14	on	on	IN	_	_	_
15	TTagar	ttagar	NN	_	_	_
16	and	and	CC	_	_	_
17	derived	derive	VBN	_	_	_
18	from	from	IN	_	_	_
19	E.	e.	FW	_	_	_
20	coli	coli	FW	_	_	_
21	B	b	NN	_	_	_
22	REL606	rel606	NN	_	_	_
23	after	after	IN	_	_	_
24	150	150	CD	_	_	_
25	days	day	NNS	_	_	_
26	of	of	IN	_	_	_
27	seasonal	seasonal	JJ	_	_	_
28	evolution	evolution	NN	_	_	_
29	experiment	experiment	NN	_	_	_
30	in	in	IN	_	_	_
31	18	18	CD	_	_	_
32	mm	mm	NN	_	_	_
33	test	test	NN	_	_	_
34	tubes	tube	NNS	_	_	_
35	in	in	IN	_	_	_
36	DMga	dmga	JJ	_	_	_
37	medium	medium	NN	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	A	a	NN	_	_	_
3	pool	pool	NN	_	_	_
4	of	of	IN	_	_	_
5	3	3	CD	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	clones	clone	NNS	_	_	_
9	forming	form	VBG	_	_	_
10	small	small	JJ	_	_	_
11	colonies	colony	NNS	_	_	_
12	when	when	WRB	_	_	_
13	plated	plate	VBN	_	_	_
14	on	on	IN	_	_	_
15	TTagar	ttagar	NN	_	_	_
16	and	and	CC	_	_	_
17	derived	derive	VBN	_	_	_
18	from	from	IN	_	_	_
19	E.	e.	FW	_	_	_
20	coli	coli	FW	_	_	_
21	B	b	NN	_	_	_
22	REL606	rel606	NN	_	_	_
23	after	after	IN	_	_	_
24	150	150	CD	_	_	_
25	days	day	NNS	_	_	_
26	of	of	IN	_	_	_
27	seasonal	seasonal	JJ	_	_	_
28	evolution	evolution	NN	_	_	_
29	experiment	experiment	NN	_	_	_
30	in	in	IN	_	_	_
31	18	18	CD	_	_	_
32	mm	mm	NN	_	_	_
33	test	test	NN	_	_	_
34	tubes	tube	NNS	_	_	_
35	in	in	IN	_	_	_
36	DMga	dmga	JJ	_	_	_
37	medium	medium	NN	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	A	a	NN	_	_	_
3	,	,	,	_	_	_
4	TP1	tp1	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	A	a	NN	_	_	_
7	,	,	,	_	_	_
8	TP2	tp2	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	A	a	NN	_	_	_
11	,	,	,	_	_	_
12	TP3	tp3	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	A	a	NN	_	_	_
15	,	,	,	_	_	_
16	TP4	tp4	NN	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	Escherichia	escherichia	FW	Organism	_	_
19	coli	coli	FW	Organism	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Frozen	frozen	JJ	_	_	_
22	bacteria	bacterium	NNS	_	_	_
23	were	be	VBD	_	_	_
24	grown	grow	VBN	_	_	_
25	overnight	overnight	RB	_	_	_
26	in	in	IN	_	_	_
27	18	18	CD	_	_	_
28	mm	mm	NN	_	_	_
29	test	test	NN	_	_	_
30	tubes	tube	NNS	_	_	_
31	containing	contain	VBG	_	_	_
32	DMga	dmga	JJ	_	_	_
33	medium	medium	NN	_	_	_
34	,	,	,	_	_	_
35	500µL	500µl	NN	_	_	_
36	of	of	IN	_	_	_
37	culture	culture	NN	_	_	_
38	was	be	VBD	_	_	_
39	transferred	transfer	VBN	_	_	_
40	to	to	TO	_	_	_
41	50mL	50ml	NN	_	_	_
42	of	of	IN	_	_	_
43	fresh	fresh	JJ	_	_	_
44	DMga	dmga	NN	_	_	_
45	in	in	IN	_	_	_
46	500mL	500ml	NN	_	_	_
47	flasks	flask	NNS	_	_	_
48	and	and	CC	_	_	_
49	grown	grow	VBN	_	_	_
50	for	for	IN	_	_	_
51	12	12	CD	_	_	_
52	hours	hour	NNS	_	_	_
53	37	37	CD	_	_	_
54	°C	°c	NN	_	_	_
55	,	,	,	_	_	_
56	250rpm	250rpm	NN	_	_	_
57	.	.	.	_	_	_

1	Extraction	extraction	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	just	just	RB	_	_	_
5	after	after	IN	_	_	_
6	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Frozen	frozen	JJ	_	_	_
3	bacteria	bacterium	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	overnight	overnight	RB	_	_	_
7	in	in	IN	_	_	_
8	18	18	CD	_	_	_
9	mm	mm	NN	_	_	_
10	test	test	NN	_	_	_
11	tubes	tube	NNS	_	_	_
12	containing	contain	VBG	_	_	_
13	DMga	dmga	JJ	_	_	_
14	medium	medium	NN	_	_	_
15	,	,	,	_	_	_
16	500µL	500µl	NN	_	_	_
17	of	of	IN	_	_	_
18	culture	culture	NN	_	_	_
19	was	be	VBD	_	_	_
20	transferred	transfer	VBN	_	_	_
21	to	to	TO	_	_	_
22	50mL	50ml	NN	_	_	_
23	of	of	IN	_	_	_
24	fresh	fresh	JJ	_	_	_
25	DMga	dmga	NN	_	_	_
26	in	in	IN	_	_	_
27	500mL	500ml	NN	_	_	_
28	flasks	flask	NNS	_	_	_
29	and	and	CC	_	_	_
30	grown	grow	VBN	_	_	_
31	for	for	IN	_	_	_
32	12hours	12hours	CD	_	_	_
33	37	37	CD	_	_	_
34	°C	°c	NN	_	_	_
35	,	,	,	_	_	_
36	250rpm	250rpm	NN	_	_	_
37	.	.	.	_	_	_

1	Extraction	extraction	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	just	just	RB	_	_	_
5	after	after	IN	_	_	_
6	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Frozen	frozen	JJ	_	_	_
3	bacteria	bacterium	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	overnight	overnight	RB	_	_	_
7	in	in	IN	_	_	_
8	18	18	CD	_	_	_
9	mm	mm	NN	_	_	_
10	test	test	NN	_	_	_
11	tubes	tube	NNS	_	_	_
12	containing	contain	VBG	_	_	_
13	DMga	dmga	JJ	_	_	_
14	medium	medium	NN	_	_	_
15	,	,	,	_	_	_
16	500µL	500µl	NN	_	_	_
17	of	of	IN	_	_	_
18	culture	culture	NN	_	_	_
19	was	be	VBD	_	_	_
20	transferred	transfer	VBN	_	_	_
21	to	to	TO	_	_	_
22	50mL	50ml	NN	_	_	_
23	of	of	IN	_	_	_
24	fresh	fresh	JJ	_	_	_
25	DMga	dmga	NN	_	_	_
26	in	in	IN	_	_	_
27	500mL	500ml	NN	_	_	_
28	flasks	flask	NNS	_	_	_
29	and	and	CC	_	_	_
30	grown	grow	VBN	_	_	_
31	for	for	IN	_	_	_
32	18	18	CD	_	_	_
33	hours	hour	NNS	_	_	_
34	37	37	CD	_	_	_
35	°C	°c	NN	_	_	_
36	,	,	,	_	_	_
37	250rpm	250rpm	NN	_	_	_
38	.	.	.	_	_	_

1	Extraction	extraction	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	just	just	RB	_	_	_
5	after	after	IN	_	_	_
6	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Frozen	frozen	JJ	_	_	_
3	bacteria	bacterium	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	overnight	overnight	RB	_	_	_
7	in	in	IN	_	_	_
8	18	18	CD	_	_	_
9	mm	mm	NN	_	_	_
10	test	test	NN	_	_	_
11	tubes	tube	NNS	_	_	_
12	containing	contain	VBG	_	_	_
13	DMga	dmga	JJ	_	_	_
14	medium	medium	NN	_	_	_
15	,	,	,	_	_	_
16	500µL	500µl	NN	_	_	_
17	of	of	IN	_	_	_
18	culture	culture	NN	_	_	_
19	was	be	VBD	_	_	_
20	transferred	transfer	VBN	_	_	_
21	to	to	TO	_	_	_
22	50mL	50ml	NN	_	_	_
23	of	of	IN	_	_	_
24	fresh	fresh	JJ	_	_	_
25	DMga	dmga	NN	_	_	_
26	in	in	IN	_	_	_
27	500mL	500ml	NN	_	_	_
28	flasks	flask	NNS	_	_	_
29	and	and	CC	_	_	_
30	grown	grow	VBN	_	_	_
31	for	for	IN	_	_	_
32	18hours	18hours	CD	_	_	_
33	37	37	CD	_	_	_
34	°C	°c	NN	_	_	_
35	,	,	,	_	_	_
36	250rpm	250rpm	NN	_	_	_
37	.	.	.	_	_	_

1	Extraction	extraction	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	just	just	RB	_	_	_
5	after	after	IN	_	_	_
6	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Frozen	frozen	JJ	_	_	_
3	bacteria	bacterium	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	overnight	overnight	RB	_	_	_
7	in	in	IN	_	_	_
8	18	18	CD	_	_	_
9	mm	mm	NN	_	_	_
10	test	test	NN	_	_	_
11	tubes	tube	NNS	_	_	_
12	containing	contain	VBG	_	_	_
13	DMga	dmga	JJ	_	_	_
14	medium	medium	NN	_	_	_
15	,	,	,	_	_	_
16	500µL	500µl	NN	_	_	_
17	of	of	IN	_	_	_
18	culture	culture	NN	_	_	_
19	was	be	VBD	_	_	_
20	transferred	transfer	VBN	_	_	_
21	to	to	TO	_	_	_
22	50mL	50ml	NN	_	_	_
23	of	of	IN	_	_	_
24	fresh	fresh	JJ	_	_	_
25	DMga	dmga	NN	_	_	_
26	in	in	IN	_	_	_
27	500mL	500ml	NN	_	_	_
28	flasks	flask	NNS	_	_	_
29	and	and	CC	_	_	_
30	grown	grow	VBN	_	_	_
31	for	for	IN	_	_	_
32	3.5	3.5	CD	_	_	_
33	hours	hour	NNS	_	_	_
34	37	37	CD	_	_	_
35	°C	°c	NN	_	_	_
36	,	,	,	_	_	_
37	250rpm	250rpm	NN	_	_	_
38	.	.	.	_	_	_

1	Extraction	extraction	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	just	just	RB	_	_	_
5	after	after	IN	_	_	_
6	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Frozen	frozen	JJ	_	_	_
3	bacteria	bacterium	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	overnight	overnight	RB	_	_	_
7	in	in	IN	_	_	_
8	18	18	CD	_	_	_
9	mm	mm	NN	_	_	_
10	test	test	NN	_	_	_
11	tubes	tube	NNS	_	_	_
12	containing	contain	VBG	_	_	_
13	DMga	dmga	JJ	_	_	_
14	medium	medium	NN	_	_	_
15	,	,	,	_	_	_
16	500µL	500µl	NN	_	_	_
17	of	of	IN	_	_	_
18	culture	culture	NN	_	_	_
19	was	be	VBD	_	_	_
20	transferred	transfer	VBN	_	_	_
21	to	to	TO	_	_	_
22	50mL	50ml	NN	_	_	_
23	of	of	IN	_	_	_
24	fresh	fresh	JJ	_	_	_
25	DMga	dmga	NN	_	_	_
26	in	in	IN	_	_	_
27	500mL	500ml	NN	_	_	_
28	flasks	flask	NNS	_	_	_
29	and	and	CC	_	_	_
30	grown	grow	VBN	_	_	_
31	for	for	IN	_	_	_
32	4	4	CD	_	_	_
33	hours	hour	NNS	_	_	_
34	37	37	CD	_	_	_
35	°C	°c	NN	_	_	_
36	,	,	,	_	_	_
37	250rpm	250rpm	NN	_	_	_
38	.	.	.	_	_	_

1	Extraction	extraction	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	just	just	RB	_	_	_
5	after	after	IN	_	_	_
6	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Frozen	frozen	JJ	_	_	_
3	bacteria	bacterium	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	overnight	overnight	RB	_	_	_
7	in	in	IN	_	_	_
8	18	18	CD	_	_	_
9	mm	mm	NN	_	_	_
10	test	test	NN	_	_	_
11	tubes	tube	NNS	_	_	_
12	containing	contain	VBG	_	_	_
13	DMga	dmga	JJ	_	_	_
14	medium	medium	NN	_	_	_
15	,	,	,	_	_	_
16	500µL	500µl	NN	_	_	_
17	of	of	IN	_	_	_
18	culture	culture	NN	_	_	_
19	was	be	VBD	_	_	_
20	transferred	transfer	VBN	_	_	_
21	to	to	TO	_	_	_
22	50mL	50ml	NN	_	_	_
23	of	of	IN	_	_	_
24	fresh	fresh	JJ	_	_	_
25	DMga	dmga	NN	_	_	_
26	in	in	IN	_	_	_
27	500mL	500ml	NN	_	_	_
28	flasks	flask	NNS	_	_	_
29	and	and	CC	_	_	_
30	grown	grow	VBN	_	_	_
31	for	for	IN	_	_	_
32	4hours	4hours	CD	_	_	_
33	37	37	CD	_	_	_
34	°C	°c	NN	_	_	_
35	,	,	,	_	_	_
36	250rpm	250rpm	NN	_	_	_
37	.	.	.	_	_	_

1	Extraction	extraction	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	just	just	RB	_	_	_
5	after	after	IN	_	_	_
6	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Frozen	frozen	JJ	_	_	_
3	bacteria	bacterium	NNS	_	_	_
4	were	be	VBD	_	_	_
5	grown	grow	VBN	_	_	_
6	overnight	overnight	RB	_	_	_
7	in	in	IN	_	_	_
8	18	18	CD	_	_	_
9	mm	mm	NN	_	_	_
10	test	test	NN	_	_	_
11	tubes	tube	NNS	_	_	_
12	containing	contain	VBG	_	_	_
13	DMga	dmga	JJ	_	_	_
14	medium	medium	NN	_	_	_
15	,	,	,	_	_	_
16	500µL	500µl	NN	_	_	_
17	of	of	IN	_	_	_
18	culture	culture	NN	_	_	_
19	was	be	VBD	_	_	_
20	transferred	transfer	VBN	_	_	_
21	to	to	TO	_	_	_
22	50mL	50ml	NN	_	_	_
23	of	of	IN	_	_	_
24	fresh	fresh	JJ	_	_	_
25	DMga	dmga	NN	_	_	_
26	in	in	IN	_	_	_
27	500mL	500ml	NN	_	_	_
28	flasks	flask	NNS	_	_	_
29	and	and	CC	_	_	_
30	grown	grow	VBN	_	_	_
31	for	for	IN	_	_	_
32	7hours	7hours	CD	_	_	_
33	37	37	CD	_	_	_
34	°C	°c	NN	_	_	_
35	,	,	,	_	_	_
36	250rpm	250rpm	NN	_	_	_
37	.	.	.	_	_	_

1	Extraction	extraction	NN	_	_	_
2	was	be	VBD	_	_	_
3	performed	perform	VBN	_	_	_
4	just	just	RB	_	_	_
5	after	after	IN	_	_	_
6	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	LA	LA	NNP	_	_	_
3	_	_	NNP	_	_	_
4	TP1	tp1	NN	_	_	_
5	_	_	CD	_	_	_
6	repl1	repl1	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	LA	LA	NNP	_	_	_
9	_	_	NNP	_	_	_
10	TP1	tp1	NN	_	_	_
11	_	_	CD	_	_	_
12	repl2	repl2	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	LA	LA	NNP	_	_	_
15	_	_	NNP	_	_	_
16	TP1	tp1	NN	_	_	_
17	_	_	CD	_	_	_
18	repl3	repl3	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	LA	LA	NNP	_	_	_
21	_	_	NNP	_	_	_
22	TP1	tp1	NN	_	_	_
23	_	_	CD	_	_	_
24	repl4	repl4	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	LA	LA	NNP	_	_	_
27	_	_	NNP	_	_	_
28	TP1	tp1	NN	_	_	_
29	_	_	CD	_	_	_
30	repl5	repl5	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	LA	LA	NNP	_	_	_
33	_	_	SYM	_	_	_
34	TP2	tp2	NN	_	_	_
35	_	_	CD	_	_	_
36	repl1	repl1	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	LA	LA	NNP	_	_	_
39	_	_	SYM	_	_	_
40	TP2	tp2	NN	_	_	_
41	_	_	CD	_	_	_
42	repl2	repl2	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	LA	LA	NNP	_	_	_
45	_	_	SYM	_	_	_
46	TP2	tp2	NN	_	_	_
47	_	_	CD	_	_	_
48	repl3	repl3	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	LA	LA	NNP	_	_	_
51	_	_	SYM	_	_	_
52	TP2	tp2	NN	_	_	_
53	_	_	CD	_	_	_
54	repl4	repl4	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	LA	LA	NNP	_	_	_
57	_	_	SYM	_	_	_
58	TP2	tp2	NN	_	_	_
59	_	_	CD	_	_	_
60	repl5	repl5	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	LA	LA	NNP	_	_	_
63	_	_	SYM	_	_	_
64	TP3	tp3	NN	_	_	_
65	_	_	CD	_	_	_
66	repl1	repl1	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	LA	LA	NNP	_	_	_
69	_	_	SYM	_	_	_
70	TP3	tp3	NN	_	_	_
71	_	_	CD	_	_	_
72	repl2	repl2	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	LA	LA	NNP	_	_	_
75	_	_	SYM	_	_	_
76	TP3	tp3	NN	_	_	_
77	_	_	CD	_	_	_
78	repl3	repl3	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	LA	LA	NNP	_	_	_
81	_	_	SYM	_	_	_
82	TP3	tp3	NN	_	_	_
83	_	_	CD	_	_	_
84	repl4	repl4	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	LA	LA	NNP	_	_	_
87	_	_	SYM	_	_	_
88	TP3	tp3	NN	_	_	_
89	_	_	CD	_	_	_
90	repl5	repl5	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	LA	LA	NNP	_	_	_
93	_	_	SYM	_	_	_
94	TP4	tp4	NN	_	_	_
95	_	_	CD	_	_	_
96	repl1	repl1	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	LA	LA	NNP	_	_	_
99	_	_	SYM	_	_	_
100	TP4	tp4	NN	_	_	_
101	_	_	CD	_	_	_
102	repl2	repl2	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	LA	LA	NNP	_	_	_
105	_	_	SYM	_	_	_
106	TP4	tp4	NN	_	_	_
107	_	_	CD	_	_	_
108	repl3	repl3	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	LA	LA	NNP	_	_	_
111	_	_	SYM	_	_	_
112	TP4	tp4	NN	_	_	_
113	_	_	CD	_	_	_
114	repl4	repl4	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	LA	LA	NNP	_	_	_
117	_	_	SYM	_	_	_
118	TP4	tp4	NN	_	_	_
119	_	_	CD	_	_	_
120	repl5	repl5	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	L	l	NN	_	_	_
123	,	,	,	_	_	_
124	TP1	tp1	NN	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	L	l	NN	_	_	_
127	,	,	,	_	_	_
128	TP2	tp2	NN	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	L	l	NN	_	_	_
131	,	,	,	_	_	_
132	TP3	tp3	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	L	l	NN	_	_	_
135	,	,	,	_	_	_
136	TP4	tp4	NN	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	SA	SA	NNP	_	_	_
139	_	_	NNP	_	_	_
140	TP1	tp1	NN	_	_	_
141	_	_	CD	_	_	_
142	repl1	repl1	NN	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	SA	SA	NNP	_	_	_
145	_	_	NNP	_	_	_
146	TP1	tp1	NN	_	_	_
147	_	_	CD	_	_	_
148	repl2	repl2	NN	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	SA	SA	NNP	_	_	_
151	_	_	NNP	_	_	_
152	TP1	tp1	NN	_	_	_
153	_	_	CD	_	_	_
154	repl3	repl3	NN	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	SA	SA	NNP	_	_	_
157	_	_	NNP	_	_	_
158	TP1	tp1	NN	_	_	_
159	_	_	CD	_	_	_
160	repl4	repl4	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	SA	SA	NNP	_	_	_
163	_	_	NNP	_	_	_
164	TP1	tp1	NN	_	_	_
165	_	_	CD	_	_	_
166	repl5	repl5	NN	_	_	_
167	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
168	SA	SA	NNP	_	_	_
169	_	_	SYM	_	_	_
170	TP2	tp2	NN	_	_	_
171	_	_	CD	_	_	_
172	repl1	repl1	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	SA	SA	NNP	_	_	_
175	_	_	SYM	_	_	_
176	TP2	tp2	NN	_	_	_
177	_	_	CD	_	_	_
178	repl2	repl2	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	SA	SA	NNP	_	_	_
181	_	_	SYM	_	_	_
182	TP2	tp2	NN	_	_	_
183	_	_	CD	_	_	_
184	repl3	repl3	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	SA	SA	NNP	_	_	_
187	_	_	SYM	_	_	_
188	TP2	tp2	NN	_	_	_
189	_	_	CD	_	_	_
190	repl4	repl4	NN	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	SA	SA	NNP	_	_	_
193	_	_	SYM	_	_	_
194	TP2	tp2	NN	_	_	_
195	_	_	CD	_	_	_
196	repl5	repl5	NN	_	_	_
197	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
198	SA	SA	NNP	_	_	_
199	_	_	SYM	_	_	_
200	TP3	tp3	NN	_	_	_
201	_	_	CD	_	_	_
202	repl1	repl1	NN	_	_	_
203	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
204	SA	SA	NNP	_	_	_
205	_	_	SYM	_	_	_
206	TP3	tp3	NN	_	_	_
207	_	_	CD	_	_	_
208	repl2	repl2	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	SA	SA	NNP	_	_	_
211	_	_	SYM	_	_	_
212	TP3	tp3	NN	_	_	_
213	_	_	CD	_	_	_
214	repl3	repl3	NN	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	SA	SA	NNP	_	_	_
217	_	_	SYM	_	_	_
218	TP3	tp3	NN	_	_	_
219	_	_	CD	_	_	_
220	repl4	repl4	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	SA	SA	NNP	_	_	_
223	_	_	SYM	_	_	_
224	TP3	tp3	NN	_	_	_
225	_	_	CD	_	_	_
226	repl5	repl5	NN	_	_	_
227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
228	SA	SA	NNP	_	_	_
229	_	_	SYM	_	_	_
230	TP4	tp4	NN	_	_	_
231	_	_	CD	_	_	_
232	repl1	repl1	NN	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	SA	SA	NNP	_	_	_
235	_	_	SYM	_	_	_
236	TP4	tp4	NN	_	_	_
237	_	_	CD	_	_	_
238	repl2	repl2	NN	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	SA	SA	NNP	_	_	_
241	_	_	SYM	_	_	_
242	TP4	tp4	NN	_	_	_
243	_	_	CD	_	_	_
244	repl3	repl3	NN	_	_	_
245	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
246	SA	SA	NNP	_	_	_
247	_	_	SYM	_	_	_
248	TP4	tp4	NN	_	_	_
249	_	_	CD	_	_	_
250	repl4	repl4	NN	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	SA	SA	NNP	_	_	_
253	_	_	SYM	_	_	_
254	TP4	tp4	NN	_	_	_
255	_	_	SYM	_	_	_
256	repl5	repl5	CD	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
258	Statistical	statistical	JJ	_	_	_
259	preprocessing	preprocess	VBG	_	_	_
260	steps	step	NNS	_	_	_
261	were	be	VBD	_	_	_
262	conducted	conduct	VBN	_	_	_
263	with	with	IN	_	_	_
264	ArrayPipe	arraypipe	NN	_	_	_
265	-LRB-	-lrb-	-LRB-	_	_	_
266	version	version	NN	_	_	_
267	1.7	1.7	CD	_	_	_
268	-RRB-	-rrb-	-RRB-	_	_	_
269	,	,	,	_	_	_
270	a	a	DT	_	_	_
271	web-based	web-based	JJ	_	_	_
272	software	software	NN	_	_	_
273	designed	design	VBN	_	_	_
274	for	for	IN	_	_	_
275	processing	processing	NN	_	_	_
276	of	of	IN	_	_	_
277	microarray	microarray	NN	_	_	_
278	data	datum	NNS	_	_	_
279	-LRB-	-lrb-	-LRB-	_	_	_
280	www.pathogenomics.ca	www.pathogenomics.ca	JJ	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	S	s	NN	_	_	_
283	,	,	,	_	_	_
284	TP1	tp1	NN	_	_	_
285	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
286	S	s	NN	_	_	_
287	,	,	,	_	_	_
288	TP2	tp2	NN	_	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
290	S	s	NN	_	_	_
291	,	,	,	_	_	_
292	TP3	tp3	NN	_	_	_
293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
294	S	s	NN	_	_	_
295	,	,	,	_	_	_
296	TP4	tp4	NN	_	_	_
297	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
298	Total	total	JJ	_	_	_
299	RNA	rna	NN	_	_	_
300	was	be	VBD	_	_	_
301	extracted	extract	VBN	_	_	_
302	using	use	VBG	_	_	_
303	Qiagen	Qiagen	NNP	_	_	_
304	RNeasy	RNeasy	NNP	_	_	_
305	Mini	Mini	NNP	_	_	_
306	Kit	kit	NN	_	_	_
307	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	removed	remove	VBN	_	_	_
4	using	use	VBG	_	_	_
5	Ambion	Ambion	NNP	_	_	_
6	DNA-free	dna-free	JJ	_	_	_
7	kit	kit	NN	_	_	_
8	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	quality	quality	NN	_	_	_
3	was	be	VBD	_	_	_
4	assessed	assess	VBN	_	_	_
5	using	use	VBG	_	_	_
6	2	2	CD	_	_	_
7	%	%	NN	_	_	_
8	agarose	agarose	NN	_	_	_
9	gels	gel	NNS	_	_	_
10	and	and	CC	_	_	_
11	OD260	od260	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	VALUEs	value	NNS	_	_	_
14	are	be	VBP	_	_	_
15	calculated	calculate	VBN	_	_	_
16	as	as	IN	_	_	_
17	log2-transformed	log2-transformed	JJ	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	test	test	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	dnaC2	dnac2	NN	_	_	_
22	30	30	CD	_	_	_
23	'	'	''	_	_	_
24	at	at	IN	_	_	_
25	30	30	CD	_	_	_
26	deg	deg	NN	_	_	_
27	,	,	,	_	_	_
28	2	2	CD	_	_	_
29	ug	ug	NN	_	_	_
30	gen	gen	NN	_	_	_
31	DNA	dna	NN	_	_	_
32	,	,	,	_	_	_
33	pdN6	pdn6	NN	_	_	_
34	RT	rt	NN	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	dnaC2	dnac2	NN	_	_	_
37	90	90	CD	_	_	_
38	'	'	''	_	_	_
39	at	at	IN	_	_	_
40	42	42	CD	_	_	_
41	deg	deg	NN	_	_	_
42	,	,	,	_	_	_
43	2	2	CD	_	_	_
44	ug	ug	NN	_	_	_
45	gen	gen	NN	_	_	_
46	DNA	dna	NN	_	_	_
47	,	,	,	_	_	_
48	pdN6	pdn6	NN	_	_	_
49	RT	rt	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	dnaC2	dnac2	NN	_	_	_
52	synchrony	synchrony	NN	_	_	_
53	30	30	CD	_	_	_
54	'	'	''	_	_	_
55	after	after	IN	_	_	_
56	shift	shift	NN	_	_	_
57	,	,	,	_	_	_
58	print	print	NN	_	_	_
59	7	7	CD	_	_	_
60	array	array	NN	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	dnaC	dnac	NN	GEN	_	_
63	fully	fully	RB	_	_	_
64	replicated	replicate	VBN	_	_	_
65	,	,	,	_	_	_
66	2	2	CD	_	_	_
67	ug	ug	NN	_	_	_
68	Sau3AI	sau3ai	NN	_	_	_
69	,	,	,	_	_	_
70	pdN6	pdn6	NN	_	_	_
71	RT	rt	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	dnaC	dnac	NN	GEN	_	_
74	fully	fully	RB	_	_	_
75	replicated	replicate	VBN	_	_	_
76	,	,	,	_	_	_
77	2	2	CD	_	_	_
78	ug	ug	NN	_	_	_
79	Say3AI	say3ai	NN	_	_	_
80	,	,	,	_	_	_
81	pdN6	pdn6	NN	_	_	_
82	RT	rt	NN	_	_	_
83	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
84	Escherichia	escherichia	FW	Organism	_	_
85	coli	coli	FW	Organism	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	Basecalls	basecall	NNS	_	_	_
88	performed	perform	VBN	_	_	_
89	using	use	VBG	_	_	_
90	Illumina	Illumina	NNP	_	_	_
91	CASAVA	CASAVA	NNP	_	_	_
92	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	induced	induce	VBN	_	_	_
5	with	with	IN	_	_	_
6	arabinose	arabinose	NN	_	_	_
7	or	or	CC	_	_	_
8	heat	heat	NN	_	_	_
9	shocked	shocked	JJ	_	_	_
10	,	,	,	_	_	_
11	then	then	RB	_	_	_
12	harvested	harvest	VBN	_	_	_
13	and	and	CC	_	_	_
14	flash	flash	VB	_	_	_
15	frozen	frozen	JJ	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	lysed	lyse	VBN	_	_	_
5	in	in	IN	_	_	_
6	liquid	liquid	JJ	_	_	_
7	nitrogen	nitrogen	NN	_	_	_
8	,	,	,	_	_	_
9	then	then	RB	_	_	_
10	samples	sample	NNS	_	_	_
11	were	be	VBD	_	_	_
12	taken	take	VBN	_	_	_
13	for	for	IN	_	_	_
14	ribosome	ribosome	NN	_	_	_
15	footprint	footprint	NN	_	_	_
16	extraction	extraction	NN	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	lysed	lyse	VBN	_	_	_
5	in	in	IN	_	_	_
6	liquid	liquid	JJ	_	_	_
7	nitrogen	nitrogen	NN	_	_	_
8	,	,	,	_	_	_
9	then	then	RB	_	_	_
10	samples	sample	NNS	_	_	_
11	were	be	VBD	_	_	_
12	taken	take	VBN	_	_	_
13	for	for	IN	_	_	_
14	total	total	JJ	_	_	_
15	RNA	rna	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	cultures	culture	NNS	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	ecoli	ecolus	NNS	_	_	_
7	_	_	VBP	_	_	_
8	k12	k12	NN	_	_	_
9	_	_	SYM	_	_	_
10	30C	30c	FW	_	_	_
11	_	_	FW	_	_	_
12	f	f	FW	_	_	_
13	_	_	SYM	_	_	_
14	1	1	CD	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	ecoli	ecolus	NNS	_	_	_
17	_	_	VBP	_	_	_
18	k12	k12	NN	_	_	_
19	_	_	SYM	_	_	_
20	30C	30c	FW	_	_	_
21	_	_	FW	_	_	_
22	f	f	FW	_	_	_
23	_	_	SYM	_	_	_
24	2	2	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	ecoli	ecolus	NNS	_	_	_
27	_	_	VBP	_	_	_
28	k12	k12	NN	_	_	_
29	_	_	SYM	_	_	_
30	30C	30c	FW	_	_	_
31	_	_	FW	_	_	_
32	f	f	FW	_	_	_
33	_	_	SYM	_	_	_
34	3	3	CD	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
36	ecoli	ecolus	NNS	_	_	_
37	_	_	VBP	_	_	_
38	k12	k12	NN	_	_	_
39	_	_	SYM	_	_	_
40	30C	30c	CD	_	_	_
41	_	_	NN	_	_	_
42	m	m	NN	_	_	_
43	_	_	NN	_	_	_
44	1	1	CD	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	ecoli	ecolus	NNS	_	_	_
47	_	_	VBP	_	_	_
48	k12	k12	NN	_	_	_
49	_	_	SYM	_	_	_
50	30C	30c	CD	_	_	_
51	_	_	NN	_	_	_
52	m	m	NN	_	_	_
53	_	_	NN	_	_	_
54	2	2	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	ecoli	ecolus	NNS	_	_	_
57	_	_	VBP	_	_	_
58	k12	k12	NN	_	_	_
59	_	_	SYM	_	_	_
60	30C	30c	CD	_	_	_
61	_	_	NN	_	_	_
62	m	m	NN	_	_	_
63	_	_	NN	_	_	_
64	3	3	CD	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	ecoli	ecolus	NNS	_	_	_
67	_	_	VBP	_	_	_
68	k12	k12	NN	_	_	_
69	_	_	SYM	_	_	_
70	42C	42c	CD	_	_	_
71	_	_	SYM	_	_	_
72	10	10	CD	_	_	_
73	min	min	NN	_	_	_
74	_	_	NN	_	_	_
75	f	f	FW	_	_	_
76	_	_	FW	_	_	_
77	1	1	CD	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	ecoli	ecolus	NNS	_	_	_
80	_	_	VBP	_	_	_
81	k12	k12	NN	_	_	_
82	_	_	SYM	_	_	_
83	42C	42c	CD	_	_	_
84	_	_	SYM	_	_	_
85	10	10	CD	_	_	_
86	min	min	NN	_	_	_
87	_	_	NN	_	_	_
88	f	f	FW	_	_	_
89	_	_	FW	_	_	_
90	2	2	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	ecoli	ecolus	NNS	_	_	_
93	_	_	VBP	_	_	_
94	k12	k12	NN	_	_	_
95	_	_	SYM	_	_	_
96	42C	42c	CD	_	_	_
97	_	_	SYM	_	_	_
98	10	10	CD	_	_	_
99	min	min	NN	_	_	_
100	_	_	NN	_	_	_
101	f	f	FW	_	_	_
102	_	_	FW	_	_	_
103	3	3	CD	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	ecoli	ecolus	NNS	_	_	_
106	_	_	VBP	_	_	_
107	k12	k12	NN	_	_	_
108	_	_	SYM	_	_	_
109	42C	42c	CD	_	_	_
110	_	_	SYM	_	_	_
111	10	10	CD	_	_	_
112	min	min	NN	_	_	_
113	_	_	NN	_	_	_
114	m	m	NN	_	_	_
115	_	_	NN	_	_	_
116	1	1	CD	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	ecoli	ecolus	NNS	_	_	_
119	_	_	VBP	_	_	_
120	k12	k12	NN	_	_	_
121	_	_	SYM	_	_	_
122	42C	42c	CD	_	_	_
123	_	_	SYM	_	_	_
124	10	10	CD	_	_	_
125	min	min	NN	_	_	_
126	_	_	NN	_	_	_
127	m	m	NN	_	_	_
128	_	_	NN	_	_	_
129	2	2	CD	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	ecoli	ecolus	NNS	_	_	_
132	_	_	VBP	_	_	_
133	k12	k12	NN	_	_	_
134	_	_	SYM	_	_	_
135	42C	42c	CD	_	_	_
136	_	_	SYM	_	_	_
137	10	10	CD	_	_	_
138	min	min	NN	_	_	_
139	_	_	NN	_	_	_
140	m	m	NN	_	_	_
141	_	_	NN	_	_	_
142	3	3	CD	_	_	_
143	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
144	ecoli	ecolus	NNS	_	_	_
145	_	_	VBP	_	_	_
146	k12	k12	NN	_	_	_
147	_	_	SYM	_	_	_
148	42C	42c	CD	_	_	_
149	_	_	SYM	_	_	_
150	20	20	CD	_	_	_
151	min	min	NN	_	_	_
152	_	_	NN	_	_	_
153	f	f	FW	_	_	_
154	_	_	FW	_	_	_
155	1	1	CD	_	_	_
156	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
157	ecoli	ecolus	NNS	_	_	_
158	_	_	VBP	_	_	_
159	k12	k12	NN	_	_	_
160	_	_	SYM	_	_	_
161	42C	42c	CD	_	_	_
162	_	_	SYM	_	_	_
163	20	20	CD	_	_	_
164	min	min	NN	_	_	_
165	_	_	NN	_	_	_
166	f	f	FW	_	_	_
167	_	_	FW	_	_	_
168	2	2	CD	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	ecoli	ecolus	NNS	_	_	_
171	_	_	VBP	_	_	_
172	k12	k12	NN	_	_	_
173	_	_	SYM	_	_	_
174	42C	42c	CD	_	_	_
175	_	_	SYM	_	_	_
176	20	20	CD	_	_	_
177	min	min	NN	_	_	_
178	_	_	NN	_	_	_
179	f	f	FW	_	_	_
180	_	_	FW	_	_	_
181	3	3	CD	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	ecoli	ecolus	NNS	_	_	_
184	_	_	VBP	_	_	_
185	k12	k12	NN	_	_	_
186	_	_	SYM	_	_	_
187	42C	42c	CD	_	_	_
188	_	_	SYM	_	_	_
189	20	20	CD	_	_	_
190	min	min	NN	_	_	_
191	_	_	NN	_	_	_
192	m	m	NN	_	_	_
193	_	_	NN	_	_	_
194	1	1	CD	_	_	_
195	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
196	ecoli	ecolus	NNS	_	_	_
197	_	_	VBP	_	_	_
198	k12	k12	NN	_	_	_
199	_	_	SYM	_	_	_
200	42C	42c	CD	_	_	_
201	_	_	SYM	_	_	_
202	20	20	CD	_	_	_
203	min	min	NN	_	_	_
204	_	_	NN	_	_	_
205	m	m	NN	_	_	_
206	_	_	NN	_	_	_
207	2	2	CD	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	ecoli	ecolus	NNS	_	_	_
210	_	_	VBP	_	_	_
211	k12	k12	NN	_	_	_
212	_	_	SYM	_	_	_
213	42C	42c	CD	_	_	_
214	_	_	SYM	_	_	_
215	20	20	CD	_	_	_
216	min	min	NN	_	_	_
217	_	_	NN	_	_	_
218	m	m	NN	_	_	_
219	_	_	NN	_	_	_
220	3	3	CD	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	ecoli	ecolus	NNS	_	_	_
223	_	_	VBP	_	_	_
224	k12	k12	NN	_	_	_
225	_	_	SYM	_	_	_
226	pBAD	pbad	FW	_	_	_
227	_	_	FW	_	_	_
228	30C	30c	FW	_	_	_
229	_	_	FW	_	_	_
230	f	f	FW	_	_	_
231	_	_	SYM	_	_	_
232	1	1	CD	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	ecoli	ecolus	NNS	_	_	_
235	_	_	VBP	_	_	_
236	k12	k12	NN	_	_	_
237	_	_	SYM	_	_	_
238	pBad	pbad	FW	_	_	_
239	_	_	FW	_	_	_
240	30C	30c	FW	_	_	_
241	_	_	FW	_	_	_
242	f	f	FW	_	_	_
243	_	_	SYM	_	_	_
244	2	2	CD	_	_	_
245	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
246	ecoli	ecolus	NNS	_	_	_
247	_	_	VBP	_	_	_
248	k12	k12	NN	_	_	_
249	_	_	SYM	_	_	_
250	pBAD	pbad	FW	_	_	_
251	_	_	FW	_	_	_
252	30C	30c	FW	_	_	_
253	_	_	FW	_	_	_
254	f	f	FW	_	_	_
255	_	_	SYM	_	_	_
256	3	3	CD	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	ecoli	ecolus	NNS	_	_	_
259	_	_	VBP	_	_	_
260	k12	k12	NN	_	_	_
261	_	_	SYM	_	_	_
262	pBAD	pbad	FW	_	_	_
263	_	_	FW	_	_	_
264	30C	30c	FW	_	_	_
265	_	_	FW	_	_	_
266	f	f	FW	_	_	_
267	_	_	SYM	_	_	_
268	4	4	CD	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	ecoli	ecolus	NNS	_	_	_
271	_	_	VBP	_	_	_
272	k12	k12	NN	_	_	_
273	_	_	CD	_	_	_
274	pBAD	pbad	NN	_	_	_
275	_	_	SYM	_	_	_
276	30C	30c	CD	_	_	_
277	_	_	NN	_	_	_
278	m	m	NN	_	_	_
279	_	_	NN	_	_	_
280	1	1	CD	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	ecoli	ecolus	NNS	_	_	_
283	_	_	VBP	_	_	_
284	k12	k12	NN	_	_	_
285	_	_	CD	_	_	_
286	pBAD	pbad	NN	_	_	_
287	_	_	SYM	_	_	_
288	30C	30c	CD	_	_	_
289	_	_	NN	_	_	_
290	m	m	NN	_	_	_
291	_	_	NN	_	_	_
292	2	2	CD	_	_	_
293	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
294	ecoli	ecolus	NNS	_	_	_
295	_	_	VBP	_	_	_
296	k12	k12	NN	_	_	_
297	_	_	CD	_	_	_
298	pBAD	pbad	NN	_	_	_
299	_	_	SYM	_	_	_
300	30C	30c	CD	_	_	_
301	_	_	NN	_	_	_
302	m	m	NN	_	_	_
303	_	_	NN	_	_	_
304	3	3	CD	_	_	_
305	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
306	ecoli	ecolus	NNS	_	_	_
307	_	_	VBP	_	_	_
308	k12	k12	NN	_	_	_
309	_	_	CD	_	_	_
310	pBAD	pbad	NN	_	_	_
311	_	_	SYM	_	_	_
312	30C	30c	CD	_	_	_
313	_	_	NN	_	_	_
314	m	m	NN	_	_	_
315	_	_	NN	_	_	_
316	4	4	CD	_	_	_
317	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
318	ecoli	ecolus	NNS	_	_	_
319	_	_	VBP	_	_	_
320	k12	k12	NN	_	_	_
321	_	_	CD	_	_	_
322	pBADsigma32I54N	pbadsigma32i54n	NN	_	_	_
323	_	_	SYM	_	_	_
324	30C	30c	FW	_	_	_
325	_	_	FW	_	_	_
326	f	f	FW	_	_	_
327	_	_	SYM	_	_	_
328	1	1	CD	_	_	_
329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
330	ecoli	ecolus	NNS	_	_	_
331	_	_	VBP	_	_	_
332	k12	k12	NN	_	_	_
333	_	_	CD	_	_	_
334	pBADsigma32I54N	pbadsigma32i54n	NN	_	_	_
335	_	_	SYM	_	_	_
336	30C	30c	FW	_	_	_
337	_	_	FW	_	_	_
338	f	f	FW	_	_	_
339	_	_	SYM	_	_	_
340	2	2	CD	_	_	_
341	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
342	ecoli	ecolus	NNS	_	_	_
343	_	_	VBP	_	_	_
344	k12	k12	NN	_	_	_
345	_	_	CD	_	_	_
346	pBADsigma32I54N	pbadsigma32i54n	NN	_	_	_
347	_	_	SYM	_	_	_
348	30C	30c	CD	_	_	_
349	_	_	NN	_	_	_
350	m	m	NN	_	_	_
351	_	_	NN	_	_	_
352	1	1	CD	_	_	_
353	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
354	ecoli	ecolus	NNS	_	_	_
355	_	_	VBP	_	_	_
356	k12	k12	NN	_	_	_
357	_	_	CD	_	_	_
358	pBADsigma32I54N	pbadsigma32i54n	NN	_	_	_
359	_	_	SYM	_	_	_
360	30C	30c	CD	_	_	_
361	_	_	NN	_	_	_
362	m	m	NN	_	_	_
363	_	_	NN	_	_	_
364	2	2	CD	_	_	_
365	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
366	ecoli	ecolus	NNS	_	_	_
367	_	_	VBP	_	_	_
368	k12	k12	NN	_	_	_
369	_	_	CD	_	_	_
370	pBADsigma32wt	pbadsigma32wt	NN	_	_	_
371	_	_	SYM	_	_	_
372	30C	30c	FW	_	_	_
373	_	_	FW	_	_	_
374	f	f	FW	_	_	_
375	_	_	SYM	_	_	_
376	1	1	CD	_	_	_
377	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
378	ecoli	ecolus	NNS	_	_	_
379	_	_	VBP	_	_	_
380	k12	k12	NN	_	_	_
381	_	_	CD	_	_	_
382	pBADsigma32wt	pbadsigma32wt	NN	_	_	_
383	_	_	SYM	_	_	_
384	30C	30c	FW	_	_	_
385	_	_	FW	_	_	_
386	f	f	FW	_	_	_
387	_	_	SYM	_	_	_
388	2	2	CD	_	_	_
389	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
390	ecoli	ecolus	NNS	_	_	_
391	_	_	VBP	_	_	_
392	k12	k12	NN	_	_	_
393	_	_	CD	_	_	_
394	pBADsigma32wt	pbadsigma32wt	NN	_	_	_
395	_	_	SYM	_	_	_
396	30C	30c	FW	_	_	_
397	_	_	FW	_	_	_
398	f	f	FW	_	_	_
399	_	_	SYM	_	_	_
400	3	3	CD	_	_	_
401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
402	ecoli	ecolus	NNS	_	_	_
403	_	_	VBP	_	_	_
404	k12	k12	NN	_	_	_
405	_	_	CD	_	_	_
406	pBADsigma32wt	pbadsigma32wt	NN	_	_	_
407	_	_	SYM	_	_	_
408	30C	30c	CD	_	_	_
409	_	_	NN	_	_	_
410	m	m	NN	_	_	_
411	_	_	NN	_	_	_
412	1	1	CD	_	_	_
413	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
414	ecoli	ecolus	NNS	_	_	_
415	_	_	VBP	_	_	_
416	k12	k12	NN	_	_	_
417	_	_	CD	_	_	_
418	pBADsigma32wt	pbadsigma32wt	NN	_	_	_
419	_	_	SYM	_	_	_
420	30C	30c	CD	_	_	_
421	_	_	NN	_	_	_
422	m	m	NN	_	_	_
423	_	_	NN	_	_	_
424	2	2	CD	_	_	_
425	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
426	ecoli	ecolus	NNS	_	_	_
427	_	_	VBP	_	_	_
428	k12	k12	NN	_	_	_
429	_	_	CD	_	_	_
430	pBADsigma32wt	pbadsigma32wt	NN	_	_	_
431	_	_	SYM	_	_	_
432	30C	30c	CD	_	_	_
433	_	_	NN	_	_	_
434	m	m	NN	_	_	_
435	_	_	SYM	_	_	_
436	3	3	CD	_	_	_
437	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
438	E.	e.	FW	_	_	_
439	coli	coli	FW	_	_	_
440	were	be	VBD	_	_	_
441	grown	grow	VBN	_	_	_
442	in	in	IN	_	_	_
443	defined	define	VBN	_	_	_
444	rich	rich	JJ	MED	_	_
445	media	media	NNS	MED	_	_
446	at	at	IN	_	_	_
447	30C	30C	NNP	_	_	_
448	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	str	str	FW	_	_	_
5	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Genome	Genome	NNP	_	_	_
4	_	_	NNP	_	_	_
5	build	build	VB	_	_	_
6	:	:	:	_	_	_
7	NC	NC	NNP	_	_	_
8	_	_	NNP	_	_	_
9	000913.2	000913.2	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	growth	growth	NN	_	_	_
12	temperature	temperature	NN	_	_	_
13	:	:	:	_	_	_
14	30C	30C	NNP	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	heat	heat	NN	_	_	_
17	shock	shock	NN	_	_	_
18	time	time	NN	_	_	_
19	:	:	:	_	_	_
20	0	0	CD	_	_	_
21	min	min	NN	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	heat	heat	NN	_	_	_
24	shock	shock	NN	_	_	_
25	time	time	NN	_	_	_
26	:	:	:	_	_	_
27	10	10	CD	_	_	_
28	min	min	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	heat	heat	NN	_	_	_
31	shock	shock	NN	_	_	_
32	time	time	NN	_	_	_
33	:	:	:	_	_	_
34	20	20	CD	_	_	_
35	min	min	NN	_	_	_
36	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
37	heat	heat	NN	_	_	_
38	shock	shock	NN	_	_	_
39	time	time	NN	_	_	_
40	:	:	:	_	_	_
41	None	none	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	induction	induction	NN	_	_	_
44	:	:	:	_	_	_
45	0.2	0.2	CD	_	_	_
46	%	%	NN	_	_	_
47	arabinose	arabinose	NN	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	induction	induction	NN	_	_	_
50	:	:	:	_	_	_
51	None	none	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	Library	Library	NNP	_	_	_
54	strategy	strategy	NN	_	_	_
55	:	:	:	_	_	_
56	Ribo-Seq	Ribo-Seq	NNP	_	_	_
57	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
58	OTHER	OTHER	NNP	_	_	_
59	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
60	plasmid	plasmid	NN	_	_	_
61	:	:	:	_	_	_
62	None	none	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	plasmid	plasmid	NN	_	_	_
65	:	:	:	_	_	_
66	pBAD	pbad	NN	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
68	plasmid	plasmid	NN	_	_	_
69	:	:	:	_	_	_
70	pBADsigma32I54N	pbadsigma32i54n	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	plasmid	plasmid	NN	_	_	_
73	:	:	:	_	_	_
74	pBADsigma32wt	pbadsigma32wt	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	Polysomes	polysome	NNS	_	_	_
77	were	be	VBD	_	_	_
78	digested	digest	VBN	_	_	_
79	with	with	IN	_	_	_
80	MNase	mnase	NN	_	_	_
81	,	,	,	_	_	_
82	monosomes	monosome	NNS	_	_	_
83	were	be	VBD	_	_	_
84	purified	purify	VBN	_	_	_
85	by	by	IN	_	_	_
86	sucrose	sucrose	NN	_	_	_
87	gradient	gradient	NN	_	_	_
88	ultracentrifugation	ultracentrifugation	NN	_	_	_
89	,	,	,	_	_	_
90	and	and	CC	_	_	_
91	the	the	DT	_	_	_
92	resulting	result	VBG	_	_	_
93	mRNA	mrna	NN	_	_	_
94	fragments	fragment	NNS	_	_	_
95	were	be	VBD	_	_	_
96	extracted	extract	VBN	_	_	_
97	with	with	IN	_	_	_
98	phenol	phenol	NN	_	_	_
99	chloroform	chloroform	NN	_	_	_
100	and	and	CC	_	_	_
101	gel-purified	gel-purified	JJ	_	_	_
102	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Reads	Reads	NNPS	_	_	_
3	were	be	VBD	_	_	_
4	aligned	align	VBN	_	_	_
5	to	to	TO	_	_	_
6	the	the	DT	_	_	_
7	MG1655	mg1655	NN	_	_	_
8	genome	genome	NN	_	_	_
9	with	with	IN	_	_	_
10	Bowtie	Bowtie	NNP	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Reads	Reads	NNPS	_	_	_
3	were	be	VBD	_	_	_
4	trimmed	trim	VBN	_	_	_
5	and	and	CC	_	_	_
6	adaptors	adaptor	NNS	_	_	_
7	removed	remove	VBN	_	_	_
8	using	use	VBG	_	_	_
9	the	the	DT	_	_	_
10	fastx	fastx	NN	_	_	_
11	_	_	NN	_	_	_
12	toolkit	toolkit	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	replicate	replicate	VBP	_	_	_
3	:	:	:	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	replicate	replicate	VB	_	_	_
7	:	:	:	_	_	_
8	2	2	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
10	replicate	replicate	VBP	_	_	_
11	:	:	:	_	_	_
12	3	3	CD	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	replicate	replicate	VB	_	_	_
15	:	:	:	_	_	_
16	4	4	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	RNA-Seq	rna-seq	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	RNA	rna	NN	_	_	_
21	was	be	VBD	_	_	_
22	dephosphorylated	dephosphorylate	VBN	_	_	_
23	,	,	,	_	_	_
24	ligated	ligate	VBN	_	_	_
25	to	to	TO	_	_	_
26	an	a	DT	_	_	_
27	adaptor	adaptor	NN	_	_	_
28	,	,	,	_	_	_
29	reverse	reverse	JJ	_	_	_
30	transcribed	transcribe	VBN	_	_	_
31	,	,	,	_	_	_
32	circularized	circularize	VBN	_	_	_
33	then	then	RB	_	_	_
34	amplified	amplify	VBN	_	_	_
35	with	with	IN	_	_	_
36	Illumina	Illumina	NNP	_	_	_
37	adaptors	adaptor	NNS	_	_	_
38	and	and	CC	_	_	_
39	barcodes	barcode	NNS	_	_	_
40	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Supplementary	Supplementary	NNP	_	_	_
3	_	_	VBD	_	_	_
4	files	file	NNS	_	_	_
5	_	_	IN	_	_	_
6	format	format	NN	_	_	_
7	_	_	NN	_	_	_
8	and	and	CC	_	_	_
9	_	_	NN	_	_	_
10	content	content	NN	_	_	_
11	:	:	:	_	_	_
12	ecoli	ecolus	NNS	_	_	_
13	_	_	VBP	_	_	_
14	heatshock	heatshock	NN	_	_	_
15	_	_	NN	_	_	_
16	normalizedcounts.txt	normalizedcounts.txt	NN	_	_	_
17	:	:	:	_	_	_
18	Tab-delimited	tab-delimited	JJ	_	_	_
19	text	text	NN	_	_	_
20	file	file	NN	_	_	_
21	has	have	VBZ	_	_	_
22	EdgeR-normalized	edger-normalize	VBN	_	_	_
23	counts	count	NNS	_	_	_
24	per	per	IN	_	_	_
25	kilobase	kilobase	NN	_	_	_
26	million	million	CD	_	_	_
27	for	for	IN	_	_	_
28	each	each	DT	_	_	_
29	E.	e.	FW	_	_	_
30	coli	coli	FW	_	_	_
31	gene	gene	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	EcoCyc	ecocyc	NN	_	_	_
34	gene	gene	NN	_	_	_
35	names	name	NNS	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Supplementary	Supplementary	NNP	_	_	_
3	_	_	VBD	_	_	_
4	files	file	NNS	_	_	_
5	_	_	IN	_	_	_
6	format	format	NN	_	_	_
7	_	_	NN	_	_	_
8	and	and	CC	_	_	_
9	_	_	NN	_	_	_
10	content	content	NN	_	_	_
11	:	:	:	_	_	_
12	ecoli	ecolus	NNS	_	_	_
13	_	_	VBP	_	_	_
14	heatshock	heatshock	NN	_	_	_
15	_	_	NN	_	_	_
16	rawcounts.txt	rawcounts.txt	NN	_	_	_
17	:	:	:	_	_	_
18	Tab-delimited	tab-delimited	JJ	_	_	_
19	text	text	NN	_	_	_
20	file	file	NN	_	_	_
21	has	have	VBZ	_	_	_
22	raw	raw	JJ	_	_	_
23	read	read	NN	_	_	_
24	counts	count	VBZ	_	_	_
25	per	per	FW	_	_	_
26	kilobase	kilobase	NN	_	_	_
27	million	million	CD	_	_	_
28	for	for	IN	_	_	_
29	each	each	DT	_	_	_
30	E.	e.	FW	_	_	_
31	coli	coli	FW	_	_	_
32	gene	gene	NN	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	EcoCyc	ecocyc	NN	_	_	_
35	gene	gene	NN	_	_	_
36	names	name	NNS	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	number	number	NN	_	_	_
4	of	of	IN	_	_	_
5	reads	read	VBZ	_	_	_
6	at	at	IN	_	_	_
7	each	each	DT	_	_	_
8	position	position	NN	_	_	_
9	in	in	IN	_	_	_
10	the	the	DT	_	_	_
11	genome	genome	NN	_	_	_
12	was	be	VBD	_	_	_
13	counted	count	VBN	_	_	_
14	using	use	VBG	_	_	_
15	in-house	in-house	JJ	_	_	_
16	Python	Python	NNP	_	_	_
17	scripts	script	NNS	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	number	number	NN	_	_	_
4	of	of	IN	_	_	_
5	reads	read	VBZ	_	_	_
6	mapping	map	VBG	_	_	_
7	to	to	TO	_	_	_
8	each	each	DT	_	_	_
9	gene	gene	NN	_	_	_
10	was	be	VBD	_	_	_
11	counted	count	VBN	_	_	_
12	and	and	CC	_	_	_
13	normalized	normalize	VBN	_	_	_
14	using	use	VBG	_	_	_
15	EdgeR	edger	NN	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Total	Total	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	was	be	VBD	_	_	_
5	extracted	extract	VBN	_	_	_
6	with	with	IN	_	_	_
7	phenol	phenol	NN	_	_	_
8	chloroform	chloroform	NN	_	_	_
9	and	and	CC	_	_	_
10	alkaline	alkaline	NN	_	_	_
11	fragmented	fragmented	JJ	_	_	_
12	,	,	,	_	_	_
13	then	then	RB	_	_	_
14	fragments	fragment	NNS	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	20-40	20-40	CD	_	_	_
17	nt	nt	NNS	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	were	be	VBD	_	_	_
20	gel-purified	gel-purified	JJ	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	temperature	temperature	NN	_	_	_
4	:	:	:	_	_	_
5	30C	30c	CD	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	treatment	treatment	NN	_	_	_
8	temperature	temperature	NN	_	_	_
9	:	:	:	_	_	_
10	42C	42c	NN	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
12	All	all	DT	_	_	_
13	data	datum	NNS	_	_	_
14	analysis	analysis	NN	_	_	_
15	was	be	VBD	_	_	_
16	performed	perform	VBN	_	_	_
17	using	use	VBG	_	_	_
18	Rockhopper	Rockhopper	NNP	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	McClure	McClure	NNP	_	_	_
21	et	et	FW	_	_	_
22	al.	al.	FW	_	_	_
23	,	,	,	_	_	_
24	2013	2013	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	and	and	CC	_	_	_
27	Escherichia	escherichia	FW	Organism	_	_
28	coli	coli	FW	Organism	_	_
29	str	str	FW	_	_	_
30	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	as	as	IN	_	_	_
3	the	the	DT	_	_	_
4	reference	reference	NN	_	_	_
5	genome	genome	NN	_	_	_
6	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Blue	blue	JJ	_	_	_
3	_	_	NN	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Blue	blue	JJ	_	_	_
7	_	_	NN	_	_	_
8	2	2	CD	_	_	_
9	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
10	Data	datum	NNS	_	_	_
11	were	be	VBD	_	_	_
12	visualized	visualize	VBN	_	_	_
13	in	in	IN	_	_	_
14	the	the	DT	_	_	_
15	Rockhopper	Rockhopper	NNP	_	_	_
16	IGV	igv	NN	_	_	_
17	genome	genome	NN	_	_	_
18	browser	browser	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	McClure	McClure	NNP	_	_	_
21	et	et	FW	_	_	_
22	al.	al.	FW	_	_	_
23	,	,	,	_	_	_
24	2013	2013	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	and	and	CC	_	_	_
27	TreeView	TreeView	NNP	_	_	_
28	3.0	3.0	CD	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Saldana	Saldana	NNP	_	_	_
31	et	et	FW	_	_	_
32	al.	al.	FW	_	_	_
33	,	,	,	_	_	_
34	2004	2004	CD	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Genome	Genome	NNP	_	_	_
6	_	_	NNP	_	_	_
7	build	build	VB	_	_	_
8	:	:	:	_	_	_
9	ASM584v2	asm584v2	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	growth	growth	NN	_	_	_
12	protocol	protocol	NN	_	_	_
13	:	:	:	_	_	_
14	Log-phase	log-phase	JJ	_	_	_
15	culture	culture	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	LB	lb	NN	MED	_	_
18	broth	broth	NN	MED	_	_
19	,	,	,	_	_	_
20	Miller	Miller	NNP	_	_	_
21	formulation	formulation	NN	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	inoculated	inoculate	VBN	_	_	_
24	with	with	IN	_	_	_
25	one	one	CD	_	_	_
26	blue	blue	JJ	_	_	_
27	colony	colony	NN	_	_	_
28	and	and	CC	_	_	_
29	grown	grow	VBN	_	_	_
30	for	for	IN	_	_	_
31	5	5	CD	_	_	_
32	hr	hr	NN	_	_	_
33	at	at	IN	_	_	_
34	37	37	CD	_	_	_
35	degrees	degree	NNS	_	_	_
36	celsius	celsius	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	growth	growth	NN	_	_	_
39	protocol	protocol	NN	_	_	_
40	:	:	:	_	_	_
41	Log-phase	log-phase	JJ	_	_	_
42	culture	culture	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	LB	lb	NN	MED	_	_
45	broth	broth	NN	MED	_	_
46	,	,	,	_	_	_
47	Miller	Miller	NNP	_	_	_
48	formulation	formulation	NN	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	inoculated	inoculate	VBN	_	_	_
51	with	with	IN	_	_	_
52	one	one	CD	_	_	_
53	pale	pale	JJ	_	_	_
54	colony	colony	NN	_	_	_
55	and	and	CC	_	_	_
56	grown	grow	VBN	_	_	_
57	for	for	IN	_	_	_
58	5	5	CD	_	_	_
59	hr	hr	NN	_	_	_
60	at	at	IN	_	_	_
61	37	37	CD	_	_	_
62	degrees	degree	NNS	_	_	_
63	celsius	celsius	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	Log-phase	log-phase	NN	_	_	_
66	cultures	culture	NNS	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	LB	lb	NN	MED	_	_
69	broth	broth	NN	MED	_	_
70	,	,	,	_	_	_
71	Miller	Miller	NNP	_	_	_
72	formulation	formulation	NN	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	inoculated	inoculate	VBN	_	_	_
75	with	with	IN	_	_	_
76	either	either	CC	_	_	_
77	blue	blue	JJ	_	_	_
78	or	or	CC	_	_	_
79	pale	pale	JJ	_	_	_
80	colonies	colony	NNS	_	_	_
81	were	be	VBD	_	_	_
82	grown	grow	VBN	_	_	_
83	for	for	IN	_	_	_
84	5	5	CD	_	_	_
85	hr	hr	NN	_	_	_
86	at	at	IN	_	_	_
87	37	37	CD	_	_	_
88	degrees	degree	NNS	_	_	_
89	celsius	celsius	NN	_	_	_
90	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	pelleted	pellete	VBN	_	_	_
4	by	by	IN	_	_	_
5	centrifugation	centrifugation	NN	_	_	_
6	and	and	CC	_	_	_
7	flash	flash	NN	_	_	_
8	frozen	freeze	VBN	_	_	_
9	on	on	IN	_	_	_
10	dry	dry	JJ	_	_	_
11	ice	ice	NN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Pale	Pale	NNP	_	_	_
3	_	_	SYM	_	_	_
4	1	1	CD	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Pale	Pale	NNP	_	_	_
7	_	_	SYM	_	_	_
8	3	3	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	parent	parent	NN	_	_	_
11	strain	strain	NN	_	_	_
12	:	:	:	_	_	_
13	BW27785	bw27785	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	phenotype	phenotype	NN	_	_	_
16	:	:	:	_	_	_
17	Blue	Blue	NNP	_	_	_
18	colony-color	colony-color	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	prion-containing	prion-containing	JJ	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
23	phenotype	phenotype	NN	_	_	_
24	:	:	:	_	_	_
25	Pale	Pale	NNP	_	_	_
26	colony-color	colony-color	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	prion-lacking	prion-lacking	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	Purified	purify	VBN	_	_	_
32	total	total	JJ	_	_	_
33	RNA	rna	NN	_	_	_
34	was	be	VBD	_	_	_
35	depleted	deplete	VBN	_	_	_
36	of	of	IN	_	_	_
37	rRNA	rrna	NN	_	_	_
38	using	use	VBG	_	_	_
39	a	a	DT	_	_	_
40	Ribo-Zero	ribo-zero	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	Bacteria	bacterium	NNS	_	_	_
43	-RRB-	-rrb-	-RRB-	_	_	_
44	rRNA	rrna	NN	_	_	_
45	Removal	removal	NN	_	_	_
46	Kit	kit	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	Illumina	Illumina	NNP	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	libraries	library	NNS	_	_	_
3	were	be	VBD	_	_	_
4	constructed	construct	VBN	_	_	_
5	and	and	CC	_	_	_
6	sequenced	sequence	VBN	_	_	_
7	on	on	IN	_	_	_
8	an	a	DT	_	_	_
9	Illumina	Illumina	NNP	_	_	_
10	NextSeq	NextSeq	NNP	_	_	_
11	500	500	CD	_	_	_
12	sequencer	sequencer	NN	_	_	_
13	at	at	IN	_	_	_
14	the	the	DT	_	_	_
15	Harvard	Harvard	NNP	_	_	_
16	Biopolymers	Biopolymers	NNP	_	_	_
17	Facility	Facility	NNP	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Specifically	specifically	RB	_	_	_
5	,	,	,	_	_	_
6	data	datum	NNS	_	_	_
7	were	be	VBD	_	_	_
8	treated	treat	VBN	_	_	_
9	as	as	IN	_	_	_
10	two	two	CD	_	_	_
11	experiments	experiment	NNS	_	_	_
12	constituting	constitute	VBG	_	_	_
13	either	either	CC	_	_	_
14	two	two	CD	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	lue	lue	NN	_	_	_
17	\	\	NN	_	_	_
18	cell	cell	NN	_	_	_
19	transcriptomes	transcriptome	NNS	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	or	or	CC	_	_	_
22	three	three	CD	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	\	\	CD	_	_	_
25	pale	pale	JJ	_	_	_
26	\	\	NN	_	_	_
27	cell	cell	NN	_	_	_
28	transcriptomes	transcriptome	NNS	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	biological	biological	JJ	_	_	_
31	replicates	replicate	VBZ	_	_	_
32	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Supplementary	Supplementary	NNP	_	_	_
3	_	_	VBD	_	_	_
4	files	file	NNS	_	_	_
5	_	_	IN	_	_	_
6	format	format	NN	_	_	_
7	_	_	NN	_	_	_
8	and	and	CC	_	_	_
9	_	_	NN	_	_	_
10	content	content	NN	_	_	_
11	:	:	:	_	_	_
12	Tab-delimited	tab-delimited	JJ	_	_	_
13	text	text	NN	_	_	_
14	file	file	NN	_	_	_
15	includes	include	VBZ	_	_	_
16	Rockhopper	Rockhopper	NNP	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	McClure	McClure	NNP	_	_	_
19	et	et	FW	_	_	_
20	al.	al.	FW	_	_	_
21	,	,	,	_	_	_
22	2013	2013	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	normalized	normalize	VBD	_	_	_
25	transcript	transcript	NN	_	_	_
26	abundance	abundance	NN	_	_	_
27	measurements	measurement	NNS	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Expression	expression	NN	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	,	,	,	_	_	_
32	transcript	transcript	NN	_	_	_
33	abundance	abundance	NN	_	_	_
34	ratios	ratio	NNS	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	Expression	expression	NN	_	_	_
37	Ratio	ratio	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	,	,	,	_	_	_
40	and	and	CC	_	_	_
41	qValues	qvalue	NNS	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	qValue	qvalue	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	for	for	IN	_	_	_
46	raw	raw	JJ	_	_	_
47	data	datum	NNS	_	_	_
48	that	that	WDT	_	_	_
49	were	be	VBD	_	_	_
50	treated	treat	VBN	_	_	_
51	as	as	IN	_	_	_
52	two	two	CD	_	_	_
53	experiments	experiment	NNS	_	_	_
54	constituting	constitute	VBG	_	_	_
55	either	either	CC	_	_	_
56	two	two	CD	_	_	_
57	-LRB-	-lrb-	-LRB-	_	_	_
58	lue	lue	NN	_	_	_
59	\	\	NN	_	_	_
60	cell	cell	NN	_	_	_
61	transcriptomes	transcriptome	NNS	_	_	_
62	;	;	:	_	_	_
63	Blue	blue	JJ	_	_	_
64	_	_	NN	_	_	_
65	1	1	CD	_	_	_
66	.	.	.	_	_	_

1	fastq	fastq	NN	_	_	_
2	,	,	,	_	_	_
3	Blue	blue	JJ	_	_	_
4	_	_	NN	_	_	_
5	2	2	CD	_	_	_
6	.	.	.	_	_	_

1	fastq	fastq	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	or	or	CC	_	_	_
4	three	three	CD	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	\	\	CD	_	_	_
7	pale	pale	JJ	_	_	_
8	\	\	NN	_	_	_
9	cell	cell	NN	_	_	_
10	transcriptomes	transcriptome	NNS	_	_	_
11	;	;	:	_	_	_
12	Pale	Pale	NNP	_	_	_
13	_	_	SYM	_	_	_
14	1	1	LS	_	_	_
15	.	.	.	_	_	_

1	fastq	fastq	NN	_	_	_
2	,	,	,	_	_	_
3	Pale	Pale	NNP	_	_	_
4	_	_	SYM	_	_	_
5	2	2	LS	_	_	_
6	.	.	.	_	_	_

1	fastq	fastq	NN	_	_	_
2	,	,	,	_	_	_
3	Pale	Pale	NNP	_	_	_
4	_	_	SYM	_	_	_
5	3	3	LS	_	_	_
6	.	.	.	_	_	_

1	fastq	fastq	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	biological	biological	JJ	_	_	_
4	replicates	replicate	VBZ	_	_	_
5	.	.	.	_	_	_

1	Gene	Gene	NNP	_	_	_
2	annotation	annotation	NN	_	_	_
3	,	,	,	_	_	_
4	gene	gene	NN	_	_	_
5	product	product	NN	_	_	_
6	description	description	NN	_	_	_
7	,	,	,	_	_	_
8	and	and	CC	_	_	_
9	strand	strand	NN	_	_	_
10	information	information	NN	_	_	_
11	is	be	VBZ	_	_	_
12	also	also	RB	_	_	_
13	included	include	VBN	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Total	total	JJ	_	_	_
3	RNA	rna	NN	_	_	_
4	extracted	extract	VBN	_	_	_
5	from	from	IN	_	_	_
6	Rho	rho	NN	_	_	_
7	prion-containing	prion-containing	JJ	_	_	_
8	cells	cell	NNS	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
10	Total	total	JJ	_	_	_
11	RNA	rna	NN	_	_	_
12	extracted	extract	VBN	_	_	_
13	from	from	IN	_	_	_
14	Rho	rho	NN	_	_	_
15	prion-lacking	prion-lacking	JJ	_	_	_
16	cells	cell	NNS	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
18	Total	total	JJ	_	_	_
19	RNA	rna	NN	_	_	_
20	was	be	VBD	_	_	_
21	extracted	extract	VBN	_	_	_
22	from	from	IN	_	_	_
23	cell	cell	NN	_	_	_
24	pellets	pellet	NNS	_	_	_
25	with	with	IN	_	_	_
26	TRI	TRI	NNP	_	_	_
27	Reagent	Reagent	NNP	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	MRC	MRC	NNP	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	precipitated	precipitated	JJ	_	_	_
4	,	,	,	_	_	_
5	resuspended	resuspended	JJ	_	_	_
6	in	in	IN	_	_	_
7	DNase	dnase	NN	_	_	_
8	Reaction	reaction	NN	_	_	_
9	Buffer	buffer	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Invitrogen	invitrogen	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	for	for	IN	_	_	_
14	30	30	CD	_	_	_
15	min	min	NN	_	_	_
16	at	at	IN	_	_	_
17	room	room	NN	_	_	_
18	temperature	temperature	NN	_	_	_
19	.	.	.	_	_	_

1	DNase-treated	dnase-treated	JJ	_	_	_
2	samples	sample	NNS	_	_	_
3	were	be	VBD	_	_	_
4	subsequently	subsequently	RB	_	_	_
5	purified	purify	VBN	_	_	_
6	with	with	IN	_	_	_
7	an	a	DT	_	_	_
8	Rneasy	Rneasy	NNP	_	_	_
9	Plus	Plus	NNP	_	_	_
10	Mini	Mini	NNP	_	_	_
11	Kit	kit	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Qiagen	qiagen	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	chemostat	chemostat	NN	_	_	_
3	STR	str	NN	_	_	_
4	culture	culture	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	chemostat	chemostat	NN	_	_	_
7	STR	str	NN	_	_	_
8	culture	culture	NN	_	_	_
9	STR	str	NN	_	_	_
10	reference	reference	NN	_	_	_
11	1	1	CD	_	_	_
12	,	,	,	_	_	_
13	rep1	rep1	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	chemostat	chemostat	NN	_	_	_
16	STR	str	NN	_	_	_
17	culture	culture	NN	_	_	_
18	STR	str	NN	_	_	_
19	reference	reference	NN	_	_	_
20	1	1	CD	_	_	_
21	,	,	,	_	_	_
22	rep2	rep2	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	chemostat	chemostat	NN	_	_	_
25	STR	str	NN	_	_	_
26	culture	culture	NN	_	_	_
27	STR	str	NN	_	_	_
28	reference	reference	NN	_	_	_
29	2	2	CD	_	_	_
30	,	,	,	_	_	_
31	rep1	rep1	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	chemostat	chemostat	NN	_	_	_
34	STR	str	NN	_	_	_
35	culture	culture	NN	_	_	_
36	STR	str	NN	_	_	_
37	reference	reference	NN	_	_	_
38	2	2	CD	_	_	_
39	,	,	,	_	_	_
40	rep2	rep2	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	chemostat	chemostat	NN	_	_	_
43	STR	str	NN	_	_	_
44	culture	culture	NN	_	_	_
45	STR	str	NN	_	_	_
46	reference	reference	NN	_	_	_
47	3	3	CD	_	_	_
48	,	,	,	_	_	_
49	rep1	rep1	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	chemostat	chemostat	NN	_	_	_
52	STR	str	NN	_	_	_
53	culture	culture	NN	_	_	_
54	STR	str	NN	_	_	_
55	reference	reference	NN	_	_	_
56	3	3	CD	_	_	_
57	,	,	,	_	_	_
58	rep2	rep2	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	chemostat	chemostat	NN	_	_	_
61	STR-PFR	str-pfr	NN	_	_	_
62	culture	culture	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	chemostat	chemostat	NN	_	_	_
65	STR-PFR	str-pfr	NN	_	_	_
66	culture	culture	NN	_	_	_
67	PFR	pfr	NN	_	_	_
68	P1	p1	NN	_	_	_
69	120	120	CD	_	_	_
70	min	min	NN	_	_	_
71	,	,	,	_	_	_
72	rep1	rep1	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	chemostat	chemostat	NN	_	_	_
75	STR-PFR	str-pfr	NN	_	_	_
76	culture	culture	NN	_	_	_
77	PFR	pfr	NN	_	_	_
78	P1	p1	NN	_	_	_
79	120	120	CD	_	_	_
80	min	min	NN	_	_	_
81	,	,	,	_	_	_
82	rep2	rep2	NN	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
84	chemostat	chemostat	NN	_	_	_
85	STR-PFR	str-pfr	NN	_	_	_
86	culture	culture	NN	_	_	_
87	PFR	pfr	NN	_	_	_
88	P1	p1	NN	_	_	_
89	25	25	CD	_	_	_
90	min	min	NN	_	_	_
91	,	,	,	_	_	_
92	rep1	rep1	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	chemostat	chemostat	NN	_	_	_
95	STR-PFR	str-pfr	NN	_	_	_
96	culture	culture	NN	_	_	_
97	PFR	pfr	NN	_	_	_
98	P1	p1	NN	_	_	_
99	25	25	CD	_	_	_
100	min	min	NN	_	_	_
101	,	,	,	_	_	_
102	rep2	rep2	NN	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	chemostat	chemostat	NN	_	_	_
105	STR-PFR	str-pfr	NN	_	_	_
106	culture	culture	NN	_	_	_
107	PFR	pfr	NN	_	_	_
108	P1	p1	NN	_	_	_
109	28h	28h	NN	_	_	_
110	,	,	,	_	_	_
111	rep1	rep1	NN	_	_	_
112	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
113	chemostat	chemostat	NN	_	_	_
114	STR-PFR	str-pfr	NN	_	_	_
115	culture	culture	NN	_	_	_
116	PFR	pfr	NN	_	_	_
117	P1	p1	NN	_	_	_
118	28h	28h	NN	_	_	_
119	,	,	,	_	_	_
120	rep2	rep2	NN	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	chemostat	chemostat	NN	_	_	_
123	STR-PFR	str-pfr	NN	_	_	_
124	culture	culture	NN	_	_	_
125	PFR	pfr	NN	_	_	_
126	P3	p3	NN	_	_	_
127	120	120	CD	_	_	_
128	min	min	NN	_	_	_
129	,	,	,	_	_	_
130	rep1	rep1	NN	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	chemostat	chemostat	NN	_	_	_
133	STR-PFR	str-pfr	NN	_	_	_
134	culture	culture	NN	_	_	_
135	PFR	pfr	NN	_	_	_
136	P3	p3	NN	_	_	_
137	120	120	CD	_	_	_
138	min	min	NN	_	_	_
139	,	,	,	_	_	_
140	rep2	rep2	NN	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	chemostat	chemostat	NN	_	_	_
143	STR-PFR	str-pfr	NN	_	_	_
144	culture	culture	NN	_	_	_
145	PFR	pfr	NN	_	_	_
146	P3	p3	NN	_	_	_
147	25	25	CD	_	_	_
148	min	min	NN	_	_	_
149	,	,	,	_	_	_
150	rep1	rep1	NN	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	chemostat	chemostat	NN	_	_	_
153	STR-PFR	str-pfr	NN	_	_	_
154	culture	culture	NN	_	_	_
155	PFR	pfr	NN	_	_	_
156	P3	p3	NN	_	_	_
157	25	25	CD	_	_	_
158	min	min	NN	_	_	_
159	,	,	,	_	_	_
160	rep2	rep2	NN	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	chemostat	chemostat	NN	_	_	_
163	STR-PFR	str-pfr	NN	_	_	_
164	culture	culture	NN	_	_	_
165	PFR	pfr	NN	_	_	_
166	P3	p3	NN	_	_	_
167	28h	28h	NN	_	_	_
168	,	,	,	_	_	_
169	rep1	rep1	NN	_	_	_
170	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
171	chemostat	chemostat	NN	_	_	_
172	STR-PFR	str-pfr	NN	_	_	_
173	culture	culture	NN	_	_	_
174	PFR	pfr	NN	_	_	_
175	P3	p3	NN	_	_	_
176	28h	28h	NN	_	_	_
177	,	,	,	_	_	_
178	rep2	rep2	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	chemostat	chemostat	NN	_	_	_
181	STR-PFR	str-pfr	NN	_	_	_
182	culture	culture	NN	_	_	_
183	PFR	pfr	NN	_	_	_
184	P5	p5	NN	_	_	_
185	10	10	CD	_	_	_
186	min	min	NN	_	_	_
187	,	,	,	_	_	_
188	rep1	rep1	NN	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	chemostat	chemostat	NN	_	_	_
191	STR-PFR	str-pfr	NN	_	_	_
192	culture	culture	NN	_	_	_
193	PFR	pfr	NN	_	_	_
194	P5	p5	NN	_	_	_
195	10	10	CD	_	_	_
196	min	min	NN	_	_	_
197	,	,	,	_	_	_
198	rep2	rep2	NN	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	chemostat	chemostat	NN	_	_	_
201	STR-PFR	str-pfr	NN	_	_	_
202	culture	culture	NN	_	_	_
203	PFR	pfr	NN	_	_	_
204	P5	p5	NN	_	_	_
205	120	120	CD	_	_	_
206	min	min	NN	_	_	_
207	,	,	,	_	_	_
208	rep1	rep1	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	chemostat	chemostat	NN	_	_	_
211	STR-PFR	str-pfr	NN	_	_	_
212	culture	culture	NN	_	_	_
213	PFR	pfr	NN	_	_	_
214	P5	p5	NN	_	_	_
215	120	120	CD	_	_	_
216	min	min	NN	_	_	_
217	,	,	,	_	_	_
218	rep2	rep2	NN	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	chemostat	chemostat	NN	_	_	_
221	STR-PFR	str-pfr	NN	_	_	_
222	culture	culture	NN	_	_	_
223	PFR	pfr	NN	_	_	_
224	P5	p5	NN	_	_	_
225	210	210	CD	_	_	_
226	min	min	NN	_	_	_
227	,	,	,	_	_	_
228	rep1	rep1	NN	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
230	chemostat	chemostat	NN	_	_	_
231	STR-PFR	str-pfr	NN	_	_	_
232	culture	culture	NN	_	_	_
233	PFR	pfr	NN	_	_	_
234	P5	p5	NN	_	_	_
235	210	210	CD	_	_	_
236	min	min	NN	_	_	_
237	,	,	,	_	_	_
238	rep2	rep2	NN	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	chemostat	chemostat	NN	_	_	_
241	STR-PFR	str-pfr	NN	_	_	_
242	culture	culture	NN	_	_	_
243	PFR	pfr	NN	_	_	_
244	P5	p5	NN	_	_	_
245	25h	25h	NN	_	_	_
246	,	,	,	_	_	_
247	rep1	rep1	NN	_	_	_
248	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
249	chemostat	chemostat	NN	_	_	_
250	STR-PFR	str-pfr	NN	_	_	_
251	culture	culture	NN	_	_	_
252	PFR	pfr	NN	_	_	_
253	P5	p5	NN	_	_	_
254	25h	25h	NN	_	_	_
255	,	,	,	_	_	_
256	rep2	rep2	NN	_	_	_
257	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
258	chemostat	chemostat	NN	_	_	_
259	STR-PFR	str-pfr	NN	_	_	_
260	culture	culture	NN	_	_	_
261	PFR	pfr	NN	_	_	_
262	P5	p5	NN	_	_	_
263	25	25	CD	_	_	_
264	min	min	NN	_	_	_
265	,	,	,	_	_	_
266	rep1	rep1	NN	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	chemostat	chemostat	NN	_	_	_
269	STR-PFR	str-pfr	NN	_	_	_
270	culture	culture	NN	_	_	_
271	PFR	pfr	NN	_	_	_
272	P5	p5	NN	_	_	_
273	25	25	CD	_	_	_
274	min	min	NN	_	_	_
275	,	,	,	_	_	_
276	rep2	rep2	NN	_	_	_
277	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
278	chemostat	chemostat	NN	_	_	_
279	STR-PFR	str-pfr	NN	_	_	_
280	culture	culture	NN	_	_	_
281	PFR	pfr	NN	_	_	_
282	P5	p5	NN	_	_	_
283	26h	26h	NN	_	_	_
284	,	,	,	_	_	_
285	rep2	rep2	NN	_	_	_
286	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
287	chemostat	chemostat	NN	_	_	_
288	STR-PFR	str-pfr	NN	_	_	_
289	culture	culture	NN	_	_	_
290	PFR	pfr	NN	_	_	_
291	P5	p5	NN	_	_	_
292	28h	28h	NN	_	_	_
293	,	,	,	_	_	_
294	rep1	rep1	NN	_	_	_
295	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
296	chemostat	chemostat	NN	_	_	_
297	STR-PFR	str-pfr	NN	_	_	_
298	culture	culture	NN	_	_	_
299	PFR	pfr	NN	_	_	_
300	P5	p5	NN	_	_	_
301	28h	28h	NN	_	_	_
302	,	,	,	_	_	_
303	rep2	rep2	NN	_	_	_
304	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
305	chemostat	chemostat	NN	_	_	_
306	STR-PFR	str-pfr	NN	_	_	_
307	culture	culture	NN	_	_	_
308	PFR	pfr	NN	_	_	_
309	P5	p5	NN	_	_	_
310	330	330	CD	_	_	_
311	min	min	NN	_	_	_
312	,	,	,	_	_	_
313	rep2	rep2	NN	_	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	chemostat	chemostat	NN	_	_	_
316	STR-PFR	str-pfr	NN	_	_	_
317	culture	culture	NN	_	_	_
318	PFR	pfr	NN	_	_	_
319	P5	p5	NN	_	_	_
320	45	45	CD	_	_	_
321	min	min	NN	_	_	_
322	,	,	,	_	_	_
323	rep1	rep1	NN	_	_	_
324	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
325	chemostat	chemostat	NN	_	_	_
326	STR-PFR	str-pfr	NN	_	_	_
327	culture	culture	NN	_	_	_
328	PFR	pfr	NN	_	_	_
329	P5	p5	NN	_	_	_
330	45	45	CD	_	_	_
331	min	min	NN	_	_	_
332	,	,	,	_	_	_
333	rep2	rep2	NN	_	_	_
334	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
335	chemostat	chemostat	NN	_	_	_
336	STR-PFR	str-pfr	NN	_	_	_
337	culture	culture	NN	_	_	_
338	PFR	pfr	NN	_	_	_
339	P5	p5	NN	_	_	_
340	5	5	CD	_	_	_
341	min	min	NN	_	_	_
342	,	,	,	_	_	_
343	rep1	rep1	NN	_	_	_
344	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
345	chemostat	chemostat	NN	_	_	_
346	STR-PFR	str-pfr	NN	_	_	_
347	culture	culture	NN	_	_	_
348	PFR	pfr	NN	_	_	_
349	P5	p5	NN	_	_	_
350	5	5	CD	_	_	_
351	min	min	NN	_	_	_
352	,	,	,	_	_	_
353	rep2	rep2	NN	_	_	_
354	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
355	chemostat	chemostat	NN	_	_	_
356	STR-PFR	str-pfr	NN	_	_	_
357	culture	culture	NN	_	_	_
358	PFR	pfr	NN	_	_	_
359	P5	p5	NN	_	_	_
360	75	75	CD	_	_	_
361	min	min	NN	_	_	_
362	,	,	,	_	_	_
363	rep2	rep2	NN	_	_	_
364	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
365	chemostat	chemostat	NN	_	_	_
366	STR-PFR	str-pfr	NN	_	_	_
367	culture	culture	NN	_	_	_
368	STR	str	NN	_	_	_
369	10	10	CD	_	_	_
370	min	min	NN	_	_	_
371	,	,	,	_	_	_
372	rep1	rep1	NN	_	_	_
373	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
374	chemostat	chemostat	NN	_	_	_
375	STR-PFR	str-pfr	NN	_	_	_
376	culture	culture	NN	_	_	_
377	STR	str	NN	_	_	_
378	10	10	CD	_	_	_
379	min	min	NN	_	_	_
380	,	,	,	_	_	_
381	rep2	rep2	NN	_	_	_
382	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
383	chemostat	chemostat	NN	_	_	_
384	STR-PFR	str-pfr	NN	_	_	_
385	culture	culture	NN	_	_	_
386	STR	str	NN	_	_	_
387	120	120	CD	_	_	_
388	min	min	NN	_	_	_
389	,	,	,	_	_	_
390	rep1	rep1	NN	_	_	_
391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
392	chemostat	chemostat	NN	_	_	_
393	STR-PFR	str-pfr	NN	_	_	_
394	culture	culture	NN	_	_	_
395	STR	str	NN	_	_	_
396	120	120	CD	_	_	_
397	min	min	NN	_	_	_
398	,	,	,	_	_	_
399	rep2	rep2	NN	_	_	_
400	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
401	chemostat	chemostat	NN	_	_	_
402	STR-PFR	str-pfr	NN	_	_	_
403	culture	culture	NN	_	_	_
404	STR	str	NN	_	_	_
405	210	210	CD	_	_	_
406	min	min	NN	_	_	_
407	,	,	,	_	_	_
408	rep1	rep1	NN	_	_	_
409	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
410	chemostat	chemostat	NN	_	_	_
411	STR-PFR	str-pfr	NN	_	_	_
412	culture	culture	NN	_	_	_
413	STR	str	NN	_	_	_
414	210	210	CD	_	_	_
415	min	min	NN	_	_	_
416	,	,	,	_	_	_
417	rep2	rep2	NN	_	_	_
418	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
419	chemostat	chemostat	NN	_	_	_
420	STR-PFR	str-pfr	NN	_	_	_
421	culture	culture	NN	_	_	_
422	STR	str	NN	_	_	_
423	25h	25h	NN	_	_	_
424	,	,	,	_	_	_
425	rep1	rep1	NN	_	_	_
426	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
427	chemostat	chemostat	NN	_	_	_
428	STR-PFR	str-pfr	NN	_	_	_
429	culture	culture	NN	_	_	_
430	STR	str	NN	_	_	_
431	25h	25h	NN	_	_	_
432	,	,	,	_	_	_
433	rep2	rep2	NN	_	_	_
434	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
435	chemostat	chemostat	NN	_	_	_
436	STR-PFR	str-pfr	NN	_	_	_
437	culture	culture	NN	_	_	_
438	STR	str	NN	_	_	_
439	25	25	CD	_	_	_
440	min	min	NN	_	_	_
441	,	,	,	_	_	_
442	rep1	rep1	NN	_	_	_
443	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
444	chemostat	chemostat	NN	_	_	_
445	STR-PFR	str-pfr	NN	_	_	_
446	culture	culture	NN	_	_	_
447	STR	str	NN	_	_	_
448	25	25	CD	_	_	_
449	min	min	NN	_	_	_
450	,	,	,	_	_	_
451	rep2	rep2	NN	_	_	_
452	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
453	chemostat	chemostat	NN	_	_	_
454	STR-PFR	str-pfr	NN	_	_	_
455	culture	culture	NN	_	_	_
456	STR	str	NN	_	_	_
457	26h	26h	NN	_	_	_
458	,	,	,	_	_	_
459	rep1	rep1	NN	_	_	_
460	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
461	chemostat	chemostat	NN	_	_	_
462	STR-PFR	str-pfr	NN	_	_	_
463	culture	culture	NN	_	_	_
464	STR	str	NN	_	_	_
465	26h	26h	NN	_	_	_
466	,	,	,	_	_	_
467	rep2	rep2	NN	_	_	_
468	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
469	chemostat	chemostat	NN	_	_	_
470	STR-PFR	str-pfr	NN	_	_	_
471	culture	culture	NN	_	_	_
472	STR	str	NN	_	_	_
473	28h	28h	NN	_	_	_
474	,	,	,	_	_	_
475	rep1	rep1	NN	_	_	_
476	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
477	chemostat	chemostat	NN	_	_	_
478	STR-PFR	str-pfr	NN	_	_	_
479	culture	culture	NN	_	_	_
480	STR	str	NN	_	_	_
481	28h	28h	NN	_	_	_
482	,	,	,	_	_	_
483	rep2	rep2	NN	_	_	_
484	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
485	chemostat	chemostat	NN	_	_	_
486	STR-PFR	str-pfr	NN	_	_	_
487	culture	culture	NN	_	_	_
488	STR	str	NN	_	_	_
489	330	330	CD	_	_	_
490	min	min	NN	_	_	_
491	,	,	,	_	_	_
492	rep1	rep1	NN	_	_	_
493	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
494	chemostat	chemostat	NN	_	_	_
495	STR-PFR	str-pfr	NN	_	_	_
496	culture	culture	NN	_	_	_
497	STR	str	NN	_	_	_
498	330	330	CD	_	_	_
499	min	min	NN	_	_	_
500	,	,	,	_	_	_
501	rep2	rep2	NN	_	_	_
502	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
503	chemostat	chemostat	NN	_	_	_
504	STR-PFR	str-pfr	NN	_	_	_
505	culture	culture	NN	_	_	_
506	STR	str	NN	_	_	_
507	45	45	CD	_	_	_
508	min	min	NN	_	_	_
509	,	,	,	_	_	_
510	rep1	rep1	NN	_	_	_
511	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
512	chemostat	chemostat	NN	_	_	_
513	STR-PFR	str-pfr	NN	_	_	_
514	culture	culture	NN	_	_	_
515	STR	str	NN	_	_	_
516	45	45	CD	_	_	_
517	min	min	NN	_	_	_
518	,	,	,	_	_	_
519	rep2	rep2	NN	_	_	_
520	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
521	chemostat	chemostat	NN	_	_	_
522	STR-PFR	str-pfr	NN	_	_	_
523	culture	culture	NN	_	_	_
524	STR	str	NN	_	_	_
525	5	5	CD	_	_	_
526	min	min	NN	_	_	_
527	,	,	,	_	_	_
528	rep1	rep1	NN	_	_	_
529	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
530	chemostat	chemostat	NN	_	_	_
531	STR-PFR	str-pfr	NN	_	_	_
532	culture	culture	NN	_	_	_
533	STR	str	NN	_	_	_
534	5	5	CD	_	_	_
535	min	min	NN	_	_	_
536	,	,	,	_	_	_
537	rep2	rep2	NN	_	_	_
538	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
539	chemostat	chemostat	NN	_	_	_
540	STR-PFR	str-pfr	NN	_	_	_
541	culture	culture	NN	_	_	_
542	STR	str	NN	_	_	_
543	75	75	CD	_	_	_
544	min	min	NN	_	_	_
545	,	,	,	_	_	_
546	rep1	rep1	NN	_	_	_
547	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
548	chemostat	chemostat	NN	_	_	_
549	STR-PFR	str-pfr	NN	_	_	_
550	culture	culture	NN	_	_	_
551	STR	str	NN	_	_	_
552	75	75	CD	_	_	_
553	min	min	NN	_	_	_
554	,	,	,	_	_	_
555	rep2	rep2	NN	_	_	_
556	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
557	E.	E.	NNP	_	_	_
558	coli	coli	NN	_	_	_
559	K12	k12	NN	_	_	_
560	substrain	substrain	NN	_	_	_
561	W3110	w3110	NN	_	_	_
562	was	be	VBD	_	_	_
563	used	use	VBN	_	_	_
564	in	in	IN	_	_	_
565	this	this	DT	_	_	_
566	study	study	NN	_	_	_
567	.	.	.	_	_	_

1	Bioreactor	Bioreactor	NNP	_	_	_
2	cultivations	cultivation	NNS	_	_	_
3	were	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	using	use	VBG	_	_	_
6	a	a	DT	_	_	_
7	two-compartment	two-compartment	JJ	_	_	_
8	bioreactor	bioreactor	NN	_	_	_
9	system	system	NN	_	_	_
10	consisting	consist	VBG	_	_	_
11	of	of	IN	_	_	_
12	an	a	DT	_	_	_
13	STR	str	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	3L	3l	NN	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	with	with	IN	_	_	_
18	a	a	DT	_	_	_
19	recycle	recycle	VB	_	_	_
20	loop	loop	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	PFR	pfr	NN	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	in	in	IN	_	_	_
25	defined	define	VBN	_	_	_
26	medium	medium	NN	_	_	_
27	at	at	IN	_	_	_
28	pH7	ph7	NN	_	_	_
29	and	and	CC	_	_	_
30	37	37	CD	_	_	_
31	°C	°c	NN	_	_	_
32	.	.	.	_	_	_

1	Bioreactor	Bioreactor	NNP	_	_	_
2	cultivations	cultivation	NNS	_	_	_
3	were	be	VBD	_	_	_
4	carried	carry	VBN	_	_	_
5	out	out	RP	_	_	_
6	with	with	IN	_	_	_
7	a	a	DT	_	_	_
8	minimal	minimal	JJ	_	_	_
9	medium	medium	NN	_	_	_
10	containing	contain	VBG	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	per	per	IN	_	_	_
13	liter	liter	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	19.0	19.0	CD	_	_	_
16	g	g	NN	_	_	_
17	glucose	glucose	NN	SUPP	_	_
18	,	,	,	_	_	_
19	1.0	1.0	CD	_	_	_
20	g	g	NN	_	_	_
21	NaH2PO4	nah2po4	NN	_	_	_
22	.	.	.	_	_	_

1	·	·	NN	_	_	_
2	2	2	CD	_	_	_
3	H2O	h2o	NN	_	_	_
4	,	,	,	_	_	_
5	2.6	2.6	CD	_	_	_
6	g	g	NN	_	_	_
7	K2HPO4	k2hpo4	NN	_	_	_
8	,	,	,	_	_	_
9	3.8	3.8	CD	_	_	_
10	g	g	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	NH4	nh4	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	2SO4	2so4	NN	_	_	_
15	,	,	,	_	_	_
16	and	and	CC	_	_	_
17	a	a	DT	_	_	_
18	trace	trace	NN	_	_	_
19	element	element	NN	_	_	_
20	solution	solution	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	0.11	0.11	CD	_	_	_
23	g	g	NN	_	_	_
24	Na3C6H5O7	na3c6h5o7	NN	_	_	_
25	,	,	,	_	_	_
26	0.00835	0.00835	CD	_	_	_
27	g	g	NN	_	_	_
28	FeCl3	fecl3	NN	_	_	_
29	·	·	NN	_	_	_
30	6	6	CD	_	_	_
31	H2O	h2o	NN	_	_	_
32	,	,	,	_	_	_
33	0.00009	0.00009	CD	_	_	_
34	g	g	NN	_	_	_
35	ZnSO4	znso4	NN	_	_	_
36	·	·	NN	_	_	_
37	7	7	CD	_	_	_
38	H2O	h2o	NN	_	_	_
39	,	,	,	_	_	_
40	0.00005	0.00005	CD	_	_	_
41	g	g	NN	_	_	_
42	MnSO4	mnso4	NN	_	_	_
43	·	·	NN	_	_	_
44	H2O	h2o	NN	_	_	_
45	,	,	,	_	_	_
46	0.0008	0.0008	CD	_	_	_
47	g	g	NN	_	_	_
48	CuSO4	cuso4	NN	_	_	_
49	·	·	NN	_	_	_
50	5	5	CD	_	_	_
51	H2O	h2o	NN	_	_	_
52	,	,	,	_	_	_
53	0.00009	0.00009	CD	_	_	_
54	g	g	NN	_	_	_
55	CoCl2	cocl2	NN	_	_	_
56	·	·	NN	_	_	_
57	6	6	CD	_	_	_
58	H2O	h2o	NN	_	_	_
59	,	,	,	_	_	_
60	0.0044	0.0044	CD	_	_	_
61	g	g	NN	_	_	_
62	CaCl2	cacl2	NN	_	_	_
63	·	·	NN	_	_	_
64	2	2	CD	_	_	_
65	H2O	h2o	NN	_	_	_
66	,	,	,	_	_	_
67	0.1	0.1	CD	_	_	_
68	g	g	NN	_	_	_
69	MgSO4	mgso4	NN	_	_	_
70	·	·	NN	_	_	_
71	7	7	CD	_	_	_
72	H2O	h2o	NN	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	STR-PFR	str-pfr	NN	_	_	_
3	was	be	VBD	_	_	_
4	operated	operate	VBN	_	_	_
5	as	as	IN	_	_	_
6	a	a	DT	_	_	_
7	chemostat	chemostat	NN	_	_	_
8	with	with	IN	_	_	_
9	ammonia	ammonia	NN	_	_	_
10	as	as	IN	_	_	_
11	the	the	DT	_	_	_
12	growth-limiting	growth-limiting	JJ	_	_	_
13	substrate	substrate	NN	_	_	_
14	.	.	.	_	_	_

1	First	first	RB	_	_	_
2	,	,	,	_	_	_
3	a	a	DT	_	_	_
4	reference	reference	NN	_	_	_
5	steady	steady	JJ	_	_	_
6	state	state	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	µ	µ	NN	_	_	_
9	=	=	JJ	_	_	_
10	0.2	0.2	CD	_	_	_
11	h	h	NN	_	_	_
12	−	−	NN	_	_	_
13	1	1	CD	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	was	be	VBD	_	_	_
16	established	establish	VBN	_	_	_
17	in	in	IN	_	_	_
18	the	the	DT	_	_	_
19	STR	str	NN	_	_	_
20	and	and	CC	_	_	_
21	sampled	sample	VBD	_	_	_
22	three	three	CD	_	_	_
23	times	time	NNS	_	_	_
24	during	during	IN	_	_	_
25	a	a	DT	_	_	_
26	16	16	CD	_	_	_
27	h	h	NN	_	_	_
28	period	period	NN	_	_	_
29	following	follow	VBG	_	_	_
30	establishment	establishment	NN	_	_	_
31	of	of	IN	_	_	_
32	the	the	DT	_	_	_
33	steady	steady	JJ	_	_	_
34	state	state	NN	_	_	_
35	.	.	.	_	_	_

1	Then	then	RB	_	_	_
2	,	,	,	_	_	_
3	the	the	DT	_	_	_
4	PFR	pfr	NN	_	_	_
5	was	be	VBD	_	_	_
6	added	add	VBN	_	_	_
7	and	and	CC	_	_	_
8	samples	sample	NNS	_	_	_
9	for	for	IN	_	_	_
10	RNA-sequencing	rna-sequencing	NN	_	_	_
11	were	be	VBD	_	_	_
12	aquired	aquire	VBN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNPS	_	_	_
5	First	First	NNP	_	_	_
6	,	,	,	_	_	_
7	ribosomal	ribosomal	JJ	_	_	_
8	RNA	rna	NN	_	_	_
9	was	be	VBD	_	_	_
10	depleted	deplete	VBN	_	_	_
11	from	from	IN	_	_	_
12	1	1	CD	_	_	_
13	μg	μg	NN	_	_	_
14	of	of	IN	_	_	_
15	total	total	JJ	_	_	_
16	RNA	rna	NN	_	_	_
17	using	use	VBG	_	_	_
18	the	the	DT	_	_	_
19	Ribo-ZeroTM	Ribo-ZeroTM	NNP	_	_	_
20	Magnetic	magnetic	JJ	_	_	_
21	Kit	kit	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Bacteria	bacterium	NNS	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	Epicentre	Epicentre	NNP	_	_	_
27	,	,	,	_	_	_
28	Madison	Madison	NNP	_	_	_
29	,	,	,	_	_	_
30	WI	WI	NNP	_	_	_
31	,	,	,	_	_	_
32	USA	USA	NNP	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	Next	next	RB	_	_	_
2	,	,	,	_	_	_
3	mRNA	mrna	NN	_	_	_
4	libraries	library	NNS	_	_	_
5	were	be	VBD	_	_	_
6	prepared	prepare	VBN	_	_	_
7	using	use	VBG	_	_	_
8	the	the	DT	_	_	_
9	TruSeq	truseq	NN	_	_	_
10	mRNA	mrna	NN	_	_	_
11	Library	Library	NNP	_	_	_
12	Prep	Prep	NNP	_	_	_
13	Kit	kit	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Illumina	Illumina	NNP	_	_	_
16	,	,	,	_	_	_
17	San	San	NNP	_	_	_
18	Diego	Diego	NNP	_	_	_
19	,	,	,	_	_	_
20	CA	CA	NNP	_	_	_
21	,	,	,	_	_	_
22	USA	USA	NNP	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	.	.	.	_	_	_

1	mRNA	mrna	NN	_	_	_
2	libraries	library	NNS	_	_	_
3	were	be	VBD	_	_	_
4	prepared	prepare	VBN	_	_	_
5	for	for	IN	_	_	_
6	sequencing	sequencing	NN	_	_	_
7	using	use	VBG	_	_	_
8	standard	standard	JJ	_	_	_
9	Illumina	Illumina	NNP	_	_	_
10	protocols	protocol	NNS	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	ASM1024v1	asm1024v1	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	NCBI	NCBI	NNP	_	_	_
9	E.	E.	NNP	_	_	_
10	coli	coli	NN	_	_	_
11	K12	k12	NN	_	_	_
12	subst	subst	NN	_	_	_
13	.	.	.	_	_	_

1	W3110	w3110	NN	_	_	_
2	genome	genome	NN	_	_	_
3	-LRB-	-lrb-	-LRB-	_	_	_
4	GenBank	genbank	NN	_	_	_
5	:	:	:	_	_	_
6	AP009048	ap009048	NN	_	_	_
7	.1	.1	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	HTseq-derived	htseq-derived	JJ	_	_	_
12	raw	raw	JJ	_	_	_
13	count	count	NN	_	_	_
14	data	datum	NNS	_	_	_
15	were	be	VBD	_	_	_
16	used	use	VBN	_	_	_
17	as	as	IN	_	_	_
18	input	input	NN	_	_	_
19	after	after	IN	_	_	_
20	a	a	DT	_	_	_
21	non-specific	non-specific	JJ	_	_	_
22	filtering	filter	VBG	_	_	_
23	step	step	NN	_	_	_
24	that	that	WDT	_	_	_
25	removed	remove	VBD	_	_	_
26	residual	residual	JJ	_	_	_
27	rRNAs	rrna	NNS	_	_	_
28	and	and	CC	_	_	_
29	tRNAs	trna	NNS	_	_	_
30	and	and	CC	_	_	_
31	low	low	JJ	_	_	_
32	coverage	coverage	NN	_	_	_
33	genes	gene	NNS	_	_	_
34	with	with	IN	_	_	_
35	fewer	fewer	JJR	_	_	_
36	than	than	IN	_	_	_
37	2	2	CD	_	_	_
38	counts	count	NNS	_	_	_
39	per	per	IN	_	_	_
40	million	million	CD	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	16-20	16-20	CD	_	_	_
43	reads	read	VBZ	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	in	in	IN	_	_	_
46	more	more	JJR	_	_	_
47	than	than	IN	_	_	_
48	25	25	CD	_	_	_
49	%	%	NN	_	_	_
50	of	of	IN	_	_	_
51	the	the	DT	_	_	_
52	dataset	dataset	NN	_	_	_
53	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Raw	raw	NN	_	_	_
3	counts	count	NNS	_	_	_
4	were	be	VBD	_	_	_
5	derived	derive	VBN	_	_	_
6	for	for	IN	_	_	_
7	each	each	DT	_	_	_
8	gene	gene	NN	_	_	_
9	based	base	VBN	_	_	_
10	on	on	IN	_	_	_
11	the	the	DT	_	_	_
12	respective	respective	JJ	_	_	_
13	annotations	annotation	NNS	_	_	_
14	available	available	JJ	_	_	_
15	from	from	IN	_	_	_
16	UCSC	UCSC	NNP	_	_	_
17	genome	genome	NN	_	_	_
18	browser	browser	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	http	http	NN	_	_	_
21	:	:	:	_	_	_
22	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
23	replicate	replicate	VBP	_	_	_
24	:	:	:	_	_	_
25	1	1	CD	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	replicate	replicate	VB	_	_	_
28	:	:	:	_	_	_
29	2	2	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	RNA-Seq	rna-seq	NN	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	sample	sample	NN	_	_	_
34	port	port	NN	_	_	_
35	:	:	:	_	_	_
36	PFR	pfr	NN	_	_	_
37	P1	p1	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	sample	sample	NN	_	_	_
40	port	port	NN	_	_	_
41	:	:	:	_	_	_
42	PFR	pfr	NN	_	_	_
43	P3	p3	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	sample	sample	NN	_	_	_
46	port	port	NN	_	_	_
47	:	:	:	_	_	_
48	PFR	pfr	NN	_	_	_
49	P5	p5	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	sample	sample	NN	_	_	_
52	port	port	NN	_	_	_
53	:	:	:	_	_	_
54	STR	str	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
56	Sampling	sample	VBG	_	_	_
57	by	by	IN	_	_	_
58	directly	directly	RB	_	_	_
59	placing	place	VBG	_	_	_
60	the	the	DT	_	_	_
61	culture	culture	NN	_	_	_
62	sample	sample	NN	_	_	_
63	into	into	IN	_	_	_
64	RNAprotect	rnaprotect	NN	_	_	_
65	Bacteria	bacterium	NNS	_	_	_
66	Reagent	reagent	NN	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	Qiagen	Qiagen	NNP	_	_	_
69	,	,	,	_	_	_
70	Hilden	Hilden	NNP	_	_	_
71	,	,	,	_	_	_
72	Germany	Germany	NNP	_	_	_
73	-RRB-	-rrb-	-RRB-	_	_	_
74	,	,	,	_	_	_
75	following	follow	VBG	_	_	_
76	short	short	JJ	_	_	_
77	centrifugation	centrifugation	NN	_	_	_
78	the	the	DT	_	_	_
79	pellet	pellet	NN	_	_	_
80	was	be	VBD	_	_	_
81	stored	store	VBN	_	_	_
82	at	at	IN	_	_	_
83	−	−	CD	_	_	_
84	70	70	CD	_	_	_
85	°C	°c	NN	_	_	_
86	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Sequenced	sequence	VBD	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	trimmed	trim	VBN	_	_	_
6	for	for	IN	_	_	_
7	adaptor	adaptor	NN	_	_	_
8	sequence	sequence	NN	_	_	_
9	using	use	VBG	_	_	_
10	Cutadapt	Cutadapt	NNP	_	_	_
11	v.	v.	CC	_	_	_
12	1.8.3	1.8.3	CD	_	_	_
13	,	,	,	_	_	_
14	then	then	RB	_	_	_
15	mapped	map	VBD	_	_	_
16	to	to	TO	_	_	_
17	E.	e.	FW	_	_	_
18	coli	coli	FW	_	_	_
19	K12	k12	NN	_	_	_
20	substr	substr	NN	_	_	_
21	.	.	.	_	_	_

1	W3110	w3110	CD	_	_	_
2	whole	whole	JJ	_	_	_
3	genome	genome	NN	_	_	_
4	from	from	IN	_	_	_
5	NCBI	ncbi	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	GenBank	genbank	NN	_	_	_
8	:	:	:	_	_	_
9	AP009048	ap009048	NN	_	_	_
10	.1	.1	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	RNA-seq	rna-seq	NN	_	_	_
15	aligner	aligner	NN	_	_	_
16	STAR	star	NN	_	_	_
17	v.	v.	CC	_	_	_
18	2.4.2	2.4.2	CD	_	_	_
19	a.	a.	NN	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	strain	strain	NN	_	_	_
22	:	:	:	_	_	_
23	K12	k12	NN	_	_	_
24	W3110	w3110	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Supplementary	supplementary	JJ	_	_	_
27	_	_	NN	_	_	_
28	files	file	NNS	_	_	_
29	_	_	IN	_	_	_
30	format	format	NN	_	_	_
31	_	_	NN	_	_	_
32	and	and	CC	_	_	_
33	_	_	NN	_	_	_
34	content	content	NN	_	_	_
35	:	:	:	_	_	_
36	xlsx	xlsx	NN	_	_	_
37	file	file	NN	_	_	_
38	format	format	NN	_	_	_
39	includes	include	VBZ	_	_	_
40	raw	raw	JJ	_	_	_
41	gene	gene	NN	_	_	_
42	counts	count	VBZ	_	_	_
43	for	for	IN	_	_	_
44	each	each	DT	_	_	_
45	sample	sample	NN	_	_	_
46	before	before	IN	_	_	_
47	and	and	CC	_	_	_
48	after	after	IN	_	_	_
49	filtering	filter	VBG	_	_	_
50	for	for	IN	_	_	_
51	low	low	JJ	_	_	_
52	coverage	coverage	NN	_	_	_
53	genes	gene	NNS	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
55	The	the	DT	_	_	_
56	bcl2fastq	bcl2fastq	NN	_	_	_
57	Conversion	conversion	NN	_	_	_
58	Software	Software	NNP	_	_	_
59	v.	v.	CC	_	_	_
60	1.8.4	1.8.4	CD	_	_	_
61	from	from	IN	_	_	_
62	Illumina	Illumina	NNP	_	_	_
63	-LRB-	-lrb-	-LRB-	_	_	_
64	http	http	NN	_	_	_
65	:	:	:	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
67	The	the	DT	_	_	_
68	RNeasy	rneasy	NN	_	_	_
69	mini	minus	NNS	_	_	_
70	kit	kit	NN	_	_	_
71	,	,	,	_	_	_
72	with	with	IN	_	_	_
73	on	on	IN	_	_	_
74	column	column	NN	_	_	_
75	RNase-Free	rnase-free	NN	_	_	_
76	DNase	dnase	NN	_	_	_
77	I	i	CD	_	_	_
78	treatment	treatment	NN	_	_	_
79	,	,	,	_	_	_
80	-LRB-	-lrb-	-LRB-	_	_	_
81	both	both	CC	_	_	_
82	Qiagen	Qiagen	NNP	_	_	_
83	,	,	,	_	_	_
84	Hilden	Hilden	NNP	_	_	_
85	,	,	,	_	_	_
86	Germany	Germany	NNP	_	_	_
87	-RRB-	-rrb-	-RRB-	_	_	_
88	was	be	VBD	_	_	_
89	used	use	VBN	_	_	_
90	for	for	IN	_	_	_
91	total	total	JJ	_	_	_
92	RNA	rna	NN	_	_	_
93	isolation	isolation	NN	_	_	_
94	-LRB-	-lrb-	-LRB-	_	_	_
95	RNA	rna	NN	_	_	_
96	≥	≥	NN	_	_	_
97	200	200	CD	_	_	_
98	bases	basis	NNS	_	_	_
99	-RRB-	-rrb-	-RRB-	_	_	_
100	,	,	,	_	_	_
101	according	accord	VBG	_	_	_
102	to	to	TO	_	_	_
103	the	the	DT	_	_	_
104	manufacturer	manufacturer	NN	_	_	_
105	's	's	POS	_	_	_
106	protocol	protocol	NN	_	_	_
107	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	quality	quality	NN	_	_	_
3	was	be	VBD	_	_	_
4	determined	determine	VBN	_	_	_
5	by	by	IN	_	_	_
6	a	a	DT	_	_	_
7	Lab-on-a-Chip-System	Lab-on-a-Chip-System	NNP	_	_	_
8	Bioanalyzer	Bioanalyzer	NNP	_	_	_
9	2100	2100	CD	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Agilent	Agilent	NNP	_	_	_
12	,	,	,	_	_	_
13	Boeblingen	Boeblingen	NNP	_	_	_
14	,	,	,	_	_	_
15	Germany	Germany	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	time	time	NN	_	_	_
3	:	:	:	_	_	_
4	0-15h	0-15h	JJ	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
6	time	time	NN	_	_	_
7	:	:	:	_	_	_
8	0-16h	0-16h	JJ	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
10	time	time	NN	_	_	_
11	:	:	:	_	_	_
12	0-2h	0-2h	JJ	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
14	time	time	NN	_	_	_
15	:	:	:	_	_	_
16	10	10	CD	_	_	_
17	min	min	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	time	time	NN	_	_	_
20	:	:	:	_	_	_
21	120	120	CD	_	_	_
22	min	min	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	time	time	NN	_	_	_
25	:	:	:	_	_	_
26	210	210	CD	_	_	_
27	min	min	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	time	time	NN	_	_	_
30	:	:	:	_	_	_
31	25h	25h	JJ	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
33	time	time	NN	_	_	_
34	:	:	:	_	_	_
35	25	25	CD	_	_	_
36	min	min	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	time	time	NN	_	_	_
39	:	:	:	_	_	_
40	26h	26h	JJ	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
42	time	time	NN	_	_	_
43	:	:	:	_	_	_
44	28h	28h	JJ	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
46	time	time	NN	_	_	_
47	:	:	:	_	_	_
48	330	330	CD	_	_	_
49	min	min	NN	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	time	time	NN	_	_	_
52	:	:	:	_	_	_
53	45	45	CD	_	_	_
54	min	min	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	time	time	NN	_	_	_
57	:	:	:	_	_	_
58	5	5	CD	_	_	_
59	min	min	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	time	time	NN	_	_	_
62	:	:	:	_	_	_
63	75	75	CD	_	_	_
64	min	min	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	0	0	CD	_	_	_
67	'	'	''	_	_	_
68	,	,	,	_	_	_
69	before	before	IN	_	_	_
70	UV	uv	NN	_	_	_
71	treatment	treatment	NN	_	_	_
72	,	,	,	_	_	_
73	25	25	CD	_	_	_
74	ug	ug	NN	_	_	_
75	total	total	JJ	_	_	_
76	RNA	rna	NN	_	_	_
77	,	,	,	_	_	_
78	2	2	CD	_	_	_
79	ug	ug	NN	_	_	_
80	pdN6	pdn6	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	0	0	CD	_	_	_
83	'	'	''	_	_	_
84	lexA	lexA	NNP	GEN	_	_
85	,	,	,	_	_	_
86	before	before	IN	_	_	_
87	UV	uv	NN	_	_	_
88	25	25	CD	_	_	_
89	ug	ug	NN	_	_	_
90	total	total	JJ	_	_	_
91	RNA	rna	NN	_	_	_
92	,	,	,	_	_	_
93	2	2	CD	_	_	_
94	ug	ug	NN	_	_	_
95	pdN6	pdn6	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	0	0	CD	_	_	_
98	'	'	''	_	_	_
99	wt	wt	JJ	_	_	_
100	,	,	,	_	_	_
101	before	before	IN	_	_	_
102	UV	uv	NN	_	_	_
103	treatment	treatment	NN	_	_	_
104	,	,	,	_	_	_
105	25	25	CD	_	_	_
106	ug	ug	NN	_	_	_
107	total	total	JJ	_	_	_
108	RNA	rna	NN	_	_	_
109	,	,	,	_	_	_
110	2	2	CD	_	_	_
111	ug	ug	NN	_	_	_
112	pdN6	pdn6	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	ATCACG-D1	atcacg-d1	NN	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	CGATGT-D2	cgatgt-d2	NN	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	DGE	dge	NN	_	_	_
119	analysis	analysis	NN	_	_	_
120	used	use	VBD	_	_	_
121	a	a	DT	_	_	_
122	false-discovery	false-discovery	JJ	_	_	_
123	rate	rate	NN	_	_	_
124	-LRB-	-lrb-	-LRB-	_	_	_
125	FDR	FDR	NNP	_	_	_
126	-RRB-	-rrb-	-RRB-	_	_	_
127	of	of	IN	_	_	_
128	0.10	0.10	CD	_	_	_
129	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Differential	differential	JJ	_	_	_
3	gene	gene	NN	_	_	_
4	expression	expression	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	DGE	dge	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	was	be	VBD	_	_	_
9	then	then	RB	_	_	_
10	performed	perform	VBN	_	_	_
11	on	on	IN	_	_	_
12	fragments	fragment	NNS	_	_	_
13	per	per	IN	_	_	_
14	kilobase	kilobase	NN	_	_	_
15	mapped	map	VBN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	FPKM	fpkm	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	values	value	NNS	_	_	_
20	in	in	IN	_	_	_
21	Cufflinks	Cufflinks	NNP	_	_	_
22	'	'	POS	_	_	_
23	Cuffdiff	cuffdiff	JJ	_	_	_
24	package	package	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	version	version	NN	_	_	_
27	0.0.7	0.0.7	CD	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	For	for	IN	_	_	_
6	the	the	DT	_	_	_
7	whole-transcriptome	whole-transcriptome	JJ	_	_	_
8	analysis	analysis	NN	_	_	_
9	,	,	,	_	_	_
10	sequencing	sequencing	NN	_	_	_
11	was	be	VBD	_	_	_
12	verified	verify	VBN	_	_	_
13	using	use	VBG	_	_	_
14	FASTQC	fastqc	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	version	version	NN	_	_	_
17	0.11.2	0.11.2	CD	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	to	to	TO	_	_	_
20	confirm	confirm	VB	_	_	_
21	base-call	base-call	JJ	_	_	_
22	quality	quality	NN	_	_	_
23	in	in	IN	_	_	_
24	each	each	DT	_	_	_
25	indexed	index	VBN	_	_	_
26	file	file	NN	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	FM180568	fm180568	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	Genome	Genome	NNP	_	_	_
9	_	_	NNP	_	_	_
10	build	build	VB	_	_	_
11	:	:	:	_	_	_
12	FM180569	fm180569	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Genome	Genome	NNP	_	_	_
15	_	_	NNP	_	_	_
16	build	build	VB	_	_	_
17	:	:	:	_	_	_
18	FM180570	fm180570	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	genotype	genotype	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Incubation	incubation	NN	_	_	_
23	and	and	CC	_	_	_
24	RNA	rna	NN	_	_	_
25	harvesting	harvesting	NN	_	_	_
26	were	be	VBD	_	_	_
27	carried	carry	VBN	_	_	_
28	out	out	RP	_	_	_
29	for	for	IN	_	_	_
30	all	all	DT	_	_	_
31	samples	sample	NNS	_	_	_
32	simultaneously	simultaneously	RB	_	_	_
33	and	and	CC	_	_	_
34	under	under	IN	_	_	_
35	RNase-free	rnase-free	JJ	_	_	_
36	conditions	condition	NNS	_	_	_
37	to	to	TO	_	_	_
38	minimize	minimize	VB	_	_	_
39	biological	biological	JJ	_	_	_
40	variability	variability	NN	_	_	_
41	in	in	IN	_	_	_
42	gene	gene	NN	_	_	_
43	expression	expression	NN	_	_	_
44	between	between	IN	_	_	_
45	each	each	DT	_	_	_
46	sample	sample	NN	_	_	_
47	.	.	.	_	_	_

1	Bacterial	bacterial	JJ	_	_	_
2	concentrations	concentration	NNS	_	_	_
3	were	be	VBD	_	_	_
4	equalized	equalize	VBN	_	_	_
5	to	to	TO	_	_	_
6	the	the	DT	_	_	_
7	same	same	JJ	_	_	_
8	density	density	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	by	by	IN	_	_	_
11	OD600	od600	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Indices	Indices	NNPS	_	_	_
3	corresponding	correspond	VBG	_	_	_
4	to	to	TO	_	_	_
5	the	the	DT	_	_	_
6	same	same	JJ	_	_	_
7	sample	sample	NN	_	_	_
8	were	be	VBD	_	_	_
9	merged	merge	VBN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	then	then	RB	_	_	_
13	uploaded	upload	VBD	_	_	_
14	to	to	TO	_	_	_
15	a	a	DT	_	_	_
16	cloud-based	cloud-based	JJ	_	_	_
17	variant	variant	NN	_	_	_
18	of	of	IN	_	_	_
19	Galaxy	Galaxy	NNP	_	_	_
20	named	name	VBD	_	_	_
21	RNA23	RNA23	NNP	_	_	_
22	Rocket	Rocket	NNP	_	_	_
23	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
24	LB	lb	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	5	5	CD	_	_	_
27	ml	ml	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	was	be	VBD	_	_	_
30	inoculated	inoculate	VBN	_	_	_
31	by	by	IN	_	_	_
32	a	a	DT	_	_	_
33	frozen	frozen	JJ	_	_	_
34	stock	stock	NN	_	_	_
35	of	of	IN	_	_	_
36	WT	WT	NNP	_	_	_
37	or	or	CC	_	_	_
38	perC-mutant	perc-mutant	JJ	_	_	_
39	strain	strain	NN	_	_	_
40	and	and	CC	_	_	_
41	incubated	incubate	VBN	_	_	_
42	at	at	IN	_	_	_
43	37	37	CD	_	_	_
44	°C	°c	NN	_	_	_
45	with	with	IN	_	_	_
46	225	225	CD	_	_	_
47	rpm	rpm	NN	_	_	_
48	shaking	shake	VBG	_	_	_
49	.	.	.	_	_	_

1	Flasks	flask	NNS	_	_	_
2	containing	contain	VBG	_	_	_
3	low-glucose	low-glucose	JJ	_	_	_
4	DMEM	dmem	NN	_	_	_
5	were	be	VBD	_	_	_
6	inoculated	inoculate	VBN	_	_	_
7	1:100	1:100	CD	_	_	_
8	with	with	IN	_	_	_
9	the	the	DT	_	_	_
10	overnight	overnight	JJ	_	_	_
11	culture	culture	NN	_	_	_
12	and	and	CC	_	_	_
13	incubated	incubate	VBN	_	_	_
14	at	at	IN	_	_	_
15	37	37	CD	_	_	_
16	°C	°c	NN	_	_	_
17	with	with	IN	_	_	_
18	225	225	CD	_	_	_
19	rpm	rpm	NN	_	_	_
20	shaking	shake	VBG	_	_	_
21	to	to	TO	_	_	_
22	mid-exponential	mid-exponential	JJ	_	_	_
23	phase	phase	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	OD600	od600	NN	_	_	_
26	0.3-0.5	0.3-0.5	CD	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Mapped	map	VBD	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	quality	quality	JJ	_	_	_
6	checked	check	VBN	_	_	_
7	with	with	IN	_	_	_
8	SAMstat	samstat	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	version	version	NN	_	_	_
11	1.08	1.08	CD	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	transcripts	transcript	NNS	_	_	_
16	were	be	VBD	_	_	_
17	assembled	assemble	VBN	_	_	_
18	in	in	IN	_	_	_
19	Cufflinks	Cufflinks	NNP	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	version	version	NN	_	_	_
22	2.0.2	2.0.2	CD	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	Resulting	result	VBG	_	_	_
26	mRNA	mrna	NN	_	_	_
27	was	be	VBD	_	_	_
28	reverse-transcribed	reverse-transcribed	JJ	_	_	_
29	to	to	TO	_	_	_
30	cDNA	cdna	NN	_	_	_
31	libraries	library	NNS	_	_	_
32	via	via	IN	_	_	_
33	SuperScript	SuperScript	NNP	_	_	_
34	III	III	NNP	_	_	_
35	First	First	NNP	_	_	_
36	Strand	Strand	NNP	_	_	_
37	reverse	reverse	VB	_	_	_
38	transcription	transcription	NN	_	_	_
39	kit	kit	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	Invitrogen	Invitrogen	NNP	_	_	_
42	,	,	,	_	_	_
43	Carlsbad	Carlsbad	NNP	_	_	_
44	,	,	,	_	_	_
45	CA	CA	NNP	_	_	_
46	,	,	,	_	_	_
47	18080051	18080051	CD	_	_	_
48	-RRB-	-rrb-	-RRB-	_	_	_
49	as	as	IN	_	_	_
50	per	per	IN	_	_	_
51	the	the	DT	_	_	_
52	manufacturer	manufacturer	NN	_	_	_
53	's	's	POS	_	_	_
54	instructions	instruction	NNS	_	_	_
55	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cDNA	cdna	NN	_	_	_
3	libraries	library	NNS	_	_	_
4	were	be	VBD	_	_	_
5	multiplexed	multiplex	VBN	_	_	_
6	to	to	TO	_	_	_
7	distinguish	distinguish	VB	_	_	_
8	replicates	replicate	VBZ	_	_	_
9	from	from	IN	_	_	_
10	one	one	CD	_	_	_
11	another	another	DT	_	_	_
12	,	,	,	_	_	_
13	barcoded	barcode	VBN	_	_	_
14	for	for	IN	_	_	_
15	sequencing	sequencing	NN	_	_	_
16	,	,	,	_	_	_
17	and	and	CC	_	_	_
18	then	then	RB	_	_	_
19	amplified	amplify	VBN	_	_	_
20	with	with	IN	_	_	_
21	random	random	JJ	_	_	_
22	hexamers	hexamer	NNS	_	_	_
23	for	for	IN	_	_	_
24	15	15	CD	_	_	_
25	PCR	pcr	NN	_	_	_
26	cycles	cycle	NNS	_	_	_
27	.	.	.	_	_	_

1	Transcripts	transcript	NNS	_	_	_
2	were	be	VBD	_	_	_
3	sequenced	sequence	VBN	_	_	_
4	for	for	IN	_	_	_
5	50	50	CD	_	_	_
6	bases	basis	NNS	_	_	_
7	in	in	IN	_	_	_
8	single-end	single-end	JJ	_	_	_
9	fashion	fashion	NN	_	_	_
10	within	within	IN	_	_	_
11	one	one	CD	_	_	_
12	lane	lane	NN	_	_	_
13	of	of	IN	_	_	_
14	an	a	DT	_	_	_
15	Illumina	Illumina	NNP	_	_	_
16	Hiseq	Hiseq	NNP	_	_	_
17	2000	2000	CD	_	_	_
18	flow	flow	NN	_	_	_
19	cell	cell	NN	_	_	_
20	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	yielded	yield	VBD	_	_	_
3	roughly	roughly	RB	_	_	_
4	30	30	CD	_	_	_
5	million	million	CD	_	_	_
6	reads	read	VBZ	_	_	_
7	per	per	IN	_	_	_
8	sample	sample	NN	_	_	_
9	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Samples	sample	NNS	_	_	_
5	were	be	VBD	_	_	_
6	diluted	dilute	VBN	_	_	_
7	1:1	1:1	CD	_	_	_
8	in	in	IN	_	_	_
9	RNA	rna	NN	_	_	_
10	Protect	protect	VB	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	Qiagen	Qiagen	NNP	_	_	_
13	,	,	,	_	_	_
14	Carlsbad	Carlsbad	NNP	_	_	_
15	,	,	,	_	_	_
16	CA	CA	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	to	to	TO	_	_	_
19	inhibit	inhibit	VB	_	_	_
20	RNase	rnase	NN	_	_	_
21	activity	activity	NN	_	_	_
22	and	and	CC	_	_	_
23	then	then	RB	_	_	_
24	centrifuged	centrifuge	VBD	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	5000	5000	CD	_	_	_
27	x	x	CC	_	_	_
28	g	g	NN	_	_	_
29	,	,	,	_	_	_
30	10	10	CD	_	_	_
31	min	min	NN	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	.	.	.	_	_	_

1	Pellets	pellet	NNS	_	_	_
2	were	be	VBD	_	_	_
3	resuspended	resuspend	VBN	_	_	_
4	in	in	IN	_	_	_
5	TE	TE	NNP	_	_	_
6	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
7	source	source	NN	_	_	_
8	:	:	:	_	_	_
9	Bustamante	Bustamante	NNP	_	_	_
10	et	et	FW	_	_	_
11	al.	al.	FW	_	_	_
12	,	,	,	_	_	_
13	2011	2011	CD	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	strain	strain	NN	_	_	_
16	:	:	:	_	_	_
17	JPEP22	jpep22	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Subsequent	subsequent	JJ	_	_	_
20	data	datum	NNS	_	_	_
21	visualizations	visualization	NNS	_	_	_
22	were	be	VBD	_	_	_
23	performed	perform	VBN	_	_	_
24	in	in	IN	_	_	_
25	R	r	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	version	version	NN	_	_	_
28	3.1.2	3.1.2	CD	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	using	use	VBG	_	_	_
31	the	the	DT	_	_	_
32	cummeRbund	cummerbund	NN	_	_	_
33	package	package	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	version	version	NN	_	_	_
36	3.0	3.0	CD	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
39	Supplementary	Supplementary	NNP	_	_	_
40	_	_	VBD	_	_	_
41	files	file	NNS	_	_	_
42	_	_	IN	_	_	_
43	format	format	NN	_	_	_
44	_	_	NN	_	_	_
45	and	and	CC	_	_	_
46	_	_	NN	_	_	_
47	content	content	NN	_	_	_
48	:	:	:	_	_	_
49	bedgraph	bedgraph	NN	_	_	_
50	:	:	:	_	_	_
51	Data	datum	NNS	_	_	_
52	presented	present	VBN	_	_	_
53	in	in	IN	_	_	_
54	a	a	DT	_	_	_
55	4	4	CD	_	_	_
56	column	column	NN	_	_	_
57	BED	bed	NN	_	_	_
58	format	format	NN	_	_	_
59	,	,	,	_	_	_
60	of	of	IN	_	_	_
61	which	which	WDT	_	_	_
62	the	the	DT	_	_	_
63	first	first	JJ	_	_	_
64	column	column	NN	_	_	_
65	is	be	VBZ	_	_	_
66	the	the	DT	_	_	_
67	chromosome	chromosome	NN	_	_	_
68	,	,	,	_	_	_
69	the	the	DT	_	_	_
70	second	second	JJ	_	_	_
71	column	column	NN	_	_	_
72	is	be	VBZ	_	_	_
73	the	the	DT	_	_	_
74	start	start	NN	_	_	_
75	position	position	NN	_	_	_
76	of	of	IN	_	_	_
77	the	the	DT	_	_	_
78	chromosome	chromosome	NN	_	_	_
79	,	,	,	_	_	_
80	the	the	DT	_	_	_
81	third	third	JJ	_	_	_
82	column	column	NN	_	_	_
83	is	be	VBZ	_	_	_
84	the	the	DT	_	_	_
85	end	end	NN	_	_	_
86	position	position	NN	_	_	_
87	,	,	,	_	_	_
88	and	and	CC	_	_	_
89	the	the	DT	_	_	_
90	fourth	fourth	JJ	_	_	_
91	column	column	NN	_	_	_
92	is	be	VBZ	_	_	_
93	the	the	DT	_	_	_
94	fragments	fragment	NNS	_	_	_
95	per	per	IN	_	_	_
96	kilobase	kilobase	NN	_	_	_
97	mapped	map	VBN	_	_	_
98	-LRB-	-lrb-	-LRB-	_	_	_
99	FPKM	fpkm	NN	_	_	_
100	-RRB-	-rrb-	-RRB-	_	_	_
101	for	for	IN	_	_	_
102	that	that	DT	_	_	_
103	sample	sample	NN	_	_	_
104	.	.	.	_	_	_

1	Chromosome	chromosome	NN	_	_	_
2	positions	position	NNS	_	_	_
3	are	be	VBP	_	_	_
4	specified	specify	VBN	_	_	_
5	as	as	IN	_	_	_
6	0-relative	0-relative	JJ	_	_	_
7	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	first	first	JJ	_	_	_
3	chromosome	chromosome	NN	_	_	_
4	position	position	NN	_	_	_
5	is	be	VBZ	_	_	_
6	0	0	CD	_	_	_
7	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	last	last	JJ	_	_	_
3	position	position	NN	_	_	_
4	in	in	IN	_	_	_
5	a	a	DT	_	_	_
6	chromosome	chromosome	NN	_	_	_
7	of	of	IN	_	_	_
8	length	length	NN	_	_	_
9	N	n	NN	_	_	_
10	would	would	MD	_	_	_
11	be	be	VB	_	_	_
12	N	n	NN	_	_	_
13	-	-	:	_	_	_
14	1	1	CD	_	_	_
15	.	.	.	_	_	_

1	Only	only	RB	_	_	_
2	positions	position	NNS	_	_	_
3	specified	specify	VBN	_	_	_
4	have	have	VBP	_	_	_
5	data	datum	NNS	_	_	_
6	.	.	.	_	_	_

1	Positions	position	NNS	_	_	_
2	not	not	RB	_	_	_
3	specified	specify	VBN	_	_	_
4	do	do	VBP	_	_	_
5	not	not	RB	_	_	_
6	have	have	VB	_	_	_
7	data	datum	NNS	_	_	_
8	and	and	CC	_	_	_
9	will	will	MD	_	_	_
10	not	not	RB	_	_	_
11	be	be	VB	_	_	_
12	graphed	graph	VBN	_	_	_
13	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	positions	position	NNS	_	_	_
3	specified	specify	VBN	_	_	_
4	in	in	IN	_	_	_
5	the	the	DT	_	_	_
6	input	input	NN	_	_	_
7	data	datum	NNS	_	_	_
8	are	be	VBP	_	_	_
9	in	in	IN	_	_	_
10	numerical	numerical	JJ	_	_	_
11	order	order	NN	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Supplementary	Supplementary	NNP	_	_	_
3	_	_	VBD	_	_	_
4	files	file	NNS	_	_	_
5	_	_	IN	_	_	_
6	format	format	NN	_	_	_
7	_	_	NN	_	_	_
8	and	and	CC	_	_	_
9	_	_	NN	_	_	_
10	content	content	NN	_	_	_
11	:	:	:	_	_	_
12	tabular	tabular	JJ	_	_	_
13	:	:	:	_	_	_
14	Tabular	tabular	JJ	_	_	_
15	data	datum	NNS	_	_	_
16	that	that	WDT	_	_	_
17	informs	inform	VBZ	_	_	_
18	the	the	DT	_	_	_
19	excel	excel	VB	_	_	_
20	spreadsheet	spreadsheet	NN	_	_	_
21	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	data	datum	NNS	_	_	_
3	are	be	VBP	_	_	_
4	averaged	average	VBN	_	_	_
5	across	across	IN	_	_	_
6	the	the	DT	_	_	_
7	three	three	CD	_	_	_
8	samples	sample	NNS	_	_	_
9	per	per	IN	_	_	_
10	strain	strain	NN	_	_	_
11	.	.	.	_	_	_

1	Both	both	DT	_	_	_
2	averaged	average	VBD	_	_	_
3	strain	strain	NN	_	_	_
4	data	datum	NNS	_	_	_
5	are	be	VBP	_	_	_
6	presented	present	VBN	_	_	_
7	for	for	IN	_	_	_
8	each	each	DT	_	_	_
9	gene	gene	NN	_	_	_
10	on	on	IN	_	_	_
11	the	the	DT	_	_	_
12	same	same	JJ	_	_	_
13	line	line	NN	_	_	_
14	.	.	.	_	_	_

1	Data	datum	NNS	_	_	_
2	contain	contain	VBP	_	_	_
3	gene	gene	NN	_	_	_
4	ID	id	NN	_	_	_
5	,	,	,	_	_	_
6	gene	gene	NN	_	_	_
7	number	number	NN	_	_	_
8	,	,	,	_	_	_
9	locus	locus	NN	_	_	_
10	,	,	,	_	_	_
11	fragments	fragment	NNS	_	_	_
12	per	per	IN	_	_	_
13	kilobase	kilobase	NN	_	_	_
14	mapped	map	VBN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	FPKM	fpkm	NN	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	for	for	IN	_	_	_
19	WT	WT	NNP	_	_	_
20	and	and	CC	_	_	_
21	mutant	mutant	JJ	_	_	_
22	strains	strain	NNS	_	_	_
23	,	,	,	_	_	_
24	log2	log2	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	fold-change	fold-change	NN	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	relative	relative	JJ	_	_	_
29	epxression	epxression	NN	_	_	_
30	of	of	IN	_	_	_
31	WT	WT	NNP	_	_	_
32	over	over	IN	_	_	_
33	mutant	mutant	JJ	_	_	_
34	strains	strain	NNS	_	_	_
35	,	,	,	_	_	_
36	test-statistic	test-statistic	JJ	_	_	_
37	,	,	,	_	_	_
38	p-value	p-value	NN	_	_	_
39	,	,	,	_	_	_
40	q-value	q-value	NN	_	_	_
41	,	,	,	_	_	_
42	and	and	CC	_	_	_
43	significance	significance	NN	_	_	_
44	analyzed	analyze	VBD	_	_	_
45	via	via	IN	_	_	_
46	the	the	DT	_	_	_
47	cummeRbund	cummerbund	NN	_	_	_
48	package	package	NN	_	_	_
49	in	in	IN	_	_	_
50	R	r	NN	_	_	_
51	whereby	whereby	WRB	_	_	_
52	a	a	DT	_	_	_
53	q-value	q-value	NN	_	_	_
54	of	of	IN	_	_	_
55	<	<	JJR	_	_	_
56	0.05	0.05	CD	_	_	_
57	is	be	VBZ	_	_	_
58	considered	consider	VBN	_	_	_
59	significant	significant	JJ	_	_	_
60	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Supplementary	Supplementary	NNP	_	_	_
3	_	_	VBD	_	_	_
4	files	file	NNS	_	_	_
5	_	_	IN	_	_	_
6	format	format	NN	_	_	_
7	_	_	NN	_	_	_
8	and	and	CC	_	_	_
9	_	_	NN	_	_	_
10	content	content	NN	_	_	_
11	:	:	:	_	_	_
12	xls	xl	NNS	_	_	_
13	:	:	:	_	_	_
14	The	the	DT	_	_	_
15	data	datum	NNS	_	_	_
16	are	be	VBP	_	_	_
17	averaged	average	VBN	_	_	_
18	across	across	IN	_	_	_
19	the	the	DT	_	_	_
20	three	three	CD	_	_	_
21	samples	sample	NNS	_	_	_
22	per	per	IN	_	_	_
23	strain	strain	NN	_	_	_
24	.	.	.	_	_	_

1	Both	both	DT	_	_	_
2	averaged	average	VBD	_	_	_
3	strain	strain	NN	_	_	_
4	data	datum	NNS	_	_	_
5	are	be	VBP	_	_	_
6	presented	present	VBN	_	_	_
7	for	for	IN	_	_	_
8	each	each	DT	_	_	_
9	gene	gene	NN	_	_	_
10	on	on	IN	_	_	_
11	the	the	DT	_	_	_
12	same	same	JJ	_	_	_
13	line	line	NN	_	_	_
14	.	.	.	_	_	_

1	Excel	Excel	NNP	_	_	_
2	spreadsheet	spreadsheet	NN	_	_	_
3	containing	contain	VBG	_	_	_
4	gene	gene	NN	_	_	_
5	ID	id	NN	_	_	_
6	,	,	,	_	_	_
7	gene	gene	NN	_	_	_
8	number	number	NN	_	_	_
9	,	,	,	_	_	_
10	locus	locus	NN	_	_	_
11	,	,	,	_	_	_
12	fragments	fragment	NNS	_	_	_
13	per	per	IN	_	_	_
14	kilobase	kilobase	NN	_	_	_
15	mapped	map	VBN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	FPKM	fpkm	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	for	for	IN	_	_	_
20	WT	WT	NNP	_	_	_
21	and	and	CC	_	_	_
22	mutant	mutant	JJ	_	_	_
23	strains	strain	NNS	_	_	_
24	,	,	,	_	_	_
25	log2	log2	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	fold-change	fold-change	NN	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	relative	relative	JJ	_	_	_
30	epxression	epxression	NN	_	_	_
31	of	of	IN	_	_	_
32	WT	WT	NNP	_	_	_
33	over	over	IN	_	_	_
34	mutant	mutant	JJ	_	_	_
35	strains	strain	NNS	_	_	_
36	,	,	,	_	_	_
37	test-statistic	test-statistic	JJ	_	_	_
38	,	,	,	_	_	_
39	p-value	p-value	NN	_	_	_
40	,	,	,	_	_	_
41	q-value	q-value	NN	_	_	_
42	,	,	,	_	_	_
43	and	and	CC	_	_	_
44	significance	significance	NN	_	_	_
45	analyzed	analyze	VBD	_	_	_
46	via	via	IN	_	_	_
47	the	the	DT	_	_	_
48	cummeRbund	cummerbund	NN	_	_	_
49	package	package	NN	_	_	_
50	in	in	IN	_	_	_
51	R	r	NN	_	_	_
52	whereby	whereby	WRB	_	_	_
53	a	a	DT	_	_	_
54	q-value	q-value	NN	_	_	_
55	of	of	IN	_	_	_
56	<	<	JJR	_	_	_
57	0.05	0.05	CD	_	_	_
58	is	be	VBZ	_	_	_
59	considered	consider	VBN	_	_	_
60	significant	significant	JJ	_	_	_
61	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	TTAGGC-D3	ttaggc-d3	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Using	use	VBG	_	_	_
5	Bowtie2	bowtie2	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	version	version	NN	_	_	_
8	2.0.2	2.0.2	CD	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	,	,	,	_	_	_
11	sequenced	sequence	VBN	_	_	_
12	reads	read	VBZ	_	_	_
13	were	be	VBD	_	_	_
14	mapped	map	VBN	_	_	_
15	to	to	TO	_	_	_
16	an	a	DT	_	_	_
17	EPEC	epec	NN	_	_	_
18	O127	o127	NN	_	_	_
19	:	:	:	_	_	_
20	H6	h6	NN	_	_	_
21	reference	reference	NN	_	_	_
22	genome	genome	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	EMBL	embl	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Whole	whole	JJ	_	_	_
27	bacterial	bacterial	JJ	_	_	_
28	cell	cell	NN	_	_	_
29	RNA	rna	NN	_	_	_
30	transcriptome	transcriptome	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	10	10	CD	_	_	_
33	min	min	NN	_	_	_
34	after	after	IN	_	_	_
35	UVtreatment	uvtreatment	NN	_	_	_
36	1	1	CD	_	_	_
37	'	'	''	_	_	_
38	,	,	,	_	_	_
39	40J	40j	NN	_	_	_
40	,	,	,	_	_	_
41	MG1655	mg1655	NN	_	_	_
42	in	in	IN	_	_	_
43	Davis	Davis	NNP	_	_	_
44	+0.4	+0.4	CD	_	_	_
45	%	%	NN	_	_	_
46	glu	glu	NN	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	10	10	CD	_	_	_
49	min	min	NN	_	_	_
50	UV	uv	NN	_	_	_
51	treated	treat	VBN	_	_	_
52	cells	cell	NNS	_	_	_
53	,	,	,	_	_	_
54	25	25	CD	_	_	_
55	ug	ug	NN	_	_	_
56	total	total	JJ	_	_	_
57	RNA	rna	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	Cells	cell	NNS	_	_	_
60	treated	treat	VBN	_	_	_
61	with	with	IN	_	_	_
62	bacterial	bacterial	JJ	_	_	_
63	protect	protect	VBP	_	_	_
64	reagent	reagent	NN	_	_	_
65	and	and	CC	_	_	_
66	freeze	freeze	NN	_	_	_
67	at	at	IN	_	_	_
68	-70	-70	CD	_	_	_
69	C	c	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	E.	e.	FW	_	_	_
72	coli	coli	FW	_	_	_
73	grow	grow	VB	_	_	_
74	in	in	IN	_	_	_
75	LB	lb	NN	_	_	_
76	rich	rich	JJ	MED	_	_
77	medium	medium	NN	MED	_	_
78	to	to	TO	_	_	_
79	OD600	od600	NN	_	_	_
80	=	=	JJ	_	_	_
81	2.4	2.4	CD	_	_	_
82	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
83	Escherichia	escherichia	FW	Organism	_	_
84	coli	coli	FW	Organism	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	Genotype	genotype	NN	_	_	_
87	:	:	:	_	_	_
88	E.	e.	FW	_	_	_
89	coli	coli	FW	_	_	_
90	K12	k12	NN	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	RNA	rna	NN	_	_	_
93	samples	sample	NNS	_	_	_
94	were	be	VBD	_	_	_
95	extracted	extract	VBN	_	_	_
96	via	via	IN	_	_	_
97	Invitrogen	Invitrogen	NNP	_	_	_
98	RNAeasy	RNAeasy	NNP	_	_	_
99	Kit	kit	NN	_	_	_
100	and	and	CC	_	_	_
101	treated	treat	VBN	_	_	_
102	with	with	IN	_	_	_
103	DNaseI	dnasei	NN	_	_	_
104	to	to	TO	_	_	_
105	remove	remove	VB	_	_	_
106	all	all	DT	_	_	_
107	DNA	dna	NN	_	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	The	the	DT	_	_	_
110	data	datum	NNS	_	_	_
111	were	be	VBD	_	_	_
112	analyzed	analyze	VBN	_	_	_
113	with	with	IN	_	_	_
114	Microarray	Microarray	NNP	_	_	_
115	Suite	Suite	NNP	_	_	_
116	version	version	NN	_	_	_
117	5.0	5.0	CD	_	_	_
118	-LRB-	-lrb-	-LRB-	_	_	_
119	MAS	mas	NN	_	_	_
120	5.0	5.0	CD	_	_	_
121	-RRB-	-rrb-	-RRB-	_	_	_
122	using	use	VBG	_	_	_
123	Affymetrix	Affymetrix	NNP	_	_	_
124	default	default	NN	_	_	_
125	analysis	analysis	NN	_	_	_
126	settings	setting	NNS	_	_	_
127	and	and	CC	_	_	_
128	global	global	JJ	_	_	_
129	scaling	scaling	NN	_	_	_
130	as	as	IN	_	_	_
131	normalization	normalization	NN	_	_	_
132	method	method	NN	_	_	_
133	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	trimmed	trim	VBN	_	_	_
3	mean	mean	NN	_	_	_
4	target	target	NN	_	_	_
5	intensity	intensity	NN	_	_	_
6	of	of	IN	_	_	_
7	each	each	DT	_	_	_
8	array	array	NN	_	_	_
9	was	be	VBD	_	_	_
10	arbitrarily	arbitrarily	RB	_	_	_
11	set	set	VBN	_	_	_
12	to	to	TO	_	_	_
13	100	100	CD	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	W3110	w3110	NN	_	_	_
3	lsrK	lsrk	NN	GEN	_	_
4	mutants	mutant	NNS	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	W3110	w3110	NN	_	_	_
7	lsrK	lsrk	NN	GEN	_	_
8	mutants	mutant	NNS	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	W3110	w3110	NN	_	_	_
11	lsrK	lsrk	NN	GEN	_	_
12	mutants	mutant	NNS	_	_	_
13	,	,	,	_	_	_
14	biological	biological	JJ	_	_	_
15	rep1	rep1	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	W3110	w3110	NN	_	_	_
18	lsrK	lsrk	NN	GEN	_	_
19	mutants	mutant	NNS	_	_	_
20	,	,	,	_	_	_
21	biological	biological	JJ	_	_	_
22	rep2	rep2	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	W3110	w3110	NN	_	_	_
25	lsrR	lsrr	NN	GEN	_	_
26	mutants	mutant	NNS	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	W3110	w3110	NN	_	_	_
29	lsrR	lsrr	NN	GEN	_	_
30	mutants	mutant	NNS	_	_	_
31	,	,	,	_	_	_
32	biological	biological	JJ	_	_	_
33	rep1	rep1	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	W3110	w3110	NN	_	_	_
36	lsrR	lsrr	NN	GEN	_	_
37	mutants	mutant	NNS	_	_	_
38	,	,	,	_	_	_
39	biological	biological	JJ	_	_	_
40	rep2	rep2	NN	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	W3110	w3110	NN	_	_	_
43	wild	wild	JJ	_	_	_
44	type	type	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	W3110	w3110	NN	_	_	_
47	wild	wild	JJ	_	_	_
48	type	type	NN	_	_	_
49	,	,	,	_	_	_
50	biological	biological	JJ	_	_	_
51	rep1	rep1	NN	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	W3110	w3110	NN	_	_	_
54	wild	wild	JJ	_	_	_
55	type	type	NN	_	_	_
56	,	,	,	_	_	_
57	biological	biological	JJ	_	_	_
58	rep2	rep2	NN	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	20	20	CD	_	_	_
61	min	min	NN	_	_	_
62	after	after	IN	_	_	_
63	UVtreatment	uvtreatment	NN	_	_	_
64	1	1	CD	_	_	_
65	'	'	''	_	_	_
66	,	,	,	_	_	_
67	40J	40j	NN	_	_	_
68	,	,	,	_	_	_
69	MG1655	mg1655	NN	_	_	_
70	in	in	IN	_	_	_
71	Davis	Davis	NNP	_	_	_
72	+0.4	+0.4	CD	_	_	_
73	%	%	NN	_	_	_
74	glu	glu	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	20	20	CD	_	_	_
77	min	min	NN	_	_	_
78	untreatedcells	untreatedcell	NNS	_	_	_
79	,	,	,	_	_	_
80	25	25	CD	_	_	_
81	ug	ug	NN	_	_	_
82	total	total	JJ	_	_	_
83	RNA	rna	NN	_	_	_
84	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
85	20	20	CD	_	_	_
86	min	min	NN	_	_	_
87	UV	uv	NN	_	_	_
88	treated	treat	VBN	_	_	_
89	cells	cell	NNS	_	_	_
90	,	,	,	_	_	_
91	25	25	CD	_	_	_
92	ug	ug	NN	_	_	_
93	total	total	JJ	_	_	_
94	RNA	rna	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	20	20	CD	_	_	_
97	min	min	NN	_	_	_
98	UVtreatment	uvtreatment	NN	_	_	_
99	control	control	NN	_	_	_
100	,	,	,	_	_	_
101	MG1655	mg1655	NN	_	_	_
102	in	in	IN	_	_	_
103	Davis	Davis	NNP	_	_	_
104	+0.4	+0.4	CD	_	_	_
105	%	%	NN	_	_	_
106	glu	glu	NN	_	_	_
107	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
108	antibody	antibody	NN	_	_	_
109	:	:	:	_	_	_
110	Monoclonal	monoclonal	JJ	_	_	_
111	ANTI-FLAG	anti-flag	NN	_	_	_
112	M2	m2	NN	_	_	_
113	antibody	antibody	NN	_	_	_
114	-LRB-	-lrb-	-LRB-	_	_	_
115	F3165	f3165	NN	_	_	_
116	-RRB-	-rrb-	-RRB-	_	_	_
117	-	-	:	_	_	_
118	Sigma	Sigma	NNP	_	_	_
119	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
120	background	background	NN	_	_	_
121	:	:	:	_	_	_
122	crp	crp	NN	GEN	_	_
123	mutant	mutant	JJ	_	_	_
124	background	background	NN	_	_	_
125	,	,	,	_	_	_
126	fis	fi	VBZ	GEN	_	_
127	flag	flag	NN	_	_	_
128	tag	tag	NN	GEN	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	background	background	NN	_	_	_
131	:	:	:	_	_	_
132	fis	fis	NN	GEN	_	_
133	mutant	mutant	JJ	_	_	_
134	background	background	NN	_	_	_
135	,	,	,	_	_	_
136	crp	crp	NN	GEN	_	_
137	flag	flag	NN	_	_	_
138	tag	tag	NN	GEN	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	background	background	NN	_	_	_
141	:	:	:	_	_	_
142	wild	wild	JJ	_	_	_
143	type	type	NN	_	_	_
144	,	,	,	_	_	_
145	crp	crp	NN	GEN	_	_
146	flag	flag	NN	_	_	_
147	tag	tag	NN	GEN	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
149	background	background	NN	_	_	_
150	:	:	:	_	_	_
151	wild	wild	JJ	_	_	_
152	type	type	NN	_	_	_
153	,	,	,	_	_	_
154	fis	fi	VBZ	GEN	_	_
155	flag	flag	NN	_	_	_
156	tag	tag	NN	GEN	_	_
157	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
158	BAM	bam	NN	_	_	_
159	files	file	NNS	_	_	_
160	of	of	IN	_	_	_
161	each	each	DT	_	_	_
162	ChIP	chip	NN	_	_	_
163	biological	biological	JJ	_	_	_
164	replicate	replicate	VB	_	_	_
165	and	and	CC	_	_	_
166	the	the	DT	_	_	_
167	input	input	NN	_	_	_
168	replicate	replicate	VB	_	_	_
169	samples	sample	NNS	_	_	_
170	were	be	VBD	_	_	_
171	used	use	VBN	_	_	_
172	in	in	IN	_	_	_
173	the	the	DT	_	_	_
174	MACS	macs	NN	_	_	_
175	peak	peak	NN	_	_	_
176	calling	call	VBG	_	_	_
177	program	program	NN	_	_	_
178	with	with	IN	_	_	_
179	the	the	DT	_	_	_
180	-	-	:	_	_	_
181	f	f	FW	_	_	_
182	BAMPE	bampe	FW	_	_	_
183	parameter	parameter	NN	_	_	_
184	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
185	Cells	cell	NNS	_	_	_
186	were	be	VBD	_	_	_
187	fixed	fix	VBN	_	_	_
188	in	in	IN	_	_	_
189	the	the	DT	_	_	_
190	required	require	VBN	_	_	_
191	growth	growth	NN	_	_	_
192	phase	phase	NN	_	_	_
193	in	in	IN	_	_	_
194	formaldehyde	formaldehyde	NN	_	_	_
195	,	,	,	_	_	_
196	quenched	quench	VBN	_	_	_
197	,	,	,	_	_	_
198	washed	wash	VBN	_	_	_
199	and	and	CC	_	_	_
200	lysed	lyse	VBN	_	_	_
201	.	.	.	_	_	_

1	Fragmented	fragmented	JJ	_	_	_
2	DNA	dna	NN	_	_	_
3	-	-	:	_	_	_
4	protein	protein	NN	_	_	_
5	complex	complex	NN	_	_	_
6	were	be	VBD	_	_	_
7	pulled	pull	VBN	_	_	_
8	using	use	VBG	_	_	_
9	the	the	DT	_	_	_
10	monoclonal	monoclonal	JJ	_	_	_
11	flag	flag	NN	_	_	_
12	tag	tag	NN	GEN	_	_
13	antibody	antibody	NN	_	_	_
14	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	complex	complex	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	washed	wash	VBN	_	_	_
6	,	,	,	_	_	_
7	reverse	reverse	VB	_	_	_
8	cross-linked	cross-linked	JJ	_	_	_
9	and	and	CC	_	_	_
10	obtained	obtain	VBN	_	_	_
11	DNA	dna	NN	_	_	_
12	purified	purify	VBN	_	_	_
13	using	use	VBG	_	_	_
14	Qiagen	Qiagen	NNP	_	_	_
15	min	min	NN	_	_	_
16	elute	elute	NN	_	_	_
17	PCR	pcr	NN	_	_	_
18	purification	purification	NN	_	_	_
19	kit	kit	NN	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	inoculated	inoculate	VBN	_	_	_
5	from	from	IN	_	_	_
6	overnight	overnight	JJ	_	_	_
7	culture	culture	NN	_	_	_
8	in	in	IN	_	_	_
9	rich	rich	JJ	_	_	_
10	Lysogeny	lysogeny	JJ	_	_	_
11	broth	broth	NN	_	_	_
12	at	at	IN	_	_	_
13	37	37	CD	_	_	_
14	degrees	degree	NNS	_	_	_
15	in	in	IN	_	_	_
16	aerobic	aerobic	JJ	_	_	_
17	conditions	condition	NNS	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	ChIP-Seq	chip-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	crp.ee.chipseq	crp.ee.chipseq	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	crp.ee.input	crp.ee.input	JJ	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	crp.me.chipseq	crp.me.chipseq	NN	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	crp.me	crp.me	NN	_	_	_
11	,	,	,	_	_	_
12	input	input	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	crp.me.input	crp.me.input	JJ	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	crpmutant.fis.ee.chipseq	crpmutant.fis.ee.chipseq	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	crpmutant.fis.ee.input	crpmutant.fis.ee.input	JJ	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	crpmutant.fis.me.chipseq	crpmutant.fis.me.chipseq	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	crpmutant.fis.me.input	crpmutant.fis.me.input	JJ	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	Escherichia	escherichia	FW	Organism	_	_
25	coli	coli	FW	Organism	_	_
26	str	str	FW	_	_	_
27	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	fis.ee.chipseq	fis.ee.chipseq	JJ	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	fis.ee.input	fis.ee.input	JJ	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	fis.me.chipseq	fis.me.chipseq	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	fis.me.input	fis.me.input	JJ	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	fismutant.crp.ee.chipseq	fismutant.crp.ee.chipseq	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	fismutant.crp.ee.input	fismutant.crp.ee.input	JJ	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	fismutant.crp.me.chipseq	fismutant.crp.me.chipseq	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	fismutant.crp.me.input	fismutant.crp.me.input	JJ	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Genome	Genome	NNP	_	_	_
20	_	_	NNP	_	_	_
21	build	build	VB	_	_	_
22	:	:	:	_	_	_
23	NC000913	nc000913	NN	_	_	_
24	.2	.2	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	growth	growth	NN	_	_	_
27	phase	phase	NN	_	_	_
28	:	:	:	_	_	_
29	Early	early	JJ	_	_	_
30	exponential	exponential	JJ	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	growth	growth	NN	_	_	_
33	phase	phase	NN	_	_	_
34	:	:	:	_	_	_
35	Mid	Mid	NNP	_	_	_
36	exponential	exponential	JJ	_	_	_
37	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
38	SAM	SAM	NNP	_	_	_
39	files	file	VBZ	_	_	_
40	thus	thus	RB	_	_	_
41	obtained	obtain	VBN	_	_	_
42	were	be	VBD	_	_	_
43	converted	convert	VBN	_	_	_
44	to	to	TO	_	_	_
45	BAM	BAM	NNP	_	_	_
46	files	file	NNS	_	_	_
47	using	use	VBG	_	_	_
48	samtools	samtool	NNS	_	_	_
49	view	view	VBP	_	_	_
50	command	command	NN	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	Samples	sample	NNS	_	_	_
53	were	be	VBD	_	_	_
54	aligned	align	VBN	_	_	_
55	to	to	TO	_	_	_
56	the	the	DT	_	_	_
57	E.	e.	FW	_	_	_
58	coli	coli	FW	_	_	_
59	K	k	NN	_	_	_
60	12	12	CD	_	_	_
61	MG1655	mg1655	NN	_	_	_
62	reference	reference	NN	_	_	_
63	sequence	sequence	NN	_	_	_
64	-LRB-	-lrb-	-LRB-	_	_	_
65	version	version	NN	_	_	_
66	NC000913	nc000913	NN	_	_	_
67	.2	.2	NN	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	,	,	,	_	_	_
70	using	use	VBG	_	_	_
71	BWA	bwa	NN	_	_	_
72	-LRB-	-lrb-	-LRB-	_	_	_
73	version	version	NN	_	_	_
74	0.5	0.5	CD	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	WITH	with	IN	_	_	_
77	-	-	:	_	_	_
78	q	q	NN	_	_	_
79	30	30	CD	_	_	_
80	parameter	parameter	NN	_	_	_
81	for	for	IN	_	_	_
82	trimming	trim	VBG	_	_	_
83	of	of	IN	_	_	_
84	reads	read	VBZ	_	_	_
85	below	below	IN	_	_	_
86	PHRED	PHRED	NNP	_	_	_
87	quality	quality	NN	_	_	_
88	score	score	NN	_	_	_
89	of	of	IN	_	_	_
90	30	30	CD	_	_	_
91	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Supplementary	Supplementary	NNP	_	_	_
3	_	_	VBD	_	_	_
4	files	file	NNS	_	_	_
5	_	_	IN	_	_	_
6	format	format	NN	_	_	_
7	_	_	NN	_	_	_
8	and	and	CC	_	_	_
9	_	_	NN	_	_	_
10	content	content	NN	_	_	_
11	:	:	:	_	_	_
12	peaks.bed	peaks.bed	VBN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	Truseq	truseq	NN	_	_	_
15	ChIP	chip	NN	_	_	_
16	kit	kit	NN	_	_	_
17	was	be	VBD	_	_	_
18	used	use	VBN	_	_	_
19	for	for	IN	_	_	_
20	the	the	DT	_	_	_
21	library	library	NN	_	_	_
22	preparation	preparation	NN	_	_	_
23	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	end	end	NN	_	_	_
4	repaired	repair	VBN	_	_	_
5	and	and	CC	_	_	_
6	adapters	adapter	NNS	_	_	_
7	were	be	VBD	_	_	_
8	ligated	ligate	VBN	_	_	_
9	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	ligation	ligation	NN	_	_	_
3	,	,	,	_	_	_
4	purify	purify	VB	_	_	_
5	ligation	ligation	NN	_	_	_
6	products	product	NNS	_	_	_
7	and	and	CC	_	_	_
8	then	then	RB	_	_	_
9	amplify	amplify	VB	_	_	_
10	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	BGI	BGI	NNP	_	_	_
3	inhouse	inhouse	NNP	_	_	_
4	software	software	NN	_	_	_
5	``	``	``	_	_	_
6	filter	filter	NN	_	_	_
7	_	_	NN	_	_	_
8	fq	fq	NN	_	_	_
9	''	''	''	_	_	_
10	for	for	IN	_	_	_
11	basecalling	basecalling	NN	_	_	_
12	and	and	CC	_	_	_
13	trimming	trim	VBG	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	Duplicate	duplicate	VB	_	_	_
16	O	o	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
18	E.	e.	FW	_	_	_
19	coli	coli	FW	_	_	_
20	MG1655	mg1655	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Escherichia	escherichia	FW	Organism	_	_
23	coli	coli	FW	Organism	_	_
24	str	str	FW	_	_	_
25	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Genome	Genome	NNP	_	_	_
4	_	_	NNP	_	_	_
5	build	build	VB	_	_	_
6	:	:	:	_	_	_
7	NC	NC	NNP	_	_	_
8	_	_	NNP	_	_	_
9	000913	000913	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	induction	induction	NN	_	_	_
12	:	:	:	_	_	_
13	induced	induce	VBN	_	_	_
14	50	50	CD	_	_	_
15	µM	µm	NN	_	_	_
16	IPTG	iptg	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	ORF1	orf1	NN	_	_	_
19	_	_	NN	_	_	_
20	1	1	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	ORF1	orf1	NN	_	_	_
23	_	_	NN	_	_	_
24	1	1	CD	_	_	_
25	_	_	CD	_	_	_
26	IPTG	iptg	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	ORF1	orf1	NN	_	_	_
29	_	_	NN	_	_	_
30	2	2	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	ORF1	orf1	NN	_	_	_
33	_	_	NN	_	_	_
34	2	2	CD	_	_	_
35	_	_	CD	_	_	_
36	IPTG	iptg	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Read-mapping	read-mapping	NN	_	_	_
39	was	be	VBD	_	_	_
40	done	do	VBN	_	_	_
41	with	with	IN	_	_	_
42	soap2	soap2	NN	_	_	_
43	.21	.21	CD	_	_	_
44	.	.	.	_	_	_

1	Mapping	mapping	NN	_	_	_
2	towards	towards	IN	_	_	_
3	genes	gene	NNS	_	_	_
4	was	be	VBD	_	_	_
5	done	do	VBN	_	_	_
6	by	by	IN	_	_	_
7	the	the	DT	_	_	_
8	following	follow	VBG	_	_	_
9	parameters	parameter	NNS	_	_	_
10	-	-	:	_	_	_
11	m	m	NN	_	_	_
12	0	0	CD	_	_	_
13	-	-	:	_	_	_
14	x	x	CC	_	_	_
15	1000	1000	CD	_	_	_
16	-	-	:	_	_	_
17	s	s	NNS	_	_	_
18	28	28	CD	_	_	_
19	-	-	:	_	_	_
20	l	l	NN	_	_	_
21	32	32	CD	_	_	_
22	-	-	:	_	_	_
23	v	v	LS	_	_	_
24	5	5	LS	_	_	_
25	-	-	:	_	_	_
26	r	r	NN	_	_	_
27	2	2	CD	_	_	_
28	-	-	:	_	_	_
29	p	p	NN	_	_	_
30	3	3	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	replicates	replicate	VBZ	_	_	_
33	:	:	:	_	_	_
34	ORF1	orf1	NN	_	_	_
35	replicate	replicate	VB	_	_	_
36	1	1	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	replicates	replicate	VBZ	_	_	_
39	:	:	:	_	_	_
40	ORF1	orf1	NN	_	_	_
41	replicate	replicate	VB	_	_	_
42	2	2	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
44	replicates	replicate	VBZ	_	_	_
45	:	:	:	_	_	_
46	Svi3-3	svi3-3	NN	_	_	_
47	replicate	replicate	VB	_	_	_
48	1	1	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	replicates	replicate	VBZ	_	_	_
51	:	:	:	_	_	_
52	Svi3-3	svi3-3	NN	_	_	_
53	replicate	replicate	VB	_	_	_
54	2	2	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
56	replicates	replicate	VBZ	_	_	_
57	:	:	:	_	_	_
58	WT	WT	NNP	_	_	_
59	replicate	replicate	VB	_	_	_
60	1	1	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	replicates	replicate	VBZ	_	_	_
63	:	:	:	_	_	_
64	WT	WT	NNP	_	_	_
65	replicate	replicate	VB	_	_	_
66	2	2	CD	_	_	_
67	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
68	RNA-Seq	rna-seq	JJ	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	Supplementary	supplementary	JJ	_	_	_
71	_	_	NN	_	_	_
72	files	file	NNS	_	_	_
73	_	_	IN	_	_	_
74	format	format	NN	_	_	_
75	_	_	NN	_	_	_
76	and	and	CC	_	_	_
77	_	_	NN	_	_	_
78	content	content	NN	_	_	_
79	:	:	:	_	_	_
80	The	the	DT	_	_	_
81	columns	column	NNS	_	_	_
82	in	in	IN	_	_	_
83	the	the	DT	_	_	_
84	processed	process	VBN	_	_	_
85	files	file	NNS	_	_	_
86	are	be	VBP	_	_	_
87	the	the	DT	_	_	_
88	following	follow	VBG	_	_	_
89	in	in	IN	_	_	_
90	order	order	NN	_	_	_
91	:	:	:	_	_	_
92	GeneID	geneid	NN	_	_	_
93	,	,	,	_	_	_
94	Length	length	NN	_	_	_
95	,	,	,	_	_	_
96	ORF1	orf1	NN	_	_	_
97	_	_	NN	_	_	_
98	1	1	CD	_	_	_
99	_	_	NN	_	_	_
100	mapped	map	VBD	_	_	_
101	_	_	CD	_	_	_
102	reads	read	VBZ	_	_	_
103	-LRB-	-lrb-	-LRB-	_	_	_
104	7655775	7655775	CD	_	_	_
105	-RRB-	-rrb-	-RRB-	_	_	_
106	,	,	,	_	_	_
107	ORF1	orf1	NN	_	_	_
108	_	_	NN	_	_	_
109	1	1	CD	_	_	_
110	_	_	CD	_	_	_
111	IPTG	iptg	NN	_	_	_
112	_	_	NN	_	_	_
113	mapped	map	VBD	_	_	_
114	_	_	CD	_	_	_
115	reads	read	VBZ	_	_	_
116	-LRB-	-lrb-	-LRB-	_	_	_
117	7178582	7178582	CD	_	_	_
118	-RRB-	-rrb-	-RRB-	_	_	_
119	,	,	,	_	_	_
120	ORF1	orf1	NN	_	_	_
121	_	_	NN	_	_	_
122	2	2	CD	_	_	_
123	_	_	NN	_	_	_
124	mapped	map	VBD	_	_	_
125	_	_	CD	_	_	_
126	reads	read	VBZ	_	_	_
127	-LRB-	-lrb-	-LRB-	_	_	_
128	7706927	7706927	CD	_	_	_
129	-RRB-	-rrb-	-RRB-	_	_	_
130	,	,	,	_	_	_
131	ORF1	orf1	NN	_	_	_
132	_	_	NN	_	_	_
133	2	2	CD	_	_	_
134	_	_	CD	_	_	_
135	IPTG	iptg	NN	_	_	_
136	_	_	NN	_	_	_
137	mapped	map	VBD	_	_	_
138	_	_	CD	_	_	_
139	reads	read	VBZ	_	_	_
140	-LRB-	-lrb-	-LRB-	_	_	_
141	7070827	7070827	CD	_	_	_
142	-RRB-	-rrb-	-RRB-	_	_	_
143	,	,	,	_	_	_
144	Svi3	svi3	NN	_	_	_
145	_	_	NN	_	_	_
146	3	3	CD	_	_	_
147	_	_	NN	_	_	_
148	1	1	CD	_	_	_
149	_	_	NN	_	_	_
150	mapped	map	VBD	_	_	_
151	_	_	CD	_	_	_
152	reads	read	VBZ	_	_	_
153	-LRB-	-lrb-	-LRB-	_	_	_
154	8018710	8018710	CD	_	_	_
155	-RRB-	-rrb-	-RRB-	_	_	_
156	,	,	,	_	_	_
157	Svi3	svi3	NN	_	_	_
158	_	_	NN	_	_	_
159	3	3	CD	_	_	_
160	_	_	NN	_	_	_
161	1	1	CD	_	_	_
162	_	_	CD	_	_	_
163	IPTG	iptg	NN	_	_	_
164	_	_	NN	_	_	_
165	mapped	map	VBD	_	_	_
166	_	_	CD	_	_	_
167	reads	read	VBZ	_	_	_
168	-LRB-	-lrb-	-LRB-	_	_	_
169	8299205	8299205	CD	_	_	_
170	-RRB-	-rrb-	-RRB-	_	_	_
171	,	,	,	_	_	_
172	Svi3	svi3	NN	_	_	_
173	_	_	NN	_	_	_
174	3	3	CD	_	_	_
175	_	_	NN	_	_	_
176	2	2	CD	_	_	_
177	_	_	NN	_	_	_
178	mapped	map	VBD	_	_	_
179	_	_	CD	_	_	_
180	reads	read	VBZ	_	_	_
181	-LRB-	-lrb-	-LRB-	_	_	_
182	7313736	7313736	CD	_	_	_
183	-RRB-	-rrb-	-RRB-	_	_	_
184	,	,	,	_	_	_
185	Svi3	svi3	NN	_	_	_
186	_	_	NN	_	_	_
187	3	3	CD	_	_	_
188	_	_	NN	_	_	_
189	2	2	CD	_	_	_
190	_	_	CD	_	_	_
191	IPTG	iptg	NN	_	_	_
192	_	_	NN	_	_	_
193	mapped	map	VBD	_	_	_
194	_	_	CD	_	_	_
195	reads	read	VBZ	_	_	_
196	-LRB-	-lrb-	-LRB-	_	_	_
197	8344539	8344539	CD	_	_	_
198	-RRB-	-rrb-	-RRB-	_	_	_
199	,	,	,	_	_	_
200	WT1	wt1	NN	_	_	_
201	_	_	CD	_	_	_
202	IPTG	iptg	NN	_	_	_
203	_	_	NN	_	_	_
204	mapped	map	VBD	_	_	_
205	_	_	CD	_	_	_
206	reads	read	VBZ	_	_	_
207	-LRB-	-lrb-	-LRB-	_	_	_
208	8074159	8074159	CD	_	_	_
209	-RRB-	-rrb-	-RRB-	_	_	_
210	,	,	,	_	_	_
211	WT2	wt2	NN	_	_	_
212	_	_	CD	_	_	_
213	IPTG	iptg	NN	_	_	_
214	_	_	NN	_	_	_
215	mapped	map	VBD	_	_	_
216	_	_	CD	_	_	_
217	reads	read	VBZ	_	_	_
218	-LRB-	-lrb-	-LRB-	_	_	_
219	8103887	8103887	CD	_	_	_
220	-RRB-	-rrb-	-RRB-	_	_	_
221	,	,	,	_	_	_
222	ORF1	orf1	NN	_	_	_
223	_	_	NN	_	_	_
224	1	1	CD	_	_	_
225	_	_	NN	_	_	_
226	coverage	coverage	NN	_	_	_
227	,	,	,	_	_	_
228	ORF1	orf1	NN	_	_	_
229	_	_	NN	_	_	_
230	1	1	CD	_	_	_
231	_	_	SYM	_	_	_
232	IPTG	iptg	SYM	_	_	_
233	_	_	SYM	_	_	_
234	coverage	coverage	NN	_	_	_
235	,	,	,	_	_	_
236	ORF1	orf1	NN	_	_	_
237	_	_	NN	_	_	_
238	2	2	CD	_	_	_
239	_	_	CD	_	_	_
240	coverage	coverage	NN	_	_	_
241	,	,	,	_	_	_
242	ORF1	orf1	NN	_	_	_
243	_	_	NN	_	_	_
244	2	2	CD	_	_	_
245	_	_	SYM	_	_	_
246	IPTG	iptg	SYM	_	_	_
247	_	_	SYM	_	_	_
248	coverage	coverage	NN	_	_	_
249	,	,	,	_	_	_
250	Svi3	svi3	NN	_	_	_
251	_	_	NN	_	_	_
252	3	3	CD	_	_	_
253	_	_	NN	_	_	_
254	1	1	CD	_	_	_
255	_	_	NN	_	_	_
256	coverage	coverage	NN	_	_	_
257	,	,	,	_	_	_
258	Svi3	svi3	NN	_	_	_
259	_	_	NN	_	_	_
260	3	3	CD	_	_	_
261	_	_	NN	_	_	_
262	1	1	CD	_	_	_
263	_	_	SYM	_	_	_
264	IPTG	iptg	SYM	_	_	_
265	_	_	SYM	_	_	_
266	coverage	coverage	NN	_	_	_
267	,	,	,	_	_	_
268	Svi3	svi3	NN	_	_	_
269	_	_	NN	_	_	_
270	3	3	CD	_	_	_
271	_	_	NN	_	_	_
272	2	2	CD	_	_	_
273	_	_	CD	_	_	_
274	coverage	coverage	NN	_	_	_
275	,	,	,	_	_	_
276	Svi3	svi3	NN	_	_	_
277	_	_	NN	_	_	_
278	3	3	CD	_	_	_
279	_	_	NN	_	_	_
280	2	2	CD	_	_	_
281	_	_	SYM	_	_	_
282	IPTG	iptg	SYM	_	_	_
283	_	_	SYM	_	_	_
284	coverage	coverage	NN	_	_	_
285	,	,	,	_	_	_
286	WT1	wt1	NN	_	_	_
287	_	_	CD	_	_	_
288	IPTG	IPTG	NNP	_	_	_
289	_	_	CD	_	_	_
290	coverage	coverage	NN	_	_	_
291	,	,	,	_	_	_
292	WT2	wt2	NN	_	_	_
293	_	_	CD	_	_	_
294	IPTG	IPTG	NNP	_	_	_
295	_	_	CD	_	_	_
296	coverage	coverage	NN	_	_	_
297	,	,	,	_	_	_
298	ORF1	orf1	NN	_	_	_
299	_	_	NN	_	_	_
300	1	1	CD	_	_	_
301	_	_	NN	_	_	_
302	rpkm	rpkm	NN	_	_	_
303	,	,	,	_	_	_
304	ORF1	orf1	NN	_	_	_
305	_	_	NN	_	_	_
306	1	1	CD	_	_	_
307	_	_	CD	_	_	_
308	IPTG	iptg	NN	_	_	_
309	_	_	NN	_	_	_
310	rpkm	rpkm	NN	_	_	_
311	,	,	,	_	_	_
312	ORF1	orf1	NN	_	_	_
313	_	_	NN	_	_	_
314	2	2	CD	_	_	_
315	_	_	CD	_	_	_
316	rpkm	rpkm	NN	_	_	_
317	,	,	,	_	_	_
318	ORF1	orf1	NN	_	_	_
319	_	_	NN	_	_	_
320	2	2	CD	_	_	_
321	_	_	CD	_	_	_
322	IPTG	iptg	NN	_	_	_
323	_	_	NN	_	_	_
324	rpkm	rpkm	NN	_	_	_
325	,	,	,	_	_	_
326	Svi3	svi3	NN	_	_	_
327	_	_	NN	_	_	_
328	3	3	CD	_	_	_
329	_	_	NN	_	_	_
330	1	1	CD	_	_	_
331	_	_	NN	_	_	_
332	rpkm	rpkm	NN	_	_	_
333	,	,	,	_	_	_
334	Svi3	svi3	NN	_	_	_
335	_	_	NN	_	_	_
336	3	3	CD	_	_	_
337	_	_	NN	_	_	_
338	1	1	CD	_	_	_
339	_	_	CD	_	_	_
340	IPTG	iptg	NN	_	_	_
341	_	_	NN	_	_	_
342	rpkm	rpkm	NN	_	_	_
343	,	,	,	_	_	_
344	Svi3	svi3	NN	_	_	_
345	_	_	NN	_	_	_
346	3	3	CD	_	_	_
347	_	_	NN	_	_	_
348	2	2	CD	_	_	_
349	_	_	CD	_	_	_
350	rpkm	rpkm	NN	_	_	_
351	,	,	,	_	_	_
352	Svi3	svi3	NN	_	_	_
353	_	_	NN	_	_	_
354	3	3	CD	_	_	_
355	_	_	NN	_	_	_
356	2	2	CD	_	_	_
357	_	_	CD	_	_	_
358	IPTG	iptg	NN	_	_	_
359	_	_	NN	_	_	_
360	rpkm	rpkm	NN	_	_	_
361	,	,	,	_	_	_
362	WT1	wt1	NN	_	_	_
363	_	_	CD	_	_	_
364	IPTG	iptg	NN	_	_	_
365	_	_	NN	_	_	_
366	rpkm	rpkm	NN	_	_	_
367	,	,	,	_	_	_
368	WT2	wt2	NN	_	_	_
369	_	_	CD	_	_	_
370	IPTG	iptg	NN	_	_	_
371	_	_	NN	_	_	_
372	rpkm	rpkm	NN	_	_	_
373	,	,	,	_	_	_
374	Symbol	symbol	NN	_	_	_
375	-LRB-	-lrb-	-LRB-	_	_	_
376	gene	gene	NN	_	_	_
377	name	name	NN	_	_	_
378	-RRB-	-rrb-	-RRB-	_	_	_
379	,	,	,	_	_	_
380	Description	description	NN	_	_	_
381	,	,	,	_	_	_
382	KEGG	KEGG	NNP	_	_	_
383	Orthology	Orthology	NNP	_	_	_
384	,	,	,	_	_	_
385	GO	GO	NNP	_	_	_
386	Component	Component	NNP	_	_	_
387	,	,	,	_	_	_
388	GO	GO	NNP	_	_	_
389	Function	function	NN	_	_	_
390	,	,	,	_	_	_
391	and	and	CC	_	_	_
392	GO	GO	NNP	_	_	_
393	Process	process	VBP	_	_	_
394	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
395	Svi3	svi3	NN	_	_	_
396	_	_	NN	_	_	_
397	3	3	CD	_	_	_
398	_	_	NN	_	_	_
399	1	1	CD	_	_	_
400	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
401	Svi3	svi3	NN	_	_	_
402	_	_	CD	_	_	_
403	3	3	CD	_	_	_
404	_	_	NN	_	_	_
405	1	1	CD	_	_	_
406	_	_	CD	_	_	_
407	IPTG	iptg	NN	_	_	_
408	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
409	Svi3	svi3	NN	_	_	_
410	_	_	CD	_	_	_
411	3	3	CD	_	_	_
412	_	_	NN	_	_	_
413	2	2	CD	_	_	_
414	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
415	Svi3	svi3	NN	_	_	_
416	_	_	CD	_	_	_
417	3	3	CD	_	_	_
418	_	_	NN	_	_	_
419	2	2	CD	_	_	_
420	_	_	CD	_	_	_
421	IPTG	iptg	NN	_	_	_
422	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
423	The	the	DT	_	_	_
424	cells	cell	NNS	_	_	_
425	for	for	IN	_	_	_
426	RNA	rna	NN	_	_	_
427	extraction	extraction	NN	_	_	_
428	were	be	VBD	_	_	_
429	immediately	immediately	RB	_	_	_
430	mixed	mix	VBN	_	_	_
431	with	with	IN	_	_	_
432	RNA	rna	NN	_	_	_
433	Protect	protect	VB	_	_	_
434	Bacterial	bacterial	JJ	_	_	_
435	reagent	reagent	NN	_	_	_
436	®	®	NN	_	_	_
437	-LRB-	-lrb-	-LRB-	_	_	_
438	Qiagen	qiagen	NN	_	_	_
439	-RRB-	-rrb-	-RRB-	_	_	_
440	and	and	CC	_	_	_
441	processed	process	VBN	_	_	_
442	by	by	IN	_	_	_
443	the	the	DT	_	_	_
444	RNAeasy	RNAeasy	NNP	_	_	_
445	Mini	Mini	NNP	_	_	_
446	Kit	kit	NN	_	_	_
447	-LRB-	-lrb-	-LRB-	_	_	_
448	Qiagen	qiagen	NN	_	_	_
449	-RRB-	-rrb-	-RRB-	_	_	_
450	according	accord	VBG	_	_	_
451	to	to	TO	_	_	_
452	the	the	DT	_	_	_
453	manufacturers	manufacturer	NNS	_	_	_
454	instructions	instruction	NNS	_	_	_
455	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	for	for	IN	_	_	_
4	whole	whole	JJ	_	_	_
5	cell	cell	NN	_	_	_
6	proteomics	proteomic	NNS	_	_	_
7	were	be	VBD	_	_	_
8	chilled	chill	VBN	_	_	_
9	in	in	IN	_	_	_
10	ice-slush	ice-slush	JJ	_	_	_
11	,	,	,	_	_	_
12	pelleted	pelleted	JJ	_	_	_
13	at	at	IN	_	_	_
14	14000	14000	CD	_	_	_
15	rpm	rpm	NN	_	_	_
16	,	,	,	_	_	_
17	4	4	CD	_	_	_
18	°C	°c	NN	_	_	_
19	and	and	CC	_	_	_
20	the	the	DT	_	_	_
21	media	media	NNS	_	_	_
22	was	be	VBD	_	_	_
23	aspirated	aspirate	VBN	_	_	_
24	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	washed	wash	VBN	_	_	_
5	with	with	IN	_	_	_
6	3	3	CD	_	_	_
7	×	×	NN	_	_	_
8	1.5	1.5	CD	_	_	_
9	mL	ml	NN	_	_	_
10	PBS	PBS	NNP	_	_	_
11	with	with	IN	_	_	_
12	pelleting	pelleting	NN	_	_	_
13	at	at	IN	_	_	_
14	as	as	IN	_	_	_
15	above	above	IN	_	_	_
16	in	in	IN	_	_	_
17	between	between	IN	_	_	_
18	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	final	final	JJ	_	_	_
3	pellet	pellet	NN	_	_	_
4	was	be	VBD	_	_	_
5	stored	store	VBN	_	_	_
6	at	at	IN	_	_	_
7	-80	-80	CD	_	_	_
8	°C	°c	NN	_	_	_
9	until	until	IN	_	_	_
10	being	be	VBG	_	_	_
11	shipped	ship	VBN	_	_	_
12	to	to	TO	_	_	_
13	the	the	DT	_	_	_
14	Proteomics	Proteomics	NNP	_	_	_
15	Core	Core	NNP	_	_	_
16	Facility	Facility	NNP	_	_	_
17	at	at	IN	_	_	_
18	University	University	NNP	_	_	_
19	of	of	IN	_	_	_
20	Gothenburg	Gothenburg	NNP	_	_	_
21	for	for	IN	_	_	_
22	processing	processing	NN	_	_	_
23	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	shipped	ship	VBN	_	_	_
5	to	to	TO	_	_	_
6	BGI	BGI	NNP	_	_	_
7	for	for	IN	_	_	_
8	total	total	JJ	_	_	_
9	RNA	rna	NN	_	_	_
10	sequencing	sequencing	NN	_	_	_
11	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	gene	gene	NN	_	_	_
4	expression	expression	NN	_	_	_
5	values	value	NNS	_	_	_
6	were	be	VBD	_	_	_
7	calculated	calculate	VBN	_	_	_
8	as	as	IN	_	_	_
9	RPKM	rpkm	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	reads	read	VBZ	_	_	_
12	per	per	IN	_	_	_
13	kilobase	kilobase	NN	_	_	_
14	transcriptome	transcriptome	NN	_	_	_
15	per	per	IN	_	_	_
16	million	million	CD	_	_	_
17	mapped	map	VBD	_	_	_
18	reads	read	VBZ	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	by	by	IN	_	_	_
21	the	the	DT	_	_	_
22	inhouse	inhouse	NNP	_	_	_
23	BGI	BGI	NNP	_	_	_
24	pipeline	pipeline	NN	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	pCA24N,-gfp	pca24n,-gfp	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	TruSeq	truseq	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	WT1	wt1	NN	_	_	_
8	_	_	CD	_	_	_
9	IPTG	iptg	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	WT2	wt2	NN	_	_	_
12	_	_	CD	_	_	_
13	IPTG	iptg	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	An	a	DT	_	_	_
16	o	o	NN	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	E.	E.	NNP	_	_	_
19	coli	coli	NN	_	_	_
20	TolC	tolc	NN	_	_	_
21	cells	cell	NNS	_	_	_
22	were	be	VBD	_	_	_
23	grown	grow	VBN	_	_	_
24	o	o	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
26	Eco	Eco	NNP	_	_	_
27	_	_	SYM	_	_	_
28	TolC	tolc	NN	_	_	_
29	_	_	NN	_	_	_
30	0	0	CD	_	_	_
31	min	min	NN	_	_	_
32	_	_	NN	_	_	_
33	A	a	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	Eco	eco	NN	_	_	_
36	_	_	CD	_	_	_
37	TolC	tolc	NN	_	_	_
38	_	_	NN	_	_	_
39	0	0	CD	_	_	_
40	min	min	NN	_	_	_
41	_	_	NN	_	_	_
42	B	b	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
44	Eco	Eco	NNP	_	_	_
45	_	_	SYM	_	_	_
46	TolC	tolc	NN	_	_	_
47	_	_	CD	_	_	_
48	15	15	CD	_	_	_
49	min	min	NN	_	_	_
50	_	_	CD	_	_	_
51	Carolacton	Carolacton	NNP	_	_	_
52	_	_	NNP	_	_	_
53	A	A	NNP	_	_	_
54	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
55	Eco	Eco	NNP	_	_	_
56	_	_	SYM	_	_	_
57	TolC	tolc	NN	_	_	_
58	_	_	CD	_	_	_
59	15	15	CD	_	_	_
60	min	min	NN	_	_	_
61	_	_	CD	_	_	_
62	Carolacton	Carolacton	NNP	_	_	_
63	_	_	NN	_	_	_
64	B	b	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
66	Eco	Eco	NNP	_	_	_
67	_	_	SYM	_	_	_
68	TolC	tolc	NN	_	_	_
69	_	_	CD	_	_	_
70	15	15	CD	_	_	_
71	min	min	NN	_	_	_
72	_	_	NN	_	_	_
73	control	control	NN	_	_	_
74	_	_	CD	_	_	_
75	A	a	DT	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	Eco	eco	NN	_	_	_
78	_	_	CD	_	_	_
79	TolC	tolc	NN	_	_	_
80	_	_	CD	_	_	_
81	15	15	CD	_	_	_
82	min	min	NN	_	_	_
83	_	_	NN	_	_	_
84	control	control	NN	_	_	_
85	_	_	CD	_	_	_
86	B	b	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
88	Eco	Eco	NNP	_	_	_
89	_	_	SYM	_	_	_
90	TolC	tolc	NN	_	_	_
91	_	_	CD	_	_	_
92	30	30	CD	_	_	_
93	min	min	NN	_	_	_
94	_	_	CD	_	_	_
95	Carolacton	Carolacton	NNP	_	_	_
96	_	_	NNP	_	_	_
97	A	A	NNP	_	_	_
98	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
99	Eco	Eco	NNP	_	_	_
100	_	_	SYM	_	_	_
101	TolC	tolc	NN	_	_	_
102	_	_	CD	_	_	_
103	30	30	CD	_	_	_
104	min	min	NN	_	_	_
105	_	_	CD	_	_	_
106	Carolacton	Carolacton	NNP	_	_	_
107	_	_	NN	_	_	_
108	B	b	NN	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
110	Eco	Eco	NNP	_	_	_
111	_	_	SYM	_	_	_
112	TolC	tolc	NN	_	_	_
113	_	_	CD	_	_	_
114	30	30	CD	_	_	_
115	min	min	NN	_	_	_
116	_	_	NN	_	_	_
117	control	control	NN	_	_	_
118	_	_	CD	_	_	_
119	A	a	DT	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
121	Eco	eco	NN	_	_	_
122	_	_	CD	_	_	_
123	TolC	tolc	NN	_	_	_
124	_	_	CD	_	_	_
125	30	30	CD	_	_	_
126	min	min	NN	_	_	_
127	_	_	NN	_	_	_
128	control	control	NN	_	_	_
129	_	_	CD	_	_	_
130	B	b	NN	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
132	Eco	Eco	NNP	_	_	_
133	_	_	SYM	_	_	_
134	TolC	tolc	NN	_	_	_
135	_	_	CD	_	_	_
136	5	5	CD	_	_	_
137	min	min	NN	_	_	_
138	_	_	CD	_	_	_
139	Carolacton	Carolacton	NNP	_	_	_
140	_	_	NNP	_	_	_
141	A	A	NNP	_	_	_
142	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
143	Eco	Eco	NNP	_	_	_
144	_	_	SYM	_	_	_
145	TolC	tolc	NN	_	_	_
146	_	_	CD	_	_	_
147	5	5	CD	_	_	_
148	min	min	NN	_	_	_
149	_	_	CD	_	_	_
150	Carolacton	Carolacton	NNP	_	_	_
151	_	_	NN	_	_	_
152	B	b	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
154	Eco	Eco	NNP	_	_	_
155	_	_	SYM	_	_	_
156	TolC	tolc	NN	_	_	_
157	_	_	CD	_	_	_
158	5	5	CD	_	_	_
159	min	min	NN	_	_	_
160	_	_	NN	_	_	_
161	control	control	NN	_	_	_
162	_	_	CD	_	_	_
163	A	a	DT	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	Eco	eco	NN	_	_	_
166	_	_	CD	_	_	_
167	TolC	tolc	NN	_	_	_
168	_	_	CD	_	_	_
169	5	5	CD	_	_	_
170	min	min	NN	_	_	_
171	_	_	NN	_	_	_
172	control	control	NN	_	_	_
173	_	_	NN	_	_	_
174	B	b	NN	_	_	_
175	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
176	Escherichia	escherichia	FW	Organism	_	_
177	coli	coli	FW	Organism	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	Genome	Genome	NNP	_	_	_
180	_	_	NNP	_	_	_
181	build	build	VB	_	_	_
182	:	:	:	_	_	_
183	CP018801	cp018801	NN	_	_	_
184	-LRB-	-lrb-	-LRB-	_	_	_
185	https	http	NNS	_	_	_
186	:	:	:	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
188	genotype	genotype	NN	_	_	_
189	:	:	:	_	_	_
190	TolC	tolc	NN	_	_	_
191	defective	defective	JJ	_	_	_
192	-LRB-	-lrb-	-LRB-	_	_	_
193	TolC	tolc	NN	_	_	_
194	-	-	:	_	_	_
195	-RRB-	-rrb-	-RRB-	_	_	_
196	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
197	Libraries	library	NNS	_	_	_
198	of	of	IN	_	_	_
199	RNA	rna	NN	_	_	_
200	fractions	fraction	NNS	_	_	_
201	were	be	VBD	_	_	_
202	constructed	construct	VBN	_	_	_
203	with	with	IN	_	_	_
204	the	the	DT	_	_	_
205	ScriptSeq	ScriptSeq	NNP	_	_	_
206	V2	v2	NN	_	_	_
207	RNA-Seq	rna-seq	NN	_	_	_
208	Library	Library	NNP	_	_	_
209	Prep	Prep	NNP	_	_	_
210	Kit	kit	NN	_	_	_
211	-LRB-	-lrb-	-LRB-	_	_	_
212	Illumina	Illumina	NNP	_	_	_
213	-RRB-	-rrb-	-RRB-	_	_	_
214	according	accord	VBG	_	_	_
215	to	to	TO	_	_	_
216	the	the	DT	_	_	_
217	manufacturers	manufacturer	NNS	_	_	_
218	guidelines	guideline	NNS	_	_	_
219	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	planktonic	planktonic	JJ	_	_	_
3	cells	cell	NNS	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
5	Raw	raw	NN	_	_	_
6	read	read	VBD	_	_	_
7	counts	count	NNS	_	_	_
8	of	of	IN	_	_	_
9	transcripts	transcript	NNS	_	_	_
10	were	be	VBD	_	_	_
11	obtained	obtain	VBN	_	_	_
12	by	by	IN	_	_	_
13	aligning	align	VBG	_	_	_
14	samples	sample	NNS	_	_	_
15	1-14	1-14	CD	_	_	_
16	to	to	TO	_	_	_
17	the	the	DT	_	_	_
18	reference	reference	NN	_	_	_
19	genome	genome	NN	_	_	_
20	and	and	CC	_	_	_
21	counting	count	VBG	_	_	_
22	mapped	map	VBN	_	_	_
23	reads	read	VBZ	_	_	_
24	per	per	IN	_	_	_
25	feature	feature	NN	_	_	_
26	using	use	VBG	_	_	_
27	Rockhopper	Rockhopper	NNP	_	_	_
28	v2	v2	NN	_	_	_
29	.0.3	.0.3	CD	_	_	_
30	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Sequenced	sequence	VBN	_	_	_
5	reads	read	VBZ	_	_	_
6	were	be	VBD	_	_	_
7	trimmed	trim	VBN	_	_	_
8	for	for	IN	_	_	_
9	adaptor	adaptor	NN	_	_	_
10	sequences	sequence	NNS	_	_	_
11	using	use	VBG	_	_	_
12	FastQC	fastqc	NN	_	_	_
13	v0	v0	NN	_	_	_
14	.11.2	.11.2	CD	_	_	_
15	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Supplementary	Supplementary	NNP	_	_	_
3	_	_	VBD	_	_	_
4	files	file	NNS	_	_	_
5	_	_	IN	_	_	_
6	format	format	NN	_	_	_
7	_	_	NN	_	_	_
8	and	and	CC	_	_	_
9	_	_	NN	_	_	_
10	content	content	NN	_	_	_
11	:	:	:	_	_	_
12	The	the	DT	_	_	_
13	tab-delimited	tab-delimited	JJ	_	_	_
14	text	text	NN	_	_	_
15	files	file	NNS	_	_	_
16	include	include	VBP	_	_	_
17	raw	raw	JJ	_	_	_
18	read	read	NN	_	_	_
19	values	value	NNS	_	_	_
20	for	for	IN	_	_	_
21	each	each	DT	_	_	_
22	time-point	time-point	NN	_	_	_
23	for	for	IN	_	_	_
24	both	both	DT	_	_	_
25	biol	biol	NN	_	_	_
26	.	.	.	_	_	_

1	replicates	replicate	VBZ	_	_	_
2	of	of	IN	_	_	_
3	control	control	NN	_	_	_
4	and	and	CC	_	_	_
5	Carolacton-treated	carolacton-treated	JJ	_	_	_
6	samples	sample	NNS	_	_	_
7	as	as	IN	_	_	_
8	obtained	obtain	VBN	_	_	_
9	from	from	IN	_	_	_
10	Rockhopper	Rockhopper	NNP	_	_	_
11	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	FASTA	fasta	NN	_	_	_
3	file	file	NN	_	_	_
4	on	on	IN	_	_	_
5	the	the	DT	_	_	_
6	series	series	NN	_	_	_
7	record	record	NN	_	_	_
8	contains	contain	VBZ	_	_	_
9	the	the	DT	_	_	_
10	transcript	transcript	NN	_	_	_
11	sequences	sequence	NNS	_	_	_
12	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	time	time	NN	_	_	_
3	point	point	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	minutes	minute	NNS	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	:	:	:	_	_	_
8	0	0	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
10	time	time	NN	_	_	_
11	point	point	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	minutes	minute	NNS	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	:	:	:	_	_	_
16	15	15	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
18	time	time	NN	_	_	_
19	point	point	NN	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	minutes	minute	NNS	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	:	:	:	_	_	_
24	30	30	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	time	time	NN	_	_	_
27	point	point	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	minutes	minute	NNS	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	:	:	:	_	_	_
32	5	5	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
34	Total	total	JJ	_	_	_
35	cellular	cellular	JJ	_	_	_
36	RNAs	rna	NNS	_	_	_
37	were	be	VBD	_	_	_
38	extracted	extract	VBN	_	_	_
39	using	use	VBG	_	_	_
40	the	the	DT	_	_	_
41	RNeasy	RNeasy	NNP	_	_	_
42	Mini	Mini	NNP	_	_	_
43	Kit	kit	NN	_	_	_
44	-LRB-	-lrb-	-LRB-	_	_	_
45	Qiagen	qiagen	NN	_	_	_
46	-RRB-	-rrb-	-RRB-	_	_	_
47	according	accord	VBG	_	_	_
48	to	to	TO	_	_	_
49	the	the	DT	_	_	_
50	manufacturers	manufacturer	NNS	_	_	_
51	protocol	protocol	NN	_	_	_
52	.	.	.	_	_	_

1	Residual	residual	JJ	_	_	_
2	DNA	dna	NN	_	_	_
3	in	in	IN	_	_	_
4	the	the	DT	_	_	_
5	fractions	fraction	NNS	_	_	_
6	was	be	VBD	_	_	_
7	digested	digest	VBN	_	_	_
8	by	by	IN	_	_	_
9	addition	addition	NN	_	_	_
10	of	of	IN	_	_	_
11	27	27	CD	_	_	_
12	Kunitz	Kunitz	NNP	_	_	_
13	units	unit	NNS	_	_	_
14	Dnase	Dnase	NNP	_	_	_
15	I	i	CD	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Qiagen	qiagen	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	,	,	,	_	_	_
20	and	and	CC	_	_	_
21	absence	absence	NN	_	_	_
22	of	of	IN	_	_	_
23	DNA	dna	NN	_	_	_
24	verified	verify	VBN	_	_	_
25	by	by	IN	_	_	_
26	Polymerase	polymerase	NN	_	_	_
27	chain	chain	NN	_	_	_
28	reaction	reaction	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	PCR	pcr	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	.	.	.	_	_	_

1	mRNA	mrna	NN	_	_	_
2	enrichment	enrichment	NN	_	_	_
3	was	be	VBD	_	_	_
4	conducted	conduct	VBN	_	_	_
5	using	use	VBG	_	_	_
6	the	the	DT	_	_	_
7	Ribo-Zero	Ribo-Zero	NNP	_	_	_
8	kit	kit	NN	_	_	_
9	for	for	IN	_	_	_
10	Gram-negative	gram-negative	JJ	_	_	_
11	bacteria	bacterium	NNS	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	epicentre	epicentre	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	quality	quality	NN	_	_	_
3	control	control	NN	_	_	_
4	of	of	IN	_	_	_
5	the	the	DT	_	_	_
6	RNA	rna	NN	_	_	_
7	extracts	extract	NNS	_	_	_
8	,	,	,	_	_	_
9	as	as	RB	_	_	_
10	well	well	RB	_	_	_
11	as	as	IN	_	_	_
12	the	the	DT	_	_	_
13	successful	successful	JJ	_	_	_
14	mRNA	mrna	NN	_	_	_
15	enrichment	enrichment	NN	_	_	_
16	,	,	,	_	_	_
17	was	be	VBD	_	_	_
18	conducted	conduct	VBN	_	_	_
19	by	by	IN	_	_	_
20	using	use	VBG	_	_	_
21	an	a	DT	_	_	_
22	Agilent	Agilent	NNP	_	_	_
23	2100	2100	CD	_	_	_
24	Bioanalyzer	Bioanalyzer	NNP	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	0.5	0.5	CD	_	_	_
5	µg	µg	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	treatment	treatment	NN	_	_	_
8	:	:	:	_	_	_
9	none	none	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	antibody	antibody	NN	_	_	_
12	:	:	:	_	_	_
13	anti-FLAG	anti-flag	JJ	_	_	_
14	mAb	mab	NN	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	antibody	antibody	NN	_	_	_
17	vendor	vendor	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Basecalls	basecall	NNS	_	_	_
20	performed	perform	VBN	_	_	_
21	using	use	VBG	_	_	_
22	CASAVA	CASAVA	NNP	_	_	_
23	version	version	NN	_	_	_
24	1.8	1.8	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Cells	cell	NNS	_	_	_
27	were	be	VBD	_	_	_
28	grown	grow	VBN	_	_	_
29	in	in	IN	_	_	_
30	LB	LB	NNP	MED	_	_
31	media	media	NNS	MED	_	_
32	with	with	IN	_	_	_
33	1mM	1mm	NN	_	_	_
34	IPTG	iptg	NN	_	_	_
35	at	at	IN	_	_	_
36	37	37	CD	_	_	_
37	°C	°c	NN	_	_	_
38	with	with	IN	_	_	_
39	shaking	shake	VBG	_	_	_
40	for	for	IN	_	_	_
41	2	2	CD	_	_	_
42	hours	hour	NNS	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	ChIP-Seq	chip-seq	JJ	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
46	CsiR	csir	NN	TF	_	_
47	_	_	CD	_	_	_
48	ChIPSeq	chipseq	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
50	CsiR	csir	NN	TF	_	_
51	_	_	CD	_	_	_
52	RNASeq	rnaseq	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	Culture	culture	NN	_	_	_
55	cells	cell	NNS	_	_	_
56	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
57	Escherichia	escherichia	FW	Organism	_	_
58	coli	coli	FW	Organism	_	_
59	K-12	k-12	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	For	for	IN	_	_	_
62	chromatin	chromatin	NN	_	_	_
63	immunoprecipitation	immunoprecipitation	NN	_	_	_
64	,	,	,	_	_	_
65	cells	cell	NNS	_	_	_
66	were	be	VBD	_	_	_
67	fixed	fix	VBN	_	_	_
68	with	with	IN	_	_	_
69	formaldehyde	formaldehyde	NN	_	_	_
70	and	and	CC	_	_	_
71	glycine	glycine	NN	_	_	_
72	and	and	CC	_	_	_
73	sheared	shear	VBD	_	_	_
74	via	via	IN	_	_	_
75	sonication	sonication	NN	_	_	_
76	.	.	.	_	_	_

1	Sheared	shear	VBN	_	_	_
2	DNA	dna	NN	_	_	_
3	from	from	IN	_	_	_
4	lysate	lysate	NN	_	_	_
5	was	be	VBD	_	_	_
6	immunoprecipitated	immunoprecipitate	VBN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	IP	IP	NNP	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	out	out	IN	_	_	_
11	using	use	VBG	_	_	_
12	an	a	DT	_	_	_
13	anti-FLAG	anti-flag	JJ	_	_	_
14	mAb	mab	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Sigma	Sigma	NNP	_	_	_
17	-RRB-	-rrb-	-RRB-	_	_	_
18	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	washed	wash	VBN	_	_	_
4	with	with	IN	_	_	_
5	IPP150	ipp150	NN	_	_	_
6	buffer	buffer	NN	_	_	_
7	and	and	CC	_	_	_
8	purified	purify	VBN	_	_	_
9	via	via	IN	_	_	_
10	ProteinaseK	ProteinaseK	NNP	_	_	_
11	digestion	digestion	NN	_	_	_
12	and	and	CC	_	_	_
13	Qiaquick	qiaquick	NN	_	_	_
14	PCR	pcr	NN	_	_	_
15	purification	purification	NN	_	_	_
16	kit	kit	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	Qiagen	qiagen	NN	_	_	_
19	-	-	:	_	_	_
20	Cat	cat	NN	_	_	_
21	.	.	.	_	_	_

1	No.	no.	NN	_	_	_
2	28106	28106	CD	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	For	for	IN	_	_	_
3	total	total	JJ	_	_	_
4	RNA	rna	NN	_	_	_
5	extraction	extraction	NN	_	_	_
6	,	,	,	_	_	_
7	cells	cell	NNS	_	_	_
8	were	be	VBD	_	_	_
9	pelleted	pellete	VBN	_	_	_
10	in	in	IN	_	_	_
11	4	4	CD	_	_	_
12	°C	°c	NN	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	U00096	u00096	NN	_	_	_
7	.2	.2	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	GenBank	genbank	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Nac	Nac	NNP	TF	_	_
13	_	_	NNP	_	_	_
14	ChIPSeq	ChIPSeq	NNP	_	_	_
15	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
16	Nac	Nac	NNP	TF	_	_
17	_	_	SYM	_	_	_
18	RNASeq	rnaseq	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	NtrC	ntrc	NN	TF	_	_
21	_	_	CD	_	_	_
22	ChIPSeq	chipseq	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	OmpR	ompr	NN	TF	_	_
25	_	_	CD	_	_	_
26	ChIPSeq	chipseq	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Peak	peak	JJ	_	_	_
29	calling	calling	NN	_	_	_
30	was	be	VBD	_	_	_
31	done	do	VBN	_	_	_
32	using	use	VBG	_	_	_
33	SPAT	SPAT	NNP	_	_	_
34	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
35	Reads	Reads	NNPS	_	_	_
36	were	be	VBD	_	_	_
37	aligned	align	VBN	_	_	_
38	to	to	TO	_	_	_
39	GenBank	genbank	NN	_	_	_
40	ID	id	NN	_	_	_
41	U00096	u00096	NN	_	_	_
42	.2	.2	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	RNA-Seq	rna-seq	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	R	r	NN	_	_	_
47	scripts	script	NNS	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	Bioconductor	bioconductor	NN	_	_	_
50	GenomicRanges	genomicrange	NNS	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	and	and	CC	_	_	_
53	custom	custom	NN	_	_	_
54	scripts	script	NNS	_	_	_
55	were	be	VBD	_	_	_
56	used	use	VBN	_	_	_
57	to	to	TO	_	_	_
58	calculate	calculate	VB	_	_	_
59	RPKMs	rpkm	NNS	_	_	_
60	.	.	.	_	_	_

1	Fold-change	fold-change	NN	_	_	_
2	was	be	VBD	_	_	_
3	calculated	calculate	VBN	_	_	_
4	as	as	IN	_	_	_
5	ratio	ratio	NN	_	_	_
6	of	of	IN	_	_	_
7	RPKMs	rpkm	NNS	_	_	_
8	after	after	IN	_	_	_
9	TF	tf	NN	_	_	_
10	induction	induction	NN	_	_	_
11	to	to	TO	_	_	_
12	control	control	VB	_	_	_
13	experiment	experiment	NN	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	strain	strain	NN	_	_	_
3	:	:	:	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
6	Supplementary	supplementary	JJ	_	_	_
7	_	_	NN	_	_	_
8	files	file	NNS	_	_	_
9	_	_	IN	_	_	_
10	format	format	NN	_	_	_
11	_	_	NN	_	_	_
12	and	and	CC	_	_	_
13	_	_	NN	_	_	_
14	content	content	NN	_	_	_
15	:	:	:	_	_	_
16	.	.	.	_	_	_

1	xlsx	xlsx	NN	_	_	_
2	files	file	NNS	_	_	_
3	contain	contain	VBP	_	_	_
4	peak	peak	JJ	_	_	_
5	region	region	NN	_	_	_
6	locations	location	NNS	_	_	_
7	and	and	CC	_	_	_
8	gene	gene	NN	_	_	_
9	expression	expression	NN	_	_	_
10	value	value	NN	_	_	_
11	for	for	IN	_	_	_
12	ChIP-Seq	chip-seq	NN	_	_	_
13	and	and	CC	_	_	_
14	RNA-Seq	rna-seq	NN	_	_	_
15	respectively	respectively	RB	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
17	The	the	DT	_	_	_
18	appropriate	appropriate	JJ	_	_	_
19	protocols	protocol	NNS	_	_	_
20	were	be	VBD	_	_	_
21	performed	perform	VBN	_	_	_
22	using	use	VBG	_	_	_
23	standard	standard	JJ	_	_	_
24	Illumina	Illumina	NNP	_	_	_
25	procedures	procedure	NNS	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	Total	Total	NNP	_	_	_
28	RNA	rna	NN	_	_	_
29	extraction	extraction	NN	_	_	_
30	was	be	VBD	_	_	_
31	done	do	VBN	_	_	_
32	using	use	VBG	_	_	_
33	TRIzol	trizol	NN	_	_	_
34	reagent	reagent	NN	_	_	_
35	and	and	CC	_	_	_
36	DNAse	dnase	NN	_	_	_
37	digested	digest	VBN	_	_	_
38	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	purfication	purfication	NN	_	_	_
3	was	be	VBD	_	_	_
4	carried	carry	VBN	_	_	_
5	out	out	RP	_	_	_
6	using	use	VBG	_	_	_
7	Rneasy	Rneasy	NNP	_	_	_
8	spin	spin	VB	_	_	_
9	columns	column	NNS	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
11	transcription	transcription	NN	_	_	_
12	factor	factor	NN	_	_	_
13	:	:	:	_	_	_
14	CsiR	csir	NN	TF	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	transcription	transcription	NN	_	_	_
17	factor	factor	NN	_	_	_
18	:	:	:	_	_	_
19	Nac	Nac	NNP	TF	_	_
20	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
21	transcription	transcription	NN	_	_	_
22	factor	factor	NN	_	_	_
23	:	:	:	_	_	_
24	NtrC	ntrc	NN	TF	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	transcription	transcription	NN	_	_	_
27	factor	factor	NN	_	_	_
28	:	:	:	_	_	_
29	OmpR	ompr	NN	TF	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	40	40	CD	_	_	_
32	min	min	NN	_	_	_
33	after	after	IN	_	_	_
34	UVtreatment	uvtreatment	NN	_	_	_
35	1	1	CD	_	_	_
36	,	,	,	_	_	_
37	40J	40j	NN	_	_	_
38	,	,	,	_	_	_
39	MG1655	mg1655	NN	_	_	_
40	in	in	IN	_	_	_
41	Davis	Davis	NNP	_	_	_
42	+0.4	+0.4	CD	_	_	_
43	%	%	NN	_	_	_
44	glu	glu	NN	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	40	40	CD	_	_	_
47	min	min	NN	_	_	_
48	untreatedcells	untreatedcell	NNS	_	_	_
49	,	,	,	_	_	_
50	25	25	CD	_	_	_
51	ug	ug	NN	_	_	_
52	total	total	JJ	_	_	_
53	RNA	rna	NN	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	batch	batch	NN	_	_	_
56	:	:	:	_	_	_
57	10	10	CD	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	batch	batch	NN	_	_	_
60	:	:	:	_	_	_
61	11	11	CD	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	batch	batch	NN	_	_	_
64	:	:	:	_	_	_
65	12	12	CD	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	batch	batch	NN	_	_	_
68	:	:	:	_	_	_
69	13	13	CD	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	batch	batch	NN	_	_	_
72	:	:	:	_	_	_
73	14	14	CD	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	batch	batch	NN	_	_	_
76	:	:	:	_	_	_
77	15	15	CD	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
79	batch	batch	NN	_	_	_
80	:	:	:	_	_	_
81	16	16	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	batch	batch	NN	_	_	_
84	:	:	:	_	_	_
85	17	17	CD	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	batch	batch	NN	_	_	_
88	:	:	:	_	_	_
89	18	18	CD	_	_	_
90	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
91	batch	batch	NN	_	_	_
92	:	:	:	_	_	_
93	19	19	CD	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	batch	batch	NN	_	_	_
96	:	:	:	_	_	_
97	20	20	CD	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	batch	batch	NN	_	_	_
100	:	:	:	_	_	_
101	21	21	CD	_	_	_
102	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
103	batch	batch	NN	_	_	_
104	:	:	:	_	_	_
105	22	22	CD	_	_	_
106	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
107	batch	batch	NN	_	_	_
108	:	:	:	_	_	_
109	23	23	CD	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	batch	batch	NN	_	_	_
112	:	:	:	_	_	_
113	24	24	CD	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	batch	batch	NN	_	_	_
116	:	:	:	_	_	_
117	25	25	CD	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	batch	batch	NN	_	_	_
120	:	:	:	_	_	_
121	26	26	CD	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	batch	batch	NN	_	_	_
124	:	:	:	_	_	_
125	27	27	CD	_	_	_
126	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
127	batch	batch	NN	_	_	_
128	:	:	:	_	_	_
129	7	7	CD	_	_	_
130	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
131	batch	batch	NN	_	_	_
132	:	:	:	_	_	_
133	8	8	CD	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	batch	batch	NN	_	_	_
136	:	:	:	_	_	_
137	9	9	CD	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	bowtie2-build	bowtie2-build	JJ	_	_	_
140	final	final	JJ	_	_	_
141	_	_	NN	_	_	_
142	reference	reference	NN	_	_	_
143	_	_	CD	_	_	_
144	seqs	seq	NNS	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
146	carbon	carbon	NN	_	_	_
147	source	source	NN	_	_	_
148	:	:	:	_	_	_
149	gluconate	gluconate	NN	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
151	carbon	carbon	NN	_	_	_
152	source	source	NN	_	_	_
153	:	:	:	_	_	_
154	glucose	glucose	NN	SUPP	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	carbon	carbon	NN	_	_	_
157	source	source	NN	_	_	_
158	:	:	:	_	_	_
159	glycerol	glycerol	NN	SUPP	_	_
160	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
161	carbon	carbon	NN	_	_	_
162	source	source	NN	_	_	_
163	:	:	:	_	_	_
164	lactate	lactate	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
166	convert	convert	VBP	_	_	_
167	back	back	RB	_	_	_
168	to	to	TO	_	_	_
169	sorted.sam	sorted.sam	NN	_	_	_
170	with	with	IN	_	_	_
171	samtools	samtool	NNS	_	_	_
172	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
173	convert	convert	VBP	_	_	_
174	bowtie	bowtie	NN	_	_	_
175	output	output	NN	_	_	_
176	.	.	.	_	_	_

1	sam	sam	NN	_	_	_
2	to	to	TO	_	_	_
3	.	.	.	_	_	_

1	bam	bam	NN	_	_	_
2	with	with	IN	_	_	_
3	samtools	samtool	NNS	_	_	_
4	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
5	Escherichia	escherichia	FW	Organism	_	_
6	coli	coli	FW	Organism	_	_
7	B	b	NN	_	_	_
8	str	str	NN	_	_	_
9	.	.	.	_	_	_

1	REL606	rel606	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	exponential	exponential	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
6	Genome	Genome	NNP	_	_	_
7	_	_	NNP	_	_	_
8	build	build	VB	_	_	_
9	:	:	:	_	_	_
10	reference	reference	NN	_	_	_
11	sequence	sequence	NN	_	_	_
12	is	be	VBZ	_	_	_
13	REL606	REL606	NNP	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	get	get	VB	_	_	_
16	raw	raw	JJ	_	_	_
17	counts	count	NNS	_	_	_
18	for	for	IN	_	_	_
19	reads	read	VBZ	_	_	_
20	mapped	map	VBN	_	_	_
21	with	with	IN	_	_	_
22	htseq-count	htseq-count	JJ	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	gluconate	gluconate	NN	_	_	_
25	_	_	NN	_	_	_
26	growth	growth	NN	_	_	_
27	:	:	:	_	_	_
28	MURI	MURI	NNP	_	_	_
29	_	_	SYM	_	_	_
30	091	091	CD	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	gluconate	gluconate	NN	_	_	_
33	_	_	NN	_	_	_
34	growth	growth	NN	_	_	_
35	:	:	:	_	_	_
36	MURI	MURI	NNP	_	_	_
37	_	_	SYM	_	_	_
38	092	092	CD	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	gluconate	gluconate	NN	_	_	_
41	_	_	NN	_	_	_
42	growth	growth	NN	_	_	_
43	:	:	:	_	_	_
44	MURI	MURI	NNP	_	_	_
45	_	_	SYM	_	_	_
46	093	093	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	gluconate	gluconate	NN	_	_	_
49	_	_	NN	_	_	_
50	growth	growth	NN	_	_	_
51	:	:	:	_	_	_
52	MURI	MURI	NNP	_	_	_
53	_	_	SYM	_	_	_
54	094	094	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	gluconate	gluconate	NN	_	_	_
57	_	_	NN	_	_	_
58	growth	growth	NN	_	_	_
59	:	:	:	_	_	_
60	MURI	MURI	NNP	_	_	_
61	_	_	SYM	_	_	_
62	095	095	CD	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	gluconate	gluconate	NN	_	_	_
65	_	_	NN	_	_	_
66	growth	growth	NN	_	_	_
67	:	:	:	_	_	_
68	MURI	MURI	NNP	_	_	_
69	_	_	SYM	_	_	_
70	096	096	CD	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	glucose	glucose	NN	SUPP	_	_
73	_	_	CD	_	_	_
74	time	time	NN	_	_	_
75	_	_	NN	_	_	_
76	course	course	NN	_	_	_
77	:	:	:	_	_	_
78	MURI	MURI	NNP	_	_	_
79	_	_	SYM	_	_	_
80	016	016	CD	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	glucose	glucose	NN	SUPP	_	_
83	_	_	CD	_	_	_
84	time	time	NN	_	_	_
85	_	_	NN	_	_	_
86	course	course	NN	_	_	_
87	:	:	:	_	_	_
88	MURI	MURI	NNP	_	_	_
89	_	_	SYM	_	_	_
90	017	017	CD	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	glucose	glucose	NN	SUPP	_	_
93	_	_	CD	_	_	_
94	time	time	NN	_	_	_
95	_	_	NN	_	_	_
96	course	course	NN	_	_	_
97	:	:	:	_	_	_
98	MURI	MURI	NNP	_	_	_
99	_	_	SYM	_	_	_
100	018	018	CD	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
102	glucose	glucose	NN	SUPP	_	_
103	_	_	CD	_	_	_
104	time	time	NN	_	_	_
105	_	_	NN	_	_	_
106	course	course	NN	_	_	_
107	:	:	:	_	_	_
108	MURI	MURI	NNP	_	_	_
109	_	_	SYM	_	_	_
110	019	019	CD	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	glucose	glucose	NN	SUPP	_	_
113	_	_	CD	_	_	_
114	time	time	NN	_	_	_
115	_	_	NN	_	_	_
116	course	course	NN	_	_	_
117	:	:	:	_	_	_
118	MURI	MURI	NNP	_	_	_
119	_	_	SYM	_	_	_
120	020	020	CD	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	glucose	glucose	NN	SUPP	_	_
123	_	_	CD	_	_	_
124	time	time	NN	_	_	_
125	_	_	NN	_	_	_
126	course	course	NN	_	_	_
127	:	:	:	_	_	_
128	MURI	MURI	NNP	_	_	_
129	_	_	SYM	_	_	_
130	021	021	CD	_	_	_
131	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
132	glucose	glucose	NN	SUPP	_	_
133	_	_	CD	_	_	_
134	time	time	NN	_	_	_
135	_	_	NN	_	_	_
136	course	course	NN	_	_	_
137	:	:	:	_	_	_
138	MURI	MURI	NNP	_	_	_
139	_	_	SYM	_	_	_
140	022	022	CD	_	_	_
141	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
142	glucose	glucose	NN	SUPP	_	_
143	_	_	CD	_	_	_
144	time	time	NN	_	_	_
145	_	_	NN	_	_	_
146	course	course	NN	_	_	_
147	:	:	:	_	_	_
148	MURI	MURI	NNP	_	_	_
149	_	_	SYM	_	_	_
150	023	023	CD	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	glucose	glucose	NN	SUPP	_	_
153	_	_	CD	_	_	_
154	time	time	NN	_	_	_
155	_	_	NN	_	_	_
156	course	course	NN	_	_	_
157	:	:	:	_	_	_
158	MURI	MURI	NNP	_	_	_
159	_	_	SYM	_	_	_
160	024	024	CD	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	glucose	glucose	NN	SUPP	_	_
163	_	_	CD	_	_	_
164	time	time	NN	_	_	_
165	_	_	NN	_	_	_
166	course	course	NN	_	_	_
167	:	:	:	_	_	_
168	MURI	MURI	NNP	_	_	_
169	_	_	SYM	_	_	_
170	025	025	CD	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	glucose	glucose	NN	SUPP	_	_
173	_	_	CD	_	_	_
174	time	time	NN	_	_	_
175	_	_	NN	_	_	_
176	course	course	NN	_	_	_
177	:	:	:	_	_	_
178	MURI	MURI	NNP	_	_	_
179	_	_	SYM	_	_	_
180	026	026	CD	_	_	_
181	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
182	glucose	glucose	NN	SUPP	_	_
183	_	_	CD	_	_	_
184	time	time	NN	_	_	_
185	_	_	NN	_	_	_
186	course	course	NN	_	_	_
187	:	:	:	_	_	_
188	MURI	MURI	NNP	_	_	_
189	_	_	SYM	_	_	_
190	027	027	CD	_	_	_
191	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
192	glucose	glucose	NN	SUPP	_	_
193	_	_	CD	_	_	_
194	time	time	NN	_	_	_
195	_	_	NN	_	_	_
196	course	course	NN	_	_	_
197	:	:	:	_	_	_
198	MURI	MURI	NNP	_	_	_
199	_	_	SYM	_	_	_
200	028	028	CD	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	glucose	glucose	NN	SUPP	_	_
203	_	_	CD	_	_	_
204	time	time	NN	_	_	_
205	_	_	NN	_	_	_
206	course	course	NN	_	_	_
207	:	:	:	_	_	_
208	MURI	MURI	NNP	_	_	_
209	_	_	SYM	_	_	_
210	029	029	CD	_	_	_
211	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
212	glucose	glucose	NN	SUPP	_	_
213	_	_	CD	_	_	_
214	time	time	NN	_	_	_
215	_	_	NN	_	_	_
216	course	course	NN	_	_	_
217	:	:	:	_	_	_
218	MURI	MURI	NNP	_	_	_
219	_	_	SYM	_	_	_
220	030	030	CD	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	glucose	glucose	NN	SUPP	_	_
223	_	_	CD	_	_	_
224	time	time	NN	_	_	_
225	_	_	NN	_	_	_
226	course	course	NN	_	_	_
227	:	:	:	_	_	_
228	MURI	MURI	NNP	_	_	_
229	_	_	SYM	_	_	_
230	031	031	CD	_	_	_
231	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
232	glucose	glucose	NN	SUPP	_	_
233	_	_	CD	_	_	_
234	time	time	NN	_	_	_
235	_	_	NN	_	_	_
236	course	course	NN	_	_	_
237	:	:	:	_	_	_
238	MURI	MURI	NNP	_	_	_
239	_	_	SYM	_	_	_
240	032	032	CD	_	_	_
241	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
242	glucose	glucose	NN	SUPP	_	_
243	_	_	CD	_	_	_
244	time	time	NN	_	_	_
245	_	_	NN	_	_	_
246	course	course	NN	_	_	_
247	:	:	:	_	_	_
248	MURI	MURI	NNP	_	_	_
249	_	_	SYM	_	_	_
250	033	033	CD	_	_	_
251	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
252	glucose	glucose	NN	SUPP	_	_
253	_	_	CD	_	_	_
254	time	time	NN	_	_	_
255	_	_	NN	_	_	_
256	course	course	NN	_	_	_
257	:	:	:	_	_	_
258	MURI	MURI	NNP	_	_	_
259	_	_	SYM	_	_	_
260	097	097	CD	_	_	_
261	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
262	glucose	glucose	NN	SUPP	_	_
263	_	_	CD	_	_	_
264	time	time	NN	_	_	_
265	_	_	NN	_	_	_
266	course	course	NN	_	_	_
267	:	:	:	_	_	_
268	MURI	MURI	NNP	_	_	_
269	_	_	SYM	_	_	_
270	098	098	CD	_	_	_
271	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
272	glucose	glucose	NN	SUPP	_	_
273	_	_	CD	_	_	_
274	time	time	NN	_	_	_
275	_	_	NN	_	_	_
276	course	course	NN	_	_	_
277	:	:	:	_	_	_
278	MURI	MURI	NNP	_	_	_
279	_	_	SYM	_	_	_
280	099	099	CD	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	glucose	glucose	NN	SUPP	_	_
283	_	_	CD	_	_	_
284	time	time	NN	_	_	_
285	_	_	NN	_	_	_
286	course	course	NN	_	_	_
287	:	:	:	_	_	_
288	MURI	MURI	NNP	_	_	_
289	_	_	SYM	_	_	_
290	100	100	CD	_	_	_
291	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
292	glucose	glucose	NN	SUPP	_	_
293	_	_	CD	_	_	_
294	time	time	NN	_	_	_
295	_	_	NN	_	_	_
296	course	course	NN	_	_	_
297	:	:	:	_	_	_
298	MURI	MURI	NNP	_	_	_
299	_	_	SYM	_	_	_
300	101	101	CD	_	_	_
301	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
302	glucose	glucose	NN	SUPP	_	_
303	_	_	CD	_	_	_
304	time	time	NN	_	_	_
305	_	_	NN	_	_	_
306	course	course	NN	_	_	_
307	:	:	:	_	_	_
308	MURI	MURI	NNP	_	_	_
309	_	_	SYM	_	_	_
310	102	102	CD	_	_	_
311	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
312	glucose	glucose	NN	SUPP	_	_
313	_	_	CD	_	_	_
314	time	time	NN	_	_	_
315	_	_	NN	_	_	_
316	course	course	NN	_	_	_
317	:	:	:	_	_	_
318	MURI	MURI	NNP	_	_	_
319	_	_	NN	_	_	_
320	103	103	CD	_	_	_
321	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
322	glucose	glucose	NN	SUPP	_	_
323	_	_	CD	_	_	_
324	time	time	NN	_	_	_
325	_	_	NN	_	_	_
326	course	course	NN	_	_	_
327	:	:	:	_	_	_
328	MURI	MURI	NNP	_	_	_
329	_	_	VBD	_	_	_
330	104	104	CD	_	_	_
331	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
332	glucose	glucose	NN	SUPP	_	_
333	_	_	CD	_	_	_
334	time	time	NN	_	_	_
335	_	_	NN	_	_	_
336	course	course	NN	_	_	_
337	:	:	:	_	_	_
338	MURI	MURI	NNP	_	_	_
339	_	_	SYM	_	_	_
340	105	105	CD	_	_	_
341	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
342	glycerol	glycerol	NN	SUPP	_	_
343	_	_	CD	_	_	_
344	time	time	NN	_	_	_
345	_	_	NN	_	_	_
346	course	course	NN	_	_	_
347	:	:	:	_	_	_
348	MURI	MURI	NNP	_	_	_
349	_	_	SYM	_	_	_
350	034	034	CD	_	_	_
351	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
352	glycerol	glycerol	NN	SUPP	_	_
353	_	_	CD	_	_	_
354	time	time	NN	_	_	_
355	_	_	NN	_	_	_
356	course	course	NN	_	_	_
357	:	:	:	_	_	_
358	MURI	MURI	NNP	_	_	_
359	_	_	SYM	_	_	_
360	035	035	CD	_	_	_
361	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
362	glycerol	glycerol	NN	SUPP	_	_
363	_	_	CD	_	_	_
364	time	time	NN	_	_	_
365	_	_	NN	_	_	_
366	course	course	NN	_	_	_
367	:	:	:	_	_	_
368	MURI	MURI	NNP	_	_	_
369	_	_	SYM	_	_	_
370	036	036	CD	_	_	_
371	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
372	glycerol	glycerol	NN	SUPP	_	_
373	_	_	CD	_	_	_
374	time	time	NN	_	_	_
375	_	_	NN	_	_	_
376	course	course	NN	_	_	_
377	:	:	:	_	_	_
378	MURI	MURI	NNP	_	_	_
379	_	_	SYM	_	_	_
380	037	037	CD	_	_	_
381	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
382	glycerol	glycerol	NN	SUPP	_	_
383	_	_	CD	_	_	_
384	time	time	NN	_	_	_
385	_	_	NN	_	_	_
386	course	course	NN	_	_	_
387	:	:	:	_	_	_
388	MURI	MURI	NNP	_	_	_
389	_	_	SYM	_	_	_
390	038	038	CD	_	_	_
391	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
392	glycerol	glycerol	NN	SUPP	_	_
393	_	_	CD	_	_	_
394	time	time	NN	_	_	_
395	_	_	NN	_	_	_
396	course	course	NN	_	_	_
397	:	:	:	_	_	_
398	MURI	MURI	NNP	_	_	_
399	_	_	SYM	_	_	_
400	039	039	CD	_	_	_
401	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
402	glycerol	glycerol	NN	SUPP	_	_
403	_	_	CD	_	_	_
404	time	time	NN	_	_	_
405	_	_	NN	_	_	_
406	course	course	NN	_	_	_
407	:	:	:	_	_	_
408	MURI	MURI	NNP	_	_	_
409	_	_	SYM	_	_	_
410	040	040	CD	_	_	_
411	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
412	glycerol	glycerol	NN	SUPP	_	_
413	_	_	CD	_	_	_
414	time	time	NN	_	_	_
415	_	_	NN	_	_	_
416	course	course	NN	_	_	_
417	:	:	:	_	_	_
418	MURI	MURI	NNP	_	_	_
419	_	_	SYM	_	_	_
420	041	041	CD	_	_	_
421	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
422	glycerol	glycerol	NN	SUPP	_	_
423	_	_	CD	_	_	_
424	time	time	NN	_	_	_
425	_	_	NN	_	_	_
426	course	course	NN	_	_	_
427	:	:	:	_	_	_
428	MURI	MURI	NNP	_	_	_
429	_	_	SYM	_	_	_
430	042	042	CD	_	_	_
431	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
432	glycerol	glycerol	NN	SUPP	_	_
433	_	_	CD	_	_	_
434	time	time	NN	_	_	_
435	_	_	NN	_	_	_
436	course	course	NN	_	_	_
437	:	:	:	_	_	_
438	MURI	MURI	NNP	_	_	_
439	_	_	SYM	_	_	_
440	043	043	CD	_	_	_
441	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
442	glycerol	glycerol	NN	SUPP	_	_
443	_	_	CD	_	_	_
444	time	time	NN	_	_	_
445	_	_	NN	_	_	_
446	course	course	NN	_	_	_
447	:	:	:	_	_	_
448	MURI	MURI	NNP	_	_	_
449	_	_	SYM	_	_	_
450	044	044	CD	_	_	_
451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
452	glycerol	glycerol	NN	SUPP	_	_
453	_	_	CD	_	_	_
454	time	time	NN	_	_	_
455	_	_	NN	_	_	_
456	course	course	NN	_	_	_
457	:	:	:	_	_	_
458	MURI	MURI	NNP	_	_	_
459	_	_	SYM	_	_	_
460	045	045	CD	_	_	_
461	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
462	glycerol	glycerol	NN	SUPP	_	_
463	_	_	CD	_	_	_
464	time	time	NN	_	_	_
465	_	_	NN	_	_	_
466	course	course	NN	_	_	_
467	:	:	:	_	_	_
468	MURI	MURI	NNP	_	_	_
469	_	_	SYM	_	_	_
470	046	046	CD	_	_	_
471	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
472	glycerol	glycerol	NN	SUPP	_	_
473	_	_	CD	_	_	_
474	time	time	NN	_	_	_
475	_	_	NN	_	_	_
476	course	course	NN	_	_	_
477	:	:	:	_	_	_
478	MURI	MURI	NNP	_	_	_
479	_	_	SYM	_	_	_
480	047	047	CD	_	_	_
481	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
482	glycerol	glycerol	NN	SUPP	_	_
483	_	_	CD	_	_	_
484	time	time	NN	_	_	_
485	_	_	NN	_	_	_
486	course	course	NN	_	_	_
487	:	:	:	_	_	_
488	MURI	MURI	NNP	_	_	_
489	_	_	SYM	_	_	_
490	048	048	CD	_	_	_
491	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
492	glycerol	glycerol	NN	SUPP	_	_
493	_	_	CD	_	_	_
494	time	time	NN	_	_	_
495	_	_	NN	_	_	_
496	course	course	NN	_	_	_
497	:	:	:	_	_	_
498	MURI	MURI	NNP	_	_	_
499	_	_	SYM	_	_	_
500	049	049	CD	_	_	_
501	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
502	glycerol	glycerol	NN	SUPP	_	_
503	_	_	CD	_	_	_
504	time	time	NN	_	_	_
505	_	_	NN	_	_	_
506	course	course	NN	_	_	_
507	:	:	:	_	_	_
508	MURI	MURI	NNP	_	_	_
509	_	_	SYM	_	_	_
510	050	050	CD	_	_	_
511	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
512	glycerol	glycerol	NN	SUPP	_	_
513	_	_	CD	_	_	_
514	time	time	NN	_	_	_
515	_	_	NN	_	_	_
516	course	course	NN	_	_	_
517	:	:	:	_	_	_
518	MURI	MURI	NNP	_	_	_
519	_	_	SYM	_	_	_
520	052	052	CD	_	_	_
521	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
522	glycerol	glycerol	NN	SUPP	_	_
523	_	_	CD	_	_	_
524	time	time	NN	_	_	_
525	_	_	NN	_	_	_
526	course	course	NN	_	_	_
527	:	:	:	_	_	_
528	MURI	MURI	NNP	_	_	_
529	_	_	SYM	_	_	_
530	053	053	CD	_	_	_
531	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
532	glycerol	glycerol	NN	SUPP	_	_
533	_	_	CD	_	_	_
534	time	time	NN	_	_	_
535	_	_	NN	_	_	_
536	course	course	NN	_	_	_
537	:	:	:	_	_	_
538	MURI	MURI	NNP	_	_	_
539	_	_	SYM	_	_	_
540	054	054	CD	_	_	_
541	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
542	glycerol	glycerol	NN	SUPP	_	_
543	_	_	CD	_	_	_
544	time	time	NN	_	_	_
545	_	_	NN	_	_	_
546	course	course	NN	_	_	_
547	:	:	:	_	_	_
548	MURI	MURI	NNP	_	_	_
549	_	_	SYM	_	_	_
550	055	055	CD	_	_	_
551	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
552	glycerol	glycerol	NN	SUPP	_	_
553	_	_	CD	_	_	_
554	time	time	NN	_	_	_
555	_	_	NN	_	_	_
556	course	course	NN	_	_	_
557	:	:	:	_	_	_
558	MURI	MURI	NNP	_	_	_
559	_	_	SYM	_	_	_
560	056	056	CD	_	_	_
561	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
562	glycerol	glycerol	NN	SUPP	_	_
563	_	_	CD	_	_	_
564	time	time	NN	_	_	_
565	_	_	NN	_	_	_
566	course	course	NN	_	_	_
567	:	:	:	_	_	_
568	MURI	MURI	NNP	_	_	_
569	_	_	SYM	_	_	_
570	057	057	CD	_	_	_
571	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
572	glycerol	glycerol	NN	SUPP	_	_
573	_	_	CD	_	_	_
574	time	time	NN	_	_	_
575	_	_	NN	_	_	_
576	course	course	NN	_	_	_
577	:	:	:	_	_	_
578	MURI	MURI	NNP	_	_	_
579	_	_	SYM	_	_	_
580	058	058	CD	_	_	_
581	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
582	glycerol	glycerol	NN	SUPP	_	_
583	_	_	CD	_	_	_
584	time	time	NN	_	_	_
585	_	_	NN	_	_	_
586	course	course	NN	_	_	_
587	:	:	:	_	_	_
588	MURI	MURI	NNP	_	_	_
589	_	_	SYM	_	_	_
590	059	059	CD	_	_	_
591	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
592	growth	growth	NN	_	_	_
593	phase	phase	NN	_	_	_
594	:	:	:	_	_	_
595	exponential	exponential	JJ	_	_	_
596	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
597	growth	growth	NN	_	_	_
598	phase	phase	NN	_	_	_
599	:	:	:	_	_	_
600	late	late	JJ	_	_	_
601	_	_	NN	_	_	_
602	stationary	stationary	JJ	_	_	_
603	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
604	growth	growth	NN	_	_	_
605	phase	phase	NN	_	_	_
606	:	:	:	_	_	_
607	stationary	stationary	JJ	_	_	_
608	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
609	growth	growth	NN	_	_	_
610	time	time	NN	_	_	_
611	-LRB-	-lrb-	-LRB-	_	_	_
612	hours	hour	NNS	_	_	_
613	-RRB-	-rrb-	-RRB-	_	_	_
614	:	:	:	_	_	_
615	10	10	CD	_	_	_
616	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
617	growth	growth	NN	_	_	_
618	time	time	NN	_	_	_
619	-LRB-	-lrb-	-LRB-	_	_	_
620	hours	hour	NNS	_	_	_
621	-RRB-	-rrb-	-RRB-	_	_	_
622	:	:	:	_	_	_
623	14	14	CD	_	_	_
624	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
625	growth	growth	NN	_	_	_
626	time	time	NN	_	_	_
627	-LRB-	-lrb-	-LRB-	_	_	_
628	hours	hour	NNS	_	_	_
629	-RRB-	-rrb-	-RRB-	_	_	_
630	:	:	:	_	_	_
631	168	168	CD	_	_	_
632	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
633	growth	growth	NN	_	_	_
634	time	time	NN	_	_	_
635	-LRB-	-lrb-	-LRB-	_	_	_
636	hours	hour	NNS	_	_	_
637	-RRB-	-rrb-	-RRB-	_	_	_
638	:	:	:	_	_	_
639	24	24	CD	_	_	_
640	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
641	growth	growth	NN	_	_	_
642	time	time	NN	_	_	_
643	-LRB-	-lrb-	-LRB-	_	_	_
644	hours	hour	NNS	_	_	_
645	-RRB-	-rrb-	-RRB-	_	_	_
646	:	:	:	_	_	_
647	26	26	CD	_	_	_
648	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
649	growth	growth	NN	_	_	_
650	time	time	NN	_	_	_
651	-LRB-	-lrb-	-LRB-	_	_	_
652	hours	hour	NNS	_	_	_
653	-RRB-	-rrb-	-RRB-	_	_	_
654	:	:	:	_	_	_
655	27	27	CD	_	_	_
656	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
657	growth	growth	NN	_	_	_
658	time	time	NN	_	_	_
659	-LRB-	-lrb-	-LRB-	_	_	_
660	hours	hour	NNS	_	_	_
661	-RRB-	-rrb-	-RRB-	_	_	_
662	:	:	:	_	_	_
663	28	28	CD	_	_	_
664	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
665	growth	growth	NN	_	_	_
666	time	time	NN	_	_	_
667	-LRB-	-lrb-	-LRB-	_	_	_
668	hours	hour	NNS	_	_	_
669	-RRB-	-rrb-	-RRB-	_	_	_
670	:	:	:	_	_	_
671	29	29	CD	_	_	_
672	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
673	growth	growth	NN	_	_	_
674	time	time	NN	_	_	_
675	-LRB-	-lrb-	-LRB-	_	_	_
676	hours	hour	NNS	_	_	_
677	-RRB-	-rrb-	-RRB-	_	_	_
678	:	:	:	_	_	_
679	3	3	CD	_	_	_
680	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
681	growth	growth	NN	_	_	_
682	time	time	NN	_	_	_
683	-LRB-	-lrb-	-LRB-	_	_	_
684	hours	hour	NNS	_	_	_
685	-RRB-	-rrb-	-RRB-	_	_	_
686	:	:	:	_	_	_
687	336	336	CD	_	_	_
688	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
689	growth	growth	NN	_	_	_
690	time	time	NN	_	_	_
691	-LRB-	-lrb-	-LRB-	_	_	_
692	hours	hour	NNS	_	_	_
693	-RRB-	-rrb-	-RRB-	_	_	_
694	:	:	:	_	_	_
695	4	4	CD	_	_	_
696	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
697	growth	growth	NN	_	_	_
698	time	time	NN	_	_	_
699	-LRB-	-lrb-	-LRB-	_	_	_
700	hours	hour	NNS	_	_	_
701	-RRB-	-rrb-	-RRB-	_	_	_
702	:	:	:	_	_	_
703	48	48	CD	_	_	_
704	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
705	growth	growth	NN	_	_	_
706	time	time	NN	_	_	_
707	-LRB-	-lrb-	-LRB-	_	_	_
708	hours	hour	NNS	_	_	_
709	-RRB-	-rrb-	-RRB-	_	_	_
710	:	:	:	_	_	_
711	5	5	CD	_	_	_
712	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
713	growth	growth	NN	_	_	_
714	time	time	NN	_	_	_
715	-LRB-	-lrb-	-LRB-	_	_	_
716	hours	hour	NNS	_	_	_
717	-RRB-	-rrb-	-RRB-	_	_	_
718	:	:	:	_	_	_
719	5.5	5.5	CD	_	_	_
720	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
721	growth	growth	NN	_	_	_
722	time	time	NN	_	_	_
723	-LRB-	-lrb-	-LRB-	_	_	_
724	hours	hour	NNS	_	_	_
725	-RRB-	-rrb-	-RRB-	_	_	_
726	:	:	:	_	_	_
727	6	6	CD	_	_	_
728	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
729	growth	growth	NN	_	_	_
730	time	time	NN	_	_	_
731	-LRB-	-lrb-	-LRB-	_	_	_
732	hours	hour	NNS	_	_	_
733	-RRB-	-rrb-	-RRB-	_	_	_
734	:	:	:	_	_	_
735	6.5	6.5	CD	_	_	_
736	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
737	growth	growth	NN	_	_	_
738	time	time	NN	_	_	_
739	-LRB-	-lrb-	-LRB-	_	_	_
740	hours	hour	NNS	_	_	_
741	-RRB-	-rrb-	-RRB-	_	_	_
742	:	:	:	_	_	_
743	7	7	CD	_	_	_
744	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
745	growth	growth	NN	_	_	_
746	time	time	NN	_	_	_
747	-LRB-	-lrb-	-LRB-	_	_	_
748	hours	hour	NNS	_	_	_
749	-RRB-	-rrb-	-RRB-	_	_	_
750	:	:	:	_	_	_
751	8	8	CD	_	_	_
752	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
753	growth	growth	NN	_	_	_
754	time	time	NN	_	_	_
755	-LRB-	-lrb-	-LRB-	_	_	_
756	hours	hour	NNS	_	_	_
757	-RRB-	-rrb-	-RRB-	_	_	_
758	:	:	:	_	_	_
759	9	9	CD	_	_	_
760	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
761	Illumina	Illumina	NNP	_	_	_
762	Ribozero	Ribozero	NNP	_	_	_
763	rRNA	rrna	NN	_	_	_
764	removal	removal	NN	_	_	_
765	followed	follow	VBN	_	_	_
766	by	by	IN	_	_	_
767	NEB	NEB	NNP	_	_	_
768	Next	next	JJ	_	_	_
769	RNA	rna	NN	_	_	_
770	library	library	NN	_	_	_
771	Prep	Prep	NNP	_	_	_
772	set	set	VBD	_	_	_
773	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	lactate	lactate	NN	_	_	_
3	_	_	NN	_	_	_
4	growth	growth	NN	_	_	_
5	:	:	:	_	_	_
6	MURI	MURI	NNP	_	_	_
7	_	_	SYM	_	_	_
8	085	085	CD	_	_	_
9	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
10	lactate	lactate	NN	_	_	_
11	_	_	NN	_	_	_
12	growth	growth	NN	_	_	_
13	:	:	:	_	_	_
14	MURI	MURI	NNP	_	_	_
15	_	_	SYM	_	_	_
16	086	086	CD	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	lactate	lactate	NN	_	_	_
19	_	_	NN	_	_	_
20	growth	growth	NN	_	_	_
21	:	:	:	_	_	_
22	MURI	MURI	NNP	_	_	_
23	_	_	SYM	_	_	_
24	087	087	CD	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	lactate	lactate	NN	_	_	_
27	_	_	NN	_	_	_
28	growth	growth	NN	_	_	_
29	:	:	:	_	_	_
30	MURI	MURI	NNP	_	_	_
31	_	_	SYM	_	_	_
32	088	088	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	lactate	lactate	NN	_	_	_
35	_	_	NN	_	_	_
36	growth	growth	NN	_	_	_
37	:	:	:	_	_	_
38	MURI	MURI	NNP	_	_	_
39	_	_	SYM	_	_	_
40	089	089	CD	_	_	_
41	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
42	lactate	lactate	NN	_	_	_
43	_	_	NN	_	_	_
44	growth	growth	NN	_	_	_
45	:	:	:	_	_	_
46	MURI	MURI	NNP	_	_	_
47	_	_	SYM	_	_	_
48	090	090	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	late	late	JJ	_	_	_
51	stationary	stationary	JJ	_	_	_
52	culture	culture	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	map	map	NN	GEN	_	_
55	trimmed	trim	VBD	_	_	_
56	reads	read	VBZ	_	_	_
57	to	to	TO	_	_	_
58	reference	reference	NN	_	_	_
59	sequence	sequence	NN	_	_	_
60	in	in	IN	_	_	_
61	indexes	index	NNS	_	_	_
62	file	file	VBP	_	_	_
63	with	with	IN	_	_	_
64	bowtie2	bowtie2	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	mg	mg	NN	_	_	_
67	+2	+2	NN	_	_	_
68	-LRB-	-lrb-	-LRB-	_	_	_
69	levels	level	NNS	_	_	_
70	-RRB-	-rrb-	-RRB-	_	_	_
71	:	:	:	_	_	_
72	baseMg	basemg	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	mg	mg	NN	_	_	_
75	+2	+2	NN	_	_	_
76	-LRB-	-lrb-	-LRB-	_	_	_
77	levels	level	NNS	_	_	_
78	-RRB-	-rrb-	-RRB-	_	_	_
79	:	:	:	_	_	_
80	highMg	highmg	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	mg	mg	NN	_	_	_
83	+2	+2	NN	_	_	_
84	-LRB-	-lrb-	-LRB-	_	_	_
85	levels	level	NNS	_	_	_
86	-RRB-	-rrb-	-RRB-	_	_	_
87	:	:	:	_	_	_
88	lowMg	lowmg	NN	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	mg	mg	NN	_	_	_
91	+2	+2	NN	_	_	_
92	-LRB-	-lrb-	-LRB-	_	_	_
93	mm	mm	NN	_	_	_
94	-RRB-	-rrb-	-RRB-	_	_	_
95	:	:	:	_	_	_
96	0.005	0.005	CD	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	mg	mg	NN	_	_	_
99	+2	+2	NN	_	_	_
100	-LRB-	-lrb-	-LRB-	_	_	_
101	mm	mm	NN	_	_	_
102	-RRB-	-rrb-	-RRB-	_	_	_
103	:	:	:	_	_	_
104	0.01	0.01	CD	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	mg	mg	NN	_	_	_
107	+2	+2	NN	_	_	_
108	-LRB-	-lrb-	-LRB-	_	_	_
109	mm	mm	NN	_	_	_
110	-RRB-	-rrb-	-RRB-	_	_	_
111	:	:	:	_	_	_
112	0.02	0.02	CD	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	mg	mg	NN	_	_	_
115	+2	+2	NN	_	_	_
116	-LRB-	-lrb-	-LRB-	_	_	_
117	mm	mm	NN	_	_	_
118	-RRB-	-rrb-	-RRB-	_	_	_
119	:	:	:	_	_	_
120	0.04	0.04	CD	_	_	_
121	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
122	mg	mg	NN	_	_	_
123	+2	+2	NN	_	_	_
124	-LRB-	-lrb-	-LRB-	_	_	_
125	mm	mm	NN	_	_	_
126	-RRB-	-rrb-	-RRB-	_	_	_
127	:	:	:	_	_	_
128	0.08	0.08	CD	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	mg	mg	NN	_	_	_
131	+2	+2	NN	_	_	_
132	-LRB-	-lrb-	-LRB-	_	_	_
133	mm	mm	NN	_	_	_
134	-RRB-	-rrb-	-RRB-	_	_	_
135	:	:	:	_	_	_
136	0.8	0.8	CD	_	_	_
137	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
138	mg	mg	NN	_	_	_
139	+2	+2	NN	_	_	_
140	-LRB-	-lrb-	-LRB-	_	_	_
141	mm	mm	NN	_	_	_
142	-RRB-	-rrb-	-RRB-	_	_	_
143	:	:	:	_	_	_
144	200	200	CD	_	_	_
145	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
146	mg	mg	NN	_	_	_
147	+2	+2	NN	_	_	_
148	-LRB-	-lrb-	-LRB-	_	_	_
149	mm	mm	NN	_	_	_
150	-RRB-	-rrb-	-RRB-	_	_	_
151	:	:	:	_	_	_
152	400	400	CD	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
154	mg	mg	NN	_	_	_
155	+2	+2	NN	_	_	_
156	-LRB-	-lrb-	-LRB-	_	_	_
157	mm	mm	NN	_	_	_
158	-RRB-	-rrb-	-RRB-	_	_	_
159	:	:	:	_	_	_
160	50	50	CD	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
162	mg	mg	NN	_	_	_
163	+2	+2	NN	_	_	_
164	-LRB-	-lrb-	-LRB-	_	_	_
165	mm	mm	NN	_	_	_
166	-RRB-	-rrb-	-RRB-	_	_	_
167	:	:	:	_	_	_
168	8	8	CD	_	_	_
169	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
170	MgSO4	mgso4	NN	_	_	_
171	_	_	CD	_	_	_
172	stress	stress	NN	_	_	_
173	_	_	RB	_	_	_
174	high	high	JJ	_	_	_
175	:	:	:	_	_	_
176	MURI	MURI	NNP	_	_	_
177	_	_	SYM	_	_	_
178	106	106	CD	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	MgSO4	mgso4	NN	_	_	_
181	_	_	CD	_	_	_
182	stress	stress	NN	_	_	_
183	_	_	RB	_	_	_
184	high	high	JJ	_	_	_
185	:	:	:	_	_	_
186	MURI	MURI	NNP	_	_	_
187	_	_	SYM	_	_	_
188	107	107	CD	_	_	_
189	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
190	MgSO4	mgso4	NN	_	_	_
191	_	_	CD	_	_	_
192	stress	stress	NN	_	_	_
193	_	_	RB	_	_	_
194	high	high	JJ	_	_	_
195	:	:	:	_	_	_
196	MURI	MURI	NNP	_	_	_
197	_	_	SYM	_	_	_
198	108	108	CD	_	_	_
199	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
200	MgSO4	mgso4	NN	_	_	_
201	_	_	CD	_	_	_
202	stress	stress	NN	_	_	_
203	_	_	RB	_	_	_
204	high	high	JJ	_	_	_
205	:	:	:	_	_	_
206	MURI	MURI	NNP	_	_	_
207	_	_	SYM	_	_	_
208	109	109	CD	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	MgSO4	mgso4	NN	_	_	_
211	_	_	CD	_	_	_
212	stress	stress	NN	_	_	_
213	_	_	RB	_	_	_
214	high	high	JJ	_	_	_
215	:	:	:	_	_	_
216	MURI	MURI	NNP	_	_	_
217	_	_	SYM	_	_	_
218	110	110	CD	_	_	_
219	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
220	MgSO4	mgso4	NN	_	_	_
221	_	_	CD	_	_	_
222	stress	stress	NN	_	_	_
223	_	_	RB	_	_	_
224	high	high	JJ	_	_	_
225	:	:	:	_	_	_
226	MURI	MURI	NNP	_	_	_
227	_	_	SYM	_	_	_
228	111	111	CD	_	_	_
229	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
230	MgSO4	mgso4	NN	_	_	_
231	_	_	CD	_	_	_
232	stress	stress	NN	_	_	_
233	_	_	RB	_	_	_
234	high	high	JJ	_	_	_
235	:	:	:	_	_	_
236	MURI	MURI	NNP	_	_	_
237	_	_	SYM	_	_	_
238	112	112	CD	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	MgSO4	mgso4	NN	_	_	_
241	_	_	CD	_	_	_
242	stress	stress	NN	_	_	_
243	_	_	RB	_	_	_
244	high	high	JJ	_	_	_
245	:	:	:	_	_	_
246	MURI	MURI	NNP	_	_	_
247	_	_	SYM	_	_	_
248	113	113	CD	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	MgSO4	mgso4	NN	_	_	_
251	_	_	CD	_	_	_
252	stress	stress	NN	_	_	_
253	_	_	RB	_	_	_
254	high	high	JJ	_	_	_
255	:	:	:	_	_	_
256	MURI	MURI	NNP	_	_	_
257	_	_	VBD	_	_	_
258	114	114	CD	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	MgSO4	mgso4	NN	_	_	_
261	_	_	CD	_	_	_
262	stress	stress	NN	_	_	_
263	_	_	RB	_	_	_
264	high	high	JJ	_	_	_
265	:	:	:	_	_	_
266	MURI	MURI	NNP	_	_	_
267	_	_	SYM	_	_	_
268	115	115	CD	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	MgSO4	mgso4	NN	_	_	_
271	_	_	CD	_	_	_
272	stress	stress	NN	_	_	_
273	_	_	RB	_	_	_
274	high	high	JJ	_	_	_
275	:	:	:	_	_	_
276	MURI	MURI	NNP	_	_	_
277	_	_	SYM	_	_	_
278	116	116	CD	_	_	_
279	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
280	MgSO4	mgso4	NN	_	_	_
281	_	_	CD	_	_	_
282	stress	stress	NN	_	_	_
283	_	_	RB	_	_	_
284	high	high	JJ	_	_	_
285	:	:	:	_	_	_
286	MURI	MURI	NNP	_	_	_
287	_	_	SYM	_	_	_
288	117	117	CD	_	_	_
289	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
290	MgSO4	mgso4	NN	_	_	_
291	_	_	CD	_	_	_
292	stress	stress	NN	_	_	_
293	_	_	RB	_	_	_
294	high	high	JJ	_	_	_
295	:	:	:	_	_	_
296	MURI	MURI	NNP	_	_	_
297	_	_	SYM	_	_	_
298	118	118	CD	_	_	_
299	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
300	MgSO4	mgso4	NN	_	_	_
301	_	_	CD	_	_	_
302	stress	stress	NN	_	_	_
303	_	_	RB	_	_	_
304	high	high	JJ	_	_	_
305	:	:	:	_	_	_
306	MURI	MURI	NNP	_	_	_
307	_	_	SYM	_	_	_
308	119	119	CD	_	_	_
309	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
310	MgSO4	mgso4	NN	_	_	_
311	_	_	CD	_	_	_
312	stress	stress	NN	_	_	_
313	_	_	RB	_	_	_
314	high	high	JJ	_	_	_
315	:	:	:	_	_	_
316	MURI	MURI	NNP	_	_	_
317	_	_	SYM	_	_	_
318	120	120	CD	_	_	_
319	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
320	MgSO4	mgso4	NN	_	_	_
321	_	_	CD	_	_	_
322	stress	stress	NN	_	_	_
323	_	_	RB	_	_	_
324	high	high	JJ	_	_	_
325	:	:	:	_	_	_
326	MURI	MURI	NNP	_	_	_
327	_	_	SYM	_	_	_
328	121	121	CD	_	_	_
329	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
330	MgSO4	mgso4	NN	_	_	_
331	_	_	CD	_	_	_
332	stress	stress	NN	_	_	_
333	_	_	RB	_	_	_
334	high	high	JJ	_	_	_
335	:	:	:	_	_	_
336	MURI	MURI	NNP	_	_	_
337	_	_	SYM	_	_	_
338	122	122	CD	_	_	_
339	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
340	MgSO4	mgso4	NN	_	_	_
341	_	_	CD	_	_	_
342	stress	stress	NN	_	_	_
343	_	_	RB	_	_	_
344	high	high	JJ	_	_	_
345	:	:	:	_	_	_
346	MURI	MURI	NNP	_	_	_
347	_	_	SYM	_	_	_
348	123	123	CD	_	_	_
349	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
350	MgSO4	mgso4	NN	_	_	_
351	_	_	CD	_	_	_
352	stress	stress	NN	_	_	_
353	_	_	RB	_	_	_
354	high	high	JJ	_	_	_
355	:	:	:	_	_	_
356	MURI	MURI	NNP	_	_	_
357	_	_	VBD	_	_	_
358	124	124	CD	_	_	_
359	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
360	MgSO4	mgso4	NN	_	_	_
361	_	_	CD	_	_	_
362	stress	stress	NN	_	_	_
363	_	_	RB	_	_	_
364	high	high	JJ	_	_	_
365	:	:	:	_	_	_
366	MURI	MURI	NNP	_	_	_
367	_	_	SYM	_	_	_
368	125	125	CD	_	_	_
369	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
370	MgSO4	mgso4	NN	_	_	_
371	_	_	CD	_	_	_
372	stress	stress	NN	_	_	_
373	_	_	RB	_	_	_
374	high	high	JJ	_	_	_
375	:	:	:	_	_	_
376	MURI	MURI	NNP	_	_	_
377	_	_	SYM	_	_	_
378	126	126	CD	_	_	_
379	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
380	MgSO4	mgso4	NN	_	_	_
381	_	_	CD	_	_	_
382	stress	stress	NN	_	_	_
383	_	_	RB	_	_	_
384	high	high	JJ	_	_	_
385	:	:	:	_	_	_
386	MURI	MURI	NNP	_	_	_
387	_	_	SYM	_	_	_
388	127	127	CD	_	_	_
389	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
390	MgSO4	mgso4	NN	_	_	_
391	_	_	CD	_	_	_
392	stress	stress	NN	_	_	_
393	_	_	RB	_	_	_
394	high	high	JJ	_	_	_
395	:	:	:	_	_	_
396	MURI	MURI	NNP	_	_	_
397	_	_	SYM	_	_	_
398	128	128	CD	_	_	_
399	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
400	MgSO4	mgso4	NN	_	_	_
401	_	_	CD	_	_	_
402	stress	stress	NN	_	_	_
403	_	_	RB	_	_	_
404	high	high	JJ	_	_	_
405	:	:	:	_	_	_
406	MURI	MURI	NNP	_	_	_
407	_	_	SYM	_	_	_
408	129	129	CD	_	_	_
409	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
410	MgSO4	mgso4	NN	_	_	_
411	_	_	CD	_	_	_
412	stress	stress	NN	_	_	_
413	_	_	RB	_	_	_
414	high	high	JJ	_	_	_
415	:	:	:	_	_	_
416	MURI	MURI	NNP	_	_	_
417	_	_	SYM	_	_	_
418	130	130	CD	_	_	_
419	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
420	MgSO4	mgso4	NN	_	_	_
421	_	_	CD	_	_	_
422	stress	stress	NN	_	_	_
423	_	_	RB	_	_	_
424	high	high	JJ	_	_	_
425	:	:	:	_	_	_
426	MURI	MURI	NNP	_	_	_
427	_	_	SYM	_	_	_
428	131	131	CD	_	_	_
429	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
430	MgSO4	mgso4	NN	_	_	_
431	_	_	CD	_	_	_
432	stress	stress	NN	_	_	_
433	_	_	RB	_	_	_
434	high	high	JJ	_	_	_
435	:	:	:	_	_	_
436	MURI	MURI	NNP	_	_	_
437	_	_	SYM	_	_	_
438	132	132	CD	_	_	_
439	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
440	MgSO4	mgso4	NN	_	_	_
441	_	_	CD	_	_	_
442	stress	stress	NN	_	_	_
443	_	_	RB	_	_	_
444	high	high	JJ	_	_	_
445	:	:	:	_	_	_
446	MURI	MURI	NNP	_	_	_
447	_	_	SYM	_	_	_
448	133	133	CD	_	_	_
449	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
450	MgSO4	mgso4	NN	_	_	_
451	_	_	CD	_	_	_
452	stress	stress	NN	_	_	_
453	_	_	RB	_	_	_
454	high	high	JJ	_	_	_
455	:	:	:	_	_	_
456	MURI	MURI	NNP	_	_	_
457	_	_	SYM	_	_	_
458	134	134	CD	_	_	_
459	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
460	MgSO4	mgso4	NN	_	_	_
461	_	_	CD	_	_	_
462	stress	stress	NN	_	_	_
463	_	_	RB	_	_	_
464	high	high	JJ	_	_	_
465	:	:	:	_	_	_
466	MURI	MURI	NNP	_	_	_
467	_	_	SYM	_	_	_
468	135	135	CD	_	_	_
469	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
470	MgSO4	mgso4	NN	_	_	_
471	_	_	CD	_	_	_
472	stress	stress	NN	_	_	_
473	_	_	RB	_	_	_
474	high	high	JJ	_	_	_
475	:	:	:	_	_	_
476	MURI	MURI	NNP	_	_	_
477	_	_	VBD	_	_	_
478	136	136	CD	_	_	_
479	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
480	MgSO4	mgso4	NN	_	_	_
481	_	_	CD	_	_	_
482	stress	stress	NN	_	_	_
483	_	_	RB	_	_	_
484	high	high	JJ	_	_	_
485	:	:	:	_	_	_
486	MURI	MURI	NNP	_	_	_
487	_	_	SYM	_	_	_
488	137	137	CD	_	_	_
489	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
490	MgSO4	mgso4	NN	_	_	_
491	_	_	CD	_	_	_
492	stress	stress	NN	_	_	_
493	_	_	RB	_	_	_
494	high	high	JJ	_	_	_
495	:	:	:	_	_	_
496	MURI	MURI	NNP	_	_	_
497	_	_	SYM	_	_	_
498	138	138	CD	_	_	_
499	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
500	MgSO4	mgso4	NN	_	_	_
501	_	_	CD	_	_	_
502	stress	stress	NN	_	_	_
503	_	_	RB	_	_	_
504	high	high	JJ	_	_	_
505	:	:	:	_	_	_
506	MURI	MURI	NNP	_	_	_
507	_	_	SYM	_	_	_
508	139	139	CD	_	_	_
509	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
510	MgSO4	mgso4	NN	_	_	_
511	_	_	CD	_	_	_
512	stress	stress	NN	_	_	_
513	_	_	RB	_	_	_
514	high	high	JJ	_	_	_
515	:	:	:	_	_	_
516	MURI	MURI	NNP	_	_	_
517	_	_	SYM	_	_	_
518	140	140	CD	_	_	_
519	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
520	MgSO4	mgso4	NN	_	_	_
521	_	_	CD	_	_	_
522	stress	stress	NN	_	_	_
523	_	_	RB	_	_	_
524	high	high	JJ	_	_	_
525	:	:	:	_	_	_
526	MURI	MURI	NNP	_	_	_
527	_	_	SYM	_	_	_
528	141	141	CD	_	_	_
529	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
530	MgSO4	mgso4	NN	_	_	_
531	_	_	CD	_	_	_
532	stress	stress	NN	_	_	_
533	_	_	RB	_	_	_
534	low	low	JJ	_	_	_
535	:	:	:	_	_	_
536	MURI	MURI	NNP	_	_	_
537	_	_	SYM	_	_	_
538	142	142	CD	_	_	_
539	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
540	MgSO4	mgso4	NN	_	_	_
541	_	_	CD	_	_	_
542	stress	stress	NN	_	_	_
543	_	_	RB	_	_	_
544	low	low	JJ	_	_	_
545	:	:	:	_	_	_
546	MURI	MURI	NNP	_	_	_
547	_	_	SYM	_	_	_
548	143	143	CD	_	_	_
549	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
550	MgSO4	mgso4	NN	_	_	_
551	_	_	CD	_	_	_
552	stress	stress	NN	_	_	_
553	_	_	RB	_	_	_
554	low	low	JJ	_	_	_
555	:	:	:	_	_	_
556	MURI	MURI	NNP	_	_	_
557	_	_	SYM	_	_	_
558	144	144	CD	_	_	_
559	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
560	MgSO4	mgso4	NN	_	_	_
561	_	_	CD	_	_	_
562	stress	stress	NN	_	_	_
563	_	_	RB	_	_	_
564	low	low	JJ	_	_	_
565	:	:	:	_	_	_
566	MURI	MURI	NNP	_	_	_
567	_	_	SYM	_	_	_
568	145	145	CD	_	_	_
569	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
570	MgSO4	mgso4	NN	_	_	_
571	_	_	CD	_	_	_
572	stress	stress	NN	_	_	_
573	_	_	RB	_	_	_
574	low	low	JJ	_	_	_
575	:	:	:	_	_	_
576	MURI	MURI	NNP	_	_	_
577	_	_	SYM	_	_	_
578	146	146	CD	_	_	_
579	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
580	MgSO4	mgso4	NN	_	_	_
581	_	_	CD	_	_	_
582	stress	stress	NN	_	_	_
583	_	_	RB	_	_	_
584	low	low	JJ	_	_	_
585	:	:	:	_	_	_
586	MURI	MURI	NNP	_	_	_
587	_	_	SYM	_	_	_
588	147	147	CD	_	_	_
589	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
590	MgSO4	mgso4	NN	_	_	_
591	_	_	CD	_	_	_
592	stress	stress	NN	_	_	_
593	_	_	RB	_	_	_
594	low	low	JJ	_	_	_
595	:	:	:	_	_	_
596	MURI	MURI	NNP	_	_	_
597	_	_	VBD	_	_	_
598	148	148	CD	_	_	_
599	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
600	MgSO4	mgso4	NN	_	_	_
601	_	_	CD	_	_	_
602	stress	stress	NN	_	_	_
603	_	_	RB	_	_	_
604	low	low	JJ	_	_	_
605	:	:	:	_	_	_
606	MURI	MURI	NNP	_	_	_
607	_	_	VBD	_	_	_
608	149	149	CD	_	_	_
609	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
610	MgSO4	mgso4	NN	_	_	_
611	_	_	CD	_	_	_
612	stress	stress	NN	_	_	_
613	_	_	RB	_	_	_
614	low	low	JJ	_	_	_
615	:	:	:	_	_	_
616	MURI	MURI	NNP	_	_	_
617	_	_	SYM	_	_	_
618	150	150	CD	_	_	_
619	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
620	MgSO4	mgso4	NN	_	_	_
621	_	_	CD	_	_	_
622	stress	stress	NN	_	_	_
623	_	_	RB	_	_	_
624	low	low	JJ	_	_	_
625	:	:	:	_	_	_
626	MURI	MURI	NNP	_	_	_
627	_	_	SYM	_	_	_
628	151	151	CD	_	_	_
629	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
630	MgSO4	mgso4	NN	_	_	_
631	_	_	CD	_	_	_
632	stress	stress	NN	_	_	_
633	_	_	RB	_	_	_
634	low	low	JJ	_	_	_
635	:	:	:	_	_	_
636	MURI	MURI	NNP	_	_	_
637	_	_	SYM	_	_	_
638	152	152	CD	_	_	_
639	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
640	MgSO4	mgso4	NN	_	_	_
641	_	_	CD	_	_	_
642	stress	stress	NN	_	_	_
643	_	_	RB	_	_	_
644	low	low	JJ	_	_	_
645	:	:	:	_	_	_
646	MURI	MURI	NNP	_	_	_
647	_	_	SYM	_	_	_
648	153	153	CD	_	_	_
649	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
650	MgSO4	mgso4	NN	_	_	_
651	_	_	CD	_	_	_
652	stress	stress	NN	_	_	_
653	_	_	RB	_	_	_
654	low	low	JJ	_	_	_
655	:	:	:	_	_	_
656	MURI	MURI	NNP	_	_	_
657	_	_	VBD	_	_	_
658	154	154	CD	_	_	_
659	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
660	MgSO4	mgso4	NN	_	_	_
661	_	_	CD	_	_	_
662	stress	stress	NN	_	_	_
663	_	_	RB	_	_	_
664	low	low	JJ	_	_	_
665	:	:	:	_	_	_
666	MURI	MURI	NNP	_	_	_
667	_	_	VBD	_	_	_
668	155	155	CD	_	_	_
669	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
670	MgSO4	mgso4	NN	_	_	_
671	_	_	CD	_	_	_
672	stress	stress	NN	_	_	_
673	_	_	RB	_	_	_
674	low	low	JJ	_	_	_
675	:	:	:	_	_	_
676	MURI	MURI	NNP	_	_	_
677	_	_	SYM	_	_	_
678	156	156	CD	_	_	_
679	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
680	MgSO4	mgso4	NN	_	_	_
681	_	_	CD	_	_	_
682	stress	stress	NN	_	_	_
683	_	_	RB	_	_	_
684	low	low	JJ	_	_	_
685	:	:	:	_	_	_
686	MURI	MURI	NNP	_	_	_
687	_	_	SYM	_	_	_
688	157	157	CD	_	_	_
689	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
690	MgSO4	mgso4	NN	_	_	_
691	_	_	CD	_	_	_
692	stress	stress	NN	_	_	_
693	_	_	RB	_	_	_
694	low	low	JJ	_	_	_
695	:	:	:	_	_	_
696	MURI	MURI	NNP	_	_	_
697	_	_	VBD	_	_	_
698	158	158	CD	_	_	_
699	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
700	MgSO4	mgso4	NN	_	_	_
701	_	_	CD	_	_	_
702	stress	stress	NN	_	_	_
703	_	_	RB	_	_	_
704	low	low	JJ	_	_	_
705	:	:	:	_	_	_
706	MURI	MURI	NNP	_	_	_
707	_	_	SYM	_	_	_
708	159	159	CD	_	_	_
709	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
710	MgSO4	mgso4	NN	_	_	_
711	_	_	CD	_	_	_
712	stress	stress	NN	_	_	_
713	_	_	RB	_	_	_
714	low	low	JJ	_	_	_
715	:	:	:	_	_	_
716	MURI	MURI	NNP	_	_	_
717	_	_	SYM	_	_	_
718	160	160	CD	_	_	_
719	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
720	MgSO4	mgso4	NN	_	_	_
721	_	_	CD	_	_	_
722	stress	stress	NN	_	_	_
723	_	_	RB	_	_	_
724	low	low	JJ	_	_	_
725	:	:	:	_	_	_
726	MURI	MURI	NNP	_	_	_
727	_	_	SYM	_	_	_
728	161	161	CD	_	_	_
729	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
730	MgSO4	mgso4	NN	_	_	_
731	_	_	CD	_	_	_
732	stress	stress	NN	_	_	_
733	_	_	RB	_	_	_
734	low	low	JJ	_	_	_
735	:	:	:	_	_	_
736	MURI	MURI	NNP	_	_	_
737	_	_	SYM	_	_	_
738	162	162	CD	_	_	_
739	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
740	MgSO4	mgso4	NN	_	_	_
741	_	_	CD	_	_	_
742	stress	stress	NN	_	_	_
743	_	_	RB	_	_	_
744	low	low	JJ	_	_	_
745	:	:	:	_	_	_
746	MURI	MURI	NNP	_	_	_
747	_	_	SYM	_	_	_
748	163	163	CD	_	_	_
749	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
750	MgSO4	mgso4	NN	_	_	_
751	_	_	CD	_	_	_
752	stress	stress	NN	_	_	_
753	_	_	RB	_	_	_
754	low	low	JJ	_	_	_
755	:	:	:	_	_	_
756	MURI	MURI	NNP	_	_	_
757	_	_	SYM	_	_	_
758	164	164	CD	_	_	_
759	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
760	MgSO4	mgso4	NN	_	_	_
761	_	_	CD	_	_	_
762	stress	stress	NN	_	_	_
763	_	_	RB	_	_	_
764	low	low	JJ	_	_	_
765	:	:	:	_	_	_
766	MURI	MURI	NNP	_	_	_
767	_	_	SYM	_	_	_
768	165	165	CD	_	_	_
769	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
770	MgSO4	mgso4	NN	_	_	_
771	_	_	CD	_	_	_
772	stress	stress	NN	_	_	_
773	_	_	RB	_	_	_
774	low	low	JJ	_	_	_
775	:	:	:	_	_	_
776	MURI	MURI	NNP	_	_	_
777	_	_	VBD	_	_	_
778	166	166	CD	_	_	_
779	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
780	MgSO4	mgso4	NN	_	_	_
781	_	_	CD	_	_	_
782	stress	stress	NN	_	_	_
783	_	_	RB	_	_	_
784	low	low	JJ	_	_	_
785	:	:	:	_	_	_
786	MURI	MURI	NNP	_	_	_
787	_	_	SYM	_	_	_
788	167	167	CD	_	_	_
789	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
790	MgSO4	mgso4	NN	_	_	_
791	_	_	CD	_	_	_
792	stress	stress	NN	_	_	_
793	_	_	RB	_	_	_
794	low	low	JJ	_	_	_
795	:	:	:	_	_	_
796	MURI	MURI	NNP	_	_	_
797	_	_	SYM	_	_	_
798	168	168	CD	_	_	_
799	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
800	MgSO4	mgso4	NN	_	_	_
801	_	_	CD	_	_	_
802	stress	stress	NN	_	_	_
803	_	_	RB	_	_	_
804	low	low	JJ	_	_	_
805	:	:	:	_	_	_
806	MURI	MURI	NNP	_	_	_
807	_	_	SYM	_	_	_
808	169	169	CD	_	_	_
809	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
810	MgSO4	mgso4	NN	_	_	_
811	_	_	CD	_	_	_
812	stress	stress	NN	_	_	_
813	_	_	RB	_	_	_
814	low	low	JJ	_	_	_
815	:	:	:	_	_	_
816	MURI	MURI	NNP	_	_	_
817	_	_	SYM	_	_	_
818	170	170	CD	_	_	_
819	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
820	MgSO4	mgso4	NN	_	_	_
821	_	_	CD	_	_	_
822	stress	stress	NN	_	_	_
823	_	_	RB	_	_	_
824	low	low	JJ	_	_	_
825	:	:	:	_	_	_
826	MURI	MURI	NNP	_	_	_
827	_	_	SYM	_	_	_
828	171	171	CD	_	_	_
829	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
830	na	na	TO	_	_	_
831	+1	+1	NN	_	_	_
832	-LRB-	-lrb-	-LRB-	_	_	_
833	levels	level	NNS	_	_	_
834	-RRB-	-rrb-	-RRB-	_	_	_
835	:	:	:	_	_	_
836	baseNa	basena	NN	_	_	_
837	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
838	na	na	TO	_	_	_
839	+1	+1	NN	_	_	_
840	-LRB-	-lrb-	-LRB-	_	_	_
841	levels	level	NNS	_	_	_
842	-RRB-	-rrb-	-RRB-	_	_	_
843	:	:	:	_	_	_
844	highNa	highna	NN	_	_	_
845	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
846	na	na	TO	_	_	_
847	+1	+1	NN	_	_	_
848	-LRB-	-lrb-	-LRB-	_	_	_
849	mm	mm	NN	_	_	_
850	-RRB-	-rrb-	-RRB-	_	_	_
851	:	:	:	_	_	_
852	100	100	CD	_	_	_
853	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
854	na	na	TO	_	_	_
855	+1	+1	NN	_	_	_
856	-LRB-	-lrb-	-LRB-	_	_	_
857	mm	mm	NN	_	_	_
858	-RRB-	-rrb-	-RRB-	_	_	_
859	:	:	:	_	_	_
860	200	200	CD	_	_	_
861	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
862	na	na	TO	_	_	_
863	+1	+1	NN	_	_	_
864	-LRB-	-lrb-	-LRB-	_	_	_
865	mm	mm	NN	_	_	_
866	-RRB-	-rrb-	-RRB-	_	_	_
867	:	:	:	_	_	_
868	300	300	CD	_	_	_
869	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
870	na	na	TO	_	_	_
871	+1	+1	NN	_	_	_
872	-LRB-	-lrb-	-LRB-	_	_	_
873	mm	mm	NN	_	_	_
874	-RRB-	-rrb-	-RRB-	_	_	_
875	:	:	:	_	_	_
876	5	5	CD	_	_	_
877	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
878	NaCl	nacl	NN	_	_	_
879	_	_	CD	_	_	_
880	stress	stress	NN	_	_	_
881	:	:	:	_	_	_
882	MURI	MURI	NNP	_	_	_
883	_	_	SYM	_	_	_
884	061	061	CD	_	_	_
885	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
886	NaCl	nacl	NN	_	_	_
887	_	_	CD	_	_	_
888	stress	stress	NN	_	_	_
889	:	:	:	_	_	_
890	MURI	MURI	NNP	_	_	_
891	_	_	SYM	_	_	_
892	063	063	CD	_	_	_
893	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
894	NaCl	nacl	NN	_	_	_
895	_	_	CD	_	_	_
896	stress	stress	NN	_	_	_
897	:	:	:	_	_	_
898	MURI	MURI	NNP	_	_	_
899	_	_	SYM	_	_	_
900	064	064	CD	_	_	_
901	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
902	NaCl	nacl	NN	_	_	_
903	_	_	CD	_	_	_
904	stress	stress	NN	_	_	_
905	:	:	:	_	_	_
906	MURI	MURI	NNP	_	_	_
907	_	_	SYM	_	_	_
908	065	065	CD	_	_	_
909	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
910	NaCl	nacl	NN	_	_	_
911	_	_	CD	_	_	_
912	stress	stress	NN	_	_	_
913	:	:	:	_	_	_
914	MURI	MURI	NNP	_	_	_
915	_	_	SYM	_	_	_
916	066	066	CD	_	_	_
917	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
918	NaCl	nacl	NN	_	_	_
919	_	_	CD	_	_	_
920	stress	stress	NN	_	_	_
921	:	:	:	_	_	_
922	MURI	MURI	NNP	_	_	_
923	_	_	SYM	_	_	_
924	067	067	CD	_	_	_
925	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
926	NaCl	nacl	NN	_	_	_
927	_	_	CD	_	_	_
928	stress	stress	NN	_	_	_
929	:	:	:	_	_	_
930	MURI	MURI	NNP	_	_	_
931	_	_	SYM	_	_	_
932	068	068	CD	_	_	_
933	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
934	NaCl	nacl	NN	_	_	_
935	_	_	CD	_	_	_
936	stress	stress	NN	_	_	_
937	:	:	:	_	_	_
938	MURI	MURI	NNP	_	_	_
939	_	_	SYM	_	_	_
940	069	069	CD	_	_	_
941	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
942	NaCl	nacl	NN	_	_	_
943	_	_	CD	_	_	_
944	stress	stress	NN	_	_	_
945	:	:	:	_	_	_
946	MURI	MURI	NNP	_	_	_
947	_	_	SYM	_	_	_
948	070	070	CD	_	_	_
949	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
950	NaCl	nacl	NN	_	_	_
951	_	_	CD	_	_	_
952	stress	stress	NN	_	_	_
953	:	:	:	_	_	_
954	MURI	MURI	NNP	_	_	_
955	_	_	SYM	_	_	_
956	071	071	CD	_	_	_
957	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
958	NaCl	nacl	NN	_	_	_
959	_	_	CD	_	_	_
960	stress	stress	NN	_	_	_
961	:	:	:	_	_	_
962	MURI	MURI	NNP	_	_	_
963	_	_	SYM	_	_	_
964	072	072	CD	_	_	_
965	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
966	NaCl	nacl	NN	_	_	_
967	_	_	CD	_	_	_
968	stress	stress	NN	_	_	_
969	:	:	:	_	_	_
970	MURI	MURI	NNP	_	_	_
971	_	_	SYM	_	_	_
972	073	073	CD	_	_	_
973	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
974	NaCl	nacl	NN	_	_	_
975	_	_	CD	_	_	_
976	stress	stress	NN	_	_	_
977	:	:	:	_	_	_
978	MURI	MURI	NNP	_	_	_
979	_	_	SYM	_	_	_
980	074	074	CD	_	_	_
981	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
982	NaCl	nacl	NN	_	_	_
983	_	_	CD	_	_	_
984	stress	stress	NN	_	_	_
985	:	:	:	_	_	_
986	MURI	MURI	NNP	_	_	_
987	_	_	SYM	_	_	_
988	075	075	CD	_	_	_
989	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
990	NaCl	nacl	NN	_	_	_
991	_	_	CD	_	_	_
992	stress	stress	NN	_	_	_
993	:	:	:	_	_	_
994	MURI	MURI	NNP	_	_	_
995	_	_	SYM	_	_	_
996	076	076	CD	_	_	_
997	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
998	NaCl	nacl	NN	_	_	_
999	_	_	CD	_	_	_
1000	stress	stress	NN	_	_	_
1001	:	:	:	_	_	_
1002	MURI	MURI	NNP	_	_	_
1003	_	_	SYM	_	_	_
1004	077	077	CD	_	_	_
1005	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1006	NaCl	nacl	NN	_	_	_
1007	_	_	CD	_	_	_
1008	stress	stress	NN	_	_	_
1009	:	:	:	_	_	_
1010	MURI	MURI	NNP	_	_	_
1011	_	_	SYM	_	_	_
1012	079	079	CD	_	_	_
1013	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1014	NaCl	nacl	NN	_	_	_
1015	_	_	CD	_	_	_
1016	stress	stress	NN	_	_	_
1017	:	:	:	_	_	_
1018	MURI	MURI	NNP	_	_	_
1019	_	_	SYM	_	_	_
1020	080	080	CD	_	_	_
1021	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1022	NaCl	nacl	NN	_	_	_
1023	_	_	CD	_	_	_
1024	stress	stress	NN	_	_	_
1025	:	:	:	_	_	_
1026	MURI	MURI	NNP	_	_	_
1027	_	_	SYM	_	_	_
1028	081	081	CD	_	_	_
1029	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1030	NaCl	nacl	NN	_	_	_
1031	_	_	CD	_	_	_
1032	stress	stress	NN	_	_	_
1033	:	:	:	_	_	_
1034	MURI	MURI	NNP	_	_	_
1035	_	_	SYM	_	_	_
1036	082	082	CD	_	_	_
1037	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1038	NaCl	nacl	NN	_	_	_
1039	_	_	CD	_	_	_
1040	stress	stress	NN	_	_	_
1041	:	:	:	_	_	_
1042	MURI	MURI	NNP	_	_	_
1043	_	_	SYM	_	_	_
1044	083	083	CD	_	_	_
1045	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1046	NaCl	nacl	NN	_	_	_
1047	_	_	CD	_	_	_
1048	stress	stress	NN	_	_	_
1049	:	:	:	_	_	_
1050	MURI	MURI	NNP	_	_	_
1051	_	_	SYM	_	_	_
1052	084	084	CD	_	_	_
1053	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1054	RNA-Seq	rna-seq	NN	_	_	_
1055	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
1056	RNAsnap	rnasnap	NN	_	_	_
1057	followed	follow	VBN	_	_	_
1058	by	by	IN	_	_	_
1059	purification	purification	NN	_	_	_
1060	through	through	IN	_	_	_
1061	Zymo	Zymo	NNP	_	_	_
1062	RNA	rna	NN	_	_	_
1063	clean	clean	JJ	_	_	_
1064	and	and	CC	_	_	_
1065	concentrator	concentrator	NN	_	_	_
1066	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	stationary	stationary	JJ	_	_	_
3	culture	culture	NN	_	_	_
4	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
5	Supplementary	Supplementary	NNP	_	_	_
6	_	_	VBD	_	_	_
7	files	file	NNS	_	_	_
8	_	_	IN	_	_	_
9	format	format	NN	_	_	_
10	_	_	NN	_	_	_
11	and	and	CC	_	_	_
12	_	_	NN	_	_	_
13	content	content	NN	_	_	_
14	:	:	:	_	_	_
15	txt	txt	NN	_	_	_
16	files	file	NNS	_	_	_
17	including	include	VBG	_	_	_
18	count	count	NN	_	_	_
19	numbers	number	NNS	_	_	_
20	of	of	IN	_	_	_
21	RNA	rna	NN	_	_	_
22	's	's	POS	_	_	_
23	and	and	CC	_	_	_
24	quality	quality	NN	_	_	_
25	control	control	NN	_	_	_
26	were	be	VBD	_	_	_
27	generated	generate	VBN	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	trim	trim	JJ	_	_	_
30	adaptors	adaptor	NNS	_	_	_
31	on	on	IN	_	_	_
32	raw	raw	JJ	_	_	_
33	reads	read	VBZ	_	_	_
34	and	and	CC	_	_	_
35	moved	move	VBD	_	_	_
36	trimmed	trimmed	RBR	_	_	_
37	reads	read	VBZ	_	_	_
38	to	to	TO	_	_	_
39	trimmed	trimmed	RBR	_	_	_
40	_	_	SYM	_	_	_
41	reads	read	VBZ	_	_	_
42	with	with	IN	_	_	_
43	flexbar	flexbar	JJ	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	BW25113	bw25113	NN	_	_	_
46	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
47	Data	Data	NNP	_	_	_
48	were	be	VBD	_	_	_
49	normalized	normalize	VBN	_	_	_
50	using	use	VBG	_	_	_
51	the	the	DT	_	_	_
52	LOWESS	LOWESS	NNP	_	_	_
53	algorithm	algorithm	NN	_	_	_
54	and	and	CC	_	_	_
55	analyzed	analyze	VBN	_	_	_
56	for	for	IN	_	_	_
57	statistical	statistical	JJ	_	_	_
58	significance	significance	NN	_	_	_
59	using	use	VBG	_	_	_
60	the	the	DT	_	_	_
61	MeV	mev	NN	_	_	_
62	package	package	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	EJW3	ejw3	NN	_	_	_
65	,	,	,	_	_	_
66	BW25113	bw25113	NN	_	_	_
67	rpoC	rpoc	NN	GEN	_	_
68	K370	k370	NN	_	_	_
69	_	_	CD	_	_	_
70	A396dup	a396dup	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	EJW3	ejw3	NN	_	_	_
73	in	in	IN	_	_	_
74	M9	m9	NN	_	_	_
75	Replicate	replicate	VB	_	_	_
76	1	1	CD	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	EJW3	ejw3	NN	_	_	_
79	in	in	IN	_	_	_
80	M9	m9	NN	_	_	_
81	Replicate	replicate	VB	_	_	_
82	2	2	CD	_	_	_
83	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
84	EJW3	ejw3	NN	_	_	_
85	in	in	IN	_	_	_
86	M9	m9	NN	_	_	_
87	supplemented	supplement	VBN	_	_	_
88	with	with	IN	_	_	_
89	0.6	0.6	CD	_	_	_
90	M	m	NN	_	_	_
91	NaCl	nacl	NN	_	_	_
92	Replicate	replicate	VB	_	_	_
93	1	1	CD	_	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	EJW3	ejw3	NN	_	_	_
96	in	in	IN	_	_	_
97	M9	m9	NN	_	_	_
98	supplemented	supplement	VBN	_	_	_
99	with	with	IN	_	_	_
100	0.6	0.6	CD	_	_	_
101	M	m	NN	_	_	_
102	NaCl	nacl	NN	_	_	_
103	Replicate	replicate	VB	_	_	_
104	2	2	CD	_	_	_
105	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
106	Escherichia	escherichia	FW	Organism	_	_
107	coli	coli	FW	Organism	_	_
108	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
109	EYG1	eyg1	NN	_	_	_
110	in	in	IN	_	_	_
111	M9	m9	NN	_	_	_
112	Replicate	replicate	VB	_	_	_
113	1	1	CD	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	EYG1	eyg1	NN	_	_	_
116	in	in	IN	_	_	_
117	M9	m9	NN	_	_	_
118	Replicate	replicate	VB	_	_	_
119	2	2	CD	_	_	_
120	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
121	EYG1	eyg1	NN	_	_	_
122	,	,	,	_	_	_
123	MG1655	mg1655	NN	_	_	_
124	rpoC	rpoc	NN	GEN	_	_
125	K370	k370	NN	_	_	_
126	_	_	CD	_	_	_
127	A396dup	a396dup	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	EYG	eyg	NN	_	_	_
130	in	in	IN	_	_	_
131	M9	m9	NN	_	_	_
132	supplemented	supplement	VBN	_	_	_
133	with	with	IN	_	_	_
134	0.6	0.6	CD	_	_	_
135	M	m	NN	_	_	_
136	NaCl	nacl	NN	_	_	_
137	Replicate	replicate	VB	_	_	_
138	1	1	CD	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	EYG	eyg	NN	_	_	_
141	in	in	IN	_	_	_
142	M9	m9	NN	_	_	_
143	supplemented	supplement	VBN	_	_	_
144	with	with	IN	_	_	_
145	0.6	0.6	CD	_	_	_
146	M	m	NN	_	_	_
147	NaCl	nacl	NN	_	_	_
148	Replicate	replicate	VB	_	_	_
149	2	2	CD	_	_	_
150	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
151	genotype	genotype	NN	_	_	_
152	:	:	:	_	_	_
153	rpoC	rpoc	NN	GEN	_	_
154	K370	k370	NN	_	_	_
155	_	_	CD	_	_	_
156	A396dup	a396dup	NN	_	_	_
157	mutant	mutant	JJ	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	genotype	genotype	NN	_	_	_
160	:	:	:	_	_	_
161	Wild-type	wild-type	JJ	_	_	_
162	strain	strain	NN	_	_	_
163	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
164	Grown	Grown	NNP	_	_	_
165	in	in	IN	_	_	_
166	glucose	glucose	NN	SUPP	_	_
167	M9	m9	NN	_	_	_
168	media	media	NNS	_	_	_
169	with	with	IN	_	_	_
170	or	or	CC	_	_	_
171	without	without	IN	_	_	_
172	supplementation	supplementation	NN	_	_	_
173	of	of	IN	_	_	_
174	0.6	0.6	CD	_	_	_
175	M	m	NN	_	_	_
176	NaCl	nacl	NN	_	_	_
177	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
178	MG1655	mg1655	NN	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	protocol	protocol	NN	_	_	_
181	:	:	:	_	_	_
182	M9	m9	NN	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
184	protocol	protocol	NN	_	_	_
185	:	:	:	_	_	_
186	M9	m9	NN	_	_	_
187	supplemented	supplement	VBN	_	_	_
188	with	with	IN	_	_	_
189	0.6	0.6	CD	_	_	_
190	M	m	NN	_	_	_
191	NaCl	nacl	NN	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	Samples	sample	NNS	_	_	_
194	were	be	VBD	_	_	_
195	grown	grow	VBN	_	_	_
196	to	to	TO	_	_	_
197	mid	mid	JJ	GrowthPhase	_	_
198	exponential	exponential	JJ	GrowthPhase	_	_
199	phase	phase	NN	GrowthPhase	_	_
200	-LRB-	-lrb-	-LRB-	_	_	_
201	OD	od	NN	_	_	_
202	approx	approx	RB	_	_	_
203	0.5	0.5	CD	_	_	_
204	-RRB-	-rrb-	-RRB-	_	_	_
205	.	.	.	_	_	_

1	Cultures	culture	NNS	_	_	_
2	were	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	quickly	quickly	RB	_	_	_
5	chilled	chill	VBN	_	_	_
6	to	to	TO	_	_	_
7	≤	≤	VB	_	_	_
8	4	4	CD	_	_	_
9	ºC	ºc	NN	_	_	_
10	on	on	IN	_	_	_
11	dry	dry	JJ	_	_	_
12	ice	ice	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	strain	strain	NN	_	_	_
15	:	:	:	_	_	_
16	BW25113	bw25113	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	strain	strain	NN	_	_	_
19	:	:	:	_	_	_
20	MG1655	mg1655	NN	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	control	control	NN	_	_	_
23	strain	strain	NN	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	Escherichia	escherichia	FW	Organism	_	_
26	coli	coli	FW	Organism	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	L-threonine	l-threonine	NN	_	_	_
29	producing	produce	VBG	_	_	_
30	strain	strain	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	L-threonine	l-threonine	NN	_	_	_
33	producing	produce	VBG	_	_	_
34	strain	strain	NN	_	_	_
35	vs	vs	CC	_	_	_
36	control	control	NN	_	_	_
37	strain	strain	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
39	The	the	DT	_	_	_
40	mean	mean	JJ	_	_	_
41	signal	signal	NN	_	_	_
42	intensity	intensity	NN	_	_	_
43	values	value	NNS	_	_	_
44	of	of	IN	_	_	_
45	the	the	DT	_	_	_
46	duplicate	duplicate	VB	_	_	_
47	spots	spot	NNS	_	_	_
48	were	be	VBD	_	_	_
49	averaged	average	VBN	_	_	_
50	and	and	CC	_	_	_
51	then	then	RB	_	_	_
52	normalized	normalize	VBN	_	_	_
53	by	by	IN	_	_	_
54	the	the	DT	_	_	_
55	global	global	JJ	_	_	_
56	normalization	normalization	NN	_	_	_
57	method	method	NN	_	_	_
58	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	genes	gene	NNS	_	_	_
3	showing	show	VBG	_	_	_
4	the	the	DT	_	_	_
5	p-values	p-value	NNS	_	_	_
6	lower	lower	JJR	_	_	_
7	than	than	IN	_	_	_
8	0.05	0.05	CD	_	_	_
9	were	be	VBD	_	_	_
10	considered	consider	VBN	_	_	_
11	to	to	TO	_	_	_
12	be	be	VB	_	_	_
13	significant	significant	JJ	_	_	_
14	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	using	use	VBG	_	_	_
3	RNeasy	RNeasy	NNP	_	_	_
4	Mini	Mini	NNP	_	_	_
5	Kit	kit	NN	_	_	_
6	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
7	W3110	w3110	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	lacI-deleted	laci-deleted	JJ	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	strain	strain	NN	_	_	_
12	harboring	harbor	VBG	_	_	_
13	pKK223-3	pkk223-3	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	ATCC2	atcc2	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	ATCC3	atcc3	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Broiler	broiler	NN	_	_	_
20	Fecal	fecal	JJ	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Escherichia	escherichia	FW	Organism	_	_
23	coli	coli	FW	Organism	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	first	first	JJ	_	_	_
26	strand	strand	NN	_	_	_
27	cDNA	cdna	NN	_	_	_
28	was	be	VBD	_	_	_
29	performed	perform	VBN	_	_	_
30	by	by	IN	_	_	_
31	the	the	DT	_	_	_
32	use	use	NN	_	_	_
33	of	of	IN	_	_	_
34	SuperScriptII	superscriptii	NN	_	_	_
35	and	and	CC	_	_	_
36	the	the	DT	_	_	_
37	second	second	JJ	_	_	_
38	strand	strand	NN	_	_	_
39	cDNA	cdna	NN	_	_	_
40	synthesis	synthesis	NN	_	_	_
41	was	be	VBD	_	_	_
42	done	do	VBN	_	_	_
43	before	before	IN	_	_	_
44	end-pair	end-pair	JJ	_	_	_
45	and	and	CC	_	_	_
46	dA-tailing	da-tailing	JJ	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
48	Following	follow	VBG	_	_	_
49	\	\	SYM	_	_	_
50	TruSeq	TruSeq	NNP	_	_	_
51	RNA	rna	NN	_	_	_
52	Sample	sample	NN	_	_	_
53	Preparation	Preparation	NNP	_	_	_
54	Guide	Guide	NNP	_	_	_
55	\	\	NNP	_	_	_
56	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	UCSC	UCSC	NNP	_	_	_
7	mm10	mm10	CD	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	Human	Human	NNP	_	_	_
10	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
11	No	No	NNP	_	_	_
12	treatment	treatment	NN	_	_	_
13	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
14	Reads	read	VBZ	_	_	_
15	longer	longer	JJR	_	_	_
16	than	than	IN	_	_	_
17	25	25	CD	_	_	_
18	nt	nt	NNS	_	_	_
19	and	and	CC	_	_	_
20	≤	≤	NN	_	_	_
21	2	2	CD	_	_	_
22	N	n	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	ambiguous	ambiguous	JJ	_	_	_
25	nucleotides	nucleotide	NNS	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	were	be	VBD	_	_	_
28	preserved	preserve	VBN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	RNA-Seq	rna-seq	NN	_	_	_
5	of	of	IN	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	were	be	VBD	_	_	_
9	done	do	VBN	_	_	_
10	using	use	VBG	_	_	_
11	blind	blind	JJ	_	_	_
12	and	and	CC	_	_	_
13	fit-only	fit-only	JJ	_	_	_
14	parameter	parameter	NN	_	_	_
15	in	in	IN	_	_	_
16	DE-Seq	de-seq	NN	_	_	_
17	pakage	pakage	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Sequenced	sequence	VBN	_	_	_
20	reads	read	VBZ	_	_	_
21	were	be	VBD	_	_	_
22	trimmed	trim	VBN	_	_	_
23	for	for	IN	_	_	_
24	adaptor	adaptor	NN	_	_	_
25	sequence	sequence	NN	_	_	_
26	,	,	,	_	_	_
27	and	and	CC	_	_	_
28	masked	mask	VBN	_	_	_
29	for	for	IN	_	_	_
30	low-complexity	low-complexity	NN	_	_	_
31	or	or	CC	_	_	_
32	low-quality	low-quality	JJ	_	_	_
33	sequence	sequence	NN	_	_	_
34	using	use	VBG	_	_	_
35	FASTX-Toolkit	fastx-toolkit	NN	_	_	_
36	version	version	NN	_	_	_
37	0.0.13	0.0.13	CD	_	_	_
38	and	and	CC	_	_	_
39	Perl	Perl	NNP	_	_	_
40	version	version	NN	_	_	_
41	5.8.8	5.8.8	CD	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	strain	strain	NN	_	_	_
44	:	:	:	_	_	_
45	E.	e.	FW	_	_	_
46	coli	coli	FW	_	_	_
47	ATCC	atcc	NN	_	_	_
48	25922	25922	CD	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	strain	strain	NN	_	_	_
51	:	:	:	_	_	_
52	Poultry	Poultry	NNP	_	_	_
53	E.	E.	NNP	_	_	_
54	coli	coli	NN	_	_	_
55	Virulent	virulent	JJ	_	_	_
56	and	and	CC	_	_	_
57	multidrug	multidrug	JJ	_	_	_
58	resistant	resistant	JJ	_	_	_
59	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
60	Strains	strain	NNS	_	_	_
61	were	be	VBD	_	_	_
62	harvested	harvest	VBN	_	_	_
63	in	in	IN	_	_	_
64	MH	mh	NN	_	_	_
65	broth	broth	NN	_	_	_
66	at	at	IN	_	_	_
67	log	log	NN	_	_	_
68	phase	phase	NN	_	_	_
69	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
70	Supplementary	Supplementary	NNP	_	_	_
71	_	_	VBD	_	_	_
72	files	file	NNS	_	_	_
73	_	_	IN	_	_	_
74	format	format	NN	_	_	_
75	_	_	NN	_	_	_
76	and	and	CC	_	_	_
77	_	_	NN	_	_	_
78	content	content	NN	_	_	_
79	:	:	:	_	_	_
80	tab-delimited	tab-delimited	JJ	_	_	_
81	text	text	NN	_	_	_
82	files	file	NNS	_	_	_
83	include	include	VBP	_	_	_
84	normalized	normalize	VBN	_	_	_
85	FPKM	fpkm	NN	_	_	_
86	values	value	NNS	_	_	_
87	and	and	CC	_	_	_
88	raw	raw	JJ	_	_	_
89	fragment	fragment	NN	_	_	_
90	counts	count	NNS	_	_	_
91	for	for	IN	_	_	_
92	each	each	DT	_	_	_
93	Sample	Sample	NNP	_	_	_
94	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
95	Total	Total	NNP	_	_	_
96	RNAs	rna	NNS	_	_	_
97	were	be	VBD	_	_	_
98	extracted	extract	VBN	_	_	_
99	from	from	IN	_	_	_
100	the	the	DT	_	_	_
101	bacterial	bacterial	JJ	_	_	_
102	isolates	isolate	NNS	_	_	_
103	using	use	VBG	_	_	_
104	TRIzol	trizol	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
106	Using	use	VBG	_	_	_
107	blind	blind	JJ	_	_	_
108	and	and	CC	_	_	_
109	fit-only	fit-only	JJ	_	_	_
110	parameter	parameter	NN	_	_	_
111	in	in	IN	_	_	_
112	DE-Seq	de-seq	NN	_	_	_
113	pakage	pakage	NN	_	_	_
114	,	,	,	_	_	_
115	expressions	expression	NNS	_	_	_
116	of	of	IN	_	_	_
117	genes	gene	NNS	_	_	_
118	in	in	IN	_	_	_
119	all	all	DT	_	_	_
120	samples	sample	NNS	_	_	_
121	were	be	VBD	_	_	_
122	changed	change	VBN	_	_	_
123	to	to	TO	_	_	_
124	count	count	VB	_	_	_
125	per	per	IN	_	_	_
126	gene	gene	NN	_	_	_
127	,	,	,	_	_	_
128	using	use	VBG	_	_	_
129	RNA-Seq	rna-seq	NN	_	_	_
130	protocol	protocol	NN	_	_	_
131	on	on	IN	_	_	_
132	Illumina	Illumina	NNP	_	_	_
133	HiSeq2500	hiseq2500	NN	_	_	_
134	platform	platform	NN	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	biomass	biomass	NN	_	_	_
137	collected	collect	VBN	_	_	_
138	in	in	IN	_	_	_
139	the	the	DT	_	_	_
140	transition	transition	NN	_	_	_
141	between	between	IN	_	_	_
142	exponential	exponential	JJ	_	_	_
143	to	to	TO	_	_	_
144	stationary	stationary	JJ	GrowthPhase	_	_
145	phase	phase	NN	GrowthPhase	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	EHEC	ehec	NN	_	_	_
148	in	in	IN	_	_	_
149	LB	LB	NNP	_	_	_
150	Experiment	Experiment	NNP	_	_	_
151	1	1	CD	_	_	_
152	-LSB-	-lsb-	-LRB-	_	_	_
153	RIBO-Seq	ribo-seq	NN	_	_	_
154	-RSB-	-rsb-	-RRB-	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	EHEC	ehec	NN	_	_	_
157	in	in	IN	_	_	_
158	LB	LB	NNP	_	_	_
159	Experiment	Experiment	NNP	_	_	_
160	1	1	CD	_	_	_
161	-LSB-	-lsb-	-LRB-	_	_	_
162	RNA-Seq	rna-seq	NN	_	_	_
163	-RSB-	-rsb-	-RRB-	_	_	_
164	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
165	EHEC	ehec	NN	_	_	_
166	in	in	IN	_	_	_
167	LB	LB	NNP	_	_	_
168	Experiment	Experiment	NNP	_	_	_
169	2	2	CD	_	_	_
170	-LSB-	-lsb-	-LRB-	_	_	_
171	RIBO-Seq	ribo-seq	NN	_	_	_
172	-RSB-	-rsb-	-RRB-	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	EHEC	ehec	NN	_	_	_
175	in	in	IN	_	_	_
176	LB	LB	NNP	_	_	_
177	Experiment	Experiment	NNP	_	_	_
178	2	2	CD	_	_	_
179	-LSB-	-lsb-	-LRB-	_	_	_
180	RNA-Seq	rna-seq	NN	_	_	_
181	-RSB-	-rsb-	-RRB-	_	_	_
182	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
183	Escherichia	escherichia	FW	Organism	_	_
184	coli	coli	FW	Organism	_	_
185	O157	o157	NN	_	_	_
186	:	:	:	_	_	_
187	H7	h7	NN	_	_	_
188	str	str	NN	_	_	_
189	.	.	.	_	_	_

1	EDL933	edl933	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	Genome	Genome	NNP	_	_	_
4	_	_	NNP	_	_	_
5	build	build	VB	_	_	_
6	:	:	:	_	_	_
7	NC	NC	NNP	_	_	_
8	_	_	NNP	_	_	_
9	002655	002655	CD	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	growth	growth	NN	_	_	_
12	media	media	NNS	_	_	_
13	:	:	:	_	_	_
14	LB	lb	NN	MED	_	_
15	medium	medium	NN	MED	_	_
16	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
17	Illumina	Illumina	NNP	_	_	_
18	fastq	fastq	NN	_	_	_
19	files	file	NNS	_	_	_
20	were	be	VBD	_	_	_
21	submitted	submit	VBN	_	_	_
22	to	to	TO	_	_	_
23	the	the	DT	_	_	_
24	galaxy	galaxy	NN	_	_	_
25	pipeline	pipeline	NN	_	_	_
26	=	=	JJ	_	_	_
27	>	>	JJR	_	_	_
28	grooming	grooming	NN	_	_	_
29	=	=	JJ	_	_	_
30	>	>	JJR	_	_	_
31	mapping	mapping	NN	_	_	_
32	to	to	TO	_	_	_
33	NC	NC	NNP	_	_	_
34	_	_	SYM	_	_	_
35	002655	002655	CD	_	_	_
36	using	use	VBG	_	_	_
37	bowtie2	bowtie2	NN	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	default	default	NN	_	_	_
40	but	but	CC	_	_	_
41	seed	seed	NN	_	_	_
42	19	19	CD	_	_	_
43	nt	nt	NNS	_	_	_
44	&	&	CC	_	_	_
45	zero	zero	CD	_	_	_
46	mismatches	mismatch	NNS	_	_	_
47	within	within	IN	_	_	_
48	seed	seed	NN	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
51	LB	lb	NN	MED	_	_
52	medium	medium	NN	MED	_	_
53	,	,	,	_	_	_
54	180	180	CD	_	_	_
55	rpm	rpm	NN	_	_	_
56	shaking	shake	VBG	_	_	_
57	,	,	,	_	_	_
58	at	at	IN	_	_	_
59	37	37	CD	_	_	_
60	°C	°c	NN	_	_	_
61	,	,	,	_	_	_
62	between	between	IN	_	_	_
63	exponential	exponential	JJ	_	_	_
64	and	and	CC	_	_	_
65	stationary	stationary	JJ	GrowthPhase	_	_
66	phase	phase	NN	GrowthPhase	_	_
67	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
68	Library	Library	NNP	_	_	_
69	strategy	strategy	NN	_	_	_
70	:	:	:	_	_	_
71	RIBO-seq	ribo-seq	JJ	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	ligation	ligation	NN	_	_	_
74	,	,	,	_	_	_
75	rt-PCR	rt-pcr	NN	_	_	_
76	,	,	,	_	_	_
77	PCR	pcr	NN	_	_	_
78	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
79	OTHER	other	JJ	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	RNA-Seq	rna-seq	NN	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	Supplementary	supplementary	JJ	_	_	_
84	_	_	NN	_	_	_
85	files	file	NNS	_	_	_
86	_	_	IN	_	_	_
87	format	format	NN	_	_	_
88	_	_	NN	_	_	_
89	and	and	CC	_	_	_
90	_	_	NN	_	_	_
91	content	content	NN	_	_	_
92	:	:	:	_	_	_
93	Reads	read	NNS	_	_	_
94	,	,	,	_	_	_
95	RPKM	rpkm	NN	_	_	_
96	,	,	,	_	_	_
97	and	and	CC	_	_	_
98	RCV	RCV	NNP	_	_	_
99	mapped	map	VBD	_	_	_
100	to	to	TO	_	_	_
101	NC	NC	NNP	_	_	_
102	_	_	SYM	_	_	_
103	002655	002655	CD	_	_	_
104	-LRB-	-lrb-	-LRB-	_	_	_
105	RCV	rcv	NN	_	_	_
106	=	=	JJ	_	_	_
107	Ribosomal	ribosomal	JJ	_	_	_
108	Coverage	Coverage	NNP	_	_	_
109	Value	value	NN	_	_	_
110	=	=	JJ	_	_	_
111	RPKM-footprint	rpkm-footprint	NN	_	_	_
112	over	over	IN	_	_	_
113	RPKM-transcription	rpkm-transcription	NN	_	_	_
114	-RRB-	-rrb-	-RRB-	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	Trizol	trizol	NN	_	_	_
117	for	for	IN	_	_	_
118	RNAseq	rnaseq	NN	_	_	_
119	,	,	,	_	_	_
120	gradient	gradient	NN	_	_	_
121	centrifugation	centrifugation	NN	_	_	_
122	=	=	JJ	_	_	_
123	>	>	JJR	_	_	_
124	RNase	rnase	NN	_	_	_
125	digestions	digestion	NNS	_	_	_
126	=	=	JJ	_	_	_
127	>	>	JJR	_	_	_
128	Trizol	trizol	NN	_	_	_
129	=	=	JJ	_	_	_
130	>	>	JJR	_	_	_
131	gel	gel	NN	_	_	_
132	extraction	extraction	NN	_	_	_
133	for	for	IN	_	_	_
134	RIBOseq	riboseq	NN	_	_	_
135	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
136	Truseq	truseq	NN	_	_	_
137	Small	small	JJ	_	_	_
138	RNA	rna	NN	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
140	Escherichia	escherichia	FW	Organism	_	_
141	coli	coli	FW	Organism	_	_
142	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
143	Genome	Genome	NNP	_	_	_
144	_	_	NNP	_	_	_
145	build	build	VB	_	_	_
146	:	:	:	_	_	_
147	NC	NC	NNP	_	_	_
148	_	_	NNP	_	_	_
149	018220	018220	CD	_	_	_
150	and	and	CC	_	_	_
151	NC	NC	NNP	_	_	_
152	_	_	SYM	_	_	_
153	000913	000913	CD	_	_	_
154	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
155	MG1655	mg1655	NN	_	_	_
156	_	_	CD	_	_	_
157	LB	lb	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	MG1655	mg1655	NN	_	_	_
160	_	_	CD	_	_	_
161	LB1	lb1	NN	_	_	_
162	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
163	MG1655	mg1655	NN	_	_	_
164	_	_	CD	_	_	_
165	LB2	lb2	NN	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	RNA	rna	NN	_	_	_
168	libraries	library	NNS	_	_	_
169	were	be	VBD	_	_	_
170	prepared	prepare	VBN	_	_	_
171	for	for	IN	_	_	_
172	sequencing	sequencing	NN	_	_	_
173	using	use	VBG	_	_	_
174	standard	standard	JJ	_	_	_
175	Illumina	Illumina	NNP	_	_	_
176	protocols	protocol	NNS	_	_	_
177	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
178	RNA-Seq	RNA-Seq	NNP	_	_	_
179	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
180	Single	single	JJ	_	_	_
181	colonies	colony	NNS	_	_	_
182	of	of	IN	_	_	_
183	P.	P.	NNP	_	_	_
184	putida	putida	NN	_	_	_
185	strain	strain	NN	_	_	_
186	DOT-T1E	dot-t1e	NN	_	_	_
187	and	and	CC	_	_	_
188	E.	e.	FW	_	_	_
189	coli	coli	FW	_	_	_
190	MG1655	mg1655	NN	_	_	_
191	were	be	VBD	_	_	_
192	grown	grow	VBN	_	_	_
193	overnight	overnight	RB	_	_	_
194	in	in	IN	_	_	_
195	Luria	Luria	NNP	_	_	_
196	--	--	:	_	_	_
197	Bertani	Bertani	NNP	_	_	_
198	-LRB-	-lrb-	-LRB-	_	_	_
199	LB	LB	NNP	_	_	_
200	-RRB-	-rrb-	-RRB-	_	_	_
201	medium	medium	NN	_	_	_
202	at	at	IN	_	_	_
203	30	30	CD	_	_	_
204	°C	°c	NN	_	_	_
205	.	.	.	_	_	_

1	Overnight	overnight	JJ	_	_	_
2	cultures	culture	NNS	_	_	_
3	were	be	VBD	_	_	_
4	diluted	dilute	VBN	_	_	_
5	to	to	TO	_	_	_
6	a	a	DT	_	_	_
7	starting	start	VBG	_	_	_
8	OD600	od600	NN	_	_	_
9	of	of	IN	_	_	_
10	0.01	0.01	CD	_	_	_
11	in	in	IN	_	_	_
12	the	the	DT	_	_	_
13	same	same	JJ	_	_	_
14	medium	medium	NN	_	_	_
15	and	and	CC	_	_	_
16	50	50	CD	_	_	_
17	ml	ml	NN	_	_	_
18	aliquots	aliquot	NNS	_	_	_
19	were	be	VBD	_	_	_
20	disposed	dispose	VBN	_	_	_
21	in	in	RP	_	_	_
22	separate	separate	JJ	_	_	_
23	250	250	CD	_	_	_
24	ml	ml	NN	_	_	_
25	Erlenmeyer	erlenmeyer	NN	_	_	_
26	flasks	flask	NNS	_	_	_
27	and	and	CC	_	_	_
28	incubated	incubate	VBN	_	_	_
29	with	with	IN	_	_	_
30	shaking	shake	VBG	_	_	_
31	at	at	IN	_	_	_
32	200	200	CD	_	_	_
33	rpm	rpm	NN	_	_	_
34	.	.	.	_	_	_

1	When	when	WRB	_	_	_
2	cultures	culture	NNS	_	_	_
3	reached	reach	VBD	_	_	_
4	exponential	exponential	JJ	GrowthPhase	_	_
5	phase	phase	NN	GrowthPhase	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	0.5	0.5	CD	_	_	_
8	at	at	IN	_	_	_
9	OD600	od600	NN	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	,	,	,	_	_	_
12	antibiotics	antibiotic	NNS	_	_	_
13	were	be	VBD	_	_	_
14	added	add	VBN	_	_	_
15	at	at	IN	_	_	_
16	sub-lethal	sub-lethal	JJ	_	_	_
17	concentrations	concentration	NNS	_	_	_
18	to	to	TO	_	_	_
19	the	the	DT	_	_	_
20	culture	culture	NN	_	_	_
21	medium	medium	NN	_	_	_
22	to	to	TO	_	_	_
23	reach	reach	VB	_	_	_
24	a	a	DT	_	_	_
25	final	final	JJ	_	_	_
26	concentration	concentration	NN	_	_	_
27	of	of	IN	_	_	_
28	1	1	CD	_	_	_
29	µg	µg	NN	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	strain	strain	NN	_	_	_
32	:	:	:	_	_	_
33	MG1655	mg1655	NN	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	Supplementary	supplementary	JJ	_	_	_
36	_	_	NN	_	_	_
37	files	file	NNS	_	_	_
38	_	_	IN	_	_	_
39	format	format	NN	_	_	_
40	_	_	NN	_	_	_
41	and	and	CC	_	_	_
42	_	_	NN	_	_	_
43	content	content	NN	_	_	_
44	:	:	:	_	_	_
45	CoK12	cok12	NN	_	_	_
46	_	_	CD	_	_	_
47	LB.xlsx	lb.xlsx	NN	_	_	_
48	:	:	:	_	_	_
49	Average	average	JJ	_	_	_
50	expression	expression	NN	_	_	_
51	values	value	NNS	_	_	_
52	of	of	IN	_	_	_
53	reads	read	VBZ	_	_	_
54	related	related	JJ	_	_	_
55	with	with	IN	_	_	_
56	MG1655	mg1655	NN	_	_	_
57	strain	strain	NN	_	_	_
58	in	in	IN	_	_	_
59	samples	sample	NNS	_	_	_
60	Co-culture	co-culture	NN	_	_	_
61	_	_	CD	_	_	_
62	LB1	lb1	NN	_	_	_
63	and	and	CC	_	_	_
64	LB2	lb2	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
66	Supplementary	supplementary	JJ	_	_	_
67	_	_	NN	_	_	_
68	files	file	NNS	_	_	_
69	_	_	IN	_	_	_
70	format	format	NN	_	_	_
71	_	_	NN	_	_	_
72	and	and	CC	_	_	_
73	_	_	NN	_	_	_
74	content	content	NN	_	_	_
75	:	:	:	_	_	_
76	CoT1E	cot1e	NN	_	_	_
77	_	_	CD	_	_	_
78	LB.xlsx	lb.xlsx	NN	_	_	_
79	:	:	:	_	_	_
80	Average	average	JJ	_	_	_
81	expression	expression	NN	_	_	_
82	values	value	NNS	_	_	_
83	of	of	IN	_	_	_
84	reads	read	VBZ	_	_	_
85	related	related	JJ	_	_	_
86	with	with	IN	_	_	_
87	DOT-T1E	dot-t1e	NN	_	_	_
88	strain	strain	NN	_	_	_
89	in	in	IN	_	_	_
90	samples	sample	NNS	_	_	_
91	Co-culture	co-culture	NN	_	_	_
92	_	_	CD	_	_	_
93	LB1	lb1	NN	_	_	_
94	and	and	CC	_	_	_
95	LB2	lb2	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
97	Supplementary	supplementary	JJ	_	_	_
98	_	_	NN	_	_	_
99	files	file	NNS	_	_	_
100	_	_	IN	_	_	_
101	format	format	NN	_	_	_
102	_	_	NN	_	_	_
103	and	and	CC	_	_	_
104	_	_	NN	_	_	_
105	content	content	NN	_	_	_
106	:	:	:	_	_	_
107	K12	k12	NN	_	_	_
108	_	_	CD	_	_	_
109	LB.xlsx	lb.xlsx	NN	_	_	_
110	:	:	:	_	_	_
111	Average	average	NN	_	_	_
112	of	of	IN	_	_	_
113	expression	expression	NN	_	_	_
114	values	value	NNS	_	_	_
115	of	of	IN	_	_	_
116	samples	sample	NNS	_	_	_
117	MG1655	mg1655	NN	_	_	_
118	_	_	CD	_	_	_
119	LB1	lb1	NN	_	_	_
120	and	and	CC	_	_	_
121	LB2	lb2	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
123	Supplementary	supplementary	JJ	_	_	_
124	_	_	NN	_	_	_
125	files	file	NNS	_	_	_
126	_	_	IN	_	_	_
127	format	format	NN	_	_	_
128	_	_	NN	_	_	_
129	and	and	CC	_	_	_
130	_	_	NN	_	_	_
131	content	content	NN	_	_	_
132	:	:	:	_	_	_
133	T1E	t1e	NN	_	_	_
134	_	_	CD	_	_	_
135	LB.xlsx	lb.xlsx	NN	_	_	_
136	:	:	:	_	_	_
137	Average	average	NN	_	_	_
138	of	of	IN	_	_	_
139	expression	expression	NN	_	_	_
140	values	value	NNS	_	_	_
141	of	of	IN	_	_	_
142	samples	sample	NNS	_	_	_
143	DOT-T1E	dot-t1e	NN	_	_	_
144	_	_	CD	_	_	_
145	LB1	lb1	NN	_	_	_
146	and	and	CC	_	_	_
147	LB2	lb2	NN	_	_	_
148	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
149	Supplementary	supplementary	JJ	_	_	_
150	_	_	NN	_	_	_
151	files	file	NNS	_	_	_
152	_	_	IN	_	_	_
153	format	format	NN	_	_	_
154	_	_	NN	_	_	_
155	and	and	CC	_	_	_
156	_	_	NN	_	_	_
157	content	content	NN	_	_	_
158	:	:	:	_	_	_
159	tab-delimited	tab-delimited	JJ	_	_	_
160	text	text	NN	_	_	_
161	files	file	NNS	_	_	_
162	include	include	VBP	_	_	_
163	the	the	DT	_	_	_
164	average	average	NN	_	_	_
165	of	of	IN	_	_	_
166	the	the	DT	_	_	_
167	expression	expression	NN	_	_	_
168	values	value	NNS	_	_	_
169	obtained	obtain	VBN	_	_	_
170	in	in	IN	_	_	_
171	Rockhopper	Rockhopper	NNP	_	_	_
172	for	for	IN	_	_	_
173	the	the	DT	_	_	_
174	replicates	replicate	VBZ	_	_	_
175	of	of	IN	_	_	_
176	each	each	DT	_	_	_
177	condition	condition	NN	_	_	_
178	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
179	We	we	PRP	_	_	_
180	use	use	VBP	_	_	_
181	Rockhopper	Rockhopper	NNP	_	_	_
182	for	for	IN	_	_	_
183	alignment	alignment	NN	_	_	_
184	and	and	CC	_	_	_
185	the	the	DT	_	_	_
186	complete	complete	JJ	_	_	_
187	analysis	analysis	NN	_	_	_
188	of	of	IN	_	_	_
189	data	datum	NNS	_	_	_
190	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
191	Adapters	adapter	NNS	_	_	_
192	trimmed	trim	VBD	_	_	_
193	with	with	IN	_	_	_
194	Cutadapt	cutadapt	NN	_	_	_
195	-LRB-	-lrb-	-LRB-	_	_	_
196	v1	v1	NN	_	_	_
197	.12	.12	CD	_	_	_
198	-RRB-	-rrb-	-RRB-	_	_	_
199	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
200	Aligned	align	VBN	_	_	_
201	to	to	TO	_	_	_
202	NC	NC	NNP	_	_	_
203	_	_	SYM	_	_	_
204	000913.3	000913.3	CD	_	_	_
205	with	with	IN	_	_	_
206	bwa	bwa	NN	_	_	_
207	version	version	NN	_	_	_
208	0.7.7	0.7.7	CD	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
210	bacterial	bacterial	JJ	_	_	_
211	cells	cell	NNS	_	_	_
212	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
213	Cells	cell	NNS	_	_	_
214	were	be	VBD	_	_	_
215	grown	grow	VBN	_	_	_
216	to	to	TO	_	_	_
217	exponential	exponential	JJ	GrowthPhase	_	_
218	phase	phase	NN	GrowthPhase	_	_
219	in	in	IN	_	_	_
220	Lysogeny	Lysogeny	NNP	_	_	_
221	broth	broth	NN	_	_	_
222	,	,	,	_	_	_
223	37oC	37oc	NN	_	_	_
224	with	with	IN	_	_	_
225	shaking	shake	VBG	_	_	_
226	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
227	Cells	cell	NNS	_	_	_
228	were	be	VBD	_	_	_
229	harvested	harvest	VBN	_	_	_
230	after	after	IN	_	_	_
231	the	the	DT	_	_	_
232	addition	addition	NN	_	_	_
233	of	of	IN	_	_	_
234	rifampicin	rifampicin	NN	SUPP	_	_
235	-LRB-	-lrb-	-LRB-	_	_	_
236	250	250	CD	_	_	_
237	μg	μg	NN	_	_	_
238	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
239	Count	count	NN	_	_	_
240	reads	read	VBZ	_	_	_
241	aligned	align	VBN	_	_	_
242	to	to	TO	_	_	_
243	each	each	DT	_	_	_
244	base	base	NN	_	_	_
245	IGVtools	igvtools	NN	_	_	_
246	-LRB-	-lrb-	-LRB-	_	_	_
247	version	version	NN	_	_	_
248	2.3.71	2.3.71	CD	_	_	_
249	-RRB-	-rrb-	-RRB-	_	_	_
250	,	,	,	_	_	_
251	window	window	NN	_	_	_
252	size	size	NN	_	_	_
253	=	=	JJ	_	_	_
254	1	1	CD	_	_	_
255	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
256	Escherichia	escherichia	FW	Organism	_	_
257	coli	coli	FW	Organism	_	_
258	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
259	Gave	give	VBD	_	_	_
260	a	a	DT	_	_	_
261	pseudocount	pseudocount	NN	_	_	_
262	of	of	IN	_	_	_
263	0.01	0.01	CD	_	_	_
264	to	to	TO	_	_	_
265	all	all	DT	_	_	_
266	values	value	NNS	_	_	_
267	of	of	IN	_	_	_
268	0	0	CD	_	_	_
269	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
270	Genome	Genome	NNP	_	_	_
271	_	_	NNP	_	_	_
272	build	build	VB	_	_	_
273	:	:	:	_	_	_
274	NC	NC	NNP	_	_	_
275	_	_	NNP	_	_	_
276	000913.3	000913.3	CD	_	_	_
277	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
278	genotype	genotype	NN	_	_	_
279	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
280	Index	Index	NNP	_	_	_
281	and	and	CC	_	_	_
282	sort	sort	NN	_	_	_
283	alignments	alignment	NNS	_	_	_
284	with	with	IN	_	_	_
285	samtools	samtool	NNS	_	_	_
286	version	version	NN	_	_	_
287	1.2	1.2	CD	_	_	_
288	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
289	Normalized	normalize	VBN	_	_	_
290	decay	decay	NN	_	_	_
291	values	value	NNS	_	_	_
292	with	with	IN	_	_	_
293	average	average	NN	_	_	_
294	of	of	IN	_	_	_
295	stable	stable	JJ	_	_	_
296	genes	gene	NNS	_	_	_
297	ssrA	ssra	NN	GEN	_	_
298	,	,	,	_	_	_
299	ssrS	ssrs	NN	GEN	_	_
300	,	,	,	_	_	_
301	and	and	CC	_	_	_
302	rnpB	rnpb	NN	GEN	_	_
303	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
304	RNA-Seq	rna-seq	NN	_	_	_
305	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
306	rnc	rnc	SYM	GEN	_	_
307	-	-	:	_	_	_
308	_	_	SYM	_	_	_
309	time0	time0	CD	_	_	_
310	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
311	rnc	rnc	SYM	GEN	_	_
312	-	-	:	_	_	_
313	_	_	SYM	_	_	_
314	time10	time10	CD	_	_	_
315	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
316	rnc	rnc	SYM	GEN	_	_
317	-	-	:	_	_	_
318	_	_	SYM	_	_	_
319	time20	time20	CD	_	_	_
320	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
321	rnc	rnc	SYM	GEN	_	_
322	-	-	:	_	_	_
323	_	_	SYM	_	_	_
324	time2	time2	CD	_	_	_
325	.5	.5	CD	_	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
327	rnc	rnc	SYM	GEN	_	_
328	-	-	:	_	_	_
329	_	_	SYM	_	_	_
330	time5	time5	CD	_	_	_
331	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
332	rnc	rnc	SYM	GEN	_	_
333	-	-	:	_	_	_
334	_	_	SYM	_	_	_
335	time7	time7	CD	_	_	_
336	.5	.5	CD	_	_	_
337	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
338	rRNA	rrna	NN	_	_	_
339	reduction	reduction	NN	_	_	_
340	with	with	IN	_	_	_
341	EpiCentre	EpiCentre	NNP	_	_	_
342	Ribo-Zero	Ribo-Zero	NNP	_	_	_
343	Gram	Gram	NNP	_	_	_
344	Negative	negative	JJ	_	_	_
345	Ribosomal	ribosomal	JJ	_	_	_
346	RNA	rna	NN	_	_	_
347	reduction	reduction	NN	_	_	_
348	kit	kit	NN	_	_	_
349	-LRB-	-lrb-	-LRB-	_	_	_
350	2.5	2.5	CD	_	_	_
351	ug	ug	NN	_	_	_
352	-RRB-	-rrb-	-RRB-	_	_	_
353	&	&	CC	_	_	_
354	TruSeq	TruSeq	NNP	_	_	_
355	RNA	rna	NN	_	_	_
356	Library	Library	NNP	_	_	_
357	Prep	Prep	NNP	_	_	_
358	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
359	strain	strain	NN	_	_	_
360	:	:	:	_	_	_
361	MG1693	mg1693	NN	_	_	_
362	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
363	strain	strain	NN	_	_	_
364	:	:	:	_	_	_
365	SK4455	sk4455	NNS	_	_	_
366	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
367	Supplementary	supplementary	JJ	_	_	_
368	_	_	NN	_	_	_
369	files	file	NNS	_	_	_
370	_	_	IN	_	_	_
371	format	format	NN	_	_	_
372	_	_	NN	_	_	_
373	and	and	CC	_	_	_
374	_	_	NN	_	_	_
375	content	content	NN	_	_	_
376	:	:	:	_	_	_
377	In	in	IN	_	_	_
378	the	the	DT	_	_	_
379	.	.	.	_	_	_

1	txt	txt	NN	_	_	_
2	files	file	VBZ	_	_	_
3	the	the	DT	_	_	_
4	first	first	JJ	_	_	_
5	column	column	NN	_	_	_
6	is	be	VBZ	_	_	_
7	the	the	DT	_	_	_
8	coordinate	coordinate	NN	_	_	_
9	of	of	IN	_	_	_
10	the	the	DT	_	_	_
11	base	base	NN	_	_	_
12	corresponding	correspond	VBG	_	_	_
13	to	to	TO	_	_	_
14	NC	NC	NNP	_	_	_
15	_	_	SYM	_	_	_
16	000913.3	000913.3	CD	_	_	_
17	and	and	CC	_	_	_
18	the	the	DT	_	_	_
19	second	second	JJ	_	_	_
20	column	column	NN	_	_	_
21	is	be	VBZ	_	_	_
22	the	the	DT	_	_	_
23	number	number	NN	_	_	_
24	of	of	IN	_	_	_
25	normalized	normalize	VBN	_	_	_
26	reads	read	VBZ	_	_	_
27	at	at	IN	_	_	_
28	that	that	DT	_	_	_
29	position	position	NN	_	_	_
30	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	0	0	CD	_	_	_
3	values	value	NNS	_	_	_
4	were	be	VBD	_	_	_
5	given	give	VBN	_	_	_
6	a	a	DT	_	_	_
7	pseudocount	pseudocount	NN	_	_	_
8	of	of	IN	_	_	_
9	0.01	0.01	CD	_	_	_
10	.	.	.	_	_	_

1	Counts	count	NNS	_	_	_
2	are	be	VBP	_	_	_
3	normalized	normalize	VBN	_	_	_
4	so	so	IN	_	_	_
5	that	that	IN	_	_	_
6	the	the	DT	_	_	_
7	averages	average	NNS	_	_	_
8	of	of	IN	_	_	_
9	ssrA	ssra	NN	GEN	_	_
10	,	,	,	_	_	_
11	ssrS	ssrs	NN	GEN	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	rnpB	rnpb	NN	GEN	_	_
15	are	be	VBP	_	_	_
16	stable	stable	JJ	_	_	_
17	throughout	throughout	IN	_	_	_
18	the	the	DT	_	_	_
19	decay	decay	NN	_	_	_
20	from	from	IN	_	_	_
21	0	0	CD	_	_	_
22	to	to	TO	_	_	_
23	20	20	CD	_	_	_
24	minutes	minute	NNS	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
26	time	time	NN	_	_	_
27	point	point	NN	_	_	_
28	:	:	:	_	_	_
29	time0	time0	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
31	time	time	NN	_	_	_
32	point	point	NN	_	_	_
33	:	:	:	_	_	_
34	time10	time10	JJ	_	_	_
35	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
36	time	time	NN	_	_	_
37	point	point	NN	_	_	_
38	:	:	:	_	_	_
39	time20	time20	JJ	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
41	time	time	NN	_	_	_
42	point	point	NN	_	_	_
43	:	:	:	_	_	_
44	time2	time2	CD	_	_	_
45	.5	.5	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
47	time	time	NN	_	_	_
48	point	point	NN	_	_	_
49	:	:	:	_	_	_
50	time5	time5	CD	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
52	time	time	NN	_	_	_
53	point	point	NN	_	_	_
54	:	:	:	_	_	_
55	time7	time7	CD	_	_	_
56	.5	.5	CD	_	_	_
57	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
58	Total	total	JJ	_	_	_
59	RNA	rna	NN	_	_	_
60	was	be	VBD	_	_	_
61	extracted	extract	VBN	_	_	_
62	and	and	CC	_	_	_
63	DNase-treated	dnase-treated	JJ	_	_	_
64	according	accord	VBG	_	_	_
65	to	to	TO	_	_	_
66	published	publish	VBN	_	_	_
67	protocols	protocol	NNS	_	_	_
68	-LRB-	-lrb-	-LRB-	_	_	_
69	Khodurksy	khodurksy	NN	_	_	_
70	A	a	NN	_	_	_
71	,	,	,	_	_	_
72	Bernstein	Bernstein	NNP	_	_	_
73	J	J	NNP	_	_	_
74	,	,	,	_	_	_
75	Peter	Peter	NNP	_	_	_
76	B	B	NNP	_	_	_
77	,	,	,	_	_	_
78	Rhodius	Rhodius	NNP	_	_	_
79	V	V	NNP	_	_	_
80	,	,	,	_	_	_
81	Wendisch	Wendisch	NNP	_	_	_
82	V	V	NNP	_	_	_
83	,	,	,	_	_	_
84	Zimmer	Zimmer	NNP	_	_	_
85	D.	D.	NNP	_	_	_
86	Escherichia	escherichia	FW	Organism	_	_
87	coli	coli	FW	Organism	_	_
88	Spotted	spot	VBN	_	_	_
89	Double-Strand	Double-Strand	NNP	_	_	_
90	DNA	DNA	NNP	_	_	_
91	Microarrays	Microarrays	NNPS	_	_	_
92	-RRB-	-rrb-	-RRB-	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
94	WTA	WTA	NNP	_	_	_
95	_	_	SYM	_	_	_
96	time0	time0	CD	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
98	WTA	WTA	NNP	_	_	_
99	_	_	SYM	_	_	_
100	time10	time10	CD	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
102	WTA	WTA	NNP	_	_	_
103	_	_	SYM	_	_	_
104	time20	time20	CD	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
106	WTA	WTA	NNP	_	_	_
107	_	_	SYM	_	_	_
108	time2	time2	CD	_	_	_
109	.5	.5	CD	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
111	WTA	WTA	NNP	_	_	_
112	_	_	SYM	_	_	_
113	time5	time5	CD	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
115	WTA	WTA	NNP	_	_	_
116	_	_	SYM	_	_	_
117	time7	time7	CD	_	_	_
118	.5	.5	CD	_	_	_
119	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
120	WTB	wtb	NN	_	_	_
121	_	_	CD	_	_	_
122	time0	time0	NN	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	WTB	wtb	NN	_	_	_
125	_	_	CD	_	_	_
126	time2	time2	NN	_	_	_
127	.5	.5	CD	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	WTB	wtb	NN	_	_	_
130	_	_	SYM	_	_	_
131	time7	time7	CD	_	_	_
132	.5	.5	CD	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	10	10	CD	_	_	_
135	pmol	pmol	NN	_	_	_
136	of	of	IN	_	_	_
137	a	a	DT	_	_	_
138	pre-adenylated	pre-adenylated	JJ	_	_	_
139	-LRB-	-lrb-	-LRB-	_	_	_
140	rApp	rapp	NN	_	_	_
141	-RRB-	-rrb-	-RRB-	_	_	_
142	adapter	adapter	NN	_	_	_
143	were	be	VBD	_	_	_
144	ligated	ligate	VBN	_	_	_
145	to	to	TO	_	_	_
146	1	1	CD	_	_	_
147	μg	μg	NN	_	_	_
148	of	of	IN	_	_	_
149	nascent	nascent	JJ	_	_	_
150	-LRB-	-lrb-	-LRB-	_	_	_
151	or	or	CC	_	_	_
152	mature	mature	JJ	_	_	_
153	-RRB-	-rrb-	-RRB-	_	_	_
154	RNA	rna	NN	_	_	_
155	in	in	IN	_	_	_
156	a	a	DT	_	_	_
157	reaction	reaction	NN	_	_	_
158	volume	volume	NN	_	_	_
159	of	of	IN	_	_	_
160	20	20	CD	_	_	_
161	μl	μl	NN	_	_	_
162	,	,	,	_	_	_
163	using	use	VBG	_	_	_
164	400	400	CD	_	_	_
165	U	U	NNP	_	_	_
166	T4	t4	NN	_	_	_
167	RNA	rna	NN	_	_	_
168	Ligase	ligase	NN	_	_	_
169	2	2	CD	_	_	_
170	,	,	,	_	_	_
171	Deletion	deletion	NN	_	_	_
172	Mutant	mutant	JJ	_	_	_
173	-LRB-	-lrb-	-LRB-	_	_	_
174	Epicentre	Epicentre	NNP	_	_	_
175	,	,	,	_	_	_
176	cat	cat	NN	_	_	_
177	.	.	.	_	_	_

1	LR2D11310K	lr2d11310k	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	in	in	IN	_	_	_
4	the	the	DT	_	_	_
5	presence	presence	NN	_	_	_
6	of	of	IN	_	_	_
7	20	20	CD	_	_	_
8	%	%	NN	_	_	_
9	PEG-8000	peg-8000	NN	_	_	_
10	,	,	,	_	_	_
11	by	by	IN	_	_	_
12	incubation	incubation	NN	_	_	_
13	at	at	IN	_	_	_
14	25	25	CD	_	_	_
15	°C	°c	NN	_	_	_
16	for	for	IN	_	_	_
17	2	2	CD	_	_	_
18	hours	hour	NNS	_	_	_
19	.	.	.	_	_	_

1	Reaction	reaction	NN	_	_	_
2	clean-up	clean-up	JJ	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	using	use	VBG	_	_	_
6	RNA	rna	NN	_	_	_
7	Clean	Clean	NNP	_	_	_
8	&	&	CC	_	_	_
9	Concentrator	Concentrator	NNP	_	_	_
10	™	™	SYM	_	_	_
11	-5	-5	CD	_	_	_
12	columns	column	NNS	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	RNA	rna	NN	_	_	_
16	was	be	VBD	_	_	_
17	eluted	elute	VBN	_	_	_
18	in	in	IN	_	_	_
19	20	20	CD	_	_	_
20	μl	μl	NN	_	_	_
21	of	of	IN	_	_	_
22	Fragmentation	fragmentation	NN	_	_	_
23	buffer	buffer	NN	_	_	_
24	-LSB-	-lsb-	-LRB-	_	_	_
25	65	65	CD	_	_	_
26	mM	mm	NN	KWSUPP	_	_
27	Tris	Tris	NNP	_	_	_
28	pH	ph	NN	_	_	_
29	8.3	8.3	CD	_	_	_
30	;	;	:	_	_	_
31	100	100	CD	_	_	_
32	mM	mm	NN	KWSUPP	_	_
33	KCl	kcl	NN	_	_	_
34	;	;	:	_	_	_
35	5	5	CD	_	_	_
36	mM	mm	NN	KWSUPP	_	_
37	MgCl2	mgcl2	NN	_	_	_
38	-RSB-	-rsb-	-RRB-	_	_	_
39	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	fragmented	fragment	VBN	_	_	_
4	by	by	IN	_	_	_
5	incubation	incubation	NN	_	_	_
6	at	at	IN	_	_	_
7	95	95	CD	_	_	_
8	°C	°c	NN	_	_	_
9	for	for	IN	_	_	_
10	8	8	CD	_	_	_
11	minutes	minute	NNS	_	_	_
12	.	.	.	_	_	_

1	Fragmented	fragmented	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	using	use	VBG	_	_	_
6	RNA	rna	NN	_	_	_
7	Clean	Clean	NNP	_	_	_
8	&	&	CC	_	_	_
9	Concentrator	Concentrator	NNP	_	_	_
10	™	™	SYM	_	_	_
11	-5	-5	CD	_	_	_
12	columns	column	NNS	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	eluted	elute	VBN	_	_	_
16	in	in	IN	_	_	_
17	5.5	5.5	CD	_	_	_
18	μl	μl	NN	_	_	_
19	of	of	IN	_	_	_
20	nuclease-free	nuclease-free	JJ	_	_	_
21	water	water	NN	_	_	_
22	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	heat-denatured	heat-denatured	JJ	_	_	_
4	at	at	IN	_	_	_
5	70	70	CD	_	_	_
6	°C	°c	NN	_	_	_
7	for	for	IN	_	_	_
8	5	5	CD	_	_	_
9	minutes	minute	NNS	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	reverse	reverse	JJ	_	_	_
13	transcription	transcription	NN	_	_	_
14	was	be	VBD	_	_	_
15	carried	carry	VBN	_	_	_
16	out	out	RP	_	_	_
17	in	in	IN	_	_	_
18	a	a	DT	_	_	_
19	final	final	JJ	_	_	_
20	volume	volume	NN	_	_	_
21	of	of	IN	_	_	_
22	10	10	CD	_	_	_
23	μl	μl	NN	_	_	_
24	,	,	,	_	_	_
25	in	in	IN	_	_	_
26	the	the	DT	_	_	_
27	presence	presence	NN	_	_	_
28	of	of	IN	_	_	_
29	0.5	0.5	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	dNTPs	dntp	NNS	_	_	_
32	,	,	,	_	_	_
33	5	5	CD	_	_	_
34	pmol	pmol	NN	_	_	_
35	of	of	IN	_	_	_
36	RT	rt	NN	_	_	_
37	primer	primer	NN	_	_	_
38	,	,	,	_	_	_
39	20	20	CD	_	_	_
40	U	U	NNP	_	_	_
41	RNaseOUT	RNaseOUT	NNP	_	_	_
42	™	™	NNP	_	_	_
43	Recombinant	recombinant	JJ	_	_	_
44	Ribonuclease	ribonuclease	NN	_	_	_
45	Inhibitor	inhibitor	NN	_	_	_
46	-LRB-	-lrb-	-LRB-	_	_	_
47	Invitrogen	Invitrogen	NNP	_	_	_
48	,	,	,	_	_	_
49	cat	cat	NN	_	_	_
50	.	.	.	_	_	_

1	10777-019	10777-019	CD	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	,	,	,	_	_	_
4	and	and	CC	_	_	_
5	100	100	CD	_	_	_
6	U	U	NNP	_	_	_
7	SuperScript	SuperScript	NNP	_	_	_
8	®	®	SYM	_	_	_
9	III	iii	CD	_	_	_
10	Reverse	reverse	JJ	_	_	_
11	Transcriptase	transcriptase	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	Invitrogen	Invitrogen	NNP	_	_	_
14	,	,	,	_	_	_
15	cat	cat	NN	_	_	_
16	.	.	.	_	_	_

1	18080-044	18080-044	CD	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	,	,	,	_	_	_
4	by	by	IN	_	_	_
5	incubation	incubation	NN	_	_	_
6	at	at	IN	_	_	_
7	50	50	CD	_	_	_
8	°C	°c	NN	_	_	_
9	for	for	IN	_	_	_
10	50	50	CD	_	_	_
11	minutes	minute	NNS	_	_	_
12	.	.	.	_	_	_

1	Template	template	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	degraded	degrade	VBN	_	_	_
5	by	by	IN	_	_	_
6	adding	add	VBG	_	_	_
7	1	1	CD	_	_	_
8	μl	μl	NN	_	_	_
9	of	of	IN	_	_	_
10	1	1	CD	_	_	_
11	M	m	NN	_	_	_
12	NaOH	naoh	NN	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	incubating	incubate	VBG	_	_	_
16	at	at	IN	_	_	_
17	95	95	CD	_	_	_
18	°C	°c	NN	_	_	_
19	for	for	IN	_	_	_
20	5	5	CD	_	_	_
21	minutes	minute	NNS	_	_	_
22	.	.	.	_	_	_

1	Reaction	reaction	NN	_	_	_
2	clean-up	clean-up	JJ	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	using	use	VBG	_	_	_
6	RNA	rna	NN	_	_	_
7	Clean	Clean	NNP	_	_	_
8	&	&	CC	_	_	_
9	Concentrator	Concentrator	NNP	_	_	_
10	™	™	SYM	_	_	_
11	-5	-5	CD	_	_	_
12	columns	column	NNS	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	cDNA	cdna	NN	_	_	_
16	was	be	VBD	_	_	_
17	eluted	elute	VBN	_	_	_
18	in	in	IN	_	_	_
19	6	6	CD	_	_	_
20	μl	μl	NN	_	_	_
21	nuclease-free	nuclease-free	JJ	_	_	_
22	water	water	NN	_	_	_
23	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	fragments	fragment	NNS	_	_	_
3	were	be	VBD	_	_	_
4	resolved	resolve	VBN	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	10	10	CD	_	_	_
8	%	%	NN	_	_	_
9	TBE-Urea	tbe-urea	NN	_	_	_
10	polyacrylamide	polyacrylamide	NN	_	_	_
11	gel	gel	NN	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	a	a	DT	_	_	_
15	gel	gel	NN	_	_	_
16	slice	slice	NN	_	_	_
17	corresponding	correspond	VBG	_	_	_
18	to	to	TO	_	_	_
19	fragments	fragment	NNS	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	range	range	NN	_	_	_
23	40-150	40-150	CD	_	_	_
24	nt	nt	NN	_	_	_
25	was	be	VBD	_	_	_
26	cut	cut	VBN	_	_	_
27	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	recovered	recover	VBN	_	_	_
4	by	by	IN	_	_	_
5	passive	passive	NN	_	_	_
6	diffusion	diffusion	NN	_	_	_
7	in	in	IN	_	_	_
8	Diffusion	Diffusion	NNP	_	_	_
9	buffer	buffer	NN	_	_	_
10	for	for	IN	_	_	_
11	16	16	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	with	with	IN	_	_	_
17	moderate	moderate	JJ	_	_	_
18	shaking	shake	VBG	_	_	_
19	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	was	be	VBD	_	_	_
3	precipitated	precipitate	VBN	_	_	_
4	by	by	IN	_	_	_
5	addition	addition	NN	_	_	_
6	of	of	IN	_	_	_
7	1	1	CD	_	_	_
8	ml	ml	NN	_	_	_
9	Isopropanol	isopropanol	NN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	2	2	CD	_	_	_
13	μl	μl	NN	_	_	_
14	Glycogen	glycogen	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	20	20	CD	_	_	_
17	μg	μg	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	10	10	CD	_	_	_
20	pmol	pmol	NN	_	_	_
21	of	of	IN	_	_	_
22	a	a	DT	_	_	_
23	pre-adenylated	pre-adenylated	JJ	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	rApp	rapp	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	adapter	adapter	NN	_	_	_
28	were	be	VBD	_	_	_
29	ligated	ligate	VBN	_	_	_
30	to	to	TO	_	_	_
31	1	1	CD	_	_	_
32	μg	μg	NN	_	_	_
33	of	of	IN	_	_	_
34	nascent	nascent	JJ	_	_	_
35	RNA	rna	NN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	either	either	CC	_	_	_
38	total	total	NN	_	_	_
39	,	,	,	_	_	_
40	or	or	CC	_	_	_
41	rRNA-depleted	rrna-depleted	JJ	_	_	_
42	using	use	VBG	_	_	_
43	Ribo-Zero	Ribo-Zero	NNP	_	_	_
44	rRNA	rrna	NN	_	_	_
45	Removal	removal	NN	_	_	_
46	Kit	kit	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	Illumina	Illumina	NNP	_	_	_
49	,	,	,	_	_	_
50	cat	cat	NN	_	_	_
51	.	.	.	_	_	_

1	MRZB12424	mrzb12424	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	in	in	IN	_	_	_
5	a	a	DT	_	_	_
6	reaction	reaction	NN	_	_	_
7	volume	volume	NN	_	_	_
8	of	of	IN	_	_	_
9	20	20	CD	_	_	_
10	μl	μl	NN	_	_	_
11	,	,	,	_	_	_
12	using	use	VBG	_	_	_
13	400	400	CD	_	_	_
14	U	U	NNP	_	_	_
15	T4	t4	NN	_	_	_
16	RNA	rna	NN	_	_	_
17	Ligase	ligase	NN	_	_	_
18	2	2	CD	_	_	_
19	,	,	,	_	_	_
20	Deletion	deletion	NN	_	_	_
21	Mutant	mutant	JJ	_	_	_
22	in	in	IN	_	_	_
23	the	the	DT	_	_	_
24	presence	presence	NN	_	_	_
25	of	of	IN	_	_	_
26	20	20	CD	_	_	_
27	%	%	NN	_	_	_
28	PEG-8000	peg-8000	NN	_	_	_
29	,	,	,	_	_	_
30	by	by	IN	_	_	_
31	incubation	incubation	NN	_	_	_
32	at	at	IN	_	_	_
33	25	25	CD	_	_	_
34	°C	°c	NN	_	_	_
35	for	for	IN	_	_	_
36	2	2	CD	_	_	_
37	hours	hour	NNS	_	_	_
38	.	.	.	_	_	_

1	Reaction	reaction	NN	_	_	_
2	clean-up	clean-up	JJ	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	using	use	VBG	_	_	_
6	RNA	rna	NN	_	_	_
7	Clean	Clean	NNP	_	_	_
8	&	&	CC	_	_	_
9	Concentrator	Concentrator	NNP	_	_	_
10	™	™	SYM	_	_	_
11	-5	-5	CD	_	_	_
12	columns	column	NNS	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	RNA	rna	NN	_	_	_
16	was	be	VBD	_	_	_
17	eluted	elute	VBN	_	_	_
18	in	in	IN	_	_	_
19	5.5	5.5	CD	_	_	_
20	μl	μl	NN	_	_	_
21	nuclease-free	nuclease-free	JJ	_	_	_
22	water	water	NN	_	_	_
23	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	heat-denatured	heat-denatured	JJ	_	_	_
4	at	at	IN	_	_	_
5	70	70	CD	_	_	_
6	°C	°c	NN	_	_	_
7	for	for	IN	_	_	_
8	5	5	CD	_	_	_
9	minutes	minute	NNS	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	reverse	reverse	JJ	_	_	_
13	transcription	transcription	NN	_	_	_
14	was	be	VBD	_	_	_
15	carried	carry	VBN	_	_	_
16	out	out	RP	_	_	_
17	in	in	IN	_	_	_
18	a	a	DT	_	_	_
19	final	final	JJ	_	_	_
20	volume	volume	NN	_	_	_
21	of	of	IN	_	_	_
22	10	10	CD	_	_	_
23	μl	μl	NN	_	_	_
24	,	,	,	_	_	_
25	in	in	IN	_	_	_
26	the	the	DT	_	_	_
27	presence	presence	NN	_	_	_
28	of	of	IN	_	_	_
29	0.5	0.5	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	dNTPs	dntp	NNS	_	_	_
32	,	,	,	_	_	_
33	5	5	CD	_	_	_
34	pmol	pmol	NN	_	_	_
35	of	of	IN	_	_	_
36	RT	rt	NN	_	_	_
37	primer	primer	NN	_	_	_
38	,	,	,	_	_	_
39	20	20	CD	_	_	_
40	U	U	NNP	_	_	_
41	RNaseOUT	RNaseOUT	NNP	_	_	_
42	™	™	NNP	_	_	_
43	Recombinant	recombinant	JJ	_	_	_
44	Ribonuclease	ribonuclease	NN	_	_	_
45	Inhibitor	inhibitor	NN	_	_	_
46	,	,	,	_	_	_
47	and	and	CC	_	_	_
48	100	100	CD	_	_	_
49	U	U	NNP	_	_	_
50	SuperScript	SuperScript	NNP	_	_	_
51	®	®	SYM	_	_	_
52	III	iii	CD	_	_	_
53	Reverse	reverse	JJ	_	_	_
54	Transcriptase	transcriptase	NN	_	_	_
55	,	,	,	_	_	_
56	by	by	IN	_	_	_
57	incubation	incubation	NN	_	_	_
58	at	at	IN	_	_	_
59	50	50	CD	_	_	_
60	°C	°c	NN	_	_	_
61	for	for	IN	_	_	_
62	50	50	CD	_	_	_
63	minutes	minute	NNS	_	_	_
64	.	.	.	_	_	_

1	Template	template	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	degraded	degrade	VBN	_	_	_
5	by	by	IN	_	_	_
6	adding	add	VBG	_	_	_
7	1	1	CD	_	_	_
8	μl	μl	NN	_	_	_
9	of	of	IN	_	_	_
10	1	1	CD	_	_	_
11	M	m	NN	_	_	_
12	NaOH	naoh	NN	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	incubating	incubate	VBG	_	_	_
16	at	at	IN	_	_	_
17	95	95	CD	_	_	_
18	°C	°c	NN	_	_	_
19	for	for	IN	_	_	_
20	5	5	CD	_	_	_
21	minutes	minute	NNS	_	_	_
22	.	.	.	_	_	_

1	Reaction	reaction	NN	_	_	_
2	clean-up	clean-up	JJ	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	using	use	VBG	_	_	_
6	RNA	rna	NN	_	_	_
7	Clean	Clean	NNP	_	_	_
8	&	&	CC	_	_	_
9	Concentrator	Concentrator	NNP	_	_	_
10	™	™	SYM	_	_	_
11	-5	-5	CD	_	_	_
12	columns	column	NNS	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	cDNA	cdna	NN	_	_	_
16	was	be	VBD	_	_	_
17	eluted	elute	VBN	_	_	_
18	in	in	IN	_	_	_
19	6	6	CD	_	_	_
20	μl	μl	NN	_	_	_
21	nuclease-free	nuclease-free	JJ	_	_	_
22	water	water	NN	_	_	_
23	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	fragments	fragment	NNS	_	_	_
3	were	be	VBD	_	_	_
4	resolved	resolve	VBN	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	10	10	CD	_	_	_
8	%	%	NN	_	_	_
9	TBE-Urea	tbe-urea	NN	_	_	_
10	polyacrylamide	polyacrylamide	NN	_	_	_
11	gel	gel	NN	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	three	three	CD	_	_	_
15	gel	gel	NN	_	_	_
16	slices	slice	NNS	_	_	_
17	corresponding	correspond	VBG	_	_	_
18	to	to	TO	_	_	_
19	fragments	fragment	NNS	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	ranges	range	NNS	_	_	_
23	of	of	IN	_	_	_
24	40-200	40-200	CD	_	_	_
25	nt	nt	NNS	_	_	_
26	,	,	,	_	_	_
27	200-400	200-400	CD	_	_	_
28	nt	nt	NNS	_	_	_
29	,	,	,	_	_	_
30	and	and	CC	_	_	_
31	400-600	400-600	CD	_	_	_
32	nt	nt	NNS	_	_	_
33	were	be	VBD	_	_	_
34	cut	cut	VBN	_	_	_
35	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	recovered	recover	VBN	_	_	_
4	by	by	IN	_	_	_
5	passive	passive	NN	_	_	_
6	diffusion	diffusion	NN	_	_	_
7	in	in	IN	_	_	_
8	Diffusion	Diffusion	NNP	_	_	_
9	buffer	buffer	NN	_	_	_
10	for	for	IN	_	_	_
11	16	16	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	with	with	IN	_	_	_
17	moderate	moderate	JJ	_	_	_
18	shaking	shake	VBG	_	_	_
19	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	was	be	VBD	_	_	_
3	precipitated	precipitate	VBN	_	_	_
4	by	by	IN	_	_	_
5	addition	addition	NN	_	_	_
6	of	of	IN	_	_	_
7	1	1	CD	_	_	_
8	ml	ml	NN	_	_	_
9	Isopropanol	isopropanol	NN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	2	2	CD	_	_	_
13	μl	μl	NN	_	_	_
14	Glycogen	glycogen	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	20	20	CD	_	_	_
17	μg	μg	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	10	10	CD	_	_	_
20	pmol	pmol	NN	_	_	_
21	of	of	IN	_	_	_
22	a	a	DT	_	_	_
23	pre-adenylated	pre-adenylated	JJ	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	rApp	rapp	NN	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	adapter	adapter	NN	_	_	_
28	were	be	VBD	_	_	_
29	ligated	ligate	VBN	_	_	_
30	to	to	TO	_	_	_
31	rnpB	rnpb	NN	GEN	_	_
32	nascent	nascent	JJ	_	_	_
33	RNA	rna	NN	_	_	_
34	in	in	IN	_	_	_
35	a	a	DT	_	_	_
36	reaction	reaction	NN	_	_	_
37	volume	volume	NN	_	_	_
38	of	of	IN	_	_	_
39	20	20	CD	_	_	_
40	μl	μl	NN	_	_	_
41	,	,	,	_	_	_
42	using	use	VBG	_	_	_
43	400	400	CD	_	_	_
44	U	U	NNP	_	_	_
45	T4	t4	NN	_	_	_
46	RNA	rna	NN	_	_	_
47	Ligase	ligase	NN	_	_	_
48	2	2	CD	_	_	_
49	,	,	,	_	_	_
50	Deletion	deletion	NN	_	_	_
51	Mutant	mutant	JJ	_	_	_
52	in	in	IN	_	_	_
53	the	the	DT	_	_	_
54	presence	presence	NN	_	_	_
55	of	of	IN	_	_	_
56	20	20	CD	_	_	_
57	%	%	NN	_	_	_
58	PEG-8000	peg-8000	NN	_	_	_
59	,	,	,	_	_	_
60	by	by	IN	_	_	_
61	incubation	incubation	NN	_	_	_
62	at	at	IN	_	_	_
63	25	25	CD	_	_	_
64	°C	°c	NN	_	_	_
65	for	for	IN	_	_	_
66	2	2	CD	_	_	_
67	hours	hour	NNS	_	_	_
68	.	.	.	_	_	_

1	Reaction	reaction	NN	_	_	_
2	clean-up	clean-up	JJ	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	using	use	VBG	_	_	_
6	RNA	rna	NN	_	_	_
7	Clean	Clean	NNP	_	_	_
8	&	&	CC	_	_	_
9	Concentrator	Concentrator	NNP	_	_	_
10	™	™	SYM	_	_	_
11	-5	-5	CD	_	_	_
12	columns	column	NNS	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	RNA	rna	NN	_	_	_
16	was	be	VBD	_	_	_
17	eluted	elute	VBN	_	_	_
18	in	in	IN	_	_	_
19	5.5	5.5	CD	_	_	_
20	μl	μl	NN	_	_	_
21	nuclease-free	nuclease-free	JJ	_	_	_
22	water	water	NN	_	_	_
23	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	heat-denatured	heat-denatured	JJ	_	_	_
4	at	at	IN	_	_	_
5	70	70	CD	_	_	_
6	°C	°c	NN	_	_	_
7	for	for	IN	_	_	_
8	5	5	CD	_	_	_
9	minutes	minute	NNS	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	reverse	reverse	JJ	_	_	_
13	transcription	transcription	NN	_	_	_
14	was	be	VBD	_	_	_
15	carried	carry	VBN	_	_	_
16	out	out	RP	_	_	_
17	in	in	IN	_	_	_
18	a	a	DT	_	_	_
19	final	final	JJ	_	_	_
20	volume	volume	NN	_	_	_
21	of	of	IN	_	_	_
22	10	10	CD	_	_	_
23	μl	μl	NN	_	_	_
24	,	,	,	_	_	_
25	in	in	IN	_	_	_
26	the	the	DT	_	_	_
27	presence	presence	NN	_	_	_
28	of	of	IN	_	_	_
29	0.5	0.5	CD	_	_	_
30	mM	mm	NN	KWSUPP	_	_
31	dNTPs	dntp	NNS	_	_	_
32	,	,	,	_	_	_
33	5	5	CD	_	_	_
34	pmol	pmol	NN	_	_	_
35	of	of	IN	_	_	_
36	RT	rt	NN	_	_	_
37	primer	primer	NN	_	_	_
38	,	,	,	_	_	_
39	20	20	CD	_	_	_
40	U	U	NNP	_	_	_
41	RNaseOUT	RNaseOUT	NNP	_	_	_
42	™	™	NNP	_	_	_
43	Recombinant	recombinant	JJ	_	_	_
44	Ribonuclease	ribonuclease	NN	_	_	_
45	Inhibitor	inhibitor	NN	_	_	_
46	,	,	,	_	_	_
47	and	and	CC	_	_	_
48	100	100	CD	_	_	_
49	U	U	NNP	_	_	_
50	SuperScript	SuperScript	NNP	_	_	_
51	®	®	SYM	_	_	_
52	III	iii	CD	_	_	_
53	Reverse	reverse	JJ	_	_	_
54	Transcriptase	transcriptase	NN	_	_	_
55	,	,	,	_	_	_
56	by	by	IN	_	_	_
57	incubation	incubation	NN	_	_	_
58	at	at	IN	_	_	_
59	50	50	CD	_	_	_
60	°C	°c	NN	_	_	_
61	for	for	IN	_	_	_
62	50	50	CD	_	_	_
63	minutes	minute	NNS	_	_	_
64	.	.	.	_	_	_

1	Template	template	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	degraded	degrade	VBN	_	_	_
5	by	by	IN	_	_	_
6	adding	add	VBG	_	_	_
7	1	1	CD	_	_	_
8	μl	μl	NN	_	_	_
9	of	of	IN	_	_	_
10	1	1	CD	_	_	_
11	M	m	NN	_	_	_
12	NaOH	naoh	NN	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	incubating	incubate	VBG	_	_	_
16	at	at	IN	_	_	_
17	95	95	CD	_	_	_
18	°C	°c	NN	_	_	_
19	for	for	IN	_	_	_
20	5	5	CD	_	_	_
21	minutes	minute	NNS	_	_	_
22	.	.	.	_	_	_

1	Reaction	reaction	NN	_	_	_
2	clean-up	clean-up	JJ	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	using	use	VBG	_	_	_
6	RNA	rna	NN	_	_	_
7	Clean	Clean	NNP	_	_	_
8	&	&	CC	_	_	_
9	Concentrator	Concentrator	NNP	_	_	_
10	™	™	SYM	_	_	_
11	-5	-5	CD	_	_	_
12	columns	column	NNS	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	cDNA	cdna	NN	_	_	_
16	was	be	VBD	_	_	_
17	eluted	elute	VBN	_	_	_
18	in	in	IN	_	_	_
19	6	6	CD	_	_	_
20	μl	μl	NN	_	_	_
21	nuclease-free	nuclease-free	JJ	_	_	_
22	water	water	NN	_	_	_
23	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	fragments	fragment	NNS	_	_	_
3	were	be	VBD	_	_	_
4	resolved	resolve	VBN	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	10	10	CD	_	_	_
8	%	%	NN	_	_	_
9	TBE-Urea	tbe-urea	NN	_	_	_
10	polyacrylamide	polyacrylamide	NN	_	_	_
11	gel	gel	NN	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	a	a	DT	_	_	_
15	gel	gel	NN	_	_	_
16	slice	slice	NN	_	_	_
17	corresponding	correspond	VBG	_	_	_
18	to	to	TO	_	_	_
19	fragments	fragment	NNS	_	_	_
20	in	in	IN	_	_	_
21	the	the	DT	_	_	_
22	range	range	NN	_	_	_
23	of	of	IN	_	_	_
24	40-300	40-300	CD	_	_	_
25	nt	nt	NNS	_	_	_
26	was	be	VBD	_	_	_
27	cut	cut	VBN	_	_	_
28	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	was	be	VBD	_	_	_
3	recovered	recover	VBN	_	_	_
4	by	by	IN	_	_	_
5	passive	passive	NN	_	_	_
6	diffusion	diffusion	NN	_	_	_
7	in	in	IN	_	_	_
8	Diffusion	Diffusion	NNP	_	_	_
9	buffer	buffer	NN	_	_	_
10	for	for	IN	_	_	_
11	16	16	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	at	at	IN	_	_	_
14	37	37	CD	_	_	_
15	°C	°c	NN	_	_	_
16	with	with	IN	_	_	_
17	moderate	moderate	JJ	_	_	_
18	shaking	shake	VBG	_	_	_
19	.	.	.	_	_	_

1	cDNA	cdna	NN	_	_	_
2	was	be	VBD	_	_	_
3	precipitated	precipitate	VBN	_	_	_
4	by	by	IN	_	_	_
5	addition	addition	NN	_	_	_
6	of	of	IN	_	_	_
7	1	1	CD	_	_	_
8	ml	ml	NN	_	_	_
9	Isopropanol	isopropanol	NN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	2	2	CD	_	_	_
13	μl	μl	NN	_	_	_
14	Glycogen	glycogen	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	20	20	CD	_	_	_
17	μg	μg	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	2	2	CD	_	_	_
20	μg	μg	NN	_	_	_
21	of	of	IN	_	_	_
22	RNA	rna	NN	_	_	_
23	from	from	IN	_	_	_
24	the	the	DT	_	_	_
25	cytoplasmic	cytoplasmic	JJ	_	_	_
26	fraction	fraction	NN	_	_	_
27	were	be	VBD	_	_	_
28	diluted	dilute	VBN	_	_	_
29	in	in	IN	_	_	_
30	20	20	CD	_	_	_
31	μl	μl	NN	_	_	_
32	of	of	IN	_	_	_
33	Fragmentation	fragmentation	NN	_	_	_
34	buffer	buffer	NN	_	_	_
35	,	,	,	_	_	_
36	and	and	CC	_	_	_
37	fragmented	fragmented	JJ	_	_	_
38	by	by	IN	_	_	_
39	incubation	incubation	NN	_	_	_
40	at	at	IN	_	_	_
41	95	95	CD	_	_	_
42	°C	°c	NN	_	_	_
43	for	for	IN	_	_	_
44	5	5	CD	_	_	_
45	minutes	minute	NNS	_	_	_
46	.	.	.	_	_	_

1	Fragmented	fragmented	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	using	use	VBG	_	_	_
6	RNA	rna	NN	_	_	_
7	Clean	Clean	NNP	_	_	_
8	&	&	CC	_	_	_
9	Concentrator	Concentrator	NNP	_	_	_
10	™	™	SYM	_	_	_
11	-5	-5	CD	_	_	_
12	columns	column	NNS	_	_	_
13	.	.	.	_	_	_

1	End	end	NN	_	_	_
2	repair	repair	NN	_	_	_
3	of	of	IN	_	_	_
4	RNA	rna	NN	_	_	_
5	fragments	fragment	NNS	_	_	_
6	was	be	VBD	_	_	_
7	performed	perform	VBN	_	_	_
8	in	in	IN	_	_	_
9	a	a	DT	_	_	_
10	final	final	JJ	_	_	_
11	volume	volume	NN	_	_	_
12	of	of	IN	_	_	_
13	20	20	CD	_	_	_
14	μl	μl	NN	_	_	_
15	,	,	,	_	_	_
16	in	in	IN	_	_	_
17	the	the	DT	_	_	_
18	presence	presence	NN	_	_	_
19	of	of	IN	_	_	_
20	20	20	CD	_	_	_
21	U	U	NNP	_	_	_
22	T4	t4	NN	_	_	_
23	Polynucleotide	Polynucleotide	NNP	_	_	_
24	Kinase	kinase	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	NEB	neb	NN	_	_	_
27	,	,	,	_	_	_
28	cat	cat	NN	_	_	_
29	.	.	.	_	_	_

1	M0201L	m0201l	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	,	,	,	_	_	_
4	and	and	CC	_	_	_
5	20	20	CD	_	_	_
6	U	U	NNP	_	_	_
7	SUPERase	SUPERase	NNP	_	_	_
8	•	•	SYM	_	_	_
9	In	in	IN	_	_	_
10	™	™	CD	_	_	_
11	RNase	rnase	NN	_	_	_
12	Inhibitor	inhibitor	NN	_	_	_
13	,	,	,	_	_	_
14	by	by	IN	_	_	_
15	incubation	incubation	NN	_	_	_
16	at	at	IN	_	_	_
17	37	37	CD	_	_	_
18	°C	°c	NN	_	_	_
19	for	for	IN	_	_	_
20	1	1	CD	_	_	_
21	hour	hour	NN	_	_	_
22	.	.	.	_	_	_

1	End-repaired	end-repaired	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	was	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	again	again	RB	_	_	_
6	using	use	VBG	_	_	_
7	RNA	rna	NN	_	_	_
8	Clean	Clean	NNP	_	_	_
9	&	&	CC	_	_	_
10	Concentrator	Concentrator	NNP	_	_	_
11	™	™	SYM	_	_	_
12	-5	-5	CD	_	_	_
13	columns	column	NNS	_	_	_
14	,	,	,	_	_	_
15	and	and	CC	_	_	_
16	eluted	elute	VBN	_	_	_
17	in	in	IN	_	_	_
18	6	6	CD	_	_	_
19	μl	μl	NN	_	_	_
20	of	of	IN	_	_	_
21	nuclease-free	nuclease-free	JJ	_	_	_
22	water	water	NN	_	_	_
23	.	.	.	_	_	_

1	6	6	CD	_	_	_
2	μl	μl	NN	_	_	_
3	of	of	IN	_	_	_
4	2X	2x	NN	_	_	_
5	RNA	rna	NN	_	_	_
6	Loading	load	VBG	_	_	_
7	Dye	dye	NN	_	_	_
8	were	be	VBD	_	_	_
9	added	add	VBN	_	_	_
10	to	to	TO	_	_	_
11	end-repaired	end-repaired	JJ	_	_	_
12	RNA	rna	NN	_	_	_
13	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	heated	heat	VBN	_	_	_
4	to	to	TO	_	_	_
5	95	95	CD	_	_	_
6	°C	°c	NN	_	_	_
7	for	for	IN	_	_	_
8	2	2	CD	_	_	_
9	minutes	minute	NNS	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	immediately	immediately	RB	_	_	_
13	placed	place	VBN	_	_	_
14	on	on	IN	_	_	_
15	ice	ice	NN	_	_	_
16	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	resolved	resolve	VBN	_	_	_
4	on	on	IN	_	_	_
5	a	a	DT	_	_	_
6	10	10	CD	_	_	_
7	%	%	NN	_	_	_
8	TBE-Urea	tbe-urea	NN	_	_	_
9	polyacrylamide	polyacrylamide	NN	_	_	_
10	gel	gel	NN	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	a	a	DT	_	_	_
14	gel	gel	NN	_	_	_
15	slice	slice	NN	_	_	_
16	corresponding	correspond	VBG	_	_	_
17	to	to	TO	_	_	_
18	fragments	fragment	NNS	_	_	_
19	above	above	IN	_	_	_
20	200	200	CD	_	_	_
21	nt	nt	NNS	_	_	_
22	was	be	VBD	_	_	_
23	cut	cut	VBN	_	_	_
24	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	gel	gel	NN	_	_	_
3	slice	slice	NN	_	_	_
4	was	be	VBD	_	_	_
5	crushed	crush	VBN	_	_	_
6	by	by	IN	_	_	_
7	centrifugation	centrifugation	NN	_	_	_
8	through	through	IN	_	_	_
9	a	a	DT	_	_	_
10	punctured	punctured	JJ	_	_	_
11	0.5	0.5	CD	_	_	_
12	ml	ml	NN	_	_	_
13	tube	tube	NN	_	_	_
14	,	,	,	_	_	_
15	and	and	CC	_	_	_
16	resuspended	resuspend	VBN	_	_	_
17	in	in	IN	_	_	_
18	500	500	CD	_	_	_
19	μl	μl	NN	_	_	_
20	of	of	IN	_	_	_
21	Diffusion	Diffusion	NNP	_	_	_
22	buffer	buffer	NN	_	_	_
23	supplemented	supplement	VBN	_	_	_
24	with	with	IN	_	_	_
25	60	60	CD	_	_	_
26	U	U	NNP	_	_	_
27	SUPERase	SUPERase	NNP	_	_	_
28	•	•	SYM	_	_	_
29	In	in	IN	_	_	_
30	™	™	CD	_	_	_
31	RNase	rnase	NN	_	_	_
32	Inhibitor	inhibitor	NN	_	_	_
33	,	,	,	_	_	_
34	then	then	RB	_	_	_
35	rotated	rotate	VBD	_	_	_
36	at	at	IN	_	_	_
37	4	4	CD	_	_	_
38	°C	°c	NN	_	_	_
39	for	for	IN	_	_	_
40	16	16	CD	_	_	_
41	hours	hour	NNS	_	_	_
42	to	to	TO	_	_	_
43	allow	allow	VB	_	_	_
44	passive	passive	JJ	_	_	_
45	diffusion	diffusion	NN	_	_	_
46	of	of	IN	_	_	_
47	RNA	rna	NN	_	_	_
48	fragments	fragment	NNS	_	_	_
49	into	into	IN	_	_	_
50	buffer	buffer	NN	_	_	_
51	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	precipitated	precipitate	VBN	_	_	_
4	by	by	IN	_	_	_
5	addition	addition	NN	_	_	_
6	of	of	IN	_	_	_
7	1	1	CD	_	_	_
8	ml	ml	NN	_	_	_
9	Isopropanol	isopropanol	NN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	2	2	CD	_	_	_
13	μl	μl	NN	_	_	_
14	Glycogen	glycogen	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	20	20	CD	_	_	_
17	μg	μg	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	3	3	CD	_	_	_
20	'	'	''	_	_	_
21	-	-	:	_	_	_
22	end	end	NN	_	_	_
23	RNA-seq	rna-seq	NN	_	_	_
24	,	,	,	_	_	_
25	Cytosolic	cytosolic	JJ	_	_	_
26	fraction	fraction	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	3	3	CD	_	_	_
29	'	'	''	_	_	_
30	-	-	:	_	_	_
31	end	end	NN	_	_	_
32	RNA-seq	rna-seq	NN	_	_	_
33	,	,	,	_	_	_
34	Cytosolic	cytosolic	JJ	_	_	_
35	fraction	fraction	NN	_	_	_
36	,	,	,	_	_	_
37	Replicate	replicate	VB	_	_	_
38	#	#	#	_	_	_
39	1	1	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	3	3	CD	_	_	_
42	'	'	''	_	_	_
43	-	-	:	_	_	_
44	end	end	NN	_	_	_
45	RNA-seq	rna-seq	NN	_	_	_
46	,	,	,	_	_	_
47	Cytosolic	cytosolic	JJ	_	_	_
48	fraction	fraction	NN	_	_	_
49	,	,	,	_	_	_
50	Replicate	replicate	VB	_	_	_
51	#	#	#	_	_	_
52	2	2	CD	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	3	3	CD	_	_	_
55	'	'	''	_	_	_
56	-	-	:	_	_	_
57	end	end	NN	_	_	_
58	RNA-seq	rna-seq	NN	_	_	_
59	,	,	,	_	_	_
60	Nucleoid	nucleoid	NN	_	_	_
61	fraction	fraction	NN	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	3	3	CD	_	_	_
64	'	'	''	_	_	_
65	-	-	:	_	_	_
66	end	end	NN	_	_	_
67	RNA-seq	rna-seq	NN	_	_	_
68	,	,	,	_	_	_
69	Nucleoid	nucleoid	NN	_	_	_
70	fraction	fraction	NN	_	_	_
71	,	,	,	_	_	_
72	Replicate	replicate	VB	_	_	_
73	#	#	#	_	_	_
74	1	1	CD	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	3	3	CD	_	_	_
77	'	'	''	_	_	_
78	-	-	:	_	_	_
79	end	end	NN	_	_	_
80	RNA-seq	rna-seq	NN	_	_	_
81	,	,	,	_	_	_
82	Nucleoid	nucleoid	NN	_	_	_
83	fraction	fraction	NN	_	_	_
84	,	,	,	_	_	_
85	Replicate	replicate	VB	_	_	_
86	#	#	#	_	_	_
87	2	2	CD	_	_	_
88	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
89	A	a	DT	_	_	_
90	single	single	JJ	_	_	_
91	colony	colony	NN	_	_	_
92	of	of	IN	_	_	_
93	Escherichia	escherichia	FW	Organism	_	_
94	coli	coli	FW	Organism	_	_
95	was	be	VBD	_	_	_
96	inoculated	inoculate	VBN	_	_	_
97	into	into	IN	_	_	_
98	250	250	CD	_	_	_
99	ml	ml	NN	_	_	_
100	of	of	IN	_	_	_
101	LB	lb	NN	MED	_	_
102	medium	medium	NN	MED	_	_
103	without	without	IN	_	_	_
104	antibiotics	antibiotic	NNS	_	_	_
105	,	,	,	_	_	_
106	and	and	CC	_	_	_
107	grown	grow	VBN	_	_	_
108	at	at	IN	_	_	_
109	37C	37c	NN	_	_	_
110	with	with	IN	_	_	_
111	shaking	shake	VBG	_	_	_
112	-LRB-	-lrb-	-LRB-	_	_	_
113	150	150	CD	_	_	_
114	RPM	rpm	NN	_	_	_
115	-RRB-	-rrb-	-RRB-	_	_	_
116	for	for	IN	_	_	_
117	approximately	approximately	RB	_	_	_
118	4	4	CD	_	_	_
119	hours	hour	NNS	_	_	_
120	,	,	,	_	_	_
121	until	until	IN	_	_	_
122	OD600	od600	NN	_	_	_
123	was	be	VBD	_	_	_
124	~	~	CD	_	_	_
125	0.3	0.3	CD	_	_	_
126	-LRB-	-lrb-	-LRB-	_	_	_
127	log	log	NN	_	_	_
128	phase	phase	NN	_	_	_
129	-RRB-	-rrb-	-RRB-	_	_	_
130	.	.	.	_	_	_

1	EDTA	edta	NN	_	_	_
2	was	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	added	add	VBN	_	_	_
5	to	to	TO	_	_	_
6	a	a	DT	_	_	_
7	final	final	JJ	_	_	_
8	concentration	concentration	NN	_	_	_
9	of	of	IN	_	_	_
10	1	1	CD	_	_	_
11	mM	mm	NN	KWSUPP	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	incubated	incubate	VBN	_	_	_
15	for	for	IN	_	_	_
16	additional	additional	JJ	_	_	_
17	5	5	CD	_	_	_
18	minutes	minute	NNS	_	_	_
19	to	to	TO	_	_	_
20	make	make	VB	_	_	_
21	bacteria	bacterium	NNS	_	_	_
22	permeable	permeable	JJ	_	_	_
23	to	to	TO	_	_	_
24	Actinomycin	Actinomycin	NNP	_	_	_
25	D.	D.	NNP	_	_	_
26	Actinomycin	Actinomycin	NNP	_	_	_
27	D	D	NNP	_	_	_
28	was	be	VBD	_	_	_
29	then	then	RB	_	_	_
30	added	add	VBN	_	_	_
31	to	to	TO	_	_	_
32	a	a	DT	_	_	_
33	final	final	JJ	_	_	_
34	concentration	concentration	NN	_	_	_
35	of	of	IN	_	_	_
36	5	5	CD	_	_	_
37	g	g	NN	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	DMS-seq	dms-seq	NN	_	_	_
40	-LRB-	-lrb-	-LRB-	_	_	_
41	Ribo	Ribo	NNP	_	_	_
42	-	-	:	_	_	_
43	RNA	rna	NN	_	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
46	DMS-seq	dms-seq	NN	_	_	_
47	-LRB-	-lrb-	-LRB-	_	_	_
48	Total	total	JJ	_	_	_
49	RNA	rna	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
52	Each	each	DT	_	_	_
53	bacteria	bacterium	NNS	_	_	_
54	pellet	pellet	NN	_	_	_
55	from	from	IN	_	_	_
56	a	a	DT	_	_	_
57	25	25	CD	_	_	_
58	ml	ml	NN	_	_	_
59	culture	culture	NN	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	OD600	od600	NN	_	_	_
62	~	~	NN	_	_	_
63	0.3	0.3	CD	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	was	be	VBD	_	_	_
66	homogeneously	homogeneously	RB	_	_	_
67	resuspended	resuspend	VBN	_	_	_
68	in	in	IN	_	_	_
69	200	200	CD	_	_	_
70	µl	µl	NN	_	_	_
71	of	of	IN	_	_	_
72	Buffer	Buffer	NNP	_	_	_
73	A	A	NNP	_	_	_
74	-LSB-	-lsb-	-LRB-	_	_	_
75	10	10	CD	_	_	_
76	mM	mm	NN	KWSUPP	_	_
77	Tris	Tris	NNP	_	_	_
78	pH	ph	NN	_	_	_
79	8.0	8.0	CD	_	_	_
80	;	;	:	_	_	_
81	20	20	CD	_	_	_
82	%	%	NN	_	_	_
83	Sucrose	sucrose	NN	_	_	_
84	;	;	:	_	_	_
85	100	100	CD	_	_	_
86	mM	mm	NN	KWSUPP	_	_
87	NaCl	nacl	NN	_	_	_
88	-RSB-	-rsb-	-RRB-	_	_	_
89	supplemented	supplement	VBN	_	_	_
90	with	with	IN	_	_	_
91	200	200	CD	_	_	_
92	U	U	NNP	_	_	_
93	SUPERase	SUPERase	NNP	_	_	_
94	•	•	SYM	_	_	_
95	In	in	IN	_	_	_
96	™	™	CD	_	_	_
97	RNase	rnase	NN	_	_	_
98	Inhibitor	inhibitor	NN	_	_	_
99	,	,	,	_	_	_
100	by	by	IN	_	_	_
101	pipetting	pipetting	NN	_	_	_
102	.	.	.	_	_	_

1	50	50	CD	_	_	_
2	µl	µl	NN	_	_	_
3	of	of	IN	_	_	_
4	Buffer	buffer	NN	_	_	_
5	B	b	NN	_	_	_
6	-LSB-	-lsb-	-LRB-	_	_	_
7	50	50	CD	_	_	_
8	mM	mm	NN	KWSUPP	_	_
9	EDTA	edta	NN	_	_	_
10	;	;	:	_	_	_
11	120	120	CD	_	_	_
12	mM	mm	NN	KWSUPP	_	_
13	Tris	Tris	NNP	_	_	_
14	pH	ph	NN	_	_	_
15	8.0	8.0	CD	_	_	_
16	-RSB-	-rsb-	-RRB-	_	_	_
17	supplemented	supplement	VBN	_	_	_
18	with	with	IN	_	_	_
19	1	1	CD	_	_	_
20	µl	µl	NN	_	_	_
21	Ready-Lyse	ready-lyse	NN	_	_	_
22	™	™	CD	_	_	_
23	Lysozyme	Lysozyme	NNP	_	_	_
24	Solution	solution	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	Epicentre	Epicentre	NNP	_	_	_
27	,	,	,	_	_	_
28	cat	cat	NN	_	_	_
29	.	.	.	_	_	_

1	R1810M	r1810m	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	were	be	VBD	_	_	_
4	added	add	VBN	_	_	_
5	dropwise	dropwise	NN	_	_	_
6	,	,	,	_	_	_
7	and	and	CC	_	_	_
8	the	the	DT	_	_	_
9	vial	vial	NN	_	_	_
10	was	be	VBD	_	_	_
11	gently	gently	RB	_	_	_
12	tilted	tilted	JJ	_	_	_
13	5	5	CD	_	_	_
14	times	time	NNS	_	_	_
15	to	to	TO	_	_	_
16	ensure	ensure	VB	_	_	_
17	homogenous	homogenous	JJ	_	_	_
18	mixing	mix	VBG	_	_	_
19	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	sample	sample	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	incubated	incubate	VBN	_	_	_
6	1	1	CD	_	_	_
7	minute	minute	NN	_	_	_
8	at	at	IN	_	_	_
9	room	room	NN	_	_	_
10	temperature	temperature	NN	_	_	_
11	.	.	.	_	_	_

1	250	250	CD	_	_	_
2	µl	µl	NN	_	_	_
3	of	of	IN	_	_	_
4	Buffer	buffer	NN	_	_	_
5	C	c	NN	_	_	_
6	-LSB-	-lsb-	-LRB-	_	_	_
7	0.5	0.5	CD	_	_	_
8	%	%	NN	_	_	_
9	Tween-20	tween-20	NN	_	_	_
10	:	:	:	_	_	_
11	0.4	0.4	CD	_	_	_
12	%	%	NN	_	_	_
13	NaDOC	nadoc	NN	_	_	_
14	;	;	:	_	_	_
15	2	2	CD	_	_	_
16	M	m	NN	_	_	_
17	NaCl	nacl	NN	_	_	_
18	;	;	:	_	_	_
19	10	10	CD	_	_	_
20	mM	mm	NN	KWSUPP	_	_
21	EDTA	edta	NN	_	_	_
22	-RSB-	-rsb-	-RRB-	_	_	_
23	were	be	VBD	_	_	_
24	immediately	immediately	RB	_	_	_
25	added	add	VBN	_	_	_
26	dropwise	dropwise	NN	_	_	_
27	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	sample	sample	NN	_	_	_
3	was	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	incubated	incubate	VBN	_	_	_
6	5	5	CD	_	_	_
7	minutes	minute	NNS	_	_	_
8	at	at	IN	_	_	_
9	room	room	NN	_	_	_
10	temperature	temperature	NN	_	_	_
11	.	.	.	_	_	_

1	At	at	IN	_	_	_
2	this	this	DT	_	_	_
3	stage	stage	NN	_	_	_
4	the	the	DT	_	_	_
5	solution	solution	NN	_	_	_
6	clears	clear	VBZ	_	_	_
7	considerably	considerably	RB	_	_	_
8	without	without	IN	_	_	_
9	increasing	increase	VBG	_	_	_
10	its	its	PRP$	_	_	_
11	viscosity	viscosity	NN	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	nucleoid	nucleoid	JJ	_	_	_
15	becomes	become	VBZ	_	_	_
16	visible	visible	JJ	_	_	_
17	.	.	.	_	_	_

1	Using	use	VBG	_	_	_
2	a	a	DT	_	_	_
3	cut	cut	NN	_	_	_
4	P1000	p1000	NN	_	_	_
5	pipette	pipette	NN	_	_	_
6	tip	tip	NN	_	_	_
7	,	,	,	_	_	_
8	the	the	DT	_	_	_
9	whole	whole	JJ	_	_	_
10	sample	sample	NN	_	_	_
11	was	be	VBD	_	_	_
12	gently	gently	RB	_	_	_
13	layered	layer	VBN	_	_	_
14	on	on	IN	_	_	_
15	the	the	DT	_	_	_
16	top	top	NN	_	_	_
17	of	of	IN	_	_	_
18	a	a	DT	_	_	_
19	5-30	5-30	CD	_	_	_
20	%	%	NN	_	_	_
21	w	w	NN	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	Escherichia	escherichia	FW	Organism	_	_
24	coli	coli	FW	Organism	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	FastQ	fastq	NN	_	_	_
27	files	file	NNS	_	_	_
28	were	be	VBD	_	_	_
29	examined	examine	VBN	_	_	_
30	using	use	VBG	_	_	_
31	the	the	DT	_	_	_
32	FastQC	fastqc	NN	_	_	_
33	tool	tool	NN	_	_	_
34	.	.	.	_	_	_

1	All	all	PDT	_	_	_
2	the	the	DT	_	_	_
3	relevant	relevant	JJ	_	_	_
4	SPET-seq	spet-seq	NN	_	_	_
5	data	datum	NNS	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	nascent	nascent	JJ	_	_	_
8	RNA	rna	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	analysis	analysis	NN	_	_	_
11	and	and	CC	_	_	_
12	normalization	normalization	NN	_	_	_
13	steps	step	NNS	_	_	_
14	were	be	VBD	_	_	_
15	performed	perform	VBN	_	_	_
16	using	use	VBG	_	_	_
17	a	a	DT	_	_	_
18	custom	custom	NN	_	_	_
19	wrapper	wrapper	NN	_	_	_
20	built	build	VBN	_	_	_
21	on	on	IN	_	_	_
22	top	top	NN	_	_	_
23	of	of	IN	_	_	_
24	the	the	DT	_	_	_
25	RNA	rna	NN	_	_	_
26	Framework13	framework13	NN	_	_	_
27	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	clipped	clip	VBN	_	_	_
6	from	from	IN	_	_	_
7	3	3	CD	_	_	_
8	'	'	''	_	_	_
9	adapter	adapter	NN	_	_	_
10	sequences	sequence	NNS	_	_	_
11	using	use	VBG	_	_	_
12	Cutadapt	cutadapt	JJ	_	_	_
13	v1	v1	NN	_	_	_
14	.10	.10	CD	_	_	_
15	,	,	,	_	_	_
16	discarding	discard	VBG	_	_	_
17	reads	read	VBZ	_	_	_
18	shorter	shorter	JJR	_	_	_
19	than	than	IN	_	_	_
20	15	15	CD	_	_	_
21	nucleotides	nucleotide	NNS	_	_	_
22	.	.	.	_	_	_

1	Escherichia	escherichia	FW	Organism	_	_
2	coli	coli	FW	Organism	_	_
3	str	str	FW	_	_	_
4	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	GenBank	genbank	NN	_	_	_
4	:	:	:	_	_	_
5	U00096	u00096	NN	_	_	_
6	.2	.2	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	was	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	as	as	IN	_	_	_
11	the	the	DT	_	_	_
12	reference	reference	NN	_	_	_
13	genome	genome	NN	_	_	_
14	to	to	TO	_	_	_
15	extract	extract	NN	_	_	_
16	transcripts	transcript	NNS	_	_	_
17	'	'	POS	_	_	_
18	sequences	sequence	NNS	_	_	_
19	.	.	.	_	_	_

1	Forward	forward	RB	_	_	_
2	and	and	CC	_	_	_
3	reverse	reverse	RB	_	_	_
4	reads	read	VBZ	_	_	_
5	were	be	VBD	_	_	_
6	independently	independently	RB	_	_	_
7	mapped	map	VBN	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	reference	reference	NN	_	_	_
11	transcriptome	transcriptome	NN	_	_	_
12	using	use	VBG	_	_	_
13	Bowtie	Bowtie	NNP	_	_	_
14	v1	v1	NN	_	_	_
15	.1.2	.1.2	CD	_	_	_
16	,	,	,	_	_	_
17	by	by	IN	_	_	_
18	allowing	allow	VBG	_	_	_
19	up	up	RP	_	_	_
20	to	to	TO	_	_	_
21	7	7	CD	_	_	_
22	mapping	mapping	NN	_	_	_
23	positions	position	NNS	_	_	_
24	to	to	TO	_	_	_
25	enable	enable	VB	_	_	_
26	mapping	map	VBG	_	_	_
27	to	to	TO	_	_	_
28	the	the	DT	_	_	_
29	7	7	CD	_	_	_
30	E.	e.	FW	_	_	_
31	coli	coli	FW	_	_	_
32	rRNA	rrna	NN	_	_	_
33	genes	gene	NNS	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	parameters	parameter	NNS	_	_	_
36	:	:	:	_	_	_
37	-	-	:	_	_	_
38	n	n	NN	_	_	_
39	2	2	CD	_	_	_
40	-	-	:	_	_	_
41	m	m	NN	_	_	_
42	7	7	CD	_	_	_
43	-	-	:	_	_	_
44	a	a	DT	_	_	_
45	--	--	:	_	_	_
46	best	best	JJS	_	_	_
47	--	--	:	_	_	_
48	strata	strata	NN	_	_	_
49	-5	-5	CD	_	_	_
50	5	5	CD	_	_	_
51	-LSB-	-lsb-	-LRB-	_	_	_
52	--	--	:	_	_	_
53	norc	norc	NN	_	_	_
54	for	for	IN	_	_	_
55	forward	forward	RB	_	_	_
56	reads	read	VBZ	_	_	_
57	,	,	,	_	_	_
58	--	--	:	_	_	_
59	nofw	nofw	NN	_	_	_
60	for	for	IN	_	_	_
61	reverse	reverse	JJ	_	_	_
62	reads	read	VBZ	_	_	_
63	-RSB-	-rsb-	-RRB-	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	.	.	.	_	_	_

1	Forward	forward	RB	_	_	_
2	and	and	CC	_	_	_
3	reverse	reverse	VB	_	_	_
4	mapped	map	VBN	_	_	_
5	reads	read	VBZ	_	_	_
6	were	be	VBD	_	_	_
7	then	then	RB	_	_	_
8	re-paired	re-paired	JJ	_	_	_
9	.	.	.	_	_	_

1	Using	use	VBG	_	_	_
2	reverse	reverse	JJ	_	_	_
3	read	read	NN	_	_	_
4	mapping	mapping	NN	_	_	_
5	positions	position	NNS	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	corresponding	correspond	VBG	_	_	_
8	to	to	TO	_	_	_
9	RNA	rna	NN	_	_	_
10	Polymerase	polymerase	NN	_	_	_
11	positions	position	NNS	_	_	_
12	along	along	IN	_	_	_
13	gene	gene	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	forward	forward	RB	_	_	_
17	reads	read	VBZ	_	_	_
18	were	be	VBD	_	_	_
19	split	split	VBN	_	_	_
20	into	into	IN	_	_	_
21	separate	separate	JJ	_	_	_
22	SAM	SAM	NNP	_	_	_
23	files	file	NNS	_	_	_
24	for	for	IN	_	_	_
25	each	each	DT	_	_	_
26	transcription	transcription	NN	_	_	_
27	intermediate	intermediate	NN	_	_	_
28	.	.	.	_	_	_

1	When	when	WRB	_	_	_
2	analysis	analysis	NN	_	_	_
3	was	be	VBD	_	_	_
4	performed	perform	VBN	_	_	_
5	in	in	IN	_	_	_
6	deciles	decile	NNS	_	_	_
7	of	of	IN	_	_	_
8	transcription	transcription	NN	_	_	_
9	,	,	,	_	_	_
10	genes	gene	NNS	_	_	_
11	were	be	VBD	_	_	_
12	split	split	VBN	_	_	_
13	into	into	IN	_	_	_
14	10	10	CD	_	_	_
15	equally	equally	RB	_	_	_
16	sized	size	VBN	_	_	_
17	deciles	decile	NNS	_	_	_
18	,	,	,	_	_	_
19	and	and	CC	_	_	_
20	reads	read	VBZ	_	_	_
21	belonging	belong	VBG	_	_	_
22	to	to	TO	_	_	_
23	transcription	transcription	NN	_	_	_
24	intermediates	intermediate	NNS	_	_	_
25	falling	fall	VBG	_	_	_
26	in	in	IN	_	_	_
27	the	the	DT	_	_	_
28	same	same	JJ	_	_	_
29	decile	decile	NN	_	_	_
30	were	be	VBD	_	_	_
31	pooled	pool	VBN	_	_	_
32	.	.	.	_	_	_

1	SAM	SAM	NNP	_	_	_
2	files	file	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	passed	pass	VBN	_	_	_
6	to	to	TO	_	_	_
7	the	the	DT	_	_	_
8	rf-count	rf-count	JJ	_	_	_
9	tool	tool	NN	_	_	_
10	of	of	IN	_	_	_
11	the	the	DT	_	_	_
12	RNA	rna	NN	_	_	_
13	Framework	framework	NN	_	_	_
14	to	to	TO	_	_	_
15	generate	generate	VB	_	_	_
16	RT-stop	rt-stop	JJ	_	_	_
17	counts	count	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	RC	rc	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	files	file	NNS	_	_	_
22	.	.	.	_	_	_

1	Resulting	result	VBG	_	_	_
2	RC	rc	NN	_	_	_
3	files	file	NNS	_	_	_
4	were	be	VBD	_	_	_
5	normalized	normalize	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	rf-norm	rf-norm	NN	_	_	_
9	tool	tool	NN	_	_	_
10	of	of	IN	_	_	_
11	the	the	DT	_	_	_
12	RNA	rna	NN	_	_	_
13	Framework	framework	NN	_	_	_
14	in	in	IN	_	_	_
15	50	50	CD	_	_	_
16	nt	nt	NNS	_	_	_
17	sliding	slide	VBG	_	_	_
18	windows	window	NNS	_	_	_
19	,	,	,	_	_	_
20	with	with	IN	_	_	_
21	a	a	DT	_	_	_
22	25	25	CD	_	_	_
23	nt	nt	NNS	_	_	_
24	offset	offset	VBP	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	parameters	parameter	NNS	_	_	_
27	:	:	:	_	_	_
28	-	-	:	_	_	_
29	sm	sm	NN	_	_	_
30	2	2	CD	_	_	_
31	-	-	:	_	_	_
32	nm	nm	NN	_	_	_
33	2	2	CD	_	_	_
34	-	-	:	_	_	_
35	ec	ec	NN	_	_	_
36	0	0	CD	_	_	_
37	-	-	:	_	_	_
38	mc	mc	NN	_	_	_
39	0	0	CD	_	_	_
40	-	-	:	_	_	_
41	n	n	NN	_	_	_
42	50	50	CD	_	_	_
43	-	-	:	_	_	_
44	nw	nw	NN	_	_	_
45	50	50	CD	_	_	_
46	-	-	:	_	_	_
47	wo	will	MD	_	_	_
48	25	25	CD	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	.	.	.	_	_	_

1	Mapping	mapping	NN	_	_	_
2	of	of	IN	_	_	_
3	DMS-seq	dms-seq	JJ	_	_	_
4	data	datum	NNS	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	mature	mature	JJ	_	_	_
7	RNA	rna	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	was	be	VBD	_	_	_
10	performed	perform	VBN	_	_	_
11	by	by	IN	_	_	_
12	using	use	VBG	_	_	_
13	the	the	DT	_	_	_
14	rf-count	rf-count	JJ	_	_	_
15	tool	tool	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	parameters	parameter	NNS	_	_	_
18	:	:	:	_	_	_
19	-	-	:	_	_	_
20	cl	cl	NN	_	_	_
21	15	15	CD	_	_	_
22	-	-	:	_	_	_
23	bm	bm	NN	_	_	_
24	7	7	CD	_	_	_
25	-	-	:	_	_	_
26	ba	ba	SYM	_	_	_
27	-	-	:	_	_	_
28	b5	b5	NN	_	_	_
29	5	5	CD	_	_	_
30	-RRB-	-rrb-	-RRB-	_	_	_
31	.	.	.	_	_	_

1	Resulting	result	VBG	_	_	_
2	RC	rc	NN	_	_	_
3	files	file	NNS	_	_	_
4	were	be	VBD	_	_	_
5	normalized	normalize	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	rf-norm	rf-norm	NN	_	_	_
9	tool	tool	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	parameters	parameter	NNS	_	_	_
12	:	:	:	_	_	_
13	-	-	:	_	_	_
14	sm	sm	NN	_	_	_
15	2	2	CD	_	_	_
16	-	-	:	_	_	_
17	nm	nm	NN	_	_	_
18	2	2	CD	_	_	_
19	-	-	:	_	_	_
20	ec	ec	NN	_	_	_
21	50	50	CD	_	_	_
22	-	-	:	_	_	_
23	mc	mc	NN	_	_	_
24	50	50	CD	_	_	_
25	-	-	:	_	_	_
26	n	n	NN	_	_	_
27	50	50	CD	_	_	_
28	-	-	:	_	_	_
29	nw	nw	NN	_	_	_
30	50	50	CD	_	_	_
31	-	-	:	_	_	_
32	wo	will	MD	_	_	_
33	25	25	CD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	rf-norm	rf-norm	JJ	_	_	_
3	tool	tool	NN	_	_	_
4	generates	generate	VBZ	_	_	_
5	a	a	DT	_	_	_
6	XML	xml	NN	_	_	_
7	file	file	NN	_	_	_
8	for	for	IN	_	_	_
9	each	each	DT	_	_	_
10	transcript	transcript	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	or	or	CC	_	_	_
13	for	for	IN	_	_	_
14	each	each	DT	_	_	_
15	transcription	transcription	NN	_	_	_
16	intermediate	intermediate	JJ	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	FastQ	fastq	NN	_	_	_
19	files	file	NNS	_	_	_
20	were	be	VBD	_	_	_
21	examined	examine	VBN	_	_	_
22	using	use	VBG	_	_	_
23	the	the	DT	_	_	_
24	FastQC	fastqc	NN	_	_	_
25	tool	tool	NN	_	_	_
26	.	.	.	_	_	_

1	All	all	PDT	_	_	_
2	the	the	DT	_	_	_
3	relevant	relevant	JJ	_	_	_
4	SPET-seq	spet-seq	NN	_	_	_
5	data	datum	NNS	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	nascent	nascent	JJ	_	_	_
8	RNA	rna	NN	_	_	_
9	-RRB-	-rrb-	-RRB-	_	_	_
10	analysis	analysis	NN	_	_	_
11	and	and	CC	_	_	_
12	normalization	normalization	NN	_	_	_
13	steps	step	NNS	_	_	_
14	were	be	VBD	_	_	_
15	performed	perform	VBN	_	_	_
16	using	use	VBG	_	_	_
17	a	a	DT	_	_	_
18	custom	custom	NN	_	_	_
19	wrapper	wrapper	NN	_	_	_
20	built	build	VBN	_	_	_
21	on	on	IN	_	_	_
22	top	top	NN	_	_	_
23	of	of	IN	_	_	_
24	the	the	DT	_	_	_
25	RNA	rna	NN	_	_	_
26	Framework13	framework13	NN	_	_	_
27	.	.	.	_	_	_

1	Briefly	briefly	RB	_	_	_
2	,	,	,	_	_	_
3	reads	read	VBZ	_	_	_
4	were	be	VBD	_	_	_
5	clipped	clip	VBN	_	_	_
6	from	from	IN	_	_	_
7	3	3	CD	_	_	_
8	'	'	''	_	_	_
9	adapter	adapter	NN	_	_	_
10	sequences	sequence	NNS	_	_	_
11	using	use	VBG	_	_	_
12	Cutadapt	cutadapt	JJ	_	_	_
13	v1	v1	NN	_	_	_
14	.10	.10	CD	_	_	_
15	,	,	,	_	_	_
16	discarding	discard	VBG	_	_	_
17	reads	read	VBZ	_	_	_
18	shorter	shorter	JJR	_	_	_
19	than	than	IN	_	_	_
20	15	15	CD	_	_	_
21	nucleotides	nucleotide	NNS	_	_	_
22	.	.	.	_	_	_

1	Forward	forward	RB	_	_	_
2	and	and	CC	_	_	_
3	reverse	reverse	RB	_	_	_
4	reads	read	VBZ	_	_	_
5	were	be	VBD	_	_	_
6	independently	independently	RB	_	_	_
7	mapped	map	VBN	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	RNase	rnase	NN	_	_	_
11	P	p	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	rnpB	rnpb	NN	GEN	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	gene	gene	NN	_	_	_
16	using	use	VBG	_	_	_
17	Bowtie	Bowtie	NNP	_	_	_
18	v1	v1	NN	_	_	_
19	.1.2	.1.2	CD	_	_	_
20	,	,	,	_	_	_
21	by	by	IN	_	_	_
22	allowing	allow	VBG	_	_	_
23	up	up	RP	_	_	_
24	to	to	TO	_	_	_
25	7	7	CD	_	_	_
26	mapping	mapping	NN	_	_	_
27	positions	position	NNS	_	_	_
28	to	to	TO	_	_	_
29	enable	enable	VB	_	_	_
30	mapping	map	VBG	_	_	_
31	to	to	TO	_	_	_
32	the	the	DT	_	_	_
33	7	7	CD	_	_	_
34	E.	e.	FW	_	_	_
35	coli	coli	FW	_	_	_
36	rRNA	rrna	NN	_	_	_
37	genes	gene	NNS	_	_	_
38	-LRB-	-lrb-	-LRB-	_	_	_
39	parameters	parameter	NNS	_	_	_
40	:	:	:	_	_	_
41	-	-	:	_	_	_
42	n	n	NN	_	_	_
43	2	2	CD	_	_	_
44	-	-	:	_	_	_
45	m	m	NN	_	_	_
46	7	7	CD	_	_	_
47	-	-	:	_	_	_
48	a	a	DT	_	_	_
49	--	--	:	_	_	_
50	best	best	JJS	_	_	_
51	--	--	:	_	_	_
52	strata	strata	NN	_	_	_
53	-5	-5	CD	_	_	_
54	5	5	CD	_	_	_
55	-LSB-	-lsb-	-LRB-	_	_	_
56	--	--	:	_	_	_
57	norc	norc	NN	_	_	_
58	for	for	IN	_	_	_
59	forward	forward	RB	_	_	_
60	reads	read	VBZ	_	_	_
61	,	,	,	_	_	_
62	--	--	:	_	_	_
63	nofw	nofw	NN	_	_	_
64	for	for	IN	_	_	_
65	reverse	reverse	JJ	_	_	_
66	reads	read	VBZ	_	_	_
67	-RSB-	-rsb-	-RRB-	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	.	.	.	_	_	_

1	Forward	forward	RB	_	_	_
2	and	and	CC	_	_	_
3	reverse	reverse	VB	_	_	_
4	mapped	map	VBN	_	_	_
5	reads	read	VBZ	_	_	_
6	were	be	VBD	_	_	_
7	then	then	RB	_	_	_
8	re-paired	re-paired	JJ	_	_	_
9	.	.	.	_	_	_

1	Using	use	VBG	_	_	_
2	reverse	reverse	JJ	_	_	_
3	read	read	NN	_	_	_
4	mapping	mapping	NN	_	_	_
5	positions	position	NNS	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	corresponding	correspond	VBG	_	_	_
8	to	to	TO	_	_	_
9	RNA	rna	NN	_	_	_
10	Polymerase	polymerase	NN	_	_	_
11	positions	position	NNS	_	_	_
12	along	along	IN	_	_	_
13	gene	gene	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	forward	forward	RB	_	_	_
17	reads	read	VBZ	_	_	_
18	were	be	VBD	_	_	_
19	split	split	VBN	_	_	_
20	into	into	IN	_	_	_
21	separate	separate	JJ	_	_	_
22	SAM	SAM	NNP	_	_	_
23	files	file	NNS	_	_	_
24	for	for	IN	_	_	_
25	each	each	DT	_	_	_
26	transcription	transcription	NN	_	_	_
27	intermediate	intermediate	NN	_	_	_
28	.	.	.	_	_	_

1	SAM	SAM	NNP	_	_	_
2	files	file	NNS	_	_	_
3	were	be	VBD	_	_	_
4	then	then	RB	_	_	_
5	passed	pass	VBN	_	_	_
6	to	to	TO	_	_	_
7	the	the	DT	_	_	_
8	rf-count	rf-count	JJ	_	_	_
9	tool	tool	NN	_	_	_
10	of	of	IN	_	_	_
11	the	the	DT	_	_	_
12	RNA	rna	NN	_	_	_
13	Framework	framework	NN	_	_	_
14	to	to	TO	_	_	_
15	generate	generate	VB	_	_	_
16	RT-stop	rt-stop	JJ	_	_	_
17	counts	count	NNS	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	RC	rc	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	files	file	NNS	_	_	_
22	,	,	,	_	_	_
23	that	that	WDT	_	_	_
24	were	be	VBD	_	_	_
25	then	then	RB	_	_	_
26	normalized	normalize	VBN	_	_	_
27	using	use	VBG	_	_	_
28	the	the	DT	_	_	_
29	rf-norm	rf-norm	NN	_	_	_
30	tool	tool	NN	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	FastQ	fastq	NN	_	_	_
3	files	file	NNS	_	_	_
4	were	be	VBD	_	_	_
5	examined	examine	VBN	_	_	_
6	using	use	VBG	_	_	_
7	the	the	DT	_	_	_
8	FastQC	fastqc	NN	_	_	_
9	tool	tool	NN	_	_	_
10	.	.	.	_	_	_

1	Reads	read	NNS	_	_	_
2	were	be	VBD	_	_	_
3	clipped	clip	VBN	_	_	_
4	from	from	IN	_	_	_
5	3	3	CD	_	_	_
6	'	'	''	_	_	_
7	adapter	adapter	NN	_	_	_
8	sequences	sequence	NNS	_	_	_
9	using	use	VBG	_	_	_
10	Cutadapt	cutadapt	JJ	_	_	_
11	v1	v1	NN	_	_	_
12	.10	.10	CD	_	_	_
13	,	,	,	_	_	_
14	discarding	discard	VBG	_	_	_
15	reads	read	VBZ	_	_	_
16	shorter	shorter	JJR	_	_	_
17	than	than	IN	_	_	_
18	15	15	CD	_	_	_
19	nucleotides	nucleotide	NNS	_	_	_
20	.	.	.	_	_	_

1	Escherichia	escherichia	FW	Organism	_	_
2	coli	coli	FW	Organism	_	_
3	str	str	FW	_	_	_
4	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	GenBank	genbank	NN	_	_	_
4	:	:	:	_	_	_
5	U00096	u00096	NN	_	_	_
6	.2	.2	NN	_	_	_
7	-RRB-	-rrb-	-RRB-	_	_	_
8	was	be	VBD	_	_	_
9	used	use	VBN	_	_	_
10	as	as	IN	_	_	_
11	the	the	DT	_	_	_
12	reference	reference	NN	_	_	_
13	genome	genome	NN	_	_	_
14	.	.	.	_	_	_

1	Reads	read	NNS	_	_	_
2	were	be	VBD	_	_	_
3	mapped	map	VBN	_	_	_
4	to	to	TO	_	_	_
5	the	the	DT	_	_	_
6	reference	reference	NN	_	_	_
7	genome	genome	NN	_	_	_
8	using	use	VBG	_	_	_
9	Bowtie	Bowtie	NNP	_	_	_
10	v1	v1	NN	_	_	_
11	.1.2	.1.2	CD	_	_	_
12	,	,	,	_	_	_
13	by	by	IN	_	_	_
14	allowing	allow	VBG	_	_	_
15	up	up	RP	_	_	_
16	to	to	TO	_	_	_
17	7	7	CD	_	_	_
18	mapping	mapping	NN	_	_	_
19	positions	position	NNS	_	_	_
20	to	to	TO	_	_	_
21	enable	enable	VB	_	_	_
22	mapping	map	VBG	_	_	_
23	to	to	TO	_	_	_
24	the	the	DT	_	_	_
25	7	7	CD	_	_	_
26	E.	e.	FW	_	_	_
27	coli	coli	FW	_	_	_
28	rRNA	rrna	NN	_	_	_
29	genes	gene	NNS	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	parameters	parameter	NNS	_	_	_
32	:	:	:	_	_	_
33	-	-	:	_	_	_
34	n	n	NN	_	_	_
35	2	2	CD	_	_	_
36	-	-	:	_	_	_
37	m	m	NN	_	_	_
38	7	7	CD	_	_	_
39	-	-	:	_	_	_
40	a	a	DT	_	_	_
41	--	--	:	_	_	_
42	best	best	JJS	_	_	_
43	--	--	:	_	_	_
44	strata	strata	NN	_	_	_
45	-5	-5	CD	_	_	_
46	5	5	CD	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	U00096	u00096	NN	_	_	_
7	.2	.2	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	In	in	FW	_	_	_
10	vitro	vitro	FW	_	_	_
11	transcription	transcription	NN	_	_	_
12	reactions	reaction	NNS	_	_	_
13	were	be	VBD	_	_	_
14	performed	perform	VBN	_	_	_
15	in	in	IN	_	_	_
16	a	a	DT	_	_	_
17	final	final	JJ	_	_	_
18	volume	volume	NN	_	_	_
19	of	of	IN	_	_	_
20	50	50	CD	_	_	_
21	µl	µl	NN	_	_	_
22	.	.	.	_	_	_

1	Each	each	DT	_	_	_
2	reaction	reaction	NN	_	_	_
3	contained	contain	VBD	_	_	_
4	2	2	CD	_	_	_
5	µl	µl	NN	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	RNA	rna	NN	_	_	_
9	Polymerase	polymerase	NN	_	_	_
10	Holoenzyme	holoenzyme	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	NEB	neb	NN	_	_	_
13	,	,	,	_	_	_
14	cat	cat	NN	_	_	_
15	.	.	.	_	_	_

1	M0551S	m0551s	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	,	,	,	_	_	_
4	5	5	CD	_	_	_
5	µl	µl	NN	_	_	_
6	E.	e.	FW	_	_	_
7	coli	coli	FW	_	_	_
8	RNA	rna	NN	_	_	_
9	Polymerase	polymerase	NN	_	_	_
10	Buffer	buffer	NN	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	10X	10x	NN	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	,	,	,	_	_	_
15	1	1	CD	_	_	_
16	µl	µl	NN	_	_	_
17	SUPERase	superase	NN	_	_	_
18	•	•	SYM	_	_	_
19	In	in	IN	_	_	_
20	™	™	CD	_	_	_
21	RNase	rnase	NN	_	_	_
22	Inhibitor	inhibitor	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Ambion	Ambion	NNP	_	_	_
25	,	,	,	_	_	_
26	cat	cat	NN	_	_	_
27	.	.	.	_	_	_

1	AM2696	am2696	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	,	,	,	_	_	_
4	and	and	CC	_	_	_
5	500	500	CD	_	_	_
6	ng	ng	NN	_	_	_
7	template	template	NN	_	_	_
8	DNA	dna	NN	_	_	_
9	.	.	.	_	_	_

1	Reactions	reaction	NNS	_	_	_
2	were	be	VBD	_	_	_
3	incubated	incubate	VBN	_	_	_
4	at	at	IN	_	_	_
5	37	37	CD	_	_	_
6	°C	°c	NN	_	_	_
7	for	for	IN	_	_	_
8	5	5	CD	_	_	_
9	minutes	minute	NNS	_	_	_
10	to	to	TO	_	_	_
11	allow	allow	VB	_	_	_
12	formation	formation	NN	_	_	_
13	of	of	IN	_	_	_
14	the	the	DT	_	_	_
15	RNA	rna	NN	_	_	_
16	Polymerase-DNA	polymerase-dna	JJ	_	_	_
17	binary	binary	JJ	_	_	_
18	complex	complex	NN	_	_	_
19	.	.	.	_	_	_

1	Transcription	transcription	NN	_	_	_
2	was	be	VBD	_	_	_
3	started	start	VBN	_	_	_
4	by	by	IN	_	_	_
5	addition	addition	NN	_	_	_
6	of	of	IN	_	_	_
7	1	1	CD	_	_	_
8	µl	µl	NN	_	_	_
9	NTPs	ntp	NNS	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	25	25	CD	_	_	_
12	mM	mm	NN	KWSUPP	_	_
13	each	each	DT	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	and	and	CC	_	_	_
17	incubated	incubate	VBN	_	_	_
18	at	at	IN	_	_	_
19	37	37	CD	_	_	_
20	°C	°c	NN	_	_	_
21	for	for	IN	_	_	_
22	5	5	CD	_	_	_
23	minutes	minute	NNS	_	_	_
24	.	.	.	_	_	_

1	Transcription	transcription	NN	_	_	_
2	was	be	VBD	_	_	_
3	stopped	stop	VBN	_	_	_
4	by	by	IN	_	_	_
5	addition	addition	NN	_	_	_
6	of	of	IN	_	_	_
7	1	1	CD	_	_	_
8	µl	µl	NN	_	_	_
9	DNase	dnase	NN	_	_	_
10	I	i	CD	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	50	50	CD	_	_	_
13	U	U	NNP	_	_	_
14	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
15	library	library	NN	_	_	_
16	strategy	strategy	NN	_	_	_
17	:	:	:	_	_	_
18	3	3	CD	_	_	_
19	'	'	''	_	_	_
20	-	-	:	_	_	_
21	end	end	NN	_	_	_
22	RNA-seq	rna-seq	NN	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	library	library	NN	_	_	_
25	strategy	strategy	NN	_	_	_
26	:	:	:	_	_	_
27	DMS-seq	dms-seq	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	library	library	NN	_	_	_
30	strategy	strategy	NN	_	_	_
31	:	:	:	_	_	_
32	SPET-seq	spet-seq	JJ	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	molecule	molecule	NN	_	_	_
35	subtype	subtype	NN	_	_	_
36	:	:	:	_	_	_
37	In	in	FW	_	_	_
38	vitro	vitro	FW	_	_	_
39	synthesized	synthesize	VBN	_	_	_
40	RNase	rnase	NN	_	_	_
41	P	p	NN	_	_	_
42	-LRB-	-lrb-	-LRB-	_	_	_
43	rnpB	rnpb	NN	GEN	_	_
44	-RRB-	-rrb-	-RRB-	_	_	_
45	RNA	rna	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	molecule	molecule	NN	_	_	_
48	subtype	subtype	NN	_	_	_
49	:	:	:	_	_	_
50	Total	total	JJ	_	_	_
51	RNA	rna	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	Cytosolic	cytosolic	JJ	_	_	_
54	fraction	fraction	NN	_	_	_
55	-RRB-	-rrb-	-RRB-	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	molecule	molecule	NN	_	_	_
58	subtype	subtype	NN	_	_	_
59	:	:	:	_	_	_
60	Total	total	JJ	_	_	_
61	RNA	rna	NN	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	Nucleoid	nucleoid	NN	_	_	_
64	fraction	fraction	NN	_	_	_
65	-RRB-	-rrb-	-RRB-	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	OTHER	other	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	RNA-Seq	rna-seq	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	RNA	rna	NN	_	_	_
72	was	be	VBD	_	_	_
73	purified	purify	VBN	_	_	_
74	on	on	IN	_	_	_
75	RNA	rna	NN	_	_	_
76	Clean	Clean	NNP	_	_	_
77	&	&	CC	_	_	_
78	Concentrator	Concentrator	NNP	_	_	_
79	™	™	SYM	_	_	_
80	-5	-5	CD	_	_	_
81	columns	column	NNS	_	_	_
82	following	follow	VBG	_	_	_
83	manufacturer	manufacturer	NN	_	_	_
84	's	's	POS	_	_	_
85	instructions	instruction	NNS	_	_	_
86	,	,	,	_	_	_
87	and	and	CC	_	_	_
88	eluted	elute	VBN	_	_	_
89	in	in	IN	_	_	_
90	6	6	CD	_	_	_
91	μl	μl	NN	_	_	_
92	of	of	IN	_	_	_
93	nuclease-free	nuclease-free	JJ	_	_	_
94	water	water	NN	_	_	_
95	.	.	.	_	_	_

1	6	6	CD	_	_	_
2	μl	μl	NN	_	_	_
3	of	of	IN	_	_	_
4	2X	2x	NN	_	_	_
5	RNA	rna	NN	_	_	_
6	Loading	load	VBG	_	_	_
7	Dye	dye	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	ThermoScientific	ThermoScientific	NNP	_	_	_
10	,	,	,	_	_	_
11	cat	cat	NN	_	_	_
12	.	.	.	_	_	_

1	R0641	r0641	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	were	be	VBD	_	_	_
4	added	add	VBN	_	_	_
5	to	to	TO	_	_	_
6	purified	purify	VBN	_	_	_
7	RNA	rna	NN	_	_	_
8	.	.	.	_	_	_

1	Both	both	DT	_	_	_
2	DMS	dms	NN	_	_	_
3	treated	treat	VBN	_	_	_
4	and	and	CC	_	_	_
5	untreated	untreated	JJ	_	_	_
6	samples	sample	NNS	_	_	_
7	were	be	VBD	_	_	_
8	heated	heat	VBN	_	_	_
9	at	at	IN	_	_	_
10	95	95	CD	_	_	_
11	°C	°c	NN	_	_	_
12	for	for	IN	_	_	_
13	2	2	CD	_	_	_
14	minutes	minute	NNS	_	_	_
15	,	,	,	_	_	_
16	and	and	CC	_	_	_
17	immediately	immediately	RB	_	_	_
18	placed	place	VBN	_	_	_
19	on	on	IN	_	_	_
20	ice	ice	NN	_	_	_
21	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	were	be	VBD	_	_	_
3	resolved	resolve	VBN	_	_	_
4	on	on	IN	_	_	_
5	a	a	DT	_	_	_
6	10	10	CD	_	_	_
7	%	%	NN	_	_	_
8	TBE-Urea	tbe-urea	NN	_	_	_
9	polyacrylamide	polyacrylamide	NN	_	_	_
10	gel	gel	NN	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	a	a	DT	_	_	_
14	gel	gel	NN	_	_	_
15	slice	slice	NN	_	_	_
16	ranging	range	VBG	_	_	_
17	from	from	IN	_	_	_
18	50	50	CD	_	_	_
19	nt	nt	NNS	_	_	_
20	to	to	TO	_	_	_
21	the	the	DT	_	_	_
22	full-length	full-length	JJ	_	_	_
23	product	product	NN	_	_	_
24	was	be	VBD	_	_	_
25	cut	cut	VBN	_	_	_
26	.	.	.	_	_	_

1	Gel	gel	NN	_	_	_
2	slices	slice	NNS	_	_	_
3	were	be	VBD	_	_	_
4	crushed	crush	VBN	_	_	_
5	by	by	IN	_	_	_
6	centrifugation	centrifugation	NN	_	_	_
7	through	through	IN	_	_	_
8	a	a	DT	_	_	_
9	punctured	punctured	JJ	_	_	_
10	0.5	0.5	CD	_	_	_
11	ml	ml	NN	_	_	_
12	tube	tube	NN	_	_	_
13	,	,	,	_	_	_
14	and	and	CC	_	_	_
15	resuspended	resuspend	VBN	_	_	_
16	in	in	IN	_	_	_
17	500	500	CD	_	_	_
18	μl	μl	NN	_	_	_
19	of	of	IN	_	_	_
20	Diffusion	Diffusion	NNP	_	_	_
21	buffer	buffer	NN	_	_	_
22	-LSB-	-lsb-	-LRB-	_	_	_
23	500	500	CD	_	_	_
24	mM	mm	NN	KWSUPP	_	_
25	Ammonium	ammonium	NN	_	_	_
26	acetate	acetate	NN	SUPP	_	_
27	;	;	:	_	_	_
28	0.05	0.05	CD	_	_	_
29	%	%	NN	_	_	_
30	SDS	sds	NN	_	_	_
31	-RSB-	-rsb-	-RRB-	_	_	_
32	supplemented	supplement	VBN	_	_	_
33	with	with	IN	_	_	_
34	60	60	CD	_	_	_
35	U	U	NNP	_	_	_
36	SUPERase	SUPERase	NNP	_	_	_
37	•	•	SYM	_	_	_
38	In	in	IN	_	_	_
39	™	™	CD	_	_	_
40	RNase	rnase	NN	_	_	_
41	Inhibitor	inhibitor	NN	_	_	_
42	,	,	,	_	_	_
43	then	then	RB	_	_	_
44	rotated	rotate	VBD	_	_	_
45	at	at	IN	_	_	_
46	4	4	CD	_	_	_
47	°C	°c	NN	_	_	_
48	for	for	IN	_	_	_
49	16	16	CD	_	_	_
50	hours	hour	NNS	_	_	_
51	to	to	TO	_	_	_
52	allow	allow	VB	_	_	_
53	passive	passive	JJ	_	_	_
54	diffusion	diffusion	NN	_	_	_
55	of	of	IN	_	_	_
56	RNA	rna	NN	_	_	_
57	fragments	fragment	NNS	_	_	_
58	into	into	IN	_	_	_
59	buffer	buffer	NN	_	_	_
60	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	precipitated	precipitate	VBN	_	_	_
4	by	by	IN	_	_	_
5	addition	addition	NN	_	_	_
6	of	of	IN	_	_	_
7	1	1	CD	_	_	_
8	ml	ml	NN	_	_	_
9	Isopropanol	isopropanol	NN	_	_	_
10	,	,	,	_	_	_
11	and	and	CC	_	_	_
12	2	2	CD	_	_	_
13	μl	μl	NN	_	_	_
14	Glycogen	glycogen	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	20	20	CD	_	_	_
17	μg	μg	NN	_	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	rnpB	rnpb	NN	GEN	_	_
20	SPET-seq	spet-seq	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	in	in	FW	_	_	_
23	vitro	vitro	FW	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	SPET-seq	spet-seq	NN	_	_	_
27	-LRB-	-lrb-	-LRB-	_	_	_
28	Ribo	Ribo	NNP	_	_	_
29	-	-	:	_	_	_
30	RNA	rna	NN	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	SPET-seq	spet-seq	NN	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	Ribo	Ribo	NNP	_	_	_
36	-	-	:	_	_	_
37	RNA	rna	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	,	,	,	_	_	_
40	Replicate	replicate	VB	_	_	_
41	#	#	#	_	_	_
42	1	1	CD	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	SPET-seq	spet-seq	NN	_	_	_
45	-LRB-	-lrb-	-LRB-	_	_	_
46	Ribo	Ribo	NNP	_	_	_
47	-	-	:	_	_	_
48	RNA	rna	NN	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	,	,	,	_	_	_
51	Replicate	replicate	VB	_	_	_
52	#	#	#	_	_	_
53	2	2	CD	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	SPET-seq	spet-seq	NN	_	_	_
56	-LRB-	-lrb-	-LRB-	_	_	_
57	Total	total	JJ	_	_	_
58	RNA	rna	NN	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	strain	strain	NN	_	_	_
62	:	:	:	_	_	_
63	K-12	k-12	NN	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	substr	substr	NN	_	_	_
66	:	:	:	_	_	_
67	MG1655	mg1655	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	Supplementary	supplementary	JJ	_	_	_
70	_	_	NN	_	_	_
71	files	file	NNS	_	_	_
72	_	_	IN	_	_	_
73	format	format	NN	_	_	_
74	_	_	NN	_	_	_
75	and	and	CC	_	_	_
76	_	_	NN	_	_	_
77	content	content	NN	_	_	_
78	:	:	:	_	_	_
79	DMS-seq	dms-seq	NN	_	_	_
80	data	datum	NNS	_	_	_
81	-LRB-	-lrb-	-LRB-	_	_	_
82	pooled	pooled	JJ	_	_	_
83	Total	total	JJ	_	_	_
84	and	and	CC	_	_	_
85	Ribo	Ribo	NNP	_	_	_
86	-	-	:	_	_	_
87	RNA	rna	NN	_	_	_
88	-RRB-	-rrb-	-RRB-	_	_	_
89	is	be	VBZ	_	_	_
90	provided	provide	VBN	_	_	_
91	in	in	IN	_	_	_
92	the	the	DT	_	_	_
93	form	form	NN	_	_	_
94	of	of	IN	_	_	_
95	RNA	rna	NN	_	_	_
96	Framework	framework	NN	_	_	_
97	's	's	POS	_	_	_
98	-LRB-	-lrb-	-LRB-	_	_	_
99	http	http	NN	_	_	_
100	:	:	:	_	_	_
101	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
102	Supplementary	supplementary	JJ	_	_	_
103	_	_	NN	_	_	_
104	files	file	NNS	_	_	_
105	_	_	IN	_	_	_
106	format	format	NN	_	_	_
107	_	_	NN	_	_	_
108	and	and	CC	_	_	_
109	_	_	NN	_	_	_
110	content	content	NN	_	_	_
111	:	:	:	_	_	_
112	Mapped	map	VBN	_	_	_
113	reads	read	VBZ	_	_	_
114	were	be	VBD	_	_	_
115	rescaled	rescale	VBN	_	_	_
116	to	to	TO	_	_	_
117	a	a	DT	_	_	_
118	size	size	NN	_	_	_
119	of	of	IN	_	_	_
120	10	10	CD	_	_	_
121	bp	bp	NN	_	_	_
122	,	,	,	_	_	_
123	and	and	CC	_	_	_
124	BEDGraph	bedgraph	NN	_	_	_
125	files	file	NNS	_	_	_
126	were	be	VBD	_	_	_
127	generated	generate	VBN	_	_	_
128	using	use	VBG	_	_	_
129	the	the	DT	_	_	_
130	genomeCoverageBed	genomecoveragebed	JJ	_	_	_
131	utility	utility	NN	_	_	_
132	of	of	IN	_	_	_
133	the	the	DT	_	_	_
134	BEDTools	bedtool	NNS	_	_	_
135	suite	suite	NN	_	_	_
136	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Supplementary	Supplementary	NNP	_	_	_
3	_	_	VBD	_	_	_
4	files	file	NNS	_	_	_
5	_	_	IN	_	_	_
6	format	format	NN	_	_	_
7	_	_	NN	_	_	_
8	and	and	CC	_	_	_
9	_	_	NN	_	_	_
10	content	content	NN	_	_	_
11	:	:	:	_	_	_
12	SPET-seq	spet-seq	NN	_	_	_
13	data	datum	NNS	_	_	_
14	is	be	VBZ	_	_	_
15	provided	provide	VBN	_	_	_
16	in	in	IN	_	_	_
17	the	the	DT	_	_	_
18	form	form	NN	_	_	_
19	of	of	IN	_	_	_
20	RNA	rna	NN	_	_	_
21	Framework	framework	NN	_	_	_
22	's	's	POS	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	http	http	NN	_	_	_
25	:	:	:	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	Supplementary	supplementary	JJ	_	_	_
28	_	_	NN	_	_	_
29	files	file	NNS	_	_	_
30	_	_	IN	_	_	_
31	format	format	NN	_	_	_
32	_	_	NN	_	_	_
33	and	and	CC	_	_	_
34	_	_	NN	_	_	_
35	content	content	NN	_	_	_
36	:	:	:	_	_	_
37	SPET-seq	spet-seq	NN	_	_	_
38	data	datum	NNS	_	_	_
39	-LRB-	-lrb-	-LRB-	_	_	_
40	pooled	pooled	JJ	_	_	_
41	Total	total	JJ	_	_	_
42	and	and	CC	_	_	_
43	Ribo	Ribo	NNP	_	_	_
44	-	-	:	_	_	_
45	RNA	rna	NN	_	_	_
46	from	from	IN	_	_	_
47	both	both	DT	_	_	_
48	replicates	replicate	VBZ	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	is	be	VBZ	_	_	_
51	provided	provide	VBN	_	_	_
52	in	in	IN	_	_	_
53	the	the	DT	_	_	_
54	form	form	NN	_	_	_
55	of	of	IN	_	_	_
56	RNA	rna	NN	_	_	_
57	Framework	framework	NN	_	_	_
58	's	's	POS	_	_	_
59	-LRB-	-lrb-	-LRB-	_	_	_
60	http	http	NN	_	_	_
61	:	:	:	_	_	_
62	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
63	10A	10a	NN	_	_	_
64	_	_	CD	_	_	_
65	MG+PMA	MG+PMA	NNP	_	_	_
66	_	_	CD	_	_	_
67	t60	t60	NN	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	10B	10b	NN	_	_	_
70	_	_	CD	_	_	_
71	MG+PMA	MG+PMA	NNP	_	_	_
72	_	_	CD	_	_	_
73	t60	t60	NN	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
75	10C	10c	CD	_	_	_
76	_	_	NN	_	_	_
77	MG+PMA	mg+pma	NN	_	_	_
78	_	_	CD	_	_	_
79	t60	t60	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	1A	1a	NN	_	_	_
82	_	_	CD	_	_	_
83	MG	mg	NN	_	_	_
84	_	_	NN	_	_	_
85	t0	t0	NN	_	_	_
86	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
87	1B	1b	NN	_	_	_
88	_	_	CD	_	_	_
89	MG	mg	NN	_	_	_
90	_	_	NN	_	_	_
91	t0	t0	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	1C	1c	NN	_	_	_
94	_	_	CD	_	_	_
95	MG	mg	NN	_	_	_
96	_	_	NN	_	_	_
97	t0	t0	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	2A	2a	NN	_	_	_
100	_	_	CD	_	_	_
101	MG	mg	NN	_	_	_
102	_	_	NN	_	_	_
103	t10	t10	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	2B	2b	NN	_	_	_
106	_	_	CD	_	_	_
107	MG	mg	NN	_	_	_
108	_	_	NN	_	_	_
109	t10	t10	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	2C	2c	NN	_	_	_
112	_	_	CD	_	_	_
113	MG	mg	NN	_	_	_
114	_	_	NN	_	_	_
115	t10	t10	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	3A	3a	NN	_	_	_
118	_	_	CD	_	_	_
119	MG	mg	NN	_	_	_
120	_	_	NN	_	_	_
121	t30	t30	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	3B	3b	NN	_	_	_
124	_	_	CD	_	_	_
125	MG	mg	NN	_	_	_
126	_	_	NN	_	_	_
127	t30	t30	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	3C	3c	NN	_	_	_
130	_	_	CD	_	_	_
131	MG	mg	NN	_	_	_
132	_	_	NN	_	_	_
133	t30	t30	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	4A	4a	NN	_	_	_
136	_	_	CD	_	_	_
137	MG	mg	NN	_	_	_
138	_	_	NN	_	_	_
139	t60	t60	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	4B	4b	NN	_	_	_
142	_	_	CD	_	_	_
143	MG	mg	NN	_	_	_
144	_	_	NN	_	_	_
145	t60	t60	NN	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	4C	4c	NN	_	_	_
148	_	_	CD	_	_	_
149	MG	mg	NN	_	_	_
150	_	_	NN	_	_	_
151	t60	t60	NN	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	5A	5a	NN	_	_	_
154	_	_	CD	_	_	_
155	MG+H	mg+h	NN	_	_	_
156	g	g	NN	_	_	_
157	_	_	CD	_	_	_
158	t10	t10	NN	_	_	_
159	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
160	5B	5b	NN	_	_	_
161	_	_	CD	_	_	_
162	MG+H	mg+h	NN	_	_	_
163	g	g	NN	_	_	_
164	_	_	CD	_	_	_
165	t10	t10	NN	_	_	_
166	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
167	5C	5c	NN	_	_	_
168	_	_	CD	_	_	_
169	MG+H	mg+h	NN	_	_	_
170	g	g	NN	_	_	_
171	_	_	CD	_	_	_
172	t10	t10	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	6A	6a	NN	_	_	_
175	_	_	CD	_	_	_
176	MG+H	mg+h	NN	_	_	_
177	g	g	NN	_	_	_
178	_	_	CD	_	_	_
179	t30	t30	NN	_	_	_
180	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
181	6B	6b	NN	_	_	_
182	_	_	CD	_	_	_
183	MG+H	mg+h	NN	_	_	_
184	g	g	NN	_	_	_
185	_	_	CD	_	_	_
186	t30	t30	NN	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	6C	6c	NN	_	_	_
189	_	_	CD	_	_	_
190	MG+H	mg+h	NN	_	_	_
191	g	g	NN	_	_	_
192	_	_	CD	_	_	_
193	t30	t30	NN	_	_	_
194	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
195	7A	7a	NN	_	_	_
196	_	_	CD	_	_	_
197	MG+H	mg+h	NN	_	_	_
198	g	g	NN	_	_	_
199	_	_	CD	_	_	_
200	t60	t60	NN	_	_	_
201	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
202	7B	7b	NN	_	_	_
203	_	_	CD	_	_	_
204	MG+H	mg+h	NN	_	_	_
205	g	g	NN	_	_	_
206	_	_	CD	_	_	_
207	t60	t60	NN	_	_	_
208	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
209	7C	7c	NN	_	_	_
210	_	_	CD	_	_	_
211	MG+H	mg+h	NN	_	_	_
212	g	g	NN	_	_	_
213	_	_	CD	_	_	_
214	t60	t60	NN	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	8A	8a	NN	_	_	_
217	_	_	CD	_	_	_
218	MG+PMA	MG+PMA	NNP	_	_	_
219	_	_	CD	_	_	_
220	t10	t10	NN	_	_	_
221	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
222	8B	8b	NN	_	_	_
223	_	_	CD	_	_	_
224	MG+PMA	MG+PMA	NNP	_	_	_
225	_	_	CD	_	_	_
226	t10	t10	NN	_	_	_
227	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
228	8C	8c	NN	_	_	_
229	_	_	CD	_	_	_
230	MG+PMA	MG+PMA	NNP	_	_	_
231	_	_	CD	_	_	_
232	t10	t10	NN	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	9A	9a	NN	_	_	_
235	_	_	CD	_	_	_
236	MG+PMA	MG+PMA	NNP	_	_	_
237	_	_	SYM	_	_	_
238	t30	t30	CD	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
240	9B	9b	NN	_	_	_
241	_	_	SYM	_	_	_
242	MG+PMA	mg+pma	JJS	_	_	_
243	_	_	SYM	_	_	_
244	t30	t30	CD	_	_	_
245	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
246	9C	9c	NN	_	_	_
247	_	_	NN	_	_	_
248	MG+PMA	mg+pma	NN	_	_	_
249	_	_	CD	_	_	_
250	t30	t30	NN	_	_	_
251	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
252	E.	E.	NNP	_	_	_
253	coli	coli	NN	_	_	_
254	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
255	Escherichia	escherichia	FW	Organism	_	_
256	coli	coli	FW	Organism	_	_
257	str	str	FW	_	_	_
258	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	For	for	IN	_	_	_
4	each	each	DT	_	_	_
5	biological	biological	JJ	_	_	_
6	RNA-Seq	rna-seq	NN	_	_	_
7	replicate	replicate	VB	_	_	_
8	E	e	NN	_	_	_
9	coli	coli	NN	_	_	_
10	K-12	k-12	NN	_	_	_
11	MG1655	mg1655	NN	_	_	_
12	was	be	VBD	_	_	_
13	subcultured	subculture	VBN	_	_	_
14	from	from	IN	_	_	_
15	cyrostorage	cyrostorage	NN	_	_	_
16	on	on	IN	_	_	_
17	Luria-Bertani	Luria-Bertani	NNP	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	LB	LB	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	agar	agar	NN	_	_	_
22	overnight	overnight	JJ	_	_	_
23	at	at	IN	_	_	_
24	37	37	CD	_	_	_
25	°C	°c	NN	_	_	_
26	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	half-dozen	half-dozen	JJ	_	_	_
3	well-isolated	well-isolated	JJ	_	_	_
4	colonies	colony	NNS	_	_	_
5	were	be	VBD	_	_	_
6	used	use	VBN	_	_	_
7	to	to	TO	_	_	_
8	inoculate	inoculate	VB	_	_	_
9	a	a	DT	_	_	_
10	20	20	CD	_	_	_
11	ml	ml	NN	_	_	_
12	starter	starter	JJ	_	_	_
13	culture	culture	NN	_	_	_
14	in	in	IN	_	_	_
15	Neidhardt	Neidhardt	NNP	_	_	_
16	MOPS	MOPS	NNP	MED	_	_
17	Minimal	minimal	JJ	_	_	_
18	Medium	medium	NN	_	_	_
19	-LRB-	-lrb-	-LRB-	_	_	_
20	NM3	nm3	NN	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Neidhardt	Neidhardt	NNP	_	_	_
24	et	et	FW	_	_	_
25	al.	al.	FW	_	_	_
26	,	,	,	_	_	_
27	1974	1974	CD	_	_	_
28	,	,	,	_	_	_
29	J	J	NNP	_	_	_
30	Bacteriol	Bacteriol	NNP	_	_	_
31	-RRB-	-rrb-	-RRB-	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	0.2	0.2	CD	_	_	_
34	%	%	NN	_	_	_
35	final	final	JJ	_	_	_
36	glucose	glucose	NN	SUPP	_	_
37	concentration	concentration	NN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	supplemented	supplement	VBN	_	_	_
40	with	with	IN	_	_	_
41	20	20	CD	_	_	_
42	mg	mg	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	Forward	forward	RB	_	_	_
45	-	-	:	_	_	_
46	and	and	CC	_	_	_
47	reverse-read	reverse-read	JJ	_	_	_
48	mate-pairs	mate-pair	NNS	_	_	_
49	were	be	VBD	_	_	_
50	assembled	assemble	VBN	_	_	_
51	and	and	CC	_	_	_
52	aligned	align	VBN	_	_	_
53	to	to	TO	_	_	_
54	the	the	DT	_	_	_
55	Escherichia	escherichia	FW	Organism	_	_
56	coli	coli	FW	Organism	_	_
57	MG1655	mg1655	NN	_	_	_
58	K-12	k-12	NN	_	_	_
59	genome	genome	NN	_	_	_
60	using	use	VBG	_	_	_
61	Bowtie2	bowtie2	NN	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	Langmead	langmead	NN	_	_	_
64	and	and	CC	_	_	_
65	Salzberg	Salzberg	NNP	_	_	_
66	,	,	,	_	_	_
67	2012	2012	CD	_	_	_
68	,	,	,	_	_	_
69	Nat	Nat	NNP	_	_	_
70	Methods	method	NNS	_	_	_
71	-RRB-	-rrb-	-RRB-	_	_	_
72	.	.	.	_	_	_

1	SAMtools	samtool	NNS	_	_	_
2	-LRB-	-lrb-	-LRB-	_	_	_
3	Li	Li	NNP	_	_	_
4	et	et	FW	_	_	_
5	al.	al.	FW	_	_	_
6	,	,	,	_	_	_
7	2009	2009	CD	_	_	_
8	,	,	,	_	_	_
9	Bioinformatics	bioinformatic	NNS	_	_	_
10	-RRB-	-rrb-	-RRB-	_	_	_
11	was	be	VBD	_	_	_
12	used	use	VBN	_	_	_
13	to	to	TO	_	_	_
14	convert	convert	VB	_	_	_
15	Bowtie2	bowtie2	NN	_	_	_
16	output	output	NN	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	.	.	.	_	_	_

1	bam	bam	NN	_	_	_
2	file	file	NN	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	to	to	TO	_	_	_
5	SAM	SAM	NNP	_	_	_
6	format	format	NN	_	_	_
7	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	ASM584v2	asm584v2	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Escherichia	escherichia	FW	_	_	_
9	_	_	FW	_	_	_
10	coli	coli	FW	_	_	_
11	_	_	SYM	_	_	_
12	str	str	FW	_	_	_
13	_	_	FW	_	_	_
14	k	k	NN	_	_	_
15	_	_	SYM	_	_	_
16	12	12	CD	_	_	_
17	_	_	SYM	_	_	_
18	substr	substr	FW	_	_	_
19	_	_	FW	_	_	_
20	mg1655.GCA	mg1655.gca	NN	_	_	_
21	_	_	SYM	_	_	_
22	000005845.2.24	000005845.2.24	CD	_	_	_
23	.	.	.	_	_	_

1	gtf	gtf	NN	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Mapped	map	VBD	_	_	_
5	read	read	VBN	_	_	_
6	counts	count	NNS	_	_	_
7	were	be	VBD	_	_	_
8	analyzed	analyze	VBN	_	_	_
9	for	for	IN	_	_	_
10	differential	differential	JJ	_	_	_
11	expression	expression	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	false	false	JJ	_	_	_
14	discovery	discovery	NN	_	_	_
15	rate	rate	NN	_	_	_
16	of	of	IN	_	_	_
17	<	<	JJR	_	_	_
18	0.01	0.01	CD	_	_	_
19	,	,	,	_	_	_
20	fold-change	fold-change	JJ	_	_	_
21	>	>	RBR	_	_	_
22	2	2	LS	_	_	_
23	-RRB-	-rrb-	-RRB-	_	_	_
24	using	use	VBG	_	_	_
25	the	the	DT	_	_	_
26	baySeq	bayseq	NN	_	_	_
27	package	package	NN	_	_	_
28	in	in	IN	_	_	_
29	R	r	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Hardcastle	hardcastle	NN	_	_	_
32	and	and	CC	_	_	_
33	Kelly	Kelly	NNP	_	_	_
34	,	,	,	_	_	_
35	2010	2010	CD	_	_	_
36	,	,	,	_	_	_
37	BMC	BMC	NNP	_	_	_
38	Bioinformatics	Bioinformatics	NNPS	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	.	.	.	_	_	_

1	Within	within	IN	_	_	_
2	baySeq	bayseq	NN	_	_	_
3	,	,	,	_	_	_
4	two-way	two-way	JJ	_	_	_
5	comparisons	comparison	NNS	_	_	_
6	using	use	VBG	_	_	_
7	quantile	quantile	JJ	_	_	_
8	normalization	normalization	NN	_	_	_
9	were	be	VBD	_	_	_
10	made	make	VBN	_	_	_
11	for	for	IN	_	_	_
12	all	all	DT	_	_	_
13	three	three	CD	_	_	_
14	biological	biological	JJ	_	_	_
15	replicate	replicate	VBP	_	_	_
16	transcriptomes	transcriptome	NNS	_	_	_
17	over	over	IN	_	_	_
18	time	time	NN	_	_	_
19	for	for	IN	_	_	_
20	HgCl2	hgcl2	NN	_	_	_
21	exposure	exposure	NN	_	_	_
22	or	or	CC	_	_	_
23	PMA	pma	NN	_	_	_
24	exposure	exposure	NN	_	_	_
25	versus	versus	CC	_	_	_
26	the	the	DT	_	_	_
27	unexposed	unexposed	JJ	_	_	_
28	control	control	NN	_	_	_
29	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	One	one	CD	_	_	_
3	cell	cell	NN	_	_	_
4	pellet	pellet	NN	_	_	_
5	from	from	IN	_	_	_
6	each	each	DT	_	_	_
7	condition	condition	NN	_	_	_
8	and	and	CC	_	_	_
9	sampling	sampling	NN	_	_	_
10	time	time	NN	_	_	_
11	was	be	VBD	_	_	_
12	thawed	thaw	VBN	_	_	_
13	on	on	IN	_	_	_
14	ice	ice	NN	_	_	_
15	;	;	:	_	_	_
16	total	total	JJ	_	_	_
17	RNA	rna	NN	_	_	_
18	was	be	VBD	_	_	_
19	isolated	isolate	VBN	_	_	_
20	by	by	IN	_	_	_
21	RNAsnap	rnasnap	NN	_	_	_
22	™	™	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Stead	stead	NN	_	_	_
25	et	et	FW	_	_	_
26	al.	al.	FW	_	_	_
27	,	,	,	_	_	_
28	2012	2012	CD	_	_	_
29	,	,	,	_	_	_
30	Nucleic	Nucleic	NNP	_	_	_
31	Acids	Acids	NNP	_	_	_
32	Res	Res	NNP	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	contamination	contamination	NN	_	_	_
3	was	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	two	two	CD	_	_	_
7	treatments	treatment	NNS	_	_	_
8	with	with	IN	_	_	_
9	Turbo-DNase	turbo-dnase	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Ambion	Ambion	NNP	_	_	_
12	;	;	:	_	_	_
13	Life	Life	NNP	_	_	_
14	Technologies	Technologies	NNPS	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	.	.	.	_	_	_

1	Ribosomal	ribosomal	JJ	_	_	_
2	RNA	rna	NN	_	_	_
3	depletion	depletion	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	with	with	IN	_	_	_
7	the	the	DT	_	_	_
8	Ribo-Zero	Ribo-Zero	NNP	_	_	_
9	™	™	NN	_	_	_
10	rRNA	rrna	NN	_	_	_
11	removal	removal	NN	_	_	_
12	kit	kit	NN	_	_	_
13	for	for	IN	_	_	_
14	Gram-negative	gram-negative	JJ	_	_	_
15	bacteria	bacterium	NNS	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Epicentre	Epicentre	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	and	and	CC	_	_	_
20	concentrated	concentrate	VBD	_	_	_
21	using	use	VBG	_	_	_
22	RNA	rna	NN	_	_	_
23	Clean	clean	JJ	_	_	_
24	and	and	CC	_	_	_
25	Concentrator	Concentrator	NNP	_	_	_
26	™	™	SYM	_	_	_
27	-5	-5	CD	_	_	_
28	columns	column	NNS	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	Zymo	Zymo	NNP	_	_	_
31	Research	Research	NNP	_	_	_
32	-RRB-	-rrb-	-RRB-	_	_	_
33	following	follow	VBG	_	_	_
34	the	the	DT	_	_	_
35	manufacturer	manufacturer	NN	_	_	_
36	's	's	POS	_	_	_
37	instructions	instruction	NNS	_	_	_
38	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Quality	Quality	NNP	_	_	_
3	control	control	NN	_	_	_
4	processing	processing	NN	_	_	_
5	of	of	IN	_	_	_
6	sequence	sequence	NN	_	_	_
7	data	datum	NNS	_	_	_
8	was	be	VBD	_	_	_
9	performed	perform	VBN	_	_	_
10	using	use	VBG	_	_	_
11	Galaxy	galaxy	NN	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	https	http	NNS	_	_	_
14	:	:	:	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	RNA-Seq	rna-seq	NN	_	_	_
17	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
18	Supplementary	supplementary	JJ	_	_	_
19	_	_	NN	_	_	_
20	files	file	NNS	_	_	_
21	_	_	IN	_	_	_
22	format	format	NN	_	_	_
23	_	_	NN	_	_	_
24	and	and	CC	_	_	_
25	_	_	NN	_	_	_
26	content	content	NN	_	_	_
27	:	:	:	_	_	_
28	raw	raw	JJ	_	_	_
29	read	read	NN	_	_	_
30	counts	count	VBZ	_	_	_
31	as	as	RB	_	_	_
32	determined	determine	VBN	_	_	_
33	by	by	IN	_	_	_
34	HTseq-Count	htseq-count	NN	_	_	_
35	,	,	,	_	_	_
36	provided	provide	VBN	_	_	_
37	in	in	IN	_	_	_
38	.	.	.	_	_	_

1	csv	csv	NN	_	_	_
2	format	format	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
4	The	the	DT	_	_	_
5	number	number	NN	_	_	_
6	of	of	IN	_	_	_
7	sequence	sequence	NN	_	_	_
8	reads	read	VBZ	_	_	_
9	that	that	IN	_	_	_
10	aligned	align	VBN	_	_	_
11	to	to	TO	_	_	_
12	features	feature	NNS	_	_	_
13	in	in	IN	_	_	_
14	annotation	annotation	NN	_	_	_
15	file	file	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Escherichia	escherichia	FW	_	_	_
18	_	_	FW	_	_	_
19	coli	coli	FW	_	_	_
20	_	_	SYM	_	_	_
21	str	str	FW	_	_	_
22	_	_	FW	_	_	_
23	k	k	NN	_	_	_
24	_	_	SYM	_	_	_
25	12	12	CD	_	_	_
26	_	_	SYM	_	_	_
27	substr	substr	FW	_	_	_
28	_	_	FW	_	_	_
29	mg1655.GCA	mg1655.gca	NN	_	_	_
30	_	_	SYM	_	_	_
31	000005845.2.24	000005845.2.24	CD	_	_	_
32	.	.	.	_	_	_

1	gtf	gtf	NN	_	_	_
2	from	from	IN	_	_	_
3	http	http	NN	_	_	_
4	:	:	:	_	_	_
5	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
6	The	the	DT	_	_	_
7	quality	quality	NN	_	_	_
8	and	and	CC	_	_	_
9	quantity	quantity	NN	_	_	_
10	of	of	IN	_	_	_
11	rRNA-depleted	rrna-depleted	JJ	_	_	_
12	RNA	rna	NN	_	_	_
13	was	be	VBD	_	_	_
14	assessed	assess	VBN	_	_	_
15	on	on	IN	_	_	_
16	a	a	DT	_	_	_
17	2100	2100	CD	_	_	_
18	Bioanalyzer	Bioanalyzer	NNP	_	_	_
19	RNA	rna	NN	_	_	_
20	pico	pico	NN	_	_	_
21	chip	chip	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	Agilent	Agilent	NNP	_	_	_
24	Technologies	Technologies	NNPS	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	using	use	VBG	_	_	_
27	manufacturer	manufacturer	NN	_	_	_
28	's	's	POS	_	_	_
29	recommendations	recommendation	NNS	_	_	_
30	.	.	.	_	_	_

1	Next	next	JJ	_	_	_
2	generation	generation	NN	_	_	_
3	sequencing	sequencing	NN	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	NGS	ngs	NN	_	_	_
6	-RRB-	-rrb-	-RRB-	_	_	_
7	libraries	library	NNS	_	_	_
8	were	be	VBD	_	_	_
9	prepared	prepare	VBN	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	Kapa	Kapa	NNP	_	_	_
13	biosystems	biosystem	NNS	_	_	_
14	NGS	NGS	NNP	_	_	_
15	stranded	strand	VBD	_	_	_
16	library	library	NN	_	_	_
17	prep	prep	JJ	_	_	_
18	kit	kit	NN	_	_	_
19	for	for	IN	_	_	_
20	RNA-Seq	rna-seq	NN	_	_	_
21	with	with	IN	_	_	_
22	dual	dual	JJ	_	_	_
23	indexed	index	VBN	_	_	_
24	Illumina	Illumina	NNP	_	_	_
25	adapters	adapter	NNS	_	_	_
26	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	mode	mode	NN	_	_	_
3	library	library	NN	_	_	_
4	insert	insert	NN	_	_	_
5	size	size	NN	_	_	_
6	was	be	VBD	_	_	_
7	~	~	CD	_	_	_
8	150	150	CD	_	_	_
9	bp	bp	NN	_	_	_
10	,	,	,	_	_	_
11	as	as	IN	_	_	_
12	determined	determine	VBN	_	_	_
13	by	by	IN	_	_	_
14	high	high	JJ	_	_	_
15	sensitivity	sensitivity	NN	_	_	_
16	NGS	ngs	NN	_	_	_
17	fragment	fragment	NN	_	_	_
18	analysis	analysis	NN	_	_	_
19	kit	kit	NN	_	_	_
20	for	for	IN	_	_	_
21	Fragment	fragment	NN	_	_	_
22	Analyzer	analyzer	NN	_	_	_
23	™	™	NN	_	_	_
24	-LRB-	-lrb-	-LRB-	_	_	_
25	Advanced	Advanced	NNP	_	_	_
26	Analytical	Analytical	NNP	_	_	_
27	Technologies	Technologies	NNPS	_	_	_
28	-RRB-	-rrb-	-RRB-	_	_	_
29	using	use	VBG	_	_	_
30	manufacturer	manufacturer	NN	_	_	_
31	's	's	POS	_	_	_
32	instructions	instruction	NNS	_	_	_
33	.	.	.	_	_	_

1	Quantification	quantification	NN	_	_	_
2	of	of	IN	_	_	_
3	each	each	DT	_	_	_
4	library	library	NN	_	_	_
5	was	be	VBD	_	_	_
6	done	do	VBN	_	_	_
7	by	by	IN	_	_	_
8	qPCR	qpcr	NN	_	_	_
9	and	and	CC	_	_	_
10	all	all	DT	_	_	_
11	30	30	CD	_	_	_
12	libraries	library	NNS	_	_	_
13	were	be	VBD	_	_	_
14	pooled	pool	VBN	_	_	_
15	in	in	IN	_	_	_
16	equal	equal	JJ	_	_	_
17	concentrations	concentration	NNS	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	treatment	treatment	NN	_	_	_
3	:	:	:	_	_	_
4	MG1655	mg1655	NN	_	_	_
5	+	+	CC	_	_	_
6	3µM	3µm	NN	_	_	_
7	HgCl2	hgcl2	NN	_	_	_
8	at	at	IN	_	_	_
9	t10	t10	NN	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	treatment	treatment	NN	_	_	_
12	:	:	:	_	_	_
13	MG1655	mg1655	NN	_	_	_
14	+	+	CC	_	_	_
15	3µM	3µm	NN	_	_	_
16	HgCl2	hgcl2	NN	_	_	_
17	at	at	IN	_	_	_
18	t30	t30	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	treatment	treatment	NN	_	_	_
21	:	:	:	_	_	_
22	MG1655	mg1655	NN	_	_	_
23	+	+	CC	_	_	_
24	3µM	3µm	NN	_	_	_
25	HgCl2	hgcl2	NN	_	_	_
26	at	at	IN	_	_	_
27	t60	t60	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	treatment	treatment	NN	_	_	_
30	:	:	:	_	_	_
31	MG1655	mg1655	NN	_	_	_
32	+	+	CC	_	_	_
33	3µM	3µm	NN	_	_	_
34	PMA	pma	NN	_	_	_
35	at	at	IN	_	_	_
36	t10	t10	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	treatment	treatment	NN	_	_	_
39	:	:	:	_	_	_
40	MG1655	mg1655	NN	_	_	_
41	+	+	CC	_	_	_
42	3µM	3µm	NN	_	_	_
43	PMA	pma	NN	_	_	_
44	at	at	IN	_	_	_
45	t30	t30	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	treatment	treatment	NN	_	_	_
48	:	:	:	_	_	_
49	MG1655	mg1655	NN	_	_	_
50	+	+	CC	_	_	_
51	3µM	3µm	NN	_	_	_
52	PMA	pma	NN	_	_	_
53	at	at	IN	_	_	_
54	t60	t60	NN	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	treatment	treatment	NN	_	_	_
57	:	:	:	_	_	_
58	MG1655	mg1655	SYM	_	_	_
59	-	-	:	_	_	_
60	unexposed	unexposed	JJ	_	_	_
61	at	at	IN	_	_	_
62	t0	t0	NN	_	_	_
63	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
64	treatment	treatment	NN	_	_	_
65	:	:	:	_	_	_
66	MG1655	mg1655	SYM	_	_	_
67	-	-	:	_	_	_
68	unexposed	unexposed	JJ	_	_	_
69	at	at	IN	_	_	_
70	t10	t10	NN	_	_	_
71	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
72	treatment	treatment	NN	_	_	_
73	:	:	:	_	_	_
74	MG1655	mg1655	SYM	_	_	_
75	-	-	:	_	_	_
76	unexposed	unexposed	JJ	_	_	_
77	at	at	IN	_	_	_
78	t30	t30	CD	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	treatment	treatment	NN	_	_	_
81	:	:	:	_	_	_
82	MG1655	mg1655	SYM	_	_	_
83	-	-	:	_	_	_
84	unexposed	unexposed	JJ	_	_	_
85	at	at	IN	_	_	_
86	t60	t60	CD	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
88	When	when	WRB	_	_	_
89	cultures	culture	NNS	_	_	_
90	reached	reach	VBD	_	_	_
91	OD595	od595	NN	_	_	_
92	≈	≈	CD	_	_	_
93	0.470	0.470	CD	_	_	_
94	-LRB-	-lrb-	-LRB-	_	_	_
95	~	~	NN	_	_	_
96	200	200	CD	_	_	_
97	min	min	NN	_	_	_
98	-RRB-	-rrb-	-RRB-	_	_	_
99	,	,	,	_	_	_
100	two	two	CD	_	_	_
101	cultures	culture	NNS	_	_	_
102	were	be	VBD	_	_	_
103	made	make	VBN	_	_	_
104	3	3	CD	_	_	_
105	µM	µm	NN	_	_	_
106	mercuric	mercuric	NN	_	_	_
107	chloride	chloride	NN	_	_	_
108	-LRB-	-lrb-	-LRB-	_	_	_
109	HgCl2	hgcl2	NN	_	_	_
110	-RRB-	-rrb-	-RRB-	_	_	_
111	or	or	CC	_	_	_
112	3	3	CD	_	_	_
113	µM	µm	NN	_	_	_
114	phenylmercuric-acetate	phenylmercuric-acetate	NN	_	_	_
115	-LRB-	-lrb-	-LRB-	_	_	_
116	PMA	pma	NN	_	_	_
117	-RRB-	-rrb-	-RRB-	_	_	_
118	and	and	CC	_	_	_
119	the	the	DT	_	_	_
120	third	third	JJ	_	_	_
121	was	be	VBD	_	_	_
122	left	leave	VBN	_	_	_
123	as	as	IN	_	_	_
124	an	a	DT	_	_	_
125	unexposed	unexposed	JJ	_	_	_
126	control	control	NN	_	_	_
127	.	.	.	_	_	_

1	Duplicate	duplicate	VB	_	_	_
2	1	1	CD	_	_	_
3	ml	ml	NN	_	_	_
4	aliquots	aliquot	NNS	_	_	_
5	of	of	IN	_	_	_
6	each	each	DT	_	_	_
7	culture	culture	NN	_	_	_
8	were	be	VBD	_	_	_
9	collected	collect	VBN	_	_	_
10	at	at	IN	_	_	_
11	0	0	CD	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	unexposed	unexposed	JJ	_	_	_
14	control	control	NN	_	_	_
15	only	only	RB	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	,	,	,	_	_	_
18	10	10	CD	_	_	_
19	,	,	,	_	_	_
20	30	30	CD	_	_	_
21	,	,	,	_	_	_
22	60	60	CD	_	_	_
23	min	min	NN	_	_	_
24	after	after	IN	_	_	_
25	mercurial	mercurial	JJ	_	_	_
26	exposure	exposure	NN	_	_	_
27	and	and	CC	_	_	_
28	immediately	immediately	RB	_	_	_
29	centrifuged	centrifuge	VBN	_	_	_
30	at	at	IN	_	_	_
31	21	21	CD	_	_	_
32	krpm	krpm	NN	_	_	_
33	,	,	,	_	_	_
34	for	for	IN	_	_	_
35	3	3	CD	_	_	_
36	min	min	NN	_	_	_
37	at	at	IN	_	_	_
38	4	4	CD	_	_	_
39	°C	°c	NN	_	_	_
40	.	.	.	_	_	_

1	Spent	spent	JJ	_	_	_
2	medium	medium	NN	_	_	_
3	was	be	VBD	_	_	_
4	aspirated	aspirate	VBN	_	_	_
5	and	and	CC	_	_	_
6	cell	cell	NN	_	_	_
7	pellets	pellet	NNS	_	_	_
8	were	be	VBD	_	_	_
9	frozen	freeze	VBN	_	_	_
10	at	at	IN	_	_	_
11	-70	-70	CD	_	_	_
12	°C	°c	NN	_	_	_
13	within	within	IN	_	_	_
14	5	5	CD	_	_	_
15	min	min	NN	_	_	_
16	after	after	IN	_	_	_
17	collection	collection	NN	_	_	_
18	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	5	5	CD	_	_	_
3	min	min	NN	_	_	_
4	after	after	IN	_	_	_
5	UVtreatment	uvtreatment	NN	_	_	_
6	1	1	CD	_	_	_
7	,	,	,	_	_	_
8	40J	40j	NN	_	_	_
9	,	,	,	_	_	_
10	MG1655	mg1655	NN	_	_	_
11	in	in	IN	_	_	_
12	Davis	Davis	NNP	_	_	_
13	+0.4	+0.4	CD	_	_	_
14	%	%	NN	_	_	_
15	glu	glu	NN	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	5	5	CD	_	_	_
18	min	min	NN	_	_	_
19	untreatedcells	untreatedcell	NNS	_	_	_
20	,	,	,	_	_	_
21	25	25	CD	_	_	_
22	ug	ug	NN	_	_	_
23	total	total	JJ	_	_	_
24	RNA	rna	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	60	60	CD	_	_	_
27	min	min	NN	_	_	_
28	after	after	IN	_	_	_
29	UVtreatment	uvtreatment	NN	_	_	_
30	1	1	CD	_	_	_
31	,	,	,	_	_	_
32	40J	40j	NN	_	_	_
33	,	,	,	_	_	_
34	MG1655	mg1655	NN	_	_	_
35	in	in	IN	_	_	_
36	Davis	Davis	NNP	_	_	_
37	+0.4	+0.4	CD	_	_	_
38	%	%	NN	_	_	_
39	glu	glu	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	60	60	CD	_	_	_
42	min	min	NN	_	_	_
43	untreatedcells	untreatedcell	NNS	_	_	_
44	,	,	,	_	_	_
45	25	25	CD	_	_	_
46	ug	ug	NN	_	_	_
47	total	total	JJ	_	_	_
48	RNA	rna	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	60	60	CD	_	_	_
51	min	min	NN	_	_	_
52	UV	uv	NN	_	_	_
53	treated	treat	VBN	_	_	_
54	cells	cell	NNS	_	_	_
55	,	,	,	_	_	_
56	25	25	CD	_	_	_
57	ug	ug	NN	_	_	_
58	total	total	JJ	_	_	_
59	RNA	rna	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	60	60	CD	_	_	_
62	min	min	NN	_	_	_
63	UVtreatment	uvtreatment	NN	_	_	_
64	control	control	NN	_	_	_
65	,	,	,	_	_	_
66	MG1655	mg1655	NN	_	_	_
67	in	in	IN	_	_	_
68	Davis	Davis	NNP	_	_	_
69	+0.4	+0.4	CD	_	_	_
70	%	%	NN	_	_	_
71	glu	glu	NN	_	_	_
72	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
73	Bacteria	bacterium	NNS	_	_	_
74	cells	cell	NNS	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	Basecalls	basecall	NNS	_	_	_
77	performed	perform	VBN	_	_	_
78	using	use	VBG	_	_	_
79	CASAVA	CASAVA	NNP	_	_	_
80	version	version	NN	_	_	_
81	1.8.2	1.8.2	CD	_	_	_
82	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
83	Escherichia	escherichia	FW	Organism	_	_
84	coli	coli	FW	Organism	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	Genome	Genome	NNP	_	_	_
87	_	_	NNP	_	_	_
88	build	build	VB	_	_	_
89	:	:	:	_	_	_
90	CP009273	cp009273	NN	_	_	_
91	.1	.1	CD	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	MT	mt	NNS	_	_	_
94	_	_	VBP	_	_	_
95	12h	12h	JJ	_	_	_
96	_	_	NN	_	_	_
97	rep1	rep1	NN	_	_	_
98	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
99	MT	mt	NNS	_	_	_
100	_	_	VBP	_	_	_
101	12h	12h	JJ	_	_	_
102	_	_	NN	_	_	_
103	rep2	rep2	NN	_	_	_
104	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
105	MT	mt	NNS	_	_	_
106	_	_	VBP	_	_	_
107	24h	24h	JJ	_	_	_
108	_	_	NN	_	_	_
109	rep1	rep1	NN	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	MT	mt	NNS	_	_	_
112	_	_	VBP	_	_	_
113	24h	24h	JJ	_	_	_
114	_	_	NN	_	_	_
115	rep2	rep2	NN	_	_	_
116	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
117	MT	mt	NNS	_	_	_
118	_	_	VBP	_	_	_
119	48h	48h	JJ	_	_	_
120	_	_	NN	_	_	_
121	rep1	rep1	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	MT	mt	NNS	_	_	_
124	_	_	VBP	_	_	_
125	48h	48h	JJ	_	_	_
126	_	_	NN	_	_	_
127	rep2	rep2	NN	_	_	_
128	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
129	MT	mt	NNS	_	_	_
130	_	_	VBP	_	_	_
131	6h	6h	JJ	_	_	_
132	_	_	NN	_	_	_
133	rep1	rep1	NN	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	MT	mt	NNS	_	_	_
136	_	_	VBP	_	_	_
137	6h	6h	JJ	_	_	_
138	_	_	NN	_	_	_
139	rep2	rep2	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	product	product	NN	_	_	_
142	:	:	:	_	_	_
143	Butanol	Butanol	NNP	_	_	_
144	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
145	Quantification	quantification	NN	_	_	_
146	of	of	IN	_	_	_
147	gene	gene	NN	_	_	_
148	expression	expression	NN	_	_	_
149	and	and	CC	_	_	_
150	analysis	analysis	NN	_	_	_
151	of	of	IN	_	_	_
152	gene	gene	NN	_	_	_
153	differential	differential	JJ	_	_	_
154	expression	expression	NN	_	_	_
155	were	be	VBD	_	_	_
156	performed	perform	VBN	_	_	_
157	using	use	VBG	_	_	_
158	Fragment	fragment	NN	_	_	_
159	Per	per	IN	_	_	_
160	Kilo	Kilo	NNP	_	_	_
161	bases	basis	NNS	_	_	_
162	per	per	IN	_	_	_
163	Million	Million	NNP	_	_	_
164	reads	read	VBZ	_	_	_
165	-LRB-	-lrb-	-LRB-	_	_	_
166	FPKM	fpkm	NN	_	_	_
167	-RRB-	-rrb-	-RRB-	_	_	_
168	value	value	NN	_	_	_
169	based	base	VBN	_	_	_
170	rsem	rsem	NN	_	_	_
171	software	software	NN	_	_	_
172	version	version	NN	_	_	_
173	1.2.4	1.2.4	CD	_	_	_
174	and	and	CC	_	_	_
175	edgeR	edger	NN	_	_	_
176	version	version	NN	_	_	_
177	3.4.2	3.4.2	CD	_	_	_
178	-LRB-	-lrb-	-LRB-	_	_	_
179	Bioconductor	bioconductor	NN	_	_	_
180	-RRB-	-rrb-	-RRB-	_	_	_
181	,	,	,	_	_	_
182	respectively	respectively	RB	_	_	_
183	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
184	RNA	rna	NN	_	_	_
185	libraries	library	NNS	_	_	_
186	were	be	VBD	_	_	_
187	prepared	prepare	VBN	_	_	_
188	for	for	IN	_	_	_
189	sequencing	sequencing	NN	_	_	_
190	using	use	VBG	_	_	_
191	standard	standard	JJ	_	_	_
192	Illumina	Illumina	NNP	_	_	_
193	protocols	protocol	NNS	_	_	_
194	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	Sequenced	sequence	VBN	_	_	_
5	reads	read	VBZ	_	_	_
6	were	be	VBD	_	_	_
7	trimmed	trim	VBN	_	_	_
8	for	for	IN	_	_	_
9	adaptor	adaptor	NN	_	_	_
10	sequence	sequence	NN	_	_	_
11	,	,	,	_	_	_
12	and	and	CC	_	_	_
13	masked	mask	VBN	_	_	_
14	for	for	IN	_	_	_
15	low-complexity	low-complexity	NN	_	_	_
16	or	or	CC	_	_	_
17	low-quality	low-quality	JJ	_	_	_
18	sequence	sequence	NN	_	_	_
19	,	,	,	_	_	_
20	then	then	RB	_	_	_
21	mapped	map	VBD	_	_	_
22	to	to	TO	_	_	_
23	CP009273	CP009273	NNP	_	_	_
24	.1	.1	CD	_	_	_
25	whole	whole	JJ	_	_	_
26	genome	genome	NN	_	_	_
27	using	use	VBG	_	_	_
28	bowtie2	bowtie2	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	strain	strain	NN	_	_	_
31	:	:	:	_	_	_
32	BW25113	bw25113	NN	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	Supplementary	supplementary	JJ	_	_	_
35	_	_	NN	_	_	_
36	files	file	NNS	_	_	_
37	_	_	IN	_	_	_
38	format	format	NN	_	_	_
39	_	_	NN	_	_	_
40	and	and	CC	_	_	_
41	_	_	NN	_	_	_
42	content	content	NN	_	_	_
43	:	:	:	_	_	_
44	Excel	Excel	NNP	_	_	_
45	file	file	NN	_	_	_
46	include	include	VBP	_	_	_
47	FPKM	fpkm	NN	_	_	_
48	values	value	NNS	_	_	_
49	of	of	IN	_	_	_
50	different	different	JJ	_	_	_
51	genes	gene	NNS	_	_	_
52	for	for	IN	_	_	_
53	each	each	DT	_	_	_
54	sample	sample	NN	_	_	_
55	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
56	Total	Total	NNP	_	_	_
57	RNAs	rna	NNS	_	_	_
58	were	be	VBD	_	_	_
59	isolated	isolate	VBN	_	_	_
60	using	use	VBG	_	_	_
61	TRIzol	trizol	NN	_	_	_
62	reagent	reagent	NN	_	_	_
63	,	,	,	_	_	_
64	followed	follow	VBN	_	_	_
65	by	by	IN	_	_	_
66	clean-up	clean-up	JJ	_	_	_
67	and	and	CC	_	_	_
68	DNase	dnase	NN	_	_	_
69	I	i	CD	_	_	_
70	treatment	treatment	NN	_	_	_
71	with	with	IN	_	_	_
72	QIAGEN	QIAGEN	NNP	_	_	_
73	RNeasy	RNeasy	NNP	_	_	_
74	mini	minus	NNS	_	_	_
75	kit	kit	NN	_	_	_
76	.	.	.	_	_	_

1	Illumina	Illumina	NNP	_	_	_
2	TruSeq	TruSeq	NNP	_	_	_
3	RNA	rna	NN	_	_	_
4	Sample	sample	NN	_	_	_
5	Prep	Prep	NNP	_	_	_
6	Kit	kit	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Cat	cat	NN	_	_	_
9	#FC	#fc	NN	_	_	_
10	-122-1001	-122-1001	CD	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	was	be	VBD	_	_	_
13	used	use	VBN	_	_	_
14	for	for	IN	_	_	_
15	the	the	DT	_	_	_
16	construction	construction	NN	_	_	_
17	of	of	IN	_	_	_
18	sequencing	sequencing	NN	_	_	_
19	libraries	library	NNS	_	_	_
20	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	WT	WT	NNP	_	_	_
3	_	_	SYM	_	_	_
4	12h	12h	CD	_	_	_
5	_	_	CD	_	_	_
6	rep1	rep1	NN	_	_	_
7	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
8	WT	wt	JJ	_	_	_
9	_	_	NN	_	_	_
10	12h	12h	NN	_	_	_
11	_	_	CD	_	_	_
12	rep2	rep2	NN	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
14	WT	wt	VBD	_	_	_
15	_	_	CD	_	_	_
16	24h	24h	JJ	_	_	_
17	_	_	NN	_	_	_
18	rep1	rep1	NN	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	WT	wt	VBD	_	_	_
21	_	_	CD	_	_	_
22	24h	24h	JJ	_	_	_
23	_	_	NN	_	_	_
24	rep2	rep2	NN	_	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	WT	wt	JJ	_	_	_
27	_	_	NN	_	_	_
28	48h	48h	NN	_	_	_
29	_	_	CD	_	_	_
30	rep1	rep1	NN	_	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	WT	wt	JJ	_	_	_
33	_	_	NN	_	_	_
34	48h	48h	NN	_	_	_
35	_	_	CD	_	_	_
36	rep2	rep2	NN	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	WT	wt	VBD	_	_	_
39	_	_	CD	_	_	_
40	6h	6h	JJ	_	_	_
41	_	_	NN	_	_	_
42	rep1	rep1	NN	_	_	_
43	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
44	WT	wt	VBD	_	_	_
45	_	_	CD	_	_	_
46	6h	6h	JJ	_	_	_
47	_	_	NN	_	_	_
48	rep2	rep2	NN	_	_	_
49	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
50	cell	cell	NN	_	_	_
51	culture	culture	NN	_	_	_
52	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
53	Escherichia	escherichia	FW	Organism	_	_
54	coli	coli	FW	Organism	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	evolved	evolve	VBD	_	_	_
57	1	1	CD	_	_	_
58	min	min	NN	_	_	_
59	rep6	rep6	NN	_	_	_
60	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
61	evolved	evolve	VBD	_	_	_
62	1	1	CD	_	_	_
63	min	min	NN	_	_	_
64	rep8	rep8	NN	_	_	_
65	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
66	evolved	evolve	VBD	_	_	_
67	5	5	CD	_	_	_
68	min	min	NN	_	_	_
69	rep6	rep6	NN	_	_	_
70	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
71	evolved	evolve	VBD	_	_	_
72	5	5	CD	_	_	_
73	min	min	NN	_	_	_
74	rep8	rep8	NN	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	evolved	evolve	VBD	_	_	_
77	9	9	CD	_	_	_
78	min	min	NN	_	_	_
79	rep6	rep6	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	evolved	evolve	VBD	_	_	_
82	9	9	CD	_	_	_
83	min	min	NN	_	_	_
84	rep7	rep7	NN	_	_	_
85	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
86	Fragmentation	fragmentation	NN	_	_	_
87	and	and	CC	_	_	_
88	reverse	reverse	JJ	_	_	_
89	transcription	transcription	NN	_	_	_
90	of	of	IN	_	_	_
91	RNA	rna	NN	_	_	_
92	with	with	IN	_	_	_
93	random	random	JJ	_	_	_
94	primers	primer	NNS	_	_	_
95	was	be	VBD	_	_	_
96	carried	carry	VBN	_	_	_
97	out	out	RP	_	_	_
98	using	use	VBG	_	_	_
99	the	the	DT	_	_	_
100	NEB	NEB	NNP	_	_	_
101	First	First	NNP	_	_	_
102	Strand	Strand	NNP	_	_	_
103	Synthesis	synthesis	NN	_	_	_
104	Module	module	NN	_	_	_
105	-LRB-	-lrb-	-LRB-	_	_	_
106	New	New	NNP	_	_	_
107	England	England	NNP	_	_	_
108	Biolabs	Biolabs	NNP	_	_	_
109	-RRB-	-rrb-	-RRB-	_	_	_
110	.	.	.	_	_	_

1	Second	second	JJ	_	_	_
2	strand	strand	NN	_	_	_
3	synthesis	synthesis	NN	_	_	_
4	was	be	VBD	_	_	_
5	done	do	VBN	_	_	_
6	with	with	IN	_	_	_
7	the	the	DT	_	_	_
8	NEBNext	nebnext	NN	_	_	_
9	Ultra	Ultra	NNP	_	_	_
10	Directional	Directional	NNP	_	_	_
11	RNA	rna	NN	_	_	_
12	Second	second	JJ	_	_	_
13	Strand	strand	NN	_	_	_
14	Synthesis	synthesis	NN	_	_	_
15	Module	module	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	New	New	NNP	_	_	_
18	England	England	NNP	_	_	_
19	Biolabs	Biolabs	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	,	,	,	_	_	_
22	then	then	RB	_	_	_
23	purified	purify	VBN	_	_	_
24	with	with	IN	_	_	_
25	1.7	1.7	CD	_	_	_
26	x	x	CC	_	_	_
27	AMPURE	AMPURE	NNP	_	_	_
28	Bead	Bead	NNP	_	_	_
29	XP	xp	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Beckman	Beckman	NNP	_	_	_
32	Coulter	Coulter	NNP	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	end	end	NN	_	_	_
3	repair	repair	NN	_	_	_
4	was	be	VBD	_	_	_
5	carried	carry	VBN	_	_	_
6	out	out	RP	_	_	_
7	with	with	IN	_	_	_
8	the	the	DT	_	_	_
9	NEBNext	nebnext	NN	_	_	_
10	end	end	NN	_	_	_
11	repair	repair	NN	_	_	_
12	module	module	NN	_	_	_
13	,	,	,	_	_	_
14	dA-tailing	da-tailing	NN	_	_	_
15	used	use	VBD	_	_	_
16	the	the	DT	_	_	_
17	NEBNext	nebnext	NN	_	_	_
18	dA-Tailing	da-tailing	NN	_	_	_
19	Module	module	NN	_	_	_
20	and	and	CC	_	_	_
21	adapter	adapter	NN	_	_	_
22	ligation	ligation	NN	_	_	_
23	used	use	VBD	_	_	_
24	the	the	DT	_	_	_
25	NEBNext	NEBNext	NNP	_	_	_
26	Quick	Quick	NNP	_	_	_
27	Ligation	ligation	NN	_	_	_
28	module	module	NN	_	_	_
29	-LRB-	-lrb-	-LRB-	_	_	_
30	New	New	NNP	_	_	_
31	England	England	NNP	_	_	_
32	Biolabs	Biolabs	NNP	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	.	.	.	_	_	_

1	PCR	pcr	NN	_	_	_
2	amplification	amplification	NN	_	_	_
3	was	be	VBD	_	_	_
4	carried	carry	VBN	_	_	_
5	out	out	RP	_	_	_
6	for	for	IN	_	_	_
7	10	10	CD	_	_	_
8	rounds	round	NNS	_	_	_
9	of	of	IN	_	_	_
10	synthesis	synthesis	NN	_	_	_
11	using	use	VBG	_	_	_
12	the	the	DT	_	_	_
13	NEBNext	nebnext	NN	_	_	_
14	High-Fidelity	high-fidelity	NN	_	_	_
15	PCR	pcr	NN	_	_	_
16	Master	master	NN	_	_	_
17	Mix	mix	VB	_	_	_
18	with	with	IN	_	_	_
19	NEBNext	nebnext	NN	_	_	_
20	USER	user	NN	_	_	_
21	Enzyme	enzyme	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	New	New	NNP	_	_	_
24	England	England	NNP	_	_	_
25	Biolabs	Biolabs	NNP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	,	,	,	_	_	_
28	samples	sample	NNS	_	_	_
29	were	be	VBD	_	_	_
30	purified	purify	VBN	_	_	_
31	with	with	IN	_	_	_
32	1.0	1.0	CD	_	_	_
33	x	x	CC	_	_	_
34	AMPURE	AMPURE	NNP	_	_	_
35	Bead	Bead	NNP	_	_	_
36	XP	xp	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	Beckman	Beckman	NNP	_	_	_
39	Coulter	Coulter	NNP	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	.	.	.	_	_	_

1	Library	Library	NNP	_	_	_
2	quality	quality	NN	_	_	_
3	was	be	VBD	_	_	_
4	verified	verify	VBN	_	_	_
5	on	on	IN	_	_	_
6	a	a	DT	_	_	_
7	Bio-Analyzer	Bio-Analyzer	NNP	_	_	_
8	DNA	DNA	NNP	_	_	_
9	chip	chip	NN	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Agilent	agilent	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Genome	Genome	NNP	_	_	_
3	_	_	NNP	_	_	_
4	build	build	VB	_	_	_
5	:	:	:	_	_	_
6	U00096	u00096	NN	_	_	_
7	.3	.3	NN	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	E.	e.	FW	_	_	_
10	coli	coli	FW	_	_	_
11	K12	k12	NN	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	NC	nc	NN	_	_	_
15	_	_	VBP	_	_	_
16	001604.1	001604.1	CD	_	_	_
17	-LRB-	-lrb-	-LRB-	_	_	_
18	T7	t7	NN	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	,	,	,	_	_	_
21	excluding	exclude	VBG	_	_	_
22	ribosomal	ribosomal	JJ	_	_	_
23	genes	gene	NNS	_	_	_
24	,	,	,	_	_	_
25	and	and	CC	_	_	_
26	with	with	IN	_	_	_
27	recoded	recode	VBN	_	_	_
28	gene	gene	NN	_	_	_
29	10	10	CD	_	_	_
30	sequence	sequence	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	Bull	bull	NN	_	_	_
33	,	,	,	_	_	_
34	2012	2012	CD	_	_	_
35	,	,	,	_	_	_
36	PMCID	pmcid	NN	_	_	_
37	:	:	:	_	_	_
38	PMC3457771	pmc3457771	NN	_	_	_
39	-RRB-	-rrb-	-RRB-	_	_	_
40	in	in	IN	_	_	_
41	place	place	NN	_	_	_
42	of	of	IN	_	_	_
43	wild-type	wild-type	JJ	_	_	_
44	sequence	sequence	NN	_	_	_
45	for	for	IN	_	_	_
46	analysis	analysis	NN	_	_	_
47	of	of	IN	_	_	_
48	recoded	recode	VBN	_	_	_
49	and	and	CC	_	_	_
50	evolved	evolve	VBD	_	_	_
51	strains	strain	NNS	_	_	_
52	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
53	infection	infection	NN	_	_	_
54	:	:	:	_	_	_
55	T7	t7	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	pseudoalignment	pseudoalignment	NN	_	_	_
58	and	and	CC	_	_	_
59	quantitation	quantitation	NN	_	_	_
60	with	with	IN	_	_	_
61	kallisto	kallisto	FW	_	_	_
62	v0	v0	FW	_	_	_
63	.42.5	.42.5	CD	_	_	_
64	with	with	IN	_	_	_
65	parameters	parameter	NNS	_	_	_
66	--	--	:	_	_	_
67	single	single	JJ	_	_	_
68	-	-	:	_	_	_
69	l	l	NN	_	_	_
70	450	450	CD	_	_	_
71	-	-	:	_	_	_
72	s	s	NNS	_	_	_
73	250	250	CD	_	_	_
74	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
75	RNA-Seq	rna-seq	JJ	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	RNA	rna	NN	_	_	_
78	was	be	VBD	_	_	_
79	isolated	isolate	VBN	_	_	_
80	using	use	VBG	_	_	_
81	Trizol	Trizol	NNP	_	_	_
82	reagent	reagent	NN	_	_	_
83	-LRB-	-lrb-	-LRB-	_	_	_
84	Thermo	Thermo	NNP	_	_	_
85	Fisher	Fisher	NNP	_	_	_
86	Scientific	Scientific	NNP	_	_	_
87	-RRB-	-rrb-	-RRB-	_	_	_
88	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
89	Supplementary	Supplementary	NNP	_	_	_
90	_	_	VBD	_	_	_
91	files	file	NNS	_	_	_
92	_	_	IN	_	_	_
93	format	format	NN	_	_	_
94	_	_	NN	_	_	_
95	and	and	CC	_	_	_
96	_	_	NN	_	_	_
97	content	content	NN	_	_	_
98	:	:	:	_	_	_
99	tab-delimitted	tab-delimitted	JJ	_	_	_
100	text	text	NN	_	_	_
101	files	file	NNS	_	_	_
102	contain	contain	VBP	_	_	_
103	TPM	tpm	NN	_	_	_
104	-LRB-	-lrb-	-LRB-	_	_	_
105	transcripts	transcript	NNS	_	_	_
106	per	per	IN	_	_	_
107	million	million	CD	_	_	_
108	-RRB-	-rrb-	-RRB-	_	_	_
109	values	value	NNS	_	_	_
110	for	for	IN	_	_	_
111	each	each	DT	_	_	_
112	sample	sample	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	t7	t7	NN	_	_	_
115	genotype	genotype	NN	_	_	_
116	:	:	:	_	_	_
117	evolved	evolve	VBD	_	_	_
118	,	,	,	_	_	_
119	codon-deoptimized	codon-deoptimized	JJ	_	_	_
120	gene	gene	NN	_	_	_
121	10	10	CD	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	t7	t7	NN	_	_	_
124	genotype	genotype	NN	_	_	_
125	:	:	:	_	_	_
126	wild-type	wild-type	JJ	_	_	_
127	gene	gene	NN	_	_	_
128	10	10	CD	_	_	_
129	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
130	t7	t7	NN	_	_	_
131	strain	strain	NN	_	_	_
132	:	:	:	_	_	_
133	evolved	evolve	VBD	_	_	_
134	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
135	t7	t7	NN	_	_	_
136	strain	strain	NN	_	_	_
137	:	:	:	_	_	_
138	wild	wild	JJ	_	_	_
139	type	type	NN	_	_	_
140	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
141	time	time	NN	_	_	_
142	:	:	:	_	_	_
143	1	1	CD	_	_	_
144	min	min	NN	_	_	_
145	post-infection	post-infection	JJ	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	time	time	NN	_	_	_
148	:	:	:	_	_	_
149	5	5	CD	_	_	_
150	min	min	NN	_	_	_
151	post-infection	post-infection	JJ	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	time	time	NN	_	_	_
154	:	:	:	_	_	_
155	9	9	CD	_	_	_
156	min	min	NN	_	_	_
157	post-infection	post-infection	JJ	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	WT	wt	NN	_	_	_
160	1	1	CD	_	_	_
161	min	min	NN	_	_	_
162	rep7	rep7	NN	_	_	_
163	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
164	WT	wt	VBD	_	_	_
165	9	9	CD	_	_	_
166	min	min	NN	_	_	_
167	rep7	rep7	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	WT	wt	VBD	_	_	_
170	9	9	CD	_	_	_
171	min	min	NN	_	_	_
172	rep8	rep8	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	3XSCOTS	3xscots	CD	_	_	_
175	cDNA	cdna	NN	_	_	_
176	24	24	CD	_	_	_
177	h	h	NN	_	_	_
178	post-infection	post-infection	JJ	_	_	_
179	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
180	3XSCOTS	3xscot	NNS	_	_	_
181	cDNA	cdna	NN	_	_	_
182	in	in	IN	_	_	_
183	RPMI	rpmi	NN	_	_	_
184	medium	medium	NN	_	_	_
185	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
186	3XSCOTS	3xscots	CD	_	_	_
187	cDNA	cdna	NN	_	_	_
188	obtained	obtain	VBN	_	_	_
189	24	24	CD	_	_	_
190	h	h	NN	_	_	_
191	post-infection	post-infection	JJ	_	_	_
192	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
193	3XSCOTS	3xscot	NNS	_	_	_
194	cDNA	cdna	NN	_	_	_
195	obtained	obtain	VBN	_	_	_
196	2h	2h	JJ	_	_	_
197	post-infection	post-infection	JJ	_	_	_
198	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
199	3XSCOTS	3xscot	NNS	_	_	_
200	cDNA	cdna	NN	_	_	_
201	obtained	obtain	VBN	_	_	_
202	8h	8h	JJ	_	_	_
203	post-infection	post-infection	JJ	_	_	_
204	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
205	3XSCOTS	3xscot	NNS	_	_	_
206	cDNA	cdna	NN	_	_	_
207	obtained	obtain	VBN	_	_	_
208	8h	8h	JJ	_	_	_
209	post-infection	post-infection	JJ	_	_	_
210	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
211	3XSCOTS	3xscot	NNS	_	_	_
212	cDNA	cdna	NN	_	_	_
213	obtained	obtain	VBN	_	_	_
214	after	after	IN	_	_	_
215	8h	8h	JJ	_	_	_
216	post-infection	post-infection	JJ	_	_	_
217	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
218	3XSCOTS	3xscot	NNS	_	_	_
219	cDNA	cdna	NN	_	_	_
220	obtained	obtain	VBN	_	_	_
221	in	in	IN	_	_	_
222	RPMI	rpmi	NN	_	_	_
223	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
224	3XSCOTS	3xscots	CD	_	_	_
225	cDNA	cdna	NN	_	_	_
226	obtained	obtain	VBN	_	_	_
227	in	in	IN	_	_	_
228	RPMI	rpmi	NN	_	_	_
229	medium	medium	NN	_	_	_
230	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
231	After	after	IN	_	_	_
232	backgroud	backgroud	NN	_	_	_
233	correction	correction	NN	_	_	_
234	and	and	CC	_	_	_
235	total	total	JJ	_	_	_
236	intensity	intensity	NN	_	_	_
237	normalization	normalization	NN	_	_	_
238	,	,	,	_	_	_
239	ratio	ratio	NN	_	_	_
240	to	to	TO	_	_	_
241	reference	reference	NN	_	_	_
242	were	be	VBD	_	_	_
243	calculated	calculate	VBN	_	_	_
244	and	and	CC	_	_	_
245	log	log	NN	_	_	_
246	base	base	NN	_	_	_
247	2	2	CD	_	_	_
248	transformed	transform	VBN	_	_	_
249	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
250	EDL933	edl933	NN	_	_	_
251	24	24	CD	_	_	_
252	h	h	NN	_	_	_
253	post	post	NN	_	_	_
254	infection	infection	NN	_	_	_
255	in	in	IN	_	_	_
256	THP-1	thp-1	NN	_	_	_
257	humans	human	NNS	_	_	_
258	cells	cell	NNS	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	EDL933	edl933	NN	_	_	_
261	8h	8h	NN	_	_	_
262	post-infection	post-infection	NN	_	_	_
263	in	in	IN	_	_	_
264	THP-1	thp-1	NN	_	_	_
265	human	human	JJ	_	_	_
266	cells	cell	NNS	_	_	_
267	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
268	EDL933	edl933	NN	_	_	_
269	8h	8h	NN	_	_	_
270	post	post	NN	_	_	_
271	THP-1	thp-1	NN	_	_	_
272	infection	infection	NN	_	_	_
273	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
274	EDL933	edl933	NN	_	_	_
275	cDNA	cdna	NN	_	_	_
276	24	24	CD	_	_	_
277	h	h	NN	_	_	_
278	post-infcetion	post-infcetion	NN	_	_	_
279	of	of	IN	_	_	_
280	THP-1	thp-1	NN	_	_	_
281	human	human	JJ	_	_	_
282	cells	cell	NNS	_	_	_
283	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
284	EDL933	edl933	NN	_	_	_
285	cDNA	cdna	NN	_	_	_
286	obtained	obtain	VBN	_	_	_
287	24	24	CD	_	_	_
288	h	h	NN	_	_	_
289	post	post	NN	_	_	_
290	-	-	:	_	_	_
291	infection	infection	NN	_	_	_
292	of	of	IN	_	_	_
293	THP-1	thp-1	NN	_	_	_
294	human	human	JJ	_	_	_
295	cells	cell	NNS	_	_	_
296	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
297	EDL933	edl933	NN	_	_	_
298	cDNA	cdna	NN	_	_	_
299	obtained	obtain	VBN	_	_	_
300	24h	24h	JJ	_	_	_
301	post-infection	post-infection	NN	_	_	_
302	of	of	IN	_	_	_
303	THP-1	thp-1	NN	_	_	_
304	human	human	JJ	_	_	_
305	cells	cell	NNS	_	_	_
306	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
307	EDL933	edl933	NN	_	_	_
308	from	from	IN	_	_	_
309	overnight	overnight	JJ	_	_	_
310	culture	culture	NN	_	_	_
311	in	in	IN	_	_	_
312	LB	lb	NN	MED	_	_
313	broth	broth	NN	MED	_	_
314	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
315	EDL933	edl933	NN	_	_	_
316	genomic	genomic	JJ	_	_	_
317	DNA	dna	NN	_	_	_
318	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
319	EDL933	edl933	NN	_	_	_
320	genomic	genomic	JJ	_	_	_
321	DNA	dna	NN	_	_	_
322	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
323	EDL933	edl933	NN	_	_	_
324	genommic	genommic	JJ	_	_	_
325	DNA	dna	NN	_	_	_
326	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
327	EDL933	edl933	NN	_	_	_
328	infection	infection	NN	_	_	_
329	of	of	IN	_	_	_
330	THP-1	thp-1	NN	_	_	_
331	cells	cell	NNS	_	_	_
332	,	,	,	_	_	_
333	recovered	recover	VBD	_	_	_
334	2	2	CD	_	_	_
335	h	h	NN	_	_	_
336	post-infection	post-infection	JJ	_	_	_
337	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
338	EDL933	edl933	NN	_	_	_
339	infection	infection	NN	_	_	_
340	of	of	IN	_	_	_
341	THP-1	thp-1	NN	_	_	_
342	cells	cell	NNS	_	_	_
343	,	,	,	_	_	_
344	recovered	recover	VBD	_	_	_
345	2h	2h	JJ	_	_	_
346	post-infection	post-infection	JJ	_	_	_
347	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
348	EDL933	edl933	NN	_	_	_
349	in	in	IN	_	_	_
350	humans	human	NNS	_	_	_
351	macrophages	macrophage	NNS	_	_	_
352	8h	8h	VBP	_	_	_
353	post-infection	post-infection	JJ	_	_	_
354	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
355	EDL933	edl933	NN	_	_	_
356	in	in	IN	_	_	_
357	RPMI	rpmi	NN	_	_	_
358	medium	medium	NN	_	_	_
359	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
360	EDL933	edl933	NN	_	_	_
361	in	in	IN	_	_	_
362	THP-1	thp-1	NN	_	_	_
363	cells	cell	NNS	_	_	_
364	8h	8h	VBP	_	_	_
365	post-infection	post-infection	JJ	_	_	_
366	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
367	Escherichia	escherichia	FW	Organism	_	_
368	coli	coli	FW	Organism	_	_
369	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
370	Genomic	genomic	JJ	_	_	_
371	DNA	dna	NN	_	_	_
372	E.	e.	FW	_	_	_
373	coli	coli	FW	_	_	_
374	EDL933	edl933	NN	_	_	_
375	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBZ	_	_	_
376	Genomic	genomic	JJ	_	_	_
377	DNA	dna	NN	_	_	_
378	from	from	IN	_	_	_
379	EDL933	edl933	NN	_	_	_
380	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
381	Genomic	genomic	JJ	_	_	_
382	DNA	dna	NN	_	_	_
383	of	of	IN	_	_	_
384	EDL933	edl933	NN	_	_	_
385	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
386	Genomic	genomic	JJ	_	_	_
387	DNA	dna	NN	_	_	_
388	was	be	VBD	_	_	_
389	extracted	extract	VBN	_	_	_
390	by	by	IN	_	_	_
391	standard	standard	JJ	_	_	_
392	phenol-chloroform	phenol-chloroform	NN	_	_	_
393	method	method	NN	_	_	_
394	-LRB-	-lrb-	-LRB-	_	_	_
395	Sambrook	Sambrook	NNP	_	_	_
396	,	,	,	_	_	_
397	J	J	NNP	_	_	_
398	,	,	,	_	_	_
399	Molecular	molecular	JJ	_	_	_
400	Cloning	cloning	NN	_	_	_
401	,	,	,	_	_	_
402	3rd	3rd	JJ	_	_	_
403	Edition	edition	NN	_	_	_
404	-RRB-	-rrb-	-RRB-	_	_	_
405	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
406	Reference	Reference	NNP	_	_	_
407	DNA	DNA	NNP	_	_	_
408	genomic	genomic	JJ	_	_	_
409	DNA	dna	NN	_	_	_
410	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
411	Reference	Reference	NNP	_	_	_
412	genomic	genomic	JJ	_	_	_
413	DNA	dna	NN	_	_	_
414	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
415	REference	reference	NN	_	_	_
416	genomic	genomic	JJ	_	_	_
417	DNA	dna	NN	_	_	_
418	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
419	RPMI	rpmi	NN	_	_	_
420	1A	1a	NN	_	_	_
421	,	,	,	_	_	_
422	Microarray	Microarray	NNP	_	_	_
423	#	#	#	_	_	_
424	1	1	CD	_	_	_
425	first	first	JJ	_	_	_
426	duplicate	duplicate	VB	_	_	_
427	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
428	RPMI	rpmi	NN	_	_	_
429	1B	1b	NN	_	_	_
430	,	,	,	_	_	_
431	Microarray	Microarray	NNP	_	_	_
432	#	#	#	_	_	_
433	1	1	CD	_	_	_
434	second	second	JJ	_	_	_
435	replicate	replicate	VBP	_	_	_
436	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
437	RPMI	rpmi	NN	_	_	_
438	2A	2a	NN	_	_	_
439	,	,	,	_	_	_
440	Microarray	Microarray	NNP	_	_	_
441	#	#	#	_	_	_
442	2	2	CD	_	_	_
443	,	,	,	_	_	_
444	first	first	RB	_	_	_
445	replicate	replicate	VB	_	_	_
446	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
447	RPMI	rpmi	NN	_	_	_
448	2B	2b	NN	_	_	_
449	,	,	,	_	_	_
450	Microarray	Microarray	NNP	_	_	_
451	#	#	#	_	_	_
452	2	2	CD	_	_	_
453	second	second	JJ	_	_	_
454	replicate	replicate	VBP	_	_	_
455	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
456	T24	t24	NN	_	_	_
457	THP-1	thp-1	NN	_	_	_
458	infection	infection	NN	_	_	_
459	,	,	,	_	_	_
460	Microarray	Microarray	NNP	_	_	_
461	#	#	#	_	_	_
462	1	1	CD	_	_	_
463	first	first	JJ	_	_	_
464	replicate	replicate	VB	_	_	_
465	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
466	T24	t24	NN	_	_	_
467	THP-1	thp-1	NN	_	_	_
468	infection	infection	NN	_	_	_
469	,	,	,	_	_	_
470	Microarray	Microarray	NNP	_	_	_
471	#	#	#	_	_	_
472	1	1	CD	_	_	_
473	second	second	JJ	_	_	_
474	replicate	replicate	VBP	_	_	_
475	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
476	T24	t24	NN	_	_	_
477	THP-1	thp-1	NN	_	_	_
478	infection	infection	NN	_	_	_
479	,	,	,	_	_	_
480	Microarray	Microarray	NNP	_	_	_
481	#	#	#	_	_	_
482	2	2	CD	_	_	_
483	first	first	JJ	_	_	_
484	replicate	replicate	VB	_	_	_
485	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
486	T24	t24	NN	_	_	_
487	THP-1	thp-1	NN	_	_	_
488	infection	infection	NN	_	_	_
489	,	,	,	_	_	_
490	Microarray	Microarray	NNP	_	_	_
491	#	#	#	_	_	_
492	2	2	CD	_	_	_
493	second	second	JJ	_	_	_
494	replicate	replicate	VBP	_	_	_
495	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
496	T2	t2	NN	_	_	_
497	THP-1	thp-1	NN	_	_	_
498	infection	infection	NN	_	_	_
499	,	,	,	_	_	_
500	Microarray	Microarray	NNP	_	_	_
501	#	#	#	_	_	_
502	1	1	CD	_	_	_
503	first	first	RB	_	_	_
504	replicate	replicate	VB	_	_	_
505	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
506	T2	t2	NN	_	_	_
507	THP-1	thp-1	NN	_	_	_
508	infection	infection	NN	_	_	_
509	,	,	,	_	_	_
510	Microarray	Microarray	NNP	_	_	_
511	#	#	#	_	_	_
512	1	1	CD	_	_	_
513	second	second	JJ	_	_	_
514	replicate	replicate	VBP	_	_	_
515	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
516	T2	t2	NN	_	_	_
517	THP-1	thp-1	NN	_	_	_
518	infection	infection	NN	_	_	_
519	,	,	,	_	_	_
520	Microarray	Microarray	NNP	_	_	_
521	#	#	#	_	_	_
522	2	2	CD	_	_	_
523	first	first	JJ	_	_	_
524	replicate	replicate	VB	_	_	_
525	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
526	T2	t2	NN	_	_	_
527	THP-1	thp-1	NN	_	_	_
528	infection	infection	NN	_	_	_
529	,	,	,	_	_	_
530	Microarray	Microarray	NNP	_	_	_
531	#	#	#	_	_	_
532	2	2	CD	_	_	_
533	second	second	JJ	_	_	_
534	replicate	replicate	VBP	_	_	_
535	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
536	T8	t8	NN	_	_	_
537	THP-1	thp-1	NN	_	_	_
538	infection	infection	NN	_	_	_
539	,	,	,	_	_	_
540	Microarray	Microarray	NNP	_	_	_
541	#	#	#	_	_	_
542	1	1	CD	_	_	_
543	first	first	RB	_	_	_
544	replicate	replicate	VB	_	_	_
545	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
546	T8	t8	NN	_	_	_
547	THP-1	thp-1	NN	_	_	_
548	infection	infection	NN	_	_	_
549	,	,	,	_	_	_
550	Microarray	Microarray	NNP	_	_	_
551	#	#	#	_	_	_
552	1	1	CD	_	_	_
553	second	second	JJ	_	_	_
554	replicate	replicate	VBP	_	_	_
555	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
556	T8	t8	NN	_	_	_
557	THP-1	thp-1	NN	_	_	_
558	infection	infection	NN	_	_	_
559	,	,	,	_	_	_
560	Microarray	Microarray	NNP	_	_	_
561	#	#	#	_	_	_
562	2	2	CD	_	_	_
563	first	first	JJ	_	_	_
564	replicate	replicate	VB	_	_	_
565	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
566	T8	t8	NN	_	_	_
567	THP-1	thp-1	NN	_	_	_
568	infection	infection	NN	_	_	_
569	,	,	,	_	_	_
570	Microarray	Microarray	NNP	_	_	_
571	#	#	#	_	_	_
572	2	2	CD	_	_	_
573	second	second	JJ	_	_	_
574	replicate	replicate	VBP	_	_	_
575	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
576	TRIzol	trizol	NN	_	_	_
577	reagent	reagent	NN	_	_	_
578	-LRB-	-lrb-	-LRB-	_	_	_
579	Gibco	Gibco	NNP	_	_	_
580	BRL	brl	NN	_	_	_
581	-RRB-	-rrb-	-RRB-	_	_	_
582	was	be	VBD	_	_	_
583	used	use	VBN	_	_	_
584	according	accord	VBG	_	_	_
585	to	to	TO	_	_	_
586	the	the	DT	_	_	_
587	manufacturer	manufacturer	NN	_	_	_
588	instruction	instruction	NN	_	_	_
589	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	treated	treat	VBN	_	_	_
4	with	with	IN	_	_	_
5	DNase	dnase	NN	_	_	_
6	-LRB-	-lrb-	-LRB-	_	_	_
7	Ambion	ambion	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	sample	sample	NN	_	_	_
3	was	be	VBD	_	_	_
4	converted	convert	VBN	_	_	_
5	to	to	TO	_	_	_
6	cDNA	cdna	NN	_	_	_
7	in	in	IN	_	_	_
8	5	5	CD	_	_	_
9	independent	independent	JJ	_	_	_
10	reverse-transcription	reverse-transcription	JJ	_	_	_
11	reactions	reaction	NNS	_	_	_
12	as	as	IN	_	_	_
13	described	describe	VBN	_	_	_
14	previously	previously	RB	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Graham	Graham	NNP	_	_	_
17	,	,	,	_	_	_
18	J.	J.	NNP	_	_	_
19	1999	1999	CD	_	_	_
20	.	.	.	_	_	_

1	PNAS	PNAS	NNP	_	_	_
2	96:11554-559	96:11554-559	CD	_	_	_
3	-RRB-	-rrb-	-RRB-	_	_	_
4	.	.	.	_	_	_

1	Bacterial	bacterial	JJ	_	_	_
2	transcript	transcript	NN	_	_	_
3	were	be	VBD	_	_	_
4	purified	purify	VBN	_	_	_
5	from	from	IN	_	_	_
6	host	host	NN	_	_	_
7	transcript	transcript	NN	_	_	_
8	by	by	IN	_	_	_
9	using	use	VBG	_	_	_
10	3	3	CD	_	_	_
11	round	round	NN	_	_	_
12	of	of	IN	_	_	_
13	the	the	DT	_	_	_
14	SCOTS	SCOTS	NNP	_	_	_
15	procedure	procedure	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Daigle	daigle	NN	_	_	_
18	,	,	,	_	_	_
19	F.	F.	NNP	_	_	_
20	2002	2002	CD	_	_	_
21	.	.	.	_	_	_

1	Methods	method	NNS	_	_	_
2	Enzymol	Enzymol	NNP	_	_	_
3	.	.	.	_	_	_

1	358:108-122	358:108-122	CD	_	_	_
2	-RRB-	-rrb-	-RRB-	_	_	_
3	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Data	Data	NNP	_	_	_
3	were	be	VBD	_	_	_
4	analyzed	analyze	VBN	_	_	_
5	with	with	IN	_	_	_
6	RMA	rma	NN	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Robust	robust	JJ	_	_	_
9	Multiarray	Multiarray	NNP	_	_	_
10	Analysis	analysis	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	using	use	VBG	_	_	_
13	Affymetrix	Affymetrix	NNP	_	_	_
14	default	default	NN	_	_	_
15	analysis	analysis	NN	_	_	_
16	settings	setting	NNS	_	_	_
17	and	and	CC	_	_	_
18	global	global	JJ	_	_	_
19	scaling	scaling	NN	_	_	_
20	as	as	IN	_	_	_
21	normalization	normalization	NN	_	_	_
22	method	method	NN	_	_	_
23	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	CRP	crp	NN	TF	_	_
5	N	n	NN	_	_	_
6	strain	strain	NN	_	_	_
7	_	_	NN	_	_	_
8	acetate	acetate	NN	SUPP	_	_
9	_	_	NN	_	_	_
10	exponential	exponential	JJ	GrowthPhase	_	_
11	phase	phase	NN	GrowthPhase	_	_
12	_	_	NN	_	_	_
13	repl1	repl1	NN	_	_	_
14	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
15	E.	e.	FW	_	_	_
16	coli	coli	FW	_	_	_
17	CRP	crp	NN	TF	_	_
18	N	n	NN	_	_	_
19	strain	strain	NN	_	_	_
20	_	_	NN	_	_	_
21	acetate	acetate	NN	SUPP	_	_
22	_	_	NN	_	_	_
23	exponential	exponential	JJ	GrowthPhase	_	_
24	phase	phase	NN	GrowthPhase	_	_
25	_	_	NN	_	_	_
26	repl2	repl2	NN	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	E.	e.	FW	_	_	_
29	coli	coli	FW	_	_	_
30	CRP	crp	NN	TF	_	_
31	N	n	NN	_	_	_
32	strain	strain	NN	_	_	_
33	_	_	NN	_	_	_
34	acetate	acetate	NN	SUPP	_	_
35	_	_	NN	_	_	_
36	stationary	stationary	JJ	GrowthPhase	_	_
37	phase	phase	NN	GrowthPhase	_	_
38	_	_	NN	_	_	_
39	repl1	repl1	NN	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	E.	e.	FW	_	_	_
42	coli	coli	FW	_	_	_
43	CRP	crp	NN	TF	_	_
44	N	n	NN	_	_	_
45	strain	strain	NN	_	_	_
46	_	_	NN	_	_	_
47	acetate	acetate	NN	SUPP	_	_
48	_	_	NN	_	_	_
49	stationary	stationary	JJ	GrowthPhase	_	_
50	phase	phase	NN	GrowthPhase	_	_
51	_	_	NN	_	_	_
52	repl2	repl2	NN	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	E.	e.	FW	_	_	_
55	coli	coli	FW	_	_	_
56	CRP	crp	NN	TF	_	_
57	N	n	NN	_	_	_
58	strain	strain	NN	_	_	_
59	_	_	NN	_	_	_
60	glucose	glucose	NN	SUPP	_	_
61	_	_	NN	_	_	_
62	exponential	exponential	JJ	GrowthPhase	_	_
63	phase	phase	NN	GrowthPhase	_	_
64	_	_	NN	_	_	_
65	repl1	repl1	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	E.	e.	FW	_	_	_
68	coli	coli	FW	_	_	_
69	CRP	crp	NN	TF	_	_
70	N	n	NN	_	_	_
71	strain	strain	NN	_	_	_
72	_	_	NN	_	_	_
73	glucose	glucose	NN	SUPP	_	_
74	_	_	NN	_	_	_
75	exponential	exponential	JJ	GrowthPhase	_	_
76	phase	phase	NN	GrowthPhase	_	_
77	_	_	NN	_	_	_
78	repl2	repl2	NN	_	_	_
79	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
80	E.	e.	FW	_	_	_
81	coli	coli	FW	_	_	_
82	CRP	crp	NN	TF	_	_
83	N	n	NN	_	_	_
84	strain	strain	NN	_	_	_
85	_	_	NN	_	_	_
86	glucose	glucose	NN	SUPP	_	_
87	_	_	NN	_	_	_
88	stationary	stationary	JJ	GrowthPhase	_	_
89	phase	phase	NN	GrowthPhase	_	_
90	_	_	NN	_	_	_
91	repl1	repl1	NN	_	_	_
92	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
93	E.	e.	FW	_	_	_
94	coli	coli	FW	_	_	_
95	CRP	crp	NN	TF	_	_
96	N	n	NN	_	_	_
97	strain	strain	NN	_	_	_
98	_	_	NN	_	_	_
99	glucose	glucose	NN	SUPP	_	_
100	_	_	NN	_	_	_
101	stationary	stationary	JJ	GrowthPhase	_	_
102	phase	phase	NN	GrowthPhase	_	_
103	_	_	NN	_	_	_
104	repl2	repl2	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	E.	e.	FW	_	_	_
107	coli	coli	FW	_	_	_
108	CRP	crp	NN	TF	_	_
109	N	n	NN	_	_	_
110	strain	strain	NN	_	_	_
111	grown	grow	VBN	_	_	_
112	in	in	IN	_	_	_
113	acetate	acetate	NN	SUPP	_	_
114	batch	batch	NN	_	_	_
115	minimal	minimal	JJ	_	_	_
116	media	media	NNS	_	_	_
117	,	,	,	_	_	_
118	cells	cell	NNS	_	_	_
119	were	be	VBD	_	_	_
120	harvested	harvest	VBN	_	_	_
121	at	at	IN	_	_	_
122	exponential	exponential	JJ	GrowthPhase	_	_
123	phase	phase	NN	GrowthPhase	_	_
124	,	,	,	_	_	_
125	biological	biological	JJ	_	_	_
126	rep1	rep1	NN	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	E.	e.	FW	_	_	_
129	coli	coli	FW	_	_	_
130	CRP	crp	NN	TF	_	_
131	N	n	NN	_	_	_
132	strain	strain	NN	_	_	_
133	grown	grow	VBN	_	_	_
134	in	in	IN	_	_	_
135	acetate	acetate	NN	SUPP	_	_
136	batch	batch	NN	_	_	_
137	minimal	minimal	JJ	_	_	_
138	media	media	NNS	_	_	_
139	,	,	,	_	_	_
140	cells	cell	NNS	_	_	_
141	were	be	VBD	_	_	_
142	harvested	harvest	VBN	_	_	_
143	at	at	IN	_	_	_
144	exponential	exponential	JJ	GrowthPhase	_	_
145	phase	phase	NN	GrowthPhase	_	_
146	,	,	,	_	_	_
147	biological	biological	JJ	_	_	_
148	rep2	rep2	NN	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	E.	e.	FW	_	_	_
151	coli	coli	FW	_	_	_
152	CRP	crp	NN	TF	_	_
153	N	n	NN	_	_	_
154	strain	strain	NN	_	_	_
155	grown	grow	VBN	_	_	_
156	in	in	IN	_	_	_
157	acetate	acetate	NN	SUPP	_	_
158	batch	batch	NN	_	_	_
159	minimal	minimal	JJ	_	_	_
160	media	media	NNS	_	_	_
161	,	,	,	_	_	_
162	cells	cell	NNS	_	_	_
163	were	be	VBD	_	_	_
164	harvested	harvest	VBN	_	_	_
165	at	at	IN	_	_	_
166	stationary	stationary	JJ	GrowthPhase	_	_
167	phase	phase	NN	GrowthPhase	_	_
168	,	,	,	_	_	_
169	biological	biological	JJ	_	_	_
170	rep1	rep1	NN	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
172	E.	e.	FW	_	_	_
173	coli	coli	FW	_	_	_
174	CRP	crp	NN	TF	_	_
175	N	n	NN	_	_	_
176	strain	strain	NN	_	_	_
177	grown	grow	VBN	_	_	_
178	in	in	IN	_	_	_
179	acetate	acetate	NN	SUPP	_	_
180	batch	batch	NN	_	_	_
181	minimal	minimal	JJ	_	_	_
182	media	media	NNS	_	_	_
183	,	,	,	_	_	_
184	cells	cell	NNS	_	_	_
185	were	be	VBD	_	_	_
186	harvested	harvest	VBN	_	_	_
187	at	at	IN	_	_	_
188	stationary	stationary	JJ	GrowthPhase	_	_
189	phase	phase	NN	GrowthPhase	_	_
190	,	,	,	_	_	_
191	biological	biological	JJ	_	_	_
192	rep2	rep2	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	E.	e.	FW	_	_	_
195	coli	coli	FW	_	_	_
196	CRP	crp	NN	TF	_	_
197	N	n	NN	_	_	_
198	strain	strain	NN	_	_	_
199	grown	grow	VBN	_	_	_
200	in	in	IN	_	_	_
201	glucose	glucose	NN	SUPP	_	_
202	batch	batch	NN	_	_	_
203	minimal	minimal	JJ	_	_	_
204	media	media	NNS	_	_	_
205	,	,	,	_	_	_
206	cells	cell	NNS	_	_	_
207	were	be	VBD	_	_	_
208	harvested	harvest	VBN	_	_	_
209	at	at	IN	_	_	_
210	exponential	exponential	JJ	GrowthPhase	_	_
211	phase	phase	NN	GrowthPhase	_	_
212	,	,	,	_	_	_
213	biological	biological	JJ	_	_	_
214	rep1	rep1	NN	_	_	_
215	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
216	E.	e.	FW	_	_	_
217	coli	coli	FW	_	_	_
218	CRP	crp	NN	TF	_	_
219	N	n	NN	_	_	_
220	strain	strain	NN	_	_	_
221	grown	grow	VBN	_	_	_
222	in	in	IN	_	_	_
223	glucose	glucose	NN	SUPP	_	_
224	batch	batch	NN	_	_	_
225	minimal	minimal	JJ	_	_	_
226	media	media	NNS	_	_	_
227	,	,	,	_	_	_
228	cells	cell	NNS	_	_	_
229	were	be	VBD	_	_	_
230	harvested	harvest	VBN	_	_	_
231	at	at	IN	_	_	_
232	exponential	exponential	JJ	GrowthPhase	_	_
233	phase	phase	NN	GrowthPhase	_	_
234	,	,	,	_	_	_
235	biological	biological	JJ	_	_	_
236	rep2	rep2	NN	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	E.	e.	FW	_	_	_
239	coli	coli	FW	_	_	_
240	CRP	crp	NN	TF	_	_
241	N	n	NN	_	_	_
242	strain	strain	NN	_	_	_
243	grown	grow	VBN	_	_	_
244	in	in	IN	_	_	_
245	glucose	glucose	NN	SUPP	_	_
246	batch	batch	NN	_	_	_
247	minimal	minimal	JJ	_	_	_
248	media	media	NNS	_	_	_
249	,	,	,	_	_	_
250	cells	cell	NNS	_	_	_
251	were	be	VBD	_	_	_
252	harvested	harvest	VBN	_	_	_
253	at	at	IN	_	_	_
254	stationary	stationary	JJ	GrowthPhase	_	_
255	phase	phase	NN	GrowthPhase	_	_
256	,	,	,	_	_	_
257	biological	biological	JJ	_	_	_
258	rep1	rep1	NN	_	_	_
259	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
260	E.	e.	FW	_	_	_
261	coli	coli	FW	_	_	_
262	CRP	crp	NN	TF	_	_
263	N	n	NN	_	_	_
264	strain	strain	NN	_	_	_
265	grown	grow	VBN	_	_	_
266	in	in	IN	_	_	_
267	glucose	glucose	NN	SUPP	_	_
268	batch	batch	NN	_	_	_
269	minimal	minimal	JJ	_	_	_
270	media	media	NNS	_	_	_
271	,	,	,	_	_	_
272	cells	cell	NNS	_	_	_
273	were	be	VBD	_	_	_
274	harvested	harvest	VBN	_	_	_
275	at	at	IN	_	_	_
276	stationary	stationary	JJ	GrowthPhase	_	_
277	phase	phase	NN	GrowthPhase	_	_
278	,	,	,	_	_	_
279	biological	biological	JJ	_	_	_
280	rep2	rep2	NN	_	_	_
281	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
282	E.	e.	FW	_	_	_
283	coli	coli	FW	_	_	_
284	CRP	crp	NN	TF	_	_
285	Q	Q	NNP	_	_	_
286	strain	strain	NN	_	_	_
287	_	_	NN	_	_	_
288	acetate	acetate	NN	SUPP	_	_
289	_	_	NN	_	_	_
290	exponential	exponential	JJ	GrowthPhase	_	_
291	phase	phase	NN	GrowthPhase	_	_
292	_	_	NN	_	_	_
293	repl1	repl1	NN	_	_	_
294	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
295	E.	e.	FW	_	_	_
296	coli	coli	FW	_	_	_
297	CRP	crp	NN	TF	_	_
298	Q	Q	NNP	_	_	_
299	strain	strain	NN	_	_	_
300	_	_	NN	_	_	_
301	acetate	acetate	NN	SUPP	_	_
302	_	_	NN	_	_	_
303	exponential	exponential	JJ	GrowthPhase	_	_
304	phase	phase	NN	GrowthPhase	_	_
305	_	_	NN	_	_	_
306	repl2	repl2	NN	_	_	_
307	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
308	E.	e.	FW	_	_	_
309	coli	coli	FW	_	_	_
310	CRP	crp	NN	TF	_	_
311	Q	Q	NNP	_	_	_
312	strain	strain	NN	_	_	_
313	_	_	NN	_	_	_
314	acetate	acetate	NN	SUPP	_	_
315	_	_	NN	_	_	_
316	stationary	stationary	JJ	GrowthPhase	_	_
317	phase	phase	NN	GrowthPhase	_	_
318	_	_	NN	_	_	_
319	repl1	repl1	NN	_	_	_
320	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
321	E.	e.	FW	_	_	_
322	coli	coli	FW	_	_	_
323	CRP	crp	NN	TF	_	_
324	Q	Q	NNP	_	_	_
325	strain	strain	NN	_	_	_
326	_	_	NN	_	_	_
327	acetate	acetate	NN	SUPP	_	_
328	_	_	NN	_	_	_
329	stationary	stationary	JJ	GrowthPhase	_	_
330	phase	phase	NN	GrowthPhase	_	_
331	_	_	NN	_	_	_
332	repl2	repl2	NN	_	_	_
333	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
334	E.	e.	FW	_	_	_
335	coli	coli	FW	_	_	_
336	CRP	crp	NN	TF	_	_
337	Q	Q	NNP	_	_	_
338	strain	strain	NN	_	_	_
339	_	_	NN	_	_	_
340	glucose	glucose	NN	SUPP	_	_
341	_	_	NN	_	_	_
342	exponential	exponential	JJ	GrowthPhase	_	_
343	phase	phase	NN	GrowthPhase	_	_
344	_	_	NN	_	_	_
345	repl1	repl1	NN	_	_	_
346	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
347	E.	e.	FW	_	_	_
348	coli	coli	FW	_	_	_
349	CRP	crp	NN	TF	_	_
350	Q	Q	NNP	_	_	_
351	strain	strain	NN	_	_	_
352	_	_	NN	_	_	_
353	glucose	glucose	NN	SUPP	_	_
354	_	_	NN	_	_	_
355	exponential	exponential	JJ	GrowthPhase	_	_
356	phase	phase	NN	GrowthPhase	_	_
357	_	_	NN	_	_	_
358	repl2	repl2	NN	_	_	_
359	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
360	E.	e.	FW	_	_	_
361	coli	coli	FW	_	_	_
362	CRP	crp	NN	TF	_	_
363	Q	Q	NNP	_	_	_
364	strain	strain	NN	_	_	_
365	_	_	NN	_	_	_
366	glucose	glucose	NN	SUPP	_	_
367	_	_	NN	_	_	_
368	stationary	stationary	JJ	GrowthPhase	_	_
369	phase	phase	NN	GrowthPhase	_	_
370	_	_	NN	_	_	_
371	repl1	repl1	NN	_	_	_
372	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
373	E.	e.	FW	_	_	_
374	coli	coli	FW	_	_	_
375	CRP	crp	NN	TF	_	_
376	Q	Q	NNP	_	_	_
377	strain	strain	NN	_	_	_
378	_	_	NN	_	_	_
379	glucose	glucose	NN	SUPP	_	_
380	_	_	NN	_	_	_
381	stationary	stationary	JJ	GrowthPhase	_	_
382	phase	phase	NN	GrowthPhase	_	_
383	_	_	NN	_	_	_
384	repl2	repl2	NN	_	_	_
385	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
386	E.	e.	FW	_	_	_
387	coli	coli	FW	_	_	_
388	CRP	crp	NN	TF	_	_
389	Q	Q	NNP	_	_	_
390	strain	strain	NN	_	_	_
391	grown	grow	VBN	_	_	_
392	in	in	IN	_	_	_
393	acetate	acetate	NN	SUPP	_	_
394	batch	batch	NN	_	_	_
395	minimal	minimal	JJ	_	_	_
396	media	media	NNS	_	_	_
397	,	,	,	_	_	_
398	cells	cell	NNS	_	_	_
399	were	be	VBD	_	_	_
400	harvested	harvest	VBN	_	_	_
401	at	at	IN	_	_	_
402	exponential	exponential	JJ	GrowthPhase	_	_
403	phase	phase	NN	GrowthPhase	_	_
404	,	,	,	_	_	_
405	biological	biological	JJ	_	_	_
406	rep1	rep1	NN	_	_	_
407	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
408	E.	e.	FW	_	_	_
409	coli	coli	FW	_	_	_
410	CRP	crp	NN	TF	_	_
411	Q	Q	NNP	_	_	_
412	strain	strain	NN	_	_	_
413	grown	grow	VBN	_	_	_
414	in	in	IN	_	_	_
415	acetate	acetate	NN	SUPP	_	_
416	batch	batch	NN	_	_	_
417	minimal	minimal	JJ	_	_	_
418	media	media	NNS	_	_	_
419	,	,	,	_	_	_
420	cells	cell	NNS	_	_	_
421	were	be	VBD	_	_	_
422	harvested	harvest	VBN	_	_	_
423	at	at	IN	_	_	_
424	exponential	exponential	JJ	GrowthPhase	_	_
425	phase	phase	NN	GrowthPhase	_	_
426	,	,	,	_	_	_
427	biological	biological	JJ	_	_	_
428	rep2	rep2	NN	_	_	_
429	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
430	E.	e.	FW	_	_	_
431	coli	coli	FW	_	_	_
432	CRP	crp	NN	TF	_	_
433	Q	Q	NNP	_	_	_
434	strain	strain	NN	_	_	_
435	grown	grow	VBN	_	_	_
436	in	in	IN	_	_	_
437	acetate	acetate	NN	SUPP	_	_
438	batch	batch	NN	_	_	_
439	minimal	minimal	JJ	_	_	_
440	media	media	NNS	_	_	_
441	,	,	,	_	_	_
442	cells	cell	NNS	_	_	_
443	were	be	VBD	_	_	_
444	harvested	harvest	VBN	_	_	_
445	at	at	IN	_	_	_
446	stationary	stationary	JJ	GrowthPhase	_	_
447	phase	phase	NN	GrowthPhase	_	_
448	,	,	,	_	_	_
449	biological	biological	JJ	_	_	_
450	rep1	rep1	NN	_	_	_
451	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
452	E.	e.	FW	_	_	_
453	coli	coli	FW	_	_	_
454	CRP	crp	NN	TF	_	_
455	Q	Q	NNP	_	_	_
456	strain	strain	NN	_	_	_
457	grown	grow	VBN	_	_	_
458	in	in	IN	_	_	_
459	acetate	acetate	NN	SUPP	_	_
460	batch	batch	NN	_	_	_
461	minimal	minimal	JJ	_	_	_
462	media	media	NNS	_	_	_
463	,	,	,	_	_	_
464	cells	cell	NNS	_	_	_
465	were	be	VBD	_	_	_
466	harvested	harvest	VBN	_	_	_
467	at	at	IN	_	_	_
468	stationary	stationary	JJ	GrowthPhase	_	_
469	phase	phase	NN	GrowthPhase	_	_
470	,	,	,	_	_	_
471	biological	biological	JJ	_	_	_
472	rep2	rep2	NN	_	_	_
473	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
474	E.	e.	FW	_	_	_
475	coli	coli	FW	_	_	_
476	CRP	crp	NN	TF	_	_
477	Q	Q	NNP	_	_	_
478	strain	strain	NN	_	_	_
479	grown	grow	VBN	_	_	_
480	in	in	IN	_	_	_
481	glucose	glucose	NN	SUPP	_	_
482	batch	batch	NN	_	_	_
483	minimal	minimal	JJ	_	_	_
484	media	media	NNS	_	_	_
485	,	,	,	_	_	_
486	cells	cell	NNS	_	_	_
487	were	be	VBD	_	_	_
488	harvested	harvest	VBN	_	_	_
489	at	at	IN	_	_	_
490	exponential	exponential	JJ	GrowthPhase	_	_
491	phase	phase	NN	GrowthPhase	_	_
492	,	,	,	_	_	_
493	biological	biological	JJ	_	_	_
494	rep1	rep1	NN	_	_	_
495	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
496	E.	e.	FW	_	_	_
497	coli	coli	FW	_	_	_
498	CRP	crp	NN	TF	_	_
499	Q	Q	NNP	_	_	_
500	strain	strain	NN	_	_	_
501	grown	grow	VBN	_	_	_
502	in	in	IN	_	_	_
503	glucose	glucose	NN	SUPP	_	_
504	batch	batch	NN	_	_	_
505	minimal	minimal	JJ	_	_	_
506	media	media	NNS	_	_	_
507	,	,	,	_	_	_
508	cells	cell	NNS	_	_	_
509	were	be	VBD	_	_	_
510	harvested	harvest	VBN	_	_	_
511	at	at	IN	_	_	_
512	exponential	exponential	JJ	GrowthPhase	_	_
513	phase	phase	NN	GrowthPhase	_	_
514	,	,	,	_	_	_
515	biological	biological	JJ	_	_	_
516	rep2	rep2	NN	_	_	_
517	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
518	E.	e.	FW	_	_	_
519	coli	coli	FW	_	_	_
520	CRP	crp	NN	TF	_	_
521	Q	Q	NNP	_	_	_
522	strain	strain	NN	_	_	_
523	grown	grow	VBN	_	_	_
524	in	in	IN	_	_	_
525	glucose	glucose	NN	SUPP	_	_
526	batch	batch	NN	_	_	_
527	minimal	minimal	JJ	_	_	_
528	media	media	NNS	_	_	_
529	,	,	,	_	_	_
530	cells	cell	NNS	_	_	_
531	were	be	VBD	_	_	_
532	harvested	harvest	VBN	_	_	_
533	at	at	IN	_	_	_
534	stationary	stationary	JJ	GrowthPhase	_	_
535	phase	phase	NN	GrowthPhase	_	_
536	,	,	,	_	_	_
537	biological	biological	JJ	_	_	_
538	rep1	rep1	NN	_	_	_
539	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
540	E.	e.	FW	_	_	_
541	coli	coli	FW	_	_	_
542	CRP	crp	NN	TF	_	_
543	Q	Q	NNP	_	_	_
544	strain	strain	NN	_	_	_
545	grown	grow	VBN	_	_	_
546	in	in	IN	_	_	_
547	glucose	glucose	NN	SUPP	_	_
548	batch	batch	NN	_	_	_
549	minimal	minimal	JJ	_	_	_
550	media	media	NNS	_	_	_
551	,	,	,	_	_	_
552	cells	cell	NNS	_	_	_
553	were	be	VBD	_	_	_
554	harvested	harvest	VBN	_	_	_
555	at	at	IN	_	_	_
556	stationary	stationary	JJ	GrowthPhase	_	_
557	phase	phase	NN	GrowthPhase	_	_
558	,	,	,	_	_	_
559	biological	biological	JJ	_	_	_
560	rep2	rep2	NN	_	_	_
561	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
562	E.	e.	FW	_	_	_
563	coli	coli	FW	_	_	_
564	CRP	crp	NN	TF	_	_
565	R	r	NN	_	_	_
566	strain	strain	NN	_	_	_
567	_	_	NN	_	_	_
568	acetate	acetate	NN	SUPP	_	_
569	_	_	NN	_	_	_
570	exponential	exponential	JJ	GrowthPhase	_	_
571	phase	phase	NN	GrowthPhase	_	_
572	_	_	NN	_	_	_
573	repl1	repl1	NN	_	_	_
574	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
575	E.	e.	FW	_	_	_
576	coli	coli	FW	_	_	_
577	CRP	crp	NN	TF	_	_
578	R	r	NN	_	_	_
579	strain	strain	NN	_	_	_
580	_	_	NN	_	_	_
581	acetate	acetate	NN	SUPP	_	_
582	_	_	NN	_	_	_
583	exponential	exponential	JJ	GrowthPhase	_	_
584	phase	phase	NN	GrowthPhase	_	_
585	_	_	NN	_	_	_
586	repl2	repl2	NN	_	_	_
587	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
588	E.	e.	FW	_	_	_
589	coli	coli	FW	_	_	_
590	CRP	crp	NN	TF	_	_
591	R	r	NN	_	_	_
592	strain	strain	NN	_	_	_
593	_	_	NN	_	_	_
594	acetate	acetate	NN	SUPP	_	_
595	_	_	NN	_	_	_
596	stationary	stationary	JJ	GrowthPhase	_	_
597	phase	phase	NN	GrowthPhase	_	_
598	_	_	NN	_	_	_
599	repl1	repl1	NN	_	_	_
600	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
601	E.	e.	FW	_	_	_
602	coli	coli	FW	_	_	_
603	CRP	crp	NN	TF	_	_
604	R	r	NN	_	_	_
605	strain	strain	NN	_	_	_
606	_	_	NN	_	_	_
607	acetate	acetate	NN	SUPP	_	_
608	_	_	NN	_	_	_
609	stationary	stationary	JJ	GrowthPhase	_	_
610	phase	phase	NN	GrowthPhase	_	_
611	_	_	NN	_	_	_
612	repl2	repl2	NN	_	_	_
613	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
614	E.	e.	FW	_	_	_
615	coli	coli	FW	_	_	_
616	CRP	crp	NN	TF	_	_
617	R	r	NN	_	_	_
618	strain	strain	NN	_	_	_
619	_	_	NN	_	_	_
620	glucose	glucose	NN	SUPP	_	_
621	_	_	NN	_	_	_
622	exponential	exponential	JJ	GrowthPhase	_	_
623	phase	phase	NN	GrowthPhase	_	_
624	_	_	NN	_	_	_
625	repl1	repl1	NN	_	_	_
626	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
627	E.	e.	FW	_	_	_
628	coli	coli	FW	_	_	_
629	CRP	crp	NN	TF	_	_
630	R	r	NN	_	_	_
631	strain	strain	NN	_	_	_
632	_	_	NN	_	_	_
633	glucose	glucose	NN	SUPP	_	_
634	_	_	NN	_	_	_
635	exponential	exponential	JJ	GrowthPhase	_	_
636	phase	phase	NN	GrowthPhase	_	_
637	_	_	NN	_	_	_
638	repl2	repl2	NN	_	_	_
639	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
640	E.	e.	FW	_	_	_
641	coli	coli	FW	_	_	_
642	CRP	crp	NN	TF	_	_
643	R	r	NN	_	_	_
644	strain	strain	NN	_	_	_
645	_	_	NN	_	_	_
646	glucose	glucose	NN	SUPP	_	_
647	_	_	NN	_	_	_
648	stationary	stationary	JJ	GrowthPhase	_	_
649	phase	phase	NN	GrowthPhase	_	_
650	_	_	NN	_	_	_
651	repl1	repl1	NN	_	_	_
652	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
653	E.	e.	FW	_	_	_
654	coli	coli	FW	_	_	_
655	CRP	crp	NN	TF	_	_
656	R	r	NN	_	_	_
657	strain	strain	NN	_	_	_
658	_	_	NN	_	_	_
659	glucose	glucose	NN	SUPP	_	_
660	_	_	NN	_	_	_
661	stationary	stationary	JJ	GrowthPhase	_	_
662	phase	phase	NN	GrowthPhase	_	_
663	_	_	NN	_	_	_
664	repl2	repl2	NN	_	_	_
665	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
666	E.	e.	FW	_	_	_
667	coli	coli	FW	_	_	_
668	CRP	crp	NN	TF	_	_
669	R	r	NN	_	_	_
670	strain	strain	NN	_	_	_
671	grown	grow	VBN	_	_	_
672	in	in	IN	_	_	_
673	acetate	acetate	NN	SUPP	_	_
674	batch	batch	NN	_	_	_
675	minimal	minimal	JJ	_	_	_
676	media	media	NNS	_	_	_
677	,	,	,	_	_	_
678	cells	cell	NNS	_	_	_
679	were	be	VBD	_	_	_
680	harvested	harvest	VBN	_	_	_
681	at	at	IN	_	_	_
682	exponential	exponential	JJ	GrowthPhase	_	_
683	phase	phase	NN	GrowthPhase	_	_
684	,	,	,	_	_	_
685	biological	biological	JJ	_	_	_
686	rep1	rep1	NN	_	_	_
687	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
688	E.	e.	FW	_	_	_
689	coli	coli	FW	_	_	_
690	CRP	crp	NN	TF	_	_
691	R	r	NN	_	_	_
692	strain	strain	NN	_	_	_
693	grown	grow	VBN	_	_	_
694	in	in	IN	_	_	_
695	acetate	acetate	NN	SUPP	_	_
696	batch	batch	NN	_	_	_
697	minimal	minimal	JJ	_	_	_
698	media	media	NNS	_	_	_
699	,	,	,	_	_	_
700	cells	cell	NNS	_	_	_
701	were	be	VBD	_	_	_
702	harvested	harvest	VBN	_	_	_
703	at	at	IN	_	_	_
704	exponential	exponential	JJ	GrowthPhase	_	_
705	phase	phase	NN	GrowthPhase	_	_
706	,	,	,	_	_	_
707	biological	biological	JJ	_	_	_
708	rep2	rep2	NN	_	_	_
709	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
710	E.	e.	FW	_	_	_
711	coli	coli	FW	_	_	_
712	CRP	crp	NN	TF	_	_
713	R	r	NN	_	_	_
714	strain	strain	NN	_	_	_
715	grown	grow	VBN	_	_	_
716	in	in	IN	_	_	_
717	acetate	acetate	NN	SUPP	_	_
718	batch	batch	NN	_	_	_
719	minimal	minimal	JJ	_	_	_
720	media	media	NNS	_	_	_
721	,	,	,	_	_	_
722	cells	cell	NNS	_	_	_
723	were	be	VBD	_	_	_
724	harvested	harvest	VBN	_	_	_
725	at	at	IN	_	_	_
726	stationary	stationary	JJ	GrowthPhase	_	_
727	phase	phase	NN	GrowthPhase	_	_
728	,	,	,	_	_	_
729	biological	biological	JJ	_	_	_
730	rep1	rep1	NN	_	_	_
731	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
732	E.	e.	FW	_	_	_
733	coli	coli	FW	_	_	_
734	CRP	crp	NN	TF	_	_
735	R	r	NN	_	_	_
736	strain	strain	NN	_	_	_
737	grown	grow	VBN	_	_	_
738	in	in	IN	_	_	_
739	acetate	acetate	NN	SUPP	_	_
740	batch	batch	NN	_	_	_
741	minimal	minimal	JJ	_	_	_
742	media	media	NNS	_	_	_
743	,	,	,	_	_	_
744	cells	cell	NNS	_	_	_
745	were	be	VBD	_	_	_
746	harvested	harvest	VBN	_	_	_
747	at	at	IN	_	_	_
748	stationary	stationary	JJ	GrowthPhase	_	_
749	phase	phase	NN	GrowthPhase	_	_
750	,	,	,	_	_	_
751	biological	biological	JJ	_	_	_
752	rep2	rep2	NN	_	_	_
753	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
754	E.	e.	FW	_	_	_
755	coli	coli	FW	_	_	_
756	CRP	crp	NN	TF	_	_
757	R	r	NN	_	_	_
758	strain	strain	NN	_	_	_
759	grown	grow	VBN	_	_	_
760	in	in	IN	_	_	_
761	glucose	glucose	NN	SUPP	_	_
762	batch	batch	NN	_	_	_
763	minimal	minimal	JJ	_	_	_
764	media	media	NNS	_	_	_
765	,	,	,	_	_	_
766	cells	cell	NNS	_	_	_
767	were	be	VBD	_	_	_
768	harvested	harvest	VBN	_	_	_
769	at	at	IN	_	_	_
770	exponential	exponential	JJ	GrowthPhase	_	_
771	phase	phase	NN	GrowthPhase	_	_
772	,	,	,	_	_	_
773	biological	biological	JJ	_	_	_
774	rep1	rep1	NN	_	_	_
775	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
776	E.	e.	FW	_	_	_
777	coli	coli	FW	_	_	_
778	CRP	crp	NN	TF	_	_
779	R	r	NN	_	_	_
780	strain	strain	NN	_	_	_
781	grown	grow	VBN	_	_	_
782	in	in	IN	_	_	_
783	glucose	glucose	NN	SUPP	_	_
784	batch	batch	NN	_	_	_
785	minimal	minimal	JJ	_	_	_
786	media	media	NNS	_	_	_
787	,	,	,	_	_	_
788	cells	cell	NNS	_	_	_
789	were	be	VBD	_	_	_
790	harvested	harvest	VBN	_	_	_
791	at	at	IN	_	_	_
792	exponential	exponential	JJ	GrowthPhase	_	_
793	phase	phase	NN	GrowthPhase	_	_
794	,	,	,	_	_	_
795	biological	biological	JJ	_	_	_
796	rep2	rep2	NN	_	_	_
797	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
798	E.	e.	FW	_	_	_
799	coli	coli	FW	_	_	_
800	CRP	crp	NN	TF	_	_
801	R	r	NN	_	_	_
802	strain	strain	NN	_	_	_
803	grown	grow	VBN	_	_	_
804	in	in	IN	_	_	_
805	glucose	glucose	NN	SUPP	_	_
806	batch	batch	NN	_	_	_
807	minimal	minimal	JJ	_	_	_
808	media	media	NNS	_	_	_
809	,	,	,	_	_	_
810	cells	cell	NNS	_	_	_
811	were	be	VBD	_	_	_
812	harvested	harvest	VBN	_	_	_
813	at	at	IN	_	_	_
814	stationary	stationary	JJ	GrowthPhase	_	_
815	phase	phase	NN	GrowthPhase	_	_
816	,	,	,	_	_	_
817	biological	biological	JJ	_	_	_
818	rep1	rep1	NN	_	_	_
819	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
820	E.	e.	FW	_	_	_
821	coli	coli	FW	_	_	_
822	CRP	crp	NN	TF	_	_
823	R	r	NN	_	_	_
824	strain	strain	NN	_	_	_
825	grown	grow	VBN	_	_	_
826	in	in	IN	_	_	_
827	glucose	glucose	NN	SUPP	_	_
828	batch	batch	NN	_	_	_
829	minimal	minimal	JJ	_	_	_
830	media	media	NNS	_	_	_
831	,	,	,	_	_	_
832	cells	cell	NNS	_	_	_
833	were	be	VBD	_	_	_
834	harvested	harvest	VBN	_	_	_
835	at	at	IN	_	_	_
836	stationary	stationary	JJ	GrowthPhase	_	_
837	phase	phase	NN	GrowthPhase	_	_
838	,	,	,	_	_	_
839	biological	biological	JJ	_	_	_
840	rep2	rep2	NN	_	_	_
841	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
842	E.	E.	NNP	_	_	_
843	coli	coli	NN	_	_	_
844	Wild	Wild	NNP	_	_	_
845	type	type	NN	_	_	_
846	_	_	CD	_	_	_
847	acetate	acetate	NN	SUPP	_	_
848	_	_	NN	_	_	_
849	exponential	exponential	JJ	GrowthPhase	_	_
850	phase	phase	NN	GrowthPhase	_	_
851	_	_	NN	_	_	_
852	repl1	repl1	NN	_	_	_
853	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
854	E.	E.	NNP	_	_	_
855	coli	coli	NN	_	_	_
856	Wild	Wild	NNP	_	_	_
857	type	type	NN	_	_	_
858	_	_	CD	_	_	_
859	acetate	acetate	NN	SUPP	_	_
860	_	_	NN	_	_	_
861	exponential	exponential	JJ	GrowthPhase	_	_
862	phase	phase	NN	GrowthPhase	_	_
863	_	_	NN	_	_	_
864	repl2	repl2	NN	_	_	_
865	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
866	E.	E.	NNP	_	_	_
867	coli	coli	NN	_	_	_
868	Wild	Wild	NNP	_	_	_
869	type	type	NN	_	_	_
870	_	_	CD	_	_	_
871	acetate	acetate	NN	SUPP	_	_
872	_	_	NN	_	_	_
873	stationary	stationary	JJ	GrowthPhase	_	_
874	phase	phase	NN	GrowthPhase	_	_
875	_	_	NN	_	_	_
876	repl1	repl1	NN	_	_	_
877	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
878	E.	E.	NNP	_	_	_
879	coli	coli	NN	_	_	_
880	Wild	Wild	NNP	_	_	_
881	type	type	NN	_	_	_
882	_	_	CD	_	_	_
883	acetate	acetate	NN	SUPP	_	_
884	_	_	NN	_	_	_
885	stationary	stationary	JJ	GrowthPhase	_	_
886	phase	phase	NN	GrowthPhase	_	_
887	_	_	NN	_	_	_
888	repl2	repl2	NN	_	_	_
889	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
890	E.	E.	NNP	_	_	_
891	coli	coli	NN	_	_	_
892	Wild	Wild	NNP	_	_	_
893	type	type	NN	_	_	_
894	and	and	CC	_	_	_
895	its	its	PRP$	_	_	_
896	mutants	mutant	NNS	_	_	_
897	were	be	VBD	_	_	_
898	grown	grow	VBN	_	_	_
899	in	in	IN	_	_	_
900	M9	m9	NN	MED	_	_
901	minimal	minimal	JJ	MED	_	_
902	medium	medium	NN	MED	_	_
903	with	with	IN	_	_	_
904	10mM	10mm	NN	_	_	_
905	glucose	glucose	NN	SUPP	_	_
906	or	or	CC	_	_	_
907	30mM	30mm	NN	_	_	_
908	acetate	acetate	NN	SUPP	_	_
909	as	as	IN	_	_	_
910	sole	sole	JJ	_	_	_
911	carbon	carbon	NN	_	_	_
912	source	source	NN	_	_	_
913	.	.	.	_	_	_

1	Samples	sample	NNS	_	_	_
2	for	for	IN	_	_	_
3	RNA	rna	NN	_	_	_
4	extraction	extraction	NN	_	_	_
5	were	be	VBD	_	_	_
6	taken	take	VBN	_	_	_
7	in	in	IN	_	_	_
8	middle	middle	JJ	_	_	_
9	exponential	exponential	JJ	GrowthPhase	_	_
10	phase	phase	NN	GrowthPhase	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	OD600	od600	NN	_	_	_
13	≈	≈	CD	_	_	_
14	0.5	0.5	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	and	and	CC	_	_	_
17	in	in	IN	_	_	_
18	stationary	stationary	JJ	GrowthPhase	_	_
19	phase	phase	NN	GrowthPhase	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	OD600	od600	NN	_	_	_
22	≈	≈	CD	_	_	_
23	1.5	1.5	CD	_	_	_
24	-RRB-	-rrb-	-RRB-	_	_	_
25	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
26	E.	E.	NNP	_	_	_
27	coli	coli	NN	_	_	_
28	Wild	Wild	NNP	_	_	_
29	type	type	NN	_	_	_
30	_	_	CD	_	_	_
31	glucose	glucose	NN	SUPP	_	_
32	_	_	NN	_	_	_
33	exponential	exponential	JJ	GrowthPhase	_	_
34	phase	phase	NN	GrowthPhase	_	_
35	_	_	NN	_	_	_
36	repl1	repl1	NN	_	_	_
37	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
38	E.	E.	NNP	_	_	_
39	coli	coli	NN	_	_	_
40	Wild	Wild	NNP	_	_	_
41	type	type	NN	_	_	_
42	_	_	CD	_	_	_
43	glucose	glucose	NN	SUPP	_	_
44	_	_	NN	_	_	_
45	exponential	exponential	JJ	GrowthPhase	_	_
46	phase	phase	NN	GrowthPhase	_	_
47	_	_	NN	_	_	_
48	repl2	repl2	NN	_	_	_
49	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
50	E.	E.	NNP	_	_	_
51	coli	coli	NN	_	_	_
52	Wild	Wild	NNP	_	_	_
53	type	type	NN	_	_	_
54	_	_	CD	_	_	_
55	glucose	glucose	NN	SUPP	_	_
56	_	_	NN	_	_	_
57	stationary	stationary	JJ	GrowthPhase	_	_
58	phase	phase	NN	GrowthPhase	_	_
59	_	_	NN	_	_	_
60	repl1	repl1	NN	_	_	_
61	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
62	E.	E.	NNP	_	_	_
63	coli	coli	NN	_	_	_
64	Wild	Wild	NNP	_	_	_
65	type	type	NN	_	_	_
66	_	_	CD	_	_	_
67	glucose	glucose	NN	SUPP	_	_
68	_	_	NN	_	_	_
69	stationary	stationary	JJ	GrowthPhase	_	_
70	phase	phase	NN	GrowthPhase	_	_
71	_	_	NN	_	_	_
72	repl2	repl2	NN	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	E.	e.	FW	_	_	_
75	coli	coli	FW	_	_	_
76	wt	wt	JJ	_	_	_
77	grown	grow	VBN	_	_	_
78	in	in	IN	_	_	_
79	acetate	acetate	NN	SUPP	_	_
80	batch	batch	NN	_	_	_
81	minimal	minimal	JJ	_	_	_
82	media	media	NNS	_	_	_
83	,	,	,	_	_	_
84	cells	cell	NNS	_	_	_
85	were	be	VBD	_	_	_
86	harvested	harvest	VBN	_	_	_
87	at	at	IN	_	_	_
88	exponential	exponential	JJ	GrowthPhase	_	_
89	phase	phase	NN	GrowthPhase	_	_
90	,	,	,	_	_	_
91	biological	biological	JJ	_	_	_
92	rep1	rep1	NN	_	_	_
93	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
94	E.	e.	FW	_	_	_
95	coli	coli	FW	_	_	_
96	wt	wt	JJ	_	_	_
97	grown	grow	VBN	_	_	_
98	in	in	IN	_	_	_
99	acetate	acetate	NN	SUPP	_	_
100	batch	batch	NN	_	_	_
101	minimal	minimal	JJ	_	_	_
102	media	media	NNS	_	_	_
103	,	,	,	_	_	_
104	cells	cell	NNS	_	_	_
105	were	be	VBD	_	_	_
106	harvested	harvest	VBN	_	_	_
107	at	at	IN	_	_	_
108	exponential	exponential	JJ	GrowthPhase	_	_
109	phase	phase	NN	GrowthPhase	_	_
110	,	,	,	_	_	_
111	biological	biological	JJ	_	_	_
112	rep2	rep2	NN	_	_	_
113	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
114	E.	e.	FW	_	_	_
115	coli	coli	FW	_	_	_
116	wt	wt	JJ	_	_	_
117	grown	grow	VBN	_	_	_
118	in	in	IN	_	_	_
119	acetate	acetate	NN	SUPP	_	_
120	batch	batch	NN	_	_	_
121	minimal	minimal	JJ	_	_	_
122	media	media	NNS	_	_	_
123	,	,	,	_	_	_
124	cells	cell	NNS	_	_	_
125	were	be	VBD	_	_	_
126	harvested	harvest	VBN	_	_	_
127	at	at	IN	_	_	_
128	stationary	stationary	JJ	GrowthPhase	_	_
129	phase	phase	NN	GrowthPhase	_	_
130	,	,	,	_	_	_
131	biological	biological	JJ	_	_	_
132	rep1	rep1	NN	_	_	_
133	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
134	E.	e.	FW	_	_	_
135	coli	coli	FW	_	_	_
136	wt	wt	JJ	_	_	_
137	grown	grow	VBN	_	_	_
138	in	in	IN	_	_	_
139	acetate	acetate	NN	SUPP	_	_
140	batch	batch	NN	_	_	_
141	minimal	minimal	JJ	_	_	_
142	media	media	NNS	_	_	_
143	,	,	,	_	_	_
144	cells	cell	NNS	_	_	_
145	were	be	VBD	_	_	_
146	harvested	harvest	VBN	_	_	_
147	at	at	IN	_	_	_
148	stationary	stationary	JJ	GrowthPhase	_	_
149	phase	phase	NN	GrowthPhase	_	_
150	,	,	,	_	_	_
151	biological	biological	JJ	_	_	_
152	rep2	rep2	NN	_	_	_
153	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
154	E.	e.	FW	_	_	_
155	coli	coli	FW	_	_	_
156	wt	wt	JJ	_	_	_
157	grown	grow	VBN	_	_	_
158	in	in	IN	_	_	_
159	glucose	glucose	NN	SUPP	_	_
160	batch	batch	NN	_	_	_
161	minimal	minimal	JJ	_	_	_
162	media	media	NNS	_	_	_
163	,	,	,	_	_	_
164	cells	cell	NNS	_	_	_
165	were	be	VBD	_	_	_
166	harvested	harvest	VBN	_	_	_
167	at	at	IN	_	_	_
168	exponential	exponential	JJ	GrowthPhase	_	_
169	phase	phase	NN	GrowthPhase	_	_
170	,	,	,	_	_	_
171	biological	biological	JJ	_	_	_
172	rep1	rep1	NN	_	_	_
173	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
174	E.	e.	FW	_	_	_
175	coli	coli	FW	_	_	_
176	wt	wt	JJ	_	_	_
177	grown	grow	VBN	_	_	_
178	in	in	IN	_	_	_
179	glucose	glucose	NN	SUPP	_	_
180	batch	batch	NN	_	_	_
181	minimal	minimal	JJ	_	_	_
182	media	media	NNS	_	_	_
183	,	,	,	_	_	_
184	cells	cell	NNS	_	_	_
185	were	be	VBD	_	_	_
186	harvested	harvest	VBN	_	_	_
187	at	at	IN	_	_	_
188	exponential	exponential	JJ	GrowthPhase	_	_
189	phase	phase	NN	GrowthPhase	_	_
190	,	,	,	_	_	_
191	biological	biological	JJ	_	_	_
192	rep2	rep2	NN	_	_	_
193	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
194	E.	e.	FW	_	_	_
195	coli	coli	FW	_	_	_
196	wt	wt	JJ	_	_	_
197	grown	grow	VBN	_	_	_
198	in	in	IN	_	_	_
199	glucose	glucose	NN	SUPP	_	_
200	batch	batch	NN	_	_	_
201	minimal	minimal	JJ	_	_	_
202	media	media	NNS	_	_	_
203	,	,	,	_	_	_
204	cells	cell	NNS	_	_	_
205	were	be	VBD	_	_	_
206	harvested	harvest	VBN	_	_	_
207	at	at	IN	_	_	_
208	stationary	stationary	JJ	GrowthPhase	_	_
209	phase	phase	NN	GrowthPhase	_	_
210	,	,	,	_	_	_
211	biological	biological	JJ	_	_	_
212	rep1	rep1	NN	_	_	_
213	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
214	E.	e.	FW	_	_	_
215	coli	coli	FW	_	_	_
216	wt	wt	JJ	_	_	_
217	grown	grow	VBN	_	_	_
218	in	in	IN	_	_	_
219	glucose	glucose	NN	SUPP	_	_
220	batch	batch	NN	_	_	_
221	minimal	minimal	JJ	_	_	_
222	media	media	NNS	_	_	_
223	,	,	,	_	_	_
224	cells	cell	NNS	_	_	_
225	were	be	VBD	_	_	_
226	harvested	harvest	VBN	_	_	_
227	at	at	IN	_	_	_
228	stationary	stationary	JJ	GrowthPhase	_	_
229	phase	phase	NN	GrowthPhase	_	_
230	,	,	,	_	_	_
231	biological	biological	JJ	_	_	_
232	rep2	rep2	NN	_	_	_
233	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
234	Escherichia	escherichia	FW	Organism	_	_
235	coli	coli	FW	Organism	_	_
236	K-12	k-12	NN	_	_	_
237	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
238	genotyp	genotyp	NN	_	_	_
239	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
240	Total	total	JJ	_	_	_
241	RNA	rna	NN	_	_	_
242	extraction	extraction	NN	_	_	_
243	using	use	VBG	_	_	_
244	Vantage	Vantage	NNP	_	_	_
245	™	™	CD	_	_	_
246	RNA	rna	NN	_	_	_
247	Purification	purification	NN	_	_	_
248	Kit	kit	NN	_	_	_
249	-LRB-	-lrb-	-LRB-	_	_	_
250	Origene	Origene	NNP	_	_	_
251	,	,	,	_	_	_
252	Rockville	Rockville	NNP	_	_	_
253	,	,	,	_	_	_
254	MD	MD	NNP	_	_	_
255	,	,	,	_	_	_
256	USA	USA	NNP	_	_	_
257	-RRB-	-rrb-	-RRB-	_	_	_
258	was	be	VBD	_	_	_
259	performed	perform	VBN	_	_	_
260	according	accord	VBG	_	_	_
261	with	with	IN	_	_	_
262	the	the	DT	_	_	_
263	manufacter	manufacter	NN	_	_	_
264	instructions	instruction	NNS	_	_	_
265	.	.	.	_	_	_

1	Purity	purity	NN	_	_	_
2	and	and	CC	_	_	_
3	concentration	concentration	NN	_	_	_
4	of	of	IN	_	_	_
5	isolated	isolate	VBN	_	_	_
6	RNA	rna	NN	_	_	_
7	were	be	VBD	_	_	_
8	assessed	assess	VBN	_	_	_
9	in	in	IN	_	_	_
10	a	a	DT	_	_	_
11	NanoDrop	NanoDrop	NNP	_	_	_
12	One	one	CD	_	_	_
13	spectrophotometer	spectrophotometer	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Thermo	Thermo	NNP	_	_	_
16	Scientific	Scientific	NNP	_	_	_
17	Incorporated	Incorporated	NNP	_	_	_
18	,	,	,	_	_	_
19	WI	WI	NNP	_	_	_
20	,	,	,	_	_	_
21	USA	USA	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	.	.	.	_	_	_

1	Quality	Quality	NNP	_	_	_
2	was	be	VBD	_	_	_
3	evaluated	evaluate	VBN	_	_	_
4	by	by	IN	_	_	_
5	microfluidic	microfluidic	JJ	_	_	_
6	capillary	capillary	JJ	_	_	_
7	electrophoresis	electrophoresis	NN	_	_	_
8	on	on	IN	_	_	_
9	an	a	DT	_	_	_
10	Agilent	Agilent	NNP	_	_	_
11	2100	2100	CD	_	_	_
12	Bioanalyzer	Bioanalyzer	NNP	_	_	_
13	-LRB-	-lrb-	-LRB-	_	_	_
14	Agilent	Agilent	NNP	_	_	_
15	Technologies	Technologies	NNPS	_	_	_
16	,	,	,	_	_	_
17	Inc	Inc	NNP	_	_	_
18	,	,	,	_	_	_
19	USA	USA	NNP	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	Adpater	adpater	NN	_	_	_
3	sequences	sequence	NNS	_	_	_
4	were	be	VBD	_	_	_
5	clipped	clip	VBN	_	_	_
6	with	with	IN	_	_	_
7	CutAdapt	cutadapt	JJ	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	AR1	ar1	NN	_	_	_
10	-	-	:	_	_	_
11	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
12	Base	base	NN	_	_	_
13	calls	call	NNS	_	_	_
14	were	be	VBD	_	_	_
15	made	make	VBN	_	_	_
16	using	use	VBG	_	_	_
17	MiSeq	MiSeq	NNP	_	_	_
18	Reporter	reporter	NN	_	_	_
19	v.	v.	CC	_	_	_
20	2.6.2.1	2.6.2.1	CD	_	_	_
21	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
22	Cell	cell	NN	_	_	_
23	pellets	pellet	NNS	_	_	_
24	were	be	VBD	_	_	_
25	lysed	lyse	VBN	_	_	_
26	in	in	IN	_	_	_
27	Tissue	tissue	NN	_	_	_
28	and	and	CC	_	_	_
29	Cell	cell	NN	_	_	_
30	lysis	lysis	NN	_	_	_
31	solution	solution	NN	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	EpiCentre	EpiCentre	NNP	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	and	and	CC	_	_	_
36	proteinase	proteinase	NN	_	_	_
37	K.	K.	NNP	_	_	_
38	RNA	rna	NN	_	_	_
39	was	be	VBD	_	_	_
40	isolated	isolate	VBN	_	_	_
41	and	and	CC	_	_	_
42	DNase	dnase	NN	_	_	_
43	treated	treat	VBN	_	_	_
44	using	use	VBG	_	_	_
45	the	the	DT	_	_	_
46	RNeasy	RNeasy	NNP	_	_	_
47	Kit	kit	NN	_	_	_
48	-LRB-	-lrb-	-LRB-	_	_	_
49	Qiagen	qiagen	NN	_	_	_
50	-RRB-	-rrb-	-RRB-	_	_	_
51	using	use	VBG	_	_	_
52	the	the	DT	_	_	_
53	manufacturer	manufacturer	NN	_	_	_
54	's	's	POS	_	_	_
55	protocol	protocol	NN	_	_	_
56	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	amount	amount	NN	_	_	_
3	of	of	IN	_	_	_
4	total	total	JJ	_	_	_
5	RNA	rna	NN	_	_	_
6	in	in	IN	_	_	_
7	each	each	DT	_	_	_
8	sample	sample	NN	_	_	_
9	was	be	VBD	_	_	_
10	quantified	quantify	VBN	_	_	_
11	using	use	VBG	_	_	_
12	the	the	DT	_	_	_
13	Qubit	Qubit	NNP	_	_	_
14	2.0	2.0	CD	_	_	_
15	Flurometer	Flurometer	NNP	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	Life	Life	NNP	_	_	_
18	Technologies	Technologies	NNPS	_	_	_
19	-RRB-	-rrb-	-RRB-	_	_	_
20	and	and	CC	_	_	_
21	quality	quality	NN	_	_	_
22	was	be	VBD	_	_	_
23	assessed	assess	VBN	_	_	_
24	using	use	VBG	_	_	_
25	the	the	DT	_	_	_
26	RNA6000	rna6000	NN	_	_	_
27	Nano	Nano	NNP	_	_	_
28	Chip	Chip	NNP	_	_	_
29	on	on	IN	_	_	_
30	the	the	DT	_	_	_
31	Bioanalyzer	Bioanalyzer	NNP	_	_	_
32	2100	2100	CD	_	_	_
33	-LRB-	-lrb-	-LRB-	_	_	_
34	Agilent	Agilent	NNP	_	_	_
35	-RRB-	-rrb-	-RRB-	_	_	_
36	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	Cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	grown	grow	VBN	_	_	_
5	in	in	IN	_	_	_
6	TB7	tb7	NN	_	_	_
7	supplemented	supplement	VBN	_	_	_
8	with	with	IN	_	_	_
9	22	22	CD	_	_	_
10	mM	mm	NN	KWSUPP	_	_
11	glucose	glucose	NN	SUPP	_	_
12	until	until	IN	_	_	_
13	OD600	od600	NN	_	_	_
14	~	~	NN	_	_	_
15	1.8	1.8	CD	_	_	_
16	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Differential	differential	JJ	_	_	_
3	expression	expression	NN	_	_	_
4	testing	testing	NN	_	_	_
5	between	between	IN	_	_	_
6	sample	sample	NN	_	_	_
7	groups	group	NNS	_	_	_
8	was	be	VBD	_	_	_
9	performed	perform	VBN	_	_	_
10	in	in	IN	_	_	_
11	Rstudio	Rstudio	NNP	_	_	_
12	-LRB-	-lrb-	-LRB-	_	_	_
13	v.	v.	CC	_	_	_
14	1.0.36	1.0.36	CD	_	_	_
15	-RRB-	-rrb-	-RRB-	_	_	_
16	using	use	VBG	_	_	_
17	DESeq2	deseq2	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	v.	v.	CC	_	_	_
20	1.14.1	1.14.1	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
23	Escherichia	escherichia	FW	Organism	_	_
24	coli	coli	FW	Organism	_	_
25	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
26	Genome	Genome	NNP	_	_	_
27	_	_	NNP	_	_	_
28	build	build	VB	_	_	_
29	:	:	:	_	_	_
30	Escherichia	escherichia	FW	Organism	_	_
31	coli	coli	FW	Organism	_	_
32	str	str	FW	_	_	_
33	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
3	genotype	genotype	NN	_	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	growth	growth	NN	_	_	_
6	phase	phase	NN	_	_	_
7	:	:	:	_	_	_
8	Late	late	JJ	_	_	_
9	exponential	exponential	JJ	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	K100Q	k100q	NN	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	K100Q	k100q	NN	_	_	_
14	rep	rep	NN	GEN	_	_
15	1	1	CD	_	_	_
16	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
17	K100Q	k100q	NN	_	_	_
18	rep	rep	NN	GEN	_	_
19	2	2	CD	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	K100Q	k100q	NN	_	_	_
22	rep	rep	NN	GEN	_	_
23	3	3	CD	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	K100R	k100r	NN	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	K100R	k100r	NN	_	_	_
28	rep	rep	NN	GEN	_	_
29	1	1	CD	_	_	_
30	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
31	K100R	k100r	NN	_	_	_
32	rep	rep	NN	GEN	_	_
33	2	2	CD	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	K100R	k100r	NN	_	_	_
36	rep	rep	NN	GEN	_	_
37	3	3	CD	_	_	_
38	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
39	Low	low	JJ	_	_	_
40	quality	quality	NN	_	_	_
41	reads	read	VBZ	_	_	_
42	were	be	VBD	_	_	_
43	trimmed	trim	VBN	_	_	_
44	with	with	IN	_	_	_
45	CutAdapt	cutadapt	JJ	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
47	Mapped	map	VBD	_	_	_
48	reads	read	VBZ	_	_	_
49	were	be	VBD	_	_	_
50	counted	count	VBN	_	_	_
51	using	use	VBG	_	_	_
52	the	the	DT	_	_	_
53	Python	Python	NNP	_	_	_
54	package	package	NN	_	_	_
55	HTSeq	htseq	NN	_	_	_
56	-LRB-	-lrb-	-LRB-	_	_	_
57	v.	v.	CC	_	_	_
58	0.6.1	0.6.1	CD	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	using	use	VBG	_	_	_
61	the	the	DT	_	_	_
62	following	follow	VBG	_	_	_
63	parameters	parameter	NNS	_	_	_
64	;	;	:	_	_	_
65	htseq-count	htseq-count	NN	_	_	_
66	-	-	:	_	_	_
67	m	m	NN	_	_	_
68	union	union	NN	_	_	_
69	-	-	:	_	_	_
70	r	r	NN	_	_	_
71	pos	pos	SYM	_	_	_
72	-	-	:	_	_	_
73	i	i	FW	_	_	_
74	gene	gene	NN	_	_	_
75	_	_	NN	_	_	_
76	name	name	NN	_	_	_
77	-	-	:	_	_	_
78	a	a	DT	_	_	_
79	10	10	CD	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
81	media	media	NNS	_	_	_
82	:	:	:	_	_	_
83	Tryptone	tryptone	NN	_	_	_
84	broth	broth	NN	_	_	_
85	buffered	buffer	VBD	_	_	_
86	to	to	TO	_	_	_
87	pH	ph	NN	_	_	_
88	7	7	CD	_	_	_
89	supplemented	supplement	VBN	_	_	_
90	with	with	IN	_	_	_
91	22	22	CD	_	_	_
92	mM	mm	NN	KWSUPP	_	_
93	glucose	glucose	NN	SUPP	_	_
94	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
95	RNA-Seq	rna-seq	NN	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	rRNA	rrna	NN	_	_	_
98	depletion	depletion	NN	_	_	_
99	,	,	,	_	_	_
100	fragmentation	fragmentation	NN	_	_	_
101	,	,	,	_	_	_
102	reverse	reverse	JJ	_	_	_
103	transcription	transcription	NN	_	_	_
104	,	,	,	_	_	_
105	tagging	tagging	NN	_	_	_
106	,	,	,	_	_	_
107	barcoding	barcoding	NN	_	_	_
108	,	,	,	_	_	_
109	limited	limited	JJ	_	_	_
110	cycle	cycle	NN	_	_	_
111	PCR	pcr	NN	_	_	_
112	-LRB-	-lrb-	-LRB-	_	_	_
113	Illumina	Illumina	NNP	_	_	_
114	-RRB-	-rrb-	-RRB-	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	ScriptSeq	scriptseq	NN	_	_	_
117	v2	v2	NN	_	_	_
118	Complete	complete	JJ	_	_	_
119	Kit	kit	NN	_	_	_
120	-LRB-	-lrb-	-LRB-	_	_	_
121	EpiCentre	EpiCentre	NNP	_	_	_
122	-RRB-	-rrb-	-RRB-	_	_	_
123	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
124	strain	strain	NN	_	_	_
125	:	:	:	_	_	_
126	K-12	k-12	NN	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	Supplementary	supplementary	JJ	_	_	_
129	_	_	NN	_	_	_
130	files	file	NNS	_	_	_
131	_	_	IN	_	_	_
132	format	format	NN	_	_	_
133	_	_	NN	_	_	_
134	and	and	CC	_	_	_
135	_	_	NN	_	_	_
136	content	content	NN	_	_	_
137	:	:	:	_	_	_
138	Comma	comma	NN	_	_	_
139	separated	separated	JJ	_	_	_
140	value	value	NN	_	_	_
141	files	file	NNS	_	_	_
142	include	include	VBP	_	_	_
143	log-fold	log-fold	JJ	_	_	_
144	changes	change	NNS	_	_	_
145	and	and	CC	_	_	_
146	associated	associate	VBN	_	_	_
147	p-values	p-value	NNS	_	_	_
148	for	for	IN	_	_	_
149	each	each	DT	_	_	_
150	comparison	comparison	NN	_	_	_
151	made	make	VBD	_	_	_
152	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
153	Supplementary	Supplementary	NNP	_	_	_
154	_	_	VBD	_	_	_
155	files	file	NNS	_	_	_
156	_	_	IN	_	_	_
157	format	format	NN	_	_	_
158	_	_	NN	_	_	_
159	and	and	CC	_	_	_
160	_	_	NN	_	_	_
161	content	content	NN	_	_	_
162	:	:	:	_	_	_
163	text	text	NN	_	_	_
164	files	file	NNS	_	_	_
165	containing	contain	VBG	_	_	_
166	gene	gene	NN	_	_	_
167	counts	count	VBZ	_	_	_
168	output	output	NN	_	_	_
169	by	by	IN	_	_	_
170	htseq-count	htseq-count	JJ	_	_	_
171	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
172	The	the	DT	_	_	_
173	resulting	result	VBG	_	_	_
174	reads	read	VBZ	_	_	_
175	were	be	VBD	_	_	_
176	mapped	map	VBN	_	_	_
177	to	to	TO	_	_	_
178	the	the	DT	_	_	_
179	reference	reference	NN	_	_	_
180	genome	genome	NN	_	_	_
181	of	of	IN	_	_	_
182	Escherichia	escherichia	FW	Organism	_	_
183	coli	coli	FW	Organism	_	_
184	str	str	FW	_	_	_
185	.	.	.	_	_	_

1	K-12	k-12	NN	_	_	_
2	substr	substr	NN	_	_	_
3	.	.	.	_	_	_

1	MG1655	mg1655	NN	_	_	_
2	using	use	VBG	_	_	_
3	Tophat2	tophat2	NN	_	_	_
4	using	use	VBG	_	_	_
5	the	the	DT	_	_	_
6	following	follow	VBG	_	_	_
7	parameters	parameter	NNS	_	_	_
8	,	,	,	_	_	_
9	--	--	:	_	_	_
10	GTF	gtf	NN	_	_	_
11	--	--	:	_	_	_
12	library	library	NN	_	_	_
13	type	type	NN	_	_	_
14	fr-secondstrand	fr-secondstrand	JJ	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	WT	wt	JJ	_	_	_
17	rep	rep	NN	GEN	_	_
18	1	1	CD	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	WT	wt	JJ	_	_	_
21	rep	rep	NN	GEN	_	_
22	2	2	CD	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	WT	wt	JJ	_	_	_
25	rep	rep	NN	GEN	_	_
26	3	3	CD	_	_	_
27	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
28	Affymetrix	Affymetrix	NNP	_	_	_
29	Microarray	Microarray	NNP	_	_	_
30	Suite	Suite	NNP	_	_	_
31	5.0	5.0	CD	_	_	_
32	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
33	Dilution	Dilution	NNP	_	_	_
34	rate	rate	NN	_	_	_
35	=	=	JJ	_	_	_
36	0.14	0.14	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	E.coli	e.coli	NNS	_	_	_
39	_	_	VBP	_	_	_
40	0	0	CD	_	_	_
41	%	%	NN	_	_	_
42	tannin	tannin	NN	_	_	_
43	_	_	NN	_	_	_
44	#	#	#	_	_	_
45	2	2	CD	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	E.coli	e.coli	NNS	_	_	_
48	_	_	VBP	_	_	_
49	0	0	CD	_	_	_
50	%	%	NN	_	_	_
51	tannin	tannin	NN	_	_	_
52	_	_	NN	_	_	_
53	#	#	#	_	_	_
54	8	8	CD	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	E.coli	e.coli	NNS	_	_	_
57	_	_	VBP	_	_	_
58	1	1	CD	_	_	_
59	%	%	NN	_	_	_
60	tannin	tannin	NN	_	_	_
61	_	_	NN	_	_	_
62	#	#	#	_	_	_
63	3	3	CD	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	e.coli	e.coli	NNS	_	_	_
66	_	_	VBP	_	_	_
67	1	1	CD	_	_	_
68	%	%	NN	_	_	_
69	tannin	tannin	NN	_	_	_
70	_	_	NN	_	_	_
71	#	#	#	_	_	_
72	5	5	CD	_	_	_
73	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
74	Escherichia	escherichia	FW	Organism	_	_
75	coli	coli	FW	Organism	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	Escherichia	escherichia	FW	Organism	_	_
78	coli	coli	FW	Organism	_	_
79	BW13711	bw13711	NN	_	_	_
80	grown	grow	VBN	_	_	_
81	anaerobically	anaerobically	RB	_	_	_
82	in	in	IN	_	_	_
83	continuous	continuous	JJ	_	_	_
84	culture	culture	NN	_	_	_
85	in	in	IN	_	_	_
86	MOPS	MOPS	NNP	MED	_	_
87	medium	medium	NN	_	_	_
88	plus	plus	CC	_	_	_
89	0.4	0.4	CD	_	_	_
90	%	%	NN	_	_	_
91	glucose	glucose	NN	SUPP	_	_
92	with	with	IN	_	_	_
93	1	1	CD	_	_	_
94	%	%	NN	_	_	_
95	Acacia	Acacia	NNP	_	_	_
96	mearnsii	mearnsii	NN	_	_	_
97	condensed	condensed	JJ	_	_	_
98	tannins	tannin	NNS	_	_	_
99	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	BW13711	bw13711	NN	_	_	_
5	grown	grow	VBN	_	_	_
6	anaerobically	anaerobically	RB	_	_	_
7	in	in	IN	_	_	_
8	continuous	continuous	JJ	_	_	_
9	culture	culture	NN	_	_	_
10	in	in	IN	_	_	_
11	MOPS	MOPS	NNP	MED	_	_
12	medium	medium	NN	_	_	_
13	plus	plus	CC	_	_	_
14	0.4	0.4	CD	_	_	_
15	%	%	NN	_	_	_
16	glucose	glucose	NN	SUPP	_	_
17	without	without	IN	_	_	_
18	Acacia	Acacia	NNP	_	_	_
19	mearnsii	mearnsii	NN	_	_	_
20	condensed	condensed	JJ	_	_	_
21	tannins	tannin	NNS	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	BW13711	bw13711	NN	_	_	_
5	grown	grow	VBN	_	_	_
6	anaerobically	anaerobically	RB	_	_	_
7	in	in	IN	_	_	_
8	continuous	continuous	JJ	_	_	_
9	culture	culture	NN	_	_	_
10	in	in	IN	_	_	_
11	MOPS	MOPS	NNP	MED	_	_
12	medium	medium	NN	_	_	_
13	plus	plus	CC	_	_	_
14	0.4	0.4	CD	_	_	_
15	%	%	NN	_	_	_
16	glucose	glucose	NN	SUPP	_	_
17	without	without	IN	_	_	_
18	Acacia	Acacia	NNP	_	_	_
19	mearnsii	mearnsii	NN	_	_	_
20	condensed	condensed	JJ	_	_	_
21	tannins	tannin	NNS	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	continous	continous	JJ	_	_	_
5	culture	culture	NN	_	_	_
6	without	without	IN	_	_	_
7	tannins	tannin	NNS	_	_	_
8	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
9	Escherichia	escherichia	FW	Organism	_	_
10	coli	coli	FW	Organism	_	_
11	continuous	continuous	JJ	_	_	_
12	culture	culture	NN	_	_	_
13	with	with	IN	_	_	_
14	1	1	CD	_	_	_
15	%	%	NN	_	_	_
16	tannins	tannin	NNS	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	Escherichia	escherichia	FW	Organism	_	_
19	coli	coli	FW	Organism	_	_
20	with	with	IN	_	_	_
21	1	1	CD	_	_	_
22	%	%	NN	_	_	_
23	tannins	tannin	NNS	_	_	_
24	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
25	Incubation	incubation	NN	_	_	_
26	temperature	temperature	NN	_	_	_
27	=	=	JJ	_	_	_
28	37C	37c	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	pH	ph	NN	_	_	_
31	=	=	JJ	_	_	_
32	5.3	5.3	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	pH	ph	NN	_	_	_
35	=	=	JJ	_	_	_
36	5.7	5.7	CD	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	Promega	Promega	NNP	_	_	_
39	RNase-free	RNase-free	NNP	_	_	_
40	DNase	dnase	NN	_	_	_
41	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
42	Qiagen	Qiagen	NNP	_	_	_
43	Rneasy	Rneasy	NNP	_	_	_
44	mini	minus	NNS	_	_	_
45	kit	kit	NN	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	50	50	CD	_	_	_
48	bp	bp	NN	_	_	_
49	single-end	single-end	JJ	_	_	_
50	reads	read	VBZ	_	_	_
51	,	,	,	_	_	_
52	were	be	VBD	_	_	_
53	mapped	map	VBN	_	_	_
54	to	to	TO	_	_	_
55	the	the	DT	_	_	_
56	genome	genome	NN	_	_	_
57	with	with	IN	_	_	_
58	using	use	VBG	_	_	_
59	bowtie2	bowtie2	NN	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	Langmead	langmead	NN	_	_	_
62	and	and	CC	_	_	_
63	Salzberg	Salzberg	NNP	_	_	_
64	,	,	,	_	_	_
65	2012	2012	CD	_	_	_
66	-RRB-	-rrb-	-RRB-	_	_	_
67	using	use	VBG	_	_	_
68	default	default	NN	_	_	_
69	parameters	parameter	NNS	_	_	_
70	.	.	.	_	_	_

1	Alignments	alignment	NNS	_	_	_
2	with	with	IN	_	_	_
3	bowtie2	bowtie2	NN	_	_	_
4	mapping	map	VBG	_	_	_
5	quality	quality	NN	_	_	_
6	values	value	NNS	_	_	_
7	lower	lower	JJR	_	_	_
8	than	than	IN	_	_	_
9	40	40	CD	_	_	_
10	were	be	VBD	_	_	_
11	not	not	RB	_	_	_
12	retained	retain	VBN	_	_	_
13	for	for	IN	_	_	_
14	further	further	JJ	_	_	_
15	analysis	analysis	NN	_	_	_
16	,	,	,	_	_	_
17	leaving	leave	VBG	_	_	_
18	128,413,654	128,413,654	CD	_	_	_
19	and	and	CC	_	_	_
20	76,508,335	76,508,335	CD	_	_	_
21	reads	read	VBZ	_	_	_
22	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	E.	E.	NNP	_	_	_
3	coli	coli	NN	_	_	_
4	3	3	CD	_	_	_
5	'	'	''	_	_	_
6	RACE	race	NN	_	_	_
7	Rep1	rep1	JJ	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
9	E.	e.	FW	_	_	_
10	coli	coli	FW	_	_	_
11	3	3	CD	_	_	_
12	'	'	''	_	_	_
13	RACE	race	NN	_	_	_
14	Rep2	rep2	JJ	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	Escherichia	escherichia	FW	Organism	_	_
17	coli	coli	FW	Organism	_	_
18	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
19	Genome	Genome	NNP	_	_	_
20	_	_	NNP	_	_	_
21	build	build	VB	_	_	_
22	:	:	:	_	_	_
23	NC	NC	NNP	_	_	_
24	_	_	NNP	_	_	_
25	000913.3	000913.3	CD	_	_	_
26	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
27	In	in	IN	_	_	_
28	order	order	NN	_	_	_
29	to	to	TO	_	_	_
30	distinguish	distinguish	VB	_	_	_
31	between	between	IN	_	_	_
32	3	3	CD	_	_	_
33	'	'	''	_	_	_
34	ends	end	NNS	_	_	_
35	of	of	IN	_	_	_
36	transient	transient	JJ	_	_	_
37	products	product	NNS	_	_	_
38	of	of	IN	_	_	_
39	RNA	rna	NN	_	_	_
40	metabolism	metabolism	NN	_	_	_
41	and	and	CC	_	_	_
42	stable	stable	JJ	_	_	_
43	3	3	CD	_	_	_
44	'	'	''	_	_	_
45	ends	end	VBZ	_	_	_
46	,	,	,	_	_	_
47	we	we	PRP	_	_	_
48	developed	develop	VBD	_	_	_
49	an	a	DT	_	_	_
50	algorithm	algorithm	NN	_	_	_
51	to	to	TO	_	_	_
52	call	call	VB	_	_	_
53	coverage	coverage	NN	_	_	_
54	peaks	peak	NNS	_	_	_
55	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	algorithm	algorithm	NN	_	_	_
3	will	will	MD	_	_	_
4	be	be	VB	_	_	_
5	discussed	discuss	VBN	_	_	_
6	in	in	IN	_	_	_
7	detail	detail	NN	_	_	_
8	in	in	IN	_	_	_
9	an	a	DT	_	_	_
10	upcoming	upcoming	JJ	_	_	_
11	manuscript	manuscript	NN	_	_	_
12	,	,	,	_	_	_
13	and	and	CC	_	_	_
14	the	the	DT	_	_	_
15	scripts	script	NNS	_	_	_
16	used	use	VBN	_	_	_
17	are	be	VBP	_	_	_
18	available	available	JJ	_	_	_
19	upon	upon	IN	_	_	_
20	request	request	NN	_	_	_
21	from	from	IN	_	_	_
22	the	the	DT	_	_	_
23	authors	author	NNS	_	_	_
24	.	.	.	_	_	_

1	In	in	IN	_	_	_
2	short	short	RB	_	_	_
3	,	,	,	_	_	_
4	positions	position	NNS	_	_	_
5	in	in	IN	_	_	_
6	the	the	DT	_	_	_
7	E.	e.	FW	_	_	_
8	coli	coli	FW	_	_	_
9	genome	genome	NN	_	_	_
10	were	be	VBD	_	_	_
11	considered	consider	VBN	_	_	_
12	in	in	IN	_	_	_
13	descending	descend	VBG	_	_	_
14	order	order	NN	_	_	_
15	of	of	IN	_	_	_
16	coverage	coverage	NN	_	_	_
17	and	and	CC	_	_	_
18	assigned	assign	VBN	_	_	_
19	a	a	DT	_	_	_
20	p-value	p-value	NN	_	_	_
21	based	base	VBN	_	_	_
22	on	on	IN	_	_	_
23	a	a	DT	_	_	_
24	Poisson	Poisson	NNP	_	_	_
25	distribution	distribution	NN	_	_	_
26	parameterized	parameterize	VBN	_	_	_
27	by	by	IN	_	_	_
28	the	the	DT	_	_	_
29	mean	mean	NN	_	_	_
30	coverage	coverage	NN	_	_	_
31	of	of	IN	_	_	_
32	all	all	DT	_	_	_
33	covered	cover	VBN	_	_	_
34	bases	basis	NNS	_	_	_
35	in	in	IN	_	_	_
36	the	the	DT	_	_	_
37	genome	genome	NN	_	_	_
38	.	.	.	_	_	_

1	Peaks	peak	NNS	_	_	_
2	were	be	VBD	_	_	_
3	rejected	reject	VBN	_	_	_
4	if	if	IN	_	_	_
5	their	they	PRP$	_	_	_
6	p-values	p-value	NNS	_	_	_
7	exceeded	exceed	VBD	_	_	_
8	1e-4	1e-4	NN	_	_	_
9	or	or	CC	_	_	_
10	if	if	IN	_	_	_
11	there	there	EX	_	_	_
12	existed	exist	VBD	_	_	_
13	a	a	DT	_	_	_
14	>	>	JJR	_	_	_
15	10-bp	10-bp	JJ	_	_	_
16	window	window	NN	_	_	_
17	containing	contain	VBG	_	_	_
18	the	the	DT	_	_	_
19	peak	peak	NN	_	_	_
20	in	in	IN	_	_	_
21	which	which	WDT	_	_	_
22	all	all	DT	_	_	_
23	positions	position	NNS	_	_	_
24	were	be	VBD	_	_	_
25	within	within	IN	_	_	_
26	2-fold	2-fold	JJ	_	_	_
27	coverage	coverage	NN	_	_	_
28	of	of	IN	_	_	_
29	the	the	DT	_	_	_
30	peak	peak	JJ	_	_	_
31	position	position	NN	_	_	_
32	.	.	.	_	_	_

1	Parameters	parameter	NNS	_	_	_
2	were	be	VBD	_	_	_
3	chosen	choose	VBN	_	_	_
4	based	base	VBN	_	_	_
5	on	on	IN	_	_	_
6	analysis	analysis	NN	_	_	_
7	of	of	IN	_	_	_
8	annotated	annotated	JJ	_	_	_
9	3	3	CD	_	_	_
10	'	'	''	_	_	_
11	ends	end	VBZ	_	_	_
12	as	as	RB	_	_	_
13	well	well	RB	_	_	_
14	as	as	IN	_	_	_
15	qualitative	qualitative	JJ	_	_	_
16	analysis	analysis	NN	_	_	_
17	of	of	IN	_	_	_
18	peaks	peak	NNS	_	_	_
19	.	.	.	_	_	_

1	This	this	DT	_	_	_
2	resulted	result	VBD	_	_	_
3	in	in	IN	_	_	_
4	20,019	20,019	CD	_	_	_
5	peaks	peak	NNS	_	_	_
6	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA-Seq	rna-seq	NN	_	_	_
3	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
4	strain	strain	NN	_	_	_
5	:	:	:	_	_	_
6	K12	k12	NN	_	_	_
7	MG1655	mg1655	NN	_	_	_
8	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
9	Supplementary	supplementary	JJ	_	_	_
10	_	_	NN	_	_	_
11	files	file	NNS	_	_	_
12	_	_	IN	_	_	_
13	format	format	NN	_	_	_
14	_	_	NN	_	_	_
15	and	and	CC	_	_	_
16	_	_	NN	_	_	_
17	content	content	NN	_	_	_
18	:	:	:	_	_	_
19	BIGWIG	bigwig	NN	_	_	_
20	file	file	NN	_	_	_
21	containing	contain	VBG	_	_	_
22	coverage	coverage	NN	_	_	_
23	tracks	track	NNS	_	_	_
24	from	from	IN	_	_	_
25	3	3	CD	_	_	_
26	'	'	''	_	_	_
27	RACE	race	NN	_	_	_
28	data	datum	NNS	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	Supplementary	supplementary	JJ	_	_	_
31	_	_	NN	_	_	_
32	files	file	NNS	_	_	_
33	_	_	IN	_	_	_
34	format	format	NN	_	_	_
35	_	_	NN	_	_	_
36	and	and	CC	_	_	_
37	_	_	NN	_	_	_
38	content	content	NN	_	_	_
39	:	:	:	_	_	_
40	GFF	gff	NN	_	_	_
41	file	file	NN	_	_	_
42	containing	contain	VBG	_	_	_
43	3	3	CD	_	_	_
44	'	'	''	_	_	_
45	end	end	NN	_	_	_
46	annotations	annotation	NNS	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	JJ	_	_	_
48	total	total	JJ	_	_	_
49	DNaseI	dnasei	NN	_	_	_
50	treated	treat	VBN	_	_	_
51	RNA	rna	NN	_	_	_
52	was	be	VBD	_	_	_
53	depleted	deplete	VBN	_	_	_
54	of	of	IN	_	_	_
55	ribosomal	ribosomal	JJ	_	_	_
56	RNA	rna	NN	_	_	_
57	using	use	VBG	_	_	_
58	the	the	DT	_	_	_
59	Ribo-Zero	Ribo-Zero	NNP	_	_	_
60	™	™	NN	_	_	_
61	RNA	rna	NN	_	_	_
62	removal	removal	NN	_	_	_
63	kit	kit	NN	_	_	_
64	for	for	IN	_	_	_
65	Gram-negative	gram-negative	JJ	_	_	_
66	bacteria	bacterium	NNS	_	_	_
67	-LRB-	-lrb-	-LRB-	_	_	_
68	Epicentre	Epicentre	NNP	_	_	_
69	-RRB-	-rrb-	-RRB-	_	_	_
70	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	3	3	CD	_	_	_
3	'	'	''	_	_	_
4	RNA	rna	NN	_	_	_
5	adapter	adapter	NN	_	_	_
6	,	,	,	_	_	_
7	based	base	VBN	_	_	_
8	on	on	IN	_	_	_
9	the	the	DT	_	_	_
10	Illumina	Illumina	NNP	_	_	_
11	multiplexing	multiplex	VBG	_	_	_
12	adapter	adapter	NN	_	_	_
13	sequence	sequence	NN	_	_	_
14	-LRB-	-lrb-	-LRB-	_	_	_
15	Oligonucleotide	oligonucleotide	NN	_	_	_
16	sequences	sequence	NNS	_	_	_
17	©	©	SYM	_	_	_
18	2007-2014	2007-2014	CD	_	_	_
19	Illumina	Illumina	NNP	_	_	_
20	,	,	,	_	_	_
21	Inc.	Inc.	NNP	_	_	_
22	.	.	.	_	_	_

1	All	all	DT	_	_	_
2	rights	rights	NNS	_	_	_
3	reserved	reserve	VBN	_	_	_
4	-RRB-	-rrb-	-RRB-	_	_	_
5	blocked	block	VBD	_	_	_
6	at	at	IN	_	_	_
7	the	the	DT	_	_	_
8	3	3	CD	_	_	_
9	'	'	''	_	_	_
10	end	end	NN	_	_	_
11	with	with	IN	_	_	_
12	an	a	DT	_	_	_
13	inverted	inverted	JJ	_	_	_
14	dT	dt	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	5	5	CD	_	_	_
17	'	'	''	_	_	_
18	-	-	:	_	_	_
19	GAUCGGAAGAGCACACGUCU	gaucggaagagcacacgucu	NN	_	_	_
20	-LSB-	-lsb-	-LRB-	_	_	_
21	idT	idt	NN	_	_	_
22	-RSB-	-rsb-	-RRB-	_	_	_
23	-3	-3	CD	_	_	_
24	'	'	''	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	,	,	,	_	_	_
27	was	be	VBD	_	_	_
28	phosphorylated	phosphorylate	VBN	_	_	_
29	at	at	IN	_	_	_
30	the	the	DT	_	_	_
31	5	5	CD	_	_	_
32	'	'	''	_	_	_
33	end	end	NN	_	_	_
34	using	use	VBG	_	_	_
35	T4	t4	NN	_	_	_
36	PNK	pnk	NN	_	_	_
37	-LRB-	-lrb-	-LRB-	_	_	_
38	New	New	NNP	_	_	_
39	England	England	NNP	_	_	_
40	Biolabs	Biolabs	NNP	_	_	_
41	-RRB-	-rrb-	-RRB-	_	_	_
42	per	per	IN	_	_	_
43	the	the	DT	_	_	_
44	manufacturer	manufacturer	NN	_	_	_
45	's	's	POS	_	_	_
46	protocol	protocol	NN	_	_	_
47	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	3	3	CD	_	_	_
3	'	'	''	_	_	_
4	RNA	rna	NN	_	_	_
5	adapter	adapter	NN	_	_	_
6	was	be	VBD	_	_	_
7	ligated	ligate	VBN	_	_	_
8	to	to	TO	_	_	_
9	the	the	DT	_	_	_
10	3	3	CD	_	_	_
11	'	'	''	_	_	_
12	ends	end	NNS	_	_	_
13	of	of	IN	_	_	_
14	the	the	DT	_	_	_
15	rRNA	rrna	NN	_	_	_
16	depleted	deplete	VBN	_	_	_
17	RNA	rna	NN	_	_	_
18	using	use	VBG	_	_	_
19	T4	t4	NN	_	_	_
20	RNA	rna	NN	_	_	_
21	ligase	ligase	NN	_	_	_
22	I	i	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	New	New	NNP	_	_	_
25	England	England	NNP	_	_	_
26	Biolabs	Biolabs	NNP	_	_	_
27	-RRB-	-rrb-	-RRB-	_	_	_
28	.	.	.	_	_	_

1	1.5	1.5	CD	_	_	_
2	mg	mg	NN	_	_	_
3	of	of	IN	_	_	_
4	RNA	rna	NN	_	_	_
5	was	be	VBD	_	_	_
6	incubated	incubate	VBN	_	_	_
7	at	at	IN	_	_	_
8	20	20	CD	_	_	_
9	°C	°c	NN	_	_	_
10	for	for	IN	_	_	_
11	6	6	CD	_	_	_
12	hours	hour	NNS	_	_	_
13	in	in	IN	_	_	_
14	1X	1x	NN	_	_	_
15	T4	t4	NN	_	_	_
16	RNA	rna	NN	_	_	_
17	ligase	ligase	NN	_	_	_
18	reaction	reaction	NN	_	_	_
19	buffer	buffer	NN	_	_	_
20	with	with	IN	_	_	_
21	1	1	CD	_	_	_
22	mM	mm	NN	KWSUPP	_	_
23	ATP	atp	NN	SUPP	_	_
24	,	,	,	_	_	_
25	30	30	CD	_	_	_
26	µM	µm	NN	_	_	_
27	3	3	CD	_	_	_
28	'	'	''	_	_	_
29	RNA	rna	NN	_	_	_
30	adapter	adapter	NN	_	_	_
31	,	,	,	_	_	_
32	10	10	CD	_	_	_
33	%	%	NN	_	_	_
34	DMSO	dmso	NN	_	_	_
35	,	,	,	_	_	_
36	10	10	CD	_	_	_
37	U	u	NN	_	_	_
38	of	of	IN	_	_	_
39	T4	t4	NN	_	_	_
40	RNA	rna	NN	_	_	_
41	ligase	ligase	NN	_	_	_
42	I	I	PRP	_	_	_
43	,	,	,	_	_	_
44	and	and	CC	_	_	_
45	40	40	CD	_	_	_
46	U	u	NN	_	_	_
47	of	of	IN	_	_	_
48	RNasin	rnasin	NN	_	_	_
49	-LRB-	-lrb-	-LRB-	_	_	_
50	Promega	promega	NN	_	_	_
51	-RRB-	-rrb-	-RRB-	_	_	_
52	in	in	IN	_	_	_
53	a	a	DT	_	_	_
54	20	20	CD	_	_	_
55	ml	ml	NN	_	_	_
56	reaction	reaction	NN	_	_	_
57	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	then	then	RB	_	_	_
4	fragmented	fragmented	JJ	_	_	_
5	in	in	IN	_	_	_
6	equivalents	equivalent	NNS	_	_	_
7	of	of	IN	_	_	_
8	100	100	CD	_	_	_
9	ng	ng	NN	_	_	_
10	using	use	VBG	_	_	_
11	the	the	DT	_	_	_
12	RNA	rna	NN	_	_	_
13	fragmentation	fragmentation	NN	_	_	_
14	reagents	reagent	NNS	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	Ambion	Ambion	NNP	_	_	_
17	®	®	NNP	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	per	per	IN	_	_	_
20	the	the	DT	_	_	_
21	manufacturer	manufacturer	NN	_	_	_
22	's	's	POS	_	_	_
23	protocol	protocol	NN	_	_	_
24	at	at	IN	_	_	_
25	70	70	CD	_	_	_
26	°C	°c	NN	_	_	_
27	for	for	IN	_	_	_
28	3	3	CD	_	_	_
29	min	min	NN	_	_	_
30	and	and	CC	_	_	_
31	subsequently	subsequently	RB	_	_	_
32	phosphorylated	phosphorylate	VBN	_	_	_
33	at	at	IN	_	_	_
34	the	the	DT	_	_	_
35	5	5	CD	_	_	_
36	'	'	''	_	_	_
37	ends	end	VBZ	_	_	_
38	using	use	VBG	_	_	_
39	T4	t4	NN	_	_	_
40	PNK	pnk	NN	_	_	_
41	-LRB-	-lrb-	-LRB-	_	_	_
42	New	New	NNP	_	_	_
43	England	England	NNP	_	_	_
44	Biolabs	Biolabs	NNP	_	_	_
45	-RRB-	-rrb-	-RRB-	_	_	_
46	per	per	IN	_	_	_
47	the	the	DT	_	_	_
48	manufacturer	manufacturer	NN	_	_	_
49	's	's	POS	_	_	_
50	protocol	protocol	NN	_	_	_
51	to	to	TO	_	_	_
52	allow	allow	VB	_	_	_
53	for	for	IN	_	_	_
54	ligation	ligation	NN	_	_	_
55	of	of	IN	_	_	_
56	the	the	DT	_	_	_
57	5	5	CD	_	_	_
58	'	'	''	_	_	_
59	adapter	adapter	NN	_	_	_
60	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	size-selected	size-selected	JJ	_	_	_
4	-LRB-	-lrb-	-LRB-	_	_	_
5	≈	≈	JJ	_	_	_
6	150-300	150-300	CD	_	_	_
7	nt	nt	NNS	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	and	and	CC	_	_	_
10	purified	purify	VBN	_	_	_
11	over	over	IN	_	_	_
12	a	a	DT	_	_	_
13	denaturing	denature	VBG	_	_	_
14	8	8	CD	_	_	_
15	%	%	NN	_	_	_
16	polyacrylamide	polyacrylamide	NN	_	_	_
17	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
18	Total	Total	NNP	_	_	_
19	RNA	rna	NN	_	_	_
20	was	be	VBD	_	_	_
21	isolated	isolate	VBN	_	_	_
22	using	use	VBG	_	_	_
23	the	the	DT	_	_	_
24	hot	hot	JJ	_	_	_
25	phenol	phenol	NN	_	_	_
26	method	method	NN	_	_	_
27	as	as	IN	_	_	_
28	described	describe	VBN	_	_	_
29	in	in	IN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	Lybecker	Lybecker	NNP	_	_	_
32	et	et	FW	_	_	_
33	al.	al.	FW	_	_	_
34	,	,	,	_	_	_
35	2014	2014	CD	_	_	_
36	-RRB-	-rrb-	-RRB-	_	_	_
37	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	0x58	0x58	NN	_	_	_
3	replicate	replicate	VBP	_	_	_
4	2	2	CD	_	_	_
5	state	state	NN	_	_	_
6	1	1	CD	_	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	IPTG	iptg	SYM	_	_	_
9	-	-	:	_	_	_
10	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
11	0x58	0x58	NN	_	_	_
12	replicate	replicate	VBP	_	_	_
13	2	2	CD	_	_	_
14	state	state	NN	_	_	_
15	2	2	CD	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	IPTG	iptg	NN	_	_	_
18	+	+	CC	_	_	_
19	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
20	0x58	0x58	NN	_	_	_
21	replicate	replicate	VBP	_	_	_
22	2	2	CD	_	_	_
23	state	state	NN	_	_	_
24	3	3	CD	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	IPTG	iptg	SYM	_	_	_
27	-	-	:	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	0x58	0x58	NN	_	_	_
30	replicate	replicate	VBP	_	_	_
31	2	2	CD	_	_	_
32	state	state	NN	_	_	_
33	4	4	CD	_	_	_
34	-LRB-	-lrb-	-LRB-	_	_	_
35	IPTG	iptg	NN	_	_	_
36	+	+	CC	_	_	_
37	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
38	0x58	0x58	NN	_	_	_
39	replicate	replicate	VBP	_	_	_
40	2	2	CD	_	_	_
41	state	state	NN	_	_	_
42	5	5	CD	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	IPTG	iptg	SYM	_	_	_
45	-	-	:	_	_	_
46	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
47	0x58	0x58	NN	_	_	_
48	replicate	replicate	VBP	_	_	_
49	2	2	CD	_	_	_
50	state	state	NN	_	_	_
51	6	6	CD	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	IPTG	iptg	NN	_	_	_
54	+	+	CC	_	_	_
55	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
56	0x58	0x58	NN	_	_	_
57	replicate	replicate	VBP	_	_	_
58	2	2	CD	_	_	_
59	state	state	NN	_	_	_
60	7	7	CD	_	_	_
61	-LRB-	-lrb-	-LRB-	_	_	_
62	IPTG	iptg	SYM	_	_	_
63	-	-	:	_	_	_
64	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
65	0x58	0x58	NN	_	_	_
66	replicate	replicate	VBP	_	_	_
67	2	2	CD	_	_	_
68	state	state	NN	_	_	_
69	8	8	CD	_	_	_
70	-LRB-	-lrb-	-LRB-	_	_	_
71	IPTG	iptg	NN	_	_	_
72	+	+	CC	_	_	_
73	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
74	0x58	0x58	NN	_	_	_
75	replicate	replicate	VBP	_	_	_
76	3	3	CD	_	_	_
77	state	state	NN	_	_	_
78	1	1	CD	_	_	_
79	-LRB-	-lrb-	-LRB-	_	_	_
80	IPTG	iptg	SYM	_	_	_
81	-	-	:	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	0x58	0x58	NN	_	_	_
84	replicate	replicate	VBP	_	_	_
85	3	3	CD	_	_	_
86	state	state	NN	_	_	_
87	2	2	CD	_	_	_
88	-LRB-	-lrb-	-LRB-	_	_	_
89	IPTG	iptg	NN	_	_	_
90	+	+	CC	_	_	_
91	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
92	0x58	0x58	NN	_	_	_
93	replicate	replicate	VBP	_	_	_
94	3	3	CD	_	_	_
95	state	state	NN	_	_	_
96	3	3	CD	_	_	_
97	-LRB-	-lrb-	-LRB-	_	_	_
98	IPTG	iptg	SYM	_	_	_
99	-	-	:	_	_	_
100	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
101	0x58	0x58	NN	_	_	_
102	replicate	replicate	VBP	_	_	_
103	3	3	CD	_	_	_
104	state	state	NN	_	_	_
105	4	4	CD	_	_	_
106	-LRB-	-lrb-	-LRB-	_	_	_
107	IPTG	iptg	NN	_	_	_
108	+	+	CC	_	_	_
109	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
110	0x58	0x58	NN	_	_	_
111	replicate	replicate	VBP	_	_	_
112	3	3	CD	_	_	_
113	state	state	NN	_	_	_
114	5	5	CD	_	_	_
115	-LRB-	-lrb-	-LRB-	_	_	_
116	IPTG	iptg	SYM	_	_	_
117	-	-	:	_	_	_
118	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
119	0x58	0x58	NN	_	_	_
120	replicate	replicate	VBP	_	_	_
121	3	3	CD	_	_	_
122	state	state	NN	_	_	_
123	6	6	CD	_	_	_
124	-LRB-	-lrb-	-LRB-	_	_	_
125	IPTG	iptg	NN	_	_	_
126	+	+	CC	_	_	_
127	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
128	0x58	0x58	NN	_	_	_
129	replicate	replicate	VBP	_	_	_
130	3	3	CD	_	_	_
131	state	state	NN	_	_	_
132	7	7	CD	_	_	_
133	-LRB-	-lrb-	-LRB-	_	_	_
134	IPTG	iptg	SYM	_	_	_
135	-	-	:	_	_	_
136	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
137	0x58	0x58	NN	_	_	_
138	replicate	replicate	VBP	_	_	_
139	3	3	CD	_	_	_
140	state	state	NN	_	_	_
141	8	8	CD	_	_	_
142	-LRB-	-lrb-	-LRB-	_	_	_
143	IPTG	iptg	NN	_	_	_
144	+	+	CC	_	_	_
145	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
146	Control	Control	NNP	_	_	_
147	pAN1201	pan1201	NN	_	_	_
148	replicate	replicate	VB	_	_	_
149	1	1	CD	_	_	_
150	-LRB-	-lrb-	-LRB-	_	_	_
151	IPTG	iptg	SYM	_	_	_
152	-	-	:	_	_	_
153	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
154	Control	Control	NNP	_	_	_
155	pAN1201	pan1201	NN	_	_	_
156	replicate	replicate	VB	_	_	_
157	2	2	CD	_	_	_
158	-LRB-	-lrb-	-LRB-	_	_	_
159	IPTG	iptg	SYM	_	_	_
160	-	-	:	_	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	Culture	culture	NN	_	_	_
163	grown	grow	VBN	_	_	_
164	in	in	IN	_	_	_
165	14	14	CD	_	_	_
166	ml	ml	NN	_	_	_
167	tube	tube	NN	_	_	_
168	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
169	Cultures	culture	NNS	_	_	_
170	were	be	VBD	_	_	_
171	spun	spin	VBN	_	_	_
172	down	down	RP	_	_	_
173	at	at	IN	_	_	_
174	4	4	CD	_	_	_
175	°C	°c	NN	_	_	_
176	,	,	,	_	_	_
177	15,000	15,000	CD	_	_	_
178	×	×	CD	_	_	_
179	g	g	NN	_	_	_
180	for	for	IN	_	_	_
181	3	3	CD	_	_	_
182	minutes	minute	NNS	_	_	_
183	.	.	.	_	_	_

1	Supernatants	supernatant	NNS	_	_	_
2	were	be	VBD	_	_	_
3	discarded	discard	VBN	_	_	_
4	after	after	IN	_	_	_
5	centrifugation	centrifugation	NN	_	_	_
6	and	and	CC	_	_	_
7	cell	cell	NN	_	_	_
8	pellets	pellet	NNS	_	_	_
9	were	be	VBD	_	_	_
10	flash	flash	NN	_	_	_
11	frozen	freeze	VBN	_	_	_
12	in	in	IN	_	_	_
13	liquid	liquid	JJ	_	_	_
14	nitrogen	nitrogen	NN	_	_	_
15	for	for	IN	_	_	_
16	storage	storage	NN	_	_	_
17	at	at	IN	_	_	_
18	-80	-80	CD	_	_	_
19	°C	°c	NN	_	_	_
20	.	.	.	_	_	_

1	Cells	cell	NNS	_	_	_
2	were	be	VBD	_	_	_
3	lysed	lyse	VBN	_	_	_
4	with	with	IN	_	_	_
5	1	1	CD	_	_	_
6	mg	mg	NN	_	_	_
7	of	of	IN	_	_	_
8	lysozme	lysozme	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Sigma	Sigma	NNP	_	_	_
11	Aldrich	Aldrich	NNP	_	_	_
12	L6871	L6871	NNP	_	_	_
13	-RRB-	-rrb-	-RRB-	_	_	_
14	in	in	IN	_	_	_
15	10	10	CD	_	_	_
16	mM	mm	NN	KWSUPP	_	_
17	Tris-HCl	tris-hcl	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	pH	ph	NN	_	_	_
20	8.0	8.0	CD	_	_	_
21	-RRB-	-rrb-	-RRB-	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	USB	usb	JJ	_	_	_
24	75825	75825	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	supplemented	supplement	VBN	_	_	_
27	with	with	IN	_	_	_
28	0.1	0.1	CD	_	_	_
29	mM	mm	NN	KWSUPP	_	_
30	EDTA	edta	NN	_	_	_
31	-LRB-	-lrb-	-LRB-	_	_	_
32	USB	usb	JJ	_	_	_
33	15694	15694	CD	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	.	.	.	_	_	_

1	RNA	rna	NN	_	_	_
2	was	be	VBD	_	_	_
3	extracted	extract	VBN	_	_	_
4	with	with	IN	_	_	_
5	PureLink	purelink	NN	_	_	_
6	RNA	rna	NN	_	_	_
7	Mini	Mini	NNP	_	_	_
8	Kit	kit	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Life	Life	NNP	_	_	_
11	Technologies	Technologies	NNPS	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	further	further	JJ	_	_	_
15	purified	purify	VBN	_	_	_
16	and	and	CC	_	_	_
17	concentrated	concentrate	VBN	_	_	_
18	with	with	IN	_	_	_
19	RNA	rna	NN	_	_	_
20	Clean	Clean	NNP	_	_	_
21	&	&	CC	_	_	_
22	Concentrator-5	Concentrator-5	NNP	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Zymo	Zymo	NNP	_	_	_
25	Research	Research	NNP	_	_	_
26	-RRB-	-rrb-	-RRB-	_	_	_
27	to	to	TO	_	_	_
28	assure	assure	VB	_	_	_
29	sample	sample	NN	_	_	_
30	quality	quality	NN	_	_	_
31	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	purified	purify	VBN	_	_	_
3	RNA	rna	NN	_	_	_
4	samples	sample	NNS	_	_	_
5	were	be	VBD	_	_	_
6	analyzed	analyze	VBN	_	_	_
7	using	use	VBG	_	_	_
8	a	a	DT	_	_	_
9	Bioanalyzer	Bioanalyzer	NNP	_	_	_
10	-LRB-	-lrb-	-LRB-	_	_	_
11	Agilent	Agilent	NNP	_	_	_
12	-RRB-	-rrb-	-RRB-	_	_	_
13	and	and	CC	_	_	_
14	Ribo-Zero	Ribo-Zero	NNP	_	_	_
15	rRNA	rrna	NN	_	_	_
16	Removal	removal	NN	_	_	_
17	Kit	kit	NN	_	_	_
18	for	for	IN	_	_	_
19	bacteria	bacterium	NNS	_	_	_
20	-LRB-	-lrb-	-LRB-	_	_	_
21	Illumina	Illumina	NNP	_	_	_
22	-RRB-	-rrb-	-RRB-	_	_	_
23	was	be	VBD	_	_	_
24	used	use	VBN	_	_	_
25	to	to	TO	_	_	_
26	deplete	deplete	VB	_	_	_
27	rRNA	rrna	NN	_	_	_
28	from	from	IN	_	_	_
29	the	the	DT	_	_	_
30	samples	sample	NNS	_	_	_
31	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Escherichia	escherichia	FW	Organism	_	_
3	coli	coli	FW	Organism	_	_
4	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
5	Genome	Genome	NNP	_	_	_
6	_	_	NNP	_	_	_
7	build	build	VB	_	_	_
8	:	:	:	_	_	_
9	NC	NC	NNP	_	_	_
10	_	_	NNP	_	_	_
11	010473.1	010473.1	CD	_	_	_
12	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
13	Individual	Individual	NNP	_	_	_
14	colonies	colony	NNS	_	_	_
15	were	be	VBD	_	_	_
16	inoculated	inoculate	VBN	_	_	_
17	into	into	IN	_	_	_
18	MOPS	MOPS	NNP	MED	_	_
19	EZ	EZ	NNP	_	_	_
20	Rich	Rich	NNP	_	_	_
21	Defined	Defined	NNP	_	_	_
22	Medium	medium	NN	_	_	_
23	-LRB-	-lrb-	-LRB-	_	_	_
24	Teknova	teknova	NN	_	_	_
25	,	,	,	_	_	_
26	CA	CA	NNP	_	_	_
27	,	,	,	_	_	_
28	M2105	m2105	NN	_	_	_
29	-RRB-	-rrb-	-RRB-	_	_	_
30	with	with	IN	_	_	_
31	0.2	0.2	CD	_	_	_
32	%	%	NN	_	_	_
33	glycerol	glycerol	NN	SUPP	_	_
34	carbon	carbon	NN	_	_	_
35	source	source	NN	_	_	_
36	and	and	CC	_	_	_
37	50	50	CD	_	_	_
38	μg	μg	NN	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	Normalized	normalize	VBN	_	_	_
41	FPKM	fpkm	NN	_	_	_
42	values	value	NNS	_	_	_
43	were	be	VBD	_	_	_
44	generated	generate	VBN	_	_	_
45	from	from	IN	_	_	_
46	the	the	DT	_	_	_
47	raw	raw	JJ	_	_	_
48	gene	gene	NN	_	_	_
49	counts	count	NNS	_	_	_
50	by	by	IN	_	_	_
51	custom	custom	NN	_	_	_
52	scripts	script	NNS	_	_	_
53	that	that	WDT	_	_	_
54	calculated	calculate	VBD	_	_	_
55	and	and	CC	_	_	_
56	applied	apply	VBD	_	_	_
57	a	a	DT	_	_	_
58	trimmed	trimmed	RBR	_	_	_
59	mean	mean	VB	_	_	_
60	of	of	IN	_	_	_
61	M-values	m-value	NNS	_	_	_
62	-LRB-	-lrb-	-LRB-	_	_	_
63	TMM	tmm	NN	_	_	_
64	-RRB-	-rrb-	-RRB-	_	_	_
65	factor	factor	NN	_	_	_
66	using	use	VBG	_	_	_
67	edgeR	edger	NN	_	_	_
68	version	version	NN	_	_	_
69	3.8.6	3.8.6	CD	_	_	_
70	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Read	Read	NNP	_	_	_
3	counts	count	VBZ	_	_	_
4	for	for	IN	_	_	_
5	each	each	DT	_	_	_
6	host	host	NN	_	_	_
7	and	and	CC	_	_	_
8	circuit	circuit	NN	_	_	_
9	gene	gene	NN	_	_	_
10	was	be	VBD	_	_	_
11	carried	carry	VBN	_	_	_
12	out	out	RP	_	_	_
13	using	use	VBG	_	_	_
14	the	the	DT	_	_	_
15	htseq-count	htseq-count	JJ	_	_	_
16	command	command	NN	_	_	_
17	of	of	IN	_	_	_
18	the	the	DT	_	_	_
19	HTSeq	htseq	NN	_	_	_
20	toolkit	toolkit	NN	_	_	_
21	with	with	IN	_	_	_
22	user-defined	user-defined	JJ	_	_	_
23	GFF	gff	NN	_	_	_
24	annotations	annotation	NNS	_	_	_
25	of	of	IN	_	_	_
26	the	the	DT	_	_	_
27	reference	reference	NN	_	_	_
28	sequences	sequence	NNS	_	_	_
29	and	and	CC	_	_	_
30	the	the	DT	_	_	_
31	options	option	NNS	_	_	_
32	'	'	POS	_	_	_
33	-	-	:	_	_	_
34	s	s	NNS	_	_	_
35	reverse	reverse	JJ	_	_	_
36	-	-	:	_	_	_
37	a	a	DT	_	_	_
38	10	10	CD	_	_	_
39	-	-	:	_	_	_
40	m	m	NN	_	_	_
41	union	union	NN	_	_	_
42	'	'	''	_	_	_
43	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Reads	read	VBZ	_	_	_
3	mapped	map	VBN	_	_	_
4	to	to	TO	_	_	_
5	reference	reference	NN	_	_	_
6	using	use	VBG	_	_	_
7	BWA	bwa	NN	_	_	_
8	versiopn	versiopn	NN	_	_	_
9	0.7.4	0.7.4	CD	_	_	_
10	with	with	IN	_	_	_
11	default	default	NN	_	_	_
12	settings	setting	NNS	_	_	_
13	PGCGROWTHCONDITIONS	pgcgrowthcondition	VBP	_	_	_
14	RNA-Seq	rna-seq	JJ	_	_	_
15	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
16	strain	strain	NN	_	_	_
17	:	:	:	_	_	_
18	NEB	NEB	NNP	_	_	_
19	10-beta	10-beta	JJ	_	_	_
20	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
21	Strand	strand	NN	_	_	_
22	specific	specific	JJ	_	_	_
23	RNAtag-seq	rnatag-seq	NN	_	_	_
24	libraries	library	NNS	_	_	_
25	were	be	VBD	_	_	_
26	created	create	VBN	_	_	_
27	by	by	IN	_	_	_
28	the	the	DT	_	_	_
29	Broad	Broad	NNP	_	_	_
30	Technology	Technology	NNP	_	_	_
31	Labs	Labs	NNPS	_	_	_
32	specialized	specialized	JJ	_	_	_
33	service	service	NN	_	_	_
34	facility	facility	NN	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	SSF	ssf	NN	_	_	_
37	-RRB-	-rrb-	-RRB-	_	_	_
38	using	use	VBG	_	_	_
39	the	the	DT	_	_	_
40	standard	standard	JJ	_	_	_
41	protocol	protocol	NN	_	_	_
42	described	describe	VBN	_	_	_
43	in	in	IN	_	_	_
44	Shishkin	Shishkin	NNP	_	_	_
45	et	et	FW	_	_	_
46	al.	al.	FW	_	_	_
47	.	.	.	_	_	_

1	Nature	Nature	NNP	_	_	_
2	Methods	method	NNS	_	_	_
3	2016	2016	CD	_	_	_
4	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
2	Supplementary	Supplementary	NNP	_	_	_
3	_	_	VBD	_	_	_
4	files	file	NNS	_	_	_
5	_	_	IN	_	_	_
6	format	format	NN	_	_	_
7	_	_	NN	_	_	_
8	and	and	CC	_	_	_
9	_	_	NN	_	_	_
10	content	content	NN	_	_	_
11	:	:	:	_	_	_
12	CSV	CSV	NNP	_	_	_
13	files	file	NNS	_	_	_
14	of	of	IN	_	_	_
15	raw	raw	JJ	_	_	_
16	read	read	NN	_	_	_
17	counts	count	NNS	_	_	_
18	and	and	CC	_	_	_
19	normalized	normalize	VBN	_	_	_
20	gene	gene	NN	_	_	_
21	expression	expression	NN	_	_	_
22	in	in	IN	_	_	_
23	FPKM	FPKM	NNP	_	_	_
24	units	unit	NNS	_	_	_
25	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	BW25113	bw25113	NN	_	_	_
3	luxS	luxs	NN	GEN	_	_
4	LB	lb	NN	_	_	_
5	30C	30c	CD	_	_	_
6	free-living	free-living	JJ	_	_	_
7	cells	cell	NNS	_	_	_
8	100	100	CD	_	_	_
9	uM	um	NN	_	_	_
10	AI2	ai2	NN	_	_	_
11	3h	3h	VBP	_	_	_
12	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
13	BW25113	bw25113	NN	_	_	_
14	luxS	luxs	NN	GEN	_	_
15	LB	lb	NN	_	_	_
16	30C	30c	CD	_	_	_
17	free-living	free-living	JJ	_	_	_
18	cells	cell	NNS	_	_	_
19	no	no	DT	_	_	_
20	AI2	ai2	NN	_	_	_
21	for	for	IN	_	_	_
22	3h	3h	JJ	_	_	_
23	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
24	BW25113	bw25113	NN	_	_	_
25	luxS	luxs	NN	GEN	_	_
26	LB	lb	NN	_	_	_
27	37C	37c	NN	_	_	_
28	free-living	free-living	JJ	_	_	_
29	cells	cell	NNS	_	_	_
30	100	100	CD	_	_	_
31	uM	um	NN	_	_	_
32	AI2	ai2	NN	_	_	_
33	3h	3h	VBP	_	_	_
34	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
35	BW25113	bw25113	NN	_	_	_
36	luxS	luxs	NN	GEN	_	_
37	LB	lb	NN	_	_	_
38	37C	37c	NN	_	_	_
39	free-living	free-living	JJ	_	_	_
40	cells	cell	NNS	_	_	_
41	no	no	DT	_	_	_
42	AI2	ai2	NN	_	_	_
43	3h	3h	NN	_	_	_
44	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
45	BW25113	bw25113	NN	_	_	_
46	sdiA	sdia	NN	GEN	_	_
47	LB	lb	NN	_	_	_
48	30C	30c	NN	_	_	_
49	OD	od	NN	_	_	_
50	4.0	4.0	CD	_	_	_
51	free-living	free-living	JJ	_	_	_
52	cells	cell	NNS	_	_	_
53	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
54	BW25113	bw25113	NN	_	_	_
55	sdiA	sdia	NN	GEN	_	_
56	mutant	mutant	JJ	_	_	_
57	LB	lb	NN	_	_	_
58	with	with	IN	_	_	_
59	1	1	CD	_	_	_
60	mM	mm	NN	KWSUPP	_	_
61	indole	indole	NN	_	_	_
62	7-h	7-h	JJ	_	_	_
63	30C	30c	NN	_	_	_
64	biofilm	biofilm	NN	_	_	_
65	cell	cell	NN	_	_	_
66	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
67	BW25113	bw25113	NN	_	_	_
68	sdiA	sdia	NN	GEN	_	_
69	mutant	mutant	JJ	_	_	_
70	LB	lb	NN	_	_	_
71	with	with	IN	_	_	_
72	DMF	dmf	NN	_	_	_
73	7-h	7-h	JJ	_	_	_
74	30C	30c	NN	_	_	_
75	biofilm	biofilm	NN	_	_	_
76	cell	cell	NN	_	_	_
77	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
78	BW25113	bw25113	NN	_	_	_
79	tnaA	tnaa	NN	GEN	_	_
80	Biofilm	biofilm	NN	_	_	_
81	100	100	CD	_	_	_
82	uM	um	NN	_	_	_
83	indole	indole	FW	_	_	_
84	7h	7h	FW	_	_	_
85	LB	lb	NN	_	_	_
86	30C	30c	NN	_	_	_
87	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
88	BW25113	bw25113	NN	_	_	_
89	tnaA	tnaa	NN	GEN	_	_
90	Biofilm	biofilm	NN	_	_	_
91	100	100	CD	_	_	_
92	uM	um	NN	_	_	_
93	indole	indole	FW	_	_	_
94	7h	7h	FW	_	_	_
95	LB	lb	NN	_	_	_
96	37C	37c	NN	_	_	_
97	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
98	BW25113	bw25113	NN	_	_	_
99	tnaA	tnaa	NN	GEN	_	_
100	Biofilm	biofilm	NN	_	_	_
101	DMF	dmf	NN	_	_	_
102	7h	7h	VBP	_	_	_
103	LB	lb	NN	_	_	_
104	37C	37c	NN	_	_	_
105	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
106	BW25113	bw25113	NN	_	_	_
107	tnaA	tnaa	NN	GEN	_	_
108	LB	lb	NN	_	_	_
109	30C	30c	NN	_	_	_
110	biofilm	biofilm	NN	_	_	_
111	cells	cell	NNS	_	_	_
112	with	with	IN	_	_	_
113	DMF	dmf	NN	_	_	_
114	7h	7h	VBP	_	_	_
115	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
116	BW25113	bw25113	NN	_	_	_
117	w	w	NN	_	_	_
118	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
119	Channel	Channel	NNP	_	_	_
120	1	1	CD	_	_	_
121	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
122	Escherichia	escherichia	FW	Organism	_	_
123	coli	coli	FW	Organism	_	_
124	PGCGROWTHCONDITIONS	pgcgrowthconditions	FW	_	_	_
125	MAS	mas	FW	_	_	_
126	5.0	5.0	CD	_	_	_
127	Expression	expression	NN	_	_	_
128	Analysis	analysis	NN	_	_	_
129	Default	Default	NNP	_	_	_
130	Setting	Setting	NNP	_	_	_
131	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
132	MAS	MAS	NNP	_	_	_
133	5.0	5.0	CD	_	_	_
134	Expression	expression	NN	_	_	_
135	Analysis	analysis	NN	_	_	_
136	Default	Default	NNP	_	_	_
137	Setting	Setting	NNP	_	_	_
138	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	extracted	extract	VBN	_	_	_
4	from	from	IN	_	_	_
5	biofilm	biofilm	NN	_	_	_
6	cells	cell	NNS	_	_	_
7	of	of	IN	_	_	_
8	E.	e.	FW	_	_	_
9	coli	coli	FW	_	_	_
10	K-12	k-12	NN	_	_	_
11	BW25113	bw25113	NN	_	_	_
12	tnaA	tnaa	NN	GEN	_	_
13	mutant	mutant	NN	_	_	_
14	after	after	IN	_	_	_
15	7	7	CD	_	_	_
16	hours	hour	NNS	_	_	_
17	of	of	IN	_	_	_
18	growth	growth	NN	_	_	_
19	in	in	IN	_	_	_
20	LB	lb	NN	_	_	_
21	with	with	IN	_	_	_
22	glasswool	glasswool	NN	_	_	_
23	and	and	CC	_	_	_
24	100	100	CD	_	_	_
25	uM	um	NN	_	_	_
26	indole	indole	NN	_	_	_
27	at	at	IN	_	_	_
28	37ºC	37ºc	NN	_	_	_
29	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
30	RNA	rna	NN	_	_	_
31	extracted	extract	VBN	_	_	_
32	from	from	IN	_	_	_
33	biofilm	biofilm	NN	_	_	_
34	cells	cell	NNS	_	_	_
35	of	of	IN	_	_	_
36	E.	e.	FW	_	_	_
37	coli	coli	FW	_	_	_
38	K-12	k-12	NN	_	_	_
39	BW25113	bw25113	NN	_	_	_
40	tnaA	tnaa	NN	GEN	_	_
41	mutant	mutant	NN	_	_	_
42	after	after	IN	_	_	_
43	7	7	CD	_	_	_
44	hours	hour	NNS	_	_	_
45	of	of	IN	_	_	_
46	growth	growth	NN	_	_	_
47	in	in	IN	_	_	_
48	LB	lb	NN	_	_	_
49	with	with	IN	_	_	_
50	glasswool	glasswool	NN	_	_	_
51	and	and	CC	_	_	_
52	DMF	dmf	NN	_	_	_
53	at	at	IN	_	_	_
54	30ºC	30ºC	NNP	_	_	_
55	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
56	RNA	RNA	NNP	_	_	_
57	extracted	extract	VBN	_	_	_
58	from	from	IN	_	_	_
59	biofilm	biofilm	NN	_	_	_
60	cells	cell	NNS	_	_	_
61	of	of	IN	_	_	_
62	E.	e.	FW	_	_	_
63	coli	coli	FW	_	_	_
64	K-12	k-12	NN	_	_	_
65	BW25113	bw25113	NN	_	_	_
66	tnaA	tnaa	NN	GEN	_	_
67	mutant	mutant	NN	_	_	_
68	after	after	IN	_	_	_
69	7	7	CD	_	_	_
70	hours	hour	NNS	_	_	_
71	of	of	IN	_	_	_
72	growth	growth	NN	_	_	_
73	in	in	IN	_	_	_
74	LB	lb	NN	_	_	_
75	with	with	IN	_	_	_
76	glasswool	glasswool	NN	_	_	_
77	and	and	CC	_	_	_
78	DMF	dmf	NN	_	_	_
79	at	at	IN	_	_	_
80	37ºC	37ºc	NN	_	_	_
81	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
82	RNA	rna	NN	_	_	_
83	extracted	extract	VBN	_	_	_
84	from	from	IN	_	_	_
85	biofilm	biofilm	NN	_	_	_
86	cells	cell	NNS	_	_	_
87	of	of	IN	_	_	_
88	E.	e.	FW	_	_	_
89	coli	coli	FW	_	_	_
90	K-12	k-12	NN	_	_	_
91	BW25113	bw25113	NN	_	_	_
92	tnaA	tnaa	NN	GEN	_	_
93	mutant	mutant	NN	_	_	_
94	after	after	IN	_	_	_
95	7	7	CD	_	_	_
96	hours	hour	NNS	_	_	_
97	of	of	IN	_	_	_
98	growth	growth	NN	_	_	_
99	in	in	IN	_	_	_
100	LB	lb	NN	_	_	_
101	with	with	IN	_	_	_
102	glasswool	glasswool	NN	_	_	_
103	and	and	CC	_	_	_
104	with	with	IN	_	_	_
105	100	100	CD	_	_	_
106	uM	um	NN	_	_	_
107	indole	indole	NN	_	_	_
108	at	at	IN	_	_	_
109	30ºC	30ºC	NNP	_	_	_
110	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
111	RNA	RNA	NNP	_	_	_
112	extracted	extract	VBN	_	_	_
113	from	from	IN	_	_	_
114	biofilm	biofilm	NN	_	_	_
115	cells	cell	NNS	_	_	_
116	of	of	IN	_	_	_
117	E.	e.	FW	_	_	_
118	coli	coli	FW	_	_	_
119	K-12	k-12	NN	_	_	_
120	BW25113	bw25113	NN	_	_	_
121	w	w	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	RNA	rna	NN	_	_	_
124	extracted	extract	VBN	_	_	_
125	from	from	IN	_	_	_
126	biofilm	biofilm	NN	_	_	_
127	cells	cell	NNS	_	_	_
128	of	of	IN	_	_	_
129	E.	e.	FW	_	_	_
130	coli	coli	FW	_	_	_
131	K-12	k-12	NN	_	_	_
132	sdiA	sdia	NN	GEN	_	_
133	mutant	mutant	NN	_	_	_
134	after	after	IN	_	_	_
135	7	7	CD	_	_	_
136	hours	hour	NNS	_	_	_
137	of	of	IN	_	_	_
138	growth	growth	NN	_	_	_
139	in	in	IN	_	_	_
140	LB	lb	NN	_	_	_
141	with	with	IN	_	_	_
142	glasswool	glasswool	NN	_	_	_
143	at	at	IN	_	_	_
144	30ºC	30ºc	NN	_	_	_
145	with	with	IN	_	_	_
146	1	1	CD	_	_	_
147	mM	mm	NN	KWSUPP	_	_
148	indole	indole	NN	_	_	_
149	presence	presence	NN	_	_	_
150	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	extracted	extract	VBN	_	_	_
4	from	from	IN	_	_	_
5	biofilm	biofilm	NN	_	_	_
6	cells	cell	NNS	_	_	_
7	of	of	IN	_	_	_
8	E.	e.	FW	_	_	_
9	coli	coli	FW	_	_	_
10	K-12	k-12	NN	_	_	_
11	sdiA	sdia	NN	GEN	_	_
12	mutant	mutant	NN	_	_	_
13	after	after	IN	_	_	_
14	7	7	CD	_	_	_
15	hours	hour	NNS	_	_	_
16	of	of	IN	_	_	_
17	growth	growth	NN	_	_	_
18	in	in	IN	_	_	_
19	LB	lb	NN	_	_	_
20	with	with	IN	_	_	_
21	glasswool	glasswool	NN	_	_	_
22	at	at	IN	_	_	_
23	30ºC	30ºc	NN	_	_	_
24	with	with	IN	_	_	_
25	DMF	dmf	NN	_	_	_
26	presence	presence	NN	_	_	_
27	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
2	RNA	rna	NN	_	_	_
3	extracted	extract	VBN	_	_	_
4	from	from	IN	_	_	_
5	free	free	JJ	_	_	_
6	living	living	NN	_	_	_
7	cells	cell	NNS	_	_	_
8	of	of	IN	_	_	_
9	E.	e.	FW	_	_	_
10	coli	coli	FW	_	_	_
11	K-12	k-12	NN	_	_	_
12	BW25113	bw25113	NN	_	_	_
13	luxS	luxs	NN	GEN	_	_
14	mutant	mutant	NN	_	_	_
15	-LRB-	-lrb-	-LRB-	_	_	_
16	when	when	WRB	_	_	_
17	growth	growth	NN	_	_	_
18	to	to	TO	_	_	_
19	OD600	od600	NN	_	_	_
20	0.5	0.5	CD	_	_	_
21	at	at	IN	_	_	_
22	30ºC	30ºC	NNP	_	_	_
23	in	in	IN	_	_	_
24	LB	LB	NNP	_	_	_
25	,	,	,	_	_	_
26	100	100	CD	_	_	_
27	uM	um	NN	_	_	_
28	AI2	ai2	NN	_	_	_
29	was	be	VBD	_	_	_
30	added	add	VBN	_	_	_
31	in	in	IN	_	_	_
32	and	and	CC	_	_	_
33	3-h	3-h	JJ	_	_	_
34	further	further	JJ	_	_	_
35	incubation	incubation	NN	_	_	_
36	was	be	VBD	_	_	_
37	applied	apply	VBN	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
40	RNA	rna	NN	_	_	_
41	extracted	extract	VBN	_	_	_
42	from	from	IN	_	_	_
43	free	free	JJ	_	_	_
44	living	living	NN	_	_	_
45	cells	cell	NNS	_	_	_
46	of	of	IN	_	_	_
47	E.	e.	FW	_	_	_
48	coli	coli	FW	_	_	_
49	K-12	k-12	NN	_	_	_
50	BW25113	bw25113	NN	_	_	_
51	luxS	luxs	NN	GEN	_	_
52	mutant	mutant	NN	_	_	_
53	-LRB-	-lrb-	-LRB-	_	_	_
54	when	when	WRB	_	_	_
55	growth	growth	NN	_	_	_
56	to	to	TO	_	_	_
57	OD600	od600	NN	_	_	_
58	0.5	0.5	CD	_	_	_
59	at	at	IN	_	_	_
60	30ºC	30ºC	NNP	_	_	_
61	in	in	IN	_	_	_
62	LB	LB	NNP	_	_	_
63	,	,	,	_	_	_
64	no	no	DT	_	_	_
65	AI2	ai2	NN	_	_	_
66	was	be	VBD	_	_	_
67	added	add	VBN	_	_	_
68	in	in	IN	_	_	_
69	and	and	CC	_	_	_
70	3-h	3-h	JJ	_	_	_
71	further	further	JJ	_	_	_
72	incubation	incubation	NN	_	_	_
73	was	be	VBD	_	_	_
74	applied	apply	VBN	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
77	RNA	rna	NN	_	_	_
78	extracted	extract	VBN	_	_	_
79	from	from	IN	_	_	_
80	free	free	JJ	_	_	_
81	living	living	NN	_	_	_
82	cells	cell	NNS	_	_	_
83	of	of	IN	_	_	_
84	E.	e.	FW	_	_	_
85	coli	coli	FW	_	_	_
86	K-12	k-12	NN	_	_	_
87	BW25113	bw25113	NN	_	_	_
88	luxS	luxs	NN	GEN	_	_
89	mutant	mutant	NN	_	_	_
90	-LRB-	-lrb-	-LRB-	_	_	_
91	when	when	WRB	_	_	_
92	growth	growth	NN	_	_	_
93	to	to	TO	_	_	_
94	OD600	od600	NN	_	_	_
95	0.5	0.5	CD	_	_	_
96	at	at	IN	_	_	_
97	37ºC	37ºc	NN	_	_	_
98	in	in	IN	_	_	_
99	LB	LB	NNP	_	_	_
100	,	,	,	_	_	_
101	100	100	CD	_	_	_
102	uM	um	NN	_	_	_
103	AI2	ai2	NN	_	_	_
104	was	be	VBD	_	_	_
105	added	add	VBN	_	_	_
106	in	in	IN	_	_	_
107	and	and	CC	_	_	_
108	3-h	3-h	JJ	_	_	_
109	further	further	JJ	_	_	_
110	incubation	incubation	NN	_	_	_
111	was	be	VBD	_	_	_
112	applied	apply	VBN	_	_	_
113	-RRB-	-rrb-	-RRB-	_	_	_
114	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
115	RNA	rna	NN	_	_	_
116	extracted	extract	VBN	_	_	_
117	from	from	IN	_	_	_
118	free	free	JJ	_	_	_
119	living	living	NN	_	_	_
120	cells	cell	NNS	_	_	_
121	of	of	IN	_	_	_
122	E.	e.	FW	_	_	_
123	coli	coli	FW	_	_	_
124	K-12	k-12	NN	_	_	_
125	BW25113	bw25113	NN	_	_	_
126	luxS	luxs	NN	GEN	_	_
127	mutant	mutant	NN	_	_	_
128	-LRB-	-lrb-	-LRB-	_	_	_
129	when	when	WRB	_	_	_
130	growth	growth	NN	_	_	_
131	to	to	TO	_	_	_
132	OD600	od600	NN	_	_	_
133	0.5	0.5	CD	_	_	_
134	at	at	IN	_	_	_
135	37ºC	37ºc	NN	_	_	_
136	in	in	IN	_	_	_
137	LB	LB	NNP	_	_	_
138	,	,	,	_	_	_
139	no	no	DT	_	_	_
140	AI2	ai2	NN	_	_	_
141	was	be	VBD	_	_	_
142	added	add	VBN	_	_	_
143	in	in	IN	_	_	_
144	and	and	CC	_	_	_
145	3-h	3-h	JJ	_	_	_
146	further	further	JJ	_	_	_
147	incubation	incubation	NN	_	_	_
148	was	be	VBD	_	_	_
149	applied	apply	VBN	_	_	_
150	-RRB-	-rrb-	-RRB-	_	_	_
151	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
152	RNA	rna	NN	_	_	_
153	extracted	extract	VBN	_	_	_
154	from	from	IN	_	_	_
155	free	free	JJ	_	_	_
156	living	living	NN	_	_	_
157	cells	cell	NNS	_	_	_
158	of	of	IN	_	_	_
159	E.	e.	FW	_	_	_
160	coli	coli	FW	_	_	_
161	K-12	k-12	NN	_	_	_
162	BW25113	bw25113	NN	_	_	_
163	sdiA	sdia	NN	GEN	_	_
164	mutant	mutant	NN	_	_	_
165	when	when	WRB	_	_	_
166	growth	growth	NN	_	_	_
167	to	to	TO	_	_	_
168	OD600	od600	NN	_	_	_
169	4.0	4.0	CD	_	_	_
170	at	at	IN	_	_	_
171	30ºC	30ºC	NNP	_	_	_
172	in	in	IN	_	_	_
173	LB	LB	NNP	_	_	_
174	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
175	RNA	RNA	NNP	_	_	_
176	extracted	extract	VBN	_	_	_
177	from	from	IN	_	_	_
178	free	free	JJ	_	_	_
179	living	living	NN	_	_	_
180	cells	cell	NNS	_	_	_
181	of	of	IN	_	_	_
182	E.	e.	FW	_	_	_
183	coli	coli	FW	_	_	_
184	K-12	k-12	NN	_	_	_
185	BW25113	bw25113	NN	_	_	_
186	wild	wild	JJ	_	_	_
187	type	type	NN	_	_	_
188	when	when	WRB	_	_	_
189	growth	growth	NN	_	_	_
190	to	to	TO	_	_	_
191	OD600	od600	NN	_	_	_
192	4.0	4.0	CD	_	_	_
193	at	at	IN	_	_	_
194	30ºC	30ºC	NNP	_	_	_
195	in	in	IN	_	_	_
196	LB	LB	NNP	_	_	_
197	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
198	RNA	RNA	NNP	_	_	_
199	extracted	extract	VBN	_	_	_
200	from	from	IN	_	_	_
201	suspension	suspension	NN	_	_	_
202	cells	cell	NNS	_	_	_
203	of	of	IN	_	_	_
204	E.	e.	FW	_	_	_
205	coli	coli	FW	_	_	_
206	K-12	k-12	NN	_	_	_
207	BW25113	bw25113	NN	_	_	_
208	w	w	NN	_	_	_
209	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
210	The	the	DT	_	_	_
211	overnight	overnight	JJ	_	_	_
212	culture	culture	NN	_	_	_
213	-LRB-	-lrb-	-LRB-	_	_	_
214	0.25	0.25	CD	_	_	_
215	ml	ml	NN	_	_	_
216	-RRB-	-rrb-	-RRB-	_	_	_
217	was	be	VBD	_	_	_
218	used	use	VBN	_	_	_
219	to	to	TO	_	_	_
220	inoculate	inoculate	VB	_	_	_
221	25	25	CD	_	_	_
222	ml	ml	NN	_	_	_
223	of	of	IN	_	_	_
224	fresh	fresh	JJ	_	_	_
225	LB	lb	NN	MED	_	_
226	medium	medium	NN	MED	_	_
227	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	at	at	IN	_	_	_
4	30	30	CD	_	_	_
5	°C	°c	NN	_	_	_
6	with	with	IN	_	_	_
7	shaking	shake	VBG	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	250	250	CD	_	_	_
10	rpm	rpm	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	to	to	TO	_	_	_
13	OD600	od600	CD	_	_	_
14	0.5	0.5	CD	_	_	_
15	,	,	,	_	_	_
16	100	100	CD	_	_	_
17	uM	um	NN	_	_	_
18	AI-2	ai-2	NN	_	_	_
19	was	be	VBD	_	_	_
20	added	add	VBN	_	_	_
21	in	in	IN	_	_	_
22	.	.	.	_	_	_

1	after	after	IN	_	_	_
2	further	further	JJ	_	_	_
3	3-h	3-h	JJ	_	_	_
4	incubation	incubation	NN	_	_	_
5	,	,	,	_	_	_
6	2.0	2.0	CD	_	_	_
7	ml	ml	NN	_	_	_
8	of	of	IN	_	_	_
9	cell	cell	NN	_	_	_
10	culture	culture	NN	_	_	_
11	was	be	VBD	_	_	_
12	removed	remove	VBN	_	_	_
13	and	and	CC	_	_	_
14	cells	cell	NNS	_	_	_
15	were	be	VBD	_	_	_
16	pelleted	pelleted	JJ	_	_	_
17	and	and	CC	_	_	_
18	frozen	frozen	JJ	_	_	_
19	in	in	IN	_	_	_
20	-80	-80	CD	_	_	_
21	C	c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	The	the	DT	_	_	_
28	overnight	overnight	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	0.25	0.25	CD	_	_	_
32	ml	ml	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	was	be	VBD	_	_	_
35	used	use	VBN	_	_	_
36	to	to	TO	_	_	_
37	inoculate	inoculate	VB	_	_	_
38	25	25	CD	_	_	_
39	ml	ml	NN	_	_	_
40	of	of	IN	_	_	_
41	fresh	fresh	JJ	_	_	_
42	LB	lb	NN	MED	_	_
43	medium	medium	NN	MED	_	_
44	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	at	at	IN	_	_	_
4	30	30	CD	_	_	_
5	°C	°c	NN	_	_	_
6	with	with	IN	_	_	_
7	shaking	shake	VBG	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	250	250	CD	_	_	_
10	rpm	rpm	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	to	to	TO	_	_	_
13	OD600	od600	CD	_	_	_
14	0.5	0.5	CD	_	_	_
15	,	,	,	_	_	_
16	no	no	DT	_	_	_
17	AI-2	ai-2	NN	_	_	_
18	was	be	VBD	_	_	_
19	added	add	VBN	_	_	_
20	in	in	IN	_	_	_
21	.	.	.	_	_	_

1	after	after	IN	_	_	_
2	further	further	JJ	_	_	_
3	3-h	3-h	JJ	_	_	_
4	incubation	incubation	NN	_	_	_
5	,	,	,	_	_	_
6	2.0	2.0	CD	_	_	_
7	ml	ml	NN	_	_	_
8	of	of	IN	_	_	_
9	cell	cell	NN	_	_	_
10	culture	culture	NN	_	_	_
11	was	be	VBD	_	_	_
12	removed	remove	VBN	_	_	_
13	and	and	CC	_	_	_
14	cells	cell	NNS	_	_	_
15	were	be	VBD	_	_	_
16	pelleted	pelleted	JJ	_	_	_
17	and	and	CC	_	_	_
18	frozen	frozen	JJ	_	_	_
19	in	in	IN	_	_	_
20	-80	-80	CD	_	_	_
21	C	c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	The	the	DT	_	_	_
28	overnight	overnight	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	0.25	0.25	CD	_	_	_
32	ml	ml	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	was	be	VBD	_	_	_
35	used	use	VBN	_	_	_
36	to	to	TO	_	_	_
37	inoculate	inoculate	VB	_	_	_
38	25	25	CD	_	_	_
39	ml	ml	NN	_	_	_
40	of	of	IN	_	_	_
41	fresh	fresh	JJ	_	_	_
42	LB	lb	NN	MED	_	_
43	medium	medium	NN	MED	_	_
44	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	at	at	IN	_	_	_
4	30	30	CD	_	_	_
5	°C	°c	NN	_	_	_
6	with	with	IN	_	_	_
7	shaking	shake	VBG	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	250	250	CD	_	_	_
10	rpm	rpm	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	to	to	TO	_	_	_
13	OD600	od600	CD	_	_	_
14	4.0	4.0	CD	_	_	_
15	,	,	,	_	_	_
16	2.0	2.0	CD	_	_	_
17	ml	ml	NN	_	_	_
18	of	of	IN	_	_	_
19	cell	cell	NN	_	_	_
20	culture	culture	NN	_	_	_
21	was	be	VBD	_	_	_
22	removed	remove	VBN	_	_	_
23	and	and	CC	_	_	_
24	cells	cell	NNS	_	_	_
25	were	be	VBD	_	_	_
26	pelleted	pelleted	JJ	_	_	_
27	and	and	CC	_	_	_
28	frozen	frozen	JJ	_	_	_
29	in	in	IN	_	_	_
30	-80	-80	CD	_	_	_
31	C	c	NN	_	_	_
32	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	The	the	DT	_	_	_
28	overnight	overnight	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	0.25	0.25	CD	_	_	_
32	ml	ml	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	was	be	VBD	_	_	_
35	used	use	VBN	_	_	_
36	to	to	TO	_	_	_
37	inoculate	inoculate	VB	_	_	_
38	25	25	CD	_	_	_
39	ml	ml	NN	_	_	_
40	of	of	IN	_	_	_
41	fresh	fresh	JJ	_	_	_
42	LB	lb	NN	MED	_	_
43	medium	medium	NN	MED	_	_
44	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	at	at	IN	_	_	_
4	37	37	CD	_	_	_
5	°C	°c	NN	_	_	_
6	with	with	IN	_	_	_
7	shaking	shake	VBG	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	250	250	CD	_	_	_
10	rpm	rpm	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	to	to	TO	_	_	_
13	OD600	od600	CD	_	_	_
14	0.5	0.5	CD	_	_	_
15	,	,	,	_	_	_
16	100	100	CD	_	_	_
17	uM	um	NN	_	_	_
18	AI-2	ai-2	NN	_	_	_
19	was	be	VBD	_	_	_
20	added	add	VBN	_	_	_
21	in	in	IN	_	_	_
22	.	.	.	_	_	_

1	after	after	IN	_	_	_
2	further	further	JJ	_	_	_
3	3-h	3-h	JJ	_	_	_
4	incubation	incubation	NN	_	_	_
5	,	,	,	_	_	_
6	2.0	2.0	CD	_	_	_
7	ml	ml	NN	_	_	_
8	of	of	IN	_	_	_
9	cell	cell	NN	_	_	_
10	culture	culture	NN	_	_	_
11	was	be	VBD	_	_	_
12	removed	remove	VBN	_	_	_
13	and	and	CC	_	_	_
14	cells	cell	NNS	_	_	_
15	were	be	VBD	_	_	_
16	pelleted	pelleted	JJ	_	_	_
17	and	and	CC	_	_	_
18	frozen	frozen	JJ	_	_	_
19	in	in	IN	_	_	_
20	-80	-80	CD	_	_	_
21	C	c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	The	the	DT	_	_	_
28	overnight	overnight	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	0.25	0.25	CD	_	_	_
32	ml	ml	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	was	be	VBD	_	_	_
35	used	use	VBN	_	_	_
36	to	to	TO	_	_	_
37	inoculate	inoculate	VB	_	_	_
38	25	25	CD	_	_	_
39	ml	ml	NN	_	_	_
40	of	of	IN	_	_	_
41	fresh	fresh	JJ	_	_	_
42	LB	lb	NN	MED	_	_
43	medium	medium	NN	MED	_	_
44	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	at	at	IN	_	_	_
4	37	37	CD	_	_	_
5	°C	°c	NN	_	_	_
6	with	with	IN	_	_	_
7	shaking	shake	VBG	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	250	250	CD	_	_	_
10	rpm	rpm	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	to	to	TO	_	_	_
13	OD600	od600	CD	_	_	_
14	0.5	0.5	CD	_	_	_
15	,	,	,	_	_	_
16	no	no	DT	_	_	_
17	AI-2	ai-2	NN	_	_	_
18	was	be	VBD	_	_	_
19	added	add	VBN	_	_	_
20	in	in	IN	_	_	_
21	.	.	.	_	_	_

1	after	after	IN	_	_	_
2	further	further	JJ	_	_	_
3	3-h	3-h	JJ	_	_	_
4	incubation	incubation	NN	_	_	_
5	,	,	,	_	_	_
6	2.0	2.0	CD	_	_	_
7	ml	ml	NN	_	_	_
8	of	of	IN	_	_	_
9	cell	cell	NN	_	_	_
10	culture	culture	NN	_	_	_
11	was	be	VBD	_	_	_
12	removed	remove	VBN	_	_	_
13	and	and	CC	_	_	_
14	cells	cell	NNS	_	_	_
15	were	be	VBD	_	_	_
16	pelleted	pelleted	JJ	_	_	_
17	and	and	CC	_	_	_
18	frozen	frozen	JJ	_	_	_
19	in	in	IN	_	_	_
20	-80	-80	CD	_	_	_
21	C	c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	The	the	DT	_	_	_
28	overnight	overnight	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	2.5	2.5	CD	_	_	_
32	ml	ml	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	was	be	VBD	_	_	_
35	used	use	VBN	_	_	_
36	to	to	TO	_	_	_
37	inoculate	inoculate	VB	_	_	_
38	250	250	CD	_	_	_
39	ml	ml	NN	_	_	_
40	of	of	IN	_	_	_
41	fresh	fresh	JJ	_	_	_
42	LB	lb	NN	MED	_	_
43	medium	medium	NN	MED	_	_
44	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	at	at	IN	_	_	_
4	30	30	CD	_	_	_
5	°C	°c	NN	_	_	_
6	with	with	IN	_	_	_
7	shaking	shake	VBG	_	_	_
8	-LRB-	-lrb-	-LRB-	_	_	_
9	250	250	CD	_	_	_
10	rpm	rpm	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	for	for	IN	_	_	_
13	7	7	CD	_	_	_
14	hours	hour	NNS	_	_	_
15	,	,	,	_	_	_
16	2.0	2.0	CD	_	_	_
17	ml	ml	NN	_	_	_
18	of	of	IN	_	_	_
19	cell	cell	NN	_	_	_
20	culture	culture	NN	_	_	_
21	was	be	VBD	_	_	_
22	removed	remove	VBN	_	_	_
23	from	from	IN	_	_	_
24	suspension	suspension	NN	_	_	_
25	part	part	NN	_	_	_
26	and	and	CC	_	_	_
27	cells	cell	NNS	_	_	_
28	were	be	VBD	_	_	_
29	pelleted	pelleted	JJ	_	_	_
30	and	and	CC	_	_	_
31	frozen	frozen	JJ	_	_	_
32	in	in	IN	_	_	_
33	-80	-80	CD	_	_	_
34	C	c	NN	_	_	_
35	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	The	the	DT	_	_	_
28	overnight	overnight	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	2.5	2.5	CD	_	_	_
32	ml	ml	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	was	be	VBD	_	_	_
35	used	use	VBN	_	_	_
36	to	to	TO	_	_	_
37	inoculate	inoculate	VB	_	_	_
38	250	250	CD	_	_	_
39	ml	ml	NN	_	_	_
40	of	of	IN	_	_	_
41	fresh	fresh	JJ	_	_	_
42	LB	lb	NN	MED	_	_
43	medium	medium	NN	MED	_	_
44	with	with	IN	_	_	_
45	10	10	CD	_	_	_
46	g	g	NN	_	_	_
47	of	of	IN	_	_	_
48	submerged	submerged	JJ	_	_	_
49	glass	glass	NN	_	_	_
50	wool	wool	NN	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	Corning	Corning	NNP	_	_	_
53	Glass	Glass	NNP	_	_	_
54	Works	Works	NNP	_	_	_
55	,	,	,	_	_	_
56	Corning	Corning	NNP	_	_	_
57	,	,	,	_	_	_
58	NY	NY	NNP	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	and	and	CC	_	_	_
61	1	1	CD	_	_	_
62	mM	mm	NN	KWSUPP	_	_
63	indole	indole	NN	_	_	_
64	for	for	IN	_	_	_
65	forming	form	VBG	_	_	_
66	biofilm	biofilm	NN	_	_	_
67	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	7	7	CD	_	_	_
5	h	h	NN	_	_	_
6	at	at	IN	_	_	_
7	30	30	CD	_	_	_
8	°C	°c	NN	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	250	250	CD	_	_	_
13	rpm	rpm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	the	the	DT	_	_	_
17	glass	glass	NN	_	_	_
18	wool	wool	NN	_	_	_
19	was	be	VBD	_	_	_
20	carefully	carefully	RB	_	_	_
21	and	and	CC	_	_	_
22	quickly	quickly	RB	_	_	_
23	removed	remove	VBD	_	_	_
24	and	and	CC	_	_	_
25	rinsed	rinse	VBD	_	_	_
26	with	with	IN	_	_	_
27	100	100	CD	_	_	_
28	ml	ml	NN	_	_	_
29	of	of	IN	_	_	_
30	sterile	sterile	JJ	_	_	_
31	0.85	0.85	CD	_	_	_
32	%	%	NN	_	_	_
33	NaCl	nacl	NN	_	_	_
34	solution	solution	NN	_	_	_
35	at	at	IN	_	_	_
36	0	0	CD	_	_	_
37	°C	°c	NN	_	_	_
38	.	.	.	_	_	_

1	Biofilm	biofilm	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	sonicating	sonicate	VBG	_	_	_
7	the	the	DT	_	_	_
8	glass	glass	NN	_	_	_
9	wool	wool	NN	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	sterile	sterile	JJ	_	_	_
15	0.85	0.85	CD	_	_	_
16	%	%	NN	_	_	_
17	NaCl	nacl	NN	_	_	_
18	solution	solution	NN	_	_	_
19	at	at	IN	_	_	_
20	0	0	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	overnight	overnight	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	2.5	2.5	CD	_	_	_
7	ml	ml	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	was	be	VBD	_	_	_
10	used	use	VBN	_	_	_
11	to	to	TO	_	_	_
12	inoculate	inoculate	VB	_	_	_
13	250	250	CD	_	_	_
14	ml	ml	NN	_	_	_
15	of	of	IN	_	_	_
16	fresh	fresh	JJ	_	_	_
17	LB	lb	NN	MED	_	_
18	medium	medium	NN	MED	_	_
19	with	with	IN	_	_	_
20	10	10	CD	_	_	_
21	g	g	NN	_	_	_
22	of	of	IN	_	_	_
23	submerged	submerged	JJ	_	_	_
24	glass	glass	NN	_	_	_
25	wool	wool	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Corning	Corning	NNP	_	_	_
28	Glass	Glass	NNP	_	_	_
29	Works	Works	NNP	_	_	_
30	,	,	,	_	_	_
31	Corning	Corning	NNP	_	_	_
32	,	,	,	_	_	_
33	NY	NY	NNP	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	and	and	CC	_	_	_
36	DMF	dmf	NN	_	_	_
37	for	for	IN	_	_	_
38	forming	form	VBG	_	_	_
39	biofilm	biofilm	NN	_	_	_
40	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	7	7	CD	_	_	_
5	h	h	NN	_	_	_
6	at	at	IN	_	_	_
7	30	30	CD	_	_	_
8	°C	°c	NN	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	250	250	CD	_	_	_
13	rpm	rpm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	the	the	DT	_	_	_
17	glass	glass	NN	_	_	_
18	wool	wool	NN	_	_	_
19	was	be	VBD	_	_	_
20	carefully	carefully	RB	_	_	_
21	and	and	CC	_	_	_
22	quickly	quickly	RB	_	_	_
23	removed	remove	VBD	_	_	_
24	and	and	CC	_	_	_
25	rinsed	rinse	VBD	_	_	_
26	with	with	IN	_	_	_
27	100	100	CD	_	_	_
28	ml	ml	NN	_	_	_
29	of	of	IN	_	_	_
30	sterile	sterile	JJ	_	_	_
31	0.85	0.85	CD	_	_	_
32	%	%	NN	_	_	_
33	NaCl	nacl	NN	_	_	_
34	solution	solution	NN	_	_	_
35	at	at	IN	_	_	_
36	0	0	CD	_	_	_
37	°C	°c	NN	_	_	_
38	.	.	.	_	_	_

1	Biofilm	biofilm	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	sonicating	sonicate	VBG	_	_	_
7	the	the	DT	_	_	_
8	glass	glass	NN	_	_	_
9	wool	wool	NN	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	sterile	sterile	JJ	_	_	_
15	0.85	0.85	CD	_	_	_
16	%	%	NN	_	_	_
17	NaCl	nacl	NN	_	_	_
18	solution	solution	NN	_	_	_
19	at	at	IN	_	_	_
20	0	0	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	The	the	DT	_	_	_
28	overnight	overnight	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	2.5	2.5	CD	_	_	_
32	ml	ml	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	was	be	VBD	_	_	_
35	used	use	VBN	_	_	_
36	to	to	TO	_	_	_
37	inoculate	inoculate	VB	_	_	_
38	250	250	CD	_	_	_
39	ml	ml	NN	_	_	_
40	of	of	IN	_	_	_
41	fresh	fresh	JJ	_	_	_
42	LB	lb	NN	MED	_	_
43	medium	medium	NN	MED	_	_
44	with	with	IN	_	_	_
45	10	10	CD	_	_	_
46	g	g	NN	_	_	_
47	of	of	IN	_	_	_
48	submerged	submerged	JJ	_	_	_
49	glass	glass	NN	_	_	_
50	wool	wool	NN	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	Corning	Corning	NNP	_	_	_
53	Glass	Glass	NNP	_	_	_
54	Works	Works	NNP	_	_	_
55	,	,	,	_	_	_
56	Corning	Corning	NNP	_	_	_
57	,	,	,	_	_	_
58	NY	NY	NNP	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	and	and	CC	_	_	_
61	DMF	dmf	NN	_	_	_
62	for	for	IN	_	_	_
63	forming	form	VBG	_	_	_
64	biofilm	biofilm	NN	_	_	_
65	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	7	7	CD	_	_	_
5	h	h	NN	_	_	_
6	at	at	IN	_	_	_
7	30	30	CD	_	_	_
8	°C	°c	NN	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	250	250	CD	_	_	_
13	rpm	rpm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	the	the	DT	_	_	_
17	glass	glass	NN	_	_	_
18	wool	wool	NN	_	_	_
19	was	be	VBD	_	_	_
20	carefully	carefully	RB	_	_	_
21	and	and	CC	_	_	_
22	quickly	quickly	RB	_	_	_
23	removed	remove	VBD	_	_	_
24	and	and	CC	_	_	_
25	rinsed	rinse	VBD	_	_	_
26	with	with	IN	_	_	_
27	100	100	CD	_	_	_
28	ml	ml	NN	_	_	_
29	of	of	IN	_	_	_
30	sterile	sterile	JJ	_	_	_
31	0.85	0.85	CD	_	_	_
32	%	%	NN	_	_	_
33	NaCl	nacl	NN	_	_	_
34	solution	solution	NN	_	_	_
35	at	at	IN	_	_	_
36	0	0	CD	_	_	_
37	°C	°c	NN	_	_	_
38	.	.	.	_	_	_

1	Biofilm	biofilm	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	sonicating	sonicate	VBG	_	_	_
7	the	the	DT	_	_	_
8	glass	glass	NN	_	_	_
9	wool	wool	NN	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	sterile	sterile	JJ	_	_	_
15	0.85	0.85	CD	_	_	_
16	%	%	NN	_	_	_
17	NaCl	nacl	NN	_	_	_
18	solution	solution	NN	_	_	_
19	at	at	IN	_	_	_
20	0	0	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	.	.	.	_	_	_

1	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
2	The	the	DT	_	_	_
3	overnight	overnight	JJ	_	_	_
4	culture	culture	NN	_	_	_
5	-LRB-	-lrb-	-LRB-	_	_	_
6	2.5	2.5	CD	_	_	_
7	ml	ml	NN	_	_	_
8	-RRB-	-rrb-	-RRB-	_	_	_
9	was	be	VBD	_	_	_
10	used	use	VBN	_	_	_
11	to	to	TO	_	_	_
12	inoculate	inoculate	VB	_	_	_
13	250	250	CD	_	_	_
14	ml	ml	NN	_	_	_
15	of	of	IN	_	_	_
16	fresh	fresh	JJ	_	_	_
17	LB	lb	NN	MED	_	_
18	medium	medium	NN	MED	_	_
19	with	with	IN	_	_	_
20	10	10	CD	_	_	_
21	g	g	NN	_	_	_
22	of	of	IN	_	_	_
23	submerged	submerged	JJ	_	_	_
24	glass	glass	NN	_	_	_
25	wool	wool	NN	_	_	_
26	-LRB-	-lrb-	-LRB-	_	_	_
27	Corning	Corning	NNP	_	_	_
28	Glass	Glass	NNP	_	_	_
29	Works	Works	NNP	_	_	_
30	,	,	,	_	_	_
31	Corning	Corning	NNP	_	_	_
32	,	,	,	_	_	_
33	NY	NY	NNP	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	and	and	CC	_	_	_
36	DMF	dmf	NN	_	_	_
37	for	for	IN	_	_	_
38	forming	form	VBG	_	_	_
39	biofilm	biofilm	NN	_	_	_
40	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	7	7	CD	_	_	_
5	h	h	NN	_	_	_
6	at	at	IN	_	_	_
7	37	37	CD	_	_	_
8	°C	°c	NN	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	250	250	CD	_	_	_
13	rpm	rpm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	the	the	DT	_	_	_
17	glass	glass	NN	_	_	_
18	wool	wool	NN	_	_	_
19	was	be	VBD	_	_	_
20	carefully	carefully	RB	_	_	_
21	and	and	CC	_	_	_
22	quickly	quickly	RB	_	_	_
23	removed	remove	VBD	_	_	_
24	and	and	CC	_	_	_
25	rinsed	rinse	VBD	_	_	_
26	with	with	IN	_	_	_
27	100	100	CD	_	_	_
28	ml	ml	NN	_	_	_
29	of	of	IN	_	_	_
30	sterile	sterile	JJ	_	_	_
31	0.85	0.85	CD	_	_	_
32	%	%	NN	_	_	_
33	NaCl	nacl	NN	_	_	_
34	solution	solution	NN	_	_	_
35	at	at	IN	_	_	_
36	0	0	CD	_	_	_
37	°C	°c	NN	_	_	_
38	.	.	.	_	_	_

1	Biofilm	biofilm	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	sonicating	sonicate	VBG	_	_	_
7	the	the	DT	_	_	_
8	glass	glass	NN	_	_	_
9	wool	wool	NN	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	sterile	sterile	JJ	_	_	_
15	0.85	0.85	CD	_	_	_
16	%	%	NN	_	_	_
17	NaCl	nacl	NN	_	_	_
18	solution	solution	NN	_	_	_
19	at	at	IN	_	_	_
20	0	0	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	The	the	DT	_	_	_
28	overnight	overnight	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	2.5	2.5	CD	_	_	_
32	ml	ml	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	was	be	VBD	_	_	_
35	used	use	VBN	_	_	_
36	to	to	TO	_	_	_
37	inoculate	inoculate	VB	_	_	_
38	250	250	CD	_	_	_
39	ml	ml	NN	_	_	_
40	of	of	IN	_	_	_
41	fresh	fresh	JJ	_	_	_
42	LB	lb	NN	MED	_	_
43	medium	medium	NN	MED	_	_
44	with	with	IN	_	_	_
45	10	10	CD	_	_	_
46	g	g	NN	_	_	_
47	of	of	IN	_	_	_
48	submerged	submerged	JJ	_	_	_
49	glass	glass	NN	_	_	_
50	wool	wool	NN	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	Corning	Corning	NNP	_	_	_
53	Glass	Glass	NNP	_	_	_
54	Works	Works	NNP	_	_	_
55	,	,	,	_	_	_
56	Corning	Corning	NNP	_	_	_
57	,	,	,	_	_	_
58	NY	NY	NNP	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	and	and	CC	_	_	_
61	with	with	IN	_	_	_
62	100	100	CD	_	_	_
63	uM	um	NN	_	_	_
64	indole	indole	NN	_	_	_
65	for	for	IN	_	_	_
66	forming	form	VBG	_	_	_
67	biofilm	biofilm	NN	_	_	_
68	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	7	7	CD	_	_	_
5	h	h	NN	_	_	_
6	at	at	IN	_	_	_
7	30	30	CD	_	_	_
8	°C	°c	NN	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	250	250	CD	_	_	_
13	rpm	rpm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	the	the	DT	_	_	_
17	glass	glass	NN	_	_	_
18	wool	wool	NN	_	_	_
19	was	be	VBD	_	_	_
20	carefully	carefully	RB	_	_	_
21	and	and	CC	_	_	_
22	quickly	quickly	RB	_	_	_
23	removed	remove	VBD	_	_	_
24	and	and	CC	_	_	_
25	rinsed	rinse	VBD	_	_	_
26	with	with	IN	_	_	_
27	100	100	CD	_	_	_
28	ml	ml	NN	_	_	_
29	of	of	IN	_	_	_
30	sterile	sterile	JJ	_	_	_
31	0.85	0.85	CD	_	_	_
32	%	%	NN	_	_	_
33	NaCl	nacl	NN	_	_	_
34	solution	solution	NN	_	_	_
35	at	at	IN	_	_	_
36	0	0	CD	_	_	_
37	°C	°c	NN	_	_	_
38	.	.	.	_	_	_

1	Biofilm	biofilm	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	sonicating	sonicate	VBG	_	_	_
7	the	the	DT	_	_	_
8	glass	glass	NN	_	_	_
9	wool	wool	NN	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	sterile	sterile	JJ	_	_	_
15	0.85	0.85	CD	_	_	_
16	%	%	NN	_	_	_
17	NaCl	nacl	NN	_	_	_
18	solution	solution	NN	_	_	_
19	at	at	IN	_	_	_
20	0	0	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	The	the	DT	_	_	_
28	overnight	overnight	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	2.5	2.5	CD	_	_	_
32	ml	ml	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	was	be	VBD	_	_	_
35	used	use	VBN	_	_	_
36	to	to	TO	_	_	_
37	inoculate	inoculate	VB	_	_	_
38	250	250	CD	_	_	_
39	ml	ml	NN	_	_	_
40	of	of	IN	_	_	_
41	fresh	fresh	JJ	_	_	_
42	LB	lb	NN	MED	_	_
43	medium	medium	NN	MED	_	_
44	with	with	IN	_	_	_
45	10	10	CD	_	_	_
46	g	g	NN	_	_	_
47	of	of	IN	_	_	_
48	submerged	submerged	JJ	_	_	_
49	glass	glass	NN	_	_	_
50	wool	wool	NN	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	Corning	Corning	NNP	_	_	_
53	Glass	Glass	NNP	_	_	_
54	Works	Works	NNP	_	_	_
55	,	,	,	_	_	_
56	Corning	Corning	NNP	_	_	_
57	,	,	,	_	_	_
58	NY	NY	NNP	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	and	and	CC	_	_	_
61	with	with	IN	_	_	_
62	100	100	CD	_	_	_
63	uM	um	NN	_	_	_
64	indole	indole	NN	_	_	_
65	for	for	IN	_	_	_
66	forming	form	VBG	_	_	_
67	biofilm	biofilm	NN	_	_	_
68	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	7	7	CD	_	_	_
5	h	h	NN	_	_	_
6	at	at	IN	_	_	_
7	37	37	CD	_	_	_
8	°C	°c	NN	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	250	250	CD	_	_	_
13	rpm	rpm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	the	the	DT	_	_	_
17	glass	glass	NN	_	_	_
18	wool	wool	NN	_	_	_
19	was	be	VBD	_	_	_
20	carefully	carefully	RB	_	_	_
21	and	and	CC	_	_	_
22	quickly	quickly	RB	_	_	_
23	removed	remove	VBD	_	_	_
24	and	and	CC	_	_	_
25	rinsed	rinse	VBD	_	_	_
26	with	with	IN	_	_	_
27	100	100	CD	_	_	_
28	ml	ml	NN	_	_	_
29	of	of	IN	_	_	_
30	sterile	sterile	JJ	_	_	_
31	0.85	0.85	CD	_	_	_
32	%	%	NN	_	_	_
33	NaCl	nacl	NN	_	_	_
34	solution	solution	NN	_	_	_
35	at	at	IN	_	_	_
36	0	0	CD	_	_	_
37	°C	°c	NN	_	_	_
38	.	.	.	_	_	_

1	Biofilm	biofilm	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	sonicating	sonicate	VBG	_	_	_
7	the	the	DT	_	_	_
8	glass	glass	NN	_	_	_
9	wool	wool	NN	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	sterile	sterile	JJ	_	_	_
15	0.85	0.85	CD	_	_	_
16	%	%	NN	_	_	_
17	NaCl	nacl	NN	_	_	_
18	solution	solution	NN	_	_	_
19	at	at	IN	_	_	_
20	0	0	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
27	The	the	DT	_	_	_
28	overnight	overnight	JJ	_	_	_
29	culture	culture	NN	_	_	_
30	-LRB-	-lrb-	-LRB-	_	_	_
31	2.5	2.5	CD	_	_	_
32	ml	ml	NN	_	_	_
33	-RRB-	-rrb-	-RRB-	_	_	_
34	was	be	VBD	_	_	_
35	used	use	VBN	_	_	_
36	to	to	TO	_	_	_
37	inoculate	inoculate	VB	_	_	_
38	250	250	CD	_	_	_
39	ml	ml	NN	_	_	_
40	of	of	IN	_	_	_
41	fresh	fresh	JJ	_	_	_
42	LB	lb	NN	MED	_	_
43	medium	medium	NN	MED	_	_
44	with	with	IN	_	_	_
45	10	10	CD	_	_	_
46	g	g	NN	_	_	_
47	of	of	IN	_	_	_
48	submerged	submerged	JJ	_	_	_
49	glass	glass	NN	_	_	_
50	wool	wool	NN	_	_	_
51	-LRB-	-lrb-	-LRB-	_	_	_
52	Corning	Corning	NNP	_	_	_
53	Glass	Glass	NNP	_	_	_
54	Works	Works	NNP	_	_	_
55	,	,	,	_	_	_
56	Corning	Corning	NNP	_	_	_
57	,	,	,	_	_	_
58	NY	NY	NNP	_	_	_
59	-RRB-	-rrb-	-RRB-	_	_	_
60	for	for	IN	_	_	_
61	forming	form	VBG	_	_	_
62	biofilm	biofilm	NN	_	_	_
63	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	incubation	incubation	NN	_	_	_
3	for	for	IN	_	_	_
4	7	7	CD	_	_	_
5	h	h	NN	_	_	_
6	at	at	IN	_	_	_
7	30	30	CD	_	_	_
8	°C	°c	NN	_	_	_
9	with	with	IN	_	_	_
10	shaking	shake	VBG	_	_	_
11	-LRB-	-lrb-	-LRB-	_	_	_
12	250	250	CD	_	_	_
13	rpm	rpm	NN	_	_	_
14	-RRB-	-rrb-	-RRB-	_	_	_
15	,	,	,	_	_	_
16	the	the	DT	_	_	_
17	glass	glass	NN	_	_	_
18	wool	wool	NN	_	_	_
19	was	be	VBD	_	_	_
20	carefully	carefully	RB	_	_	_
21	and	and	CC	_	_	_
22	quickly	quickly	RB	_	_	_
23	removed	remove	VBD	_	_	_
24	and	and	CC	_	_	_
25	rinsed	rinse	VBD	_	_	_
26	with	with	IN	_	_	_
27	100	100	CD	_	_	_
28	ml	ml	NN	_	_	_
29	of	of	IN	_	_	_
30	sterile	sterile	JJ	_	_	_
31	0.85	0.85	CD	_	_	_
32	%	%	NN	_	_	_
33	NaCl	nacl	NN	_	_	_
34	solution	solution	NN	_	_	_
35	at	at	IN	_	_	_
36	0	0	CD	_	_	_
37	°C	°c	NN	_	_	_
38	.	.	.	_	_	_

1	Biofilm	biofilm	NN	_	_	_
2	cells	cell	NNS	_	_	_
3	were	be	VBD	_	_	_
4	removed	remove	VBN	_	_	_
5	by	by	IN	_	_	_
6	sonicating	sonicate	VBG	_	_	_
7	the	the	DT	_	_	_
8	glass	glass	NN	_	_	_
9	wool	wool	NN	_	_	_
10	in	in	IN	_	_	_
11	200	200	CD	_	_	_
12	ml	ml	NN	_	_	_
13	of	of	IN	_	_	_
14	sterile	sterile	JJ	_	_	_
15	0.85	0.85	CD	_	_	_
16	%	%	NN	_	_	_
17	NaCl	nacl	NN	_	_	_
18	solution	solution	NN	_	_	_
19	at	at	IN	_	_	_
20	0	0	CD	_	_	_
21	°C	°c	NN	_	_	_
22	.	.	.	_	_	_

1	After	after	IN	_	_	_
2	breaking	break	VBG	_	_	_
3	the	the	DT	_	_	_
4	cells	cell	NNS	_	_	_
5	with	with	IN	_	_	_
6	a	a	DT	_	_	_
7	bead	bead	NN	_	_	_
8	beater	beater	NN	_	_	_
9	,	,	,	_	_	_
10	and	and	CC	_	_	_
11	the	the	DT	_	_	_
12	total	total	JJ	_	_	_
13	RNA	rna	NN	_	_	_
14	was	be	VBD	_	_	_
15	isolated	isolate	VBN	_	_	_
16	with	with	IN	_	_	_
17	Qiagen	Qiagen	NNP	_	_	_
18	RNeasy	RNeasy	NNP	_	_	_
19	mini	minus	NNS	_	_	_
20	Kit	kit	NN	_	_	_
21	-LRB-	-lrb-	-LRB-	_	_	_
22	Cat	cat	NN	_	_	_
23	#	#	#	_	_	_
24	74104	74104	CD	_	_	_
25	-RRB-	-rrb-	-RRB-	_	_	_
26	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
27	10	10	CD	_	_	_
28	_	_	CD	_	_	_
29	ESBL019	esbl019	NN	_	_	_
30	Filamented	Filamented	NNP	_	_	_
31	Repl	Repl	NNP	_	_	_
32	3	3	CD	_	_	_
33	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
34	11	11	CD	_	_	_
35	_	_	NN	_	_	_
36	ESBL019	esbl019	NN	_	_	_
37	Transition	transition	NN	_	_	_
38	Repl	repl	NN	_	_	_
39	3	3	CD	_	_	_
40	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
41	12	12	CD	_	_	_
42	_	_	NN	_	_	_
43	ESBL019	esbl019	NN	_	_	_
44	Reverted	revert	VBD	_	_	_
45	Repl	repl	JJ	_	_	_
46	3	3	CD	_	_	_
47	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
48	13	13	CD	_	_	_
49	_	_	NN	_	_	_
50	ESBL019	esbl019	NN	_	_	_
51	Coliform	coliform	NN	_	_	_
52	Repl	repl	NN	_	_	_
53	4	4	CD	_	_	_
54	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
55	14	14	CD	_	_	_
56	_	_	CD	_	_	_
57	ESBL019	esbl019	NN	_	_	_
58	Filamented	Filamented	NNP	_	_	_
59	Repl	Repl	NNP	_	_	_
60	4	4	CD	_	_	_
61	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
62	15	15	CD	_	_	_
63	_	_	NN	_	_	_
64	ESBL019	esbl019	NN	_	_	_
65	Transition	transition	NN	_	_	_
66	Repl	repl	NN	_	_	_
67	4	4	CD	_	_	_
68	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
69	16	16	CD	_	_	_
70	_	_	NN	_	_	_
71	ESBL019	esbl019	NN	_	_	_
72	Reverted	revert	VBD	_	_	_
73	Repl	repl	JJ	_	_	_
74	4	4	CD	_	_	_
75	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
76	1	1	CD	_	_	_
77	_	_	NN	_	_	_
78	ESBL019	esbl019	NN	_	_	_
79	Coliform	coliform	NN	_	_	_
80	Repl	repl	NN	_	_	_
81	1	1	CD	_	_	_
82	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
83	2	2	CD	_	_	_
84	_	_	CD	_	_	_
85	ESBL019	esbl019	NN	_	_	_
86	Filamented	Filamented	NNP	_	_	_
87	Repl	Repl	NNP	_	_	_
88	1	1	CD	_	_	_
89	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
90	3	3	CD	_	_	_
91	_	_	NN	_	_	_
92	ESBL019	esbl019	NN	_	_	_
93	Transition	transition	NN	_	_	_
94	Repl	repl	NN	_	_	_
95	1	1	CD	_	_	_
96	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
97	4	4	CD	_	_	_
98	_	_	NN	_	_	_
99	ESBL019	esbl019	NN	_	_	_
100	Reverted	revert	VBD	_	_	_
101	Repl	repl	NN	_	_	_
102	1	1	CD	_	_	_
103	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
104	5	5	CD	_	_	_
105	_	_	NN	_	_	_
106	ESBL019	esbl019	NN	_	_	_
107	Coliform	coliform	NN	_	_	_
108	Repl	repl	NN	_	_	_
109	2	2	CD	_	_	_
110	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
111	6	6	CD	_	_	_
112	_	_	NN	_	_	_
113	ESBL019	esbl019	NN	_	_	_
114	Filamented	filament	VBD	_	_	_
115	Repl	repl	NN	_	_	_
116	2	2	CD	_	_	_
117	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
118	75th	75th	JJ	_	_	_
119	percentile	percentile	NN	_	_	_
120	shift	shift	NN	_	_	_
121	normalisation	normalisation	NN	_	_	_
122	and	and	CC	_	_	_
123	baseline	baseline	NN	_	_	_
124	adjusted	adjusted	JJ	_	_	_
125	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
126	7	7	CD	_	_	_
127	_	_	NN	_	_	_
128	ESBL019	esbl019	NN	_	_	_
129	Transition	transition	NN	_	_	_
130	Repl	repl	NN	_	_	_
131	2	2	CD	_	_	_
132	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
133	8	8	CD	_	_	_
134	_	_	NN	_	_	_
135	ESBL019	esbl019	NN	_	_	_
136	Reverted	revert	VBD	_	_	_
137	Repl	repl	NN	_	_	_
138	2	2	CD	_	_	_
139	PGCGROWTHCONDITIONS	pgcgrowthcondition	NNS	_	_	_
140	9	9	CD	_	_	_
141	_	_	NN	_	_	_
142	ESBL019	esbl019	NN	_	_	_
143	Coliform	coliform	NN	_	_	_
144	Repl	repl	NN	_	_	_
145	3	3	CD	_	_	_
146	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
147	ESBL019	esbl019	NN	_	_	_
148	Coliform	coliform	NN	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	ESBL019	esbl019	NN	_	_	_
151	Filamented	filamented	JJ	_	_	_
152	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
153	ESBL019	esbl019	NN	_	_	_
154	Reverted	revert	VBD	_	_	_
155	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
156	ESBL019	esbl019	NN	_	_	_
157	Transition	transition	NN	_	_	_
158	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
159	Escherichia	escherichia	FW	Organism	_	_
160	coli	coli	FW	Organism	_	_
161	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
162	Four	four	CD	_	_	_
163	morphologic	morphologic	JJ	_	_	_
164	states	state	NNS	_	_	_
165	of	of	IN	_	_	_
166	ESBL019	esbl019	NN	_	_	_
167	were	be	VBD	_	_	_
168	used	use	VBN	_	_	_
169	during	during	IN	_	_	_
170	the	the	DT	_	_	_
171	experiments	experiment	NNS	_	_	_
172	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	first	first	JJ	_	_	_
3	ESBL019	esbl019	NN	_	_	_
4	morphological	morphological	JJ	_	_	_
5	state	state	NN	_	_	_
6	was	be	VBD	_	_	_
7	prepared	prepare	VBN	_	_	_
8	by	by	IN	_	_	_
9	resuspension	resuspension	NN	_	_	_
10	of	of	IN	_	_	_
11	ESBL019	esbl019	NN	_	_	_
12	in	in	IN	_	_	_
13	cell	cell	NN	_	_	_
14	culture	culture	NN	_	_	_
15	medium	medium	NN	_	_	_
16	-LRB-	-lrb-	-LRB-	_	_	_
17	CCM	ccm	NN	_	_	_
18	-RRB-	-rrb-	-RRB-	_	_	_
19	without	without	IN	_	_	_
20	ceftibuten	ceftibuten	NN	_	_	_
21	supplementation	supplementation	NN	_	_	_
22	prior	prior	RB	_	_	_
23	to	to	TO	_	_	_
24	its	its	PRP$	_	_	_
25	inoculation	inoculation	NN	_	_	_
26	of	of	IN	_	_	_
27	primary	primary	JJ	_	_	_
28	human	human	JJ	_	_	_
29	bladder	bladder	NN	_	_	_
30	epithelial	epithelial	JJ	_	_	_
31	cells	cell	NNS	_	_	_
32	-LRB-	-lrb-	-LRB-	_	_	_
33	HBEP	hbep	NN	_	_	_
34	-RRB-	-rrb-	-RRB-	_	_	_
35	-LRB-	-lrb-	-LRB-	_	_	_
36	designated	designate	VBN	_	_	_
37	;	;	:	_	_	_
38	ESBL019	esbl019	NN	_	_	_
39	Coliform	coliform	NN	_	_	_
40	-RRB-	-rrb-	-RRB-	_	_	_
41	.	.	.	_	_	_

1	A	a	DT	_	_	_
2	second	second	JJ	_	_	_
3	ESBL019	esbl019	NN	_	_	_
4	morphological	morphological	JJ	_	_	_
5	state	state	NN	_	_	_
6	was	be	VBD	_	_	_
7	prepared	prepare	VBN	_	_	_
8	by	by	IN	_	_	_
9	resuspension	resuspension	NN	_	_	_
10	in	in	IN	_	_	_
11	CCM	CCM	NNP	_	_	_
12	and	and	CC	_	_	_
13	then	then	RB	_	_	_
14	used	use	VBN	_	_	_
15	to	to	TO	_	_	_
16	inoculate	inoculate	VB	_	_	_
17	HBEP	hbep	NN	_	_	_
18	cells	cell	NNS	_	_	_
19	with	with	IN	_	_	_
20	ceftibuten	ceftibuten	NN	_	_	_
21	supplementation	supplementation	NN	_	_	_
22	-LRB-	-lrb-	-LRB-	_	_	_
23	480ng	480ng	CD	_	_	_
24	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
25	morphology	morphology	NN	_	_	_
26	:	:	:	_	_	_
27	Coliform	coliform	NN	_	_	_
28	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
29	morphology	morphology	NN	_	_	_
30	:	:	:	_	_	_
31	Filamented	filamented	JJ	_	_	_
32	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
33	morphology	morphology	NN	_	_	_
34	:	:	:	_	_	_
35	Reverted	revert	VBN	_	_	_
36	-LRB-	-lrb-	-LRB-	_	_	_
37	reverted	revert	VBD	_	_	_
38	back	back	RB	_	_	_
39	from	from	IN	_	_	_
40	a	a	DT	_	_	_
41	Filamented	filamented	JJ	_	_	_
42	shape	shape	NN	_	_	_
43	into	into	IN	_	_	_
44	a	a	DT	_	_	_
45	coli	coli	NN	_	_	_
46	shape	shape	NN	_	_	_
47	-RRB-	-rrb-	-RRB-	_	_	_
48	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
49	morphology	morphology	NN	_	_	_
50	:	:	:	_	_	_
51	Transition	transition	NN	_	_	_
52	-LRB-	-lrb-	-LRB-	_	_	_
53	from	from	IN	_	_	_
54	Coli	Coli	NNP	_	_	_
55	into	into	IN	_	_	_
56	Filamented	Filamented	NNP	_	_	_
57	-RRB-	-rrb-	-RRB-	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	RNA	rna	NN	_	_	_
60	isolation	isolation	NN	_	_	_
61	was	be	VBD	_	_	_
62	performed	perform	VBN	_	_	_
63	using	use	VBG	_	_	_
64	an	a	DT	_	_	_
65	RNeasy	rneasy	NN	_	_	_
66	mini	minus	NNS	_	_	_
67	kit	kit	NN	_	_	_
68	-LRB-	-lrb-	-LRB-	_	_	_
69	Qiagen	Qiagen	NNP	_	_	_
70	Technologies	Technologies	NNPS	_	_	_
71	,	,	,	_	_	_
72	Hilden	Hilden	NNP	_	_	_
73	,	,	,	_	_	_
74	Germany	Germany	NNP	_	_	_
75	-RRB-	-rrb-	-RRB-	_	_	_
76	,	,	,	_	_	_
77	according	accord	VBG	_	_	_
78	to	to	TO	_	_	_
79	the	the	DT	_	_	_
80	manufacturer	manufacturer	NN	_	_	_
81	's	's	POS	_	_	_
82	protocol	protocol	NN	_	_	_
83	.	.	.	_	_	_

1	DNA	dna	NN	_	_	_
2	decontamination	decontamination	NN	_	_	_
3	treatment	treatment	NN	_	_	_
4	was	be	VBD	_	_	_
5	performed	perform	VBN	_	_	_
6	using	use	VBG	_	_	_
7	Turbo	Turbo	NNP	_	_	_
8	DNase	dnase	NN	_	_	_
9	-LRB-	-lrb-	-LRB-	_	_	_
10	Qiagen	qiagen	NN	_	_	_
11	-RRB-	-rrb-	-RRB-	_	_	_
12	and	and	CC	_	_	_
13	the	the	DT	_	_	_
14	quantity	quantity	NN	_	_	_
15	and	and	CC	_	_	_
16	purity	purity	NN	_	_	_
17	of	of	IN	_	_	_
18	the	the	DT	_	_	_
19	purified	purify	VBN	_	_	_
20	RNA	rna	NN	_	_	_
21	samples	sample	NNS	_	_	_
22	were	be	VBD	_	_	_
23	determined	determine	VBN	_	_	_
24	using	use	VBG	_	_	_
25	a	a	DT	_	_	_
26	spectrophotometer	spectrophotometer	NN	_	_	_
27	Nanodrop-1000	nanodrop-1000	NN	_	_	_
28	-LRB-	-lrb-	-LRB-	_	_	_
29	Nanodrop	Nanodrop	NNP	_	_	_
30	Technologies	Technologies	NNPS	_	_	_
31	Inc.	Inc.	NNP	_	_	_
32	,	,	,	_	_	_
33	Wilmington	Wilmington	NNP	_	_	_
34	,	,	,	_	_	_
35	DE	de	NN	_	_	_
36	,	,	,	_	_	_
37	USA	USA	NNP	_	_	_
38	-RRB-	-rrb-	-RRB-	_	_	_
39	by	by	IN	_	_	_
40	measuring	measure	VBG	_	_	_
41	the	the	DT	_	_	_
42	absorbance	absorbance	NN	_	_	_
43	-LRB-	-lrb-	-LRB-	_	_	_
44	A260	a260	NN	_	_	_
45	,	,	,	_	_	_
46	230	230	CD	_	_	_
47	,	,	,	_	_	_
48	280	280	CD	_	_	_
49	-RRB-	-rrb-	-RRB-	_	_	_
50	and	and	CC	_	_	_
51	calculating	calculate	VBG	_	_	_
52	absorbance	absorbance	NN	_	_	_
53	ratios	ratio	NNS	_	_	_
54	-LRB-	-lrb-	-LRB-	_	_	_
55	A260	a260	NN	_	_	_
56	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
57	strain	strain	NN	_	_	_
58	:	:	:	_	_	_
59	beta-lactamase	beta-lactamase	NN	_	_	_
60	-LRB-	-lrb-	-LRB-	_	_	_
61	ESBL	esbl	NN	_	_	_
62	-RRB-	-rrb-	-RRB-	_	_	_
63	-	-	:	_	_	_
64	producing	produce	VBG	_	_	_
65	UPEC	upec	NN	_	_	_
66	-LRB-	-lrb-	-LRB-	_	_	_
67	ESBL019	esbl019	NN	_	_	_
68	-RRB-	-rrb-	-RRB-	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	The	the	DT	_	_	_
71	E.	e.	FW	_	_	_
72	coli	coli	FW	_	_	_
73	isolate	isolate	NN	_	_	_
74	ESBL019	esbl019	NN	_	_	_
75	was	be	VBD	_	_	_
76	originally	originally	RB	_	_	_
77	isolated	isolate	VBN	_	_	_
78	from	from	IN	_	_	_
79	a	a	DT	_	_	_
80	patient	patient	NN	_	_	_
81	at	at	IN	_	_	_
82	Örebro	Örebro	NNP	_	_	_
83	University	University	NNP	_	_	_
84	hospital	hospital	NN	_	_	_
85	,	,	,	_	_	_
86	Sweden	Sweden	NNP	_	_	_
87	and	and	CC	_	_	_
88	was	be	VBD	_	_	_
89	maintained	maintain	VBN	_	_	_
90	on	on	IN	_	_	_
91	tryptic	tryptic	JJ	_	_	_
92	soy	soy	NN	_	_	_
93	agar	agar	NN	_	_	_
94	-LRB-	-lrb-	-LRB-	_	_	_
95	TSA	tsa	NN	_	_	_
96	-RRB-	-rrb-	-RRB-	_	_	_
97	-LRB-	-lrb-	-LRB-	_	_	_
98	Becton	Becton	NNP	_	_	_
99	Dickinson	Dickinson	NNP	_	_	_
100	,	,	,	_	_	_
101	Le	Le	NNP	_	_	_
102	Pont	Pont	NNP	_	_	_
103	Claix	Claix	NNP	_	_	_
104	,	,	,	_	_	_
105	France	France	NNP	_	_	_
106	-RRB-	-rrb-	-RRB-	_	_	_
107	.	.	.	_	_	_

1	ESBL019	esbl019	NN	_	_	_
2	was	be	VBD	_	_	_
3	grown	grow	VBN	_	_	_
4	in	in	IN	_	_	_
5	Luria	Luria	NNP	MED	_	_
6	broth	broth	NN	MED	_	_
7	-LRB-	-lrb-	-LRB-	_	_	_
8	Difco	Difco	NNP	_	_	_
9	Laboratories	Laboratories	NNPS	_	_	_
10	,	,	,	_	_	_
11	Detroit	Detroit	NNP	_	_	_
12	,	,	,	_	_	_
13	MI	MI	NNP	_	_	_
14	,	,	,	_	_	_
15	USA	USA	NNP	_	_	_
16	-RRB-	-rrb-	-RRB-	_	_	_
17	overnight	overnight	JJ	_	_	_
18	on	on	IN	_	_	_
19	shake	shake	NN	_	_	_
20	at	at	IN	_	_	_
21	200	200	CD	_	_	_
22	rpm	rpm	NN	_	_	_
23	37	37	CD	_	_	_
24	°C	°c	NN	_	_	_
25	prior	prior	RB	_	_	_
26	to	to	TO	_	_	_
27	experiments	experiment	NNS	_	_	_
28	.	.	.	_	_	_

1	The	the	DT	_	_	_
2	bacteria	bacterium	NNS	_	_	_
3	were	be	VBD	_	_	_
4	resuspended	resuspend	VBN	_	_	_
5	in	in	IN	_	_	_
6	sterile	sterile	JJ	_	_	_
7	phosphate	phosphate	NN	_	_	_
8	buffered	buffer	VBN	_	_	_
9	saline	saline	NN	_	_	_
10	prior	prior	RB	_	_	_
11	to	to	TO	_	_	_
12	inoculation	inoculation	NN	_	_	_
13	of	of	IN	_	_	_
14	CnT-21	cnt-21	NN	_	_	_
15	cell	cell	NN	_	_	_
16	culture	culture	NN	_	_	_
17	medium	medium	NN	_	_	_
18	-LRB-	-lrb-	-LRB-	_	_	_
19	CCM	ccm	NN	_	_	_
20	-RRB-	-rrb-	-RRB-	_	_	_
21	with	with	IN	_	_	_
22	or	or	CC	_	_	_
23	without	without	IN	_	_	_
24	ceftibuten	ceftibuten	NN	_	_	_
25	-LRB-	-lrb-	-LRB-	_	_	_
26	480	480	CD	_	_	_
27	ng	ng	NN	_	_	_
28	PGCGROWTHCONDITIONS	PGCGROWTHCONDITIONS	NNP	_	_	_
29	Escherichia	escherichia	FW	Organism	_	_
30	coli	coli	FW	Organism	_	_
31	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
32	lexA	lexa	NN	GEN	_	_
33	10	10	CD	_	_	_
34	'	'	''	_	_	_
35	after	after	IN	_	_	_
36	UV	uv	NN	_	_	_
37	vs.	vs.	CC	_	_	_
38	0	0	CD	_	_	_
39	'	'	''	_	_	_
40	,	,	,	_	_	_
41	MG1655	mg1655	NN	_	_	_
42	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
43	lexA	lexa	NN	GEN	_	_
44	10	10	CD	_	_	_
45	min	min	NN	_	_	_
46	after	after	IN	_	_	_
47	UV	uv	NN	_	_	_
48	treatment	treatment	NN	_	_	_
49	,	,	,	_	_	_
50	25	25	CD	_	_	_
51	ug	ug	NN	_	_	_
52	total	total	JJ	_	_	_
53	RNA	rna	NN	_	_	_
54	,	,	,	_	_	_
55	2	2	CD	_	_	_
56	ug	ug	NN	_	_	_
57	pdN6	pdn6	NN	_	_	_
58	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
59	lexA	lexa	NN	GEN	_	_
60	20	20	CD	_	_	_
61	'	'	''	_	_	_
62	after	after	IN	_	_	_
63	NOuv	NOuv	NNP	_	_	_
64	vs.	vs.	CC	_	_	_
65	0	0	CD	_	_	_
66	'	'	''	_	_	_
67	,	,	,	_	_	_
68	MG1655	mg1655	NN	_	_	_
69	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
70	lexA	lexa	NN	GEN	_	_
71	20	20	CD	_	_	_
72	'	'	''	_	_	_
73	after	after	IN	_	_	_
74	UV	uv	NN	_	_	_
75	vs.	vs.	CC	_	_	_
76	0	0	CD	_	_	_
77	'	'	''	_	_	_
78	,	,	,	_	_	_
79	MG1655	mg1655	NN	_	_	_
80	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
81	lexA	lexa	NN	GEN	_	_
82	20	20	CD	_	_	_
83	min	min	NN	_	_	_
84	after	after	IN	_	_	_
85	NOuv	NOuv	NNP	_	_	_
86	,	,	,	_	_	_
87	25	25	CD	_	_	_
88	ug	ug	NN	_	_	_
89	total	total	JJ	_	_	_
90	RNA	rna	NN	_	_	_
91	,	,	,	_	_	_
92	2	2	CD	_	_	_
93	ug	ug	NN	_	_	_
94	pdN6	pdn6	NN	_	_	_
95	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
96	lexA	lexa	NN	GEN	_	_
97	20	20	CD	_	_	_
98	min	min	NN	_	_	_
99	after	after	IN	_	_	_
100	UV	uv	NN	_	_	_
101	treatment	treatment	NN	_	_	_
102	,	,	,	_	_	_
103	25	25	CD	_	_	_
104	ug	ug	NN	_	_	_
105	total	total	JJ	_	_	_
106	RNA	rna	NN	_	_	_
107	,	,	,	_	_	_
108	2	2	CD	_	_	_
109	ug	ug	NN	_	_	_
110	pdN6	pdn6	NN	_	_	_
111	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
112	lexA	lexa	NN	GEN	_	_
113	40	40	CD	_	_	_
114	'	'	''	_	_	_
115	after	after	IN	_	_	_
116	UV	uv	NN	_	_	_
117	vs.	vs.	CC	_	_	_
118	0	0	CD	_	_	_
119	'	'	''	_	_	_
120	,	,	,	_	_	_
121	MG1655	mg1655	NN	_	_	_
122	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
123	lexA	lexa	NN	GEN	_	_
124	40	40	CD	_	_	_
125	min	min	NN	_	_	_
126	after	after	IN	_	_	_
127	UV	uv	NN	_	_	_
128	treatment	treatment	NN	_	_	_
129	,	,	,	_	_	_
130	25	25	CD	_	_	_
131	ug	ug	NN	_	_	_
132	total	total	JJ	_	_	_
133	RNA	rna	NN	_	_	_
134	,	,	,	_	_	_
135	2	2	CD	_	_	_
136	ug	ug	NN	_	_	_
137	pdN6	pdn6	NN	_	_	_
138	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
139	lexA	lexa	NN	GEN	_	_
140	5	5	CD	_	_	_
141	'	'	''	_	_	_
142	after	after	IN	_	_	_
143	UV	uv	NN	_	_	_
144	vs.	vs.	CC	_	_	_
145	0	0	CD	_	_	_
146	'	'	''	_	_	_
147	,	,	,	_	_	_
148	MG1655	mg1655	NN	_	_	_
149	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
150	lexA	lexa	NN	GEN	_	_
151	5	5	CD	_	_	_
152	min	min	NN	_	_	_
153	after	after	IN	_	_	_
154	UV	uv	NN	_	_	_
155	treatment	treatment	NN	_	_	_
156	,	,	,	_	_	_
157	25	25	CD	_	_	_
158	ug	ug	NN	_	_	_
159	total	total	JJ	_	_	_
160	RNA	rna	NN	_	_	_
161	,	,	,	_	_	_
162	2	2	CD	_	_	_
163	ug	ug	NN	_	_	_
164	pdN6	pdn6	NN	_	_	_
165	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
166	lexA	lexa	NN	GEN	_	_
167	60	60	CD	_	_	_
168	'	'	''	_	_	_
169	after	after	IN	_	_	_
170	NOuv	NOuv	NNP	_	_	_
171	vs.	vs.	CC	_	_	_
172	0	0	CD	_	_	_
173	'	'	''	_	_	_
174	,	,	,	_	_	_
175	MG1655	mg1655	NN	_	_	_
176	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
177	lexA	lexa	NN	GEN	_	_
178	60	60	CD	_	_	_
179	'	'	''	_	_	_
180	after	after	IN	_	_	_
181	UV	uv	NN	_	_	_
182	vs.	vs.	CC	_	_	_
183	0	0	CD	_	_	_
184	'	'	''	_	_	_
185	,	,	,	_	_	_
186	MG1655	mg1655	NN	_	_	_
187	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
188	lexA	lexa	NN	GEN	_	_
189	60	60	CD	_	_	_
190	min	min	NN	_	_	_
191	after	after	IN	_	_	_
192	NOuv	NOuv	NNP	_	_	_
193	,	,	,	_	_	_
194	25	25	CD	_	_	_
195	ug	ug	NN	_	_	_
196	total	total	JJ	_	_	_
197	RNA	rna	NN	_	_	_
198	,	,	,	_	_	_
199	2	2	CD	_	_	_
200	ug	ug	NN	_	_	_
201	pdN6	pdn6	NN	_	_	_
202	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
203	lexA	lexa	NN	GEN	_	_
204	60	60	CD	_	_	_
205	min	min	NN	_	_	_
206	after	after	IN	_	_	_
207	UV	uv	NN	_	_	_
208	treatment	treatment	NN	_	_	_
209	,	,	,	_	_	_
210	25	25	CD	_	_	_
211	ug	ug	NN	_	_	_
212	total	total	JJ	_	_	_
213	RNA	rna	NN	_	_	_
214	,	,	,	_	_	_
215	2	2	CD	_	_	_
216	ug	ug	NN	_	_	_
217	pdN6	pdn6	NN	_	_	_
218	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
219	lexA	lexa	NN	GEN	_	_
220	vs.	vs.	CC	_	_	_
221	wt	wt	JJ	_	_	_
222	,	,	,	_	_	_
223	before	before	IN	_	_	_
224	UV	uv	NN	_	_	_
225	treatment	treatment	NN	_	_	_
226	,	,	,	_	_	_
227	MG1655	mg1655	NN	_	_	_
228	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_
229	untreated	untreated	JJ	_	_	_
230	cells	cell	NNS	_	_	_
231	,	,	,	_	_	_
232	25	25	CD	_	_	_
233	ug	ug	NN	_	_	_
234	total	total	JJ	_	_	_
235	RNA	rna	NN	_	_	_
236	PGCGROWTHCONDITIONS	pgcgrowthconditions	NN	_	_	_